Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystals
Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystals
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改善含有 H、C、N 和 O 原子的分子的分子间力场，应用于核苷和肽晶体
DOI：
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发表时间：
2001
影响因子：
3
通讯作者：
Donald E. Williams
中科院分区：
文献类型：
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作者：
Donald E. Williams
从76个观察到的氮杂烃晶体结构和11个观察到的升华热的训练数据集导出了一个新的有机分子中氮原子的分子间力场。先前发表的氢、碳和氧的W 99力场因此扩展到包括氮原子。氮原子分为四类：N（1）为三键氮，N（2）为没有键合氢的氮（除了三键的情况），N（3）为有一个键合氢的氮，N（4）为有两个或更多键合氢的氮。H（4）表示与氮键合的氢。计算每个分子的6 - 31 g ** 质量的波函数，并用净原子和补充位点电荷模拟分子电势（MEP）。孤对电子电荷网站包括氮原子在适当的情况下，和亚甲基平分线电荷用于CH 2和CH 3基团时，拟合MEP。将X-OH键距设置为用于波函数计算的标准值，然后将其缩短0.1 μ m用于MEP和力场拟合。使用针对训练数据集优化的力场，通过分子间能量最小化来松弛每个氮杂烃晶体结构。每个晶体的晶胞边长预测的最大变化为3%或更小。完整的力场为H，C，N和O原子进行了测试，通过核苷和肽分子晶体的分子间能量弛豫。尽管这些分子没有包含在力场的任何训练数据集中，但与它们观察到的晶体结构的一致性非常好，预测的晶胞边缘位移通常小于2%。这些测试包括在DNA和RNA中发现的所有八种常见核苷的代表的晶体结构，15种二肽，四种三肽，两种四肽和一种在不对称单元中具有两个分子的五肽。John Wiley & Sons，Inc. J Comput Chem 22：1154-1166，2001
A new intermolecular force field for nitrogen atoms in organic molecules was derived from a training dataset of 76 observed azahydrocarbon crystal structures and 11 observed heats of sublimation. The previously published W99 force field for hydrogen, carbon, and oxygen was thus extended to include nitrogen atoms. Nitrogen atoms were divided into four classes: N(1) for triply bonded nitrogen, N(2) for nitrogen with no bonded hydrogen (except the triple bonded case), N(3) for nitrogen with one bonded hydrogen, and N(4) for nitrogen with two or more bonded hydrogens. H(4) designated hydrogen bonded to nitrogen. Wavefunctions of 6‐31g** quality were calculated for each molecule and the molecular electric potential (MEP) was modeled with net atomic and supplementary site charges. Lone pair electron charge sites were included for nitrogen atoms where appropriate, and methylene bisector charges were used for CH2 and CH3 groups when fitting the MEP. XH bond distances were set to standard values for the wave function calculation and then foreshortened by 0.1 Å for the MEP and force field fitting. Using the force field optimized to the training dataset, each azahydrocarbon crystal structure was relaxed by intermolecular energy minimization. Predicted maximum changes in unit cell edge lengths for each crystal were 3% or less. The complete force field for H, C, N, and O atoms was tested by intermolecular energy relaxation of nucleoside and peptide molecular crystals. Even though these molecules were not included in any of the training datasets for the force field, agreement with their observed crystal structures was very good, with predicted unit cell edge shifts usually less than 2%. These tests included crystal structures of representatives of all eight common nucleosides found in DNA and RNA, 15 dipeptides, four tripeptides, two tetrapeptides, and a pentapeptide with two molecules in the asymmetric unit. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1154–1166, 2001