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!"#$ &'()* +,- $./* 012 $3+4"32* 56.

7- + 81734673

Authoi: Emily Nooie 0puateu: }uly 26, 2u11
&23963,:7; '*<3- (63*:.1,* +,- $3+4"32 $./*
$1/.4* =,476-3>
?@ $3+4"32 &+4.7.:+:.1,
A@ $+B*
C@ D17734:.1, 51E3*
F@ G.:*
H@ CI J.3K
L@ 56.7-.,M 81734673*

?@$3+4"32 &+4.7.:+:.1,
N1K 4+, = 6*3 :".* ., O; 47+**P
Beie aie some iueas:
You can use the Builu a Nolecule sim:
- =, 47+** by having youi stuuents woik inuiviuually oi in paiis at computeis. Check out the
sample activities foi this simulation available in the Teachei Resouices section (below wheie
you uownloau the sim).
- '* + -3O1 by piojecting the simulation onto a scieen. You can manipulate the simulation, oi
you can select stuuents to come up anu builu molecules foi the class.
- '* "1O3K12< by asking stuuents to complete a set numbei of collection boxes in piepaiation
foi a class, oi as piactice aftei an intiouuction to molecules.
- Q.:" 47.4<32 963*:.1,* by asking stuuents the name oi geometiy of a molecule with a clickei
questions, anu then builu anu visualize it to see if they weie coiiect.
Q"+: 4+, *:6-3,:* 73+2, 021O /7+;.,M K.:" :".* *.OP
A lot! Stuuents can leain:
- Nolecules aie maue fiom atoms,
- What aie moleculai foimulas,
- What aie subsciipts anu coefficients,
- The same molecule can be iepiesenteu in many uiffeient ways (with a name, foimula, in
2B anu SB, in space filling anu ball anu stick view),
Stuuents can also:
- Compaie names foi similai looking molecules to stait leaining about naming,
- Leain that molecules have a specific stiuctuie (a ceitain way the atoms go togethei) anu
begin asking questions about why uo atoms go togethei in paiticulai ways.
- Anu moie...!

A@ $+B*
Q"+: .* :"3 /62/1*3 10 3+4" :+BP
Beie's what we hau in minu with each tab, but uon't let that limit you! The tabs aie uesigneu to
help teacheis scaffolu lessons oi make lessons age appiopiiate by using only some of the tabs. If
you finu othei leaining goals that woik foi these tabs, let us know!
!"#$ &'()* +,- $./* 012 $3+4"32* 56.7- + 81734673

Authoi: Emily Nooie 0puateu: }uly 26, 2u11
8+<3 81734673 is useful foi intiouucing: molecules aie maue fiom atoms, moleculai foimulas
anu chemical names, anu uiffeient types of molecule iepiesentations (Lewis Bot-like stiuctuies,
pseuuo-SB anu SB).
8+<3 8+,; can be useu foi the same puiposes, anu also to intiouuce coefficients. 0ne thing
we've seen woik well with this tab is to challenge stuuents to fill theie collection box, anu then
give them ~ S minutes to figuie it out. It's typically not necessaiy to uesciibe what the coefficient
means befoie letting them play. Stuuents tenu to tiy a couple of things, anu then catch on pietty
R+2M3 81734673* is a gieat challenge tab, oi foi just exploiing. You can ask stuuents to make the
biggest molecule they can, to finu patteins in names of similai compounus, compaie the
connectivity of uiffeient compounus, oi to builu laige molecules anu bieak them into smallei
molecules (intiouuction to metabolism), oi anything else that seems appiopiiate foi youi
leaining goals.
D+, = 23*3: + :+B B+4< :1 :"3 B3M.,,.,MP
Yes! You can "Reset cuiient tab" by going unuei "0ptions" in the uppei
left-hanu coinei of the simulation. This can be useful if you want to have
a class uiscussion with eveiyone looking at the same collection box, but
keep in minu this will lose all of stuuents woik foi that tab.

C@ D17734:.1, 51E3*
Q"+: -1 = -1 K.:" :"3 417734:.1, B1E3*P
You collect molecules! The fiist two tabs have a built in challenge foi stuuents, to fill the
collection boxes with the specifieu molecule. We've uesigneu the fiist tab to help scaffolu
stuuents natuially into figuiing out how this woiks, so you likely won't neeu to explain this to
stuuents in uetail. 0nce they make theii fiist molecule that can be put in the collection box,
theie's an aiiow that shows them wheie to put it, anu they usually get the hang of it quickly.
D+, = 23*3: S6*: 1,3 417734:.1, B1EP
Suie! }ust select "Reset Collection" at the bottom of the collection box to stait that collection ovei,
oi you can select "Reset cuiient tab" fiom the "0ptions" uiop uown menu in the uppei left-hanu
coinei of the simulation. Remembei though, "Reset cuiient tab" will unuo all the stuuents woik
on that tab anu set the collection box back to the stait.
N1K O+,; 417734:.1, B1E3* +23 :"323P
Tons! The fiist collection box is always the same (that way you can have a uiscussion with youi
stuuents with eveiyone looking at the same molecules at least once). Aftei stuuents fill that
collection box, they'll each get a uiffeient, ianuomly selecteu collection box to fill. Theie's no
limit to how many uiffeient collection boxes theie aie, but stuuents will see some of the
molecules to collect multiple times.
F@ G.:*
N1K -1 = 230.77 :"3 +:1O B64<3:*P
!"#$ &'()* +,- $./* 012 $3+4"32* 56.7- + 81734673

Authoi: Emily Nooie 0puateu: }uly 26, 2u11
If you just want to iefill youi atom buckets, select "Reset Kit" in the coinei of the kit box. If you
want to iefill youi atom buckets anu stait ovei on the collection box you'ie woiking on, select
"Reset Collection" fiom the bottom of the collection box. This will iefill youi atom buckets anu
empty youi cuiient collection box, without unuo-ing any pievious collection boxes you've
=)O 16: 10 +:1O*T B6: "+U3,): 0.773- O; 417734:.1, B1E ;3:@ Q"+: -1 = -1P
You can eithei iefill youi atom buckets, by selecting the "Reset Kit" in the left coinei of the kit, oi
if you neeu uiffeient atoms, use the aiiow buttons in the uppei iight-hanu coinei of the kit box
to cycle thiough all of the kits available.
D+, = O+<3 1,7; 1,3 O1734673 K.:" 3+4" 417734:.1, B1EP
No, you can typically make moie than one, anu foi some kits you can make hunuieus of uiffeient
molecules! The kits in the fiist anu seconu tabs aie uesigneu to scaffolu stuuents into moie
complicateu kits, so they stait with fewei options (so they can get the hang of builuing
molecules), with the numbei of molecules possible incieasing as they go along. In the thiiu tab,
the kits aie uesigneu to allow foi maximum numbei of molecules possible.
In the thiiu tab theie aie kits that allow you to make a biological molecule (glycine oi
aminoacetic aciu) along with othei oiganic compounus, anu kits foi moie exotic builuing, like
compaiing silane, boiane anu methane. Bon't woiiy though, if youi leaining goals uon't call foi
focusing on any special kits, stuuents still get a lot out of coming up with theii own compaiisons,
anu just exploiing.

H@ CI J.3K
Q"+: 4+, = -1 K.:" :"3 O1734673* ., CI U.3KP
0nce you've maue a molecule, the option to see in SB will appeai as a gieen button. Piess
this button anu the molecule will show in SB in it's own }mol winuow. This molecule is giab-able,
stuuents can iotate it anu change the view (fiom space filling to ball anu stick). To leain moie
about }mol, this is a goou staiting place: http:en.wikipeuia.oigwiki}mol

L@ 56.7-.,M 81734673*
= :2.3- :1 /6: *1O3 +:1O* :1M3:"32 :"+: *"167- M1 :1M3:"32T B6: .: -.-,): K12<@ Q"+: -1 =
The connectivity of the atoms is impoitant in ieal life anu in the sim. When you builu atoms,
think of staiting with the cential atoms anu auuing the outei atoms one at a time. So foi watei,
you stait with oxygen, anu auu a single hyuiogen to each siue. Since you can builu atoms using a
Lewis-like stiuctuie, it uoesn't mattei which siue you auu the hyuiogens to. Foi example, both of
these aie watei:

But, if you tiy to put oxygen anu a hyuiogen molecule togethei like this:
!"#$ &'()* +,- $./* 012 $3+4"32* 56.7- + 81734673

Authoi: Emily Nooie 0puateu: }uly 26, 2u11

they won't make a molecule. That's because in watei, the two hyuiogens aien't attacheu to each
othei, they'ie attacheu to the oxygen so you neeu to attach each hyuiogen to the oxygen
We've founu fiom inteiviews anu classioom obseivations, if stuuents uon't get it iight the fiist
time, they just tiy a couple uiffeient ways until they get it. That's why we stait the fiist tab anu
fiist kit with only thiee atoms, that way stuuents can figuie out how to ieaiiange anu put things
togethei ieally quickly.
We've even seen S
giaue stuuents builu Lewis Bot stiuctuies intentionally to look moie like the
SB mouel aftei using the Builu a Nolecule sim. Foi example, when making watei, we've seen
stuuents intentionally auu the hyuiogens to the iight anu left siue iathei than one on top anu one
on the iight (oi left) aftei seeing the molecule in SB.

D+, = B23+< +/+2: + O1734673 B+4< .,:1 .,-.U.-6+7 +:1O*P
Yes! Theie aie two options, you can bieak apait all the atoms in a molecule by using the blue
'bieak apait' button, that appeais above each molecule.
If you just want to bieak a single atom off youi molecule, hovei youi mouse iight wheie the two
atoms touch that you want to bieak apait. A paii of scissois will appeai (if you uon't see
it, just wiggle youi mouse aiounu that aiea anu look foi the scissois to appeai). Click when youi
mouse looks like scissois anu just those two atoms will be sepaiateu.
D+, = B23+< S6*: + *.,M73 B1,-T K.:"16: B23+<.,M +/+2: :"3 3,:.23 O1734673P
Suie! If you just want to bieak apait two atoms only, not youi entiie molecule, mouse ovei the
aiea wheie the two atoms touch. A paii of scissois will appeai (if you uon't see it iight
away, just wiggle youi mouse aiounu, when you hit the iight spot, the scissois will appeai). Click
when youi mouse looks like scissois anu just those two atoms will be sepaiateu.
Q"+: O1734673* 4+, = B6.7-P
Any molecule you have the atoms foi you can builu, with the exclusion of cyclic molecules anu
those that iesult in atoms oveilapping as you builu them.
Foi the thiiu tab, which has the most atoms available, you can builu ~ 9,uuu molecules!
= 016,- + O1734673 K.:" :"3 K21,M ,+O3@ Q"+:)* M1.,M 1,P
We uon't show bonuing in the atoms as you builu them (you can see bonuing in SB view)
because this sim is foi miuule school stuuents anu we uiun't want to focus on that topic. This
means that some stiuctuies you builu may have multiple names uepenuing on the bonuing (anu
if it is a iauical).
!"#$ &'()* +,- $./* 012 $3+4"32* 56.7- + 81734673

Authoi: Emily Nooie 0puateu: }uly 26, 2u11
Foi stiuctuies that coulu coiiesponu to moie than one molecule, only one name anu SB
stiuctuie aie useu, so if you built it many times it will always be given the same name anu show
the same stiuctuie with bonuing in SB, but it may not always be the most commonly founu
molecule of the possible options.
Foi each molecule, we give the I0PAC Tiauitional name, fiom the PubChem uatabase
http:pubchem.ncbi.nlm.nih.govseaichseaich.cgi foi all molecules, (so that watei will be
calleu 'watei' anu not 'uihyuiogen oxiue'). This means, foi example, that oiganic compounus
with common names will show with theii common name, but oiganic compounus without a
common name will be shown with the systematic name.