1. Computational Systems Biology Lab. 2011.04.13
계산 화학
Computational Systems Biology Lab.

2. Contents Introduction Exercise (Gaussian 03w) HW Coordinate system
Draw Z-matrix
Calculate single point energy
Minimization and calculate property
Electrostatic potential map
Potential energy surface HW

3. Coordinate System (1) Cartesian coordinates Most common system
Given as x, y, z coordinates
Three axes are orthogonal
TITLE guanyl-3',5'-cytidine
(X, Y, Z cell lengths)
(X, Y, Z cell angles)
No. Atom X Y Z C C C N N C .
connectivity table (sometimes)
atom types (sometimes)
bond types (sometimes) 1 2 3 4 5 6 7 8 9

4. Coordinate System (2) Crystallographic Coordinates
In natural crystal axes, called notional axes
Notional axes are not generally perpendicular
TITLE guanyl-3',5'-cytidine
(a, b, c cell lengths)
(a, b, g cell angles)
No Atom a b c C C C N N C .
connectivity table (sometimes)
atom types (sometimes)
bond types (sometimes) 1 2 3 4 5 6 7 8 9

5. Coordinate System (3) Internal Coordinates
Described by reference to another atom
Distance, Angel, Torsion Angle
primarily used for more sophisticated calculations
molecular orbital calculation
ab initio calculations …

6. Coordinate System (4) Less Common Coordinates Spherical Coordinates
More sophisticated calculations
Polar Coordinates
Hydrogen bonds

7. Exercise : Z-matrix
Ethane

8. Exercise : Z-matrix Acetic acid의 Z-matrix 짜보기 시작 – 보조 프로그램 – 메모장(워드패드)
Z-matrix를 완성한 후 Aceticacid.gjf로 저장
Gaussview에서 구조 확인하면서 변수 고치기
Atom간 결합 길이(간격은 space bar, 소수점 표시)
C - C
1.5
C - O
1.4
C = O
1.25
C - H
1.09
O - H
1.0

9. Coordinate System – gjf file
gjf file format
%chk=B.chk
# opt sto-3g
Title card Required
0 1 C
H B1
H B A1
H B A D1
Jop type, method, basis set, option
Compound name
Charge, Spin multiplicity

10. Coordinate System – gjf file
Jop type
SP : single point energy (default)
Opt : geometry optimization
Freq : frequency and thermochemical analysis
IRC : reaction path following
Scan : potential energy surface scan
Option
Pop(Population) : atomic charge, dipole moment, molecular orbital, multipole moments (default)

11. Coordinate System – gjf file
Gaussian input file format
Angle
Name
Bond length
Torsion angle

12. Exercise : SPE calculation
Option
# (SP) (Methd)/(basis set)
Ex) # SP AM1/ZDO
# SP HF/STO-3G

13. Exercise : SPE calculation
시작  모든프로그램  Gaussian 03W  Gaussian 03W

14. Exercise : SPE calculation
gjf file  gaussian 창으로 drag & drop

15. Exercise : SPE calculation
Ready for processing start  Run  C: Save

16. Exercise : SPE calculation
Processing complete  GaussView실행

17. Exercise : SPE calculation
File  Open  파일형식 수정  out  열기

18. Exercise : SPE calculation
Results  Summary

19. Exercise : Minimization and PC
Option
# (Opt) Freq (Methd)/(basis set)
Ex) # SP AM1/ZDO
# SP HF/STO-3G

20. Exercise : Minimization and PC
Result  Vibration  check  Start

21. Exercise : Minimization and PC
Spectrum

22. Exercise : Minimization and PC
Result  Veiw file ★Energy Unit : 1HF = kcal/mol

23. Molecular Orbital Molecular Orbital
A space in a molecule where electrons are most likely to be found
Describe behavior of one electron in the electric field
Bonding / Anti-bonding orbital
HOMO, LUMO, …

24. Diatomic Molecular Orbital

25. Exercise : Molecular orbital
Edit  MOs

26. Exercise : Molecular orbital
New  Generate

27. Exercise : Molecular orbital
Visualize  Add Type : HOMO, LUMO  Update

28. Exercise : Molecular orbital
Right Drag : size

29. Exercise : Molecular orbital
Right One Click  Display format

30. Exercise : Electrostatic potential map
gjf file  gaussian 창으로 drag & drop

31. Exercise : Electrostatic potential map
Ready for processing start  Run  C: Save

32. Exercise : Electrostatic potential map
Processing complete  Utilities  FormChk

33. Exercise : Electrostatic potential map
Utilities  CubeGen

34. Exercise : Electrostatic potential map
The following dialog box appears:
Property[Density]? Density
Formatted Checkpoint File? C:\Filename.fch (note that you wil l need to specify the path to your .fch file here)
Cube File [ ]? Filename.cube (this is the name of your cube fil e Cubegen will create)
Approximate Points per Side [0]? 40 (This puts roughly 40 poin ts on each side of the cube, giving it 403 points)
Header in cube file [H]? H (make sure to have a header so you can get the exact dimensions of the cube file. T3D will require them)

35. Exercise : Electrostatic potential map

36. Exercise : Electrostatic potential map
File  Open  파일형식 수정  fch  열기

37. Exercise : Electrostatic potential map
Results  Surface

38. Exercise : Electrostatic potential map
Cube Actions  New Cube

39. Exercise : Electrostatic potential map
Kind : Total Density  OK  Surface Actions  New Mapped Surface

40. Exercise : Electrostatic potential map
Default option  OK

41. Potential Energy Surface
PEF : Functional Representation of PES

42. Potential Energy Surface
PEF (Force Field)
An empirical set of energy function

43. Exercise : Potential Energy Surface
Option
#p (SP) Freq (Methd)/(basis set) Scan
Ex) #p AM1 Scan
Define variable

44. Exercise : Potential Energy Surface
Example
operation
Z-matrix
Variables
(B1에 대해여 1.0부터 5단계로 -0.1)

45. Exercise : Potential Energy Surface
시작  모든프로그램  Gaussian 03W  Gaussian 03W

46. Exercise : Potential Energy Surface
gjf file  gaussian 창으로 drag & drop

47. Exercise : Potential Energy Surface
Ready for processing start  Run  C: Save

48. Exercise : Potential Energy Surface
Processing complete  GaussView실행

49. Exercise : Potential Energy Surface
File  Open  파일형식 수정  out  열기

50. Exercise : Potential Energy Surface
Result  Scan 선택
click

51. Exercise : Potential Energy Surface
Dipeptide(Ala-Ala)

52. PES for SN2 Reaction Nucleophilic Substitution
“Incoming group” replaces the “leaving group” in one step
From Wikipedia, SN2 Reaction

53. PES for SN2 Reaction

54. PES for SN2 Reaction 시작  모든 프로그램  Gaussian 03W  Gaussian 03W
Calculation using Gaussian
1. Select gjf file!
2. Drag & Drop 2 1

55. PES for SN2 Reaction 시작  모든 프로그램  Gauss view  Gauss view1 2
1. File - Open
2. Open “.log” file

56. PES Generation 시작  모든 프로그램  Golden Software Surfer 8  Surfer 8
1. Grid-Data
2. Open
“PES_data.xls”
3. Click OK

57. PES Generation 1. Map – Contour Map – New Contour Map 2. Open
“PES_data.grd”

58. PES Generation 1. Double Click Map 2. Check Fill Contours
3. Check Color Scale
4. OK

59. H.W.
가우시안에서 사용하는 대표적인 Method와 그에 해 당하는 basis set 을 3가지 조사하여 정리(Pair로 조사 해야 함)
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제출일 : 4월 20일
장소 : 분자 설계 연구소(BMDRC)