Recent Publications
1998-2010
- “Cooperative Effects in the Structuring of Fluoride Water Clusters: Ab Initio Hybrid Quantum Mechanical/Molecular Mechanical Model Incorporating Polarizable Fluctuating Charge Solvent”, R.A.Bryce, M.A.Vincent, N.O.J.Malcolm, I.H.Hillier and N.A.Burton, J. Chem. Phys., 109, 3077-3085 (1998)
- “Prediction of the Mechanisms of Enzyme-Catalysed Reactions using Hybrid Quantum Mechanical Molecular Mechanical Methods”, N.A.Burton, M.J.Harrison, J.C.Hart, I.H.Hillier and D.W.Sheppard, Faraday Discuss., 110, 463-475 (1998)
- “An alternative role for the conserved Asp residue in phosphoryl transfer reactions”, J.C.Hart, I.H.Hillier, N.A.Burton and D.W.Sheppard, J. Amer. Chem. Soc., 120, (1998) 13535-13536
- “Ab initio study of single and double point adsorption of carbon monoxide on clusters representing zeolites.”, A.Khodakov, S.P.Bates, J.Dwyer, C.M.Windsor, N.A.Burton, Phys. Chem. Chem. Phys., 1, 507-512 (1999)
- “What is the mechanism of phosphoryl transfer in protein kinases? A hybrid quantum mechanical/molecular mechanical study”, J.C.Hart, D.W.Sheppard, I.H.Hillier and N.A.Burton, Chem. Commun., 1, 79-80 (1999)
- “Monte Carlo simulations of water clusters on a parallel computer using an ab initio potential.”, E.V.Akhmatskaya, M.D.Cooper, N.A.Burton, A.J.Masters, I.H.Hillier, Int. J. Quantum Chem., 74, 709-719 (1999)
- “Ab initio hybrid quantum mechanical/molecular mechanical studies of the mechanisms of the enzymes protein kinase and thymidine phosphorylase.” D.W.Sheppard, N.A.Burton, I.H.Hillier, J. Mol. Struc. (Theochem) 506, 35-44 (2000)
- “Aspects of hybrid QM/MM calculations: The treatment of the QM/MM interface region and geometry optimisation with an application to chorismate mutase.”, R.A.Hall, S.A.Hindle, N.A.Burton, I.H.Hillier, J. Comp. Chem. 21, 1433-1441 (2000)
- “QM/MM methods and the study of kinetic isotope effects: Modelling the covalent junction region and application to the enzyme Xylose Isomerase.”, R.M.Nicoll, S.A.Hindle, G.MacKenzie, I.H.Hillier, N.A.Burton, Theor. Chem. Acc. 106, 105-112 (2001)
- “QM/MM studies show substantial tunnelling for the hydrogen-transfer reaction in methylamine dehydrogenase.” P.F.Faulder, G.Tresadern, K.K.Chohan, N.S.Scrutton, M.J.Sutcliffe, I.H.Hillier, N.A.Burton, J. Amer. Chem. Soc. 123, 8604-8605 (2001), (DOI:10.1021/ja016219a)
- “Calculations of hydrogen tunnelling and enzyme catalysis: a comparison of liver alcohol dehydrogenase, methylamine dehydrogenase and soybean lipoxygenase.”, G. Tresadern, J.P.McNamara, M.Mohr, H.Wang, N.A.Burton, I.H.Hillier, Chem. Phys. Lett., 358, 489-494 (2002), (DOI:10.1016/S0009-2614(02)00654-1).
- “Direct dynamics calculations of reaction rate and kinetic isotope effects in enzyme catalyzed reactions.”, G.Tresadern, S.Nunez, P.Faulder, H.Wang, I.H.Hillier, N.A.Burton, Faraday Discussions 122 (Time-Resolved Chemistry: From Structure to Function, 2002), 223-242 (2003).
- “Recent advances in quantum mechanical/molecular mechanical calculations of enzyme catalysis: hydrogen tunnelling in liver alcohol dehydrogenase and inhibition of elastase by a-ketoheterocycles.”, G.Tresadern, P.F.Faulder, M.P.Gleeson, Z.Tai, G.MacKenzie, N.A.Burton, I.H.Hillier, Theoretical Chemistry Accounts 109, 108-117 (2003).
- “Prediction of the potency of inhibitors of adenosine deaminase by QM/MM calculations.”, M.P.Gleeson, N.A.Burton, I.H.Hillier, Chem. Commun. 2180-2181 (2003).
- “What form of NG-hydroxy-L-arginine is the intermediate in the mechanism of NO synthase? QM and QM/MM calculations of substrate-active site interactions.”, I.Morao, Z.Tai, I.H.Hillier, N.A.Burton, J.Mol.Struc. (Theochem) 632, 277-285 (2003).
- “The mechanism of adenosine deaminase catalysis studied by QM/MM calculations: The role of histidine 238 and the activity of the alanine 238 mutant.”, M.P.Gleeson, N.A.Burton, I.H.Hillier, Phys. Chem. Chem. Phys., 5, 4272-4278 (2003).
- “Extreme tunnelling in methylamine dehydrogenase revealed by hybrid QM/MM calculations: potential energy surface profile for methylamine and ethanolamine substrates and kinetic isotope effect values.”, G.Tresadern, H.Wang, P.F.Faulder, N.A.Burton, I.H.Hillier, Mol. Phys. 101, 2775-2784 (2003).
- “Theoretical Analyses of the Peptidyl α-Ketoheterocyclic Inhibitors of Human Neutrophil Elastase: Insight into the Mechanism of Inhibition and the Application of QM/MM Calculations in Structure-Based Drug Design.”, M.P.Gleeson, I.H.Hillier, N.A.Burton, J. Org. Biomol. Chem., 2, 2275-2280 (2004), (DOI:10.1039/B402399D).
- “Assessment of a mechanism for reactive inhibition of carboxypeptidase A with QM/MM methods.”, L. Phoon and N.A. Burton, J. Mol. Graph. Soc. 24, 94-101 (2005).
- “The development of a PM3 parameter set to describe iron-sulfur proteins.”, M. Sundararajan, J.P. McNamara, I.H. Hillier, H. Wang, N.A. Burton, Chem. Phys. Lett. 404, 9-12 (2005).
- “Structure and Redox Properties of the Protein, Rubredoxin, and Its Ligand and Metal Mutants Studied by Electronic Structure Calculation.”, M. Sundararajan, I.H. Hillier, N.A. Burton, J. Phys. Chem. A 110, 785-790 (2006).
- “Exploring Reaction Pathways with Transition Path and Umbrella Sampling: Application to Methyl Maltoside.”, R.J. Dimelow, R.A. Bryce, A.J. Masters, I.H. Hillier, and N.A Burton, J. Chem. Phys. (2006) 124(11), 114113/1-114113/16 (DOI:10.1063/1.2172604).
- “An analysis of reaction pathways for proton tunnelling in methylamine dehydrogenase.”, S. Nuñez, G. Tresadern, I.H. Hillier and N.A. Burton, Phil. Trans. R. Soc. B (2006), 361(1472), 1387-1398, (DOI:10.1098/rstb.2006.1867).
- “Structure and Ionization Energies of some analogues of iron-only hydrogenases studied by Density Functional Theory methods”, P. Jayapal, M. Sundararajan, I.H. Hillier, N.A. Burton, J. Organometallic. Chem. (2006), 691(21), 4532-4538.
- “ How are the ready and unready states of nickel-iron hydrogenase activated by H2? A density functional theory study.”, P. Jayapal, M. Sundararajan, I.H. Hillier, N.A. Burton, Phys. Chem. Chem. Phys. (2006), 8(35), 4086-4094 (DOI:10.1039/b608069c).
- “The dithiolene ligand- innocent' or non-innocent'? A theoretical and experimental study of some cobalt-dithiolene complexes.”, G. Periyasamy, N.A. Burton, I.H. Hillier, M.A. Vincent, H. Disley, J. McMaster, C.D. Garner, Faraday Discussions (2006), 135 469-488.
- “The dynamics of water exchange in gadolinium DOTA complexes studied by transition path sampling and potential of mean force methods.”, R.J. Dimelow, N.A. Burton, I.H. Hillier, Phys. Chem. Chem. Phys. (2007), 9(11), 1318-1323, (DOI:10.1039/b617068d)
- “The mechanism of nitrite reduction at T2Cu(II) centres: Electronic structure calculations of catalysis by copper nitrite reductase and by synthetic model compounds”, M. Sundararajan, I.H. Hillier, N.A. Burton, J. .Phys. Chem. B (2007), 111, 5511-5517 (DOI:10.1021/jp066852o).
- “The binding of nitric oxide at the Cu(I) site of copper nitrite reductase and of inorganic models: DFT calculations of the energetics and EPR parameters of side-on and end-on structures.”, G. Periyasamy, M. Sundararajan, I.H. Hillier, N.A. Burton, J.J. McDouall, Phys. Chem. Chem. Phys. (2007), 9., 2498-2506.
- “Density Functional and Semiempirical Molecular Orbital Methods Including Dispersion Corrections for the Accurate Description of Noncovalent Interactions Involving Sulfur-Containing Molecules.”, C.A. Morgado, J.P. McNamara, I.H. Hillier, N.A. Burton, M.A. Vincent, J. Chem. Theor. Comp. (2007), 3, 1656-1664 (DOI:10.1021/ct700072a).
- “The structure and binding energies of the van der Waals complexes of Ar and N2 with phenol and its cation, studied by high level ab initio and density functional theory calculations.”, M.A. Vincent, I.H. Hillier, Ian H., C.A. Morgado, N.A. Burton, X. Shan., J. Chem. Phys., (2008), 128, 044313/1-044313/7 (DOI:10.1063/1.2828369).
- “A computational study of the intramolecular deprotonation of a carbon acid in aqueous solution", R. Sharma, M. Thorley, J. P. McNamara, C. I. F. Watt and N. A. Burton, Phys. Chem. Chem. Phys., (2008), 10, 2475 - 2487 (DOI: 10.1039/b717524h)
- "A QM/MM study of fluoroaromatic interactions at the binding site of carbonic anhydrase II, using a DFT method corrected for dispersive interactions.", C.A. Morgado, I.H. Hillier, N.A. Burton, J.J.W. McDouall, Phys. Chem. Chem. Phys., (2008), 10(19), 2706-2714, (DOI:10.1039/b715514j).
- “QM/MM studies of Ni–Fe hydrogenases: the effect of enzyme environment on the structure and energies of the inactive and active states”, P. Jayapal, M. Sundararajan, I.H. Hillier and N.A. Burton, Phys. Chem. Chem. Phys., (2008), 10(29), 4249-4257, DOI:10.1039/B804035D
- “Electron delocalisation in the metallabenzenes - a computational analysis of ring currents.”, G. Periyasamy, N.A. Burton, I.H. Hillier, J. Thomas, J. Phys. Chem. A, (2008), 112(26), 5960-5972, DOI:10.1021/jp7106044.
- “The primary kinetic hydrogen isotope effect in the deprotonation of a nitroalkane by an intramolecular carboxylate group.”, N. Backstrom, S. Turega, N.A. Burton, and C.I F. Watt, J. Phys. Org.Chem., (2008), 21(7-8), 603-613, DOI:10.1002/poc.1330
- “Carbohydrate-protein recognition probed by density functional theory and ab initio calculations including dispersive interactions.”, R.K. Raju, A. Ramraj, M.A. Vincent, I.H. Hillier, N.A. Burton, Phys. Chem. Chem. Phys. (2008), 10(43), 6500-6508, DOI: 0.1039/b809164a
- “Which density functional should be used to study actinyl complexes?”, J.P. Austin, N.A. Burton, I.H. Hillier, M. Sundararajan, M.A. Vincent, Phys. Chem. Chem. Phys. (2009), 11(8), 1143-1145, DOI:10.1039/b821577d
- “Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force.”, S. Doudou, N.A. Burton, R. Henchman, J. Chem. Theor. Comp. (2009), 5(4), 909-918, DOI: 10.1021/ct8002354
- “Carbohydrate-aromatic pi interactions: a test of density functionals and the DFT-D method.”, R. K. Raju, A. Ramraj.; I. H. Hillier, M. A. Vincent, N. A. Burton, Phys. Chem. Chem. Phys. (2009), 11(18), 3411-3416, DOI: 10.1039/b822877a
- “Why does the enzyme SyrB2 chlorinate, but does not hydroxylate, saturated hydrocarbons? A density functional theory (DFT) study”,
S. Pandian, M. A. Vincent, I. H. Hillier and N. A. Burton, Dalton Trans., (2009), 6201-6207, DOI: 10.1039/b906866j
- “Prediction of ring formation efficiency via diene ring closing metathesis (RCM) reactions using the M06 density functional.”, S. Pandian, I. H. Hillier, M. A. Vincent, N. A. Burton, I. W. Ashworth, D. J. Nelson, J. M. Percy and G. Rinaudo, Chem. Phys. Lett., (2009), 476(1-3), 37-40, DOI: 10.1016/j.cplett.2009.06.021
- “Inhibitors of PIM-1 Kinase: A Computational Analysis of the Binding Free Energies of a Range of Imidazo [1,2-b] Pyridazines”,
S. Doudou, R. Sharma, R. H. Henchman, D. W. Sheppard and N. A. Burton, Journal of Chemical Information and Modeling, (2010), 50(3), 368-379, DOI: 10.1021/ci9003514
- “A DFT study of the possible role of vinylidene and carbene intermediates in the mechanism of the enzyme acetylene hydratase”, M. A. Vincent, I. H. Hillier, G. Periyasamy and N. A. Burton, Dalton Trans., (2010), 39(16), 3816-3822, DOI:
10.1039/b924800e
- “Assessment of approximate quantum chemical methods for calculating the interaction energy of nucleic acid bases with graphene and carbon nanotubes”, A. Ramraj, I. H. Hillier, M. A. Vincent and N. A. Burton,
Chem. Phys. Lett., (2010), 484(4-6), 295-298, DOI: 10.1016/j.cplett.2009.11.068
- “Factors controlling material deposition in the CVD of nickel sulfides, selenides or phosphides from dichalcogenoimidodiphosphinato complexes: deposition, spectroscopic and computational studies”,
A. Panneerselvam, G. Periyasamy, K. Ramasamy, M. Afzaal, M. A. Malik, P. O’Brien,* N. A. Burton, J. Waters and B. E. van Dongen, submitted to Dalton Trans., (2010)
- “Modelling the binding of HIV-reverse transcriptase and Nevirapine: An assessment of quantum mechanical and force field approaches and predictions of the effect of mutations on binding”,
R. K. Raju, N. A. Burton and I. H. Hillier, Phys. Chem. Chem. Phys., (2010), in print
- “The Effects of Perfluorination on Carbohydrate-pi Interactions: Computational studies of the interaction of Benzene and Hexafluorobenzene with Fucose and Cyclodextrin”, R. K. Raju, I. H. Hillier, N. A. Burton, M. A. Vincent, S. Doudou and R. A Bryce, Phys. Chem. Chem. Phys., (2010), accepted for publication.