Electronic circular dichroism of fluorescent proteins: a computational study.

The electronic circular dichroism (ECD) properties of the green fluorescent protein and other fluorescent proteins have been calculated with density functional theory. The influence of different embedding models on the ECD signal of the chromophore has been investigated by modeling the protein environment by the polarizable continuum model (QM/PCM), by the polarizable embedding model (PE-QM/MM), by treating the minimal environment quantum mechanically at the same footing as the chromophore (QM/QM), and by adding the remaining part of the protein by means of PCM (QM/QM/PCM). The rotatory strength is found to be more sensitive than the oscillatory strength to changes in the geometry of the chromophore and its surroundings and to the type of embedding model used. In general, explicit embedding of the surrounding protein (PE-QM/MM or QM/QM) induces an increase in the rotatory strength of the chromophore. Explicit inclusion of the whole protein through polarizable embedding is found to be an affordable embedding model that gives the correct sign of the rotatory strength for all fluorescent proteins. PCM is useful as a first approximation to protein environment effects, but as a rule seems to underestimate the rotatory strength.

Circular dichroism and optical rotation of lactamide and 2-aminopropanol in aqueous solution.

The performance of implicit and explicit solvent models (polarizable continuum model (PCM) and microsolvation with positions of water molecules obtained either from molecular dynamics (MD) simulations or quantum mechanical geometry optimization) for calculations of electronic circular dichroism (CD) and optical rotation (OR) is examined for two polar and flexible molecules: lactamide and 2-aminopropanol. The vibrational structure of the CD spectrum is modeled for lactamide. The results are compared with the newly obtained experimental data. The signs of the bands are correctly reproduced using all three methods under investigation and the CAM-B3LYP functional for the CD spectrum of lactamide, but not for 2-aminopropanol. The sign of the calculated optical rotation is correctly predicted by means of PCM, but its magnitude is somewhat underestimated in comparison with experiment for lactamide and overestimated for 2-aminopropanol. To some extent it is rectified by employing explicit hydration. Overall, microsolvation with geometry optimization seems more cost-effective than classical MD, but this is likely to be a consequence of inadequate classical potential and electronic structure model.

Theoretical prediction of the spin-spin coupling constants between an axis and macrocycle of a rotaxane.

The indirect nuclear spin-spin coupling constants between nuclei belonging to the axis and to the macrocycle of three structurally related rotaxanes have been calculated by means of density functional theory. It has been shown that the through-space axis-macrocycle proton-proton coupling constants can be as large as 0.4-0.5 Hz and therefore of measurable values. The largest through-space axis-macrocycle carbon-proton and nitrogen-proton coupling constants are 0.2-0.3 Hz. Visualization of coupling pathways by means of the coupling energy density method indicates that the larger proton-proton couplings are indeed transmitted through the space between the coupled nuclei. Thus, it seems that measurement of such couplings should be possible and that indirect spin-spin couplings can be actually transmitted through-space, with no covalent or hydrogen bonds between the coupled nuclei.