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Theoretical and Computational Chemistry

Working Paper

WaterKit: thermodynamic profiling of protein hydration sites

Jerome Eberhardt, Stefano Forli

Version 1 posted 01 November 2022

319

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Theoretical and Computational Chemistry

Working Paper

Estimating Free Energy Barriers for Heterogeneous Catalytic Reactions with Machine Learning Potentials and Umbrella Integration

Sina Stocker, Hyunwook Jung, Gábor Csányi, C. Franklin Goldsmith, Karsten Reuter, Johannes T. Margraf

Version 1 posted 30 May 2023

677

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1

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Physical Chemistry

Working Paper

Theoretical Study of Stability, Structure, and Optical Spectra of Ultra-Small Silver Clusters Using Density Functional Theory

Mohsen Farshad, Duwage Perera, jayendran Rasaiah

Version 1 posted 24 November 2020

455

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Biological and Medicinal Chemistry

Working Paper

Evaluating the use of absolute binding free energy in the fragment optimization process.

Irfan Alibay, Aniket Magarkar, Daniel Seeliger, Philip Biggin

Version 3 posted 02 February 2022

1,912

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Theoretical and Computational Chemistry

Working Paper

Impact of SARS-CoV-2 3CL Protease Mutations on Nirmatrelvir Inhibitory Efficiency. Computational Insights into Potential Resistance Mechanisms

Carlos A. Ramos-Guzmán, Milorad Andjelkovic, Kirill Zinovjev, J. Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 23 November 2022

239

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Physical Chemistry

Working Paper

A consistent picture of phosphate–divalent cation binding from models with implicit and explicit electronic polarization

Julie Puyo, Marie Juillé, Jérôme Hénin, Carine Clavaguéra, Elise Duboué-Dijon

Version 2 posted 27 April 2022

403

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Biological and Medicinal Chemistry

Working Paper

pyCHARMM: Embedding CHARMM Functionality in a Python Framework

Joshua Buckner, Xiaorong Liu, Arghya Chakravorty, Yujin Wu, Luis Cervantes, Thanh Lai, Charles Brooks

Version 2 posted 30 March 2023

1,206

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Theoretical and Computational Chemistry

Working Paper

Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations

Sigbjørn L. Bore, Pablo M. Piaggi, Roberto Car, Francesco Paesani

Version 1 posted 29 April 2022

665

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1

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Physical Chemistry

Working Paper

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

Wenxin Hu, Pengfei Li, Jia-Ning Wang, Yuanfei Xue, Yan Mo, Jun Zheng, Xiaoliang Pan, Yihan Shao, Ye Mei

Version 1 posted 29 July 2020

290

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Theoretical and Computational Chemistry

Working Paper

Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics

Paolo Raiteri, Alicia Schuitemaker, Julian Gale

Version 2 posted 02 April 2020

946

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60 results in Free energy in Keywords: Free energy

WaterKit: thermodynamic profiling of protein hydration sites

Estimating Free Energy Barriers for Heterogeneous Catalytic Reactions with Machine Learning Potentials and Umbrella Integration

Theoretical Study of Stability, Structure, and Optical Spectra of Ultra-Small Silver Clusters Using Density Functional Theory

Evaluating the use of absolute binding free energy in the fragment optimization process.

Impact of SARS-CoV-2 3CL Protease Mutations on Nirmatrelvir Inhibitory Efficiency. Computational Insights into Potential Resistance Mechanisms

A consistent picture of phosphate–divalent cation binding from models with implicit and explicit electronic polarization

pyCHARMM: Embedding CHARMM Functionality in a Python Framework

Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics

60 results in Keywords: Free energy