Stochastic generator of chemical structure .2. Using simulated annealing to search the space of constitutional isomers
Stochastic generator of chemical structure .2. Using simulated annealing to search the space of constitutional isomers
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DOI：
10.1021/ci950179a
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发表时间：
1996-07-01
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影响因子：
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通讯作者：
Faulon, JL
中科院分区：
文献类型：
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作者：
Faulon, JL
虽然已经有许多理论和应用研究来探索构象异构体的空间，但是关于构象异构体的结构（即，结构）异构体。过去曾提出过确定性算法，但仅限于小分子，因为组成空间大小随原子数量呈指数级变化。本文提出了一种基于模拟退火算法的随机算法，用于搜索具有所需性质的结构异构体。该算法是通用的，足以用于任何类别的有机和无机化合物，包括环状和交联结构。理论上，该算法被证明是有效的（即，多项式）。实际上，即使在非常大的宪法空间大小（高达10（32）），该算法执行得非常好。该算法的应用程序中提出的计算机辅助分子设计的背景下。文中给出的实例包括寻找具有特定拓扑指数的结构，寻找具有低logP（辛醇/水）分配系数的结构，以及寻找结构空间中能量的全局最小值。该算法似乎是第一个搜索化学结构，而不限制搜索空间。
While there have been many theoretical and applied studies to explore the space of conformational isomers, little has been reported regarding constitutional (i.e., structural) isomers. Deterministic algorithms have been proposed in the past but are limited to small molecules because constitutional space sizes scale exponentially with the number of atoms. The present paper proposes a stochastic algorithm based on the simulated annealing method that searches constitutional isomers with desired properties. The algorithm is general enough to be used for any class of organic and inorganic compounds, including cyclic and crosslinked structures. Theoretically, the algorithm is shown to be efficient (i.e., polynomial). Practically, the algorithm performs remarkably well even in very large constitutional space sizes (up to 10(32)). Applications of this algorithm are suggested in the context of computer-aided molecular design. The practical examples given in the paper include the search for structures having specific topological indices, the search for structures having low log P (octanol/water) partition coefficient, and the search for global minimum of energy in constitutional spaces. The proposed algorithm appears to be the first one that searches chemical structures without restricting the search space.