" "

-
HyperChem
-

2013

: ..-.., ..
- HyperChem: .-. / "
"; . .. . , 2013. 175 .
HyperChem.

HyperChem. , -,
, . HyperChem. .
, 011200.62
. , ,
.

4
"15" 2012 .

3
"12" 2012 .

_______________________
. .

_________________________
. .

..

I. -
HYPERCHEM
1.


.
- ,
,
,
, , , [1-14].
, - .

-
. . -- - () - , , .
() .

. -
( ab initio
( . ) ), , ( )
.

, . [15]. , Gaussian (www.gaussian.com), Gamess
(www.msg.ameslab.gov/GAMESS), ChemCraft, 3

 Gaussian Gamess
(www.chemcraftprog.com), MOPAC (openmopac.net), Molden . HyperChem,
. 10-, ,
Hypercube (www.hyper.com).
( ) : CDK.pdf, GetStart.pdf, Referenc.pdf
( 5.0), hyperchem_getting_started.pdf (
7.5), hyper8.pdf ( 8.0).
HyperChem , -
(. 1.1). ,
,
. ,
HyperChem +, Amber,
OPLS BIO+ ( CHARMM).
: , CNDO, INDO, MINDO/3,
MNDO, AM1, PM3, ZINDO/1, ZINDO/S . : ab initio (-)
.
- ,
, HyperChem 6.0.

HyperChem 8.07.
HyperChem , ,
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. 1.1. HyperChem
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HyperChem 8.0 , ,
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HyperChem. , ab initio 3-21G

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HyperChem (. 1.1)
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, Windows.
2. Hyperhem
2.1. HyperChem
HyperChem . 1.2.
, Windows, , , ,
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, . ,
untitled. , ,
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 HyperChem : File (), Edit (),

Build ( ), Select (), Display (),
Databases ( ), Setup (), Compute (), Annotations (), Script (), Cancel (), Help ().

. 1.2. HyperChem

, , , , ,
.

,

Windows.

. . , ,

 , Preferences () File ().

,
, , , , , ..
,
.
( ),
. , ,
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. 1.1 ,
. 1.2 +.
2.2.
HyperChem
. :
1. L- - .
2. R- - . , R L-.
3. -
.
4. L- R- -
, , (),
.
5. LR- - , .
6. RL- - , LR-, .
. :
8

1.
(Draw - ).
2. .
: .
(Select - 3.
) .
4. . :.
.
Rotate out of plane (XY-, 3- )
Rotate in plane (Z-, )
Translate ( )
Z-translate ( Z-, )
Maghify/Shrink (, / )
Z-clipping planes ( z )
, .
2.3.
HyperChem , :
1. (2D) HyperChem (3D) (.
. 3).
2. HyperChem () .
3. , HyperChem
( HIN) -

 Brookhaven Protein Data Bank (

ENT), .
HIN :
1. (L-) File.
2. Open ().
3. ,
L-
.

. 1.3. HIN
Samples

, ,
Samples ( ), .
60, . 1.4, Samples > Aromatic c60.hin.
.
2.4.
HyperChem
. ,
Display ().

10

. 1.4. - 60

2.4.1.
, ,
, :
1. L- Display > Labels
() (. 1.5).
2. ,
None ().
3. L- OK .

2.5.

( ,
, , ..) . , -

11

 , .
Display > Colors Atom
( ) .
2.4.2.
:
1. Renderings () Display.
2. Rendering method , , Balls () (. 1.6).
3. Balls
(. 1.6).

. 1.6. Balls ()

, (. 1.7).
.
[F2] , (. 1.8). - Last
Rendering ( ).
Rendering method Balls & Cylinders ( ) , . 1.9. ,
, .

12

. 1.7. : Sticks ()
Balls ()

. 1.8. : Sticks

. 1.9. Balls & Cylinders

.
2.5. HyperChem
Exit File.
.
No, , Yes .
Hin ,
, 13

 . , .
3.
HyperChem
.
.
3.1. HyperChem

, .
File () New ().
(. 1.10), :
? , . HyperChem .

. 1.10.

3.2.
,
HIN. , 2-D .
1. Build Default element (
) ().
Draw
Element Table
(. 1.11).
2.
.
14

. 1.11. (Element Table)

3. Properties..., , (. 1.12).

. 1.12. N ()

4. Allow Arbitrary Valence (

). Explicit hydrogens (
) . .
5. Element Table.
6. . . ,
Draw

15

7. , .

, , , . 1.13.
8. Default Element
..
3.3.
1. ""
, (L-),
. , ,
, .. . ,
(. 1.14).

. 1.13 . ( )

2. .
, , (L-)
, ,
. .
3. ,
,

16

 ,
Rotate out of plane.
4. ( (.
1.14), , ), , ( ) .
(single,
double, triple, aromatic, . 1.1).

. 1.14.

5. ,
R-
. , .
1.1.

_____________________

===================

()

--------------------------------

(,
), , .

17

3.4. ()
() .

.
Select ()
( ).
1. ()
Select. Atoms (),
Residues (), (Moleculs), .
2. , (, Atoms), L- . (. 1.18). : Preferences File , .

. 1.18.

. 1.19.
7 8

3. . Select
Atoms
Multiple Selections.
(. 1.19).

18


(
Edit).
Select Sphere Select .

,
(
Fail > Preferences > Tool ( ) whole molecular
translation).


.
. , , 
.
: ,
, ..
, , .
3.5.

.
1. Select Select Sphere.
2. ,
,
(LR -) . , .
LR-,
( . 1.20).
3. , (. 1.21).
2. .
Select ( ) Multiple Selections.

19

 .
.

. 1.20.

. 1.21.

, 
.
, .
3.6.
:
1.
(Draw) .
2. R. .
:
LR-
,
Edit () Clear ().
, : " ?". "".

1.
2.

3.7.
Select Atoms.
.

20

 Edit () Copy ().

.
4. Past ().
3.

4.
4.1. 2-D
,
.
HyperChem ,

.
1--3--2 .
Build > Default element
2. Allow Arbitrary Valence ( ). Explicit hydrogens ( ) ,
.
3. () .
.
4. . 1.22 ( ).
1.

. 1.22. 2D 1--3--2

, , L- . -

21

 . L .

, , . ,
.
4.2.
:
1. File > Save ().
2. (. 1.23).
, . File name
( ) (, ).
, _ab_initio _mndo).
3. , Save as type ( ) - HIN.
4. L- OK.
.

. 1.23.

22

 .
HyperChem , : hin
protein data bank ent. Hin ,
, Hyperhem, , ent .
,
(
Save File ).
, .
4.3. .
3-D
, , . :
1. L-
(Oxygen).
2. .
C ( ) O (
). .
3. Build Add
Hydrogens ( ).
4.
, Build Add H & Model Build (
). 2D () 3D (. 1.24) .

, . .
5. ,
23

 ,

(Rotate out-of plane), (Translate).

. 1.24. 1-hydroxy-3-phenyl-2-propene

, Display
Show Hydrogens ( ) Add
Hydrogens.
7. .
6.

4.4.
:
1. Display Labels ().

1.25.

. 1.26.
()

24

 (. 1.25) Atoms ()
None - .
Symbol ( . 1.24),
Name, Number ( . 1.26) OK.
3. .
, .
.
2.

5. ,
HIN- , , , .
5.1. XY-
XY- (Translate)
.
, . , XY- L , ,
Translate.
XY-:
1. L- XY- (Translate).
2. .

.
3. L- , . 1.27.
Translate:
1. XY-, , Translate Edit, Translate (. 1.28).
2. dx 5.0.
3. L- OK.
5.0 .

25

. 1.27. ,

. 1.28. XY-

5.2. Z-

,
(.. Z) Z-
(Z-translate).
Z-:
1. Display, Rendering, ,
Perspective (. 1.29) Vector and Line
Options. Perspective
. .
2. L- Z-.
3. . Z-.

26

4. L- .
.
5. , , Z .

. 1.29. Perspective

Translate:
1. Translate (. 1.28)
( Z-,
Translate Edit).
2. dx dy 0.
3. dz, -5, OK.
HyperChem 5 .
: (Spacebar),
, . Scale to Fit
Display.
5.3.
,
Maghi
fy/Shrink. , , .

27

 :
1. L-
Maghify/Shrink.
2. . .
3. L- .
.
. 1.30.
, , Zoom (. 1.31):
Zoom Edit;
.

. 1.30.

. 1.31.

5.4. XY-
x
y , XY-
(Rotate out of plane).

28

 XY-:
1. L- XY .
2. .
3. L-.
y .
4. L-.
x .
5. L- , x y (. 1.32).
5.5. Z-
(Rotate in plane),
Z-
z , ..
.
Z-:
1. L- Z .
2. .
3. L-
.
(. 1.33).
4. L- . .
Rotate:
1. Rotate (. 1.34)
( Z- XY, Translate Edit).
2. (X, Y Z).
3. Angle () , , 90 OK.

29

. 1.32. XY-

. 1.33. Z-

. 1.34. Rotate

1.
Show Inertial Axes Display, 3- .
2. , , Molecules Select,
, R- L .
6.
, ,
.

30

6.1.
. , Select, Atoms,
Multiple Selections. : ,
,
, - . x, y z- (. 1.36).
Build
(Set Atom Type), (Set Charge), (Set
Mass) (Constrain Geometry) (. 1.37,
1.38), ,
.

. 1.36.

. 1.37.

. 1.38.

31

6.2.
, N ,
(N-1), (N-2) (N-3). 3N-6 .
HyperChem ,
(Model Builder).
, HyperChem
.

(Select) .
, Select, Atoms Multiple Selections ( ).
, () (. 1.39).

. 1.39.

, .
Build Constrain
bond length,
, , .

32

, , Select Multiple Selections. . L-

( ) , .
6.3.
, , .
.

,
.
,
, .
.
(. 1.40).

. 1.40.

(Numbers), .. .

33

 . L- 4
6 (.. ,
),
(. 1.41).
HyperChem ,
, (Model
Builder). ,
109 , - 120 , 180 .
Build Constrain Bond Angle, .

. 1.41.

6.4.

, ,
.
, ( ) , ,
.
,
,
(. 1.42). L .

34

 Constrain Bond Torsion

Build ,
.

. 1.42. CH-

6.5.
, HyperChem
(. 1.43). ,
- 3,2
- 120 .

. 1.43.

35

 Display Show Hydrogen Bonds ( ).

2. Recompute H Bonds ( ).
HyperChem .
, , , .
1.

7. HyperChem
HyperChem
Compute
.
Setup () - - ,
(. 1.2). HyperChem :
(MM+, AMBER, BIO+ OPLS), - (12 ,
, CNDO, INDO, MINDO3, MNDO,
AM1, PM3, ZINDO/S TNDO), (ab initio) (DFT)
.
1.2. Setup
Molecular mechanics
Semiempirical
Ab Initio Ab Initio -

Density
Functional
. Periodic
, box
.
-

36

 1.2.
Restraints . (
) 1, 2, 3 4 . ,
Set velocity . , .

Set Finite .

Field
. Network

.
Edit
parameters
. Select
parameter
set
.
Compile
parameter , HyperChem
file
Reaction .
, ..
map
.
,

, Setup, Compute,
.
7.1.
7.1.1.
Setup Molecular Mechanics (
) (. 1.43)
, . , .

, 37

 .
, ,
( -, ).

, , . , ,
, .. , .

,
.
.
,
, ..
: ,
.
,
, ,
.
Force fild ( )
. (MM+, AMBER, BIO+, OPLS),
(. 1.43).
MM+ . , ,
, , , , , . -

38

 , Options
(Force field).

. 1.43.

AMBER .
, ,
.
.
BIO+
AMBER.
OPLS . AMBER, .
7.1.2. +
+ Options (. 1.44):
Electrostatics ()
: .
Bond dipoles ( ) .
MM+.
Atomic charges ( )
.
()
Build, Set Charge, ab initio ,

39

. 1.44. MM+

Cutoffs () , .. . Periodic
Box .
None ()
.
.
Switched .
Shifted ,
0 . .
9 Outer radius Switched Shifted ,
0. , 4 , . .
9 Inner radius
Switched cutoffs.
.

40

 4 , , 0.
, Cutoffs
, .
Components
.
, , ..
7.1.3.
Force Field Options (. 1.45) AMBER, BIO+ OPLS.

. 1.45. AMBER

Dielectric (epsilon) ( )
Constant () Distance dependent ( )
, , .
Constant () .
,
, .
Distance dependent ( )
.
41

 . OPLS.
, , .
Constant
(epsilon), , (Scale factor). 1,
.
>=1.
Distance dependent
- 14 Scale factor.
Electrostatic () , . 0 1. AMBER OPLS 0.5,
BIO+ 1.0, 0.5 0.4
.
Van-der-Waals (--) - ,
, 0 1.
AMBER 0.5, OPLS 0.125,
BIO+ 1.0.
Cutoffs () , .
, Periodic Box, +.
7.2. (semi-empirical)

HyperChem , -
(semi-empirical) (. 1.46),
- (ab-initio) (. ).

42


Compute. ,
, . . , :
;
;

;
, ().
,
.

. 1.46.

. , HyperChem
, , .

43

 , ,
, INDO (Intermediate Neglecting of
Differential Overlap) , .
HyperChem , . ,
,
. ,
, Select,
Setup Compute. , ,
. , , ,
Select.
7.2.1.
HyperChem .
Extended Huckel ( , )

. (SCF, self-consistent field).

CNDO (Complete Neglect of Differential Overlap,
) .
, .
INDO (Intermediate Neglect of Differential Overlap, )
44

 CNDO
.
MINDO3 (Modified INDO - INDO 3)
INDO. .
.
SCF, .
MNDO (Modified Neglect of Differential Overlap, )
MINDO3, .
.

, 1- 2- ( ).
MNDO/d
MNDO d-.
AM1 (Austin model) MNDO
, , .
.
, MNDO, , 1 2 .
PM3 ( , 3)
AM1 .
PM3
. , PM3 , AM1. PM3
, , .

45

 ZINDO/1 INDO, , .
ZINDO/S INDO,
.
.
TNDO (Typed Neglect of Differential Overlap, . )
, . , ,
.

. HyperChem
. , , . ,
.
. .
7.2.2.
()

(. 1.47).
:
Total charge ( )

.
.
46

Spin multiplicity ( )
2S+1, S .
, 1/2. ( ) , 1(S=0). , (2S+1=2). 3 (S=1, ) ..
, 1
6. , , HyperChem . , , 1, - = 2*1/2 + 1 = 2.
Huckel constant ( ) -
. 1,75.
, .

. 1.47.

Unweightet constant .
,
.

47

 Weight diffuseness ( ) , ,
,
.
d-orbitals on (d- ) d- Si, P, S, Cl.
Scale factor ( )

(- -) .

, ( ),
(. 1.48).
Total charge Spin multiplicity ( ) .

. 1.48.

State (). .
Lowest () ,

.

48

 Next Lowest ( )
,
.
Convergence Limit ( , .. )
SCF () ,
, , .
0,01 /, 1 0,001. 1 /
, 0,001 / , . .
Iteration limit ( )
. 50, , , 100 200,
, .
Accelerate convergence ( )
SCF .
Spin pairing ( ) :
- (UHF Unrestricted
Hartree-Fock)
() ().
. ,
. ,
. , - ,
. , .
- (RHF Restricted
Hartree-Fock) ,
, -

49

 , . . ,
.
Overlap Weighting Factors ( )
ZINDO , .
Sigma-Sigma . 1.0 ZINDO/1 1.67 ZINDO/S.
Pi-Pi .
1.0 ZINDO/1. ZINDO/S
0.640 0.585
.
7.3. (b-initio) -
b initio Setup . -
, - - , , , .
Ab initio ,
- .
- .

, , ,
. , Model
Builder Build ,
.
ab initio (,
) -

50

 (. ).
. ab initio ,
. , , , .
,
. , ,
.
:
,
,
.
. , , , -.
7.3.1.
( ) ( ,
LCAO) .

, . , b initio
. HyperChem ( *.BAS),
(. 1.49).
.

51


( ), .
, - .

. 1.49. b initio

HyperChem. :
STO-1G and STO-1G* ( H He);
STO-2G and STO-2G* (H Xe);
STO-3G and STO-3G* (H Xe);
STO-4G and STO-4G* (H Xe);
STO-5G and STO-5G* (H Xe);
STO-6G and STO-6G* (H Xe);
3-21G, 3-21G*, and 3-21G** (H Ar);
4-21G, 4-21G*, and 4-21G** (H Ne);
6-21G, 6-21G*, and 6-21G** (H Ar);
4-31G, 4-31G*, and 4-31G** (H Ne);
5-31G, 5-31G*, and 5-31G** (H F);
6-31G, 6-31G*, and 6-31G** (H Ar);
6-311G, 6-311G*, and 6-311G** (H Ar);
D95, D95* and D95** (H Cl).
STO-3G
( ) (1s),
52

 Li Ne (1s, 2s, 2px, 2py 2z) Na Ar (1s, 2s, 2x, 2, 2pz,

3s, , y z).
7.3.2.
: HF.
1.
(STO-N):
1. SZ single-: STO-1
HF = H (1s) + F (1s + 2s + 2p*3) = 6
2. DZ double-: STO-2
HF = H (1s)*2 + F (1s + 2s + 2p*3)*2 = 12
3. TZ triple-: STO-3
HF = H (1s)*3 + F (1s + 2s + 2p*3)*3 = 18
2. (STONG):
STO-NG, N = 2, 3, 4, 5, 6:
HF = H (1s)*N + F (1s + 2s + 2p*3)*N=6*N. N=3, 18
.
7.3.3. ab initio
HyperChem . (. 1.49) Apply Basis
Set ( ) ,
, ,
. ,
6-31G ( d-),
6-31G* ( d-).
Basis Set
( Apply Basis Set).
No Basis Set ,
. , .

53

 Minimal (STO-3G) STO-3G . (3-21G, 6-31G)

, .
Other Assign Other Basis
Set, , (
) (. 1.51).
Assign Other Basis Set ( ).

(. 1.50),
( , ).

OK , Ab Initio Method
. , ,
.BAS.

,
[basisset] CHEM.INI
Windows.
Extra Basis Functions ( ).
,
(. 1.50).
Options ( )
, ab initio (. . 1.51).
Advanced options ( )
, ,
.
OK . , Apply Basis Set
. Cancel
.
, HyperChem .

54

. 1.50. b initio

7.3.4. ab initio
(. 1.51) .
, .
ab initio.
Gradient (
). RMS-
.
(single point only). ,

,
, . HyperGauss, , , - .
MP2 Correlation included
-. , .
,
(
).

55

 .
- . , , : E = E - E < 0. ,
.

. 1.51. b initio

Total charge Spin multiplicity ( )

.
SCF Controls ( ).

SCF () .
Convergence Limit ( ) ,
SCF ,
. ab initio , , 0,00001 /,
1 0,00000001 /. , 10-10,
, -
. .
Iteration Limit ( ) SCF-. -

56

 , .
,
, . ,
(, 200) .
Accelerate Convergence ( ). SCF .
HyperChem , (Direct Inversion of
Iterative Subspase, DIIS),
.
Spin pairing ( ). ,
.
- (Unrestricted Hartree-Fock method, UHF)
- (Restricted Hartree-Fock method, RHF).
.
, HyperChem - (RHF) ab initio .
8.
HyperChem ,
, ,
. Compute ( 1.3) .
(Single
Point), c
(Single Point CI), (Geometry Optimization),
(Molecular Dynamics),
(Langevin Dynamics), -,
- (Vibration, Rotation Analysis),
(Entropy and Free Energy). ,

57

 +,
ab initio.
. 1.3. Compute
.
Single Point


Single Point CI
(CI)

Geometry
,
Optimization

Vibration, Rota- .
MP2. tion Analysis
Vibrational Spectrum
Entropy and Free . Energy
. Properties
() Molecular

Dynamics
. ,
, .
Langevin Dynam- ,

ics
,
Monte Carlo


Transition State
, ,


Rate Constant
- 1H, 13C, 15N, 15O,
Invoke NMR
19F, 31P , H Ar
Properties
, , , , .
Plot
Molecular
: Graphs
, , .

Orbitals
( ),
,

58

. 1.3.

Vibrational
Spectrum
()
Electronic
.
Spectrum
Single Point CI
Potential

. , Conformational

Search

QSAR Properties :
, , ,
,

.
8.1. (Geometry Optimization)

. .
Compute > Geometry optimization
(. 1.52).

. 1.52.

59

 .
, ,
Polak-Ribiere (-).
(in
vacuo, ) (periodic boundary condition, ). In vacuo
, .
Termination Condition ( )
RMS . ,
,
. /.
(, 0,001
0,1).
100 1000. .
. Hyperchem , ,
Cancel.
8.2. (Single Point)
. . ..
, . , . , , , . Single Point
:

.
, .

60

 ( , 1000 ).
.
8.3. c
(Single Point CI)
Single Point CI (Configuration Interaction - )
(. 1.53).
,
.
,
.
8.3.1.
. (SCF)
,
, ,
. ,
. , ,
. ,
SCF , , , .
(CI) , , SCF-.
SCF , . , () . ,
61

 .
, (single point).
.

Configuration Interaction ( ) (. 1.53). .
:

. 1.53.

None ( )
.
Singly Exited ( ) .
Microstate () , - .
Orbital Criterion ( ) , , .
Occupied () ,
(
HOMO), .

62

 Unoccupied ()
() ,
(), .
Energy Criterion ( )
( ),

.
(Singly Exited).
Maximum Exitation ( ) ( ) , CI . ,
. , CI .
8.3.2.

:
;
;
,
;
;
-
.

.
. .
,
. , , . , CI
,
CI , , .

63

II.

HyperChem

. , , ,
, .
,
.
9.

:





HyperChem,
. ,
, C6H12. ,
, .

. , , . , , ,
. . ,
,

64

.
, ,
- .
.
- , - .
: , , . .
,
.

, log-, . File >
Start Log.
- Mechanics Print
Level = 9 - Quantum print level
= 9. log ,
, Append.
9.1.
,
,
,
HyperChem. , , . , AMBER.
:
1. Molecular Mechanics Setup.
2. AMBER.
3. L- Options, Force
Field Options.
4. Distance Dependent Dielectric.
, , , ,
65

 ~ 1/r2, .. , ~ 1/r
.
5. Scale factor 1.
6. Electrostatic van der Waals 1-4
0.5 (. 2.1).
, .
7. Cutoffs None.
,
, . , ,
.
8. OK .

. 2.1. Amber

AMBER ,
. Select Parameter Set Setup
, amber2.
9.2.

1. Default Element , Draw.

2. Select Atoms.
3. Display > Labels .
4. , Build Explicit Hydrogens.
5. 2-D , . 2.2.

66

6. Add H & Model Build Build.

7. Show Hydrogens Display.
8. , . 2.2.
,
, .

.

. 2.2. 2D

1. Select.
2. Atoms Multiple Selection.
3. -, c
.
-:
:
:

1,54
109,47 .
60

4. R-
.
(single point)
,
. Single
Point Compute.

67

 / (RMS)
kcal/( ) :

1,64 kcal/mol
3,02 kcal/(A mol)

, .
, - ,
AMBER.
, . -, Compute > Properties (. 2.3).

. 2.3.

-, log- (. 2.4).
.

. 2.4. log- amber

9.3.
, 68

. ,
.

1. Geometry Optimization Compute.
2. RMS - 0.1.
L- OK . . :

1.33 kcal/mol
0.07 kcal/(A mol)

, , .

(, ) .
:
:
:

1.54
109.47 .
60

1.53
110.2
58.0

,

2 .
9.4.


.
:
1. Multiple Selections Select.
2. Select.
3. Select, .

69

4. 1-2 5-4,
, . 2.5.

. 2.5.

5. Name Selection Select.

6. PLANE (of Selection), OK.

1. Show Hydrogens Zoom, , .
2. LR- ,
( .2.6).
3. Reflect Edit.

. 2.6.

PLANE,
(. 2.7).
4.
.

70

. 2.7.

12 17
(1,84 ).
, .
.
9.5.

Compute > Geometry Optimization. . , ,
:

1.33 kcal/mol
0.07 kcal/(A mol)

8.31 kcal/mol
0.08 kcal/(A mol)

2,28 .
.
9.6. -
- .
,
.

71

1. Show Hydrogens.
2. , : 6-1, 1-2, 2-3 (. 2.8).

. 2.8.

3. Constrain Bond Torsion Build, Other,

30.
4. R-
.

Select. HyperChem
, .
9.7. -
-,
.
, (. 2.9) :

-
7.22 kcal/mol
0.07 kcal/(A mol)

. 2.9. -

9.8.
/
/( ), :

72

1.33 kcal/mol
0.07 kcal/(A mol)

8.31 kcal/mol
0.08 kcal/(A mol)

-
7.22 kcal/mol
0.07 kcal/(A mol)

-
, .
.



:


-, kcal/mol
6,98
--, kcal/mol 5,89

6,9
5,3

log- .
:
1. , MM+, Amber.
2.
MNDO.
10.
HyperChem ,
HyperChem.
AMBER
.


,
( )

73

 .
() ,
. , ,

() () .
(N, O, F, Cl, I, Br)
. . (
, ) .
, , .
, . ,
- -
, ..
.
.
,
, . . - .
10.1.
HyperChem,
,
.
(. 2.10).
:
1. Show Hydrogens Display.
74

2. Default Element Allow arbitrary valence

Explicit hydrogens ( ).
3. .
, .
.
.
.
- .

. 2.10. . 2.11. 2D

:
1. Default Element .
2. L- ,
, :
3. .
4. L- ,
, .
5. , .
. 2.11.


, .
HyperChem,
:
- ,
() .

75

 , + 1.0 -0.5 .
1. , Select Atoms Multiple
Selections.
3. .
4. Set Charge Build, 1.0.
5. R- , .
6. , -0.5
.
7. R- .

, (Model Builder), Model Builder
. , , Calculate Types
Build.
1. Molecular Mechanics Setup.
2. AMBER Options. Force
Field Options.
3. AMBER
.2.1 .
4. OK Force Field Options.

(. 2.12), OK.

. 2.12.

3D
1. Select
Model Build Build. HyperChem (. 2.13).

76

2. ,
.
3. .hin.

. 2.13.

. 2.14. NCCO

1. Select O-C-O .
120 .
2. L-
(. 2.14). N-C-C-O 60 120 , ,
.
3. R- ,
.
Single Point
,
.
Single Point Compute. .

, .
- C-N C-O .

77

 Geometry Optimization
Compute.
.

74.59 kcal/mol
95.70 kcal/(A mol)

-18.10 kcal/mol
0.10 kcal/(A mol)

O-C-O (123.9 )
N-C-C-O (-53 96.4 )
.
O-C-O
N-C-C-O

120 .
60 120

123.9
53.0 96.4

N-C-C-O - .
, , Name Selection
Select. Other ncco, OK.
N-C-C-O
.

, .
-.hin.
10.2.


HyperChem , .. , ,
,
. , , ,
. , , .
1. , Labels
Display.
2. Periodic Box Setup,
Periodic Box Options (. 2.15).
-

78

. 2.15.

=1000 /3. HyperChem ,

, ( ,
2,7 ). ,
. , - 45 .
Periodic Box
, . ,
Smallest box enclosing solute Periodic Box
Options.
, , , , - .
, , 18,7 . , 18,7 ,
.

79

 12 10 12 .
HyperChem
40 . ,
. , ,
, . , , ,
.

1. Rendering Display.
2. Perspective Vector and Line Options, OK.
3. Select Molecules.
4. , . 2.16.
.

,
(Cutoffs) Force Field Options.
. :
1. Molecular Mechanics Setup.
2. Amber Options,
Force Field Options (. 2.17).
3. Cutoffs .
Periodic box, HyperChem Inner Outer,

. Outer
, Inner 4 , , .
4. Dielectric, ,
.
Constant Distance dependent.
80

. 2.16. ,

. 2.17. Amber

5. OK .


( ), , , .
( )
.
( ), .
1. Geometry Optimization Compute.
2. OK,
, . .
3. :

-955.83 kcal/mol
0.09 kcal/(A mol)

:
, .

81


. , ,
, .

-.hin.
10.3. ()
- .
.
HyperChem, , .

,
.
1. Select > Molecules.
2. L- , .
3. Select Complement Selection.
, .. .
4. Clear Edit.
5. , , , Yes.
6. Show Periodic Box.
.
-.hin.
. , ,
, .
:
1. Merge File, -.hin.

.
82

 . Merge ,
. .
2. , Translate,
, .
3. , ( Preferences), .
4. Complement Selection Select.
5.
, .
6. R- , .
, , ,
, HyperChem .
. ,
.

1. Select toms
Multiple Selections.
2. N-C-C . , .
3. Overlay Display.
4. R- , .
. 2.18.

. 2.18.

83

 .

, . .
O-C-O
N-C-C-O

123.9
-53.0 96.4

122.9
-26.0 176

:
1.
. Hin-
HyperChem 9, .
11.
,
HyperChem
.
() ,
. .

,
.
- . , .
( ) .
. (-

84

)
. , , . , [1,2].
,
.

-.hin,
.
, Show Periodic Box Display,
.


(force field) .
- . Switched Shifted utoffs . 2.17 AMBER.
11.1.

1. Molecular Dynamics Compute.

Molecular Dynamics Options (.2.19) .
: ,
.
2. Heat time ( ) 0.1 . , , - .
3. Temperature step () 30 , Starting temperature ( ) 100 .
85

- (, ),
0,1 ,
100 K 300
30 .

. 2.19.

4. Run time ( ) 0.5 .

,
.
, . , , (
), , , .
5. , Periodic boundary
conditions. HyperChem , .
6. Step Size ( ) 0,0005 .
7. Data Collection period 4.
, , , Data collection period 4.

86

8. Constant Temperature.
11.2.
- , .
1. Snapshots Molecular Dynamics
Options. Molecular Dynamics Snapshots.
2. -. HyperChem -. , .hin, HIN ,
. , -.snp, , .
3. Snapshot period 1 .
4. OK, Molecular
Dynamics Options.
11.3.
,
, . , ,

.
:
1. Averages,
Molecular Dynamics Averages.
2. L- Selection EKIN, EPOT, ETOT
ncco, L- Add,
Average only.
3. L- EKIN, EPOT, ETOT ncco
Average only, L- Add,
Avg. & graph (. 2.20).
.. , , N-C-C-O , ,
( ).
87

. 2.20.

HyperChem -.csv,
, , Excel.
4. OK, Molecular
Dynamics Options.
11.4.
1. Proceed , . Molecular
Dynamics Results.
2. , . , ,
, , .
3. , Rescale,
.
(
), , (. 2.21).
, 1 , .
: ,
Done. ,
Playback .

88

. 2.21.

-
, , Compute Molecular
Dynamics, Playback Proceed.
( ) time steps ( 1). .
11.5.
, , .
1. Geometry Optimization Compute.
2. OK, .
, , , , ,
, .

.
-955.83 kcal/mol
0.09 kcal/(A mol)

89

.
-1029.8 kcal/mol
0.09 kcal/(A mol)

 , , ,
. , , .
:

,
10 . .

O-C-O
123.9
N-C-C-O -53.0 96.4

122.9
-26.0 176

,

. ,
()
.
. . .
.
9.
12. ,
,
:

HyperChem

,
,

90

 .
12.1.
1. Display, , Show
Hydrogens, Perspective Rendering.
2. Default Element, Explicit Hydrogens,
, .
3.
4. Select Add H and Model Build.
.
5. .
. 2.22.
,
109 . .

. 2.22.

, ,
,
( ) y .
:
1. Align Molecules Edit.
2. Align () Secondary,
With Y Axis (. 2.23).
3. , , Minor Axix.
Y, 2.24.

91

. 2.23.

. 2.24.

H2O.hin.
12.2.

.
.
1. Semi-empirical Setup.
2. CNDO, Options.
, - CNDO.
3. Semi-empirical
Options (. 2.25).
4. OK, .
5. Single Point Compute, .. , .
12.3.
, ,
Set Charge Build. , ,
.
:

92

. 2.25. CNDO

1. Display > Labels.

2. Charge Atoms, OK. (. 2.26).

.
, .

,
. ,
, ,
, .

. 2.26.

Q = ZA Ze
(2.1),
93

 ZA , ,
Ze , ..
. , .
12.4.
2- 3- .
, , ,
.

.
,
: , ,
.

HyperChem
.
XY ( )
Z ().
:
1. .
2. Plot Molecular Graphs Compute, Plot Molecular Properties Options.
3. - Electrostatic Potential 2-D .
HyperChem
(. 2.27).
4. Contour Grid Contour
Grid:
Horizontal grid 60.
Vertical grid, 60.
Contour levels 30.
Plane Offset 0.5 .
5. OK.

94

. 2.27. 2D

6. Plot Molecular Properties Options,

3-D . HyperChem 3-D (. 2.28).
Total Charge Density ( )
. , CNDO , HyperChem
(, 1s ),
, .. .
:
1. Plot Molecular Graphs Compute, Plot Molecular Properties Options.
2. - Total Charge Density, 2D Contours, .
3-D (. 2.29).
12.5.

.

95

. 2.28. 3D

. 2.29. 3D

,
,
.

(2.2),

R - I- ZI, .
(. 2.30)
Display Show Dipole moment.
, , Compute > Single Point
Geometry Optimization.
-
(D). 1D = 3,33.10-30 ..
, . (, , ) . ,
, (

96

NH3, H2O) ,
CO2 .

.2.30. : , CNDO

12.6. ()
.
(, HOMO - highest occupied molecular orbital) (, LUMO lowest unoccupied molecular orbital).

,
,
. ,

.

.
-
.
, CNDO ( 2s, 2p 1s ) .
( ) . 1s-
.

97

 :
1. Orbitals, Orbitals Compute.
2. HOMO-, , 3 (. 2.31).
, 3
, , .
.
,
.
3. 3D Isosurface.
4. , Orbital squared.
5. Plot OK.

.2.31.

HyperChem 3-D . 2s .
6. Isosurface Options,
Isosurface Display, , F4.
, . -

98

 Rendering - Wire mesh, Orbital contour value

0.05, OK (. 2.32).

.2.32. 2s

7. Orbitals,
2 1 HOMO- . Options, , 7 .
2x 2py (. 2.33).

.2.33. 2x 2py

8. - (. 2.34,
), 0
HOMO- .
,
XZ (,
), XY .
9. Rotate Edit. X Axis,
Angle 90, Apply to Viewer, OK.

99

.2.34. 2pz ()

.2.35. 4 ()

10. Orbitals,
LUMO+ 0 1, 2
(. 2.35).
, .
Save, .hin.
:
1. PM3 (H,
CH3, O, OH, Cl, N, NO2, COOH)
.
2. ,
Model Builder. 1,510 (C-C ) 1,089 (C-H ).
RHF , , .
.
3. log- ,
, AM1.
-51,9
/ 2,88 . .
.

100

4.
NDO .
Semi-empirical Options ( ) State - Next Lowest (
).
Lowest () .
13.
:

ab initio
, MP2

13.1. 3O+
1. Explicit Hydrogens Allow Arbitrary Valence
Build. Allow Arbitrary Valence
,
.
2. Labels Display
Symbol.
3. Default Element Build O
(Oxygen).
4. Draw , .
, ,
, .
5. ,
3O (. 2.36).
3D
Select
Model Build Build.
(. 2.37) 109.470
1.05 .

101

.2.36. 3O

.2.37. 3D 3O

1. Ab initio Setup.
2. Options.
3. 1 Total charge.
+1 , 1. .
Ab initio 3O+ . 2.38.

.2.38. ab initio

13.2. H3O+
ab initio
1. Ab initio Setup.
2. Other (Basis set).
3. Assign Other Basis Set.
4. 4-31G OK.

102

 4-31G, .
5. Minimal (STO-3G).
6. Apply Basis Set (. 2.39) OK.
.
HyperChem . ,
, (. 2.40):
1. Labels Display.
2. Basis Set.

.2.39. ab initio

.2.40.

(Geometry Optimization
Compute) ,
STO-3G 3O+ 113.75
0.99.
,
1. Ab initio Setup,
Options, MP2 Correlation included (
MP2) (. 2.41).
2. Single Point Compute (
,
).

103

 H3O+ STO-3G 47270.57 / -47301.07 /

MP2, -30.50 /
(. 2.41).

.2.41. MP2 3O

13.3.
STO-3G
H2O 3O+ (2O ++),
.
1. Draw R- , H3O+ 2O.
+ , 2O,
H3O+ 2O.
2. Ab initio Setup, Options
Total charge 1 0. OK,
.
3. Geometry Optimization Compute, 2O, H3O+.
2O
STO-3G 97,3 (. 2.42) 1,01
.
0,957 104,5 0. ab initio,

104

AM1 PM3, 0,01 , 1-2 . ,

.
4. Single Point Compute.
2O STO-3G -47067.06
/ -47040.93 / MP2,
-26.13 / .
, 229.64 / 234.01 /
MP2. . ,
164,5 /.
6-31G* .

.2.42. 2
H3O+
, /
-47270.57
MP2, /
-47301.07
MP2, / -30.50

2O
-47040.93
-47067.06
-26.13

E, .
229.64
234.01

:
1. 3-21G 6-31G*.
, - ( - -) 3-21G H3O+ 120 . 6-31G*, . 3-21G - . s p
H3O+ NH3
105

 .
, D-.

. , - 3-21G
, .
2. HF, HCl, NH3,
CH4, H2O2, BH3, LiH, H2S, PH3, 66 PM3 3-21G. .
14.

:

,



NH3.
14.1.
1. Explicit Hydrogens Build.
2. .
3. Add H & Model Build Build,
NH3 .

3-21G d- .
1. Labels Display.
2. Basis Set, Labels.
3. Ab initio Setup.

106

4. Small (3-21G)
Apply Basis Set.
- 3-21G (. 2.43).

.2.43. 3-21G

5. Select.
6. Ab initio Setup.
7. Advanced Options, ,
Six Number of d orbitals ( d ).
8. Ab Initio Method Extra Basis function D 1.0 (. 2.44).

.2.44. d-

6 d-, 1.0.
.

107

9.
.
14.2.
( -
).
1. Geometry Optimization Compute.
(H-N-H - 106.5
N-H - 1.008 ) ,
. , .
2. Single Point Compute, , MP2.
- -35086.49 /, ,
MP2 - -35191.11 /.

1. Vibration, Rotation Analysis Compute, .
.
, , , : ,
.
. - () . - ;
.
2. (100% ) Vibrational Spectrum Compute, (. 2.45).
,
. ,

108

 . -1 .

. 2.45. ()

, .. , , . ,
,
(2.3).
3. Animate Vibrations. ,
Apply. ,
. - ,
, ( ). (,
>3000 -1).
, -
.

109

 , , (Zoom)
(Pan). (Line Width)
, . , , log-.
-
File > Start Log.
OK Vibrational Spectrum. , . Cancel, .
.
,
, , , .
14.3.
. ,
. - , , , , .
,
.

1. Select .
2. Name Selection Select, Other,
"imptor". "imptor" . (, 180 ) .
.
3. .

110

. 2.46.

4. Restraints Setup. 4-imptor (

4- , imptor) Add,
. Other Restrained
Value 180 (. 2.46).
Other Force Constant 500,
. OK Restraint Forces.
5. Compute .
120 1.00 .
6. Single Point Compute,
, MP2 .
-34795,85 /, , MP2
, -34863,33 /.
~ 290 /.
14.4.
1. Restraints Setup. 4-imptor Remove, .
2. Vibration, Rotation Analysis Compute, .

111

3. Vibrational Spectrum Compute, .

,
. -
(.. ) . ,
- - , . ()
, - ,
.
4.
. " " ,
.
" " .
:
1. (
) PM3, ZINDO/s, ab initio . .
O2
1580
, -1

NO
2273

HF
4139

HCl
2991

HBr
2649

HI
2310

CO
1725

F2
892

CH4
2950

- ,
. ,
ZINDO/S (Zerners Intermediate Neglect of Differential OverlapSpectroscopic) - .

, ZINDO/S PM3.
2. PH3, AsH3, SbH3,
BiH3. .
, .

112

15. ()
:
-
-

(, ) , *

15.1.
1. , Explicit Hydrogens Select .
2. Default Element - ( ).
, =.
3. Add H & Model Build Build,
(. 2.47).
15.2.
Ab initio Setup.
(STO-3G) .
.2.48.

. 2.47.

. 2.48. ab initio

Geometry Optimization Compute. -

113

 C-C 1.345 ,
C-H 1.098 , H-C-H 116.52 .

Single Point Compute.
-48362,6 / MP2 -48441.4
/, -78.8 / .

.
1. Orbitals Compute. , () -8,718
() () 8,61 , 2.49.

. 2.49.

2pz () 2p*z
() .
* .
- * , ,
, * .
2. Plot
3D ( 2.50).
, , .

114

. 2.50. 2pz () 2p*z ()

15.3. ()
,
. , .
,
. .
. , , (, CI).
:
1. Single Point CI Compute.
2. Singly Excited CI .
3. Energy Criterion. 1000 Maximum Excitation Energy (. 2.51). OK.
- ( ). -

115

. 2.51.

,
(Orbital Criterion) (Energy Criterion),
. 1000 , .
4. CI Compute > Electronic Spectrum . Electronic Spectrum,
(. 2.52).
54,24 nm ()
* .
( )
392,2 nm ( * ).
( ),
-. * 112,4 nm.
, 8,718+8,61 = 17,328 . ,
-, , () = 1240/ (). -

116

, 100 = 12,4 , 10 = 124 , 0,1 = 12400 , ..

. 2.52.

.. 1240/17,328 = 71,61 400 /.

(112,4 ) - (71,61 ) .
* - 162 [2].
15.4.
, , . HyperChem
.

1.
Model Build .

117

2. ,
Set Bond Torsion Edit, 45 . HyperChem
( ),
.
, .
3. Ab initio Setup. Spin
pairing ( ) - UHF 3
() Spin Multiplicity () (. 2.53).

. , -
Minimal (STO-3G) .
4. (Geometry optimization
Compute).
. , 90 (. 2.54), . C-C 1,494 ( 1,345 ). , . C-H
1,08 , H-C-H 116,2 .

. 2.53.

C-C,
1.345
1.494

. 2.54.
C-H,
1.098
1.081

118

H-C-H, .
116.52
116.20


Orbitals Compute.
.
, * (.
2.55). (. 2.56).

. 2.55.

. 2.56. 2pz 2p*z

15.5.
Single Point Compute. 48329,02 / ( MP2), 33,58 /
(851,4 ) , (-48362,6 /). , 1 () = 28591,2 /
(/).
33,58 / (851,4 ) -
119

, .
.
MP2
(-45,11 /). , (-78,8 /). , , 67,27 /
(425 ).

(91,14 / 313,7 ) . ( ) , ,
, .
:
1. (Orbital Criterion = 4). .
2. n * , , , . ( , =
117 194 ).
3.

S0 () T1 :
1
CH4

2
3
4
CCl3F CF3Cl CCl4

5
CF4

6
SiH4

7
8
CCl3H CF3H

9
CCl2F2

10
CH3Cl

.
16.

, (),
,
.

120

 , , ,
.
.
- HyperChem , :
1. (Electronic Energy),
.
2. (
) (Nuclear Energy).
3. (Total Energy) E = Ee + E,
.
4. (Binding Energy) Eb,
, .
5. ( , Heat of Formation) Hf,
(2.4),

Hf(I) E(I)
I- (.. ).
(, ), . , .. ,
, .
6. (MP2 Energy,
ab initio CI).
, ,
Compute Properties,
Details Total Energy (. 2.57).
16.1. ()

121

 . , ( , ..).
HyperChem (. 2.57).
HyperChem
( 0
) (2.4).

. 2.57.

,
(2.4). ,

2 B2 [7]:
(2.5),
fH () = E() E(2) E(2)
E() , E(2) E(2)
2 2 .
(2.4)
CH4 ab initio . -24928,9 /. STO-3G -

122

 () = - 23274,1 /, () =-292,8
/ ( ).
.., ()
(2.6)
: D = () + 4 () (4) = -23274,1 1171,2 +
24928,9 = 483,6 /. .

. () 170,9 /
52,1 /.
, (4) = () + 4 () ()
=170,9 +208,4 483,6 = -104,3 (/).
(2.5). fH (4) = E(4) E(2)
.
4 E(2) = -24928,9 + 46700,6 + 4. 701,2 = - 176,2 /.
.
PM3 -13,07 / 392,3
/.
.

16.2.

, . , -, - ( ,
), .

,
.
.
, .

123

 ,
( ) .
, , ( ). ,

(2.7)
I = - E

(2.8).
= E
,
, .. .


(2.9)
I/ = (M+) E (M)
+
(M ), (M) - ,
(Single Point )
.

- -. ,
() ,
,
E = E - E
(2.10)

,
.
(2.11)
Eb i
(), Ei i- -

124

 ( ) E
.
(D) ,
(2.6 2.11). .
, ..
,
.
, .
HyperChem
() (. . 2.67), . (2.11).
- , .
:
1. 1
2 PM3. ,
(2.4) . .
2. PM3 (I), (A)
(D) ,
2.1.
2.1.

1
2
3
4
5
6
7

H2
Li2
C2
N2
O2
F2
P2
I,
A,
D, /

125

8
S2

9
Cl2

10
Br2

17.

.
. ,

( ) HCCH, - , .
.

().
. HyperChem
( ) .
,
.
17.1.
(, , ),
Setup, , . , - ( , , --), .
Compute > Potential.
Inititial Bond Length ( ), Final Bond Length
( ), Step
. Outliers , .
. 2.58. Ok .
126

 ,
,
(. 2.59)
=
.

. 2.58.

. 2.59. ( 2,5 )

(.. , .2.60).
, , 2- : .

127

 . 2.61. .

. 2.60. 2
[2]

. 2.61. [2]

Properties (. 2.59), . ,
System .
, .

128

 :
1. E(RAA) H2, He2, Li2,
Be2, B2, C2, N2, O2, F2, Ne2, , HF. 0,5 3 , 0,05 .
2. NH- , . .
18.

,

- I II .

,
.
. , 2- - 2 4
2s, 2px, 2py, 2pz - 8 2s (), 2px (), 2py (), 2pz (), 2s (), 2px (), 2py
(), 2pz ().

Z. -, - -.

- 2s (), 2pz (), 2s (B), 2pz (B),
- - 2px (), 2py (), 2px (B), 2py (B).
2pm .

, .
, :
129

- = 1 2s () + 2 2pz () + 3 2s (B) + 4 2pz (B),

- = 1 2px () + 2 2py () + 3 2px (B) + 4 2py (B).
2py 2px
- :
-x = 1 2px () + 3 2px (B) -y = 2 2py () + 4 2py (B).
,
-.

.
.
.
. 2- 4 :
- 1, 2, 3, 4
- 1x, 2, 3x, 4y

.
, .. . : sp-, sp2-, sp3 . .
.
i , .
2- , , .
:
- = 1 2s () + 2 2pz () + 3 2s (B) + 4 2pz (B) = 1 [2s () +
(2/c1) 2pz ()] + 3 [2s (B) + (4/c3) 2pz (B)] = c1 sp1 + 3 sp2
i:
1. 1 = 3
2. 1 3
3. |1| >> |c3| |1| << |c3|

130

 . 2-
, .
:
1. ,
.
2. ,
.
3. , 1 .
-.

, .
.
, .

.
18.1.
BeO. c MNDO
( Log-).
Compute >
Properties. D = 5,326 .
(. 2.62).
Compute >
Orbitals (. 2.63). (8) .

131

 8 : 2s (Be), 2px (Be), 2py (Be), 2pz (Be), 2s

(O), 2px (O), 2py (O), 2pz (O).

. 2.62.

. 2.63. BeO

(. 2.64).

BeO :
- = 1 2s (Be) + 2 2py (Be) + 3 2s (O) + 4 2py (O),
-x = 1 2px (Be) + 3 2px (O)
-y = 2 2pz (Be) + 4 2pz (O).
-. Y
(. 2.64). -.

132

 - ( Eigenvalues (eV) and Eigenvectors) 2.2.

2.2.
MO
1
2
3
4
5
6
Symmetry
1
2
1
1
3
2
Eigenvalue -36.572 -11.575 -11.234 -11.234 -1.658 3.646
2S Be
0.257 0.452 -0.000 -0.000 0.762 0.000
2Px Be
-0.000 -0.000 -0.447 0.069 0.000 -0.892
2Py Be
0.291 0.107 -0.000 0.000 -0.552 -0.000
2Pz Be
-0.000 0.000 0.069 0.447 0.000 0.012
2S O
0.913 -0.270 0.000 0.000 0.004 -0.000
2Px O
0.000 0.000 -0.881 0.136 -0.000 0.452
2Py O
-0.117 -0.843 -0.000 0.000 0.337 0.000
2Pz O
0.000 0.000 0.136 0.881 -0.000 -0.006

7
2
3.646
-0.000
0.013
0.000
0.892
0.000
-0.006
-0.000
-0.452

8
4
7.656
-0.384
0.000
-0.774
0.000
0.303
0.000
-0.402
0.000

2.2 :
1- = 0,257.2s (Be)+0,291.2py (Be) + 0,913.2s (O)0,117 . 2py (O).
( .2.64) 2s (3 ~ 1). .
2- = 0,452.2s (Be)+0,107.2py (Be) - 0,270.2s (O) 0,843.2py (O).
(. 2.65), ..
.

. 2.64. (1)

. 2.65. (2)

- (.
2.66) ( ):
1-x = -0,447 . 2px (Be) 0,881 . 2px (O)
2-z = 0,447 . 2pz (Be) + 0,881 . 2pz (O).

133

1-x (. 2.67). , , 2z - (. 2.68).

3 (. 2.69), 3x (. 2.70),
4z , 4 .

. 2.66. BeO ( )

. 2.67. (1x)

. 2.68. (2z)

. 2.69. (3)

. 2.70. (3x )

i , , , -

134

 sp- , , ,
, BeO. ,
.
1 2
- = 1 2s (Be) + 2 2py (Be) + 3 2s (O) + 4 2py (O) = 1 [2s
(Be) + (2/c1) 2py (Be)] + 3 [2s (O) + (4/c3) 2py (O)] = c1 sp1 + 3 sp2.
1 = 0,257.[2s (Be) + 1,132.2py (Be)] + 0,913.[2s (O) 0,128.2py (O)]
= 0,257 . s.p1 + 0,913 . s.p2
2 = 0,452.[2s (Be) + 0,236.2py (Be)] - 0,270.[2s (O) + 3,122.2py (O)]
= 0,452 . s.p1 - 0,270 . s.p2
, 1 3 |1| > |c3| ( |1| < |c3|) . q(Be) = -q(O) = 0,446
.
, ..
. < 0,
BeO.
:
1.
H2O2+.
2. H2C=O.
19.

.
HyperChem , , 16 .
, ,
. 2.71.
- PM3 (8 ) (RHH) =
0,71 , 1,8 (. 2.72).
19.1.
2- (.
2.73). , 135

 (. 2.74, ) R = 1,79 .

. 2.71.

. 2.72.

. 2.73.

. 2.74.

H3O+ (a)
HO- (b) ( )
RHO=1,81 .
RHO=0,96 , - (. 2.75).

. 2.75.

19.2. 1- 2-


136

 . ( ) ( ) (N+H3 -OOC-) (. 2.76).

(
--)
H-.
.

. 2.76.

2.77 (), ()
.

. 2.77. () ()

HyperChem ( )
(. 2.78-79).
19.3.

137

 . .
, .

. 2.78.

. 2.79.

(. 2.80, )
PM3.
10, .
,
. PM3.

138

 Display
Show Hydrogen Bonds.
Display > Recompute H Bonds (. 2.80, ).

.2.80. () ()

2.3.
:
(2.12),
+2 ,
, 2 .

-217,2 -7492,7 / .
,
7,3 / ( 30 /), . :
6,9 /.
2 5,
2-3
( ) . .

139

 2.3.

+H2O

N1
0,902
0,889
-0,013
2
-0,504
-0,453
0,051
Q ( 3
0,479
0,464
-0,015
)
4
-0,474
-0,470
0,004
5
-0,609
-0,626
-0,015
N1-C2
1,4783
1,4861
0,008
,
C2-C3
1,6463
1,6102
0,036

131,91
129,39
-2,52
,
11,5
13,32
1,82
, /
-24509,6
-32009,6
7,3 *
, /
-892,7
-1116,8
6,9 *
. 2.81. * - (2.12).

. 2.81.

- 0,013
0,9 .

-
=, - .
:
1. + 2O, ab
initio .
2. (C2H5OH) .
3. NH3 H2= . N-C 2,6 .

140

III. -
-
HYPERCHEM
1
-
: - (
+) - MNDO .

1. HyperChem.

Windows Chem.exe
(:\Hyper8\Program\).
2. .
,
: ( , ),
( !),
.
. .

HyperChem . 3 .
() C6H5NO2.
3.
.



. Build
141

Add H & Model build. .

, Display Show hydrogens.
hin- HyperChem
(, .hin).
4. log- .
File Start Log. Mechanics print level = 9.
5. .
: .
Setup (+)
(Molecular Mechanics);
MM+.
Compute >
Geometry Optimization.

Converged=YES .
- .
6.
6.1. . ( , , ).

- MNDO, (
) , +.
HyperChem . 4 . 5 -

142

 3 ( ). ( )
() .
,
+, MNDO ( ). .
MNDO 0.04
3-4 .
3.1. ( )
+
MNDO
( . 3.1)
1,212
1,177
O2 N1
1,499
1,424
C5 N1
1,405
1,343
6 C7
1,091
1,103
C6 H11
119,27
118,2
C4 C5 C6
120,46
121,0
C5 C6 C7
120,09
117,5
O1 N2 3

1,229
1,465
1,385
1,095
118,1
120,3
123,2

, Edit > Copy image (F9). ,

.
.
,
Display > Labels, Number
Symbol. 3-
Display > Rendering.
7. log-.
File > Stop Log.
MM+ MNDO .
hin- HyperChem

(,
_MM+.hin).
8. log- .
143

 File Start Log. Quantum print level = 9.

Rendering Balls and Cylinders

. 3.1

9. .
: MNDO.
Setup Semi-empirical;
MNDO ( III MNDO/d). Options , ,
(Lowest) (Next Lowest) .

Compute > Geometry Optimization. ,
Conv=YES
.
10.
10.1. . ( , , ).

.
( 10.2-10.10)
MNDO, .

144

10.2.

, Display > Show dipole moment.
( ),
( Compute > Single Point).
log-.

log-
Dipole (Debyes)
x
y
z
Total
Point-Chg.
4.134 -2.368 -0.000
4.764
sp Hybrid
0.419 -0.240 -0.000
0.483
pd Hybrid
0.000
0.000 0.000
0.000
Sum
4.553 -2.608 -0.000
5.247
(D)
. 3.2.

.
,
Edit > Copy image (F9),
.
10.3.

, : (2) = 1,83 D, (C3H) = 1,69 D
( ).

145



.

5,25 D, ..
, .. .
. CClF3
0,27 D, , CClF3
.

10.4. ,
, Display > Labels, Charge.

. 3.3.

.

Compute Plot Molecular graphs. Electrostatic potential 3D 2D
.
.
.

146

 ,
.

2D

3D

2D

. 3.4. (2 3 D)
(2 D)

, , . ,
, .
, (NH2)(C6H5)
(NH2)(C6H5)(NO2), ,
, .
Compute Plot Molecular graphs.
Total charge density 3D 2D
.

,
.
10.5. ,
() ()

Compute > Orbitals.
(ab-initio), , (, MNDO) . ,
147

 F 7 9.
N, O C MNDO 1s .
( , ),
Labels.
Orbitals
(Number),
. 3D 2D
, Plot Ok.
(23) = -10,312

(24) = -1,221 .

. 3.5. 2D

( Eigenvalues
(eV) and Eigenvectors )
Mol. Orbital
Eigenvalue

Pz
Pz
Pz
Pz
Pz
Pz
Pz
Pz
Pz

N
O
O
C
C
C
C
C
C

2
1
3
4
5
6
7
8
9

23
-10.312

24
-1.221

-0.00000
-0.00134
0.00128
0.49900
0.00010
-0.49892
-0.50111
-0.00013
0.50097

-0.30188
0.21777
0.21781
0.36765
-0.46746
0.36775
0.18258
-0.50831
0.18267

148

 , .
, - .
10.7. ()
(
) : + ;
- - . .

(24) = -1,221 .
, , .

,
, , . , , , .., , . ,
E > 0 . , E < 0, ,
, ,
, .. .
10.8. .
:
E= E - E.
:
= ( )/2.
:
S=1/(2), .. S=1/( ).
,
1 ; ,
1 .

> 1
. : .
: = ()/2 = (-1,221 + 10,312)/2 = 4,545 .

10.9.

149


.
.
. :
(3.1),

ci - ( ) ,
. f
.
.
.
:
O3
-0,342
O2
-0,342
N1
0,487
. : .

( ),
( ).

.
.
10.10. () .
,
+, MNDO. -

150


Compute > Vibration, Rotation Analysis. , Calculating
Vibrational Spectrum 100% . ,
,
.

Compute > Vibrational Spectrum.
Vibrational Spectrum 3-4
: ,
. ( -1)
log- (. ).
- ( log-)
========== IR Spectrum ==========
-1
31 Normal Mode Frequency 1827.60 cm Intensity 285.13387

28 Normal Mode Frequency 1605.93 Intensity 221.70650

-1
11 Normal Mode Frequency 726.64 cm Intensity 102.257

NO CN ,
.

Animate Vibrations
Apply.
Cancel . - .
? .
10.11. log-
( 1).

ENERGIES AND GRADIENT
Total Energy =
-35381.2387025 (kcal/mol)
Binding Energy =
-1503.6380795 (kcal/mol)
Isolated Atomic Energy = -33877.6006230 (kcal/mol)
Electronic Energy =
-150210.5977513 (kcal/mol)
Core-Core Interaction = 114829.3590488 (kcal/mol)
Heat of Formation =
14.3299205 (kcal/mol)
Gradient =
0.0952986 (kcal/mol/Ang)

151

11. log-.
File > Stop Log.
hin- HyperChem

(,
_MNDO.hin).
12. Word OpenOffice.


+ MNDO , , .
3- ,
:
1.

+.
2. MNDO.
3. .
, , .
2

: , ,
.
, , , , ..
.
1.

152

1. .
. , .
- 1). CH3-CH3, 2). CH2=CH2, 3). C6H6, 4). CHCH,
5). CH3Cl, 6). C6H4Cl2, 7). CO2, 8). BH3,

9). CCl4, 10). BCl3

, 1). H2O2, 2). (CH3)2CO, 3). HCOOH, 4). CH3OH,

5). CH3NH2, 6). CH3COH, 7) (CH3)2SO, 8).
KHCO3, 9). KSCN, 10). C4H4O

2. 4 , CNDO, INDO, MNDO AM1 ( ).

3.
log- :
( ),
( ),
( ) ,
().
.

RAB

ABC

fH0

CNDO
INDO
MNDO
AM1

4.
() .
5*. ab initio STO 4-21G.
2.

1. , (CNDO, INDO, MNDO AM1) (I), (A),

153

 (R) (D) , .
3.2.

1
2
3
4
5
6
7
8
9

H2
Li2
C2
N2
O2
F2
P2
S2
Cl2
I,
15,4 5,1
12,4 15,6 12,1 15,7 11,1 9,4
11,5
A,
0,45 3,27 -1.80 0,45 3,08 0,59 1,67 2,38
R,
0,74 2,67 1,24 1,10 1,21 1,41 1,89 1,89 1,99
D, / 103 24
143 225 118 37
116 101 57

10
Br2
10,7
2,22
2,28
46

: 3d- , MNDO MNDO/d, AM1 PM3.

.

. CNDO
I,
A,
R,
D, /

INDO

MNDO

AM1

2. , (CNDO, INDO, MNDO PM3) (Hf, ) , 3.3.

3. (CNDO, INDO, MNDO
PM3)
3.4.
3.3.

1
2
3
4
5
6
7
8
LiH BeH2 B2H6 CH4 NH3 H2O HF
PH3
30,7 78,1 7,5
-20,3 -11
-57,8 -64,2 2,2
Hf,
/

9
H2S
-4,8

10
HCl
-22,1

3.4.

1
2
3
4
5
6
7
8
9
10
BH CH NH HO HF
HCl HBr HI
CO CS
0,58 0,89 1,49 1,98 1,83 1,08 0,78 0,38 0,11 1,96
, D

154


3.4 . ?
4.
() .
5*. ab initio 6-31G*.
. 3.4.

1
2

NH3
PH3
AsH3
H2O
H2S
H2Se
1,48
0,89
0,18
1,87
1,17
0,24
, D

3
4
C3H8 CH3-CH=CH2 CH3-CCH CH3Cl
CH2Cl2
CCl3H
0,09
0,364
0,78
1,83
1,62
1,01
, D

5
6

CH3Br
CH2Br2
CBr3H

1,80
1,40
0,99
2,15
2,83
0,38
, D

3

: () .

1. AM1 ,
C2H2, C3H3, C4H4, C5H5, C6H6, C7H7, C8H8,
C9H9, C10H10 - . C-H
100 /. : ).
; ). ; ). .
2. CNDO , (8, 20, 60, 80, 180, 240, 540) - . hin.

155

3. S3, S4, S5, S6, S7, S8, S9, S10

PM3 S-S . ,
.
4. 1-3 ,
- - .
?
5. CNDO : 6H6, C18H12, C24H12, C42H18, C54H18,
C84H24.
hin-.
4

:
.

.
1. - MNDO: ,
. Log-.
2. - -.
2. 2- - ,
(, , ).
3. (,
).
4. .
. 3.5.

1
2
3
4

Si2
Li2
C2
N2

156

5
O2

6
F2

7
P2

8
S2

9
Cl2

10
B2

. 3.6.

1
2
3
4
5
6
7
8
9
10
LiF CN NO BN BF
LiCl BeO BC
CO CN+
CN, NO

( ) 2.

CN-, NO- ..

5
-
:
.

1. .

C2H5OH ( .3.6).

. 3.6 .

hin-.
2. log- .
File Start Log. Quantum print level = 9.
3. ab-initio

, STO-3G.

157

 Setup ab initio; minimal

basis STO-3G. Options , ,
. . 3.7.

Compute > Geometry Optimization.
10-15 10
Pentium 4.

. 3.7.

C2H5OH STO3G
3 . ,
C2H5OH 63 : 2*C*(3*(1s) + 3*(2s + 3*2p)) + 1*O*(3*(1s) + 3*(2s + 3*2p)) +
6*H*(3*(1s)) = 63.
4.
4.1. . ( , ).
,
ab initio (
). .
4.2. .
,

158

 / .
4.3.

1.
4.4. ,
4.5. ,
() ()
4.6.

4.7. .
4.8. ()

.
.
5. log-.
File > Stop Log.
6. Word OpenOffice.
(), , .

, abinitio STO-3G , ,

.
6

: ,
,

159

.
.
1.
ab initio

1. .

2
CCl3F
7
CCl3H

CH4
6
SiH4

3
CF3Cl
8
CF3H

CCl4

CF4

9
CCl2F2

10
CH3Cl

2. 6 ab initio (
STO-3G RHF, 3-21G RHF, 3-21G UHF, 3-21G RHF + MP2, 6-31G
RHF, 6-31G** RHF ).
3.
log- :
( ),
( ,
),
( ) .
.

RAB,
RB

ABC

STO-3G RHF
3-21G RHF
3-21G UHF
3-21G RHF + MP2
6-31G RHF
6-31G** RHF

MP2 ( % ).
4. .
5.
.
2.

160

1. , (STO-3G RHF, 3-21G RHF, 3-21G

UHF, 6-31G RHF) (I), (A),
(R)
(D) , 3.7.
3.7.

1
2
3
4
5
6
7
8
9

H2
Li2
C2
N2
O2
F2
P2
S2
Cl2
I,
15,4 5,1
12,4 15,6 12,1 15,7 11,1 9,4
11,5
A,
0,45 3,27 -1,80 0,45 3,08 0,59 1,67 2,38

10
Br2
10,7
2,22

3.7.

1
2

H2
Li2
R,
0,74 2,67
D, / 103 24

10
Br2
2,28
46

3
C2
1,24
143

4
N2
1,10
225

5
O2
1,21
118

6
F2
1,41
37

7
P2
1,89
116

8
S2
1,89
101

9
Cl2
1,99
57

. STO-3G RHF 3-21G RHF 3-21G UHF 6-31G RHF

I,
A,
R,
D, /

2. (STO-3G RHF, 3-21G RHF, 3-21G UHF, 6-31G

RHF)
3.8.
3.
.
3.8.

1
2
3
4
5
6
7
8
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1 ... = 1 = 2 = 27,212 = 219350 -1 = 627,5
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168


1. / .. , .. , .. . : - , 2009. 48 .
2. :
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3. ..
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4. .., .., .. : . . 2-. - : -, 2005. 32 .
5. .. , , / IV -
-, , 1416 2009 . . .: ., 2009. . 282289.
6. .. . - : ,
2009. 138 . URL: http://window.edu.ru/resource/668/65668 (
13.10.2012).
7. - // . .. . [, 2004]. URL:
http://quant.distant.ru/files/pdf/study/lab/lab1.pdf ( 13.10.2012).
8. - // . .. . [, 2004]. URL:
http://quant.distant.ru/files/pdf/study/lab/lab2.pdf ( 13.10.2012).
9. HyperChem Word //
[2007]. URL: http://a-kosmonavt.narod.ru/prog/hyperchem.rar ( 13.10.2012).
10. .. - HyperChem // / . [, 2010]. URL: educons.net/atlas_last/nanoobjfiles/61/ComplexHYPERCHEM.doc (
13.10.2012).
11. .., .. :
-
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. ., 2001. II. 40 .
12. :
/ . . , .. , . . , . . . - : , 2002. 223 . URL: http://www.kirensky.ru/
books/book ( 13.10.2012).

169

13. .., .. / ..,

.. .: -, 2005. 536 .
14. .. : . .: , 2008. 180 .
15. .. ( ). - :
, 2006. 52 .
16. (.): HyperChem ver. 5.0 CDK.pdf, GetStart.pdf, Referen.pdf., HyperChem ver. 7.5 hyperchem_getting_started.pdf,
HyperChem ver. 8.0 hyper8.pdf.

16. .. . ,
: . .: . , 2010. 495 .
17. .. . .: , 2001.
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19. .., .., ..
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20. .. : . . / . . . -.: , 2008. 384 .
21. .. :
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22. .., .. : /
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23. .., ., .. . /
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24. . :
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25. ..
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26. .. . . .II: . .:
, 2004. 176 .
27. .. : Gaussian GaussView. .: -, 2011. 224 .

170


I. - HYPERCHEM .. 3
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2.1. HyperChem ............................................................................ 6
2.2. ...................................................... 8
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2.4. ....................... 10
2.4.1. .................................... 11
2.4.2. ............... 12
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3. ................................... 14
3.1. HyperChem ..................................................... 14
3.2. ................................................................... 14
3.3. ........................................................................................ 16
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3.6. ..................................................................... 20
3.7. ........................................... 20
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4.2. ............................................................... 22
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5.2. Z- ........................................................................................... 26
5.3. ...................................................................................... 27
5.4. XY- .............................................................................................. 28
5.5. Z- ................................................................................................. 29
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6.2. ............................................................................ 32
6.3. ............................................................. 33
6.4. .................................................................. 34
6.5. ............................................................ 35
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7.1.1. ...................................................... 37
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7.1.3. ..................................................... 41
7.2. (semi-empirical) ............................. 42
7.2.1. .................... 44

171

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7.3. (b-initio) - .................................... 50
7.3.1. .................................................................... 51
7.3.2. ....................................... 53
7.3.3. ab initio ...................................................... 53
7.3.4. ab initio ............................... 55
8. ....................................................................................... 57
8.1. (Geometry Optimization) ................. 59
8.2. (Single Point) .............................. 60
8.3. c
(Single Point CI) ..................................................................... 61
8.3.1.
............................................................................................. 61
8.3.2. ............. 63
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9.2. ............ 66
9.3. ........................................ 68
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9.7. - .......................... 72
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172

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13.2. H3O+ ............................. 102
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14.2. ................................. 108
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173

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............................................................. 170

174

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