Computers in Chemistry

Computational methods play a crucial role in modern chemistry, providing both fundamental theoretical insights as well as supporting the interpretation of experimental data. This interplay between theory and experiment is vital. Theory helps experimental chemists to understand their results and in return experimental results provide data that helps validate and develop theoretical methods. The computational group within the Department of Chemistry at York has a very diverse range of interests and aims to target demanding problems important to today’s world. Expertise spans quantum chemistry, structural biology, molecular recognition, applied organometallics, materials chemistry, chemometrics, atmospheric modelling, unconventional computation, spectroscopy and more. This diversity allows us to tackle problems in both fundamental and applied research in chemistry and related fields. The group has strong interdisciplinary links at the international, national and departmental level.

Click here for information on computing facilities available to the group

Click here to view training and PhD/PDRA opportunities in the group

Areas of Interest

Quantum chemistry

Ab initio method development in modern valence-bond theory, excited state methods and calculation of magnetic properties; ground-state and excited state aromaticity and antiaromaticity; electronic structure of Möbius aromatic hydrocarbons (Dr Peter B Karadakov);  electronic structure and reactivity of unusual main-group-element compounds (Dr John Slattery); electronic structure of aromatic molecules and molecular complexes (Dr Martin Cockett, Dr John Moore, Dr Laurence Abbott); reaction mechanisms (Dr Peter B Karadakov, Dr John Slattery, Dr Jason M Lynam, Dr Martin Cockett, Professor Simon Duckett, Dr Paul Clarke, Professor Robin Perutz); computational catalysis (Dr John Slattery, Dr Martin Cockett, Dr Jason M Lynam, Professor Simon Duckett, Professor Robin Perutz, Professor Ian Fairlamb); electronic structure and properties of halogen bonded complexes (Dr Peter B Karadakov, Professor Duncan W Bruce); structure and energetics of ionic molecules and clusters (Dr Caroline Dessent); electron diffraction, electronic structure calculations, photochemistry (Dr Derek Wann)

PES for alkyne-vinylidene tautomerisation

Spectroscopy, photochemistry and excited states

Ground and excited-state structure and dynamics of organic dyes and transition metal complexes (Dr Laurence Abbott and Dr John Moore); non-covalent interactions in molecular complexes (Dr Martin Cockett); multidimensional Franck-Condon calculations and simulation of electronic spectra (Dr Martin Cockett); excited-state magnetic properties (Dr Peter B Karadakov)

Simulations in materials science and biochemistry

Simulation of liquid crystals and complex systems (Dr Martin Bates); virtual screening of potential pharmaceuticals (Hubbard); computational chemistry of small, conformationally flexible biomolecular ions (Dr Caroline Dessent)

Atmospheric modelling

Understanding the composition of the troposphere through box, regional and global modelling including the use of observations to constrain uncertainties (Professor Mat Evans , Dr Rickard)

Complexity figure

Nuclear Magnetic Resonance

Spin dynamics as a platform to implement computation; development of NMR pulse sequences by means of numerical simulations and novel search algorithms such as genetic alogorithms (Sebald); ab initio calculation of NMR properties (Dr Peter B Karadakov); understanding hyperpolarisation in NMR spectroscopy (Professor Simon Duckett)

Statistical thermodynamics

Molecular theory of solubility, thermodynamics of protein solvation and statistical thermodynamics of solution (Dr Seishi Shimizu)

Chemometric algorithm development

Chemometrics, biostatistics and image analysis (Dr Julie Wilson)

Cluster figure

Crystallographic software development

Software tools for protein crystallography (Dr Kevin Cowtan)

Miscellaneous

‘Artificial chemistries’ (Dr Angelika Sebald/Dr Stepney)

Selected Publications

2012

  • How Lewis acidic is your cation? Putting phosphenium ions on the fluoride-ion affinity scale. John M. Slattery and Sharifa Hussein, Dalton Trans., 41, 1808–1815 (2012).
  • Charged Behaviour from Neutral Ligands: Synthesis and Properties of N-Heterocyclic Pseudo-amides. Robert J. Thatcher, David G. Johnson, John M. Slattery and Richard E. Douthwaite, Chem. Eur. J., 18, 4329-36 (2012).
  • White phosphorus as a ligand for the coinage metals. Laura C. Forfar, Timothy J. Clark, Michael Green, Stephen M. Mansell, Chris A. Russell, Rajashekharayya Sanguramatha and John M. Slattery, Chem. Commun., 48, 1970-1972 (2012).
  • Green, R. A., Adams, R. W., Duckett, S. B., Mewis, R. E., Williamson D. C. and Green. G. G. R., The theory and practice of hyperpolarization in magnetic resonance using parahydrogen. Progress Prog. Nucl. Magn. Reson. Spectros., 10.1016/j.pnmrs.2012.03.001 (2012).
  • A nuclear magnetic resonance implementation of a classical Deutsch-Josza algorithm. A. Abbot, M. Bechmann, C. Calude and A. Sebald, Int. J. Unconvent. Comp., 8, 161-175 (2012).
  • Boolean logic gate design principles in unconventional computers: an NMR case study. M. Bechmann, A. Sebald and S. Stepney, Int. J. Unconvent. Comp., 8, 139-159 (2012).
  • P. B. Karadakov, D. L. Cooper, B. J. Duke and J. Li, Spin-Coupled Theory for ‘N in M ’ Active Spaces, J. Phys. Chem. A116, 7238–7244, (2012).

2011

  • Cowley, M. J., Adams, R. W., Atkinson, K. D., Cockett, M. C. R., Duckett, S. B., Green, G. G. R. Lohman, J. A. B., Kerssebaum, R., Kilgour, D. and Mewis, R. E., Iridium N-Heterocyclic Carbene Complexes as Efficient Catalysts for Magnetization Transfer from para-Hydrogen. J. Am. Chem. Soc., 133, 6134-6137 (2011).
  • Analysis of complex mixtures using high-resolution nuclear magnetic resonance spectroscopy and chemometrics.  McKenzie, JS, Donarski JA, Wilson JC, Charlton AJ.  Prog. Nucl. Magn. Reson. Spectros., 59(4), 336-359 (2011).
  • L. J. McAllister, D. W. Bruce and P. B. Karadakov, Halogen Bonding Interaction between Fluorohalides and Isocyanides, J. Phys. Chem. A,115, 11079–11086 (2011).

2010

  • Pugliesi. I, Gosling, M.P. and *Cockett, M.C.R. The role of the methyl group in stabilising the weak N–H···p hydrogen bond in the 4-fluorotoluene–ammonia complex. Phys. Chem. Chem., Phys., 12, 132 (2010).
  • Peak Matching in 2D 1H-13C HSQC NMR Spectra for Metabolomic Studies. James S. McKenzie, Adrian J. Charlton, James Donarski, Julie C. Wilson. Metabolomics, 6, 574-582 (2010).
  • Automated classification of starch granules using supervised pattern recognition of morphological properties. Julie Wilson, Karen Hardy, Richard Allen, Les Copeland, Richard Wrangham and Matthew Collins. J. Arch.Sci., 2010, 37, 594–604.
  • L. C. Roper, C. Prasang, V. N. Kozhevnikov, A. C. Whitwood, P. B. Karadakov and D. W. Bruce, An Experimental and Theoretical Study of Halogen-bonded Complexes of DMAP with Di- and Tri-Iodofluorobenzenes. A Complex with a Very Short N• • •I Halogen Bond, Cryst. Growth Des., 10, 3710–3720, (2010).
  • Insights into the intramolecular acetate-mediated formation of ruthenium vinylidene complexes: a ligand-assisted proton shuttle (LAPS) mechanism. D. G. Johnson, J. M. Lynam, J. M. Slattery and C. E. Welby, Dalton Trans.,39, 10432–10441 (2010).

Pre-2010

  • Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Michael Buckley, Matthew Collins, Jane Thomas-Oates and Julie C. Wilson. Rapid Commun. Mass Spectrom. 2009, 23,  3843–3854.
  • D. L. Cooper and P. B. Karadakov, Spin-Coupled Descriptions of Organic Reactivity, Int.Rev. Phys. Chem.,28, 169–206 (2009).
  • Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Michael Buckley, Matthew Collins, Jane Thomas-Oates and Julie C. Wilson. Rapid Commun. Mass Spectrom., 23, 3843–3854 (2009).
  • Exceptional Sensitivity of Metal-Aryl Bond Energies to ortho-Fluorine Substituents: Influence of the Metal, the Coordination Sphere, and the Spectator Ligands on M-C/H-C Bond Energy Correlations Clot E, Mégret C, Eisenstein O and Perutz R N, J. Am. Chem. Soc.,131, 7817-7827 (2009).
  • Pugliesi. I, Tonge, N.M. and *Cockett, M.C.R.  An excited state ab initio and multidimensional Franck-Condon analysis of the A1B2-X1A1 band system of fluorobenzene.J. Chem. Phys., 129, 104303 (2008).
  • P. B. Karadakov, Ground and Excited State Aromaticity and Antiaromaticity in Benzene and Cyclobutadiene, J. Phys. Chem. A.,112, 7303–7309, (2008).
  • P. B. Karadakov, Aromaticity and Antiaromaticity in the Low-Lying Electronic States of Cyclooctatetraene, J. Phys. Chem. A.,112, 12707–12713, (2008).
  • Competing C-F Activation Pathways in the Reaction of Pt(0) with Fluoropyridines: Phosphine-Assistance versus Oxidative Addition. Nova Flores A, Erhardt S, Jasim N A, Perutz R N, Macgregor S A, McGrady J E and Whitwood A C,  J. Am. Chem., Soc., 130, 15499–15511 (2008).
  • Ground- and Excited-State Infrared Spectra of an Azacrown-Substituted [(bpy)Re(CO)3L]+ Complex: Structure and Bonding in Ground and Excited States and Effects of Ba2+ Binding. J D Lewis, M Towrie and J N Moore, J Phys Chem A, 2008, 112, 3852-3864.
  • A natural light induced regioselective 6π-electrocyclisation / oxidative aromatisation reaction: Experimental and theoretical insights. B E Moulton, H Dong, C T O’Brien, S B Duckett, Z Lin and I J S Fairlamb, Org Biomol Chem, 2008, 6, 4523–4532.
  • Tonge, N.M., MacMahon, E.C., Pugliesi. I and *Cockett, M.C.R. The weak hydrogen bond in the fluorobenzene-ammonia van der Waals complex: Insights into the effects of electron withdrawing substituents on pi versus in-plane bonding.J Chem Phys., 126, 154319 (2007).
  • Ground and excited state resonance Raman spectra of an azacrown-substituted [(bpy)Re(CO)3L]+ complex: characterisation of excited states, determination of structure and bonding, and observation of metal cation release from the azacrown. J D Lewis, I P Clark and J N Moore, J Phys Chem A, 2007, 111, 50-58.
  • In-silico prediction of Pd-catalysed cross-coupling processes: dibenzylidene acetone (dba) ligand control.
    I J S Fairlamb and A F Lee, Organometallics, 2007, 26, 4087-4089.
  • López-Serrano, J., Duckett S. B. and Lledós. A. Palladium catalysed hydrogenation: detection of palladium hydrides, a joint study using parahydrogen enhanced NMR spectroscopy and density functional theory. J. Am. Chem. Soc.,128, 9596-9597, (2006).
  • The effect of the leaving ligand X on transmetallation of organostannanes (vinylSnR3) with LnPd(Ar)(X) in Stille cross-coupling reactions. A density functional theory study. A Ariafard, Z Lin and I J S Fairlamb, Organometallics, 2006, 25, 5788-5794
  • Experimental and Computational Studies of Structure and Bonding in Parent and Reduced Forms of the Azo Dye Orange II. L C Abbott, S N Batchelor, J Oakes, B C Gilbert, A C Whitwood, J R Lindsay Smith and J N Moore, J Phys Chem A, 2005, 109, 2894-2905.
  • Semi-empirical and ab initio studies of the structure and spectroscopy of the azo dye Direct Blue 1: comparison with experiment. L C Abbott, S N Batchelor, J Oakes, J R Lindsay Smith and J N Moore, J Phys Chem A, 2004, 108, 10208-10218.
  • Schott,D., Callaghan,P., Dunne, J.,  Duckett,S. B., Godard, C.,  Goicoechea, J. M., Harvey,  J. N., Lowe, J. P., Mawby, R. J., Müller, G., Perutz, R. N., Poli, R.  and Whittlesey, M. K. The reaction of M(CO)3(Ph2PCH2CH2PPh2) (M  Fe, Ru) with parahydrogen: probing the electronic structure of reaction intermediates and the internal rearrangement mechanism for the dihydride products. Dalton. Trans., 3218-3224 (2004).
  • Anwar, M. S., Blazina, D., Carteret, H., Duckett, S. B. and Jones, J. A.  Implementation of quantum computation with pure quantum states derived from parahydrogen in liquid state NMR. Phys. Rev. A., 70, 032324-1-032324-5 (2004).

Quick links

Postgraduate courses

Staff research interests

Current News

  • The Chemistry Department plan to develop the first dedicated laboratory building in the UK for atmospheric chemistry research, supported in part by a £1.25M grant from the Wolfson Foundation.
  • David Johnson (Lynam and Slattery groups) presents his computational mechanistic chemistry at the Dalton Regional Meeting in Leeds (June 2012)
  • Several members of the computational group (Slattery, Lynam, Perutz, Bates and Karadakov) move into the new chemistry research building (July 2012)
  • Neetisha Mistry (Lynam and Slattery groups) wins the KMS prize (July 2012)
  • Lynam, Perutz and their groups attend the 25th International Conference on Organometallic Chemistry in Lisbon (September 2012)
  • Andrew Rickard (NCAS) moves from Leeds to York
  • Karadakov has given a talk at the 21st IUPAC International Conference on Physical Organic Chemistry in Durham (September 2012)