No description available.

This thesis explores mathematical optimization techniques to address the computeraided molecular and mixture design problems (CAMD/CAMxD). In particular, we leverage the power of mixed-integer linear programs (MILPs) to quickly and efficiently design over the massive chemical search space. These MILPs, when coupled with state-ofthe- art derivative-free optimization (DFO) methods, make for an efficient optimization strategy when designing mixtures of molecules or when considering a single molecule design problem that involves difficult thermodynamics or process models. In the first chapter, we provide a very general overview of the field of CAMD as addressed from the perspective of mathematical optimization. We discuss many relevant quantitative structure-property relationships (QSPRs) and provide constraints typically used in CAMD/CAMxD optimization problems. The second chapter introduces our DFO-based molecular/mixture design algorithm and describes how this approach enables a much greater molecular diversity to be considered in the search space as compared to traditional methods. Additionally, this chapter looks at a few case studies relevant to crystallization solvents and provides a detailed comparison of 27 different DFO algorithms for solving these problems. The third chapter introduces COSMO-RS/-SAC as alternatives to UNIFAC as the method used to capture mixture thermodynamics for a variety of CAMD/CAMxD problems. To fully incorporate COSMO-RS/-SAC into CAMD, we introduce group contribution (GC) methods for estimating a few necessary parameters for COSMO-based methods. We demonstrate the utility of COSMO-RS/-SAC in a few case studies for which UNIFAC-like methods are insufficient. In the fourth chapter, we investigate reaction solvent design using COSMO-based methods. COSMO-RS is particularly suitable for these problems as they allow for modeling of many relevant species in chemical reactions (transition states, charges, etc.) directly at the quantum level. This information can be immediately passed to the CAMD problem. We investigate a number of solvent design problems for a few difficult reactions. We summarize the work and provide a few future directions in the final chapter. Overall, this thesis serves to push the field of CAMD forward by introducing new methods to more efficiently explore the massive chemical search space and to enable a few new classes of problems which were previously untenable.

This work presents heuristics for searching large sets of molecular structures for low-energy, stable systems. The goal is to find the globally optimal structures in less time or by consuming less computational resources. The strategies intermittently evaluate and rank structures during molecular dynamics optimizations, culling possible weaker solutions from evaluations earlier, leaving better solutions to receive more simulation time. Although some imprecision was introduced from not allowing all structures to fully optimize before ranking, the strategies identify metrics that can be used to make these searches more efficient when computational resources are limited.

Control of solid state ordering in conjugated small molecules is paramount to the continued development and implementation of organic materials in electronic devices. However, there exists no reliable method on which to predicatively determine how a change to the molecular structure will impact the solid-state packing. As such, the molecule must be synthesized before its solid-state packing can be definitively evaluated. However, once the packing structure of a material is known there exist both qualitative structure- function relationships derived from the literature, as well as quantitative computational methods that can be employed to suggest if a material will perform well in a given device. This type of bottom-up strategy is used in Chapter 2 to design and synthesize a high performance material for organic field effect transistors. A core molecule is synthesized, and through rigorous optimization of pendant and solubilizing groups a material with exceptional solid-state packing is developed and its performance in an organic field effect transistor is discussed. Chapter 3 discusses the use of conjugated organic molecules in conjunction with inorganic materials to develop hybrid organic/inorganic materials. A scalable synthesis is developed so derivatives can be rapidly synthesized and their properties evaluated. Two classes of materials are developed and synthesized: tetracene-based ligands for quantum dots and diammonium-substituted anthracene and tetracene derivatives for 2D-perovskites. Initial results for both classes of materials are presented. Chapter 4 discusses the topochemical photopolymerization of heptacene [4+4] dimers. Multiple derivatives were synthesized in order to give the ideal alignment of molecules in the crystal, followed by irradiation of crystals to give crystal templated polymerization. In Chapter 5, triarylmethane derivatives are synthesized and their performance as radiochromic sensors is evaluated. Chapter 6 involves the development of a robust synthetic scheme toward a difficult to attain π- extended regioisomer of pyrene. Photophysical characterization reveals that the direction of π-extension from the pyrene core has a profound effect on electron delocalization.

Incorporating consideration for safety issues while designing solvent processes has become crucial in light of the chemical process incidents involving solvents that have taken place in recent years. The implementation of inherently safer design concepts is considered beneficial to avoid hazards during early stages of design. The application of existing process design and modeling techniques that aid the concepts of ‘substitution’, ‘intensification’ and ‘attenuation’ has been shown in this work. For ‘substitution’, computer aided molecular design (CAMD) technique has been applied to select inherently safer solvents for a solvent operation. For ‘intensification’ and ‘attenuation’, consequence models and regulatory guidance from EPA RMP have been integrated into process simulation. Combining existing techniques provides a design team with a higher level of information to make decisions based on process safety. CAMD is a methodology used for designing compounds with desired target properties. An important aspect of this methodology concerns the prediction of properties given the structure of the molecule. This work also investigates the applicability of Quantitative Structure Property Relationship (QSPR) and topological indices to CAMD. The evaluation was based on models developed to predict flash point properties of different classes of solvents. Multiple linear regression and neural network analysis were used to develop QSPR models, but there are certain limitations associated with using QSPR in CAMD which have been discussed and need further work. Practical application of molecular design and process design techniques have been demonstrated in a case study on liquid-liquid extraction of acetic acid-water mixture. Suitable inherently safer solvents were identified using ICAS-ProCAMD, and consequence models were integrated into Aspen Plus simulator using a calculator sheet. Upon integrating flammable and toxic hazard modeling, solvents such as 5-nonanone, 2-nonanone and 5-methyl-2-hexanone provide inherently safer options, while conventionally-used solvent, ethyl acetate, provides higher degree of separation capability. A conclusive decision regarding feasible solvents and operating conditions would depend on design requirements, regulatory guidance, and safety criteria specified for the process. Inherent safety has always been an important consideration to be implemented during early design steps, and this research presents a methodology to incorporate the principles and obtain inherently safer alternatives.

Type III secretion is a virulence system utilized by several clinically important Gram-negative pathogens. Computational methods have been used to develop two classes of type III secretion inhibitors, the salicylidene acylhydrazides and the acetylated salicylanilides. For these classes of compounds, quantitative structure-activity relationship models have been constructed with data from focused libraries obtained by statistical molecular design. The models have been validated and shown to provide useful predictions of untested compounds belonging to these classes. Scaffold hopping of the salicylidene acylhydrazides have resulted in a number of synthetic targets that might mimic the scaffold of the compounds. The synthesis of two libraries of analogs to two of these scaffolds and the biological evaluation of them is presented.

No description available.

A number of novel hydrocarbon cage systems have been designed and characterized using ab initio molecular orbital calculations at the MP2 and B3-LYP levels. In particular,equilibrium structures for five families of molecules, hemialkaplanes, hemispiroalkaplanes, alkaplanes, spiroalkaplanes and dimethanospiroalkaplanes, have been examined in detail with the aim of designing a saturated hydrocarbon with a planar-tetracoordinate carbon atom and with a view to identifying appropriate synthetic targets. ¶ The hemialkaplanes and hemispiroalkaplanes are constructed from a spiropentane or neopentane subunit, respectively, which is capped by a cyclic hydrocarbon. The hemispiroalkaplanes are predicted to contain a pyramidal-tetracoordinate carbon atom possessing a lone pair of electrons. Protonation at this apical carbon atom is found to be highly favorable, resulting in a remarkably high basicity for a saturated hydrocarbon. The proton affinities of the hemispiroalkaplanes are calculated to be more than 1170 kJ mol[superscript -1] , even greater than those for the diamine "proton sponges". ¶ The alkaplanes and the spiroalkaplanes, which are constructed by bicapping a neopentane or spiropentane subunit, respectively, with a pair of cyclic hydrocarbons, show unprecedented flattening of a tetracoordinate carbon atom. Linking the spiroalkaplane caps with methano bridges gives the dimethanospiroalkaplanes, two of which, dimethanospirooctaplane and dimethanospirobinonaplane, achieve exact planarity at the central carbon atom. They are the first neutral saturated hydrocarbons predicted to contain an exactly planartetracoordinate carbon atom. This has been achieved through structural constraints alone. The electronic structure at the central carbon atom results in a highest occupied molecular orbital corresponding to a p-type lone pair. Consequently, the adiabatic ionization energies for octaplane, spirooctaplane and dimethanospirooctaplane (approximately 5 eV) are predicted to be similar to those of lithium and sodium - incredibly low for a saturated hydrocarbon. ¶ Some consideration has been given to likely pathways for unimolecular decomposition for all species. Predicted structures, heats of formation and strain energies for all the novel hydrocarbons are also detailed. Tetramethylhemispirooctaplane and dimethanospirobinonaplane are identified as the preferred synthetic targets.

<p>Rheumatoid arthritis (RA) is an autoimmune disease affecting approximately 1% of the population in the western world. It is characterised by a tissue specific attack of cartilage in peripheral joints. Collagen induced arthritis (CIA) is one of the most commonly used animal models for (RA), with similar symptoms and histopathology. CIA is induced by immunisation of mice with type II collagen (CII), and the immunodominant part was previously found to be located between residues 256-270. This thesis describes the interaction between the MHC molecule, glycopeptide antigens from CII and the T cells that is essential in development of CIA. The glycopeptide properties for binding to the mouse MHC molecule Aq have been studied, as well as interaction points in the glycopeptide that are critical for stimulation of a T-cell response.</p><p>The thesis is based on five studies. In the first paper the minimal glycopeptide core, that is required for binding to the Aq molecule while still giving a full T cell response was determined. The second paper studied the roles of amino acid side-chains and a backbone amide bond as T-cell contact points. In the third paper the hydrogen bond donor-acceptor characteristics of the 4-OH galactose hydroxyl group of the glycopeptide was studied in detail. In the fourth paper we established a structure activity relationship (QSAR model) for (glyco)peptide binding to the Aq molecule. Finally, the stereochemical requirements for glycopeptide binding to the Aq molecule and for T-cell recognition was studied in the fifth paper.</p><p>The study was performed using collagen glycopeptide analogues, which were synthesised on solid phase. Amide bond and hydroxyl group isosteres were introduced for study of hydrogen bond donor-acceptor characteristics. Statistical methods were used to design a representative peptide test set and in establishing a QSAR model.</p><p>The results give a deeper understanding of the interactions involved in the ternary MHC-glycopeptide-T cell complex. This information contributes to research directed towards finding new treatments for RA.</p>

This thesis describes studies directed towards development of novel antiadhesive agents, with particular emphasis on compounds that prevent attachment of bacteria to a host-cell. Three different proteins involved in the assembly or function of adhesive pili in uropathogenic Escherichia coli have been targeted either by rational structure based design or statistical molecular methods. A library of substituted galabiose (Galα1-4Gal) derivatives was screened for binding to the E. coli adhesin PapG in an assay based on surface plasmon resonance, and for inhibition of Streptococcus suis adhesins PN and PO in a hemagglutination assay. The results were used to generate QSAR models which had good predictive powers and provided further insight in the structural requirements needed for high affinity binding. 2-pyridones and amino acid derivatives were modelled into the binding site of chaperones involved in pilus assembly in E. coli and a heuristic method, VALIDATE, was used for affinity prediction. The affinity of the compounds for the chaperones PapD and FimC were assessed in assays based on surface plasmon resonance and relaxation-edited NMR spectroscopy. Their ability to disrupt chaperone/subunit complexes was investigated in vitro through a FPLC assay and their capacity to inhibit pilus formation in vivo was determined via hemagglutination and confirmed with atomic force microscopy. Statistical molecular design was used to design a diverse peptide library targeting pili subunits, and an ELISA was developed to investigate the ability of the peptides to inhibit chaperone/subunit complexation. The resulting QSAR model provided extensive information regarding binding of the peptides to the subunits. Because the peptides were suggested to bind in an extended β-strand formation, β-strand mimetics consisting of oligomeric enaminones were designed. Finally, new methods to synthesize enaminone building blocks were developed using microwave assisted chemistry. The projects described have generated compounds that besides their value as leads for developing novel antibacterial agents, also constitute new chemical tools to study the mechanisms underlying bacterial virulence.