Publications

30. Gaigeot, M.-P., Besley, N.A. & Hirst, J.D, Modelling the infrared and circular dichroism spectroscopy of linear and cyclic diamides. J. Phys. Chem. B, 115, 5562–5535 (2011).
DOI: http://dx.doi.org/10.1021/jp111140f
29. Robinson, D., Besley, N.A., O'Shea, P. & Hirst, J.D., Di-8-ANEPPS Emission Spectra in Phospholipid / Cholesterol Membranes: A Theoretical Study. J. Phys. Chem. B, 115, 4160–4167 (2011).
DOI: http://dx.doi.org/10.1021/jp1111372
28. Jiang, J., Abramavicius, D., Falvo, C., Bulheller, B.M., Hirst, J.D. & Mukamel, S., Simulation of two-dimensional ultraviolet spectroscopy of amyloid fibrils. J. Phys. Chem. B., 114, 12150–12156 (2010).
DOI: http://dx.doi.org/10.1021/jp1046968
27. Jiang, J., Abramavicius, D., Bulheller, B.M., Hirst, J.D. & Mukamel, S., Ultraviolet spectroscopy of protein backbone transitions in aqueous solution: QM/MM simulations. J. Phys. Chem. B, 114, 8270–8277 (2010).
DOI: http://dx.doi.org/10.1021/jp101980a
26. Abramavicius, D., Jiang, J., Bulheller, B.M., Hirst, J.D. & Mukamel, S., Simulation Study of Chiral Two-Dimensional Ultraviolet Spectroscopy of the Protein Backbone. J. Am. Chem. Soc., 132, 7769–7775 (2010).
DOI: http://dx.doi.org/10.1021/ja101968g
25. Bulheller, B.M., Rodger, A., Hicks, M.R., Dafforn, T.R., Serpell, L.C., Marshall, K.E., Bromley, E.H.C., King, P.J.S., Channon, K.J., Woolfson, D.N. & Hirst, J.D., Flow linear dichroism of some prototypical proteins. J. Am. Chem. Soc., 131, 13305–13314 (2009).
DOI: http://dx.doi.org/10.1021/ja902662e

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24. Bulheller, B.M., Pantoş G.D., Sanders, J.K.M. & Hirst, J.D., Electronic structure and circular dichroism spectroscopy of naphthalenediimide nanotubes. Phys. Chem. Chem. Phys., 11, 6060–6065 (2009).
DOI: http://dx.doi.org/10.1039/b905187b

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23. Bulheller, B.M. & Hirst, J.D., DichroCalc–circular and linear dichroism online. Bioinformatics, 25, 539–540 (2009).
DOI: http://dx.doi.org/10.1093/bioinformatics/btp016
22. Bulheller, B.M., Miles, A.J., Wallace, B.A. & Hirst, J.D., Charge-Transfer Transitions in the Vacuum-Ultraviolet of Protein Circular Dichroism Spectra. J. Phys. Chem. B, 112, 1866–1874 (2008).
DOI: http://dx.doi.org/10.1021/jp077462k
21. Bulheller, B.M., Rodger, A. & Hirst, J.D., Circular and Linear Dichroism of Proteins. Phys. Chem. Chem. Phys., 9, 2020–2035 (2007).
DOI: http://dx.doi.org/10.1039/b615870f

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20. Oakley, M.T. & Hirst, J.D., Charge-Transfer Transitions in Protein Circular Dichroism Calculations. J. Am. Chem. Soc., 128, 12414–12415 (2006).
DOI: http://dx.doi.org/10.1021/ja0644125

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19. Jansen, T.L.C., Dijkstra, A.G., Watson, T.M., Hirst, J.D. & Knoester, J., Modeling the amide I bands of small peptides. J. Chem. Phys., 125, 44312/1 – 44312/9 (2006).
DOI: http://dx.doi.org/10.1063/1.2218516
18. Oakley, M.T., Bulheller, B.M. & Hirst, J.D., First Principles Calculations of Protein Circular Dichroism in the Far-Ultraviolet and Beyond. Chirality, 18, 340–347 (2006).
DOI: http://dx.doi.org/10.1002/chir.20264
17. Watson, T.M. & Hirst, J.D., Theoretical Studies of the Amide I Vibrational Frequencies of [Leu]-enkephalin. Mol. Phys., 103, 1531–1546 (2005).
DOI: http://dx.doi.org/10.1080/00268970500052387
16. Rogers, D.M. & Hirst, J.D., First Principles Calculations of Protein Circular Dichroism in the Near-Ultraviolet. Biochemistry, 43, 11092–11102 (2004).
DOI: http://dx.doi.org/10.1021/bi049031n

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15. Watson, T.M. & Hirst, J.D., Vibrational Analysis of Capped [Leu]Enkephalin. Phys. Chem. Chem. Phys., 6, 2580–2587 (2004).
DOI: http://dx.doi.org/10.1039/b315501c
14. Rogers, D.M. & Hirst, J.D., Calculations of Protein Circular Dichroism from First Principles. Chirality, 16, 234–243 (2004).
DOI: http://dx.doi.org/10.1002/chir.20018
13. Watson, T.M. & Hirst, J.D., Calculating Vibrational Frequencies of Amides: from Formamide to Concanavalin A. Phys. Chem. Chem. Phys., 6, 998–1005 (2004).
DOI: http://dx.doi.org/10.1039/b312181j
12. Rogers, D.M. & Hirst, J.D., Ab Initio Studies of Aromatic Side-Chains in Gas Phase and Solution. J. Phys. Chem. A, 107, 11191–11200 (2003).
DOI: http://dx.doi.org/10.1021/jp036081d
11. Hirst, J.D., Colella, K. & Gilbert, A.T.B., Electronic Circular Dichroism Spectra of Proteins from First Principles Calculations. J. Phys. Chem. B, 107, 11813–11819 (2003).
DOI: http://dx.doi.org/10.1021/jp035775j
10. Bhattacharjee, S., Tóth, G., Lovas, S. & Hirst, J.D., Influence of Tyrosine on the Electronic Circular Dichroism of Helical Peptides. J. Phys. Chem. B, 107, 8682–8688 (2003).
DOI: http://dx.doi.org/10.1021/jp034517j
9. Hirst, J.D., Bhattacharjee, S. & Onufriev, A.V., Theoretical Studies of Time-Resolved Protein Folding. Faraday Discussions, 122, 253–267 (2003).
DOI: http://dx.doi.org/10.1039/b200714b
8. Andrew, C.D., Bhattacharjee, S., Kokkoni, N., Hirst, J.D., Jones, G.R. & Doig, A.J., Stabilizing Interactions between Aromatic and Basic Side Chains in α-Helical Peptides. Tyrosine Effects on Helix Circular Dichroism. J. Am. Chem. Soc., 124, 12706–12714 (2002).
DOI: http://dx.doi.org/10.1021/ja027629h

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7. Watson, T.M. & Hirst, J.D., DFT Vibrational Frequencies of Amides and Amide Dimers. J. Phys. Chem. A, 106, 7858–7867 (2002).
DOI: http://dx.doi.org/10.1021/jp025551l
6. Rodger, A., Rajendra, J., Mortimer, R., Andrews, T., Hirst, J.D., Gilbert, A.T.B., Marrington, R., Dafforn, T.R., Hasall, D.J., Ardhammar, M., Nordén, B., Woolhead, C.A., Robinson, C., Pinheiro, T., Kazlauskaite, J., Seymour, M., Perez, N. & Hannon, M.J., Flow Oriented Linear Dichroism to Probe Protein Orientation in Membrane Environments. Phys. Chem. Chem. Phys., 4, 4051–4057 (2002).
DOI: http://dx.doi.org/10.1039/b205080n
5. Dang, Z. & Hirst, J.D., Short Hydrogen Bonds, Circular Dichroism and Over- Estimates of Peptide Helicity. Angew. Chemie Intl. Ed., 40, 3619–3621 (2001).
DOI: http://dx.doi.org/10.1002/1521-3773(20011001)40:19<3619::AID-ANIE3619>3.0.CO;2-4
4. Hirst, J.D. & Besley, N.A., Response to »Comment on 'Improving Protein Circular Dichroism Calculations in the Far-Ultraviolet through Reparametrizing the Amide Chromophore'«. J. Chem. Phys. [J. Chem. Phys. 109, 782-788 (1998)], 111, 2846–2847 (1999).
DOI: http://dx.doi.org/10.1063/1.479563
3. Hirst, J.D., Improving Protein Circular Dichroism Calculations through Better Ab Initio Models of the Amide Chromophore. Enantiomer, 3, 215–220 (1998).
2. Hirst, J.D., Improving Protein Circular Dichroism Calculations in the Far-Ultraviolet through Reparametrizing the Amide Chromophore. J. Chem. Phys., 109, 782–788 (1998).
DOI: http://dx.doi.org/10.1063/1.476617
1. Hirst, J.D. & Brooks III, C.L., Helicity, Circular Dichroism and Molecular Dynamics of Proteins. J. Mol. Biol., 243, 173–178 (1994).
DOI: http://dx.doi.org/10.1006/jmbi.1994.1644