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分子熵的面积定律:超越简谐近似

The Area Law of Molecular Entropy: Moving beyond Harmonic Approximation.

作者信息

Roy Amitava, Ali Tibra, Venkatraman Vishwesh

机构信息

Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT 59812, USA.

Department of Mathematics and Natural Sciences, School of Data and Science, BRAC University, Dhaka 1212, Bangladesh.

出版信息

Entropy (Basel). 2024 Aug 14;26(8):688. doi: 10.3390/e26080688.

DOI:10.3390/e26080688
PMID:39202158
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11353761/
Abstract

This article shows that the gas-phase entropy of molecules is proportional to the area of the molecules, with corrections for the different curvatures of the molecular surface. The ability to estimate gas-phase entropy by the area law also allows us to calculate molecular entropy faster and more accurately than currently popular methods of estimating molecular entropy with harmonic oscillator approximation. The speed and accuracy of our method will open up new possibilities for the explicit inclusion of entropy in various computational biology methods.

摘要

本文表明,分子的气相熵与分子面积成正比,并对分子表面的不同曲率进行了校正。通过面积定律估算气相熵的能力,也使我们能够比目前流行的用简谐振荡器近似估算分子熵的方法,更快、更准确地计算分子熵。我们方法的速度和准确性将为在各种计算生物学方法中明确纳入熵开辟新的可能性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bf01/11353761/df158e4e8b0c/entropy-26-00688-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bf01/11353761/6114dc413dc9/entropy-26-00688-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bf01/11353761/df158e4e8b0c/entropy-26-00688-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bf01/11353761/6114dc413dc9/entropy-26-00688-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bf01/11353761/df158e4e8b0c/entropy-26-00688-g002.jpg

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本文引用的文献

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Thermodynamic Properties of Organic Substances: Experiment, Modeling, and Technological Applications.有机物质的热力学性质:实验、建模与技术应用
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Does a Machine-Learned Potential Perform Better Than an Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins.机器学习势能是否优于最优调谐传统力场?以氟醇为例的研究。
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Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.
Open Force Field v1.0.0-帕利西小分子力场的开发与基准测试。
J Chem Theory Comput. 2021 Oct 12;17(10):6262-6280. doi: 10.1021/acs.jctc.1c00571. Epub 2021 Sep 22.
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Testing the Black-Hole Area Law with GW150914.利用GW150914检验黑洞面积定律。
Phys Rev Lett. 2021 Jul 2;127(1):011103. doi: 10.1103/PhysRevLett.127.011103.
5
Understanding Conformational Entropy in Small Molecules.理解小分子中的构象熵。
J Chem Theory Comput. 2021 Apr 13;17(4):2099-2106. doi: 10.1021/acs.jctc.0c01213. Epub 2021 Mar 24.
6
Surprising Non-Additivity of Methyl Groups in Drug-Kinase Interaction.药物激酶相互作用中甲基的惊人非加和性。
ACS Chem Biol. 2019 Dec 20;14(12):2585-2594. doi: 10.1021/acschembio.9b00476. Epub 2019 Nov 4.
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Predicting gas phase entropy of select hydrocarbon classes through specific information-theoretical molecular descriptors.通过特定的信息论分子描述符预测选择的碳氢化合物类的气相熵。
SAR QSAR Environ Res. 2019 Jul;30(7):491-505. doi: 10.1080/1062936X.2019.1624613. Epub 2019 Jun 20.
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Small Molecule Thermochemistry: A Tool for Empirical Force Field Development.小分子热化学:经验力场开发的一种工具
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The Alexandria library, a quantum-chemical database of molecular properties for force field development.亚历山大图书馆,一个用于力场开发的分子性质量子化学数据库。
Sci Data. 2018 Apr 10;5:180062. doi: 10.1038/sdata.2018.62.
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