Department of Chemistry, Faculty of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania.
Department of Chemistry, Faculty of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania.
J Mol Graph Model. 2014 May;50:125-33. doi: 10.1016/j.jmgm.2014.04.001. Epub 2014 Apr 13.
Potential energy surface (PES) were built for nineteen amino acids using density functional theory (PW91 and DFT M062X/6-311**). Examining the energy as a function of the φ/ψ dihedral angles in the allowed regions of the Ramachandran plot, amino acid groups that share common patterns on their PES plots and global minima were identified. These patterns show partial correlation with their structural and pharmacophoric features. Differences between these computational results and the experimentally noted permitted conformations of each amino acid are rationalized on the basis of attractive intra- and inter-molecular non-covalent interactions. The present data are focused on the intrinsic properties of an amino acid - an element which to our knowledge is typically ignored, as larger models are always used for the sake of similarity to real biological polypeptides.
使用密度泛函理论（PW91 和 DFT M062X/6-311**）为十九种氨基酸构建了势能面（PES）。通过检查允许的 Ramachandran 图区域中 φ/ψ 二面角的能量，确定了在 PES 图和全局最小值上具有共同模式的氨基酸基团。这些模式与它们的结构和药效特征具有部分相关性。基于吸引力的分子内和分子间非共价相互作用，对这些计算结果与每种氨基酸实验观察到的允许构象之间的差异进行了合理化。目前的数据集中于氨基酸的固有特性 - 据我们所知，这通常被忽略，因为为了与真实的生物多肽相似，总是使用更大的模型。
