Asymmetry in methyl group of ethane during internal rotation:Ab initio study

Mastryukov, V. S.; Samdal, Svein

doi:10.1002/(sici)1096-987x(19980730)19:10<1141::aid-jcc3>3.0.co;2-m

Cited by 2 publications

(1 citation statement)

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“…A possibility to address this problem is to treat the methyl group as a rigid symmetric rotor with local C 3 v symmetry (see Table S2). However, the results will be not realistic because the neighbor group to which the methyl group is attached, the C α N′C′H α group, does not have 3-fold symmetry. On the other hand, for other AA residues, all except glycine and alanine, it is necessary to fix the χ 1 angle (N′–C α –C β –X γ ), choosing an X γ substituent.…”

Section: Results and Discussionmentioning

confidence: 99%

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

Fabián

Omar

Vega

2019

J. Chem. Theory Comput.

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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 χ 1 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.

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Section: Results and Discussionmentioning

confidence: 99%