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

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

NRC publication: Ye

Theoretical analysis of electronic absorption spectra of vitamin B\u2081\u2082 models

Time-dependent density-functional theory (TD-DFT) is applied to analyze the electronic absorption spectra of vitamin B\u2081\u2082. To accomplish this two model systems were considered: CN-[CoIII-corrin]-CN (dicyanocobinamide, DCC) and imidazole-[CoIII-corrin]-CN (cyanocobalamin, ImCC). For both models 30 lowest excited states were calculated together with transition dipole moments. When the results of TD-DFT calculations were directly compared with experiment it was found that the theoretical values systematically overestimate experimental data by approximately 0.5 eV. The uniform adjustment of the calculated transition energies allowed detailed analysis of electronic absorption spectra of vitamin B\u2081\u2082 models. All absorption bands in spectral range 2.0\ufffd5.0 eV were readily assigned. In particular, TD-DFT calculations were able to explain the origin of the shift of the lowest absorption band caused by replacement of the\ufffdCN axial ligand by imidazole.Peer reviewed: YesNRC publication: Ye

DFT analysis of Co-alkyl and Co-adenosyl vibrational modes in B12-cofactors

Density functional theory (DFT)-based normal mode calculations have been carried out on models for B12-cofactors to assign reported isotope-edited resonance Raman spectra, which isolate vibrations of the organo-Co group. Interpretation is straightforward for alkyl-Co derivatives, which display prominent Co-C stretching vibrational bands. DFT correctly reproduces Co-C distances and frequencies for the methyl and ethyl derivatives. However, spectra are complex for adenosyl derivatives, due to mixing of Co-C stretching with a ribose deformation coordinate and to activation of modes involving Co-C-C bending and Co-adenosyl torsion. Despite this complexity, the computed spectra provide a satisfactory re-assignment of the experimental data. Reported trends in adenosyl-cobalamin spectra upon binding to the methylmalonyl CoA mutase enzyme, as well as on subsequent binding of substrates and inhibitors, provide support for an activation mechanism involving substrate-induced deformation of the adenosyl ligand.NRC publication: Ye

Time-dependent density functional theory study of cobalt corrinoids: Electronically excited states of coenzyme B-12

The analysis of the electronic spectra of adenosylcobalamin (AdoCbl) and its derivative in which the trans axial base was replaced by a water molecule (AdoCbi\u2013H2O) has been performed by means of time-dependent density functional theory (TDDFT). The latter corresponds to the situation encountered in strongly acidic conditions. The TDDFT electronic transitions and oscillator strengths were calculated at the optimized B3LYP and BP86 ground state equilibrium geometries. A comparison of the orbital energy diagrams obtained with the B3LYP and BP86 functionals reveals a different orbital order and composition of the highest occupied and lowest unoccupied molecular orbitals. In B3LYP the lowest-energy transitions are of \u3c0/d\u2192\u3c0*, \u3c0/d\u2192\u3c3*, and \u3c0/d\u2192d characters while in the case of BP86 they are mainly d/\u3c0\u2192\u3c0* and d\u2192\u3c0*. The long range charge transfer transitions involving excitations from adenine \u3c0 orbitals to antibonding corrin \u3c0* orbital can be observed at low energies, especially in BP86 results. Calculated electronic excitations were used to simulate the absorption spectra for a direct comparison with the absorption spectra recorded for AdoCbl at different pH values. As previously found for methylcobalamin [ see Andruni\uf3w et al., J. Chem. Phys. 129, 085101 (2008) ] also for AdoCbl the two-parameter scaling technique is required to obtain a satisfactory agreement between theoretical and experimental spectra. Both functionals correctly predict the shifting of the lowest intense transition toward blue by approximately 13 nm upon changing pH from 7 to 1.Peer reviewed: YesNRC publication: Ye