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Yoshizawa K, Hirata K, Ishiuchi SI, Fujii M, Zehnacker A. Do Stereochemical Effects Overcome a Charge-Induced Perturbation in Isolated Protonated Cyclo(Tyr-Tyr)? J Phys Chem A 2022; 126:6387-6394. [PMID: 36098637 DOI: 10.1021/acs.jpca.2c03789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two diastereomers of the protonated diketopiperazine (DKP) dipeptide cyclo(Tyr-Tyr), namely, cyclo(LTyr-LTyr)H+ and cyclo(LTyr-DTyr)H+, are studied in a cryogenic ion trap by means of IR photodissociation spectroscopy combined with quantum chemical calculations. The two diastereomers have similar structures in which one of the rings is folded over the DKP ring and the other one is extended in a trans geometry, allowing a strong OH+···π interaction to take place. This contrasts to the observation of a stacked geometry for neutral cyclo(LTyr-LTyr) only under supersonic expansion conditions that do not exist for cyclo(LTyr-DTyr). In the protonated form, the strength of the OH+···π interaction is different for the two diastereomers, resulting in a ∼110 cm-1 difference in the ν(OH+) frequency and a smaller but clearly identifiable difference in the protonated amide ν(NH) frequency. Stereochemical effects are therefore still evidenced despite the strong perturbation due to the excess charge.
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Affiliation(s)
- Koki Yoshizawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.,International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Anne Zehnacker
- International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.,Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, Orsay F-91405, France
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Pérez-Mellor A, Alata I, Lepère V, Zehnacker A. Conformational Study of the Jet-Cooled Diketopiperazine Peptide Cyclo Tyrosyl-Prolyl. J Phys Chem B 2019; 123:6023-6033. [PMID: 31268717 DOI: 10.1021/acs.jpcb.9b04529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The conformational landscape of the diketopiperazine (DKP) dipeptide built on tyrosine and proline, namely, cyclo Tyr-Pro, is studied by combining resonance-enhanced multiphoton ionization, double resonance infrared ultraviolet (IR-UV) spectroscopy, and quantum chemical calculations. Despite the geometrical constraints due the two aliphatic rings, DKP and proline, cyclo Tyr-Pro is a flexible molecule. For both diastereoisomers, cyclo LTyr-LPro and cyclo LTyr-DPro, two structural families coexist under supersonic jet conditions. In the most stable conformation, the aromatic tyrosine substituent is folded over the DKP ring (g+ geometry of the aromatic ring) as it is in the solid state. The other structure is completely extended (g- geometry of the aromatic ring) and resembles that proposed for the vapor phase. IR-UV results are not sufficient for unambiguous assignment of the observed spectra to either folded or extended conformations and the simulation of the vibronic pattern of the S0-S1 transition is necessary. Still, the comparison between IR-UV results and anharmonic calculations allows explanation of the minor structural differences between cyclo LTyr-LPro and cyclo LTyr-DPro in terms of different NH···π and CH···π interactions.
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Affiliation(s)
- Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
| | - Valeria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
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BenNasr F, Pérez-Mellor A, Alata I, Lepere V, Jaïdane NE, Zehnacker A. Stereochemistry-dependent hydrogen bonds stabilise stacked conformations in jet-cooled cyclic dipeptides: (LD) vs. (LL) cyclo tyrosine-tyrosine. Faraday Discuss 2018; 212:399-419. [PMID: 30229773 DOI: 10.1039/c8fd00079d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Tyrosine-containing cyclic dipeptides based on a diketopiperazine (DKP) ring are studied under jet-cooled conditions using resonance-enhanced multi-photon ionisation (REMPI), conformer-selective IR-UV double resonance vibrational spectroscopy and quantum chemical calculations. The conformational landscape of the dipeptide containing natural L tyrosine (Tyr), namely c-LTyr-LTyr strongly differs from that of its diastereomer c-LTyr-DTyr. A similar family of conformers exists in both systems, with one aromatic ring folded on the dipeptide DKP ring and the other one extended. Weak NHπ and CHπ interactions are observed, which are slightly different in c-LTyr-LTyr and c-LTyr-DTyr. These structures are identical to those of LL and LD cyclo diphenylalanine, which only differ from c-Tyr-Tyr by the absence of hydroxyl on the benzene rings. While this is the only conformation observed for c-LTyr-DTyr, c-LTyr-LTyr exhibits an additional form stabilised by the interaction of the two hydroxyls, in which the two aromatic rings are in a stacked geometry. Stereochemical effects are still visible in the radical cation, for which one structure is observed for c-LTyr-DTyr, while the spectrum of the c-LTyr-LTyr radical cation is explained in terms of two co-existing structures.
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Affiliation(s)
- Feriel BenNasr
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France. and Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Nejm-Eddine Jaïdane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
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Uporov IV, Forlemu NY, Nori R, Aleksandrov T, Sango BA, Mbote YEB, Pothuganti S, Thomasson KA. Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory. Int J Mol Sci 2015; 16:21237-76. [PMID: 26370961 PMCID: PMC4613251 DOI: 10.3390/ijms160921237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 06/09/2015] [Accepted: 06/30/2015] [Indexed: 01/23/2023] Open
Abstract
The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.
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Affiliation(s)
- Igor V Uporov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Faculty of Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia.
| | - Neville Y Forlemu
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, GA 30043, USA.
| | - Rahul Nori
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Tsvetan Aleksandrov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Boris A Sango
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Yvonne E Bongfen Mbote
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- James E. Hurley College of Science & Mathematics, Oklahoma Baptist University, OBU Box 61772, 500 W. University, Shawnee, OK 74804, USA.
| | - Sandeep Pothuganti
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Kathryn A Thomasson
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
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Gaigeot MP, Besley NA, Hirst JD. Modeling the infrared and circular dichroism spectroscopy of a bridged cyclic diamide. J Phys Chem B 2011; 115:5526-35. [PMID: 21344909 DOI: 10.1021/jp111140f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory based molecular dynamics simulations are used to study the structure, infrared (IR) spectroscopy, circular dichroism (CD) spectroscopy, and coupling between the amide I vibrations of a bridged cyclic diamide in the gas phase and in aqueous solution. IR spectra computed via the dipole moment time correlation function show a large red-shift of 30 cm(-1) in the amide I vibration in solution compared to the gas phase, and are in good agreement with experiment. Conformationally averaged CD spectra computed using the CIS(D) method are highly sensitive to the structures used, and structures sampled in the aqueous phase simulation are required to obtain qualitatively correct CD spectra. Analysis of the coupling between the amide I modes shows that in the aqueous phase there is an increased localization of the vibrations on the individual peptide groups and a reduction in the mode coupling parameter compared to the gas phase. Overall, the results illustrate the significance of incorporating molecular dynamics in the simulation of IR and CD spectra.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry Val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environment, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France
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Fu H, Hou RY, Zhou XM, Zhou ZY, Zhang AG, Jia ZK. Optical rotation and two chiral C atoms of aliphatic cyclic dipeptides. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2009. [DOI: 10.1134/s0036024409110168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Goerigk L, Grimme S. Calculation of Electronic Circular Dichroism Spectra with Time-Dependent Double-Hybrid Density Functional Theory. J Phys Chem A 2008; 113:767-76. [DOI: 10.1021/jp807366r] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Lars Goerigk
- Theoretische Organische Chemie, Organisch-Chemisches Institut, Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany, and NRW Graduate School of Chemistry, Corrensstrasse 36, D-48149 Münster, Germany
| | - Stefan Grimme
- Theoretische Organische Chemie, Organisch-Chemisches Institut, Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany, and NRW Graduate School of Chemistry, Corrensstrasse 36, D-48149 Münster, Germany
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Seino J, Honda Y, Hada M, Nakatsuji H. SAC and SAC−CI Calculations of Excitation and Circular Dichroism Spectra of Straight-Chain and Cyclic Dichalcogens. J Phys Chem A 2006; 110:10053-62. [PMID: 16913679 DOI: 10.1021/jp0627271] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate quantum-chemical calculations of the excitation energies and the rotatory strengths of dichalcogens R-Ch-Ch-R (Ch = S, Se, Te) were carried out with the symmetry adapted cluster (SAC) and SAC-configuration interaction (CI) methods. A series of straight-chain molecules (dihydrogen dichalcogenide, dimethyl dichalcogenide, and (+)-bis(2-methylbutyl) dichalcogenide) and one cyclic molecule (2,3-(R,R)-dichalcogenadecalin) were adopted for comparative analysis. The calculated excitation and circular dichroism (CD) spectra were in good agreement with experimental ones (Laur, P. H. A. In Proceedings of the Third International Symposium on Organic Selenium and Tellurium Compounds; Cagniant, D., Kirsch, G., Eds.; Universite de Metz: Metz, 1979; pp 219-299) within 0.3 eV. The fitting CD spectra also reasonably reproduced the experimental ones. In all the molecules adopted, the first and second lowest bands were assigned to the n-sigma(Ch-Ch) transition and the third and fourth lowest bands to the n-sigma(Ch-R) transition. The first and second lowest bands apparently depended on the R-Ch-Ch-R dihedral angle, suggesting that the orbital energies of two sigma(Ch-Ch) change with the R-Ch-Ch-R dihedral angle. This calculated trend agrees with two empirical rules: the C(2) rule and the quadrant rule.
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Affiliation(s)
- Junji Seino
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-shi, Tokyo 192-0397, Japan
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Carlson KL, Lowe SL, Hoffmann MR, Thomasson KA. Theoretical UV Circular Dichroism of Cyclo(l-Proline-l-Proline). J Phys Chem A 2006; 110:1925-33. [PMID: 16451026 DOI: 10.1021/jp052924k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MP2, DFT, and molecular mechanics (AMBER, CVFF, and CFF91) geometry optimizations were performed on the cyclic dipeptide cyclo(L-Pro-L-Pro) starting from crystal structure data. Three stable conformations were identified as energy minima by all methods, but assignment of relative energy varied between the methods. The pi-pi transition feature of the UV circular dichroic (CD) spectrum was predicted for each minimized structure using the classical physics method of the dipole interaction model. The model was sensitive to the different conformations. The UV-CD predictions were compared individually and as a Boltzmann-weighted composite with published experimental CD spectra [Bowman, R. L.; Kellerman, M.; Johnson, W. C., Jr. Biopolymers 1983, 22, 1045]. For all structures, the original parameters of Applequist [Applequist, J. J. Chem. Phys. 1979, 71, 4324] with a bandwidth of 3000 cm(-1) most accurately replicated experiment, except for the CFF91 structures, which matched experiment best with a bandwidth of 4000 cm(-1). The inclusion of solvent by a continuum model did not significantly alter the minimized geometries obtained by molecular or quantum mechanics, but it did have an effect on the relative predicted energies of CFF91 and B3LYP conformations. The overall effect of solvent inclusion was negligible when Boltzmann-weighted spectra were considered. Gas-phase CFF91 structures were also reasonably good for prediction of CD spectra, and when water was included via a continuum model for energy calculations, the weighting scheme resembled that of the higher-level weightings. The CD calculated using the MP2/6-311G structures and energies for weighting were most descriptive of the 180 nm negative band in the experimental CD, but red-shifted the location of the 205 nm band. DFT structures were comparably, though not identically, as descriptive of the first pi-pi band, and did a better job with placement of the second (positive) pi-pi band. DFT calculations were less sensitive to basis set effect than the MP2 calculations, with 6-31G results in close agreement with 6-311G. The results suggest that it is possible to use geometries obtained from a variety of different methods (molecular mechanical or quantum mechanical) with the classical physics dipole interaction model to qualitatively reproduce the UV CD of model amides.
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Affiliation(s)
- Kristine L Carlson
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202-9024, USA
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Furo T, Mori T, Origane Y, Wada T, Izumi H, Inoue Y. Absolute configuration determination of donor-acceptor [2.2]paracyclophanes by comparison of theoretical and experimental vibrational circular dichroism spectra. Chirality 2006; 18:205-11. [PMID: 16432922 DOI: 10.1002/chir.20233] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Vibrational circular dichroism (VCD) spectra were obtained for the assignments of the absolute configurations of diastereomeric 4,7-bis(methoxycarbonyl)-12,15-dimethoxy-[2.2]paracyclophanes (1 and 2), and density functional theory (DFT) calculations were performed at the B3LYP/6-31G(d) level for all possible conformations of both 1 and 2 to give the theoretical VCD spectra. Comparisons of the experimental and theoretical VCD spectra obtained unambiguously established the absolute configurations of the dextrorotatory (+)-enantiomers as (4S(p);12S(p))-1 and (4S(p);12R(p))-2, respectively.
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Affiliation(s)
- Takahiro Furo
- Department of Molecular Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan
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Oakley MT, Bulheller BM, Hirst JD. First-principles calculations of protein circular dichroism in the far-ultraviolet and beyond. Chirality 2006; 18:340-7. [PMID: 16557524 DOI: 10.1002/chir.20264] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding the relationship between the amino acid sequence of a protein and its unique, compact three-dimensional structure is one of the grand challenges in molecular biophysics. One exciting approach to the protein-folding problem is fast time-resolved spectroscopy in the ultra-violet (UV). Time-resolved electronic circular dichroism (CD) spectroscopy offers resolution on a nanosecond (or faster) timescale, but does not provide the spatial resolution of techniques like X-ray crystallography or NMR. There is a need to underpin fast timescale spectroscopic studies of protein folding with a stronger theoretical foundation. We review some recent studies in this regard and briefly highlight how modern quantum chemical models of aromatic groups have improved the accuracy of calculations of protein CD spectra near-UV. On the other side of the far-UV, we describe calculations indicating that charge-transfer transitions are likely to be responsible for bands observed in the vacuum UV in protein CD.
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Affiliation(s)
- Mark T Oakley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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