Crystallographic analysis of atomic structures and the phenomenological mechanism of crystallization

A theoretical study of the structure and vibrational spectrum of methyl-β-D-glucopyranoside is performed with allowance for the hydrogen bond effect on them. At the density functional theory level with the use of the B3LYP functional in the 6–31G(d) basis set the structural dynamic models of a free molecule of methyl-β-D-glucopyranoside and its simplest complexes with hydrogen bonding in the form of dimers with different structures are constructed. Energies are minimized; structures, electro optical parameters, force constants, and normal vibrational frequencies in the harmonic approximation and their intensities in IR spectra are calculated; the hydrogen bond energy is estimated. Based on the calculation, the conclusions are drawn about the structure of the methyl-β-D-glucopyranoside sample, the formation and interpretation of its IR spectrum, and the possibilities of the used density functional theory method.     

Investigation of structure of liquid 2,2,2 trifluoroethanol: neutron diffraction, molecular dynamics, and ab initio quantum chemical study

The molecular conformation and intermolecular H bonding in liquid 2,2,2 trifluoroethanol (TFE) have been studied by neutron diffraction with hydrogen/deuterium isotopic substitution at room temperature. For comparison, conformations of molecules and their dimers in the gas phase have also been calculated, based on the density functional theory. Energies, geometry, and vibrational frequencies of dimers were analyzed. Diffraction data analyzed by the "Monte Carlo determination of g(r)" (MCGR) method resulted in a molecular structure in agreement with the findings from gas phase electron diffraction experiments and density functional calculations. The intermolecular structure functions were compared to the same functions obtained from a molecular dynamics simulation. All of the composite radial distribution functions are in good agreement with the simulation results. According to our calculation the hydrogen-bonded aggregation size is smaller in pure liquid TFE than in pure liquid ethanol.     

Quantum dynamic of sticking of a H atom on a graphite surface

A quantum study of the sticking of a hydrogen atom chemisorbed onto graphite (0001) surface was carried out also including the phonon modes of the system in the collinear scattering approximation. A new model was developed to extract the substrate vibrational modes from density functional theory (DFT) calculation and include them in the total system dynamics. The resulting coupled-channel equations are numerically developed along time using the wave packet methods. The sticking coefficients are calculated for hydrogen atoms incident energies ranging from 0.17 and 1.3 eV for a surface temperature of 10 K and between 0.17 and 0.2 eV for a surface temperature of 150 K. The results are found to be in good agreement with the experimental work.     

Toward understanding mobile proton behavior from first principles calculation: the short hydrogen bond in crystalline urea-phosphoric acid

The dynamics of the intermolecular short hydrogen bond in the molecular complex of urea and phosphoric acid are investigated using plane-wave density functional theory. Results indicate migration of the proton toward the center of the hydrogen bond as temperature is increased, in line with recent experimental measurements. Computed vibrational frequencies show favorable agreement with experimental measurement. An analysis of existing neutron diffraction data leads us to conclude that the effective potential well experienced by the proton is temperature-dependent. Inspired by our computations and theoretical analysis, we offer a possible explanation for the proton migration phenomenon.     

Experimental and theoretical vibrational study of silyl trifluoromethanesulfonate, CF3SO2OSiH3

Infrared and Raman spectra were obtained for liquid silyl trifluoromethanesulfonate, a silylating agent of limited stability. The molecular geometry was optimized by means of density functional theory and M?ller-Plesset second order perturbation theory methods, using different basis sets. The optimized structure presents a gauche conformation, similar to that adopted by methyl trifluoromethanesulfonate, which was determined experimentally a short time ago. The wavenumbers for the normal modes of vibration and the corresponding force constants were also calculated, facilitating the interpretation of the vibrational data. The harmonic force constants given by theory were scaled to reproduce adequately the experimental wavenumbers.     

Inelastic neutron scattering spectrum of cyclotrimethylenetrinitramine: a comparison with solid-state electronic structure calculations

Solid-state geometry optimizations and corresponding normal-mode analysis of the widely used energetic material cyclotrimethylenetrinitramine (RDX) were performed using density functional theory with both the generalized gradient approximation (BLYP and BP functionals) and the local density approximation (PWC and VWN functionals). The structural results were found to be in good agreement with experimental neutron diffraction data and previously reported calculations based on the isolated-molecule approximation. The vibrational inelastic neutron scattering (INS) spectrum of polycrystalline RDX was measured and compared with simulated INS constructed from the solid-state calculations. The vibrational frequencies calculated from the solid-state methods had average deviations of 10 cm(-1) or less, whereas previously published frequencies based on an isolated-molecule approximation had deviations of 65 cm(-1) or less, illustrating the importance of including crystalline forces. On the basis of the calculations and analysis, it was possible to assign the normal modes and symmetries, which agree well with previous assignments. Four possible "doorway modes" were found in the energy range defined by the lattice modes, which were all found to contain fundamental contributions from rotation of the nitro groups.     

Intermolecular charge transfer and hydrogen bonding in solid furan

The calculated structures of furan as a monomer, a dimer that was isolated from the crystal structure, and the full crystal structure have been thoroughly investigated by a combination of density functional theory (DFT) calculations and inelastic neutron scattering (INS) measurements. To improve our understanding of the nature and magnitude of the intermolecular interactions in the solid, the atoms in molecules (AIM) theory has been applied to the dimer and a cluster of eight monomers. After a careful topological study of the theoretical charge density and of its Laplacian, we have established the existence of C-H...pi, C-H...O, and H...H interactions between adjacent molecules in solid furan. The electron distribution has also been analyzed by performing natural bond orbital (NBO) calculations for the monomer and a H-bonded dimer. When the hydrogen bond is established between two adjacent furan rings, some electron charge is transferred from the pi electronic system of one furan ring to the other molecule in the dimer. This result provides a model of the interaction between end groups of neighboring chains of polyfuran and could be applicable to other conjugated polymers where the pi system is responsible for their conducting properties. To determine how the intermolecular bonds in the solid affect the vibrational dynamics in the periodic system, INS data were analyzed by performing molecular and periodic density functional calculations. Reasonable agreement is achieved, although we note that the poorest agreement is for modes involving hydrogen atoms.     

Theoretical DFT and experimental Raman and NMR studies on thiophene, 3-methylthiophene and selenophene

The results of extended MO calculations using density functional theory (DFT) approximation supported by experimental Raman, ¹H and ¹³C NMR studies on thiophene are reported. Raman spectra of liquid thiophene were re-examined and the performance of a hybrid B3PW91 density functional was compared with the ab initio restricted Hartree–Fock (RHF) method. With the basis sets of the 6-311++G^** quality, the DFT calculated bond lengths, dipole moments and harmonic vibrations were predicted in a very good agreement with available experimental data.

Additionally, the results on thiophene were extended by calculations on 3-methylthiophene and selenophene. In this case, a significant change in geometry and charge distribution in thiophene ring due to a methyl group substituent or replacement of sulphur by selene atom was observed.

A linear correlation between the predicted harmonic vibrational frequencies (scaled using SQM method) and experimental ones for thiophene, selenophene and 3-methylthiophene was shown. The theoretically calculated spectra have satisfactorily reproduced the available experimental spectra for thiophene and selenophene.     

Inelastic X-ray scattering and vibrational effects at the K-edges of gaseous N2, N2O, and CO2

We report non-resonant inelastic X-ray scattering experiments of several gaseous samples in the inner-shell excitation energy range. The experimental near-edge spectra from all the K-edges of N(2), N(2)O, and CO(2) including the momentum transfer dependence are presented. The results are analyzed using density functional theory calculations that accurately reproduce the experimental spectral features. We observe vibrational effects in the measured spectrum and in the calculations the atomic motion is modeled using the Franck-Condon approximation and the linear coupling model. Our findings show that vibrational effects cannot be neglected in the analysis of high resolution inelastic X-ray scattering spectroscopy. The results also support the validity of the transition potential approximation for calculating core excited state potential energy surfaces.     

Ab initio calculation of resonance Raman cross sections based on excited state geometry optimization

A method for the calculation of resonance Raman cross sections is presented on the basis of calculation of structural differences between optimized ground and excited state geometries using density functional theory. A vibrational frequency calculation of the molecule is employed to obtain normal coordinate displacements for the modes of vibration. The excited state displacement relative to the ground state can be calculated in the normal coordinate basis by means of a linear transformation from a Cartesian basis to a normal coordinate one. The displacements in normal coordinates are then scaled by root-mean-square displacement of zero point motion to calculate dimensionless displacements for use in the two-time-correlator formalism for the calculation of resonance Raman spectra at an arbitrary temperature. The method is valid for Franck-Condon active modes within the harmonic approximation. The method was validated by calculation of resonance Raman cross sections and absorption spectra for chlorine dioxide, nitrate ion, trans-stilbene, 1,3,5-cycloheptatriene, and the aromatic amino acids. This method permits significant gains in the efficiency of calculating resonance Raman cross sections from first principles and, consequently, permits extension to large systems (>50 atoms).     

Molecular structure, vibrational spectra and NBO analysis of phenylisothiocyanate by density functional method

The molecular geometry, vibrational frequencies and NBO analysis of phenylisothiocyanate (PITC) in the ground state have been calculated by using density functional theory calculation (B3LYP) with 6-311++G(d,p) basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with experimental values. Comparison of the observed fundamental vibrational frequencies of the PITC and calculated result by density functional theory (B3LYP) indicates B3LYP is superior for molecular vibrational problems. The entropy of the title compound was also performed at HF/B3LYP/6-311++G(d,p) levels of theory. Natural bond orbital (NBO) analysis of title molecule is also carried out. A detailed interpretation of the IR and Raman spectra of PITC is reported on the basis of the calculated potential energy distribution (PED). The theoretical spectrogram for IR spectrum of the title molecule has been constructed.     

Electrical transport properties of potassium germanide tungstates (K10Ge18WO4): A theoretical study

The total and partial density of states, electronic charge density and optical properties of the monoclinic structure K₁₀Ge₁₈WO₄ compound have been investigated using a full relativistic version of the full-potential augmented plane-wave method based on the density functional theory, within local density approximation (LDA), generalized gradient approximation (GGA) and Engel-Vosko GGA (EVGGA). Density of states discloses the semiconductor nature of the calculated compound. There exists a strong hybridization between K-p and K-s, W-d and O-p, W-f and K-p. The analysis of the chemical bonding shows that the bonding possesses strong covalent nature. The dielectric optical properties were also calculated and discussed in detail. The electrical transport coefficients of the under observation compound have been investigated using the density functional theory calculation within EVGGA.     

Analytical approach for the excited-state Hessian in time-dependent density functional theory: formalism, implementation, and performance

The paper presents the formalism, implementation, and performance of the analytical approach for the excited-state Hessian in the time-dependent density functional theory (TDDFT) that extends our previous work [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011)] on the analytical Hessian in TDDFT within Tamm-Dancoff approximation (TDA) to full TDDFT. In contrast to TDA-TDDFT, an appreciable advantage of full TDDFT is that it maintains the oscillator strength sum rule, and therefore yields more precise results for the oscillator strength and other related physical quantities. For the excited-state harmonic vibrational frequency calculation, however, full TDDFT does not seem to be advantageous since the numerical tests demonstrate that the accuracy of TDDFT with and without TDA are comparable to each other. As a common practice, the computed harmonic vibrational frequencies are scaled by a suitable scale factor to yield good agreement with the experimental fundamental frequencies. Here we apply both the optimized ground-state and excited-state scale factors to scale the calculated excited-state harmonic frequencies and find that the scaling decreases the root-mean-square errors. The optimized scale factors derived from the excited-state calculations are slightly smaller than those from the ground-state calculations.     

Proton momentum distribution in water: an open path integral molecular dynamics study

Recent neutron Compton scattering experiments have detected the proton momentum distribution in water. The theoretical calculation of this property can be carried out via "open" path integral expressions. In this work, present an extension of the staging path integral molecular dynamics method, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases. We utilize a flexible, single point charge empirical force field to model the system's interactions. The calculated momentum distributions depict both agreement and discrepancies with experiment. The differences may be explained by the deviation of the force field from the true interactions. These distributions provide an abundance of information about the environment and interactions surrounding the proton.     

X-ray scattering intensities of water at extreme pressure and temperature

We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure using the ab initio density functional theory (DFT). Our calculations span the molecular liquid, ice VII, and superionic solid phases, including the recently predicted symmetrically hydrogen bonded region. We compute simulated spectra for ice VII and superionic water. We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We show that our modified atomic form factors allow for a nearly exact comparison with the total x-ray scattering intensities calculated from DFT. Finally, we analyze the effect of their new form factors have on the determination of the oxygen-oxygen radial distribution function from experiment.     

Single particle scattering and momentum distributions in solid hydrogen

The incoherent inelastic neutron scattering function of solid para-hydrogen was recorded. It was shown that at momentum transfers above 5Å⁻¹ the data can be interpreted as recoil spectra from single particle scattering at hydrogen molecules. The evaluation of the momentum distribution and kinetic energy of the scattering particles from such data is discussed.     

First principles molecular dynamics simulation of liquid rubidium

We present a first principles molecular dynamics simulation of liquid rubidium. The atomic forces are obtained from a quantum mechanical calculation of its electronic structure within the local density approximation of the density functional formalism and using the pseudopotential plane-wave method. We compare our results with the structure and dynamics predicted by classical molecular dynamics simulations.     

The effect of electron charge transfer in biological activity and vibrational wavenumbers of 2′-Deoxyuridine and 5-Fluoro-2′-Deoxyuridine: DFT approach

Vibrational analysis of the 2′-Deoxyuridine and 5-Fluoro-2′-deoxyuridine compounds has been performed using FT-Raman and FTIR spectroscopic techniques. The optimized geometry, various bonding features and harmonic vibrational wavenumbers have been computed with the help of B3LYP/6-31G (d, p) density functional theory method. The natural bond orbital analysis, Mulliken population analysis on atomic charges and the HOMO–LUMO energy have been calculated to explore the reasons for the change in biological activity and vibrational wavenumbers of the title compounds. Potential energy distribution analysis has been used to assign the normal modes of vibrations unambiguously.     

Spectroscopic and theoretical study on peramine and some pyrrolopyrazinone compounds

The comparative analysis of IR and Raman spectra of peramine and its four derivatives in solid state was carried out. The harmonic vibrational frequencies, infrared intensities, and Raman scattering activities were calculated at density functional B3LYP methods with 6-311++G(d,p) basis set. For the predicted spectra, a potential energy distribution of normal modes was also calculated. For peramine derivatives the conjugation effect of pyrrole with pyrazinone ring was observed as a result of introduction of double bond. Moreover, ¹H NMR analysis indicated that pyrrole protons are deshielded in comparison with the pyrrolopyrazinone model ring system.     

Experimental and theoretical vibrational study of 2,2,2-trifluoroethyl trifluoromethanesulfonate, CF3SO2OCH2CF3

The infrared spectra of 2,2,2-trifluoroethyl trifluoromethanesulfonate (CF3SO2OCH2CF3) were obtained in the gaseous, liquid and solid states as well as the Raman spectrum of the liquid. Quantum chemistry calculations using the density functional theory were used to predict the most stable geometry and conformation of the studied molecule. Subsequently, the harmonic vibrational frequencies and force field were calculated. An assignment of the observed spectral features made after comparison with the related molecules and with the predicted frequencies was used as the basis of a scaling of the original force field in order to reproduce as well as possible the experimental frequencies. With this purpose a set of scale factors was calculated by a least square procedure, leading to a final root mean square deviation (RMSD) of 9.7 cm(-1).