Raman optical activity: An incisive probe of chirality, and of biomolecular structure and behaviour

Barron, Laurence D.; Zhu, Fujiang; Hecht, Lutz

doi:10.1016/j.vibspec.2006.04.020

Cited by 41 publications

(34 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…with / 5 2908 and 1908) that provide the same Raman signal. 30 As a reference spectrum we have chosen that / 5 908. Obviously, an experimental ROA spectrum of this conformer cannot be obtained because of the fast enantiomer (2908 $ 1908) exchange.…”

Section: One-dimensional Modelmentioning

confidence: 99%

Molecular dynamics with restrictions derived from optical spectra

2008

View full text Add to dashboard Cite

The information about molecular structure coded in the optical spectra must often be deciphered by complicated computational procedures. A combination of spectral modeling with the molecular dynamic simulations makes the process simpler, by implicit accounting for the inhomogeneous band broadening and Boltzmann averaging of many conformations. Ideally, geometries of studied systems can be deduced by a direct confrontation of such modeling with the experiment. In this work, the comparison is enhanced by restrictions to molecular dynamics propagations based on the Raman and Raman optical activity spectra. The methodology is introduced and tested on model systems comprising idealized H 2 O 2 , H 2 O 3 molecules, and the alanine zwitterion. An additional gradient term based on the spectral overlap smoothed by Fourier transformation is constructed and added to the molecular energy during the molecular dynamics run. For systems with one prevalent conformation the method did allow to enrich the Boltzmann ensemble by a spectroscopically favored structure. For systems with multiconformational equilibria families preferential conformations can be selected. An alternative algorithm based on the comparison of the averaged spectra with the reference enabling iterative updates of the conformer probabilities provided even more distinct distributions in shorter times. It also accounts for multiconformer equilibria and provided realistic spectra and conformer distribution for the alanine.

show abstract

Section: One-dimensional Modelmentioning

confidence: 99%

Molecular dynamics with restrictions derived from optical spectra

2008

View full text Add to dashboard Cite

show abstract

“…[3][4][5] ROA spectrum is a difference in scattering of right and left circularly polarized light, as dependent on the Raman frequency shift. 6 Not only do enantiomeric species provide spectra of opposite signs, but also smaller differences in molecular structure can be amplified as changes of the ROA signal.…”

Section: Introductionmentioning

confidence: 99%

Interpretation of Raman and Raman Optical Activity Spectra of a Flexible Sugar Derivative, the Gluconic Acid Anion

et al. 2009

View full text Add to dashboard Cite

Raman scattering and its polarized extension, Raman optical activity (ROA), are commonly used for monitoring of molecular conformational equilibria in solutions. This is complicated for saccharides due to extensive motions of the hydroxyl groups and other molecular parts. Standard interpretation procedures involving ab initio spectral simulations for a limited set of conformers are not adequate. In this study, a more general approach is proposed for the gluconic acid anion taken as a model compound, where quantum simulations of the spectra are directly coupled with molecular dynamics (MD) techniques. Such a multiscale approach reveals how the structural information is encoded in the broadened spectral lines. The spectra were simulated for solvent-solute clusters generated by MD. Conformational averaging was enabled by a limited library of conformers for which the spectral parameters could be calculated ab initio and moved on the MD geometries by Cartesian coordinate tensor transfer techniques. The B3LYP/CPCM/6-31+G** approximation was used as a default for computation of the source force fields and polarizability derivatives. The spectra thus obtained relatively faithfully reproduced most of the experimental features. The Amber and polarizable Amoeba MD force fields produced similar results; application of the latter, however, was limited by the long time necessary to achieve a converged conformational equilibrium. Both MD simulation and spectral averaging suggest that the hydroxyl groups as well as the backbone C-C bonds rotate relatively freely, with some restrictions in the vicinity of the carboxyl group. In spite of the averaging, spectral response of characteristic vibrational normal mode families, such as CH and OH bending, can clearly be identified in the spectra. The simulations thus confirm the experimental fact that flexible saccharides exhibit significant vibrational activity that reveals precious information about molecular structure and dynamics encoded in the Raman and ROA spectral shapes.

show abstract

“…More recently the chiroptical variants of both were utilized to distinguish protein conformations and to deconvolve components of mixed structures as found in globular proteins. [2][3][4][5][6] Of the structural types, a-helices and b-sheets yield the more characteristic vibrational transitions, since they are repeating structures of some uniformity in amide conformation, resulting in excitonic bands of higher intensity and characteristic chirality. This has led to a number of useful analyses and, for peptides, to some exceptionally detailed spectral assignments, recently enhanced by use of isotopic labeling to create localized transitions.…”

Section: Introductionmentioning

confidence: 99%

“…[7][8][9][10][11][12][13][14][15][16][17][18] A key element of peptide conformational studies is use of chiroptical techniques such as circular dichroism (CD) and more recently vibrational CD (VCD) and Raman optical activity (ROA), the latter of which can have useful sensitivity to isotopic variants. [4][5][6]14,[19][20][21] Here chirality is not used to determine absolute configuration, which is, of course, known from the synthetic method used (e.g. employing L-amino acids), but is useful to determine oligomer conformation which can be uniform (as in helices or sheets) or highly variable, lacking repeating character, particularly in /, w torsions.…”

Section: Introductionmentioning

confidence: 99%

Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide

et al. 2008

View full text Add to dashboard Cite

A model cyclohexapeptide, cyclo-(Phe-(D)Pro-Gly-Arg-Gly-Asp) was synthesized and its IR and VCD spectra were used as a test of density functional theory (DFT) level predictions of spectral intensities for a peptide with a nonrepeating but partially constricted conformation. Peptide structure and flexibility was estimated by molecular dynamics (MD) simulations and the spectra were simulated using full quantum mechanical (QM) approaches for the complete peptide and for simplified models with truncated side chains. After simulated annealing, the backbone conformation of the ring structure is relatively stable, consisting of a normal beta-turn and a tight loop (no H-bond) which does not vary over short trajectories. Only in quite long MD runs at high temperatures do other conformations appear. MD simulations were carried out for the cyclic peptide in water and in TFE, which match experimental solvents, as well as with and without protonation of the Asp carboxyl group. DFT spectral simulations were made using the annealed structure and were extended to include basis set variation, to determine an optimal computational approach, and solvent simulation with a polarized continuum model (PCM). Stepwise full DFT simulation of spectra was done for various sequences with the same backbone geometry but based on (1) solely Gly residues, (2) Ala substitution except Gly and Pro, and (3) complete sequences with side chains. Additionally, a selection of structures was used to compute IR and VCD spectra with the optimal method to determine structural variation effects. The side chains, especially the Asp-COOH and Arg-NH(2) transitions, had an impact on the computed amide frequencies, IR intensities and VCD pattern. Since experimentally these groups would have little chirality, due to conformational variation, they do not impact the observed VCD spectra. Correcting for frequency shifts, the Ala model for the cyclopeptide gives the clearest representation of the amide VCD. The experimental sign pattern for the amide I' band in D(2)O and also the sharper, more intense amide I VCD band in TFE was seen to some degree in one conformer with Type II' turns, but the data favor a mix of structures.

show abstract

Raman optical activity: An incisive probe of chirality, and of biomolecular structure and behaviour

Cited by 41 publications

References 38 publications

Molecular dynamics with restrictions derived from optical spectra

Molecular dynamics with restrictions derived from optical spectra

Interpretation of Raman and Raman Optical Activity Spectra of a Flexible Sugar Derivative, the Gluconic Acid Anion

Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide

Contact Info

Product

Resources

About