Modeling the sorption dynamics of NaH using a reactive force field

We have parametrized a reactive force field for NaH, ReaxFF(NaH), against a training set of ab initio derived data. To ascertain that ReaxFF(NaH) is properly parametrized, a comparison between ab initio heats of formation of small representative NaH clusters with ReaxFF(NaH) was done. The results and trend of ReaxFF(NaH) are found to be consistent with ab initio values. Further validation includes comparing the equations of state of condensed phases of Na and NaH as calculated from ab initio and ReaxFF(NaH). There is a good match between the two results, showing that ReaxFF(NaH) is correctly parametrized by the ab initio training set. ReaxFF(NaH) has been used to study the dynamics of hydrogen desorption in NaH particles. We find that ReaxFF(NaH) properly describes the surface molecular hydrogen charge transfer during the abstraction process. Results on heat of desorption versus cluster size shows that there is a strong dependence on the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. To gain more insight into the structural transformations of NaH during thermal decomposition, we performed a heating run in a molecular dynamics simulation. These runs exhibit a series of drops in potential energy, associated with cluster fragmentation and desorption of molecular hydrogen. This is consistent with experimental evidence that NaH dissociates at its melting point into smaller fragments.     

DFT and ab initio quantum chemical studies on p-cyanobenzoic acid

The Fourier transform infrared (FTIR) and FT-Raman spectra of p-cyanobenzoic acid (CBA) have been recorded in the range 4000-400 and 4000-100 cm(-1), respectively. The complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman data. The vibrational frequencies determined experimentally were compared with theoretical wavenumbers obtained from ab initio HF and DFT-B3LYP gradient calculations employing 6-31G**, 6-311++G** and cc-pVTZ basis sets for the optimised geometry of the compound. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The normal coordinate analysis was also carried out with ab initio force fields utilising Wilson's FG matrix method. The interactions of cyano and carboxylic acid groups with the skeletal vibrational modes were investigated.     

An ab initio study of intermolecular hydrogen bonding between small peptide fragments

Several small peptide fragments are investigated with ab initio (Hartree-Fock) calculations, using Gaussian basis sets. Complexation energies, net atomic charges, and optimum geometries are obtained. The geometries predicted by the STO -6G, and 6–31G* basis sets are quite similar, whereas the binding energies obtaiend by the 6–31G calculations are higher than those obtained with STO -6G and 6–31G* basis sets.     

Intermolecular electrostatic energies using density fitting

A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H2O dimer, Mg2+-H2O, Cu+-H2O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies.     

Vibrational spectroscopy (FTIR and FTRaman) investigation using ab initio (HF) and DFT (B3LYP) calculations on the structure of 3-Bromo phenol

The FT-IR and FT-Raman spectra of 3-Bromo phenol (3-BP) molecule have been recorded using Bruker IFS 66V spectrometer in the range of 4000-100 cm(-1). The molecular geometry and vibrational frequencies in the ground state are calculated by using the ab initio Hartree-fock (HF) and DFT (B3LYP) methods with 6-31G (d, p) and 6-311G (d, p) basis sets. 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 differences between the observed and scaled wave number values of most of the fundamentals are very small in DFT than HF. The inductive effect of halogen atom in the molecule has also been investigated.     

Interactions between anionic and neutral bromine and rare gas atoms

High-quality, ab initio potential energy functions are obtained for the interaction of bromine atoms and anions with atoms of the six rare gases (Rg) from He to Rn. The potentials of the nonrelativistic (2)Sigma(+) and (2)Pi electronic states arising from the ground-state Br((2)P)-Rg interactions are computed over a wide range of internuclear separations using a spin-restricted version of the coupled cluster method with single and double excitations and noniterative correction to triple excitations [RCCSD(T)] with an extrapolation to the complete basis set limit, from basis sets of d-aug-cc-pVQZ and d-aug-cc-pV5Z quality. These are compared with potentials derived previously from experimental measurements and ab initio calculations. The same approach is used also to refine the potentials of the Br(-)-Rg anions obtained previously [Buchachenko et al., J. Chem. Phys. 125, 064305 (2006)]. Spin-orbit coupling in the neutral species is included both ab initio and via an atomic approximation; deviations between two approaches that are large enough to affect the results significantly are observed only in the Br-Xe and Br-Rn systems. The resulting relativistic potentials are used to compute anion zero electron kinetic energy photoelectron spectra, differential scattering cross sections, and the transport coefficients of trace amounts of both anionic and neutral bromine in the rare gases. Comparison with available experimental data for all systems considered proves a very high precision of the present potentials.     

Molecular dynamics and Monte Carlo simulations for the structure of the aqueous trimethylammonium chloride solution in the 0.2-1 molar range

Molecular dynamics and Monte Carlo simulations have been performed for characterizing the structure of the 0.2 and 1 molar aqueous trimethylammonium chloride solutions. Atomic charges were derived through the CHELPG and RESP fits to the molecular electrostatic potentials calculated for the cation in water at the IEF-PCM/B3LYP level using the 6-31G* and 6-311++G** basis sets. Maxima and minima of the calculated radial distribution functions were not sensitive to the four atomic charge sets. Simulated solution structures suggest non-negligible solute-solute interactions and remarkable inhomogeneity at both concentrations. This means that equilibrium ratios, derived for conformers/tautomers by means of ab initio calculations with the IEF-PCM continuum dielectric solvent model, should be corrected for free energy changes following solute association when compared to experimental data obtained for the 0.1-1 molar aqueous solutions.     

High level ab initio study of the structure and vibrational spectra of HO(2)NO(2)

A high-level ab initio study has been performed on the conformational structure and vibrational spectra of HO(2)NO(2). Calculations carried out with coupled-cluster methods using a series of Pople and Dunning basis sets reveal that there is a significant basis set dependence on the predicted ab initio structure. Higher angular momentum basis sets are shown to be necessary in order to bring the calculated structure into agreement with experimental rotational constants. Harmonic vibrational frequencies of HO(2)NO(2) are computed at the CCSD(T)/aug-cc-pVTZ level of theory while the corresponding vibrational anharmonicities are calculated at the MP2/cc-pVTZ level. In addition, the absorption cross sections of OH stretching overtones in HO(2)NO(2) are calculated using a dipole function computed at the QCISD level of theory and found to be in good agreement with the available experimental data.     

Interaction potentials for Br(-)-Rg (Rg=He-Rn): spectroscopy and transport coefficients

High-level ab initio CCSD(T) calculations are performed in order to obtain accurate interaction potentials for the Br(-) anion interacting with each rare gas (Rg) atom. For the Rg atoms from He to Ar, two approaches are taken. The first one implements a relativistic core potential and an aug-cc-pVQZ basis set for bromine, an aug-cc-pV5Z basis set for Rg, and a set of bond functions placed at the midpoint of the Rg-Br distance. The second one uses the all-electron approximation with aug-cc-pV5Z bases further augmented by an extra diffuse function in each shell. Comparison reveals close similarity between both sets of results, so for Rg atoms from Kr to Rn only the second approach is exploited. Calculated potentials are assessed against the previous empirical, semiempirical, and ab initio potentials, and against available beam scattering data, zero electron kinetic energy spectroscopic data, and various sets of the measured ion mobilities and diffusion coefficients. This multiproperty analysis leads to the conclusion that the present potentials are consistently good for the whole series of Br(-)-Rg pairs over the whole range of internuclear distances covered.     

Evaluation of the charge penetration energy between non-orthogonal molecular orbitals using the Spherical Gaussian Overlap approximation

An overlap dependent formula for evaluating the charge penetration energy between non-orthogonal molecular orbitals is derived using the Spherical Gaussian Overlap approximation. When combined with an accurate multipole representation of the electrostatic energy, such as in the effective fragment potential method, ab initio electrostatic energies are generally reproduced to within 0.2 kcal/mol for a variety of molecular dimers and basis sets. The only larger error is for the DMSO dimer, where the electrostatic energy is overestimated by 0.7 kcal/mol.     

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.     

Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit

Structural properties of liquid water at ambient temperature were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (CPAIMD) simulations combined with the Kohn-Sham (KS) density functional theory and the BLYP exchange-correlation functional for the electronic structure. Unlike other recent work on the same subject, where plane-wave (PW) or hybrid Gaussian/plane-wave basis sets were employed, in the present paper, a discrete variable representation (DVR) basis set is used to expand the KS orbitals, so that with the real-space grid adapted in the present work, the properties of liquid water could be obtained very near the complete basis set limit. Structural properties of liquid water were extracted from a 30 ps CPAIMD-BLYP/DVR trajectory at 300 K. The radial distribution functions (RDFs), spatial distribution functions, and hydrogen bond geometry obtained from the CPAIMD-BLYP/DVR simulation are generally in good agreement with the most up to date experimental measurements. Compared to recent ab initio MD simulations based on PW basis sets, less significant overstructuring was found in the RDFs and the distributions of hydrogen bond angles, suggesting that previous plane-wave and Gaussian basis set calculations have exaggerated the tendency toward overstructuring.     

More user-friendly phosphines? Molecular structure of methylphosphine and its adduct with borane, studied by gas-phase electron diffraction and quantum chemical calculations

The molecular structures of methylphosphine (CH(3)PH(2)) and methylphosphine-borane (CH(3)PH(2).BH(3)) have been determined from gas-phase electron diffraction data and rotational constants, employing the SARACEN method. The experimental geometric parameters generally showed a good agreement with those obtained using ab initio calculations and previous microwave spectroscopy studies. In order to assess the accuracy of the calculated structures a range of ab initio methods were used, including the CCSD(T) method, with correlation-consistent basis sets. The structural environment around the phosphorus atom was found to change significantly upon complexation with borane, with the P-C bond length shortening and the bond angles widening.     

Prediction of the thermophysical properties of pure neon, pure argon, and the binary mixtures neon-argon and argon-krypton by Monte Carlo simulation using ab initio potentials

Gibbs ensemble Monte Carlo simulations were used to test the ability of intermolecular pair potentials derived ab initio from quantum mechanical principles, enhanced by Axilrod-Teller triple-dipole interactions, to predict the vapor-liquid phase equilibria of pure neon, pure argon, and the binary mixtures neon-argon and argon-krypton. The interaction potentials for Ne-Ne, Ar-Ar, Kr-Kr, and Ne-Ar were taken from literature; for Ar-Kr a different potential has been developed. In all cases the quantum mechanical calculations had been carried out with the coupled-cluster approach [CCSD(T) level of theory] and with correlation consistent basis sets; furthermore an extrapolation scheme had been applied to obtain the basis set limit of the interaction energies. The ab initio pair potentials as well as the thermodynamic data based on them are found to be in excellent agreement with experimental data; the only exception is neon. It is shown, however, that in this case the deviations can be quantitatively explained by quantum effects. The interaction potentials that have been developed permit quantitative predictions of high-pressure phase equilibria of noble-gas mixtures.     

Density embedded VB/MM: a hybrid ab initio VB/MM with electrostatic embedding

A hybrid QM/MM method that combines ab initio valence-bond (VB) with molecular mechanics (MM) is presented. The method utilizes the ab initio VB approach to describe the reactive fragments and MM to describe the environment thus allows VB calculations of reactions in large biological systems. The method, termed density embedded VB/MM (DE-VB/MM), is an extension of the recently developed VB/MM method. It involves calculation of the electrostatic interaction between the reactive fragments and their environment using the electrostatic embedding scheme. Namely, the electrostatic interactions are represented as one-electron integrals in the ab initio VB Hamiltonian, hence taking into account the wave function polarization of the reactive fragments due to the environment. Moreover, the assumptions that were utilized in an earlier version of the method, VB/MM, to formulate the electrostatic interactions effect on the off-diagonal matrix elements are no longer required in the DE-VB/MM methodology. Using DE-VB/MM, one can calculate, in addition to the adiabatic ground state reaction profile, the energy of the diabatic VB configurations as well as the VB state correlation diagram for the reaction. The abilities of the method are exemplified on the identity SN2 reaction of a chloride anion with methyl chloride in aqueous solution. Both the VB configurations diagram and the state correlation diagram are presented. The results are shown to be in very good agreement with both experimental and other computational data, suggesting that DE-VB/MM is a proper method for application to different reactivity problems in biological systems.     

Green's function calculation of through‐bond electronic coupling in donor–bridge–acceptor model systems II: Importance factors applied to atomic sites

Importance factors, associated with the Green's function formalism, are introduced. They are applied for the determination of the relative atomic site contribution to the electronic interaction propagation in a molecular system. The calculation is performed at the Hartree–Fock (self‐consistent) level, using ab initio STO‐3G, 4‐31G, and D95 basis sets. The results are compared with those obtained from the charge densities of the appropriate molecular orbitals at the ab initio STO‐3G level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

A systematic ab initio study of the equilibrium geometry and vibrational wave numbers of bismuthine

The equilibrium structure and the harmonic and anharmonic force fields of BiH(3) are determined by high-level ab initio calculations using a variety of correlation treatments, basis sets, and pseudopotentials, partly in combination with core polarization potentials. Spin-orbit effects are included by a configuration interaction treatment. This systematic study serves to establish a reliable computational protocol for such calculations and, in particular, to minimize basis set superposition errors through an improved new basis set and/or counterpoise corrections. Using the recommended procedures, the best ab initio results for the equilibrium geometry and the fundamental vibrational wave numbers are in good agreement with the available experimental data, which further supports the recent spectroscopic identification of BiH(3). The ground-state total atomization energy of BiH(3) is predicted to be 153.1 kcal/mol.