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HyperChem 5.

0 Windows

HC50-00-01-00

1996

1996 Hypercube, Inc.



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Hypercube, Inc.

Microsoft, MS-DOS, Exel .
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CARMm Molecular Simulation Inc.
IBM International Business Machines Inc.


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51

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53


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54

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56


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57

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58

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59


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60

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6 .
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ALA58 VAL.
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61


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77

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79

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82

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83

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85

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92

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94


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95

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96

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97

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HyperChem 5 Windows.

12
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2. Labels Atom Symbol.
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.
4. , 2-D :
5. , :
C-O .
6. ,
3-D .

- -NMA
98

, ,
trans-NMA, -NMA.
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O-C-N-C C-N-C-O,

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4. Trans, .
5. R- , .
6. , .
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,
CH - - , - NH . Set Torsion Edit
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NMA
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:
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..., "".
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3. :
4. .
99

5. -
. ,
; , .
6. Select Parameter Set Setup.
7. amber3, .
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10. , RMS
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HyperChem
.


11, ,
. ,
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.
:
1. , .
, 0.00.
2. Semi-empirical Setup.
3. CNDO , .
4. Single Point Compute.
HyperChem .
, ,
:
5. nma.hin.



, NMA 11
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NMA :
1. , Marge File.
2. water.hin.
NMA .
100


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101

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7. .
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:
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NMA, .
NMA.
:
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2. CNDO , .
3. Single Point Compute.
.
4. , .
, .
:


102

1. - .
, -

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.
2.
.

13

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.
2. testbpti.hin.
103

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3. , Show Hydrogens
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4. Rendering Display.
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7. , , Ribbons Rendering/Sticks ,
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8. , , :
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, sp3.
105

, , N-C . ,
sp3, .


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,
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2. Semi-empirical Setup.
3. , CNDO , L- Options.
4. Options, Convergence Limit 0.1.
,
, .
5. Total charge 2 .
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c.
8. Plot Molecular Properties.
9. Total Charge Density 2-D Contour .
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11. .
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106

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, 7, ,
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3
Ab Initi
3 ab initio ,
HyperChem.
, , ,
- , ab initio .
ab initio ,
107

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3 , :

Ab initio
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ab initio .
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ab initio
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,
ab initio .


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2. , Allow Ions Build.
, Allow Ions,
, ,
.
. Allow Ions
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108

3. Labels Display, .
4. Symbols , .
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O (),
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. H3O+ ,
.

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H3O+:
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2. , H3O
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3-D :
1. .
, Model Build Build,
,
.

:
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2. Options.
3. 1 Total charge L- OK,
Ab Initio.
4. L- OK,
Ab Initio.
+1 -
, .

.


:
1. Ab Initio Setup.
2. Other .
109

3. Assign Other Basis Set.


4. 4-31G .
4-31G ,
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6. , Apply Basis Set ,
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-
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. HyperChem
. , ,
.
, :
1. Labels Display.
2. Basis Set , .
:


H3O +:
1. Ab Initio Setup.
2.
Options, Total charge = 1, Spin multiplicity = 1,
Spin pairing = RHF, Convergence limit = 0.01, Iteration limit = 50, Accelerate convergence =
Yes. Single Point only
.
3. L- , Ab Initio
L- , Ab Initio.
4. Geometry Optimization Compute.
110

5. Polak-Ribiere 0.1 RMS


L- , .
HyperGauss .
, STO-3G H3O+ 113.74
0.99.
H3O+,
:
1. Ab Initio Setup, Options
MP2 , Ab Initio
Ab Initio , .
2. Single Point Compute.
H3O+ STO-3G -47270.57
/ SCF -47300.98 / MP2 , 30.50 / .


STO-3G H2O+H +:
1. R-
H3O +, H2O.
H + - , H2O

H3O+

H2O.
2. Ab Initio Setup Options,
Total charge 1 0. .
3. Geometry Optimization Compute H2O,
H3O +.
STO-3G 100.0
0.99.
4. Single Point Compute.
H2O STO-3G -47041.82
/ SCF -47066.21/ MP2 ,
-24.45 / .
228.75 / SCF 234.77 / MP2.
.


111

1. 3-21G 6-31G* .
, H3O +,
. , , ( SCF)

3-21G

. , s p
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NH3

. D-
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2. HF, H2O, NH3 CH4
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3. H + H2O, Ab Initio
-

HyperChem REACT.SCR.


Ab Initio
- , HyperChem ,
7, , HyperChem 5
Windows.

15

,


,
, -


NH3.


112

:
1. L- Explicit Hydrogens Build, .
2. Default Element Build,
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3. N (),
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4. L- , .
5. L- ,
.
6. Add H & Model Build Build, NH3
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3-21G
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2. Basis Set,
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4. Small (3-21G) , L- Apply Basis
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, , 3-21G.
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. ,
Atoms Select ,
Residues Molecules.
6. Ab Initio Setup .
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8. Extra Basis Function D Exponent 1.0
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Ab Initio .
113

6
d-, 1.0, .
.
9. R- , .
Ab Initio
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1. Geometry Optimization Compute Polak-Ribiere
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.
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2. Single Point Compute, ,
MP2 .
SCF -35086.49 / ,
MP2 -35191.11 /.
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.

.
4. HyperChem
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5. Vibrational Spectrum Compute,
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HyperChem.
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,
114

. ,
.
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. Apply,
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115

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, MP2 .
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-
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, 0.05 /.


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,

116

- Ab Initio
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117

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118

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119


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120

3. NH3 CH3- OH3+.


4.
.
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[CH2CHO]-;
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Ab Initio
- , HyperChem,
7, , HyperChem 5
Windows.

16
-
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-


-
, * .


Ab Initio
,
.
STO-3G :
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121

2. , Explicit Hydrogens .
3. -
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.
,
C-C 1.31, C-H 1.08, H-C-H 115.7 .
:
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correlation energy. , ,
.
2. Single Point Compute.
SCF -48364.64 / MP2
-48438.61 /, -74.97 / .

.
,
,
.
.


:
1. Orbitals Compute.
(HOMO) (LUMO)
:

122

(HOMO) *(LUMO) .

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. ,
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1000, Maximum Excitation Energy. ,
, .
-
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.
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123

7. Electronic Specrum Compute, ,


:
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124

(STO-3G)
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90 .
C-C 1.49
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. C-H 1.08

H-C-H -

117.8 .
:
1. Ab Initio Setup, Options, , MP2
correlation energy .
.
2. Single Point Compute.
SCF -48328.65
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MP2

(-45.02 /) -

(-74.43 /), ,

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125

1. * CI
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.
3. n p*
.
4. *
CI.
.


ab initio
- , HyperChem ,
7, , HyperChem 5
Windows.

4
HyperChem & DDE
4 , Windows
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Windows. 4 , :

HyperChem
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126

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4. .
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6. -
.


:
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2. L- benzene A2 plot.xls.
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133

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137

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