STRUCTURE OPTIMIZATION & RMS FITTING

Structure Optimization & RMS Fitting

Structure Optimization & RMS Fitting

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed (Lada, 2010).

Aim

The aim of this experiment is to create realistic models using conformational analysis and geometry optimisation. Bufotenine molecular model will be experimented by usage of the CSD structure as a reference and the bufotenine structure builded to find out the lowest optimisation and RMS fitting of bufotinine.

Method

Bufotenine was drawn using Scigress and the geometry was optimised using MM3 method.

Three dihedral angles were measured using 12 step of 30 degrees. The CSD structure (reference bufotenine structure) was then downloaded. Finally the conformational analysis was carried out (rotating the three dihedral angles) on bufotenine (that I built) using an optimised map calculation (MM3). The colour of the CSD structure was changed to blue and the colour of the builded structure was changed to red to be easier distinguished (Tom, 2010).

The conformers were tested one by one via selecting three atoms (same atoms in both structures) from both structures and superimposing them to find the best fitted superimposed structure of the bufotenine and the CSD structure. RMS values of all energy conformers were recorded which helps in recognition of the superimposable structures.

Results

The energy of Bufotenine structure is 28.5548 kcal/mol.

The dihedral angles are 174.65 o (C-C-C-C), 177.04 o (C-C-C-N) and -169.42 o (C-C-N-C).

Conformational analysis table

Conformer

RMS value

Energy

(kcal/mole)

1

0.0387

27.283651

2

0.0388

27.292459

3

0.0393

27.391516

4

0.0380

27.393360

5

0.0377

27.400194

6

0.0377

27.401468

7

0.0365

27.414959

8

0.0383

27.422382

9

0.0376

27.428066

10

0.0383

27.429008

The conformational analysis formed 68 conformers with the lowest being 27.283651 kcal/mol and the highest being 35.193905 kcal/mol. The lowest energy conformers were the closest to the CSD structure and the highest energy conformers were the furthest as there were so many differences ...