How Does The Relocation Of Internal Water Affect Resonance Raman Spectra Of Rhodopsin? An Insight From Casscf/amber Calculations

The effect of relocation of the W2 crystallographic water in bovine rhodopsin has been investigated by comparing and analyzing simulated resonance Raman spectra of I HZX-and 1U19-based quantum mechanics/molecular mechanics (CASSCF/MM) models. The main target is to explore the sensitivity of the simulated resonance Raman spectra to protein cavity change. In particular, we focus on a quantitative investigation of the changes in the vibrational activity of rhodopsin induced by modifications in the protein cavity structure and in the water position. Comparison of the simulated FIR spectra of the Rh-1U19 and Rh-1HZX models with the measured spectrum of rhodopsin reveals that the Rh-1U19 model provides a slightly better rhodopsin model consistently with the simulations of the absorption maxima. On the other hand, and irrespective of the comparison with the experimental data, the analysis of two different computational models for the same protein and chromophore makes it possible to investigate and disentangle the relationship between structural features and change in the FIR intensities in an unusually detailed way

On the Franck-Condon Effects in the Absorption Spectrum of C10\text{}_{10}H8\text{}_{8} Anion. the Analysis Based on the AB Initio MCSCF Method

The near-IR, visible and UV regions of the absorption spectrum of naphthalene anion (C$\text{}_{10}$H$\text{}_{8}^{–}$) are studied in terms of full optimized reaction space multiconfiguration self-consistent field method applied with Dunning's double-zeta basis set including polarization and diffuse functions on the all hydrogen atoms. Computed Franck-Condon activity of the all (nine) totally symmetric vibrations in the seven low-energy transitions is discussed and compared to the available experimental data. The assignment for some electronic transitions in the visible part of the naphthalene anion absorption spectrum is corrected on the base of full optimized reaction space multiconfiguration self-consistent field computations. We have argued that two (overlapping) bands at 21700 cm$\text{}^{-1}$ and 26800 cm$\text{}^{-1}$ are due to 1$\text{}^{2}$B$\text{}_{1g}$ → 1$\text{}^{2}$A$\text{}_{u}$ and 1$\text{}^{2}$B$\text{}_{1g}$ → 2$\text{}^{2}$A$\text{}_{u}$ transitions rather than to the short-axis and long-axis polarized ones as was suggested in an earlier semiempirical treatment. An experimental method appropriate to verify this result is proposed

Theoretical determination of the Co-C bond energy dissociation in cobalamins

NRC publication: Ye