2,038 research outputs found

    Kinetic model construction using chemoinformatics

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    Kinetic models of chemical processes not only provide an alternative to costly experiments; they also have the potential to accelerate the pace of innovation in developing new chemical processes or in improving existing ones. Kinetic models are most powerful when they reflect the underlying chemistry by incorporating elementary pathways between individual molecules. The downside of this high level of detail is that the complexity and size of the models also steadily increase, such that the models eventually become too difficult to be manually constructed. Instead, computers are programmed to automate the construction of these models, and make use of graph theory to translate chemical entities such as molecules and reactions into computer-understandable representations. This work studies the use of automated methods to construct kinetic models. More particularly, the need to account for the three-dimensional arrangement of atoms in molecules and reactions of kinetic models is investigated and illustrated by two case studies. First of all, the thermal rearrangement of two monoterpenoids, cis- and trans-2-pinanol, is studied. A kinetic model that accounts for the differences in reactivity and selectivity of both pinanol diastereomers is proposed. Secondly, a kinetic model for the pyrolysis of the fuel “JP-10” is constructed and highlights the use of state-of-the-art techniques for the automated estimation of thermochemistry of polycyclic molecules. A new code is developed for the automated construction of kinetic models and takes advantage of the advances made in the field of chemo-informatics to tackle fundamental issues of previous approaches. Novel algorithms are developed for three important aspects of automated construction of kinetic models: the estimation of symmetry of molecules and reactions, the incorporation of stereochemistry in kinetic models, and the estimation of thermochemical and kinetic data using scalable structure-property methods. Finally, the application of the code is illustrated by the automated construction of a kinetic model for alkylsulfide pyrolysis

    A treatment of stereochemistry in computer aided organic synthesis

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    This thesis describes the author’s contributions to a new stereochemical processing module constructed for the ARChem retrosynthesis program. The purpose of the module is to add the ability to perform enantioselective and diastereoselective retrosynthetic disconnections and generate appropriate precursor molecules. The module uses evidence based rules generated from a large database of literature reactions. Chapter 1 provides an introduction and critical review of the published body of work for computer aided synthesis design. The role of computer perception of key structural features (rings, functions groups etc.) and the construction and use of reaction transforms for generating precursors is discussed. Emphasis is also given to the application of strategies in retrosynthetic analysis. The availability of large reaction databases has enabled a new generation of retrosynthesis design programs to be developed that use automatically generated transforms assembled from published reactions. A brief description of the transform generation method employed by ARChem is given. Chapter 2 describes the algorithms devised by the author for handling the computer recognition and representation of the stereochemical features found in molecule and reaction scheme diagrams. The approach is generalised and uses flexible recognition patterns to transform information found in chemical diagrams into concise stereo descriptors for computer processing. An algorithm for efficiently comparing and classifying pairs of stereo descriptors is described. This algorithm is central for solving the stereochemical constraints in a variety of substructure matching problems addressed in chapter 3. The concise representation of reactions and transform rules as hyperstructure graphs is described. Chapter 3 is concerned with the efficient and reliable detection of stereochemical symmetry in both molecules, reactions and rules. A novel symmetry perception algorithm, based on a constraints satisfaction problem (CSP) solver, is described. The use of a CSP solver to implement an isomorph‐free matching algorithm for stereochemical substructure matching is detailed. The prime function of this algorithm is to seek out unique retron locations in target molecules and then to generate precursor molecules without duplications due to symmetry. Novel algorithms for classifying asymmetric, pseudo‐asymmetric and symmetric stereocentres; meso, centro, and C2 symmetric molecules; and the stereotopicity of trigonal (sp2) centres are described. Chapter 4 introduces and formalises the annotated structural language used to create both retrosynthetic rules and the patterns used for functional group recognition. A novel functional group recognition package is described along with its use to detect important electronic features such as electron‐withdrawing or donating groups and leaving groups. The functional groups and electronic features are used as constraints in retron rules to improve transform relevance. Chapter 5 details the approach taken to design detailed stereoselective and substrate controlled transforms from organised hierarchies of rules. The rules employ a rich set of constraints annotations that concisely describe the keying retrons. The application of the transforms for collating evidence based scoring parameters from published reaction examples is described. A survey of available reaction databases and the techniques for mining stereoselective reactions is demonstrated. A data mining tool was developed for finding the best reputable stereoselective reaction types for coding as transforms. For various reasons it was not possible during the research period to fully integrate this work with the ARChem program. Instead, Chapter 6 introduces a novel one‐step retrosynthesis module to test the developed transforms. The retrosynthesis algorithms use the organisation of the transform rule hierarchy to efficiently locate the best retron matches using all applicable stereoselective transforms. This module was tested using a small set of selected target molecules and the generated routes were ranked using a series of measured parameters including: stereocentre clearance and bond cleavage; example reputation; estimated stereoselectivity with reliability; and evidence of tolerated functional groups. In addition a method for detecting regioselectivity issues is presented. This work presents a number of algorithms using common set and graph theory operations and notations. Appendix A lists the set theory symbols and meanings. Appendix B summarises and defines the common graph theory terminology used throughout this thesis

    Computational Studies on Bimetallic Catalysis and X-ray Absorption Spectroscopy

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    Computational studies are very important to gain an insight into reaction mechanisms and in interpreting and understanding complicated experimental observations. This report contains a discussion on computational studies performed on bimetallic catalysis and on X-ray absorption spectroscopy of insulators. The viability of a bimetallic rhodium and cobalt catalysts for industrially important hydroformylation and aldehyde-water shift catalysis (AWS) is discussed. Density functional theory (DFT) studies were used for bimetallic catalysis and time-dependent DFT studies were used for excited state dynamics. These studies were performed using Gaussian 09 package and NWChem. Hydroformylation is experimentally performed in acetone and 30% water/acetone systems and results in dicationic dirhodium complexes and monocationic dirhodium complexes respectively. DFT studies were used to determine the active catalyst and possible intermediates. Computational studies support the mechanism proposed by Prof. Stanley for hydrofomylation in acetone, but DFT studies demonstrate a different mechanism for hydroformylation in water/acetone which contains mono-bridging complexes. A detailed discussion on this is given in chapter 2. DFT studies were used to study the AWS catalysis with the bimetallic [rac-Rh2(μ-CO)2(CO)2(et,ph-P4)]2+ complex. These studies were performed in both vacuum and using explicit water molecules, and lower energies were obtained when explicit water molecules were used. The computations support an alternate mechanism with protonated acid intermediates different from the originally proposed mechanism. This mechanism is discussed in great detail in chapter 3. DFT studies are also performed to study the suitability of dicobalt analogs for hydroformylation and AWS catalysis. The most suitable active catalyst and possible mechanism for hydroformylation using Co2(μ-H)(μ-CO)(CO)3(H)(et,ph-P4)]2+ (Co_2), [rac- and [rac-Co2(μ-H)2(CO)4(et,ph-P4)]2+ (Co_2*) and [rac-Co2(μ-CO)2(CO)2(H)2(et,ph-P4)]2+ (Co_2**) are discussed in chapter 4. The capability of [rac-Co2(CO)4(et,ph-P4)]2+ (Co_4*) catalyst for AWS catalysis is also discussed in chapter 4. Chapter 5 discusses a method to generate X-ray absorption spectra of insulators using time-dependent DFT. α-Quartz was used as a model for insulators. Bulk-mimicking embedded finite cluster models, atom-centered basis sets, tuned range-separated functionals and molecular orbital-based absorbing boundary conditions were utilized to model near and above ionization spectral features without experimental parameterization. The calculated spectra match well with the experimental results over the range of approximately 105 – 130 eV

    Novel pericyclic routes to strained organic molecules: Theoretical and experimental studies

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    The chemistry of cyclobutyne (20) and 1,2-cyclobutadiene (21) has been investigated. Research efforts were focused on attempting to independently generate and trap these highly reactive species. The trapping experiments were inconclusive in each case. Calculations using MCSCF theory indicate that perfluorination of cyclobutyne will have a profound effect that stabilizes the cyclobutyne relative to rearrangement. However, experiments designed to generate and trap perfluorocyclobutyne (73) did not provide evidence for this compound. The development of new routes to strained organic compounds through the extension of known pericyclic reactions is described. These novel pericyclic reactions have been investigated by ab initio calculations and flash vacuum pyrolysis (FVP) experiments. MP4/6-31G*//MP2/6-31G* calculations support the possibility that strained six-membered rings can be prepared by replacement of a double bond with a triple bond in the prototypical Diels/Alder cycloaddition eq. (1) or electrocyclic reaction eq. (7). The novel cycloadditions explored involve the replacement of the traditional 1,3-butadiene component of (4+2) cycloadditions with vinylacetylene (19), 1,3-butadiyne (160), and strans-butadiene (233). Electrocyclic reactions of 1,2,3-cyclohexatriene (167), 1,2,4-cyclohexatriene (166), cyclohexen-3-yne (247), and 1,2,3,4-cyclohexatetraene (243) have been investigated. Experimental evidence is presented for the first example of intramolecular diyne + alkene and diyne + alkyne cycloadditions. The latter process is believed to give an o-benzyne intermediate, which is subsequently reduced to indan. This cycloaddition is unique in that it may be considered a cycloaromatization because an aromatic ring is directly generated. The mechanism and generality of diyne cycloadditions is examined

    Aerospace medicine and biology: A continuing bibliography with indexes (supplement 406)

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    This bibliography lists 346 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during Oct. 1995. Subject coverage includes: aerospace medicine and physiology, life support systems and man/system technology, protective clothing, exobiology and extraterrestrial life, planetary biology, and flight crew behavior and performance

    Metal-free catalysis using boron-based systems : from designed frustrated Lewis Pairs to boranes

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    La catalyse est la pierre angulaire de la chimie verte et elle permet de performer des transformations chimiques difficiles de manière efficace et sélective. Au niveau industriel, l'utilisation de la catalyse se traduit habituellement en une économie de temps et d'argent. Le développement de systèmes catalytiques pratiques s'est initialement fait à l'aide de métaux des secondes et troisièmes rangées de transition. Au cours des deux dernières décennies, ce domaine de recherche a atteint une certaine maturité. Néanmoins, les catalyseurs à base de métaux de transitions sont souvent dispendieux et polluants. Une quantité considérable de gaz à effet de serre est également engendrée par l'extraction minière de ces métaux. Afin de palier à ces problèmes, d'intéressantes alternatives commencent à faire leur place. Notamment, de nouvelles stratégies de catalyse sans métal de transition ont été développées et l'étude des mécanismes réactionnels nous permet de maximiser leur efficacité. Dans cette thèse, l'optimisation d'une paire de Lewis frustrée (FLP) de type aminoborane (1-NR₂-2-BH₂-C₆H₄) est exploré afin d'améliorer ses performances dans la borylation catalytique de liens C-H de molécules hétéroaromatiques (pyrroles, indoles, thiophènes). Dans les premiers chapitres, le mécanisme réactionnel de cette réaction de borylation est étudié en détail. Une première étude théorique nous permet de déterminer l'impact de l'ajout d'un groupement fonctionnel en position ortho du -BH₂ sur l'activation du lien C-H. Par la suite, la performance d'aminoboranes possédant un encombrement stérique varié au niveau de l'amine est testée pour la catalyse. Les résultats obtenus combinés avec des études cinétiques démontrent que l'aminoborane possédant un groupement pipéridyl effectue la borylation catalytique jusqu'à 15 fois plus rapidement que l'espèce possédant le groupement le plus encombrée tetraméthylpipéridyl. L'activation C-H est donc favorisée lorsque le site réactionnel est plus dégagé. Pour compléter l'étude du mécanisme de la borylation, nous avons également étudié l'étape de la métathèse des liens sigma, qui se révèle être un élément critique et important lors de la borylation du thiophène. En explorant la réaction de FLPs de type aminoborane, nous avons découvert que l'acide borique pouvait agir comme précatalyseur pour l'hydroboration catalytique de composés insaturés. Cette espèce de bore peu dispendieuse et stable peut être utilisée comme précatalyseur remplaçant le BH₃ qui est une molécule très réactive. Une étude mécanistique à l'aide de réactions stœchiométriques et d'analyses cinétiques démontre que la réaction d'hydroboration est plus rapide que la génération et la régénération du catalyseur. Finalement, un système catalytique à base d'acide borique utilisant l'irradiation micro-ondes sans conditions inertes a donc été développé pour l'hydroboration d'esters et d'alcynes. Une dernière étude portant sur la combinaison de deux types de chimie sans métal, les FLPs et les phosphines biphiliques, vient clore le travail présenté. Nous avons exploré deux stratégies pour évaluer s'il est possible de générer une synergie avec les deux systèmes. Tout d'abord, nous avons adapté le ligand de la phosphine triamide P{N[o-NMe-C₆H₄]₂} pour y installer une base de Lewis intramoléculaire. Des tests d'activation de l'hydrogène gazeux avec la phosphine biphilique modifiée nous ont permis de réaliser qu'il n'est pas possible d'atteindre de la réactivité FLP de cette manière. Nous avons ensuite décidé de mélanger la phosphine biphilique P{N[o-NMe-C₆H₄]₂} avec l'aminoborane de type FLP le moins encombrée (1-NMe₂-2-BH₂-C₆H₄). L'objectif était de produire un complexe sans métal ayant une plateforme d'oxydoréduction sur l'atome de phosphore et des orbitales vides et pleines fournies par l'acide de Lewis et la base de Lewis de l'aminoborane. Le complexe attendu n'est pas généré. À la place de celui-ci, une réaction entre les deux espèces produit le benzodiazaborole correspondant et un solide orangé insoluble. À l'aide d'études comparatives, nous sommes venus à la conclusion que le solide produit est un mélange de polymères de phosphore polyhydrures et que la réaction observée est caractéristique des aminophosphines possédant au moins un hydrogène.Catalysis is the cornerstone of green chemistry, and it allows to perform efficient and selective transformations that are usually challenging to achieve. At the industrial level, catalysis usually offers time and cost-efficient processes. Initially, the development of practical catalysis was done using transition metals of the second and third rows. Over the last two decades, this field of research reached a certain level of maturity. However, the use of transition metal-based catalysts is generally expensive due to the costs associated with their production and their removal from final products. Additionally, a considerable amount of greenhouse gases is liberated during the mining processes of the metals. To overcome these problems, interesting alternatives are starting to appear. Notably new metal-free strategies have been developed and the study of the mechanism allows to maximize their efficiency. In this thesis, the optimisation of an aminoborane (1-NR₂-2-BH₂-C₆H₄) frustrated Lewis pair (FLP) is explored to improve its performance for the catalytic borylation of C-H bonds of heteroaromatic molecules (pyrroles, indoles, thiophenes). In the first chapters, the mechanism of this borylation reaction is thoroughly studied. First, a theoretical study allows us to evaluate the effect of adding a functional group in ortho position of the -BH₂ for the first reaction step of the catalytic cycle: C-H activation. Subsequently, the catalysis performance of aminoboranes with various steric hindrance were tested. These results combined with kinetic studies shows that the aminoborane with a piperidyl group can perform catalysis 15 times faster than the aminoborane with the most encumbered amino group tetramethylpiperidyl. Therefore, the C-H activation is favored when the reaction site is more accessible. To complete the mechanistic investigation of the borylation reaction, the sigma bond metathesis reaction step was also studied. We discovered that this step is a critical and important element for the borylation of thiophene. While screening the aminoborane FLPs reactivity, we discovered that boric acid could act as a precatalyst for the catalytic hydroboration of unsaturated compounds. This inexpensive and stable boron species can be used as a precatalyst to replace the very reactive BH₃. A mechanistic study done with stoichiometric reactions and kinetic analysis show that the hydroboration reaction is faster than the generation and the regeneration of the borane catalyst. Finally, a boric acid based catalytic system using microwave irradiation has been developed for the hydroboration of esters and alkynes. To conclude, a study on the combination of two metal-free strategies was done using FLPs and biphilic phosphines. We explored two strategies to evaluate if it is possible to generate a synergy with both systems. First, we installed an intramolecular Lewis base on the phosphine triamide P{N[o-NMe-C₆H₄]₂}. It was not possible to reach FLP reactivity when looking at hydrogen activation tests with the adapted biphilic phosphine. Following these results, we mixed the biphilic phosphine P{N[o-NMe-C₆H₄]₂} with the least sterically encumbered aminoborane FLP (1-NMe₂-2-BH₂-C₆H₄). The objective was to produce a metal-free complex with a redox platform on the phosphorus atom and with filled and vacant orbitals provided by the Lewis acid and the Lewis base of the aminoborane. Unfortunately, this complex was not generated. Instead, a reaction between the two species produced the corresponding benzodiazaborole and an insoluble orange solid. Using comparative studies, we concluded that the insoluble solid generated is a mixture of phosphorus polyhydride polymers and that the observed reaction is characteristic to aminophosphine bearing at least one hydrogen

    Hetero-interpenetrated metal-organic frameworks : supramolecular interactions between ligands in metal-organic framework formation : a thesis presented in fulfilment of the requirements of the degree of Doctor of Philosophy in Chemistry at Massey University, Manawatū, New Zealand

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    Metal-organic frameworks are an exciting class of materials formed through the self-assembly of their metal ion and organic ligand components into ordered, nanoporous lattice structures whose pore spaces are open to solvent, gas, and other guest molecules. Their consequently high surface areas render them suitable for diverse applications including gas storage, separations, and catalysis. The ability to precisely engineer the chemistry of the pores in framework materials and thus tune their properties is one of their most attractive features. Interpenetration, a phenomenon where multiple lattices are woven through each other, is an important handle on tuning their properties, mediating between pore shapes and volumes, chemistries, and robustness. In this thesis new frameworks are presented where two chemically distinct lattices are interpenetrated, a longstanding target in the field. These frameworks therefore have two orthogonal handles on both pore shape and functionalisation and have been applied to asymmetric organocatalysis by embedding an achiral catalytic site within a chiral pore space. Additionally, some insight is gained into the underlying principles of the formation of complex types of interpenetration through the exploitation of several analogous novel ligands

    The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes

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    Computational techniques provide accurate descriptions of the structure and dynamics of biological systems, contributing to their understanding at an atomic level.Classical MD simulations are a precious computational tool for the processes where no chemical reactions take place.QM calculations provide valuable information about the enzyme activity, being able to distinguish among several mechanistic pathways, provided a carefully selected cluster model of the enzyme is considered.Multiscale QM/MM simulation is the method of choice for the computational treatment of enzyme reactions offering quantitative agreement with experimentally determined reaction parameters.Molecular simulation provide insight into the mechanism of both the catalytic activity and inhibition of monoamine oxidases, thus aiding in the rational design of their inhibitors that are all employed and antidepressants and antiparkinsonian drugs. Aging society and therewith associated neurodegenerative and neuropsychiatric diseases, including depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease, urgently require novel drug candidates. Targets include monoamine oxidases A and B (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and various receptors and transporters. For rational drug design it is particularly important to combine experimental synthetic, kinetic, toxicological, and pharmacological information with structural and computational work. This paper describes the application of various modern computational biochemistry methods in order to improve the understanding of a relationship between the structure and function of large biological systems including ion channels, transporters, receptors, and metabolic enzymes. The methods covered stem from classical molecular dynamics simulations to understand the physical basis and the time evolution of the structures, to combined QM, and QM/MM approaches to probe the chemical mechanisms of enzymatic activities and their inhibition. As an illustrative example, the later will focus on the monoamine oxidase family of enzymes, which catalyze the degradation of amine neurotransmitters in various parts of the brain, the imbalance of which is associated with the development and progression of a range of neurodegenerative disorders. Inhibitors that act mainly on MAO A are used in the treatment of depression, due to their ability to raise serotonin concentrations, while MAO B inhibitors decrease dopamine degradation and improve motor control in patients with Parkinson disease. Our results give strong support that both MAO isoforms, A and B, operate through the hydride transfer mechanism. Relevance of MAO catalyzed reactions and MAO inhibition in the context of neurodegeneration will be discussed
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