Popelier Paul L A, Aicken Fiòna M
Department of Chemistry, UMIST Manchester, M60 1QD, Great Britain.
Chemistry. 2003 Mar 3;9(5):1207-16. doi: 10.1002/chem.200390138.
Molecular electron densities are generated at B3LYP/6-311+G(2d,p)//HF/6-31G(d) level for 57 molecules, including one conformation of each naturally occurring amino acid and smaller derived molecules. The electron densities are partitioned into atomic fragments according to the approach of quantum chemical topology (QCT). A set of 547 unique topological atoms is obtained, containing 421 hydrogens, 63 oxygens, 57 nitrogens and 6 sulfurs. Each atom is described by seven properties: volume, kinetic energy, monopole, dipole, quadrupole, octupole and hexadecapole moment. Cluster analysis groups atoms into atom types based on their similarity expressed in the discrete 7D space of atomic properties. Using a separation criterion we distinguish seven hydrogen, six oxygen, two nitrogen and six sulfur atom types.
在B3LYP/6 - 311 + G(2d,p)//HF/6 - 31G(d)水平上，为57个分子生成了分子电子密度，其中包括每种天然存在的氨基酸的一种构象以及较小的衍生分子。根据量子化学拓扑学（QCT）方法，将电子密度划分为原子片段。得到了一组547个独特的拓扑原子，其中包括421个氢原子、63个氧原子、57个氮原子和6个硫原子。每个原子由七个属性描述：体积、动能、单极矩、偶极矩、四极矩、八极矩和十六极矩。聚类分析根据原子在离散的七维原子属性空间中表达的相似性，将原子分组为原子类型。使用一个分离标准，我们区分出七种氢原子类型、六种氧原子类型、两种氮原子类型和六种硫原子类型。
