pinecone/core-2020-05-10-deduplication huggingface dataset:
Modeling emission features of salicylidene aniline molecular crystals: A QM/QM' approach

A new computational protocol relying on the use of electrostatic embedding, derived from QM/QM' ONIOM calculations, to simulate the effect of the crystalline environment on the emission spectra of molecular crystals is here applied to the beta-form of salicylidene aniline (SA). The first singlet excited states (S-1) of the SA cis-keto and trans-keto conformers, surrounded by a cluster of other molecules representing the crystalline structure, were optimized by using a QM/QM' ONIOM approach with and without electronic embedding. The model system consisting of the central salicylidene aniline molecule was treated at the DFT level by using either the B3LYP, PBE0, or the CAM-B3LYP functional, whereas the real system was treated at the HF level. The CAM-B3LYP/HF level of theory provides emission energies in good agreement with experiment with differences of 220/232 nm (cis-keto form) and 28/214 nm (trans-keto form), respectively, whereas notably larger differences are obtained using global hybrids. Though such differences on the optical properties arise from the density functional choice, the contribution of the electronic embedding is rather independent of the functional used. This plays in favor of a more general applicability of the present protocol to other crystalline molecular systems
Additive CHARMM force field for naturally occurring modified ribonucleotides

International audienceMore than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. (C) 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc
Interacting quantum fragments-rooted preorganized-interacting fragments attributed relative molecular stability of the Be-II complexes of nitrilotriacetic acid and nitrilotri-3-propionic acid

A method designed to investigate, on a fundamental level, the
origin of relative stability of molecular systems using BeII complexes
with nitrilotriacetic acid (NTA) and nitrilotri-3-propionic
acid (NTPA) is described. It makes use of the primary and
molecular fragment energy terms as defined in the IQA/F
(Interacting Quantum Atoms/Fragments) framework. An extensive
classical-type investigation, focused on single descriptors
(bond length, density at critical point, the size of metal ion or
coordination ring, interaction energy between BeII and a donor
atom, etc.) showed that it is not possible to explain the experimental
trend. The proposed methodology is fundamentally different
in that it accounts for the total energy contributions
coming from all atoms of selected molecular fragments, and
monitors changes in defined energy terms (e.g., fragment
deformation, inter- and intra-fragment interaction) on complex
formation. By decomposing combined energy terms we identified
the origin of relative stability of BeII(NTA) and BeII(NTPA)
complexes. We found that the sum of coordination bonds’
strength, as measured by interaction energies between BeII ion
and donor atoms, favours BeII(NTA) but the binding energy of
BeII ion to the entire ligand correlates well with experimental
trend. Surprisingly, the origin of BeII(NTPA) being more stable is
due to less severe repulsive interactions with the backbone of
NTPA (C and H-atoms). This general purpose protocol can be
employed not only to investigate the origin of relative stability
of any molecular system (e.g., metal complexes) but, in principle,
can be used as a predictive tool for, e.g., explaining reaction
mechanism.The National Research Foundation of South Africa (Grant Numbers 87777) and the University of Pretoria.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-987X2017-06-30hb2016Chemistr
ORBKIT - A Modular Python Toolbox for Cross-Platform Post-Processing of
  Quantum Chemical Wavefunction Data

ORBKIT is a toolbox for post-processing electronic structure calculations
based on a highly modular and portable Python architecture. The program allows
computing a multitude of electronic properties of molecular systems on
arbitrary spatial grids from the basis set representation of its electronic
wavefunction, as well as several grid-independent properties. The required data
can be extracted directly from the standard output of a large number of quantum
chemical programs. ORBKIT can be used as a standalone program to determine
standard quantities, for example, the electron density, molecular orbitals, and
derivatives thereof. The cornerstone of ORBKIT is its modular structure. The
existing basic functions can be arranged in an individual way and can be easily
extended by user-written modules to determine any other desired quantities.
ORBKIT offers multiple output formats that can be processed by common
visualization tools (VMD, Molden, etc.). Additionally, ORBKIT possesses
routines to order molecular orbitals computed at different nuclear
configurations according to their electronic character and to interpolate the
wavefunction between these configurations. The program is open-source under
GNU-LGPLv3 license and freely available at
http://sourceforge.net/projects/orbkit/. This article provides an overview of
ORBKIT with particular focus on its capabilities and applicability, and
includes several example calculations
Quantum Monte Carlo with very large multideterminant wavefunctions

An algorithm to compute efficiently the first two derivatives of (very) large
multideterminant wavefunctions for quantum Monte Carlo calculations is
presented. The calculation of determinants and their derivatives is performed
using the Sherman-Morrison formula for updating the inverse Slater matrix. An
improved implementation based on the reduction of the number of column
substitutions and on a very efficient implementation of the calculation of the
scalar products involved is presented. It is emphasized that multideterminant
expansions contain in general a large number of identical spin-specific
determinants: for typical configuration interaction-type wavefunctions the
number of unique spin-specific determinants $N_{\rm det}^\sigma$
($\sigma=\uparrow,\downarrow$) with a non-negligible weight in the expansion is
of order ${\cal O}(\sqrt{N_{\rm det}})$. We show that a careful implementation
of the calculation of the $N_{\rm det}$-dependent contributions can make this
step negligible enough so that in practice the algorithm scales as the total
number of unique spin-specific determinants, $\; N_{\rm det}^\uparrow + N_{\rm
det}^\downarrow$, over a wide range of total number of determinants (here,
$N_{\rm det}$ up to about one million), thus greatly reducing the total
computational cost. Finally, a new truncation scheme for the multideterminant
expansion is proposed so that larger expansions can be considered without
increasing the computational time. The algorithm is illustrated with
all-electron Fixed-Node Diffusion Monte Carlo calculations of the total energy
of the chlorine atom. Calculations using a trial wavefunction including about
750 000 determinants with a computational increase of $\sim$ 400 compared to a
single-determinant calculation are shown to be feasible.Comment: 9 pages, 3 figure
Ecoupling server: A tool to compute and analyze electronic couplings

Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user-friendly tools to compute and analyze electronic coupling from external wave functions will be of high value. The first server to provide a friendly interface for evaluation and analysis of electronic couplings under two different approximations (FDC and GMH) is presented in this communication. Ecoupling server accepts inputs from common QM and QM/MM software and provides useful plots to understand and analyze the results easily. The web server has been implemented in CGI-python using Apache and it is accessible at http://ecouplingserver.bsc.es. Ecoupling server is free and open to all users without login.This work has been funded by the Spanish Ministry of Education and Science through the Project CTQ2013-48287.Peer ReviewedPostprint (author's final draft
Theoretical Study of Lithium Ionic Conductors by Electronic Stress
  Tensor Density and Electronic Kinetic Energy Density

We analyze the electronic structure of lithium ionic conductors, ${\rm
Li_3PO_4}$ and ${\rm Li_3PS_4}$, using the electronic stress tensor density and
kinetic energy density with special focus on the ionic bonds among them. We
find that, as long as we examine the pattern of the eigenvalues of the
electronic stress tensor density, we cannot distinguish between the ionic bonds
and bonds among metalloid atoms. We then show that they can be distinguished by
looking at the morphology of the electronic interface, the zero surface of the
electronic kinetic energy density.Comment: 30 pages, 7 figure
Geometrical Control of the Interatomic Coulombic Decay Process in Quantum Dots for Infrared Photodetectors

n electron dynamics calculations the interatomic Coulombic decay  ICD  process has recently been shown to take place in two vertically aligned quantum dots  QDs . Energy emitted during the relaxation of one electron in one QD is converted into kinetic energy of another electron ejected from a neighboring QD.    As the electronic structure of QDs can be controlled by their geometries, we prove here in thorough scans of the transversal and vertical QD confinement potentials  widths that geometries are likewise control parameters for ICD. Such a comprehensive investigation has been enabled by a significant development of the calculations in terms of speed achieved among others by optimization of the grid and Coulomb interaction operator representations. As key result of this study we propose two cigar shaped singly charged GaAs QDs vertically aligned in the direction of their long side for a most efficient QD ICD realization useful for an infrared photodetector
Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels

Microscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 1/Å^3 have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent.Postprint (author's final draft
On the stability of cis- and trans-2-butene isomers. An insight based on the FAMSEC, IQA and ETS-NOCV schemes

In the present account, the real space fragment attributed molecular system energy change (FAMSEC) approach, interacting quantum atoms energy decomposition scheme as well as molecular orbitals based the extended transition state scheme coupled with natural orbitals for chemical valence (ETS-NOCV) have been, for the first time, successfully used to delineate factors of importance for stability of the 2-butene conformers (cis-eq, cis-TS, trans-eq, trans-TS). Our results demonstrate that atoms of the controversial H–H contact in cis-eq (i) are involved in attractive interaction dominated by the exchange-correlation term, (ii) are weekly stabilized, (iii) show trends in several descriptors found in other typical H-bonds, and (iv) are part of most stabilized CH–HC fragment (loc-FAMSEC =-3.6 kcal/mol) with most favourably changed intrafragment interactions on trans-eq →cis-eq. Moreover, lower stability of cis-eq vs. trans-eq is linked with the entire HC[DOUBLE BOND]CH (ethylenic) fragment which destabilized cis-eq (mol-FAMSEC, +3.9 kcal/mol) the most. Although the H–H contact can be linked with smaller, relative to trans-, rotational energy barrier in cis-2-butene, we have proven that to rationalize this phenomenon one must account for changes in interactions between various fragments that constitute the entire molecule. Importantly, we discovered a number of comparable trends in fundamental properties of equivalent molecular fragments on a methyl group rotation; for example, interaction between BP-free H-atoms in trans-eq (involving C[BOND]H bonds of the methyl and ethylenic units) and BP-linked H-atoms in cis-eq. Clearly, rotational energy barrier cannot be entirely (i) rationalized by the properties of or (ii) attributed to the H–H contact in cis-eq.The National Research Foundation of South Africa (Grant Numbers 87777) and the University of Pretoria, Pretoria, South Africa.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-987X2017-12-15Chemistr
Predicting core level binding energies shifts: suitability of the projector augmented wave approach as implemented in VASP

Here, we assess the accuracy of various approaches implemented in Vienna ab initio simulation package code to estimate core-level binding energy shifts (ΔBEs) using a projector augmented wave method to treat core electrons. The performance of the Perdew-Burke-Ernzerhof (PBE) and the Tao-Perdew-Staroverov-Scuseria (TPSS) exchange-correlation density functionals is examined on a dataset of 68 molecules containing B→F atoms in diverse chemical environments, accounting for 185 different 1s core level binding energy shifts, for which both experimental gas-phase X-ray photoemission (XPS) data and accurate all electron ΔBEs are available. Four procedures to calculate core-level shifts are investigated. Janak-Slater transition state approach yields mean absolute errors of 0.37 (0.21) eV at PBE (TPSS) level, similar to highly accurate all electron ΔSCF approaches using same functionals, and close to XPS experimental accuracy of 0.1 eV. The study supports the use of these procedures to assign ΔBEs of molecular moieties on material surfaces of interest in surface science, nanotechnology, and heterogeneous catalysis
Electronic structure of stoichiometric and reduced ZnO from periodic relativistic all electron hybrid density functional calculations using numeric atom-centered orbitals

The atomic and electronic structure of stoichiometric and reduced ZnO wurtzite has been studied using a periodic relativistic all electron hybrid density functional (PBE0) approach and numeric atom-centered orbital basis set with quality equivalent to aug-cc-pVDZ. To assess the importance of relativistic effects, calculations were carried out without and with explicit inclusion of relativistic effects through the zero order regular approximation. The calculated band gap is ∼0.2 eV smaller than experiment, close to previous PBE0 results including relativistic calculation through the pseudopotential and ∼0.25 eV smaller than equivalent nonrelativistic all electron PBE0 calculations indicating possible sources of error in nonrelativistic all electron density functional calculations for systems containing elements with relatively high atomic number. The oxygen vacancy formation energy converges rather fast with the supercell size, the predicted value agrees with previously hybrid density functional calculations and analysis of the electronic structure evidences the presence of localized electrons at the vacancy site with a concomitant well localized peak in the density of states ∼0.5 eV above the top of the valence band and a significant relaxation of the Zn atoms near to the oxygen vacancy. Finally, present work shows that accurate results can be obtained in systems involving large supercells containing up to ∼450 atoms using a numeric atomic-centered orbital basis set within a full all electron description including scalar relativistic effects at an affordable cost
Mutantelec : AnIn Silicomutation simulation platform for comparative electrostatic potential profiling of proteins.

The electrostatic potential plays a key role in many biological processes like determining the affinity of a ligand to a given protein target, and they are responsible for the catalytic activity of many enzymes. Understanding the effect that amino acid mutations will have on the electrostatic potential of a protein, will allow a thorough understanding of which residues are the most important in a protein. MutantElec, is a friendly web application for in silico generation of site-directed mutagenesis of proteins and the comparison of electrostatic potential between the wild type protein and the mutant(s), based on the three-dimensional structure of the protein. The effect of the mutation is evaluated using different approach to the traditional surface map. MutantElec provides a graphical display of the results that allows the visualization of changes occurring at close distance from the mutation and thus uncovers the local and global impact of a specific chang
Systematic study of the effect of HSE functional internal parameters on the electronic structure and band gap of a representative set of metal oxides

The effect of the amount of Hartree-Fock mixing parameter (α) and of the screening parameter (w) defining the range separated HSE type hybrid functional is systematically studied for a series of seven metal oxides: TiO2, ZrO2, CuO2, ZnO, MgO, SnO2, and SrTiO3. First, reliable band gap values were determined by comparing the optimal α reproducing the experiment with the inverse of the experimental dielectric constant. Then, the effect of the w in the HSE functional on the calculated band gap was explored in detail. Results evidence the existence of a virtually infinite number of combinations of the two parameters which are able to reproduce the experimental band gap, without a unique pair able to describe the full studied set of materials. Nevertheless, the results point out the possibility of describing the electronic structure of these materials through a functional including a screened HF exchange and an appropriate correlation contribution
Toward deformation densities for intramolecular interactions without radical reference states using the fragment, atom, localized, delocalized, and interatomic (FALDI) charge density decomposition scheme

A novel approach for calculating deformation densities is presented, which enables to calculate the deformation density resulting from a change between two chemical states, typically conformers, without the need for radical fragments. The Fragment, Atom, Localized, Delocalized, and Interatomic (FALDI) charge density decomposition scheme is introduced, which is applicable to static electron densities (FALDI-ED), conformational deformation densities (FALDI-DD) as well as orthodox fragment-based deformation densities. The formation of an intramolecular NH⋅⋅⋅N interaction in protonated ethylene diamine is used as a case study where the FALDI-based conformational deformation densities (with atomic or fragment resolution) are compared with an orthodox EDA-based approach. Atomic and fragment deformation densities revealed in real-space details that (i) pointed at the origin of density changes associated with the intramolecular H-bond formation and (ii) fully support the IUPAC H-bond representation. The FALDI scheme is equally applicable to intra- and intermolecular interactions.National Research Foundation of South Africa and University of Pretoria.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-987X2018-05-15Chemistr
An Open-Source Framework for Analyzing $N$-Electron Dynamics: I.
  Multi-Determinantal Wave Functions

The aim of the present contribution is to provide a framework for analyzing
and visualizing the correlated many-electron dynamics of molecular systems,
where an explicitly time-dependent electronic wave packet is represented as a
linear combination of $N$-electron wave functions. The central quantity of
interest is the electronic flux density, which contains all information about
the transient electronic density, the associated phase, and their temporal
evolution. It is computed from the associated one-electron operator by reducing
the multi-determinantal, many-electron wave packet using the Slater-Condon
rules. Here, we introduce a general tool for post-processing multi-determinant
configuration-interaction wave functions obtained at various levels of theory.
It is tailored to extract directly the data from the output of standard quantum
chemistry packages using atom-centered Gaussian-type basis functions. The
procedure is implemented in the open-source Python program detCI@ORBKIT, which
shares and builds upon the modular design of our recently published
post-processing toolbox [J. Comput. Chem. 37 (2016) 1511]. The new procedure is
applied to ultrafast charge migration processes in different molecular systems,
demonstrating its broad applicability. Convergence of the $N$-electron dynamics
with respect to the electronic structure theory level and basis set size is
investigated. This provides an assessment of the robustness of qualitative and
quantitative statements that can be made concerning dynamical features observed
in charge migration simulations
Comparison of the periodic slab approach with the finite cluster ansatz
  for metal-organic interfaces at the example of PTCDA on Ag(110)

We present a comparative study of metal-organic interface properties obtained
from dispersion corrected density functional theory calculations based on two
different approaches: the periodic slab supercell technique and cluster models
with 18 to 290 Ag atoms. Fermi smearing and fixing of cluster borders are
required to make the cluster calculation feasible and realistic. The considered
adsorption structure and energy of a PTCDA molecule on the Ag(110) surface is
not well reproduced with clusters containing only two metallic layers. However,
clusters with four layers of silver atoms and sufficient lateral extension
reproduce the adsorbate structure within 0.02 \AA\ and adsorption energies
within 10\% of the slab result. A consideration of the computational effort
shows that the cluster approach is a competitive alternative to methods using
periodic boundary conditions and of particular interest for research at surface
defects and other systems that do not show periodic symmetry