Raman optical activity comes of age

Barron, Laurence D.; Hecht, Lutz; McColl, Iain H.; Blanch, Ewan W.

doi:10.1080/00268970410001704399

Cited by 200 publications

(219 citation statements)

References 72 publications

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“…3,4 The extension of the optical activity techniques into the vibrational domain opened further possibilities, as the vibrational transitions are numerous and better resolved than the electronic ones. The vibrational circular dichroism (VCD) 5 and the Raman optical activity (ROA) 6 gave unique information about structure of many organic compounds, proteins, or nucleic acids. 7,8 Other important ways to increase effective resolution of the optical spectra include site-specific labeling with stable isotopes 9 and twodimensional multiphoton spectra sampling the chromophore coupling.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics with restrictions derived from optical spectra

2008

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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.

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Section: Introductionmentioning

confidence: 99%

Molecular dynamics with restrictions derived from optical spectra

2008

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“…1,2 Moreover, vibrational optical activity techniques, such as vibrational circular dichroism (VCD) and Raman optical activity (ROA), make the structural information encoded in the spectra more apparent and add chiral and conformational sensitivity to the unpolarized techniques. [3][4][5][6] Thus, more detailed information about the structure of many peptides, proteins, and nucleic acids could be deciphered in the past. [7][8][9][10][11] However, due to the inhomogeneous broadening of vibrational bands, their overlap, and the coupling of many motions in bigger systems, it is often difficult to assign vibrational spectral features to certain transitions and structural features unambiguously.…”

Section: Introductionmentioning

confidence: 99%

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

2007

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The cis-platin binding to the d(CCTGGTCC)*d(GGACCAGG) model DNA octamer was monitored with infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopies. The spectra were modeled with the aid of density functional computations and a Cartesian coordinate-based transfer of molecular property tensors from smaller DNA fragments. Because of the fragmentation, the tensors could be calculated with a higher precision. Environmental effects, such as the presence of the solvent or the cis-platin ligand, could be included in the modeling. The solvent was modeled by an explicit inclusion of hydrogen-bound water molecules, positions of which were estimated from a molecular dynamics simulation, or by the polarized continuum COSMO model. The B3LYP and BPW91 functionals used for the calculations of the spectral parameters were combined with the relativistic LANL2DZ platinum pseudo-potentials. The simulations reproduced the main IR and VCD DNA spectral features and explained most of the changes observed experimentally upon metal binding. The results confirmed that the influence of the ligand on DNA vibrational properties is quite complex; it originates in the geometry deformation and normal mode coupling pattern changes of the platinated octamer, as well as in local perturbations of the electronic structure and force field of the GC base pairs to which the platinum is bound. Many of the local effects could be accounted for by a point charge used in place of the metal in the GC complex.

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“…Vibrational optical activity (VOA) 6,[8][9][10][11] is comprised of two principal areas, infrared vibrational circular dichroism (VCD) 12 and vibrational Raman optical activity (ROA), 13,14 based on infrared absorption spectroscopy and Raman scattering spectroscopy, respectively. Both arise from a differential response with respect to left (LCP) and right circularly polarized (RCP) radiation for a chiral molecule undergoing a vibrational transition.…”

Section: Introductionmentioning

confidence: 99%

Observation and calculation of vibrational circular birefringence: A new form of vibrational optical activity

Lombardi

Nafie

2009

Chirality

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We report the first mid-infrared observation of vibrational circular birefringence (VCB) arising from individual chiral molecules. VCB can also be called vibrational optical rotatory dispersion (VORD) and is the Kramers-Kronig transform of vibrational circular dichroism (VCD). The method of measurement involves a simple change in the optical set-up and electronic processing of a VCD spectrometer such that the VCB spectrum appears at twice the polarization modulation frequency as a pseudo vibrational linear dichroism (VLD) spectrum. VCB spectra are also calculated with density function theory (DFT) for the first time using a commercially available program for rotational strengths where the calculated intensities are convolved with the real, dispersive part of a normalized complex Lorentzian lineshape rather than the imaginary, absorptive part, normally used for IR and VCD intensity calculations. Comparison of the measured and calculated VCB, VCD, and IR spectra of (1)-R-limonene and (2)-S-apinene show close agreement and confirm the validity of the new VCB measurements. Chirality 21:E277-E286, 2009. V

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Raman optical activity comes of age

Cited by 200 publications

References 72 publications

Molecular dynamics with restrictions derived from optical spectra

Molecular dynamics with restrictions derived from optical spectra

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

Observation and calculation of vibrational circular birefringence: A new form of vibrational optical activity

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