Publications

46. Robinson, D., Alarfaji, S. & Hirst, J.D., Benzene and mono-substituted derivatives: diabatic nature of the oscillator strengths of S1 <-- S0 transitions. . J. Phys. Chem. A, 125, 5237–5245 (2021).
DOI: http://dx.doi.org/10.1021/acs.jpca.1c01685

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45. Ye, S., Zhong, K., Zhang, J., Hu, W., Hirst, J.D., Zhang, G., Mukamel, S., Jiang, J., A transferable machine learning protocol for predicting protein amide-I infrared spectra. J. Am. Chem. Soc., 142, 19071–19077 (2020).
DOI: http://dx.doi.org/10.1021/jacs.0c06530

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44. Li, Z. & Hirst, J.D., Computed optical spectra of SARS-CoV-2 proteins. Chem. Phys. Lett., 758, 137935 (2020).
DOI: http://dx.doi.org/10.1016/j.cplett.2020.137935

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43. Baiz, C.R.; Blasiak, B.; Bredenbeck, J.; Cho, M.; Choi, J.-H.; Corcelli, S.A.; Dijkstra, A.G.; Feng, C.J.; Garrett-Roe, S.; Nien-Hui Ge, N.-H.; Hanson-Heine, M.W.D.; Hirst, J.D.; Jansen, T.L.C.; Kwac, K.; Kubarych, K.J.; Londergan, C.H.; Maekawa, H.; Reppert, M.; Saito, S.; Roy, S.; Skinner, J.L.; Stock, G.; Straub, J.E.; Thielges, M.C.; Tominaga, K.; Tokmakoff, A.; Torii, H.; Wang, L.; Webb, L.J.; Zanni, M.T., Vibrational Frequency Map, Vibrational Spectroscopy, and Intermolecular Interaction. . Chem. Rev., 120, 7152–7218 (2020).
DOI: http://dx.doi.org/10.1021/acs.chemrev.9b00813

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42. Auvray, F. & Hirst, J.D., Unfolding dynamics of a photo-switchable helical peptide. J. Phys. Chem. B, 124, 5380–5392 (2020).
DOI: http://dx.doi.org/10.1021/acs.jpcb.0c04017

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41. Rogers, D.M, Jasim, S.B, Dyer, N.T, Auvray, F, Rèfrègiers, M, Hirst, J.D., Electronic circular dichroism of proteins. Chem, 5, 2751–2774 (2019).
DOI: http://dx.doi.org/10.1016/j.chempr.2019.07.008
40. Auvray, F, Dennetiere D, Giulianib A, Jamme F, Wien F, Polack F, Menneglier C, Lagarde B, Hirst JD, Rèfrègiers M., Time resolved transient circular dichroism spectroscopy based on synchrotron natural polarization. Stuct Dynamics, 6, 54307 (2019).
DOI: http://dx.doi.org/10.1063/1.5120346
39. Michaelis M, Hildebrand N, Meissner RH, Wurzler N, Li Z, Hirst JD, Micsonai A, Kardos J, Delle Piane M & Colombi Ciacchi L., Impact of the conformational variability of oligopeptides on the computational prediction of their CD spectra. J Phys Chem B, 123, 6694–6704 (2019).
DOI: http://dx.doi.org/10.1021/acs.jpcb.9b03932
38. Hildebrand, N., Michaelis, M., Wurzler, N., Li, Z., Hirst, J.D., Misconai, A., Kardoe, J., Koeppen, S., delle Piane, M., Bussi, G. & Ciacchi, L.C. , Atomistic details of protein conformational changes upon adsorption on silica. ACS Biomat. Sci. Eng., 4, 4036–4050 (2018).
DOI: http://dx.doi.org/10.1021/acsbiomaterials.8b00819
37. Jasim, S.B., Li, Z., Guest, E.E. & Hirst, J.D., DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet. J. Mol. Biol., 430, 2196–2202 (2018).
DOI: http://dx.doi.org/10.1016/j.jmb.2017.12.009
36. Shaw, D.J., Hill, R.E., Simpson, N., Husseini, F.S., Robb, K., Greetham, G.M., Towrie, M., Parker, A.W., Robinson, D., Hirst, J.D., Hoskisson, P.A. & Hunt, N.T., Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. Chem. Sci., 8, 8384–8399 (2017).
DOI: http://dx.doi.org/10.1039/c7sc03336b
35. Li, Z. & Hirst, J.D., Vibrational structure in the near-ultraviolet electronic circular dichroism spectra of proteins. Chem. Sci., 8, 4318–4333 (2017).
DOI: http://dx.doi.org/10.1039/C7SC00586E
34. Husseini, F.S., Robinson, D., Hunt, N.T., Parker, A.W. & Hirst, J.D. , Computing infrared spectra of proteins using the exciton model. J. Comput. Chem., 38, 1362–1375 (2017).
DOI: http://dx.doi.org/10.1002/jcc.24674
33. Hanson-Heine, M.W.D., Husseini, F., Hirst, J.D. & Besley, N.A., Simulation of the two-dimensional infrared spectroscopy of peptides using localized normal modes. J. Chem. Theor. Comput., 12, 1905–1918 (2016).
DOI: http://dx.doi.org/10.1021/acs.jctc.5b01198
32. Li, Z., Robinson, D. & Hirst, J.D., Vibronic structure in the far-UV electronic circular dichroism spectra of proteins. Faraday Discussion, 177, 329–344 (2015).
DOI: http://dx.doi.org/10.1039/C4FD00163J
31. Hill R.E., Hunt N.T. & Hirst J.D., Studying biomacromolecules with two-dimensional infrared spectroscopy. Adv. Prot. Chem. Str. Biol., 93, 13150 (2013).
DOI: http://dx.doi.org/10.1016/B978-0-12-416596-0.00001-4
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