Ab initio melting curve of molybdenum by the phase coexistence method

Ab initio calculations of the melting curve of molybdenum for the pressure range 0-400 GPa are reported. The calculations employ density functional theory (DFT) with the Perdew-Burke-Ernzerhof exchange-correlation functional in the projector augmented wave (PAW) implementation. Tests are presented showing that these techniques accurately reproduce experimental data on low-temperature body-centered cubic (bcc) Mo, and that PAW agrees closely with results from the full-potential linearized augmented plane-wave implementation. The work attempts to overcome the uncertainties inherent in earlier DFT calculations of the melting curve of Mo, by using the "reference coexistence" technique to determine the melting curve. In this technique, an empirical reference model (here, the embedded-atom model) is accurately fitted to DFT molecular dynamics data on the liquid and the high-temperature solid, the melting curve of the reference model is determined by simulations of coexisting solid and liquid, and the ab initio melting curve is obtained by applying free-energy corrections. The calculated melting curve agrees well with experiment at ambient pressure and is consistent with shock data at high pressure, but does not agree with the high-pressure melting curve deduced from static compression experiments. Calculated results for the radial distribution function show that the short-range atomic order of the liquid is very similar to that of the high-T solid, with a slight decrease of coordination number on passing from solid to liquid. The electronic densities of states in the two phases show only small differences. The results do not support a recent theory according to which very low dT(m)dP values are expected for bcc transition metals because of electron redistribution between s-p and d states.     

Tests of Monte Carlo perturbation theory for the free energy of liquid copper

Monte Carlo perturbation theory, in which terms in the thermodynamic perturbation series are evaluated by Monte Carlo averaging, has potentially large advantages in efficiency for calculating free energies of liquids from ab initio potential surfaces. In order to test the accuracy of perturbation theory for liquid metals, a series of calculations has been done on liquid copper, modeled by an embedded atom potential. A simple 1/r(12) pair potential is used as the reference system. The free energy is calculated to third order in perturbation theory, and the results are compared to an exact formula. It is found that for optimal reference potential parameters, second order perturbation theory is essentially exact. Second and third order theories give accurate results for significantly nonoptimal reference parameters. The relation between perturbation theory and reweighting is discussed, and an approximate formula is derived that shows an exponential dependence of the efficiency of reweighting on the second order free energy correction. Finally, techniques for application to ab initio potentials are discussed. It is shown that with samples of 100 configurations, it is possible to obtain accuracy and precision at the level of approximately 1 meV/atom.     

Ab initio calculations of the melting temperatures of refractory bcc metals

We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental values. We compare the melting temperatures to those obtained from direct ab initio molecular dynamics simulations and see if they are in excellent agreement with each other. The small remaining discrepancies with experiment are thus likely due to inherent limitations associated with exchange-correlation energy approximations within density-functional theory.     

Conformational Analysis of 2,2′-bifuran: Correlated High-level Ab initio and DFT Results

The torsional potential for inter-ring rotation in 2,2′-bifuran has been systematically tackled using highly accurate ab initio calculations as well as cost-effective DFT methods. The successful convergence of the ab initio results allowed to confirm the presence of a shallow gauche minimum in the torsional potential curve. The standard DFT methods failed to capture such a tiny energy barrier but, interestingly, the results could be remarkably improved by a mixture of wavefunction and DFT energies in a multi-coefficient fashion; thus, accurate DFT-based and ab initio reference data also become available. Since the experimental evaluation of torsional potentials faces quantitative problems, the outcome of high-level theoretical calculations is expected to be reliably used in further investigation on structure and conformational distribution of this system.     

Interaction energies in hydrogen-bonded systems: a testing ground for subsystem formulation of density-functional theory

The formalism based on the total energy bifunctional (E[rhoI,rhoII]) is used to derive interaction energies for several hydrogen-bonded complexes (water dimer, HCN-HF, H2CO-H2O, and MeOH-H2O). Benchmark ab initio data taken from the literature were used as a reference in the assessment of the performance of gradient-free [local density approximation (LDA)] and gradient-dependent [generalized gradient approximation (GGA)] approximations to the exchange-correlation and nonadditive kinetic-energy components of E[rhoI,rhoII]. On average, LDA performs better than GGA. The average absolute error of calculated LDA interaction energies amounts to 1.0 kJ/mol. For H2CO-H2O and H2O-H2O complexes, the potential-energy curves corresponding to the stretching of the intermolecular distance are also calculated. The positions of the minima are in a good agreement (less than 0.2 A) with the reference ab initio data. Both variational and nonvariational calculations are performed to assess the energetic effects associated with complexation-induced deformations of molecular electron densities.     

High pressure-high temperature phase diagram of ammonia

The high pressure (P)-high temperature (T) phase diagram of solid ammonia has been investigated using diamond anvil cell and resistive heating techniques. The III-IV transition line has been determined up to 20 GPa and 500 K both on compression and decompression paths. No discontinuity is observed at the expected location for the III-IV-V triple point. The melting line has been determined by visual observations of the fluid-solid equilibrium up to 9 GPa and 900 K. The experimental data are well fitted by a Simon-Glatzel equation in the covered P-T range. These transition lines and their extrapolations are compared to the reported ab initio calculations.     

Infrared and Raman spectra, ab initio calculations of structure and vibrational assignment of 1-fluoro-2-butyne.

The infrared spectra (3500-50 cm(-1)) of the gas and solid and the Raman spectra (3500-50 cm(-1)) of the liquid and solid have been recorded for 1-fluoro-2-butyne, CH3-C-triple bond-C-CH2F. Equilibrium geometries and energies have been determined by ab initio and hybrid DFT methods using a number of basis sets. A vibrational assignment is proposed based on the force constants, relative intensities, depolarization ratios from the ab initio and DFT calculations and on vibrational-rotational band contours obtained using the calculated equilibrium geometries. From calculated energies it is shown that the CH3 group exhibits almost completely free rotation which is in agreement with the observation of Coriolis sub-band structure in two of the degenerate methyl vibrations. The results are compared to the corresponding quantities for some similar molecules.     

Frozen density functional free energy simulations of redox proteins: computational studies of the reduction potential of plastocyanin and rusticyanin

The evaluation of reduction potentials of proteins by ab initio approaches presents a major challenge for computational chemistry. This is addressed in the present investigation by reporting detailed calculations of the reduction potentials of the blue copper proteins plastocyanin and rusticyanin using the QM/MM all-atom frozen density functional theory, FDFT, method. The relevant ab initio free energies are evaluated by using a classical reference potential. This approach appears to provide a general consistent and effective way for reproducing the configurational ensemble needed for consistent ab initio free energy calculations. The FDFT formulation allows us to treat a large part of the protein quantum mechanically by a consistently coupled QM/QM/MM embedding method while still retaining a proper configurational sampling. To establish the importance of proper configurational sampling and the need for a complete representation of the protein+solvent environment, we also consider several classical approaches. These include the semi-macroscopic PDLD/S-LRA method and classical all-atom simulations with and without a polarizable force field. The difference between the reduction potentials of the two blue copper proteins is reproduced in a reasonable way, and its origin is deduced from the different calculations. It is found that the protein permanent dipole tunes down the reduction potential for plastocyanin compared to the active site in regular water solvent, whereas in rusticyanin it is instead tuned up. This electrostatic environment, which is the major effect determining the reduction potential, is a property of the entire protein and solvent system and cannot be ascribed to any particular single interaction.     

Quantum wave-packet dynamics of H+HLi scattering: reaction cross section and thermal rate constant

The channel specific and initial state-selected reaction cross section and temperature-dependent rate constant for the title system is calculated with the aid of a time-dependent wave-packet approach and using the ab initio potential energy surface of Dunne et al. [Chem. Phys. Lett. 336, 1 (2001)]. All partial-wave contributions up to the total angular momentum J=74 are explicitly calculated within the coupled states (CS) approximation. Companion calculations are also carried out employing the standard as well as the uniform J-shifting (JS) approximation. The overall variation of reaction cross sections corresponds well to the behavior of a barrierless reaction. The hydrogen exchange channel yielding HLi+H products is seen to be more favored over the HLi depletion channel yielding Li+H(2) products at low and moderate collision energies. Sharp resonance features are observed in the cross-section results for the HLi depletion channel at low energies. Resonance features in the reaction cross sections average out with various partial-wave contributions, when compared to the same observed in the individual reaction probability curve. Except near the onset of the reaction, the vibrational and rotational excitation of the reagent HLi, in general, does not dramatically influence the reactivity of either channel. The thermal rate constants calculated up to 4000 K show nearly Arrhenius type behavior. The rate constant decreases with vibrational excitation of the reagent HLi, indicating that the cold HLi molecules are efficiently depleted in the reactive encounter with H at relatively low temperatures. The results obtained from the JS approximation are found to agree well qualitatively with the CS results.     

Conformational stability,barriers to internal rotation,structural parameters,ab initio calculations,and vibrational assignment of cyclopropanecarboxaldehyde

The asymmetric torsional potential function, conformational energy difference, vibrational frequencies, and structural parameters of Cyclopropane-carboxaldehyde have been obtained from ab initio calculations at the 3–21G and/or 6-31G^* baiss set levels. These results have allowed for a reinterpretation or clarification of some of the corresponding results obtained from experiment. The conformations that have the oxygen atom oriented cis and trans to the three-membered ring are observed and calculated to be the most stable and high energy forms in the gaseous phase, respectively. From the ab initio calculations using the 6–31 G^* basis set, the energy difference between the two conformers is 114 cm^–1. For the liquid, the trans conformer is more stable and is the only rotamer present in the annealed solid. Based on a combination of results obtained from ab initio calculations, microwave spectroscopy, and the electron diffraction technique,r _o structural parameters have been obtained for both conformations.     

Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy

In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.     

Quantum and classical studies of vibrational motion of CH5+ on a global potential energy surface obtained from a novel ab initio direct dynamics approach

We report a full dimensional, ab initio based potential energy surface for CH(5) (+). The ab initio electronic energies and gradients are obtained in direct-dynamics calculations using second-order M?ller-Plesset perturbation theory with the correlation consistent polarized valence triple zeta basis. The potential energy and the dipole moment surfaces are fit using novel procedures that ensure the full permutational symmetry of the system. The fitted potential energy surface is tested by comparing it against additional electronic energy calculations and by comparing normal mode frequencies at the three lowest-lying stationary points obtained from the fit against ab initio ones. Well-converged diffusion Monte Carlo zero-point energies, rotational constants, and projections along the CH and HH bond lengths and the tunneling coordinates are presented and compared with the corresponding harmonic oscillator and standard classical molecular dynamics ones. The delocalization of the wave function is analyzed through comparison of the CH(5) (+) distributions with those obtained when all of the hydrogen atoms are replaced by (2)H and (3)H. The classical dipole correlation function is examined as a function of the total energy. This provides a further probe of the delocalization of CH(5) (+).     

A combination of pseudopotentials and density functionals: Results for Cun, Cun, Agn, and Agn clusters (n ≤ 4)

Structures and binding energies have been calculated for neutral and singly ionized Cu and Ag clusters with up to four atoms. The valence-electron system is treated at the ab initio SCF level; core-valence interaction is accounted for by semi-empirical pseudopotentials, corrected for core polarization; valence correlation is included using a local spin-density-functional approximation, corrected for self-interaction. The results are compared to previous calculations for Li, Na and K clusters, and it is shown that, in spite of the different bulk crystal structure, small group 1a and 1b clusters have many properties in common.     

Infrared spectra of the complexes of trifluoroethene with dimethyl ether, acetone, and oxirane: a cryosolution study

Infrared spectra of solutions of trifluoroethene and dimethyl ether, acetone, or oxirane in liquid krypton and liquid argon have been studied. For each Lewis base the formation of a 1:1 complex with the Lewis acid was observed. The C-H stretching of trifluoroethene being perturbed by a strong Fermi resonance, the complexes with trifuloroethene-d were also investigated and showed that in each case the hydrogen bond between the acid and base is of the traditional, red-shifting type. The structures of the complexes were investigated using ab initio calculations. These indicate that with dimethyl ether and acetone two different isomeres can be formed, but with a single one detected in the solution in each case. The Fermi resonance in the complex with unlabeled trifluoroethene is discussed using data derived form ab initio potential and dipole hypersurface calculations. The complexation enthalpies of the complexes were obtained from temperature dependent studies of the solutions and are discussed in relation to the ab initio complexation energies and Monte Carlo free energy perturbation calculations of solvent effects.     

Comparison of AM1 and PM3 semiempirical to ab initio methods in the study of Diels-Alder reactions of butadiene and cyclopentadiene with cyanoethylenes

Assuming a concerted synchronous mechanism with one transition state of the Diels-Alder reactions, the structures of the transition states and the activation energies for the reactions of butadiene and cyclopentadiene with cyanoethylenes were calculated by AM1 and PM3 semiempirical methods. The structural parameters were compared with those obtained by high level Gaussian calculations, whereas the activation energies were compared both with the ab initio calculations and those obtained experimentally. The structural properties calculated with PM3 methods are in general in better agreement with the ab initio calculations. The low level ab initio calculations are in many cases worse than the semiempirical methods. All predicted activation energies with both semiempirical methods are up to 300% higher than the experimental values. The predicted reactivity is also opposite to the experimental data. Only the very high level Gaussian calculations are in good correlation with experimental results. The predicted selectivity of the reaction is also opposite to the experimental facts. Two explanations are offered for this discrepancy: AM1 and PM3 methods cannot handle the calculation of the concerted Diels-Alder transition states and are not recommended to be used for that purpose, or this Diels-Alder reaction is not concerted but is stepwise.     

FTIR and FT-Raman spectra, molecular geometry, vibrational assignments, first-order hyperpolarizability, ab initio and DFT calculations for 3,4-dimethoxybenzonitrile

Quantum chemical calculations of energies, geometrical structure and vibrational wave numbers of 3,4-dimethoxybenzonitrile (DMBN) were carried out by the ab initio Hartree-Fock (HF) and density functional theory (DFT) with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. Making use of the recorded data, the complete vibrational assignments are made and analysis of the observed fundamental bands of molecule is carried out. The geometries and normal modes of vibrations obtained from ab initio HF and B3LYP calculations are in good agreement with the experimentally observed data. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. The theoretical FTIR and FT-Raman spectra for the title molecule have been constructed.     

Simulations of the solid, liquid, and melting of 1-n-butyl-4-amino-1,2,4-triazolium bromide

Molecular dynamics simulations are used to study the solid and liquid properties and to predict the melting point of 1-n-propyl-4-amino-1,2,4-triazolium bromide ([patr][Br]) using a force field based on the one developed by Canongia Lopes et al. (J. Phys. Chem. B 2004, 108, 2038) for dialkyl substituted imidazolium salts, which was modified by including terms from the general AMBER force field. Electrostatic charges for the intermolecular interactions were determined from gas-phase ab initio electron structure calculations of the triazolium cation. Simulations of the solid state at 100 K reproduced the experimental density to within 4%. Simulations from 100 K to the melting point and the liquid from 333 to 500 K were performed to determine the temperature dependence of the densities of the two phases. The structures of the solid and liquid phases are characterized with radial distribution functions, which show that there are strong spatial correlations among neighboring ion pairs in liquid [patr][Br]. The dynamic behavior of the ions in the liquid state is also studied by computing velocity autocorrelation functions and the mean-square displacements between the ions. The melting point is determined by simulating void-induced melting. Changes in the density, intermolecular energy, and Lindemann index are used as indicators of the melting transition. The computed melting point is 360 +/- 10 K, which is within 10% of the experimental value 333 K.     

Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods

Optimized geometries and total energies of some conformers of alpha- and beta-D-galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of alpha- and beta-D-galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units alpha 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles psi and phi of the glycosidic linkage are considered. In each calculation, at each increment of psi and phi, using a step of 30 degrees from 0 to 330 degrees, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*.     

Equation-of-motion coupled-cluster study on exciton states of polyethylene with periodic boundary condition

Equation-of-motion coupled cluster with singles and doubles (EOM-CCSD) method has been applied to exciton states of polyethylene using ab initio crystal Hartree-Fock method with one-dimensional periodic boundary condition. Full transformation of two-electron integrals from atomic-orbital basis to crystal-orbital basis has been performed for EOM-CCSD calculations. In order to make transformed integrals to have correct properties of translational symmetry, a lattice summation scheme has been proposed. The EOM-CCSD excitation energies have been obtained for the lowest singlet and triplet exciton states of polyethylene. The excitation energies converge with system size much faster than oligomer calculations using n-alkanes. Quasiparticle energy-level calculations by second-order many-body perturbation theory and by solving the inverse Dyson equation have also been performed to obtain exciton binding energies. Basis set dependencies on excitation energy, quasiparticle band gap, and exciton binding energy have been investigated. At the 6-31+G level, the excitation energy of the lowest singlet-exciton state and its binding energy are calculated to be 8.1 and 3.2 eV, respectively. The calculated excitation energy is well comparable with the corresponding experimental value, 7.6 eV.     

Free energy perturbation study of water dimer dissociation kinetics

An efficient approach is described for using accurate ab initio calculations to determine the rates of elementary condensation and evaporation processes that lead to nucleation of aqueous aerosols. The feasibility of the method is demonstrated in an application to evaporation rates of water dimer at 230 K. The method, known as ABC-FEP (ab initio/classical free energy perturbation), begins with a calculation of the potential of mean force for the dissociation (evaporation) of small water clusters using a molecular dynamics (MD) simulation with a model potential. The free energy perturbation is used to calculate how changing from the model potential to a potential calculated from ab initio methods would alter the potential of mean force. The difference in free energy is the Boltzmann-weighted average of the difference between the ab initio and classical potential energies, with the average taken over a sample of configurations from the MD simulation. In principle, the method does not require a highly accurate model potential, though more accurate potentials require fewer configurations to achieve a small sampling error in the free energy perturbation step. To test the feasibility of obtaining accurate potentials of mean force from ab initio calculations at a modest number of configurations, the free energy perturbation method has been used to correct the errors when some standard models for bulk water (SPC, TIP4P, and TIP4PFQ) are applied to water dimer. To allow a thorough exploration of sampling issues, a highly accurate fit to results of accurate ab initio calculations, known as SAPT-5s, as been used a proxy for the ab initio calculations. It is shown that accurate values for a point on the potential of mean force can be obtained from any of the water models using ab initio calculations at only 50 configurations. Thus, this method allows accurate simulations of small clusters without the need to develop water models specifically for clusters.