Comparative vibrational spectroscopic studies, HOMO-LUMO, NBO analyses and thermodynamic functions of p-cresol and 2-methyl-p-cresol based on DFT calculations

DFT computations on vibrational spectra: Scaling procedures to improve the wavenumbers

The performance of ab initio and density functional theory (DFT) methods in calculating the vibrational wavenumbers in the isolated state was analyzed. To correct the calculated values, several scaling procedures were described in detail. The two linear scaling equation (TLSE) procedure leads to the lowest error and it is recommended for scaling. A comprehensive compendium of the main scale factors and scaling equations available to date for a good accurate prediction of the wavenumbers was also shown. Examples of each case were presented, with special attention to the benzene and uracil molecules and to some of their derivatives. Several DFT methods and basis sets were used. After scaling, the X3LYP/DFT method leads to the lowest error in these molecules. The B3LYP method appears closely in accuracy, and it is also recommended to be used. The accuracy of the results in the solid state was shown and several additional corrections are presented.

Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet

Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation of and insight into biophysical and simulation studies of protein dynamics and folding. We have developed new models of the aromatic side chain chromophores toluene, p-cresol and 3-methylindole, which incorporate ab initio calculations of the Franck-Condon effect into first principles calculations of CD using an exciton approach. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures.