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| Content Provider | PubMed Central |
|---|---|
| Author | Senthilkumar, Kittusamy Mujika, Jon I. Ranaghan, Kara E. Manby, Frederick R. Mulholland, Adrian J. Harvey, Jeremy N. |
| Copyright Year | 2008 |
| 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. |
| Related Links | http://dx.doi.org/10.1098/rsif.2008.0243.focus |
| Ending Page | 216 |
| Starting Page | 207 |
| File Format | |
| ISSN | 17425689 |
| e-ISSN | 17425662 |
| Journal | Journal of the Royal Society Interface |
| Issue Number | Suppl 3 |
| Volume Number | 5 |
| Language | English |
| Publisher | The Royal Society |
| Publisher Date | 2008-12-06 |
| Access Restriction | Open |
| Rights Holder | The Royal Society |
| Subject Keyword | Biotechnology Biophysics Biochemistry Bioengineering Biomaterials Biomedical Engineering Research in Higher Education |
| Content Type | Text |
| Resource Type | Article |
| Subject | Biochemistry Biomaterials Biophysics Bioengineering Biomedical Engineering Biotechnology |
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