Development of many body potential for simulation of mucleic acid base

基于从头算分子轨道计算结果，建立了腺嘌呤(A)、胞嘧啶(C)、鸟嘌呤(G)、胸腺嘧啶(T)和尿嘧啶(U)的极化模型电位（PMP）函数。分子轨道的能级计算为MP2/6-31+G^*。PMP函数由库仑项、伦纳德-琼斯项和极化项组成。用静电势法确定了库仑项的部分点电荷。用可极化单电子势法确定了极化项的多中心极化率。采用原子极化率作为多中心极化率。原子极化模型很好地再现了核酸的极化。在PMP函数计算中，沃森-克里克型A-T和G-C碱基对的相互作用能分别为-15.6和-29.2 kcal/mol。Hoogsteen型A-T碱基对的相互作用能为-17.7 kcal/mol。这些结果很好地再现了MP2/6-311++G（3df,2pd）的量子化学计算结果。A-T和C-G的层能分别为-9.3和-10.7 kcal/mol。这些结果很好地再现了MP2/6-311++G （2d,2p）的计算结果。此外，还计算了钠离子或氯离子与核酸碱基相邻的模型的势能面。能量表面的再现非常好。虽然核酸碱基是一种极化各向异性非常大的分子，但用简单的原子极化率可以很好地再现高级量子化学计算结果的势函数。

A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculation results. The level of the molecular orbital calculation is MP2/6-31+G^*. The PMP function consists of Coulomb, Lennard-Jones, and polarization terms. The partial point charges of the Coulomb term are determined by using electrostatic potential method. The multicenter polarizabilities of the polarization term are determined by using polarizable one-electronic potential method. Atomic polarizabilities are adopted as the multicenter polarizabilities. The atomic polarization model reproduce well the polarization of the nucleic acid. In the calculations using PMP function, the interaction energies of Watson-Crick type A-T and G-C base pairs were -15.6 and -29.2 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.7 kcal/mol. These results reproduce well the quantum chemistry calculations of MP2/6-311++G(3df,2pd). The stacking energies of A-T and C-G were -9.3 and -10.7 kcal/mol, respectively. These results reproduce well the calculations of MP2/6-311++G (2d,2p). Moreover, the potential energy surfaces of the models in which a sodium ion or a chloride ion is adjacent to the nucleic acid bases are calculated. The reproduction of the energy surfaces was very well. The potential function in which a high-level quantum chemistry calculation results are reproduced well by taking the simple atomic polarizabilities can be made though the nucleic acid base is a molecule with a very large polarization anisotropy.