Satoh Hiroko, Oda Tomohiro, Nakakoji Kumiyo, Uno Takeaki, Tanaka Hiroaki, Iwata Satoru, Ohno Koichi
Research Organization of Information and Systems (ROIS), Tokyo 105-0001, Japan.
Department of Chemistry, University of Zurich , 8057 Zurich, Switzerland.
J Chem Theory Comput. 2016 Nov 8;12(11):5293-5308. doi: 10.1021/acs.jctc.6b00439. Epub 2016 Oct 5.
This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map (r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for β-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of C and C chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of C conformations; that is, the potential energy of the global minimum of C is lower than that of C (thermodynamic predominance) and that the highest energy of those of all the TS structures along a route from C to C is lower than that of C to C (kinetic predominance).
本文描述了我们基于势能面(PES)的构象分析方法。该方法通过使用非谐向下畸变跟随方法的缩放超球面搜索(SHS - ADDF)自动推导构象转变网络,即构象反应路线图(r - map)。基于PES的构象搜索是通过使用大型ADDF实现的,这使得在限制键长和高自由能结构的同时,仅追踪低过渡态(TS)势垒成为可能。它通过简单地考虑PES的数学特征自动对极小值和TS结构进行采样,而无需对可变内部坐标进行任何先验指定。得到的r - map由通过TS构象体经由反应路线连接的平衡(EQ)构象体组成,其中所有反应路线在使用内禀反应坐标(IRC)方法的推导过程中已得到确认。使用我们开发的RMapViewer软件对推导的r - map进行计算后分析。本文介绍了基于PES的构象分析的计算细节及其在d - 葡萄糖上的应用。计算是在气相中于RHF / 6 - 31G水平对孤立的葡萄糖分子进行的。得到的α - d - 葡萄糖的构象r - map由201个EQ和435个TS构象体组成,β - d - 葡萄糖的构象r - map由202个EQ和371个TS构象体组成。对于使用RMapViewer软件程序对构象r - map进行计算后分析,我们在C和C椅式构象的全局极小值之间发现了多个最小能量路径(MEP)。使用RMapViewer进行的分析使我们能够确认C构象的热力学和动力学优势;也就是说,C全局极小值的势能低于C(热力学优势),并且从C到C的所有TS结构中沿着一条路线的最高能量低于从C到C的(动力学优势)。