Gleeson, Duangkamol

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A theoretical study of cis-trans isomerisation in H-ZSM5: Probing the impact of cluster size and zeolite framework on energetics and structure
(2008-01-01)
Gleeson, Duangkamol
In this study the results from a series of calculations are reported that probe the influence of the QM cluster size and the extended framework treatment in ONIOM calculations. This is done by comparing the differences in the structures and energetics obtained during simulations of cis-trans isomerisation of butene in H-ZSM-5 at varying level of accuracy. Seven different models have been employed; 3T, 5T and 10T DFT cluster models, and to more effectively encode the extended framework of ZSM-5; 3T:46T, 5T:46T, 10T:46T DFT:MM ONIOM models, and a 46T DFT cluster model. The results show that irrespective of the exact QM cluster size, relatively small gasphase clusters show clear limitations due to the neglect of the extended framework. In particular, the structural and electronic implications of using the different zeolite models have been rigorously assessed using the multivariate statistical method principal components analysis (PCA). © Springer Science+Business Media B.V. 2008.
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QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors
(2009-06-22)
Gleeson, M. Paul
;
Gleeson, Duangkamol
The use of QM/MM based methods to optimize and rescore GOLD derived cross-docked protein-ligand poses has been investigated using a range of fragment-like kinase inhibitors where experimental data have been reported. Particular emphasis has been placed on rationalizing the potential benefits of the method in the increasingly popular fragment based drug discovery area. The results of this cross-docking, rescoring study on 9 protein ligand complexes suggest that the hybrid QM/MM calculations could prove useful in kinase fragment based drug discovery (FBDD). B3LYP/6-31G<sup>**</sup>//UFF derived enthalphies allow us to identify the correct X-ray pose from a range of plausible decoys 77% of the time, almost a doubling of the retrieval rate compared to GOLD (44%). In addition, this method provides us with a means to rapidly and accurately generate virtual protein-ligand complexes that will allow a program team to probe the existing interactions between the ligand and protein and search for additional interactions. © 2009 American Chemical Society.
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The catalytic conversion of acetonitrile to acrylonitrile in zeolitic systems: Rationalization of experimental observations using theoretical simulations
(2007-12-15)
Gleeson, Duangkamol
;
Limtrakul, Jumras
Quantum mechanical calculations have been performed on faujasite and silicalite models to investigate reported experimental differences in yields of two key catalytic products (propionitrile and acrylonitrile) formed from the reaction of acetonitrile with either methanol or formaldehyde, respectively. The calculations were performed using 12T and 10T cluster representations of faujasite and silicalite, respectively, and the results are in good overall agreement with experimental observations. Both reactions are predicted to proceed in a concerted manner, with the transfer of a proton to the basic zeolite oxygen atom in conjunction with the methyl group migration to form a reaction intermediate. The stationary points found on the reaction surface in both zeolites have been systematically assessed using principal components analysis to give us an insight into the correlated nature of the structural/electronic changes that occur on the reaction surfaces. © 2007 Elsevier B.V. All rights reserved.
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QM/MM calculations in drug discovery: A useful method for studying binding phenomena?
(2009-03-23)
Gleeson, M. Paul
;
Gleeson, Duangkamol
Herein we investigate whether QM/MM could prove useful as a tool to study the often subtle binding phenomena found within pharmaceutical drug discovery programs. The goal of this investigation is to determine whether it is possible to employ high level QM/MM calculations to answer specific questions around a binding event in a cycle time that is aligned with medicinal chemistry synthesis. To this end QM/MM calculations have been performed on four protein kinase-ligand complexes using five different levels of theory, using standard hardware, in an effort to assess their utility. We conclude that the accuracy and turnaround time of such calculations mean they could prove valuable to (1) probe the subtle nature of the interactions within protein active sites, (2) facilitate the interpretation of poorly resolved electron density, and (3) study the impact of substituent changes on the binding conformation or in the assessment of alternate scaffolds. In practice, the successful application of such methods will be limited by the size of the system under investigation, the level of theory used, and whether there is a need for conformational sampling. © 2009 American Chemical Society.
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Application of QM simulations and multivariate analysis in the study of alkene reactivity in the zeolite H-ZSM5
(2008-01-01)
Gleeson, Duangkamol
Reported herein are the results of an investigation into the effect of the extended framework of the zeolite ZSM-5 on the reaction energetics and structures of (a) the physisorbed complex formed between the zeolite and six alkenes, (b) the corresponding chemisorbed alkoxide intermediate and (c) the transition states (TS) connecting the two. For this, quantum mechanical (QM) simulations of ZSM-5 in the presence and absence of the zeolite framework have been employed. A 46T density functional theory (DFT) cluster model and a 3T:46T DFT:UFF ONIOM model are used to represent the former scenario and a simple 3T DFT cluster model for the latter. The structural implications of neglecting the zeolite framework have been rigorously compared using the multivariate statistical method principal components analysis (PCA). This method allows one to assess the correlated nature of the changes in structure along the reaction coordinate, for multiple different alkenes, in a facile, reliable way. Copyright © 2008 John Wiley & Sons, Ltd.

Gleeson, Duangkamol

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