Conformational Analysis of Arabinofuranosides: Prediction of 3JH,H Using MD Simulations with DFT-Derived Spin-Spin Coupling Profiles
Conformational Analysis of Arabinofuranosides: Prediction of 3JH,H Using MD Simulations with DFT-Derived Spin-Spin Coupling Profiles
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DOI：
10.1021/ct900477x
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发表时间：
2010-01-01
影响因子：
5.5
通讯作者：
Roy, Pierre-Nicholas
中科院分区：
文献类型：
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作者：
Taha, Hashem A.;Castillo, Norberto;Roy, Pierre-Nicholas
报道了一系列α-阿拉伯呋喃低聚糖苷(1-8)的分子动力学(MD)研究。该方法的验证是通过将实验的邻近质子-质子耦合常数((3)J(H，H))与由经验确定的Karplus方程和专门针对α-阿拉伯呋喃糖基体系的密度泛函理论(DFT)推导的关系式得到的结果进行直接比较来进行的。开发了一个简单的程序来实现(3)J(H，H)的确定，通过将这些关系应用于模拟所显示的OTAMERS和环构象的概率分布。在大多数情况下，经验Karplus关系和DFT导出的方程与环内J(H，H)值的实验趋势相同。这种直接比较绕过了由反卷积程序引入的假设可能产生的额外误差来源，这些假设通常用于从实验(3)J(H，H)计算旋转体和环构象的数量。
A molecular dynamics (MD) investigation on a series of oligo-alpha-arabinofuranosides (1-8) using the AMBER force field and the GLYCAM carbohydrate parameter set is reported. The validation of the method was carried out by direct comparison of experimental vicinal proton-proton coupling constants ((3)J(H,H)) With those obtained by using an empirically determined Karplus equation and density functional theory (DFT)-derived relationships specifically tailored for alpha-arabinofuranosyl systems. A simple code was developed to implement the determination of (3)J(H,H) by applying these relationships to the probability distributions of otamers and ring conformations displayed by the simulations. The empirical Karplus relationship and the DFT-derived equations yielded, in most cases, the same trend as experiment for intra-ring (3)J(H,H) values. This direct comparison circumvents additional sources of errors that may arise from the assumptions introduced by the deconvolution procedures often used to calculate population of rotamers and ring conformations from experimental (3)J(H,H).