Phonon spectra and thermal properties of some fcc metals using embedded-atom potentials /

By employing the embedded-atom potentials of Mei et ai.[l], we have calculated the dynamical matrices and phonon dispersion curves for six fee metals (Cu,Ag,Au,Ni,Pd and Pt). We have also investigated, within the quasiharmonic approximation, some other thermal properties of these metals which depend on the phonon density of states, such as the temperature dependence of lattice constant, coefficient of linear thermal expansion, isothermal and adiabatic bulk moduli, heat capacities at constant volume and constant pressure, Griineisen parameter and Debye temperature. The computed results are compared with the experimental findings wherever possible. The comparison shows a generally good agreement between the theoretical values and experimental data for all properties except the discrepancies of phonon frequencies and Debye temperature for Pd, Pt and Au. Further, we modify the parameters of this model for Pd and Pt and obtain the phonon dispersion curves which is in good agreement with experimental data.

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.

Simultaneous extraction of order parameters and orientational distribution fuctions from 31[superscript]P NMR spectra of magnetically partially oriented phospholipid bilayers

Order parameter profiles extracted from the NMR spectra of model membranes are a valuable source of information about their structure and molecular motions. To al1alyze powder spectra the de-Pake-ing (numerical deconvolution) ~echnique can be used, but it assumes a random (spherical) dist.ribution of orientations in the sample. Multilamellar vesicles are known to deform and orient in the strong magnetic fields of NMR magnets, producing non-spherical orientation distributions. A recently developed technique for simultaneously extracting the anisotropies of the system as well as the orientation distributions is applied to the analysis of partially magnetically oriented 31p NMR spectra of phospholipids. A mixture of synthetic lipids, POPE and POPG, is analyzed to measure distortion of multilamellar vesicles in a magnetic field. In the analysis three models describing the shape of the distorted vesicles are examined. Ellipsoids of rotation with a semiaxis ratio of about 1.14 are found to provide a good approximation of the shape of the distorted vesicles. This is in reasonable agreement with published experimental work. All three models yield clearly non-spherical orientational distributions, as well as a precise measure of the anisotropy of the chemical shift. Noise in the experimental data prevented the analysis from concluding which of the three models is the best approximation. A discretization scheme for finding stability in the algorithm is outlined

The measurement of the optical absorption cross section of photosystem 1 and photosystem 2 from whole live cells of porphyridium cruentum, in light state 1 and light state 2

The optical cross section of PS I in whole cells of Porphyridium cruentum (UTEX 161), held in either state 1 or state 2, was determined by measuring the change in absorbance at 820nm, an indication of P700+; the X-section of PS2 was determined by measuring the variable fluorescence, (Fv-Fo)/Fo, from PS2. Both cross-sections were 7 determined by fitting Poisson distribution equations to the light saturation curves obtained with single turnover laser flashes which varied in intensity from zero to a level where maximum yield occurred. Flash wavelengths of 574nm, 626nm, and 668nm were used, energy absorbed by PBS, by PBS and chla, and by chla respectively. There were two populations of both PSi and PS2. A fraction of PSi is associated with PBS, and a fraction of PS2 is free from PBS. On the transition S1->S2, only with PBS-absorbed energy (574nm) did the average X-section of PSi increase (27%), and that of PS2 decrease (40%). The fraction of PSi associated with PBS decreased, from 0.65 to 0.35, and the Xsection of this associated PS 1 increased, from 135±65 A2 to 400±300A2. The cross section of PS2 associated with PBS decreased from 150±50 A2 to 85±45 A2, but the fraction of PS2 associated with PBS, approximately 0.75, did not change significantly. The increase in PSi cross section could not be completely accounted for by postulating that several PSi are associated with a single PBS and that in the transition to state2, fewer PSi share the same number of PBS, resulting in a larger X-section. It is postulated that small changes occur in the attachment of PS2 to PBS causing energy to be diverted to the attached PSi. These experiments support neither the mobile-PBS model of state transitions nor that of spillover. From cross section changes there was no evidence of energy transfer from PS2 to PSi with 668nm light. The decrease in PS2 fluorescence which occurred at this wavelength cannot be explained by energy transfer; another explanation must be sought. No explanation was found for an observed decrease in PSi yield at high flash intensities.

The vibrational spectra and the normal coordinate analysis of thiocarbonye halides /|nby C. R. Subramaniam. -- 260 St. Catharines, Ont. : [s. n.],

The infrared and the Raman spectra of eSelF has been obtained for the first time and has been analysed to give the in-plane normal vibrational frequencies of the molecule, in the ground state. A normal co-ordinate analysis has been carried out for the molecules CSF2, CSClF and eSel 2 using a Urey-Bradley type of potential function and the elements of the [L] matrix elements, the distribution of the potential energy in Urey-Bradley space, and the displacement vector diagrams for the normal modes of vibration for these molecules, have been obtained. The bond for~e constants obtained through the normal co-ordinate analysis, have given some interesting results. The stretching force constant, Kes ' varies markedly with halogen substitution and the force constants KeF and Keel also vary with substitution.

Transmission measurements using a new far-infrared set-up

A system comprised of a Martin-Puplett type polarizing interferometer and a Helium-3 cryostat was developed to study the transmission of materials in the very-far-infrared region of the spectrum. This region is of significant interest due to the low-energy excitations which many materials exhibit. The experimental transmission spectrum contains information concerning the optical properties of the material. The set-up of this system is described in detail along with the adaptations and improvements which have been made to the system to ensure the best results. Transmission experiments carried out with this new set-up for two different varieties of materials: superconducting thin films of lead and biological proteins, are discussed. Several thin films of lead deposited on fused silica quartz substrates were studied. From the ratio of the transmission in the superconducting state to that in the normal state the superconducting energy gap was determined to be approximately 25 cm-1 which corresponds to 2~/kBTc rv 5 in agreement with literature data. Furthermore, in agreement with theoretical predictions, the maximum in the transmission ratio was observed to increase as the film thickness was increased. These results provide verification of the system's ability to accurately measure the optical properties of thin low-Tc superconducting films. Transmission measurements were carried out on double deionized water, and a variety of different concentrations by weight of the globular protein, Bovine Serum Albumin, in the sol, gel and crystalline forms. The results of the water study agree well with literature values and thus further illustrate the reproducibility of the system. The results of the protein experiments, although preliminary, indicate that as the concentration increases the samples become more transparent. Some weak structure in the frequency dependent absorption coefficient, which is more prominent in crystalline samples, may be due to low frequency vibrations of the protein molecules.

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.

Cognitive set, absorption, and achievement as moderators of the perceptual closure effect in picture priming /

The present study examined individual differences in Absorption and fantasy, as well as in Achiievement and achievement striving as possible moderators of the perceptual closure effect found by Snodgrass and Feenan (1990). The study also examined whether different instructions (experiential versus instrumental) interact with the personality variables to moderate the relationship between priming and subsequent performance on a picture completion task. 1 28 participants completed two sessions, one to fill out the MPQ and NEO personality inventories and the other to complete the experimental task. The experimental task consisted of a priming phase and a test phase, with pictures presented on a computer screen for both phases. Participants were shown 30 pictures in the priming phase, and then shovm the 30 primed pictures along with 30 new pictures for the test phase. Participants were randomly assigned to receive one of the two different instruction sets for the task. Two measures of performance were calculated, most fragmented measure and threshold. Results of the present study confirm that a five-second exposure time is long enough to produce the perceptual closure effect. The analysis of the two-way interaction effects indicated a significant quadratic interaction of Absorption with priming level on threshold performance. The results were in the opposite direction of predictions. Possible explanations for the Absorption results include lack of optimal conditions, lack of intrinsic motivation and measurement problems. Primary analyses also revealed two significant between-subject effects of fantasy and achievement striving on performance collapsed across priming levels. These results suggest that fantasy has a beneficial effect on performance at test for pictures primed at all levels, whereas achievement striving seems to have an adverse effect on performance at test for pictures primed at all levels. Results of the secondary analyses with a revised threshold performance measure indicated a significant quadratic interaction of Absorption, condition and priming level. In the experiential condition, test performance, based on Absorption scores for pictures primed at level 4, showed a positive slope and performance for pictures primed at levels 1 and 7 based on Absorption showed a negative slope. The reverse effect was found in the instrumental condition. The results suggest that Absorption, in combination with experiential involvement, may affect implicit memory. A second significant result of the secondary analyses was a linear three-way interaction of Achievement, condition and priming level on performance. Results suggest that as Achievement scores increased, test performance improved for less fragmented primed pictures in the instrumental condition and test performance improved for more highly fragmented primes in the experiential condition. Results from the secondary analyses suggest that the revised threshold measure may be more sensitive to individual differences. Results of the exploratory analyses with Openness to Experience, Conscientiousness and agentic positive emotionality (PEM-A) measures indicated no significant effects of any of these personality variables. Results suggest that facets of the scales may be more useful with regard to perceptual research, and that future research should examine narrowly focused personality traits as opposed to broader constructs.

Pigment orientation changes detected by low temperature linear dichroism spectroscopy: cold-hardening transition in phycobilisome-containing organisms

Low temperature (77K) linear dichroism spectroscopy was used to characterize pigment orientation changes accompanying the light state transition in the cyanobacterium, Synechococcus sp. pee 6301, and cold-hardening in winter rye (Secale cereale L. cv. Puma). Samples were oriented for spectroscopy using the gel squeezing method (Abdourakhmanov et aI., 1979) and brought to 77K in liquid nitrogen. The linear dichroism (LD) spectra of Synechococcus 6301 phycobilisome/thylakoid membrane fragments cross-linked in light state 1 and light state 2 with glutaraldehyde showed differences in both chlorophyll a and phycobilin orientation. A decrease in the relative amplitude of the 681nm chlorophyll a positive LD peak was observed in membrane fragments in state 2. Reorientation of the phycobilisome (PBS) during the transition to state 2 resulted in an increase in core allophycocyanin absorption parallel to the membrane, and a decrease in rod phycocyanin parallel absorption. This result supports the "spillover" and "PBS detachment" models of the light state transition in PBS-containing organisms, but not the "mobile PBS" model. A model was proposed for PBS reorientation upon transition to state 2, consisting of a tilt in the antenna complex with respect to the membrane plane. Linear dichroism spectra of PBS/thylakoid fragments from the red alga, Porphyridium cruentum, grown in green light (containing relatively more PSI) and red light (containing relatively more PSll) were compared to identify chlorophyll a absorption bands associated with each photosystem. Spectra from red light - grown samples had a larger positive LD signal on the short wavelength side of the 686nm chlorophyll a peak than those from green light - grown fragments. These results support the identification of the difference in linear dichroism seen at 681nm in Synechococcus spectra as a reorientation of PSll chromophores. Linear dichroism spectra were taken of thylakoid membranes isolated from winter rye grown at 20°C (non-hardened) and 5°C (cold-hardened). Differences were seen in the orientation of chlorophyll b relative to chlorophyll a. An increase in parallel absorption was identified at the long-wavelength chlorophyll a absorption peak, along with a decrease in parallel absorption from chlorophyll b chromophores. The same changes in relative pigment orientation were seen in the LD of isolated hardened and non-hardened light-harvesting antenna complexes (LHCII). It was concluded that orientational differences in LHCII pigments were responsible for thylakoid LD differences. Changes in pigment orientation, along with differences observed in long-wavelength absorption and in the overall magnitude of LD in hardened and non-hardened complexes, could be explained by the higher LHCII monomer:oligomer ratio in hardened rye (Huner et ai., 1987) if differences in this ratio affect differential light scattering properties, or fluctuation of chromophore orientation in the isolated LHCII sample.

Studies in the mass spectra of perfluoroaromatic derivatives of phosphorus and some selected transition metals

The mass spectra and fragmentation of a variety of fluoroaromatic compounds of Group V and some selected transition elements are discussed in some detail, aided by data from metastable defocussed experiments. Results of ,studies on the coupling reaction using unstable organotitanium chloride intermediate species are reported. The preparation of some 5-substituted octafluorodibenzophospho1es is also discussed. Rearrangements under electron bombardment resulting in the loss of heteroatom-fluoride fragments are discussed in the light of presently accepted mechanisms for these processes as are rearrangements observed in compounds involving thionophosphoryl bonds ( p=s ).

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.

Developing a numerical inverse-theory-based extraction of orientation-dependent relaxation rates from partially- relaxed spectra

Second-rank tensor interactions, such as quadrupolar interactions between the spin- 1 deuterium nuclei and the electric field gradients created by chemical bonds, are affected by rapid random molecular motions that modulate the orientation of the molecule with respect to the external magnetic field. In biological and model membrane systems, where a distribution of dynamically averaged anisotropies (quadrupolar splittings, chemical shift anisotropies, etc.) is present and where, in addition, various parts of the sample may undergo a partial magnetic alignment, the numerical analysis of the resulting Nuclear Magnetic Resonance (NMR) spectra is a mathematically ill-posed problem. However, numerical methods (de-Pakeing, Tikhonov regularization) exist that allow for a simultaneous determination of both the anisotropy and orientational distributions. An additional complication arises when relaxation is taken into account. This work presents a method of obtaining the orientation dependence of the relaxation rates that can be used for the analysis of the molecular motions on a broad range of time scales. An arbitrary set of exponential decay rates is described by a three-term truncated Legendre polynomial expansion in the orientation dependence, as appropriate for a second-rank tensor interaction, and a linear approximation to the individual decay rates is made. Thus a severe numerical instability caused by the presence of noise in the experimental data is avoided. At the same time, enough flexibility in the inversion algorithm is retained to achieve a meaningful mapping from raw experimental data to a set of intermediate, model-free

Spectroscopic and theoretical considerations of cyclopropenone

Please consult the paper edition of this thesis to read. It is available on the 5th Floor of the Library at Call Number: Z 9999 P65 D53 2007

Spectral Reflectance Characteristics of Kimberlite Indicator Minerals and Other Selected Mineral Grains

High chromium content in kimberlite indicator minerals such as pyrope garnet and diopside is often correlated with the presence of diamonds. In this study, kimberlite indicator minerals were examined using visible light reflectance spectroscopy to determine if chromium content can be correlated with spectral absorption features. The depth of absorption features in the visible spectral region were correlated with the molecular percentage of chromium and other first series transition metal elements obtained by electron microprobe data. In the visible part of the spectrum, chromium is evident by 3 absorption features in the pyrope reflectance spectrum; one isolated and narrow feature at the wavelength 689 nm was used to correlate with the chromium mol %. The isolation of this feature in the pyrope spectra is advantageous since it is not directly affected by other proximal absorption bands that could be caused by other transition metals. Analysis of the feature indicates that as grain volume increases the depth of the absorption feature will also increase. Clustering grain volumes into fractions yields better correlation between absorption depth and mol % chromium. Other types of garnet (almandine, grossular, spessartine) and kimberlite indicator minerals (olivine, diopside, chromite, ilmenite) were analyzed to determine if other absorption features could be used to predict the proportion of specific transition metal elements. Diopside in particular illustrates the same isolated chromium absorption feature as pyrope and may indicate mol percent but needs further study with larger sample sets.

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.