29,100 research outputs found
Efficient model chemistries for peptides. I. Split-valence Gaussian basis sets and the heterolevel approximation in RHF and MP2
We present an exhaustive study of more than 250 ab initio potential energy
surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries
(MCs) used are constructed as homo- and heterolevels involving possibly
different RHF and MP2 calculations for the geometry and the energy. The basis
sets used belong to a sample of 39 selected representants from Pople's
split-valence families, ranging from the small 3-21G to the large
6-311++G(2df,2pd). The reference PES to which the rest are compared is the
MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the more
accurate PES of a dipeptide in the literature. The aim of the study presented
is twofold: On the one hand, the evaluation of the influence of polarization
and diffuse functions in the basis set, distinguishing between those placed at
1st-row atoms and those placed at hydrogens, as well as the effect of different
contraction and valence splitting schemes. On the other hand, the investigation
of the heterolevel assumption, which is defined here to be that which states
that heterolevel MCs are more efficient than homolevel MCs. The heterolevel
approximation is very commonly used in the literature, but it is seldom
checked. As far as we know, the only tests for peptides or related systems,
have been performed using a small number of conformers, and this is the first
time that this potentially very economical approximation is tested in full
PESs. In order to achieve these goals, all data sets have been compared and
analyzed in a way which captures the nearness concept in the space of MCs.Comment: 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Che
Effects of constraints in general branched molecules: A quantitative ab initio study in HCO-L-Ala-NH2
A general approach to the design of accurate classical potentials for protein
folding is described. It includes the introduction of a meaningful statistical
measure of the differences between approximations of the same potential energy,
the definition of a set of Systematic and Approximately Separable and Modular
Internal Coordinates (SASMIC), much convenient for the simulation of general
branched molecules, and the imposition of constraints on the most rapidly
oscillating degrees of freedom. All these tools are used to study the effects
of constraints in the Conformational Equilibrium Distribution (CED) of the
model dipeptide HCO-L-Ala-NH2. We use ab initio Quantum Mechanics calculations
including electron correlation at the MP2 level to describe the system, and we
measure the conformational dependence of the correcting terms to the naive CED
based in the Potential Energy Surface (PES) without any simplifying assumption.
These terms are related to mass-metric tensors determinants and also occur in
the Fixman's compensating potential. We show that some of the corrections are
non-negligible if one is interested in the whole Ramachandran space. On the
other hand, if only the energetically lower region, containing the principal
secondary structure elements, is assumed to be relevant, then, all correcting
terms may be neglected up to peptides of considerable length. This is the first
time, as far as we know, that the analysis of the conformational dependence of
these correcting terms is performed in a relevant biomolecule with a realistic
potential energy function.Comment: 8 pages, 1 figure, LaTeX, aipproc style (included
Geometrical and spectral study of beta-skeleton graphs
We perform an extensive numerical analysis of beta-skeleton graphs, a particular type of proximity graphs. In beta-skeleton graph (BSG) two vertices are connected if a proximity rule, that depends of the parameter beta is an element of (0, infinity), is satisfied. Moreover, for beta > 1 there exist two different proximity rules, leading to lune-based and circle-based BSGs. First, by computing the average degree of large ensembles of BSGs we detect differences, which increase with the increase of beta, between lune-based and circle-based BSGs. Then, within a random matrix theory (RMT) approach, we explore spectral and eigenvector properties of random BSGs by the use of the nearest-neighbor energy-level spacing distribution and the entropic eigenvector localization length, respectively. The RMT analysis allows us to conclude that a localization transition occurs at beta = 1
Hyperon ordering in neutron star matter
We explore the possible formation of ordered phases in neutron star matter.
In the framework of a quantum hadrodynamics model where neutrons, protons and
Lambda hyperons interact via the exchange of mesons, we compare the energy of
the usually assumed uniform, liquid phase, to that of a configuration in which
di-lambda pairs immersed in an uniform nucleon fluid are localized on the nodes
of a regular lattice. The confining potential is calculated self-consistently
as resulting from the combined action of the nucleon fluid and the other
hyperons, under the condition of beta equilibrium. We are able to obtain stable
ordered phases for some reasonable sets of values of the model parameters. This
could have important consequences on the structure and cooling of neutron
stars.Comment: 6 pages, 2 figures. To appear in the proceedings of the 4th Catania
Relativistic Ion Studies: Exotic Clustering (CRIS 2002), Catania, Italy,
10-14 Jun 200
- …