Computational Protocol to Evaluate Side-Chain Vicinal Spin–Spin Coupling Constants and Karplus Equation in Amino Acids: Alanine Dipeptide Model

A computational protocol has been applied to the alanine dipeptide model in order to study the side-chain conformation, the calculated spin–spin coupling constants involved in the side-chain χ1 angle, and theoretical extended Karplus equations developed for amino acids. Two structures within the bac...

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Bibliographic Details
Published in:Journal of chemical theory and computation 2019-07, Vol.15 (7), p.4252-4263
Main Authors: San Fabián, J, Omar, S, García de la Vega, J. M
Format: Article
Language:English
Subjects:
Alanine
Amino acids
Chains
Computation
Constants
Couplings
Mathematical models
Molecular conformation
Solvent effect
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Summary:A computational protocol has been applied to the alanine dipeptide model in order to study the side-chain conformation, the calculated spin–spin coupling constants involved in the side-chain χ1 angle, and theoretical extended Karplus equations developed for amino acids. Two structures within the backbone secondary conformation are used to predict coupling constants which in addition are employed to analyze the effect of those structures on the resulting Karplus extended equations. The number of Fourier coefficients to be included within the Karplus equations is critically analyzed. Wave function and density functional methods as well as different basis sets are compared to find appropriate Karplus coefficients in the most efficient way. The influence of exchange and correlation functionals and the solvent effect on the calculated couplings are considered.
ISSN:1549-9618
1549-9626
DOI:10.1021/acs.jctc.9b00131