Conformational Evaluation of Indol-3-yl-N-alkyl-glyoxalylamides and Indol-3-yl-N,N-dialkyl-glyoxalylamides

Restricted rotation in indol-3-yl-N-alkyl- and indol-3-yl-N,N-dialkyl-glyoxalylamides can in principle give the syn-periplanar and anti-periplanar rotamers. In asymmetrically disubstituted glyoxalylamides, steric effects lead to the occurrence of both rotamers, as observed by NMR spectroscopy. The predominant peak corresponds with the anti rotamer, in which the bulkier alkyl group is orientated trans to the amide carbonyl group. In monoalkylated glyoxalylamides, only one set of peaks is observed, consistent with the presence of only one rotamer. Crystal structures of 5-methoxyindole-3-yl-N-tert-butylglyoxalylamide, indole-3-yl-N-tert-butylglyoxalylamide, and indole-3-yl-N-isopropylglyoxalylamide reported here reveal a syn conformation held by an intramolecular N-HO hydrogen bond.

Anisotropic surface energetics and wettability of macroscopic form I paracetamol crystals

Advancing (θA) and receding (θR) contact angles were measured with several probe liquids on the external facets (201), (001), (011), and (110) of macroscopic form I paracetamol crystals as well as the cleaved (internal) facet (010). For the external crystal facets, dispersive surface energies γd calculated from the contact angles were found to be similar (34 ± 1 mJ/m2), while the polar components varied significantly. Cleaving the crystals exposed a more apolar (010) surface with very different surface properties, including γd = 45 ± 1 mJ/m2. The relative surface polarity (γp/γ) of the facets in decreasing order was (001) > (011) > (201) > (110) > (010), which agreed with the fraction of exposed polar hydroxyl groups as determined from C and O 1s X-ray photoelectron spectroscopy (XPS) spectra, and could be correlated with the number of non-hydrogen-bonded hydroxyl groups per unit area present for each crystal facet, based on the known crystal structures. In conclusion, all facets of form I paracetamol crystals examined exhibited anisotropic wetting behavior and surface energetics that correlated to the presence of surface hydroxyl groups.  © 2006 American Chemical Society.

X-ray crystallographic and theoretical studies of an anticonvulsant enaminone:methyl 4-(4'-bromophenyl)amino-6-methyl-2-oxocyclohex-3-en-1-oate

Objective: The aims of this study were to establish the structure of the potent anticonvulsant enaminone methyl 4-(4′-bromophenyl)amino-6-methyl-2- oxocyclohex-3-en-1-oate (E139), and to determine the energetically preferred conformation of the molecule, which is responsible for the biological activity. Materials and Methods: The structure of the molecule was determined by X-ray crystallography. Theoretical ab initio calculations with different basis sets were used to compare the energies of the different enantiomers and to other structurally related compounds. Results: The X-ray crystal structure revealed two independent molecules of E139, both with absolute configuration C11(S), C12(R), and their inverse. Ab initio calculations with the 6-31G, 3-21G and STO-3G basis sets confirmed that the C11(S), C12(R) enantiomer with both substituents equatorial had the lowest energy. Compared to relevant crystal structures, the geometry of the theoretical structures shows a longer C-N and shorter C=O distance with more cyclohexene ring puckering in the isolated molecule. Conclusion: Based on a pharmacophoric model it is suggested that the enaminone system HN-C=C-C=O and the 4-bromophenyl group in E139 are necessary to confer anticonvulsant property that could lead to the design of new and improved anticonvulsant agents. Copyright © 2003 S. Karger AG, Basel.

Novel strategies to improve recombinant membrane protein production in yeast

Approximately 60% of pharmaceuticals target membrane proteins; 30% of the human genome codes for membrane proteins yet they represent less than 1% of known unique crystal structures deposited in the Protein Data Bank (PDB), with 50% of structures derived from recombinant membrane proteins having been synthesized in yeasts. G protein-coupled receptors (GPCRs) are an important class of membrane proteins that are not naturally abundant in their native membranes. Unfortunately their recombinant synthesis often suffers from low yields; moreover, function may be lost during extraction and purification from cell membranes, impeding research aimed at structural and functional determination. We therefore devised two novel strategies to improve functional yields of recombinant membrane proteins in the yeast Saccharomyces cerevisiae. We used human adenosine A2A receptor (hA2AR) as a model GPRC since it is functionally and structurally well characterised.In the first strategy, we investigated whether it is possible to provide yeast cells with a selective advantage (SA) in producing the fusion protein hA2AR-Ura3p when grown in medium lacking uracil; Ura3p is a decarboxylase that catalyzes the sixth enzymatic step in the de novo biosynthesis of pyrimidines, generating uridine monophosphate. The first transformant (H1) selected using the SA strategy gave high total yields of hA2AR-Ura3p, but low functional yields as determined by radio-ligand binding, leading to the discovery that the majority of the hA2AR-Ura3p had been internalized to the vacuole. The yeast deletion strain spt3Δ is thought to have slower translation rates and improved folding capabilities compared to wild-type cells and was therefore utilised for the SA strategy to generate a second transformant, SU1, which gave higher functional yields than H1. Subsequently hA2AR-Ura3p from H1 was solubilised with n-dodecyl-β-D-maltoside and cholesteryl hemisuccinate, which yielded functional hA2AR-Ura3p at the highest yield of all approaches used. The second strategy involved using knowledge of translational processes to improve recombinant protein synthesis to increase functional yield. Modification of existing expression vectors with an internal ribosome entry site (IRES) inserted into the 5ˊ untranslated region (UTR) of the gene encoding hA2AR was employed to circumvent regulatory controls on recombinant synthesis in the yeast host cell. The mechanisms involved were investigated through the use of yeast deletion strains and drugs that cause translation inhibition, which is known to improve protein folding and yield. The data highlight the potential to use deletion strains to increase IRES-mediated expression of recombinant hA2AR. Overall, the data presented in this thesis provide mechanistic insights into two novel strategies that can increase functional membrane protein yields in the eukaryotic microbe, S. cerevisiae.

Lars Vegard:key communicator and pioneer crystallographer

The Norwegian physicist Lars Vegard studied with William H. Bragg in Leeds and then with Wilhelm Wien in Würzburg. There, in 1912, he heard a lecture by Max Laue describing the first X-ray diffraction experiments and took accurate notes which he promptly sent to Bragg. Although now remembered mainly for his work on the physics of the aurora borealis, Vegard also did important pioneering work in three areas of crystallography. He derived chemical insight from a series of related crystal structures that he determined, Vegard's Law relates the unit-cell dimensions of mixed crystals to those of the pure components, and he determined some of the first crystal structures of gases solidified at cryogenic temperatures. © 2013 Taylor and Francis.

Structural basis for receptor activity-modifying protein-dependent selective peptide recognition by a G protein-coupled receptor

Association of receptor activity-modifying proteins (RAMP1-3) with the G protein-coupled receptor (GPCR) calcitonin receptor-like receptor (CLR) enables selective recognition of the peptides calcitonin gene-related peptide (CGRP) and adrenomedullin (AM) that have diverse functions in the cardiovascular and lymphatic systems. How peptides selectively bind GPCR:RAMP complexes is unknown. We report crystal structures of CGRP analog-bound CLR:RAMP1 and AM-bound CLR:RAMP2 extracellular domain heterodimers at 2.5 and 1.8 Å resolutions, respectively. The peptides similarly occupy a shared binding site on CLR with conformations characterized by a β-turn structure near their C termini rather than the α-helical structure common to peptides that bind related GPCRs. The RAMPs augment the binding site with distinct contacts to the variable C-terminal peptide residues and elicit subtly different CLR conformations. The structures and accompanying pharmacology data reveal how a class of accessory membrane proteins modulate ligand binding of a GPCR and may inform drug development targeting CLR:RAMP complexes.

Comparative physical, mechanical and crystallographic properties of a series of gemfibrozil salts

Objectives Understanding the impact of the counterion on the properties of an acidic or basic drug may influence the choice of salt form, especially for less potent drugs with a high drug load per unit dose. The aim of this work was to determine the influence of the hydrogen bonding potential of the counterion on the crystal structure of salts of the poorly soluble, poorly compressible, acidic drug gemfibrozil and to correlate these with mechanical properties. Methods Compacts of the parent drug and the salts were used to determine Young's modulus of elasticity using beam bending tests. Crystal structures were determined previously from X-ray powder diffraction data. Key findings The free acid, tert-butylamine, 2-amino-2-methylpropan-1-ol and 2-amino-2-methylpropan-1, 3-diol salts had a common crystal packing motif of infinite hydrogen-bonded chains with cross-linking between pairs of adjacent chains. The tromethamine (trsi) salt, with different mechanical properties, had a two-dimensional sheet-like network of hydrogen bonds, with slip planes, forming a stiffer compact. Conclusions The type of counter ion is important in determining mechanical properties and could be selected to afford slip and plastic deformation. © 2010 Royal Pharmaceutical Society of Great Britain.

Formation and investigation of nanostructured thin films

Small devices, in the range of nanometers, are playing a major role in today's technology. The field of nanotechnology is concerned with materials and systems whose structures and components exhibit novel and significantly improved physical, chemical and biological properties, phenomena and processes due to their small nanoscale size. Researches more and more are finding that structural features in the range of about 1 to 100 nanometers behave quite differently than isolated molecules (1 nanometer) or bulk materials. For comparison, a 10 nanometer structure is 1000 times smaller than the diameter of a human hair. The virtues of working in the nanodomain are increasingly recognized by the scientific community and discussed in the popular press. The use of such devices is expected to revolutionize our industries and lives. ^ This work mainly focuses on the fabrication, characterization and discovery of new nanostructured thin films. This research consists of the design of a new high-deposition rate nanoparticle machine for depositing nanostructured films from beams of nanoparticles and investigation film's unique optical and physical properties.^ A high-deposition rate nanoparticle machine was designed, built and successfully tested. Different nanostructured thin films were deposited from Copper, Gold, Iron and Zirconium targets with the grain size of between 1 to 20 nm under different conditions. Transmission Electron Microscopy (TEM), Atomic Force Microscopy (AFM), and x-ray diffraction (XRD) confirmed nanoscale grain size structures of deposited films. The optical properties of the nanostructured films deposited from copper, Iron and Zirconium targets were significantly different from optical properties of bulk and thin films. Zr, Cu and Fe films were transparent. Gold films revealed an epitaxial contact with the silicon substrate with interesting crystal structures. ^ The new high-deposition rate nanoparticle machine was able to deposit new nanostructured films with different properties from bulk and thin films reported in the literatures. ^

Pigmentos a base de Cobalto para aplicação em revestimentos cerâmicos

Ceramic pigments that own mainly the spinel structure AB2O4 are becoming a matter of great scientific and technological interest due to the ability of accommodate different cations in its structure, allowing different dopings and thus obtaining different colors. Studies on ceramic pigments currently are being directed to the development of stable and pigments obtained at low temperatures and with greater reproducibility. This work aims at the use of inorganic pigments for applications in ceramic tiles, investigating the influence of doping and calcination temperature on the coloring pigments and ceramic glazes. the based pigments of CoCr2O4, CoAl2O4, Co0,8Zn0,2Cr2O4 and Co0,8Zn0,2Al2O4 were synthesized by a chemical route using commercial gelatin as organic precursor. The materials were characterized by thermogravimetric analysis (TG), X-ray diffraction (XRD), infrared spectroscopy (FTIR) spectroscopy scanning electron microscopy (SEM) in the UVVisible region and colorimetry. The results confirmed the feasibility of synthesis used, the route presented pigments crystal structures and the desired phases were obtained from 500 °C with increased crystallinity and the crystallite size. The pigments have hues ranging from green to violet according to their doping and calcination temperatures.

Síntese e caracterização de complexos de Co(II) e Ni(II) com l-dopa, carbidopa e benzimidazol

Were synthesized in this work in the following aqueous solution coordination compounds: [Ni(LDP)(H2O)2Cl2].2H2O, [Co(LDP)Cl2].3H2O, [Ni(CDP)Cl2].4H2O, [Co(CDP)Cl2].4H2O, [Ni(BDZ)2Cl2].4H2O and [Co(BDZ)2Cl2(H2O)2]. These complexes were synthesized by stoichiometric addition of the binder in the respective metal chloride solutions. Precipitation occurred after drying the solvent at room temperature. The characterization and proposed structures were made using conventional analysis methods such as elemental analysis (CHN), absorption spectroscopy in the infrared Fourier transform spectroscopy (FTIR), X-ray diffraction by the powder method and Technical thermoanalytical TG / DTG (thermogravimetry / derivative thermogravimetry) and DSC (differential scanning calorimetry). These techniques provided information on dehydration, coordination modes, thermal performance, composition and structure of the synthesized compounds. The results of the TG curve, it was possible to establish the general formula of each compound synthesized. The analysis of X-ray diffraction was observed that four of the synthesized complex crystal structure which does not exhibit the complex was obtained from Ldopa and carbidopa and the complex obtained from benzimidazole was obtained crystal structures. The observations of the spectra in the infrared region suggested a monodentate ligand coordination to metal centers through its amine group for all complexes. The TG-DTG and DSC curves provide important information and on the behavior and thermal decomposition of the synthesized compounds. The molar conductivity data indicated that the solutions of the complexes formed behave as a nonelectrolyte, which implies that chlorine is coordinated to the central atom in the complex.

Síntese e caracterização de complexos de Co(II) e Ni(II) com l-dopa, carbidopa e benzimidazol

Were synthesized in this work in the following aqueous solution coordination compounds: [Ni(LDP)(H2O)2Cl2].2H2O, [Co(LDP)Cl2].3H2O, [Ni(CDP)Cl2].4H2O, [Co(CDP)Cl2].4H2O, [Ni(BDZ)2Cl2].4H2O and [Co(BDZ)2Cl2(H2O)2]. These complexes were synthesized by stoichiometric addition of the binder in the respective metal chloride solutions. Precipitation occurred after drying the solvent at room temperature. The characterization and proposed structures were made using conventional analysis methods such as elemental analysis (CHN), absorption spectroscopy in the infrared Fourier transform spectroscopy (FTIR), X-ray diffraction by the powder method and Technical thermoanalytical TG / DTG (thermogravimetry / derivative thermogravimetry) and DSC (differential scanning calorimetry). These techniques provided information on dehydration, coordination modes, thermal performance, composition and structure of the synthesized compounds. The results of the TG curve, it was possible to establish the general formula of each compound synthesized. The analysis of X-ray diffraction was observed that four of the synthesized complex crystal structure which does not exhibit the complex was obtained from Ldopa and carbidopa and the complex obtained from benzimidazole was obtained crystal structures. The observations of the spectra in the infrared region suggested a monodentate ligand coordination to metal centers through its amine group for all complexes. The TG-DTG and DSC curves provide important information and on the behavior and thermal decomposition of the synthesized compounds. The molar conductivity data indicated that the solutions of the complexes formed behave as a nonelectrolyte, which implies that chlorine is coordinated to the central atom in the complex.

Synthesis and Properties of a Series of 1,1,n,n-Tetramethyl[n](2,11)teropyrenophanes

The work described in this thesis revolves around the 1,1,n,ntetramethyl[n](2,11)teropyrenophanes, which are a series of [n]cyclophanes with a severely bent, board-shaped polynuclear aromatic hydrocarbons (PAH). The thesis is divided into seven Chapters. The first Chapter conatins an overview of the seminal work on [n]cyclophanes of the first two members of the “capped rylene” series of PAHs: benzene and pyrene. Three different general strategies for the synthesis of [n]cyclophanes are discussed and this leads in to a discussion of some slected syntheses of [n]paracyclopahnes and [n](2,7)pyrenophanes. The chemical, structural, spectroscopic and photophysical properties of these benzene and pyrene-derived cyclophanes are discussed with emphasis on the changes that occur with changes in the structure of the aromatic system. Chapter 1 concludes with a brief introduction to [n]cyclophanes of the fourth member of the capped rylene series of PAHs: teropyrene. The focus of the work described in Chapter 2 is the synthesis of of 1,1,n,ntetramethyl[n](2,11)teropyrenophane (n = 6 and 7) using a double-McMurry strategy. While the synthesis 1,1,7,7-tetramethyl[7](2,11)teropyrenophane was successful, the synthesis of the lower homologue 1,1,6,6-tetramethyl[6](2,11)teropyrenophane was not. The conformational behaviour of [n.2]pyrenophanes was also studied by 1H NMR spectroscopy and this provided a conformation-based rationale for the failure of the synthesis of 1,1,6,6-tetramethyl[6](2,11)teropyrenophane. Chapter 3 contains details of the synthesis of 1,1,n,n-tetramethyl[n](2,11)teropyrenophanes (n = 7-9) using a Wurtz / McMurry strategy, which proved to be more general than the double McMurry strategy. The three teropyrenophanes were obtained in ca. 10 milligram quantities. Trends in the spectroscopic properties that accompany changes in the structure of the teropyrene system are discussed. A violation of Kasha’s rule was observed when the teropyrenophanes were irradiated at 260 nm. The work described in the fourth Chapter concentrates on the development of gram-scale syntheses of 1,1,n,n-tetramethyl[n](2,11)teropyrenophanes (n = 7–10) using the Wurtz / McMurry strategy. Several major modifications to the orginal synthetic pathway had to be made to enable the first several steps to be performed comfortably on tens of grams of material. Solubility problems severely limited the amount of material that could be produced at a late stage of the synthetic pathways leading to the evennumbered members of the series (n = 8, 10). Ultimately, only 1,1,9,9- tetramethyl[9](2,11)teropyrenophane was synthesized on a multi-gram scale. In the final step in the synthesis, a valence isomerization / dehydrogenation (VID) reaction, the teropyrenophane was observed to become unstable under the conditions of its formation at n = 8. The synthesis of 1,1,10,10-tetramethyl[10](2,11)teropyrenophane was achieved for the first time, but only on a few hundred milligram scale. In Chapter 5, the results of an investigation of the electrophilic aromatic bromination of the 1,1,n,n-tetramethyl[n](2,11)teropyrenophanes (n = 7–10) are presented. Being the most abundant cyclophane, most of the work was performed on 1,1,9,9-tetramethyl[9](2,11)teropyrenophane. Reaction of this compound with varying amounts of of bromine revealed that bromination occurs most rapidly at the symmetryrelated 4, 9, 13 and 18 positions (teropyrene numbering) and that the 4,9,13,18- tetrabromide could be formed exclusively. Subsequent bromination occurs selectively on the symmetry-related 6, 7, 15 and 16 positions (teropyrene numbering), but considerably more slowly. Only mixtures of penta-, hexa-, hepta and octabromides could be formed. Bromination reactions of the higher and lower homologues (n = 7, 8 and 10) revealed that the reactivity of the teropyrene system increased with the degree of bend. Crystal structures of some tetra-, hexa-, hepta- and octa-brominated products were obtained. The goal of the work described in Chapter 6 is to use 1,1,9,9- tetramethyl[9](2,11)teropyrenophane as a starting material for the synthesis of warped nanographenophanes. A bromination, Suzuki-Miyaura, cyclodehydrogenation sequence was unsuccessful, as was a C–H arylation / cyclodehydrogenation approach. Itami’s recently-developed K-region-selective annulative -extension (APEX) reaction proved to be successful, affording a giant [n]cyclophane with a C84 PAH. Attempted bay-region Diels-Alder reactions and some cursory host-guest chemistry of teropyrenophanes are also discussed. In Chapter 7 a synthetic approach toward a planar model compound, 2,11-di-tbutylteropyrene, is described. The synthesis could not be completed owing to solubility problems at the end of the synthetic pathway.

Membrane protein production in the Yeast, S. cerevisiae

The first crystal structures of recombinant mammalian membrane proteins were solved in 2005 using protein that had been produced in yeast cells. One of these, the rabbit Ca2+-ATPase SERCA1a, was synthesized in Saccharomyces cerevisiae. All host systems have their specific advantages and disadvantages, but yeast has remained a consistently popular choice in the eukaryotic membrane protein field because it is quick, easy and cheap to culture, whilst being able to post-translationally process eukaryotic membrane proteins. Very recent structures of recombinant membrane proteins produced in S. cerevisiae include those of the Arabidopsis thaliana NRT1.1 nitrate transporter and the fungal plant pathogen lipid scramblase, TMEM16. This chapter provides an overview of the methodological approaches underpinning these successes.

Cocrystallisation involving the thioamide, amide and imide functional groups

The work presented in this dissertation focused on the development and characterisation of novel cocrystals that incorporated the thioamide, amide and imide functional groups. A particular emphasis was placed on the characterisation of these cocrystals by single crystal X-ray diffraction methods. In Chapter One a summary of the intermolecular interactions utilised in this work and a short review of the solid state and multicomponent systems is provided. A brief introduction to the ways in which different multicomponent systems can be distinguished, crystal engineering strategies and a number of cocrystal applications highlights the importance the understanding of intermolecular interactions can have on the physical and chemical properties of crystalline materials. Chapter Two is the first Results and Discussion chapter and includes an introduction that is specific to the chapter. The main body of this work focuses on the primary aromatic thioamide functional group and its propensity to cocrystallise with a number of sulfoxides. Unlike the amide functional group, thioamides are not commonly employed in cocrystallisation studies. This chapter presents the first direct comparison between the cocrystallisation abilities of these two functional groups and the intermolecular hydrogen bonding interactions present in the cocrystal structures are examined. Chapter Three describes the crystal landscape of a short series of secondary aromatic amides and their analogous thioamides. Building on the results obtained in Chapter Two, a cocrystal screen of the secondary thioamides with the sulfoxide functional group was carried out in order to determine the effect removing a hydrogen bond had on the supramolecular synthons observed in the cocrystals. These secondary thioamides are also utilised in Chapter Four, which examines their halogen bonding capabilities with two organoiodine coformers: 1,2- and 1,4-diiodotetrafluorobenzene. Chapter Five explores the cocrystallisation abilities of three related cyclic imides as coformers for cocrystallisation with a range of commonly used coformers. Chapter Six is an overall conclusions chapter that highlights the findings of the results presented in Chapters Two to Five. Chapter Seven details the instrument and experimental data for the compounds and cocrystals discussed in the Results and Discussion Chapters. The accompanying CD contains all of the crystallographic data in .cif format for the novel single crystal structures characterised in this work.

Interactions of Cytochrome P450 3A4 with Phospholipid Bilayer Nanodiscs

Thesis (Ph.D.)--University of Washington, 2016-08