Ab initio circular dichroism and conformational flexibility of amino acids

We present the application of our recently developed ab-initio code for circular dichroism (CD) calculations [1] to some amino acids, with a particular focus on the conformational dependence of CD spectra. The ability to reproduce the CD spectrum of amino acids can be regarded as a preliminary step towards the more complex case of peptides. Our code computes the CD spectrum starting from (complex) momentum matrix elements obtained via existing density functional theory (DFT) codes (in particular Abinit [2]). Amino acids, although smaller than peptides or proteins, display a certain degree of conformational flexibility, which cannot be neglected when calculating their electronic spectra. An understanding of the influence this flexibility exerts on spectra, and of the best way to treat it from a computational point of view, is therefore needed. Moreover one should take into account the effect of the solvent, and the two possible forms amino acids can assume, namely the neutral and the zwitterionic one (displaying NH+ 3 and COO−). In this work we investigated the effect on CD spectra both of amino acid sidechain conformation, resulting in the presence of several different rotamers, and of the orientation of the amino and carboxyl groups, described by ' and à dihedrals. We found interesting results on the sensitivity of our calculated gas phase spectra to structural details, and on the relative importance of different degrees of freedom, e.g. of sidechain vs. backbone conformation. In the presence of water, the zwitterionic form (unstable in vacuo) is favored, and the local arrangement of water molecules surrounding the amino acid seems to have a large influence on CD features. References: [1] E. Molteni, G. Onida, G. Tiana, in preparation. [2] X. Gonze et al., ABINIT: First-principles approach of materials and nanosystem properties, Computer Phys. Commun. 180, 2582 (2009).