Theoretical and computational investigations on thermodynamic properties, effective site diameters, and molecular free volume of carbon disulfide fluid

A newly proposed theory [R. Laghaei et al., J. Chem. Phys. 124, 154502 (2006)] was extended to polyatomics and applied to compute the density and temperature dependence of the effective site diameters of carbon disulfide fluids. The generic van der Waals (GvdW) theory was also extended to polyatomics in order to calculate the GvdW parameters and the molecular free volume using the effective site diameters as the repulsion-attraction separation distance. A three-site Lennard-Jones potential available in the literature was slightly modified and used in Monte Carlo simulations to obtain the functions appearing in the effective site diameter and GvdW expressions. The interaction potential was examined to reproduce the fluid phase thermodynamic properties using Gibbs ensemble Monte Carlo simulations and also the equation of state in the liquid phase using NVT Monte Carlo (NVT-MC) simulations. Comparison between the simulation results and experimental data shows excellent agreement for the densities of the coexisting phases, the vapor pressure, properties of the predicted critical point, and the equation of state. NVT-MC simulations were performed over a wide range of densities and temperatures in sub- and supercritical regions to compute the effective site diameters, the GvdW parameters, and the molecular free volume. The molecular structure in terms of the site-site pair correlation functions, the density dependence of the effective site diameters, and the density and temperature dependence of the GvdW parameters and molecular free volume were studied and discussed. The GvdW parameters were fitted to empirical expressions as a function of density and temperature. The computed molecular free volume will be used in future investigations to study the transport properties of carbon disulfide.     

Quantum vibrational analysis of hydrated ions using an ab initio potential

We present full-dimensional potential energy surfaces (PESs) for hydrated chloride based on the sum of ab initio (H(2)O)Cl(-), (H(2)O)(2), and (H(2)O)(3) potentials. The PESs are shown to predict minima and corresponding harmonic frequencies accurately on the basis of comparisons with previous and new ab initio calculations for (H(2)O)(2)Cl(-), (H(2)O)(3)Cl(-), and (H(2)O)(4)Cl(-). An estimate of the effect of the 3-body water interaction is made using a simple 3-body water potential that was recently fit to tens of thousands of ab initio 3-body energies. Anharmonic, coupled vibrational calculations are presented for these clusters, using the "local monomer model" for the high frequency intramolecular modes. This model is tested against previous "exact" calculations for (H(2)O)Cl(-). Radial distribution functions at 0 K obtained from quantum zero-point wave functions are also presented for the (H(2)O)(2)Cl(-) and (H(2)O)(3)Cl(-) clusters.     

Comparative studies on the structures,infrared spectrum,and thermodynamic properties of phthalocyanine using ab initio Hartree–Fock and density functional theory methods

The molecular structure, vibrational spectrum, standard thermodynamic functions, and enthalpy of formation of free base phthalocyanine (Pc) have been studied using the density functional theory B3LYP procedure, as well as the ab initio Hartree–Fock method. Various basis sets 3‐21G, 6‐31G*, and LANL2DZ have been employed. The results obtained at various levels are discussed and compared with each other and with the available experimental data. It is shown that calculations performed at the Hartree–Fock level cannot produce a reliable geometry and related properties such as the dipole moment of Pc and similar porphyrin‐based systems. Electron correlation must be included in the calculations. The basis set has comparatively less effect on the calculated results. The results derived at the B3LYP level using the smaller 3‐21G and LANL2DZ basis sets are very close to those produced using the medium 6‐31G* basis set. The geometry of Pc obtained at the B3LYP level has D_2h symmetry and the diameter of the central macrocycle is about 4 Å. The enthalpy of formation of Pc in the gas phase has been predicted to be 1518.50 kJ/mol at the B3LYP/6‐311G(2d,2p)//B3LYP/6‐31G* level via an isodesmic reaction. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Ab initio effective core potential studies on polymers

Ab initio crystal orbital calculation with the effective core potential (ECP) approximation is performed on infinite poly-yne, all-trans-polyethylene, and all-trans-polysilane. The optimized bond lengths of poly-yne are predicted to be 1.130 Å and 1.321 Å with the split valence LP-31G basis set and agree fairly well with 4-31G results, 1.166 Å and 1.339 Å. The energy band structures of poly-yne and all-trans-polyethylene obtained from ECP calculations are in reasonable agreement with those from the all electron calculations. The fully optimized geometries of all-trans-polysilane are also predicted with the LP-31G basis set asr _SiSi = 2.264 Å,r _SiH = 1.493 Å, \(\sphericalangle\) SiSiSi = 118.97 °, and \(\sphericalangle\) HSiH = 100.35 °. The computational time for calculations of polysilane is found roughly to be comparative to that of polyethylene under ECP approximations.     

Quantum vibrational analysis and infrared spectra of microhydrated sodium ions using an ab initio potential

We present a full-dimensional potential energy surface and a dipole moment surface (DMS) for hydrated sodium ion. These surfaces are based on an n-body expansion for both the potential energy and the dipole moment, truncated at the two-body level for the H(2)O-Na(+) interaction and also for the DMS. The water-water interaction is truncated at the three-body level. The new full-dimensional two-body H(2)O-Na(+) potential is a fit to roughly 20,000 coupled-cluster single double (triple)/aug-cc-pVTZ energies. Properties of this two-body potential and the potential describing (H(2)O)(n)Na(+) clusters, with n up to 4 are given. We then report anharmonic, coupled vibrational calculations with the "local-monomer model" to obtain infrared spectra and also 0 K radial distribution functions for these clusters. Some comparisons are made with the recent infrared predissociation spectroscopy experiments of Miller and Lisy [J. Am. Chem. Soc. 130, 15381 (2008).].     

Critical and phase-equilibrium properties of an ab initio based potential model of methanol and 1-propanol using two-phase molecular dynamics simulations

Two-phase molecular dynamics simulations employing a Monte Carlo volume sampling method were performed using an ab initio based force field model parameterized to reproduce quantum-mechanical dimer energies for methanol and 1-propanol at temperatures approaching the critical temperature. The intermolecular potential models were used to obtain the binodal vapor-liquid phase dome at temperatures to within about 10 K of the critical temperature. The efficacy of two all-atom, site-site pair potential models, developed solely from the energy landscape obtained from high-level ab initio pair interactions, was tested for the first time. The first model was regressed from the ab initio landscape without point charges using a modified Morse potential to model the complete interactions; the second model included point charges to separate Coulombic and dispersion interactions. Both models produced equivalent phase domes and critical loci. The model results for the critical temperature, density, and pressure, in addition to the sub-critical equilibrium vapor and liquid densities and vapor pressures, are compared to experimental data. The model's critical temperature for methanol is 77 K too high while that for 1-propanol is 80 K too low, but the critical densities are in good agreement. These differences are likely attributable to the lack of multi-body interactions in the true pair potential models used here.     

Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose conformations

Ab initio geometry optimization was carried out on 10 selected conformations of maltose and two 2‐methoxytetrahydropyran conformations using the density functional denoted B3LYP combined with two basis sets. The 6‐31G* and 6‐311++G** basis sets make up the B3LYP/6‐31G* and B3LYP/6‐311++G** procedures. Internal coordinates were fully relaxed, and structures were gradient optimized at both levels of theory. Ten conformations were studied at the B3LYP/6‐31G* level, and five of these were continued with full gradient optimization at the B3LYP/6‐311++G** level of theory. The details of the ab initio optimized geometries are presented here, with particular attention given to the positions of the atoms around the anomeric center and the effect of the particular anomer and hydrogen bonding pattern on the maltose ring structures and relative conformational energies. The size and complexity of the hydrogen‐bonding network prevented a rigorous search of conformational space by ab initio calculations. However, using empirical force fields, low‐energy conformers of maltose were found that were subsequently gradient optimized at the two ab initio levels of theory. Three classes of conformations were studied, as defined by the clockwise or counterclockwise direction of the hydroxyl groups, or a flipped conformer in which the ψ‐dihedral is rotated by ∼180°. Different combinations of ω side‐chain rotations gave energy differences of more than 6 kcal/mol above the lowest energy structure found. The lowest energy structures bear remarkably close resemblance to the neutron and X‐ray diffraction crystal structures. © 2000 John Wiley & Sons, Inc. * J Comput Chem 21: 1204–1219, 2000     

Insight into the electronic,optical, thermodynamic,and thermoelectric properties of novel chalcogenides: An ab initio study

Ternary chalcogenides with direct band gaps are remarkable for being used in many optoelectronic applications. We investigated for structural, electronic, optical, and transport characteristics of new Ba₂CdCh₃ (Ch = S, Se, Te) semiconductors using the full-potential linearized augmented plane wave (FP-LAPW) approach. The band structures of these compounds confirm a direct type of band gap. The phonon dispersion plots along with the predicted negative formation energies suggest these compounds to be thermodynamically stable. Additionally, important optical characteristics were computed and thoroughly explained. The different ELF spectra were calculated in which strong peak correlate precisely with plasma resonance. Moreover, we also explored the thermodynamic characteristics of the ternary systems by employing the quasi-harmonic Debye model. These compounds were also suitable for thermoelectric applications based on the detailed discussion of the computed significant thermoelectric properties. In general, the advancement of various and promising semiconducting devices and their applications will be supported by the present study.     

Structural, vibrational and ab initio studies of L-histidine oxalate

Single crystals of L-histidine oxalate were obtained by slow evaporation of an aqueous solution at room temperature. The grown crystals have been subjected to X-ray diffraction (XRD), Infrared, and Raman spectroscopy. The title compound crystallises in the non-centrosymmetric space group P2(1)2(1)2(1,) the crystal cohesion is achieved by relatively strong hydrogen bonds, so that the NH3 groups show significant distortion with respect to the tetrahedral symmetry. Raman and infrared spectra of the title compound were recorded in the frequency range 300-3200 and 400-4000 cm-1, respectively. To obtain a reliable assignment of the observed spectral lines, we have calculated the geometry and the frequencies of the vibrational modes of histidine cation and the oxalate anion using the semi empirical PM3 method.     

Structure and properties of a model of deoxyheme,an ab initio SCF calculation

Ab initio SCF calculations have been used to study the structure and the electronic properties of four- and five-coordinate Fe(II) porphyrins. The following systems have been considered: FeP (P = porphine dianion) (S = 1 and S = 2) and Fe(NH₂)₄ (S = 1) as four-coordinate systems. FePNH₃, Fe(NH₂)₄NH₃ and Fe(NH₂)₄1m as models of the deoxyheme (S = 2). Fe(NH₂)₄SH (S = 2) as a model of the reduced cytochrome P450. The basis sets used are either of the split-valence type or of double-zeta quality. The ground-state electronic configurations have been assigned. The potential energy curve of FePNH₃, as a function of the out-of-plane displacement of the iron atom, has a minimum for a displacement of 0.32 Å. a value significantly smaller than the accepted value of 0.6 Å in human deoxyhemoglobin. The out-of-plane displacement is larger, by ≈ 0.2 Å, when a mercaptide ligand replaces the ammonia or imidazole ligand. The electric field gradient tensor, the quadrupole splitting and the asymmetry parameter have been calculated and compared with the experimental values derived from the ⁵⁷Fe Mössbauer spectra.     

Kinetic study on the H + SiH4 abstraction reaction using an ab initio potential energy surface

Variational transition state theory calculations with the correction of multidimensional tunneling are performed on a 12-dimensional ab initio potential energy surface for the H + SiH(4) abstraction reaction. The surface is constructed using a dual-level strategy. For the temperature range 200-1600 K, thermal rate constants are calculated and kinetic isotope effects for various isotopic species of the title reaction are investigated. The results are in very good agreement with available experimental data.     

Vibrational levels of methanol calculated by the reaction path version of MULTIMODE, using an ab initio, full-dimensional potential

An accurate potential energy surface has been determined for methanol from ab initio potential data at the CCSD(T) level of theory with an aug-cc-pVTZ basis. The resulting potential function is valid over all twelve vibrational degrees of freedom for all near-equilibrium and torsional configurations. A torsional reaction path has been derived for this potential, from which the low-lying vibrational levels of methanol have been calculated by the reaction path version of MULTIMODE. Comparisons with experiment and other calculations are made.     

Monte Carlo simulation of liquid hydroxylamine using ab initio intermolecular potential functions

A potential model for intermolecular interactions between hydroxylamine (NH₂OH) molecules based on ab initio quantum mechanical calculations is reviewed and critically assessed by analyzing results from a Monte Carlo simulation of liquid hydroxylamine. The liquid structure is studied in detail using radial, energy, and angular distribution functions, coordination numbers, and their distribution. Results indicate a large first solvation shell (5.3 Å), which contains 13 molecules, out of which only 4 are truly bonded by nonlinear, low-energy hydrogen bonds. These are of either the OH…O or the OH…N type, as NH…O and NH…N linear bonds are considerably suppressed, and no cyclic dimers are found. The dependence of the structural and physical properties on the simulation characteristics has also been investigated.     

Conformational studies on L-serine phosphate and hydrated L-serine phosphate using ab initio SCF calculations

Ab initio MO -LCAO -SCF calculations using an STO -3G basis set were performed to find the most stable conformations of L -serine phosphate and hydrated L -serine phosphate. The most favorable conformation of L -serine phosphate is found to be one where the bond sequence O? C? C? C is trans and P? O? C? C gauche, and a very short hydrogen bond is formed between an oxygen atom of the phosphate group and a hydrogen atom of the ammonium group. For hydrated L -serine phosphate, a bridge-type hydration in which a water molecule links a phosphate oxygen and an ammonium hydrogen displays particularly low energy. In the four-hydrated L -serine phosphate anion, the most favorable conformation is such a bridged one having a rather extended configuration with regard to the bond sequences O? C? C? C and P? O? C? C.     

A comparative study of nitrogen physisorption on different C70 crystal structures using an ab initio based potential

Quantum mechanical calculations are performed using the recently developed hybrid method for interaction energies to determine atom site Lennard-Jones potential parameters for the interactions of molecular nitrogen with C(70) molecules. This ab initio based potential is used in grand canonical Monte Carlo simulations to predict surface adsorption properties of N(2) on five known C(70) structures: rhombohedral, fcc, ideal hcp, deformed hcp, and monoclinic crystals. Because of the presence of five-membered carbon rings and the surface curvature of C(70) molecule, the Lennard-Jones potential parameters for nitrogen-carbon interactions obtained from ab initio based calculations are found to be different from that with planar graphite. The simulation results obtained from these two sets of force fields are compared and shown to differ, particularly at low coverage, where the nitrogen-carbon interactions are more important than the nitrogen-nitrogen interactions. The surface area, monolayer capacity, and isosteric heat of adsorption are calculated for various C(70) crystals and found to change appreciably as a result of the shear-induced phase transformation from hcp to rhombohedral lattice.     

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.     

Full-dimensional vibrational calculations for H5O2+ using an ab initio potential energy surface

We report quantum diffusion Monte Carlo (DMC) and variational calculations in full dimensionality for selected vibrational states of H(5)O(2) (+) using a new ab initio potential energy surface [X. Huang, B. Braams, and J. M. Bowman, J. Chem. Phys. 122, 044308 (2005)]. The energy and properties of the zero-point state are focused on in the rigorous DMC calculations. OH-stretch fundamentals are also calculated using "fixed-node" DMC calculations and variationally using two versions of the code MULTIMODE. These results are compared with infrared multiphoton dissociation measurements of Yeh et al. [L. I. Yeh, M. Okumura, J. D. Myers, J. M. Price, and Y. T. Lee, J. Chem. Phys. 91, 7319 (1989)]. Some preliminary results for the energies of several modes of the shared hydrogen are also reported.     

Structural and electronic properties of boron-doped lithium clusters: ab initio and DFT studies

The lowest-energy structures and electronic properties of the BLi(n) (n = 1-7) clusters are reported using the B3LYP, MP2, and CCSD(T) methods with the aug-cc-pVDZ basis set. Though the results at the B3LYP level agree well with those at the CCSD(T) level, the MP2 method is rather unsatisfactory. The first three-dimensional ground state in the BLi(n) clusters occurs for BLi(4), and the impurity B atom is seen to be trapped in a Li cage from the BLi(6) cluster onwards. The evolution of the binding energies, vertical ionization potentials, and polarizability with size of cluster shows the BLi(5) cluster to be most stable among the BLi(n) clusters. Besides, the BLi(5) cluster is also found to have the largest reaction enthalpy (49.8 kcal/mol) upon losing a Li atom, which is different from the previous prediction. The unique stability of the 8-valence electron BLi(5) can be understood from the cluster electronic shell model (CSM). However, in contradiction to the prediction of the CSM, the 2s level is filled prior to the 1d level in the BLi(n) clusters.