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The limitations of quantum chemistry in this still early era motivated Fernand to embrace atomistic modeling, a bold move and a possibly disappointing perspective to his mentors that he met again when returning to Toulouse at the end of the 1980s. Published as part of the special collection of articles "Festschrift in honor of Fernand Spiegelman". His expertise in quantum chemistry has also kept recognition as he maintained fruitful collaborations in the related areas of cold atoms and molecules but also in alkali spectral broadenings in dense astrophysical environments. [Extracted from the article]

This is part of a series dealing with the formation of benzene from acetylene on iron clusters, Fe[sub n][sup q+] (n=1–4, q=0,1). In this paper, we show that the formation of benzene from acetylene on Fe and Fe[sub n][sup +] (n=1–4) is favorable from a thermodynamic point of view. We explain the variation of the rate constants observed for the successive adsorption of acetylene molecules on an iron cation and the experimental observations about the cyclodimerization of acetylene molecules in Fe(C[sub 2]H[sub 2])[sub 2][sup +] by referring to the spin conservation principle. Our results indicate that the complexes resulting from the cyclodimerization of Fe[sub n](C[sub 2]H[sub 2])[sub 2][sup +]/Fe(C[sub 2]H[sub 2])[sub 2] and Fe[sub n](C[sub 2]H[sub 2])[sub 3][sup +]/Fe(C[sub 2]H[sub 2])[sub 3](n=1–4) contain an n-C[sub 4]H[sub 4] ligand (formation of a metallacycle) rather than a cyclobutadiene molecule. However, it is possible to observe the formation of cyclobutadiene from Fe(C[sub 2]H[sub 2])[sub 2][sup +] and Fe[sub 2](C[sub 2]H[sub 2])[sub 3][sup +] only if spin–orbit coupling is significant. A post-self-consistent-field method that includes a multideterminantal treatment is needed to get a quantitative energetic description of the various steps of the reaction. Finally, we discuss various difficulties met in this study and possible ways to deal with them. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

This is the first paper in a series dealing with the formation of benzene from acetylene on iron clusters, Fe[sub n]/Fe[sub n][sup +] (n=1–4). In the present study, we have performed all-electron Kohn–Sham density-functional theory calculations on the adsorption of acetylene and vinylidene on small iron clusters. Many starting structures were fully optimized without geometric and symmetric constraints for at least three different spin states (numbers of unpaired electrons) using gradient corrected functionals. Vibrational analyses have been performed on all the optimized structures. There is a large number of low-lying electronic states within a window of 50 kJ/mol above the lowest-energy structure for each cluster size and charge state. Various types of coordination and numbers of unpaired electrons are encountered in these electronic states. According to our energetic error bar, all of these states are possible candidates for the ground state of a given complex. Inclusion of corrections beyond the gradient of the density in generalized gradient approximation functionals for correlation stabilizes electronic states with high magnetic moment and destabilizes the low spin states. Electronic states corresponding to the adsorption of an acetylene or a vinylidene molecule on only one iron atom are also more stable when higher corrections are included in the correlation functional. Finally, we have excluded the participation of the vinylidene molecule in the reaction mechanism of the formation of benzene from acetylene on small iron clusters. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Investigates the use of density functional calculations combined with embedded cluster approach in the study of chemisorption on metal surfaces. Comparison between bare and embedded clusters; Role of molecular orbitals embedding potential; Details on the adsorption of oxygen on aluminum surface.

Our recently developed method for the calculation of indirect nuclear spin–spin coupling constants is studied in more detail. For the couplings between nuclei other than N, O, and F (which have lone pairs) the method yields very reliable results. The results for 1J(Si–H) couplings are presented and their dependence on the basis set quality is analyzed. Also, 2J(H–H) and 1J(X–H) couplings (X=C, Si, Ge, Sn) in XH4 molecules are presented and the relativistic effects on 1J(X–H) are discussed. The limitations of the method, which is based on density functional theory, are connected with the inability of the present LDA and GGA exchange-correlation functionals to describe properly the spin-perturbations (through the Fermi-contact mechanism) on atoms to the right of the periodic table (containing lone pairs). However, the deviations from experiment of the calculated couplings for such nuclei are systematic, at least for one-bond couplings, and therefore these calculated couplings should still be useful for NMR structure determinations. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The binding energies, structural parameters, and vibrational frequencies of FeCO, FeCO-, and FeCO+ were studied with a linear combination of Gaussian-type orbitals-density functional (LCGTO-DF) method. The ground state of FeCO is found to be 3Σ- and the calculated dissociation energy, with respect to ground state Fe(5D,3d64s2) and CO (1Σ+), is 30 kcal/mol; after correcting for the atomic states separation of the iron atom this value becomes 17 kcal/mol, which is relatively close to the most recent experimental values 8.1±3.5–10.5±3.7 kcal/mol. Quartet ground states were found for both FeCO+ and FeCO- and the calculated dissociation energies (with respect to ground state Fe+, Fe-, and CO) are 50 and 31 kcal/mol, respectively. There is agreement between theory and experiment in that D(FeCO+)>=D(FeCO-)>=D(FeCO). The ωe’s we calculate for FeCO are, in cm-1, 658 (Fe–C stretch), 1982 (C–O stretch), and 368 (bend). These values are reasonably close to their experimental counterparts, 530±10, 1950±10, and 330±50. For FeCO- we have found 566 and 272 cm-1 for the Fe–C stretch and bend modes while the experimental values are 465±10 and 230±40 cm-1. A frequency of 1831 cm-1 is predicted for the C–O stretch of FeCO-. The σ-donation (CO→Fe) and π-back-donation (Fe→CO) charge transfer mechanism is operative in these species. [ABSTRACT FROM AUTHOR]

The electronic structure of the allyl radical C3H5 and the polyene radicals C5H7, C7H9, C9H11, and C11H13 have been calculated using the linear combination of Gaussian-type orbitals-local spin density method. In contrast to the results obtained using the Hartree–Fock model, which show large errors, the geometries are in excellent agreement with multiconfiguration self-consistent-field calculations and with experiment. LSD yields a C2v symmetry for the allyl radical, while the polyenes C5H7 to C11H13 have C–C bonds alternating between single and double bonds. The harmonic vibrational frequencies were calculated for the allyl radical and C5H7 (the 1,4-pentadienyl radical). The unscaled vibrational frequencies calculated for the allyl radical are in excellent agreement with experiment. [ABSTRACT FROM AUTHOR]

In recent years, double perovskite oxides have been considered as highly promising electrode materials, with use in different energy production applications. Proposing new perovskite solid solutions, however, is a great challenge due to the analytical complexity introduced by disorder. Here, we investigate the structural formability and electro-optical properties of the possible Ba 2 ZrTiO 6 double perovskite which can be also considered as a solid solution of BaZrO 3 and BaTiO 3 perovskites. Based on our calculations, by considering the (τ) − tolerance factor and the (μ) -octahedral factor, the Ba 2 SrTiO 6 double perovskite exhibits a perfectly cubic structure with the space group Fm3m (space group no: 225). Our electrical properties calculations show that Ba 2 ZrTiO 6 is a direct semiconductor with a Γ point band gap about 3.14 ​eV obtained with the modified Becke-Johnson (mBJ) approximation. We also discovered remarkable optical properties of the proposed double perovskite. Furthermore, the effect of hydrostatic pressure in the 0–35 ​GPa range on the electronic properties of the compound is investigated. It was found that the hydrostatic pressure slightly increases the energy gap of the material while the band gap remains direct (Γ to Γ). Also, the optical spectra experience blue shifts under pressure. Analyzing the thermoelectric features shows that the material exhibits a good Seebeck coefficient and thermoelectric power factors which suggest this structure as a promising material for thermoelectric applications. The results suggest Ba 2 ZrTiO 6 double perovskite for use in electrical, optical and thermoelectric applications. [Display omitted] • Ba2ZrTiO6 double perovskite shows a cubic structure with the space group of Fm3m. • Ba 2 ZrTiO 6 double perovskite is a mechanically stabile structure and shows brittle property at its ground state. • Ba2ZrTiO6 double perovskite shows a Γ point direct band gap of about of 3.14 ​eV. • Ba2ZrTiO6 double perovskite shows interesting strain tunable electrical and optical properties. • Ba2ZrTiO6 double perovskite shows a good Seebeck coefficient and power factor. [ABSTRACT FROM AUTHOR]

Since the form of the exact functional in density functional theory is unknown, we must rely on density functional approximations (DFAs). In the past, very promising results have been reported by combining semi-local DFAs with exact, i.e. Hartree–Fock, exchange. However, the spin-state energy ordering and the predictions of global minima structures are particularly sensitive to the choice of the hybrid functional and to the amount of exact exchange. This has been already qualitatively described for single conformations, reactions, and a limited number of conformations. Here, we have analyzed the mixing of exact exchange in exchange functionals for a set of several hundred isomers of the transition metal carbide, Mo4C2. The analysis of the calculated energies and charges using PBE0-type functional with varying amounts of exact exchange yields the following insights: (1) The sensitivity of spin-energy splitting is strongly correlated with the amount of exact exchange mixing. (2) Spin contamination is exacerbated when correlation is omitted from the exchange-correlation functional. (3) There is not one ideal value for the exact exchange mixing which can be used to parametrize or choose among the functionals. Calculated energies and electronic structures are influenced by exact exchange at a different magnitude within a given distribution; therefore, to extend the application range of hybrid functionals to the full periodic table the spin-energy splitting energies should be investigated. [ABSTRACT FROM AUTHOR]

The catalytic transformation of the heavy aromatics in bitumen into lighter components is the key to the upgrading and refining of the oil sands. To understand the chemical bonding in molybdenum carbide nanoparticle (MCNP) catalysts and the chemisorption bonds between the MCNPs and unsaturated hydrocarbons, the topological analysis of the electron localization function was applied to various MCNPs and their complexes with unsaturated hydrocarbons. For some of the smaller complexes, comparisons are made with the atoms in molecules approach, including the calculation of delocalization indices. The results are interpreted in the Lewis bonding scheme. It was found that the Mo-C bonding can be highly ionic in cases like Mo8C12 and MoC but shows significant covalent character in Mo2C, Mo3C, and Mo28C14. The chemisorption bonds between hydrocarbons and the MCNPs involve electron sharing of various types with strong covalent character. The strong three- or four-center interactions determine the adsorption configurations of the hydrocarbons on the MCNPs. Derivatives of benzene show some different bonding features, which depend strongly on the substituent or the heteroatom. [ABSTRACT FROM AUTHOR]

Explicit description of atomic polarizability is critical for the accurate treatment of inter-molecular interactions by force fields (FFs) in molecular dynamics (MD) simulations aiming to investigate complex electrostatic environments such as metal-binding sites of metalloproteins. Several models exist to describe key monovalent and divalent cations interacting with proteins. Many of these models have been developed from ion–amino-acid interactions and/or aqueous-phase data on cation solvation. The transferability of these models to cation–protein interactions remains uncertain. Herein, we assess the accuracy of existing FFs by their abilities to reproduce hierarchies of thousands of Ca2+–dipeptide interaction energies based on density-functional theory calculations. We find that the Drude polarizable FF, prior to any parameterization, better approximates the QM interaction energies than any of the non-polarizable FFs. Nevertheless, it required improvement in order to address polarization catastrophes where, at short Ca2+–carboxylate distances, the Drude particle of oxygen overlaps with the divalent cation. To ameliorate this, we identified those conformational properties that produced the poorest prediction of interaction energies to reduce the parameter space for optimization. We then optimized the selected cation–peptide parameters using Boltzmann-weighted fitting and evaluated the resulting parameters in MD simulations of the N-lobe of calmodulin. We also parameterized and evaluated the CTPOL FF, which incorporates charge-transfer and polarization effects in additive FFs. This work shows how QM-driven parameter development, followed by testing in condensed-phase simulations, may yield FFs that can accurately capture the structure and dynamics of ion–protein interactions. [ABSTRACT FROM AUTHOR]

Heterogeneous reactions catalyzed by transition-metal-containing nanoparticles represent a crucial type of reaction in chemical industry. Because of the existing gap in understanding heterogeneous catalysis between a cluster of a few atoms and a bulk model of periodic slabs, reactions catalyzed by transition-metal-containing nanoparticles are still not well understood. Herein, we provide a multiscale modeling approach to study the benzene hydrogenation reactions on molybdenum carbide nanoparticles (MCNPs) in the process of in situ heavy oil upgrading. By coupling the quantum mechanical (QM) density functional tight-binding (DFTB) method with a molecular mechanical (MM) force field, a QM/MM model was built to describe the reactants, the nanoparticles and the surroundings. Umbrella sampling (US) was used to calculate the free energy profiles of the benzene hydrogenation reactions in a model aromatic solvent in the in situ heavy oil upgrading conditions. By comparing with the traditional method in computational heterogeneous catalysis, the results reveal new features of the metallic MCNPs. Rather than being rigid, they are very flexible under working condition due to the entropic contributions of the MCNPs and the solvent, which greatly affect the free energy profiles of these nanoscale heterogeneous reactions. [ABSTRACT FROM AUTHOR]

The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes. [ABSTRACT FROM AUTHOR]

Although potentially powerful, molecular oxygen is an inert oxidant due to the triplet nature of its ground state. Therefore, many enzymesse various metal cations (M) to produce singlet active species MO. In this communication we investigate the topology of the Electron Localization Function (ELF) within five biomimetic complexes which are representative of the strategies followed by metalloenzymes to activate O. Thanks to its coupling to the constrained DFT methods the ELF analysis reveals the tight connection between the spin state of the adduct and the spatial organization of the oxygen lone pairs. We suggest that enzymes could resort to spin state control to tune the regioselectivity of substrate oxidations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011 [ABSTRACT FROM AUTHOR]

Abstract: The constrained DFT approach of Wu and Van Voorhis is a promising tool for the study of long range biological electron transfers within Marcus theory. This approach allows one to define chemically relevant non-adiabatic states and to compute the three key parameters entering the rate constant expression; the driving force (ΔG°), the reorganization energy (λ) and the electronic coupling H DA. Here we present the implementation of the method in deMon2k and we then successively use it to derive new parameters for the pathway model which is one of the most common interpretative models used in biochemistry to relate the H DA amplitude to the composition of proteins. This original application of CDFT also opens the door towards more elaborate models. [Copyright &y& Elsevier]

Abstract: A new density functional combining the TPSS meta-GGA exchange and the τ1 meta-GGA correlation is studied. The parameters in the τ1 meta-GGA correlation model are reoptimized in a synchronized way to match the original TPSS meta-GGA exchange functional. This reparametrized meta-GGA exchange-correlation functional, named TPSSτ3, yields improved results for hydrogen-bonded and van der Waals complexes compared to Bmτ1 and TPSSτ1. [Copyright &y& Elsevier]

Ni‐CeO2 nanoparticles (NPs) are promising nanocatalysts for water splitting and water gas shift reactions due to the ability of ceria to temporarily donate oxygen to the catalytic reaction and accept oxygen after the reaction is completed. Therefore, elucidating how different properties of the Ni‐Ceria NPs relate to the activity and selectivity of the catalytic reaction, is of crucial importance for the development of novel catalysts. In this work the active learning (AL) method based on machine learning regression and its uncertainty is used for the global optimization of Ce(4‐x)NixO(8‐x) (x = 1, 2, 3) nanoparticles, employing density functional theory calculations. Additionally, further investigation of the NPs by mass‐scaled parallel‐tempering Born‐Oppenheimer molecular dynamics resulted in the same putative global minimum structures found by AL, demonstrating the robustness of our AL search to learn from small datasets and assist in the global optimization of complex electronic structure systems. [ABSTRACT FROM AUTHOR]

Reinforcement learning (RL) methods have helped to define the state of the art in the field of modern artificial intelligence, mostly after the breakthrough involving AlphaGo and the discovery of novel algorithms. In this work, we present a RL method, based on Q‐learning, for the structural determination of adsorbate@substrate models in silico, where the minimization of the energy landscape resulting from adsorbate interactions with a substrate is made by actions on states (translations and rotations) chosen from an agent's policy. The proposed RL method is implemented in an early version of the reinforcement learning software for materials design and discovery (RLMaterial), developed in Python3.x. RLMaterial interfaces with deMon2k, DFTB+, ORCA, and Quantum Espresso codes to compute the adsorbate@substrate energies. The RL method was applied for the structural determination of (i) the amino acid glycine and (ii) 2‐amino‐acetaldehyde, both interacting with a boron nitride (BN) monolayer, (iii) host‐guest interactions between phenylboronic acid and β‐cyclodextrin and (iv) ammonia on naphthalene. Density functional tight binding calculations were used to build the complex search surfaces with a reasonably low computational cost for systems (i)–(iii) and DFT for system (iv). Artificial neural network and gradient boosting regression techniques were employed to approximate the Q‐matrix or Q‐table for better decision making (policy) on next actions. Finally, we have developed a transfer‐learning protocol within the RL framework that allows learning from one chemical system and transferring the experience to another, as well as from different DFT or DFTB levels. [ABSTRACT FROM AUTHOR]

Analyzes the structure, bonding and vibrations of Fe(N2)n transition metal with molecular species. Use of the LCGTO-KS-DF method; Estimation of dissociation energies; Vibrational analysis of ground states; Effect of 15N isotopic substitution on vibrational frequencies; Comparisons of the isoelectronic species Fe(CO)n; Fe-N2 bonding.

The time-dependent density functional theory (TD-DFT) calculation of excitation spectra places certain demands on the DFT exchange-correlation potential, v[sub xc], that are not met by the functionals normally used in molecular calculations. In particular, for high-lying excitations, it is crucial that the asymptotic behavior of v[sub xc] be correct. In a previous paper, we introduced a novel asymptotic-correction approach which we used with the local density approximation (LDA) to yield an asymptotically corrected LDA (AC-LDA) potential [Casida, Casida, and Salahub, Int. J. Quantum Chem. 70, 933 (1998)]. The present paper details the theory underlying this asymptotic correction approach, which involves a constant shift to incorporate the effect of the derivative discontinuity (DD) in the bulk region of finite systems, and a spliced asymptotic correction in the large r region. This is done without introducing any adjustable parameters. We emphasize that correcting the asymptotic behavior of v[sub xc] is not by itself sufficient to improve the overall form of the potential unless the effect of the derivative discontinuity is taken into account. The approach could be used to correct v[sub xc] from any of the commonly used gradient-corrected functionals. It is here applied to the LDA, using the asymptotically correct potential of van Leeuwen and Baerends (LB94) in the large r region. The performance of our AC-LDA v[sub xc] is assessed for the calculation of TD-DFT excitation energies for a large number of excitations, including both valence and Rydberg states, for each of four small molecules: N[sub 2], CO, CH[sub 2]O, and C[sub 2]H[sub 4]. The results show a significant improvement over those from either the LB94 or the LDA functionals. This confirms that the DD is indeed an important element in the design of functionals. The quality of TDLDA/LB94 and TDLDA/AC-LDA oscillator strengths were also assessed in what we believe to be the first rigorous assessment ... [ABSTRACT FROM AUTHOR]

In this work, we explore the possibility of using computationally inexpensive electronic structure methods, such as semiempirical and DFTB calculations, for the search of the global minimum (GM) structure of chemical systems. The basic prerequisite that these inexpensive methods will need to fulfill is that their lowest energy structures can be used as starting point for a subsequent local optimization at a benchmark level that will yield its GM. If this is possible, one could bypass the global optimization at the expensive method, which is currently impossible except for very small molecules. Specifically, we test our methods with clusters of second row elements including systems of several bonding types, such as alkali, metal, and covalent clusters. The results reveal that the DFTB3 method yields reasonable results and is a potential candidate for this type of applications. Even though the DFTB2 approach using standard parameters is proven to yield poor results, we show that a re-parametrization of only its repulsive part is enough to achieve excellent results, even when applied to larger systems outside the training set. [ABSTRACT FROM AUTHOR]

The development of the cyclic cluster model (CCM) formalism for Kohn-Sham auxiliary density functional theory (KS-ADFT) methods is presented. The CCM is a direct space approach for the calculation of perfect and defective systems under periodic boundary conditions. Translational symmetry is introduced in the CCM by integral weighting. A consistent weighting scheme for all two-center and three-center interactions appearing in the KS-ADFT method is presented. For the first time, an approach for the numerical integration of the exchange-correlation potential within the cyclic cluster formalism is derived. The presented KS-ADFT CCM implementation was applied to covalent periodic systems. The results of cyclic and molecular cluster model (MCM) calculations for trans-polyacetylene, graphene, and diamond are discussed as examples for systems periodic in one, two, and three dimensions, respectively. All structures were optimized. It is shown that the CCM results represent the results of MCM calculations in the limit of infinite molecular clusters. By analyzing the electronic structure, we demonstrate that the symmetry of the corresponding periodic systems is retained in CCM calculations. The obtained geometric and electronic structures are compared with available data from the literature. [ABSTRACT FROM AUTHOR]

The development and implementation of sum-over-states density-functional-perturbation theory (SOS-DFPT) [V.G. Malkin, O.L. Malkina, M.E. Casida, and D.R. Salahub, J. Am. Chem. Soc. 116, 5898 (1994)] has allowed a significant improvement in the accuracy of nuclear magnetic resonance (NMR) chemical shift values over the Hartree-Fock approximation. Furthermore, due to its computational efficiency, SOS-DFPT has opened the way to the study of systems of increased size compared to those that may be approached by more sophisticated but also computationally more intensive methods, such as Møller-Plesset perturbation theory or coupled-cluster theory. The success of SOS-DFPT relies on the introduction of an ad hoc correction to the excitation energy that improves the calculation of the paramagnetic component of the NMR shielding tensor. The lack of a clear physical basis for this approximation has left the SOS-DFPT open to some criticism. We have shown in a previous article [E. Fadda, M.E. Casida, and D.R. Salahub, Int. J. Quantum Chem. 91, 67 (2003)] that the electric field and magnetic field responses are given by equivalent expressions within the Tamm-Dancoff approximation of time-dependent density-functional theory (TD-DFT). This provides an SOS-DFPT expression which, upon restriction to diagonal contributions, yields a new rigorous "Loc.3" approximation. In this article, we more than double our original test set of 10 molecules for [sup 13]C, [sup 15]N, and [sup 17]O chemical shifts to a set of 25 molecules. In addition, we compare the results of "Loc.3" SOS-DFPT with the results of promising recent functionals for DFT calculations of chemical shifts. The results show not only that the "Loc.3" approximation represents the rigorous physical connection between SOS-DFPT and TD-DFT, but also that it has very good potential for the prediction of NMR shielding constants, opening the way to further developments in DFT-based NMR parameter calculations. [ABSTRACT FROM AUTHOR]

A density functional study of neutral and anionic vanadium trimer monoxides is presented. The calculations were of all-electron type employing a newly developed basis set for the vanadium atom. Different isomers of V[sub 3]O and V[sub 3]O[sup -] were studied in order to determine the ground state structures. For both systems a planar C[sub 2v] structure with an edge-bonded oxygen atom was found as the ground state. Equilibrium structure parameters of ground states as well as low-lying excited states, harmonic frequencies, the adiabatic electron affinity, and Kohn-Sham orbital diagrams are reported. The experimental negative ion photoelectron spectra of V[sub 3]O was simulated by calculating multidimensional Franck-Condon factors, using the geometries and harmonic frequencies of the calculated ground states of V[sub 3]O[sup -] and V[sub 3]O. The good agreement between the experimental and the theoretical spectra allows the determination of the ground state structure of V[sub 3]O and V[sub 3]O[sup -]. This represents the first work in which a simulation of a vibrationally resolved negative ion photoelectron spectra of a transition metal oxide is presented. [ABSTRACT FROM AUTHOR]

The optimized effective potential (OEP) is (within a certain linear response approximation) the exact exchange-correlation potential of density-functional theory (DFT). In the program DEMON-DYNARHO, we have implemented the OEP at the exchange-only level without the evaluation of four-center integrals using resolution-of-the-identity techniques. We point out that great care must be taken in treating the asymptotic behavior of the OEP in finite basis set methods. Our results are compared with previous work using OEP-like potentials. Our OEP orbital energies are compared with experimental ionization potentials, Hartree-Fock (HF) orbital energies, and with orbital energies from the local density approximation (LDA) potential, with and without asymptotic correction (AC). We find that OEP orbital energies are a much better approximation to experimental ionization potentials than are HF orbital energies. LDA orbital energies also correlate well with OEP orbital energies, except for a molecule-dependent rigid shift, due to the well-known fact that the LDA potential falls off too rapidly at large distances. The resultant underbinding is largely corrected by the AC-LDA potential whose orbital energies correlate well with OEP orbital energies, with typical differences on the order of 0.5 eV. However larger differences between AC-LDA and OEP orbital energies are also observed, particularly for unoccupied orbitals and the reason for this is discussed. As an illustration of how the OEP might be used in practical calculations, we give an example from time-dependent DFT where use of the OEP instead of the AC-LDA potential leads to significant improvement in a key σ→π* excitation energy of ethylene. [ABSTRACT FROM AUTHOR]

Finding the optimum material with improved properties for a given application is challenging because data acquisition in materials science and chemistry is time consuming and expensive. Therefore, dealing with small datasets is a reality in chemistry, whether the data are obtained from synthesis or computational experiments. In this work, we propose a new artificial intelligence method based on active learning (AL) to guide new experiments with as little data as possible, for optimum experimental design. The AL method is applied to ABO3 perovskites, where a descriptor based on atomic properties was developed. Several regressor algorithms were employed: artificial neural network, Gaussian process, and support vector regressor. The developed AL method was applied in the experimental design of two important materials: non-stoichiometric perovskites (Ba(1−x)AxTi(1−y)ByO3) due to substituting ionic sites with different concentrations and elements (A = Ca, Sr, Cd; B = Zr, Sn, Hf), aiming at the maximization of the energy storage density, and stoichiometric ABO3 perovskites where different elements are changed in the A and B sites for the minimization of the formation energy. AL for experimental design is implemented in the machine learning agent for chemistry and design (MLChem4D) software, which has the potential to be applied in inorganic and organic synthesis (e.g., search for the optimum concentrations, catalysts, reactants, temperatures, and pH to improve the yield) and materials science (e.g., search the periodic table for the proper elements and their concentrations to improve the materials properties). The latter marks the first MLChem4D application for the design of perovskites. [ABSTRACT FROM AUTHOR]

Examines the results of the density functional study of the mononitrosyl of first-row transition-metal atoms. Geometries and frequencies of the complexes in different states; Bent geometry found for the systems with higher multiplicities; Description of binding mechanism described through an analysis of the molecular orbitals.

We report the implementation of time-dependent density-functional response theory (TD-DFRT) for molecules using the time-dependent local density approximation (TDLDA). This adds exchange and correlation response terms to our previous work which used the density-functional theory (DFT) random phase approximation (RPA) [M. E. Casida, C. Jamorski, F. Bohr, J. Guan, and D. R. Salahub, in Theoretical and Computational Modeling of NLO and Electronic Materials, edited by S. P. Karna and A. T. Yeates (ACS, Washington, D.C., in press)], and provides the first practical, molecular DFT code capable of treating frequency-dependent response properties and electronic excitation spectra based on a formally rigorous approach. The essentials of the method are described, and results for the dynamic mean dipole polarizability and the first eight excitation energies of N2 are found to be in good agreement with experiment and with results from other ab initio methods. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Molecular structures, harmonic vibrational frequencies, dissociation energies, and barriers to internal rotation have been determined using a Gaussian density functional method. Both local and nonlocal levels of theory have been employed. The calculated equilibrium geometry and harmonic vibrational frequencies for BH3NH3 compare well with those determined by microwave and infrared experiments. The rotational barrier is found to be 2.09 kcal/mol in very good agreement with the experimental data. The calculated properties for ammonia-alane (AlH3NH3) are compared with those obtained previously from high level correlated methods. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Density-functional calculations using gradient-corrected functionals have been performed for aluminum clusters up to Al4 (neutral and cationic) using the linear-combination-of-Gaussian- type-orbitals approach. Two different types of calculations (all electron and model core potential) were performed to obtain full geometry and spin optimization. A comparison between both methods and with other experimental and theoretical values has been done. Bond distances, equilibrium geometries, atomization energies, ionization potentials, and harmonic frequencies are in good agreement between them. The nature of the ground state of Al2 was examined in detail. This work shows that all electron and model core potential calculations generate the same results. © 1994 American Institute of Physics. [ABSTRACT FROM AUTHOR]

LCGTO-MP-LSD results are reported for the spectroscopic constants and electronic structure of the diatomic molecules Si2, Ge2, Sn2, SiGe, SiSn, and GeSn in their low-lying electronic states. For the homonuclear molecules we found that the ground state is 3Σ-g with the most important lower-lying excited states being 3Πu, 1Πu, and 1Σ+g, respectively. Our results are in good agreement with the available experimental data and also in qualitative agreement with other theoretical studies. We present here the first theoretical study on the heteronuclear molecules, for which experimental data are not available. We found the 3Σ- state to be the lowest, followed by 3Π and 1Σ+ states. Model potentials (MP) are reported for the Si, Ge, and Sn atoms. The reliable results for molecules complement those for the atoms and show that the LSD model potentials presented here allow for an accurate description of chemical bonding and spectroscopic properties in the title molecules. [ABSTRACT FROM AUTHOR]

The model potential (MP) method originally proposed by Huzinaga and Bonifacic is extended to spin-polarized local-spin-density calculations, including scalar relativistic effects. The theoretical justification of the MP method in this case is studied and the method of optimization of the basis functions and MP parameters is given. The validity of the frozen core approximation is studied for Mo2, Ru2, and Ag2. It is found that the MP can very accurately reproduce all-electron (AE) results if the 4p electrons of Ag and the 3d electrons of Mo are also considered as valence electrons, although inclusion of these electrons in the core still yields a useful level of accuracy. It is shown that the present MP results are not sensitive to basis set superposition errors (BSSE). Upon inclusion of the scalar relativistic effects the calculated bond length and vibrational frequency of Ag2 are in near perfect agreement with experiment, while the dissociation energy is overestimated by 23% with the ‘‘best’’ local potential (VWN). MP calculations have also been performed for AgH, AgO, and AgF. The same level of agreement with experiment as for Ag2 was found, with the exception of the bond length for AgO. Our calculated bond length is 0.05 Å shorter than the presently accepted experimental value. Since some uncertainty is associated with the spectroscopic assignments for AgO we believe an experimental reexamination would be in order. [ABSTRACT FROM AUTHOR]

Explores density functional theory (DFT) for charge-transfer complexes. Generalized gradient approximation; Hybrid functionals with Hartree-Fock exchange; Consideration of two hybrid approaches; Underestimation of intermolecular distances for hydrogen bonds.

Genetic algorithms (GAs) are stochastic global search methods inspired by biological evolution. They have been used extensively in chemistry and materials science coupled with theoretical methods, ranging from force‐fields to high‐throughput first‐principles methods. The methodology allows an accurate and automated structural determination for molecules, atomic clusters, nanoparticles, and solid surfaces, fundamental to understanding chemical processes in catalysis and environmental sciences, for instance. In this work, we propose a new genetic algorithm software, GAMaterial, implemented in Python3.x, that performs global searches to elucidate the structures of atomic clusters, doped clusters or materials and atomic clusters on surfaces. For all these applications, it is possible to accelerate the GA search by using machine learning (ML), the ML@GA method, to build subsequent populations. Results for ML@GA applied for the dopant distributions in atomic clusters are presented. The GAMaterial software was applied for the automatic structural search for the Ti6O12 cluster, doping Al in Si11 (4Al@Si11) and Na10 supported on graphene (Na10@graphene), where DFTB calculations were used to sample the complex search surfaces with reasonably low computational cost. Finally, the global search by GA of the Mo8C4 cluster was considered, where DFT calculations were made with the deMon2k code, which is interfaced with GAMaterial. [ABSTRACT FROM AUTHOR]

The crystal structure, the electronic structure and the mechanical properties were investigated for (CrB 2 ) n CrAl with n = 1, 2, 3 by using the all-electron projector augmented wave method with the Perdew-Burke Ernzerhof functional. The calculated bulk moduli for Cr 2 AlB 2 , Cr 3 AlB 4 and Cr 4 AlB 6 were 202, 222 and 234 GPa, respectively, and the Young moduli were estimated to be 397, 412 and 434 GPa, respectively. All three materials were identified as stiff and hard materials; however, the density of states and the projected density of states analysis predicted a metallic behavior for all investigated materials. The partially filled d-orbitals of Cr atoms have an important role in attributing metallic behavior to these materials. The hardness of these materials was related to the presence of quite strong B B covalent bonds and the metallic characteristic arises from Cr Cr interactions. The chemical interpretation of the physical properties was made with the electron localization function and the investigation of the topology of the electron densities was provided, based on the quantum theory of atoms in molecules. Surface properties were explored for slab models, arbitrarily chosen to be along the a-axis. The metallic behavior of the compounds (CrB 2 ) n CrAl continues in the surface model. Using the electron localization function and Bader's charge analysis, a small increase of the number of electronic carriers was observed, due to the localization of some Al Al bonds in the slab models. [ABSTRACT FROM AUTHOR]

Heterogeneous reactions at the surfaces of mineral dusts represent a key process in the formation of atmospheric aerosols. To quantify the rate of aerosol formation in climate modeling as well as combat hazardous aerosols, a deep understanding of the mechanisms of these reactions is essential. In the present work, density functional theory calculations, including a Hubbard-like +U correction, were employed to elucidate the reaction between SO2 and the hematite(0001) surface. Three reaction conditions are considered: dry, wet, and aerobic. In the absence of water and oxygen, adsorption energies of SO2 on the clean Fe–O3–Fe-termination were found to be about −0.8 to −1.0 eV and resulted in the formation of an adsorbed SO3-like species. The addition of water leads to surface hydroxylation and has little effect on promoting the SO2 adsorption. Under such circumstances, an HSO3-like species was formed with a smaller adsorption energy of about −0.5 eV. By contrast, the presence of molecular oxygen enhances the SO2 adsorption significantly as the two species combine to form sulfate SO42−, with adsorption energies of −1.31 to −1.64 eV. The calculated vibrational frequencies of the adsorbate species provide insight into the surface bonding and a useful spectral fingerprinting for experimental measurements. These results elucidate the atomistic mechanism of the reaction between SO2 and hematite and highlight the important role of atmospheric O2 in the formation of sulfates. [ABSTRACT FROM AUTHOR]

Adsorbate interactions with substrates (e.g. surfaces and nanoparticles) are fundamental for several technologies, such as functional materials, supramolecular chemistry, and solvent interactions. However, modeling these kinds of systems in silico, such as finding the optimum adsorption geometry and energy, is challenging, due to the huge number of possibilities of assembling the adsorbate on the surface. In the current work, we have developed an artificial intelligence (AI) approach based on an active learning (AL) method for adsorption optimization on the surface of materials. AL uses machine learning (ML) regression algorithms and their uncertainties to make a decision (based on a policy) for the next unexplored structures to be computed, increasing, though, the probability of finding the global minimum with a small number of calculations. The methodology allows an accurate and automated structural elucidation of the adsorbate on the surface, based on the minimization of the total electronic energy. The new AL method for adsorption optimization was developed and implemented in the quantum machine learning software/agent for material design and discovery (QMLMaterial) program and was applied for C60@TiO2 anatase (101). It marks another software extension with a new feature in addition to the automatic structural elucidation of defects in materials and of nanoparticles as well. SCC-DFTB calculations were used to build the complex search surfaces with a reasonably low computational cost. An artificial neural network (NN) was employed in the AL framework evaluated together with two uncertainty quantification methods: K-fold cross-validation and non-parametric bootstrap (BS) resampling. Also, two different acquisition functions for decision-making were used: expected improvement (EI) and the lower confidence bound (LCB). [ABSTRACT FROM AUTHOR]

Born-Oppenheimer molecular dynamics (BOMD) in combination with density functional theory, augmented with a damped empirical dispersion term, has been used to study the behavior of dilauroyl phosphatidylcholine (DLPC) isomers with temperature. In contrast to dimyristoyl phosphatidylcholine (DMPC), the BOMD results show the presence of various conformations at different temperatures. The molecular order-disorder process, quantified by the distance-fluctuation criterion as a function of temperature, is characterized by two transitions. This is in line with the known two-phase transitions of DLPC bilayers, involving trans to gauche conformational changes in the alkane chains. The different temperature dependence of the DLPC and DMPC molecules suggests that the experimentally observed unusual dynamics of DLPC bilayers compared to that of longer chain lipids is governed to a large extent by the intramolecular dynamics. A first-principles methodology applied at the molecular level can thus be an appropriate tool for microscopic analysis of the order-disorder transitions, which are related to the molecular structural transformations within large assemblies. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

We present a new local meta-GGA exchange-correlation density functional by combining the TPSS meta-GGA exchange and the τ1 meta-GGA correlation functionals. The TPSS meta-GGA exchange-correlation and the τ1 meta-GGA correlation functionals have been implemented in the deMon code. The parameters in the τ1 meta-GGA correlation model are reoptimized in a synchronized way to match the original TPSS meta-GGA exchange counterpart. This reparametrized meta-GGA functional is referred to as “TPSSτ3”. The TPSSτ3 and TPSSτ1 meta-GGAs are validated using a test set that consists of covalent molecules, hydrogen-bonded complexes, and van der Waals interactions. The calculated results from TPSSτ1 and TPSSτ3 are analyzed and compared with reliable experimental data and theoretical data, as well as with those from Bmτ1 and TPSS calculations. The τ1 correlation model describes the aromatic compounds better than TPSS. TPSSτ3 yields satisfactory results for the covalent molecules, the hydrogen-bonded complexes, and the van der Waals complexes in the test set compared with TPSS, Bmτ1 and TPSSτ1. [ABSTRACT FROM AUTHOR]

Active learning (AL) has been successfully applied in materials science for the global optimization of clusters and defects in materials. Many important chemistry problems require the structural elucidation of molecules as a first step to the mechanistic elucidation of complex heterogeneous catalysis phenomena. Theoretical methods coupled with global optimization algorithms are successfully used for this purpose. However, it is challenging to find the global minimum structure together with the proper electronic spin multiplicity. In this work, we present an AL implementation for global optimization of atomic clusters where the spin multiplicity is considered in the search loop (SM@AL). The method was implemented in the QMLMaterial software, interfaced with the deMon2k program to perform local structure optimizations. In this work, we present applications of SM@AL for the global optimization, in terms of molecular structure and electronic spin of 3Al@Si11, where Si11 is doped by 3 Al, and Mo4C2 with spin multiplicities 2, 4 and 6 and 1, 3, 5, 7, 9 and 11, respectively. [ABSTRACT FROM AUTHOR]

We examine the hyperfine structure of the paramagnetic active sites in two oxidized blue copper proteins (azurin and stellacyanin), using a combined quantum mechanics/molecular mechanics (QM/MM) approach. In our implementation, the QM region (treated with density functional theory (DFT)) is truncated by one-electron carbon capping potentials. The effects from surroundings are modeled by including the electric field, due to the MM domain, in the DFT Hamiltonian. The hyperfine structure of the active sites is well described by a small QM region, embedded in MM partial charges. Because of the simplicity of the implementation, the present approach enables us to investigate the hyperfine parameters of large, realistic models of biological active sites. [Copyright &y& Elsevier]

Generally, the chemistry of VPO-based catalysts is controlled by the properties of surface defects. Therefore, the effect of isolated vacancies on the reactivity of vanadyl pyrophosphate, the main component of VPO catalysts, seems to be a natural starting point for a theoretical analysis to understand better the real material. Here, we report density functional calculations of the electronic structure for different clusters modeling the defective (VO)2P2O7(1 0 0) surface, where a neutral oxygen monovacancy is incorporated. This study is complementary to our previous investigations on the energetics and the Lo¨wdin charge analysis of the same type of defects. The electronic structure of the defective (1 0 0) surface is discussed by means of the total and atomic (partial) density of states to show modifications of the electronic states caused by the differently located vacancies. A theoretical estimation of the density of states reveals evidence for the presence of color center-induced levels for high-coordinated vacant sites and their absence in the case of low-coordinated vacancies. It is shown that only in the case of high-coordinated oxygen vacancies the band gap is reduced relative to the clean surface. Specific features of the density of states projected onto different cationic and anionic surface sites agree with experimental evidence on their implications for catalytic performance. [Copyright &y& Elsevier]

Sum-over-states density functional perturbation theory (SOS-DFPT) (Malkin, V. G.; Malkina, O. L.; Casida, M. E.; Salahub, D. R. J Am Chem Soc 1994, 116, 5898) has been successful as a method for calculating nuclear magnetic resonance (NMR) chemical shifts. The key to this success is the introduction of an ad hoc correction to the excitation energies represented by simple orbital energy differences in uncoupled density functional theory. It has been suggested (Jamorski, C.; Casida, M. E.; Salahub, D. R. J Chem Phys 1996, 104, 5134) that the good performance of this methodology could be partly explained by the resemblance of the corrected excitation energy to the orbital energy difference given by time-dependent density functional theory (TDDFT). In fact, according to exact (wave function) time-dependent perturbation theory, both magnetic and electric perturbations may be described using essentially the same simple SOS expression. However in adiabatic TDDFT, with no explicit relativistic or current density functional dependence, the functional is approximate and so the magnetic and electric SOS expressions are different. Because TDDFT (neglecting relativistic and current density functional dependence) is formally exact for electric perturbations but not magnetic perturbations and because the two SOS expressions should have the same form, we propose that the SOS expression for electric perturbations should also be used for magnetic perturbations. We then go on to realize our theory by deriving a “Loc.3” approximation that is explicitly designed by applying the electric field SOS expression to magnetic fields within the two-level model and Tamm–Dancoff approximation. Test results for 13 small organic and inorganic molecules show that the Loc.3 approximation performs at least as well as the “Loc.1” and “Loc.2” approximations of SOS-DFPT. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003 [ABSTRACT FROM AUTHOR]

In catalysis, an accurate structural elucidation of molecules, atomic clusters, nanoparticles and solid surfaces is required to understand chemical processes. Therefore, an efficient and automatic structure determination for these systems is of great benefit since it requires a global search within huge chemical spaces. In this work, we propose a new active learning (AL) method intended for atomic clusters that uses different supervised machine learning techniques and their uncertainties to decide the promising non-observed (virtual) structures to be evaluated from quantum calculations. The method was developed for structural elucidation of (I) clusters where all atomic coordinates are allowed to change in a continuous chemical space and (II) doped ones where the atoms exchange in a sufficiently rigid structure, thus, a discrete search space where all cluster descriptors are known. Particularly for case I, a genetic algorithm operator was used to create the unknown virtual structures (and then their descriptors) from the observed ones to improve the performance of the AL search. The proposed AL was applied to the global optimization of heteronuclear (Al4Si7 and 4Al@Si11) and homonuclear (Na20) clusters using self-consistent charge density-functional tight-binding (SCC-DFTB), where a new repulsion parameter was developed to reproduce isomers evaluated from high-level calculations. The performance of the Gaussian process and artificial neural network algorithms was evaluated together with several uncertainty quantification methods: from Gaussian process, K-fold cross-validation and nonparametric bootstrap (BS) resampling. The efficiency of the AL was compared to conventional global optimization methods, such as random search and a genetic algorithm. The results show that the AL can find efficiently the global minimum of atomic clusters. [ABSTRACT FROM AUTHOR]

The study of materials in the nanoscale regime has important applications for catalytic reactions, the energy industry and medicine. We performed exploratory density functional theory calculations for molybdenum disulphide (MoS2) and calcium carbonate (CaCO3) nanoparticles (NPs), the former being developed as a hydrogenation and coke-prevention catalyst and the latter representing the catalytic support in some reservoirs. Utilizing Born–Oppenheimer Molecular Dynamics with reduced masses as a global optimization method, we found Mo8S16 and Mo16S32 NPs with lower-lying energies than those of locally optimized crystal geometries. Our results suggest that MoS2 NPs prefer a tetragonal lattice arrangement which is in agreement with previous studies of smaller MoS2 NPs. It remains to be seen how prenucleation MoS2 clusters of the hexagonal phase are formed. The CaCO3 NPs showed small energy differences between vastly different conformations. Therefore, in order to capture only their supporting effects in reservoirs, one should consider keeping a substantial part of the models fixed. [ABSTRACT FROM AUTHOR]

van Wüllen has correctly commented on the lack of gauge invariance of our sum-over-states density functional perturbation theory (SOS-DFPT) method for NMR chemical shifts. It is shown that, for practical basis sets, the improvement of the SOS-DFPT method over an uncoupled approach is greater than the difference in gauge dependence between these two methods. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The Roothaan-Hartree-Fock (HF) method has been implemented in deMon-DynaRho within the resolution-of-the-identity (RI) auxiliary-function approximation. While previous studies have focused primarily upon the effect of the RI approximation on total energies, very little information has been available regarding the effect of the RI approximation on orbital energies, even though orbital energies play a central role in many theories of ionization and excitation. We fill this gap by testing the accuracy of the RI approximation against non-RI-HF calculations using the same basis sets, for the occupied orbital energies and an equal number of unoccupied orbital energies of five small molecules, namely CO, N[sub 2], CH[sub 2]O, C[sub 2]H[sub 4], and pyridine (in total 102 orbitals). These molecules have well-characterized excited states and so are commonly used to test and validate molecular excitation spectra computations. Of the deMon auxiliary basis sets tested, the best results are obtained with the (44) auxiliary basis sets, yielding orbital energies to within 0.05 eV, which is adequate for analyzing typical low resolution polyatomic molecule ionization and excitation spectra. Interestingly, we find that the error in orbital energies due to the RI approximation does not seem to increase with the number of electrons. The absolute RI error in the orbital energies is also roughly related to their absolute magnitude, being larger for the core orbitals where the magnitude of orbital energy is large and smallest where the molecular orbital energy is smallest. Two further approximations were also considered, namely uniterated ("zero-order") and single-iteration ("first-order") calculations of orbital energies beginning with a local density approximation initial guess. We find that zero- and first-order orbital energies are very similar for occupied but not for unoccupied orbitals, and that the first-order orbital energies are fairly close to the corresponding fully c... [ABSTRACT FROM AUTHOR]