324 research outputs found
Defect chemistry of Ti and Fe impurities and aggregates in Al2O3
We report a theoretical evaluation of the properties of iron and titanium impurities in sapphire (corundum structured α-Al2O3). Calculations using analytical force fields have been performed on the defect structure with the metals present in isolated, co-doped and tri-cluster configurations. Crystal field parameters have been calculated with good agreement to available experimental data. When titanium and iron are present in neighbouring face and edge-sharing orientations, the overlap of the d-orbitals facilitates an intervalence charge transfer (FeIII/TiIII → FeII/TiIV) with an associated optical excitation energy of 1.85 eV and 1.76 eV in the respective configurations. Electronic structure calculations based on density functional theory confirm that FeIII/TiIII is the ground-state configuration for the nearest-neighbour pairs, in contrast to the often considered FeII/TiIV pair. Homonuclear intervalence charge transfer energies between both FeIII/FeII and TiIV/TiIII species have also been calculated, with the energy lying in the infra-red region. Investigation of multiple tri-clusters of iron and titanium identified one stable configuration, TiIII–(TiIV/FeII), with the energy of electron transfer remaining unchanged
Metadynamic sampling of the free energy landscapes of proteins coupled with a Monte Carlo algorithm
Metadynamics is a powerful computational tool to obtain the free energy
landscape of complex systems. The Monte Carlo algorithm has proven useful to
calculate thermodynamic quantities associated with simplified models of
proteins, and thus to gain an ever-increasing understanding on the general
principles underlying the mechanism of protein folding. We show that it is
possible to couple metadynamics and Monte Carlo algorithms to obtain the free
energy of model proteins in a way which is computationally very economical.Comment: Submitted to Gen
Thermodynamics of beta-amyloid fibril formation
Amyloid fibers are aggregates of proteins. They are built out of a peptide
called --amyloid (A) containing between 41 and 43 residues,
produced by the action of an enzyme which cleaves a much larger protein known
as the Amyloid Precursor Protein (APP). X-ray diffraction experiments have
shown that these fibrils are rich in --structures, whereas the shape of
the peptide displays an --helix structure within the APP in its
biologically active conformation. A realistic model of fibril formation is
developed based on the seventeen residues A12--28 amyloid peptide, which
has been shown to form fibrils structurally similar to those of the whole
A peptide. With the help of physical arguments and in keeping with
experimental findings, the A12--28 monomer is assumed to be in four
possible states (i.e., native helix conformation, --hairpin, globular
low--energy state and unfolded state). Making use of these monomeric states,
oligomers (dimers, tertramers and octamers) were constructed. With the help of
short, detailed Molecular Dynamics (MD) calculations of the three monomers and
of a variety of oligomers, energies for these structures were obtained. Making
use of these results within the framework of a simple yet realistic model to
describe the entropic terms associated with the variety of amyloid
conformations, a phase diagram can be calculated of the whole many--body
system, leading to a thermodynamical picture in overall agreement with the
experimental findings. In particular, the existence of micellar metastable
states seem to be a key issue to determine the thermodynamical properties of
the system
A folding inhibitor of the HIV-1 Protease
Being the HIV-1 Protease (HIV-1-PR) an essential enzyme in the viral life
cycle, its inhibition can control AIDS. The folding of single domain proteins,
like each of the monomers forming the HIV-1-PR homodimer, is controlled by
local elementary structures (LES, folding units stabilized by strongly
interacting, highly conserved, as a rule hydrophobic, amino acids). These LES
have evolved over myriad of generations to recognize and strongly attract each
other, so as to make the protein fold fast and be stable in its native
conformation. Consequently, peptides displaying a sequence identical to those
segments of the monomers associated with LES are expected to act as competitive
inhibitors and thus destabilize the native structure of the enzyme. These
inhibitors are unlikely to lead to escape mutants as they bind to the protease
monomers through highly conserved amino acids which play an essential role in
the folding process. The properties of one of the most promising inhibitors of
the folding of the HIV-1-PR monomers found among these peptides is demonstrated
with the help of spectrophotometric assays and CD spectroscopy
Designability of lattice model heteropolymers
Protein folds are highly designable, in the sense that many sequences fold to
the same conformation. In the present work we derive an expression for the
designability in a 20 letter lattice model of proteins which, relying only on
the Central Limit Theorem, has a generality which goes beyond the simple model
used in its derivation. This expression displays an exponential dependence on
the energy of the optimal sequence folding on the given conformation measured
with respect to the lowest energy of the conformational dissimilar structures,
energy difference which constitutes the only parameter controlling
designability. Accordingly, the designability of a native conformation is
intimately connected to the stability of the sequences folding to them.Comment: in press on Phys. Rev.
Measuring shared electrons in extended molecular systems: Covalent bonds from plane-wave representation of wave function
In the study of materials and macromolecules by first-principle methods, the bond order is a useful tool to represent molecules, bulk materials and interfaces in terms of simple chemical concepts. Despite the availability of several methods to compute the bond order, most applications have been limited to small systems because a high spatial resolution of the wave function and an all-electron representation of the electron density are typically required. Both limitations are critical for large-scale atomistic calculations, even within approximate density-functional theory (DFT) approaches. In this work, we describe our methodology to quickly compute delocalization indices for all atomic pairs, while keeping the same representation of the wave function used in most compute-intensive DFT calculations on high-performance computing equipment. We describe our implementation into a post-processing tool, designed to work with Quantum ESPRESSO, a popular open-source DFT package. In this way, we recover a description in terms of covalent bonds from a representation of wave function containing no explicit information about atomic types and positions
ORGANOMETALLIC CHEMISTRY FROM THE INTERACTING QUANTUM ATOM APPROACH
The Interacting Quantum Atoms approach(IQA) is a recent development of Bader\u2019s QTAM(Quantum Theory of Atoms in Molecules). During the PhD studies the use of pseudopotential inside IQA was implemented allowing the study of transition metal compounds with this techniques. Furthermore IQA concepts were joined with Pon\ue8c\u2019s DAFH (Domain Avaraged Fermi Hole) giving the so-called IQA-EDF-DAFH analysis (EDF= electron-number distribution function) which provide a complete description of the chemical bond in terms of electron density. In order to make benchmark of this new technique classic metal-organic molecules like metal carbonyls, metal hydrides and simple metal dimeric compounds were studied
Evolution of frustrated and stabilising contacts in reconstructed ancient proteins
Energetic properties of a protein are a major determinant of its evolutionary fitness. Using a reconstruction algorithm, dating the reconstructed proteins and calculating the interaction network between their amino acids through a coevolutionary approach, we studied how the interactions that stabilise 890 proteins, belonging to five families, evolved for billions of years. In particular, we focused our attention on the network of most strongly attractive contacts and on that of poorly optimised, frustrated contacts. Our results support the idea that the cluster of most attractive interactions extends its size along evolutionary time, but from the data, we cannot conclude that protein stability or that the degree of frustration tends always to decrease
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