Vuong Van Quan, Nishimoto Yoshio, Fedorov Dmitri G, Sumpter Bobby G, Niehaus Thomas A, Irle Stephan
Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee , Knoxville , Tennessee 37996 , United States.
Fukui Institute for Fundamental Chemistry , Kyoto University , Kyoto 606-8501 , Japan.
J Chem Theory Comput. 2019 May 14;15(5):3008-3020. doi: 10.1021/acs.jctc.9b00108. Epub 2019 Apr 30.
The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), which hampers the simulation of zwitterionic systems such as biopolymers or ionic liquids. Here we report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. The scaling of FMO-LC-DFTB with system size N is shown to be almost linear, O( N), and its numerical accuracy is established for a variety of representative systems including neutral and charged polypeptides. It is shown that pair interaction energies between fragments for two mini-proteins are in excellent agreement with results from long-range corrected density functional theory. The new method was employed in long time scale (1 ns) molecular dynamics simulations of the tryptophan cage protein (PDB: 1L2Y ) in the gas phase for four different protonation states and in stochastic global minimum structure searches for 1-ethyl-3-methylimidazolium nitrate ionic liquid clusters containing up to 2300 atoms.
目前基于片段分子轨道（FMO）方法的密度泛函紧束缚（DFTB）线性标度方法，因自相互作用误差（SIE）导致的人工电荷转移问题而受到严重影响，这阻碍了对两性离子体系（如生物聚合物或离子液体）的模拟。在此，我们报告了FMO-DFTB的扩展，其中我们纳入了一种旨在减轻DFTB SIE的长程校正（LC）泛函，称为FMO-LC-DFTB方法，从而得到一种能够成功模拟两性离子体系的稳健方法。我们针对气相和可极化连续介质溶剂化模型开发了能量和解析梯度。FMO-LC-DFTB随系统大小N的标度显示几乎是线性的，为O(N)，并且其数值精度在包括中性和带电多肽在内的各种代表性系统中得到了确立。结果表明，两个微型蛋白质片段之间的对相互作用能与长程校正密度泛函理论的结果高度一致。该新方法被用于对气相中四种不同质子化状态的色氨酸笼蛋白（PDB：1L2Y）进行长时间尺度（1 ns）的分子动力学模拟，以及对含有多达2300个原子的硝酸1-乙基-3-甲基咪唑鎓离子液体簇进行随机全局最小结构搜索。
