Literature DB >> 31922746

Comparing Alchemical Free Energy Estimates to Experimental Values Based on the Ben-Naim Formula: How Much Agreement Can We Expect?

T Ryan Rogers1, Feng Wang1.   

Abstract

The solvation free energy (SFE) plays a key role in thermodynamics. One well-established method for computing the SFE is through an alchemical transformation. However, experimental SFEs are generally determined according to the Ben-Naim equations relying on vapor pressure or density ratios. It is important to establish whether, or to what extent, typical alchemical-based free energy computations provide results comparable to experimental SFEs. In this work, we mimic experimental measurements by simulating the liquid-vapor coexistence of water without alchemical operations. The SFEs measured through vapor pressure and density ratios are used to validate the SFEs obtained through alchemical transformations. It is shown that proper consideration of the nonideal behavior of the vapor is important to ensure that the alchemical SFEs are consistent with the Ben-Naim SFEs. Alchemical transformations in the vapor phase should be performed in addition to solution phase transformations for strongly interacting solutes, such as those with low boiling temperatures and large second virial coefficients. A formula based on the virial expansion of pressure is proposed to provide a better estimate of the true SFE from the simulated vapor pressures. The proposed formula is also applicable to experimental determinations of SFE when the pressure-based route is used.

Entities:  

Mesh:

Substances:

Year:  2020        PMID: 31922746      PMCID: PMC7661276          DOI: 10.1021/acs.jpcb.9b08965

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  33 in total

1.  Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study.

Authors:  M A Wilson; A Pohorille
Journal:  J Phys Chem B       Date:  1997-04-17       Impact factor: 2.991

2.  Theory of a systematic computational error in free energy differences.

Authors:  Daniel M Zuckerman; Thomas B Woolf
Journal:  Phys Rev Lett       Date:  2002-10-15       Impact factor: 9.161

3.  Rapid calculation of partition functions and free energies of fluids.

Authors:  Hainam Do; Jonathan D Hirst; Richard J Wheatley
Journal:  J Chem Phys       Date:  2011-11-07       Impact factor: 3.488

4.  Efficient Algorithms for Langevin and DPD Dynamics.

Authors:  N Goga; A J Rzepiela; A H de Vries; S J Marrink; H J C Berendsen
Journal:  J Chem Theory Comput       Date:  2012-06-13       Impact factor: 6.006

Review 5.  Free energy via molecular simulation: applications to chemical and biomolecular systems.

Authors:  D L Beveridge; F M DiCapua
Journal:  Annu Rev Biophys Biophys Chem       Date:  1989

6.  Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.

Authors:  Michael R Shirts; Vijay S Pande
Journal:  J Chem Phys       Date:  2005-04-08       Impact factor: 3.488

7.  Etomica: an object-oriented framework for molecular simulation.

Authors:  Andrew J Schultz; David A Kofke
Journal:  J Comput Chem       Date:  2015-01-06       Impact factor: 3.376

8.  Perspective: Alchemical free energy calculations for drug discovery.

Authors:  David L Mobley; Pavel V Klimovich
Journal:  J Chem Phys       Date:  2012-12-21       Impact factor: 3.488

9.  A potential model for sodium chloride solutions based on the TIP4P/2005 water model.

Authors:  A L Benavides; M A Portillo; V C Chamorro; J R Espinosa; J L F Abascal; C Vega
Journal:  J Chem Phys       Date:  2017-09-14       Impact factor: 3.488

10.  Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations.

Authors:  Yilin Meng; Danial Sabri Dashti; Adrian E Roitberg
Journal:  J Chem Theory Comput       Date:  2011-09-13       Impact factor: 6.006

View more
  1 in total

1.  Anion-cation contrast of small molecule solvation in salt solutions.

Authors:  Stefan Hervø-Hansen; Jan Heyda; Mikael Lund; Nobuyuki Matubayasi
Journal:  Phys Chem Chem Phys       Date:  2022-02-02       Impact factor: 3.676

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.