Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, USA.
Phys Chem Chem Phys. 2011 Mar 14;13(10):4311-7. doi: 10.1039/c0cp02177f. Epub 2011 Jan 21.
In the present work, the conventional static ab initio picture of a water-assisted mechanism of the tautomerization of Nucleic Acid Bases (NABs) in an aqueous environment is enhanced by the classical and Car-Parrinello molecular dynamics simulations. The inclusion of the dynamical contribution is vital because the formation and longevity of the NAB-water bridge complexes represent decisive factors for further tautomerization. The results of both molecular dynamic techniques indicate that the longest time when such complexes exist is significantly shorter than the time required for proton transfer suggested by the static ab initio level of theory. New rate constants of tautomerization corrected for the dynamic effect of environment are proposed based on the first principles molecular dynamics data. Those values are used for the evaluation of a water-assisted mechanism that is feasible in such biological systems as E. coli cell.
在本工作中，通过经典和 Car-Parrinello 分子动力学模拟增强了水辅助的核酸碱基（NAB）互变异构在水相环境中的经典从头算静态图像。包含动力学贡献是至关重要的，因为 NAB-水桥复合物的形成和稳定性是进一步互变异构的决定性因素。这两种分子动力学技术的结果都表明，这种复合物存在的最长时间明显短于静态从头算理论所建议的质子转移所需的时间。基于第一性原理分子动力学数据，提出了修正环境动力学效应后的新的互变异构速率常数。这些值用于评估在大肠杆菌细胞等生物体系中可行的水辅助机制。
