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标题: 求助：簇模型解析酶催化机理时溶剂模型的选择问题 [打印本页]
作者Author: sun877469558 时间: 2022-4-30 13:52
标题: 求助：簇模型解析酶催化机理时溶剂模型的选择问题
请问各位，在使用簇模型进行酶的催化机制相关计算时，在Fahmi Himo老师的文章里经常看到使用SMD或CPCM模型，但是在sob老师的帖子，“谈谈隐式溶剂模型下溶解自由能和体系自由能的计算”（http://sobereva.com/327），有以下一段话
“隐式溶剂模型的缺点是无法表现溶剂与溶质之间的强相互作用，如氢键。反应过程中若溶剂起到催化作用，也显然没法靠隐式溶剂模型表现。某些电子激发可能涉及到溶质与溶剂之间电荷转移，这显然也没法靠隐式溶剂模型恰当体现。而且对于溶质是离子的情况，隐式溶剂模型计算溶解自由能的精度明显低于溶质是中性分子的情况。”
既然溶剂在催化中起到催化作用，比如水解酶吧，溶剂水分子起到催化作用，那为什么Fahmi Himo老师文章在做Limonene Epoxide Hydrolase中还是使用了隐式溶剂模型？
以下是文章计算细节
All calculationswere performed using the hybrid density functional B3LYP [1] asimplemented inthe Gaussian03 program package. [2] Geometry optimizations werecarried outemploying the 6-31G(d,p) basis set. More accurate energies were obtainedbysingle-point calculations on the optimized geometries using the larger6-311+G(2d,2p)basis set. The polarization effects of the enzyme environment notexplicitly includedin the model were taken into account by single-point calculationsusing theconductor-like polarizable continuum model (CPCM) [3] with a dielectricconstantof 4 and the UA0 radii. Analytical frequencies were calculated at the samelevelof theory as the geometry optimizations to confirm the nature of the stationarypointsand also to obtain zero-point energies (ZPE). Fixing coordinates introduces afewsmall imaginary frequencies, in this case all below 50i cm -1 . These smallfrequencieshave little impact on the ZPE and can therefore be disregarded. Allenergiesreported in the paper include also the dispersion effect according to theB3LYP-D2method of Grimme.
作者Author: wzkchem5 时间: 2022-4-30 15:15
因为他们显式考虑了参与反应的那些水分子。溶剂参与反应意味着那几个参与反应的溶剂分子必须显式描述，但是不影响用隐式溶剂模型描述那些没参与反应的溶剂分子。sob老师的话如果说得更明确，应该是，“反应过程中若溶剂起到催化作用，也显然没法【仅】靠隐式溶剂模型表现。”那些没参与催化的溶剂还是要靠隐式溶剂模型描述的。
作者Author: sun877469558 时间: 2022-4-30 15:34
豁然开朗，谢谢老师！
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