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Stem Cells, Biology, Endoplasmic Reticulum Stress, Medicine, Ion Channels, and 15 moreNeuroprotection, Amyotrophic Lateral Sclerosis, Biological Sciences, Caspases, Cell Differentiation, Humans, Mutation, Female, Male, Phenotype, Middle Aged, Aminopyridine, Induced Pluripotent Stem Cells, Motor Neurons, and Medical and Health Sciences
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We try to decompose the interaction energy of the hydrogen bonded dimer systems HOH⋯NH3, H2O⋯HNH2, and H2O⋯HNH3+ into several well-defined quantities, using the fragment-based density-functional calculations, Symmetry-adapted perturbation... more
We try to decompose the interaction energy of the hydrogen bonded dimer systems HOH⋯NH3, H2O⋯HNH2, and H2O⋯HNH3+ into several well-defined quantities, using the fragment-based density-functional calculations, Symmetry-adapted perturbation theory, and as well the Heitler–London approach to interaction energies. The theoretical considerations and the numerical results show that despite the different nature of the decomposition schemes common terms beyond the electrostatic
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ABSTRACT The periodic Hartree-Fock approach is used in all-electron calculations on bulk rutile (TiO2) and various slabs modeling the (001), (100), and (110) surface to study possible geometric and electronic surface relaxations,... more
ABSTRACT The periodic Hartree-Fock approach is used in all-electron calculations on bulk rutile (TiO2) and various slabs modeling the (001), (100), and (110) surface to study possible geometric and electronic surface relaxations, convergence of properties with slab thickness, and the relative stability of the different surfaces. Results are discussed by means of a Mulliken population analysis, band structures, and the density of states. We find displacements of surface atoms ranging from 5 to nearly 40 pm; the (001) surface appears to be significantly unstable with respect to the other two [(100) and (110)], in accord with experimental findings. Specific features of the density of states projected onto different Ti sites and the relative stability of the different surfaces agree with a possible dissociation behavior of the rutile structure into TiO2 chains, which are calculated to be stable.
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ABSTRACT The dressed diagonal approximation to the self-consistent – size consistent CI, corrected for off-diagonal Fock matrix elements in localized orbitals is developed and applied to the ammoniac dimer system. A quite correct... more
ABSTRACT The dressed diagonal approximation to the self-consistent – size consistent CI, corrected for off-diagonal Fock matrix elements in localized orbitals is developed and applied to the ammoniac dimer system. A quite correct correlation energy can be obtained for this system, with a significantly reduced dependence of the results on the choice of the localization procedure. When calculating an interaction energy, the choice of the monomer orbitals and the application of the Boys–Bernardi counterpoise procedure shows in this case an unusual behavior: the correlation energy does not increase with the size of the atomic basis sets. Nevertheless a reasonable potential curve can be obtained.
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ABSTRACT The geometrical structure of the polar, Al-terminated surface of corundum has been investigated by different theoretical methods ranging from empirical pair potentials to periodic Hartree–Fock or density functional theory... more
ABSTRACT The geometrical structure of the polar, Al-terminated surface of corundum has been investigated by different theoretical methods ranging from empirical pair potentials to periodic Hartree–Fock or density functional theory calculations. The different methods agree in predicting a structure for the bulk, which is close to the experimental one, and an inward relaxation of more than 50% in agreement with experiment. However, a rather strong disagreement exists concerning the quantitative amount of relaxation of the surface layers. Accurate density functional theory calculations for slab models considering up to 18 layers with 30 atoms in the unit cell strongly suggest that the degree of relaxation of the outermost Al atomic layer is much larger than the values obtained by other methods. Reasons for the different description are given and implications for the use of pair potentials discussed.
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Human adult germline stem cells (haGSCs) were established from human testicular biopsies and were claimed to be pluripotent. Recently, the gene expression profile of haGSCs demonstrated that these cells presented with a fibroblast rather... more
Human adult germline stem cells (haGSCs) were established from human testicular biopsies and were claimed to be pluripotent. Recently, the gene expression profile of haGSCs demonstrated that these cells presented with a fibroblast rather than a pluripotent identity. Nevertheless, haGSCs were reported to generate teratomas. In this report, we address this discrepancy. Instead of using haGSCs, which are no longer available for the stem cell community, we used a human testicular fibroblastic cell (hTFC) line that presents with a gene expression profile highly similar to that of haGSCs. Indeed, as shown by microarray analysis, the similarity between hTFCs and haGSCs is comparable to human embryonic stem cell (hESC) lines derived by different laboratories. We argue that the almost identical gene expression profile of hTFCs and haGSCs should result in a very similar if not identical differentiation potential. Strikingly, hTFCs were not able to generate teratomas after injection into nude ...
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A method is proposed for the solution of the self-consistent field equations that can lead to localized occupied and virtual molecular orbitals, avoiding the need for solving for the canonical molecular orbitals. The method starts with... more
A method is proposed for the solution of the self-consistent field equations that can lead to localized occupied and virtual molecular orbitals, avoiding the need for solving for the canonical molecular orbitals. The method starts with strongly localized “guess molecular orbitals”, it is nonperturbative and proceeds through the diagonalization of single configuration interaction matrices which may be rendered size-consistent through
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ABSTRACT Starting with self-consistent fields (SCFs), localized orbitals should facilitate the calculation of the correlation energy in extended, and in particular periodic, systems. This idea is exploited on model ring systems (H4n+2).... more
ABSTRACT Starting with self-consistent fields (SCFs), localized orbitals should facilitate the calculation of the correlation energy in extended, and in particular periodic, systems. This idea is exploited on model ring systems (H4n+2). It is shown that for insulating materials [(H2)2n+1, presenting a large gap in the band structure], most of the energy lowering brought by the orders larger than 2 in the canonical many-body perturbation expansion are due to the local-hole–local-particle interaction and that the localized Epstein–Nesbet second-order energies are close to the best correlation-energy estimates. The situation is completely different for small-gap (metalliclike) systems, such as cyclic H4n+2, where the localized second-order approach misses a large fraction of the correlation energy, involving the propagation of the holes and of the particles and implying specific higher-order diagrams. © 1998 American Institute of Physics.
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ABSTRACT In this work we test two ab initio methodologies which allow the decomposition of the total intermolecular interaction energy into physically meaningful contributions, namely, the symmetry adapted perturbation theory (SAPT) and... more
ABSTRACT In this work we test two ab initio methodologies which allow the decomposition of the total intermolecular interaction energy into physically meaningful contributions, namely, the symmetry adapted perturbation theory (SAPT) and the use of localized orbitals within a Møller–Plesset perturbation scheme. The accuracy of the two different methods is compared to supermolecular results, within MP2 and coupled-cluster theory within single and double excitations, with perturbative estimates of the amplitudes of triple excitations [CCSD(T)]. Some relations between the different approaches are conjectured from theoretical considerations, and are confirmed by numerical results. The corresponding calculations have been performed for three model dimers: two NH3⋯H2O dimers, with NH3 acting once as a proton acceptor and once as a proton donor, and the NH4+⋯H2O considered as a prototype of the ion–molecule interaction. We may conclude that third-order terms in SAPT help significantly to reproduce the Hartree–Fock induction and the relaxed, total dispersion in the LMP2 decomposition. © 2003 American Institute of Physics.
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Starting from localized bond or lone-pair Hartree-Fock molecular orbitals, one may define contracted doubly excited functions for each pair of bond molecular orbitals. These functions are obtained from local single- and... more
Starting from localized bond or lone-pair Hartree-Fock molecular orbitals, one may define contracted doubly excited functions for each pair of bond molecular orbitals. These functions are obtained from local single- and double-configuration interaction (CISD) of moderate size. Then one may build a contracted CISD matrix for the whole molecule, spanned by the Hartree-Fock determinant and these contracted doubly excited functions, the number of which is indeed moderate, as scaling at most as the square of the number of bonds. The calculation of the off-diagonal elements of this matrix is straightforward. Its diagonalization provides an upper bound to the lowest CISD eigenvalue. The well-known size-consistency error may be overcome through self-consistent dressings such as coupled-electron pair approximations, and cutoff criteria will lead to linear scaling. Numerical tests on a series of covalent and ionic systems show that the results are very close to that of coupled-cluster calculations. Possible improvements of this already efficient algorithm are suggested.
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ABSTRACT Localized molecular Hartree–Fock orbitals have been determined by means of an iterative procedure consisting of orthogonalization and configuration interaction employing single excitations. For ring systems the rotational... more
ABSTRACT Localized molecular Hartree–Fock orbitals have been determined by means of an iterative procedure consisting of orthogonalization and configuration interaction employing single excitations. For ring systems the rotational symmetry has been included explicitly to obtain Wannier-like orbitals suited for a posteriori correlation calculations using only the most important contributions within a limited region around one reference ring segment. Applications involving different estimates of the correlation energy include as model systems (H2)2n+1, the ionic LinHn, and a weakly bound beryllium ring as well as the strongly covalent molecule (CH2)36 forming a closed ring. In all cases, the localized and canonical MP2 results are close, and the localized Epstein–Nesbet second-order gives a good estimate of more expensive MP4 or CEPA-0 values. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 167–180, 1998
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This article recalls basic properties of Slater type Orbital (STO) basis sets, in particular, with respect to satisfying Kato's electron-nucleus cusp condition. It is shown that a suitable starting point is the set of... more
This article recalls basic properties of Slater type Orbital (STO) basis sets, in particular, with respect to satisfying Kato's electron-nucleus cusp condition. It is shown that a suitable starting point is the set of hydrogen-like orbitals or, more flexibly, their generalization as Coulomb Sturmians. A case study is presented on the Hartree-Fock density obtained for a water molecule, N2, and
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ABSTRACT In the present paper it is proposed—without a formal physical demonstration—that the probability to select the lifetime of an activated complex possibly yielding ozone and formed by reactions involving distinguishable isotopes is... more
ABSTRACT In the present paper it is proposed—without a formal physical demonstration—that the probability to select the lifetime of an activated complex possibly yielding ozone and formed by reactions involving distinguishable isotopes is not equal to the probability to select the lifetime of the same complex but formed by reaction involving indistinguishable isotopes.The origin of this effect is supposed to be linked to the quantum mechanical principle according to which it is not permitted, in a scattering process, to separate the probabilities describing the recoil from the incident particle, if the two particles are indistinguishable. We ascribe the mass independent isotopic fractionation factor to the lifetime ratio of the complexes formed by reactions involving distinguishable and indistinguishable isotopes.In order to illustrate the consequences of this principle, all the accompanying scattering calculations of O+O2→O3*→O+O2 were performed in a thermal gas with oxygen isotopes having the same mass (16 amu). It is numerically shown that the origin of the experimentally observed mass-independent isotope fractionation in ozone is well accounted for within this single assumption.The effect is a priori not restricted to ozone or to oxygen isotopes and may have played a role in several other isotopic anomalies found in meteorites.
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All electron, first principles, periodic calculations have been carried out to investigate the relaxation of the Al-terminated corundum surface. Different theoretical formalisms, Hartree–Fock (HF) and density functional theory using... more
All electron, first principles, periodic calculations have been carried out to investigate the relaxation of the Al-terminated corundum surface. Different theoretical formalisms, Hartree–Fock (HF) and density functional theory using either the LDA or the hybrid B3LYP exchange-correlation functional, have been employed. In the past, many ab initio studies of surface structure have been performed using the experimental, rather than the
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The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn2+ are derived from gas-phase ab initio calculation of the... more
The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn2+ are derived from gas-phase ab initio calculation of the Zn2+-water dimer. The Thole-based dipole polarization is adjusted on the basis of the constrained space orbital variations (CSOV) calculation, while the symmetry adapted perturbation theory (SAPT) approach is also discussed. The vdW parameters of Zn2+ have been obtained by comparing the AMOEBA Zn2+ water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn2+ solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time, and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive reduced variati...
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As for generating localized Hartree−Fock orbitals, we propose a potentially linear-scaling singles-CI scheme to construct fragment-localized density functional theory (DFT) orbitals for molecular systems as water clusters. Due to the use... more
As for generating localized Hartree−Fock orbitals, we propose a potentially linear-scaling singles-CI scheme to construct fragment-localized density functional theory (DFT) orbitals for molecular systems as water clusters. Due to the use of a deformation step instead of a localization step, the influence of the environment on each separate molecule can be studied in detail. The generated orbital set for the whole molecular system is strictly equivalent to a set of canonical orbitals and is a subsequent energy decomposition of intermolecular interactions into electrostatic, exchange repulsion, and orbital interaction, well beyond dimer systems. Beyond this, the correspondence of the individual orbitals to the initial monomer orbitals permits to assess how an interaction deforms an electron density. We show this for dipole moments, which may be decomposed into monomer contributions, polarization, and charge-transfer contribution. Applications to a water and an ammonia dimer and chains...
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In this contribution, we propose accurate intermolecular benchmarks for the 10 standardized water dimers initially proposed by van Duijneveldt et al., following a study by Smith et al. (J Chem Phys, 1990, 92, 1240). Using the popular... more
In this contribution, we propose accurate intermolecular benchmarks for the 10 standardized water dimers initially proposed by van Duijneveldt et al., following a study by Smith et al. (J Chem Phys, 1990, 92, 1240). Using the popular triple-zeta aug-cc-pVTZ basis set, symmetry-adapted perturbation theory (SAPT) computations have been performed and compared with supermolecular post-Hartree-Fock techniques up to most recent explicitly correlated methods. Effects of approximated inclusion of third-order corrections to induction and exchange-induction energies are discussed. As SAPT results are close to the best available ab initio ones, detailed analysis of the available individual SAPT contributions to the interaction energy confirms that electron correlation acts not only on its long-range dispersion part but also on its separated physical components. This permits to assess the validity of the usual HF+Dispersion model as approximation to add pure correlation effects to orbital-based...
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ABSTRACT We present electronic and structural parameters for bulk rutile (TiO2) determined by means of different theoretical methods, namely, the periodic Hartree-Fock approach, subsequent post-Hartree-Fock density functional correlation... more
ABSTRACT We present electronic and structural parameters for bulk rutile (TiO2) determined by means of different theoretical methods, namely, the periodic Hartree-Fock approach, subsequent post-Hartree-Fock density functional correlation correction, and a linear-combination-of-atomic-orbitals approach based entirely on density functionals. Differences between the use of effective core potentials, a frozen-core treatment, and all-electron calculations are investigated. © 1996 John Wiley & Sons, Inc.
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Selecting excitations in localized orbitals to calculate long-range correlation contributions to range-separated density-functional theory can reduce the overall computational effort significantly. Beyond simple selection schemes of... more
Selecting excitations in localized orbitals to calculate long-range correlation contributions to range-separated density-functional theory can reduce the overall computational effort significantly. Beyond simple selection schemes of excited determinants, the dispersion-only approximation, which avoids counterpoise-corrected monomer caculations, is shown to be particularly interesting in this context, which we apply to the random-phase approximation. The approach has been tested on dimers of formamide, water, methane and benzene.
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We consider several spin-unrestricted random-phase approximation (RPA) variants for calculating correlation energies, with and without range separation, and test them on datasets of atomization energies and reaction barrier heights. We... more
We consider several spin-unrestricted random-phase approximation (RPA) variants for calculating correlation energies, with and without range separation, and test them on datasets of atomization energies and reaction barrier heights. We show that range separation greatly improves the accuracy of all RPA variants for these properties. Moreover, we show that a RPA variant with exchange, hereafter referred to as RPAx-SO2, first proposed by Szabo and Ostlund [J. Chem. Phys. 67, 4351 (1977)] in a spin-restricted closed-shell formalism, and extended here to a spin-unrestricted formalism, provides on average the most accurate range-separated RPA variant for atomization energies and reaction barrier heights. Since this range-separated RPAx-SO2 method had already been shown to be among the most accurate range-separated RPA variants for weak intermolecular interactions [J. Toulouse et al., J. Chem. Phys. 135, 084119 (2011)], this works confirms range-separated RPAx-SO2 as a promising method for general chemical applications.