Phonon spectra and thermodynamic properties of rare gas solids based on empirical and semi-empirical (ab initio) two-body potentials : a comparative study /

We study the phonon dispersion, cohesive and thermal properties of raxe gas solids Ne, Ar, Kr, and Xe, using a variety of potentials obtained from different approaches; such as, fitting to crystal properties, purely ab initio calculations for molecules and dimers or ab initio calculations for solid crystalline phase, a combination of ab initio calculations and fitting to either gas phase data or sohd state properties. We explore whether potentials derived with a certain approaxih have any obvious benefit over the others in reproducing the solid state properties. In particular, we study phonon dispersion, isothermal ajid adiabatic bulk moduli, thermal expansion, and elastic (shear) constants as a function of temperatiue. Anharmonic effects on thermal expansion, specific heat, and bulk moduli have been studied using A^ perturbation theory in the high temperature limit using the neaxest-neighbor central force (nncf) model as developed by Shukla and MacDonald [4]. In our study, we find that potentials based on fitting to the crystal properties have some advantage, particularly for Kr and Xe, in terms of reproducing the thermodynamic properties over an extended range of temperatiures, but agreement with the phonon frequencies with the measured values is not guaranteed. For the lighter element Ne, the LJ potential which is based on fitting to the gas phase data produces best results for the thermodynamic properties; however, the Eggenberger potential for Ne, where the potential is based on combining ab initio quantum chemical calculations and molecular dynamics simulations, produces results that have better agreement with the measured dispersion, and elastic (shear) values. For At, the Morse-type potential, which is based on M0ller-Plesset perturbation theory to fourth order (MP4) ab initio calculations, yields the best results for the thermodynamic properties, elastic (shear) constants, and the phonon dispersion curves.

Fluorescence spectra and ab initio theoretical studies of HCOOH /

A fluorescence excitation spectrum of formic acid monomer (HCOOH) , has been recorded in the 278-246 nm region and has been attributed to an n >7r* electron promotion in the anti conformer. The S^< S^ electronic origins of the HCOOH/HCOOD/DCOOH/DCOOD isotopomers were assigned to weak bands observed at 37431.5/37461.5/37445.5/37479.3 cm'''. From a band contour analysis of the 0°^ band of HCOOH, the rotational constants for the excited state were estimated: A'=1.8619, B'=0.4073, and C'=0.3730 cm'\ Four vibrational modes, 1/3(0=0), j/^(0-C=0) , J/g(C-H^^^) and i/,(0-H^yJ were observed in the spectrum. The activity of the antisymmetric aldehyde wagging and hydroxyl torsional modes in forming progressions is central to the analysis, leading to the conclusion that the two hydrogens are distorted from the molecular plane, 0-C=0, in the upper S. state. Ab initio calculations were performed at the 6-3 IG* SCF level using the Gaussian 86 system of programs to aid in the vibrational assignments. The computations show that the potential surface which describes the low frequency OH torsion (twisting motion) and the CH wagging (molecular inversion) motions is complex in the S^ excited electronic state. The OH and CH bonds were calculated to be twisted with respect to the 0-C=0 molecular frame by 63.66 and 4 5.76 degrees, respectively. The calculations predicted the existence of the second (syn) rotamer which is 338 cm'^ above the equilibrium configuration with OH and CH angles displaced from the plane by 47.91 and 41.32 degrees.

Effects of large anphiphilic ligands upon the spectra and kinetics of cytochrome C oxidase

Cytoch ro me c oxidase (ferrocytochrome c : 02 oxidoreductase ; EC 1.9. 3.1) is the terminal enzyme in the mitochondrial electron transport chain, catalyzing the transfer of electrons from ferrocytochrome c to molecular oxygen. The effects of two large amphiphilic molecules .. valinomycin and dibucaine upon the spectra of the isolated enzyme and upon the activity of both isolated enzyme and enzyme in membrane systems are investigated by using spectrophotometric and oxygen electrode techniques. The results show that both valinomycin and dibucaine change the Soret region of the spectrum and cause a partial inhibition in a concentration range higher than that in which they act as ionophores. It is concluded that both valinomycin and dibucain~ binding induce a conformational change of the protein structure which modifies the spectrum of the a3 CUB centre and diminishes the rate of electron transfer between cytochrome a and the binuclear centre.

The satellite band patterns in the near ultraviolet absorption spectra of isotopic compounds of acetaldehyde

The 3700 A - 3000 A absorption spectra of CH3CHO and its isotopic compounds such as CH3CDO, CD3CHO and CD3CDO were studied in the gas phase at room temperature and low temperatures. The low resolution spectra of the compounds were recorded by a 1.5 m Baush and Lomb grating spectrograph. The high resolution spectra were recorded by a Ebert spectrograph with the Echelle grating and the holographic grating separately. The multiple reflection cells were used to achieve the long path length. The pressure-path length used for the absorption spectrum of CH 3CHO was up to 100 mm Hg )( 91 . 43mo The emission spectrum and the excitation spectrum of CH3CHO were also recorded in this research. The calculated satellite band patterns \vhich were ob-tailied by the method of Lewis were used to compare with the observed near UV absorption spectrum of acetaldehyde. These calculated satellite band patterns belonged to two cases: namely, the barriers-in-phase case and the barriers- out-of-phase case. Each of the calculated patterns corresponded to a stable conformation of acetaldehyde in the excited state . The comparisons showed that the patterns in the observed absorption spectra corresponded to the H-H eclipsed conformations of acetaldehyde in the excited state . The least squares fitting analysis showed that the barrier heights in the excited state were higher than in the ground state. Finally, the isotopic shifts for the isotopic compounds of acetaldehyde were compared to the compounds with the similar deuterium substitution.

An analysis of the methyl rotation dynamics in the So (x' A) and T (a A) states of thioacetaldehyde from Pyrolysis jet spectra /

Jet-cooled, laser-induced phosphorescence excitation spectra (LIP) of thioacetaldehyde CH3CHS, CH3CDS, CD3CHS and CD3CDS have been observed over the region 15800 - 17300 cm"^ in a continuous pyrolysis jet. The vibronic band structure of the singlet-triplet n -* n* transition were attributed to the strong coupling of the methyl torsion and aldehydic hydrogen wagging modes . The vibronic peaks have been assigned in terms of two upper electronic state (T^) vibrations; the methyl torsion mode v^g, and the aldehydic hydrogen wagging mode v^^. The electronic origin O^a^ is unequivocally assigned as follows: CH3CHS (16294.9 cm"'' ), CH3CDS (16360.9 cm"'' ), CD3CHS (16299.7 cm"^ ), and CD3CDS (16367.2 cm"'' ). To obtain structural and dynamical information about the two electronic states, potential surfaces V(e,a) for the 6 (methyl torsion) and a (hydrogen wagging) motions were generated by ab initio quantum mechanical calculations with a 6-3 IG* basis in which the structural parameters were fully relaxed. The kinetic energy coefficients BQ(a,e) , B^(a,G) , and the cross coupling term B^(a,e) , were accurately represented as functions of the two active coordinates, a and 9. The calculations reveal that the molecule adopts an eclipsed conformation for the lower Sq electronic state (a=0°,e=0"') with a barrier height to internal rotation of 541.5 cm"^ which is to be compared to 549.8 cm"^ obtained from the microwave experiment. The conformation of the upper T^ electronic state was found to be staggered (a=24 . 68° ,e=-45. 66° ) . The saddle point in the path traced out by the aldehyde wagging motion was calculated to be 175 cm"^ above the equilibrium configuration. The corresponding maxima in the path taken by methyl torsion was found to be 322 cm'\ The small amplitude normal vibrational modes were also calculated to aid in the assignment of the spectra. Torsional-wagging energy manifolds for the two states were derived from the Hamiltonian H(a,e) which was solved variationally using an extended two dimensional Fourier expansion as a basis set. A torsionalinversion band spectrum was derived from the calculated energy levels and Franck-Condon factors, and was compared with the experimental supersonic-jet spectra. Most of the anomalies which were associated with the interpretation of the observed spectrum could be accounted for by the band profiles derived from ab initio SCF calculations. A model describing the jet spectra was derived by scaling the ab initio potential functions. The global least squares fitting generates a triplet state potential which has a minimum at (a=22.38° ,e=-41.08°) . The flatter potential in the scaled model yielded excellent agreement between the observed and calculated frequency intervals.

Effects of large anphiphilic ligands upon the spectra and kinetics of cytochrome C oxidase

Cytoch ro me c oxidase (ferrocytochrome c : 02 oxidoreductase ; EC 1.9. 3.1) is the terminal enzyme in the mitochondrial electron transport chain, catalyzing the transfer of electrons from ferrocytochrome c to molecular oxygen. The effects of two large amphiphilic molecules - valinomycin and dibucaine upon the spectra of the isolated enzyme and upon the activity of both isolated enzyme and enzyme in membrane systems are investigated by using spectrophotometric and oxygen electrode techniques. The results show that both valinomycin and dibucaine change the Soret region of the speetrum and cause a partial inhibition in a concentration range higher than that in which they act as ionophores. It is concluded that both valinomycin and dibucaine binding induce a conformational change of the protein structure which modifies the spectrum of the a3 CUB centre and diminishes the rate of electron transfer between cytochrome a and the binuclear centre.

Phonon spectra and temperature variation of thermodynamic properties of fcc metals via Finnis-Sinclair type many body potentials: Sutton-Chen and improved Sutton-Chen models

Volume(density)-independent pair-potentials cannot describe metallic cohesion adequately as the presence of the free electron gas renders the total energy strongly dependent on the electron density. The embedded atom method (EAM) addresses this issue by replacing part of the total energy with an explicitly density-dependent term called the embedding function. Finnis and Sinclair proposed a model where the embedding function is taken to be proportional to the square root of the electron density. Models of this type are known as Finnis-Sinclair many body potentials. In this work we study a particular parametrization of the Finnis-Sinclair type potential, called the "Sutton-Chen" model, and a later version, called the "Quantum Sutton-Chen" model, to study the phonon spectra and the temperature variation thermodynamic properties of fcc metals. Both models give poor results for thermal expansion, which can be traced to rapid softening of transverse phonon frequencies with increasing lattice parameter. We identify the power law decay of the electron density with distance assumed by the model as the main cause of this behaviour and show that an exponentially decaying form of charge density improves the results significantly. Results for Sutton-Chen and our improved version of Sutton-Chen models are compared for four fcc metals: Cu, Ag, Au and Pt. The calculated properties are the phonon spectra, thermal expansion coefficient, isobaric heat capacity, adiabatic and isothermal bulk moduli, atomic root-mean-square displacement and Gr\"{u}neisen parameter. For the sake of comparison we have also considered two other models where the distance-dependence of the charge density is an exponential multiplied by polynomials. None of these models exhibits the instability against thermal expansion (premature melting) as shown by the Sutton-Chen model. We also present results obtained via pure pair potential models, in order to identify advantages and disadvantages of methods used to obtain the parameters of these potentials.