ArticleJournal of the Royal Society, Interface2008
Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds.
Article in Journal of the Royal Society, Interface, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
9 citing papers in PubMed.
- Nanotechnology-Driven Drug Delivery Systems for Lung Cancer: Computational Advances and Clinical Perspectives.Thoracic cancer · 2025Review
- Arginine Kinase Activates Arginine for Phosphorylation by Pyramidalization and Polarization.ACS catalysis · 2024Article
- The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin.Scientific reports · 2020Article
- Theoretical Studies Applied to the Evaluation of the DFPase Bioremediation Potential against Chemical Warfare Agents Intoxication.International journal of molecular sciences · 2018Article
- Electronic Absorption Spectra from MM andJournal of chemical theory and computation · 2012Article
- Does compound I vary significantly between isoforms of cytochrome P450?Journal of the American Chemical Society · 2011Article
- Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes.Photosynthesis research · 2011Article
- Recent developments of the quantum chemical cluster approach for modeling enzyme reactions.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2009Review
- Introduction. Biomolecular simulation.Journal of the Royal Society, Interface · 2008Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly important for the study of chemical reactions and systems in condensed phases. Here, we have tested the accuracy of a density functional theory-based QM/MM implementation (B3LYP/6-311+G(d,p)/CHARMM27) on a set of biologically relevant interactions by comparison with full QM calculations. Intermolecular charge transfer due to hydrogen bond formation is studied to assess the severity of spurious polarization of QM atoms by MM point charges close to the QM/MM boundary. The changes in total electron density and natural bond orbital atomic charges due to hydrogen bond formation in selected complexes obtained at the QM/MM level are compared with full QM results. It is found that charge leakage from the QM atoms to MM atomic point charges close to the QM/MM boundary is not a serious problem, at least with limited basis sets. The results are encouraging in showing that important properties of key biomolecular interactions can be treated well at the QM/MM level employing good-quality levels of QM theory.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.