文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期,新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

Expanded ensemble predictions of toluene-water partition coefficients in the SAMPL9 log  challenge.

作者信息

Goold Steven R, Raddi Robert M, Voelz Vincent A

机构信息

Department of Chemistry, Temple University, Philadelphia, PA, USA.

出版信息

Phys Chem Chem Phys. 2025 Mar 19;27(12):6005-6013. doi: 10.1039/d4cp03621b.


DOI:10.1039/d4cp03621b
PMID:40042168
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12023009/
Abstract

The logarithm of the partition coefficient (log ) between water and a nonpolar solvent is useful for characterizing a small molecule's hydrophobicity. For example, the water-octanol log  is often used as a predictor of a drugs lipophilicity and/or membrane permeability, good indicators of its bioavailability. Existing computational predictors of water-octanol log  are generally very accurate due to the wealth of experimental measurements, but may be less so for other non-polar solvents such as toluene. In this work, we participate in a Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) log  challenge to examine the accuracy of a molecular simulation-based absolute free energy approach to predict water-toluene log  in a blind test for sixteen drug-like compounds with acid-base properties. Our simulation workflow used the OpenFF 2.0.0 force field, and an expanded ensemble (EE) method for free energy estimation, which enables efficient parallelization over multiple distributed computing clients for enhanced sampling. The EE method uses Wang-Landau flat-histogram sampling to estimate the free energy of decoupling in each solvent, and can be performed in a single simulation. Our protocol also includes a step to optimize the schedule of alchemical intermediates in each decoupling. The results show that our EE workflow is able to accurately predict free energies of transfer, achieving an RMSD of 2.26 kcal mol (1.65 log  units), and of 0.80. An examination of outliers suggests that improved force field parameters could achieve better accuracy. Overall, our results suggest that expanded ensemble free energy calculations provide reasonably accurate log  prediction for a general-purpose force field.

摘要

相似文献

[1]
Expanded ensemble predictions of toluene-water partition coefficients in the SAMPL9 log  challenge.

Phys Chem Chem Phys. 2025-3-19

[2]
Development and test of highly accurate endpoint free energy methods. 3: partition coefficient prediction using a Poisson-Boltzmann method combined with a solvent accessible surface area model for SAMPL challenges.

Phys Chem Chem Phys. 2023-12-21

[3]
Prediction of octanol-water partition coefficients for the SAMPL6- molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields.

J Comput Aided Mol Des. 2020-5

[4]
SAMPL9 blind predictions for toluene/water partition coefficients using nonequilibrium alchemical approaches.

J Chem Phys. 2023-3-28

[5]
Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge.

J Comput Aided Mol Des. 2020-4

[6]
Prediction of toluene/water partition coefficients in the SAMPL9 blind challenge: assessment of machine learning and IEF-PCM/MST continuum solvation models.

Phys Chem Chem Phys. 2023-7-12

[7]
Blind prediction of toluene/water partition coefficients using COSMO-RS: results from the SAMPL9 challenge.

Phys Chem Chem Phys. 2023-11-29

[8]
Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge.

Phys Chem Chem Phys. 2023-12-6

[9]
Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge.

J Comput Aided Mol Des. 2020-4

[10]
Integrating multiscale and machine learning approaches towards the SAMPL9 log  challenge.

Phys Chem Chem Phys. 2024-2-28

引用本文的文献

[1]
Local Chemotherapy of Skin Pre-Neoplastic Lesions and Malignancies from the Perspective of Current Pharmaceutics.

Pharmaceutics. 2025-8-1

本文引用的文献

[1]
Multiple Topology Replica Exchange of Expanded Ensembles for Multidimensional Alchemical Calculations.

J Chem Theory Comput. 2025-1-14

[2]
Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability.

J Chem Theory Comput. 2024-7-23

[3]
Development and test of highly accurate endpoint free energy methods. 3: partition coefficient prediction using a Poisson-Boltzmann method combined with a solvent accessible surface area model for SAMPL challenges.

Phys Chem Chem Phys. 2023-12-21

[4]
Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge.

Phys Chem Chem Phys. 2023-12-6

[5]
Blind prediction of toluene/water partition coefficients using COSMO-RS: results from the SAMPL9 challenge.

Phys Chem Chem Phys. 2023-11-29

[6]
Prediction of toluene/water partition coefficients in the SAMPL9 blind challenge: assessment of machine learning and IEF-PCM/MST continuum solvation models.

Phys Chem Chem Phys. 2023-7-12

[7]
RNA-ligand molecular docking: advances and challenges.

Wiley Interdiscip Rev Comput Mol Sci. 2022

[8]
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.

J Chem Theory Comput. 2023-6-13

[9]
Folding@home: Achievements from over 20 years of citizen science herald the exascale era.

Biophys J. 2023-7-25

[10]
Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method.

J Comput Chem. 2023-5-15

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

推荐工具

医学文档翻译智能文献检索