Department of Chemistry and Biochemistry, University of San Diego, 5998 Alcala Park, San Diego, California 92110, USA.
J Phys Chem A. 2013 Apr 11;117(14):2997-3008. doi: 10.1021/jp312202j. Epub 2013 Mar 29.
A computational protocol utilizing density functional theory calculations, including Poisson-Boltzmann implicit solvent and free energy corrections, is applied to study the thermodynamic and kinetic energy landscape of glycolaldehyde in solution. Comparison is made to NMR measurements of dissolved glycolaldehyde, where the initial dimeric ring structure interconverts among several species before reaching equilibrium where the hydrated monomer is dominant. There is good agreement between computation and experiment for the concentrations of all species in solution at equilibrium, that is, the calculated relative free energies represent the system well. There is also relatively good agreement between the calculated activation barriers and the estimated rate constants for the hydration reaction. The computational approach also predicted that two of the trimers would have a small but appreciable equilibrium concentration (>0.005 M), and this was confirmed by NMR measurements. Our results suggest that while our computational protocol is reasonable and may be applied to quickly map the energy landscape of more complex reactions, knowledge of the caveats and potential errors in this approach need to be taken into account.
利用密度泛函理论计算，包括泊松-玻尔兹曼隐溶剂和自由能修正，应用于研究乙二醇醛在溶液中的热力学和动能景观。与溶解的乙二醇醛的 NMR 测量进行了比较，其中初始二聚环结构在达到平衡之前在几种物质之间相互转化，其中水合单体占主导地位。在平衡时，所有物种在溶液中的浓度上，计算和实验之间有很好的一致性，也就是说，计算的相对自由能很好地代表了体系。计算的活化能垒与水合反应的估计速率常数之间也有较好的一致性。计算方法还预测了两个三聚体将具有较小但可察觉的平衡浓度（>0.005 M），这通过 NMR 测量得到了证实。我们的结果表明，虽然我们的计算方案是合理的，并且可以快速绘制更复杂反应的能量景观，但需要考虑到这种方法的注意事项和潜在误差。
