Molecular Model Building Instruction Manual

Molecular Model of Caffeine

!"#$% '( " )*$+,#-./ 01) $2-." 3.$%,- 4.'5$3-6 7"88 9::;

Models of organlc molecules provlde a physlcal represenLaLlon of Lhe Lhree-dlmenslonal arrangemenL
of aLoms ln space. uslng a molecular model klL LhroughouL your sLudy of organlc chemlsLry wlll
enable you Lo beLLer undersLand boLh Lhe chemlcal and physlcal properLles of Lhe molecules you
encounLer.

1. 1he flrsL sLep Lo successfully uslng your molecular model klL ls Lo become acqualnLed wlLh
Lhe conLenLs of your klL and whaL each unlL represenLs.
?our model klL conLalns several polyhedrons and spheres LhaL wlll represenL Lhe
aLoms you work wlLh. 1he ALom 1able speclfles Lhe number of holes on each
polyhedron and sphere and ldenLlfles whlch are used Lo form a speclflc hybrldlzaLlon.


1he 8ond 1able speclfles Lhe #3"8$% bond lengLh represenLed by each of Lhe
connecLors ln your klL along wlLh a llsL of common bonds you wlll encounLer
LhroughouL your sLudy of organlc chemlsLry and Lhe correspondlng connecLor LhaL
you should use. (for bonds ln grey, more Lhan one connecLor can be used)






!"#$
&'()*
+)',-

.'/- +)0*

1*2

3/**4

.'/- 3/*5

6789" +)0*

6789" 3/*5

6789" +)0*
:;<9*/*=

# of holes 4 4 4 4 3 3 14 2
sp
3
x x x x
sp
2
x x
sp x
+#42 &'()*
>/'48*
1.10

P-C

P-n P-C C-C C=C C-n C=n n=n n-n
3/**4
1.40

C=C C-C C-n C=n C-n n-n
?97"*
1.34

C-C C-n C-C n-n
@*))#A
1.80

C-Cl C-8r C-l
+)0*
1.33

C=C C-C C=C C=n C-n C=n n=n n-n
LlecLron lone palrs can be represenLed uslng elLher Lhe green or blue orblLal plaLes ln your klL.


2. now LhaL you are famlllar wlLh whaL your model klL conLalns, Lhe nexL sLep ls Lo learn how
and when Lo use each unlL.
When bulldlng a molecular model lL wlll be helpful Lo deslgnaLe whlch polyhedron
you wlll use for each aLom ln a molecular formula. uslng dlfferenL polyhedrons wlLh
dlfferenL colors for dlfferenL aLoms wlll make lL easler for you Lo keep Lrack of aLoms
when creaLlng and analyzlng lsomers. lurLhermore, uslng Lhe approprlaLe connecLors
Lo represenL your bonds (slngle, double or Lrlple) wlll enable you Lo beLLer vlsuallze
whlch molecules can do resonance, whlch molecules are con[ugaLed and/or
aromaLlc, and whlch molecules have barrler(s) Lo roLaLlon and are or are noL planar.
keep ln mlnd LhaL whlle some bonds may be represenLed by more Lhan one
connecLor, lL may be useful Lo plck connecLors ln a way LhaL wlll make lL easlesL for
you do recognlze sigma and pi bonds.

! !)-'4*BC Slngle bonds are consLrucLed by connecLlng Lwo polyhedrons or a
polyhedron and a sphere wlLh a slngle connecLor (noL lncludlng a blue connecLor)
LhaL corresponds Lo Lhe aLoms you are bondlng.
Lxample: eLhane (CP
3
CP
3
)

! !)-*4*BC uouble bonds (one sigma bond and one pi bond) can be consLrucLed ln
Lwo dlfferenL ways.
1) 1wo polyhedrons (usually four-holed) are connecLed wlLh Lwo blue
connecLors. 1hls meLhod of consLrucLlon hlghllghLs Lhe planarlLy of a molecule
and Lhe barrler(s) Lo roLaLlon LhaL exlsL because of Lhe pl bond. Powever, Lhls
meLhod wlll noL enable you Lo dlsLlngulsh beLween Lhe slgma and pl bond.
Lxample: eLhene (CP
2
CP
2
)



2) 1wo polyhedrons (usually flve-holed) are connecLed wlLh a slngle connecLor
(noL lncludlng a blue connecLor) LhaL corresponds Lo Lhe aLoms you are
bondlng. 1hls wlll represenL Lhe slgma bond. Cne orblLal plaLe of each color ls
aLLached Lo each polyhedron wlLh same colored orblLal plaLes ad[acenL. 1hls
wlll represenL Lhe pl bond. 1hls meLhod enables you Lo clearly dlsLlngulsh
beLween slgma and pl bonds, however, lL wlll make lL more dlfflculL Lo see Lhe
barrler(s) Lo roLaLlon LhaL exlsL because of Lhe pl bond.
Lxample: eLhene (CP
2
CP
2
)




! !)-54*BC 1rlple bonds (one sigma bond and two pi bonds) can be consLrucLed ln
Lwo dlfferenL ways.
1) 1wo polyhedrons (usually flve-holed) are connecLed wlLh Lhree blue
connecLors. 1hls meLhod of consLrucLlon hlghllghLs Lhe barrler(s) Lo roLaLlon
LhaL exlsL because of Lhe Lwo pl bonds. Powever, Lhls meLhod wlll noL enable
you Lo dlsLlngulsh beLween Lhe slgma and pl bonds.
Lxample: eLhyne (PC!CP)


2) 1wo polyhedrons (usually fourLeen-holed) are connecLed wlLh a slngle
connecLor (noL lncludlng a blue connecLor) LhaL corresponds Lo Lhe aLoms you
are bondlng. 1hls wlll represenL Lhe slgma bond. lour orblLal plaLes (Lwo of
each color) are aLLached Lo each polyhedron wlLh same colored orblLal plaLes
ad[acenL Lo one anoLher and dlfferenL colored orblLal plaLes opposlLe one
anoLher. 1hls wlll represenL Lhe Lwo pl bonds. 1hls meLhod hlghllghLs Lhe
llnearlLy of a molecule and clearly dlsLlngulshes beLween slgma and pl bonds.
Powever, lL wlll make lL dlfflculL Lo see Lhe barrler(s) Lo roLaLlon LhaL exlsL
because of Lhe pl bonds
Lxample: eLhyne (PC!CP)



! D5,)7, E#)*,0)*B: Cycllc alkanes, alkenes, and alkynes can be consLrucLed uslng
Lhe same meLhods prevlously menLloned.
Lxample: 8enzene (C
6
P
6
) ls a common cycllc molecule (one LhaL you wlll
repeaLedly encounLer ln your sLudy of organlc chemlsLry) LhaL applles many of
Lhe model bulldlng rules llsLed above.


lurLhermore, consLrucLlon of cycllc molecules wlll enable you Lo beLLer vlsuallze
chalr conformaLlons and "2,"8 and $<="-'.,"8 lnLeracLlons for cycllc molecules
wlLh subsLlLuenLs. MasLery of Lhls sklll ls crlLlcally lmporLanL when deallng wlLh
carbohydraLes.
Lxample: 1-chlorocyclohexane











(Cl = axlal) (Cl = equaLorlal)

* When bulldlng a molecular model, you wlll ofLen encounLer molecules LhaL are
noL only composed of dlfferenL aLoms, buL also of seLs of Lhe same aLoms wlLh
dlfferenL hybrldlzaLlons. 8ecause your model klL conLalns a llmlLed supply of
dlfferenL colored polyhedrons, lL ls up Lo you Lo declde wheLher you wanL Lo
represenL all Lhe same aLoms wlLh Lhe same colored polyhedrons or wheLher
you wanL Lo dlsplay Lhe dlfferences ln Lhelr hybrldlzaLlon by uslng dlfferenL
colored polyhedrons. lf you choose Lo represenL slmllar aLoms uslng same
colored polyhedrons, and Lhus use polyhedrons LhaL do noL necessarlly
correspond Lo Lhe correcL hybrldlzaLlon of an aLom, make sure you Lake Lhls
lnLo accounL when observlng/deLermlnlng Lhe bond angles of your model.

* C-P bonds do noL always have Lo be used/lncluded ln your model ln order for
you Lo undersLand a molecules sLrucLure. Powever, lf you are havlng a dlfflculL
Llme vlsuallzlng Lhe formal charges [lf any] or hybrldlzaLlon of Lhe aLoms ln your
molecule, lL may be ln your besL lnLeresL Lo lnclude Lhem.

3. now LhaL you know how Lo use Lhe conLenLs of your model klL Lo consLrucL varlous molecular
sLrucLures, Lhe nexL sLep ls Lo learn how Lo use Lhe sLrucLures you consLrucL Lo help you
beLLer undersLand Lhe characLerlsLlcs of a molecule.
FB#$*/B: lsomers are molecules wlLh Lhe same chemlcal formula buL dlfferenL speclal
arrangemenLs of aLoms. uslng Lhe models you consLrucL, you can alLer Lhe sLrucLure
of your molecule Lo creaLe dlfferenL lsomers.

! D#4G#/$'"7#4') FB#$*/B: 1o creaLe a conformaLlonal lsomer you can roLaLe Lhe
subsLlLuenL(s) of your molecule around a slngle bond. 8oLaLlng Lhe subsLlLuenL(s)
of your molecule wlll enable you Lo vlsuallze ecllpsed and sLaggered (gauche and
anLl) conformaLlons as well as deLermlne wheLher your molecule ls #,# or -."(#.
1hls ln Lurn wlll enhance your undersLandlng of Lhe varlous Lypes of sLraln and
consequenL relaLlve energles of Lhe lsomers and conformaLlons of Lhe varlous
molecules you wlll encounLer LhroughouL your sLudy of organlc chemlsLry.
Lxample: buLane (CP
3
CP
2
CP
2
CP
3
)

(ecllpsed) (gauche) (anLl)

! D#4B"7"0"7#4') FB#$*/B: 1o creaLe a consLlLuLlonal lsomer, you can alLer Lhe
connecLlvlLy of Lhe aLoms LhaL comprlse your molecule Lo creaLe dlfferenL
molecules. 1hese molecules wlll have dlfferenL sLrucLures and as a resulL wlll
exhlblL dlfferenL properLles.

! ;"*/*#7B#$*/B: 1here exlsL Lwo Lypes of sLereolsomers (enanLlomers and
dlasLereomers). 1o creaLe an enanLlomer (nonsuperposable mlrror lmage of a
molecule) lnverL all of your molecules sLereocenLers by changlng Lhe poslLlon of
one of Lhe aLoms around each sLereocenLer. 1o creaLe a dlasLereomer lnverL aL
leasL one buL noL all of your molecules sLereocenLers by changlng Lhe poslLlon of
one of Lhe aLoms around Lhe sLereocenLer. 1he Lhree-dlmenslonal sLrucLure of
your molecular models wlll also enable you Lo more easlly deLermlne Lhe
conflguraLlons of Lhe sLereocenLer(s) of your molecule. 1o deLermlne Lhe
conflguraLlon of Lhe sLereocenLer(s) of your molecule, hold Lhe aLom or group of
aLoms wlLh Lhe lowesL prlorlLy ln your hand so LhaL Lhe sLereocenLer ls faclng you
and so LhaL Lhe aLom or group of aLoms wlLh Lhe lowesL prlorlLy ls faclng away
from you. lf Lhe remalnlng aLoms or groups of aLoms faclng you decrease
clockwlse ln prlorlLy, Lhe absoluLe conflguraLlon of your sLereocenLer ls >. lf Lhe
remalnlng aLoms or groups of aLoms faclng you decrease counLerclockwlse ln
prlorlLy, Lhe absoluLe conflguraLlon of your sLereocenLer ls ?.












Lxample:


(8r)

(Cl) (P)






(l)



(? conflguraLlon)

1*B#4'4,*H D#4I08'"7#4H J !/#$'"7,7"5: 8ulldlng Lhree-dlmenslonal models of a
molecules sLrucLure by uslng Lhe varlous unlLs ln your model klL Lo deplcL noL only Lhe
arrangemenL of aLoms ln space and Lhelr connecLlvlLy's buL also Lhe presence of 4
orblLals and lone palr elecLrons, wlll enable you Lo deLermlne wheLher a molecule
can do resonance, has con[ugaLlon, and/or ls aromaLlc. 1hls ablllLy wlll greaLly
enhance your undersLandlng of Lhe properLles of Lhe molecules you encounLer ln
organlc chemlsLry.