Comparison of conformational behavior of the short alanine peptides and their boron analogues
| Autor: | M. Vaultier, Jaroslav Koča, Martin Černohorský |
|---|---|
| Rok vydání: | 1999 |
| Předmět: |
Alanine
Quantitative Biology::Biomolecules 010405 organic chemistry Ab initio chemistry.chemical_element Dihedral angle 010402 general chemistry Condensed Matter Physics 01 natural sciences Biochemistry Stationary point Quantum chemistry 0104 chemical sciences Maxima and minima chemistry.chemical_compound Crystallography Monomer chemistry Computational chemistry Physics::Atomic and Molecular Clusters Physical and Theoretical Chemistry Boron |
| Zdroj: | ResearcherID |
| ISSN: | 0166-1280 |
| DOI: | 10.1016/s0166-1280(99)00056-1 |
| Popis: | Conformational behavior of short terminally blocked alanine peptides up to three residues has been analyzed by means of a new computer program Vader . The program is based on Single-Coordinate-Driving method and it employs quantum chemistry energy calculation. The semiempirical AM1 method has been used in this study. Conformational behavior of alanine peptides has been compared with their boron analogues. It has been found that: 1. Semiempirical AM1 method creates an artifact in energy calculation of boron analogues for geometries where the dihedral angles are around zero value. In such a case, ab initio methods have to be employed. 2. Boron analogues appear conformationally more flexible. They exhibit much higher number of energy minima along the PES. It has also been concluded that the program Vader is able to give quite a good estimation of stationary points. All stationary points found by Vader for monomers and those stationary points with relative energy less that 2.0 kcal/mol found for the dimers were subjected to frequency analysis of the Hessian matrix. In all cases, they were confirmed as stationary points of the same category as predicted by Vader . |
| Databáze: | OpenAIRE |
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