Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase
Quantum mechanics/molecular mechanics (QM/MM) methods are a popular tool in the investigation of enzyme reactions. Here, we compare B3LYP density functional theory (DFT) and ab initio QM/MM methods for modelling the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate in chorismate synthas...
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Elsevier
2014
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th-cmuir.6653943832-48882014-08-30T02:55:55Z Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase Lawan N. Ranaghan K.E. Manby F.R. Mulholland A.J. Quantum mechanics/molecular mechanics (QM/MM) methods are a popular tool in the investigation of enzyme reactions. Here, we compare B3LYP density functional theory (DFT) and ab initio QM/MM methods for modelling the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate in chorismate synthase. Good agreement with experimental data is only obtained at the SCS-MP2/CHARMM27 level for a reaction mechanism in which phosphate elimination precedes proton transfer. B3LYP predicts reaction energetics that are qualitatively wrong, stressing the need for ab initio QM/MM methods, and caution in interpretation of DFT results for this enzyme. © 2014 Elsevier B.V. All rights reserved. 2014-08-30T02:55:55Z 2014-08-30T02:55:55Z 2014 Article 00092614 10.1016/j.cplett.2014.06.010 CHPLB http://www.scopus.com/inward/record.url?eid=2-s2.0-84903707057&partnerID=40&md5=5e4ddfa423529ab4b1c462e38a67ee48 http://cmuir.cmu.ac.th/handle/6653943832/4888 English Elsevier |
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| description |
Quantum mechanics/molecular mechanics (QM/MM) methods are a popular tool in the investigation of enzyme reactions. Here, we compare B3LYP density functional theory (DFT) and ab initio QM/MM methods for modelling the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate in chorismate synthase. Good agreement with experimental data is only obtained at the SCS-MP2/CHARMM27 level for a reaction mechanism in which phosphate elimination precedes proton transfer. B3LYP predicts reaction energetics that are qualitatively wrong, stressing the need for ab initio QM/MM methods, and caution in interpretation of DFT results for this enzyme. © 2014 Elsevier B.V. All rights reserved. |
| format |
Article |
| author |
Lawan N. Ranaghan K.E. Manby F.R. Mulholland A.J. |
| spellingShingle |
Lawan N. Ranaghan K.E. Manby F.R. Mulholland A.J. Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase |
| author_facet |
Lawan N. Ranaghan K.E. Manby F.R. Mulholland A.J. |
| author_sort |
Lawan N. |
| title |
Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase |
| title_short |
Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase |
| title_full |
Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase |
| title_fullStr |
Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase |
| title_full_unstemmed |
Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase |
| title_sort |
comparison of dft and ab initio qm/mm methods for modelling reaction in chorismate synthase |
| publisher |
Elsevier |
| publishDate |
2014 |
| url |
http://www.scopus.com/inward/record.url?eid=2-s2.0-84903707057&partnerID=40&md5=5e4ddfa423529ab4b1c462e38a67ee48 http://cmuir.cmu.ac.th/handle/6653943832/4888 |
| _version_ |
1681420321810284544 |