Density Functional Theory Description Research Articles

Hybrid density functional theory description of N- and C-doping of NiO

The large intrinsic bandgap of NiO hinders its potential application as a photocatalyst under visible-light irradiation. In this study, we have performed first-principles screened exchange hybrid density functional theory with the HSE06 functional calculations of N- and C-doped NiO to investigate the effect of doping on the electronic structure of NiO. C-doping at an oxygen site induces gap states due to the dopant, the positions of which suggest that the top of the valence band is made up primarily of C 2p-derived states with some Ni 3d contributions, and the lowest-energy empty state is in the middle of the gap. This leads to an effective bandgap of 1.7 eV, which is of potential interest for photocatalytic applications. N-doping induces comparatively little dopant-Ni 3d interactions, but results in similar positions of dopant-induced states, i.e., the top of the valence band is made up of dopant 2p states and the lowest unoccupied state is the empty gap state derived from the dopant, leading to bandgap narrowing. With the hybrid density functional theory (DFT) results available, we discuss issues with the DFT corrected for on-site Coulomb description of these systems.

DFT and MM description of the structure and magnetic properties of manganese complexes with X-phenylcyanamido bridging ligand

Magnetic properties of the complexes [Mn(3-Clpcyd)(H2O)-(phen)2]+, [{Mn(3-Fpcyd)(MeOH)(phen)}2(μ-3-Fpcyd)2], [{Mn(3-Fpcyd)(EtOH)(phen)}2(μ-3-Fpcyd)2], [{Mn(3-Clpcyd)(MeOH)(phen)}2(μ-3-Clpcyd)2], and [{Mn(4-Clpcyd)(EtOH)(phen)}2(μ-4-Clpcyd)2] (where Xpcyd = halogeno-phenylcyanamido; phen = 1,10-phenanthroline) have been explored by means of density functional theory (DFT). Exchange coupling constants were calculated from the energy differences between the high-spin and broken-symmetry states. Very good agreement between theoretical and experimental data was achieved. The g-tensor calculations were performed employing the coupled perturbed Kohn–Sham equations. Molecular mechanics calculations have been performed to elucidate structural features in the five complexes. Finally, the reliability of the molecular mechanics results was confirmed by comparing the magnetic couplings calculated on optimized structures with experimental data.

Coordinate space translation technique for simulation of electronic process in the ion–atom collision

Recently we developed a theoretical model of ion-atom collisions, which was made on the basis of a time-dependent density functional theory description of the electron dynamics and a classical treatment of the heavy particle motion. Taking advantage of the real-space grid method, we introduce a "coordinate space translation" technique to allow one to focus on a certain space of interest such as the region around the projectile or the target. Benchmark calculations are given for collisions between proton and oxygen over a wide range of impact energy. To extract the probability of charge transfer, the formulation of Lüdde and Dreizler [J. Phys. B 16, 3973 (1983)] has been generalized to ensemble-averaging application in the particular case of O((3)P). Charge transfer total cross sections are calculated, showing fairly good agreements between experimental data and present theoretical results.

A molecular dynamics study of 1,1-diamino-2,2-dinitroethylene (FOX-7) crystal using a symmetry adapted perturbation theory-based intermolecular force field

A dimer potential energy function for 1,1-diamino-2,2-dinitroethylene (FOX-7) has been developed using symmetry adapted perturbation theory based on a Kohn-Sham density functional theory description of the monomers [SAPT(DFT)]. Interaction energies of 1008 dimer configurations were computed in an augmented double zeta basis set and fitted to an atom-atom intermolecular potential energy function of Coulomb plus Buckingham exp-6 form. The potential was used in isothermal-isostress molecular dynamics simulations to study the structure and thermal/pressure response of FOX-7 crystal. The simulated structure is in very good agreement with experiment and the computed thermal/pressure response of the crystal shows significant anisotropy with respect to crystallographic direction, in-line with experimental observations. It is concluded that SAPT(DFT) is an excellent method for development of intermolecular potentials for energetic molecular crystals.

Influence of exchange correlation on the symmetry and properties of siderite according to density-functional theory

Density-functional theory (DFT) without spin-orbit coupling (SOC), as implemented in CASTEP, yields structural, energetic, and elastic properties of siderite $({\text{FeCO}}_{3})$ in good agreement with available data from the literature. The electronic ground state is however found ferromagnetic (FM) with a nonzero density of states at the Fermi level, whereas real siderite is antiferromagnetic (AFM) and insulating. We show in both cases how the paradox can be removed. Concerning the metallic/insulating character, a symmetry analysis of the electronic structure performed with the help of ISOTROPY shows that the absence of gap is due to an essential degeneracy of monoelectronic wave functions in the experimental $R\overline{3}c$ symmetry. The small dispersion of individual bands establishes a clear difference with the case of a real metal. Complemented by $\text{DFT}+\text{SOC}$ computations performed using ABINIT this shows the consistency of the DFT description with crystal-field theory data taken from the literature. Thus for DFT the electronic structure of siderite is characterized by correlation, but of exchange origin, as opposed to electrostatic origin. The AFM nature of the ground state is also restored by SOC. Without SOC the total energies of the FM and AFM states are very close. After introducing some modifications in a classical model of superexchange we obtain a satisfactory interpretation of our DFT results in terms of spin polarization in the iron-carbonate bonds, spin-coupling mechanisms between neighboring iron ions and finally of the observed FM over AFM stability. Hence, siderite emerges as an original model system among transition-metal compounds for the application of DFT to open-shell electronic structures.

Hybrid density functional theory description of oxygen vacancies in the CeO 2 (1 1 0) and (1 0 0) surfaces

In ceria the formation of oxygen vacancies plays a key role. Density functional theory, corrected for on-site Coulomb interactions (DFT + U) provides a reasonable description of oxygen vacancies, but has issues with the U dependence. We present a hybrid HSE06 study of oxygen vacancies in the (1 1 0) and (1 0 0) ceria surfaces. We find (i) the oxygen vacancy formation energy is larger with hybrid DFT compared with DFT + U, (ii) localised Ce 3+ ions form and (iii) the position of the Ce 3+ gap state is in good agreement with experiment. Our results provide important information for assessing the reliability of the DFT + U approach.

Comprehensive Solid-State NMR Characterization of Electronic Structure in Ditechnetium Heptoxide

A relativistic density functional theory description of the electronic structure of Tc(2)O(7) has been evaluated by comparison with solid-state (99)Tc and (17)O NMR spectroscopic data (the former isotope is a weak β emitter). Every site in the molecule can be populated by a nucleus with favorable NMR characteristics, providing the rare opportunity to obtain a comprehensive set of chemical shift and electric field gradient tensors for a small molecular transition-metal oxide. NMR parameters were computed for the central molecule of a (Tc(2)O(7))(17) cluster using standard ZORA-optimized all-electron QZ4P basis sets for the central molecule and DZ basis sets for the surrounding atoms. The magnitudes of the predicted tensor principal values appear to be uniformly larger than those observed experimentally, but the discrepancies were within the accuracy of the approximation methods used. The convergence of the calculated and measured NMR data suggests that the theoretical analysis has validity for the quantitative understanding of structural, magnetic, and chemical properties of Tc(VII) oxides in condensed phases.

Improving the density functional theory description of water with self-consistent polarization

We applied the self-consistent polarization density functional theory (SCP-DFT) to water. SCP-DFT requires only minimal parametrization, self-consistently includes the dispersion interaction neglected by standard DFT functionals, and has a cost similar to standard DFT despite its improved performance. Compared to the DFT functionals BLYP and BLYP-D (where the latter contains a simple dispersion correction), SCP-DFT yields interaction energies per molecule and harmonic frequencies of clusters in better agreement with experiment, with errors in the former of only a few tenths of a kcal/mol. BLYP and BLYP-D underbind and overbind the clusters, respectively, by up to about 1 kcal/mol. For liquid water, both BLYP and SCP-DFT predict radial distribution functions that are similar and overstructured compared to experiment. However, SCP-DFT improves over BLYP in predicting the experimental enthalpy of vaporization. A decomposition of the dimer interaction energy attempts to rationalize the performance of SCP-DFT. The SCP-DFT approach holds promise as an efficient and accurate method for describing large hydrogen-bonded systems, and has the potential to model complex systems with minimal parametrization.

Combining ab initio quantum mechanics with a dipole-field model to describe acid dissociation reactions in water: First-principles free energy and entropy calculations

We introduce a novel approach to compute dissociation free energy and entropy values in simulations that employ a density functional theory description of the acidic moiety and of the solvent. The approach consists of utilizing an alchemical transformation of a weak acid A-COOH into the strong acid B-COOH, which makes it practical to employ alchemical free energy perturbation methods in the context of ab initio molecular dynamics simulations. The present alchemical transformation circumvents the need to tackle changes in the total number of electrons and atoms by replacing the chemical residue responsible for the change in acidity with an easily tunable external effective potential. Our investigation demonstrates that (1) a simple but effective class of external potentials that control acidity changes in the acetic/trifluoroacetic acid series can be achieved by replacing the methyl and trifluoromethyl substituents by screened dipoles. Using this dipole-field/quantum-mechanics (DF/QM) approach one can predict gas-phase geometries, proton dissociation energies, total dipole moments, and water binding energies in good agreement with full-QM values. (2) The resulting alchemical perturbation calculations are stable and well converged and allow one to compute absolute pK(a) values whose accuracy is limited primarily by the exchange-correlation functional employed: H-COOH=2.5+/-0.6 (full-QM calculation), 3.7 (exp); F(3)C-COOH=0.4+/-0.6 (DF/QM calculation), 0.5 (exp); H(3)C-COOH=3.1+/-0.7 (DF/QM calculation), 4.7 (exp); 3) Our DF/QM model predicts that the difference in acidity between H-COOH and H(3)C-COOH is dominated by solvent entropy effects, in excellent agreement with experimental observations. The calculated difference between the dissociation energies of these acids is DeltaDelta(d)U=0.0+/-0.26 kcal/mol while the experimental value is 0.0+/-0.1 kcal/mol.

Interactions of graphene sheets deduced from properties of polycyclic aromatic hydrocarbons

Intermolecular interactions of coronene dimer were studied with symmetry-adapted perturbation theory based on the density functional theory description of the monomers [SAPT(DFT)]. The most stable stacked structure was found to have the interaction energy of -17.45 kcal/mol, slightly lower than the structure analogous to graphite (-17.36 kcal/mol). The latter energy was extrapolated to the interaction energy of two graphene sheets. The effects of interactions of multiple layers were also estimated leading to the exfoliation energy of graphite equal to 45.3 meV per carbon atom. The SAPT(DFT)-based decomposition into physical quantities of the interaction energies shows the dominant effect of the dispersion interactions with a weaker electrostatic contribution due to penetration effects. The extrapolated physical picture of the graphene-graphene interaction is very similar to that of smaller stacked polycyclic aromatic hydrocarbons.

Density functional theory description of the mechanism of ferromagnetism in nitrogen-doped SnO 2

Based on first-principles calculations, we have studied the occurrence of spin polarization in the magnetic metal oxide SnO 2 doped with nonmagnetic nitrogen (N) impurities. It was found that the local magnetic moments are localized mainly on the N dopant, causing a total moment of 0.95 μ B per cell. The long-range magnetic coupling of N-doped SnO 2 may be attributed to a p – p coupling interaction between the N impurity and host valence states.

Role of exchange in density-functional theory for weakly interacting systems: Quantum Monte Carlo analysis of electron density and interaction energy

We analyze the density-functional theory (DFT) description of weak interactions by employing diffusion and reptation quantum Monte Carlo (QMC) calculations, for a set of benzene-molecule complexes. While the binding energies depend significantly on the exchange-correlation approximation employed for DFT calculations, QMC calculations show that the electron density is accurately described within DFT, including the quantitative features in the reduced density gradient. We elucidate how the enhancement of the exchange-energy density at a large reduced density gradient plays a critical role in obtaining accurate DFT description of weakly interacting systems.

Quantum interference effects in electron transport through nitrobenzene with pyridil anchor groups

We present density functional theory (DFT) based non-equilibrium Green's function (NEGF) calculations for the conductance through a nitrobenzene molecule, which is anchored by pyridil-groups to Au electrodes. This work is building up on earlier theoretical studies where quantum interference effects (QIE) have been identified both in qualitative tight binding and in DFT descriptions for the same molecule with different chemical connections to the leads. The novelty in the current contribution is two-fold: i) The pyridil-anchors guarantee for the conductance to be determined by rather narrow peaks situated closely to the Fermi energy which is relevant because it might maximize the impact of quantum interferences on the I/V behaviour. In a scan of eight different junction setups, where the connection sites of aromatic rings, their torsion angle with respect to each other and the surface structure have been varied, QIE was found to dominate the conductance for only one planar geometry. For finite torsion angles between aromatic rings the effect moves to higher energies and would therefore only be accessible for experimental observation in a gated junction. ii) A detailed comparison between simple topological models and DFT results for the investigated systems aims at assessing the usefulness of such models as analysis tools for a better understanding of the physics of QIE and its structure dependence.

Accurate DFT Descriptions for Weak Interactions of Molecules Containing Sulfur.

Dispersion corrected atom centered potentials (DCACPs) have been shown to significantly improve the density functional theory (DFT) description of weak interactions. In this work, we have calibrated a DCACP for sulfur in combination with the widely used Generalized Gradient Approximation (GGA) BLYP, thereby augmenting the existing library of DCACPs for the first- and second-row elements H, C, N, O, and rare gases. Three weakly bound complexes as well as elemental (orthorhombic) sulfur are used as test cases to evaluate the transferability of the DCACP to different chemical environments. It is found that the sulfur DCACP systematically improves the agreement of DFT-calculated weak interactions with respect to MP2 and CCSD(T) level results.

Potential energy curves and electronic structure of 3d transition metal hydrides and their cations

We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to Cu with density functional theory (DFT) methods. The performance of two exchange-correlation functionals, Boese-Martin for kinetics (BMK) and Tao-Perdew-Staroverov-Scuseria (TPSS), in predicting bond lengths and energetics, electronic structures, dipole moments, and ionization potentials is evaluated in comparison with available experimental data. To ensure a unique self-consistent field (SCF) solution, we use stability analysis, Fermi smearing, and continuity analysis of the potential energy curves. Broken-symmetry approach was adapted in order to get the qualitatively correct description of the bond dissociation. We found that on average BMK predicted values of dissociation energies and ionization potentials are closer to experiment than those obtained with high level wave function theory methods. This agreement deteriorates quickly when the fraction of the Hartree-Fock exchange in DFT functional is decreased. Natural bond orbital (NBO) population analysis was used to describe the details of chemical bonding in the systems studied. The multireference character in the wave function description of the hydrides is reproduced in broken-symmetry DFT description, as evidenced by NBO analysis. We also propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states (pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs). The high spin states are build with canonical natural orbitals and do not require SCF convergence.

QMC Assessments of Weak-interaction Described by DFT within various XC approximations / Effects of Carbon Nanotube Oxidation on Molecular Interactions

ABSTRACTThis paper first presents the fixed-node diffusion and reptation quantum Monte Carlo (QMC) assessment of density functional theory (DFT) description of weak molecular interactions within several exchange-correlation (XC) approximations. The case of Benzene-molecule complex was studied with a number of small molecules. We found that the binding energy for the set of complexes depend significantly on XC approximation employed although its trend appears rather consistent. Analysis of the reduced density gradient revealed that the binding energy trend among different XC approximation is highly correlated with the exchange enhancement factor behaviors at large reduced density gradients. Our findings point to the importance of accurate exchange energy functional in describing the weak interactions, in addition to the more obvious correlation part in DFT description.We then present DFT investigation on molecular interaction of NO3 toward a single-wall carbon nanotube (CNT). We aim to explain the atomistic processes that are responsible for the recently observed CNT conductance changes in the redox process. We found that molecular physisorption and chemisorption to be energetically stable states, and the chemisorbed configuration becomes less endothermic with an increased oxidation state of the CNT. Our results also show that the dissociative incorporation of the molecule can become highly favored energetically in the process. This chemical state may play an important role of the occasionally-observed CNT conductance irreversibility in the experiment.

Current–voltage curves for molecular junctions: the issue of the basis set for the metal contacts

We present current–voltage (I–V) curves for a chain of six Au atoms and for benzene-1,4-dithiol between two Au (111) surfaces computed using a self-consistent, non-equilibrium, Green’s Functions approach in conjunction with a density functional theory (DFT) description of the extended molecule. The solutions are expanded in Gaussian basis sets. In an attempt to improve the description of the molecule-surface bond, we consider one- and two-layer clusters of metal atoms in the extended molecule. To avoid non-physical charging of the bulk metal clusters we add a shift to the diagonal elements of the Fock Matrix of the metal atoms in the DFT treatment; this can be viewed as correcting the self-energies or shifting the Fermi level. The Au6 cluster with the full minimal basis set represents a compromise between accuracy and cost. The Au31(12/19) two-layer cluster results are of about the same quality as the one-layer Au21 cluster, but allows one to study more binding sites. Using a double zeta basis set for three of the top-layer Au atoms of the Au31(12/19) cluster yields result similar to the all minimal basis set, while using all double zeta atoms yields inferior results.

The Reactivity of Calicheamicin γ1I in the Minor Groove of DNA: The Decisive Role of the Environment

Triggering and Bergman cyclization of calicheamicin gamma(1) (I) outside and inside the minor groove of the duplex 9mer-B-DNA sequence d(CACTCCTGG).d(CCAGGAGTG) were investigated by using density functional theory and molecular mechanics (DFT and MM) descriptions in which the ligand is completely described at the DFT and the receptor at the MM level. The calculated docking energy of calicheamicin gamma(1) (I) (-12.5 kcal mol(-1)) is close to the measured value of -9.7 kcal mol(-1) and the site specificity is in line with experimental observations. Calicheamicin is triggered in the minor groove in such a way that out of a cyclohexenone by Michael addition an E rather than a Z form of a cyclohexanone is formed, which in turn adopts a chair rather than a twistboat form. Decisive for the stereochemistry of the Michael addition is the orientation of the carbamate substituent at the headgroup of calicheamicin. Triggered calicheamicin can undergo the Bergman cyclization at body temperature only if present in its E chair form (activation enthalpy 16.4 kcal mol(-1)). An intermediate biradical is formed (docking energy -13.6 kcal mol(-1)), which has a sufficient lifetime to abstract two hydrogen atoms. Hydrogen abstraction is a two- rather than one-step process and involves the C5(H5') atom first and then the T22(H4') atom in line with experimental observations. The decisive role of using a DFT rather than an MM description for the ligand is documented.

On the performance of local, semilocal, and nonlocal exchange-correlation functionals on transition metal molecules

The lowest singlet-triplet transition (X (1)Sigma+-(3)Sigma+) of AgI has been used to study systematically the performance of local [local density approximation (LDA)], semilocal [generalized gradient approximation (GGA)], and nonlocal (semiempiric hybrid and meta)-type exchange-correlation functionals on a transition metal molecule where dynamic electronic correlation effects are essential. Previous benchmark ab initio calculations showed that the triplet ground state possesses a shallow well in the Franck-Condon region before becoming repulsive at longer internuclear distance [A. Ramirez-Solis, J. Chem. Phys. 118, 104 (2003)]. Several density functional theory (DFT) descriptions are compared with the benchmark complete active space self-consistent-field+averaged coupled pair functional results, using the same relativistic effective core potentials and optimized Gaussian basis sets. A rather unreliable performance of exchange-correlation functionals was found when ascending the various rungs in DFT Jacob's ladder for this complex molecule. While some of the simpler (LDA and GGA) functionals correctly predict the presence of a short-distance maximum for the (3)Sigma+ state, more sophisticated hybrid and meta-functionals lead to totally repulsive or oscillating curves for the ground triplet state. A thorough discussion addressing the local versus nonlocal character of the exchange and correlation effects on the triplet potential curve is presented. The author concludes that any new efforts directed at producing more accurate exchange-correlation functionals must take into account the more complex electronic structure arising in transition metal molecules, whether these efforts follow the dominant pragmatic semiempiric trend or the more philosophically correct nonempiric pathway to develop better exchange-correlation functionals; only then will the Kohn-Sham version of DFT make the necessary improvements to correctly describe the electronic structure of complex transition metal systems.

Basis Set Superposition Error along the Free-Energy Surface of the Water Dimer.

In this article we review the behavior of static plane wave basis set calculations in comparison to Gaussian basis set calculations. This was done in the framework of density functional theory for description of hydrogen bonds with the water dimer as an example. Furthermore we carried out molecular dynamics simulations enforcing the self-dissociation reaction of the water dimer to study the influence of the basis set onto the reaction. Not surprisingly, we find strongly varying results of the calculated forces for a chosen cutoff along the reaction coordinates. The basis set superposition errors of the dimer interaction energy are analyzed along the free-energy surface, i.e., along the trajectories. Based on the analysis along the trajectories a qualitative and quantitative estimate depending on the particular point of the free-energy surface can be provided. Namely, at the intermolecular O···H distance close to the equilibrium geometry the errors are smaller than at shorter O···H distances. However, the distribution at the equilibrium distance is more unsymmetrical than the distribution at short distances. It is wider, and the standard deviation is larger than at shorter distances where the basis set superposition error is larger.