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Chemical crystallography

Fang-Fang Shen, Kai Chen, Yun-Qian Zhang, Qian-Jiang Zhu, Zhu Tao, Hang Cong
Mono- and dihydroxylated symmetrical octamethylcucurbit[6]urils {(OH)OMeQ[6] and (OH)2OMeQ[6]} were prepared using a photochemical method to introduce limited alcohol group(s) directly to the parent symmetrical octamethylcucurbit[6]uril (OMeQ[6]), and the resulting compounds were verified by (1)H NMR, Xevo Q-TOF MS, and X-ray crystallography. Further chemical modification of mono- and dihydroxylated OMeQ[6] was also performed.
October 21, 2016: Organic Letters
Gregory J O Beran, Joshua D Hartman, Yonaton N Heit
Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties...
October 18, 2016: Accounts of Chemical Research
Ewa Kober, Zofia Janas, Julia Jezierska
A series of oxidovanadium(V) complexes [VO(L-κ(4)O,N,N,O)(OR)] (1a, R = Et, L = L(1); 1b, R = Me, L = L(1); 2, R = Me, L = L(2); 3, R = Me, L = L(3)) were synthesized by the σ-bond metathesis reaction between [VO(OR)3] and the linear diaminebis(phenol) derivatives H2L (salans) containing different para-substituents on the phenoxo group [CMe3CH2CMe2, L(1); Me, L(2); Cl, L(3)]. As shown by X-ray crystallography complexes 1a, 1b, and 2 exhibit cis-α geometry, do have a stereogenic vanadium center, and exist as a racemic mixture of the Δ cis-α and Λ cis-α enantiomers...
October 18, 2016: Inorganic Chemistry
John Lee
The molecular mechanisms of the bioluminescence systems of the firefly, bacteria, and those utilizing imidazopyrazinone luciferins such as coelenterazine, are gradually being uncovered using modern biophysical methods such as dynamic (ns-ps) fluorescence spectroscopy, NMR, X-ray crystallography, and computational chemistry. The chemical structures of all reactants are well defined and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high energy species that undergoes decarboxylation to form directly the product in its S1 state, the bioluminescence emitter...
October 17, 2016: Photochemistry and Photobiology
Maria B Mesch, Kilian Bärwinkel, Yaşar Krysiak, Charlotte Martineau, Francis Taulelle, Reinhard B Neder, Ute Kolb, Jürgen Senker
Poly(triazine imide) with incorporated lithium chloride has recently attracted substantial attention due to its photocatalytic activity for water splitting. However, an apparent H/Li disorder prevents the delineation of structure-property relationships, for example, with respect to band-gap tuning. Herein, we show that through a combination of one- and two-dimensional, multinuclear solid-state NMR spectroscopy, chemical modelling, automated electron diffraction tomography, and an analysis based on X-ray pair distribution functions, it is finally possible to resolve the H/Li substructure...
October 13, 2016: Chemistry: a European Journal
Jodi L Brewster, James L O McKellar, Thomas J Finn, Janet Newman, Thomas S Peat, Monica L Gerth
Chemoreceptors enable bacteria to detect chemical signals in the environment and navigate towards niches that are favourable for survival. The sensor domains of chemoreceptors function as the input modules for chemotaxis systems, and provide sensory specificity by binding specific ligands. Cache-like domains are the most common extracellular sensor module in prokaryotes, however only a handful have been functionally or structurally characterised. Here, we have characterised a chemoreceptor Cache-like sensor domain (PscD-SD) from the plant pathogen Pseudomonas syringae pv...
October 13, 2016: Scientific Reports
Andrey S Orekhov, Feruza T Tuyakova, Ekaterina A Obraztsova, Artem B Loginov, Andrey L Chuvilin, Alexander N Obraztsov
Diamond is attractive for various applications due to its unique mechanical and optical properties. In particular, single crystal diamond needles with high aspect ratios and sharp apexes of nanometer size are demanded for different types of optical sensors including optically sensing tip probes for scanning microscopy. This paper reports on electron microscopy and Raman spectroscopy characterization of the diamond needles having geometrically perfect pyramidal shapes with rectangular atomically flat bases with (001) crystallography orientation, 2-200 nm sharp apexes, and with lengths from about 10-160 μm...
October 11, 2016: Nanotechnology
Junji Uchida, Takashi Nakamura, Masaki Yamamura, Gento Yamaguchi, Tatsuya Nabeshima
The effectiveness of a m-phenylene linker, which has rigidity as well as rotational flexibility, is presented to produce a series of variously shaped macrocyclic oligomers of dipyrrins and BODIPYs, whose structures were revealed by X-ray crystallography and (1)H NMR analysis. Although the chemical structures of the repeating units are the same for dipyrrin/BODIPY oligomers, their absorbance and emission properties changed significantly depending on the size and shape of the macrocycles.
October 10, 2016: Organic Letters
Michiko Tawada, Shinkichi Suzuki, Yasuhiro Imaeda, Hideyuki Oki, Gyorgy Snell, Craig A Behnke, Mitsuyo Kondo, Naoki Tarui, Toshimasa Tanaka, Takanobu Kuroita, Masaki Tomimoto
A novel approach was conducted for fragment-based lead discovery and applied to renin inhibitors. The biochemical screening of a fragment library against renin provided the hit fragment which showed a characteristic interaction pattern with the target protein. The hit fragment bound only to the S1, S3, and S3(SP) (S3 subpocket) sites without any interactions with the catalytic aspartate residues (Asp32 and Asp215 (pepsin numbering)). Prior to making chemical modifications to the hit fragment, we first identified its essential binding sites by utilizing the hit fragment's substructures...
September 28, 2016: Bioorganic & Medicinal Chemistry
Dingqing Li, Jan Schwabedissen, Hans-Georg Stammler, Norbert W Mitzel, Helge Willner, Xiaoqing Zeng
Dichlorophosphanyl isocyanate, Cl2PNCO, was synthesized and characterized by IR, Raman and (31)P NMR spectroscopy. The conformational properties and molecular structures were studied by using gas electron diffraction (GED), X-ray crystallography and quantum-chemical calculations. Extensive DFT and ab initio calculations show that the potential energy surface of Cl2PNCO upon rotating the P-N bond is rather flat; three conformers, namely syn, anti and gauche between the NCO group and the bisector of the ClPCl angle, were theoretically predicted...
September 21, 2016: Physical Chemistry Chemical Physics: PCCP
Russell W Driver, Timothy D W Claridge, Steve Scheiner, Martin D Smith
The precise role of non-conventional hydrogen bonds such as the C-H⋅⋅⋅O interaction in influencing the conformation of small molecules remains unresolved. Here we survey a series of β-turn mimetics using X-ray crystallography and NMR spectroscopy in conjunction with quantum calculation, and conclude that favourable torsional and electronic effects are important for the population of states with conformationally influential C-H⋅⋅⋅O interactions. Our results also highlight the challenge in attempting to deconvolute a myriad of interdependent noncovalent interactions in order to focus on the contribution of a single one...
October 6, 2016: Chemistry: a European Journal
Mahmoud Saleh, Douglas R Powell, Rudolf J Wehmschulte
Fully chlorinated carborate and dodecaborate cages such as [CHB11Cl11](-) and [Me3NB12Cl11](-) are prominent examples of valuable and chemically rather inert weakly coordinating anions. While both anions can be obtained by chlorination of the precursors [CH12B11](-) and [H3NB12H11](-) with SO2Cl2 followed by methylation for the synthesis of [Me3NB12Cl11](-), best results were found using photochemical chlorination with SO2Cl2 for [CH12B11](-) and thermal chlorination with SO2Cl2 for [H3NB12H11](-). The hexachlorinated anion [n-Pr3NB12H5Cl6](-) was formed readily within 30 min by chlorination of [n-Pr3NB12H11](-), but attempts to synthesize isopropyl-substituted ammonio-dodecaborates with a higher chlorination number resulted in the formation of mixtures and partial decomposition...
October 5, 2016: Inorganic Chemistry
Zachary N Vealey, Brandon Q Mercado, Patrick H Vaccaro
Tropolone long has served as a model system for unraveling the ubiquitous phenomena of proton transfer and hydrogen bonding. This molecule, which juxtaposes ketonic, hydroxylic, and aromatic functionalities in a framework of minimal complexity, also has provided a versatile platform for investigating the synergism among competing intermolecular forces, including those generated by hydrogen bonding and aryl coupling. Small members of the troponoid family typically produce crystals that are stabilized strongly by pervasive π-π, C-H...
October 1, 2016: Acta Crystallographica. Section C, Structural Chemistry
Suzanne G Mays, C Denise Okafor, Richard J Whitby, Devrishi Goswami, J Oacutezef Stec, Autumn R Flynn, Michael C Dugan, Nathan T Jui, Patrick R Griffin, Eric A Ortlund
Liver receptor homolog 1 (NR5A2, LRH-1) is an orphan nuclear hormone receptor that regulates diverse biological processes, including metabolism, proliferation, and the resolution of endoplasmic reticulum stress. While preclinical and cellular studies demonstrate that LRH-1 has great potential as a therapeutic target for metabolic diseases and cancer, development of LRH-1 modulators has been difficult. Recently, systematic modifications to one of the few known chemical scaffolds capable of activating LRH-1 failed to improve efficacy substantially...
September 30, 2016: Journal of Biological Chemistry
George D Geromichalos, Constantinos E Alifieris, Elena G Geromichalou, Dimitrios T Trafalis
Conventional drug design embraces the "one gene, one drug, one disease" philosophy. Nowadays, new generation of anti- cancer drugs, able to inhibit more than one pathway, is believed to play a major role in contemporary anticancer drug research. In this way, polypharmacology, focusing on multi-target drugs, has emerged as a new paradigm in drug discovery. A number of recent successful drugs have in part or in whole emerged from a structure-based research approach. Many advances including crystallography and informatics are behind these successes...
July 2016: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
Tobias A Schaub, Eva M Zolnhofer, Dominik P Halter, Tatyana E Shubina, Frank Hampel, Karsten Meyer, Milan Kivala
Triarylphosphine oxides (Ar3 P=O) are being intensely studied as electron-accepting (n-type) materials. Despite the widespread application of these compounds as electron conductors, experimental data regarding the structural and electronic properties of their negatively charged states remain scarce owing to their propensity for follow-up chemistry. Herein, a carefully designed triarylphosphine oxide scaffold is disclosed that comprises sterically demanding spirofluorenyl moieties to shield the central phosphoryl (P=O) moiety...
October 17, 2016: Angewandte Chemie
Corina G Heidrich, Sanya Mitova, Andreas Schedlbauer, Sean R Connell, Paola Fucini, Judith N Steenbergen, Christian Berens
Omadacycline is an aminomethylcycline antibiotic with potent activity against many Gram-positive and Gram-negative pathogens, including strains carrying the major efflux and ribosome protection resistance determinants. This makes it a promising candidate for therapy of severe infectious diseases. Omadacycline inhibits bacterial protein biosynthesis and competes with tetracycline for binding to the ribosome. Its interactions with the 70S ribosome were, therefore, analyzed in great detail and compared with tigecycline and tetracycline...
2016: Antibiotics
Ivan Guerra, Susan J Schroeder
The folding landscape for an RNA sequence contains many diverse structures and motifs, which are often sampled rather than completely explored. Today's supercomputers make the complete enumeration of all possible folds for an RNA and a detailed description of the RNA folding landscape a more feasible task. This chapter provides protocols for using the Crumple folding algorithm, an efficient tool to generate all possible non-pseudoknotted folds for an RNA sequence. Crumple in conjunction with Sliding Windows and Assembly can incorporate experimental constraints on the global features of an RNA, such as the minimum number and lengths of helices, which may be determined by crystallography or cryo-electron microscopy...
2016: Methods in Molecular Biology
Andrew J Knappenberger, Md Faiz Ahmad, Rajesh Viswanathan, Chris G Dealwis, Michael E Harris
Class I ribonucleotide reductase (RR) maintains balanced pools of deoxyribonucleotide substrates for DNA replication by converting ribonucleoside diphosphates (NDPs) to 2'-deoxyribonucleoside diphosphates (dNDPs). Binding of deoxynucleoside triphosphate (dNTP) effectors (ATP/dATP, dGTP, and dTTP) modulates the specificity of class I RR for CDP, UDP, ADP, and GDP substrates. Crystal structures of bacterial and eukaryotic RRs show that dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop (loop 2)...
October 3, 2016: Biochemistry
Vassilios Myrianthopoulos, Nicolas Gaboriaud-Kolar, Cynthia Tallant, Michelle-Lynn Hall, Stylianos Grigoriou, Peter Moore Brownlee, Oleg Fedorov, Catherine Rogers, David Heidenreich, Marek Wanior, Nikolaos Drosos, Nikitia Mexia, Pavel Savitsky, Tina Bagratuni, Efstathios Kastritis, Evangelos Terpos, Panagis Filippakopoulos, Susanne Müller, Alexios-Leandros Skaltsounis, Jessica Ann Downs, Stefan Knapp, Emmanuel Mikros
Bromodomains (BRDs) are epigenetic interaction domains currently recognized as emerging drug targets for development of anticancer or anti-inflammatory agents. In this study, development of a selective ligand of the fifth BRD of polybromo protein-1 (PB1(5)) related to switch/sucrose nonfermenting (SWI/SNF) chromatin remodeling complexes is presented. A compound collection was evaluated by consensus virtual screening and a hit was identified. The biophysical study of protein-ligand interactions was performed using X-ray crystallography and isothermal titration calorimetry...
October 13, 2016: Journal of Medicinal Chemistry
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