Th.

s BI TH THU QUNH
Th.s NGUYN XUN TRUNG

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GIO TRNH
NG DNG TIN HC
TRONG HO HC

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Hi Phng, thng 7 nm 2009
 GIO TRNH NG DNG TIN HC TRONG HO HC

GIO TRNH
NG DNG TIN HC TRONG
HO HC
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Th.s BI TH THU QUNH

NGUYN XUN TRUNG

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Th.s BI TH THU QUNH- Th.s NGUYN XUN TRUNG
BI 2 S DNG PHN MM HYPERCHEM

I. GII THIU
- Phn mm Hyperchem tp hp mt s phng php bn king nghim: MIND, ZINDO,
ZINDO/S, MNDOS l DO(xen ph vi phn) da trn nhng cch khc nhau tham s ho
vic tnh tch phn 1tm, y 2tm v tch phn tng tc ht nhn v electron thu c kt qu
tt hn.
- Phn ct li ca Hyperchem:
BUILD: xy dng bng con ng trc gic cc m hnh phn t
SETUP: la chn cc phng php tnh
+ c hc phn t: MOLECULAR MECHANICS
+ bn kinh nghim: SEMI- EMPIRICAL
+ phng php: AB- INITIO
+ hp tun hon: PERIODIC BOX
COMPUTE: thc hin tnh ton
SINGLE POIN: xc nh nng lng tng cng ( kcal/mol )
GRADIENT ( kcal/mol.A): gi tr ca cn bc 2 bnh phng trung bnh ca tt c cc lc
trn cc nguyn t - tc bin i nng lng tng cng tnh theo s chuyn dch theo cc hng
x,y,z.
II. CC BC C BN KHI S DNG HYPERCHEM
1. Xy dng phn t : Bt ch lm vic - Chn file\ start log
a. V phn t
*Chn nguyn t
- Nhp chut vo menu: Build \ Default element ( xo du x trc allow lons; explicit)
- Chn nguyn t, mun thay i nguyn t: Select atom
Ch thch :
- s dng nguyn t c nhiu lin kt hn ho tr ca n, nh du hp allow lons
- ngm nh nguyn t ngoi cng l Hyro, nh du hp Explicit Hyrogens
*V cu trc phn t
- Nhp vo trn mn hnh to nguyn t ban u
- Gi chut tri v ko chut ti mt v tr hoc 1 nguyn t no v lin kt n
- To lin kt bi bng cch nhp p chut vo lin kt
- Xo lin kt hoc nguyn t bng cch nhp p chut phi vo lin kt hoc nguyn t
* Quay phn t
- Nhp nt quay phn t trong mt phng mn hnh
- Nhp nt quay phn t trong khng gian ba chiu
Cch quay :
Nhp tri chut ln mn hnh dch chuyn chut quay phn t ti mt gc cn thit
*Phng to, thu nh phn t
Nhp vo nt sau nhp v gia tri chut v ko phng to phn t trn mn hnh
*Dch chuyn phn t
Nhp vo nt sau nhp v gi tri chut v ko xc nh phn t trn mn hnh
*Lp li cc bc cho n khi hon thin c khung phn t
b. Chuyn cu trc 3 chiu
- Nhp chut vo menu: Build \ AddH & Model Build
2. Ti u ho cu hnh
- Nhp chut vo menu: Setup \ Molecular Mechanich \ chn trng lc MN+ \ options \
Atomic charges.
- Nhp chut vo menu: Compute \ Geometry optimization \ Polak Riviere
RMS gradient = 0,1 OK
Khi my bo Conv = Yes l c.

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 GIO TRNH NG DNG TIN HC TRONG HO HC
3. Tnh cc thng s
a. Chn phng php tnh
- Setup\ Semi-empirical\ AM1\ options
t Convergence limit ( t): 0,01
Iteration limit (gii hn t): 50
UHF
OK
- Compute \Geometry Optimization\ Polak-Ribiere : 200 (phn t cng ln cng cn vng lp cao)
b. Tnh im n ( nng lng tng cng)
- Compute \ single point
- Xem kt qu:
+ in tch, di lin kt trn phn t
+ Gc lin kt: nhp biu tng , kch vo nh cn xem gc. kt qu hin thanh di
khung phn t.
+ Display \Labels: Symbol: nguyn t
Charge: in tch
Bond length: di lin kt
Bond urder: bc lin kt
c. QSAR
- Compute\ properties
Pratical charger : in tch ring phn Surface area : in tch b mt
Volume : th tch Hyration Energy : nng lng hyrat ho
LogP Refractivity : h s khc x
Mass : khi lng Polarizability : h s phn cc
Cop QSAR : Option\output to\ Resultf window\ok
d. Chp ph v xem dao ng phn t
- Compute\ Vibration, Rotation analysis
- Xem kt qu : Compute\Vibration Spectum \ Frequency : tn s, Intensity : cng
- Xem dao ng phn t : Compute\Vibratinal Spectrum\ chn tch vo Animate Vibration\ sau
chn dao ng cn xem ri Apply\OK
4. Lu phn t: Vo file \ save
5. Thot, xem kt qu, in bng chng trnh win: m file.log

III. CHUYN CC DNG NG PHN

1. Chuyn dng gh 


thuyn




- Xy dng phn t
- Chn 2 lin kt C-C song song : Select\ Name Selection/Plane (of selection)
- B lin kt : Edit\ Reflect , sau chn 8 lin kt cn b
2. Chuyn cis 




trans
- Xy dng phn t
- Chn lin kt cn b C-H, C=C
- Eit\ Setbond torsion\ 0 (chn gc b)
IV. THC HNH
Bi 1 : Tnh cc thng s ho l cho phn t cis-but-2-en
1 4
H3C CH3
2 3
C C

H H

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Th.s BI TH THU QUNH- Th.s NGUYN XUN TRUNG
Bc 1 : Xy dng phn t
a. V phn t
- Chn nguyn t C : nhp vo nt
- V cu trc phn t

- Cu trc 3 chiu (dng trans-C4H8 : cu trc bn do nng lng cc tiu)

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 GIO TRNH NG DNG TIN HC TRONG HO HC
b. Chuyn dng cis
- Chn cnh b : nhp chut vo select sau chn cc nguyn t c lin kt cn b C1-C2,
2 3 3 4
C =C ,C -C bng cch nhp chut tri chn nguyn t

- Chn gc b : Eit\ Setbond torsion\ 0\ OK

- Kt qu dng cis

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Th.s BI TH THU QUNH- Th.s NGUYN XUN TRUNG
c. Ti u ho cu hnh dng cis v phng php tnh
* Chn phng php tnh : - Setup\ Semi-empirical\ AM1\ options
t Convergence limit ( t): 0,01
Iteration limit (gii hn t): 50
UHF \ OK
- Geometry Optimization\ Polak-Ribiere : 200 (phn t cng ln cng cn vng lp cao)

* Kt qu ti u

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 GIO TRNH NG DNG TIN HC TRONG HO HC
* Tnh im n : Compute \ single point
- Gi tr nng lng nguyn t no th nhp chut vo nt ri sau ch hoc nhp chut tri
vo nguyn t cn xem

- Xem di lin kt th nhp chut tri vo nt ri sau nhn chut tri vo 2 nguyn t
lin kt cn xem

di lin kt gia nguyn t cacbon th 4 v cacbon th 3 l 1,47579 A0

- Xem gi tr gc lin kt th nhp chut tri vo nt ri sau nhn chut tri vo 3 nguyn t
to gc cn xem

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Th.s BI TH THU QUNH- Th.s NGUYN XUN TRUNG

Gc lin kt to bi C4-C3-C2 l 123,8960

- QSAR : Compute\ properties

Surface area (in tch b mt) = 257,35 A2

Cop QSAR : Option\output to\ Resultf window\ok
- Chp ph:
Compute\ Vibration, Rotation analysis
Xem kt qu : Compute\Vibration Spectum \ Frequency : tn s, Intensity : cng
Frequency (tn s) = -51,07 , Intensity (cng ) = 0,564

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 GIO TRNH NG DNG TIN HC TRONG HO HC
- Dao ng phn t : - Xem dao ng phn t : Compute\Vibratinal Spectrum\ chn tch vo
Animate Vibration\ sau chn dao ng cn xem ri Apply\OK

V. BI TP
Tnh cc thng s ho l cho cc phn t: Buta-1,3- ien; Anilin; Phenol; Stiren; Axit axetic.

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BI 3
VIOLET
*Ch
- K hiu di : H2O th vit latex(H_2)O
- K hiu trn : sp3d2 th vit l latex(sp^2d^3)
I. BI TP TRC NGHIM DNG MT P N NG
1. Giao din

2. To mc
- Thm mc
- To tiu : in cc thng tin cho ch \mc\tiu \tip tc

3. To bi trc nghim mt p n ng

- Chn cng c\ bi tp trc nghim

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 GIO TRNH NG DNG TIN HC TRONG HO HC

- Chn kiu mt p n ng

- To nhiu phng n hoc bt phng n

- Nhp cu hi cho bi tp

- Thm nh cho bi trc nghim

4. Hon thnh v lu bi trc nghim
- Nhp ng hon thnh bi trc nghim

- Lu bi trc nghim vo cn thit

II. BI TP TRC NGHIM DNG NHIU P N NG

III. BI TP TRC NGHIM DNG NG SAI

IV. BI TP TRC NGHIM DNG GHP I

V. BI TP DNG CH

VI. BI TP DNG KO TH CH

VII. BI KIM TRA TRC NGHIM

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CHEMSKET

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BI 5
FLASH 8
I. TO TIU

II. TO CHUYN NG

III. TO QU O

IV. TO NT PLAY

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MCMIX

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