HyperChem7 (Tiengviet)

Hng dn s dng HyperChem 7.
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Bi 1 Bt u s dng phn mm
Nhp chut vo biu tng HyperChem, mn hnh lm vic hin ln nh sau:
Thanh tiu (title bar)

Biu din tn file ang biu din trn ca s. Nu cha lu file th tn s l untitled
Thanh cng c la chn (menu bar)

Cha cc cng c tnh ton khc: File, Edit (hiu chnh), Build (xy dng), Databases (d liu), Setup (t phng php tnh), Compute (tnh ton), Annotations (ghi ch, din gii), cancel (thot), Script, v Help (tr gip).
Thanh biu tng cng c (tool bar)

Cha cc cng c cho php ta v, chn, biu din, v di chuyn cc nguyn t, phn t. Phn bn phi thanh cng c c cha cc cng c gip ta ghi ch thm, lu nhanh, ct, dn, in, tr gip.
Mn lm vic (workspace)
L ni biu din h phn t hin ti. 1
Hng dn s dng HyperChem 7.04
Dng hin trng tnh ton (status line)

Cho ta bit thng tin nh l s nguyn t trong mt phn t, hin trng tnh ton, gi tr tnh ton
Tr gip (help)
Cha cc hng dn thm cho ngi s dng.
Cch s dng chut:

Mun thao tc trn cng c no ta ch vic nhp tri chut (L-Click) vo biu tng cng c . V d mun s dng cng c v, ta di chuyn biu tng chut n biu tng v nhp chut:
S dng bn phm
Thay v phi dng chut ta c th dng bn phm di chuyn n nhng la chn cn thit. V d m select menu ta nhn ng thi hai phm [Alt] + [S] ([Alt] v [S]). chn cc la chn khc trong hp thoi ta nhp tip vo k t tt c gch di trong mi la chn. V d chn tip select all ta nhp ch e trn bn phm.
Cc phm tt khc:
Ctrl + N Ctrl + O Ctrl + S Ctrl + X Ctrl + C Ctrl + V Alt + F4 Ctrl + D Ctrl + K Ctrl + L Ctrl + F Ctrl + B Spacebar F2 F9 Esc To trang lm vic mi M file Lu file (save) trong File menu Ct (cut) trong File menu Copy (copy) trong Edit menu Dn (paste) trong Edit menu Thot khi HyperChem Xo (delete) trong Annotations menu La chn tip (select next) trong Annotations menu La chn phn trc (select previous) trong Annotations menu Di chuyn tip (move forward) trong Annotations menu Di chuyn tr li (move backward) trong Annotations menu Di chuyn h phn t vo trung tm v biu din theo t l mn lm vic. Tr li kiu biu din lc trc (last rendering) trong Display menu Copy hnh nh (copy image) trong Edit menu Nh mc thot (cancel) trn thanh cng c
Cc cng c quan trng trn thanh cng c
Cc thao tc trn HyperChem M mt file v d: V d m file c ui HIN.

1. Di chuyn con tr chut n File trn thanh cng c. 2. Nhp tri chut (L-click) vo File mn hnh s hin ra nh sau:
3. Nhp tri chut vo Open. Mn hnh s hin ra nh sau:
4. Nu mn hnh list vn cn cc cht khc, c th ko thanh trt tm kim.
ko thanh trt ta nhp tri biu tng chut vo thanh trt, gi nguyn nh th v r chut theo chiu mun ko. 5. Mun m file no ta ch cn nhp tri (L-click) chut vo file ri nhn tip vo nt Open trn list
Trn mn hnh s hin ra phn t cha trong file
Cch s dng Display Settings

Display settings cha cc la chn biu din h phn t trn trang lm vic m Display menu ta thc hin nh sau 1. Nhp tri chut vo biu tng Display trn thanh cng c. Mn hnh khi hin ra nh sau:
S dng nhn (Labels)
Hng dn s dng HyperChem 7.04 Nhp tri chut vo Labels trong Display. Hp thoi Labels hin ra vi cc la chn khc nhau, ta c th la chn hnh thc nhn biu hin ca cc nguyn t trong h.
Atoms None B tt c cc nhn. Symbol Biu tng nguyn t, v d C, O, N.. Name Tn ca nguyn t theo ngn hng d liu, v d CA, CB i vi cacbon alpha v beta. S th t to nguyn t. Number Type Kiu nguyn t, theo tc ng ca trng lc, v d CT i vi cacbon t din trong trng lc AMBER. Charge in tch thc ca nguyn t. Spin Tng spin thc (alpha-beta) ca mt nguyn t Poputation Mass Khi lng nguyn t Basis set Tp hp hm c bn p dng cho nguyn t Chirality R hoc S RMS Gradient Ga tr v hng ca vect bin thin m t trng lc trn mt nguyn t. Custom t tu chn. Residues None B tt c cc nhn. Name Tn hp phn, v d: TRP, ILE. Sequence Th t hp phn t hp phn ui N (Nteminus).1,2,3 Name+Seq C tn ln th t. Bonds
Hng dn s dng HyperChem 7.04 None B tt c cc nhn Bond Length di lin kt gia cc nguyn t Bond Order Th t lin kt tnh ton theo c hc lng t.
Hnh thc biu din phn t:

Ta hon ton c th biu din cc phn t khc nhau trong h.
Thay i hnh thc biu din:

1. Nhp tri chut vo Rendering trong Display menu Hp thoi la chn hin ra nh sau:
Nhp tri chut vo mt trong nhng hnh thc biu din, v d chn Balls and Cylinders (kiu hnh cu v hnh tr) th trn m hnh cc nguyn t ca h c biu din di dng hnh cu, lin kt dng hnh tr nh sau:
Ch : HyperChem cn c cc kiu biu din khc: - Sticks: Kiu que. - Balls : Kiu hnh cu. - Overlapping Spheres: Kiu hnh cu chng ln nhau. - Dots: Kiu chm. - Sticks & Dots: Kiu chm - gch.
t mu nn trang lm vic
t mu nn trang lm vic ta lm nh sau: 1. Nhp tri chut tch chn Preferences trong File menu. 2. Tch chn mc Window Color trong hp thoi Preferences. Mu ngm nh cho trang lm vic ca HyperChem l mu en:
Hng dn s dng HyperChem 7.04 3. Tch chn White ri nhp OK xem biu din mu nn ca mn lm vic. Mu nn lc ny l mu trng:
Ch : Nu ta t mu khc th nn s c mu khc: - Black: Mu en. - Blue: Mu xanh nc bin. - Green: Mu xanh da tri. - Cyan: Mu lc lam. - Red: Mu . - Violet: Mu ta. - Yellow: Mu vng. - White: Mu trng.
t mu sc lin kt trong phn t

1. Tch chn Preferences trong File menu.
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2. Chn mc Bond Color trong hp thoi Preferences. Tch chn mu m ta mun t cho lin kt. V d ta chn mu en (Black). Hnh nh biu din trn mn lm vic s nh sau:
Ch : Tu theo ta chn mu no, lin kt s c biu din theo mu y. HyperChem ngm nh mu cho lin kt theo cc nguyn t, nh ta c th quan st d dng cc lin kt khc nhau, tuy nhin iu khng c li trong khi ta phi in en trng.
Mu sc ca nguyn t
HyperChem ngm nh mu sc ca cc nguyn t c trng nh sau: Nguyn t Mu ngm nh 11
Hng dn s dng HyperChem 7.04 Cacbon Nit Oxy Flo Lu hunh Natri Kali St Coban ng Brom Iot Vng Tt c cc nguyn t cn li Lc lam Xanh Vng Vng Ta Ta Xanh Xanh l cy Vng Vng Mu trng
Ta c th t li mu sc biu din cc nguyn t theo su mu chun, cng vi mu trng v mu en. HyperChem s dng mt tp hp mu ngm nh. Nu ta thay i mu sc ca mt nguyn t, ta vn c th tr li vi mu ngm nh bng cch nhp vo Revert trong hp thoi sau:
t mu mi cho nguyn t ta lm nh sau: 1. Nhp tri chut chn Element color trong Display menu. 2. Nhp tri chut vo tn nguyn t mun i mu. 3. Nhp tri chut vo mu mun i. 4. Nhp OK chn. 5. tr li mu ngm nh nhp Revert.
t ch Copy hnh nh
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Hng dn s dng HyperChem 7.04 y l phn kh th v nu ta mun ly hnh nh ca HyperChem chuyn qua trnh ng dng khc, v d nh trnh Word ca Microsoft. 1. Nhp tri chut chn Preferences trong File menu. Chn mc Setup Image. Hnh nh hp thoi lc ny nh sau:
2. t cc la chn nh trn hnh v. Nhp OK chn. 3. Nhp F9 hoc nhp tri chut chn Copy Image trong Edit menu. 4. Nhp OK nu HyperChem t ra cu cnh bo no. C ca s mn lm vic ca HyperChem s c Copy. Nu ta dn qua Word th s thy nh sau:
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Ch : HyperChem cho ta nhiu la chn copy hnh nh. Top leve Copy c cc hp thoi v menu ko Window xung nu ta nhp vo Copy image (Ca s) thay v nhp F9. Workspace Ch Copy phn mn lm vic. HyperChem Copy c ca s lm vic HyperChem Full screen Copy c mn hnh, k c cc ca s khc. Bitmap Lu kiu file c ui .bmp. Dng File format mu chun. Thch hp lu cho biu (Kiu file) din phn t kiu hnh cu, cc biu ca tnh ton im n, tnh ton bn kinh nghim. RGB Bitmap Ging nh .bmp, dng 24 mu. Kh hn ch trong cc ng dng khc khng c ch 24 mu. Metafile File ui m rng l .wmf. Thch hp lu vi cc kiu biu din phn t nh Sticks, Ball and Cylinder, Dots v Stick & Dots. Detination(Ni File HyperChem lu nh c phn ui l t file) .bmp hay .wmf vo trong file. Clipboard Lu nh vo b nh tm thi, mi ln c mt nh. Color Tch chn lu hnh nh vi mu sc y , nu khng n ch c 14
Hng dn s dng HyperChem 7.04 dng en trng. Tch chn im tr chut c trong nh. Dng t tn v v tr file t nh.
Cursor Filename
Thot khi HyperChem

C nhiu cch thot khi chng trnh lm vic 1. Nhp tri chut vo Exit trong Menu file 2. Nhp Alt + F4 c thm: Chng 1 trong HyperChem for Windows Reference Manual.
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Bi 2. V v hiu chnh
V nguyn t v lin kt
v nguyn t ta cn c bng la chn cc nguyn t.
C hai cch thc hin iu ny

1. Nhp tri chut vo Default Element trong Menu Build. 1. Nhp lin tc hai ln chut tri (Double-click) vo cng c V
Bng la chn cc nguyn t hin ra nh sau: la chn nguyn t no ta ch vic nhp tri chut vo nguyn t . 2. Mun bit thuc tnh ca tng nguyn t ta ch vic nhp vo biu tng thuc tnh (Properties) trong thoi, bng cc thuc tnh ca nguyn t s xut hin.
Sau khi la chn nguyn t mun v, nhp tri chut ln mn lm vic ta s c nguyn t mun v. Mn hnh hin ra c dng nh sau:
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3. Mun v lin kt ta ch vic nhn nt tri chut v r t v tr ny n v tr khc mun v. Nu u kia l mt nguyn t khc th ta phi la chn nguyn t li sau cng nhn nt tri chut v r t v tr nguyn t ban u n v tr m nguyn t th hai mun biu din.
4. v phn t dng vng ta nhn v r chut ni cc nguyn t vi nhau.
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5. To lin kt i, ba bng cch nhp tri chut vo chnh lin kt . 6. To vng lin hp bng cch nhp lin tip hai ln chut tri vo lin kt vng c v. 7. Thm nhanh nhng nguyn t Hydro cn thiu trong phn t, nu c bng cch nhp lin tip hai ln chut tri vo biu tng cng c la chn trn thanh cng c.
Chn nguyn t (Selecting Atoms)

Trong phn ny ta hc nhng k thut c bn la chn mt nguyn t, nhm nguyn t hay mt tp hp no ang biu din trn trang lm vic.
t cc hnh thc chn c mt s bc sau:

1. Nhp tri chut vo Select menu. Trn mn hnh hin ra nh sau:
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2. Nu cc nguyn t cha c chn th hy nhp chut tri vo Atoms chn. Tip theo tt chn nhiu (Multiple Selections) bng cch nhp chut tri b du tch (). Khi ta tch chn Atoms, n v la chn nh nht chn nguyn t, vi cng c la chn, khi ta c th la chn cc nguyn t, lin kt v gc ring. Gii hn ny vn hot ng cho n khi ta chn Residures hoc Molecules. Ch : S dng la chn Atoms nu ta khng mun chn cc hp phn hay cc phn t.
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Chn nguyn t
1. Nhp tri chut vo cng c la chn (select) trn thanh cng c, sau di chuyn con tr xung mn lm vic. 2. t con tr chut vo nguyn t mun chn v nhp tri chut. Nguyn t c chn s c khoanh vng sng hn cc nguyn t khc. 3. Mun chn lin kt no ta nhp tri chut vo lin kt . 4. Mun chn tt c cc nguyn t trong mn lm vic, ta thc hin bng cch di chuyn chut n khong trng ca trang lm vic v nhp phi chut (R-click)
Ch : nguyn t c la chn c m t trn dng hin trng: S ch th t to ra nguyn t trong phn t Atom number Tn nguyn t. Element name Tn nguyn t, xut hin khi chn nguyn t trong Atom name protein hoc amino axit. Trng lc p dng cho kiu nguyn t (amber, Force Field mm+, bio+ hoc opls). Kiu nguyn t Atom type in tch nguyn t Charge To ca nguyn t theo h to ca phn t. Atomic coordinates
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Chn nhm nguyn t

chn mt nhm nguyn t ta dng kiu chn hnh ch nht 1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp ng thi tri v phi chut, gia nh vy v r to hnh ch nht cha cc nguyn t mun chn. 3. Nh chut th tt c cc nguyn t trong hnh ch nht c chn
Chn thm mt nhm nguyn t

1. Nhp tri chut tch chn Multiple select trong Select menu 2. R chut chn nhm nguyn t mi theo hnh ch nht nh trn.
Chn cc hp phn (Residures)

Khi ta tch chn Residures, n v la chn nh nht chn cc hp phn. Hp phn phi c ngun gc t Databases menu hoc t ngn hng d liu Protein. HyperChem khng nhn ra nhng hp phn do ta v t cc nguyn t. Ch : Nu khng c hp phn no trong phn t th Residures hot ng nh Atoms. 21
chn hp phn ta c cc cch sau: 1. Nhp tri chut vo hp phn ta mun chn. Nu cng c la chn chn ln mt phn t, n s chn hp phn gn nht vi n. 2. Nhp phi chut vo hp phn b la chn n. 3. Chn Muiltiple trong Select menu chn nhiu m khng phi loi b bt k la chn no trc . 4. Nhp tri chut vo vng trng trn mn lm vic chn tt c cc nguyn t trong h phn t. Nhp phi chut vo vng trng mn lm vic loi b tt c cc la chn. Hp phn la chn c m t trn dng hin trng:
Number of residures selected Residure name and number
S th t to hp phn c th s l 0 cho tt c cc hp phn. y l tn v th t ni tip ca hp phn ta chn.
Chn c phn t (Molecules)

Khi ta tch chn Molecules, n v la chn nh nht chn phn t ring. Hnh thc la chn ny hot ng cho n khi ta tch chn kiu chn khc. Cc kiu la chn phn t ging nh i vi la chn hp phn v la chn nguyn t: 1. Nhp tri chut ln mt phn t chn n. Nu cng c la chn gn hai phn t th n s chn phn t gn nht. 22
Loi b la chn
1. Nhp phi chut vo nguyn t chn, nu khng mun chn nguyn t na. 2. Nhp phi chut vo gia lin kt nu mun khng chn lin kt . 3. Nhp phi chut vo khong trng trong trang lm vic loi b tt c cc nguyn t chn.
Mu sc biu din khi la chn
Tch chn mc Select Color trong hp thoi Preferences. Tch chn Thick line (ng m) th khi la chn cc ng biu din s la chn s m hn:
Ch : Khi ta chn cc mu khc th khi la chn phn la chn s c 23
Hng dn s dng HyperChem 7.04 kiu mu tng ng.
Chn phn b (Complement Selection)

Ta thc hin chn phn b chn tt c nhng phn cha c chn v b la chn i vi phn chn. Cch thc hin l nhp vo Complement Selection trong Select menu.
Hp thoi la chn (Select Dialog Box) Ta thng quan tm n hp thoi la chn khi c s la chn c bit, v d nh ch chn nguyn t no hoc ch chn mt hp phn no .
By string
Chn nguyn t vi gi tr xc nh theo mt chui gi tr khc nhau. Nhp tri chut vo mt nt xem chui gi tr thch hp trong bn phi. Chui gi tr khc nhau m t tp hp cc nguyn t c th chn c nh sau: Atom Symbol Biu tng nguyn t quy c cho mi nguyn t, 24
Hng dn s dng HyperChem 7.04 nh l C, N, O, F Tn quy c cho mt nguyn t trong amino axit hoc nucleic axit. Ch p dng cho cho tn nh ngha trong cc mu i vi cc thnh phn ca phn t ln. V d l CA, 1HA, 2HA i vi cacbon alpha ni vi hydro. Kiu nguyn t trong c hc phn t nh l CT, HC Tn ca mt hp phn amino axit hoc nucleic axit, nh l GLY, ALA, Tp hp hm c bn tnh theo Ab initio hoc DFT quy cho nguyn t. V d: 6-31G*. S bt i xng, R hoc S, quy cho nguyn t bt i. Dy cc phn la chn c t tn trc . Dy ny gm c cc la chn nh trc nh l LINE, POINT v PLANE, c c cc tn theo biu tng nguyn t quy c nh l C, N, O, F Loi b phn la chn c t tn no khi list. Chn mt nguyn t theo mt gi tr xc nh t mt dy cc gi tr s khc nhau. Nhp tri chut vo mt nt chn kiu s mun chn sau nh gi tr s vo cc thch hp bn phi. Chn nguyn t theo s th t to ra n trong phn t. Chn hp phn theo s th t ni tip trong phn t. Theo th t to phn t. Theo khi lng nguyn t Theo s th t nguyn t trong bng h thng tun hon. Theo in tch nguyn t tnh trong c hc lng t. Chn theo cn bc hai bnh phng trung bnh ca gradient. Chn theo mt spin, da theo lng electron alpha (hng ln) v electrong beta(hng xung) 25
Atom Name
Atom Type Residue Name Basis Set Chirality Named Selection
Remove By Number
Atome Number Residue Number Molecule Number Atomic Mass Atomic Number Electric Charge RMS gradient Spin Population
Hng dn s dng HyperChem 7.04 Value Gi tr s dng t cho kiu la chn thch hp. For Molecule(s) Chn tt c cc phn t, nu khng tch th s gii hn theo list.
Chn theo chui (String)

1. 2. 3. 4. 5. Chn Select trong Select menu. Nhp tri chut chn By String trong hp thoi. Nhp tri chut vo mt trong cc nt thch hp. Nhp tri chut vo mt trong cc gi tr biu din bn phi. Nhp OK chn.
Chn theo s
Chn Select trong Select menu. Chn By Number trong hp thoi. Tch chn vo nt thch hp chn. nh gi tr ph hp theo khong hoc xc nh. Nu tch chn For Molecule (s) xc nh mt tp hp hoc gii hn cc phn t. Nu khng tch chn tt c cc phn t l ngm nh. 6. Nhp OK chn. 1. 2. 3. 4. 5.
Tn phn la chn (Name Selection)

t tn phn la chn gip ta d dng chn li chng vo ln sau. Tn phn la chn c th l: POINT, LINE, PLANE, REACTANT, PRODUCT, PLOT1, PLOT2, GHOST ATOMS, NMR ATOMS, QUANTUM ATOMS hoc tn do ta t (ti a 19 k t)
POINT LINE
Tm khi ca cc nguyn t chn. ng thng gia hai hay nhiu nguyn t, hoc l 26
Hng dn s dng HyperChem 7.04 trc qun tnh th nht. Mt phng to bi trc th nht v trc qun tnh th hai ca cc nguyn t chn Tn phn cc nguyn t cht phn ng. Dng tm trng thi chuyn tip trong phn ng. Ch hot ng khi ta chn mt na s nguyn t trn mn lm vic. Tn cc nguyn t ca sn phm. Dng tm trng thi chuyn tip. Hot ng ng thi vi Reactant. Tn cha mt tp hp ca 2, 3 hay 4 nguyn t cng xc nh mt di lin kt, mt gc lin kt hay mt xon lin kt xc nh s bin thin th nng trong khng gian mt chiu hoc hai chiu. Dng xc nh s bit thin th nng trong khng gian hai chiu. Cha tp hp cc nguyn t c coi l cc nguyn t m (ma) khi tnh ton Ab initio hoc DFT. Cha cc nguyn t c quy cho spin nhn v s dng trong tnh ton HyperNMR. Cha tp hp cc nguyn t c xc nh l cc nguyn t lng t trong s pha trng gia tnh ton c hc lng t v c hc phn t (MM/QM). Tn do ta t
PLANE REACTANT PRODUCT PLOT1
PLOT2 GHOST ATOMS NMR ATOMS QUANTUM ATOMS Other
Xo nguyn t
Xo mt nguyn t n hoc mt lin kt n 1. Nhp tri chut vo cng c v trn thanh cng c. 2. Nhp phi chut vo nguyn t hoc vo gia lin kt mun xo. Khi nguyn t hoc lin kt s bin mt.
Xo nhiu nguyn t
1. Nhp tri chut vo cng c chn trn thanh cng c. 2. R chut chn nhng nguyn t mun xo. 3. Nhp tri chut vo Clear (xo sch) trong Edit menu. Hp thoi xut hin hi c thc s mun xo phn la chn khng. 4. Chn Yes nu mun xo. 5. Chn No nu khng mun xo.
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Copy nguyn t vo b nh tm thi (Clipboard)

1. 2. 3. 4. Nhp tri chut vo cng c chn trn thanh cng c. Nhp tri chut vo lin kt hoc nguyn t mun chn. Chn Copy trong Edit menu. Chn Paste trong Edit menu. Mt bn copy ca cc nguyn t chn s c dn vo trong mn lm vic.
t in tch hnh thc cho nguyn t trong h

Ta hon ton c th t in tch hnh thc cho mt nguyn t no trong phn t. in tch hnh thc trong HyperChem nh sn l cc gi tr nguyn. N ta mun t in tch hnh thc cho nguyn t no th cch lm nh sau: 1. Chn nguyn t mun t in tch hnh thc. 2. Nhp tri chut chn Set Formal Charge trong Build menu. Hp thoi la chn xut hin nh sau:
Ta c th t in tch hnh thc thch hp cho nguyn t chn. 0-Neutral +1-Singly Positive -1-Singly Negative +2-Doubly Positive -2-Doubly Negative +3-Triply Positive -3-Triply Negative Trung tnh Dng mt m mt Dng hai m hai Dng ba m ba
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Hng dn s dng HyperChem 7.04 Nu nh nhiu nguyn t c chn th Set Formal Charge khng hot ng, khi ta c kiu t in tch khc. Ch : in tch hnh thc ch c ngha biu din, khng c gi tr tnh ton.
t in tch thc
HyperChem c th tnh ton in tch ca tng nguyn t ring bit trong phn t, nhng ta cng c th t in tch theo mun. Cch lm nh sau: 1. Chn nguyn t hay nhm nguyn t mun t in tch. Hp thoi t in tch xut hin:
nh gi tr in tch thch hp m ta mun. Nhp OK chn. Khi cc nguyn t chn s c cng in tch m ta nh vo.
t khi lng nguyn t

Cch lm tng t nh t in tch nguyn t trn, bng cch nhp tri chut vo Set mass trong Build menu.
t di lin kt
t di lin kt cho php ta t di lin kt chn theo mun. 1. Nhp chn lin kt mun t li di. 2. Nhp chn Set Bond Length trong Edit menu. nh gi tr mun t vo hp thoi la chn.
Nhp OK thc hin thay i di lin kt chn.
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Ch : Lin kt chn thay i khng c l lin kt trong vng. t gc lin kt Cch lm tng t nh t di lin kt trn, nhng ta phi chn gc lin kt v tch chn Set Bond Angle trong Edit menu m hp thoi la chn.
t xon lin kt
Ta cng thc hin nh cch t di lin kt trn, nhng ta phi chn bn nguyn t lin tip to gc xon mun thay i, tch chn Set Bond Torsion trong Edit menu.
t nhn ring
Ta c th ghi ch nhn tu cho nguyn t la chn, cch lm tng t nh t in tch nguyn t trn. Ta tch chn Set Custom Label trong Build menu m hp thoi v nh nhn m mnh mun vo .
t kiu nguyn t (Atom Type)

Kiu nguyn t ch c ngha khi ta thc hin tnh ton theo c hc phn t, khng c gi tr g khi ta tnh ton bn kinh nghim. Kiu nguyn t cng c ngm nh theo cc thit lp nh sn nu ta khng thay i g. Ta khng nn t li kiu nguyn t nu khng r v n. Cch t kiu nguyn t nh cch t in tch trn, ta chn nguyn t mun t li kiu, tch chn Compile Type Rules trong Build menu. Hp thoi la chn xut hin v ta chn kiu nguyn t m mnh mong mun. c thm: Atom types trang 177- chng 11-quyn Computational Chemistry.
Thay i cc thuc tnh hnh hc Cng bc hnh hc

Vi cc kiu cng bc trong HyperChem gip ta un, thay i gc, di lin kt theo mong mun. Vic cng bc nh vy lun nh hng n tnh ton v kt qu cui cng. Tuy nhin HyperChem khng phi lc no cng
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Hng dn s dng HyperChem 7.04 cho ta c ngay hnh hc mong mun, v vy y l mt trong nhng cng c hu ch. Ch : Cng bc hnh hc ch hot ng khi mt nguyn t c chn. cng bc hnh hc ta lm nh sau: 1. Chn mt nguyn t trong h. 2. Tch chn Constrain Geometry trong Build menu. Hp thoi la chn xut hin:
3. Tch chn hnh thc cng bc m ta mun, nhp OK chn. 4. Loi b la chn nguyn t. 5. Nhp vo Model Build thc hin cng bc chn. Tt c cc gc lin kt ni vi nguyn t c chn s chu cng bc. Ch : Ta cng c th b nhng cng bc va thc hin bng cch tch chn Computed trong hp thoi cng bc v nhp vo Model Build trong Build Menu xy dng li cu trc theo trnh xy dng. Computed Linear Trigonal Tetrahedral Square Planar Bipyramidal Octahedral Khng cng bc. Trnh xy dng quyt nh hnh hc. Cng bc hai lin kt to gc 1800.. Cng bc to mt phng tam gic, mi cp lin kt to gc 1200. Cng bc to t din, mi cp lin kt to gc 109.470. Cng bc to mt phng, mi cp lin kt lin nhau to to gc 900. To hai chp tam gic chng ln nhau. To bt din.
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Cng bc di lin kt
Ta c th gii hn di lin kt theo mun. Cch lm nh sau: 1. Chn lin kt mun thay i di. 2. Nhp chn Constrain Bond Length trong Build menu. Hp thoi la chn xut hin:
3. Tch chn Other v nh gi tr di mong mun vo. Nhp OK chn. 4. B chn lin kt. 5. Nhp chn Model Build trong Build menu thc hin cng bc lin kt. Ch : Vic cng bc lin kt lun nh hng n tnh ton, ta ch nn t khi thy cn thit. loi b cng bc ta chn li lin kt, tch chn Computed trong hp thoi cng bc v thc hin nh vi cch cng bc trn.
Cng bc gc lin kt
cng bc gc lin kt no ta lm nh sau: 1. Chn gc lin kt mun thay i. 2. Chn Constrain Bond Angle trong Build menu. 32
Hng dn s dng HyperChem 7.04 Hp thoi la chn xut hin:
3. Tch chn kiu gc mun thay i. Nhp OK chn. 4. B chn gc lin kt. 5. Nhp chn Model Build thc hin cng bc. Ch : Vic cng bc gc lin kt c nh hng n gi tr tnh ton. loi b cng bc ta lm tng t nh khi cng bc nhng tch chn Computed trong hp thoi la chn. Cc kiu la chn gc nh sau: Computed Linear Trigonal Tetrahedral Orthogonal Other Khng cng bc 1800 1200 109.470 900 Tu t gi tr t 3600 n +3600
Cng bc lin kt xon

Cch lm tng t nh kiu cng bc gc lin kt trn. Tuy nhin y ta phi chn lin kt xon gm t nht bn nguyn t. Hp thoi la chn cng bc nh sau:
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Cc kiu la chn: Computed Trans Cis Gauche+ GaucheOther Khng cng bc Cng bc 1800 00 600 -600 Tu gi tr t vo t 1800 n +1800
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Bi 3. To nhng phn t nh trong khng gian hai chiu (2D) v ba chiu (3D).
Cch v phn t trong khng gian hai chiu. Hiu chnh lin kt v cc nguyn t. Biu din phn t trn khng gian ba chiu. Lu cu trc phn t.
V phn t trn khng gian hai chiu

1. Nhp hai ln lin tip tri chut (Double-click) vo cng c v. Hp thoi la chn nguyn t s hin ra. 2. Tch (4) trong phn Allow Arbitrary Valence, v b tch trong phn Explicit Hydrogens. Nu ta khng b tch Explicit Hydrogens, th hydro lun t ng thm vo. 3. Chn nguyn t mun v, y ly v d chn Carbon.
4. Nhp tri chut, gi v r n cc im theo cng thc phn t mun v.
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Lu bc v vo trong mt File
Trc khi thc hin sa i bc v, ta hy lu bc v li. iu ny gip ta khng phi v li bc v ban u nu trong qu trnh chnh sa b hng.
Cch lu nh sau
1. Nhp tri chut vo Save (lu) trong File menu. HyperChem s hin ln hp thoi c dng nh sau:
2. nh tn file m bn mun t vo mc File name. 3. t kiu ui HIN lu dng nh trong phn Save as type. 4. Nhp tri chut vo nt Save lu file. Lc ny hp thoi lu t ng thot v ta c c hnh nh phn t hin ti lu. 5. Nhng thao tc lc sau trn phn t v, mun lu ta ch vic nhp vo Save. Nu mun lu vo tn file khc th ta nhp vo Save as trong File menu.
Thay i hnh thc lin kt

Vic sa i gip ta c th biu din phn t c cha cc lin kt i, ba hay l to vng benzen. 1. Nhp tri chut vo cng c v. 2. to lin kt i ta ch vic nhp tri chut vo gia lin kt n to ra trc .
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3. To lin kt ba bng cch nhp tip tri chut vo lin kt i to ra.
4. Ch : Mun sa tr li thnh lin kt n ta ch vic ln lt nhp phi chut vo gia lin kt i, ba to ra.To vng benzen bng cch nhp lin tip hai ln tri chut vo mch vng.
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Biu din nguyn t di cc dng nhn khc nhau

Ta hon ton c th biu din cc nguyn t trn trang lm vic di dng biu tng, tn, in tch, khi lng ca n.
Cch biu din nhn nguyn t

1.Nhp tri chut vo Labels trong Display menu.
Hp thoi nhn (label) hin ra nh sau: 38
2. Tch vo kiu nhn m ta mun biu din. 3. Nhp tri chut vo OK chn. Nu ta chn kiu biu tng (symbol) th trn mn lm vic cc nguyn t s c biu din di dng biu tng.
Chnh sa cc nguyn t
Nu trong phn t v, ta mun thay i nguyn t ny thnh nguyn t khc th cch lm nh sau. 1. Nhp hai ln tri chut vo cng c v trn thanh cng c. Bng cc nguyn t s hin ra. 2. Chn nguyn t mun thay th. V d chn oxi. 3. Nhp tri chut vo nguyn t mun thay th trong phn t v. V d nh cacbon.
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Nguyn t cacbon s c thay th bng nguyn t oxi.
Thm nhanh hydro cn thiu

nhanh chng thm nhng hydro cn thiu trong phn t ta c th thc hin d dng, cu trc sau khi thm hydro nhanh s dng khng gian ba chiu. Cch lm nh sau. 1. Nhp tri chut chn Add H & Model Build trong Build menu.
HyperChem s thc hin biu din phn t ta v trn khng gian ba chiu v t ng thm nhng hydro cn thiu.
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Nu vn khng thy hydro xut hin th hy tch (4) chn Show Hydrogens trong Display menu.
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Bi 4. Dch chuyn, quay v biu din h phn t theo t l mn lm vic.

Dch chuyn phn t theo cc trc. Quay phn t theo cc trc. Phng to, thu nh. Chuyn phn t thnh nhng lt nh theo trc z.
H to trong HyperChem
HyperChem c hai h to biu din phn t: H to ca ngi quan st v h to phn t. Mi h to u c cc trc to Decac x, y v z.
H to phn t tu thuc vo phn t , do khi dch chuyn phn t th h to cng thay i theo. Cn h to ca ngi quan st l khng i trong HyperChem, n c biu din nh hnh trn. Trong HyperChem khi ta s dng cc cng c ta dng nhp tri chut dch chuyn, quay l thc hin theo h to ngi quan st, vic dch chuyn ny xy ra cho ton b h phn t. Ta dng phi chut dch chuyn, quay theo h to phn t. Vic dch chuyn ny ch xy ra i vi cc nguyn t, hp phn, phn t c chn.
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H to ca ngi quan st
H to ca ngi quan st (Viewers Coordinate System) nh r v tr ca cc nguyn t lin h vi ta, ngi quan st. H to ca ngi quan st gn vi dng hnh hc mn hnh. Trc y thng ng, trc x nm ngang, trc z thng gc vi mt phng mn hnh. Trong h to ca ngi quan st, ta c th di chuyn phn t m khng lm thay i cc to nguyn t. Vi cc cng c trong HyperChem, ta dng tri chut dch chuyn cc phn t theo h to ca ngi quan st. Cc phn t dch chuyn nh ta nag thay i v tr quan st ca mnh. S dch chuyn nh hng ln ton b h phn t. Vi mt s hp thoi lc chn ca HyperChem, nh l Align Viewer (t thng ngi quan st), s dch chuyn l t ng theo to ca ngi quan st nu khng c nguyn t no c chn. Khi ta to mt phn t u tin, HyperChem t thng h to ca ngi quan st v h to ca phn t do cc trc x, y v z l tng ng nhau. Khi ta dch chuyn phn t, cc h to khng cn tng ng nhau na. Dng Align Viewer trong Edit menu dch chuyn h to ca ngi quan st n tng ng vi h to ca phn t. Khi ta lu h phn t vo file HIN, HyperChem cng lu c h to ca ngi quan st. Khi m li file ny ta s c ng h to lu.
H to ca phn t
H to ca phn t gn lin vi h phn t v nh r to ca cc nguyn t, cc ta ny c s dng trong tt c cc tnh ton ho hc ca HyperChem. Ta c th xc nh to phn t ca bt k nguyn t no bng cch la chn nguyn t . To ca nguyn t c chn xut hin trn dng hin trng (status line). Vi cc cng c ca HyperChem, ta dch chuyn cc nguyn t theo h to phn t bng cch s dng nt phi chut. Vic dch chuyn ny ch tc ng ln cc nguyn t, hp phn, v cc phn t c chn. Cng c (Tool) Chc nng ca nt phi chut 43
Hng dn s dng HyperChem 7.04 Quay theo XY Ch quay khi c phn t c chn. Quay theo Z Ch quay c phn t hay nhnh c th quay c. Dch chuyn theo XY Dch chuyn cc nguyn t hay phn t chn.(a) Dch chuyn theo Z Dch chuyn cc nguyn t hay phn t chn.(a) a. Chc nng ca nt phi c gii hn cho ton b phn t nu Whole molecule translation trong mc Tool ca hp thoi Preferences (trong File menu) c tch chn. Vi cc hp thoi ca HyperChem, nh l Align Molecules, s dch chuyn t ng theo h to ca phn t.
Trc qun tnh

i vi cc nguyn t hay c h phn t c chn, HyperChem c th tnh ton s chuyn ng theo qun tnh v c cc trc qun tnh. HyperChem bo s chuyn ng theo qun tnh trn dng hin trng v biu din cc trc qun tnh l cc ng nt t, c nh trong h to ca phn t. C ba s chuyn ng v ba trc (trc th nht, th hai v th ba) thc hin chc nng theo v tr v khi lng ca cc nguyn t. Cc trc qun tnh ph thuc vo h phn t v khng ph thuc vo h to ca ngi quan st ln h to ca phn t. Tch chn Show inertial Axes trong Display menu biu din cc trc qun tnh. C s trc dao (vung gc) v c nh s th t 1, 2 v 3 cho cc trc th nht, th hai v th ba ring. Cc trc vn hin trn mn lm vic cho n khi ta b tch Show inertial Axes trong Display menu. Trc qun tnh th nht thng biu th khong cch di nht qua h phn t, v trc qun tnh th ba biu th khong cch ngn nht.
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HyperChem dng cc trc qun tnh b tr cc phn t (Xem t phn t thng trc: Align Molecules) trn mn lm vic v khi nh r POINT, LINE v PLANE (xem phn chn: Select). Nhng s nh r ny l trong cc s hng ca cc trc qun tnh. in giao nhau ca cc trc qun tnh ti tm khi ca cc nguyn t chn. LINE Trc th hai ca cc nguyn t chn. (1) PLANE Mt phng hnh thnh t trc th nht v trc th hai, vung gc (trc giao) vi trc th ba ca cc nguyn t chn. (1) Trc th nht ng vi gi tr c trng nh nht trong s chuyn ng ca ma trn qun tnh. POINT
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t ch lm vic cho cc cng c

Tch chn Preferences trong File menu. Tch chn mc Tool trong hp thoi Preferences. Hnh nh hp thoi lc ny c dng nh sau:
Cc la chn gip ta trong qu trnh s dng cc cng c quay, phng to, dch chuyn trn mn lm vic. Gi tr t cho vic di chuyn chut t mp ny n mp i din trong mn lm vic. XY rotation Nu ta t l 360 th khi dch chuyn t mp ny n mp i din phn t s quay c 3600. Mc ny t c gi tr t > 0 n 36000. t c gi tr t > 0 n 36000. t c gi tr t > 0 n 1000A0. t c t l t > 0 n 1000 ln. t c di dch chuyn mt ct t > 0 n 1000A0. Khi tch chn, gip ta chuyn dch nhanh hnh nh h phn t. Nu ta tch chn mc ny th khi dng cng c hay hp thoi u dch chuyn c c phn t. Nu khng tch chn thi khi dch chuyn theo to ca phn t s ch dch chuyn c phn la chn trong phn t. (Dch chuyn quan st l nh nhau khi ta tch hay khng tch, ch c s khc nhau khi dch chuyn theo to phn t)
Z rotation Z translation Zoom Clip Fast translation Whole molecule translation
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Hng dn s dng HyperChem 7.04 Ch : Tng t ta cng t c ch cho cc cng c khi s dng bn phm bng cch t cc la chn trong mc Key ca hp thoi Preferences.
Nghch chuyn (Invert: chuyn (ho) thnh)

Nghch chuyn tin hnh chuyn ho hnh hc phn t (nghch chuyn) qua mt im (POINT). POINT l tm khi ca mt hay nhiu nguyn t chn. S dng hp thoi Name Selection trong Select menu xc nh POINT. Nu to ca mt nguyn t l x, y v z (lin h vi POINT), Invert chuyn chng thnh x, -y v -z. Khi ta thit lp mt POINT, ta c th nghch chuyn bt k nguyn t no chn, hoc nu khng c la chn th s nghch chuyn c h phn t. Ch : Invert chuyn qua mu xm hot ng c khi h chn POINT trong Name Selection.
nghch chuyn cc nguyn t v phn t ta lm nh sau:

1. Chn mt hoc nhiu nguyn t nh nghch chuyn POINT. 2. Chn Name Selection trong Select menu. Sau tch chn POINT trong hp thoi ny v nhp OK chn. 3. B chn tt c cc nguyn t. 4. Chn Invert trong Edit menu. Ch : Nu ta nghch chuyn cc nguyn t chn trong mt phn t HyperChem ch nghch chuyn cc nguyn t ny v c th bp mo cc lin kt ni vi cc nguyn t t phn ng yn ca phn t. Ta nn t Chirality trong hp thoi Labels d dng quan st s nghch chuyn. V d: nghch chuyn amino axit alanine. Khi carbon alpha l mt tm bt i, s nghch chuyn thay i s bt i ca nguyn t ny.
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Ta cng c th dng s nghch chuyn nghch chuyn cu hnh dng gh v dng thuyn.
Phn chiu (Reflect)

Phn chiu tin hnh chuyn ho hnh hc phn t (s phn chiu) qua mt mt phng (PLANE). S chuyn ho phn t ny c th to ra mt hnh nh qua gng cc nguyn t hoc ton b phn t chn. Nu PLANE l mt phng XY, khi Reflect chuyn to ca nguyn t t x, y v z (lin h vi PLANE) thnh x, y v -z. S dng hp thoi Name Selection nh r PLANE. PLANE l mt phng c xc nh theo trc qun tnh th nht v th hai ca cc nguyn t. Phn chiu tc ng ln cc phn t c chn, hoc nu khng chn th n tc ng ln ton b h phn t. Nu cc nguyn t c phn chiu c mt hay nhiu tm bt i, HyperChem lm thay i s bt i ca chng. Ch : Phn chiu chuyn qua mu xm hot ng c khi h phn t c phn la chn vi tn l PLANE. Ta nn t Chirality trong hp thoi Labels d quan st s thay i.
phn chiu cc nguyn t v phn t ta lm nh sau:

1. Chn t nht ba nguyn t phn chiu PLANE. 2. Chn Name Selection trong Select menu. Tch chn PLANE trong hp thoi v nhp OK chn. 3. B la chn cc nguyn t. 4. Chn Reflect trong Edit menu.
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Hng dn s dng HyperChem 7.04 V d: Phn chiu mt nhm bn ca cyclohexane:
Dch chuyn phn t theo trc xy

Ta c th dng cng c dch chuyn dch chuyn phn t n cc v tr trn mn hnh theo cc trc X v Y. Cch tin hnh nh sau 1. Nhp tri chut vo cng c dch chuyn. 2. Di chuyn con tr ln mn lm vic. 3. Nhp tri chut, gi v r phn t n v tr mi.
4. Nu mun dch chuyn n to c th ta c th dng hp thoi la chn. C hai cch lm xut hin hp thoi ny: 49
Hng dn s dng HyperChem 7.04 - Nhp tri chut chn Translation trong Edit menu. - Nhp lin tip hai ln tri chut vo cng c dch chuyn. Hp thoi xut hin nh sau:
5. Nhp tri chut vo tng la chn dx, dy, dz v nh s thch hp vo . C th dch chuyn gia cc phn la chn khc nhau nh s bng cc nhp phm Tab trn bn phm. 6. Nhp OK chn sau khi nh cc s theo mun. Cc mc trong hp thoi dch chuyn:
Translate Viewer (chuyn dch quan st) dx dy dz Translate Selection (Chuyn phn la chn)
Dch chuyn ton b phn t trong mn lm vic, nhng cho php to cc nguyn t khng thay i. y ging nh dng nt tri chut vi cng c dch chuyn trn mn lm vic. Lng chuyn sang phi, A0. Lng chuyn ln trn, A0. Lng chuyn ra pha ngi quan st, A0. Chuyn tm khi ca cc nguyn t c chn n mt im mi, lm thay i to nguyn t. y ging nh dng phi chut vi cng c dch chuyn trn mn lm vic. Nu ch mt phn phn t c chn, v khng c tch chn Whole Molecule translation (trong mc Tool ca hp thoi Preferences) th HyperChem s ch dch chuyn phn la chn. POINT Dch chuyn phn t hoc cc nguyn t chn n POINT (im) xc nh trong hp thoi Name Selection. Origin Dch chuyn phn t hoc cc nguyn t chn n h to ban u. 50
Hng dn s dng HyperChem 7.04 Other Dch chuyn phn t hoc cc nguyn t chn n to mi do ta t.
Dch chuyn theo trc Z

Trong HyperChem thit k cng c ta dch chuyn nhanh phn t theo trc XY ring v trc Z ring. Tuy nhin cch lm u ging nhau. Nhng hp thoi la chn c th to mun dch chuyn l nh nhau. Cng c dch chuyn nhanh theo trc Z c dng sau: Ch : a phn t dch chuyn tr li trung tm mn lm vic ta ch cn nhp vo phm trn bn phm. S dch chuyn ch c tc dng khi ta dch chuyn cng c sao cho phng dc theo cng c lun song song vi trc z ngm nh ca HyperChem, iu c ngha l ta phi dch chuyn cng c ln xung theo trc thng ng (trc Y).
S dng cng c phng to

i khi phi xem chi tit v tr no trn phn t ta cn phng to v tr , cng c khi ta mun xem ton b h th li phi thu nh va phi. Do vic s dng cng c phng to, thu nh l cn thit.
Cch s dng cng c phng to (zoom tool)

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Hng dn s dng HyperChem 7.04 1. Nhn phm Shift ng thi nhp tri chut vo gn nh phi ca biu tng phng to, gi nh vy cho n khi phn t trn mn hnh nh nh mong mun. 2. phng to ta cng lm tng t nhng lc ny nhp tri chut vo gc di bn tri ca biu tng phng to. Phn t c phng to c dng nh:
Ch : ch s dng c vi phm Shift khi HyperChem trn my l ci t. i vi phn mm ch c copy gia cc my th khng thc hin c nh vy m ta phi dng cc phng php khc. Ta cng c th phng to hay thu nh bng cch iu khin trc tip chut hoc s dng hp thoi chn kch c c th. 1. Thao tc bng chut - Nhp tri chut vo biu tng phng to. - Di chuyn con tr xung mn lm vic. - Nhp tri chut v r theo phng to-nh ca biu tng phng to hay thu nh phn t. 2. S dng hp thoi - Ta nhp lin tip hai ln tri chut vo biu tng phng to trn thanh cng c hoc nhp vo Zoom trong Edit menu. Hp thoi la chn hin ra. - nh vo kch c m ta mun phng to hay thu nh. - Nhp OK chn. 52
+Zoom Factor: h s phng to.
t phn t tr li tm v biu din theo t l

Khi mt h phn t c m t File, n c biu din tm mn lm vic theo kch c chun nh sn. Nhng do qu trnh thao tc lm lch v tr ban u ca n i. Nhng ta hon ton c th a n tr li tm mn lm vic vi t l chun nh sn.
Cch lm nh sau
1. Nhp tri chut chn Scale to Fit trong Display menu, hoc nhp nt Spacebar trn bn phm. Phn t s c a tr li kch c ban u v n c t vo tm mn lm vic. Ch : Ta c th a phn t tr li tm vi kch c chun ban u bng cch chn gi tr 1 trong hp thoi ca cng c phng to.
Quay phn t theo phng XY

quay phn t theo cc trc x, y ta dng cng c quay. Cch lm nh sau 1. Nhp tri chut vo cng c quay theo trc XY. 2. Di chuyn con tr xung mn lm vic. 3. Nhp tri chut, gi v r theo phng x, y m ta mun xoay phn t. Hnh nh trn mn hnh c dng nh sau:
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Quay phn t theo trc Z

quay phn t theo trc z ta s dng cng c quay theo trc z.
Cch lm nh sau
1. Nhp tri chut vo cng c quay theo trc z.
2. a con tr xung mn hnh. 3. Nhp tri chut v r qua tri hay phi xoay phn t theo mun.
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Hng dn s dng HyperChem 7.04 Ch : R chut theo chiu ln xung khng c tc dng g trong cch quay ny. Ta cng c th s dng hp thoi la chn quay. Vic ny thc hin bng cch nhp chn Rotate trong Edit menu hoc nhp lin tip hai ln tri chut vo cng c quay trn thanh cng c hp thoi la chn xut hin. Hp thoi la chn quay:
Rotate About
X Axis Y A xis Z Axis LINE Angle Apply to Molecules Viewer
Ta c th quay cc nguyn t la chn, hoc khng la chn, hoc c h phn t quanh mt trc theo h to ca ngi quan st hay h to phn t, hoc quanh mt LINE (ng). LINE l phn la chn c t tn ph thuc vo h phn t. Nu ta khng th quay cc nguyn t chn, HyperChem biu din mt dng thng tin trn thanh hin trng. L trc trong mt phng nm ngang ca mn hnh Trc trong mt phng thng ng ca mn hnh Trc vung gc vi mt phng mn hnh L tn ca phn la chn. Ta dng Name Selection t LINE chon h phn t. t gc quay. Gi tr thay i t 360 n +3600 Quay cc nguyn t chn hay ton b h phn t theo cc cch: Quay theo h to ca phn t, lm thay i to ca cc nguyn t. Quay theo h to ca ngi quan st, to ca cc nguyn t khng i.
Ct phn t thnh tng lt nh theo trc Z
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Hng dn s dng HyperChem 7.04 Vi cng c ct phn t theo trc z s gip cho ta quan st k hn bn trong phn t t nhng lt ct nh
Cch lm nh sau
1. Xoay phn t bng cng c xoay sao cho khi ct ta d quan st.
2. Nhp hai ln tri chut vo cng c ct theo trc Z, hoc nhp tri chut vo Z Clip trong Edit menu.
Hp thoi la chn xut hin:
3. Ta c th ko thanh cun hoc chn ch s thch hp ct phn t theo mun. Sau khi chn ct xong ta nhp OK thc hin. Hnh nh phn t b ct v d nh sau:
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4. Mun ct tip ta thc hin nhp li vo cng c ct v thc hin nh trn. Ch : Ta cng c th thc hin ct phn t bng chut trn mn lm vic. Cch lm nh sau: 1. Nhp tri chut chn cng c ct theo trc Z trn thanh cng c v di chuyn cng c ct ln mn lm vic. 2. Nhp tri chut gi v r thng ng iu chnh v tr ct mt phng pha trc ca phn t. 3. Nhp Phi chut, gi v r thng ng iu chnh v tr ct mt sau ca phn t.
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Hng dn s dng HyperChem 7.04 4. Di chuyn chut t mp trn xung mp di mn lm vic ta s dch chuyn mt phng ct c khong 10A0 (Ngm nh). Ta c th xem dch chuyn trn dng hin trng bn di ca s HyperChem. Ch : a phn t tr li trng thi ban u ta ch vic nhp vo nt Spacebar trn bn phm.
Ch thch hp thoi Z Clip
System Slab
V tr xa nht ng trc v ng sau ca ton b phn t trn mn lm vic. V tr mt phng ct trc v sau gn vi ngi quan st.
Dng cc dng nm (Wedge) biu din lin kt trong khng gian

HyperChem cho php ta biu din cc lin kt trong khng gian bng cch biu din lin kt di dng cc hnh nm. Cc hnh nm c s dng vi quy c nh sau:
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Cch thc hin nh sau: 1. Nhp chn Rendering trong Display menu, sau chn mc Sticks v tch chn Wedges, nhp OK ng hp thoi. 2. Nhp tri chut chn cng c v trn thanh cng c. 3. Nhn phm Shift trn bn phm ng thi nhp tri chut vo lin kt mun biu din cho n khi c dng mong mun. 4. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c dng trnh xy dng biu din li cu trc trong khng gian, nu mun.
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Bi 5. Xem thuc tnh cu trc phn t

Trong bi ny ta hc cch o cc thuc tnh cu trc ca phn t nh l gc lin kt, di lin kt, gc vn
Xem thuc tnh ca nguyn t Cch lm nh sau:

1. Nhp tri chut tch vo Atoms v b tch Multiple Selections trong Select menu. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp tri chut vo nguyn t mun bit c tnh. Nguyn t c la chn s sng hn v c tnh ca phn t hin ra thanh hin trng bn di.
Dng hin trng cho ta bit s nguyn t, tn nguyn t, in tch nguyn t theo trng c hc phn t hin ti, to theo cc phng x, y v z.
o di lin kt
Ta hon ton c th xc nh c di cc lin kt trong phn t. Gi tr di ny trnh by trong dng hin trng bn di.
Cch o nh sau
1. Nhp tri chut vo cng c la chn trn thanh cng c. 60
Hng dn s dng HyperChem 7.04 2. Nhp tri chut vo nguyn t th nht mun o ko n nguyn t th hai ri nh chut ra. Lin kt gia hai nguyn t s sng hn, di o c biu din dng hin trng. Ch : Sau khi thc hin tnh ton ti u h phn t ta c th bit c gi tr thuc tnh khc ca h bng cch nhp chn phn mun xem hoc xem thuc tnh c h (khng cn chn phn no) tip theo chn Propeties trong Computer menu. Mt hp thoi thuc tnh hnh hc xut hin trn mn lm vic, vi c h c th c c cc gi tr v nng lng ton phn, nhit hnh thnh, momen lng cc...
o gc lin kt
o gc lin kt ta nhp tri chut vo nguyn t th nht v r n nguyn t th ba (theo th t lp thnh gc). Cch o gc lin kt 1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp tri chut vo nguyn t th nht r n nguyn t th ba (theo th t to nn gc) ri nh chut.
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o gc vn
Ta c th o gc vn bng cch r chut chn hai phn t u v cui trong bn phn t to nn gc vn.
Cch lm nh sau
1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp tri chut vo phn t u r n phn t th t trong bn phn t to nn gc vn ri gii phng chut. Hnh nh v d nh sau:
3. Gi tr gc vn hin th trong dng tnh trng di. 62
o khong cch khng lin kt o khong cch khng lin kt ta lm nh sau

1. Nhp tri chut tch vo Multiple Selections trong Select menu. Vic bt Multiple Selections cho php ta chn nhiu nhm, ngoi ra khi ta la chn nhm th hai th nhm th nht vn c chn. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp phi chut vo phn trng trn mn lm vic. Vic ny gip ta hu b tt c cc la chn trc . 4. Nhp tri chut ln lt vo hai nguyn t khng lin kt. Khong cch gia chng hin th trn dng hin trng.
Lin kt Hydro
gip ta xc nhn iu kin to lin kt hydro, HyperChem cho php ta tnh ton v biu din lin kt ny. Lin kt hydro c hnh thnh khi khong cch t hydro cho n nguyn t nhn b hn 3,2 A0.
biu din lin kt hydro ta lm nh sau

1. 2. 3. 4. Nhp tri chut vo cng c la chn trn thanh cng c. Nhp phi chut vo vng trng trn trang lm vic. Nhp tri chut tch vo Show Hydrogen Bonds trong Display menu. Nhp tri chut chn Recompute H Bonds trong Display menu. HyperChem s biu din cc lin kt hydro nu c di dng ng nt t nh sau:
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Hng dn s dng HyperChem 7.04 Lin kt hydro khng t ng tnh ton ng thi vi qu trnh ti u hnh hc phn t. Do ta phi tnh lin kt hydro li mi khi cn thit.
Recompute Hydrogen Bonds

Tnh ton li lin kt hydro xc nh cc lin kt hydro gia cc phn t chn hoc nu khng c s la chn, th n xc nh lin kt hydro gia tt c cc nguyn t trong h phn t. HyperChem to ra cc lin kt hydro nu khong cch gia cc hydro cho v nguyn t nhn b hn 3.2A0 v gc to bi lin kt cng ho tr t hydro cho n cc nguyn t nhn ln hn 1500. Tuy nhin ta cng c th thay i cc tiu chun ny.
Biu din momen lng cc

Khi ta tch chn Show Dipole Moment, HyperChem s biu din momen lng cc tnh ton cho cc nguyn t c chn hoc cho c h phn t. Show Dipole Moment ch hot ng sau khi ta thc hin tnh ton im n. Momen lng cc biu din trn mn hnh dng ng nt t tm khi ca cc nguyn t chn. Dng hin trng cho bit tng gi tr ca momen lng cc v gi tr momen theo cc trc khc nhau theo n v Debye.
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Bi 6. Databases Menu
To chui Polypeptide
Ni cc hp phn li vi nhau Thm phn cn thiu cho chui Thay i hp phn v tr c bit
S dng hp thoi la chn cc Amino Axit

Hp thoi la chn cha cc hp phn amino axit c cu trc ho hc chun. Trong hp thoi ta chn cc cu hnh bc hai ca polypeptit (Xon apha, mng beta hay cc kiu gc khc ta t: gc Phi, Psi v Omega). Ta chn xy dng chui bt u t amino axit c im N cui (N-Terminus: ui nit). Trong hp thoi gm c: 20 amino axit chun. Hai kiu trung tnh v mt kiu proton ho ca histidine (Hid, Hie v His). pH sinh l, histidine c th mang in tch dng hoc trung ho tu thuc vo mi trng. Half-Cyx (bn Cystine) dng to lin kt ngang i sunfua. Mt nhm c im N cui (N-teminal: Ace). N ch c dng lm hp phn khi u cho chui. Mt nhm c im C cui (C-teminal: Nme). N ch c dng kt thc chui.
m hp thoi cch lm nh sau

1. Nhp tri chut vo Amino Acids trong Databases menu. Hp thoi Amino axit xut hin nh sau:
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Hng dn s dng HyperChem 7.04 Hp thoi Amino axit hin cho ti khi no ta nhp vo nt tt trn gc phi. - Ala Alanine, thuc cht bo trung tnh, khng cc. - Gly Glycine, trung tnh, c cc. - Ser Serine, trung tnh, c cc. - Thr Threorine, trung tnh, c cc. - Leu Leucine, trung tnh, thuc cht bo, khng cc. - Ile Isoleucine, trung tnh, thuc cht bo, khng cc. - Val Valine, trung tnh, thuc cht bo, khng cc. - Asn Asparagine, trung tnh, c cc. - Gln Glutamine, trung tnh, c cc. - Arg Arginine, tch in dng. - Hid Histidine, trung tnh, c hydro nit delta. - Hie Histidine, trung tnh, c hydro nit epsilon. - Hip, His Histidine, tch in dng, c hydro c nit delta v epsilon. - Trp Tryptophan, vng thm trung tnh, khng cc. - Phe Phenylalanine, vng thm trung tnh, khng cc. - Tyr Tyrosine, vng thm trung tnh, c cc. - Glu Axit Glutamic, tch in m. - Asp Axit Aspartic, tch in m. - Lys Lysine, tch in dng. - Pro Proline, trung tnh, khng cc. - Cys Cysteine, trung tnh, c cc. - Cyx Bn Cystine, trung tnh, c cc. Nu ly t file PDB ta s c hp phn Cystine y . - Met Methionine, trung tnh, khng cc. - Ace Acetyl, Nhm c im N cui (N-teminal). - Nme N-Methyl amino, Nhm c im C cui (C-teminal).
To dng v biu din chui Polypeptide

Cc chui Polypeptide thng c hnh dng rt phc tp. d dng trong vic to dng v quan st ta phi la chn hnh dng biu din thch hp c v mt ho hc ln kh nng quan st. Trong phn ny ta hc cch dng cu trc bc hai ca polypeptide. Ch : Ta khng thm bt hay sa i g cc hp phn bng cch dng cng c v. sa i ta s hc cc bc sau (xem Thay th monome trong hp phn bng amino axit khc; To ion lng cc).
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Hng dn s dng HyperChem 7.04 HyperChem ni kt cc hp phn li vi nhau theo th t ta chn chng. Khi nhp chn hp phn c C-teminal (cn gi l np bt: cap), n s ngn cn khng cho ni thm cc hp phn khc vo chui. Nu ta chn tip th mt chui khc s c hnh thnh. Khi ko di chui, ta c th thay i cc thuc tnh ca cc hp phn tip theo: - Cu trc bc hai(xon alpha, mng beta, hay cc gi tr do ta t Other) - Cu hnh ca lin kt peptit (Omega) - ng phn L hoc D ca mi hp phn.
Cch lm nh sau:
1. Nhp tri chut chn Amino Acids trong Databaes menu. 2. Tch chn Beta sheet trong hp thoi Amino Acids. iu ny gip biu din cc gc vn phi v psi 1800. 3. t gc vn omega l 1800.
To chui
1. Nhp tri chut ln lt vo cc amino axit m ta mun ni thm vo. V d nh sau: Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg. Ch : Ta khng s dng trnh xy dng (Model Builder) dng li ton b cu trc chui. Trnh xy dng s lm hng cu trc ti u ca phn t v khng th ly li chnh xc cu trc ban u. Tuy nhin ta c th dng trnh xy dng i vi cc nguyn t c chn no . Nu chui polypeptide khng c np bt, ta c th thm tip cc hp phn n hp phn c C-teminus. Nu ta thc hin to ion lng cc (Make Zwitterion), ta cng khng th thm cc hp phn c na, khi chn thm hp phn th mt chui khc s c xy dng. Hp phn ca chui c th c cu hnh bc hai khc nhau. Chui polypeptide c th cng c cu trc xon alpha, cu trc gp beta cng nh cc cu hnh chuyn ho khc.
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Xon Alpha (Alpha helix: xon c alpha) Mng beta (Beta sheet)
t chun cc gc vn Phi v Psi l -58 v -470 cho xon alpha, cng vi lin kt peptit chuyn tip (transpeptide) (Omega = 1800). t chun cc gc Phi v Psi cng l 1800 v cng t tm gp khc tm beta l 1800, cng vi mi lin kt peptit chuyn tip (Omega = 1800).
Other Chp nhn gi tr khng chun cho cc gc vn Phi, Psi v Omega. Phi Gc vn () ca C-N-C-C: Thay i t 360 n +3600 Psi Gc vn () ca N-C-C-N. Thay t 360 n +3600. Omega Gc vn lin kt peptit (),thng thay i t 170 n 69
Hng dn s dng HyperChem 7.04 1800. p dng cho hp phn amino axit tip theo. Thay i t 360 n +3600. Cho php ta chn ng phn lp th L thng thng (Khng i xng S) hoc ng phn lp th D (khng i xng R).
Isomer
Ch : Ta c th dch chuyn hp thoi amino axit trn mn hnh v s dng c cc cng c khc (v d nh t nhn trong Display menu).
To ion lng cc (Make Zwitterion)

Trong dung dch c pH trung tnh, cc polypeptide tn ti di dng cc ion lng cc, cha cc nhm ui l -NH3+ v -COO-. Thc hin to ion lng tnh cho phn t polypeptide chn nhm chuyn cu trc theo file d liu thnh ion lng tnh. Nu khng c polypeptide no c chn th Make Zwitterion s thc hin cho tt c cc polypeptide trong h. Cc polypeptide thc hin c Make Zwitterion phi c nhm ui thng thng (-NH v -CO) ch khng phi l cc nhm np bt (cap: Ace v Nme). Khi ta dng chui peptit vi HyperChem, cc phn ui cha y (cn l -N-H v -C-O). Make Zwitterion chuyn i cc phn ui thnh NH3+ v -COO-.
Cch lm nh sau
1. Chn none ( phn Atoms) trong hp thoi Labels d nhn. 2. Dch chuyn v quay phn t polypeptide gip ta d quan st.
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3. Nhp tri chut chn Make Zwitterion trong Databases menu. HyperChem s thm vo oxi cn thiu trn nguyn t C.
HyperChem cng thm c cc proton cn thiu vo nguyn t N.
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Hng dn s dng HyperChem 7.04 Ch : Cc hp phn amino axit trong file d liu (Trong Database hay File PDB) bao gm cc nguyn t vi phn din tch ring. Khi thc hin Make Zwitterion s lm thay i in tch nhm nguyn t ui (Teminal). N khng lm thay i in tch ca cc nhm bin ca cc amino axit (v d xem cc nhm bin axit, baz hay cc nhm imio C3H4N2).
B Ion cc ui (Remove Ionic Ends)

B ion ui ngc li vi kt qu Make Zwitterion. iu ny tc l chuyn cc nhm NH3+ v -COO- trong polypeptide thnh NH v -CO.
Thay th mt monome trong hp phn bng mt amino axit khc

Th t ca cc amino axit trong chui ng mt vai tr quan trng trong cu trc chui. Mi s thay i th t hay thay th mt monome ny bng mt monome khc u dn thay i cu trc v thuc tnh ca protein, do cng thay i chc nng ca n.
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Cch lm nh sau
Trc tin cn phi bit tn v v tr amino axit hp phn cn thay th. 1. Nhp tri chut vo Labels trong Display menu. 2. Nhp tri chut tch chn Name + seq trong hp thoi Labels. Nhp OK mn hnh s hin ra nh sau.
3. Nhp tri chut tch chn Residues trong Select menu. 4. Nhp tri chut vo cng c la chn trn thanh cng c. 5. Nhp phi chut vo vng trng mn lm vic loi b tt c cc la chn c th c trc . 6. Nhp tri chut vo PHE 5. Hp phn ny s sng hn ln. 7. Nhp tri chut chn Mutate trong Databases menu.
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Ch : Mutate s khng hot ng nu ta cha tch chn Residues trong Select menu. 8. Trong hp thoi Mutate, ko thanh cun chn amino axit mun thay th. V d chn Thr.
iu ny c ngha l phenylalanine c thay th bng threonine:
Ch : Nh lu tn phn t m bn mi to bng mt tn thch hp. i vi nucleic axit ta cng lm tng t.
Cc Axit Nucleic
V c bn cch xy dng chui polycucleotide tng t nh cch xy dng polypeptide trn. Ta s dng cc Axit Nucleic xy dng chui polynucleotide (AND v ARN). Cc hp phn ny c cu trc ho hc chun.
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Hng dn s dng HyperChem 7.04 Trong hp thoi Nucleic Acids, ta c th chn cc cu trc bc hai cho cc hp phn thm vo (A, B, Z hoc cc kiu gc cu hnh khc m ta t). Ta c th to chui polynucleotide bt u t cc ui 5 hoc 3 bng cch nhp chn cc hp phn axit nucleic ny: - Bn deoxyribonucleotide (monophosphat) - Bn ribonucleotide (monophosphat) - Np bt (Cap) A 3 cn tr ko di chui thm. - Np bt A 5 cn tr ko di chui thm. Ch : Ta khng chnh sa cc hp phn bng cng c v. Ta c th thm bt hay chnh sa cc hp phn nh trng hp Amino axit trn. HyperChem ni kt cc hp phn li vi nhau theo th t ta chn cc hp phn, bt u t phn ui 5. y l trt t t nhin ca qu trnh tng hp AND v ARN. Nu ta mun xy dng chui bt u t ui 3 th phi tch chn Backward (ngc) trong hp thoi. Cc u bt (cap) ngn cn vic thm tip cc hp phn k c cc hp phn ui 5 v 3. Sau khi thm mt u bt, vic chn thm hp phn mi s to mt chui khc. Nu chui cha c u bt, ta c th thm c nhiu hp phn na cho n khi c u bt. Khi ko di chui, ta c th thay i thuc tnh ca cc hp phn tip theo m ta thm vo: - Cu hnh bc hai (A, B, Z hay cc kiu khc). - K c kiu gp 2 Endo (gp ni) hay 3 Endo cho vng ng. Kiu A ca AND thng cha ng deoxyribose dng C3-endo bn vng hn. Kiu B ca AND cha ng C2-endo. - Double-Stranded (Kt i thnh phn). Tch chn phn ny th khi nhp chn axit, ngoi axit ta chn cn c thm baz lin hp ca chnh n, gia chng c cu ni hydro vi nhau (Tch chn Recompute H Bonds trong Display menu xem lin kt hydro). HyperChem quan tm ch yu n cp baz; mt s lin kt trong hp phn lin hp c di lin kt khng ng v mt s cp baz cng khng c cc gc cun chnh xc. Ta cn phi ti u hnh hc li sa cc li trong cu trc.
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Hng dn s dng HyperChem 7.04 Ch : Khng s dng trnh xy dng (Model Builder) i vi polynucleotide xy dng. Trnh xy dng s lm hng hnh hc ca phn t v khng th xy dng li chnh xc c. Cc la chn ta t c nh hng n cc hp phn sau cho n khi ta thay i kiu la chn khc. Ta khng th thay i thuc tnh sau khi tch chn hp phn . Hp thoi Nucleic Acids c dng nh sau:
Cc kiu hp phn trong hp thoi nh sau: - dA Deoxyadenosine 5 monophosphate, hp phn ca AND. - dT Deoxythymindine 5 monophosphate, hp phn ca AND. - dC Deoxycytidine 5 monophosphate, hp phn ca AND. - dG Deoxyguanosine 5 monophosphate, hp phn ca DNA. - rA Adenosine 5 monophosphate, hp phn ca ARN. - rU Uridine 5 monophosphate, hp phn ca ARN. - rG Guanosine 5- monophosphate, hp phn ca ARN. - rC Cytidine 5 monophosphate, hp phn ca ARN. - 5CAP u bt kiu A (-OH) kt thc chui ui 5. - 3CAP u bt kiu A (-OH) kt thc chui ui 3. Cc la chn cho hp phn nh sau: Helix Form t cu hnh bc hai cho cc hp phn ca chui. (Kiu xon c) Mi dng xon c c gc vn, cun (s vng quay ca mi phn) v cao (Chiu cao ca mt vng) c trng ring. A Form Cu hnh xon phi trong AND kt i, kh nc, c (Kiu A) khong 11 hp phn mi vng.
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Hng dn s dng HyperChem 7.04 B Form (Kiu B) Z Form (Kiu Z) Other (Kiu khc) Cu hnh xon phi trong AND kt i, kh nc, vi khong 10 hp phn mi vng. Cu hnh xon phi ca AND kt i, vi khong 12 hp phn mi vng. Xen k cc hp phn (c nh s chn l: odd, even) trong mi phn ca Z AND c cc gc vn khc nhau. Nhn cc gi tr ta t cho gc vn trong lin kt khung chui polynuleotide.
Alpha Beta Gama Chi Delta Epsilon Zeta
() Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600.
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- Sugar Form 2 Endo 3 Endo - Double Strand
- Backward
Cu hnh ca vng ribo. C2 l ngoi mt phng vng, trn cng mt phng nh C5. C3 l ngoi mt phng vng, trn cng mt phng nh C5. Khi phn ny c tch chn, HyperChem thm hp phn lin hp ca chnh n, theo quy tc cp baz ca Watson-Crick, v dng ln mt polynucleotide khng song song. Ta c th tch hoc khng tch dng cc phn t c baz kt i mt phn. Khi tch chn phn ny, HyperChem bt u xy dng chui t phn ui 3, thm dn cc hp phn n phn ui 5. iu ny ngc li vi qu trnh tng hp AND v ARN thng thng. Vic t nh vy nh hng n ton b chui, do ta phi t n trc khi bt u xy dng chui.
Ch : Ta vn c th s dng cc cng c khc khi hp thoi Nucleic Acids cn trn mn hnh.
Thm cc ion tri du (Add Counter Ions)
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Hng dn s dng HyperChem 7.04 Add Counter Ions t mt ion natri gn mt nhm photphat trn khung lin kt ca chui polynucleotide. Ion Na+ cch u mi oxy ca nhm photphat mt khong 1.688A0.
Nu ta chn Add Counter Ions v sau thm cc hp phn khc, th ch cc hp phn u mi c ion tri du. Ta phi chn li Add Counter Ions li thm cc ion Na+ cho cc hp phn mi. Ch : loi b cc ion Na+ ta s dng chn cc ion mun loi b v dng Clear hoc Cut trong Edit menu. Nu ta lu h vo file HIN th cc ion tri du cng c lu. Dng tinh th (Crystal Builder) Crystal Builder l mt modun dng c, to v quan st cu trc tinh th trong HyperChem. Cc cu trc tinh th c th c lu, chnh sa hoc tnh ton nh bt k h no khc. Crystal Builder c cc tnh nng nh sau: - D dng xy dng cc tinh th nguyn t da trn cc kiu tinh th c bn: lp phng, t din, trc thoi (orthorhombic), hnh lng din (rhombohedral:c cc mt hnh thoi), su cnh, n t (monoclinic) v tam t (triclinic) - Cc cu trc mu nh l NaCl, CsCl, CaF2, PbS, MgO, ZnS - C th hiu chnh d liu nguyn t nh l vi to ca chng trc khi to tinh th. - C kh nng quan st cc mt khc nhau ca tinh th, xc nh ch s Miller. 79
Hng dn s dng HyperChem 7.04 - C kh nng c v vit cc file trong ngun d liu b tr bn ngoi.
Cc lnh s dng trong xy dng tinh th

File/new File/Open File/save None Xem dng a Xem dng cu Xo trng mn lm vic M file lu trc Lu kt qu trn mn lm vic Bt Stick trong Rendering Bt Disk trong Rendering Bt Sphere trong Rendering
Xem b mt tinh th HyperChem/Get t t bo n v t HyperChem HyperChem/Put Gi tinh th n HyperChem Tm tr gip
To tinh th kim loi Natri

Phn ny minh ho cho ta cch to cu trc tinh th Natri 1. Khi ng HyperChem, tip theo tch chn Crystal trong Databases menu. 2. Trong mc Crystal Type, tch vo Cubic (lp phng) chn t bo n v dng lp phng.
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3. Nhp s t bo n v: 3x3x3 bng cch nh gi tr 3 vo trong ba tng ng. 4. Trong mc Unit Cell Parameters, nhp kch thc ca t bo cho Na: 4.225 cho u tin t a, b, c =. Gi tr ca b v c s c t ng t l 4.225. 5. nh s th t ca cc nguyn t trong t bo n v Na (bcc): 2 cho thch hp. 6. Nhp tri chut vo Edit Atom Date.. m hp thoi d liu nguyn t (Atom Data). 7. Trong hp thoi nn biu din s th t nguyn t l 1. Thay i tn nguyn t t - thnh NA1. i nguyn t thnh Na. 8. Nhn ln dng trn trong nt spin hoc nhp s 2 cho s th t nguyn t, d liu ca 2 nguyn t s c biu din. Thay i a, b v c t 0 n 0.5. Chuyn tn nguyn t t - thnh NA2. Nhp vo nt Close. 9. Nhp chn nt lnh: HyperChem/Put chuyn cu trc to c vo cho HyperChem, hoc ln lt nhn nt Toolbar i n khi cc cht lng mu xanh xut hin. 10. Tinh th natri 3x3x3 s xut hin trn mn lm vic ca HyperChem. 11. quan st mt phng tinh th [111], chn lnh View/Crystal Face trong Crystal Builder hoc nhp vo nt View trn thanh cng c. Mt hp thoi s xut hin. Nhp gi tr 1 cho cc h, k v l, nhp OK, v HyperChem s quay tinh th v t ct mt phng nhm biu din cho ta mt [111]. Dng lnh Display/Rendering trong HyperChem chuyn dng biu din nguyn t sang dng cu. 12. Lu t bo n v bng cch nhp lnh File/Save as (Nhp Save as trong File menu). nh tn mun lu vo mt file mi: NA.CSD. Nhp OK, v t bo n v c lu vo kiu D liu tinh th Cambridge.
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Hng dn s dng HyperChem 7.04 13. Lu ton b tinh th bng cch nhp vo ca s HyperChem v chn lnh File/Save as... Lu file vi tn mi l: NA.HIN.
To tinh th NaCl
Phn ny ta s hc cch to tinh th ca natri clorua. 1. Tch chn Crystal Builder bng cch nhp Crystals.. trong Database menu. 2. Nhn nt Samples.. vo hp thoi cu trc tinh th mu (Sample Crystal Structure) 3. Chn kiu tinh th NaCl bng cch nhp vo nt thch hp v nhn OK chn. 4. Nhp s t bo n v l: 3x3x3 bng cch nhp gi tr 3 vo trong ba hiu chnh. Khng nn hiu chnh g n tham s t bo n v: Trnh xy dng tinh th (Crystal Builder) t cc gi tr thch hp cho NaCl. 5. Chn lnh: HyperChem/Put gi cu trc cho HyperChem, hoc nhn nt Toolbar i khi c dung dch mu xanh xut hin. 6. Tinh th NaCl 3x3x3 s xut hin trn mn lm vic. 7. quan st mt phng tinh th [111], chn lnh View/Crystal Face trong Crystal Builder hoc nhp vo nt View trn thanh cng c. Mt hp thoi s xut hin. Nhp gi tr 1 cho cc h, k v l, nhp OK, v HyperChem s quay tinh th v t ct mt phng nhm biu din cho ta mt [111]. Dng lnh Display/Rendering trong HyperChem chuyn dng biu din nguyn t sang dng cu(nu mun).
Dng mt ct [111].
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Xy dng phn t ng (Sugar Builder)

Trnh xy dng ng (Sugar Builder) cho php ta xy dng cu trc polysaccharite tng t nh xy dng chui amino axi hay chui axit nucleic. Ta c th to cc hp phn theo mun ch khng nht thit phi l saccharite (sacarit), v dng Sugar Builder ni kt cc hp phn li vi nhau. Cc tnh nng ca Sugar Builder - C 32 mu monosaccharite thng thng, bao gm c aldose v ketose, k c dng D, L, alpha, beta v dng xp xon (acyclic). - C kh nng thm cc nhm thng thng, k c OAc v Nac. - C kh nng to chui t cc mono hnh thnh nn chui polysaccharite. - Tham s ho trng lc AMBER cho chui (aldose). - C kh nng ni kt cc chui to cc nhnh. - C kh nng thm ln n 21 hp phn ca ngi s dng vo file d liu. To chui Phn ny minh ho cho ta cch to poly(1-4)--D-Glucose 1. Nhp tri chut chn Saccharides trong Database menu. 2. Dng lnh Add/Aldoses m hp thoi Aldoses. 3. Chn D v chn Dng phn D v anome . 4. Chn Glucoses to ra hp phn glucose trong HyperChem. 5. Chn kiu ni kt 1-4 bng cch chn n t list. 6. t v ln lt l 48.05 v -20. 7. Nhp tri chut lp i lp li vo Glucose cho n khi nhn c chui mong mun. 8. Chuyn ra mn hnh HyperChem v quan st chui mi to.
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Dng chui polymer

dng mt chui polyme, hy ch n kh nng xem phn t n trn mn lm vic c kh nng to chui khng. Nhng vic cn lm l xc nh phn u v phn ui ca phn t, ng thi xc nh gc vn, gc lin kt s c dng ni kt lp i lp li u vi ui cho n khi to thnh chui vi di mong mun. Trnh xy dng polyme ch xy dng cu trc ca polyme, n khng phn tch thuc tnh nh HyperChem thc hin i vi cc phn t khc. Khi cu trc polyme vi kch thc nh sn xy dng c, n to nn mt phn t bnh thng nh HyperChem quan tm. nh r monome. u v ui cc monome c th dng xy dng chui phi c mt u, xem nh l a v mt ui b. iu c ngha l monome phi c kiu, b-R-a. Bt k phn t no c t nht ba nguyn t u c th l mt monome. Polyme ho bng s tch Phn ng polyme ho l phn ng to ra s tch (ngng t) ca a-b. l: R-R-R-R bng cch lp i lp li
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Nu gc vn R-R c xem l ngu nhin, khi u (a) v ui (b) phi c xc nh xy dng chui. Xc nh gc vn Khi tch a v b, hnh hc bn trong ca R c xem nh khng i. Tuy nhin, vn c s quay quanh lin kt R-R. C mt la chn cho qu trnh polyme ho ngu nhin, nt nm ngay bn phi. Kh nng khc na l gc c xc nh theo ngi s dng nh mt gi tr hng cho qu trnh ni kt. Trong trng hp ny ta cn xem xt thm n hnh hc ca lin kt RR. Tha nhn l a c ni vi nguyn t x ln lt ni vi x. Tng t, nguyn t b ni vi y v y ni vi y. C th, s ngng t monome l:
Trong trng hp, gc vn c xc nh l xon x-x-y-y. Mi nguyn t ny, a, b, x, x, y, y, c xc nh trong monome bng cc phn la chn c t tn. Nu chng khng c t tn, khi ta s thy dng bo li sau xut hin: V d:
Ta s xy dng mt polyme t monome 1-3 butadien. Phn t monome trng nh sau, y ta dng custom labels v ch thch ch ra cc phn la chn c t tn
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Nu phn la chn c t tn ph hp c thc hin, khi nhp chn Polymers trong Databases menu. Hp thoi la chn nh sau xut hin:
Nhng la chn phi c thc hin t ngu nhin cc gc x-x-y-y hoc t cc gi tr hng xc nh. Hn na ta phi chn di ca chui polyme mun xy dng. Ch : Tch chn Branching Enabled ch khi cc nguyn t khc cng c t tn tng ng. V d cnh b ta t b cnh a t a Nu ta chn 300 cho gc xon v xy dng chui bng 20 n v. Ta s thu c cu trc nh sau:
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To polyme cho cc monome khc Trong kiu mu trn ta c th s dng bt k monome no khc m ta mun vi iu kin ta xc nh chnh xc cc nguyn t cn c, a, b, x, x, y v y. Vi cc phn u v ui ngn, vic xc nh x v x c th trng vi vic xc nh y v y nhng iu khng thnh vn vi iu kin a, x v x (hoc b, y v y) xem nh l cc nguyn t lin kt ni tip nhau. Do , v d, x v y hoc x v b c th l cng mt nguyn t. Cc phn la chn c t tn a (hoc b) c th xem nh l mt nhm cc nguyn t, ch khng phi l mt nguyn t n, vi iu kin cc nguyn t ny lin kt vi x (hoc y) bng mt lin kt.
Cc bc tun t to Polyme nh sau (v d cho butadien) 1. V phn t Butadien ln mn lm vic. 87
Hng dn s dng HyperChem 7.04 2. Chn cng c la chn trn thanh cng c. 3. Chn nguyn t hydro u tin, tip theo chn Name Selection trong Select menu. 4. Chn mc Other, ri nh b vo . Tip theo ln lt chn cc nguyn t khc v nh tn theo th t nh hng dn trn. 5. Nhp chn Polymer.. trong Database menu, hp thoi la chn xut hin, hy nhp cc gi tr nh gc vn, s monome n v.. thch hp:
6. Nhp OK thc hin to chui polyme. Ch : Ta hon ton c th thc hin cc tnh ton kho st h polyme m mnh va to ra. Tuy nhin do polyme l phn t ln nn thng ngi ta ch kho st mt phn no ca h bng cch chn phn v thc hin tnh ton nh i vi cc phn t nh khc.
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Bi 7. La chn v biu din mt nhm cc nguyn t trn mn lm vic

To vng xon c. Chn nhm nguyn t. t nhn v t mu nhm nguyn t.
To vng xon c alpha.

Ta hc cch to vng xon cho chui polypeptide.
Cch lm nh sau
1. Nhp tri chut chn Amino Acids trong Databases menu. Hp thoi amino axit xut hin. 2. Nhp tri chut tch chn Alpha helix mc Conformation (hnh dng) 3. t gc Omega l 1800. 4. Nhp ln lt su ln tri chut vo Phe. 5. Nhp vo nt tt hp thoi. Cu trc ca chui xut hin nh sau:
(Cu trc ny c tt Show Hydrogens trong Display menu v c xoay n nh vy cho d nhn, vi cc bc trn ta s thu c 89
Hng dn s dng HyperChem 7.04 cng thc phn t nh vy nhng cha c xoay theo gc nhn thch hp). 6. Nu cu trc xut hin vn cn biu din cc nguyn t hydro th hy nhp tri chut b tch Show Hydrogens trong Display menu. 7. Xoay phn t n gc nhn thch hp.
t nhn cho u v ui chui

nhn c r hn ta nn t nhn cho cc nguyn t N v C cc ui ca chui.
Cch lm nh sau
1. Nhp tri chut tch vo Atoms v Multiple Selections trong Select menu. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp tri chut nguyn t nit ui.
4. Nhp tri chut vo C ui cn li.
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5. Nhp tri chut chn Labels trong Display menu. Hp thoi Labels xut hin. 6. Nhp tri chut tch chn Symbol trong mc Atom ca hp thoi Labels v nhp OK la chn. Cc nguyn t N-ui v C-ui s c biu din di dng nhn biu tng (symbol) nh sau:
Chn lin kt khung

nghin cu vng xon c alpha t nhin ca chui polypeptide, vic chn ny gip ta hnh dung d dng hn.
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Hng dn s dng HyperChem 7.04 Bc u tin chn lin kt khung, ta c th thc hin mt trong hai cch sau: - Chn ng ngn nht gia hai im chn lm ui. - S dng Select Backbone (chn lin kt khung) trong Select menu.
Chn ng ngn nht gia hai ui chn.

1. Nu cn thit nhp b tch Show hydrogn trong Display menu. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp tri chut vo nguyn t C-ui chn v r n nguyn t Nui chn ri nh chut.
S dng lnh Select Backbone: 1. u tin, nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp phi chut vo vng trng trn mn lm vic. Vic lm ny gip loi b nhng la chn trc . 3. Nhp tri chut chn Select Backbone trong Select menu. Hnh nh lin kt khung s xut hin nh sau:
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T mu lin kt khung t mu lin kt khung ta lm nh sau

1. Nhp tri chut chn Color trong Display menu. Hp thoi la chn mu s xut hin. 2. Nhp tri chut chn mu m ta mun biu din, v d chn mu vng (Yellow) v nhp OK chn. 3. Nhp phi chut vo vng trng mn lm vic. HyperChem s biu din khung lin kt dng mu vng.
Ch biu din lin kt khung trn mn lm vic biu din mi lin kt khung ta lm nh sau
1. Nhp tri chut chn Show Selection Only (ch biu din phn c chn) trong Display menu. Khi ch c phn lin kt khung v nhn ca n c biu din. 2. Nu mun khng xut hin c phn nhn th ta vo hp thoi Labels trong Display menu v chn none mc Atom ri nhp OK chn. Lc ny ch c lin kt khung c biu din trn mn lm vic. Ch : Nu nh ta th thc hin v d ny ngay cho lin kt khung c t mu trn th s khng cn g xut hin trn mn hnh, s d nh vy v trong phn trn hin th mu ta nhp phi chut ng ngha vi vic b tt c cc la chn.
Biu din lin kt nhnh (lin kt bin)

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biu din lin kt nhnh ta lm nh sau

1. Quay v chuyn lin kt khung sao cho trc vng xon c lin kt khung hng ra ngoi mt phng mn hnh.
2. Nhp tri chut chn Show All trong Display menu. Mn hnh s hin ra nh sau:
Biu din cc nhm nguyn t khng chn

i khi ta mun chn v biu din cc phn cn li ca h phn t ch khng phi l phn la chn hin ti. Ta c th s dng Complement Selection (lu chn b xung) trong Select menu.
Cch lm nh sau
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Hng dn s dng HyperChem 7.04 1. Nhp tri chut chn Complement Selection trong Select menu. HyperChem s chn biu din tt c cc phn tr nhng phn c chn trc s dng bnh thng.
2. Nu ta nhp tip tri chut chn Show Selection Only trong Display menu th HyperChem s du lun phn lin kt chn trc. Ch : a phn t v trng thi bnh thng ta nhp tri chut chn Show All trong Display menu.
Chn theo hnh ch nht chn cc nguyn t theo hnh ch nht ba chiu ta lm nh sau
1. 2. 3. 4. Chn Show Hydrogens v chn Show All trong Display menu. B tch nu c Select Sphere trong Select menu. Nhp tri chut vo cng c la chn trn thanh cng c. Nhp ng thi tri v phi chut gi nh vy v r ph ht nhng nguyn t mun chn vo hnh ch nht.
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5. Nh chut v tr thch hp th tt c cc nguyn t trong hnh ch nht c chn s sng hn
Chn theo hnh cu chn cc nguyn t trong mt hnh cu ta lm nh sau

1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp phi chut vo khong trng trn mn lm vic b tt c cc la chn trc . 3. Nhp tri chut tch chn Select Sphere trong Select menu. 4. t con tr la chn vo mt nguyn t no c chn lm tm hnh cu
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5. Nhp ng thi tri v phi chut, gi v r to mt hnh cu cha cc nguyn t mun chn. 6. Nh chut th tt c cc nguyn t trong phn hnh cu s sng hn.
Ch : nu ta chn mt im trng no lm tm th khi nhp v r chut s l kiu chn hnh ch nht ch khng phi kiu chn hnh cu.
t tn phn la chn
HyperChem gip ta d dng t tn cc phn la chn v th c th d dng biu din li chng sau ny.
t tn phn la chn ta lm nh sau

1. Chn Name Selection trong Select menu. Hp thoi Name Selection xut hin. 2. Nhp tri chut tch vo mc Other v nh tn ca nhm la chn ngay trng cnh .
3. Nhp OK chn. HyperChem s lu tt c phn la chn vi tn m ta nh vo, v d y l n_sub. 4. Nhp phi chut vo vng trng trn mn lm vic loi b la chn. 5. Nhp tri chut chn Select trong Select menu. 97
Hng dn s dng HyperChem 7.04 Hp thoi Select s hin ra. 6. Nhp tri chut chn Named Selection trong mc By String. 7. Nhp tri chut chn n_sub trong list cc tn bn cnh, nhp OK chn. Phn la chn vi tn tng ng s c chn tr li.
Chn lin kt vng chn vng lin kt ta lm nh sau

1. Nhp tri chut chn cng c la chn trn thanh cng c. 2. Nhp phi chut vo vng trng trn mn lm vic b tt c cc la chn trc . 3. Nhp lin tip hai ln tri chut vo mt trong cc lin kt ca vng. Vng lin kt s c chn.
Ch : Nu tch chn Multiple Selection trong Select menu th ta c th chn c tt c cc lin kt vng.
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Bi 8. Thao tc vi nhng phn t ln

c v m cc file PDB. Biu din cc thuc tnh cu trc ca cc phn t ln. Biu din lin kt hydro Thay th cc monome. Quay lin kt nhnh Mt nt c trng quan trng ca HyperChem l kh nng thao tc bng tay v tnh ton thuc tnh ca cc phn t ln, nh l cc protein v nucleic acid. Ngoi kh nng xy dng v nghin cu cc phn t nh. By gi chng ta nghin cu cc phn t ln lu trong ngn hng d liu Protein Brookhaven (Brookhaven Protein Data Bank, PDB). Trong phn ny ta thc hnh trn trypsin, cht c ch tuyn tu (BPTI).
c ngun file d liu PDB .

Cc file (PDB) trong ngn hng d liu Protein Brookhaven c phn ui m rng l .ent . HyperChem c th c cc file ny t cc ngun cung cp khc nhau. Cc file ny trc tin phi c chuyn t ngun gc n HyperChem.
m file PDB ta lm nh sau

1. Nhp tri chut chn Open trong File menu. Hp thoi Open file xut hin. 2. Chuyn n th mc samples ca HyperChem. 3. Chn m th mc Pdb. 4. Chn phn ui m rng l Brookhaven PDB (*.ENT) trong mc Files of type. Cc file c ui ent hin ra. 5. Nhp tri chut chn pdb5pti.ent trong list file. Dng ch gii bn di (Comment) s cho bit s qua v ngun gc ca cht. 6. Nhp OK chn Mn lm vic s xut hin phn t nh sau
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Trong h c c cc phn t nc. 7. Nu cu trc xut hin c c nhn ca cc nguyn t th ta nn chn none hp thoi Label trong Display menu d quan st. 8. Ta cng nn loi b biu din cc lin kt hydro tin quan st phn t.
Loi b cc phn t nc
Trong phn ny ta hc cch loi b cc phn t nc bao quanh phn t BPTI (bovine pancreatic trypsin inhibitor) m ta ang nghin cu.
Cch lm nh sau
1. Nhp tri chut chn Molecules trong Select menu. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp tri chut vo phn t BPTI chn phn t ny. Phn t BPTI s sng hn ln 4. Nhp tri chut chn Complement Selection trong Select menu. Vic ny gip ta ch la chn cc phn t nc. 5. Nhp tri chut chn Clear trong Edit menu. Lc ny s c hp thoi hi ta c thc s mun xo cc nguyn t chn xut hin
6. Chn Yes. Cc phn t nc s b xo i v cu trc ca BPTI s xut hin trn mn lm vic nh sau: 100
Ch : trnh trng hp mun kho st cu trc BPTI trn m li phi loi b cc phn t nc khi m file PDB, ta nn lu cu trc hin ti vo mt tn khc khi m sn c. - Nhp tri chut chn Save as trong File menu. - nh tn mun lu vo mc File name v chn phn ui m rng l hin (HyperChem (*.HIN)). - Nhp Save chn HyperChem s lu li tn file m bn nh vo vi phn ui m rng l hin.
Biu din cu trc phn t Biu din cu trc chnh Biu din cu trc chnh ca phn t ta lm nh sau
1. Nhp tri chut b tch Show Hydrogens trong Display menu. iu ny gip ta d quan st phn t hn. 2. Nhp tri chut chn Backbone trong Select menu. Lin kt khung s sng hn. 3. Nhp phm Spacebar trn bn phm. iu ny gip cho phn t c biu din ph hp vi t l mn hnh v cho php ta nhn r hn. 4. Nhp tri chut chn Show Selection Only trong Display menu.
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Lc ny trn mn hnh ch biu din lin kt khung. 5. Nhp phi chut ln vng trng ca mn lm vic loi b la chn lin kt khung. Lin kt khung s tr v trng thi bnh thng. Ch : biu din li cc lin kt nhnh ta nhp tri chut chn Show All trong Display menu.
Biu din vng xon Alpha biu din vng xon Alpha ta lm nh sau
1. Nhp tri chut tch chn Multiple Selections v Residues trong Select menu. 2. Nhp tri chut chn Select trong Select menu. Hp thoi Select xut hin. 3. Nhp tri chut tch chn Residue number trong mc By number. 4. nh s 47 vo mc value = v nhp OK chn. iu ny ng ngha vi SER 47 c chn. Vi cch ny gip ta d dng chn nhng monome hp phn c bit trong phn t. 5. Nhp tri chut chn Select trong Select menu m hp thoi Selecct mt ln na v nhp chn Residue number vi s ch 55. Ta thy trn mn hnh cc hp phn th 47 v 55 sng ln. 6. Nhp tri chut vo hp phn 47 v r n hp phn 55. iu ny gip cho cc hp phn t 47 n 55 c chn. Ta cng c th chn cc hp phn t 47 n 55 bng cch nh s 47 v 55 ln lt vo v tr value >= v <=. 7. Nhp tri chut chn Show Selection Only trong Display menu. iu ny gip ta biu din nhng phn chn gn gh hn. 102
Hng dn s dng HyperChem 7.04 8. Nhp Spacebar HyperChem biu din phn la chn theo t l mn lm vic. 9. Nhp phi chut vo vng trng mn lm vic loi b la chn cc hp phn. 10. Chn Select Backbone trong Select menu, sau nhp chn Show Selection Only trong Display menu. HyperChem s biu din cc hp phn t 47 n 55. Nhng phn khng c chn s khng xut hin trn mn hnh. 11. Chuyn v quay vng xon c Alpha sao cho trc ca n hng ra mt phng mn hnh. Lc ny phn c chn s c dng biu din nh sau:
12. Nhp tri chut chn Show All v Scale to Fit biu din phn t theo t l mn lm vic. 13. Nhp tri chut vo cng c la chn trn thanh cng c v nhp phi chut vo vng trng mn lm vic loi b la chn.
Biu din cu ni i sunfua

Trong phn t PBTI c cha cc hp phn cystin (C6H12N2S2) to nn cc hnh thc lin kt ngang dc theo lin kt khung ca chui peptit. Trong phn ny ta hc cch phng to mt phn phn t xem biu din cc lin kt ngang ny.
phng to phn c cu ni i sunfua ta lm nh sau

1. Nhp tri chut chn Show All trong Display menu sau nhp phm Spacebar trn bn phm biu din ton b phn t theo t l mn lm vic. iu ny s gip biu din cu trc phn t vo tm mn lm vic. 103
Hng dn s dng HyperChem 7.04 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp ng thi tri v phi chut gi nh vy v r chn theo hnh ch nht vng c hp phn xystin. C th mt vi hp phn khc ln cn vi xystin cng c chn Ch : HyperChem ngm nh mu ca lu hunh l mu vng, do c th d dng pht hin ra hp phn xystin v tr no. Ta cng c th chn xystin theo kiu hnh cu nh sau: - Nhp tri chut tch chn Select Sphere. - Nhp tri chut vo cng c la chn trn thanh cng c. - Nhp ng thi tri v phi chut vo phn t lu hunh mun chn, gi v r sao cho bn knh hnh cu tri rng ht vng ta mun chn.
4. Nhn vo dng hin trng lm vic bit chc chn hp phn CYX c chn. 5. Nhp phm Spacebar biu din phn la chn vo tm theo t l mn lm vic. 6. Nhp tri chut chn Labels trong Display menu. Hp thoi Labels hin ra. 7. Nhp tri chut tch chn Symbol trong mc Atoms sau nhp OK chn. 8. Nhp tri chut b tch Show Hydrogens trong Display menu d quan st. 9. Quay v phng to n khi c th quan st c cu ni S-S- mt cch d dng.
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10. Nhp tri chut vo cng c la chn trn thanh cng c sau nhp phi chut vo vng trng trn mn lm vic b la chn.
Chn cu trc vng

Ta c th s dng tnh nng tm vng ca HyperChem biu din cc hp phn hnh thnh nn vng trong protein.
biu din cu trc vng ta lm nh sau 1. Nhp tri chut chn Atoms trong Select menu. 2. Nhp tri chut chn cng c la chn trn thanh cng c. 3. Nhp lin tip hai ln tri chut vo lin kt S-S-.
Vng lin kt c cha lin kt S-S- s c chn. (Ta cng chn c vng nu nhp lin tip hai ln tri chut vo bt k lin kt no thuc vng m ta bit) Nhp phm Spacebar trn bn phm a vng lin kt chn vo tm mn lm vic. Nhp tri chut chn Show Selection Only trong Display menu. Nhp tri chut chn Labels trong Display menu. Hp thoi Labels xut hin. Nhp tri chut tch chn Name+Seq mc Residues trong hp thoi, sau nhp OK chn. HyperChem s biu din cc hp phn to nn vng v nhn tn km theo ca chng. Quay vng cho n khi c th nhn c r nh sau:
4. 5. 6. 7.
8.
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Biu din lin kt hydro

tnh ton v biu din lin kt hydro ta lm nh sau
1. Nhp tri chut vo cng c la chn trn thanh cng c, sau nhp phi chut vo vng trng trn mn lm vic loi b nhng la chn trc . 2. Nhp tri chut chn Show All v Scale to Fit trong Display menu biu din ton b phn t vo tm theo t l mn lm vic. 3. Nhp tri chut chn Labels trong Display menu. Hp thoi Labels xut hin. 4. Chn none trong tt c cc mc ca hp thoi ri nhp OK chn. 5. Nhp tri chut tch chn Show Hydrogen Bonds trong Display menu. HyperChem s biu din ton b cc lin kt hydro c th c trong h. 6. Nhp tri chut chn Recompute H Bonds trong Display menu. HyperChem biu din cc lin kt hydro dng ng nt t. 7. Nhn phm PgDn trn bn phm phng to cho n khi c th quan st d dng cc lin kt hydro. 8. Nhn phm Spacebar trn bn phm chuyn phn t tr li tm theo t l mn lm vic.
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Ch : Nu ta thay i s sp xp ca cc phn t trong h hoc l HyperChem thay i hnh dng trong qu trnh tnh ton, th ta nn chn Recompute H Bonds li xem lin kt hydro.
Thay th hp phn v tr c bit

Trong bi 6 ta hc cch thay th cc hp phn cu trc bn trong. Trong phn ny, ta s hc cch thay th cc hp phn cu trc ngoi.
thay th ta lm nh sau
1. Nhp tri chut b tch Multiple Selections trong Select menu. 2. Nhp tri chut chn Labels trong Display menu. Hp thoi Labels xut hin. 3. Nhp tri chut tch chn Name+Seq mc Residues ri nhp OK chn. 4. Nhp tri chut chn Select... trong Select menu. Hp thoi Select xut hin. 5. Tch chn Residue number trong mc By number, tip theo nh s 58 vo phn value =. 6. Nhp OK chn. Hp phn 58 s c chn. 7. Phng to phn c chn d quan st, cu trc phn t lc ny c dng:
107
8. Khi hp phn ALA 58 cn ang c chn, nhp tri chut chn Mutate trong Databases menu. Hp thoi Mutate (thay th) xut hin. 9. Nhp tri chut chn VAL trong list cc hp phn ri nhp OK chn. 10. Tip tc dng hp thoi Select chn GLY 57 v thay th bng PHE. Thay th 56 bng ALA v 55 bng VAL. Ch : Ta c th thay th bng cc hp phn khc theo mnh.
Quay nhnh lin kt

Ta c th thay i gc vn ca cc nhnh bng vic la chn nhnh v chn quay bn trong bng cng c quay theo trc Z.
quay nhnh lin kt ta lm nh sau

1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp phi chut vo vng trng trn mn lm vic loi b cc la chn trc . 3. Nhp tri chut tch chn Atoms trong Select menu. 4. Cu trc phn t v d c dng nh trn hnh
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5. Nhp lin tip hai ln tri chut vo C trong lin kt C-C ca VAL chn nhnh lin kt ny.
6. Nhp tri chut vo cng c quay theo trc Z trn thanh cng c. 7. a con tr chut vo mn lm vic, nhp tri gi v r sang bn phi quay nhnh valin.
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Ch : Vic dng cng c quay v thao tc quay bng tay l rt lu, v thng l c phn t cng quay. thc hin ch quay nhnh ta nn dng hp thoi quay theo trc chn gc quay thch hp theo mong mun.
Cch lm nh sau
- Nhp lin tip hai ln tri chut vo cng c quay theo trc Z. Hp thoi la chn gc quay xut hin. (Ta cng c th ly hp ny ra bng cch nhp tri chut vo Rotate trong Edit menu.) - Nhp tri chut tch chn trc Z (Z axis) trong hp thoi, tip theo tch chn Molecules trong mc Apply to. - nh gi tr gc m ta mun quay nhnh vo v tr Angle, nhp OK chn. Nhnh s quay mt gc m ta chn.
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Bi 9. Cc tiu ho nng lng ca h.

Ti u ho hnh hc phn t theo phng php c hc phn t. Tnh ton im n. S dng lin kt xon bt buc. o v so snh thuc tnh cu trc ca h. S dng hnh nh phn chiu qua mt phng xc nh ca trnh xy dng. Lu vo trong log file kt qu tnh ton. Trong bi ny, chng ta thc hin cc tiu ho nng lng ca xiclohexan s dng trng lc AMBER. Trc khi thc hin ta nn hiu qua mt cht v s cc tiu ho nng lng. Cc tiu ho nng lng lm bin i hnh hc phn t n nhng mc h c nng lng thp hn, v cui cng l to ra mt cu hnh n nh nht. Trong qu trnh cc tiu ho, qu trnh i n cu trc phn t m nng lng khng cn c th thay i vi phn c na. iu ny c ngha l bt ngun t nng lng lin h theo cc to Decac, c gi l gradient, l gn nh bng khng. y c bit l im dng (stationary point) trn mt th nng. Nu c s thay i no trong cc thng s hnh hc lm tng nng lng ca phn t, cu hnh s nhanh chng sa i a v trng thi nng lng cc tiu. Mt h phn t c th c nhiu cc tiu nng lng. Nng lng c gi tr thp nht c gi l cc tiu ton phn, nhng im cc tiu cn li gi l cc tiu b phn.
Lu kt qu tnh ton vo Log file.

Dng hin trng bn di ca s HyperChem biu din nhng kt qa tnh ton ph hp nht. Ta c th lu nhng kt qa ny km nhng thng tin tnh ton lin quan vo trong mt Log file. iu ny thc hin c d dng nh sau: 1. Nhp tri chute chn Start Log trong File menu. Hp thoi Start Log xut hin vi tn ngm nh l chem.log. 2. nh tn file mun lu vo mc File name. 111
Hng dn s dng HyperChem 7.04 3. Nhp OK chn. Log file s lu li tt c cc kt qu trong qu trnh tnh ton m ta tin hnh. 4. Sau khi tnh ton xong ta nhp tri chut vo Stop log kho vic ghi chp tip nhng sa i khng cn thit vo phn kt qu tnh ton.
Chn trng lc
Trc khi dng cu trc dng gh ca xiclohexan v tin hnh ti u theo phng php c hc phn t, ta nn hc cch chn trng lc c hc phn t do HyperChem cung cp. Trong phn ny ta s dng trng lc AMBER.
chn trng lc ta lm nh sau

1. Nhp tri chut chn Molecular Mechanics trong Setup menu. 2. Lc ny hp thoi la chn phng php xut hin, nhp tri chut chn phng php AMBER. 3. Nhp vo nt Options m hp thoi la chn thm cho phng php. 4. Nhp tri chut chn Distance Dipendent (ph thuc khong cch) trong mc Dielectric.
5. Chn Scale factor (h s t l) l 1. 6. t c hai h s Electrostatic (tnh in) ln van der Waals trong mc 1-4 Scale Factor l 0.5. 7. t none mc Cutoffs (lc b). 8. Nhp OK ng hp thoi. 9. Nhp tri chut chn Select Parameter Set trong Setup menu. 10. Hp thoi la chn xut hin, chn tham s thch hp m ta mong mun, v d chn amber2. 11. Nhp OK ng hp thoi.
Dng cu trc dng gh ca Xiclohexan. Cch lm nh sau

1. Nhp lin tip hai ln tri chut vo cng c v trn thanh cng c, hp thoi la chn nguyn t hin ra. 112
Hng dn s dng HyperChem 7.04 2. 3. 4. 5. 6. Chn nguyn t cacbon v ng hp thoi li. Nhp tri chut tch chn Atoms trong Select menu. Chn Labels trong Display menu v t Label l number. Nhp tri chut b tch Exlicit Hydrogens nu c trong Build menu. a chut ln mn hnh v v cu trc phn t:
7. Nhp tri chut chn Add H & Model Build trong Build menu thm nhanh cc hydro cn thiu v biu din li phn t. C th thc hin lnh ny bng cch nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c. 8. Nhp tri chut b tch, nu c, Show Hydrogens trong Display menu. 9. Quay v chuyn cu trc n khi nhn c nh sau:
113
Trnh xy dng (Model Builder) dng cu trc dng gh ca xiclohexan nh l mt cu trc ngm nh. Cu trc ny cha c ti u ho, nhng n c t chun v chiu di lin kt, gc, v gc vn.
o thuc tnh cu trc dng gh ca xiclohexan.

By gi chng ta o cc thuc tnh cu trc theo cu trc ca trnh xy dng nh sn ca HyperChem. Sau , ta em so snh gi tr o c vi gi tr ca cu trc c ti u.
o thuc tnh cu trc ta lm nh sau

1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp tri chut tch Atoms v b tch Multiple Selection trong Select menu. 3. Chn mt vi lin kt, gc lin kt, gc vn xc nh gi tr ca chng. Cc gi tr nh sau s xut hin trn dng hin trng sau khi ta tin hnh chn: di lin kt: 1.54A0 Gc lin kt: 109.470. Gc vn: 600. 4. Nhp phi chut b cc la chn.
Tnh ton im n
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Hng dn s dng HyperChem 7.04 Tip theo, ta tin hnh tnh ton im n thu nng lng ton phn ca cu hnh cha c ti u.
Cch lm nh sau
1. Nhp tri chut chn Single Point trong Cumpute menu. Tnh ton im n biu din nng lng dng kcal/mol v cn bc hai tng bnh phng trung bnh (RMS) gradient l kcal/mol.A0 cho cu hnh ca cc nguyn t hin ti. Cc gi tr nng lng v gradient xut hin trn dng hin trng
Ghi ch vo Log file

Ta c th ghi ch thm vo d liu tnh ton lu trong Log file. Tuy nhin ghi ch ny ch thc hin c khi Start Log ang hot ng.
Cch lm nh sau
1. Nhp tri chut chn Log comments trong File menu. Hp thoi Log comments xut hin:
2. nh ghi ch m ta mun vo vng trng, sau nhp OK chn.
Ti u ho cu trc
Tip theo ta hc cch cc tiu ho cu trc dng gh bng phng php ti u c hc phn t. u tin l t cc bin s cc tiu ho, gm c hnh thc cc tiu v tip theo l chy tnh ton.
t bin ti u
1. Nhp tri chut chn Geometry Optimization trong Computer menu. Hp thoi xut hin:
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Hp thoi la chn cho php ta chn thut ton ti u v tiu chun hi t cho qu trnh cc tiu ho m ta tin hnh. 2. Nhp tri chut chn thut ton Polak-Ribiere. Thut ton ny ni chung cho kt qu ti u tt. 3. Chn gi tr 0.1 kcal/A0mol cho RMS gradient v ngm nh gi tr ny cho cc h khc. Maximum cycles trong mc RMS gradient cho php ta t iu kin kt thc tnh ton. Khi tnh ton t c mt trong cc tiu chun ny th tnh ton s dng li. Mc In vacuo (trong chn khng) c tch ngm nh sn nu ta khng t Periodic Box trong Setup menu. Hp thoi la chn ti u hnh hc l nh nhau i vi mi phng php. Algorithm HyperChem s dng cc thut ton tnh ton cho h chn. Steepest Descent Chuyn trc tip xung ng dc nht (ca lc tng tc) trn mt th nng. Nu nng lng ca h gim i, n tip tc thc hin nh vy nhng vi bc nhy ln hn (tng thm 1.2 ln) nu nng lng tng sau bc nhy, t l iu chnh hnh hc gim xung: bc nhy tip theo bng mt na bc nhy trc . Phng php ny to ra cc in tch c gii hn cho h, dng nhanh chng hiu chnh hnh hc khi u km hoc loi b cc tip im km; n c tc ng tt khi h cn xa so vi cc tiu. Tnh ton khng sn sng hi t v c th dao ng. Fletcher-Reeves y l phng php gradient lin hp, c ngha l n chn hng gim ( c nng lng thp hn) bng cch xt gradient hin ti, s lin hp ca n, vi gradient ca bc trc . y l 116
Hng dn s dng HyperChem 7.04 phng php c hi t tuyn tnh cao; n hi t tt hn phng php trn. y l phng php gradient lin hp s dng s thm d mt chiu. N ci tin t phng php Fletcher-Reeves cng bng cch xem xt hng lin hp trc . L phng php nhanh hn Fletcher-Reeves. C gi tr cho cc ti u bn kinh nghim v thun tu l thuyt; khng c gi tr cho ng lc hc phn t.n dng cc vect c trng ca ma trn cho ho Hesian xc nh hng ti u cho s chuyn ng ca nguyn t. c on ban u c tnh theo kinh nghim. Ch c gi tr cho trng lc MM+. y ch l phng php dng tnh trc tip cc o hm bc hai, hoc cc hng s lc. y l phng php c hiu qu trong vic xc nh cc tiu nhng i hi hnh hc khi u hp l. C gi tr cho tnh ton bn kinh nghim, thun tu l thuyt v DFT. N ch dng nng lng v o hm ca nng lng. Do n c th s dng rng ri hn mc d n khng c kh nng so snh vi cc phng php o hm. c th s dng ti u hnh hc MP2 hay trng thi kch thch hnh hc CI. Dng cc hp thoi ny t cc iu kin kt thc tnh ton. Khi RMS gradient ca nng lng b hn gi tr ny, tnh ton s dng li. Gi tr t thay i t 10-3 n 0.1. t gi tr b hn na c th my s bo li. Ta c th t gi tr cao hn 0.1 tnh ton nhanh hn, nhng km chnh xc. S vng tnh ton ti a. Ngm didnh bng 15 ln s nguyn t. Gi tr c th thay i t 100 n 1000. Tch loi b cc iu kin bin tun hon khi tnh ton. ch chn in vacuo nu h trong mt hp tun hon. y s dng iu kin bin tun hon thit lp cho h tnh ton. ch c gi tr vi h trong hp tun hon. 117
Polak-Ribiere
EigenvectorFollow
Block Diagonal Newton-Raphson
Conjugate Dierections
Termination condition RMS gradient
max. Cycles In vacuo Periodic boudary conditions
Hng dn s dng HyperChem 7.04 Variable Nhp nt la chn thm. cho php ta chonk ti u nng lng SCF hay SCF + MP2 (ch Ab initio) hoc nng lng trng thi kch thch (cung cp cho tng tc cu hnh c chn trc ). Screen refresh y l tn s, trong cc vng ti u ho, biu period din kt qu ln mn hnh.
Chy tnh ton

Sau khi t xong cc bin cho vic ti u, by gi ta bt u thc hin tnh ton ti u . 1. Nhp tri chut chn OK ng hp thoi v HyperChem s bt u tnh ton Ti u ho bt u v hin trng tnh ton s hin trn dng hin trng. Sau mt lc tnh ton hon thnh v gi tr nng lng ln gradient hin ra trn dng hin trng.
o thuc tnh cu trc ca h ti u

By gi ta so snh thuc tnh cu trc ca cu trc c cc tiu ho vi cu trc ca trnh xy dng trong HyperChem. 1. Chn o mt vi lin kt, gc lin kt, gc vn. Cc gi tr o c xut hin trn dng hin trng nh sau: di lin kt: 1.53A0. Gc lin kt: 110.20 Gc vn: 58.00. 2. So snh cc gi tr ny vi cc gi tr ca cu trc cha c ti u. di lin kt: 1.54A0 Gc lin kt: 109.40 Gc vn: 600 Ta thy cu trc c ti u gc lin kt tng ln mt t khi gc t din v gc vn gim i hai . Ch : Sau khi tnh ton xong ta c th xem thuc tnh ca h hay mt phn la chn no bng cch nhp chn phn v chn Propeties trong Compute menu xem thuc tnh.
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Chuyn t xiclohexan dng gh sang dng thuyn

Trong phn ny ta s hc cch phn chiu (Reflect) mt ui ca phn t to ra cu trc xiclohexan dng gh.
nh mt phng phn chiu ta lm nh sau 1. Nhp tri chut tch chn Multiple Selections trong Select menu. 2. Nhp tri chut chn cng c la chn trn thanh cng c. 3. Nhp lin tip hai ln tri chut vo cng c la chn to cu trc theo
trnh xy dng. 4. Nhp tri chut vo lin kt 1-2 v 4-5 chn lm mt phng phn chiu.
5. Nhp tri chut chn Name Selection trong Select menu. 6. Nhp chn PLANE (mt phng) v nhp OK ng hp thoi. phn chiu ui ca phn t ta lm nh sau
1. Nu cn thit, chn Show Hydrogens trong Display menu v dng cng c phng to phng to thu nh phn t cho d nhn. 2. Nhp ng thi tri v phi chut, gi v r chn tt c cc nguyn t ta mun phn chiu.
119
3. Nhp tri chut chn Reflect (phn chiu) trong Edit menu. Cc nguyn t c chn s phn chiu theo mt mt phng to ra cu trc xiclohexan dng thuyn.
4. Nhp phi chut vo vng trng trn mn lm vic b cc la chn. Ch : Nu nh ta khng t Show Hydrogen trc khi la chn phn chiu, ta s khng phn chiu c chng.
o khong cch gia cc Hydro trc
120
o khong cch gia cc hydro trc ta lm nh sau

1. Nhp tri chut tch chn Multiple Selections trong Select menu. 2. Nhp tri chut chn cng c la chn trn thanh cng c. 3. Nhp phi chut vo hai hydro trc.
Dng hin trng cho bit khong cch gia cc nguyn t l 1.84A0. gi tr ny kh ph hp vi khong cch gia cc nguyn t khng lin kt.
Ti u ho cu trc xiclohexan dng thuyn ti u ho cu trc dng thuyn ta lm nh sau

1. Nhp phi chut trn vng trng loi b tt c cc la chn trc . 2. Chn Geometry Optimization trong Cumputer menu. 3. Nhp OK bt u ti u, s dng nhng la chn ln trc. Khi cu hnh c ti u ho xong, gi tr nng lng v gradient hin trn dng hin trng.
o li khong cch gia cc Hydro trc

1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp tri chut chn Multiple Selections trong Select menu. 3. Nhp tri chut vo hai hydro trc. Dng hin trng biu din khong cch mi ca H-H (2.28A0). Cu trc ti u c lm dt nh lm cho cc hydro trc dn xa nhau ra mt trc.
121
To cu trc dng thuyn xon

Hnh thc th ba ca xiclohexan l cu trc dng thuyn xon. Cch n gin to ra cu trc ny l thay i mt chc cu trc dng thuyn bng cch xon cng bc lin kt.
xon cng bc ta lm nh sau.

1. Nhp phi chut ln vng trng loi b tt c nhng la chn trc . 2. Nhp tri chut b tch Show Hydrogens trong Display menu. 3. Chn gc vn gia bn nguyn t cc bon bng cch chn cc lin kt 61, 1-2 v 2-3.
Ta phi chn cc lin kt theo ng nh vy vn cng bc. 4. Nhp tri chut chn Constrain Bond Torsion trong Build menu, sau nhp chn Other v nhp vo s 30 vn cng bc 300. Nhp OK chn.
5. Nhp phi chut vo vng trng loi b tt c cc la chn trc . Gc vn cng bc c thc hin.
xy dng li phn t vi lin kt c vn cng bc ta lm nh sau

122
1. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c
gi trnh xy dng. HyperChem s xy dng li cu trc vi s cng bc xon to ra cu trc xon dng thuyn hp vi tiu chun.
Ti u ho cu trc xon dng thuyn

Cch lm nh nhng cu trc trn.
Ngng Log file

Sau khi tnh ton xong ta ngng Log file v kim tra kt qu bng Notepad hoc Wordpad.
ngng Log (ghi) cng vic ta lm nh sau

1. Nhp tri chut vo Stop Log trong File menu.
kim tra kt qu tnh ton ta lm nh sau

1. 2. 3. 4. M NotePad. M tm file log m ta mun xem,v d chem.log Xem kt qu tnh c. ng NotePad khi xem xong kt qu.
123
Bi 10. C hc phn t
Xy dng v hiu chnh phn t Ti u hnh hc theo c hc phn t S dng iu kin bin chu k Chng cht hai phn t ng lc hc phn t Biu din li ng lc hc phn t v tnh trung bnh. ng lc hc Langevin v Monte Carlo
Trong phn ny ta s hc v chc nng v cch s dng cc phng php c hc phn t ca HyperChem. Cc tnh ton c hc phn t x l cc nguyn t nh s tng tc ca cc ht Newton bng mt hm th nng. Cc th nng ph thuc vo di lin kt, gc lin kt, gc vn v cc tng tc khng lin kt (gm c lc Van de Waals, tng tc tnh in v cc lin kt hydro). Trong cc tnh ton ny, lc tc dng ln nguyn t l hm v tr ca cc nguyn t. Ch : Nu ch phn no ca h trn mn lm vic c chn, khi ch cc tng tc lin quan n t nht mt nguyn t c chn mi c trong cc tnh ton. Nhng tng tc lin quan n nhng nguyn t khng c chn khng xut hin trong tnh ton. Vi tnh ton ti u ho cu trc, ch nhng nguyn t c chn c php dch chuyn, trong khi cc phn khng chn vn ng yn. S dng trng lc AMBER ta s ti u ion lng tnh alanin dng c lp v trong dung dch xc nh nh hng ca dung mi ln cu trc ti u. Ta cng biu din ng lc hc phn t trong dung dch m phng tc ng ca n vi cc h sinh hc. Trong bi by c nm bi thc hnh: Bi thc hnh 1: To ion lng tnh alanin c ti u ho s dng cc k nng xy dng v hiu chnh nhng bi trc. Bi thc hnh 2: S dng iu kin bin tun hon (periodic boundary conditons) solvat ho ion lng tnh. Bi thc hnh 3: S dng s chng cht so snh th gic phn t c lp v phn t c solvat ho. 124
Bi thc hnh 4: S dng ng lc hc phn t tm dng c nng lng thp nht. Bi thc hnh 5: Dng ng lc hc Langevin m phng s c mt ca dung mi trong qu trnh thc hin dao ng ng lc. Dng phng php Monte Carlo ly mu cu hnh theo phn b Boltzmann.
Bi thc hnh 1: To ion lng tnh alanin c lp

Phc tho ion lng tnh alanin
Mc d ta c th d dng dng th vin amino axit ca HyperChem biu din alanin, y ta s hc cch xy dng cu trc dng th ca n.
phc ho ion lng tnh alanin ta lm nh sau

1. Nhp lin tip hai ln tri chut vo cng c v trn thanh cng c. Hp thoi la chn nguyn t hin ra. 2. Tch chn Allow Arbitrary Valence v Explicit hydrogens. 3. Chn cacbon v ng hp thoi li. 4. M hp thoi Label trong Display menu v t Symbol ri ng hp thoi. 5. Nhp tri chut vo cng c v trn thanh cng c. 6. V phc ho nh sau: Ch : Hydro lun t thm vo trong khi ta v.
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Ch : C mt cacbon ch c hai hydro. Ta s hiu chnh cc hydro ny thnh oxi.
Hiu chnh cu trc

Cu trc ny ch c hydro v cacbon, ta cn phi hiu chnh cu trc to ra ion lng tnh alanin. c bit, ta cn chuyn mt s nguyn t thnh nit hoc oxi v to lin hp trong nhm cacboxyl.
hiu chnh cu trc ta lm nh sau

1. Nhp lin tip hai ln tri chut vo cng c v m hp thoi cc nguyn t, chn nit v ng hp thoi li. 2. Nhp tri chut vo cacbon nhm metyl chuyn n thnh nit nh sau:
126
3. M hp thoi la chn cc nguyn t v chn oxi. 4. Nhp tri chut vo hai nguyn t hydro chuyn chng thnh oxi. 5. Nhp lin tip hai ln tri chut vo cc lin kt cacbon-oxi chuyn chng thnh lin kt lin hp. 6. Hnh v phc tho ca ta s trng nh sau:
t in tch nguyn t
Bc tip theo ta t in tch hnh thc cho mt s nguyn t biu din mt cch xp x phn b in tch trn ion lng tnh hin ti. Ta c th tm in tch nguyn t bng cc phng php sau vi HyperChem: Nu mt phn t c xy dng t mt mu cho sn, nh PDB file, mu cha sn in tch. Bng tnh ton c hc lng t. 127
Hng dn s dng HyperChem 7.04 Bng cch ly xp x in tch. Trong bi ny, ta t xp x n gin in tch ca nit l +1 v mi nguyn t oxi l -0.5.
quy in tch cho cc nguyn t ta lm nh sau:

Nhp tri chut tch chn Atoms trong Select menu. nhp tri chut tch chn Multiple Selections trong Select menu. Nhp tri chut chn cng c la chn trn thanh cng c. Chn nguyn t nit. Nhp tri chut chn Set Charge trong Build menu. Hp thoi la chn xut hin, nhp in tch 1.0 v ng hp thoi li. 6. Nhp phi chut vo vng trng trn trang lm vic b la chn. 7. Chn c hai nguyn t oxi v quy cho in tch l - 0.5 cho mi nguyn t. 8. Nhp phi chut vo vng trng b tt c cc la chn. 1. 2. 3. 4. 5.
Chn trng lc
Tip theo y ta s hc cch chn trng lc. Ta nn chn trng lc trc khi s dng n Trnh xy dng (Model Builder) bi v trnh xy dng quy cho kiu nguyn t cho mi nguyn t theo trng lc m bn chn. Nh mt s la chn, ta c th quy cho chnh xc cc kiu nguyn t bt k lc no bng vic s dng hnh thc tnh ton (Calculate Types) trong Build menu. Tuy nhin, cch n gin nht l quy cho trng lc chnh xc trc khi ta s dng trnh xy dng.
Hp thoi trng lc c hc phn t biu din cc trng lc (hm th) cho ta la chn tnh ton. MM+ Pht trin cho cc phn t hu c. y l trng lc ton b nguyn t. HyperChem b sung trng lc MM2 bng cch cung cp thm cc tham s (cc hng s lc). iu ny m rng phm vi cho cc hp cht ho hc m MM+ c th 128
Hng dn s dng HyperChem 7.04 cung cp. MM+ cng cung cp cc gii hn cho vic tnh ton cc tng tc khng lin kt, iu kin bin tun hon v s hng gim bt s cng lin kt nhm trnh lin kt qu di. Pht trin cho cc protein v nucleic axit. Ta c AMBER th chn m phng nguyn t ton din (all-atom) hay nguyn t hp nht (united-atom). La chn United-atom x l cc nhm nguyn t nht nh nh mt nguyn t, bng mt kiu nguyn t. Ta cng c th chn t cc tp hp tham s khc nhau hin hnh cho Amber. BIO+(CHARMM) Pht trin cho cc phn t sinh hc ln. Ta c th chn m phng all-atom hoc united-atom. La chn united-tom x l nhm nguyn t nht nh nh mt nguyn t, vi cng kiu nguyn t. Ta c th chn cc tp hp tham s khc nhau. Pht trin cho cc phn t protein v axit nucleic. OPLS N tng t nh AMBER nhng x l cc tng tc khng lin kt chnh xc hn. Trng lc ny ch cung cp kiu m phng united-atom. Nhp tri chut la chn thm cho trng lc Options Nhp tri chut n cc thnh phn ca trng Components lc. iu ny cho php ta chn thnh phn no ca trng lc c tnh n trong tnh ton.
chn trng lc ta lm nh sau

1. Nhp tri chut chn Molecular Mechanics trong Setup menu. Hp thoi la chn trng lc xut hin. 2. Chn AMBER v nhp vo nt Options. Hp thoi la chn thm cho trng lc xut hin. 3. S dng cc gi tr ngm nh ri nhp OK ng hp thoi ny li.
4. Chn OK ng hp thoi la chn trng lc. 5. Nu xut hin hp thoi nhc nh sau th nhp OK chn. 129
Ch : S dng hp thoi la chn trng lc t cc iu kin cho cc trng lc c hc phn t AMBER, BIO+, v OPLS. HyperChem lu cc thit lp la chn ny. Dielectric permittivity (epsilon) Constant Distance dependent Hng s hoc ph thuc khong cch xc nh phng php tnh ton epsilon, h s gim bt cc tng tc in tch-in tch (v th tnh in). Epsilon l hng s in mi. y lm cho epsilon l mt hng s. y l hnh thc thch hp cho cc h trong pha kh hoc trong mt dung mi r rng. y lm cho epsilon t l vi s phn li tn ti gia cc nguyn t. iu ny gn ng cho nh hng ca dung mi khi thiu dung mi thch hp, v cho php tnh ton nhanh hn. S dng Distance dependent vi trng lc OPLS. Khi m phng ny chn biu din cho mt dung mi, ta thng chn Constant (hng s) khi dung mi hin din. Vi hng s, epsilon = (hng s in mi ca khong trng t do)x(H s t l). Vi ph thuc khong cch, epsilon = (hng s in mi ca khng gian t do)x(h s t l)x(s phn li gia cc nguyn t). Scale factor (h s t l) phi 1. Ga tr ngm nh l 1.0 l thch hp cho tt c cc h. Cc tng tc khng lin kt (Van de Waals v tnh in) gia cc nguyn t c tch t cc lin kt ba c bi s bng h s ny. y lm thay i ln tng tc in gia cc nguyn t tch ra t cc lin kt ba. Thay i t 0 n 1. Vi AMBER v OPLS, s dng gi tr 0.5. vi BIO+ s dng gi tr 1.0, 0.5, hoc 0.4 Lm thay i ln tng tc Van de Waals gia cc nguyn t tch t cc lin kt ba. Thay i t 0 n 1. Vi AMBER dng 0.5. vi OPLS dng 0.125. vi BIO+ dng gi tr c nh l 1. Cc la chn ny xc nh gii hn khong cch cho vic tnh ton cc tng tc khng lin kt v 130
Scale factor
1-4 Scale factor Electrostatic
Van de Waals
Cutoffs
Hng dn s dng HyperChem 7.04 ng nht vi cc la chn trong MM+. Hp thoi la chn MM+. S dng hp thoi la chn MM+ t cc iu kin cho trng lc c hc phn t MM+. HyperChem lu thit lp la chn ny, ngoi tr cc gii hn, trong S ng k (Registry) hoc trong file chem.ini v s dng chng cho cc phn HyperChem mi.
Cc tng tc tnh in khng lin kt c tnh ton s dng cc tng tc lng cc lin kt hoc mt phn in tch ca cc nguyn t. Bond dipoles y s dng cc lng cc lin kt tnh ton cc tng tc tnh in khng lin kt. Cc gi tr lng cc lin kt ly t file tham s cng (stretch) MM+. Atomic charges y s dng mt phn in tch nguyn t tnh ton cc tng tc tnh in khng lin kt. Ta c th quy in tch ny theo cch t in tch trong Build hoc ta c th tnh ton bn kinh nghim hay AB initio trc tnh in tch nguyn t vi mi nguyn t s dng cc phn tch khu tr Muliken. La chn ny xc nh khong cch gii hn cho Cutoffs vic tnh ton cc tng tc khng lin kt. Chn Periodic Box trong Setup menu t ng thit lp Switched (bt) vi cc gi tr ngm nh. Gii hn l cn thit ngn vic tnh ton cc tng tc vi cc hnh nh tun hon ln cn. None Tnh ton tt c cc tng tc khng lin kt. None ngm nh cho cc h in vacuo (chn khng). Khng dung la chn ny cho cc iu kin bin tun hon bi v n cho kt qu trong gii hn khng m t hon ton v gy nn s gin on trong mt th nng. Electrostatics 131
Hng dn s dng HyperChem 7.04 Switched Mt hm trn, p dng cho bn knh trong n bn knh ngoi (The inner radius to the outer radius), gim t t cc tng tc khng lin kt n khng. Nu h phn t trong mt hp tun hon, HyperChem chn Switched (bt) v t Outer v Inner Radius. Ta c th cng dng Shifted (tt). Shifted Hm trn, p dng ln ton b khong cch khng lin kt, t khng n bn knh ngoi, gim dn cc tng tc khng lin kt n khng. Outer radius bt (Switched) v tt (Shifted) cc gii hn, y l khong cch cc tiu ti cc tng tc khng lin kt c t l khng. y thng c t gi tr t nht l 4A0, ln hn bn knh trong. Vi cc iu kin bin tun hon, gi tr ny bng mt na chiu nh nht ca hp tun hon. Inner radius Ch bt gii hn, y l khong cch nh nht gia cc nguyn t i vi cc tng tc khng lin kt hon ton. Vi cc iu kin bin tun hon, gi tr ny l 4A0, b hn mt na chiu nh nht ca hp tun hon hoc c gi tr cc tiu l khng. Ch : Cc gii hn c thit lp s tr v gi tr ngm nh khi ta thit lp mt h phn t mi trn mn lm vic.
Cc thnh phn trng lc
S dng thnh phn trng lc t cc thnh phn ca trung lc MM+, AMBER, BIO+ v OPLS lin quan n tnh ton ca ta. HyperChem lu s thit lp cc thnh phn ny, p dng cho tt c cc trng lc, trong Registry v s dng chng cho cc phn HyperChem mi.
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Bond
Angle
Torsion Non-Bonded Electrosstatic Hydrogen-Bonded
Thnh phn bao hm trong tt c cc s hng trng lc kt hp vi s cng lin kt. Vi MM+ y l s hng bao hm s hng cng bc ba v s hng cng bnh thng. Thnh phn ny bao hm tt c cc s hng trng lc kt hp vi s un gc lin kt. Vi MM+ y l s hng bao hm s hng uncng ngang v un mt phng ngoi cng nh s hng un thng thng. Vi BIO+ (Charmm) n bao hm s hng Urey-Bradley cng nh s hng un thng thng. Bao hm tt c cc s hng vn, .v.v. s xon thch hp v khng thch hp. Bao hm tt c cc s hng kiu 6-12 van der Waals gia cc nguyn t khng lin kt. Bao hm tt c cc tng tc culomb v lng cc (MM+). Bao hm bt k s hng lin kt hydro nh s bao hm trong cc phin bn trc ca Amber v Charmm.
Dng v kho st cu trc 3D

Bn sn sng xy dng cu trc 3D cho alanin v quan st hnh dng ca n.
xy dng v nh hng cu trc ta lm nh sau

1. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c thc hin dng cu trc theo trnh xy dng. HyperChem xy dng v biu din gn ng bc nht cho ion lng tnh alanin. 2. Quay v chuyn cu trc n khi hnh dng ca n trng nh sau:
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Cu trc ca trnh xy dng ch l cu trc gn ng ca ion alanin. 3. M hp thoi Labels t Display menu v chn Chirality (tnh khng i xng gng) cho cc nguyn t. Nu cacbon trung tm c gn nhn l R ch khng phi l S, ta hy nhp tri chut vo cng c v, nhn phm Shift v nhp tri chut vo cacbon trung tm. Ta cng c th s dng nhn phm Shift v nhp tri chut quay hai nguyn t bn cnh, theo thay i tnh i xng gng ca phn t. 4. i kiu nhn ca cc nguyn t tr li dng Symbol v nhp tri chut bt li cng c la chn. 5. Lu cu trc vi tn l alaz.hin
o thuc tnh cu trc ca phn t ta lm nh sau:

1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp tri chut vo nguyn t oxi gi v r chut n nguyn t oxi cn li Trnh xy dng dng gc O-C-O l 1200. 3. Nhp phi chut vo vng trng b la chn. 4. Nhp tri chut vo nguyn t oxi gi v r n nguyn t nit ri nh chut.
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Gc vn O-C-C-N l 600 hoc 1200, tu thuc vo th t m ta s dng v cc nguyn t trong cu trc. 5. Nhp phi chut vo vng trng trn trang lm vic loi b cc la chn gc.
biu din kiu nguyn t MBER ta lm nh sau:

1. M hp thoi Labels trong Display menu v kiu nhnh l Type.
Thc hin tnh ton im n cho phn t

By gi ta thc hin tnh ton im n tnh nng lng v gradient cho phn t. 135
tnh ton im n ta lm nh sau:

1. Nhp tri chut chn Single Point trong Compute menu. Sau mt lc tnh ton hon thnh dng hin trng xut hin kt qu nng lng v gradient tnh ton c.
Ti u ho cu trc phn t c lp
Gi tr nng lng v gradient ln cho bit rng cu trc ca trnh xy dng kh xa cu trc ti u. Sc cng ch yu ph thuc vo khong cch ca lin kt C-N v C-O.
ti u ho cu trc ta lm nh sau
1. Nhp tri chut chn Geometry Optimization trong Compute menu. Hp thoi la chn ti u hnh hc xut hin
2. Nhp cc gi tr nh trong hp thoi trn v nhp OK thc hin tnh ton. Sau mt lc, ti u ho hon thnh. Trn dng hin trng xut hin kt qu v nng lng v gradient tnh ton c. 3. Khi ti u hon thnh, tin hnh o gc O-C-O v gc vn O-C-C-N: Gc O-C-O = 123.90. Gc O-C-C-N = -510 v 990. M li cu trc cha c ti u c gc O-C-O l 1200 v gc O-C-CN l 600 v 1200. Cui cng trong bi ny ta s dng gc O-C-C-N biu din cc tnh nng ca ng lc hc phn t ca HyperChem, v th hy lu gc ny. Nhp tri, gi v r chn gc vn O-C-C-N. Nhp tri chut chn Name Selection trong Select menu. Tch chn Other, nhp tn ncco ri nhp OK chn.
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4. Nhp phi chut vo vng trng b tt c cc la chn.
Lu cu trc
Ta nn lu cu trc alanin c lp ti u, nh th ta c th em so snh n vi cu trc trong dung mi m ta s to ra bi tip theo.
Lu cu trc
1. Nhp vo Save trong File menu hoc nhp ng thi hai phm Ctrl v S trn bn phm. Hp thoi xut hin. 2. nh tn ala-gas vo mc File name. 3. Chn ui HIN trong mc Save as Type. 4. Nhp tri chut vo phn ghi ch v nh ch thch nh sau:
5. Nhp OK chn.
Bi thc hnh 2: Solvat ho h phn t
137
Hng dn s dng HyperChem 7.04 HyperChem cho php ta t h phn t trong mt hp tun hon ca cc phn t nc m phng tc ng trong dung mi nc nh trong mt h sinh hc. Trong bi ny ta solvat ho ion lng tnh alanin to bi 1.
Trc khi tip tc, hy lm theo cc bc sau

1. Nhp tri chut chn none v chn Labels trong Display menu v t none, nhp OK chn. 2. Nhp trri chut chn Periodic Box trong Setup menu m hp thoi la chn.
Smallest box enclosing solute
Ch c chc nng thng tin. X, Y, Z cho ta bit kch c hp nh nht ta c th bao quanh h phn t (cht tan). Hp thoi c kch c cc tiu ny khng th iu tit s phn t nc trong h v n ch c ngha tham kho. Periodic box size Kch c cc chiu ca hp. Ta c th t li theo mun. Ch c ngha thng tin. N cho bit s phn t Maximum number of Water nc ti a trong hp. molecules Khong cch cc tiu gia cc phn t dung mi Minimum distance between v cht tan. Ngm nh l 2.3A0. C th t li t 1-5A0. solvent and solute atoms
t iu kin bin tun hon

solvat ho mt h bng HyperChem ta s dng mt hnh ch nht hoc hnh lp phng cha cc phn t nc trng thi cn bng. Ta xc nh cc chiu ca hp, t cht tan vo tm v xc nh khong cch cc tiu 138
Hng dn s dng HyperChem 7.04 gia cc nguyn t dung mi v cht tan. HyperChem s loi b tt c cc phn t nc n gn phn t cht tan hn khong cch l thuyt.
Xc nh kch c hp tun hon

C nhiu yu t xem xt khi ta xc nh kch c ca hp tun hon. v d, n phi ln hn hp nh nht cha c cht tan hin ra trong hp thoi la chn. Kch c ca hp t nht gp hai ln kch c ca cht tan ln nht trnh s tng tc gia cht tan-cht tan khi s dng cc ngng gii hn ngm nh. Tng tc gia cht tan-cht tan c th cng c trnh i vi hp nh hn bng cch lm nh bn knh ngng sau khi solvat ho( v th kch c cht tan ln nht bao gi cng b hn kch c ca hp nh nht). ln ln nht ca cnh hnh lp phng l 56.10408A0, do ta khng th t kch thc cc cnh ca hp bn ngoi gi tr nh nht v ln nht trong hp thoi la chn.
Chn kch c hp
1. Ly kch thc hp theo cc chiu l 12.0, 10.0 v 12.0 A0, nh trnh by trong minh ho sau:
2. Nhp OK chn. iu ny c ngha la t cu trc vo tm ca hp bao quanh bi 40 phn t nc.
Biu din h solvat ha

1. Nhp tri chut chn Rendering trong Display menu. 2. Chn Sticks, m phn la chn Sticks tch chn Perspective (phi cnh) ri nhp OK chn. 3. Nhp tri chut chn Molecules trong Select menu. 4. Chn vo lin kt hay mt nguyn t bt k thuc phn t alanin, quay h cho n khi nhn c nh sau:
139
iu chnh cc gii hn v la chn cht in mi

Khi ta s dng iu kin bin tun hon, ta cn kim tra cc la chn i vi cc gii hn v cht in mi trong hp thoi la chn trng lc.
kim tra la chn ngng v cht in mi ta lm nh sau

1. Nhp tri chut chn Molecular Mechanics trong Setup menu. 2. Chn Options m hp thoi la chn thm cho trng lc. 3. Nhn vo mc la chn Cutoff (ngng, gii hn) bn phi hp thoi.
Khi ta chn cc la chn trong hp thoi, HyperChem t ng thay i cc la chn cho cc ngng ta la chn chnh xc ngng bn trong v bn ngoi cho h c solvat ho. Ngng ngoi c t bng mt na kch thc hp nh nht, ngng trong t b hn 4A0 bo m khng c im khng lin tc trong mt th. 4. By gi nhn vo la chn Dielectric (cht in mi), trn nh ca hp thoi Khi ta s dng dung mi r rng, ta nn s dng hng s in mi. 5. Chn Constant (hng s) thay v Distance dependent (ph thuc khong cch). Ch : Hng s in mi khng t ng thay i bi v khi t mi n c lu vo trong file Chem.ini. 140
Hng dn s dng HyperChem 7.04 6. Nhp OK ng ln lt cc hp thoi.
Ti u ho phn t c solvat ho
Tip theo y ta thc hin ti u h solvat ho s dng iu kin bin tun hon. Bi trc phn t alanin c ti u hnh hc dng c lp. Trong phn ny ta thc hin ti u ho di nh hng ca dung mi.
ti u phn t trong dung mi ta lm nh sau

1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp phi chut vo vng trng loi b la chn trc . 3. Nhp tri chut chn Geometry Optimization trong Compute menu. Hp thoi la chn ti u hnh hc theo phng php c hc phn t xut hin. 4. Nhp OK bt u ti u ho phn t alanin solvat ho, k c cc phn t nc. Tnh ton thc hin trong mt vi pht. 5. Khi tnh ton hon thnh, cc gi tr tnh c xut hin trn dng hin trng. 6. Lu cu trc vi tn l ala-liq.hin.
Bi thc hnh 3: S dng s chng cht cc phn t

H ang biu din l h c cu trc c cc tiu ho ca ion lng tnh alanin trong nc. Ta s dng n so snh vi cu trc c lp. Thay v so snh cc phn t bng cch o thuc tnh cu trc ca tng phn t, ta s dng tnh nng chng cht ca HyperChem so snh mt cch trc quan hai cu trc bng vic chng cht cc phn t ln nhau.
Xo cc phn t nc
Trc khi tin hnh chng cht, ta cn xo cc phn t nc trong h.
xo cc phn t nc ta lm nh sau
1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp tri chut chn Molecules trong Select menu. 3. Nhp tri chut vo alanin. Phn t alanin s c chn.
141
4. Nhp tri chut chn Complement Selection trong Select menu Thao tc ny gip ch chn cc phn t nc. 5. Nhp tri chut chn Clear trong Edit menu. 6. Nu hp thoi xut hin hi ta c mun xo cc nguyn t chn khng, nhp Yes.
7. Nhp tri chut b tch Show Periodic box trong Display menu mn hnh ch cn biu din phn t alanin. 8. Lu kt qu thc hin vo file tn l ala-sol.hin.
Hp nht hai h
Bc tip theo l hp nht h ny vi h c lp. Trc khi hp nht hai h, ta nn chn h hin ti ta c th phn bit n trn mn hnh sau khi hp nht.
hp nht hai h ta lm nh sau

1. Nhp tri chut chn alanin. 2. Nhp tri chut chn Name Selection trong Select menu, vo mc Other v lu vi tn solvated ( solvat). Thc hin iu ny tin li cho ta biu din li n v sau.
142
Hng dn s dng HyperChem 7.04 3. Nhp tri chut chn Merge trong File menu, hp thoi m file xut hin, nhp m ala-gas.hin lu ln trc. C hai cu trc c lp v cu trc c solvat ho by gi trng nh trn mn hnh. Cu trc c solvat ho vn cn c chn nn sng hn.
4.
5.
6. 7. 8. 9.
Chng cht cho php ta kt hp h hin ti vi h khc c lu trc . H kt hp tr thnh h ang lm vic trn mn hnh. Nu cn thit, s dng cng c dch chuyn (Translation tool) dch chuyn quan st cho r. - Nhp tri chut vo cng c dch chuyn trn thanh cng c. - Nhp phi chut gi v r, phn la chn s dch chuyn theo chiu r chut. Nhp tri chut chn Color trong Display menu, hp thoi la chn m ra, chn Yellow ri nhp OK. Mu ca phn la chn s biu din l mu vng nu ta b la chn i. Nhng chng ta khoan hy b la chn. Nu mun chn h c lp th nhp tri chut chn Complement Selection trong Select menu. H c solvat ho s b b la chn cn h c lp c chn. Chn mu cho h c lp l mu ta (violet). Nhp phi chut vo vng trng b la chn. Chn Labels l symbol cho c h.
Chng cht cc phn t

Khi mt h c t nht hai phn t, nh trong v d ny, HyperChem c th chng cht cc phn t. S chng cht da trn s la chn ba nguyn t khng thng hng trong mi phn t. bt u, u tin chn cc nguyn t trong mi phn t trng khp nhau. Tip theo, gia cc lin kt 143
Hng dn s dng HyperChem 7.04 la chn cc nguyn t u tin v th hai mi phn t phi thng hng. Cui cng, la chn nguyn t th ba mi phn t phi t trn cng mt phng.
thc hin chng cht ta lm nh sau

1. Nhp tri chut chn cng c la chn trn thanh cng c. 2. Nhp tri chut chn Atoms v tch chn Multiple Selections trong Select menu. 3. Nhp tri chut v r chn gc lin kt N-C-C mi phn t. Ta c th quay cc cu trc nhn c nh sau
4. Nhp tri chut chn Overlay (ph) trong Display menu. 5. Nhp phi chut vo vng trng loi b la chn. 6. Nhp phm Spacebar trn bn phm a cu trc chng cht vo tm mn lm vic. H lc ny s trng nh sau:
144
7. Lu kt qu lm vic vo file vi tn l ala-sup.hin. Cc phn t hu nh trng kht vo nhau.
Bi thc hnh 4: Ti u m phng

M phng ng lc hc phn t kho st khng gian pha (vng xc nh theo v tr v tc ca nguyn t) bng cch gii cc phng trnh chuyn ng Newton. Khng nh tnh ton im n v ti u hnh hc, ng lc hc phn t tnh ton cc chuyn ng nhit. Cc phn t c th c nhit nng vt qua hng ro th. Tnh ton ng lc hc phn t cung cp cho ta cc thng tin v cc cu hnh c th c, cc thuc tnh ng lc hc v hot ng ng lc ca cc phn t. Trong bi ny ta s dng ng lc hc ti u h nhm thu c nc c cc tiu nng lng thp hn. u tin ta phi m li h ion lng tnh alanin c solvat ho thc hin ng lc hc phn t vi n.
m li h c solvat ho ta lm nh sau
1. Nhp tri chut chn Open trong File menu. 2. Chn m file ala-liq trong hp thoi Open. 3. Nu cn thit nhp tri chut tch bt li Show Periodic Box trong Display menu biu din hp tun hon gip ta xc nh d dng hn. 4. Nu cn thit chn li labels l none d nhn.
t m phng ng lc hc
1. Nhp tri chut chn Molecular Dinamics trong Compute menu.
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Hp thoi la chn ng lc hc phn t xut hin cho php ta t cc la chn cho tnh ton ng lc hc phn t Chy tnh ng lc hc phn t c ba giai on la chn: nung nng, chy v thi gian lm lnh. Giai on u tin xut hin giai on m phng thi gian gia nhit, s dng nhit bt u t vn tc khi u theo t l vi vn tc nhit tng ln n nhit m phng. Giai on gia, vn tc c thay i ch khi nu hng s nhit c chn. Giai on cui cng xut hin qua giai on m phng thi gian lm lnh vi s thay i vn tc t nhit tng thm n nhit cui cng. t Heat time (thi gian gia nhit) l 0.1 pico giy. t Temperature step (bc nhy nhit) l 30K. Bi v gradient l rt nh lc h khi u, mt thi gian gia nhit ngn 0.1 pico giy dng tng nhit t 100K n nhit m phng l 300K tng theo bc nhy nhit l 30K. t thi gian chy l 0.5 pico giy. Nhit c s dng y t vn tc nguyn t khi u hoc iu chnh vn tc nguyn t. ng nng ny c th c bin i thnh th nng trong qu trnh m phng, nguyn nhn do nhit tnh ton c l gim xung. Nu nhit cui cng tng ln (nh trong v d ny), c ngha l th nng ang chuyn thnh ng nng khi h chuyn v cu hnh n nh hn. Thc hin chc chn l iu kin bin tun hon trng thi bt. La chn ny c HyperChem t ng bt khi iu kin bin tun hon c s dng, nhng n c th b gt ra nu ta t In vacuo trong mc Option. t Step size (kch c bc) l 0.0005 pico giy. t Data Collection period (giai on la chn d liu) l 4. iu ny gip cho qu trnh tnh ton c nhanh hn. B tch Constant Temperature tt nhit khng i. t cc iu kin nh trong hp thoi sau
2. 3.
4.
5.
6. 7. 8. 9.
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La kch c thi gian cho qu trnh m phng ng lc hc v ng lc hc Langevin. Vi Monte Carlo, l s bc trong mi pha, v s chuyn ng cc i ca nguyn t trong mi bc. Giai on bt u v kt thc u cng mt nhit . La chn cho ng lc hc phn t (Molecular Dynamics ) v ng lc hc Langevin (Langevin Dinamics). Heat time Thi gian tnh bng poco giy (ps) cho qu trnh chuyn nhit t lc bt u n nhit m phng. Gi tr nn thay i t 0 n 10 ps Run time Thi gian theo pico giy gi h nhit m phng. Thay i t 0 n 103 ps. Cool time Thi gian chuyn nhit t nhit m phng n nhit cui cng. Thay i t 0 n 10 ps. Step size Khong thi gian gia cc gi tr ca nng lng ton phn v nhit ca h. Thay i t 10-4 n 10-3 ps, v ln hn 0. t cho Monte Carlo: Heat S bc t nhit khi u n nhit m phng. Run steps S bc thc hin tnh ton nhit m phng. Cool S bc chuyn nhit m phng v nhit cui cng. Max delta y l khong cch cc i (A0) m bt k nguyn t no trong h s di chuyn trong mi bc theo tnh ton. thay i t 0.01 n 0.1 A0. Ngm nh l 0.05A0. Temperature Cc mc nhit m phng. Trong qu trnh nung nng v lm lnh, HyperChem t nhit bng cch iu chnh nh k cc vn tc. Trong qu trnh chy vi nhit khng i, HyperChem iu chnh vn tc mi bc thi gian. Nu hng s nhit khng tch, s Times
147
Hng dn s dng HyperChem 7.04 hiu chnh xut hin mt ln lc bt u m phng. Nu thi gian gia nhit ln hn khng, vn tc ban u ca nguyn t c hiu chnh n nhit ny. gi tr thay i t 0 n 300 K. Ti im khi u thi gian chy, vn tc nguyn t c hiu chnh n nhit ny. nu ta mun nung nng lc u trong qu trnh m phng, nhit ny cn ln hn nhit khi u. Gi tr thay i t 0 n 300K. Nu thi gian lm lnh ln hn khng, vn tc nguyn t c hiu chnh n gn nhit ny im kt thc ca thi gian lm lnh. Nu ta mun, y dng t kch c bc nhy, theo K, cho qu trnh nung nng v lm lnh. Gi tr thay i trong khong 0 n 100K.
Starting temperature Simulation temperature
Final temperature Temperature step
Options In vacuo Tch chn khng tnh n iu kin bin tun hon t trong tnh ton. Ta ch chn In vacuo (trong chn khng) nu h c t hp tun hon, nu khng th HyperChem ngm nh sn cho ta. Periodic Tch chn phn ny bao gm c cc iu kin bin boudary tun hon vo trong tnh ton. Vi iu kin h phi conditions c t hp tun hon ta mi c th t la chn ny c. Constant Dng iu chnh nhit ca h phn t hng v temperature nhit m phng, ch p dng trong qu trnh chy m phng (Run time). iu ny to ra iu kin khng cn bng; qu trnh m phng hiu chnh vn tc nguyn t iu chnh nhit . Bath Hng s thi gian dng cho qu trnh hiu chnh nhit relaxation trong qu trnh chy. gi tr ny nh hng n cng hiu chnh. Cc gi tr hng tng t nh Step size (kch c bc nhy) gip cho qu trnh hiu chnh tt hn, nhng lm cho h xa khi cn bng hn. Thi gian ln nn t cho qu trnh hiu chnh nh, nhng thng dng gi tr nhm chng li cc sai s lm trn tch t trong qu trnh m phng lu. gi tr ngm nh l 0.1 ps. Random seed S ny l im khi u cho qu trnh to ra s ngu nhin s dng m phng. N c dng xc nh vn tc khi u cho cc nguyn t trong qu 148
Hng dn s dng HyperChem 7.04 trnh tnh ton ng lc hc phn t. Friction La chn ny dng cho ng lc hc Langevin. N coeficient m t h s ma st s dng cho vic m phng tng tc ca dung mi. Gi tr ly c t 0 n v cng. y l tn s, theo cc bc thi gian, qu trnh m Data phng a gi tr tnh ton c vo HyperChem . C collection th t t 1 n 32,767. period Screen refresh y l tn s, theo cc bc d liu, biu din kt qu tnh ton ln mn lm vic. t c gi tr t 1 n period 32,767. Tch chn phn ny qu trnh m phng lu vo Playback mt file HIN cc nh chp nhanh (SNP). Nu mun Playback li h phn t t file HIN ta phi trn m lm vic. Nu tch Playback, th ch c giai on tp hp d liu, lm mi mn hnh, chp nh nhanh v tnh trung bnh l c gi tr. Nhp tri chut vo Snapshots xem hp thoi biu din li ng lc hc phn t. Nhp vo Averages tnh trung bnh hoc v biu cc gi tr trong qu trnh biu din li. Nu Restart c tch chn, tnh ton thit lp vn tc Restart ban u ca nguyn t cho cc gi tr c xc nh trc . Nu Playback khng tch, khi chn, nt ny s biu Snapshots din hp thoi chp nh nhanh ng lc hc phn t. Nu Playback tch chn, Snapshots biu din hp thoi Playback ng lc hc phn t. Biu din hp thoi tnh trung bnh ng lc hc phn Averages t, v th ta c th tnh trung bnh v v biu kt qu tnh ton c. Dng hp thoi ny sau khi tnh ton hoc chy li snapshots file. Tnh trung bnh ch c gi tr cho ng lc hc phn t. Biu xut hin trong hp thoi kt qu ng lc hc phn t. Bt u tin hnh ng lc hc phn t, Monte Carlo Proceed hay l biu din li Snapshot file.
t biu din li ng lc hc
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Hng dn s dng HyperChem 7.04 Bc tip theo ta s hc cch t biu din li ng lc hc. Biu din li ng lc hc phn t l thch hp bi v n lu li thi gian m phng ng lc khng nh trc ta phn tch sau ny. ng lc hc phn t m phng din bin ca mt h theo thi gian, cho ta bit c vn tc v v tr ca cc nguyn t (qu o ca n). Cc tnh ton ny c th rt tn thi gian, v kt qu c ngha thng k, thi gian m phng lu ph thuc vo hng nghn bc cn thit. Thng ta s mun lu qu o tnh ton c biu din li v sau hoc phn tch, hn l phi lp li m phng.
t biu din li ng lc hc
1. Nhp tri chut chn Snapshots (chp nh nhanh) y hp thoi la chn ng lc hc phn t (Molecular Dynamics Option). Hp thoi chp nh nhanh ng lc hc phn t xut hin (Molecular Dynamics Snapshots) cho php ta nh tn v ghi ch cn thit vo file. 2. nh tn ala-run mc File name. Mt file c tn ala-run.hin c lu li, l file HIN cha nh chp nhanh. Mt file khc, ala-run.snp, l mt file nh nguyn cha ng thi vn tc v to ca nguyn t. 3. t mc Snap Shot period gi tr 1. 4. Nhp OK tr v hp thoi la chn ng lc hc phn t. 5. Nhp Proceed tin hnh ng lc hc phn t. Ch : Sau khi tin hnh ng lc hc phn t, nu mun xem li qu trnh ng lc hc phn t thc hin ta li m hp thoi la chn Molecular Dinamics trong Compute menu. Tch chn Playback, lc ny hp thoi la chn biu din li ng lc hc s hin ra. Ta ch vic t nhng la chn cn thit v nhp Nt Proceed nh trc xem biu din li qu trnh ng lc hc.
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Trajectory Snapshot file Step count Step side Start time End time AVI Movie Create file Movie file Frame rate
Phn ny cho ta nhng thng tin v file snapshot, v cho php ta xc nh biu din li tt c hay ch mt phn. Ch biu din file ngun. Bao gm ng dn. Ch biu din s nh chp nhanh lu trong qu trnh m phng. Ch biu din khong thi gian gia cc nh chp nhanh (theo ps). Thi gian trong qu trnh m phng bt u biu din li. Nhp gi tr t 0.000 (ngm nh) n End time. Thi gian trong qu trnh m phng kt thc biu din li. Nhp s t Start time n gi tr ngm nh (tng thi gian m phng). Phn ny c cc la chn to ra mt phim AVI t cc nh chp nhanh. C th xem t Multimedia player hay cc trnh ng dng tng thch khc. Nu la chn ny c tch, mt AVI movie s c to ra. nh tn file AVI ta mun to vo ny. t t l hnh nh vo y.
t tnh trung bnh theo ng lc hc phn t

ng lc hc phn t thng c s dng thu nhng thng tin v m bng cch ly mu m phng ln qua mt thi gian di. N cng hu dng
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Hng dn s dng HyperChem 7.04 theo di s lng hnh hc v nng lng trong qu trnh m phng nhm xem h c n nh cho vic ly mu c gi tr thng k hay khng. Ch : Khi bt u tnh hm trung bnh, HyperChem to ra mt file vi phn ui m rng l .csv trong th mc lm vic hin ti. Tuy nhin, nu ta ang c file snapshot t CD, th mc hin ti trn CD; ta khng th to ra file ny c. Ta cn copy file Snapshot vo cng ca my.
t tnh trung bnh

1. Nhp tri chut vo Averages y hp thoi la chn ng lc hc phn t m hp thoi tnh trung bnh ng lc hc phn t.
2. Nhp tri chut vo EKIN, EPOT, ETOT v ncco trong mc Selecton, sau nhp tri chut vo nt Add chuyn chng vo hp thoi Average only.
3. Nhp tri chut chn EKIN, EPOT, ETOT v ncco trong mc Average only, tip theo nhp vo nt Add chuyn chng vo mc Avg. & graph.
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Hng dn s dng HyperChem 7.04 iu ny gip cho vic lu d dng hn biu nng lng ton phn, th nng, ng nng v gc vn vo phn la chn c t tn. HyperChem to ra mt file vi tn l ala-run.csv (hoc chem.csv nu ta khng t biu din li ng lc hc), ghi li nhng con s c tnh trung bnh h biu din gip ta c c d dng bng biu hoc chng trnh bng tnh phn tch. y l list cc la chn, cng vi cc phn la chn Selection c t tn m HyperChem c th v biu v tnh trung bnh. EKIN ng nng (kcal/mol) EPOT Th nng (kcal/mol) ETOT Nng lng ton phn(kcal/mol) TEMP Nhit (Kelvin) ACCR T l chp nhn (ch c gi tr cho m phng Mote Carlo) Named Cc phn la chn c t tn cng c lit k trong selections list. D EKIN lch RMS so vi gi tr ng nng trung bnh. D EPOT lch RMS so vi gi tr th nng trung bnh. D ETOT lch RMS so vi gi tr nng lng ton phn trung bnh. D TEMP lch RMS so vi gi tr nhit trung bnh. ACCR lch so vi t l chp nhn trung bnh (ch cho Monte Carlo). D Named lch RMS so vi trung bnh cc phn la chn c selections t tn. Average only y l list cc gi tr HyperChem tnh trung bnh khi kt thc tnh ton ng lc hc phn t. y l list bn gi tr HyperChem tnh trung bnh v v Avg. & biu trong qu trnh m phng ng lc hc phn t. Graph Biu din gi tr tnh trung bnh gn nht. na c ngha Value l cha tnh trung bnh. Average/Gra y t khong cho d liu tnh trung bnh hay v biu cho n. ph period
Tin hnh ng lc hc
1. Nhp OK tr v hp thoi la chn ng lc hc phn t, tip theo nhp vo nt Proceed bt u ng lc hc.
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Hng dn s dng HyperChem 7.04 Hp thoi kt qu dng biu xut hin trn mn lm vic. 2. Di chuyn hp thoi sang mt bn c th nhn qu trnh m phng c r hn. Trong khi tnh ton ang chy, ta c th quay, dch chuyn hoc phng to h quan st c r. Ta cng c th s dng cc ng dng khc ca Window, nhng iu ny c th lm chm qu trnh m phng. 3. Khi qu trnh m phng vn ang tip tc, ta c th nhp vo nt Rescale thay i t l cc gi tr ang v biu . Khi giai on gia nhit hon thnh, (khi nng lng ang c thm vo) nng lng ton phn vn l hng s, v ng nng phn nh th nng ca h. Cn trng: Ta khng th v li biu nu nhp tri chut vo Done. v li biu ta phi thc hin li qu trnh ng lc hc. Trong phn u lc chy v sau khi gia nhit th nng v nhit ca h tr nn kh n nh, nhng khi nhit tng ln. Th nng trong qu trnh chy cui cng gim xung ng k. ng lc hc phn t nhit phng cho php h gii quyt hng ro nng lng trn mt th v tm kim vng th nng thp hn khng c nghin cu bi thut ton cc tiu. Khi chy ng lc hc hon thnh ta c th ti u ho h xc nh cc tiu mi.
Sau khong 10 pht th vic chy s hon thnh.
Ti u ho li cu trc mi
By gi chy ng lc hc hon thnh, ta c th ti u ho cu trc xc nh cc tiu b phn mi. 1. Nhp tri chut chn Geometry Optimization trong Compute menu. 2. Nhp tri chut chn OK ti u ho bng phng php c hc phn t theo nhng la chn trc. Sau khi ti u hon thnh, dng hin trng cho bit cu trc c nng lng thp hn cc tiu cu trc c solvat ho trc . Trong hnh thc tnh ton ny, kch c hp v giai on m phng khng quan trng bng khi ta tnh trung bnh kt qu so snh vi thc nghim. Nh l ly mu nn bt u khi h c cn bng, thng c nh
154
Hng dn s dng HyperChem 7.04 gi theo th nng v ng nng dao ng trong khong gi tr thch hp i vi giai on m phng di.
Bi thc hnh 5: M phng Langevin v Monte Carlo.

Trong phn ny ta s dng phng php m phng Langevin v Monte Carlo kho st thm cc cu hnh ca h ion lng tnh alanin. Phng php ng lc hc Langevin m phng chuyn ng ca cc phn t chu va chm ngu nhin cng nh chu tc dng ca cc lc ma st v c th c dng lm m hnh cho cc h c solvat ho khng bao gm cc phn t dung mi.
Phn 1: ng lc hc Langevin
Cc phn t trong dung dch chu s va chm vi cc phn t khc v chu tc dng ca cc lc ma st khi chng chuyn ng trong dung mi. Dng ng lc hc Langevin, ta c th m hnh ho cc tc ng ny v nghin cu v hot ng ng lc ca cc h phn t trong mi trng lng. Cc m phng ny c th nhanh hn nhiu so vi m phng ng lc hc phn t. Thay v bao hm c th cc phn t dung mi, phng php ng lc hc Langevin m hnh ho cc nh hng qua cc lc ngu nhin tc dng ln phn t c quan tm m phng cc va chm v lc ma st c thm vo m hnh ho nng lng b mt i qua cc tng tc ny. ng lc hc Langevin c th dng nghin cu cc vn ging nh ng lc hc phn t: cc thuc tnh ph thuc vo thi gian ca h solvat nhit khc khng. Do x l n dung mi, phng php ny c bit thch hp cho vic nghin cu cc phn t ln trong dung dch. M phng ng lc hc Langevin c thit lp ging nh m phng ng lc hc phn t, nhng c s khc nhau nh tu thuc vo vic thm h s ma st m t nh hng ca dung mi. ng lc hc Langevin dng tnh ton cc thuc tnh ph thuc vo thi gian ca phn t c lp. Tuy nhin, ngi ta thng quan tm n tnh cht phn t ny nh hng n phn t khc. Vi HyperChem, ta cng c th thm cc phn t dung mi, nhng vic thm nhiu phn t dung mi s lm cho qu trnh m phng chm hn.
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Hng dn s dng HyperChem 7.04 1. Khi phc li ion alanin trng thi kh, ta lu trong file ala-gas.hin t trc. 2. t cc la chn trong hp thoi la chn ng lc hc Langevin nh ng lc hc phn t bi trc. 3. t Friction coefficient l 0.05 ps-1. Khi h s ma st c t l 0, HyperChem thc hin tnh ton s nh ng lc hc phn t, v ta cng nn s dng time step (thi gian nhy) thch hp cho phng php.Vi gi tr h s ma st ln hn, cc chuyn ng xut hin qua mt thi gian ngn, thi gian nhy ln hn c th c s dng. 4. t thi gian Time Step l 0.001 pico giy. 5. t Averages v Snapshots nh bi ng lc hc phn t trc. 6. Nhp tri chut vo nt Proceed bt u m phng ng lc hc Langevin. Nh vi k thut ng lc hc phn t, giai on nung nng v lm lnh cng c thm vo m phng ng lc hc Langevin. Cn bng ca h khng quyt nh cho vic xc nh thm cu trc c nng lng thp, nhng n quan trng khi so snh gi tr c m phng vi cc thuc tnh thc nghim.
Phn 2: M phng Monte Carlo

Phng php Monte Carlo kho st khng gian pha bng cch to ra cc cu hnh ngu nhin t mt phn b Boltzmann nhit cho trc. Phng php Monte Carlo c th c s dng tm nng lng trung bnh v thuc tnh cu trc cn bng ca cc h tng tc phc tp. Phng php Monte Carlo cung cp cch tip cn to ra cc cu hnh bn.
Thit lp m phng Monte Carlo

1. M li h ion lng tnh alanin c solvat ho m ta lu bi trc. 2. Nhp tri chut chn Monte Carlo trong Compute menu. Hp thoi la chn xut hin cho php ta t cc tham s m phng Monte Carlo. Trong v d ny chng ta s chy m phng nhit khng i vi 1000 bc. i vi mt s h, c l nn thm giai on gia nhit v lm lnh. 3. t Run Steps l 1000, t Heat v Cool steps l 0. 4. t kch c bc nhy cc i, Max Delta, l 0.05 A0. y l t s di ch ti a ca cc nguyn t th. 5. t Simulation Temperature l 300K. 6. Tch chn Periodic boundary conditions. 156
Hng dn s dng HyperChem 7.04 7. t Data Collection period l 4 bc (steps).
t biu din li Monte Carlo

8. t file Snapshot, nu mun.
t tnh trung bnh theo Monte Carlo

9. t tnh trung bnh v v th nu mun. (nh bi thc hnh ng lc hc phn t)
Tin hnh m phng v phn tch

Khng c s khc nhau ng k gia cc bc s dng HyperChem phn tch m phng Monte Carlo v m phng ng lc hc phn t. Window c th copy cc kt qu m phng Monte Carlo vo b nh tm thi v dn vo trong cc ng dng khc.
Xem li kt qu
1. Theo nhng bc sau xem li ng lc hc: M file ala-run.hin. M hp thoi la chn ng lc hc phn t v tch chn Playback. Chn Snapshots xc nh phn m phng lp li. Chn Proceed bt u biu din li ng lc hc. M phng s biu din li v cn bn l nhanh hn khi tnh ton ng lc hc lc u. 2. To cc phn la chn t tn cho hai, ba hoc bn nguyn t v s dng biu din li ng lc hc phn t v biu gi tr tnh c.
Bi cc phng php bn kinh nghim

Chn Semi-empirical s dng phng php tnh ton c hc lng t bn kinh nghim. S tch chn ny hot ng mi cho n khi ta chn Molecular Mechanics hay Ab initio. Ta c th dng mt phng php c hc lng t bn kinh nghim cho tt c cc tnh ton trong Compute menu. Cc tnh ton bn kinh nghim gii phng trnh Schrodinger, vi s xp x no , nhm m t thuc tnh ca cc nguyn t v phn t. tnh nhanh v n gin, cc phng php bn kinh nghim thc hin s n gin ho nh sau: ch tnh cho cc electrong ho tr; b qua mt s tch phn tng tc; s dng cc hm obital in t c bn chun, khng c ti u; dng cc tham s xc nh t thc nghim. Cc tham s thc nghim loi b mt 157
Hng dn s dng HyperChem 7.04 lng tnh ton cn thit no v sa cc li kt qu thu c t s gn ng. Quan trng: Cc phng php bn kinh nghim trong HyperChem c th x l tt c cc nguyn t nhm chnh, c tham s ho trong cc file tham s x l n c xenon. Extended Huckel, ZINDO/1, ZINDO/S c th x l hai hng kim loi chuyn tip u tin. Tt c cc phng php bn kinh nghim hin hnh c thit lp nhm loi b nhng tnh ton tn nhiu thi gian ca cc tch phn xen ph. Phng php b qua xen ph vi phn khng tnh cc tch phn y c gi tr nh.
Hp thoi la chn phng php bn kinh nghim:
Extended Huckel
CNDO
INDO
S dng tnh ton obital phn t ca cc phn t. Khng c gi tr ti u hnh hc hoc tnh ton ng lc hc phn t. Dng s ng gin ho mt electron quy cho l khng c s tng tc r rng gia cc electron. y khng phi l phng php trng t hp (SCF) B qua hon ton xen ph vi phn. y l phng php trng t hp n gin nht. N c gi tr tnh cc thuc tnh electron trng thi c bn ca cc h v h v h v kn, dng ti u hnh hc, tnh nng lng ton phn. Gin tip b qua xen ph vi phn. Ci tin t CNDO bng cch tnh n lc y mt tm gia cc electron trong cng mt nguyn t. Dng tnh thuc tnh electrong trng thi c bn ca h v h v v kn, dng ti u hnh hc, tnh nng lng ton phn, y 158
Hng dn s dng HyperChem 7.04 l mt phng php SCF. L phng php m rng t INDO bng cch s dng cc tham s, thay v tnh ton i vi nhiu tng tc. s dng cho cc phn t hu c ln, tnh ton thuc tnh in t, ti u hnh hc, tnh nng lng ton phn. y l phng php SCF. S dng cho nhiu loi phn t hu c khc nhau c cha cc nguyn t thuc hng 1 v 2 trong bng h thng, khng c gi tr cho cc kim loi chuyn tip. Loi b mt s sai s trong MINDO3. Tnh thuc tnh in t, ti u hnh hc, nng lngt ton phn, v nhit hnh thnh. y l phng php SCF. L phin bn ca MNDO vi vic thm cho cc obital d. S dng cho cc nguyn t nhm chnh c cc obital-d ng vai tr quan trng (nh l Sunfua). c tham s ho tt hn, dng cho cc kim loi chuyn tip. Tnh ton thuc tnh in t, ti u hnh hc, nng lng ton phn, nhit hnh thnh. y l phng php SCF. Ci tin t MNDO,v l phng php chnh xc nht. Dng cho cc phn t hu c c cha cc nguyn t thuc hng th nht v hng th hai trong bng h thng, khng dng cho kim loi chuyn tip. C th tnh tt hn MNDO cho cc hp cht cha c nit v oxi. Tnh thuc tnh in t, ti u hnh hc, nng lng ton phn, nhit hnh thnh. y l phng php SCF. c tham s ho t AM1. PM3 khc AM1 ch cc gi tr tham s. Cc tham s cho PM3 ly bng cch so snh s lng ln v rng ri t thc nghim. Tiu biu, cc tng tc khng lin kt t y hn trong PM3 so vi AM1. PM3 u tin c s dng cho cc phn t hu c, nhng n cng c s dng cho nhiu nguyn t nhm chnh. y l phng php SCF. S i t INDO m rng cho cc kim loi chuyn tip. Tng ng vi phin bn gn y nht ca phng php INDO/1, s khc u tin l s dng hng s m obital. ZINDO/1 cho php ta tnh nng lng trng thi chuyn tip, ti hu hnh hc ca cc phn t cha kim loi chuyn tip. L phng php INDO c tham s ho thm nhm m phng s chuyn ph UV/Visible (t ngoi/kh
MINDO3
MNDO
MNDO/d
AM1
PM3
ZINDO/1
ZINDO/S
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Hng dn s dng HyperChem 7.04 kin) khi dng phng php CI n (tng tc cu hnh n) dng e d on ph UV/Visible nhng khng ph hp tnh ti u hnh hc hay ng lc hc phn t. L phng php b qua xen ph vi phn, bao gm cc tham s khng ch cho s th t nguyn t m cn cho kiu nguyn t. C gng thu c phng php bn kinh nghim nng cao chnh xc nhiu hn. S dng phng php ny nh mt cng c nghin cu cho mt khong gii hn cc phn t c cc tham s c pht trin v ang hin hnh. Nhp tri chut biu din la chn bn kinh nghim nhm thit lp cc iu kin tnh ton. C ba phin bn, tu thuc vo phng php bn kinh nghim m ta chn.
TNDO
Options..
Phng php p dng cho cc nguyn t:

Cc bng sau y biu din cho ta bit cc nguyn t c x l theo cc phng php bn kinh nghim khc nhau trong HyperChem. y biu tng ca cc nguyn t x l theo mi phng php c t m: Ch : Phng php Huckel m rng c th p dng cho tt c cc nguyn t trong bng h thng, tp hp tham s ngm nh bao hm tt c cc tham s cn thit
160
161
La chn bn kinh nghim cho phng php Huckel

Hp thoi ny dng t ring cho phng php Huckel. Tt c cc phng php bn kinh nghim khc s dng hp thoi khc.
Total charge
Spin mutiplicity
in tch ht nhn d so vi in tch electron. N bng khng i vi h trung ho, l gi tr nguyn dng i vi cation v l gi tr nguyn m i vi anion. y l bi spin, 2S+1, y S l tng spin electron ca h. Mi electron khng kt i c tnh l 1/2. H v kn (singlet) c bi l 1. Trng thi doublet (biu din hai mi tn hng ln) v triplet (biu din ba mi tn hng ln) c bi l 2 v 3. Ta c th thay i gi tr t 1 n
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Hng dn s dng HyperChem 7.04 6. Huckel Constant Hng s t l gia cc yu t ma trn khng cho ho v cc yu t ca ma trn cho ho. Gi tr thng l 1.75. Ga tr ln t cho trng lng ln ng vai tr l xen ph obital nguyn t trong vic xc nh nng lng. Gi tr nh t cho trong lng ln nhm kt hp nng lng ca cc electron trong cc obital nguyn t. Unweighted Dng hng s Huckel khng sa i g. constant Weight Tng hng s Huckel bng mt h s c coi l difuseness s khuch tn ca cc obital nguyn t. H s ny ch c quy cho cc h phn t c cc obital khuc tn rt khc nhau. iu ny him khi xut hin i vi cc hp cht hu c v cc nguyn t nhm chnh. Tch chn thm cc obital d cho Si, P, S v Cl. d orbitals y l h s t l. Scale Factor
Hp thoi la chn cho cc phng php bn kinh nghim khc

Total charge Spin multiplicity in tch ht nhn d so vi in tch electron. Bng khng trong h trung ho, nguyn dng trong cation v nguyn m trong anion. L bi spin ton phn, 2S + 1, S l tng spin electron ca h. Mi electron khng kt i c tnh l 1/2. H v kn c bi l 1. H v h c th c bi l 2, 3, 4 hoc cao hn. Dng cc s nguyn thay i t 1 n 6. 163
Hng dn s dng HyperChem 7.04 State Lowest Next lowest Convergence limit M t trng thi kch thch ca cc electron ho tr trong h. Trng thi in t c nng lng thp nht bi spin cho trc. Trng thi kch thch in t u tin ca bi spin cho trc. (singlet, doublet, triplet, hoc quartet) Kt thc tnh ton SCF khi s khc nhau v nng lng sau hai ln lp li lin tip b hn gi tr t. y l gii hn hi t cho nng lng electron ton phn trong tnh ton SCF. Ga tr cc i cho s lp li ca mt tnh ton SCF. Tnh ton s ngng sau khi lp gi tr ta t d cha n kt qa cui cng. Tch chn t hi t nhanh hn cho qu trnh lp SCF. t cho phng php tnh ton cc kiu tc ng spin. C hai kiu nh sau: Phng php Hartree-Fock khng gii hn cung cp cc obital c khng gian ring (alph v beta) cho cc electron cng vi kiu spin. Phng php ny dng cho cc h v h v v kn. Phng php Hartree-Fock gii hn i hi spin cp i ca cc electron nh c trong cng khng gian obital. L phng php dng cho h v h v h v kn. Tham s ho thm cho cc phng php ZINDO nhm thay i phn ng gp trong lin kt sigma v pi. Hiu chnh xen ph obital nguyn t sigmasigma. Nn t cho ZINDO/1 gi tr 1, cho ZINDOS gi tr 1.267. Hiu chnh xen ph obital nguyn t pi-pi. Nn t 1 cho ZINDO/1. Ngm nh 0.64 cho ZINDOS l thch hp cho cc kim loi chuyn tip, v gi tr 0.585 cho cc phn t hu c. La chn chn hai phin bn TNDO ta mun dng. La chn ny lp li cc h s mc xen ph m t trn khi chn TNDO. TNDO c ngun gc l CNDO v INDO v ta 164
Iteration limit Accelerate convergence Spin pairing UHF
RHF
Overlap Weighting Factors Sigma Sigma Pi-Pi
TNDO Version
Hng dn s dng HyperChem 7.04 c th chn mt trong hai TNDO/1 hay TNDO/2. La chn ny t hot ng v t cc la chn cho tnh ton tng tc cu hnh. iu ny l cn thit nu ta mun tnh ph UV visible.
Configuration interaction
La chn tng tc cu hnh

Cc tnh ton CI c th dng ci tin cht lng ca hm sng v trng thi nng lng. Cc tnh ton trng t hp (SCF) da trn m hnh mt electron, mi electron di chuyn trong trng trung bnh c to nn bi n-1 electron cn li trong phn t. Thc t, cc electron tng tc ngay tc thi v do c khuynh hng t nhin trnh xa electron khc, tho mn nguyn l loi tr. S tng quan (tc ng qua li ln nhau) ny dn n kt qu l lc y trung bnh gia cc electron thp hn v do c trng thi nng lng thp hn.
C hai kiu tng quan electron: tnh v ng. Tng quan tnh c quy cho l s suy bin gn trng thi cho trc; tng quan ng l s trnh xa tc thi ca cc electron vi nhau. Chn None, Singly Excited (kch thch n), Microstate (vi trng thi) None Chn None nu khng mun s dng tng tc cu hnh. Singly Excited Ch cc cu hnh kch thch n c tnh. Microstate Gm nhiu trng thi kch thch, k c cc trng thi kch thch n. t phm vi cc obital v t cc electron c Orbital kch thch to ra mt tp hp cu hnh tng tc. Criterion CI Method
165
Hng dn s dng HyperChem 7.04 Occupied Phm vi ca cc obital nh c bt u t HOMO, t cc electron c kch thch. Unoccupied Phm vi ca cc obital o bt u t LUMO n khi cc electron c kch thch ln. L la chn cho Orbital Criterion, gi tr ny t Energy nng lng gii hn cho s to tp hp cc cu hnh Criterion tng tc. Nng lng obital cao nht khc nhau (eV) gia cc Maximum obital nh c v khng nh c, c tnh trong tnh Excitation ton CI. Ni chung cc cu hnh c nng lng cao khng tng tc mnh trong tnh ton ta ni y. Tng thm nng lng cc i s lm tng thm s tng tc cu hnh trong tnh ton CI.
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Bi 11 Tnh ton Obital phn t

Tnh cc hm sng. V biu th tnh in, mt in tch v obital phn t. Tnh in tch nguyn t. t cu trc thng trc.
Bi ny cho ta bit nhiu kiu tnh ton bn kinh nghim khc nhau m HyperChem c th lm. Phn t ta s dng trong bi ny l nc.
To phn t nc to phn t nc theo trnh xy dng ta lm nh sau

1. Nhp tri chut chn Show Hydrogens trong Display menu v b tch Perpective nu c trong mc Sticks ca hp thoi la chn Rendering. 2. Nhp lin tip hai ln tri chut vo cng c v trn thanh cng c m hp thoi la chn cc nguyn t. 3. B tch Explicit Hydrogens, nhp chn oxi ri ng hp thoi li. 4. Nhp tri chut vo cng c v, chuyn con tr ln mn lm vic v v mt nguyn t oxi. 5. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c thm hydro cn thiu vo oxi. HyperChem s t ng thm nhng hydro cn thiu v biu din phn t nc theo trnh xy dng. 6. Nhp tri chut vo Labels trong Display menu v chn Symbol trong hp thoi Labels mc Atoms, sau nhp OK chn. Bc v ca ta s trng nh sau;
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Gc lin kt ca cu trc theo trnh xy dng ny l gc t din 1090. Ta c th ci tin cu trc ny, nhng vi bi tp ny ta thc hin tnh hm sng cho cu trc ca trnh xy dng.
t cu trc thng trc

Trc khi tnh ton hm sng, ta t phn t vo nh hng chun bng cch t thng trc qun tnh th hai ca nc (trc i xng trong mt phng phn t) l trc y.
t thng cu trc ta lm nh sau

1. Nhp tri chut chn Align Molecules trong Edit menu. 2. Trong hp thoi la chn Align Molecules tch chn Secondary, trong mc With chn Y Axit (trc Y).
3. B tch nu c mc Minor Axit; ta khng mun nh r s thng dc theo trc th hai. 4. Nhp OK chn. Phn t nc s c quay trn mn lm vic trng nh th ny:
168
5. Lu cu trc vi tn l h2o.hin.
Biu din in tch nguyn t

Trong bi 10 ta quy in tch nguyn t bng vic s dng Set Charges (t in tch) trong Build menu. in tch c th c quy t ng nu phn t ta ang dng c c t mt file mu, nh l file PDB. Trong bi ny, ta thu c in tch nguyn t bng tnh ton c hc lng t bn kinh nghim. u tin, xem khng thy khng c in tch c quy cho phn t nc.
biu din in tch ta lm nh sau:

1. Nhp tri chut m hp thoi Labels trong Display menu. 2. Nhp tri chut tch chn Charge trong mc Atoms ca hp thoi Labels, ri nhp OK chn. Nhn cho bit l trn phn t khng c in tch c quy cho phn t nc.
Tnh hm sng
Hm sng c lp nn t cc obital phn t v m t s phn b ca cc electron trong phn t. Trong bi tp ny, ta tnh hm sng cho ton b phn t nc. Sau trong bi 12, ta tnh hm sng cho phn c la chn trong cu trc.
tnh hm sng ta lm nh sau

1. Nhp tri chut chn Semi-empirical trong Setup menu. 169
Hng dn s dng HyperChem 7.04 2. Nhp tri chut tch chn CNDO, ri nhp vo nt Options. Ta cng c th chn mt trong cc phng php khc trong , nhng v d ny s dng CNDO lm phng php tnh. 3. Dng cc gi tr nh sau t vo hp thoi la chn bn kinh nghim (Semi-empirical Options):
Cc la chn ny t tnh Hartree-Fock gii hn (RHF) vi Convergence limit (gii hn hi t trung bnh) l 0.0001, c ngha l tnh ton kt thc khi s khc nhau v nng lng sau hai ln lp li lin tip b hn 0.0001 kcal/mol. Gii hn lp li (Iteration limit), t l 50, l s ln lp li cc i c s dng i n mt hm sng t hp. Total charge (in tch ton phn) t l 0 v Spin multiplicity ( bi spin) t l 1. Tnh ton c tin hnh trng thi thp nht khng c s gia tc hi t c bit (b tch mc Acceleration convergence) 4. Nhp OK ng hp thoi la chn bn kinh nghim v nhp tip OK ng hp thoi la chn phng php bn kinh nghim. 5. Nhp tri chut chn Single Point trong Compute menu. Kt qu nng lng, gradientv in tch nguyn t tnh c nh sau:
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Hng dn s dng HyperChem 7.04 (Gi tr tnh ton ca bn c th khc mt cht)
V biu th tnh in
By gi ta tnh c hm sng, ta c th biu din bn th tnh in. V biu th tnh in c l i hi nhiu thi gian hn tnh hm sng c hc lng t. iu ny bi v cc gi tr phi c tnh lng ln cc im k c c bn . Bn th tnh in c ph ln trn trang lm vic ca HyperChem v gi nguyn cho n khi ta dch chuyn hoc thay i phn t hoc biu din bn khc. Mt phng ca bn lun song song vi mt phng XY (Mt phng mn lm vic).
v biu th tnh in ta lm nh sau

1. Chn none trong hp thoi Labels. 2. Nhp tri chut chn Plot Molecular Graphs trong Compute menu m hp thoi la chn. 3. Nhp tri chut tch chn Electrostactic Potential trong mc Molecular Properties v chn biu din trn khng gian hai chiu (2D Contour). HyperChem s tnh ton v biu din biu th tnh in trn khng gian hai chiu. 4. Nhp tri chut vo mc Contour Grid la chn biu din cc ng biu trn mn hnh. 5. t Horizotal grid points l 60. 6. t Vertical grid points l 60. 7. t Contour levels l 30. 8. t Plane Offset l 0.5 . 9. Nhp OK bt u tnh ton. 10. Sau mt lc, th tnh in s c tnh ton v biu din trn mn lm vic. Ch : Biu m bn v c th khc vi biu in trong sch mt cht.
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(Mu xanh th hin in tch dng, mu ta th hin mang in m, ta c th t mu sc biu din trong mc Isosurface Color ca hp thoi Preference ) 11. M li hp thoi la chn v biu th tnh in v chn 3D isosurface biu din biu trn khng gian ba chiu. HyperChem s biu din li biu th tnh in trn khng gian ba chiu (3D). 12. Nhp tri chut chn mc Isosurface Rendering. t gi tr Electrostatic potential contour value l 0.1, v tnh chn Shaded surface . Th tnh in s c biu din trn khng gian ba chiu, c t m v khng c khong trng. 13. Nhp tri chut chn mc Isosurface Grid, tch chn Medium. Mc ny cho php ta chn nn v b mt vi mt vi im (hnh v g gh nhng v nhanh) hay l nhiu im (hnh v mn v v lu). 14. Nhp OK bt u tnh ton cho mt phng. iu ny s mt mt lc tnh ton. Khi mt phng s biu din nh sau:
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15. M li hp thoi la chn v biu th tnh in, tch chn 3D Mapped Isosurface. iu ny cho php biu din mt phng v vi gi tr c xc nh bng tng mt in tch nhng t mu theo th tnh in. 16. Nhp tri chut chn mc Isosurface Rendering. nh gi tr 0.135 vo mc Total charge density contour value, ri tch chn Gouraud shaded surface. Mt phng s biu din trn khng gian ba chiu mt in tch ton phn. Mt phng s rt nhn. 17. Nhp tri chut chn mc Mapped Function. nh gi tr -1.0 vo Minimum value v vo Maximum value l 1.0. Nhp tri chut tch chn Display range legend. Mt phng s c t mu theo th tnh in, mu sc thay i, mt ghi ch c v km biu din s khc nhau v gi tri theo mu sc. 18. Nhp tri chut chn OK bt u tnh ton b mt. S mt mt lc hon thnh. Khi b mt s c biu din nh sau:
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Ch thch hp thoi v biu thuc tnh phn t

Ta dng hp thoi ny v biu cho nhiu thuc tnh khc nhau:
Property Electrostactic potential Total spin density Total charge density Representation
Mc ny cho php ta la chn thuc tnh mun biu din. Chn v biu trng th tnh in theo s phn b in tch in t v in tch ht nhn. Chn v biu kh nng tm thy electron c spin hng ln (electron alpha) nhiu hn electron c spin hng xung im bt k trong khng gian. V biu hm mt in tch cho cc electron ho tr ca phn t. Mc ny cho php ta xc nh mun biu din biu thuc tnh phn t dng no. 174
Hng dn s dng HyperChem 7.04 2D Contours 3D Isourface 3D Mapped Isourface La chn v biu dng ng vin hai chiu. La chn v thuc tnh dng mt ba chiu. V theo dng mt ba chiu kt hp vi mu sc biu din thuc tnh c chn.
Mc la chn Isosurface Grid trong hp thoi

Ta dng la chn ny xc nh gi tr cho li 3D (3D Grid) dng biu din mt ng hng (isosurface).
Grid Mesh Size
Grid Layout Grid point step size Grid ponit counts Spatial extents Adjust points Adjust Extents
Mc ny cho php chn kiu li Coarse (th), Medium (trung bnh), hay Fine (p) hoc chn theo mun sau xc nh cc kiu la chn li c th ta mun v. Dng la chn ny xc nh la chn cho li 3D. Xc nh khong cch gia hai im d liu trong li 3D, theo A0. Kch c li 3D theo cc phng x, y, z, theo n v s im li. Kch c li 3D theo cc phng, theo n v A0. Dng nt ny p dng s hiu chnh cho Grid point counts Dng nt ny p dng s hiu chnh cho Spatial extents
Mc la chn Contour Grid

Dng mc ny t cc gi tr cho li 2D dng biu din cc ng biu .
175
Horizontal grid points Vertical grid points Contour levels Plane offset Starting value Default Other Increment Default Other
phn gii ngang ca cc ng biu . C th thay i t 2 n 8,172. phn gii thng ng ca cc ng biu . Gi tr thay i t 2 n 8,172. S ng ta mun dng v biu , gi tr thay i t 1 n 32,767. S mt phng ca tp hp cc ng dng v biu , vung gc vi trc z ca ngi quan st. Gi tr ca ng thp nht. Gi tr khi u HyperChem tnh cho cc im li v t ngm nh, (khi u tnh t trong ra ngoi). Gi tr ta mun thay i cho ng khi u. Khong cch gia cc ng gn k. Gi tr ngm nh tnh theo HyperChem. Ga tr do ta t.
Mc Isosurface colors (mu sc th hin tnh m-dng trong biu )

Mc ny kh quan trng cho vic biu din biu cc thuc tnh khc nhau ca h. Qua mu sc ta c th phn bit c phn no th hin tnh m (negative), phn no th hin tnh dng (positive). Ta hon ton c th chn cc mu sc biu din khc nhau tu theo s thch.
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Cc mc cn li khng quan trng lm, c th tham kho trong HyperChem reference, chng 7.
V bn mt in tch ton phn

Ta c th v biu dng ng cho mt in tch (electron) ton phn. Khi phng php CNDO v cc phng php bn kinh nghim khc c hiu lc trong HyperChem khng bao hm cc electron lp bn trong (v d, electron 1s ca oxy trong nc), mt in tch biu din ch l mt in tch cng ho tr.
v biu mt in tch ta lm nh sau

1. Nhp tri chut chn Plot Molecular graphs trong Compute menu. 2. Nhp tri chut chn 2D contour trong mc Molecular properties v nhp chn Total Charge Density, sau nhp OK ng hp thoi. Sau mt lc, biu mt in tch ton phn xut hin:
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Mt in tch ton phn cng c th c v trn khng gian ba chiu.
V bn mt spin ton phn

Mt spin ton phn c th v biu c theo cng cch nh mt in tch ton phn. Tuy nhin, trong trng hp phn t nc (v tt c cc h khc trong tt c cc electron c ghp i), gi tr ca mt in spin ton phn l 0 mi im, v khng c biu no c v. Mt spin c th c tnh v biu din cho cc h ho hc c electron khng ghp i.
V bn obital phn t ring

Ta c th v biu tt c cc obital ring l no. Obital c xc nh c th l obital phn t nh c nng lng cao nht (HOMO) v obital phn t khng nh c nng lng thp nht (LUMO). Vi phn thc hnh ny, ta v obital phn t theo th t nng lng tng. Vi nc, CNDO s dng tp hp ca su obital nguyn t c bn (2s, 2p trn nguyn t oxi v 1s trn hai nguyn t hydro) v tnh ton cho su obital phn t. Bn trong cc obital ny (2a1, 1b2, 3a1, v 1b1 bt u nng lng thp nht) c nh c v hai obital (4a1 v 2b2) khng nh c. Obital phn t nh c nng lng cao nht (HOMO) l 1b1, v obital phn t khng nh c nng lng thp nht (LUMO) l 4a1. S thiu cc electron 1s lp v bn trong ca oxi m t s thiu obital 1a1. Do obital u tin, 2a1 l HOMO3.
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v biu obital phn t ring ta lm nh sau

1. Nhp tri chut chn cng c la chn trn thanh cng c v nhp phi chut vo vng trng mn lm vic loi b cc la chn. 2. Nhp tri chut vo Obitals m hp thoi la chn trong Compute menu. 3. Nhp tri chut chn HOMO-, tip theo nhp tri chut vo mc ghi ch (text box) cho obital v t gi tr l 3. iu ny gip chn obital thp th 3 theo th t sp xp nng lng ca HOMO. Trong v d ny, n l obital c tnh l thp nht. Quan st mc thp nht trong biu mc nng lng obital thay i mu sc. Ta cng c th chn obital bng cch nhp tri chut vo mc obital c nng lng thp nht trong biu . 4. Nhp tri chut tch chn 3D Isosurface. 5. B tch nu c Orbital Squared. Hp thoi la chn v Obital c dng nh sau:
Pan
Thanh cun ln xung trong s nng lng obital.
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Hng dn s dng HyperChem 7.04 Orbital Alpha Cho bit thng tin v obital c chn. Cho bit obital c chn c spin alpha hay khng. Nu obital chn c spin beta, nhp tri chut vo Alpha thay i la chn chuyn thnh obital alpha. La chn ny ch hot ng sau khi ta tnh ton bn kinh nghim UHF. Cho bit obital c chn c spin beta hay khng. Nu obital c chn c spin alpha, nhp tri chut vo Beta chuyn s la chn v obital c spin beta. La chn ny ch hot ng sau khi ta tnh ton bn kinh nghim UHF. Cho bit v tr obital la chn hin ti c lin quan n LUMO. V d, khi ta chn obital LUMO phn trn (ng gch) trong s nng lng, gi tr +1 xut hin trong hp thoi ch s, ngc li nu ta chn LUMO bn di, ch s 1 s xut hin. Tng t nh s la chn LUMO, nhng khc ch ch s ngc vi LUMO. Cho bit tr s tuyt i ca obital c chn, bt u t obital nng lng thp nht (bn di). Vi tnh ton UHF y c c hai ct obital alpha v beta c biu din, s th t c thc hin phn chia trong mi nhm. Cho bit nng lng ca obital c chn theo n v electron volt (ev). Cho bit dng biu din ti gin ca obital c chn. Biu din electron nh c trong mi obital. Vi tnh ton RHF s eletron nh c ti a trong mi obital l 2, ngc li trong tnh ton UHF, s electron nh c ti a l 1. Sau khi ta phng to s nng lng (nhp tri chut v r trong khung s ), chuyn tr li dng ban u ta nhp vo nt ny. Cung cp cho ta nhng la chn biu din biu obital. V biu obital trn khng gian hai chiu. V biu obital trn khng gian ba chiu. Khi chn, biu biu din bnh phng gi tr obital trong mt phng xc nh. 180
Beta
LUMO+
HOMONumber
Energy Symmetry Labels
Zoom Out Orbital Plotting 2D Contours 3D Isosurface Orbital squared
Hng dn s dng HyperChem 7.04 Options Dng la chn thm cho dng biu din obital. Plot Thc hin v biu obital chn. Copy s nng lng vo trnh ng dng khc, vo b nh tm thi.
Copy
6. Nhp OK thc hin v biu obital. HyperChem v biu obital cho obital 2a1, v biu din hin trng cng vic trn dng hin trng. 7. Nhp tri chut chn Isosurface trong Display menu, hoc nhn F4. Hp thoi la chn Plot molecular properties xut hin. 8. Nhp tri chut tch chn Wire mesh (Li dy) trong mc Rendering option, nh gi tr 0.05 vo Obital contour value, v nhp OK chn. HyperChem biu din biu obital 2a1 nh sau:
9. M li hp thoi la chn v obital trong Compute menu, nh gi tr 1 vo number cho HOMO. Nhp vo nt Options v s dng nhng la chn nh la chn th tnh in, nhng tch chn mc Rendering l Jorgensen-Salem. iu ny HyperChem s biu din obital 3a1:
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C th dng cng c quay quay cu trc nhn cho r. 10. Lp li tnh ton v s dng gi tr 2 cho HOMO v chn Lines trong mc Rendering. HyperChem s biu din obital 1b2:
11. Nhp tri chut chn Rotate trong Edit menu. 12. Tch chn X Axis, nh gi tr Angle (gc) l 90, chn Apply to View, ri nhp OK chn. B tch Show isosurface hoc nhp F3 th HyperChem s khng biu din obital phn t trn mn lm vic na. Tch li Show isosurface hoc nhp F3 th HyperChem s biu din obital tr li. 13. Nhp tri chut m hp thoi Orbital trong Compute menu ly gi tr 0 cho HOMO.
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Hng dn s dng HyperChem 7.04 14. Nhp vo nt Option, trong mc Isosurface Rendering chn Flat surface v nh gi tr 0.05 vo Obital contour value, ri nhp OK chn. HyperChem biu din obital phn t nh c cao nht ca nc cho 1b1:
15. Nhp tri chut chn Rotate trong Edit menu, nh gi tr Angle l -90, ri nhp OK chn. 16. Nhp tri chut m hp thoi Obital trong Compute menu v tch chn LUMO+, nh cc gi tr 0 v 1 biu din cc obital khng nh c.
V biu th nng mt chiu (1D) v hai chiu (2D)

Vi cc cng c la chn cho php tnh nng lng nh Amber94, PM3, cho php ta tnh c cc gi tr v nng lng nh sau: - Biu th nng mt chiu. - Biu th nng hai chiu. Biu th mt chiu biu din nng lng l hm ca mt s thay i. Biu th hai chiu biu din nng lng l hm ca hai s thay i. Cc s thay i ny c th l di lin kt, gc lin kt, gc vn.
Th mt chiu
Ta c th to ra th mt chiu mt cch d dng. u tin l chn kiu hm nng lng s dng. C th chn l AMBER, PM3, STO-3G Sau chn 2, 3 hoc 4 nguyn t trong mt lin kt, gc hay mt gc vn l nhng thay i c lp. Cc bc to th mt chiu nh sau: 1. Chn lin kt, hoc gc lin kt, gc vn mun v biu th. 183
Hng dn s dng HyperChem 7.04 2. Nhp chn Name Selection trong Select menu, tip theo tch chn mc PLOT1, nhp OK chn. 3. Nhp chn Potetial trong Compute menu. Nu phn la chn ta vn t ch chn th hp thoi sau xut hin:
Nu ta khng cn t ch chn phn la chn th hp thoi sau xut hin:
t li cc gi tr v biu nu mun, hoc s dng ch ngm nh. 4. Nhp OK thc hin tnh ton v biu . Trong phn ny ta chn v biu th cho H2.
Cc la chn biu din biu th Nhn nt Propeties m hp thoi la chn biu din biu :
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Ta c th t cc la chn thch hp biu din th.
Th hai chiu
v biu th hai chiu ta phi t ng thi PLOT1 v PLOT2. Phn la chn hin ti ch c th l mt s thay i do , ta phi t PLOT1 cho phn la chn u v PLOT2 cho bt k lin kt, gc lin kt hoc gc vn no. S thay i hai khng cn thit l phi cng loi. Nhp vo Rotential trong Compute menu to ra biu 3 chiu. V d: V biu th 2D cho cc gc vn C1-C2 v C2-C3 trong Pentan. Ta t la chn v biu nh sau:
Tnh ton bng trng lc MM+. Cc tiu (mu ) xut hin gi tr gc 180, -60, 60 v 1800. Cc i xut hin cc gc -120, 0 v 1200.
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Cng th nh quan st trn khng gian 3D s nh sau:
Lu phn t
Ta c th lu phn t nc tnh vo file water.hin. C th s dng log file lu cc kt qu chi tit tnh ton c.
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Bi 12: Tng tc ca nc vi N-metylaxetamit.

Dng gc xon cng bc Ti u hnh hc cho mt tp hp con S dng cc m phng dung mi Tin hnh tnh ton hm sng tnh in tch nguyn t Hp nht hai phn t vo mt h n
Trong bi ny, ta chy c tnh ton bn kinh nghim ln c hc phn t trong HyperChem v tnh in tch nguyn t cho vic s dng tnh ton c hc phn t tip theo. u tin, ta to ra cu trc N-metylaxtamit (NMA) theo trnh xy dng, s dng hnh hc cng bc thay i t kiu cis sang kiu trans, v dng li phn t. Tip theo, ta tnh hm sng cho cu trc trc v sau khi ta solvat ho phn t vi nc.
To ra phn t NMA to N-metylaxetamit ta lm nh sau:

1. Chn New trong File menu. 2. M hp thoi Labels trong Display menu v t Symbol. 3. Trong hp thoi la chn cc nguyn t, b tch nu c Explicit Hydrogens, v chn Carbon l nguyn t ngm nh. 4. Nhp tri chut vo cng c v trn thanh cng c v v lin kt khung nh sau:
187
5. Chnh sa cu trc trng nh sau:
To lin kt i cho lin kt C-O. 6. Nhp lin tip hai ln tri chut vo cng c la chn trnh xy dng xy dng li cu trc theo khng gian ba chiu v thm nhng hydro cn thiu.
Chuyn dng cis- sang dng trans-NMA

Tu thuc vo vic ta v lin kt khung, trnh xy dng s xy dng li phn t theo dng trans hay dng cis-NMA. Trnh xy dng dng gc nh din dng trans- nh l gc ngm nh.
188
Hng dn s dng HyperChem 7.04 Nu ta v lin kt khung theo th t O-C-N-C hoc C-N-C-O, nguyn t ln cn (O v C) s l trans v kt qu s l cis-NMA:
Nu ta v lin kt khung theo th t C-C-N-C hoc C-N-C-C, cc nguyn t ln cn (C v C) s l trans v kt qu l trans-NMA:
1. Quay cu trc ca trnh xy dng v xc nh xem cu trc l dng cis hay dng trans. Nu dng cis nh trong v d u tin trn c biu din, ta cn chuyn n v dng trans bng cch thm s xon lin kt bt buc v xy dng li cu trc theo cc bc m t di y. Nu ta dng c cu trc dng trans, gi nguyn n cho phn tip theo, Ti u ho cu trc NMA.
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Hng dn s dng HyperChem 7.04 chuyn cu trc dng cis v dng trans cho NMA ta lm nh sau: 1. Nhp tri chut chn cng c la chn trn thanh cng c, v tch chn Atoms trong Select menu. 2. Nhp tri chut t nguyn t oxi, gi v r n nguyn t hydro ni vi nit chn bn nguyn t nh sau:
3. 4. 5. 6.
Nhp tri chut chn Constrain Bond Torsion trong Build menu. Tch chn Trans, ri nhp OK ng hp thoi. Nhp phi chut vo vng trng loi b la chn. Xy dng li phn t bng cch nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c. H phn t lc ny s biu din l dng trans-NMA. Cc tnh ton sau tha nhn s nh hng ca nhm metyl nh l dng trans i vi lin kt CO, nhng cis cho lin kt NH. S dng t gc vn trong Edit menu thu c cu hnh cn thit.
Ti u ho cu trc NMA.
Trc khi tnh hm sng cho phn t, ta ti u cu trc phn t s dng trng lc AMBER.
ti u cu trc ta lm nh sau:
1. Nhp tri chut chn Molecular Mechanics trong Setup menu. Nu hp thoi cnh bo Recalculate atom types.. xut hin th nhp chn OK. 2. Chn trng lc AMBER, v nhp vo nt Options. 3. S dng cc la chn ngm nh nh sau.
190
4. Nhp OK ng hp thoi la chn. 5. Nhp OK ng hp thoi la chn trng lc c hc phn t. C th s c dng cnh bo Recalculate atom type . Nu th, nhp OK chn. 6. Nhp tri chut chn Select Parameter Set trong Setup menu. 7. Chn amber3, ri nhp OK. 8. Nu HyperChem hi ta c mun tnh li kiu nguyn t khng, nhp OK chn. 9. Nhp tri chut chn Geometry Optimization trong Compute menu. 10. Trong hp thoi, s dng cc la chn ngm nh, nhng t RMS gradient l 0.001, ri nhp OK bt u tnh ton. Sau mt lc, tnh ton hon thnh v HyperChem biu din kt qu trong dng hin trng.
Tnh in tch nguyn t

Trong bi 11, ta thu c in tch cc nguyn t trong phn t nc bng cch tnh hm sng. Trong phn thc hnh sau y, ta tnh in tch nguyn t v s dng chng tnh ton c hc phn t cho NMA v nc v sau.
tnh in tch nguyn t ta lm nh sau:

1. u tin, ly Label l Charge (in tch) cho h. HyperChem biu din tt c cc nguyn t c in tch l 0.00. 2. Nhp tri chut chn Semi-empirical trong Setup menu. 3. Tch chn CNDO v nhp OK ng hp thoi. 4. Nhp tri chut chn Single Point trong Compute menu. HyperChem biu din in tch nguyn t khi tnh ton hon thnh. Cc gi tr in tch, nng lng, v gradient bn tnh c th sai khc vi gi tr bn di mt cht:
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5. Lu phn t ny vi tn l nma.hin.
Solvat ho nhm Cacbonyl
Hp nht hai cu trc

Trong bi ny, ta hp nht phn t NMA vi phn t nc trong bi 11 v tnh ton tng tc ca chng.
biu din NMA v phn t nc nh mt h ta lm nh sau

1. Nhp tri chut chn Merge trong File menu. 2. Chn m file water.hin lu t trc. Mn lm vic by gi biu din c NMA v nc.
Dch chuyn phn t nc

Tip theo ta dch chuyn phn t nc n v tr c kh nng to lin kt hydro gia oxi ca nhm cacbonyl vi nguyn t hydro ca nc.
di chuyn phn t nc ta lm nh sau:

1. Nhp tri chut vo cng c la chn trn thanh cng c, ri nhp phi chut vo vng trng loi b cc la chn trc . 2. Chn Symbol trong hp thoi Labels. 3. V tr ca phn t nc c di chuyn n nh minh ho di y. Ch : di chuyn mt phn t ta lm nh sau - Nhp tri chut vo cng c la chn trn thanh cng c. 192
Hng dn s dng HyperChem 7.04 Nhp tri chut tch chn Molecules trong Select menu. Nhp tri chut vo phn t mun chn. Nhp tri chut vo cng c dch chuyn trn thanh cng c. Nhp phi chut vo phn t chn, gi v r n v tr mun chuyn n. - Nhp tri chut vo cng c la chn, ri nhp phi chut vo vng trng loi b la chn.
Ti u mt tp hp con ca h
Trong bi thc hnh ny, ta ti u ho hnh hc ca nc s dng c hc phn t. Khi ta tin hnh ti u ho hnh hc ln mt h trong ch tp hp con c chn chu tc ng ca php ti u, v tr ca cc nguyn t c chn b thay i trong qu trnh ti u. iu ny c ngha l nu ta la chn ch c phn t nc, khi ta ti u, phn t NMA gi nguyn khng i khi phn t nc di chuyn n v tr thun li. iu ny ni chung nhanh hn cho php tt c cc bc t do. Khi nc gn v tr thun li, ta c th ti u ton b h, nu mun.
ti u tp hp con ta lm nh sau
1. Nhp tri chut chn Molecular Mechanics trong Setup menu. 2. Tch chn trng lc AMBER, nhp OK s dng cc la chn ngm nh cho trng lc.
193
Hng dn s dng HyperChem 7.04 3. Chn phn t nc nu n cha c chn. Ta c th s nhn c li cnh bo l kiu nguyn t s c tnh ton li, nu th nhp OK chn. 4. Nhp tri chut chn Geometry Optimization trong Compute menu. 5. S dng RMS gradient l 0.01. 6. Nhp OK bt u tnh ton. 7. Sau mt lc, tnh ton hon thnh.
Tnh ton li lin kt Hydro tnh ton li lin kt hydro ta lm nh sau:

1. Nhp tri chut tch chn Show Hydrogen bonds v nhp tri chut vo Recompute H bonds trong Display menu. Cu hnh khi trng tng t nh sau:
Biu th c im ca h tng tc
gip biu th c im s solvat ho NMA, ta thc hin tnh ton c hc lng t trn h tng tc. Ta khi c th so snh kt qu vi tnh ton cc moneme (n th) ca nc v NMA trc .
tnh hm sng cho h ta lm nh sau:

1. Nhp tri chut chn Semi-empirical trong Setup menu. 2. Tch chn CNDO, ri nhp OK ng hp thoi. 3. Nhp tri chut chn Single Point trong Compute menu. iu ny gip tnh ton hm sng cho h lin kt. 4. Chn Charge trong hp thoi Labels biu din in tch nguyn t tnh ton c. 194
Hng dn s dng HyperChem 7.04 Kt qu trnh by nh sau:
195
Bi 13: Thuc tnh in t ca Protein

Tnh mt in t S dng cc bin lng t c in trong tnh ton Tnh hm sng Vi HyperChem, ta c th pha trn tnh ton c hc lng t vi tnh ton c in cho cng mt h phn t. iu ny cho php ta nghin cu c hc lng t trn cc phn ca cc phn t ln, nh l v tr hot ng ca enzim, khi khng th tnh cho ton b h phn t. Bi ny minh ho tnh ton mt in tch cho vng ui-N ca cht c ch tripsin tuyn tu ca b (BPTI). Tnh ton protein minh ho trong bi c thc hin ch yu cng cch nh tnh ton c hc lng t bn kinh nghim ta thc hin trong bi 11 v 12, ngoi tr bin gii (boundary) gia phn c in ca phn t vi phn lng t ca phn t c nh r.
Trc khi ta bt u
Bi ny s dng file testbpti.hin, ta lu trong bi 8. Nu ta khng thc hin bi 8, hy lm theo cc bc trong bi 8 li (bc m file PDB, v xo cc phn t nc) trc khi thc hin bi 13 ny.
c v biu din phn t c v quan st phn t BPTI ta lm nh sau

1. Nhp tri chut chn Labels trong Display menu, ri nhp OK ng li. Ta khng chn g v HyperChem gip ta t chn none cho labels. 2. M file tesbpti.hin. Cu trc c lu trong bi 8. 3. Nu cu trc c biu din c hydro, b tch Show hydrogens trong Display menu khng biu din hydro. 4. Nhp tri chut chn Rendering trong Display menu. 5. Biu din phn t dng cc la chn khc nhau ca hp thoi Rendering. iu ny gip ta quan st phn t c d dng hn.
196
Hng dn s dng HyperChem 7.04 6. S dng cc cng c trong Select menu v Display menu biu din ch lin kt khung ca phn t. (tham kho biu din lin kt khung cc bi trc). 7. Dng cng c la chn, nhp phi chut vo vng trng loi b la chn, nhp tri chut chn Riddbons (di) trong hp thoi Rendering mc Sticks. iu ny gip biu din cu trc bc hai ca phn t nh mt di ruy bng. 8. Quay cu trc thu c s nh hng phn t nh sau:
9. M hp thoi Rendering trong Display menu, trong mc Sticks tch chn thm Stereo. iu ny gip biu din di dng lp th. Nu lt qua bng mt chng cht cc hnh nh, hoc nu ta nhn bng knh nhn ni, th di s xut hin dng ba chiu.
Chn vng ta quan tm

Bc tip theo l chn phn ca h ta mun m t theo c hc c in v phn ta mun m t theo c hc lng t. thc hin iu ny ta chn mt tp hp con ca h. Cc nguyn t chn cng thi im ta tin hnh tnh ton c hc lng t l cc nguyn t m HyperChem tin hnh tnh ton c hc lng t trn . V d, ta s chn dng hnh cu cc nguyn t v xem xt ch cc nguyn t trong vng bn knh chn. Ta cng c th la chn theo hnh ch nht. Trong v d ny ta chn phn u thc hin tnh ton c hc lng t.
197
chn phn u Acginin ta lm nh sau

1. B tch Stereo, b la chn lin kt khung, v biu din ton b cc nguyn t. 2. Nhp tri chut chn Select trong Select menu, trong mc By number tch chn Residue number v ly gi tr l 1 value =. iu ny ARG1 s c chn. Phn ny ta s dng tnh c hc lng t. 3. Quay v chuyn phn t cho n khi trng c nh sau:
4. Nhn phm Spacebar a phn la chn vo tm mn lm vic. Khi phn la chn trng c dng nh sau:
198
Chn bin c in lng t.

Phn tip theo l t chnh xc bin gii gia tnh ton c hc lng t v tnh ton c in. Vn tt l, y din t HyperChem gii quyt vn gii hn nh th no: Mi nguyn t c chn s c x l bng c hc lng t v mi nguyn t khng c chn, nhng c lin kt vi nguyn t c chn, c x l nh mt nguyn t bin. Cc nguyn t bin c t vo cho tnh ton c hc lng t bng cc nguyn t flo gi.
t bin lng t c in ta lm nh sau

1. Nhp tri chut tch chn Extend to sp3 trong Select menu. iu ny m rng la chn phn u acginin ti bin thch hp. HyperChem x l cacbon lin kt vi bn nguyn t, nit lin kt vi ba nguyn t, v oxi lin kt vi hai nguyn t.
Tnh hm sng
Tip theo, ta tnh hm sng. u tin, xc nh xem h c in tch in t hnh thc khng, bng cch xem nhm nitro c b proton ho khng.
xem nhm nitro c c proton ho khng ta lm nh sau:

1. Biu din phn t c c hydro v chn Symbol trong hp thoi Labels.
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Hng dn s dng HyperChem 7.04 C ba hydro c ni vi nit. Cng nh th, ui acginin, cacbon ni vi ba nguyn t nit, hai nguyn t nit trong s c ni vi hai nguyn t hydro, iu ny to nhm lin hp c in tch dng. Khi ui nit (N-terminal) c ba nguyn t hydro, nit ny c in tch hnh thc l +1. Theo phn c la chn tnh ton c hc lng t l cation ho tr hai vi in tch l +2. Ta phi xc nh iu ny t ng s electron trong tnh ton c hc lng t.
tnh hm sng ta lm nh sau

1. Chn none trong hp thoi Labels. 2. Nhp tri chut chn Semi-empirical trong Setup menu. 3. Trong hp thoi, tch chn phng php CNDO, v nhp tri chut vo nt Options. 4. t gii hn hi t (Convergence limit) l 0.1. Khi ta quan tm n in tch v hnh nh nh tnh ca obital ch khng phi l nng lng, gii hn hi t t nghim ngt c s dng. 5. t Total charge l 2 nh r cation ho tr hai. 6. t cc la chn khc nh trnh by di y, khi nhp OK chn.
7. Nhp tri chut chn Single point trong Compute menu. Nng lng v gradient xut hin trn dng hin trng tnh ton khi tnh ton hon thnh. 8. Nhp tri chut chn Plot Molecular graphs trong Compute menu. 9. Tch chn Total Charge Density v chn biu din trn khng gian hai chiu (2D Contour). 10. Chn mc Contour Grid, t Horizontal grid points v Vertical grid points l 60, t Contour level l 30. 11. Nhp OK bt u v biu mt . Khi tnh ton hon thnh, biu xut hin nh sau:
200
Nu v biu trn khng gian ba chiu (3D), s dng Gouraud Shading v Total charge density contour value l 0.09 trong mc Isosurface rendering, kt qu trng nh sau:
201
Phn tnh ton thun tu l thuyt (Ab Initio Calculations) Bi Thit lp la chn tnh ton Ab Initio v Density Functional
Tnh ton Ab Initio (thun tu l thuyt) v Density Functional (hm mt ) c rt nhiu im chung v v th ta m t c hai y. xc nh tnh ton Ab initio ta c bn phi chn tp hp hm c bn. Vi tnh ton hm mt ta cng phi chn tp hp hm, nhng phi chn thm mt hm (functional). Cc phn SCF ca hai kiu tnh ton c bn tng t nhau. Tnh ton Ab initio hay DFT tn nhiu thi gian hn cc phng php bn kinh nghim. u tin ta nn chy ti u theo c hc phn t chuyn hnh hc n mc ti u no , v ti u thm bng phng php bn kinh nghim trc khi ti u hnh hc theo Ab initio. Ring vi cc cu trc v c, ti u theo c hc phn t hay bn kinh nghim u cho kt qu km do thiu cc tham s thch hp, nhng ta dng trnh xy dng (Model Builder) cho cu trc v c s c c im khi u hp l hn.
Chn tp hm c bn
Chn tp hm c bn l cng vic quan trng i vi tnh ton Ab initio v tnh hm mt . Bt k tp hm mt electron no u c th l tp hm c bn trong php tnh gn ng LCAO. Tuy nhin, tp hm c bn tt s d on c cc tnh cht ca in t, s dng cc s hng t hn so vi tp hp hm khng tt. V th, chn tp hm c bn thch hp cho tnh ton Ab initio v hm mt quyt nh n tnh thc t v chnh xc kt qu tnh ton c. Cc tp hm c trong la chn ca mi hp thoi u s dng c cho phng php .
La chn cho phng php Ab initio v Density Functional

Hai hp thoi ca hai phng php kh ging nhau, ch khc mt s t chi tit. Ta c th dng nhiu tp hm c bn trong mt h phn t. Nt Apply Basis Set trong hp thoi dng p dng tp hm la chn hin ti cho cc nguyn t c chn hoc cho ton b cc nguyn t trong HyperChem nu 202
Hng dn s dng HyperChem 7.04 khng c s la chn no. V d, mt s nguyn t nng dng tp hm 631G (ch cho s v p) trong khi mt s nguyn t khc dng 6-31G* (c cho obital d) (xem Basis set trong HyperChem computational chemistry).
Basis Set No basis set Minimal (STO3G) Small (3-21G) Medium (6-31G*) Large (6-31G**) Other Assign Other Basis Set.. Extra Basis Function Options Advanced Options Apply Basis Set Grid
Xc nh tp hm cho phn la chn hoc c h phn t. Khng dng tp hm no c. La chn ny nn dng ch khi p dng mt hm c bn ph cho cc nguyn t. t tp hm STO-3G t tp hm 3-21g t tp hm 6-31G* t tp hm 6-31G** Tch chn tp hm theo mun. Nhp chut vo nt ny m hp thoi la chn tp hm theo mun. Tch chn hm c bn m rng, cho php ta m rng hm c bn cho cc nguyn t chn. t cc la chn thc hin tnh ton t cc la chn cao cp cho tnh ton. Nhp p dng tp hm hin ti cho cc nguyn t chn. (DFT) Nhp nt ny m hp thoi chn khung li (grid) tch phn dng cho cc tnh phn s. La chn n gin nht l Standard Grids. Nh mt la chn, ta c th xc nh r rng (DFT) Nhp chn hp thoi th tng quan trao i nhm xc nh hm mt tng quan 203
Exchange
Hng dn s dng HyperChem 7.04 Corelation OK Cancel trao i dng cho tnh ton. Lu thit lp hin ti, p dng cc hm cho phn la chn v ng hp thoi li. Thot khi hp thoi v khng lu thit lp hin ti cng nh khng p dng tp hm hin ti cho phn la chn.
Hp thoi la chn thm cho Ab initio v Density Functional

Dng hp thoi Otions chn cc la chn c bn cho tnh ton Ab initio v Density Functional. Cc la chn ny c bn ging trong la chn bn kinh nghim.
and Vng ny dng xc nh in tch thc trn h phn t hin ti v xt xem h dng singlet, hay doublet Phn d in tch ca ht nhn so vi electron. Bng Total charge khng vi h trung ho, nguyn dng vi h cation, nguyn m vi h anion. bi spin dng cho h hin ti. H v kn c Spin bi spin l 1 (singlet), h v h c bi spin l 2, Multiplicity 3, 4 hoc cao hn. gi tr c th thay i t 1 n 6. Phn ny dng xc nh chnh xc mong mun SCF controls cho hm sng SCF v s lng lp li cc tiu n chnh xc cho php. t kt thc tnh ton SCF khi s khc nhau gia hai Convergence ln lp li lin tip b hn gi tr ta t. limit Iteration limit S ln lp li cc i. Tch chn phn ny, HyperChem s thc hin nhanh Accelerate qu trnh tnh ton SCF. convergence Charge spin
204
Hng dn s dng HyperChem 7.04 Point Phn ny xc nh xem c tnh ton gradient v nng lng tng quan MP2 hay khng. La chn ny ch dng cho tnh ton Single Point v b qua bt k kiu tnh ton no khc. Chn tnh gradient. Gradient Tch chn tnh nng lng tng quan. MP2 correlation energy Phn ny chn phng php tnh cc tng tc Spin pairing spin. Phng php Hartree-Fock khng gii hn. dng cho UHF h v h v v kn. Phng php Hartree-Fock gii hn spin, i hi cc RHF electron c spin cp i trong mi khng gian obital nh c. Ngi ta thng dng cho cc h v singlet kn. Tch chn t tng tc cu hnh. Cl Cp nhn s thay i thc hin trong hp thoi. OK Thot ht thoi, khng chp nhn s thay i no. Cancel Single only
La chn cao cp cho Ab initio v Density Functional

Ta dng hp thoi Advanced options hiu chnh qa trnh tnh ton ab initio.
iu khin tnh ton tch phn hai electron v Two-electro lu tr. integral control Cutoff Ch gi cc tch phn hai electron vi mt gi tr hon ton ln hn hoc bng gi tr ny. gi tr ngm nh l 10-10 Hartree. Buffer size t kch c nh lu trn cng. Integral format Xc nh kiu lu cc tch phn hai 205
Hng dn s dng HyperChem 7.04 electron. Lu kiu nguyn bn. Lu kiu Raffenetti tng tc hnh thnh ma trn Fock. Tnh trc tip SCF. Cc tch phn hai electron c tnh trc tip. S chm hn tnh ton thng thng, nhng khng mt nhiu a trng v b nh. Dng cho cc phn t ln. iu khin s dng phn la chn ghost atoms. Tch dng phn la chn ghost-atoms. La chn ny c gi tr khi phn la chn c t tn l ghost-atoms. Xc nh c lng ban u cho cc h s MO. Chn nt ny dng cc h s MO thu c t s cho ho Hamilton li. Dng nt ny dng cc h s MO to ra t tnh ton Huckel. Dng nt ny dng cc h s MO to ra t tnh ton INDO. Xc nh s dng Gaussians Decac (6) hay Gaussians Hermite (5) Chn dng Gaussian Hermite bao gm nng obital d: d0, d+1, d-1, d+2, d-2. Chn dng Gaussian Decac bao gm su obital d: dxx, dyy, dzz, dxy, dxz, dyz. Chp nhn s thay i. ng hp thoi, khng chp nhn s thay i.
Regular Raffenetti Direct SCF calculation Ghost-atoms control Use ghostatoms selection MO initial guess Core Hamiltonian Projected CNDO Projected INDO Number of d orbitals Five Six OK Cancel
La chn m rng hm c bn
Hp thoi ny cho php ta hiu chnh cc tp hp hm hin c bng cch thm cc hm c bn m rng cho cc nguyn t. Nu ta mun thm hm phn cc cho hydrogen hay hm khuch tn cho cc nguyn t nng. Mt v ch mt v ph thm (kiu S, P, D, SP hay SPD) c th c p dng cho bt k nguyn t no vi phin bn hin ti ca HyperChem. S khc nhau gia cc v m rng l c th p dng c cho cc nguyn t khc nhau nhng mi nguyn t ch nhn thm mt lp v m rng. Nu ta mun 206
Hng dn s dng HyperChem 7.04 thm v m rng cho nguyn t no, ta cn phi hiu chnh file tp hm c bn v to ra mt tp hm mi.
Shell type None S P D SP SPD Exponent OK Cancel
nh kiu v thm cho cc nguyn t chn, hoc cho c h phn t. Khng chn thm. Thm hm c bn m rng kt hp vi kiu v S. Thm hm c bn m rng kt hp vi kiu v P. Thm hm c bn m rng kt hp vi kiu v D. Thm hm c bn m rng kt hp kiu v SP. Thm hm c bn m rng kt hp kiu v SPD. t s m cho kiu hm chn. Chp nhn cc la chn. Khng chp nhn cc la chn.
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Bi 14: S Proton ho ca nc
To h phn t tch mang in tch. Chn tp hp hm c bn. Chn cc la chn cho tnh ton im n thun tu l thuyt (Ab initio) v ti u ho. Kho st tnh ton nng lng tng tc MP2. Phn hng dn ny s gii thiu cho ta nhng bc c bn cn thit thc hin tnh ton thun tu l thuyt.
t v phn t chun b v H3O vi cc nguyn t hydro c th ta lm nh sau:

1. Nhp tri chut tch chn Explicit Hydrogens trong Build menu. 2. Nhp tri chut tch chn Allow Arbitrary Valence trong Build menu. Nu ta khng chn Allow Arbitrary Valence th s khng th v c ba lin kt t nguyn t oxi khi m Oxi c ho tr thng thng l hai. 3. Nhp tri chut chn Labels trong Display menu. 4. Chn Symbol trong hp thoi Labels v nhp OK ng hp thoi li. 5. Nhp tri chut chn Default Elemen trong Build menu, tch chn Oxi trong hp thoi v ng hp thoi li. 6. Nhp tri chut vo cng c v trn thanh cng c. By gi ta chun b sn sng v H3O+.
To H3O+
V H3O
1. Nhp tri chut vo mn lm vic to ra nguyn t oxi. 2. V ba lin kt t Oxi to H3O nh sau:
Chuyn hnh v thnh cu trc 3D

1. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c.
Thm in tch dng cho tnh ton c hc lng t.

1. Nhp tri chut chn Ab Initio trong Setup menu. 2. Nhp chut vo nt Options. 3. nh gi tr 1 cho Total charge v nhp tri chut vo nt OK ng hp thoi la chn ring ny li.
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Hng dn s dng HyperChem 7.04 4. Nhp tri chut vo nt OK ng hp thoi la chn phng php tnh thun tu l thuyt. Nh vy ta thm in tch +1 cho phn t thc hin tnh c hc lng t, c bn gim s in t thnh mt. in tch ton phn c s dng xc nh s electron s dng trong tnh ton c hc lng t.
Chn tp hp hm c bn tnh chn tp hp hm c bn ta lm nh sau

Nhp tri chut chn Ab Initio trong Setup menu. Tch chn Other trong phn Basis Set. Nhn nt Assign Other Basis Set. Chn 4-31G trong list v nhp OK chn. iu ny gip thm tp hn c bn 4-31G cho list cc tp hp hm c bn m ta c th nhanh chng chn n. Cc tp hp hm c bn xut hin trong Assign Other Basis Set bao gm tt c cc tp hp hm c bn c lit k trong file CHEM.INI theo tn file tp hp hm c bn c nh r ca chng (*.BAS). Cc tp hp hm c bn do ta t c th c thm cho list bng cch to file c ui .BAS mi v thm n vo cho file CHEM.INI. Tuy nhin ta c th t cc tp hp khc theo yu cu kho st phn t. 5. Tch chn Minimal (STO-3G) cho mc Basis set. 6. Nhp chut vo nt Apply Basis Set v nhp OK hoc ch cn nhp lun OK ng hp thoi la chn phng php Ab Initio. By gi ta chn tp hp hm c bn cho mi nguyn t ca phn t, tp hp hm c bn cc tiu STO-3G. N c th la chn c th cc nguyn t v s dng nt Apply Basis Set t tp hp hm c bn chn ch trn cc nguyn t c chn vi s sp xp tip sau ca mt tp hp hm c bn khc trn cc nguyn t c la chn khc. HyperChem cho php t cc tp hp c s khc nhau cho cc nguyn t khc nhau. xem tp hp hm c bn no c p dng cho mi nguyn t, ta c th biu din cc nhn thch hp. 1. 2. 3. 4.
xem tp hp hm c bn p dng cho mi nguyn t ta lm nh sau:

1. Nhp tri chut chn Labels trong Display menu. 2. Chn Basis Set v nhp OK chn. By gi ta s xem c nhn ca tp hp hm c bn p dng cho cc nguyn t trn mn lm vic.
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Cc tiu ho cu trc tnh hnh hc ti u ca H3O+ ta lm nh sau:

1. Chn Ab Initio trong Setup menu. 2. t cc la chn thch hp ti u hnh hc bng cch nhp vo nt Options v t cc gi tr nh sau: Total charge = 1, Spin multiplicity = 1, Spin pairing = RHF, Convergence limit = 0.01, Iteration limit = 50, v Accelerate convergence = Yes (3). Phn Single Point only khng c chn s dng trong ti u hnh hc v c th c bt k gi tr no. 3. Nhp tri chut chn OK ng hp thoi Options v nhp tip OK ng hp thoi la chn phng php. 4. Nhp tri chut chn Geometry Optimization trong Compute menu. 5. Chn Polak-Ribiere cho phng php ti u v t RMS gradient l 0.1 ri nhp tri chut vo OK bt u ti u.
tnh nng lng ton phn ca H3O+ ti u k c nng lng tng tc ta lm nh sau:
1. Chn Ab Initio trong Setup menu, nhn nt Options v chn tnh MP2 correlation energy, ri nhp OK ng hp thoi ny v nhp tip OK ng hp thoi la chn phng php. 2. Chn Single point trong Compute menu. Ta thy rng nng lng ton phn ca H3O+ vi tp hp hm c bn STO-3G l -47270.57 kcal/mol mc SCF v l -47300.98 kcal/mol mc MP2 khi ta bao gm c -30.50 kcal/mol nng lng tng tc tnh ton c.
Nng lng Proton ho tnh nng lng ti u theo STO-3G ca H2O + H+ ta lm nh sau:
1. Nhp tri chut vo cng c v, v nhp phi chut vo mt hydro ca H3O+ xo n v to thnh H2O. Nng lng in t ca H+ l khng v th tnh nng lng proton ho ca H2O ta ch cn tr nng lng tnh ton trc ca H3O+ cho nng lng ng vi H2O. 2. Chn Ab Initio trong Setup menu v nhn nt Options chuyn Total charge t 1 v 0. Khi nhp ln lt hai ln nt OK ng cc hp thoi. 3. Chn Geometry Optimization trong Compute menu v ti u phn t nc nh i vi H3O+. 210
Hng dn s dng HyperChem 7.04 4. Chn Single point trong Compute menu. Ta thy rng nng lng ton phn ca H2O theo tp hp hm c bn STO-3G l -47041.82 kcal/mol mc SCF v -47066.21 kcal/mol mc MP2 khi ta bao gm c -24.45 kcal/mol ca nng lng tng tc tnh c. Kt qu nng lng proton ho l 228.75 kcal/mol mc SCF hoc 234.77 kcal/mol mc MP2. nh hng ca s tng tc trong v d ny l khng ln.
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Bi 15: Dao ng v trng thi chuyn tip ca Amoni.

Phn tch dao ng. Thm tng tc lp ph vo cc hm c bn. Xc nh s i xng. Tm trng thi chuyn tip theo vc t c trng hay phng php chuyn ho ng thi.
Trong phn ny ta s kho st dao ng ca amoni v s khc nhau gia dng hnh chp v dng phng ca amoni.
To Amoni
v amoni ta lm nh sau:
1. Nhp tri chut b tch Explicit Hydrogens trong Build menu. 2. Nhp chn Default Element trong Build menu m hp thoi la chn cc nguyn t. 3. Nhp lin tip hai ln tri chut vo N (nit) chn nguyn t ny ng thi ng hp thoi li. 4. Nhp tri chut chn cng c v trn thanh cng c. 5. Nhp tri chut mt ln vo mn lm vic to ra nguyn t nit n. 6. Chn Add H & Model Build trong Build menu to NH3 theo hnh hc chun ca trnh xy dng.
Chn tp hp hm c bn chn tp hp hm c bn ta lm nh sau:

1. Nhp tri chut tch chn Labels trong Display menu. 2. Chn Basis set v nhp OK ng hp thoi. Nhn trn mi nguyn t by gi biu din l tp hp hm c bn cho nguyn t . Lc ny l None. 3. Chn Ab Initio trong Setup menu. 4. Chn Small (3-21G) l tp hp hm c bn v nhp tri chut vo Apply Basis Set, ri nhp OK ng hp thoi li. By gi tp hp hm c bn trn mi nguyn t s l 3-21G. 5. Dng cng c la chn chn nit trong phn t amoni. (Tch chn Atoms trong Select menu khi chn ch chn mt nguyn t mong mun). 6. Nhp tri chut chn Ab Initio trong Setup menu. 212
Hng dn s dng HyperChem 7.04 7. Nhn nt Advanced Options v tch chn Six (su) trong phn Number of d Orbitals ri nhp OK tr v hp thoi la chn phng php . 8. Nhn nt Extra Basis Function v chn D trong mc shell type (kiu v) v t Exponent (s m) l 1.0 trong hp thoi Extra Basis Function. Tip theo nhp ln lt hai ln OK ng cc hp thoi li. 9. Nhp phi chut vo vng trng b la chn. (Dng cng c la chn). By gi ta sn sng tnh ton Ab Initio i vi amoni bng tp hp hm c bn va t.
Phn tch dao ng ca Amoni dng hnh chp, ph dao ng

Dng Vibrations tnh ton chuyn ng dao ng ca ht nhn, v dng Vibrations Spetrum biu din dng biu cu trc ph ca cc dao ng. Ta c th tnh dao ng bng cc phng php ab initio, DFT hay cc phng php bn kinh nghim, ngoi tr phng php Huckel m rng.
thc hin phn tch dao ng ta lm nh sau:

1. Chn Geometry Optimization trong Compute menu v tin hnh ti u theo Polak-Ribiere vi RMS gradient l 0.1. hi t SCF thch hp nn s dng l 0.01. C l mt mt vi pht tnh ton tu thuc vo tc my tnh ca ta. Kt qu tnh ton v cu trc (gc H-N-H = 106.5 v di lin kt N-H = 1.01A0) cho thy rt st vi gi tr thc nghim. 2. Chn Single Point trong Compute menu tnh nng lng ton phn bao gm c nng lng tng tc MP2. Nng lng ton phn mc SCF l -35086.49 kcal/mol v nng lng ton phn k c nng lng tng tc MP2 l -35191.11 kcal/mol. 3. Chn Vibrations trong Compute menu tin hnh phn tch dao ng trn hnh hc c ti u. Tnh ton ny i hi mt vi pht. 4. Nhp tri chut chn Vibrational Spectrum trong Compute menu biu din ph dao ng nh trnh by di y:
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Tn s c sp xp gim dn t tri qua phi. 5. Tch chn Animate Vibrations biu din. Tch vo dao ng nng lng thp nht bn phi bn ph v nhn nt Apply. Dch chuyn ca s bn ph n khi c th quan st c dao ng trong mn hnh lm vic. Nu s dao ng qu nhanh, ta c th thay i gi tr mc Frames iu chnh. iu ny s biu din chuyn ng mt cch sinh ng vi tn s thp cho amoni. N gi kiu i xng C3v v thay i ch yu l gc lin kt. Ta c th quan st cc dao ng khc bng cch nhp chut trc tip vo ph tng ng v nhn Apply. Cc vch trn trong ca s biu din tt c cc mc chuyn dao ng, cn dng di ca ca s biu din cc mc chuyn dao ng km theo cng hng ngoi ca chng (cc mc chuyn thc t xy ra c). Khi ta nhp vo mt vch, tn s (Frequency) v cng (intesity) tng ng ca vch biu din gc tri ca ca s. 6. Chn mc chuyn nng lng thp nht ( pha bn phi) ln na. Nhn vo nt Apply v nhp OK ng ca s ph dao ng li. Quay phn t amoni bng cng c quay theo trc XY quan st c y dao ng c tn s thp nht. 7. Nhp vo nt Cancel trn thanh cng c hoc nhn nt Esc ngng biu din dao ng. Nhp tri chut chn Labels trong Display menu v nhp OK khi hp thoi Labels m ra loi b nhn ang biu din. Nhp tri chut chn Rendering trong Display menu. Trong mc Sticks tch chn IR Vectors v nhp OK chn biu din cc vc t c trng ca kiu dao ng. Quay phn t theo trc XY quan st y cc vc t IR ca kiu dao ng th. 8. Nhp tri chut chn Vibrational Spectrum trong Compute menu biu din li ph dao ng. Nhp vo vch c kiu dao ng th quan st chuyn ng th km cc vc t IR ca n. Ch : Lun cn phi thc hin ti u hnh hc to phn t c cc tr v nng lng trc khi tnh ton phn tch dao ng.
Ti u amoni phng
By gi ta s to ra mt co trc amoni phng ti u nht. to cu trc c bit ny ta s s dng cch cng bc. y ta dng gc vn khng ng to ra amoni dng phng.
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to amoni phng ta lm nh sau:

1. Loi b tt c cc nhn cng nh vect IR vn cn ang biu din. 2. Tch chn Multiple Selections trong Select menu. Tch chn Atoms trong Select menu. 3. Nhp tri chut vo cng c la chn trn thanh cng c. Ln lt nhp chn bn nguyn t hnh thnh nn phn t amoni. 4. Chn Name Selection trong Select menu. Tch chn Other, v nh vo mt tn tu , chng hn nh l imptor. Nhp OK ng hp thoi ny li. By gi ta c th t nn to mt gc 1800 (1800 = phng) bng cch thm lc nn cho gc. iu ny gip chuyn amoni v dng phng. 5. Nhp phi chut vo vng trng trn mn lm vic loi b cc la chn. 6. Chn Restraints (cng li) trong Setup menu. Chn 4-imptor (bn nguyn t c chn c tn ta t l imptor) v nhn nt Add them phn tn c chn ny vo list ca Restraints. Tch chn Other cho Restrained Value (gi tr c cng li) v nh gi tr 180 cho gc vn (torsion). Tch chn Other cho Force Constant v nh gi tr ln hp l, 500, bo m l amoni c gi phng. Nhp OK ng hp thoi Restraints li. 7. Chn Geometry Optimization trong Compute menu ti u to ra cu trc phng nht. Chn phng php Polak-Ribiere, chn RMS gradient l 0.1. Nhp OK bt u ti u. 8. Cu trc ti u ta thu c l phng vi di lin kt l 0.99A0. 9. Chn Single Point trong Compute menu tnh nng lng ca cu trc phng bao gm c nng lng tng tc MP2. Nng lng ton phn mc SCF l -35079.16 kcal/mol v nng lng ton phn k c nng lng tng tc MP2 l -35183.80 kcal/mol. S khc nhau gia nng lng ny v nng lng ti u ca amoni kiu chp l hng ro nghch chuyn ca amoni. Gi tr SCF cho hng ro nghch chuyn ny l 7.33 kcal/mol. nh hng ca nng lng tng tc i vi hng ro nghch chuyn ny c d on l khng ng k c 0.05 kcal/mol.
Phn tch dao ng ca amoni phng tin hnh phn tch dao ng ca amoni phng ta lm nh sau
1. Chn Restraints (cng li) trong Setup menu. Chn 4-imptor trong mc Restraint v nhn nt Remove chuyn gc xon khng ng ny khi list. Nhp OK ng hp thoi Restraint li.
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Hng dn s dng HyperChem 7.04 Nu ta khng chuyn 4-imptor khi mc Restraint, phn tch dao ng s bao gm c cc thnh phn dn xut bc hai theo lc km ch c hc phn t v cn thm tnh ton thun tu l thuyt c hc lng t i vi amoni phng. 2. Chn Vibrations trong Compute menu tin hnh phn tch dao ng cho amoni phng c ti u. Tnh ton ny i hi tnh s cc dn xut bc hai theo s thay i to Decac ca cc nguyn t v phi mt mt vi pht tnh ton. 3. Kch c ca s HyperChem xp x bng mt phn ba mn hnh v ta hy t n gc phi mn hnh. 4. Chn Vibrational Spectrum trong Compute menu biu din ph dao ng nh bn di y:
Ch l dao ng c nng lng thp nht c tn s m. Thc t, gii cc phng trnh bnh thng cho ta cc gi tr c trng l bnh phng ca cc tn s dao ng. Khi mt trong cc bnh phng ny ca tn s dao ng l m, HyperChem v biu cho n l cn bc hai ln ch khng phi nh mt s o. Theo gi tr m ny, -, chnh xc c ngha l mt tn s dao ng o. Tn s o n l vi tt c cc tn s cn li c ng r rng rng cu trc phng l mt trng thi chuyn tip, ch khng phi l cu trc c cc tiu nng lng, nh cu trc kiu chp ta nghin cu. 5. Nhp vo vch dao ng c tn s m v xem trng thi dao ng ca n. Ta s thy rng kiu bnh thng ny tng t nh kiu th ca amoni. y l ng phn ng lin hp vi trng thi chuyn tip. HyperChem khng gii trc tip vi hnh hc cng bc cng nh vi cc to ni cng bc, m n lm vic ch vi cc to Decac. Tuy nhin, n vn c th, qua s cng bc, bng nhin tc ng khc thu c kt qu qua to cng bc. 6. Nhp chut vo nt OK ng ca s Vibrational Spectrum v tip theo l nhp Cancel ngng s dao ng. Chn New trong File menu xo mn lm vic.
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Tm trng thi chuyn tip theo vect c trng

Trong tnh ton ny ta s s dng phng php theo vect c trng (Eigenvector Follow) tm kim trng thi chuyn tip tm trng thi chuyn tip ca s nghch chuyn amoni chp, m khng cn cng bc thm cu trc. Phng php ny c bit hu dng nu mt trong cc kiu dao ng t nhin cu trc ca ta c hng chuyn n mt trng thi chuyn tip. Ta c th tm trng thi chuyn tip theo ab initio, DFT hay cc phng php bn kinh nghim, tr phng php Huckel m rng. 1. M cu trc chp amoni ti u ta lu phn trc trong phn tch dao ng amoni chp ln mn lm vic. 2. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c xy dng li cu trc theo trnh xy dng. Ti u theo vect c trng khng lm vic tt c nu nh im khi u l cu trc dng cc tiu no ; ngay c nu kiu dao ng i theo c xc nh, cc chuyn ng nguyn t ti u dn dt t mt cc tiu khng xc nh tt c. 3. Chn Transition State trong Compute menu. 4. Trong hp thoi m ra, chn Eigenvector following, v nhp OK chn. Dng hin trng cho bit HyperChem ang tin hnh tnh ton dao ng. Khi tnh ton hon thnh, hp thoi thm d trng thi chuyn tip xut hin.
5. Nhp vo vect c trng c nng lng thp nht bn phi ca ph. Nh trc, vct ny tng ng vi kiu th, tn s thp nht ca amoni, trong s chuyn ng ca cc nguyn t trc tip dn n s nghch chuyn ca amoni dng chp.
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Hng dn s dng HyperChem 7.04 Dao ng c nng lng thp nht thng l kiu gn nht vi trng thi chuyn tip. 6. t RMS gradient limit l 0.1 kcal/(A0 mol), v nhp OK chn. HyperChem fm trng thi chuyn tip phng. 7. Trng thi chuyn tip l dng phng vi di lin kt l 0.99A0. Chn ln lt t nguyn t N v ba nguyn t H xem gc xon khng ng c trnh by trong dng hin trng. N rt gn vi 00 hoc 1800.
Tm trng thi chuyn tip bng s chuyn ho ng thi

Trong tnh ton ny ta s s dng phng php chuyn ho ng thi (Synchronous Transit) tm trng thi chuyn tip tm trng thi chuyn tip phng cho s nghch chuyn ca amoni chp, m khng cn cng bc cu trc thm. Phng php ny cho php ta tnh cc trng thi chuyn tip khi h cc cht phn ng v sn phm rt khc nhau, hoc nu ta mun xc nh cn thn nh th no cc nguyn t c sp xp li qua trng thi chuyn tip. Cc nguyn t ca cht phn ng v sn phm c lm cho tng ng, v im bt u tm c ni suy t cc cu hnh ban u v lc sau. 1. M li cu trc amoni m ta lu ln trc. 2. t Number hp thoi Labels trong Display menu. 3. Nhp tri chut vo cng c v trn thanh cng c, nhn phm Shift gi nh vy v nhp tri chut vo nguyn t N. Khi nh chut v nh phm ra, nguyn t H s chuyn n mt v tr trng ca chp amoni, o chiu s khng i xng ca h c xt n th t nguyn t. Thng thng ta s dng thao tc ny thay i s ni khc nhau n tm bt i. 4. Ti u hnh hc ca h vi gradient l 0.1 kcal/(A0 mol) nh trc. C tp hp nguyn t cht phn ng v sn phm c ti u trc khi ta tm trng thi chuyn tip vi phng php i qua ng thi. 5. Nhp chn Merge trong File menu nhp m thm bn copy khc ca cu trc amoni c ti u lu trc cho mn lm vic. 6. Nhp tri chut vo cng c la chn trn tranh cng c. Chn mt phn t trn mn lm vic. 7. Nhp chn Name Selection trong Select menu, v nhp chn REACTANT.
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8. Nhp tri chut chn Complement Selection loi b s la chn phn t th nht v chn phn t cn li. 9. Nhp vo Name Selection trong Select menu v tch chn PRODUCT. 10. Nhp phi chut vo vng trng trn mn lm vic loi b cc la chn. 11. Nhp chn Reaction Map trong Setup menu m hp thoi Transition State Mapping. 12. Trong hp thoi chn nguyn t N t mc Reactant v nguyn t H trong mc Product. Mi nguyn t trong list c nh r theo s th t ca n trong phn t. Khi ta chn mt nguyn t trong list, n s c sng hn trn mn lm vic:
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Hng dn s dng HyperChem 7.04 Bi v hai nguyn t ta chn khng tng ng vi nhau (Nguyn t N trong cht phn ng khng th tr thnh nguyn t H trong sn phm), nt Add s khng hot ng. 13. Chn li nguyn t N trong c list Reactant v Product. Bi v cc nguyn t l tng ng, nt Add s hot ng.
14. Nhp tri chut vo nt Add. Cc nguyn t c chuyn t list Reactant v Product thnh mt cp tng ng trong list Map. 15. Chn nguyn t #2 trong list Reactant v Product v chuyn cp ny cho list Map. Tng t lm cho cc cp nguyn t cn li. Bi v ta ang tm cch nghch chuyn phn t amoni, do th t ca cc nguyn t rt quan trng. Khi tt c cc nguyn t c chuyn qua cho list Map, nhp OK bt u thc hin cc bc cn thit tip theo. 16. t gi tr 0.49 cgi mc Lambda. (Lambda) l tham s ni suy; gi tr ca n xp t 0 cho trng thi cht phn ng n 1 cho trng thi sn phm. Bi v tp hp nguyn t cht phn ng v sn phm l nh qua gng, gi tr ; 0.5 s cho mt im khi u i xng tuyt i cho vic tm trng thi chuyn tip. S lm vic khng c kt qu tt vi khi u i xng tuyt i. Gi tr 0.49 cho ta im khi u i xng va phi cho vic tm kim.
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17. Nhp OK chn. Cc nguyn t ca sn phm b xo i, v cc nguyn t ca cht phn ng c gi li lm to cho im khi u ni suy cho vic tm kim trng thi chuyn tip. 18. Nhn nt Spacebar a cu trc vo tm mn lm vic, v quay n sao cho c th trng c d dng. im khi u nn l cu trc phng. 19. Chn Transition State trong Compute menu. Hp thoi la chn tm trng thi chuyn tip m ra.
Eigenvector following
Phng php ny cho php vect c trng ca kiu dao ng tm kim trng thi chuyn tip. Nu ta chn phn ny v nhp OK, HyperChem s thc hin tnh ton dao ng v ra hp thoi n trng thi chuyn tip cho php ta xc nh kiu dao ng no xy ra. Phng php ny hu dng cho vic tm kim trng thi chuyn tip theo kiu dao ng t nhin. Phng php ny dng kiu chuyn ho ng thi, Synchronous thch hp cho vic tm kim trng thi chuyn tip transit trong phn ng ho hc. Linear HyperChem dng php ni tuyn xc nh trng thi ca cht phn ng v sn phm. Quadratic HyperChem dng php ni suy ton phng xc nh trng thi cht phn ng v sn phm. Dng phn ny t cc iu kin kt thc tm trng Synchronous thi chuyn tip. Transit Termination 221
Hng dn s dng HyperChem 7.04 Condition RMS gradient Tnh ton s ngng khi RMS gradient ca nng lng b hn gi tr ny. c th t gi tr thay i t 10-2 n 0.1, nu dng gi tr ln hn th tnh ton s nhanh hn, nhng kt qu km hn. S vng cc i dng tnh ton. Max. cycles 20. t Synchronous Transit, tch chn Quadratic (bc hai), v RMS gradient t chun l 0.1 kcal/(A0 mol). Nhp OK chn. HyperChem thc hin tnh ton dao ng, chn cc vect c trng ca n, v sau tm trng thi chuyn tip. Khi cng vic tm kim bt u im khi u tt, n s tm ra trng thi chuyn tip mt cch nhanh chng. Ta cng c th s dng im khi u c ni suy t hp thoi Reaction Map nh im khi u cho vic tm kim trng thi chuyn tip vi phng php theo vect c trng.
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Bi 16: Trng thi in t kch thch thp nht ca Etilen.

Nghin cu biu nng lng obital ca phn t. Thc hin tnh ton tng tc cu hnh kch thch n. Nghin cu ph in t ca phn t. Tnh ton hnh hc vi trng thi kch thch triplet
Trong phn ny ta s kho st tnh ton ph kch thch in t, tho lun v s chuyn mc vch ba -> * trong etilen.
Ti u trng thi c bn ca Etilen.

By gi ta s c mt cht kh khn trong vic tnh ton thun tu l thuyt, v th phn ny s tm lc cho ta mt s ch dn.
to Etilen theo tp hp hm c bn STO-3G ta lm nh sau:

1. Nhp tri chut chn New trong File menu. 2. B tch Explicit Hydrogens trong Build menu. 3. Chn cacbon trong hp thoi la chn nguyn t v v to lin kt i C = C. 4. Chn Add H & Model Build trong Build menu to ra etilen. 5. Chn Ab Initio trong Setup menu v chn Minimal (STO-3G) cho tp hp hm c bn. t Total charge = 0, Spin multiplity = 1, Spin pairing = RHF, Accelerate convergence = Yes (tch chn), v gi tr SCF Convergence Limit t thch hp l 0.0001. Nhp nt CI (Cofiguration Interaction) v t None ri nhp OK ln lt ng cc hp thoi.
ti u trng thi c bn ca etilen ta lm nh sau:

1. Chn Geometry Optimization trong Compute menu. Tch chn phng php Polak-Ribiere v t gi tr 0.01 cho RMS gradient. Nhp OK ng hp thoi v bt u ti u. Ta s tm hnh hc c ti u ca etilen c di lin kt C-C l 1.31 A0, di lin kt C-H l 1.08 A0, v gc H-C-H l 115.70.
tnh nng lng tng tc ta lm nh sau:

1. Chn Ab Initio trong Setup menu, nhn nt Options, v chn MP2 correlation energy. Nhp OK ng hp thoi ny li tr v mn lm vic. 2. Chn Single Point trong Compute menu.
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Hng dn s dng HyperChem 7.04 Ta s tm nng lng SCF l -48364.64 kcal/mol v tng nng lng MP2 l -48438.61 kcal/mol trong bao gm c -74.97 kcal/mol nng lng tng tc. S khc nhau nh gia nng lng c ti u v nng lng tnh ton theo Single Point i khi c th xy ra.
Obital trng thi c bn ca Etilen quan st biu nng lng obital v cc obital ta lm nh sau:
1. Chn Orbitals trong Compute menu. Nhp tri chut vo vng biu din cc vch mc nng lng obital, gi v r phng to cho n khi c th nhn cc vch mc c nh sau:
C hai obital c quy cho l obital c in y (HOMO) v obital * trng (LUMO) ca etilen. Cc trng thi kch thch thp nht ca etilen tng ng vi s chuyn mt electron t obital p n obital *. C ngha l t -> * (HOMO n LUMO) s chuyn dn n c hai trng thi mc n b kch thch, y cc electron kiu i nhau, v mt trng thi bi ba, y cc electron trong obital v * c spin song song. 2. Chn cc obital ny bng cch nhp tri chut vo n, v v biu obital. nh hng phn t etilen sao cho c th quan st c nh trong v d. y biu din obital *, sau khi phn t c t dc trc x bng cng c hiu chnh Align Molecules trong Edit menu.
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CI v ph in t ca Etilen tnh ph ca Etilen ta lm nh sau

Nhp chn Ab Initio trong Setup menu. Nhp chn Minimal (STO-3G). Nhp vo nt Options. Nhp vo nt CI (Configuration Interaction). Tch chn Singly Excited. Chn Energy Criterion (Chun nng lng). nh gi tr 1000 cho Maximum Excitation Energy. Nhp ln lt OK tr li mn lm vic. Khi tin hnh tnh ton tng tc cu hnh (CI) kch thch n, n trn s lng ln cc th ca cc cu hnh. Cc cu hnh ny bao hm s kch thch mt electron t mt obital nh c n mt obital trng. Cn thit phi quyt nh c nhiu yu t nh th no lin quan n s trn. iu ny c th thc hin trn c s ca tt c cc kch thch c lin quan bao gm s lng c th cc obital khng nh c thp nht v obital nh c cao nht hoc trn c s chun nng lng kt hp vi s khc nhau v nng lng ca hai obital c lin quan. Chn gi tr 1000 s cho kt qu trong bao gm tt c cc cu hnh kch thch n trong CI (tng tc cu hnh). 7. Chn Single Point trong Compute menu. iu ny gip ta bt u tnh CI kt hp vi tnh ton im n. Khi tnh ton hon thnh, mc Electronic Spectrum s chuyn qua mu en v hot ng c. 8. Chn Electronic Spectrum trong Compute menu biu din ph nh sau: 1. 2. 3. 4. 5. 6.
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Vch cao nht l 52.7 nm v n khng lin h g vi s chyn -> *. Mc chuyn nng lng thp nht (bc sng di nht) pha bn phi c bc sng l 3.3.7 nm v l s chuyn bi ba (triplet) -> *. Tt nhin, y c s cm (mt bng khng) khi tt c s chuyn l t singlet (bi mt, mc n) n triplet. Nng lng thp nht cho php chuyn 106.4 nm l s chuyn singlet -> *. Wavelength Zoom Oscillator Strength Pan Transition S ch gc cao bn tri v phi cho bit gii hn ph ang c biu din. Thanh trt phng to v thu nh gip d dng quan st biu din ph. T l ca cng dao ng (intensity). Thanh trt h tr quan st. Biu din s ca s chuyn, mc ca s chuyn c chn. S chuyn theo th t t bc sng di nht n bc sng ngn nht (tri qua phi). Ta c th chn mt s chuyn bng cch nh vo s ca s chuyn. Xc nh s suy bin ca trng thi kch thch theo s chuyn chn. L bi spin ton phn, 2S+1, y S l tng spin electron ca h. Mi electron khng kt i c spin l 1/2,. H v kn (singlet) c bi l 1, trng thi doublet, triplet ln lt c bi l 2 v 3. Bc sng (nm) ca s chuyn c chn. Lng khng th nguyn t l vi cng ca s chuyn c chn. 226
Degeneracy Spin multiplicity Wavelength Oscillator Strength
Hng dn s dng HyperChem 7.04 Copy Copy hnh nh hp thoi biu din ph vo trnh ng dng khc, vo b nh tm thi.
Hnh hc v nng lng ca Etilen bi ba

Do trng thi kch thch thp nht ca etilen c trng thi spin khc (triplet) ch khng phi trng thi c bn (singlet), vi HyperChem ta c th tnh d dng v trc tip hm sng SCF ti u cho n. y khng phi l mt tnh ton n gin khi trng thi b kch thch c s i xng spin nh trng thi c bn v HyperChem hin ti khng c kh nng tnh trc tip trng thi singlet b kch thch cho etilen, ngoi thng tin c gi tr phng php CI cho trng thi c bn ra, nh l ta thc hin trn ra. Trng thi Triplet c th tnh ton c bng trc tip bng tnh ton SCF yu t n.
tnh hnh hc cho trng Etilen bi ba ta lm nh sau:

1. To etilen chun theo trnh xy dng trn mn lm vic nu ta cha c. Khi ta tin hnh ti u hnh hc, hnh hc khi u hin ti khng ti hn v etilen ca ta c th l cu trc c ti u cho trng thi c bn theo STO-3G thu c t trc. 2. Chn mt gc vn trong etilen phng v khi chn Set Bond Torsion trong Edit menu i gc vn thnh 300. Nhng ngi ti u dn xut u tin theo HyperChem c th khng d dng tm thy s thun li ca s khng phng nu ta bt u vi mt cu hnh phng cho mt phn t. Ta ang gip cho s ti u i lch hng so vi mt cu trc khng phng. 3. Chn Ab Initio trong Setup menu v chn 3 (triplet) cho Spin Multiplicity v t UHF cho Spin Pairing. iu ny s tnh ton cho trng thi triplet electron khng cp i ch khng phi tnh bnh thng RHF cho trng thi c bn singlet electron cp i. t 0.0001 cho SCF convergence. S dng Minimal (STO-3G) Basis set v nhp OK tr li mn lm vic. 4. Chn Geometry optimization trong Compute menu. Tin hnh ti u vi RMS gradient l 0.01. S ti u mt mt lc kh lu. Tuy nhin kt qu l trng thi triplet c kch thch c xon n 900 so vi trng thi c bn. Lin kt i C C c dn rng n 1.49A0 so vi trng thi c bn l 1.31A0, ch yu, l lin kt i c ph v v gi li gn vi lin kt n. Khong cch C H cn li l 1.08A0 v gc H C H by gi l 117.80.
tnh nng lng kch thch on nhit ta lm nh sau:

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Hng dn s dng HyperChem 7.04 1. Chn AbInitio trong Setup menu, nhn nt Options, tch chn MP2 correlation energy. Nhp OK ng hp thoi thot ra mn lm vic. 2. Chn Single Point trong Compute menu. Nng lng SCF ca trng thi triplet kch thch c ti u l -48328.65 kcal/mol cao hn 35.99 kcal/mol (794.4 nm) so vi trng thi c bn singlet c ti u. y l nng lng kch thch on nhit o c t cc tiu nng lng ca mi trng thi. Nng lng tng tc MP2 trong trng thi triplet kch thch (-45.02 kcal/mol) b hn nhiu so vi trng thi c bn (-74.43 kcal/mol) do , di nh hng ca s tng tc, nng lng kch thch on nhit l 65.84 kcal/mol (434.3 nm). Nhng con s ny c th so snh vi nng lng kch thch cc im (91.14 kcal/mol hay 313.7 nm) tnh theo CI cho s chuyn ny. Nng lng kch thch cc im (ging nh hnh hc ca trng thi kch thch vi trng thi c bn) r rng cn phi ln hn nng lng kch thch on nhit.
kho st obital ca trng thi triplet ta lm nh sau:

1. Chn Orbitals trong Compute menu. Phng to vo cc obital alpha xem biu nh sau:
Ch rng hai obital nh c v * xuy bin. Nhp vo cc obital ny chn v v biu tng ng kho st.
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Bi 17 Kh nng phn cc DFT ca H2

Tnh hm mt Chn hm tng tc trao i Thm trng in v tnh kh nng phn cc Thuyt hm mt (DFT) l phng php mi, n c nhiu im chung vi cc phng php tnh ton thun tu l thuyt. Phng php ny dng thuyt hm mt d on nng lng ph thuc vo mt . Phng php ny thay th cc th Hartree-Fock ca tnh ton thun tu l thuyt bng th tng tc trao i ca mt electron. L phng php chnh xc hn tnh ton thun tu l thuyt. Trong phn ny s gii thiu cho ta nhng bc c bn cn thit thc hin tnh ton DFT.
To H2 v to phn t hydro ta lm nh sau:

1. Tch chn Explicit Hydrogens trong Build menu. 2. Chn Labels trong Display menu v tch chn Symbols. 3. Nhp tri chut vo cng c v trn thanh cng c v r v mt ng trn mn lm vic. Nu v sai th dng phi chut xo hnh nh va to.
4. Nhp tri chut vo Model Build trong Build menu to phn t hydro theo trnh xy dng vi di lin kt l 0.74 A0 quay dc theo trc Y. 229
By gi ta c mt phn t thc hin tnh ton. Ta s tin hnh tnh ton trn hnh hc ca trnh xy dng c di lin kt l 0.74 A0 mc d ta c th ti u hnh hc nu ta mun.
Chn th tng tc trao i biu th kiu tnh ton DFT ta mun thc hin cn lm nh sau: 1. Nhp chn Density Functional trong Setup menu. 2. Chn tp hp hm c bn 6-31G** nh trnh by di y. Kiu tp hp
hm c bn ny c thm hm phn cc kiu p cho cp tp hp hm c bn zeta 6-31G kiu s cho H2.
3. Nhp vo nt Options v chn cc la chn ngm nh sn nh bn di

y:
Ring hi t ca SCF (1.0e-008) nn t nh hn bnh thng ( tnh kt qu SCF c chnh xc hn) khi ta gi nguyn cc gi tr khc. 4. Nhp vo nt Grid trong hp thoi Density Functional Method v chn Standard Grid #1 theo nh sn ca Pople v cc cng s.
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Thuyt hm mt (DFT) i hi ta c lng cc yu t ma trn ca ton t Hamilton trong bt k phng php c hc lng t no. Trong trng hp DFT, cc s hng trong ton t Hamilton (cc th trao i v tng tc) c hnh thc hm qu phc tp c th khai thc cc cng thc gii tch cho cc tch phn thch hp. DFT ni chung i hi s tch phn tnh ton cc tch phn ny v iu ny ch cho ta phi chn mt li to biu din s tch phn ny. Standard Grid #1 l mt s ho hp gia chnh xc v phc tp (s cc im trn li). Nhiu im s cho cc tch phn chnh xc hn nhng s i hi nhiu thi gian tnh ton. 5. Nhp vo nt Exchange Corelation v tch chn c hm trao i ln hm tng tc. Chn phng php HCTH98 cho c hai.
Ta c th chn bt k hm trao i no kt hp vi bt k hm tng tc no hoc c th chn c s lin h nh c ti u theo cc tc gi. Nhiu trong s cc hm c pht trin vi s tha nhn chng s c s dng thnh tng i xc nh mc d HyperChem khng i hi iu ny. HyperChem cho php chn c lp cho trao i v chn c lp cho tng tc. Trong trng hp ca ta ta s chn c hai hm trao i v tng tc nh nhau (HCTH98) c nhm Handy thuc trng i hc Cambridge pht trin. Mt cht kinh nghim c l c gi tr s dng ch cho mt trong cc
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Hng dn s dng HyperChem 7.04 cp hm. C chng ngi ta c th pht trin mt th trao i ti u nht trong chnh n m khng n s tng tc (hoc ngc li). Chn None trn l xt on ton din cho th tng tc khi tnh ton Hatree-Fock khng cha s tng tc. Tuy nhin chnj None chn s trao i l c vn ng ng mc d n lin quan n tnh ton Hatree.
Tnh ton DFT im n trong trng in. kho st ng dng ca trng in trn mn lm vic ta lm nh sau:
1. Nhp chn Single Point tin hnh tnh ton DFT thiu s c mt ca trng in 0.74 A0. Ta thu c nng lng -743.850760 kcal/mol. 2. Nhp chn Show Dipole Moment trong Display menu. Momen lng cc bng khng (hoc gn khng) nh mong i. 3. Nhp chn Set Finite Field trong Setup menu v thm gi tr 0.001 cho trng in nh trnh by di y.
4. Nhp OK thm trng. 5. Nhp Single Point trong Compute menu tnh ton im n li nhng by gi c thm trng in c p dng. Ta thu c nng lng l -743.852747 kcal/mol b hn mt cht so vi khng c trng in. Momen lng cc trong trng in s khng bng khng. 6. Nhp vo Show Dipole Moment trong Display menu. Kt qa momen lng cc dc theo trc y l 0.16096 Debye hay l 0.16096/2.541765 = 0.00633 a.u. S phn cc dn n kt qa c momen lng cc theo trng p vo. Do , s phn cc dc theo trc y l 0.00633/0.001 = 6.33 n v nguyn t. Ta tin hnh tnh ton s lo lng hn ch v s phn cc ca H2 bng hm DFT hcth98. Tuy nhin, HyperChem cho php ta tnh trc tip s phn cc nh ta s thy sau y.
Tnh s cng phn cc
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tnh s phn cc ta lm nh sau

1. Nhp chn Set Finite Field trong Setup menu v b tch Electric ta t phn trc. 2. Nhp chn Density Functional trong Setup menu. Nhp vo nt Options v nhp tip vo Polarizabilities. Ta by gi c th yu cu tnh phn cc trong qu trnh tnh im n, t cc gi tr nh sau:
Dng gi tr 0.001 nh ta s dng trc y ch khng nn dng gi tr ngm nh 0.0005. Ga tr ngm nh l s ho hp gia chnh xc ca s thay i c th theo di c v gi tr chnh xc tuyt i ch trong gii hn trng bng khng p vo. 3. Nhp chn Single Point trong Compute menu tnh im n li nhng thi gian i hi nhiu hn. Tnh ton i hi mt 6 ln thi gian tnh ton khng c tnh s phn cc trong c tnh n c trng lc p vo cho cc trc X, Y v Z. xem kt qa tnh ton sau khi tnh ton hon thnh, nhp vo Properties trong Compute menu. Nhp vo Details xem y s cng.
Ta thy rng hp phn YY ch c gi tr l 6.33 nh tnh ton phn trn.
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Bi 18 Ch thch
Thm ch thch cho phn t Chn, chnh sa v dch chuyn ch thch Th t lp ch thch theo trc Z, ghi ch thch vo lp ch thch. Phn ny s gii thiu cho ta bn kiu ch thch c bn-kiu ghi, kiu ng thng, elip (trn) v kiu ch nht. N gip ta lm cch no ghi ch v sa i kch c, mu sc v cc thuc tnh khc.
To mt h phn t
to mt h phn t lm mu ta lm nh sau: 1. Chn Open trong File menu. 2. M chn file ethanol.hin m ta lu t trc (C th v trc tip trn trang lm vic cng c). Chn ball and cylinder mc Rendering ca Display menu. Hnh nh biu din trn m lm vic s c dng nh sau:
Ch thch kiu ch nht

Ch thch kiu ch nht v elip c bn l nh nhau. Phn ny ch minh ho cho kiu ch thch ch nht. Bn hy th li vi kiu elip.
to v thao tc vi ch thch kiu ch nht ta lm nh sau

1. Chn Options mun: trong Annotations menu v chn cc la chn mong
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Tch chn nh trong hnh v. 2. Chn Color trong Annotations menu v chn mu xanh (blue). y s l mu sc ca bt k ng thng, elip hay ch nht no m ta v ra sau . 3. Nhp vo biu tng hnh ch nht trn thanh cng c. Ch l, sau khi ta nhp vo biu tng ny th khi chuyn ln mn lm vic chut cng c hnh dng ch nht. 4. t tr chut ln gc tri mn lm vic, nhp tri chut gi v r to hnh ch nht nh mong mun ri nh chut ra. Ch thch kiu ch nht khi xut hin nh sau:
Tt c phn t nm lp bn trong ri vi lp ch thch nm bn ngoi. Chnh v chn Annotation Layer in Front nn phn t ca ta b che mt. 5. Chn Options trong Annotations menu v b tch Annotation Layer in Front t lp ch thch ng sau, khi mn lm vic biu din nh sau: 235
6. Nhp chn cng c la chn trn thanh cng c v nhp tri chut vo ch thch ch nht chn ch thch ny. Ch nht ch thch s xut hin ng vin la chn mu (ngm nh l mu xanh). Nu cn thit loi b la chn ta ch vic nhp phi chut vo vng trng mn lm vic. Tng t ta cng c th chn phn t nh nhng bi trc. 7. Dng cng c dch chuyn v phng to iu chnh kch c v v tr ph hp. Ch , nu phn t cng c chn th n s c u tin i vi tc ng ca cc cng c. Nu ch ch thch c chn, th n s chu tc ng ca cng c phng to v cng c dch chuyn; cc cng c khc khng c tc dng vi n. 8. Ch chn hnh ch nht. 9. Chn Options trong Annotations menu v b tch Fill Circles and Rectangles. Nhp OK chn. 10. B la chn hnh ch nht. Ta s thy s lp y bin mt, thay vo l hnh nh nh sau:
236
Hng dn s dng HyperChem 7.04 11. Chn hnh ch nht li ln na v nhp chn Options trong Annotaions menu. Chn kiu ng thng (line type) l Dashed (Nt t). Ta s thy hnh ch nht lin trn chuyn thnh hnh nt t. Ch : - Hide Annotation layer: giu ch thch. - Fill Circles and Rectangles: Lm y ch thch (T y mu la chn) - Use Gravity on lines: Dng lc ht cho cc ng thng. - Line Width: rng ca ng. - Line type: Kiu ng: Solid (nt lin), Dashed (nt t), Dotted (chm chm), DashDotted (gch chm), DashDotDotted (gch chm chm).
Ch thch dng ng thng

Ch thch dng ng thng cng ging nh ch thch kiu elip v ch nht nhng khng c ch lm y. Chng cng khc nhau v lc ht lm cho cc ng ni c vi nhau. Kho st ch thch kiu ng thng ta lm nh sau: 1. Chn cng c ch thch ng thng trn thanh cng c, v mt vi ng, chn, t mu, dch chuyn v phng to nh ch thch kiu ch nht trn. Th kho st kh nng ht ca u mt cc ng khi v gn nhau bng cch tch chn Use gravity in lines trong hp thoi Options ca Annotation menu.
Ch thch kiu vn bn
Ghi ch bng t cng nh bng biu tng hu nh ging nhau ngoi tr biu tng l mt k t n. Ch thch kiu vn bn khc v mu sc so vi kiu ng, elip v kiu ch nht. Mu chn cho kiu vn bn ch c 16 mu. Cng ch c duy nht cc kiu phng ch, kch c ch cng nh mt s kiu biu din ch.
Kho st vic to v hiu chnh ch thch kiu vn bn ta lm nh sau:

1. Nhp tri chut tch chn ch thch kiu vn bn trn thanh cng c.
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Hng dn s dng HyperChem 7.04 2. Nhp tri chut ln gc trn bn tri hnh ch nht to trc (t chut v tr mun ghi ch). Khi hp thoi la chn ghi ch kiu vn bn xut hin:
3. Chn cc la chn nh trong hnh v, vit ch thch vo ca s trng bn di, nhp OK th mn hnh s xut hin nh sau:
Ta c th thu c hnh nh sai khc mt cht nu cha chnh sa v hon ton c th vit ting vit nu my tnh c ci phng ting vit.
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Hng dn s dng HyperChem 7.04 4. Dng cng c la chn chn dng ch thch bng cch nhp chut vo v tr thch hp trn dng . N s c vy li bng hp la chn ca cng c la chn. 5. Chn Edit Text trong Annotations menu v thay i kch c ch t 40 v 30. 6. S dng cng c dch chuyn v dch chuyn dng ch thch n v tr nh trnh by sau:
7. Chn Symbols (biu tng) trong Annotations menu v nhp vo mt biu tng, v d nhp vo mi tn v nhp OK chn.
Tu thuc vo phng ta ci t trn my m ta s c kiu biu tng khc. Mu sc ngm nh ca biu tng l mu trng (mu ngm nh ca nn HyperChem l mu en), do nu ta chn mu nn l mu trng th khng th nhnh thy biu tng. Biu tng mi ly ra lun nm gc
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Hng dn s dng HyperChem 7.04 trn bn tri mn lm vic, n vn cn ang c la chn v ta c th dng cng c dch chuyn chuyn n n v tr cn thit. 8. Chn Edit Text trong Annotations menu v chn mu thch hp cho biu tng mi ly. Ch , biu tng ta ly l mt k t trong phng hin hnh trong hp thoi. Nhp OK chn.
9. Chuyn mi tn n nguyn t oxy. B la chn, ta c th b mi la chn bng cch dng cng c la chn v nhp phi chut vo vng trng trn mn lm vic. 10. Dng cng c ch thch dng vn bn to mt ch thch khc l Oxygen Atom v t n vo v tr nh sau:
Nu ta lo lng v vic la chn cc ch thch ring th c th s dng Select Next hay Select Previous trong Annotations menu. Ta ch c th s dng chng khi mt ch thch c chn. Ta ch c th hiu chnh c ch thch dng vn bn khi mt ch thch dng vn bn c chn.
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Lu ch thch
Ch thch cng c HyperChem lu vo file HIN. Ta c th lu n vi h phn t hoc khng cng c. lu ch thch vo file HIN ta lm nh sau: 1. Lu phn t trn cng vi ch thch bng cch nhp chn Save trong File menu. 2. Sau khi lu vo file HIN, chn New trong File menu. 3. Chn Open trong File menu v c file m ta mi lu. Ch thch s xut hin nh ta biu din trc .
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Bi 19 Cc File tham s TNDO

Tnh TNDO. Hiu chnh trc tip tham s TNDO (V nhng phng php khc) To cc tham s mi xc nh kiu Phn ny s gii thiu cho ta nhng thao tc bng tay c bn v tnh ton kiu b qua xen ph vi phn (TNDO). Ta s kho st tng c bn v kiu nguyn t trong cc tnh ton bn kinh nghim v pht trin cc tham s mi cho phng php TNDO. Vi mt tp hp tham s ngm nh, TNDO ch l phng php CNDO (hoc l INDO). Ta s kho st nh th no CNDO d on r rng di lin kt C C trong etan v eten v pht trin cc tham s mi xc nh cho cc h sp2 v sp3.
Tham s ngm nh CNDO/INDO. kho st di lin kt CNDO ca etan v eten ta lm nh sau:

1. To mt phn t etan trn mn lm vic v p dng nhn (Labels) theo kiu nguyn t (type).
2. Chn Semi-empirical trong Setup menu v chn TNDO s dng phng php bn kinh nghim ny. Nhp vo nt Options v chn cc gi tr ngm nh nh trnh by bn di:
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c bit, khng chn Add INDO Terms. Khng tch chn phn ny, TNDO tng ng vi CNDO (cng vi hoc khng cng vi cc tham s ring). 3. Chn Select Parameter Set trong Setup menu v chn tp hp tham s ngm nh. Nhp OK ng hp thoi. 4. Dng Polak-Ribiere ti u cu trc ca Etan, t RMS gradient l 0.01. Ta nn thy rng di lin kt c ti u vo khong 1.457 A0. Ta c th thch tnh ton li vi phng php CNDO. Lp li tnh ton cho Eten v thu c di lin kt khong 1.310 A0.
Kim tra tham s TNDO kim tra tham s TNDO ta lm nh sau: 1. Chn mt nguyn t cacbon ca etan v chn Edit Parameters trong Setup
menu. Hp thoi vi cc tham s TNDO ngm nh nh sau xut hin hon ton ng nht vi cc tham s theo CNDO/INDO.
Trong TNDO cc tham s ny c kt hp vi mt kiu nguyn t ring ch khng theo s th t nguyn t. Trong trng hp ny kiu l CT. Ch c bit gi tr beta l 21. Lng beta ny l tham s c bn cho di lin kt v cc yu t ngoi ng cho ca ma trn Fock. Gi tr beta ln nn c t cho lin kt mnh hn v gi tr beta nh hn nn t cho 243
Hng dn s dng HyperChem 7.04 lin kt yu. Trc khi hiu chnh cc gi tr ngm nh ny ta nn to ra mt file tham s mi th nghim vi n. Ch : Ta cng c th kim tra cc tham s cho cc phng php bn kinh nghim khc hoc phng php c hc phn t. Vi phng php c hc phn t, ta s thy tham s khc pht trin da trn ta chn nguyn t, lin kt, gc lin kt hay gc vn.
Copy tham s TNDO cho tp hp mi

copy tp hp tham s ngm nh cho tp hp vi tn tutorial s dng cho th nghim. 1. Chn Select Parameter Set trong Setup menu nh trc xem cc tp hp tham s TNDO. Chn tp hp ngm nh v nhp vo nt Copy. HyperChem by gi s hi ta chn tn cho bn copy:
2. Tn tp hp tham s mi c nh vo l tutorial trong hp thoi hiu chnh. Nhp OK. By gi ta s c th xem tp hp tham s mi ny m t trong Registry nu ta mun.
Hiu chnh tham s TNDO hiu chnh tp hp tutorial (t trn) ta lm nh sau:

1. Chn Select Parameter Set trong Setup menu v chn tp hp tham s tutorial mi ca ta lm tp hp s dng. 2. Chn mt nguyn t cacbon ca etan v chn Edit Parameters trong Setup menu. 3. Nhn nt Edit v nh vo gi tr mi cho Beta. Nhp vo OK. Th vi cc gi tr khc ca beta v nh hng ca chng ln di lin kt C C c ti u. Ta nn c th cc gi tr beta b hn 21 xem ta c th ci tin di lin kt C C t 1.457 A0 n gn vi 1.54A0. Ga tr CT cho beta vo khong 16 s cho ta di lin kt tt hn nhiu.
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Hng dn s dng HyperChem 7.04 4. Th vi eten. Ta s thy rng gi tr ngm nh cho beta 21 a n di lin kt C=C l 1.310 A0 nh hn nhiu so vi 1.34 A0 c trng ca lin kt i C=C. 5. Tham s beta CX mi khong 19 s cho di lin kt tt hn nhiu cho eten. Kt qu ca bi hc ny l ta s to ra c file tham s TNDO mi, tutorial.abp, cha cc tham s beta mi cho lin kt n C-C sp3 sp2 (kiu CT-CT) v cho lin kt i C=C sp2-sp2 (kiu CX-CX). Ta by gi c th th chng cho propen xem chng hot ng tt th no trong tnh hung mi.
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Ch gii Glossary
Ab Initio. Hnh thc tnh ton c hc lng t trong mi obital c tnh l tng ca mt tp hp cc hm hnh hc c bn (tp hm c bn). Bng cch tnh ton s nh hng ca nhiu hm sng obital, cc tnh ton ab initio c th cho kt qu rt chnh xc, phng php ny i hi nhiu phn a trng ghi v thi gian tnh ton rt lu. AM1. M hnh Austin. L phng php SCF, bn kinh nghim, dng cho tnh ton ho hc. L mt trong cc phng php MOPAC [Stewart, J.J.P., J. Comp.-Aided Molec. Thit k 4(1):1-108, 1990]. Phng php ny ci tin t phng php MNDO. N c dng tnh cho cc phn t hu c c cha cc nguyn t kim loi. Ni chung n l phng php bn kinh nghim chnh xc nht trong HyperChem. Tnh ton cc thuc tnh in t, hnh hc ti u, nng lng ton phn v nhit hnh thnh. Tham kho: Dewar, M.J.S., et at., J. Am. Chem. Soc. 107: 3902, 1985. ALL atom. L mt phng php tnh ton c hc phn t trong mi nguyn t c biu din nh mt ht ring bit. Tri ngc vi united atom. AMBER. L phng php c hc phn t, hay cn gi l phng php trng lc(force field), dng tnh ton ho hc. Phng php ny c thit lp tnh ton cho cc protein v cc nucleic axit. Trng lc ny cung cp cho c hai hnh thc tnh all atom v united atom. Tham kho: Weiner, S.J., et al., J. Comp. Chem. 7:230-252, 1986. Atom type. Kiu nguyn t biu din cc loi mi trng ho hc quy cho mi nguyn t s dng trong tnh ton trng lc. Cc tnh cht ca mi trng gm c s lai ho, in tch hnh thc v cc lin kt trc tip bn cnh. V d, kiu nguyn t AMBER ca C biu din l mt cacbon cacbonyl sp2, kiu CT biu din l mt cacbon t din, v kiu CH l s biu din nguyn t cacbon c lai ho sp3 cng vi mt nguyn t hiro. Mi trng lc c mt tp hp cc kiu nguyn t khc nhau. HyperChem c th quy kiu nguyn t cho mt h nguyn t bng vic dng cc quy tc trong chem.rul. Backbone (Lin kt khung). L mch lin kt cng ho tr lin tc trong mt phn t. Vi polypeptide, lin kt khung bao gm tt c cc lin kt peptide, xen k gia cc cacbon alpha cng vi cu ni isunfua. Vi polynucleotide, lin kt khung bao gm tt cc cc lin kt photpho ieste, ln lt gia cc cacbon C3-C4 trong phn t ng (ribo hoc deoxyribose). 246
Back end. Phn mm tnh ton HyperChem. HyperChem c thit k thnh cc modul, vi phn mm front-end chy trn mt PC v phn mm back-end chy trn cng PC hoc trn mt my tnh khc. Back-end gm c HyperNewton (AMBER, BIO+, v OPLS), HyperMM+ (MM+), HyperGauss (Ab Initio), HyperEHT (Extended Huckel), v HyperNDO (CNDO, INDO, MINDO/3, MNDO, AM1, v PM3). Bio+. B xung thm cho trng lc CHARMM (Chemistry at HARvard Macromolecular Mechanics), do nhm Martin Karplus thuc trng i hc Harvard pht trin ln. L phng php c hc phn t, cn gi l force field (trng lc), dng cho tnh ton ho hc. Dng tnh ton cho cc phn t protein. Tham kho: Brook, B.R., ET AL., J. Comp. Chem. 4:187-217, 1983; Reiher, W.E., II, Theoretical Studies of Hydrogen Bonding, Ph. D. thesis, Harvard University, 1985. Bitmap. Bc nh mn lm vic to nn t tp hp cc im (dots). Bc nh c phn gii nh trn mn hnh. Brookhaven Protein Data Bank (PDB). L d liu v cc cu trc ca protein v cc nucleic axit. Thng tin v mi cu trc phn t gm c to nguyn t, kh nng lin kt ca nguyn t v nhng vn lin quan khc. HyperChem c th c v gii thch tt c cc file PDF cng vi nhng thng tin v to hoc kh nng lin kt ca nguyn t. Cc file PDF c ui m rng l .ent. Charge density. S phn b mt in tch electron trong phn t. Hnh dng ca phn t thng kt hp vi b mt in tch c mt khng i. HyperChem tnh ton mt in tch bng tng ca cc mt obital phn t, l tng bnh phng ca cc hm sng obital. Clipboard. Vng nh tm thi cho d liu v th do Window cung cp. Lnh Cut v Copy trong HyperChem s t mt m t dng vn bn vo trong b nh tm thi. Copy nh trong HyperChem s t hnh nh vo trong b nh tm thi. Ta c th xem nhng g c trong b nh tm thi bng cch s dng trnh Clipboard trong nhm trnh ng dng chnh ca Window. Click. Nhn v gii phng nt chut mt cch nhanh chng. Clipping. Biu din mt phn trong h phn t trn mn lm vic (Workspace) ca HyperChem. Giu nhng nguyn t cn cnh v cc nguyn t pha sau khng cn thit v th ta c th tp trung vo vng cn quan tm. Phn quan tm c gi 247
Hng dn s dng HyperChem 7.04 l clipping slab. y l hp thoi hnh ch nht c th iu chnh chiu su, chiu cao v chiu rng bng chiu cao v chiu rng mn lm vic ca HyperChem. Xem clipping planes. Clipping planes. Cc bin trc v sau ca mt mt ct, c th iu chnh ring t 0 A0 n mt s no theo Angstrom tu theo kch c v phng i ca h phn t. Clipping slab. Phn hnh ch nht trong mt h phn t c gii hn bi hai mt phng ct c th iu chnh c. Closed-shell. Phn t khng c cc electron k i. CNDO. Hon ton b qua xen ph vi phn (xem NDO). y l phng php SCF n gin nht trong cc phng php tnh ton c hc lng t bn kinh nghim. N thch hp cho tnh ton thuc tnh in t trng thi c bn cc h v kn v v h, ti u hnh hc v tnh ton nng lng ton phn. HyperChem s dng CNDO/2. Tham kho: Pople, J.A. and Beveridge, DL., Approximate Molecular Orbital Theory, McGraw-Hill, 1970. Connectivity. Thng tin v s hnh thnh lin kt cng ho tr ca nguyn t vi cc nguyn t ln cn. File PDF c th cha cc thng tin ny trong cc tp CONECT. Cc file HIN c cha cc thng tin ny cui cc tp ghi nguyn t, trong dng <nbor#nbor-bonds>. Constraint. Cng bc gi tr ca Model Build (trnh xy dng) ph hp vi ca cc cu trc thc khi xy dng cu trc 3D gn ng. Convergence. Tiu chun kt thc mt tnh ton ho hc. Tnh ton c hc SCF bn kinh nghim hi t (kt thc) khi s khc nhau v nng lng sau hai ln lp li lin tip b hn gii hn hi t (ngm nh l 0.01kcal/mol) hoc tnh ton t n gii hn lp (ngm nh l 50). Vi tnh ton ti u hnh hc phn t, gii hn hi t l s vng tnh ton (s ngm nh bng 15 ln s nguyn t) hoc l gradient RMS ca h phn t (ngm nh 0.1 kcal/Angstrom mol). Coordinate system. Khng gian ba chiu (3D) cha cc to Decac x, y v z ca mi nguyn t trong h. HyperChem c h to ca ngi quan st v h to ca phn t. T h ta ca ngi quan st ta c th dch chuyn, quay h phn t n v tr quan st thch hp. Quay v dch chuyn theo h to phn t s lm thay i v tr ring ca cc nguyn t.
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Hng dn s dng HyperChem 7.04 Correlation Energy. Nng lng m phng php Hartree-Fock m t nng lng c c t s tng tc theo v tr c th ca cc electron, ch khng phi l t v tr trung bnh ca chng. Cc tnh ton Ab initio c th tnh ton nng lng tng tc theo thuyt Moller-Plesset bc hai (MP2). Thuyt hm mt (DFT) s l nng lng tng tc theo thuyt trng t hp cng vi cc phng trnh (Cc phng trnh Kohn-Sham) tng t nh cc phng trnh Hartree-Fock. Cc phng trnh Kohn-Sham i hi mt hm trao i v mt hm tng quan (tng tc qua li). Chng chuyn thnh thuyt Hartree-Fock khi hm trao i l hm Hartree-Fock v hm tng quan coi nh b b qua. CPK. Cc k t u ca Corey-Pauling-Koltun; quy cho tp hp nguyn t ph bin radii dng miu t khng gian nhiu hnh nh hay xy dng cc m hnh cht do. Cursor keys. (Phm tr chut) l cc phm . S dng ring tng phm ny, cng vi phm Shift, hoc kt hp vi phm Ctrl+Shift quay hoc dch chuyn cc phn t trn mn lm vic (Workspace). Cursor. im tr chut hoc cng c trn mn hnh m ta dch chuyn khi dng chut. S dng im tr chut chn cc mc t cc menu, dng v v dch chuyn cc phn t, dng thc hin cc la chn trong hp thoi v hiu chnh. Cycle. Trong qu trnh ti u hnh hc (Geometry optimization), s vng (cycle) ch ra s ln tnh ton trn mt th nng xc nh im cc tiu. Mi vng c mt hoc nhiu im, dng tnh ton nhm c lng nng lng v gradient trong qu trnh tnh ton. HyperChem cho bit s vng v s im tnh ton trn dng hin trng. DDE. Trao i d liu ng lc hc. Mt h dng trao i d liu gia HyperChem v cc ng dng Window khc. HyperChem th hin nh mt trnh phc v (server): n cung cp thng tin ch khi mt trnh ng dng khch (client) yu cu d liu ring. Default element. Nguyn t cng c v ca HyperChem dng xy dng cc phn t. N c th ch l mt nguyn t ngm nh thi im no , v ta c th thay i n khi cn thit. Density functional. S ph thuc ca nng lng vo mt hm (mt electron). Cc hm khc nhau m t s ph thuc khc nhau vo mt electron. Thuyt hm
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Hng dn s dng HyperChem 7.04 mt m t phng php tnh ton nng lng tp trung vo mt electron ch khng phi vo hm sng. Desktop. Mn biu din Microsoft Window dng biu din cc ca s v cc biu tng. Dialog box. Kiu ca s dng chp nhn thng tin hoc biu din thng tin. S biu din cc hp thoi lm cn tr cc chc nng khc ca HyperChem. Ta phi ng cc hp thoi ny HyperChem hot ng tr li. Cc hp thoi lin tc (v d: hp thoi Amino Axit) khng lm cn tr cc chc nng ca HyperChem. Dielectric constant. H s (epsilon) dng hiu chnh cc tng tc trong qu trnh tnh ton c hc phn t. Khi thiu dung mi, hng s in mi ph thuc khong cch tc l hng s in mi c gi tr ln hn 1 m phng s c mt ca dung mi. Khi biu din dung mi, nh l trong hp tun hon hyrat ho, hng s in mi l mt hng s ch ph thuc vo khong cch. Hng s in mi, epsilon = (hng s in mi trong khng gian t do)x((h s t l). Vi hng in mi ph thuc khong cch, epsilon = (hng s in mi trong khng gian t do)x(h s t l)x(h s phn ly gia cc nguyn t). Xem electrostatic potential. Drag. Dch chuyn mt vt th trn mn hnh bng cch gi mt nt chut trong khi ch chuyn chut. Cc vt th c th l cc phn t hoc cc mc trong mt menu. Khi ta hon thnh qu trnh chuyn, gii phng nt chut. V d: ta c th dch chuyn mt phn t c chn bng cch r (drag) cng c dch chuyn trn mn lm vic ca HyperChem trong qu trnh ta phi gi nt phi chut. Ta c th gi nt tri chut v dch chuyn n biu tng no trn menu mun chn. Gii phng nt chut chn biu tng . Dynamic Data Exchange. Xem DDE. Electrostatic potential. Th nng mi im trong khng gian xut hin do s phn b ca cc nguyn t tch in. Th tnh in )U) khong cch r so vi in tch im c xc nh theo nh lut Coulomb: U = Cq/(r), y C l hng s (ph thuc vo cc n v) v l hng s in mi (hay epsilon). Vi nhiu in tch trong khng gian 3D (k c cc in tch ht nhn v cc electron trong cc obital phn t), phng trnh ny tr thnh h phc tp. HyperChem tnh ton th tnh in nh th nng ca mt n v in tch dng tng tc vi h phn t. Trong qu trnh tnh ton tng tc vi cc electron trong cc obtal phn t, HyperChem b qua cc hp phn tu thuc vo s xen ph vi phn gia cc nguyn t (xem NDO). HyperChem tnh ton v v biu th tnh in t cc kt
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Hng dn s dng HyperChem 7.04 qu tnh ton im n, tnh ton c hc lng t bn kinh nghim. Ta c th s dng cc kt qu ny d on v tr tn cng ca cc proton v cc ion khc trong qu trnh phn ng. Exchange Functional. S ph thuc ca nng lng trao i vo mt electron. Cch thc lin h mt electron l nng lng trao i. Thuyt hm mt xut phng php tnh nng lng trao i v nng lng tng quan t mt electron. Explicit hydrogens. Khi Explicit hydrogent hot ng trong qu trnh v, HyperChem mong mun tt c cc nguyn t hydro c v. Cc nguyn t ch vi mt lin kt c v l hydro ch khng nh default element. iu ny tri ngc vi vic thm cc nguyn t hydro bng Model Builder sau khi cc nguyn t nng hn c v. Force constant. S hng trong mi phng trnh ca mt trng lc l s chuyn cc d liu t to nguyn t thnh gi tr th nng. V d, nng lng cng lin kt: Ebond = K r (r r0 ) 2 , y E l th nng, r l di lin kt, r0 l di lin
bonds
kt trng thi cn bng (strain-free), v Kr l hng s lc. Vi mi trng lc, mt hay nhiu tp hp tham s xc nh cc hng s lc v cc hnh hc cn bng (v d, r0). Force field. L phng php c hc phn t dng tnh ton ho hc. Cc tnh ton ny c th l tnh im n, ti u hnh hc, hay ng lc hc phn t. HyperChem cung cp bn trng lc: MM+, AMBER, BIO+ v OPLS. Mi trng lc c ba thnh phn: cc phng trnh xc nh th nng ca mt h phn t l hm to ca cc nguyn t, cc kiu nguyn t (atom types) v cc tp tham s ph hp cho cc phng trnh ly t d liu thc nghim. Xem u vo khc nhau gia atom type v parameter set. Front end. Xem back end. Geometry optimization. L mt tnh ton, dng cho c phng php c hc phn t ln c hc lng t, tm cu hnh c nng lng cc tiu (bn vng) ca mt h phn t. Tnh ton iu chnh cc to nguyn t tng bc tm mt cu hnh trong cc tc ng thc ln mi nguyn t c gim n khng. y thng l mt cc tiu a phng local minimum) trn mt th, khng nht thit phi l cc tiu ton phn (global minimum). Global minimum. Cu hnh ca mt h phn t c th nng thp nht. 251
Gradient. Tc bin i (xut pht im u tin) ca nng lng mt h phn t, l hm cc v tr ca nguyn t. bin thin (gradient) bng khng cho bit cu hnh vi nng lng cc tiu l cc tiu a phng hay cc tiu ton phn hoc l trng thi chuyn tip. Khi HyperChem bo mt gi tr n ca Gradient, l RMS gradient ca cc lc trong ton b cc nguyn t. Ground state. Trng thi in t c nng lng thp nht. Xem lowest state. Group selection. Mt la chn mt tp hp con cc nguyn t, cc hp phn hoc cc phn t trong mt h phn t. La chn cc nguyn t, cc hp phn hay cc phn t trong Select menu hiu chnh mc nhm la chn. Cng vi cng c la chn ng hot ng, ta la chn nhm bng cch r mt ng bin bao quanh cc cu trc phn t mun chn, kt hp vi vic nhn ng thi c nt tri v nt phi chut (nhn nt tri trc nt phi). La chn cu (Select Sphere) trong Select menu nhm vo qu trnh la chn nhm 2D hay 3D. La chn 2D bao gm tt c cc nguyn t nh ra trong mt hnh ch nht hai chiu c chn. La chn 3D bao gm tt c cc nguyn t trong mt hnh cu ly tm trn mt nguyn t. HIN. File u vo ca HyperChem. y l kiu file c bn HyperChem dng lu cc h phn t. cc file c phn m rng l .hin. HOMO. Obital phn t nh c c nng lng cao nht. iu ny cho bit tt c cc obital phn t khc u c v tr di obital ny trong biu nng lng. Cc obital phn t l t hp tuyn tnh ca cc obital nguyn t (LCAO). Huckel method. Phng php n gin v gn ng dng cho cc tnh ton c hc lng t bn kinh nghim. Phng php Huckel m rng dng trong HyperChem ch c tc dng cho tnh ton im n (single point), khng dng ti u hnh hc hoc tnh ton ng lc hc phn t. Cc tnh ton Huckel m rng cho nhng m t nh tnh hoc bn nh lng cc obital phn t v thuc tnh ca in t (v d, in tch thc ca nguyn t v phn b spin). y khng phi l phng php trng t hp (Self-Consistent Field: SCF). Tham kho: Hoffman, R., J. Chem. Phys. 39(6):1397-1412, 1963. Icon. Biu tng hnh hc nh biu din mt cng c hay mt chng trnh ng dng. INDO. Gin tip b qua xen ph vi phn (xem NDO). L phng php SCF dng tnh ton c hc lng t bn kinh nghim. N ci tin t CNDO bng cch tnh 252
Hng dn s dng HyperChem 7.04 ton cc tng tc y mt tm c th gia cc electron trong cng nguyn t. Dng cho tnh ton cc thuc tnh in t trng thi c bn ca cc h v h v v kn, ti u hnh hc v tnh ton nng lng ton phn. Tham kho: Pople, J. A. and Beveridge, D.L., Approximate Molecular Orbital Theory, McGraw-Hill, 1970. Improper torsion. Gc vn (gc nh din) khng c hnh thnh do s ni tip ca ba lin kt. Mt s trng lc c hc phn t dng cc gc nh th trong cc s hng nng lng duy tr mt phng hoc ngn s nghch chuyn ca cc carbon t din c mt hydrogen biu din kiu nguyn t lin kt (united atom). Inertial axes. (Trc qun tnh) c ba trc (trc th nht, th hai v th ba) kt hp vi cc momen qun tnh ca mt h phn t hay mt h con c chn. Cc trc l cc hm v tr v khi lng ca nguyn t. chng ph thuc vo h v khng ph thuc vo h to phn t hay h to ca ngi quan st. Trc qun tnh th nht thng biu th di nht qua h phn t, trc th ba thng biu din di ngn nht. Isosurface. (ng mt) Mt ba chiu biu din trong khng gian ba chiu, tnh cht c nh ngha theo gi tr cho trc; n nh l lp da ca mt vt th rn. V d, i vi hm ton hc s = x2 + y2 + z2, biu ng mt (isosurface plot) vi s = 1 s l mt mt cu vi bn knh l 1; cc biu ng mt vi cc gi tr khc ca s s l cc mt cu vi cc kch c khc nhau. Interation. Trong mt phng php c hc lng t SCF, mi tnh ton cc obital phn t bt u cng s phng on v kiu ca cc obital. Mi th nghim (hay interaction: s lp li) lc ra s phng on cho th nghim tip theo. Khi s khc nhau gia hai ln lp li lin tip b hn gii hn hi t (do ta t), th tnh ton SCF i n hi t (convergence). Label. Thng tin v cc hp phn ca mt h phn t HyperChem c th biu din cng h. Nhn (Label) cng c p dng cho nguyn t hay cc phn d (residue). Nhn nguyn t l Symbol (biu tng) (ho hc), Name (tn) (theo file PDB thch hp), Number (s ca v tr ni), Type (Atom type), Basis Set, Mass, Charge, hay Chirality (R hay S). Nhn Residue l Name, Sequence, hay Name+Sequence. HyperChem gn cc nhn cho la chn hin hnh. LINE. Gii hn trc, Named selection nhn bit cc nguyn t trong phn la chn, cng vi trc qun tnh chnh ca cc nguyn t c chn. (Trc qun tnh chnh tng ng vi gi tr c trng nh nht ca moment ma trn qun tnh.) Mt h phn t c th ch c mt la chn LINE ring bit.
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Hng dn s dng HyperChem 7.04 Local minimum. Mt cc tiu trn mt nng lng i vi h phn t biu din cu hnh th nng thp. Cc mt nng lng phn t c th c nhiu cc tiu a phng (local minimum), cc tiu a phng nh nht l global minimum (cc tiu ton phn). Cc tnh ton Geometry optimization c th a n mt cu trc cc tiu a phng. Log. Mt file cha kt qu tnh ton ho hc v nhng li ch gii. HyperChem t ng tp hp nhng thng tin ny nu ta chn Start Log trong Menu File (xem Start Log). Tn file (filename) ngm nh l chem.log v file thng c phn m rng l .log. Lowest state. Trng thi in t thp nht ca bi spin ring bit; nht thit khng phi l ground state. LUMO. Orbital phn t khng nh c thp nht. iu ny c dng nh mt im ch dn miu t v tr ca bt k orbital phn t no bng hay trn orbital ny. Cc orbital phn t l mt t hp tuyn tnh ca cc orbital nguyn t (LCAO). Metafile. Hnh nh bao gm cc lnh v. S chuyn mt hnh metafile khng ph thuc vo mn hnh (monitor), v l s chuyn ca thit b u ra. V d, nu ta in mt metafile bng my in laser, s chuyn l 300 dpi. MINDO/3. B qua c mc cc xen ph vi phn trung gian, phin bn 3. y l mt phng php SCF ca tnh ton c hc lng t bn kinh nghim. M rng t INDO, MINDO/3 dng cc tham s thch hp cho kt qu thc nghim, thay v tnh ton chnh xc. Dng cho cc phn t hu c ln, cation, v cc hp cht polynitro. Tnh ton cc thuc tnh in t, ti u hnh hc v nng lng ton phn. Tham kho: Dewar, M.J.S. et al., J. Am. Chem. Soc. 97: 1285, 1975. MM+. Phng php chung nht i vi cc tnh ton c hc phn t, pht trin cho cc phn t hu c. y l mt trng lc all atom. MM+ da trn cc hm MM2 (77), tc gi l Dr. Norman Allinger thuc i hc Georgia. HyperChem n nh cc kiu nguyn t v cc tham s khng c gi tr thng thng l MM2, m rng phm vi ca cc hp cht ho hc m trng lc ny c th thch nghi. MM+ m rng MM2 cho php cc la chn nh l cc iu kin bin tun hon v ng lc hc phn t chung vi cc trng lc khc. Tham kho: Allinger, N.L., J. Am. Chem. Soc. 99:8127-8134, 1977.
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Hng dn s dng HyperChem 7.04 MNDO. Gim bt s b qua xen ph hai nguyn t. y l phng php SCF i vi cc tnh ton c hc lng t bn kinh nghim. Dng cho cc hp cht hu c khc nhau cha cc nguyn t t dng 1 v 2 ca bng h thng tun hon, tr kim loi chuyn tip. Loi b mt s li trong MINDO/3. Tnh ton cc thuc tnh in t, ti u hnh hc, nng lng ton phn, v nhit hnh thnh. Tham kho: Dewar, M.J.S. v Theil, W., J. Am. Chem. Soc. 99:4899, 1977. Model Builder. Trnh thun tin trong HyperChem dng dng m hnh 3D ca cc cu trc ho hc t hnh v 2D. HyperChem dng cc quy tc gn lin quy nh di lin kt, gc lin kt, gc xon v ho lp th chun. Trnh xy dng (Model Builder) cng quy nh kiu nguyn t i vi force field ang hot ng, v c th t ng thm cc nguyn t hydrogen tho mn ho tr cn thit. C cc cu trc gn ng v c th cn lc bng geometry optimization. Moleculer dynamics. Tnh ton m phng chuyn ng ca mi nguyn t trong h phn t nng lng c nh, nhit c nh, hay vi s bin i nhit c iu khin. Kt qu tnh ton ng lc hc phn t c gi l trajectory (qu o). HyperChem c th dng c hc phn t hay phng php c hc lng t bn kinh nghim tnh qu o ng lc hc phn t. Ta c th dng tnh ton ny nhn c mt s ln cc tnh cht v cu trc v tnh cht v nhit ng lc hc, bao gm ln lt cc local minimum, nng lng khc nhau gia cc cu hnh khc nhau, v c ch cng nh ng phn ng. Molecular mechanics. Cc phng php khc nhau tnh ton th nng ca cc h phn t nh hm to ca cc ht nhn nguyn t, b qua x l cc electron. Tc ng ca in t c ngm nh trong cc kiu hm gii tch v qu trnh tham s ho. Tt c cc phng php dng d liu kinh nghim xc nh cc hng s lc ring (v d, cc hng s cng lin kt) v thng bng (cng t do strain-free) cc gi tr i vi mi i lng hnh hc (v d, di lin kt). HyperChem cung cp cc phng php sau: MM+, AMBER, BIO+ v OPLS. Multiplicity. bi spin ton phn l 2S + 1, y S l tng spin electron ca h. Mi electron khng cp i tnh c spin l +1/2. Cc electron cp i c spin thc l khng (+1/2 -1/2 = 0). Mt h v kn (closed-shell) c bi l 1 (singlet mc n). Mt h v h (open-shell) c th c bi l 2, 3, 4 (doublet, triplet, quartet tng ng), hay cao hn. Dng cc gi tr nguyn t 1 n 6 trong HyperChem. Named selection. Mt tp hp cc nguyn t c n nh tn, nh gii hn (POINT, LINE, hay PLANE) hay tn khc di n 19 k t. Ta c th dng cc phn la chn c t tn lp li phn la chn hay chuyn n nhng qu 255
Hng dn s dng HyperChem 7.04 trnh c bit (v d, nghch chuyn-inversion, phn chiu-reflection, quay-rotation, tnh trung bnh-averaging v v th trong ng lc hc phn t, hay t kim ch (restraints) trong tnh ton). NDO. B qua xen ph vi phn. i vi cc tnh ton c hc lng t bn kinh nghim, y l s n gin ho loi tr nhiu tch phn m t tng tc ca cc electron. Phng php CNDO b qua vic tnh ton tt c cc tch phn xen ph vi phn. Cc phng php NDO khc (INDO, MNDO/3, MNDO v AM1) b qua mt s tch phn. Open shell. Mt h phn t cha cc electron cha kt i. OPLS. Cc th c ti u ho i vi cc m phng cht lng. Mt phng php c hc phn t, hay force field, tnh ton ho hc. Pht trin cho cc protein v nucleic acid. N tng t AMBER nhng xem xt cc tng tc khng lin kt chnh xc hn. Trng lc ny ch cung cp cho miu t united atom (nguyn t lin kt). Orbital. Hm m t s phn b trong khng gian ca mt electron. Cc orbital nguyn t m t cc electron trong cc nguyn t. Orbital phn t, bt ngun l s t hp tuyn tnh ca cc orbital nguyn t (LCAO), m t cc electron trong phn t. Parameter set. i vi cc trng lc c hc phn t, kinh nghim hay l thuyt nhn c t cc hng s lc v cc gi tr cu trc p dng cho cc t hp lin kt xc nh ca cc nguyn t (mi m t bng mt atom type). Mi trng lc c th c nhiu hn mt tp hp tham s, nhng ta c th ch dng mt tp hp ring bit. Vi MM+, HyperChem cung cp cc tham s khi chng khng c sn trong tp tham s MM2. Vi cc tnh ton bn kinh nghim, cc file tham s (c phn m rng l .abp) cha cc gi tr kinh nghim cho cc tch phn trong tnh ton. PDB. Xem Brookhaven Protein Data Bank. Periodic box/ boundary conditions. Hp tun hon l mt hnh lp phng bao quanh h phn t. HyperChem thm cc phn t nc chun (TIP3P, cn bng 300K v 1 atmosphere) hp, cung cp mt hng s t trng dung mi. Trong cc tnh ton c hc phn t, hp c xem nh l c bao quanh bng 26 hp ging ht nhau (hnh nh), mi hp cha cc phn t ging ht nhau. Cc nguyn t trong mi hnh chu cng cc lc (biu l cc chuyn ng nh nhau) nh cc phn t 256
Hng dn s dng HyperChem 7.04 trong hp trung tm. Nu trong qu trnh tnh ton, cc phn t chuyn ng ra ngoi hp, mt ht ging ht vo t hp ln cn. Cc iu kin bin tun hon ny m phng mt h lin tc vi mt hng t trng ca cc phn t. Ta c th tch loi cc phn t nc, nhng gi nguyn hp tun hon v cc iu kin bin, m phng mng tinh th. Vi cc iu kin bin tun hon ca HyperChem, mt nguyn t ch tng tc vi hnh nh gn nht ca cc nguyn t khc v khng bao gi vi hnh nh ca chnh n trong cc tnh ton c hc phn t. PLANE. Xc nh trc, named selection ng nht cc nguyn t trong phn la chn, cng vi mt phng hnh thnh bi trc qun tnh th nht v th hai ca cc nguyn t c chn. Mt h phn t c th ch c mt la chn PLANE ring bit. Potential (energy) surface. Mt biu nhiu chiu ca th nng mt h phn t l hm ca tt c cc bin s (cc t do) trong h (v d, cc gc lin kt). Mt th nng ca phn t khng thng c N nguyn t (ln hn 2) c 3N 6 t do c lp (6 = ba duy tr s quay v ba cho s chuyn dch ca ton b h phn t). Cc mt th nng thng c v biu ch trong mt hoc hai chiu. Mt th 1D biu din nng lng lin kt theo di. Mt th 2D biu din biu ng vin nng lng l hm ca hai gc xon. Nhng nt quan trng trong mt th nng l cc cc tiu vi HyperChem c th nh v bng ti u hnh hc v cc tnh ton ng lc hc phn t - v cc im yn nga, biu din cu trc cc trng thi chuyn tip. Quantum mechanics. Thuyt nng lng c hp th hay pht x trong cc phn ri rc, gi l cc lng t. Kt qu l cc electron di chuyn trong mt s orbital gii hn quanh ht nhn nguyn t, v mi orbital c trng bng mt nng lng xc nh. S chuyn ng ca cc electron c tnh cht ca ht v sng. Phng trnh Schrodinger v cc o hm ca n m t hon ton hot ng ca cc electron v ht nhn, v do tc ng ca cc hp cht ho hc. Cc tnh ton bn kinh nghim trong HyperChem tha nhn cc ht nhn ng yn v gii gn ng phng trnh Schrodinger, cng vi d liu kinh nghim (cc tham s), d on tnh cht ca cc electron ca h phn t. Cc tnh ton ab initio ca HyperChem gii cc phng trnh Roothaan (xem computationa Chemistry ) m khng c s gn ng no thm ngoi vic dng mt tp hm hn ch xc nh. Chng bao gm nhiu hm gn ng vi li gii phng trnh Schrodinger hn cc phng php bn kinh nghim. 257
Rendering. Biu din kiu nhn mt h phn t di cc hnh thc. Phin bn HyperChem ny cung cp nm kiu: Sticks, Disks, Spheres (CDK kiu m hnh), Dots, v Sticks & Dots. RHF. Thuyt Hartree-Fock gii hn. Biu din hm sng cng vi cc electron c spin cp i (hng ln v hng xung) hn ch c ng cc orbital phn t cng khng gian. Mi orbital khng gian c th cng cha cc electron n (spin hng ln hay spin hng xung). RMS gradient. Gradient ( dc) nng lng ton phn c tnh bng gi tr cn bc hai bnh phng trung bnh. Gradient (G) l tc bin thin (o hm u tin) nng lng ton phn (E) xem xt n s chuyn di ca mi nguyn t theo cc hng x, y v z. T nguyn t 1 n n,
2 2 2 1 n E E E = x + y + z 3n i =1 i i i
GRMS
n v l kcal/mol Angstrom. HyperChem bo gi tr ny cho tnh ton geometry optimization v single point. Gradient RMS l khng c ngha cu trc mt local minimum hay im yn nga trong mt th nng, khng nht thit cu trc v trng thi nng lng thp nht (global minimum). Restraint. Restraint tnh ton mnh cng vi hon li cc lc cho cc nguyn t c chn. Kim ch (restraint) p dng cho khong cch nguyn t (mt hoc hai nguyn t), gc lin kt (ba nguyn t), v gc xon (bn nguyn t). Scale to fit. Mt mc trong Display menu (biu din) ly t l cc nguyn t v phn t nhn thy thch va vi workspace (mn lm vic). Nu c phn la chn, cc nguyn t c chn c chim y mn lm vic. Khng c phn la chn, HyperChem t ton b h phn t va vi mn lm vic. SCF. Trng t hp (Self-Consistent Field). y l mt phng php lp, dng trong tt c cc phng php tnh ton c hc lng t NDO, semi-empirical. N gii thch nng lng y ca electron trong cc li gii phng trnh Schrodinger. Phng php SCF hay Hartree-Fock n gin ho bi ton ny bng vic tha nhn s chuyn ng ca cc electron l c lp v mt electron tng tc vi mt trng trung bnh ca cc electron khc trong phn t. Trong HyperChem, tt c cc phng php c hc lng t bn kinh nghim, ngoi tr phng php Huckel m rng, u l cc phng php SCF. 258
Mt tnh ton SCF bt u bng vic c lng hm sng m t cc orbital electron v cc tng tc y electron. Da trn c on ny, HyperChem tnh ton mt hm sng mi v so snh kt qu vi kt qu c on. HyperChem lp li qu trnh ny cho n khi gi tr c on v kt qu hi t tr thnh t hp. Mi s lp li ci tin cc orbital cho n khi kt qu t n gii hn hi t (convergence). Script. Mt tp hp cc d liu, lu trong mt file vi phn m rng l .scr, chy HyperChem. Tng t nh mt chng trnh ln p dng. HyperChem vit tp hp hay c cc bin s, truyn cc lnh, v lm hot ng cc mc menu. Dng mt trnh thu thp ch to ra file script, sau dng menu Script trong HyperChem chy mt Script. Self-consistent field method. Xem SCF. Semi-empirical. Kiu tnh ton ho c hc lng t dng cc tham s xut pht t thc nghim n gin ho qu trnh tnh ton. Single point. Mt tnh ton xc nh nng lng ton phn (theo kcal/mol) v gradient ca mt h phn t hay ca cc nguyn t c chn. Bng phng php c hc lng t, tnh ton im n cng xc nh s phn b electron (in tch) trong h. Tnh ton ch biu din cu hnh phn t hin ti, mt im n trn mt th i vi h phn t. Snapshot. Ghi im n theo thi gian trong mt m phng molecular dynamic. Ta c th ch th HyperChem thc hin chp nh nhanh (snapshot) cc khong thi gian khng i trong qu trnh m phng. To v vn tc i vi mt h phn t c lu trong cc file SNP. Ta c th biu din li sau cc nh chp nhanh xem s bin thin cu hnh ca h, v biu cc gi tr d liu, v tnh trung bnh cc gi tr d liu. D liu chn bin s (nh l nng lng ton phn hay gc xon) c lu trong file CSV. Spin density. Kh nng tm thy nhiu electron c spin hng ln hn cc electron c spin hng xung mt im trong khng gian. i vi h v kn, mt spin (spin density) l bng khng mi im. HyperChem c th v biu mt spin ton phn cho mt h phn t sau khi thc hin tnh im n, tnh ton c hc lng t bn kinh nghim hay ab initio. Ta c th dng cc biu mt spin ht nhn d on kt qu ph cng hng spin electron (ESR). Xem Spin pairing v multiplicity.
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Hng dn s dng HyperChem 7.04 Spin multiplicity. Xem multiplicity. Spin pairing. Hai electron c ng cng orbital phi c cp i v c cc spin i nhau, mt spin hng ln v mt spin hng xung. Cc h v knh ch cha cc electron kt i. Cc h v h cha cc electron khng kt i. Status line. Dng y ca s HyperChem biu din thng tin v d liu. 3D surface. Xem isosurface. Tool. Con tr thc hin cc nhim v, nh l v hay dch chuyn, trong workspace ca HyperChem. Biu tng cng c (Tool icon) trong mt ct hay mt hng v tr bn trn hay bn tri ca s HyperChem. Nhp tri chut (Lclick) vo biu tng cng c chuyn tr chut thnh cng c. Trajectory. Lch s ca chuyn ng nguyn t theo thi gian. Thut ng ny thng c p dng cho m phng ng lc hc phn t (molecular dynamics). C th lu c trong file snapshot. Translation. Dch chuyn phn t m khng quay. Type rules. Quy tc i vi mi force field, tm trong file chem.rul (hay ng lng nh phn ca n, typerule.bin), n nh kiu nguyn t cho cc nguyn t hay nhm nguyn t ring. UHF. Phng php Hartree-Fock khng gii hn. Biu din hm sng cung cp cc orbital khng gian tch ri vi cc electron c spin hng ln () v spin hng xung (). Mi orbital v c th khng cha hoc cha mt electron. Ta c th dng cc tnh ton UHF tnh ton cc phn ng phn tch ca cc h v h. United atom. S n gin ho force field xem xt cc nhm nguyn t c th (cc nguyn t nng nh C v N v cc lin kt hydrogen ca chng) l mt nguyn t n. T hp nguyn t (united atom) i hi x l cc kiu nguyn t kt hp cc tnh cht ca cc nguyn t hp phn v cc kiu quy tc bng s ch nh cc kiu ny. Biu din t hp nguyn t l cc la chn vi AMBER v MM+, t ng quy cho nhiu nguyn t vi OPLS, v biu din ngm nh cho BIO+. Thut ng khc i vi t hp nguyn t l nguyn t m rng. Ln lt cho cc t hp l all atom, biu din mi nguyn t tch ring, vi atom type ring. Wave function. Xem orbital.
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Window. Vng lm vic trn mn hnh cha chng trnh phn mm (nh l HyperChem). Mt ca s c mt thanh tiu trn nh, cha tn ca chng trnh. Ch mt ca s c th hot ng mi thi im. Ca s hot ng nhn d liu u vo t chut v bn phm. Mt hp thoi l mt kiu ca s. Workspace. Vng ca s cha d liu; vi HyperChem, l mt h phn t. Z Clipping. Xem clipping. Zoom. Hm HyperChem phng to hay thu nh kch c h phn t trong mn lm vic. Zwitterion. Mt phn t c cc vng tnh in m v in dng hnh thc. y l trng thi bnh thng ca polypeptide pH trung tnh trong dung dch, vi cc nhm tn cng lNH3+ v -COO-. Polypeptide c xy dng t d liu HyperChem cha hon thnh, on cui khng tch in (-N-H v -C-O), tr phi cc nhm tn cng c s dng.
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Bi 1 Bt u s dng phn mm.........................................................................1 Thanh tiu (title bar) .....................................................................................1 Thanh cng c la chn (menu bar) ..................................................................1 Thanh biu tng cng c (tool bar)..................................................................1 Mn lm vic (workspace) .................................................................................1 Dng hin trng tnh ton (status line) ..............................................................2 Tr gip (help) ...................................................................................................2 Cch s dng chut:...........................................................................................2 S dng bn phm...............................................................................................2 Cc phm tt khc: .............................................................................................3 Cc cng c quan trng trn thanh cng c.......................................................3 Cc thao tc trn HyperChem ................................................................................4 M mt file v d: V d m file c ui HIN...................................................4 Cch s dng Display Settings...............................................................................6 S dng nhn (Labels) .......................................................................................6 Hnh thc biu din phn t:..............................................................................8 Thay i hnh thc biu din: ............................................................................8 t mu nn trang lm vic ...................................................................................9 t mu sc lin kt trong phn t ......................................................................10 Mu sc ca nguyn t.........................................................................................11 t ch Copy hnh nh....................................................................................12 Thot khi HyperChem....................................................................................15 Bi 2. V v hiu chnh 16 V nguyn t v lin kt ......................................................................................16 Chn nguyn t (Selecting Atoms) ......................................................................18 Chn nguyn t ....................................................................................................20 Chn nhm nguyn t..........................................................................................21 Chn thm mt nhm nguyn t..........................................................................21 Chn cc hp phn (Residures) ...........................................................................21 Chn c phn t (Molecules) ...............................................................................22 Loi b la chn...................................................................................................23 Mu sc biu din khi la chn ...........................................................................23 Chn phn b (Complement Selection) ...............................................................24 Chn theo chui (String) ......................................................................................26 Chn theo s.........................................................................................................26 Tn phn la chn (Name Selection) ...................................................................26 Xo nguyn t ......................................................................................................27 Xo nhiu nguyn t ........................................................................................27 Copy nguyn t vo b nh tm thi (Clipboard)................................................28 t in tch hnh thc cho nguyn t trong h...................................................28
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Hng dn s dng HyperChem 7.04 t in tch thc.................................................................................................29 t khi lng nguyn t ....................................................................................29 t di lin kt................................................................................................29 t xon lin kt ..................................................................................................30 t nhn ring......................................................................................................30 t kiu nguyn t (Atom Type) .........................................................................30 Thay i cc thuc tnh hnh hc.........................................................................30 Cng bc hnh hc .............................................................................................30 Cng bc di lin kt ....................................................................................32 Cng bc gc lin kt ........................................................................................32 Cng bc lin kt xon ......................................................................................33 Bi 3. To nhng phn t nh trong khng gian hai chiu (2D) v ba chiu (3D). 35 V phn t trn khng gian hai chiu ..................................................................35 Lu bc v vo trong mt File .............................................................................36 Thay i hnh thc lin kt ..................................................................................36 Biu din nguyn t di cc dng nhn khc nhau............................................38 Chnh sa cc nguyn t ......................................................................................39 Thm nhanh hydro cn thiu ...............................................................................40 Bi 4. Dch chuyn, quay v biu din h phn t theo t l mn lm vic. .....42 H to trong HyperChem ................................................................................42 H to ca ngi quan st...........................................................................43 H to ca phn t ......................................................................................43 Trc qun tnh ......................................................................................................44 t ch lm vic cho cc cng c...................................................................46 Nghch chuyn (Invert: chuyn (ho) thnh).......................................................47 Phn chiu (Reflect).............................................................................................48 Dch chuyn phn t theo trc xy ........................................................................49 Dch chuyn theo trc Z ......................................................................................51 S dng cng c phng to....................................................................................51 t phn t tr li tm v biu din theo t l.....................................................53 Quay phn t theo phng XY ............................................................................53 Quay phn t theo trc Z .....................................................................................54 Ct phn t thnh tng lt nh theo trc Z ..........................................................55 Cch lm nh sau 56 Dng cc dng nm (Wedge) biu din lin kt trong khng gian ................58 Bi 5. Xem thuc tnh cu trc phn t..............................................................60 Xem thuc tnh ca nguyn t .............................................................................60 o di lin kt.................................................................................................60 o gc lin kt .....................................................................................................61 o gc vn ...........................................................................................................62 263
Hng dn s dng HyperChem 7.04 o khong cch khng lin kt ...........................................................................63 Lin kt Hydro .....................................................................................................63 Recompute Hydrogen Bonds ...........................................................................64 Biu din momen lng cc.................................................................................64 Bi 6. Databases Menu 66 To chui Polypeptide..........................................................................................66 S dng hp thoi la chn cc Amino Axit .......................................................66 To dng v biu din chui Polypeptide ............................................................67 To chui..............................................................................................................68 To ion lng cc (Make Zwitterion)..................................................................70 B Ion cc ui (Remove Ionic Ends) .................................................................72 Thay th mt monome trong hp phn bng mt amino axit khc .....................72 Cc Axit Nucleic..................................................................................................74 Thm cc ion tri du (Add Counter Ions) ..........................................................78 Dng tinh th (Crystal Builder)............................................................................79 Cc lnh s dng trong xy dng tinh th ...........................................................80 To tinh th kim loi Natri...............................................................................80 To tinh th NaCl .............................................................................................82 Xy dng phn t ng (Sugar Builder) ............................................................83 Dng chui polymer ............................................................................................84 To polyme cho cc monome khc..................................................................87 Cc bc tun t to Polyme nh sau (v d cho butadien).............................87 Bi 7. La chn v biu din mt nhm cc nguyn t trn mn lm vic .......89 To vng xon c alpha. ......................................................................................89 t nhn cho u v ui chui...........................................................................90 Chn lin kt khung .............................................................................................91 T mu lin kt khung .........................................................................................93 Ch biu din lin kt khung trn mn lm vic ..................................................93 Biu din lin kt nhnh (lin kt bin) ...............................................................93 Biu din cc nhm nguyn t khng chn.........................................................94 Chn theo hnh ch nht ......................................................................................95 Chn theo hnh cu ..............................................................................................96 t tn phn la chn ..........................................................................................97 Chn lin kt vng ...............................................................................................98 Bi 8. Thao tc vi nhng phn t ln ...............................................................99 c ngun file d liu PDB . ...............................................................................99 Loi b cc phn t nc ...................................................................................100 Biu din cu trc phn t..................................................................................101 Biu din cu trc chnh.................................................................................101 Biu din vng xon Alpha............................................................................102 Biu din cu ni i sunfua............................................................................103
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Hng dn s dng HyperChem 7.04 Chn cu trc vng ............................................................................................105 Thay th hp phn v tr c bit.....................................................................107 Quay nhnh lin kt ...........................................................................................108 Bi 9. Cc tiu ho nng lng ca h............................................................ 111 Lu kt qu tnh ton vo Log file.....................................................................111 Chn trng lc..................................................................................................112 Dng cu trc dng gh ca Xiclohexan. ..........................................................112 o thuc tnh cu trc cu trc dng gh ca xiclohexan.................................114 Tnh ton im n ............................................................................................114 Ghi ch vo Log file ..........................................................................................115 Ti u ho cu trc ............................................................................................115 t bin ti u................................................................................................115 Chy tnh ton ................................................................................................118 o thuc tnh cu trc ca h ti u .............................................................118 Chuyn t xiclohexan dng gh sang dng thuyn............................................119 o khong cch gia cc Hydro trc..............................................................120 Ti u ho cu trc xiclohexan dng thuyn .....................................................121 o li khong cch gia cc Hydro trc............................................................121 To cu trc dng thuyn xon ..........................................................................122 Ti u ho cu trc xon dng thuyn...............................................................123 Ngng Log file...................................................................................................123 Bi 10. C hc phn t 124 Bi thc hnh 1: To ion lng tnh alanin c lp .......................................... 125 Phc tho ion lng tnh alanin..........................................................................125 Hiu chnh cu trc ............................................................................................126 t in tch nguyn t......................................................................................127 Chn trng lc..................................................................................................128 Cc thnh phn trng lc .................................................................................132 Dng v kho st cu trc 3D ............................................................................133 Thc hin tnh ton im n cho phn t.........................................................135 Ti u ho cu trc phn t c lp.....................................................................136 Lu cu trc .......................................................................................................137 Bi thc hnh 2: Solvat ho h phn t ........................................................... 137 t iu kin bin tun hon .............................................................................138 Xc nh kch c hp tun hon.....................................................................139 Biu din h solvat ha ......................................................................................139 iu chnh cc gii hn v la chn cht in mi .......................................140 Ti u ho phn t c solvat ho ...................................................................141 Bi thc hnh 3: S dng s chng cht cc phn t ...................................... 141 Xo cc phn t nc.........................................................................................141 Hp nht hai h ..................................................................................................142
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Hng dn s dng HyperChem 7.04 Chng cht cc phn t ......................................................................................143 Bi thc hnh 4: Ti u m phng.................................................................. 145 t biu din li ng lc hc ...........................................................................149 t tnh trung bnh theo ng lc hc phn t ..................................................151 Tin hnh ng lc hc......................................................................................153 Ti u ho li cu trc mi ................................................................................154 Bi thc hnh 5: M phng Langevin v Monte Carlo................................... 155 Phn 1: ng lc hc Langevin.........................................................................155 Phn 2: M phng Monte Carlo.........................................................................156 Xem li kt qu ..................................................................................................157 Bi cc phng php bn kinh nghim ........................................................... 157 Phng php p dng cho cc nguyn t:..........................................................160 Hp thoi la chn cho cc phng php bn kinh nghim khc .....................163 La chn tng tc cu hnh..............................................................................165 Bi 11 Tnh ton Obital phn t...................................................................... 167 To phn t nc................................................................................................167 t cu trc thng trc.......................................................................................168 Biu din in tch nguyn t ............................................................................169 Tnh hm sng....................................................................................................169 V biu th tnh in.....................................................................................171 Ch thch hp thoi v biu thuc tnh phn t ........................................174 Mc la chn Isosurface Grid trong hp thoi ..............................................175 Mc la chn Contour Grid ...........................................................................175 Mc Isosurface colors (mu sc th hin tnh m-dng trong biu ) ......176 V bn mt in tch ton phn ...............................................................177 V bn mt spin ton phn.......................................................................178 V biu th nng mt chiu (1D) v hai chiu (2D).....................................183 Th mt chiu ................................................................................................183 Cc la chn biu din biu th ................................................................184 Th hai chiu..................................................................................................185 Lu phn t ........................................................................................................186 Bi 12: Tng tc ca nc vi N-metylaxetamit. ......................................... 187 To ra phn t NMA ..........................................................................................187 Chuyn dng cis- sang dng trans-NMA...........................................................188 Ti u ho cu trc NMA. .................................................................................190 Tnh in tch nguyn t ....................................................................................191 Solvat ho nhm Cacbonyl.................................................................................192 Dch chuyn phn t nc .................................................................................192 Ti u mt tp hp con ca h...........................................................................193 Tnh ton li lin kt Hydro ...............................................................................194 Biu th c im ca h tng tc ....................................................................194
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Hng dn s dng HyperChem 7.04 Bi 13: Thuc tnh in t ca Protein............................................................ 196 Trc khi ta bt u ...........................................................................................196 c v biu din phn t ...................................................................................196 Chn vng ta quan tm ......................................................................................197 Chn bin c in lng t. ..........................................................................199 Tnh hm sng....................................................................................................199 Phn tnh ton thun tu l thuyt (Ab Initio Calculations) ........................... 202 Bi Thit lp la chn tnh ton Ab Initio v Density Functional .................. 202 Chn tp hm c bn..........................................................................................202 La chn cho phng php Ab initio v Density Functional ............................202 Hp thoi la chn thm cho Ab initio v Density Functional .........................204 La chn cao cp cho Ab initio v Density Functional .....................................205 La chn m rng hm c bn ..........................................................................206 Bi 14: S Proton ho ca nc ...................................................................... 208 t v phn t ...............................................................................................208 Chn tp hp hm c bn tnh.......................................................................209 Cc tiu ho cu trc..........................................................................................210 Nng lng Proton ho ......................................................................................210 Bi 15: Dao ng v trng thi chuyn tip ca Amoni. ................................ 212 To Amoni 212 Chn tp hp hm c bn...................................................................................212 Phn tch dao ng ca Amoni dng hnh chp, ph dao ng ........................213 Ti u amoni phng ...........................................................................................214 Phn tch dao ng ca amoni phng ................................................................215 Tm trng thi chuyn tip theo vect c trng ...............................................217 Tm trng thi chuyn tip bng s chuyn ho ng thi................................218 Bi 16: Trng thi in t kch thch thp nht ca Etilen............................. 223 Ti u trng thi c bn ca Etilen. ...................................................................223 Obital trng thi c bn ca Etilen ....................................................................224 CI v ph in t ca Etilen...............................................................................225 Hnh hc v nng lng ca Etilen bi ba .........................................................227 Bi 17 Kh nng phn cc DFT ca H2 .......................................................... 229 To H2 ................................................................................................................229 Chn th tng tc trao i................................................................................230 Tnh ton DFT im n trong trng in.......................................................232 Tnh s cng phn cc........................................................................................232 Bi 18 Ch thch 234 To mt h phn t.............................................................................................234 Ch thch kiu ch nht .................................................................................234 Ch thch dng ng thng ..............................................................................237 Ch thch kiu vn bn.......................................................................................237
267
Hng dn s dng HyperChem 7.04 Lu ch thch .....................................................................................................241 Bi 19 Cc File tham s TNDO ...................................................................... 242 Tham s ngm nh CNDO/INDO. ...................................................................242 Kim tra tham s TNDO....................................................................................243 Copy tham s TNDO cho tp hp mi...............................................................244 Hiu chnh tham s TNDO ................................................................................244 Ch gii 246
268

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Hng dn s dng HyperChem 7.

Thanh tiu (title bar)

Thanh cng c la chn (menu bar)

Thanh biu tng cng c (tool bar)

Hng dn s dng HyperChem 7.04

Dng hin trng tnh ton (status line)

Cch s dng chut:

Hng dn s dng HyperChem 7.04

Cc cng c quan trng trn thanh cng c

Hng dn s dng HyperChem 7.04

Cc thao tc trn HyperChem M mt file v d: V d m file c ui HIN.

3. Nhp tri chut vo Open. Mn hnh s hin ra nh sau:

Hng dn s dng HyperChem 7.04

4. Nu mn hnh list vn cn cc cht khc, c th ko thanh trt tm kim.

Trn mn hnh s hin ra phn t cha trong file

Hng dn s dng HyperChem 7.04

Cch s dng Display Settings

S dng nhn (Labels)

Hnh thc biu din phn t:

Thay i hnh thc biu din:

Hng dn s dng HyperChem 7.04

t mu sc lin kt trong phn t

Hng dn s dng HyperChem 7.04

Hng dn s dng HyperChem 7.04

Thot khi HyperChem

Hng dn s dng HyperChem 7.04

C hai cch thc hin iu ny

Hng dn s dng HyperChem 7.04

4. v phn t dng vng ta nhn v r chut ni cc nguyn t vi nhau.

Hng dn s dng HyperChem 7.04

Chn nguyn t (Selecting Atoms)

t cc hnh thc chn c mt s bc sau:

Hng dn s dng HyperChem 7.04

Hng dn s dng HyperChem 7.04

Hng dn s dng HyperChem 7.04

Chn nhm nguyn t

Chn thm mt nhm nguyn t

Chn cc hp phn (Residures)

Hng dn s dng HyperChem 7.04

Number of residures selected Residure name and number

S th t to hp phn c th s l 0 cho tt c cc hp phn. y l tn v th t ni tip ca hp phn ta chn.

Chn c phn t (Molecules)

Hng dn s dng HyperChem 7.04

Mu sc biu din khi la chn

Ch : Khi ta chn cc mu khc th khi la chn phn la chn s c 23

Hng dn s dng HyperChem 7.04 kiu mu tng ng.

Chn phn b (Complement Selection)

Atom Type Residue Name Basis Set Chirality Named Selection

Chn theo chui (String)

Tn phn la chn (Name Selection)

PLANE REACTANT PRODUCT PLOT1

PLOT2 GHOST ATOMS NMR ATOMS QUANTUM ATOMS Other

Hng dn s dng HyperChem 7.04

Copy nguyn t vo b nh tm thi (Clipboard)

t in tch hnh thc cho nguyn t trong h

t khi lng nguyn t

Nhp OK thc hin thay i di lin kt chn.

Hng dn s dng HyperChem 7.04

t kiu nguyn t (Atom Type)

Thay i cc thuc tnh hnh hc Cng bc hnh hc

Hng dn s dng HyperChem 7.04

Hng dn s dng HyperChem 7.04 Hp thoi la chn xut hin:

Cng bc lin kt xon