Literature DB >> 24765118

Can quantum-chemical NMR chemical shifts be used as criterion for force-field development.

Thomas E Exner1, Andrea Frank2, Heiko M Möller2, Martin Dračínský3.   

Abstract

Entities:  

Year:  2014        PMID: 24765118      PMCID: PMC3980060          DOI: 10.1186/1758-2946-6-S1-O2

Source DB:  PubMed          Journal:  J Cheminform        ISSN: 1758-2946            Impact factor:   5.514


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Fragment-based quantum chemical calculations based on our adjustable density matrix assembler (ADMA) are able to calculate NMR chemical shifts even for proteins and protein-protein complexes [1,2]. The agreement between the calculated and experimental chemical shifts in these calculations is, however, highly dependent on including conformational sampling and explicit solvent molecules. On the one hand, ensembles taken from classical MD simulations are suited for 13C and 1H chemical shift calculations if polar protons are neglected [3]. On the other hand, input structures from a Car–Parrinello MD resulted in landmark improvements over calculations based on classical MD especially for amide protons, which are predicted too high-field shifted based on the latter ensembles [4]. The better results are caused by the solute–solvents interactions forming shorter hydrogen bonds as well as by the internal degrees of freedom of the solute. With the obtained accuracy and the possibility of identifying the structural reasons for discrepancies between the experimental and calculated data, NMR chemical-shift calculations are now a perfect tool for e.g. the validation of new, improved force fields.
  4 in total

1.  Conformational Sampling by Ab Initio Molecular Dynamics Simulations Improves NMR Chemical Shift Predictions.

Authors:  Martin Dračínský; Heiko M Möller; Thomas E Exner
Journal:  J Chem Theory Comput       Date:  2013-07-02       Impact factor: 6.006

2.  Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 2. Level of Theory, Basis Set, and Solvents Model Dependence.

Authors:  Andrea Frank; Heiko M Möller; Thomas E Exner
Journal:  J Chem Theory Comput       Date:  2012-03-30       Impact factor: 6.006

3.  Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins.

Authors:  Andrea Frank; Ionut Onila; Heiko M Möller; Thomas E Exner
Journal:  Proteins       Date:  2011-05-09

4.  Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 3. Conformational Sampling and Explicit Solvents Model.

Authors:  Thomas E Exner; Andrea Frank; Ionut Onila; Heiko M Möller
Journal:  J Chem Theory Comput       Date:  2012-10-15       Impact factor: 6.006

  4 in total

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