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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Analysis of the Pyramidalization of the Peptide Group Nitrogen: Implications for Molecular Mechanics Energy Functions
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Analysis of the Pyramidalization of the Peptide Group Nitrogen: Implications for Molecular Mechanics Energy Functions

机译:肽基团氮的金字塔化分析:对分子力学能量函数的影响

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Pyramidalization at the peptide group nitrogen atom is analyzed using N-methylacetamide (NMA) as a model molecule. Mutually orthogonal peptide CN torsion and NH out-of-plane bend coordinates are necessary for a correct description of the energetics of nonplanar deformations of the peptide group. Using such coordinates, ab initio calculations at the MP2/6-31++G(d,p) level of theory show that the energy minimum of the NH out-of-plane bend angle shifts significantly away from zero for nonzero CN torsion angles. Not being due to nonbonded interactions alone, this energy behavior needs to be taken explicitly into account in molecular mechanics force fields. By use of different schemes for calculating potential-derived atomic charges, the charge distribution of NMA was also investigated in connection with the pyramidalization. Large variations in the charges were found as a function of the NH out-of-plane angle. These could not be reproduced only by polarization through the (molecular mechanics) electric field. An enhanced electrostatic model, using geometry-dependent charges (charge fluxes) is shown to provide a satisfactory physical description of this effect.
机译:使用N-甲基乙酰胺(NMA)作为模型分子分析在肽基团氮原子处的金字塔化。相互正交的肽CN扭转和NH面外弯曲坐标对于正确描述肽组非平面形变的能量学是必要的。使用这样的坐标,在MP2 / 6-31 ++ G(d,p)的理论水平上从头算起显示,对于非零的CN扭转角,NH面外弯曲角的能量最小值明显偏离零。 。不仅仅是由于非键相互作用,还需要在分子力学力场中明确考虑这种能量行为。通过使用不同的方案来计算电位衍生的原子电荷,还研究了NMA的电荷分布与锥体化的关系。发现电荷的较大变化是NH面外角的函数。这些不能仅通过(分子力学)电场的极化来复制。使用与几何形状有关的电荷(电荷通量)的增强静电模型显示出可以令人满意地描述这种效应。

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