Literature DB >> 20445813

Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide.

Alexander D Mackerell1, Ji Hyun Shim, Victor M Anisimov.   

Abstract

The accuracy of empirical force fields is inherently related to the quality of the target data used for optimization of the model. With the heat of vaporization (ΔH(vap)) of N-methylacetamide (NMA), a range of values have been reported as target data for optimization of the nonbond parameters associated with the peptide bond in proteins. In the present work, the original experimental data and Antoine constants used for the determination of the ΔH(vap) of NMA are reanalyzed. Based on this analysis, the wide range of ΔH(vap) values reported in the literature are shown to be due to incorrect reporting of the temperatures at which the original values were extracted and limitations in the quality of experimental vapor pressure-temperature data over a wide range of temperatures. Taking these problems into account, a consistent ΔH(vap) value is extracted from three studies for which experimental data are available. This analysis suggests that the most reliable value for ΔH(vap) is 13.0±0.1 at 410 K for use in force field optimization studies. The present results also indicate that similar analyses, including analysis of Antoine constants alone, may be of utility when reported ΔH(vap) values are not consistent for a given neat liquid.

Entities:  

Year:  2008        PMID: 20445813      PMCID: PMC2863105          DOI: 10.1021/ct8000969

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  12 in total

Review 1.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

Review 2.  Empirical force fields for biological macromolecules: overview and issues.

Authors:  Alexander D Mackerell
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

3.  A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Authors:  Chris Oostenbrink; Alessandra Villa; Alan E Mark; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

4.  The Antoine equation for vapor-pressure data.

Authors:  G W THOMSON
Journal:  Chem Rev       Date:  1946-02       Impact factor: 60.622

5.  A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model.

Authors:  Sandeep Patel; Charles L Brooks
Journal:  J Chem Phys       Date:  2005-01-08       Impact factor: 3.488

Review 6.  From structure to function: methods and applications.

Authors:  Haim J Wolfson; Maxim Shatsky; Dina Schneidman-Duhovny; Oranit Dror; Alexandra Shulman-Peleg; Buyong Ma; Ruth Nussinov
Journal:  Curr Protein Pept Sci       Date:  2005-04       Impact factor: 3.272

7.  Can molecular dynamics simulations provide high-resolution refinement of protein structure?

Authors:  Jianhan Chen; Charles L Brooks
Journal:  Proteins       Date:  2007-06-01

8.  Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.

Authors:  Wangshen Xie; Jingzhi Pu; Alexander D Mackerell; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2007       Impact factor: 6.006

9.  Understanding the dielectric properties of liquid amides from a polarizable force field.

Authors:  Edward Harder; Victor M Anisimov; Troy Whitfield; Alexander D MacKerell; Benoît Roux
Journal:  J Phys Chem B       Date:  2008-02-27       Impact factor: 2.991

10.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991

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  2 in total

1.  Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

Authors:  Bin Lin; Pedro E M Lopes; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Phys       Date:  2013-08-28       Impact factor: 3.488

2.  Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization.

Authors:  Junmei Wang; Hou Tingjun
Journal:  J Chem Theory Comput       Date:  2011-07-12       Impact factor: 6.006

  2 in total

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