J Comput Aided Mol Des. 2013 Sep;27(9):793-805. doi: 10.1007/s10822-013-9677-z.
Fast and reliable prediction of bond orders in organic systems based upon experimentally measured quantities can be performed using electron density features at bond critical points (J Am Chem Soc 105:5061–5068, 1983; J Phys Org Chem 16:133–141, 2003; Acta Cryst B 61:418–428, 2005; Acta Cryst B 63:142–150, 2007). These features are outcomes of low-temperature high-resolution X-ray diffraction experiments. However, a time-consuming procedure of gaining these quantities makes the prediction limited. In the present work we have employed an empirical approach AlteQ (J Comput Aided Mol Des 22:489–505, 2008) for evaluation of electron density properties. This approach uses a simple exponential function derived from comparison of electron density, gained from high-resolution X-ray crystallography, and distance to atomic nucleus what allows calculating density distribution in time-saving manner and gives results which are very close to experimental ones. As input data AlteQ accepts atomic coordinates of isolated molecules or molecular ensembles (for instance, protein–protein complexes or complexes of small molecules with proteins, etc.). Using AlteQ characteristics we have developed regression models predicting Cioslowski–Mixon bond order (CMBO) indexes (J Am Chem Soc 113(42):4142–4145, 1991). The models are characterized by high correlation coefficients lying in the range from 0.844 to 0.988 dependently on the type of covalent bond, thereby providing a bonding quantification that is in reasonable agreement with that obtained by orbital theory. Comparative analysis of CMBOs approximated using topological properties of AlteQ and experimental electron densities has shown that the models can be used for fast determination of bond orders directly from X-ray crystallography data and confirmed that AlteQ characteristics can replace experimental ones with satisfactory extent of accuracy.
基于实验测量量,通过键临界点的电子密度特征,可以快速可靠地预测有机体系中的键级(J Am Chem Soc 105:5061–5068, 1983; J Phys Org Chem 16:133–141, 2003; Acta Cryst B 61:418–428, 2005; Acta Cryst B 63:142–150, 2007)。这些特征是低温高分辨率 X 射线衍射实验的结果。然而,获得这些量的耗时过程使得预测受到限制。在本工作中,我们采用了一种经验方法 AlteQ(J Comput Aided Mol Des 22:489–505, 2008)来评估电子密度特性。该方法使用了一个简单的指数函数,该函数是通过比较从高分辨率 X 射线晶体学获得的电子密度和到原子核的距离得出的,这使得能够以节省时间的方式计算密度分布,并给出非常接近实验结果的结果。作为输入数据,AlteQ 接受孤立分子或分子集合的原子坐标(例如,蛋白质-蛋白质复合物或小分子与蛋白质的复合物等)。我们使用 AlteQ 特征开发了预测 Cioslowski–Mixon 键级(CMBO)指数的回归模型(J Am Chem Soc 113(42):4142–4145, 1991)。这些模型的特征是相关系数很高,范围从 0.844 到 0.988,具体取决于共价键的类型,从而提供了与轨道理论获得的定量结果相当吻合的定量结果。使用 AlteQ 拓扑特性和实验电子密度近似 CMBO 的比较分析表明,这些模型可用于直接从 X 射线晶体学数据快速确定键级,并证实 AlteQ 特性可以在令人满意的精度范围内替代实验特性。