369 research outputs found
Density functional theory study of Fe(II) adsorption and oxidation on goethite surfaces
We study the interactions between Fe(II) aqua complexes and surfaces of
goethite (alpha-FeOOH) by means of density functional theory calculations
including the so-called Hubbard U correction to the exchange-correlation
functional. Using a thermodynamic approach, we find that (110) and (021)
surfaces in contact with aqueous solutions are almost equally stable, despite
the evident needlelike shape of goethite crystals indicating substantially
different reactivity of the two faces. We thus suggest that crystal anisotropy
may result from different growth rates due to virtually barrierless adsorption
of hydrated ions on the (021) but not on the (110) surface. No clear evidence
is found for spontaneous electron transfer from an adsorbed Fe(II) hex-aqua
complex to a defect-free goethite substrate. Crystal defects are thus inferred
to play an important role in assisting such electron transfer processes
observed in a recent experimental study. Finally, goethite surfaces are
observed to enhance the partial oxidation of adsorbed aqueous Fe(II) upon
reaction with molecular oxygen. We propose that this catalytic oxidation effect
arises from donation of electronic charge from the bulk oxide to the oxidizing
agent through shared hydroxyl ligands anchoring the Fe(II) complexes on the
surface
Subspace representations in ab initio methods for strongly correlated systems
We present a generalized definition of subspace occupancy matrices in ab
initio methods for strongly correlated materials, such as DFT+U and DFT+DMFT,
which is appropriate to the case of nonorthogonal projector functions. By
enforcing the tensorial consistency of all matrix operations, we are led to a
subspace projection operator for which the occupancy matrix is tensorial and
accumulates only contributions which are local to the correlated subspace at
hand. For DFT+U in particular, the resulting contributions to the potential and
ionic forces are automatically Hermitian, without resort to symmetrization, and
localized to their corresponding correlated subspace. The tensorial invariance
of the occupancies, energies and ionic forces is preserved. We illustrate the
effect of this formalism in a DFT+U study using self-consistently determined
projectors.Comment: 15 pages, 8 figures. This version (v2) matches that accepted for
Physical Review B on 15th April 201
Generalized Wannier functions: a comparison of molecular electric dipole polarizabilities
Localized Wannier functions provide an efficient and intuitive means by which
to compute dielectric properties from first principles. They are most commonly
constructed in a post-processing step, following total-energy minimization.
Nonorthogonal generalized Wannier functions (NGWFs) [Skylaris et al., Phys.
Rev. B 66, 035119 11 (2002); Skylaris et al., J. Chem. Phys. 122, 084119
(2005)] may also be optimized in situ, in the process of solving for the
ground-state density. We explore the relationship between NGWFs and
orthonormal, maximally localized Wannier functions (MLWFs) [Marzari and
Vanderbilt, Phys. Rev. B 56, 12847 (1997); Souza, Marzari, and Vanderbilt,
ibid. 65, 035109 (2001)], demonstrating that NGWFs may be used to compute
electric dipole polarizabilities efficiently, with no necessity for
post-processing optimization, and with an accuracy comparable to MLWFs.Comment: 5 pages, 1 figure. This version matches that accepted for Physical
Review B on 4th May 201
Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U
Myoglobin modulates the binding of diatomic molecules to its heme group via
hydrogen-bonding and steric interactions with neighboring residues, and is an
important benchmark for computational studies of biomolecules. We have
performed calculations on the heme binding site and a significant proportion of
the protein environment (more than 1000 atoms) using linear-scaling density
functional theory and the DFT+U method to correct for self-interaction errors
associated with localized 3d states. We confirm both the hydrogen-bonding
nature of the discrimination effect (3.6 kcal/mol) and assumptions that the
relative strain energy stored in the protein is low (less than 1 kcal/mol). Our
calculations significantly widen the scope for tackling problems in drug design
and enzymology, especially in cases where electron localization, allostery or
long-ranged polarization influence ligand binding and reaction.Comment: 15 pages, 3 figures. Supplementary material 8 pages, 3 figures. This
version matches that accepted for J. Phys. Chem. Lett. on 10th May 201
Renormalization of myoglobin-ligand binding energetics by quantum many-body effects
We carry out a first-principles atomistic study of the electronic mechanisms
of ligand binding and discrimination in the myoglobin protein. Electronic
correlation effects are taken into account using one of the most advanced
methods currently available, namely a linear-scaling density functional theory
(DFT) approach wherein the treatment of localized iron 3d electrons is further
refined using dynamical mean-field theory (DMFT). This combination of methods
explicitly accounts for dynamical and multi-reference quantum physics, such as
valence and spin fluctuations, of the 3d electrons, whilst treating a
significant proportion of the protein (more than 1000 atoms) with density
functional theory. The computed electronic structure of the myoglobin complexes
and the nature of the Fe-O2 bonding are validated against experimental
spectroscopic observables. We elucidate and solve a long standing problem
related to the quantum-mechanical description of the respiration process,
namely that DFT calculations predict a strong imbalance between O2 and CO
binding, favoring the latter to an unphysically large extent. We show that the
explicit inclusion of many body-effects induced by the Hund's coupling
mechanism results in the correct prediction of similar binding energies for
oxy- and carbonmonoxymyoglobin.Comment: 7 pages, 5 figures. Accepted for publication in the Proceedings of
the National Academy of Sciences of the United States of America (2014). For
the published article see
http://www.pnas.org/content/early/2014/04/09/1322966111.abstrac
Projector self-consistent DFT+U using non-orthogonal generalized Wannier functions
We present a formulation of the density-functional theory + Hubbard model
(DFT+U) method that is self-consistent over the choice of Hubbard projectors
used to define the correlated subspaces. In order to overcome the arbitrariness
in this choice, we propose the use of non-orthogonal generalized Wannier
functions (NGWFs) as projectors for the DFT+U correction. We iteratively refine
these NGWF projectors and, hence, the DFT+U functional, such that the
correlated subspaces are fully self-consistent with the DFT+U ground-state. We
discuss the convergence characteristics of this algorithm and compare
ground-state properties thus computed with those calculated using hydrogenic
projectors. Our approach is implemented within, but not restricted to, a
linear-scaling DFT framework, opening the path to DFT+U calculations on systems
of unprecedented size.Comment: 4 pages, 3 figures. This version (v2) matches that accepted for
Physical Review B Rapid Communications on 26th July 201
Tracing potential energy surfaces of electronic excitations via their transition origins: application to Oxirane
We show that the transition origins of electronic excitations identified by
quantified natural transition orbital (QNTO) analysis can be employed to
connect potential energy surfaces (PESs) according to their character across a
widerange of molecular geometries. This is achieved by locating the switching
of transition origins of adiabatic potential surfaces as the geometry changes.
The transition vectors for analysing transition origins are provided by linear
response time-dependent density functional theory (TDDFT) calculations under
the Tamm-Dancoff approximation. We study the photochemical CO ring opening of
oxirane as an example and show that the results corroborate the traditional
Gomer-Noyes mechanism derived experimentally. The knowledge of specific states
for the reaction also agrees well with that given by previous theoretical work
using TDDFT surface-hopping dynamics that was validated by high-quality quantum
Monte Carlo calculations. We also show that QNTO can be useful for considerably
larger and more complex systems: by projecting the excitations to those of a
reference oxirane molecule, the approach is able to identify and analyse
specific excitations of a trans-2,3-diphenyloxirane molecule.Comment: 14 pages, 12 figure
Accurate ionic forces and geometry optimization in linear-scaling density-functional theory with local orbitals
Linear scaling methods for density-functional theory (DFT) simulations are formulated in terms of localized orbitals in real space, rather than the delocalized eigenstates of conventional approaches. In local-orbital methods, relative to conventional DFT, desirable properties can be lost to some extent, such as the translational invariance of the total energy of a system with respect to small displacements and the smoothness of the potential-energy surface. This has repercussions for calculating accurate ionic forces and geometries. In this work we present results from onetep, our linear scaling method based on localized orbitals in real space. The use of psinc functions for the underlying basis set and on-the-fly optimization of the localized orbitals results in smooth potential-energy surfaces that are consistent with ionic forces calculated using the Hellmann-Feynman theorem. This enables accurate geometry optimization to be performed. Results for surface reconstructions in silicon are presented, along with three example systems demonstrating the performance of a quasi-Newton geometry optimization algorithm: an organic zwitterion, a point defect in an ionic crystal, and a semiconductor nanostructure.<br/
How to Collect your Water Sample and Interpret the Results for the Poultry Analytical Package
Rapidly growing birds may consume up to twice as much water as feed (Scantling and Watkins 2013), which means a plentiful supply of clean water is crucial for poultry health and productivity. To determine the quality of your poultry’s water resources, periodic sampling and analysis is needed. Analyzing water supplies can also be a crucial tool in identifying existing or potential challenges. The Arkansas Water Resources Center (AWRC) in cooperation with the UA Cooperative Extension Service offers several analytical packages to assess the quality of your water resources. This document is intended to provide guidance to poultry producers on collecting water samples for analysis and understanding the “Poultry Water Report Form” provided by the AWRC’s Water Quality Laboratory (Lab). The information contained within this fact sheet should be used as general guidance, and the reader is encouraged to seek advice from Extension specialists regarding the interpretation of individual reports and water testing results that may be of concern
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