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2013 , Vol. 71 >Issue 11: 1547 - 1552

DOI: https://doi.org/10.6023/A13060606

研究论文

应用QM与ABEEM/MM结合的方法研究NAMI-A的结构性质

  • 邹惠园 ,
  • 赵东霞 ,
  • 杨忠志
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  • 辽宁师范大学化学化工学院 大连 116029

收稿日期: 2013-06-07

  网络出版日期: 2013-07-26

基金资助

项目受中国国家自然科学基金(Nos. 21133005, 21073080)资助.

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Studies on the Structural Properties of NAMI-A in Aqueous Solution by Combined QM and ABEEM/MM Method

  • Zou Huiyuan ,
  • Zhao Dongxia ,
  • Yang Zhongzhi
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  • Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian 116029

Received date: 2013-06-07

  Online published: 2013-07-26

Supported by

Project supported by the National Natural Science Foundation of China (Nos. 21133005, 21073080).

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摘要

应用量子力学(QM)与ABEEM浮动电荷力场(ABEEM/MM)相结合的方法研究了抗癌药物NAMI-A在水溶液中的结构性质. 所有的结构优化都是在DFT的B3LYP方法下采用6-31G(d,p)和LanL2DZ基组完成的, 没有加入任何限制性条件. 结果表明, 优化得到的NAMI-A构型受不同环境及方法的影响均有变化. 与气相中得到的构型相比, QM/MM迭代优化得到构型要比PCM的构型变化更明显. QM/MM (ABEEM/MM)迭代优化得到的NAMI-A构型比QM/MM (OPLS-AA)的变化要小. 总之, 溶剂通过极化效应对NAMI-A结构、电荷分布及径向分布函数等性质均有影响, 客观地处理极化效应才能正确地反映QM区的性质.

关键词： ABEEM/MM; QM; QM/MM; NAMI-A; 钌

本文引用格式

邹惠园 , 赵东霞 , 杨忠志 . 应用QM与ABEEM/MM结合的方法研究NAMI-A的结构性质[J]. 化学学报, 2013 , 71(11) : 1547 -1552 . DOI: 10.6023/A13060606

Abstract

Since 1970s carried out by Warshel et al. QM/MM method has been successfully applied to a wide range of reactions in solution, enzyme and proteins. Up to now, QM has been combined with some popular force fields, like OPLS-AA, Amber or CHARMM. In this work, QM has been combined with ABEEM fluctuating charge force field (ABEEM/MM). ABEEM/MM is a polarizable force field in which the ABEEMσπ method has been fused. ABEEMσπ method, the atom-bond electronegativity equalization method, was proposed and developed by Yang et al. based on electronegativity equalization principle in density functional theory (DFT). In order to further improve the feasibility of combining QM with ABEEM/MM, the properties of anticancer drug imidazolium[trans-tetrachloro(DMSO)(imidazole)ruthenate(Ⅲ)](NAMI-A) in aqueous solution have been investigated, such as structures, polarization energies, charge distributions and radial distribution functions. All the configurations were optimized at B3LYP/6-31G(d,p)//LanL2DZ (for Ru) level by using the Gaussian 03 program. The isoelectric focusing polarized continuum model (IEF-PCM) with UAHF atomic radii was employed for PCM model, and the dielectric constant of water (ε=78.39) was used to approximate the effect of aqueous solution. In QM/MM method, QM and MM regions were optimized by using different methods. The convergence criteria that the maximum gradient of energy is less than 5×10-4 a.u. in QM region and the RMS gradient is less than 1×10-3 kcal·mol-1·A-1 in MM region was adopted for the iterative optimization. After MM minimization, MM region participated as point charges to impact the optimization of QM. No cutoff was introduced to QM and MM interactions. Iterative optimizations have accomplished until reaching the convergence criteria. All the MD simulations were performed by using the modified Tinker program in the NVT ensemble at 298 K with Berendsen thermostats, the velocity Verlet integrator, and a time step of 1 fs. To prepare a reasonable structure of solvent, the periodic boundary condition and the minimum image convention were used. The cutoff radius for nonbonded interactions was 9.0 Å. Dynamic simulations consisted of 150 ps of equilibration run and 50 ps of averaging run. Comparisons of structure for NAMI-A obtained by PCM model, QM/MM (OPLS-AA) and QM/MM (ABEEM/MM) methods have been carried out. Our results show that NAMI-A interact with aqueous solution by forming hydrogen bonds, and the solvent does have a great impact on both structure and atomic charge of NAMI-A by polarization effect. How to deal with the polarization plays a key role in accurately describing the properties of NAMI-A. Since ABEEM/MM can fast and accurately describe the electrostatic interaction between molecules, thus combining QM with ABEEM/MM has been further proved to be a development of QM/MM method.

Key words： ABEEM/MM; QM; QM/MM; NAMI-A; ruthenium

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