Data di Pubblicazione:
2014
Citazione:
Ab initio circular dichroism and conformational flexibility of amino acids / E. Molteni, G. Onida, G. Tiana. ((Intervento presentato al 19. convegno ETSF Workshop on Electronic Excitations, Complex systems in Biology and Nanoscience tenutosi a Zaragoza nel 2014.
Abstract:
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).
Tipologia IRIS:
14 - Intervento a convegno non pubblicato
Elenco autori:
E. Molteni, G. Onida, G. Tiana
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