No description available.

The London dispersion interaction is responsible for attraction between non-polar molecules and is of great importance in describing structure and reactivity in many areas of chemistry. Dispersion is difficult to model accurately. Density Functional Theory (DFT) methods, widely used in computational chemistry today, do not include the necessary physics. This often leads to qualitatively incorrect predictions when DFT is applied to dispersion-bound systems. A novel DFT method has been developed which is capable of accurately modeling dispersion. Dispersion attraction between molecules arises when an instantaneous dipole moment in one molecule induces a dipole moment in a second molecule. Our approach proposes that the source of these instantaneous dipole moments is the position-dependent dipole moment of the exchange hole. The model is no more computationally expensive than existing DFTs and gives remarkably accurate dispersion coefficients, intermolecular separations, intermolecular binding energies, and intramolecular conformational energies. Our dispersion theory is also combined with previous post-exact-exchange models of dynamical and nondynamical correlation, yielding a unified exact-exchange-based energy functional called DF07. DF07 overcomes many of the outstanding problems in DFT arising from local exchange approximations. The DF07 model is shown to provide highly accurate results for thermochemistry, kinetics, and van der Waals interactions. / Thesis (Ph.D, Chemistry) -- Queen's University, 2007-11-29 21:57:09.045

Fluids are associated with a wide range of physical and chemical processes in the Earth, including transporting and concentrating important ore elements such as Cu, Au, Zn, and Pb. Significant amounts of fluid may be generated as a result of dehydration or decarbonation reactions, and the volatile content of a magma is directly linked to the explosivity of eruptions. In most cases, small amounts of the fluids involved in the formation or alteration of rocks are trapped within minerals in the form of fluid inclusions. These fluid inclusions may be studied to understand the composition and pressure and temperature of the original fluid involved in the geologic process of interest, however, an understanding of the composition of the fluid as well as how the fluid behaves under changing pressure and temperature conditions is essential to reconstruct the fluid evolution path based on data obtained from fluid inclusions. Several analytical techniques are involved in the study of fluids, including fluid inclusion microthermometry and Raman spectroscopy. Microthermometry is the heating/cooling of fluid inclusions to observe and record temperatures of phase changes which, in turn, are used to determine properties such as salinity (based on the freezing point depression of liquid), or density based on the temperature at which all phases within the fluid inclusion homogenize to a single phase. Raman spectroscopy is a non-destructive analytical technique that measures the vibrational frequency of molecules in a given material. The Raman spectral properties of fluids act as a "fingerprint" of the chemical species within the fluid and serve to identify both the presence of chemical species, such as H2O, N2, CO2, and CH4, and the density of the fluid. Microthermometric and Raman spectroscopic experiments involving synthetic fluid systems are necessary to elucidate the pressure-volume-temperature-composition (PVTX) and Raman spectral behavior of the fluid systems, which then aids in the study and characterization of natural fluids. In chapter 1, the partitioning of NaCl and KCl between coexisting immiscible fluid phases during boiling is experimentally determined at temperatures and pressures relevant to magmatic-hydrothermal systems using synthetic fluid inclusions. The partitioning behavior is then combined with literature data to calculate the Na/K ratio of the original silicate melt phase in a magma body before the exsolution of a fluid phase. In chapter 2, we explore the Raman spectral behavior of N2, CO2, and CH4 in pure, single-component systems from PT conditions corresponding to the liquid-vapor curve to elevated temperatures and pressures, and relate the changes in the spectral behavior to changes in the bonding environment of the molecules through intermolecular attraction and repulsion. In chapter 3, the observations and relationships determined for pure fluids and described in chapter 2 are used to explore the Raman spectral properties of N2, CO2, and CH4 in the N2-CO2-CH4 ternary system and the manner in which the spectral behavior of each component in the system varies with changing temperature, pressure, molar volume, and fugacity. / Doctor of Philosophy / Water and other fluids play an important role in the formation of mineral deposits that are the source of the many metals, such as copper, silver, gold, and others, that are needed by a modern technological society. In addition, water and other fluids affect the way rocks behave under stress and can promote earthquakes and influence the explosivity of volcanoes. When minerals in a rock form, often small amounts of the fluid will be trapped within the minerals in the form of fluid inclusions. These fluid inclusions contain samples of the fluid involved in the geologic process of interest and can be studied using a variety of methods to determine the chemistry and the temperature and pressure conditions of rock formation. Two of the many methods used to study fluid inclusions are microthermometry and Raman spectroscopy. Microthermometry involves heating and/or cooling the fluid inclusion while it is being observed on a microscope, and this method can be used to determine the salinity of water in the inclusion and the fluid density. The density of the fluid may then be used to determine the pressure or temperature at which the fluid was encapsulated into the rock, and by extension the temperature and pressure at which the rock formed. Raman spectroscopy is an analytical technique in which a rock or fluid is illuminated using a laser. The laser light interacts with the rock or fluid and gains or loses energy, and this change in energy serves as a "fingerprint" to identify the molecules in the rock or fluid. The Raman spectrum can also be used to determine fluid density because the signal generated when the laser interacts with the fluid depends on the density of the fluid. Experiments on fluids at carefully-controlled laboratory conditions are necessary to understand the behavior of fluids trapped in natural samples. In chapter 1, the preference of sodium and potassium to go into either a liquid or a gas phase during boiling at high pressures and temperatures is determined. In chapter 2, gases containing only nitrogen, carbon dioxide, or methane are studied using Raman spectroscopy and the changes in the Raman behavior of the gases with changing pressure and temperature are related to molecular interactions. In chapter 3, the results from chapter 2 are used to understand the Raman behavior of nitrogen, carbon dioxide, and methane in gas mixtures as pressure and temperature are changed and how this relates to the interactions of the molecules.

Quantum chemistry is plagued by the presence of high-rank quantities, stemming from the N-body nature of the electronic Schrödinger equation. These high-rank quantities present a significant mathematical and computational barrier to the computation of chemical observables, and also drastically complicate the pedagogical understanding of important interactions between particles in a molecular system. The application of physically-motivated rank reduction approaches can help address these to problems. This thesis details recent efforts to apply rank reduction techniques in both of these arenas. With regards to computational tractability, the representation of the 1/r Coulomb repulsion between electrons is a critical stage in the solution of the electronic Schrödinger equation. Typically, this interaction is encapsulated via the order-4 electron repulsion integral (ERI) tensor, which is a major bottleneck in terms of generation, manipulation, and storage. Many rank reduction techniques for the ERI tensor have been proposed to ameliorate this bottleneck, most notably including the order-3 density fitting (DF) and pseudospectral (PS) representations. Here we detail a new and uniquely powerful factorization - tensor hypercontraction (THC). THC decomposes the ERI tensor as a product of five order-2 matrices (the first wholly order-2 compression proposed for the ERI) and offers great flexibility for low-scaling algorithms for the manipulations of the ERI tensor underlying electronic structure theory. THC is shown to be physically-motivated, markedly accurate, and uniquely efficient for some of the most difficult operations encountered in modern quantum chemistry. On the front of chemical understanding of electronic structure theory, we present our recent work in developing robust two-body partitions for ab initio computations of intermolecular interactions. Noncovalent interactions are the critical and delicate forces which govern such important processes as drug-protein docking, enzyme function, crystal packing, and zeolite adsorption. These forces arise as weak residual interactions leftover after the binding of electrons and nuclei into molecule, and, as such, are extremely difficult to accurately quantify or systematically understand. Symmetry-adapted perturbation theory (SAPT) provides an excellent approach to rigorously compute the interaction energy in terms of the physically-motivated components of electrostatics, exchange, induction, and dispersion. For small intermolecular dimers, this breakdown provides great insight into the nature of noncovalent interactions. However, SAPT abstracts away considerable details about the N-body interactions between particles on the two monomers which give rise to the interaction energy components. In the work presented herein, we step back slightly and extract an effective 2-body interaction for each of the N-body SAPT terms, rather than immediately tracing all the way down to the order-0 interaction energy. This effective order-2 representation of the order-N SAPT interaction allows for the robust assignment of interaction energy contributions to pairs of atoms or functional groups (the A-SAPT or F-SAPT partitions), allowing one to discuss the interaction in terms of atom- or functional-group-pairwise interactions. These A-SAPT and F-SAPT partitions can provide deep insight into the origins of complicated noncovalent interactions, e.g., by clearly shedding light on the long-contested question of the nature of the substituent effect in substituted sandwich benzene dimers.

Nonheme iron(II) oxygenases within a common 2-His-1-carboxylate binding motif catalyze a wide range of oxidation reactions involved in biological functions like DNA repair and secondary metabolic processes. The mechanism of O2 activation catalyzed by this enzyme family has been examined by spectroscopic, crystallographic, and computational studies, where it is clear the iron(II) center works with substrate, and cosubstrate to activate O2 by forming a highly oxidizing iron species (iron(IV)-oxo). From a thermodynamic perspective, substrate and/or co-substrate binding organizes the active site for O2 activation, and understanding the interactions among metal, substrate, cosubstrate, and enzyme provides insight into the intramolecular contacts that guide the reaction catalyzed by the enzymes. This dissertation is focused on elucidating the interactions between metal, substrate, and co-substrate in a representative enzyme subfamily of nonheme iron(II) oxygenases, namely the 2-oxoglutarate dependent dioxygenases. Specifically, we investigated the thermodynamic properties of divalent metal ions binding to taurine-dependent dioxygenase (TauD), using Mn2+, Fe2+, and Co2+ ions. Additionally, the thermodynamics associated with substrate and co-substrate binding to Fe·TauD and iron(II)-ethylene forming enzyme (Fe·EFE) were explored using calorimetry and other biophysical techniques.

The localized model of a chemical bond has had a long and prominent role in chemistry, but situations of extended charge delocalization and dipole effects remain topics in need of greater understanding. Both orbital delocalization in isolated molecules and induced molecular dipoles in condensed phases serve to move electron density and influence the chemical and physical properties of a system. This dissertation studies these aspects of electronic structure for selected organic, inorganic, and organometallic systems by means of electronic structure calculations and photoelectron spectroscopy, which is well-suited for studying both intramolecular and intermolecular effects by providing a direct probe of orbital energies and characters. Photoelectron spectra of P₄ and AsP₃ reveal differences in the molecular symmetry and cationic state effects between the two molecules in Chapter 3. Despite these differences, AsP₃ is found to have electron delocalization and vibrational structures that are comparable to P₄. A similar study of the delocalized -system of 2H-1,2,3-triazole in Chapter 4 relates the vibrational structure in photoelectron spectroscopy data to a series of Rydberg excitations in the vacuum UV photoabsorption spectrum. Chapters 5 and 6 examine extended electronic structures in organometallic complexes. The electron delocalization and charge transfer between two Ru centers along a bridging ethynediyl ligand is studied in [CpRu(CO)₂]₂(μC≡C). Details of the Ru-alkynyl interaction were explored by comparing the spectra of CpRu(CO)₂C≡CMe with CpRu(CO)₂Cl, including the -backbonding ability of alkynyl ligands. Chapter 6 moves from the realm of intramolecular effects to intermolecular interactions to understand how surrounding media affect electronic properties of molecules. The reversal of ionization energies between the gas and solid phases of M(CO)₄dmpe and M(CO)₄dppe, where M = Mo, W, is explored with photoelectron spectroscopy. The surrounding molecular environment stabilizes the cation, resulting in this reversal that extends to core ionization energies. The variety of systems presented illustrates the wide applicability of photoelectron spectroscopy and computations to different electronic structure studies, including how gas phase results can be related to condensed phase studies. This work continues the progress of photoelectron spectroscopy from small molecules to larger molecular systems and even further to bulk systems.

Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / A family of three 2-aminopyrazine derivatives were prepared and co-crystallized with thirty carboxylic acids. Our theoretical charge calculations and experimental results from 90 reactions demonstrated that decreasing the charge on the hydrogen-bond acceptor sites results in a decrease of the supramolecular yield (the frequency of occurrence of the desired outcome). However, synthon crossover (undesired connectivity) was observed 7/12 times and was unavoidable due to competitive binding sites present in the N-heterocyclic bases chosen. To avoid synthon crossover, we used a strategy based on geometric bias. We utilized hydrogen-bonding two-point contacts and halogen-bonding single-point contacts for supramolecular reactions with the 2-aminopyrazine family of compounds. The desired two-point contact and single-point contact (N•••I or N•••Br) appeared in 9/9 times even in the presence of other potentially interfering intermolecular interactions. In addition, the role of charge in controlling the presence/absence of proton transfer was also highlighted. To establish a hierarchy in halogen-bonding interactions we designed and synthesized a library of eight molecules equipped with two different halogen bond donors and combined with variety of halogen-bond acceptors. 11 Halogen-bonded co-crystals were obtained; however, positional disorder of I/Br atoms obscures a complete analysis. This problem was solved by introducing asymmetry in the halogen-bond donor molecules. Finally, successfully demonstrated an unprecedented hierarchy in halogen-bond interactions based on electrostatics. We developed high-yielding Suzuki-Miyaura coupling reactions of tetraboronic pinacolyl ester cavitand to iodoarenes with a range of functional groups (electron withdrawing/donating group and a heterocycle) that show robustness and versatility, making it a ‘launch pad’ for the synthesis of many new cavitands in a facile manner. We have also successfully demonstrated cavitand functionalization from tetraaldehyde to tetraoximes using ‘solvent assisted grinding’, irrespective of the position of the aldehyde. Finally, we prepared tetra-substituted pyridyl and carboxylic acid cavitands having an ellipsoidal cavity capable of encapsulating asymmetric guest molecules and was subsequently obtained the first of its kind, C[subscript]2v symmetric molecular capsule with encapsulated asymmetric guest molecule.

No description available.

O tema interações intermoleculares é um conceito central dentro do conhecimento químico por permitir, por exemplo, a interpretação de uma série de transformações e propriedades físicas dos materiais. Considerando a carência de estudos que investigam especificamente os processos de ensino e aprendizagem em nível superior, a presente pesquisa objetivou analisar o aprendizado de graduandos em química durante uma disciplina de química geral I, relacionando-o as aulas ministradas aos alunos e a abordagem do tema nos livros didáticos sugeridos para estudo. Para isso, as aulas da disciplina, oferecidas aos alunos ingressantes do curso de química do Instituto de Química da Universidade de São Paulo, foram acompanhadas e gravadas em vídeo; os estudantes responderam alguns questionários para o levantamento das principais dificuldades e lacunas na aprendizagem e os livros didáticos sugeridos foram analisados através de mapas conceituais. A análise dos livros mostrou a complexidade e amplitude do tema por apresentar uma rede de relações conceituais extensa e distribuídas ao longo de diferentes capítulos. Nas análises dos livros e das aulas chamou atenção a abordagem classificatória com que o tema é tratado começando pelas interações que envolvem moléculas polares e depois interações entre moléculas apolares. Na análise das explicações dos alunos foi possível perceber a presença de várias dificuldades ou lacunas como na interpretação das equações das energias potenciais das interações e identificação dos tipos de interações que atuam em distintos contextos. A partir das análises foi feita uma triangulação dos dados que permitiu elencar ideias fundamentais que os alunos precisam compreender sobre o tema sendo essas relacionadas a: uma melhor compreensão da estrutura molecular considerando a geometria da molécula e a distribuição da densidade eletrônica na mesma, parâmetro expresso pelos conceitos polaridade, polarizabilidade e nuvem eletrônica (propriedades moleculares); necessidade de fazer uma correta diferenciação entre as interações intermoleculares e as ligações químicas; compreender que as mudanças de estado físico estão correlacionadas aos diferentes tipos de interações intermoleculares que atuam nos sistemas; entender que vários tipos de interações intermoleculares podem estar atuando no mesmo sistema e que as forças dispersivas de London são universais; interpretar as equações das energias potenciais que são diretamente proporcionais a propriedade molecular e inversamente a distância; interpretar os valores de energia típicos das interações e também relacionar a intensidade e o alcance; considerar nas ligações de hidrogênio a direcionalidade da interação e a necessidade de sítios para esse tipo de interação (pares de elétrons livres). Essas ideias integraram sugestões para o ensino do tema que vão desde a repensar a forma como as interações intermoleculares são ensinadas na química geral até uma possível retomada da abordagem do tema em disciplinas mais avançadas ampliando e ressignificando a compreensão dos conceitos. Defende-se aqui a necessidade de superar o ensino classificatório do tema interações intermoleculares abordando separadamente os tipos de interações intermoleculares: íon-dipolo, dipolo-dipolo, dipolo-dipolo induzido, forças dispersivas de London e ligação de hidrogênio para um ensino com ênfase na estrutura molecular e propriedades moleculares. / The subject of intermolecular interactions is a central concept within the chemical knowledge because it allows, for example, the interpretation of a series of transformations and physical properties of the materials. Considering the lack of studies that specifically investigate teaching and learning processes at the higher level, the present study is aimed at analyzing the chemistry students\' learning in during a general chemistry course, relating the classes given to the students and the approach to the subject suggested textbooks for study. For this, the classes of the course, offered to the incoming chemistry\'s course students of the Institute of Chemistry of the University of São Paulo, were accompanied and recorded in video; the students answered some questionnaires to survey the main difficulties and gaps in learning and the suggested textbooks were analyzed through concept maps. The analysis of the books showed the complexity and amplitude of the theme by presenting a network of extensive conceptual relationships distributed throughout different chapters. In the analysis of books and classes, the classificatory approach with which the topic is treated, starting with the interactions involving polar molecules and then interactions between apolar molecules, was called attention. In the analysis of the students\' explanations, it was possible to perceive the presence of several difficulties or gaps as in the interpretation of the equations of the potential energies of the interactions and identification of the types of interactions that operate in different contexts. From the analyzes, a triangulation of the data was made which allowed to list fundamental ideas that the students need to understand about the subject being related to: a better understanding of the molecular structure considering the geometry of the molecule and its distribution of the electronic density in, expressed parameter by the concepts polarity and polarizability and electronic cloud (molecular properties); the need to make a proper differentiation between intermolecular interactions and chemical bonds; to understand that the changes of physical state are correlated to the different types of intermolecular interactions that operate in the systems; to understand that various types of intermolecular interactions may be operating in the same system and that London\'s dispersive forces are universal; interpret the equations of potential energies that are directly proportional to the molecular property and inversely the distance; interpret the energy values typical of the interactions and also relate intensity and range; to consider in the hydrogen bonds the directionality of the interaction and the need of sites for this type of interaction (free electron pairs). These ideas have included suggestions for teaching the subject, ranging from rethinking how intermolecular interactions is taught in general chemistry to a possible resumption of the subject approach in more advanced courses by broadening and redefining the understanding of concepts. It is argued here the need to overcome classificatory teaching of intermolecular interactions by addressing separately the types of intermolecular interactions: ion-dipole, dipole-dipole, dipole-induce dipole, London\'s dispersive forces and hydrogen bonding for teaching with an emphasis on molecular structure and molecular properties.

We have used ab initio computational simulation techniques to investigate both intra- and intermolecular interactions in a novel family of ionic organophosphonate molecular crystals. We have examined the influence of various numerical approximations on the computed geometry and binding energies of a selection of well-characterised hydrogen bonded systems. It was found that numerical basis sets provided the efficiency required to study the large hydrogen bonded dimer anions present in the organophosphonate system, while also producing accurate geometries and binding energies. We then calculated the relaxed structures and binding energies of phenylphosphonic acid dimer in the two arrangements in which it is present in the bulk crystal. The computed geometries were in excellent agreement with the experimental structures and the binding energies were consistent with those found for other ionic hydrogen bonded systems. Electron density maps were used to gain insight into the nature of the hydrogen bonding interaction between phenylphosphonic acid dimers. We also examined the effect of aromatic ring substituents on the geometry and energetics of the hydrogen bonding interaction. The nitro-substituted dimer was predicted to have a stronger binding energy than its unsubstituted parent while the methyl-substituted dimer was predicted to have a similar binding energy to its unsubstituted parent. An analysis of crystal field effects showed that the structure of the phenylphosphonic acid dimers in the organophosphonates is a complex product of competing intra- and intermolecular forces and crystal field effects. Cooperative effects in the organophosphonate system were also investigated and it was found that the interactions were mostly one-body (local) in nature. We have examined the intramolecular charge-transfer interaction between copper-halogen cations in the organophosphonate materials. The origin of geometric differences between the Cu(I) starting material and Cu(II) product cations was attributed to the electronic configuration of the Cu ion, not crystal field effects. To gain further insight into the difference in electronic structure between the starting material and product, we attempted to simulate the step-by-step dissociation of the [CuI]+ system. Although this investigation was not successful, we were able to expose some of the pitfalls of simulating dissociating odd-electron systems. We also analysed and compared the charge-transfer interaction in the chloro-, bromo- and iodo-forms of the organophosphonate family. The charge-transfer interaction was predicted to increase on going from the chloro- to the iodo-form, consistent with solid-state UV-visible data. Finally, we used the highly accurate Quantum Monte Carlo (QMC) method to investigate the hydrogen bonding interaction in water dimer and to calculate the dissociation energy. The accuracy of the experimental estimate for the dissociation energy has recently been questioned and an alternative value has been put forward. Our results lend support to the validity of the alternative value and are also in excellent agreement with those from other high-level calculations. Our results also indicate that QMC techniques are a promising alternative to traditional wavefunction techniques in situations where both high accuracy and efficiency are important.