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Henriques JCG, Ventura GB, Fernandes CDM, Peres NMR. Optical absorption of single-layer hexagonal boron nitride in the ultraviolet. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:025304. [PMID: 31553957 DOI: 10.1088/1361-648x/ab47b3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this paper we theoretically describe the absorption of hexagonal boron nitride (hBN) single layer. We develop the necessary formalism and present an efficient method for solving the Wannier equation for excitons. We give predictions for the absorption of hBN on quartz and on graphite. We compare our predictions with recently published results (Elias et al 2019 Nat. Commun. 10 2639) for a monolayer of hBN on graphite. The spontaneous radiative lifetime of excitons in hBN is also computed. We argue that the optical properties of hBN in the ultraviolet are very useful for the study of peptides and other biomolecules.
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Affiliation(s)
- J C G Henriques
- Department and Centre of Physics, and QuantaLab, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
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2
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Jiang S, Liu L, Xu J, Zeng M, Zhao Y. Amino acid composition and digestibility of Pacific oyster (Crassostrea gigas) proteins isolated from different parts. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.108591] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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3
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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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Li Z, Robinson D, Hirst JD. Vibronic structure in the far-UV electronic circular dichroism spectra of proteins. Faraday Discuss 2015; 177:329-44. [DOI: 10.1039/c4fd00163j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Franck–Condon effect is considered and the vibrational structure of the πnbπ* transition of the peptide backbone is incorporated into matrix method calculations of the electronic circular dichroism (CD) spectra of proteins in the far-ultraviolet. We employ the state-averaged CASPT2 method to calculate the ground and πnbπ* excited state geometries and frequencies of N-methylacetamide (NMA), which represents the peptide chromophore. The results of these calculations are used to incorporate vibronic levels of the excited states into the matrix method calculation. The CD spectra of a set of 49 proteins, comprising a range of structural types, are calculated to assess the influence of the vibrational structure. The calculated spectra of α-helical proteins are better resolved using the vibronic parameters and correlation between the experimental and the calculated intensity of less regular β structure proteins improves over most wavelengths in the far-UV. No obvious improvement is observed in the calculated spectra of regular β-sheet proteins. Our high-level ab initio calculations of the vibronic structure of the πnbπ* transition in NMA have provided some further insight into the physical origins of the nature of protein CD spectra in the far-UV.
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Affiliation(s)
- Zhuo Li
- School of Chemistry
- University of Nottingham
- Nottingham NG7 2RD
- UK
| | - David Robinson
- School of Chemistry
- University of Nottingham
- Nottingham NG7 2RD
- UK
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Stern AC, Belof JL, Eddaoudi M, Space B. Understanding hydrogen sorption in a polar metal-organic framework with constricted channels. J Chem Phys 2012; 136:034705. [DOI: 10.1063/1.3668138] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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6
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Woody RW. A significant role for high-energy transitions in the ultraviolet circular dichroism spectra of polypeptides and proteins. Chirality 2010; 22 Suppl 1:E22-9. [DOI: 10.1002/chir.20857] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Kruschel D, Zagrovic B. Conformational averaging in structural biology: issues, challenges and computational solutions. MOLECULAR BIOSYSTEMS 2009; 5:1606-16. [PMID: 20023721 DOI: 10.1039/b917186j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most experimental methods in structural biology provide time- and ensemble-averaged signals and, consequently, molecular structures based on such signals often exhibit only idealized, average features. Second, most experimental signals are only indirectly related to real, molecular geometries, and solving a structure typically involves a complicated procedure, which may not always result in a unique solution. To what extent do such conformationally-averaged, non-linear experimental signals and structural models derived from them accurately represent the underlying microscopic reality? Are there some structural motifs that are actually artificially more likely to be "seen" in an experiment simply due to the averaging artifact? Finally, what are the practical consequences of ignoring the averaging effects when it comes to functional and mechanistic implications that we try to glean from experimentally-based structural models? In this review, we critically address the work that has been aimed at studying such questions. We summarize the details of experimental methods typically used in structural biology (most notably nuclear magnetic resonance, X-ray crystallography and different types of spectroscopy), discuss their individual susceptibility to conformational (motional) averaging, and review several theoretical approaches, most importantly molecular dynamics simulations that are increasingly being used to aid experimentalists in interpreting structural biology experiments.
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Affiliation(s)
- Daniela Kruschel
- Laboratory of Computational Biophysics, Mediterranean Institute for Life Sciences, Mestrovicevo setaliste bb, Split, HR-21000, Croatia
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Woody RW. Circular Dichroism Spectrum of Peptides in the Poly(Pro)II Conformation. J Am Chem Soc 2009; 131:8234-45. [DOI: 10.1021/ja901218m] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Robert W. Woody
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
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Belof JL, Stern AC, Eddaoudi M, Space B. On the Mechanism of Hydrogen Storage in a Metal−Organic Framework Material. J Am Chem Soc 2007; 129:15202-10. [DOI: 10.1021/ja0737164] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jonathan L. Belof
- Contribution from the Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250
| | - Abraham C. Stern
- Contribution from the Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250
| | - Mohamed Eddaoudi
- Contribution from the Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250
| | - Brian Space
- Contribution from the Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250
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Two Dimensional Electronic Correlation Spectroscopy of the npi* and pipi* Protein Backbone Transitions: A Simulation Study. Chem Phys 2007; 341:29-36. [PMID: 19011677 DOI: 10.1016/j.chemphys.2007.03.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The two dimensional (2D) photon echo spectrum of the amide ultraviolet (UV) bands of proteins are simulated. Two effective exciton Hamiltonian parameter sets developed by Woody and Hirst, which predict similar CD spectra, may be distinguished by their very different 2DUV spectra. These differences are enhanced in specific configurations of pulse polarizations which provide chirality-induced signals.
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11
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Abstract
Circular dichroism (CD) is an important technique in the structural characterisation of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the so-called matrix method, with an accuracy which is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. Linear dichroism (LD) can be calculated using analogous methodology and has been used to establish the relative orientations of subunits in proteins and protein orientation in an environment such as a membrane. However, simple analysis of LD data is not possible, due to overlapping transitions. So coupling the calculations and experiment is an important strategy. In this paper, the use of LD for the determination of protein orientation and how these data can be interpreted with the aid of calculations, are discussed. We review methods for the calculation of CD spectra, focusing on semiempirical and ab initio parameter sets used in the matrix method. Lastly, a new web interface for online CD and LD calculation is presented.
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Affiliation(s)
- Benjamin M Bulheller
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK NG7 2RD
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12
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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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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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14
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Carlson KL, Lowe SL, Hoffmann MR, Thomasson KA. Theoretical UV Circular Dichroism of Aliphatic Cyclic Dipeptides. J Phys Chem A 2005; 109:5463-70. [PMID: 16839074 DOI: 10.1021/jp046580u] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four cyclic dipeptides (piperazine-2,5-diones), cyclo(L-Pro-Gly), cyclo(L-Pro-L-Leu), cyclo(L-Ala-L-Ala), and cyclo(L-Pro-L-Ala), were modeled from crystal structure data. Conformations resulting from energy minimization using molecular mechanics were compared with traditional ab initio and density functional theory geometric optimizations for each dipeptide. In all computational cases, the gas phase was assumed. The pi-pi transition feature of the UV circular dichroic (CD) spectra was predicted for each peptide structure via the classical dipole interaction model. The dipole interaction model predicted CD spectra that qualitatively agreed with experiment when MP2 or DFT geometries were used. By coupling MP2 or DFT geometric optimizations with the classical physics method of the dipole interaction model, significantly better CD spectra were calculated than those using geometries obtained by molecular mechanics. Thus, one can couple quantum mechanical geometries with a classical physics model for calculation of circular dichroism.
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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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15
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Abramavicius D, Mukamel S. Coherent third-order spectroscopic probes of molecular chirality. J Chem Phys 2005; 122:134305. [PMID: 15847463 DOI: 10.1063/1.1869495] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The third-order optical response of a system of coupled localized anharmonic vibrations is studied using a Green's function solution of the nonlinear exciton equations for bosonized excitons, which are treated as interacting quasiparticles. The explicit calculation of two-exciton states is avoided and the scattering of quasiparticles provides the mechanism of optical nonlinearities. To first-order in the optical wave vector we find several rotationally invariant tensor components for isotropic ensembles which are induced by chirality. The nonlocal nonlinear susceptibility tensor is calculated for infinitely large periodic structures in momentum space, where the problem size reduces to the exciton interaction radius. Applications are made to alpha and 3(10) helical infinite peptides.
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Woody RW. Heme-heme interactions in tetramers and dimers of hemoglobin subunits: DeVoe theory calculations. Chirality 2005; 17:450-5. [PMID: 16096988 DOI: 10.1002/chir.20192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Detectable exciton couplets arising from heme-heme interactions in the hemoglobin (Hb) tetramers of HbO(2) and deoxyHb were predicted by DeVoe theory. This prediction was supported by the observation of an exciton couplet in the CD difference spectrum between the Hb tetramer and the alphabeta dimer of HbCO. In this paper, DeVoe theory is used to calculate the heme-heme interactions in the CO complex of the Hb tetramer (alpha(2)beta(2)) and dimer (alphabeta), the systems studied by Goldbeck et al. The couplet strength of the resulting theoretical CD difference spectrum agrees well with experiment, thus confirming that heme-heme interactions contribute significantly to the CD of HbCO. Given that the heme-heme distances in HbCO are 25 A and more, it is highly likely that heme-heme interactions also contribute significantly to the CD of other multi-heme proteins, e.g., cytochrome c(3), cytochrome oxidase, cytochrome bc(1), etc., where the hemes are in closer proximity.
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Affiliation(s)
- Robert W Woody
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA.
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17
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Superchi S, Giorgio E, Rosini C. Structural determinations by circular dichroism spectra analysis using coupled oscillator methods: An update of the applications of the DeVoe polarizability model. Chirality 2004; 16:422-51. [PMID: 15236342 DOI: 10.1002/chir.20056] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The exciton (coupled oscillator) model for optical activity is a very useful and powerful method which allows to analyze a circular dichroism (CD) spectrum in a nonempirical way, arriving at a safe assignment of the absolute configuration of organic and inorganic compounds. Usually in this model only the exciton coupling of two electrically allowed transitions (oscillators) is taken into account. This approach has the important advantage of an easy application but, sometimes, it may lead to wrong results. Thus, in this review article a more general treatment, which allows considering the simultaneous coupling of several oscillators, i.e., the DeVoe model, is presented and critically analyzed, discussing in detail the latest applications reported in the literature. In the authors opinion, since the DeVoe model joins generality and reliability requiring an almost negligible computational effort, it represents the method of choice for stereochemical assignments, even by nonspecialists.
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Affiliation(s)
- Stefano Superchi
- Dipartimento di Chimica, Università della Basilicata, Potenza, Italy
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DeVane R, Ridley C, Space B, Keyes T. A time correlation function theory for the fifth order Raman response function with applications to liquid CS2. J Chem Phys 2003. [DOI: 10.1063/1.1601607] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Liang W, Yokojima S, Chen G. Localized-density-matrix calculation of circular dichroism spectrum of optically active molecule. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00019-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Lowe SL, Pandey RR, Czlapinski J, Kie-Adams G, Hoffmann MR, Thomasson KA, Pierce KS. Dipole interaction model predicted pi-pi* circular dichroism of cyclo(L-Pro)3 using structures created by semi-empirical, ab initio, and molecular mechanics methods. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2003; 61:189-201. [PMID: 12605604 DOI: 10.1034/j.1399-3011.2003.00046.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cyclo(l-Pro)3 (CP3) is a synthetic peptide created to model cis and torsionally strained peptide bonds that also exhibits a strong distinctive UV circular dichroic (CD) spectrum. Circular dichroic spectra were computed for the amide pi-pi* transition using the dipole interaction model for various conformations of the peptide. Conformations of CP3 were created initially from crystal data, and followed by energy minimizations via molecular mechanics using the cvff force field; the effects of additional geometric optimizations by semi-empirical and ab initio quantum mechanics were investigated. The CD spectra for each conformation were calculated using a variety of different parameters, and each result was compared with the published experimental spectrum [Deber, C.M., Scatturin, A., Vaidya, V.M. & Blout, E.R. (1970) Small cyclic proline peptides: UV absorption and CD. In: Peptides: Chemistry and Biochemistry, Proceedings of the First American Peptide Symposium (Weinstein, B., ed.), Marcel Dekker, New York pp. 163-173]. Herein, two distinct conformations, a C3 symmetric and an asymmetric form, gave CD predictions that separately did not resemble the experimental spectrum. Energy differences were predicted at various theoretical levels, including MP2 and density functional theory. When the predicted CD spectra for each conformation were multiplied by Boltzmann weighting factors created using heats of formation determined by the AM1 optimizations, the weighted composite CD spectrum created did resemble experiment for the pi-pi* transition indicating that both conformations may exist simultaneously in solution.
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Affiliation(s)
- S L Lowe
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202-9024, USA
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Ji X, Ahlborn H, Space B, Moore PB. A theoretical investigation of the temperature dependence of the optical Kerr effect and Raman spectroscopy of liquid CS2. J Chem Phys 2000. [DOI: 10.1063/1.1318772] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Applequist J, Bode KA. Fully Extended Poly(β-amino acid) Chains: Translational Helices with Unusual Theoretical π−π* Absorption and Circular Dichroic Spectra. J Phys Chem A 2000. [DOI: 10.1021/jp000862m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jon Applequist
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Kimberly A. Bode
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
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Applequist J. Electronic Normal Modes and Polarization Waves in Translational Polymer Helices. Application to Fully Extended Poly[(R)-β-aminobutyric acid] Chains. J Phys Chem A 2000. [DOI: 10.1021/jp000863e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jon Applequist
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
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Ji X, Ahlborn H, Space B, Moore PB, Zhou Y, Constantine S, Ziegler LD. A combined instantaneous normal mode and time correlation function description of the optical Kerr effect and Raman spectroscopy of liquid CS2. J Chem Phys 2000. [DOI: 10.1063/1.481539] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Applequist J, Bode KA. Solvent Effects on Ultraviolet Absorption and Circular Dichroic Spectra of Helical Polypeptides and Globular Proteins. Calculations Based on a Lattice-Filled Cavity Model. J Phys Chem B 1999. [DOI: 10.1021/jp984233c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jon Applequist
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Kimberly A. Bode
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
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27
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Bode KA, Applequist J. Globular Protein Ultraviolet Circular Dichroic Spectra. Calculation from Crystal Structures via the Dipole Interaction Model. J Am Chem Soc 1998. [DOI: 10.1021/ja982509o] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kimberly A. Bode
- Contribution from the Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011
| | - Jon Applequist
- Contribution from the Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011
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Applequist J, Bode KA, Appella DH, Christianson LA, Gellman SH. Theoretical and Experimental Circular Dichroic Spectra of the Novel Helical Foldamer Poly[(1R,2R)-trans-2-aminocyclopentanecarboxylic acid]. J Am Chem Soc 1998. [DOI: 10.1021/ja9742186] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jon Applequist
- Department of Biochemistry and Biophysics Iowa State University, Ames, Iowa 50011 Department of Chemistry, University of Wisconsin Madison, Wisconsin 53706
| | - Kimberly A. Bode
- Department of Biochemistry and Biophysics Iowa State University, Ames, Iowa 50011 Department of Chemistry, University of Wisconsin Madison, Wisconsin 53706
| | - Daniel H. Appella
- Department of Biochemistry and Biophysics Iowa State University, Ames, Iowa 50011 Department of Chemistry, University of Wisconsin Madison, Wisconsin 53706
| | - Laurie A. Christianson
- Department of Biochemistry and Biophysics Iowa State University, Ames, Iowa 50011 Department of Chemistry, University of Wisconsin Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Biochemistry and Biophysics Iowa State University, Ames, Iowa 50011 Department of Chemistry, University of Wisconsin Madison, Wisconsin 53706
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Abstract
The dipole interaction model is used to investigate the effects of interactions between helices and supertwisting of helices by determining whether the predicted UV absorption and CD spectra for the three-helix bundle and coiled coil are significantly different from spectra for the single straight alpha-helix. Crystallographic data by Yan et al. for alpha-spectrin are used to construct a three-helix bundle of poly(L-alanine) modeling the protein. Backbone torsion angles represented by Fourier series are used to generate supertwisted helices and coiled coil models of poly(L-alanine) that have pitch, radius, and residue repeat similar to experimental crystallographic data on tropomyosin. Calculated CD spectra are compared with available experimental data. Theoretical spectra for the three-helix bundle and the supertwisted structures are quite similar to predictions for the straight alpha-helix of the same length with similar torsion angles, suggesting that CD is primarily dependent on the average backbone conformation and would not be a sensitive tool for distinguishing between single straight helices and closely packed or twisted alpha-helices.
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Affiliation(s)
- K A Bode
- Department of Biochemistry and Biophysics, Iowa State University, Ames 50011, USA
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Bode KA, Applequist J. Poly(β-amino acid) Helices. Theoretical π−π* Absorption and Circular Dichroic Spectra. Macromolecules 1997. [DOI: 10.1021/ma961210s] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kimberly A. Bode
- Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011
| | - Jon Applequist
- Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011
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Bode KA, Applequist J. A New Optimization of Atom Polarizabilities in Halomethanes, Aldehydes, Ketones, and Amides by Way of the Atom Dipole Interaction Model. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp962119t] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kimberly A. Bode
- Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011
| | - Jon Applequist
- Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011
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