ArticleJournal of biomolecular NMR2015
Converging nuclear magnetic shielding calculations with respect to basis and system size in protein systems.
Article in Journal of biomolecular NMR, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- NMR crystallography reveals active-site protonation states of Toho-1 β-lactamase in complex with avibactam.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems.Journal of computational chemistry · 2025Article
- Solid-state NMR chemical shift analysis for determining the conformation of ATP bound to Na,K-ATPase in its native membrane.RSC advances · 2023Article
- Convergence in determining enzyme functional descriptors across Kemp eliminase variants.Electronic structure (Bristol, England) · 2022Article
- Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition.Journal of chemical theory and computation · 2022Article
- Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensionalProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Mutation of βGln114 to Ala Alters the Stabilities of Allosteric States in Tryptophan Synthase Catalysis.Biochemistry · 2021Article
- Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.Journal of chemical theory and computation · 2021Article
- PredictingAngewandte Chemie (International ed. in English) · 2020Article
- A benchmark for the size of the QM system required for accurate hybrid QM/MM calculations on the metal site of the protein copper, zinc superoxide dismutase.Journal of molecular modeling · 2019Article
- TensorView: A software tool for displaying NMR tensors.Magnetic resonance in chemistry : MRC · 2019Article
- Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation.Reaction chemistry & engineering · 2019Article
- Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters.Molecules (Basel, Switzerland) · 2018Article
- Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer.Physical chemistry chemical physics : PCCP · 2018Article
- Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM.Physical chemistry chemical physics : PCCP · 2018Article
- Computational Understanding of the Selectivities in Metalloenzymes.Frontiers in chemistry · 2018Review
- NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity.Journal of the American Chemical Society · 2016Article
- How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase.The journal of physical chemistry. B · 2016Article
- Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions.Crystal growth & design · 2016Article
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5 authors.
Funding
Abstract
Ab initio chemical shielding calculations greatly facilitate the interpretation of nuclear magnetic resonance (NMR) chemical shifts in biological systems, but the large sizes of these systems requires approximations in the chemical models used to represent them. Achieving good convergence in the predicted chemical shieldings is necessary before one can unravel how other complex structural and dynamical factors affect the NMR measurements. Here, we investigate how to balance trade-offs between using a better basis set or a larger cluster model for predicting the chemical shieldings of the substrates in two representative examples of protein-substrate systems involving different domains in tryptophan synthase: the N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F9) ligand which binds in the α active site, and the 2-aminophenol quinonoid intermediate formed in the β active site. We first demonstrate that a chemically intuitive three-layer, locally dense basis model that uses a large basis on the substrate, a medium triple-zeta basis to describe its hydrogen-bonding partners and/or surrounding van der Waals cavity, and a crude basis set for more distant atoms provides chemical shieldings in good agreement with much more expensive large basis calculations. Second, long-range quantum mechanical interactions are important, and one can accurately estimate them as a small-basis correction to larger-basis calculations on a smaller cluster. The combination of these approaches enables one to perform density functional theory NMR chemical shift calculations in protein systems that are well-converged with respect to both basis set and cluster size.
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