[NMR paper] Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.

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Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.

Related Articles Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.

J Chem Theory Comput. 2016 Dec 19;

Authors: Steinmann C, Bratholm LA, Olsen JM, Kongsted J

Abstract
Full-protein NMR shielding constants based on ab initio calculations are desirable since they can assist in elucidating protein structures from NMR experiments. In this work we present NMR shielding constants computed using a new automated fragmentation (J. Phys. Chem. B 2009, 113, 10380--10388) approach in the framework of polarizable embedding density functional theory. We extend our previous work to give both basis set recommendations and comment on how large the quantum mechanical region should be in order to successfully compute (13)C NMR shielding constants that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we can obtain a representative subset of snapshots that gives the smallest predicted error compared to experiment. Finally, we use this subset of snapshots to calculate the NMR shielding constants at the PE-KT3/pcSseg-2 level of theory for all atoms in the protein GB3.


PMID: 27992211 [PubMed - as supplied by publisher]



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