Quantum magnetic materials provide pathways to exotic spin-disordered phases. We study two broad classes of quantum spin systems and their ground states. The first class is that of spin-dimer systems, which form valence-bond-solid states. In such systems, competition between interactions among the dimers can lead to interesting magnetization behaviour. We explain the magnetization of Ba3Cr2O8 as a Bose-Einstein condensate of spin-carrying excitations. Furthermore, we investigate possible dimerized and nearby magnetically ordered states in the Shastry-Sutherland compound (CuCl)LaNb2O7. The second class of spin systems feature geometric frustration, which may stabilize spin-liquid states without any order or particular dimerization. We argue the proximity of the face-centred-cubic double perovskite La2LiMoO6 to such a phase, to explain its lack of long-range order. We argue for the coexistence of such a state, along with spiral magnetic order, to explain the anomalous thermodynamic measurements in the spin-density-wave phase of powder samples of Volborthite, a distorted kagome-lattice spin system. Finally, we study spin liquid phases that have spin correlations consistent with those found from inelastic neutron scattering of the disordered kagome-lattice material Herbertsmithite. We predict electron spin resonance absorption lineshapes associated with these phases.

Enantioselective reactions are one of the ways to produce pure chiral compounds. Understanding the basis of this selectivity makes it possible to guide enzyme design towards more efficient catalysts. One approach to study enzymes involved in chiral chemistry is through the use of computational models that are able to simulate the chemical reaction taking place. The potato epoxide hydrolase is one enzyme that is known to be both highly enantioselective, while still being robust upon mutation of residues to change substrate scope. The enzyme was used to investigate the epoxide hydrolysis mechanism for a number of different substrates, using the EVB approach to the reaction both in solution and in several enzyme variants. In addition to this, work has been performed on new ways of performing simulations of divalent transition metals, as well as development of new simulation software.

In the search for a sustainable and environmentally friendly energy source, artificial photosynthesis has been proposed  as a promising solution. Using water as a substrate, solar energy can be utilised to store energy in the chemical form of hydrogen fuel. In part of this global scientific effort, this thesis work focuses on enabling molecular dynamics simulations of a particular set of ruthenium centred  water oxidation catalysts. The new catalysts show great success because of a binuclear  reaction  pathway in aqueous solution which makes it very interesting to model and investigate. Utilising quantum  mechanical tools, a set of molecular mechanics force field parameters for Ru-involved bonds, angles, torsions, and partial charges was successfully obtained and examined. The work allows future large scale simulation of water  oxidation and oxygen evolution in order to gain understanding and improve artificial photosynthesis.

The reaction mechanisms for the hemoglobin degrading enzymes in the Plasmodium falciparum malaria parasite, plasmepsin II (Plm II) and histo-aspartic protease (HAP), have been analyzed by molecular simulations. The reaction free energy profiles, calculated by the empirical valence bond (EVB) method in combination with molecular dynamics (MD) and free energy perturbation (FEP) simulations are in good agreement with experimental data. Additional computational methods, such as homology modelling and automated substrate docking, were necessary to generate a 3D model and a reactive substrate conformation before the reaction mechanism in HAP could be investigated. HAP is found to be an aspartic protease with a peptide cleaving mechanism similar to plasmepsin II. The major difference between these enzymes is that the negatively charged tetrahedral intermediate is stabilized by the charged histidine in HAP while in Plm II it is a neutral aspartic acid. Also the reaction mechanism for two other aspartic proteases, cathepsin D and HIV-1 protease, was simulated. These enzymes are relevant both for the inhibitor selectivity and for obtaining a general picture of catalysis in aspartic proteases. Another project involves inhibitor design towards plasmepsins. In particular, Plm II directed inhibitors based on the dihydroxyethylene scaffold have been characterized computationally. Molecular dynamics (MD) simulations were used to propagate the investigated system through time and to generate ensembles used for the calculation of free energies. The ligand binding affinities were calculated with the linear interaction energy (LIE) method. The most potent inhibitor had a Ki value of 6 nM and showed 78 % parasite inhibition when tested on red blood cells infected by malaria parasite P. falciparum. Citrate synthase is part of the citric acid cycle and is present in organisms that live in cold sea water as well as hot springs. The temperature adaptation of citrate synthase to cold and heat was investigated in terms of the difference in transition state stabilization between the psychrophilic, mesophilic and hyperthermophilic homologues. The EVB, FEP and MD methods were used to generate reaction free energy profiles. The investigated energetics points toward the electrostatic stabilization during the reaction as the major difference between the different citrate synthase homologues. The electrostatic stabilization of the transition state is most effective in the following order of the citrate synthase homologues: hyperthermophile, mesophile, psycrophile. This could be a general rule for temperature adaptation of enzyme catalysis.

Through the development of physical chemistry and chemical physics over the late-nineteenth and early-twentieth centuries, the relationship between physics and chemistry changed to create a broad interdisciplinary framework in which chemists and physicists could make contributions to problems of common value. It is here argued that evolving disciplinary factors such as physical and chemical responses to the atomic hypothesis, the nature of disciplinary formation in Germany and the United States, the reception of quantum mechanics within physics and chemistry, and the application of quantum mechanics to the problem of chemical bonding by physicists and chemists, formed the chemical bond into a physico-chemical theory. In the late nineteenth-century context of early physical chemistry, the chemical bond was known as a physical link between atoms, which could not be studied by chemical means because of the lack of an adequate atomistic framework. Both chemists and physicists broadly accepted the atomistic hypothesis following the discovery of the electron at the turn of the twentieth century, which afforded theoretical study of chemical bonding. Between 1916 and 1919, Gilbert N. Lewis and Irving Langmuir proposed the valence bond to be a pair of electrons shared between two atoms, within the context of a cubic model of the atom. However, the lack of a physical mechanism for the shared electron pair prevented the formation of a fully physico-chemical view of bonding. In 1927, physicists Walter Heitler and Fritz London showed the stability of the valence bond was caused by the wave mechanical phenomenon of resonance. Chemist Linus Pauling extended their treatment of the valence bond to a theory of structural chemistry in The Nature of the Chemical Bond. His synthesis of the physical and chemical views, his value as a physico-chemical researcher during the 1930s, and the research of his contemporaries John Slater and Robert Mulliken show that a true physico-chemical blend was only realized within the amorphous discipline of chemical physics. Finally, it is seen that this interdisciplinarity of chemical bonding and its supporting framework force a reevaluation of the reductionist criteria, and a re-definition of the chemical bond as a physico-chemical work.

Through the development of physical chemistry and chemical physics over the late-nineteenth and early-twentieth centuries, the relationship between physics and chemistry changed to create a broad interdisciplinary framework in which chemists and physicists could make contributions to problems of common value. It is here argued that evolving disciplinary factors such as physical and chemical responses to the atomic hypothesis, the nature of disciplinary formation in Germany and the United States, the reception of quantum mechanics within physics and chemistry, and the application of quantum mechanics to the problem of chemical bonding by physicists and chemists, formed the chemical bond into a physico-chemical theory. In the late nineteenth-century context of early physical chemistry, the chemical bond was known as a physical link between atoms, which could not be studied by chemical means because of the lack of an adequate atomistic framework. Both chemists and physicists broadly accepted the atomistic hypothesis following the discovery of the electron at the turn of the twentieth century, which afforded theoretical study of chemical bonding. Between 1916 and 1919, Gilbert N. Lewis and Irving Langmuir proposed the valence bond to be a pair of electrons shared between two atoms, within the context of a cubic model of the atom. However, the lack of a physical mechanism for the shared electron pair prevented the formation of a fully physico-chemical view of bonding. In 1927, physicists Walter Heitler and Fritz London showed the stability of the valence bond was caused by the wave mechanical phenomenon of resonance. Chemist Linus Pauling extended their treatment of the valence bond to a theory of structural chemistry in The Nature of the Chemical Bond. His synthesis of the physical and chemical views, his value as a physico-chemical researcher during the 1930s, and the research of his contemporaries John Slater and Robert Mulliken show that a true physico-chemical blend was only realized within the amorphous discipline of chemical physics. Finally, it is seen that this interdisciplinarity of chemical bonding and its supporting framework force a reevaluation of the reductionist criteria, and a re-definition of the chemical bond as a physico-chemical work.

<p>In this thesis I present three publications about the use of<br />valence bonds to gain information about quantum spin systems.<br />Valence bonds are an essential ingredient of low energy states present<br />in many compounds.<br /><br />The first part of this thesis is dedicated to<br />two studies of the antiferromagnetic J₁-J₂ chain with<br />S=1/2. We show how automated variational calculations based on<br />valence bond states can be performed close to the Majumdar-Ghosh point<br />(MG-point). At this point, the groundstate is a product state of<br />dimers (valence bonds between nearest neighbours). In the dimerized<br />region surrounding the MG-point, we find such variational computations<br />to be reliable.<br /><br />The first publication is about<br />the entanglement properties of an impurity attached to the chain. We show<br />how to use the variational method to calculate the negativity, an<br />entanglement measure between the impurity and a distant part of the<br />chain. We find that increasing the impurity coupling and a<br />minute explicit dimerization, suppress the long-ranged entanglement<br />present in the system for small impurity coupling at the MG-point. <br /><br />The second publication is about a<br />transition from commensurate to incommensurate behaviour and how its<br />characteristics depend on the parity of the length of the chain. The<br />variational technique is used in a parameter regime inaccessible to<br />DMRG. We find that in odd chains, unlike in even chains, a very<br />intricate and interesting pattern of level crossings can be observed. <br /><br />The publication of the second part is about novel worm algorithms for<br />a popular quantum Monte Carlo method called valence bond quantum Monte<br />Carlo (VBQMC). The algorithms are based on the notion of a worm<br />moving through a decision tree. VBQMC is entirely formulated in<br />terms of valence bonds. In this thesis, I explain how the approach<br />of VBQMC can be translated to the S_z-basis. The algorithms explained<br />in the publication can be applied to this S_z-method.</p> / Doctor of Philosophy (PhD)

Ground state destabilization is a hypothesis to explain enzyme catalysis. The most popular interpretation of it is the entropic effect, which states that enzymes accelerate biochemical reactions by bringing the reactants to a favorable position and orientation and the entropy cost of this is compensated by enthalpy of binding. Once the enzyme-substrate complex is formed, the reaction could proceed with negligible entropy cost. Deamination of cytidine catalyzed by E.coli cytidine deaminase appears to agree with this hypothesis. In this reaction, the chemical transformation occurs with a negligible entropy cost and the initial binding occurs with a large entropy penalty that is comparable to the entropic cost of the uncatalyzed reaction. Our calculations revealed that this reaction occurs with different mechanisms in the cytidine deaminase and water. The uncatalyzed reaction involves a concerted mechanism and the entropy cost of this reaction appears to be dominated by the reacting fragments and first solvation shell. The catalyzed reaction occurs via a stepwise mechanism in which a hydroxide ion acts as the nucleophile. In the active site, the entropy cost of hydroxide ion formation is eliminated due to pre-organization of the active site. Hence, the entropic effect in this reaction is due to a pre-organized active site rather than ground state destabilization. In the second part of this thesis, we investigated peptide bond formation and peptidyl-tRNA hydrolysis at the peptidyl transferase center of the ribosome. Peptidyl-tRNA hydrolysis occurs by nucleophilic attack of a water molecule on the ester carbon of peptidyl-tRNA. Our calculations showed that this reaction proceeds via a base catalyzed mechanism where the A76 O2’ is the general base and activates the nucleophilic water. Peptide bond formation occurs by nucleophilic attack of the α-amino group of aminoacyl-tRNA on the ester carbon of peptidyl-tRNA. For this reaction we investigated two mechanisms: i) the previously proposed proton shuttle mechanism which involves a zwitterionic tetrahedral intermediate, and ii) a general base mechanism that proceeds via a negatively charged tetrahedral intermediate. Although both mechanisms resulted in reasonable activation energies, only the proton shuttle mechanism found to be consistent with the pH dependence of peptide bond formation.

Orientador: Ricardo Luís Doretto / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-09-03T02:41:35Z (GMT). No. of bitstreams: 1 Leite_LeonardoDaSilvaGarcia_M.pdf: 1468749 bytes, checksum: 2f4e22a34c4a72b7b68eec6673285298 (MD5) Previous issue date: 2017 / Resumo: Nesse trabalho, calculamos a entropia de emaranhamento de um antiferromagneto de Heisenberg dimerizado em uma rede quadrada. Dois padrões de dimerização distintos são considerados: colunar e alternado. Em ambos os casos, focamos na fase de sólidos de singletos (VBS) que é descrita pela representação dos operadores de ligação. Nesse formalismo, o hamiltoniano de spin original é mapeado em um modelo efetivo de bósons interagentes com excitações de tripleto. O hamiltoniano efetivo é estudado na aproximação harmônica e o espectro das excitações elementares e o diagrama de fase dos dois modelos dimerizados são determinados. Consideramos um subsistema unidimensional (cadeia) de comprimento $L$ dentro de uma rede quadrada com condições periódicas de contorno e calculamos a entropia de emaranhamento. Seguimos um procedimento analítico baseado na teoria de ondas de spin modificadas que havia sido desenvolvido originalmente para calcular a entropia de emaranhamento em fases magneticamente ordenadas. Em particular, esse procedimento nos permite considerar subsistemas unidimensionais compostos por até 200 sítios. Combinamos esse procedimento com o formalismo dos operadores de ligação na aproximação harmônica e mostramos que, para os dois modelos de Heisenberg dimerizados, a entropia de emaranhamento da fase VBS obedece uma lei de área. Tanto para a dimerização colunar quanto para a alternada, mostramos que a entropia de emaranhamento aumenta à medida que o sistema se aproxima da transição de fase quântica entre as fases Néel-VBS / Abstract: Nesse trabalho, calculamos a entropia de emaranhamento de um antiferromagneto de Heisenberg dimerizado em uma rede quadrada. Dois padrões de dimerização distintos são considerados: colunar e alternado. Em ambos os casos, focamos na fase de sólidos de singletos (VBS) que é descrita pela representação dos operadores de ligação. Nesse formalismo, o hamiltoniano de spin original é mapeado em um modelo efetivo de bósons interagentes com excitações de tripleto. O hamiltoniano efetivo é estudado na aproximação harmônica e o espectro das excitações elementares e o diagrama de fase dos dois modelos dimerizados são determinados. Consideramos um subsistema unidimensional (cadeia) de comprimento $L$ dentro de uma rede quadrada com condições periódicas de contorno e calculamos a entropia de emaranhamento. Seguimos um procedimento analítico baseado na teoria de ondas de spin modificadas que havia sido desenvolvido originalmente para calcular a entropia de emaranhamento em fases magneticamente ordenadas. Em particular, esse procedimento nos permite considerar subsistemas unidimensionais compostos por até 200 sítios. Combinamos esse procedimento com o formalismo dos operadores de ligação na aproximação harmônica e mostramos que, para os dois modelos de Heisenberg dimerizados, a entropia de emaranhamento da fase VBS obedece uma lei de área. Tanto para a dimerização colunar quanto para a alternada, mostramos que a entropia de emaranhamento aumenta à medida que o sistema se aproxima da transição de fase quântica entre as fases Néel-VBS / Mestrado / Física / Mestre em Física / 1547615/2015 / CAPES

In this thesis, we investigate strongly correlated phenomena in quantum spin systems. In the first part of this work, we study geometrically frustrated antiferromagnets (AFMs). Generalizing the SU(2) Heisenberg Hamiltonian to Sp(N) symmetry, we obtain, in the large-N limit, the mean-field phase diagrams for the planar pyrochlore and cubic AFMs. We then use gauge theories to consider fluctuation effects about their respective mean-field configurations. We find, in addition to conventional Neel states, a plethora of novel magnetically disordered phases: two kinds of spin liquids, Z2 in 2+1D and U(1)in 3+1D, and several valence bond solids such as two and three-dimensional plaquette and columnar singlet states. We use the same approach to study the diamond lattice AFM which possesses extended classical ground state degeneracy. We demonstrate that quantum and entropic fluctuations lift this degeneracy in different ways. In the second part of the thesis, we study ultracold spinor atoms confined in optical lattices. We first demonstrate the feasibility of experimental realization of rotor models using ultracold spin-one Bose atoms in a spin-dependent and disordered optical lattice. We show that the ground state of such disordered rotor models with quadrupolar interactions can exhibit biaxial nematic ordering in the disorder-averaged sense, and suggest an imaging experiment to detect the biaxial nematicity in such systems. Finally, using variational wavefunction methods, we study the Mott phases and superfluid-insulator transition of spin-three bosons in an optical lattice with an anisotropic two dimensional optical trap. We chart out the phase diagrams for Mott states with n = 1 and n = 2 atoms per lattice site. We show that the long-range dipolar interaction stabilizes a state characterized by antiferromagnetic chains made of ferromagnetically aligned spins. We also obtain the mean-field phase boundary for the superfluid-insulator transition, and show that inside the superfluid phase and near the superfluid-insulator phase boundary, the system undergoes a first order antiferromagnetic-ferromagnetic spin ordering transition.