Literature DB >> 34496578

A comparison of three DFT exchange-correlation functionals and two basis sets for the prediction of the conformation distribution of hydrated polyglycine.

Ying Yuan1, Feng Wang1.   

Abstract

The performance of three density functional theory (DFT) exchange-correlation functionals, namely, Perdew-Burke-Ernzerhof (PBE), BP86, and B3LYP, in predicting conformational distributions of a hydrated glycine peptide is tested with two different basis sets in the framework of adaptive force matching (AFM). The conformational distributions yielded the free energy profiles of the DFT functional and basis set combinations. Unlike traditional validations of potential energy and structural parameters, our approach allows the free energy of DFT to be validated. When compared to experimental distributions, the def2-TZVP basis set provides better agreement than a slightly trimmed aug-cc-pVDZ basis set. B3LYP is shown to be better than BP86 and PBE. The glycine model fitted against B3LYP-D3(BJ) with the def2-TZVP basis set is the most accurate and named the AFM2021 model for glycine. The AFM2021 glycine model provides better agreement with experimental J-coupling constants than C36m and ff14SB, although the margin is very small when compared to C36m. Our previously published alanine model is also refitted with the slightly simplified AFM2021 energy expression. This work shows good promise of AFM for developing force fields for a range of proteinogenic peptides using only DFT as reference.

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Year:  2021        PMID: 34496578      PMCID: PMC8425985          DOI: 10.1063/5.0059669

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   4.304


  46 in total

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Authors:  Omololu Akin-Ojo; Feng Wang
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Journal:  Biochem Soc Trans       Date:  2008-02       Impact factor: 5.407

4.  Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method.

Authors:  Omololu Akin-Ojo; Yang Song; Feng Wang
Journal:  J Chem Phys       Date:  2008-08-14       Impact factor: 3.488

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Journal:  Phys Rev B Condens Matter       Date:  1986-11-15

6.  Effect of the damping function in dispersion corrected density functional theory.

Authors:  Stefan Grimme; Stephan Ehrlich; Lars Goerigk
Journal:  J Comput Chem       Date:  2011-03-01       Impact factor: 3.376

7.  Dihedral angles of trialanine in D2O determined by combining FTIR and polarized visible Raman spectroscopy.

Authors:  R Schweitzer-Stenner; F Eker; Q Huang; K Griebenow
Journal:  J Am Chem Soc       Date:  2001-10-03       Impact factor: 15.419

8.  Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides.

Authors:  D J Tobias; C L Brooks
Journal:  Biochemistry       Date:  1991-06-18       Impact factor: 3.162

9.  Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association.

Authors:  Robert B Best; Wenwei Zheng; Jeetain Mittal
Journal:  J Chem Theory Comput       Date:  2014-10-16       Impact factor: 6.006

10.  Development and Validation of a DFT-Based Force Field for a Hydrated Homoalanine Polypeptide.

Authors:  Ying Yuan; Zhonghua Ma; Feng Wang
Journal:  J Phys Chem B       Date:  2021-02-08       Impact factor: 2.991

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  1 in total

1.  Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching.

Authors:  Dong Zheng; Ying Yuan; Feng Wang
Journal:  J Phys Chem A       Date:  2022-04-14       Impact factor: 2.944

  1 in total

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