Horta Bruno A C, Merz Pascal T, Fuchs Patrick F J, Dolenc Jozica, Riniker Sereina, Hünenberger Philippe H
Laboratory of Physical Chemistry, ETH Zürich , CH-8093 Zürich, Switzerland.
Instituto de Química, Universidade Federal do Rio de Janeiro , Rio de Janeiro 21941-909, Brazil.
J Chem Theory Comput. 2016 Aug 9;12(8):3825-50. doi: 10.1021/acs.jctc.6b00187. Epub 2016 Jul 8.
This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The calibration is based on 62 organic molecules spanning the chemical functions alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, and disulfide, as well as aromatic compounds and nucleic-acid bases. For 57 organic compounds, the calibration targets are the experimental pure-liquid density ρliq and the vaporization enthalpy ΔHvap, as well as the hydration free energy ΔGwat and the solvation free energy ΔGche in cyclohexane, at atmospheric pressure and at (or close to) room temperature. The final root-mean-square deviations (RMSD) for these four quantities over the set of compounds are 32.4 kg m(-3), 3.5 kJ mol(-1), 4.1 kJ mol(-1), and 2.1 kJ mol(-1), respectively, and the corresponding average deviations (AVED) are 1.0 kg m(-3), 0.2 kJ mol(-1), 2.6 kJ mol(-1), and 1.0 kJ mol(-1), respectively. For the five nucleic-acid bases, the parametrization is performed by transferring the final 2016H66 parameters from analogous organic compounds followed by a slight readjustment of the charges to reproduce the experimental water-to-chloroform transfer free energies ΔGtrn. The final RMSD for this quantity over the five bases is 1.7 kJ mol(-1), and the corresponding AVED is 0.8 kJ mol(-1). As an initial validation of the 2016H66 set, seven additional thermodynamic, transport, and dielectric properties are calculated for the 57 organic compounds in the liquid phase. The agreement with experiment in terms of these additional properties is found to be reasonable, with significant deviations typically affecting either a specific chemical function or a specific molecule. This suggests that in most cases, a classical force-field description along with a careful parametrization against ρliq, ΔHvap, ΔGwat, and ΔGche results in a model that appropriately describes the liquid in terms of a wide spectrum of its physical properties.
本文报道了一种新的适用于凝聚相中小有机分子的与GROMOS兼容的参数集2016H66的校准和验证。校准基于62种有机分子，涵盖醇、醚、醛、酮、羧酸、酯、胺、酰胺、硫醇、硫化物和二硫化物等化学官能团，以及芳香化合物和核酸碱基。对于57种有机化合物，校准目标是实验测得的纯液体密度ρliq、汽化焓ΔHvap，以及在大气压和（或接近）室温下环己烷中的水合自由能ΔGwat和溶剂化自由能ΔGche。在这组化合物上，这四个量的最终均方根偏差（RMSD）分别为32.4 kg m(-3)、3.5 kJ mol(-1)、4.1 kJ mol(-1)和2.1 kJ mol(-1)，相应的平均偏差（AVED）分别为1.0 kg m(-3)、0.2 kJ mol(-1)、2.6 kJ mol(-1)和1.0 kJ mol(-1)。对于五种核酸碱基，通过从类似有机化合物转移最终的2016H66参数，然后对电荷进行轻微调整以重现实验测得的水到氯仿的转移自由能ΔGtrn来进行参数化。在这五个碱基上，该量的最终RMSD为1.7 kJ mol(-1)，相应的AVED为0.8 kJ mol(-1)。作为对2016H66集的初步验证，对57种液相有机化合物计算了另外七种热力学、输运和介电性质。发现这些额外性质与实验的一致性是合理的，显著偏差通常影响特定的化学官能团或特定的分子。这表明在大多数情况下，经典力场描述以及针对ρliq、ΔHvap、ΔGwat和ΔGche进行仔细的参数化会产生一个能够根据其广泛的物理性质适当地描述液体的模型。
