1,721,143 research outputs found
Ab initio circular dichroism and conformational flexibility of amino acids
No full textWe 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)
The Bethe-Salpeter equation and ab-initio calculations : from the first adventure to a well established tool
No full textEFFECT OF SIZE AND GEOMETRY ON THE ELECTRONIC-PROPERTIES OF SMALL HYDROGENATED SILICON CLUSTERS
No full textWe have calculated the geometrical characteristics and electronic properties of small SinHm clusters, using the local-density approximation of density functional theory and the pseudopotential approach. Both for passivated crystal fragments and octasilacubane our results indicate nontrivial and so far unexpected effects of the cluster structure on the nature of the low-lying electronic excitations. Comparison with previous calculations as well as with experimental data, where available, is made. For the sake of comparison, calculations on (carbon) cubane are also presented
Comment on Imaging the atomic orbitals of carbon atomic chains with field-emission electron microscopy
No full textThe observation of a stable doublet pattern in the field-emission electron microscopy of a linear atomic chain requires a stable mechanism breaking the axial symmetry, which is not identified correctly by Mikhailovskij et al. [Phys. Rev. B 80, 165404 (2009)]. Using microscopic calculations, we attribute the observed pattern to the symmetry breaking produced by the ligand where the chain is attached, plus carbon π-bonding alternation
VIBRATIONAL-SPECTRUM OF C-60 - A BOND-CHARGE MODEL CALCULATION
No full textWe present a calculation of the vibrational spectrum of the C60 cluster by means of an adiabatic bond-charge model, which is directly derived from a calculation reproducing the intralayer phonons in crystalline graphite. Despite the very restricted number of adjustable parameters (four), the fourteen experimental Raman and infrared-active frequencies are reproduced within 3.0% (mean-square relative deviation). Good agreement is found also for other optically inactive modes, recently detected by neutron scattering and reflection electron energy loss spectroscopy
BULK AND SURFACE DYNAMICS OF GRAPHITE WITH THE BOND CHARGE MODEL
No full textThe bond charge model (BCM), originally designed by Weber for the dynamics of tetrahedrally coordinated semiconductors, is shown to be applicable, with minor adjustments, to sp2 configurations. Calculations for the bulk and surface dynamics of graphite, based on a comparatively small number of adjustable parameters (five or six), are shown to be in excellent agreement with recent inelastic helium atom scattering data and high-resolution electron-energy-loss spectroscopy. The parameter transferability to other forms of sp2-bonded carbons is discussed with the indication that BCM is easily applicable to large structures (e.g., giant fullerenes) presently inaccessible to ab initio methods, with a comparatively modest computational effort
Effects of local fields in time-dependent density functional theory shown in oxidized silicon clusters
No full textWe studied the influence of oxygen and oxygen-related bonds on the structural, electronic, and optical properties of a prototypical silicon dot, the adamantanelike Si10H16 nanocrystal. The optical photoabsorption spectra have been calculated keeping into account both local field effects and the effects of pseudopotential nonlocality. While the effects of the latter show up essentially as a change of a few percent of the f-sum rule integral, the former are shown to modify substantially both the optical absorption edge and the size of its redshift as induced by oxidation of the nanocrystal. Exchange-correlation contributions have also been evaluated, within the adiabatic local density approximation
Surface versus crystal-termination effects in the optical properties of surfaces
No full textWe prove, by realistic microscopic calculations within the sp(3)s(*) tight-binding method for GaAs(110) and GaAs(100), that the surface optical properties are not influenced by long-range crystal termination effects, and hence that they can be consistently studied considering slabs of limited thickness (20-30 Angstrom). The origin of derivative like and bulklike line shapes in reflection anisotropy spectra is also discussed, analyzing the effects arising from possible surface-induced reduction, broadening, and shifting of the bulk spectrum near the surface. [S0163-1829(99)01123-61]
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