On the role of DMSO-O(lone pair)⋯π(arene), DMSO-S(lone pair)⋯π(arene) and SO⋯π(arene) interactions in the crystal structures of dimethyl sulphoxide (DMSO) solvates

CrystEngComm ◽  
2014 ◽  
Vol 16 (28) ◽  
pp. 6398-6407 ◽  
Author(s):  
Julio Zukerman-Schpector ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structures ◽  
Lone Pair ◽  
Dimethyl Sulphoxide

DMSO-O(lone pair)⋯π(arene), DMSO-S(lone pair)⋯π(arene) and SO⋯π(arene) interactions are found in DMSO solvates.

Different cationic forms of (–)-cytisine in the crystal structures of its simple inorganic salts

2018 ◽  
Vol 74 (11) ◽  
pp. 1518-1530 ◽  
Author(s):  
Agata Owczarzak ◽  
Anna K. Przybył ◽  
Maciej Kubicki
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Lone Pair ◽  
Piperidine Ring ◽  
Coulombic Interactions ◽  
Laburnum Anagyroides ◽  
Almost All ◽  
Chloride Monohydrate

The crystal structures of 13 simple salts of cytisine, an alkaloid isolated from the seeds of Laburnum anagyroides, have been determined, namely cytisinium (6-oxo-7,11-diazatricyclo[7.3.1.02,7]trideca-2,4-dien-11-ium) bromide, C11H15N2O+·Br−, cytisinium iodide, C11H15N2O+·I−, cytisinium perchlorate, C11H15N2O+·ClO4 −, cytisinium iodide triiodide, C11H15N2O+·I−·I3 −, cytisinium chloride monohydrate, C11H15N2O+·Cl−·H2O, cytisinium iodide monohydrate, C11H15N2O+·I−·H2O, cytisinium nitrate monohydrate, C11H15N2O+·NO3 −·H2O, hydrogen dicytisinium tribromide, C22H31N4O2 3+·3Br−, hydrogen dicytisinium triiodide, C22H31N4O2 3+·3I−, hydrogen dicytisinium triiodide diiodide, C22H31N4O2 3+·I3 −·2I−, hydrogen dicytisinium bis(triiodide) iodide, C22H31N4O2 3+·2I3 −·I−, cytisinediium (6-oxidaniumylidene-7,11-diazatricyclo[7.3.1.02,7]trideca-2,4-dien-11-ium) bis(perchlorate), C11H16N2O2+·2ClO4 −, and cytisinediium dichloride trihydrate, C11H16N2O2+·2Cl−·3H2O. Cytisine has two potential protonation sites, i.e. the N atom of the piperidine ring and the carbonyl O atom of the pyridone ring. Three forms of the cytisinium cation were identified, namely the monocation, which is always protonated at the N atom, the dication, which utilizes both protonation sites, and the third form, which contains two cytisine moieties connected by very short and linear O...H...O hydrogen bonds, with an O...O distance of approximately 2.4 Å. This third form may therefore be regarded as a 3+ species, or sesqui-cation, and is observed solely in the salts with bromide, iodide or triiodide (heavier halogen) anions. The cation is quite rigid and all 19 cytisinium fragments in the studied series have very similar conformations. The crystal structures are determined mainly by Coulombic interactions and hydrogen bonds, and the latter form is determined by different networks. Additionally, some anion–π and lone-pair...π secondary interactions are identified in almost all of the crystal structures. Hirshfeld surface analysis generally confirms the role of different interactions in the determination of the crystal architecture.

scholarly journals Spotlight on Alkali Metals: The Structural Chemistry of Alkali Metal Thallides

Crystals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1013
Author(s):  
Stefanie Gärtner
Keyword(s):  
Crystal Structure ◽  
Alkali Metal ◽  
Crystal Structures ◽  
Alkali Metals ◽  
Valence Electron ◽  
Oxidation States ◽  
Valence Electron Concentration ◽  
Base Metals ◽  
Charge Balancing

Alkali metal thallides go back to the investigative works of Eduard Zintl about base metals in negative oxidation states. In 1932, he described the crystal structure of NaTl as the first representative for this class of compounds. Since then, a bunch of versatile crystal structures has been reported for thallium as electronegative element in intermetallic solid state compounds. For combinations of thallium with alkali metals as electropositive counterparts, a broad range of different unique structure types has been observed. Interestingly, various thallium substructures at the same or very similar valence electron concentration (VEC) are obtained. This in return emphasizes that the role of the alkali metals on structure formation goes far beyond ancillary filling atoms, which are present only due to charge balancing reasons. In this review, the alkali metals are in focus and the local surroundings of the latter are discussed in terms of their crystallographic sites in the corresponding crystal structures.

The Through-Bond Interaction of a Sulfur Lone Pair with Oxygenated Substituents in the Thiacyclohexane Framework

2005 ◽  
Vol 58 (7) ◽  
pp. 531
Author(s):  
Laura Andrau ◽  
Jonathan M. White
Keyword(s):  
Low Temperature ◽  
Crystal Structures ◽  
Bond Distance ◽  
Lone Pair ◽  
X Ray ◽  
Ester Derivative ◽  
Bond Interaction ◽  
Derivatives Of ◽  
Electron Demand

Low-temperature X-ray crystal structures were determined on a range of derivatives of 4-thiacyclohexanol 5a of varying electron demand with a view to finding evidence for a through-bond interaction between the sulfur lone pair and the oxygenated substituent. In contrast to earlier suggestions, plots of C–OR bond distance versus pKa (ROH) showed that any interaction between the sulfur and the OR group is unlikely to be of a through-bond origin. Furthermore, unimolecular solvolysis rate measurements on the nosylate ester derivative 5g showed that the sulfur actually retards the reaction slightly in comparison with the corresponding sulfur-free analogue 6.

p-Type conductivity of GeTe: The role of lone-pair electrons

2012 ◽  
Vol 249 (10) ◽  
pp. 1902-1906 ◽  
Author(s):  
Alexander V. Kolobov ◽  
Paul Fons ◽  
Junji Tominaga
Keyword(s):  
Lone Pair ◽  
Type Conductivity ◽  
P Type ◽  
Lone Pair Electrons

scholarly journals Investigation of the role of cytochrome P450 2B4 active site residues in substrate metabolism based on crystal structures of the ligand-bound enzyme

2006 ◽  
Vol 455 (1) ◽  
pp. 61-67 ◽  
Author(s):  
Cynthia E. Hernandez ◽  
Santosh Kumar ◽  
Hong Liu ◽  
James R. Halpert
Keyword(s):  
Cytochrome P450 ◽  
Crystal Structures ◽  
Active Site ◽  
Active Site Residues ◽  
Substrate Metabolism ◽  
Cytochrome P450 2B4

scholarly journals The role of BamA in the biogenesis of beta-barrel membrane proteins

2014 ◽  
Vol 70 (a1) ◽  
pp. C578-C578
Author(s):  
Nicholas Noinaj ◽  
Adam Kuszak ◽  
Curtis Balusek ◽  
JC Gumbart ◽  
Petra Lukacik ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Crystal Structures ◽  
Outer Membrane Proteins ◽  
Hydrophobic Surface ◽  
Md Simulations ◽  
Structural Features ◽  
Bam Complex ◽  
Beta Barrel

Beta-barrel membrane proteins are essential for nutrient import, signaling, motility, and survival. In Gram-negative bacteria, the beta-barrel assembly machinery (BAM) complex is responsible for the biogenesis of beta-barrel outer membrane proteins (OMPs), with homologous complexes found in mitochondria and chloroplasts. Despite their essential roles, exactly how these OMPs are formed remains unknown. The BAM complex consists of a central and essential component called BamA (an OMP itself) and four lipoproteins called BamB-E. While the structure of the lipoproteins have been reported, the structure of full length BamA has been elusive. Recently though, we described the structure of BamA from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. BamA consists of a large periplasmic domain attached to a 16-strand transmembrane beta-barrel domain. Together, our crystal structures and molecule dynamics (MD) simulations revealed several structural features which gave clues to the mechanism by which BamA catalyzes beta-barrel assembly. The first is that the interior cavity is accessible in one BamA structure and conformationally closed in the other. Second, an exterior rim of the beta-barrel has a distinctly narrowed hydrophobic surface, locally destabilizing the outer membrane. Third, the beta-barrel can undergo lateral opening, suggesting a route from the interior cavity in BamA into the outer membrane. And fourth, a surface exposed exit pore positioned above the lateral opening site which may play a role in the biogenesis of extracellular loops. In this presentation, the crystal structures and MD simulations of BamA will be presented along with our work looking at the role of these four structural features in the role of BamA within the BAM complex.

scholarly journals Organic Stabilization of Extracellular Elemental Sulfur in a Sulfurovum-Rich Biofilm: A New Role for Extracellular Polymeric Substances?

2021 ◽  
Vol 12 ◽  
Author(s):  
Brandi Cron ◽  
Jennifer L. Macalady ◽  
Julie Cosmidis
Keyword(s):  
Crystal Structures ◽  
Extracellular Polymeric Substances ◽  
Elemental Sulfur ◽  
Dense Matrix ◽  
Cave System ◽  
Carboxylic Groups ◽  
Sulfur Oxidizing ◽  
New Evidence ◽  
Sulfur Oxidizing Bacteria

This work shines light on the role of extracellular polymeric substance (EPS) in the formation and preservation of elemental sulfur biominerals produced by sulfur-oxidizing bacteria. We characterized elemental sulfur particles produced within a Sulfurovum-rich biofilm in the Frasassi Cave System (Italy). The particles adopt spherical and bipyramidal morphologies, and display both stable (α-S8) and metastable (β-S8) crystal structures. Elemental sulfur is embedded within a dense matrix of EPS, and the particles are surrounded by organic envelopes rich in amide and carboxylic groups. Organic encapsulation and the presence of metastable crystal structures are consistent with elemental sulfur organomineralization, i.e., the formation and stabilization of elemental sulfur in the presence of organics, a mechanism that has previously been observed in laboratory studies. This research provides new evidence for the important role of microbial EPS in mineral formation in the environment. We hypothesize that the extracellular organics are used by sulfur-oxidizing bacteria for the stabilization of elemental sulfur minerals outside of the cell wall as a store of chemical energy. The stabilization of energy sources (in the form of a solid electron acceptor) in biofilms is a potential new role for microbial EPS that requires further investigation.

scholarly journals Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain

2019 ◽  
Author(s):  
Ming Lei ◽  
Wolfram Tempel ◽  
Ke Liu ◽  
Jinrong Min
Keyword(s):  
Crystal Structures ◽  
Transcriptional Repression ◽  
Consensus Sequence ◽  
Complex Structure ◽  
Structural Basis ◽  
Structural Studies ◽  
Transcription Activator ◽  
Methylated Dna ◽  
Attachment Region

AbstractMeCP2 is an abundant protein, involved in transcriptional repression by binding to CG and non-CG methylated DNA. However, MeCP2 might also function as a transcription activator as MeCP2 is found bound to sparsely methylated promoters of actively expressed genes. Furthermore, Attachment Region Binding Protein (ARBP), the chicken ortholog of MeCP2, has been reported to bind to Matrix/scaffold attachment regions (MARs/SARs) DNA with an unmethylated 5’-CAC/GTG-3’ consensus sequence. In this study, we investigated how MeCP2 recognizes unmethylated 5’-CAC/GTG-3’ motif containing DNA by binding and structural studies. We found that MeCP2-MBD binds to MARs DNA with a comparable binding affinity to mCG DNA, and the MeCP2-CAC/GTG complex structure revealed that MeCP2 residues R111 and R133 form base-specific interactions with the GTG motif. For comparison, we also determined crystal structures of the MeCP2-MBD bound to mCG and mCAC/GTG DNA, respectively. Together, these crystal structures illustrate the adaptability of the MeCP2-MBD toward the GTG motif as well as the mCG DNA, and also provide structural basis of a biological role of MeCP2 as a transcription activator and its disease implications in Rett syndrome.

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