Showing papers on "Ab initio quantum chemistry methods published in 2002"
TL;DR: In this paper, an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias.
Abstract: We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density-functional theory (DFT) as implemented in the well tested SIESTA approach (which uses nonlocal norm-conserving pseudopotentials to describe the effect of the core electrons, and linear combination of finite-range numerical atomic orbitals to describe the valence states). We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including self-consistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme involving the scattering states. As an illustration, the method is applied to three systems where we are able to compare our results to earlier ab initio DFT calculations or experiments, and we point out differences between this method and existing schemes. The systems considered are: (i) single atom carbon wires connected to aluminum electrodes with extended or finite cross section, (ii) single atom gold wires, and finally (iii) large carbon nanotube systems with point defects.
4,674 citations
TL;DR: In this article, the binding energies of the benzene dimer were investigated at the second-order Moller−Plesset perturbation theory (MP2) level, and it was shown that more modest basis sets such as aug-cc-pVDZ are sufficient for geometry optimizations of intermolecular parameters.
Abstract: State-of-the-art electronic structure methods have been applied to the simplest prototype of aromatic π−π interactions, the benzene dimer. By comparison to results with a large aug-cc-pVTZ basis set, we demonstrate that more modest basis sets such as aug-cc-pVDZ are sufficient for geometry optimizations of intermolecular parameters at the second-order Moller−Plesset perturbation theory (MP2) level. However, basis sets even larger than aug-cc-pVTZ are important for accurate binding energies. The complete basis set MP2 binding energies, estimated by explicitly correlated MP2−R12/A techniques, are significantly larger in magnitude than previous estimates. When corrected for higher-order correlation effects via coupled cluster with singles, doubles, and perturbative triples [CCSD(T)], the binding energies De (D0) for the sandwich, T-shaped, and parallel-displaced configurations are found to be 1.8 (2.0), 2.7 (2.4), and 2.8 (2.7) kcal mol-1, respectively.
1,206 citations
TL;DR: In this paper, a new version of MOLVIB, a program for vibrational force field calculations, has recently been prepared, which is now possible to perform scale factor calculations according to several methods, which are described.
718 citations
TL;DR: In this article, the authors performed ab initio electronic structure and total energy calculations for bcc, fcc and hcp Al structures to study the equations of state, volume dependences of elastic constants, and relative stability diagram for these structures.
Abstract: We have performed ab initio electronic structure and total-energy calculations for bcc, fcc, and hcp Al structures to study the equations of state, volume dependences of elastic constants, and relative stability diagram for these structures. A technique for elastic constant calculation in the case of initial isotropic pressure is presented. In this study we used the accurate full-potential linear muffin-tin orbital method to describe electrons of the crystal and the Debye treatment of the vibrating lattice. The volume dependence of the Debye temperature is derived from the volume dependence of the elastic constants. Our calculations show that at pressures of 1–2 Mbar and temperatures of about 1000 K and higher, the aluminium structure must have a lower symmetry than the structures considered.
696 citations
662 citations
TL;DR: The complexes formed by a variety of anions with perfluoro derivatives of benzene, naphthalene, pyridine, thiophene, and furan have been calculated using DFT (B3LYP/6-31++G**) and MP2 and the AIM analysis of the electron density shows a varieties of topologies depending on the aromatic system considered.
Abstract: The complexes formed by a variety of anions with perfluoro derivatives of benzene, naphthalene, pyridine, thiophene, and furan have been calculated using DFT (B3LYP/6-31++G**) and MP2 (MP2/6-31++G** and MP2/6-311++G**) ab initio methods. The minimum structures show the anion interacting with the π-cloud of the aromatic compounds. The interaction energies obtained range between −8 and −19 kcal mol-1. The results obtained at the MP2/6-31++G** and MP2/6-311++G** levels are similar. However, the B3LYP/6-31++G** results provide longer interaction distances and smaller interaction energies than do the MP2 results. The interaction energies have been partitioned using an electrostatic, polarization, and van der Waals scheme. The AIM analysis of the electron density shows a variety of topologies depending on the aromatic system considered.
458 citations
TL;DR: In this article, an extended Lagrangian is used to propagate the density matrix in a basis of atom centered Gaussian functions, and the results of trajectory calculations obtained by this method are compared with the Born-Oppenheimer approach (BO), in which the density is converged at each step rather than propagated.
Abstract: In a recently developed approach to ab initio molecular dynamics (ADMP), we used an extended Lagrangian to propagate the density matrix in a basis of atom centered Gaussian functions. Results of trajectory calculations obtained by this method are compared with the Born–Oppenheimer approach (BO), in which the density is converged at each step rather than propagated. For NaCl, the vibrational frequency with ADMP is found to be independent of the fictitious electronic mass and to be equal to the BO trajectory result. For the photodissociation of formaldehyde, H2CO→H2+CO, and the three body dissociation of glyoxal, C2H2O2→H2+2CO, very good agreement is found between the Born–Oppenheimer trajectories and the extended Lagrangian approach in terms of the rotational and vibrational energy distributions of the products. A 1.2 ps simulation of the dynamics of chloride ion in a cluster of 25 water molecules was used as a third test case. The Fourier transform of the velocity–velocity autocorrelation function showed ...
411 citations
28 Apr 2002
347 citations
TL;DR: In this paper, a force field for liquid-state simulations on ionic liquids containing 1-ethyl-3-methylimidazolium and 1-n-butyl-3methyloroaluminate and tetrafluoroborate anions is presented.
Abstract: We present a complete force field for liquid-state simulations on ionic liquids containing 1-ethyl-3-methylimidazolium and 1-n-butyl-3-methylimidazolium cations and the tetrachloroaluminate and tetrafluoroborate anions. The force field is compatible with the AMBER methodology and is easily extendable to other dialkylimidazolium salts. On the basis of the general AMBER procedures to develop lacking intramolecular parameters and the RESP approach to calculate the atomic point charges, we obtained an all-atom force field which was validated against the experimental density, diffusion coefficient, vibrational frequencies, as well as X-ray (crystal state) and neutron (liquid state) diffraction structural data. Moreover, molecular mechanics calculations for the developed force field produce the cation's structures and dipole moments in very good agreement with quantum mechanical ab initio calculations. In addition, a basic study concerning the simulated liquid structure in terms of the radial distribution funct...
311 citations
TL;DR: In this article, the authors used ab initio techniques based on density functional theory in the projector-augmented-wave implementation to calculate the free energy and a range of other thermodynamic properties of liquid iron at high pressures and temperatures relevant to the Earth's core.
Abstract: Ab initio techniques based on density functional theory in the projector-augmented-wave implementation are used to calculate the free energy and a range of other thermodynamic properties of liquid iron at high pressures and temperatures relevant to the Earth’s core. The ab initio free energy is obtained by using thermodynamic integration to calculate the change of free energy on going from a simple reference system to the ab initio system, with thermal averages computed by ab initio molecular dynamics simulation. The reference system consists of the inverse-power pair-potential model used in previous work. The liquid-state free energy is combined with the free energy of hexagonal close packed Fe calculated earlier using identical ab initio techniques to obtain the melting curve and volume and entropy of melting. Comparisons of the calculated melting properties with experimental measurement and with other recent ab initio predictions are presented. Experiment-theory comparisons are also presented for the pressures at which the solid and liquid Hugoniot curves cross the melting line, and the sound speed and Gruneisen parameter along the Hugoniot. Additional comparisons are made with a commonly used equation of state for high-pressure–high-temperature Fe based on experimental data.
295 citations
TL;DR: In this article, it is shown how ab initio techniques based on density functional theory can be used to calculate the chemical potentials of the leading candidate impurity elements (S, O and Si) in the Earth's solid inner core and liquid outer core.
TL;DR: In this paper, a fitting database for high-temperature simulations of B2-NiAl using molecular dynamics and Monte Carlo methods has been proposed to enhance the transferability of the obtained potential.
Abstract: database that includes both experimental properties of B2-NiAl and a large set of structural energies generated by ab initio calculations. Additional ab initio data, not included in the fitting database, are used to test the potential. The fitting database samples a large area of configuration space in order to enhance the transferability of the obtained potential. The potential proposed in this work can be used effectively in atomistic simulations of plastic deformation, fracture, and especially atomic disorder and diffusion. It is designed to be particularly reliable in high-temperature simulations of B2-NiAl using molecular dynamics and Monte Carlo methods.
TL;DR: In this article, the authors explored the chemical sensitivity of these features in C 1s and O 1s NEXAFS spectra for a series of polymers containing the carbonyl group in a range of different bonding environments.
Abstract: Carbonyl core (C 1s, O 1s) → π*CO transitions are distinctive in the near-edge X-ray absorption fine structure (NEXAFS) spectra of species containing carbonyl groups. These features are used for the chemical microanalysis of organic materials using X-ray microscopy. We have explored the chemical sensitivity of these features in C 1s and O 1s NEXAFS spectra for a series of polymers containing the carbonyl group in a range of different bonding environments. Ab initio calculations are used to explain the origin of the observed trends and to explore the effect that orbital interactions have on the energy of these core (C 1s, O 1s) → π*CO features. The differences between the experimental and the calculated carbonyl core (C 1s, O 1s) → π*CO transition energies are systematic and can be used to develop a semiempirical method for predicting the absolute (experimental) transition energies from the calculated transition energies. This relationship is applied to a large body of calculated transition energy data to ...
TL;DR: In this paper, the authors investigated the fluorescence emission and excitation spectra of para-phenylene vinylenes nPV with n=1-4 styryl units as a function of temperature and the polarizability of the solvent.
Abstract: Fluorescence emission and excitation spectra of para-phenylene vinylenes nPV with n=1–4 styryl units are investigated experimentally and theoretically as a function of the temperature and the polarizability of the solvent. At low temperatures, the vibronic structures of the S0↔S1 emission and excitation bands are mirror symmetrical with negligible 0–0 energy gaps. The frequencies of the prominent vibrational modes are assigned to the second longitudinal acoustic phonon modes of the entire molecules and to localized carbon–carbon stretching vibrations. The complete vibronic structures of the spectra are calculated at the ab initio Hartree–Fock (HF/6-311G*) and restricted configuration interaction singles (RCIS/6-311G*) levels of theory assuming planar C2h molecular symmetry. The theoretically predicted spectra are in good agreement with the experiments. At room temperature, a 0–0 energy gap between the first band maxima opens, and the mirror symmetry between absorption and emission is lost. The vibronic band shapes and 0–0 band gaps are successfully simulated with a combination of Gaussian and exponential broadening of the low temperature spectra. The exponential term reflects the differences in thermal population of the phenyl-vinyl torsional modes in the S0 and S1 electronic states. Spectral shifts upon changes in temperature and solvents are quantitatively explained by changes in the refractive index of the environment. From extrapolation of the experimental data the vertical and adiabatic transition energies of the oligomers in vacuo are obtained and compared to RCIS and semiempirical quantum chemical calculations, respectively.
TL;DR: In this article, the authors used the difference dedicated configuration interaction (CI) technique to analyze the magnetic coupling in binuclear complexes of Cu (d9) ions and performed numerical analysis of their respective roles.
Abstract: Accurate estimates of the magnetic coupling in binuclear complexes can be obtained from ab initio configuration interaction (CI) calculations using the difference dedicated CI technique. The present paper shows that the same technique also provides a way to analyze the various physical contributions to the coupling and performs numerical analysis of their respective roles on four binuclear complexes of Cu (d9) ions. The bare valence-only description (including direct and kinetic exchange) does not result in meaningful values. The spin-polarization phenomenon cannot be neglected, its sign and amplitude depend on the system. The two leading dynamical correlation effects have an antiferromagnetic character. The first one goes through the dynamical polarization of the environment in the ionic valence bond forms (i.e., the M+⋯M− structures). The second one is due to the double excitations involving simultaneously single excitations between the bridging ligand and the magnetic orbitals and single excitations of...
TL;DR: In this paper, an inner-valence ionized cluster, which releases its excess energy by emitting an electron, is characterized by an efficient energy transfer between monomers in the cluster.
TL;DR: In this paper, the authors examined the consequences of incorporating the ab initio derived monomer potential-energy surface and nonlinear dipole surface of Partridge and Schwenke [J. Phys. 106, 4618 (1997)] into the previously developed TTM2-R model of Burnham et al. in order to develop a new all-atom polarizable, flexible model for water.
Abstract: In this work we examine the consequences of incorporating the ab initio derived monomer potential-energy surface and nonlinear dipole surface of Partridge and Schwenke [J. Chem. Phys. 106, 4618 (1997)] into the previously developed TTM2-R model of Burnham et al. [J. Chem. Phys. 116, 1500 (2002)] in order to develop a new, all-atom polarizable, flexible model for water (TTM2-F). We found that the use of the nonlinear dipole surface is essential in modeling the change in the internal geometry of interacting water molecules and, in particular, the increase in the internal H–O–H bend angle with cluster size. This is the first demonstration of a flexible model which shows an increase in the bending angle in clusters. An explanation for this behavior is presented using the concept of geometric polarizabilities. The model furthermore reproduces the n=2–6 cluster binding energies to within an RMS deviation of 0.05 kcal/mol per hydrogen bond with respect to the MP2 complete basis set estimates. Preliminary results...
TL;DR: In this paper, Hartree-Fock vibration-rotation interaction constants have been calculated for 18 single-configuration dominated molecules containing hydrogen and first-row atoms at various standard levels of ab initio theory.
Abstract: rotation interaction constants a r . The vibration‐rotation interaction constants have been calculated for 18 single-configuration dominated molecules containing hydrogen and first-row atoms at various standard levels of ab initio theory. Comparisons with the experimental data and tests for the internal consistency of the calculations show that the equilibrium structures generated using Hartree‐Fock vibration‐rotation interaction constants have an accuracy similar to that obtained by a direct minimization of the CCSD~T! energy. The most accurate vibration‐rotation interaction constants are those calculated at the CCSD~T!/cc-pVQZ level. The equilibrium bond distances determined from these interaction constants have relative errors of 0.02%‐0.06%, surpassing the accuracy obtainable either by purely experimental techniques ~except for the smallest systems such as diatomics! or by ab initio methods. © 2002 American Institute of Physics. @DOI: 10.1063/1.1459782#
TL;DR: In this article, density-functional theory calculations in the local density approximation of the structural, electronic, and optical properties of single-walled carbon nanotubes were performed under light polarized parallel and perpendicular to the tube axis.
Abstract: We performed density-functional theory calculations in the local-density approximation of the structural, electronic, and optical properties of 4-$\mathrm{\AA{}}$-diameter single-walled carbon nanotubes. The calculated relaxed geometries show significant deviations from the ideal rolled graphene sheet configuration. We study the effect of the geometry on the electronic band structure finding the metallic character of the (5,0) nanotube to be a consequence of the high curvature of the nanotube wall. Calculations of the dielectric function and optical absorption of the isolated nanotubes were performed under light polarized parallel and perpendicular to the tube axis. We compare our results to measurements of the optical absorption of zeolite-grown nanotubes and are able to assign the observed maxima to the nanotube chiralities.
TL;DR: In this article, the first molecular simulation study of 1-n-butyl-3-methylimidazolium hexafluorophosphate [bmim][PF6], a widely studied ionic liquid, is reported.
TL;DR: In this article, it is shown that spin polarization may change the sign of the direct exchange interaction, and that dynamical correlation results in a dramatic reduction of the effective repulsion U.
Abstract: Most interpretations of the magnetic coupling J between two unpaired electrons rest upon simple valence models that involve essentially the ferromagnetic direct exchange contribution, Kab, and the antiferromagnetic effect of the delocalization resulting from the interaction between neutral and ionic determinants, tab, whose energy difference is U. Ab initio valence-only calculations give very poor estimates of J, whatever the definition of the magnetic orbitals, and large CI expansions are required to evaluate it properly. It is, however, possible to define valence effective Hamiltonians from the knowledge of the eigenenergies and the eigenvectors of these accurate CI calculations. When applied to four different complexes, this strategy shows that spin polarization may change the sign of the direct exchange interaction, Kab, and that dynamical correlation results in a dramatic reduction of the effective repulsion U. The present article also shows how Kab, tab, and U effective parameters can be extracted from density functional theory (DFT) calculations and that the typical overestimation of J in DFT can be attributed to an excessive lowering of the effective on-site repulsion.
TL;DR: In this article, a force field for liquid SiO2 has been parametrized using the forces, stresses and energies extracted from ab initio calculations and compared with the most widely used force fields for silica.
Abstract: We present a classical interatomic force field for liquid SiO2 which has been parametrized using the forces, stresses and energies extracted from ab initio calculations. We show how inclusion of more electronic effects in a phenomenological way and parametrization at the relevant conditions of pressure and temperature allow the creation of more accurate force fields. We compare the results of simulations with this force field both to experiment and to the results of ab initio molecular dynamics simulations and show how our procedure leads to comparisons which are greatly improved with respect to the most widely used force fields for silica.
TL;DR: In this article, the effect of fluctuating structural distortions on the efficiency of hole migration in some DNA double strands was studied, and a parametrization of the coupling in terms of the overlap between the localized wave functions was found by a large number of ab initio calculations.
Abstract: We have studied the effect of fluctuating structural distortions on the efficiency of hole migration in some DNA double strands. Standard molecular dynamics (MD) simulations of DNA embedded in water have been performed over a time intervals of 40 ps. The MD study was followed by quantum chemical calculations of time-dependent electronic coupling between all the pairs of adjacent bases and by the subsequent evaluation of the fluctuating effective electronic coupling between donor and acceptor (HDA) guanine bases. A convenient parametrization of the coupling in terms of the overlap between the localized wave functions was found by a large number of ab initio calculations. The MD results show that HDA undergoes large fluctuations and that its quadratic average is 1 order of magnitude larger than its mean value. Furthermore, the MD analysis shows that the base-pair couplings are due predominantly to the transverse motions of the DNA strands, while longitudinal motions are surprisingly ineffective.
TL;DR: In this article, the electronic structure and chemical bonding of B5− and B5 were investigated using anion photoelectron spectroscopy and ab initio calculations, and the experimental spectra were obtained and compared to theoretical calculations performed at various levels of theory.
Abstract: The electronic structure and chemical bonding of B5− and B5 were investigated using anion photoelectron spectroscopy and ab initio calculations. Vibrationally resolved photoelectron spectra were obtained for B5− and were compared to theoretical calculations performed at various levels of theory. Extensive searches were carried out for the global minimum of B5−, which was found to have a planar C2v structure with a closed-shell ground state (1A1). Excellent agreement was observed between ab initio detachment energies and the experimental spectra, firmly establishing the ground-state structures for both B5− and B5. The chemical bonding in B5− was investigated and compared to that in Al5−. While both B5− and Al5− have a similar C2v planar structure, their π-bonding orbitals are different. In Al5−, a π-bonding orbital was previously observed to delocalize over only the three central atoms in the C2v ground-state structure, whereas a similar π orbital (1b1) was found to completely delocalize over all five atom...
TL;DR: In this article, the potential energy function of the lowest 3s Rydberg state of 9H-adenine was found to be dissociative with respect to the stretching of the NH bond length of the azine group.
Abstract: Minimum-energy reaction paths and corresponding potential-energy proles have been com- puted for the lowest excited states of the amino form of 9H-adenine. Complete-active- space self-consistent- eld (CASSCF) and density functional theory (DFT) methods have been employed. The potential-energy function of the lowest 1 state, nominally a 3s Rydberg state, is found to be dissociative with respect to the stretching of the NH bond length of the azine group. The 1 potential-energy function inter- sects not only those of the 1 and 1 n excited states, but also that of the electronic ground state. The 1 { 1 and 1 {S0 intersections are converted into conical intersections when the out-of-plane motion of the active hydrogen atom is taken into account. It is argued that the predissociation of the 1 and 1 n states by the 1 state and the conical intersection of the 1 state with the S0 state provide the mechanism for the ultrafast radiationless deactivation of the excited singlet states of adenine.
TL;DR: The basicity of 1,3-di-tert-butylimidazol-2-ylidene was measured in THF against three hydrocarbon indicators and both ion pairs and free ions were found and the corresponding equilibrium constants were measured.
Abstract: The basicity of 1,3-di-tert-butylimidazol-2-ylidene (1) was measured in THF against three hydrocarbon indicators. Both ion pairs and free ions were found and the corresponding equilibrium constants...
TL;DR: In this article, the equilibrium structure and potential energy surface of calcium monohydroxide in its ground doublet state, X2Σ+ CaOH, were determined from large-scale ab initio calculations using the spin-r...
Abstract: The equilibrium structure and potential energy surface of calcium monohydroxide in its ground doublet state, X2Σ+ CaOH, have been determined from large-scale ab initio calculations using the spin-r...
TL;DR: In this article, a dipole interaction model for calculating the polarizability of molecular clusters is proposed, where a damping of the interatomic interaction at short distances is introduced in such a way as to retain a traceless interaction tensor and a good description of the damping over a wide range of interatomic distances.
Abstract: We have developed and investigated a dipole interaction model for calculating the polarizability of molecular clusters. The model has been parametrized from the frequency-dependent molecular polarizability as obtained from quantum chemical calculations for a series of 184 aliphatic, aromatic, and heterocyclic compounds. A damping of the interatomic interaction at short distances is introduced in such a way as to retain a traceless interaction tensor and a good description of the damping over a wide range of interatomic distances. By adopting atomic polarizabilities in addition to atom-type parameters describing the damping and the frequency dependence, respectively, the model is found to reproduce the molecular frequency-dependent polarizability tensor calculated with ab initio methods. A study of the polarizability of four dimers has been carried out: the hydrogen fluoride, methane, benzene, and urea dimers. We find in general good agreement between the model and the quantum chemical results over a wide ...
TL;DR: The magnitude of the stabilizing interaction between an aliphatic C−H bond attached to an ammonium nitrogen and a carbonyl oxygen was evaluated by ab initio calculations at the MP2/6-311++G** level of theory as mentioned in this paper.
Abstract: The magnitude of the stabilizing interaction between an aliphatic C−H bond attached to an ammonium nitrogen and a carbonyl oxygen was evaluated by ab initio calculations at the MP2/6-311++G** level of theory. Attractive R3N+−C−H···OC interactions play an important role in supramolecular recognition and various types of stereoselective catalysis. Our calculations show that R3N+−C−H···OC is the strongest hydrogen bond of the C−H···O type known to date. Such hydrogen bonds remain as stabilizing interactions even in water for amide acceptors.
TL;DR: In this paper, the authors combine crystallographic and computational evidences to demonstrate an attractive interaction between the anion and the π-cloud of 1,3,5-trinitrobenzene.