257 research outputs found
First-principles molecular structure search with a genetic algorithm
The identification of low-energy conformers for a given molecule is a
fundamental problem in computational chemistry and cheminformatics. We assess
here a conformer search that employs a genetic algorithm for sampling the
low-energy segment of the conformation space of molecules. The algorithm is
designed to work with first-principles methods, facilitated by the
incorporation of local optimization and blacklisting conformers to prevent
repeated evaluations of very similar solutions. The aim of the search is not
only to find the global minimum, but to predict all conformers within an energy
window above the global minimum. The performance of the search strategy is: (i)
evaluated for a reference data set extracted from a database with amino acid
dipeptide conformers obtained by an extensive combined force field and
first-principles search and (ii) compared to the performance of a systematic
search and a random conformer generator for the example of a drug-like ligand
with 43 atoms, 8 rotatable bonds and 1 cis/trans bond
Impact of vibrational entropy on the stability of unsolvated peptide helices with increasing length
Helices are a key folding motif in protein structure. The question which
factors determine helix stability for a given polypeptide or protein is an
ongoing challenge. Here we use van der Waals corrected density-functional
theory to address a part of this question in a bottom-up approach. We show how
intrinsic helical structure is stabilized with length and temperature for a
series of experimentally well studied unsolvated alanine based polypeptides,
Ac-Alan-LysH+. By exploring extensively the conformational space of these
molecules, we find that helices emerge as the preferred structure in the length
range n=4-8 not just due to enthalpic factors (hydrogen bonds and their
cooperativity, van der Waals dispersion interactions, electrostatics), but
importantly also by a vibrational entropic stabilization over competing
conformers at room temperature. The stabilization is shown to be due to softer
low-frequency vibrational modes in helical conformers than in more compact
ones. This observation is corroborated by including anharmonic effects
explicitly through \emph{ab initio} molecular dynamics, and generalized by
testing different terminations and considering larger helical peptide models
Thermodynamic equilibrium conditions of graphene films on SiC
First-principles surface phase diagrams reveal that epitaxial monolayer
graphene films on the Si side of 3C-SiC(111) can exist as thermodynamically
stable phases in a narrow range of experimentally controllable conditions,
defining a path to the highest-quality graphene films. Our calculations are
based on a van der Waals corrected density functional. The full, experimentally
observed (6 sqrt(3)x 6 sqrt(3))-R30 supercells for zero- to trilayer graphene
are essential to describe the correct interface geometries and the relative
stability of surface phases and possible defects
Length Dependence of Ionization Potentials of Trans-Acetylenes: Internally-Consistent DFT/GW Approach
We follow the evolution of the Ionization Potential (IP) for the paradigmatic
quasi-one-dimensional trans-acetylene family of conjugated molecules, from
short to long oligomers and to the infinite polymer trans-poly-acetylene (TPA).
Our results for short oligomers are very close to experimental available data.
We find that the IP varies with oligomer length and converges to the given
value for TPA with a smooth, coupled inverse-length-exponential behavior. Our
prediction is based on an "internally-consistent" scheme to adjust the exchange
mixing parameter of the PBEh hybrid density functional, so as to
obtain a description of the electronic structure consistent with the
quasiparticle approximation for the IP. This is achieved by demanding that the
corresponding quasiparticle correction, in the GW@PBEh approximation, vanishes
for the IP when evaluated at PBEh(). We find that is
also system-dependent and converges with increasing oligomer length, allowing
to capture the dependence of IP and other electronic properties.Comment: 22 pages with 9 figures, submitted to Physical Review
Molecular Virology of Hepatitis C Virus (HCV): 2006 Update
Fascinating progress in the understanding of the molecular biology of hepatitis C virus (HCV) was achieved recently. The replicon system revolutionized the investigation of HCV RNA replication and facilitated drug discovery. Novel systems for functional analyses of the HCV glycoproteins allowed the validation of HCV receptor candidates and the investigation of cell entry mechanisms. Most recently, recombinant infectious HCV could be produced in cell culture, rendering all steps of the viral life cycle, including entry and release of viral particles, amenable to systematic analysis. In this review, we summarize recent advances and discuss future research directions
Large-scale surface reconstruction energetics of Pt(100) and Au(100) by all-electron DFT
The low-index surfaces of Au and Pt all tend to reconstruct, a fact that is
of key importance in many nanostructure, catalytic, and electrochemical
applications. Remarkably, some significant questions regarding their structural
energies remain even today, in particular for the large-scale quasihexagonal
reconstructed (100) surfaces: Rather dissimilar reconstruction energies for Au
and Pt in available experiments, and experiment and theory do not match for Pt.
We here show by all-electron density-functional theory that only large enough
"(5 x N)" approximant supercells capture the qualitative reconstruction energy
trend between Au(100) and Pt(100), in contrast to what is often done in the
theoretical literature. Their magnitudes are then in fact similar, and closer
to the measured value for Pt(100); our calculations achieve excellent agreement
with known geometric characteristics and provide direct evidence for the
electronic reconstruction driving force.Comment: updated version - also includes EPAPS information as auxiliary file;
related publications can be found at http://www.fhi-berlin.mpg.de/th/th.htm
Tunable Semiconductors: Control over Carrier States and Excitations in Layered Hybrid Organic-Inorganic Perovskites
For a class of 2D hybrid organic-inorganic perovskite semiconductors based on
-conjugated organic cations, we predict quantitatively how varying the
organic and inorganic component allows control over the nature, energy and
localization of carrier states in a quantum-well-like fashion. Our
first-principles predictions, based on large-scale hybrid density-functional
theory with spin-orbit coupling, show that the interface between the organic
and inorganic parts within a single hybrid can be modulated systematically,
enabling us to select between different type-I and type-II energy level
alignments. Energy levels, recombination properties and transport behavior of
electrons and holes thus become tunable by choosing specific organic
functionalizations and juxtaposing them with suitable inorganic components
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