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    Key role of hydrazine to the interaction between oxaloacetic against phosphoenolpyruvic carboxykinase (PEPCK): ONIOM calculations
    (2013-08-01)
    Prajongtat, Pongthep
    ;
    Phromyothin, Darinee Sae Tang
    ;
    Hannongbua, Supa
    The interactions between oxaloacetic (OAA) and phosphoenolpyruvic carboxykinase (PEPCK) binding pocket in the presence and absence of hydrazine were carried out using quantum chemical calculations, based on the two-layered ONIOM (ONIOM2) approach. The complexes were partially optimized by ONIOM2 (B3LYP/6-31G(d):PM6) method while the interaction energies between OAA and individual residues surrounding the pocket were performed at the MP2/6-31G(d,p) level of theory. The calculated interaction energies (INT) indicated that Arg87, Gly237, Ser286, and Arg405 are key residues for binding to OAA with the INT values of -1.93, -2.06, -2.47, and -3.16 kcal mol<sup>-1</sup>, respectively. The interactions are mainly due to the formation of hydrogen bonding interactions with OAA. Moreover, using ONIOM2 (B3LYP/6-31G(d):PM6) applied on the PEPCKHS complex, two proton transfers were observed; first, the proton was transferred from the carboxylic group of OAA to hydrazine while the second one was from Asp311 to Lys244. Such reactions cause the generation of binding strength of OAA to the pocket via electrostatic interaction. The orientations of Lys243, Lys244, His264, Asp311, Phe333, and Arg405 were greatly deviated after hydrazine incorporation. These indicate that hydrazine plays an important role in terms of not only changing the conformation of the binding pocket, but is also tightly bound to OAA resulting in its conformation change in the pocket. The understanding of such interaction can be useful for the design of hydrazine-based inhibitor for antichachexia agents. [Figure not available: see fulltext.] © 2013 Springer-Verlag Berlin Heidelberg.
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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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    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.
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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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    Application of ONIOM calculations in the study of the effect of the zeolite framework on the adsorption of alkenes to ZSM-5
    (2006-08-18)
    Namuangruk, Supawadee
    ;
    Tantanak, Duangkamol
    ;
    Limtrakul, Jumras
    The structures and energetics associated with the adsorption of ethene and four butene isomers on H-ZSM-5 zeolite have been studied using a 46T cluster and calculated at the ONIOM2(B3LYP/6-311++G(d,p):UFF) level. The adsorption energy for ethene-zeolite complex is predicted to be -8.17 kcal/mol, which is in good agreement with the experimental data of -9.0 kcal/mol. The trend of the calculated adsorption energies (kcal/mol) for the butene isomers is as follows: 1-butene (-16.06) > cis-2-butene (-13.62) ≅ trans-2-butene (-13.25) > isobutene (-6.96). The isobutene-zeolite complex is the least stable due to the greatest steric repulsion between the methyl substituents around the C{double bond, long}C bond and zeolite framework; the more substituted the lower the adsorption energy. Although our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) calculation results indicate that isobutene hardly approaches the acid site and has a weak interaction with the zeolite framework, NBO analysis shows that it has the maximum charge transfer from the active site and the largest stabilization energy. These findings explain the reason why ZSM-5 is selective towards isobutene produced from n-butene and indicate that the acidic proton from the zeolite is easy to transfer to isobutene. Thus, further catalytic conversion of isobutene would be facile. © 2006 Elsevier B.V. All rights reserved.