Oh Kwang-Im, Choi Jun-Ho, Lee Joo-Hyun, Han Jae-Beom, Lee Hochan, Cho Minhaeng
Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul, Republic of Korea.
J Chem Phys. 2008 Apr 21;128(15):154504. doi: 10.1063/1.2904558.
Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C[Triple Bond]N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9 cm(-1), respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, beta-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.
已发现腈基和硫氰酸酯衍生的氨基酸是用于研究其在蛋白质中局部静电环境的有用红外探针。为了阐明与氢键溶剂分子相互作用引起的C≡N伸缩频率位移和光谱线形变化，我们对水中的乙腈（MeCN）和甲基硫氰酸盐（MeSCN）进行了经典和量子力学/分子力学（QM/MM）分子动力学（MD）模拟。发现这些QM/MM和传统力场MD模拟结果与实验结果以及MeCN-水和MeSCN-水势能的高水平从头计算结果不一致。因此，获得了一组新的MeCN和MeSCN原子部分电荷。通过使用MD模拟轨迹和最近开发的静电势模型，获得了C≡N和SCN伸缩模式频率轨迹，并用于模拟红外光谱。与气相值相比，水中MeCN和MeSCN的C≡N频率蓝移估计分别为9.0和1.9 cm-1。发现这些值与水中和其他极性溶剂中MeCN、MeSCN、β-氰基-L-丙氨酸和氰化半胱氨酸的实验测量红外光谱合理一致。
