Burger Steven K, Yang Weitao
Department of Chemistry, Duke University, P.O. Box 90346, Durham, North Carolina 27708-0346, USA.
J Chem Phys. 2007 Oct 28;127(16):164107. doi: 10.1063/1.2780147.
A new method, referred to as the sequential quadratic programming method, is presented for determining minimum energy paths. The method is based on minimizing the points representing the path in the subspace perpendicular to the tangent of the path while using a penalty term to prevent kinks from forming. Rather than taking one full step, the minimization is divided into a number of sequential steps on an approximate quadratic surface. The resulting method can efficiently determine the reaction mechanism, from which transition state can be easily identified and refined with other methods. To improve the resolution of the path close to the transition state, points are clustered close to this region with a reparametrization scheme. The usefulness of the algorithm is demonstrated for the Muller-Brown potential, amide hydrolysis, and an 89 atom cluster taken from the active site of 4-oxalocrotonate tautomerase for the reaction which catalyzes 2-oxo-4-hexenedioate to the intermediate 2-hydroxy-2,4-hexadienedioate.
提出了一种新的方法,即序列二次规划法,用于确定最小能量路径。该方法基于在垂直于路径切线的子空间中最小化表示路径的点,同时使用惩罚项来防止扭结的形成。与采取完整的一步不同,最小化在近似二次曲面上被划分为多个连续的步骤。由此产生的方法可以有效地确定反应机理,从中可以很容易地识别过渡态并用其他方法进行优化。为了提高靠近过渡态的路径分辨率,通过重新参数化方案将点聚集在该区域附近。该算法对穆勒-布朗势、酰胺水解以及从4-草酰巴豆酸互变异构酶活性位点提取的89原子簇用于催化2-氧代-4-己烯二酸酯生成中间体2-羟基-2,4-己二烯二酸酯的反应的有效性进行了证明。