Conformational analysis of spiro-epoxides by principal component analysis of molecular dynamics trajectories,Physical Chemistry Chemical Physics

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Conformational analysis of spiro-epoxides by principal component analysis of molecular dynamics trajectories
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2017-11-07 00:00:00 , DOI: 10.1039/c7cp05600a
T. Hrenar _{1,

2,

3,

4,

5} , I. Primožič _{1,

2,

3,

4,

5} , D. Fijan _{1,

2,

3,

4,

5} , M. Majerić Elenkov _{5,

6,

7,

8}

Affiliation

A new procedure for full conformational analyses comprising the statistical analysis of molecular dynamics trajectories was developed and applied. This method included a coordinate space for sampling using molecular dynamics simulations, reduction of dimensionality using tensor decomposition tools, determination of probability distributions in a reduced space, and finally the search for all of the strict extrema points of probability distributions. These extracted extrema points formed an initial guess for geometry optimization and clustering of conformers. A complete conformational space of 1-oxaspiro[2,5]octane and its cis- and trans-4-, 5- and 6-methyl substituted derivatives was also determined. In each case, eight conformers were found with two chair-like conformers predominant at room temperature. It was found that chair-like conformers with an epoxide ring oxygen atom in the pseudo-axial position had less strain, as well as all of their conformers with the methyl substituent in an equatorial position on a cyclohexane moiety.

中文翻译：

通过分子动力学轨迹的主成分分析对螺环氧化物进行构象分析

开发并应用了一种新的全构象分析方法，包括分子动力学轨迹的统计分析。该方法包括使用分子动力学模拟进行采样的坐标空间，使用张量分解工具降低维数，确定缩小空间中的概率分布以及最后搜索概率分布的所有严格极值点。这些提取的极值点构成了几何优化和构象聚类的初步猜测。1-氧杂螺[2,5]辛烷及其顺式和反式的完整构象空间还确定了-4-，5-和6-甲基取代的衍生物。在每种情况下，均发现八个构象异构体，其中两个在室温下主要呈椅子样的构象异构体。发现在伪轴向位置具有环氧化物环氧原子的椅子状构象异构体以及在环己烷部分的赤道位置具有甲基取代基的所有其构象异构体具有较小的应变。

更新日期：2017-11-22

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