Structure change of liquid GaSb under pressure: an ab initio molecular-dynamics simulation

We have performed ab initio molecular-dynamics simulation of liquid GaSb (l-GaSb) up to 20.0 GPa. The calculated structure factors are consistent with the recent experimental results, and the partial structure parameters show that the structure of l-GaSb under pressure contracts nonuniformly. In the whole calculated pressure region, the contraction of l-GaSb can be divided into three substages: 1.8-5.4, 5.4-10.0, and 10.0-20.0 GPa. It is further confirmed by analyzing the bond-angle distributions of Ga-Ga-Ga and Sb-Sb-Sb that the rearrangement of Sb atoms under pressure plays a crucial role in the structure change of l-GaSb.     

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study

Using quantum chemistry plus ab initio molecular dynamics and classical molecular dynamics methods, we address the relationship between molecular conformation and the biomedical function of arylamide polymers. Specifically, we have developed new torsional parameters for a class of these polymers and applied them in a study of the interaction between a representative arylamide and one of its biomedical targets, the anticoagulant drug heparin. Our main finding is that the torsional barrier of a C(aromatic)-C(carbonyl) bond increases significantly upon addition of an o-OCH2CH2NH3+ substituent on the benzene ring. Our molecular dynamics studies that are based on the original general AMBER force field (GAFF) and GAFF modified to include our newly developed torsional parameters show that the binding mechanism between the arylamide and heparin is very sensitive to the choice of torsional potentials. Ab initio molecular dynamics simulation of the arylamide independently confirms the degree of flexibility we obtain by classical molecular dynamics when newly developed torsional potentials are used.     

Viscosities of liquid CdTe near melting point from ab initio molecular-dynamics calculations

Recent experimental results for the viscosity of liquid CdTe exhibit disparate behavior as a function of temperature. While some measurements show the expected Arrhenius-type behavior, other measurements show an anomalous temperature dependence indicating an increase in viscosity with increasing temperature. We present ab initio molecular-dynamics simulations of liquid cadmium telluride near its melting point and use the Stokes-Einstein relation to extract values of the viscosity constant. We find no anomalous behavior; the viscosity decreases monotonically with temperature and is consistent with an Arrhenius like behavior. Although calculated values are slightly smaller than those measured, the predicted activation energy agrees well with experiment.     

Water mediated proton transfer in a mesostructured aluminosilicate framework: an ab initio molecular dynamics study

The proton transfer process mediated by water molecules adsorbed in an aluminosilicate framework has been studied using ab initio molecular dynamics simulations. This investigation has been carried out using a quasi-one-dimensional model simulating the mesoporous aluminosilicate channel structures. The effects of both the water loading and temperature of the system have been considered. At low coverage (one water molecule per acid site), the hydroxonium ion (H(3)O)(+) is found to be a transition state, in agreement with earlier studies on zeolites. At a higher water coverage (two water molecules per acid site), the (H(5)O(2))(+) species and the hydrogen bonded "neutral complex" structure are both found to be stable complexes at finite temperatures. The vibrational frequency spectrum is simulated by performing a Fourier transform of the velocity autocorrelation function (VAF), and the peak positions in the VAF are compared with IR measurements and zero-temperature calculations.     

Ab initio molecular-dynamics study of liquid formamide

Properties of neat liquid formamide (HCONH2) have been studied by the combination of gradient-corrected density-functional theory, norm-conserving pseudopotentials, and the adaptive finite-element method. The structural and dynamical quantities have been calculated through molecular dynamics simulations under the Born-Oppenheimer approximation. Satisfactory agreement with experimental data was obtained for both intramolecular and intermolecular properties. Our results are also compared with those of the empirical potential functions to clarify their accuracies.     

A combined matrix isolation and ab initio study of bromine oxides

Bromine oxides have been generated by passing a mixture of Br(2)/O(2)/Ar through a microwave discharge. The products were stabilized at 6.5 K in an excess amount of argon. Infrared spectroscopy was used to analyze the species formed; experiments with enriched (18)O(2) and ab initio calculations were carried out to assist in the assignment of the spectra. Besides the known species BrO, OBrO, and BrBrO, spectroscopic evidence for BrOBrO, BrBrO(2), and a new isomer of Br(2)O(3) is reported for the first time. Extensive comparisons are drawn between the present studies and previous experimental and theoretical works. The chemistry involved in the production of the observed compounds is discussed. The assignments are corroborated by the good correlation between observed and calculated band positions and intensities.     

An ab initio study of the proton transfer and tautomerization processes in hydroxycarbene

We have investigated the hydrogen-bonded complexes formed by hydroxycarbene in trans configuration at MP2 and CCSD computational levels. In addition, these complexes have been used as starting point in the potential tautomerization of hydroxycarbene to produce formaldehyde. The presence of molecules that can be involved in the tautomerization significantly reduces its barrier. The electron density of the different structures obtained has been analyzed with the Atoms in Molecules methodology.     

A comparative ab initio study of intramolecular proton transfer in model alpha-hydroxyalkoxides

A comparative ab initio study was performed on the intramolecular proton-transfer reaction that occurs in alpha-hydroxyethanoxy, alpha-hydroxyphenoxide, and alpha-hydroxyethenoxy anions. The intramolecular proton transfer occurs in a five-member atom arrangement, between two oxygen atoms separated by a carbon-carbon bond. The chosen systems serve as models for alpha-hydroxyalkoxide molecules where the carbon-carbon bond varies from a single bond (the glycolate anion or alpha-hydroxyethanoxide anion) to a part of an aromatic ring (the alpha-hydroxyphenoxide anion), and finally to a double bond (the alpha-hydroxyethenoxide anion). Particular attention was given to the evolution along the intrinsic reaction coordinate of such properties as energies, relevant structural parameters, Mulliken charges, dipole moments, and 1H-NMR chemical shifts to reveal the similarities and differences for the proton transfer in the model systems.     

Trimethyl phosphate-acetylene interaction: a matrix-isolation infrared and ab initio study

Trimethyl phosphate (TMP) and acetylene were codeposited in nitrogen and argon matrices and adducts of these species were identified using infrared spectroscopy. Formation of the adducts was evidenced by shifts in the vibrational frequencies of the modes involving the TMP and acetylene submolecules. The structures of these adducts, energies and the vibrational frequencies were computed at the HF/6-31G** level. Both the experimental and computational studies indicated that two types of TMP-acetylene complexes were formed; one in which the hydrogen in acetylene was bonded to the phosphoryl oxygen and another in which the bonding was at the alkoxy oxygen of the phosphate. In addition to the primary hydrogen bonded interaction at the phosphoryl oxygen, this complex, also appeared to be stablilized by a secondary and weaker interaction involving a methyl hydrogen in TMP and the pi cloud in acetylene--a case of a H...pi interaction. The computed vibrational frequencies in the adducts agreed well with the observed frequencies for the modes involving the TMP submolecule, while the agreement was relatively poor for the modes involving the acetylene submolecule. The stabilization energies of these adducts, corrected for both zero-point energies and basis set superposition errors, were approximately 3 kcal/mol for the phosphoryl complex and, approximately 1 kcal/mol for the alkoxy complex.     

The rotational spectrum and dynamical structure of LiOH and LiOD: a combined laboratory and ab initio study

Millimeter wave rotational spectroscopy and ab initio calculations are used to explore the potential energy surface of LiOH and LiOD with particular emphasis on the bending states and bending potential. New measurements extend the observed rotational lines to J=7<--6 for LiOH and J=8<--7 for LiOD for all bending vibrational states up to (03(3)0). Rotation-vibration energy levels, geometric expectation values, and dipole moments are calculated using extensive high-level ab initio three-dimensional potential energy and dipole moment surfaces. Agreement between calculation and experiment is superb, with predicted Bv values typically within 0.3%, D values within 0.2%, ql values within 0.7%, and dipole moments within 0.9% of experiment. Shifts in Bv values with vibration and isotopic substitution are also well predicted. A combined theoretical and experimental structural analysis establishes the linear equilibrium structure with re(Li-O)=1.5776(4) A and re(O-H)=0.949(2) A. Predicted fundamental vibrational frequencies are v1=923.2, v2=318.3, and v3=3829.8 cm(-1) for LiOH and v1=912.9, v2=245.8, and v3=2824.2 cm(-1) for LiOD. The molecule is extremely nonrigid with respect to angular deformation; the calculated deviation from linearity for the vibrationally averaged structure is 19.0 degrees in the (000) state and 41.9 degrees in the (03(3)0) state. The calculation not only predicts, in agreement with previous work [P. R. Bunker, P. Jensen, A. Karpfen, and H. Lischka, J. Mol. Spectrosc. 135, 89 (1989)], a change from a linear to a bent minimum energy configuration at elongated Li-O distances, but also a similar change from linear to bent at elongated O-H distances.     

Ab initio molecular-dynamics study of supercritical carbon dioxide

Car-Parrinello molecular-dynamics simulations of supercritical carbon dioxide (scCO(2)) have been performed at the temperature of 318.15 K and at the density of 0.703 g/cc in order to understand its microscopic structure and dynamics. Atomic pair correlation functions and structure factors have been obtained and good agreement has been found with experiments. In the supercritical state the CO(2) molecule is marginally nonlinear, and thus possesses a dipole moment. Analyses of angle distributions between near neighbor molecules reveal the existence of configurations with pairs of molecules in the distorted T-shaped geometry. The reorientational dynamics of carbon dioxide molecules, investigated through first- and second-order time correlation functions, exhibit time constants of 620 and 268 fs, respectively, in good agreement with nuclear magnetic resonance experiments. The intramolecular vibrations of CO(2) have been examined through an analysis of the velocity autocorrelation function of the atoms. These reveal a red shift in the frequency spectrum relative to that of an isolated molecule, consistent with experiments on scCO(2). The results have also been compared to classical molecular-dynamics calculations employing an empirical potential.     

Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-Hartree-Fock ab initio study

The results of a comprehensive study on the double-proton transfer in Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs at room temperature in gas phase and with the inclusion of environmental effects are obtained. The double-proton-transfer process has been investigated in the AT and GC base pairs at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. It has been predicted that the hydrogen-bonded bases possess nonplanar geometries due to sp3 hybridization of nitrogen atoms and because of the soft intermolecular vibrations in the molecular complexes. An analysis of the energetic parameters of the local minima suggests that rare AT base pair conformation is not populated due to the shallowness of this minimum, which completely disappears from the Gibbs free energy surface. The stabilization of canonic or rare forms of the DNA bases by water molecules and metal cations has been predicted by calculating the optimal configuration of charges (using differential product/transition state stabilization approach) followed by calculations of the interactions between the base pair and a water/sodium cation.     

A combined ab initio and photoionization mass spectrometric study of polyynes in fuel-rich flames

Polyynic structures in fuel-rich low-pressure flames are observed using VUV photoionization molecular-beam mass spectrometry. High-level ab initio calculations of ionization energies for C2nH2 (n=1-5) and partially hydrogenated CnH4 (n=7-8) polyynes are compared with photoionization efficiency measurements in flames fuelled by allene, propyne, and cyclopentene. C2nH2 (n=1-5) intermediates are unambiguously identified, while HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH=C=CH2, HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH=CH2 (vinyltriacetylene) and HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH[double bond, length as m-dash]CH-C[triple bond, length as m-dash]CH are likely to contribute to the C7H4 and C8H4 signals. Mole fraction profiles as a function of distance from the burner are presented. C7H4 and C8H4 isomers are likely to be formed by reactions of C2H and C4H radicals but other plausible formation pathways are also discussed. Heats of formation and ionization energies of several combustion intermediates have been determined for the first time.     

Size-expanded yDNA bases: an ab initio study

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.     

Solvent-dependent stereoselectivity in a Still-Wittig rearrangement: an experimental and ab initio study

[see reaction]. The Still-Wittig rearrangement gave opposite selectivities for (Z:E)-alkenes in THF (3:1) vs toluene (1:3) in the synthesis of serine-proline dipeptide amide isosteres. Four transition states leading to (Z)-and (E)-alkenes with THF and without (representing toluene) were identified by ab initio calculations at the 3-21G* level. The calculated (Z:E)-ratios with THF (4.7:1) and without THF (1:3.2) suggested that the transition state geometries and energies were well-represented by the calculations.     

The structure of ionically conductive chalcogenide glasses: a combined NMR,XPS and ab initio calculation study

This paper reports on the structural investigation of lithium and sodium thiosilicate crystals and glasses by means of X-ray photoelectron spectroscopy and ab initio calculation. The results are analysed in conjunction with previously reported ²⁹Si NMR data. While NMR proved to be an effective tool for the quantitative discrimination of edge- and corner-sharing tetrahedra existing in these materials, X-ray photoelectron spectroscopy (XPS) gives information on the nature of SiS bonds, i.e. bridging and non-bridging bonds. The main result is the noticeable difference existing between the structures of lithium and sodium thiosilicate glasses, which, according to XPS data, is due to different electronic redistributions over the network when one or the other alkali is added, the sodium addition resulting in a change in the electronic distribution over the entire network.     

Pseudorotation motion in tetrahydrofuran: an ab initio study

The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.     

Vibrational inelastic and charge transfer processes in H(+)+H2 system: an ab initio study

State-resolved differential cross sections, total and integral cross sections, average vibrational energy transfer, and the relative probabilities are computed for the H(+)+H2 system using the newly obtained ab initio potential energy surfaces at the full CI/cc-pVQZ level of accuracy which allow for both the direct vibrational inelastic and the charge transfer processes. The quantum dynamics is treated within the vibrational close-coupling infinite-order-sudden approximation approach using the two ab initio quasidiabatic potential energy surfaces. The computed collision attributes for both the processes are compared with the available state-to-state scattering experiments at E(c.m.)=20 eV. The results are in overall good agreement with most of the observed scattering features such as rainbow positions, integral cross sections, and relative vibrational energy transfers. A comparison with the earlier theoretical study carried out on the semiempirical surfaces (diatomics in molecules) is also made to illustrate the reliability of the potential energy surfaces used in the present work.