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研究论文

基于化学键偶极的糖类分子势函数的构建

王新茹, 李越欣, 董婉婷, 郝强*, 王长生*   

  1. 辽宁师范大学 化学化工学院 大连 116029
  • 投稿日期:2026-04-29
  • 通讯作者: *E-mail: qh@lnnu.edu.cn; chwangcs@lnnu.edu.cn
  • 基金资助:
    国家自然科学基金(No. 21773102)资助.

A Carbohydrate Molecular Potential Based on Chemical Bond Dipoles

Wang Xin-Ru, Li Yue-Xin, Dong Wan-Ting, Hao Qiang*, Wang Chang-Sheng*   

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
  • Received:2026-04-29
  • Supported by:
    National Natural Science Foundation of China (No. 21773102).

本文针对糖类分子中的C-O、O-H和C-H键, 引入化学键偶极描述符, 其偶极矩大小可随周围环境发生变化. 采用偶极-偶极作用描述静电作用、Lennard-Jones 12-6函数描述范德华作用, 并引入键长、键角、二面角和氢键作用项, 构建了糖类分子势函数并确定了相关参数. 将该势函数用于快速计算8种糖分子共计42个构象的构象能和分子偶极矩以及8个糖分子-水团簇的分子间作用能和多体极化作用能, 并与量子力学方法及CHARMM36、GLYCAM06和AMOEBA力场方法的计算结果进行比较. 结果表明, 本文方法的计算精度接近或优于AMOEBA可极化力场方法, 同时具有更高计算效率, 可望应用于糖类分子模拟与药物设计.

关键词: 糖类分子, 化学键偶极, 极化, 构象能, 多体极化作用

A carbohydrate-specific molecular potential is developed by explicitly representing bond polarity through an environment-dependent bond-dipole framework. The C-O, O-H, and C-H bonds in carbohydrate molecules are treated as bond dipoles whose dipole moment magnitudes vary with the surrounding chemical environment, allowing polarization effects to be incorporated without introducing atomic charges. Electrostatic interactions are described using pairwise dipole-dipole interactions, while van der Waals interactions are modeled with a Lennard-Jones 12-6 potential. In addition, standard bonded interaction terms, including bond stretching, angle bending, and dihedral torsions, are included, together with an explicit hydrogen-bond interaction term. All parameters of the potential are determined by fitting to high-level quantum mechanical reference data. The resulting carbohydrate potential is applied to compute conformational energies and molecular dipole moments for a benchmark set of eight carbohydrate molecules comprising a total of 42 distinct conformations. Furthermore, intermolecular interaction energies and many-body polarization energies are evaluated for eight carbohydrate-water cluster systems. The calculated results are systematically compared with those obtained from quantum mechanical methods, including CCSD(T)/CBS for conformational energies, B3LYP/aug-cc-pVTZ for molecular dipole moments, and DLPNO-MP2/aug-cc-pVTZ for cluster interaction and polarization energies, as well as with predictions from the fixed-charge force fields CHARMM36 and GLYCAM06 and the polarizable force field AMOEBA. For conformational energies, the proposed method yields a root-mean-square deviation (RMSD) of 11.48 kJ·mol-1 relative to CCSD(T)/CBS results, comparable to CHARMM36 and significantly better than GLYCAM06 and AMOEBA. For molecular dipole moments, an RMSD of 0.78 × 10-30 C·m is obtained relative to B3LYP/aug-cc-pVTZ, outperforming all three reference force fields. In carbohydrate-water clusters, the method reproduces DLPNO-MP2/aug-cc-pVTZ total interaction energies with an RMSD of 13.72 kJ·mol-1 and a relative deviation of 1.55%, achieving accuracy slightly lower than AMOEBA but superior to CHARMM36 and GLYCAM06. Many-body polarization energies are also reasonably captured, with an RMSD of 7.96 kJ·mol-1. Timing statistics for single-point energy calculations demonstrate that the proposed method is more than twice as fast as AMOEBA for the cluster systems considered. These results indicate that the environment-dependent bond-dipole potential provides an effective balance between accuracy and efficiency, making it well suited for molecular simulations of carbohydrates and for applications in carbohydrate-related drug design.

Key words: carbohydrate molecules, chemical bond dipoles, polarization, conformational energy, many-body polarization