Variational Monte Carlo study of core-valence separation schemes for first-row atoms and positive ions /

All-electron partitioning of wave functions into products ^core^vai of core and valence parts in orbital space results in the loss of core-valence antisymmetry, uncorrelation of motion of core and valence electrons, and core-valence overlap. These effects are studied with the variational Monte Carlo method using appropriately designed wave functions for the first-row atoms and positive ions. It is shown that the loss of antisymmetry with respect to interchange of core and valence electrons is a dominant effect which increases rapidly through the row, while the effect of core-valence uncorrelation is generally smaller. Orthogonality of the core and valence parts partially substitutes the exclusion principle and is absolutely necessary for meaningful calculations with partitioned wave functions. Core-valence overlap may lead to nonsensical values of the total energy. It has been found that even relatively crude core-valence partitioned wave functions generally can estimate ionization potentials with better accuracy than that of the traditional, non-partitioned ones, provided that they achieve maximum separation (independence) of core and valence shells accompanied by high internal flexibility of ^core and Wvai- Our best core-valence partitioned wave function of that kind estimates the IP's with an accuracy comparable to the most accurate theoretical determinations in the literature.

Study of colossal magnetoresistance and pressure effects in La2/3Ca1/3MnO2 thin films /

The main purpose of this thesis is to study properties of La2/3Cai/3Mn03, both polycrystalline ceramics and thin films. This material has striking related electrical and magnetic properties. Thin films show colossal negative magnetoresistance (CMR) near transition from an insulating to a metallic state accompanied closely by transition from a paramagnetic to a ferromagnetic state. The double exchange mechanism (DE) and the Jahn-Teller deformations play an important role in CMR effect. Applied pressure has a very similar effect as does an applied magnetic field, except, at low temperatures (Telectrons. Oxygen stoichiometry plays an important role in the magnitude and position of MR(T) maximum. The distortions of structure and Mn-O-Mn bonds in applied pressure axe discussed. The fabrication of La2/3Cai/3Mn03 thin films by pulsed laser deposition was successfully developed. The films grown on (100) SrTiOs substrate are c-axis oriented and exhibit negative magnetoresistance Ap/p(H) of over 400% at 245°C and 4200% at 90 K.

An experimental investigation of dechanneling in copper single crystals

This investigation comprises a comparison of experimental and theoretical dechanneling of MeV protons in copper single crystals. Dechanneling results when an ion's transverse energy increases to the value where the ion can undergo small impact parameter collisions with individual atoms. Depth dependent dechanneling rates were determined as functions of lattice temperature, ion beam energy and crystal axis orientation. Ion beam energies were IMeV and 2MeV,temperatures ranged from 35 K to 280 K and the experiment was carried out along both the (lOa) and <110) axes. Experimental data took the form of aligned and random Rutherford backscattered energy spectra. Dechanneling rates were extracted from these spectra using a single scattering theory that took explicit account of the different stopping powers experienced by channeled and dechanneled ions and also included a correction factor to take into account multiple scattering effects along the ion's trajectory. The assumption of statistical equilibrium and small angle scattering of the channeled ions allows a description of dechanneling in terms of the solution of a diffusion like equation which contains a so called diffusion function. The diffusion function is shown to be related to the increase in average transverse energy. Theoretical treatments of increase in average transverse energy due to collisions of projectiles with channel electrons and thermal perturbations in the lattice potential are reviewed. Using the diffusion equation and the electron density in the channel centre as a fitting parameter dechanneling rates are extracted. Excellent agreement between theory and experiment has been demonstrated. Electron densities determined in the fitting procedure appear to be realistic. The surface parameters show themselves to be good indicators of the quality of the crystal.

Application of [Lambda] to the fourth perturbation theory in calculating the equation of state of rare gas solids and fcc metals

We have calculated the thermodynamic properties of monatomic fcc crystals from the high temperature limit of the Helmholtz free energy. This equation of state included the static and vibrational energy components. The latter contribution was calculated to order A4 of perturbation theory, for a range of crystal volumes, in which a nearest neighbour central force model was used. We have calculated the lattice constant, the coefficient of volume expansion, the specific heat at constant volume and at constant pressure, the adiabatic and the isothermal bulk modulus, and the Gruneisen parameter, for two of the rare gas solids, Xe and Kr, and for the fcc metals Cu, Ag, Au, Al, and Pb. The LennardJones and the Morse potential were each used to represent the atomic interactions for the rare gas solids, and only the Morse potential was used for the fcc metals. The thermodynamic properties obtained from the A4 equation of state with the Lennard-Jones potential, seem to be in reasonable agreement with experiment for temperatures up to about threequarters of the melting temperature. However, for the higher temperatures, the results are less than satisfactory. For Xe and Kr, the thermodynamic properties calculated from the A2 equation of state with the Morse potential, are qualitatively similar to the A 2 results obtained with the Lennard-Jones potential, however, the properties obtained from the A4 equation of state are in good agreement with experiment, since the contribution from the A4 terms seem to be small. The lattice contribution to the thermal properties of the fcc metals was calculated from the A4 equation of state, and these results produced a slight improvement over the properties calculated from the A2 equation of state. In order to compare the calculated specific heats and bulk moduli results with experiment~ the electronic contribution to thermal properties was taken into account~ by using the free electron model. We found that the results varied significantly with the value chosen for the number of free electrons per atom.

Calculation of the optical conductivity for the Anderson impurity model using the slave boson technique

The optical conductivity of the Anderson impurity mode l has been calculated by emp l oying the slave boson technique and an expansion in powers of l i N, where N is the d egeneracy o f the f electron level . This method has been used to find the effective mass of the conduction electrons for temperatures above and below the Kondo tempera ture. For low temperatures, the mass enhancement is f ound to be large while a t high t emperatures, the mass enhancement is sma ll. The conductivity i s f ound to be Drude like with frequency dependent effective mass and scattering time for low independent effective mass and temperatures and scattering time f requency for high t emperatures. The behavior of both the effective mass and the conductivity is in qualitative agreement with experimental r esul t 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 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.

Exchange energy calculation of He-He with supermolecular one-matrix

Exch~nge energy of the He-He system is calculated using the one-density matrix which has been modified according to the supermolecular density formula quoted by Kolos. The exchange energy integrals are computed analytically and by the Monte Carlo method. The results obtained from both ways compared favourably,with the results obtained from the SCF program HONDO

Investigations into the determinations of hydride-forming elements

Analytical methods for the determination of trace amounts of germanium, tin and arsenic were established using hydride generation coupled with direct current plasma atomic emission spectrometry. A continuous gas flowing batch system for the hydride generation was investigated and was applied to the determination of germanium(Ge), tin(Sn), antimony(Sb) and lead(Pb) (Preliminary results suggest that it is also applicable to arsenic)As) ). With this system, the reproducibility of signals was improved and the determination was speeded up, compared with the conventional batch type hydride generation system. Each determination was complete within one minute. Interferences from a number of transition metal ions, especially from Pd(II), Pt(IV), Ni(II), Cu(II), Co(II), and Fe(II, III), have proven to be very serious under normal conditions, in the determination of germanium, tin, and arsenic. These interference effects were eliminated or significantly reduced in the presence of L-cystine or L-cysteine. Thus, a 10-1000 fold excess of Ni(II), Cu(II), Co(II), Fe(II), Pt(IV), Pd(II), etc. can be tolerated without interference, In the presence of L-cystine or L-cysteine, compared with absence of interference reducing agent. The methods for the determination of Ge, Sn, and As were examined by the analyses of standard reference materials. Interference effects from the sample matrix, for example, in transition metal-rich samples, copper, iron and steel, were eliminated by L-cystine (for As and Sn) and by LI cysteine (for Ge). The analysis of a number of standard reference materials gave excellent results of As and Sn contents in agreement with the certified values, showing there was no systematic interference. The detection limits for both germanium and tin were 20 pg ml- I . Preliminary studies were carried out for the determination of antimony and lead. Antimony was found to react with NaBH4, remaInIng from the previous determinations, giving an analytical signal. A reversed injection manner, i.e., injection of the NaBH4 solution prior to the analyte solution was used to avoid uncertainty caused by residual NaBH4 present and to ensure that an excess of NaB H4 was available. A solution of 0.4% L-cysteine was found to reduce the interference from selected transition metal ions, Co(II), Cu(II), Ni(II) and Pt(IV). Hydrochloric acid - hydrogen peroxide, nitric acid - ammonium persulphate, and potassium dichromate malic acid reaction systems for lead hydride generation were compared. The potassium dichromate - malic acid reaction medium proved to be the best with respect to reproducibility and minimal interference. Cu(II), Ni(II), and Fe(II) caused strong interference In lead determinations, which was not reduced by L-cysteine or Lcystine. Sodium citrate, ascorbic acid, dithizone, thiosemicarbazide and penicillamine reduced interferences to some extent. Further interference reduction studies were carried out uSIng a number of amino acids, glycine, alanine, valine, leucine and histidine, as possible interference reducing agents in the determination of germanium. From glycine, alanine, valine to leucine, the interference reduction effect in germanium determinations decreased. Histidine II was found to be very promising In the reduction of interference. In fact, histidine proved more efficient than L-cystine and L-cysteine In the reduction of interference from Ni(II) in the determination of germanium. Signal enhancement by easily ionized elements (EIEs), usually regarded as an interference effect in analysis by DCP-AES, was studied and successfully applied to advantage in improving the sensitivity and detection limit in the determination of As, Ge, Sn, Sb, and Pb. The effect of alkali and alkaline-earth elements on the determination of the above five hydride forming elements was studied. With the appropriate EIE, a signal enhancement of 40-115% was achieved. Linear calibration and good reproducibility were also obtained in the presence of EIEs. III

Optimization of the valence energy variance of the CuH molecule

We developed the concept of split-'t to deal with the large molecules (in terms of the number of electrons and nuclear charge Z). This naturally leads to partitioning the local energy into components due to each electron shell. The minimization of the variation of the valence shell local energy is used to optimize a simple two parameter CuH wave function. Molecular properties (spectroscopic constants and the dipole moment) are calculated for the optimized and nearly optimized wave functions using the Variational Quantum Monte Carlo method. Our best results are comparable to those from the single and double configuration interaction (SDCI) method.

Reduced local energy calculations on X¹Sigmaâ ½gHâ and 1¹S He /|nGerald F. Thomas. -- 260 St. Catharines [Ont.] : Dept. of Chemistry, Brock University,

The one-electron reduced local energy function, t ~ , is introduced and has the property < tL)=(~>. It is suggested that the accuracy of SL reflects the local accuracy of an approximate wavefunction. We establish that <~~>~ <~2,> and present a bound formula, E~ , which is such that where Ew is Weinstein's lower bound formula to the ground state. The nature of the bound is not guaranteed but for sufficiently accurate wavefunctions it will yield a lower bound. ,-+ 1'S I I Applications to X LW Hz. and ne are presented.

Solute effects on the production and decay of primary species in the flash photolysis of indole

Maximum production rates ofs and decay kinetics for the hydrated electron, the indolyl neutral radical and the indole triplet state have been obtained in the microsecond, broadband (X > 260 nm) flash photolysis of helium-saturated, neutral aqueous solutions of indole, in the absence and in the presence of the solutes NaBr, BaCl2*2H20 and CdSCV Fluorescence spectra and fluorescence lifetimes have also been obtained in the absence and in the presence of the above solutes, The hydrated electron is produced monophotonically and biphotonically at an apparent maximum rate which is increased by BaCl2*2H20 and decreased by NaBr and CdSOif. The neutral indolyl radical may be produced monophotonically and biphotonically or strictly monophotonically at an apparent maximum rate which is increased by NaBr and CdSO^ and is unaffected by BaCl2*2H20. The indole triplet state is produced monophotonically at a maximum rate which is increased by all solutes. The hydrated electron decays by pseudo first order processes, the neutral indolyl radical decays by second order recombination and the indole triplet state decays by combined first and second order processes. Hydrated electrons are shown to react with H , H2O, indole, Na and Cd"*""1"". No evidence has been found for the reaction of hydrated electrons with Ba . The specific rate of second order neutral indolyl radical recombination is unaffected by NaBr and BaCl2*2H20, and is increased by CdSO^. Specific rates for both first and second order triplet state decay processes are increased by all solutes. While NaBr greatly reduced the fluorescence lifetime and emission band intensity, BaCl2*2H20 and CdSO^ had no effect on these parameters. It is suggested that in solute-free solutions and in those containing BaCl2*2H20 and CdSO^, direct excitation occurs to CTTS states as well as to first excited singlet states. It is further suggested that in solutions containing NaBr, direct excitation to first excited singlet states predominates. This difference serves to explain increased indole triplet state production (by ISC from CTTS states) and unchanged fluorescence lifetimes and emission band intensities in the presence of BaCl2*2H20 and CdSOt^., and increased indole triplet state production (by ISC from S^ states) and decreased fluorescence lifetime and emission band intensity in the presence of NaBr. Evidence is presented for (a) very rapid (tx ^ 1 us) processes involving reactions of the hydrated electron with Na and Cd which compete with the reformation of indole by hydrated electron-indole radical cation recombination, and (b) first and second order indole triplet decay processes involving the conversion of first excited triplet states to vibrationally excited ground singlet states.

Orientation of Non-Native 2-Monosubstituted and 2,3-Disubstituted 1,4-Naphthoquinones in the A1 binding site of PSI and the effect on the rate of electron transfer : an electron paramagnetic resonance spectroscopy study

The proce-ss ofoxygenic photosynthesis is vital to life on Earth. the central event in photosynthesis is light induced electron transfer that converts light into energy for growth. Ofparticular significance is the membrane bound multisubunit protein known as Photosystem I (PSI). PSI is a reaction centre that is responsible for the transfer of electrons across the membrane to reduce NADP+ to NADPH. The recent publication ofa high resolution X-ray structure of PSI has shown new information about the structure, in particular the electron transfer cofactors, which allows us to study it in more detail. In PSI, the secondary acceptor is crucial for forward electron transfer. In this thesis, the effect of removing the native acceptor phylloquinone and replacing it with a series of structurally related quinones was investigated via transient electron paramagnetic resonance (EPR) experiments. The orientation of non native quinones in the binding site and their ability to function in the electron transfer process was determined. It was found that PSI will readily accept alkyl naphthoquinones and anthraquinone. Q band EPR experiments revealed that the non-native quinones are incorporated into the binding site with the same orientation of the headgroup as in the native system. X band EPR spectra and deuteration experiments indicate that monosubstituted naphthoquinones are bound to the Al site with their side group in the position occupied by the methyl group in native PSI (meta to the hydrogen bonded carbonyl oxygen). X band EPR experiments show that 2, 3- disubstituted methyl naphthoquinones are also incorporated into the Al site in the same orientation as phylloquinone, even with the presence of a halogen- or sulfur-containing side chain in the position normally occupied by the phytyl tail ofphylloquinone. The exception to this is 2-bromo-3-methyl --.- _. -. - -- - - 4 _._ _ _ - _ _ naphthoquinone which has a poorly resolved spectrum, making determination of the orientation difficuh. All of the non-native quinones studied act as efficient electron acceptors. However, forward electron transfer past the quinone could only be demonstrated for anthraquinone, which has a more negative midpoint potential than phylloquinone. In the case of anthraquinone, an increased rate of forward electron transfer compared to native PSI was found. From these results we can conclude that the rate ofelectron transfer from Al to Fx in native PSI lies in the normal region ofthe Marcus Curve.

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.

Towards reverse engineering of Photosystem II: Synergistic Computational and Experimental Approaches

ABSTRACT Photosystem II (PSII) of oxygenic photosynthesis has the unique ability to photochemically oxidize water, extracting electrons from water to result in the evolution of oxygen gas while depositing these electrons to the rest of the photosynthetic machinery which in turn reduces CO2 to carbohydrate molecules acting as fuel for the cell. Unfortunately, native PSII is unstable and not suitable to be used in industrial applications. Consequently, there is a need to reverse-engineer the water oxidation photochemical reactions of PSII using solution-stable proteins. But what does it take to reverse-engineer PSII’s reactions? PSII has the pigment with the highest oxidation potential in nature known as P680. The high oxidation of P680 is in fact the driving force for water oxidation. P680 is made up of a chlorophyll a dimer embedded inside the relatively hydrophobic transmembrane environment of PSII. In this thesis, the electrostatic factors contributing to the high oxidation potential of P680 are described. PSII oxidizes water in a specialized metal cluster known as the Oxygen Evolving Complex (OEC). The pathways that water can take to enter the relatively hydrophobic region of PSII are described as well. A previous attempt to reverse engineer PSII’s reactions using the protein scaffold of E. coli’s Bacterioferritin (BFR) existed. The oxidation potential of the pigment used for the BFR ‘reaction centre’ was measured and the protein effects calculated in a similar fashion to how P680 potentials were calculated in PSII. The BFR-RC’s pigment oxidation potential was found to be 0.57 V, too low to oxidize water or tyrosine like PSII. We suggest that the observed tyrosine oxidation in BRF-RC could be driven by the ZnCe6 di-cation. In order to increase the efficiency of iii tyrosine oxidation, and ultimately oxidize water, the first potential of ZnCe6 would have to attain a value in excess of 0.8 V. The results were used to develop a second generation of BFR-RC using a high oxidation pigment. The hypervalent phosphorous porphyrin forms a radical pair that can be observed using Transient Electron Paramagnetic Resonance (TR-EPR). Finally, the results from this thesis are discussed in light of the development of solar fuel producing systems.