Showing papers on "Ab initio published in 2008"

Ab-initio simulations of materials using VASP: Density-functional theory and beyond.

Abstract: During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science—promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces, interfaces and thin films, chemical reactions, and catalysis) are reviewed. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008

Pillared graphene: a new 3-D network nanostructure for enhanced hydrogen storage.

Abstract: A multiscale theoretical approach was used to investigate hydrogen storage in a novel three-dimensional carbon nanostructure. This novel nanoporous material has by design tunable pore sizes and surface areas. Its interaction with hydrogen was studied thoroughly via ab initio and grand canonical Monte Carlo calculations. Our results show that, if this material is doped with lithium cations, it can store up to 41 g H2/L under ambient conditions, almost reaching the DOE volumetric requirement for mobile applications.

Highly accurate first-principles benchmark data sets for the parametrization and validation of density functional and other approximate methods. Derivation of a robust, generally applicable, double-hybrid functional for thermochemistry and thermochemical kinetics.

Abstract: We present a number of near-exact, nonrelativistic, Born-Oppenheimer reference data sets for the parametrization of more approximate methods (such as DFT functionals). The data were obtained by means of the W4 ab initio computational thermochemistry protocol, which has a 95% confidence interval well below 1 kJ/mol. Our data sets include W4-08, which are total atomization energies of over 100 small molecules that cover varying degrees of nondynamical correlations, and DBH24-W4, which are W4 theory values for Truhlar's set of 24 representative barrier heights. The usual procedure of comparing calculated DFT values with experimental atomization energies is hampered by comparatively large experimental uncertainties in many experimental values and compounds errors due to deficiencies in the DFT functional with those resulting from neglect of relativity and finite nuclear mass. Comparison with accurate, explicitly nonrelativistic, ab initio data avoids these issues. We then proceed to explore the performance of B2x-PLYP-type double hybrid functionals for atomization energies and barrier heights. We find that the optimum hybrids for hydrogen-transfer reactions, heavy-atoms transfers, nucleophilic substitutions, and unimolecular and recombination reactions are quite different from one another: out of these subsets, the heavy-atom transfer reactions are by far the most sensitive to the percentages of Hartree-Fock-type exchange y and MP2-type correlation x in an (x, y) double hybrid. The (42,72) hybrid B2K-PLYP, as reported in a preliminary communication, represents the best compromise between thermochemistry and hydrogen-transfer barriers, while also yielding excellent performance for nucleophilic substitutions. By optimizing for best overall performance on both thermochemistry and the DBH24-W4 data set, however, we find a new (36,65) hybrid which we term B2GP-PLYP. At a slight expense in performance for hydrogen-transfer barrier heights and nucleophilic substitutions, we obtain substantially better performance for the other reaction types. Although both B2K-PLYP and B2GP-PLYP are capable of 2 kcal/mol quality thermochemistry, B2GP-PLYP appears to be the more robust toward nondynamical correlation and strongly polar character. We additionally find that double-hybrid functionals display excellent performance for such problems as hydrogen bonding, prototype late transition metal reactions, pericyclic reactions, prototype cumulene-polyacetylene system, and weak interactions.

Li−Fe−P−O2 Phase Diagram from First Principles Calculations

Abstract: We present an efficient way to calculate the phase diagram of the quaternary Li−Fe−P−O2 system using ab initio methods. The ground-state energies of all known compounds in the Li−Fe−P−O2 system were calculated using the generalized gradient approximation (GGA) approximation to density functional theory (DFT) and the DFT+U extension to it. Considering only the entropy of gaseous phases, the phase diagram was constructed as a function of oxidation conditions, with the oxygen chemical potential, μO2, capturing both temperature and oxygen partial pressure dependence. A modified Ellingham diagram was also developed by incorporating the experimental entropy data of gaseous phases. The phase diagram shows LiFePO4 to be stable over a wide range of oxidation environments, being the first Fe2+-containing phase to appear upon reduction at μO2 = −11.52 eV and the last of the Fe-containing phosphates to be reduced at μO2 = −16.74 eV. Lower μO2 represents more reducing conditions, which generally correspond to higher t...

Ab initio determination of light hadron masses.

Abstract: More than 99% of the mass of the visible universe is made up of protons and neutrons. Both particles are much heavier than their quark and gluon constituents, and the Standard Model of particle physics should explain this difference. We present a full ab initio calculation of the masses of protons, neutrons, and other light hadrons, using lattice quantum chromodynamics. Pion masses down to 190 mega-electron volts are used to extrapolate to the physical point, with lattice sizes of approximately four times the inverse pion mass. Three lattice spacings are used for a continuum extrapolation. Our results completely agree with experimental observations and represent a quantitative confirmation of this aspect of the Standard Model with fully controlled uncertainties.

Electronic properties of semiconductor nanowires.

Abstract: This paper provides a review of the state-of-the-art electronic-structure calculations of semiconductor nanowires. Results obtained using empirical k.p, empirical tight-binding, semi-empirical pseudopotential, and with ab initio methods are compared. For conciseness, we will restrict our detailed discussions to free-standing plain and modulated nanowires. Connections to relevant experimental data, particularly band gaps and polarization anisotropy, will be made since these results depend crucially on the electronic properties. For completeness, a brief review on the synthesis of nanowires is included.

Benchmarks for electronically excited states: Time-dependent density functional theory and density functional theory based multireference configuration interaction

Abstract: Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole moments are computed using the same geometries (MP2/6-31G∗) and basis set (TZVP) as in our previous ab initio benchmark study on electronically excited states. The results from TD-DFT (with the functionals BP86, B3LYP, and BHLYP) and from DFT/MRCI are compared against the previous high-level ab initio results, and, in particular, against the proposed best estimates for 104 singlet and 63 triplet vertical excitation energies. The statistical evaluation for the latter reference data gives the lowest mean absolute deviations for DFT/MRCI (0.22 eV for singlets and 0.24 eV for triplets) followed by TD-DFT/B3LYP (0.27 and 0.44 eV, respectively), whereas TD-DFT/BP86 and TD-DFT/BHLYP are significantly less accurate. The ene...

Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.

Abstract: Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.

Compression curves of transition metals in the Mbar range: Experiments and projector augmented-wave calculations

Abstract: The ambient temperature equations of state (EoS) of iron, cobalt, nickel, zinc, molybdenum, and silver have been measured by x-ray diffraction. These transition metals were compressed using diamond anvil cells with a helium pressure transmitting medium. The maximum pressure reached during these experiments varied between 65 GPa (for cobalt) and 200 GPa (for iron). This work completes previous measurements on six other metals [Phys. Rev. B 70, 094112 (2004)] to quantify the differences between ab initio calculations and experiment on a large experimental set of transition metals. The compression curves of iron, cobalt, nickel, zinc, molybdenum, silver, platinum, and gold are also calculated ab initio within the density-functional theory (DFT) formalism using the projector augmented-wave (PAW) method and different exchange-correlation functionals (LDA, GGA-PBE, GGA-PBEsol). The difference between PAW and available all-electron calculations is found to be negligible up to very high pressures. The success of each exchange-correlation functional is correlated with the atomic number. For all metals, the bulk modulus becomes overestimated at high pressure. In addition, this extended data set of metals' EoS enables to reduce further, but marginally, the systematic uncertainty of the high-pressure metrology based on the ruby standard.

High-accuracy extrapolated ab initio thermochemistry. III. Additional improvements and overview

Abstract: Effects of increased basis-set size as well as a correlated treatment of the diagonal Born-Oppenheimer approximation are studied within the context of the high-accuracy extrapolated ab initio thermochemistry (HEAT) theoretical model chemistry. It is found that the addition of these ostensible improvements does little to increase the overall accuracy of HEAT for the determination of molecular atomization energies. Fortuitous cancellation of high-level effects is shown to give the overall HEAT strategy an accuracy that is, in fact, higher than most of its individual components. In addition, the issue of core-valence electron correlation separation is explored; it is found that approximate additive treatments of the two effects have limitations that are significant in the realm of <1kJmol−1 theoretical thermochemistry.

Cholesky Decomposition-Based Multiconfiguration Second-Order Perturbation Theory (CD-CASPT2): Application to the Spin-State Energetics of Co(III)(diiminato)(NPh).

Abstract: The electronic structure and low-lying electronic states of a Co-III(diiminato)(NPh) complex have been studied using mulficonfigurational wave function theory (CASSCF/CASPT2) The results have been compared to those obtained with density functional theory. The best agreement with ab initio results is obtained with a modified B3LYP functional containing a reduced amount (15%) of Hartree-Fock exchange. A relativistic basis set with 869 functions has been employed in the most extensive ab initio calculations, where a Cholesky decomposition technique was used to overcome problems arising from the large size of the two-electron integral matrix. It is shown that this approximation reproduces results obtained with the full integral set to a high accuracy, thus opening the possibility to use this approach to perform multiconfigurational wave-function-based quantum chemistry on much larger systems relative to what has been possible until now.

Rotationally invariant ab initio evaluation of Coulomb and exchange parameters for DFT+U calculations

Abstract: Conventional density functional theory (DFT) fails for strongly correlated electron systems due to large intra-atomic self-interaction errors. The DFT+U method provides a means of overcoming these errors through the use of a parametrized potential that employs an exact treatment of quantum mechanical exchange interactions. The parameters that enter into this potential correspond to the spherically averaged intra-atomic Coulomb (U) and exchange (J) interactions. Recently, we developed an ab initio approach for evaluating these parameters on the basis of unrestricted Hartree-Fock (UHF) theory, which has the advantage of being free of self-interaction errors and does not require experimental input [Mosey and Carter, Phys. Rev. B 76, 155123 (2007)]. In this work, we build on that method to develop a more robust and convenient ab initio approach for evaluating U and J. The new technique employs a relationship between U and J and the Coulomb and exchange integrals evaluated using the entire set of UHF molecular orbitals (MOs) for the system. Employing the entire set of UHF MOs renders the method rotationally invariant and eliminates the difficulty in selecting unambiguously the MOs that correspond to localized states. These aspects overcome two significant deficiencies of our earlier method. The new technique is used to evaluate U and J for Cr(2)O(3), FeO, and Fe(2)O(3). The resulting values of U-J are close to empirical estimates of this quantity for each of these materials and are also similar to results of constrained DFT calculations. DFT+U calculations using the ab initio parameters yield results that are in good agreement with experiment. As such, this method offers a means of performing accurate and fully predictive DFT+U calculations of strongly correlated electron materials.

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

Abstract: RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 A deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNA(Phe), pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses.

Ab initio evaluation of the thermodynamic and electrochemical properties of alkyl halides and radicals and their mechanistic implications for atom transfer radical polymerization.

Abstract: High-level ab initio molecular orbital calculations are used to study the thermodynamics and electrochemistry relevant to the mechanism of atom transfer radical polymerization (ATRP). Homolytic bond dissociation energies (BDEs) and standard reduction potentials (SRPs) are reported for a series of alkyl halides (R−X; R = CH2CN, CH(CH3)CN, C(CH3)2CN, CH2COOC2H5, CH(CH3)COOCH3, C(CH3)2COOCH3, C(CH3)2COOC2H5, CH2Ph, CH(CH3)Ph, CH(CH3)Cl, CH(CH3)OCOCH3, CH(Ph)COOCH3, SO2Ph, Ph; X = Cl, Br, I) both in the gas phase and in two common organic solvents, acetonitrile and dimethylformamide. The SRPs of the corresponding alkyl radicals, R•, are also examined. The computational results are in a very good agreement with the experimental data. For all alkyl halides examined, it is found that, in the solution phase, one-electron reduction results in the fragmentation of the R−X bond to the corresponding alkyl radical and halide anion; hence it may be concluded that a hypothetical outer-sphere electron transfer (OSET) in ...

Ab initio GW many-body effects in graphene.

Abstract: We present an ab initio numerical many-body GW calculation of the band plot in freestanding graphene. We consider the full ionic and electronic structure introducing e-e interaction and correlation effects via a self-energy containing non-Hermitian and dynamical terms. With respect to the density-functional theory local-density approximation, the Fermi velocity is renormalized with an increase of 17%, in better agreement with the experiment. Close to the Dirac point the linear dispersion is modified by the presence of a kink, as observed by angle-resolved photoemission spectroscopy. We demonstrate that the kink is due to low-energy pi-->pi* single-particle excitations and to the pi plasmon. The GW self-energy does not open the band gap.

An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport

Abstract: A new multistate empirical valence bond model (MS-EVB3) is developed for proton solvation and transport in aqueous solutions. The new model and its quantum version (qMS-EVB3) are based on the MS-EVB2 model [Day et al., J. Chem. Phys. 2002, 117, 5839] and recently developed flexible water modelsthe SPC/Fw model [Wu et al. J. Chem. Phys. 2006, 124, 24503] and the qSPC/Fw model [Paesani et al. J. Chem. Phys. 2006, 125, 184507]for classical and quantum simulations, respectively. Using ab initio data as benchmarks, the binding energies and optimized geometries calculated with the new model for protonated water clusters, as well as the potential energy surface for proton shuttling between water molecules in a cluster environment, are improved in comparison to the MS-EVB2 model. For aqueous solutions, classical and quantum molecular dynamics simulations with the MS-EVB3 model yield a more accurate description of the solvation structure and diffusive dynamics of the excess proton. New insight is also provided int...

Ab Initio Study of the Hydroxylated Surface of Amorphous Silica: A Representative Model

Abstract: A new complete, representative model for the hydroxylated surface of amorphous silica is presented and characterized by means of periodic DFT calculations. This model accounts for the experimentally encountered ring size distribution, Si-O-Si and O-Si-O angles, silanols density, and distribution (isolated, associated, geminals). Properties such as NMR shifts, dehydrogenation energies, OH vibrational frequencies, and the interaction with water are investigated. The results are compared with former experimental and theoretical results. This new representative model for this complex surface would probably help the investigation of its reactivity toward amino acids or other organic molecules, opening new perspectives in the understanding of the chemistry of amorphous materials.

Role of electron-hole pair excitations in the dissociative adsorption of diatomic molecules on metal surfaces.

Abstract: We quantitatively evaluate the contribution of electron-hole pair excitations to the reactive dynamics of H2 on Cu(110) and N2 on W(110), including the six dimensionality of the process in the entire calculation. The interaction energy between molecule and surface is represented by an ab initio six-dimensional potential energy surface. Electron friction coefficients are calculated with density functional theory in a local density approximation. Contrary to previous claims, only minor differences between the adiabatic and nonadiabatic results for dissociative adsorption are found. Our calculations demonstrate the validity of the adiabatic approximation to analyze adsorption dynamics in these two representative systems.

Superconducting high pressure phase of germane

Abstract: High-pressure structures of germane (GeH4) are explored through ab initio evolutionary methodology to reveal a metallic monoclinic structure of C2/c (4 molecules/cell). The C2/c structure consists of layerlike motifs containing novel "H2" units. Enthalpy calculations suggest a remarkably wide decomposition (Ge+H2) pressure range of 0-196 GPa, above which C2/c structure is stable. Perturbative linear-response calculations for C2/c GeH4 at 220 GPa predict a large electron-phonon coupling parameter lambda of 1.12 and the resulting superconducting critical temperature reaches 64 K.

An ab initio Study of Reduction of V2O5 through the Formation of Oxygen Vacancies and Li Intercalation

Abstract: Two methods of reduction of V2O5 have been investigated: oxygen vacancy formation and lithium intercalation. The electronic structure, geometry, and energetics of these reduced systems are examined...

The charge flipping algorithm

Abstract: This paper summarizes the current state of charge flipping, a recently developed algorithm of ab initio structure determination. Its operation is based on the perturbation of large plateaus of low electron density but not directly on atomicity. Such a working principle radically differs from that of classical direct methods and offers complementary applications. The list of successful structure-solution cases includes periodic and aperiodic crystals using single-crystal and powder diffraction data measured with X-ray and neutron radiation. Apart from counting applications, the paper mainly deals with algorithmic issues: it describes and compares new variants of the iteration scheme, helps to identify and improve solutions, discusses the required data and the use of known information. Finally, it tries to foretell the future of such an alternative among well established direct methods.

Implementation of ab initio multiple spawning in the Molpro quantum chemistry package

Abstract: The ab initio multiple spawning (AIMS) method has been developed to solve the electronic and nuclear Schrodinger equations simultaneously for application to photochemical reaction dynamics. We discuss some details of the implementation of AIMS in the M olpro program package. A few aspects of the implementation are highlighted, including a new multiple timescale integrator and a scheme for solving the coupled-perturbed multiconfiguration self-consistent field (CP-MCSCF) equations in the context of ab initio molecular dynamics. The implementation is very efficient and we demonstrate calculations on the photoisomerization of ethylene using more than 5000 trajectory basis functions. We have included the capability for hybrid quantum mechanics/molecular mechanics (QM/MM) simulations within AIMS, and we investigate the role of an argon solvent in the photoisomerization of ethylene. Somewhat surprisingly, the surrounding argon has little effect on the timescale of non-adiabatic quenching in ethylene.

Density matrix renormalization group calculations on relative energies of transition metal complexes and clusters.

Abstract: The accurate first-principles calculation of relative energies of transition metal complexes and clusters is still one of the great challenges for quantum chemistry. Dense lying electronic states and near degeneracies make accurate predictions difficult, and multireference methods with large active spaces are required. Often density functional theory calculations are employed for feasibility reasons, but their actual accuracy for a given system is usually difficult to assess (also because accurate ab initio reference data are lacking). In this work we study the performance of the density matrix renormalization group algorithm for the prediction of relative energies of transition metal complexes and clusters of different spin and molecular structure. In particular, the focus is on the relative energetical order of electronic states of different spin for mononuclear complexes and on the relative energy of different isomers of dinuclear oxo-bridged copper clusters.

Application of static charge transfer within an ionic-liquid force field and its effect on structure and dynamics.

Abstract: The effects of linear scaling of the atomic charges of a reference potential on the structure, dynamics, and energetics of the ionic liquid 1,3-dimethylimidazolium chloride are investigated. Diffusion coefficients that span over four orders of magnitude are observed between the original model and a scaled model in which the ionic charges are +/-0.5 e. While the three-dimensional structure of the liquid is less affected, the partial radial distribution functions change markedly--with the positive result that for ionic charges of +/-0.7 e, an excellent agreement is observed with ab initio molecular dynamics data. Cohesive energy densities calculated from these partial-charge models are also in better agreement with those calculated from the ab initio data. We postulate that ionic-liquid models in which the ionic charges are assumed to be +/-1 e overestimate the intermolecular attractions between ions, which results in overstructuring, slow dynamics, and increased cohesive energy densities. The use of scaled-charge sets may be of benefit in the simulation of these systems--especially when looking at properties beyond liquid structure--thus providing an alternative to computationally expensive polarisable force fields.