To Gibbs or Not to Gibbs Effect of Entropic Contribution in the NMR Calculations of Flexible and Polar Molecules-Updating the DP4+App.

IF 1.9 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Magnetic Resonance in Chemistry Pub Date : 2024-10-30 DOI:10.1002/mrc.5491
Milagros Amichetti, Bruno A Franco, María Marta Zanardi, Ariel M Sarotti
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Abstract

The application of quantum-based NMR methods for the structural elucidation of natural and unnatural products has grown significantly. However, accurately calculating the conformational landscape of flexible molecules with intricate intramolecular hydrogen bonding (IHB) networks continues to be a major challenge. In this work, we thoroughly studied the effect of entropic contributions (trough Gibbs free energies calculations) in the DP4+ performance. Our results show that to solve biased systems with strong IHB interactions requires computing the Boltzmann contributions using Gibbs free energies computed with at least triple-ξ basis set and SMD solvation model. In response to this finding, we have updated our DP4+App, a user-friendly Python applet that automates the entire process of calculating DP4+ probabilities. In the new version, the program allows for calculating of conformational contributions at any selected theory level, using either SCF or Gibbs free energies.

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柔性和极性分子核磁共振计算中熵贡献的吉布斯效应(To Gibbs or Not to Gibbs Effect of Entropic Contribution in the NMR Calculations of Flexible and Polar Molecules)-更新 DP4+App.
基于量子的核磁共振方法在天然和非天然产物的结构阐释方面的应用已大幅增长。然而,精确计算具有复杂分子内氢键(IHB)网络的柔性分子的构象格局仍然是一项重大挑战。在这项工作中,我们深入研究了熵贡献(通过吉布斯自由能计算)对 DP4+ 性能的影响。结果表明,要求解具有强 IHB 相互作用的偏态系统,需要使用至少三ξ基集和 SMD 溶解模型计算的吉布斯自由能来计算玻尔兹曼贡献。针对这一发现,我们更新了 DP4+App 程序,这是一个用户友好的 Python 小程序,可以自动完成 DP4+ 概率的整个计算过程。在新版本中,该程序允许使用 SCF 或吉布斯自由能计算任何选定理论水平的构象贡献。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
4.70
自引率
10.00%
发文量
99
审稿时长
1 months
期刊介绍: MRC is devoted to the rapid publication of papers which are concerned with the development of magnetic resonance techniques, or in which the application of such techniques plays a pivotal part. Contributions from scientists working in all areas of NMR, ESR and NQR are invited, and papers describing applications in all branches of chemistry, structural biology and materials chemistry are published. The journal is of particular interest not only to scientists working in academic research, but also those working in commercial organisations who need to keep up-to-date with the latest practical applications of magnetic resonance techniques.
期刊最新文献
Issue Information A New qNMR Compliant Savitzky-Golay Apodization Function for Resolution Enhancement. NMR Relaxometry to Monitor In Situ the Loading of Amberlite IR120 and Dowex Marathon MSC Resins With Ni2+ and Cu2+ During a Column Experiment. To Gibbs or Not to Gibbs Effect of Entropic Contribution in the NMR Calculations of Flexible and Polar Molecules-Updating the DP4+App. Deciphering the Conformations of Glutathione Oxidized Peptide: A Comparative NMR Study in Solution and Solid-State Environments.
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