生物活性化合物的精确生成焓从高级从头计算与详细构象处理:大麻素的一个例子。

IF 5.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Journal of Chemical Theory and Computation Pub Date : 2025-01-28 Epub Date: 2025-01-09 DOI:10.1021/acs.jctc.4c01177
Andrei Kazakov, Eugene Paulechka
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引用次数: 0

摘要

我们最近开发的基于单、双和微扰三重激发的局部耦合簇[LCCSD(T)]模型的方法为计算理想气体的生成焓提供了非常有效的方法。对于中等大小的化合物,该方法的扩展不确定度(95%置信度)约为3 kJ·mol-1,与典型的实验测量值相当。较大的感兴趣的化合物通常表现出许多构象,这些构象在分子内相互作用中可以显着不同。虽然目前的能力允许处理给定化合物的几百种不同的构象结构,但许多感兴趣的系统显示出的数字远远超过1000。在本研究中,我们研究了如何在控制近似误差的同时减少大型共形集成的昂贵LCCSD(T)计算次数。发现的最佳策略是以系统的方式纠正较低级别的替代模型(密度泛函理论,DFT)的结果。研究还发现,替代模型引入的构象贡献误差主要是由系统(偏差)驱动的,而不是由DFT能量偏离LCCSD(T)目标的随机成分驱动的。在DFT基准测试研究中,这一区别通常被忽视。作为这项工作的结果,得到了20大麻素和大麻素相关化合物的生成焓。综合不确定度分析表明,所得值的扩展不确定度在4 kJ·mol-1以下。
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Accurate Enthalpies of Formation for Bioactive Compounds from High-Level Ab Initio Calculations with Detailed Conformational Treatment: A Case of Cannabinoids.

Our recently developed approach based on the local coupled-cluster with single, double, and perturbative triple excitation [LCCSD(T)] model gives very efficient means to compute the ideal-gas enthalpies of formation. The expanded uncertainty (95% confidence) of the method is about 3 kJ·mol-1 for medium-sized compounds, comparable to typical experimental measurements. Larger compounds of interest often exhibit many conformations that can significantly differ in intramolecular interactions. Although the present capabilities allow processing even a few hundred distinct conformer structures for a given compound, many systems of interest exhibit numbers well in excess of 1000. In this study, we investigate how to reduce the number of expensive LCCSD(T) calculations for large conformer ensembles while controlling the error of the approximation. The best strategy found was to correct the results of the lower-level, surrogate model (density functional theory, DFT) in a systematic manner. It was also found that the error in the conformational contribution introduced by a surrogate model is mainly driven by a systematic (bias) rather than a random component of the DFT energy deviation from the LCCSD(T) target. This distinction is usually overlooked in DFT benchmarking studies. As a result of this work, the enthalpies of formation for 20 cannabinoid and cannabinoid-related compounds were obtained. Comprehensive uncertainty analysis suggests that the expanded uncertainties of the obtained values are below 4 kJ·mol-1.

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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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