AN EFFICIENT ALGORITHM FOR SEARCHING LOW-ENERGY CONFORMERS OF CYCLIC AND ACYCLIC MOLECULES
AN EFFICIENT ALGORITHM FOR SEARCHING LOW-ENERGY CONFORMERS OF CYCLIC AND ACYCLIC MOLECULES
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DOI：
10.1039/p29930000187
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发表时间：
1993-02-01
期刊：
影响因子：
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通讯作者：
OSAWA, E
中科院分区：
文献类型：
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作者：
GOTO, H;OSAWA, E
提出了一套寻找环状、非环状或脂环族分子低能构象的策略。从任何构象开始，局部扰动系统地应用于所讨论的分子的所有柔性部分，以产生新构象的候选者。微扰包括挥舞和/或翻转的内环键和逐步旋转的无环键。它们产生的构象被认为接近构象空间中的初始几何形状。构象空间起始域的全局能量最小（GEM）结构可以通过总是选择在最后一个扰动循环中产生的最稳定的构象作为下一个初始结构来快速达到。一旦达到该域的GEM，局部扰动将搜索逐渐引导到越来越高的能量区域，同时穷尽地找到其中的所有低能构象。可变的搜索限制策略允许使用不稳定的构象作为扰动的初始结构，以确保在低能量区域的搜索的穷尽性。通过进一步增加搜索限制，新的领域的构象spaces.A程序CONFLEX3包含几个额外的策略，以提高性能已被测试的正构烷烃癸烷和环烷烃环十二烷。
A set of strategies for exhaustively finding low-energy conformers of cyclic, acyclic or alicyclic molecules is presented. Starting from any conformation, local perturbation is systematically applied to all the flexible portions of the molecule in question to produce candidates of new conformation. The perturbations consist of flapping and/or flipping for endocyclic bonds and stepwise rotation for acyclic bonds. The conformations they produced are believed to lie close to the initial geometry in the conformational space. The global energy minimum (GEM) structure of the starting domain of conformational space can be quickly reached by always choosing the most stable of the conformers produced in the last perturbation cycle as the next initial structure. Once GEM of the domain is reached, the local perturbations direct the search gradually to higher and higher energy regions while exhaustively finding all the low-energy conformers therein. The variable search-limit strategy allows one to use unstable conformers as the initial structure for perturbation to ensure the exhaustiveness of the search in the low-energy region. By further increasing the search-limit, new domains of conformational space may be found. A program CONFLEX3 containing several additional strategies for improved performance has been tested for n-alkanes up to decane and cycloalkanes up to cyclododecane.