Theoretical UV Circular Dichroism of Cyclo(l-Proline-l-Proline)

Abstract

MP2, DFT, and molecular mechanics (AMBER, CVFF, and CFF91) geometry optimizations were performed on the cyclic dipeptide cyclo(L-Pro-L-Pro) starting from crystal structure data. Three stable conformations were identified as energy minima by all methods, but assignment of relative energy varied between the methods. The pi-pi transition feature of the UV circular dichroic (CD) spectrum was predicted for each minimized structure using the classical physics method of the dipole interaction model. The model was sensitive to the different conformations. The UV-CD predictions were compared individually and as a Boltzmann-weighted composite with published experimental CD spectra [Bowman, R. L.; Kellerman, M.; Johnson, W. C., Jr. Biopolymers 1983, 22, 1045]. For all structures, the original parameters of Applequist [Applequist, J. J. Chem. Phys. 1979, 71, 4324] with a bandwidth of 3000 cm(-1) most accurately replicated experiment, except for the CFF91 structures, which matched experiment best with a bandwidth of 4000 cm(-1). The inclusion of solvent by a continuum model did not significantly alter the minimized geometries obtained by molecular or quantum mechanics, but it did have an effect on the relative predicted energies of CFF91 and B3LYP conformations. The overall effect of solvent inclusion was negligible when Boltzmann-weighted spectra were considered. Gas-phase CFF91 structures were also reasonably good for prediction of CD spectra, and when water was included via a continuum model for energy calculations, the weighting scheme resembled that of the higher-level weightings. The CD calculated using the MP2/6-311G structures and energies for weighting were most descriptive of the 180 nm negative band in the experimental CD, but red-shifted the location of the 205 nm band. DFT structures were comparably, though not identically, as descriptive of the first pi-pi band, and did a better job with placement of the second (positive) pi-pi band. DFT calculations were less sensitive to basis set effect than the MP2 calculations, with 6-31G results in close agreement with 6-311G. The results suggest that it is possible to use geometries obtained from a variety of different methods (molecular mechanical or quantum mechanical) with the classical physics dipole interaction model to qualitatively reproduce the UV CD of model amides.

Asymmetric Catalysis in Confined Space Provided by l-Proline Functionalized Mesoporous Silica with Plugs in the Pore

“…As result, the CD spectra of the L-proline silane in water/ethanol solution (Fig. 1) shows a consistent pattern with LPro-L-Pro having peptide bond [29]. It can be concluded that proline precursor was successfully synthesized and retain the chirality.…”

The close-packed triple helix as a possible new structural motif for collagen

“…In short, both quantum mechanical exciton based calculation, and classical dipole based calculation fails to adequately describe the experimental data. For a related discussion with comparative results for different theoretical approaches, see Carlson et al [41]. Perhaps, the most straightforward explanation for this is that the current structural understanding of the collagen molecule is inadequate.…”

Circular and linear dichroism of proteins

“…For the calculation of the optical spectra of large molecules, such as proteins and crystals, several methods have been developed specifically to cope with the size of the systems. The dipole interaction model [24][25][26][27][28][29][30][31] considers atoms and chromophores to act as point dipole oscillators, which interact through mutually induced dipole moments in the presence of an electric field. Another approach is the matrix method, 32 which we discuss in detail below.…”