Woodcock H Lee, Moran Damian, Pastor Richard W, MacKerell Alexander D, Brooks Bernard R
Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
Biophys J. 2007 Jul 1;93(1):1-10. doi: 10.1529/biophysj.106.099986.
A range of ab initio calculations were carried out on the axial and equatorial anomers of the model carbohydrate 2-ethoxy tetrahydropyran to evaluate the level of theory required to accurately evaluate the glycosyl dihedral angle and the anomeric ratio. Vacuum CCSD(T)/CBS extrapolations at the global minimum yield DeltaE = E(equatorial) - E(axial) = 1.42 kcal/mol. When corrected for solvent (by the IEFPCM model), zero-point vibrations and entropy, DeltaG(298) = 0.49 kcal/mol, in excellent agreement with the experimental value of 0.47 +/- 0.3 kcal/mol. A new additivity scheme, the layered composite method (LCM), yields DeltaE to within 0.1 kcal/mol of the CCSD(T)/CBS result at a fraction of the computer requirements. Anomeric ratios and one-dimensional torsional surfaces generated by LCM and the even more efficient MP2/cc-pVTZ level of theory are in excellent agreement, indicating that the latter is suitable for force-field parameterization of carbohydrates. Hartree-Fock and density functional theory differ from CCSD(T)/CBS for DeltaE by approximately 1 kcal/mol; they show similar deviations in torsional surfaces evaluated from LCM. A comparison of vacuum and solvent-corrected one- and two-dimensional torsional surfaces indicates the equatorial form of 2-ethoxy tetrahydropyran is more sensitive to solvent than the axial.
对模型碳水化合物2-乙氧基四氢吡喃的轴向和赤道异头物进行了一系列从头算计算,以评估准确评估糖基二面角和异头物比例所需的理论水平。在全局最小值处的真空CCSD(T)/CBS外推得出ΔE = E(赤道) - E(轴向) = 1.42千卡/摩尔。当校正溶剂(通过IEFPCM模型)、零点振动和熵时,ΔG(298) = 0.49千卡/摩尔,与0.47±0.3千卡/摩尔的实验值非常吻合。一种新的加和方案,即分层复合方法(LCM),在计算机需求的一小部分情况下,能使ΔE与CCSD(T)/CBS结果的偏差在0.1千卡/摩尔以内。由LCM和效率更高的MP2/cc-pVTZ理论水平生成的异头物比例和一维扭转面非常吻合,表明后者适用于碳水化合物的力场参数化。Hartree-Fock和密度泛函理论在ΔE方面与CCSD(T)/CBS相差约1千卡/摩尔;它们在从LCM评估的扭转面中表现出类似的偏差。真空和溶剂校正后的一维和二维扭转面的比较表明,2-乙氧基四氢吡喃的赤道形式比轴向形式对溶剂更敏感。