ASSIGNMENT

MOLECULAR MODELLING OF ANY 5 AMINO OR

NUCLEIC ACIDS

CHE 6505
Biochemical Engineering

Submitted to
DR. MOHIDUS SAMAD KHAN
Assistant Professor
Department of Chemical Engineering, BUET

Submitted by
TANVIR AHMED
Student No. 1015022027
Department of Chemical Engineering, BUET

MOLECULAR MODELLING OF ANY 5 AMINO ACIDS

No.: 01
Name: ALANINE
Input Geometry:

Output Geometry:
Using Semi Empirical PM6 Method:

Using MP2 6-31G Method:

Calculated Energy:
Using Semi Empirical PM6 Method: -0.15737769 a.u.
Using MP2 6-31G Method: -322.34422939 a.u.
Dipole Moment:
Using Semi Empirical PM6 Method: 2.9012 Debye
Using MP2 6-31G Method: 1.8059 Debye

Bond Name

Bond Lengths (Armstrong)

Semi
Empirical
MP2 6-31G
PM6

Bond Angle
Name

Bond Angle (Degree)

Semi
Empirical
MP2 6-31G
PM6
27.646
122.061

- C-H-

1.12764

1.11087

-O-C=O

- C-C-

1.52996

1.52249

-C-C-C-

108.307

112.172

-C-O-

1.37470

1.39845

-C-C-N-

106.209

107.734

-C=O

1.20566

1.25001

- C-N-

1.48260

1.47154

-N-H-

1.01558

1.01452

-H-O-

0.99439

0.98514

No.: 02
Name: LEUCINE
Input Geometry:

Output Geometry:
Using Semi Empirical PM6 Method:

Using MP2 6-31G Method:

Calculated Energy:
Using Semi Empirical PM6 Method: -0.18220359 a.u.
Using MP2 6-31G Method: -441.54369791 a.u.
Dipole Moment:
Using Semi Empirical PM6 Method: 3.15991 Debye
Using MP2 6-31G Method: 1.8625 Debye

Bond Name

Bond Lengths (Armstrong)

Semi
Empirical
MP2 6-31G
PM6

Bond Angle
Name

Bond Angle (Degree)

Semi
Empirical
MP2 6-31G
PM6
120.256
122.145

- C-H-

1.12837

1.09320

-O-C=O

- C-C-

1.52780

1.51391

-C-C-C-

108.840

109.893

-C-O-

1.37555

1.37798

-C-C-N-

106.028

106.935

-C=O

1.20604

1.23430

- C-N-

1.48304

1.46087

-N-H-

1.01540

1.01103

-H-O-

0.99400

0.98305

No.: 03
Name: LYSINE
Input Geometry:

Output Geometry:
Using Semi Empirical PM6 Method:

Using MP2 6-31G Method:

Calculated Energy:
Using Semi Empirical PM6 Method: -0.12430592 a.u.
Using MP2 6-31G Method: -495.22106047 a.u.
Dipole Moment:
Using Semi Empirical PM6 Method: 5.7817 Debye
Using MP2 6-31G Method: 0.9080 Debye

Bond Name

Bond Lengths (Armstrong)

Semi
Empirical
MP2 6-31G
PM6

Bond Angle
Name

Bond Angle (Degree)

Semi
Empirical
MP2 6-31G
PM6
120.210
122.457

- C-H-

1.12718

1.09776

-O-C=O

- C-C-

1.52722

1.51937

-C-C-C-

108.842

109.962

-C-O-

1.37529

1.39740

-C-C-N-

106.005

106.840

-C=O

1.20649

1.25042

- C-N-

1.48412

1.47700

-N-H-

1.01836

1.01609

-H-O-

0.99359

0.98632

No.: 04
Name: GLYCINE
Input Geometry:

Output Geometry:
Using Semi Empirical PM6 Method:

Using MP2 6-31G Method:

Calculated Energy:
Using Semi Empirical PM6 Method: -0.14829389 a.u.
Using MP2 6-31G Method: -283.22927934 a.u.
Dipole Moment:
Using Semi Empirical PM6 Method: 1.0479 Debye
Using MP2 6-31G Method: 1.8879 Debye

Bond Name

Bond Lengths (Armstrong)

Semi
Empirical
MP2 6-31G
PM6

Bond Angle
Name

- C-H-

1.11915

1.10924

-O-C=O

- C-C-

1.51610

1.51613

-C-C-C-

-C-O-

1.37305

1.39836

-C-C-N-

-C=O

1.20747

1.24826

- C-N-

1.47363

1.46685

-N-H-

1.01785

1.01462

-H-O-

0.99530

0.98497

Bond Angle (Degree)

Semi
Empirical
MP2 6-31G
PM6
120.486
122.722

114.072

109.364

No.: 05
Name: SERINE
Input Geometry:

Output Geometry:
Using Semi Empirical PM6 Method:

Using MP2 6-31G Method:

Calculated Energy:
Using Semi Empirical PM6 Method: -0.21715500 a.u.
Using MP2 6-31G Method: -397.27948887 a.u.
Dipole Moment:
Using Semi Empirical PM6 Method: 1.0066 Debye
Using MP2 6-31G Method: 0.6000 Debye

Bond Name

Bond Lengths (Armstrong)

Semi
Empirical
MP2 6-31G
PM6

Bond Angle
Name

Bond Angle (Degree)

Semi
Empirical
MP2 6-31G
PM6
120.642
122.726

- C-H-

1.13194

1.09485

-O-C=O

- C-C-

1.52577

1.52731

-C-C-C-

109.366

109.040

-C-O-

1.37369

1.39237

-C-C-N-

106.159

112.425

-C=O

1.20528

1.25216

- C-N-

1.47733

1.47748

-N-H-

1.01547

1.01611

-H-O-

0.99579

0.98595

10