Saccharide Recognition by a Three‐Arm‐Shaped Host Having Preorganized Three‐Dimensional Hydrogen‐Bonding Sites

2020 ◽  
Author(s):  
Yuki Ohishi ◽  
Kentaro Masuda ◽  
Kazuki Kudo ◽  
Hajime Abe ◽  
Masahiko Inouye
Keyword(s):  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Saccharide Recognition

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

Elastomers Based on Polycyclic Bisphenol Polycarbonates

1966 ◽  
Vol 39 (4) ◽  
pp. 1008-1018
Author(s):  
K. P. Perry ◽  
W. J. Jackson ◽  
J. R. Caldwell
Keyword(s):  
Hydrogen Bonding ◽  
Bisphenol A ◽  
Methylene Chloride ◽  
Three Dimensional ◽  
Pyridine Solution ◽  
Designed Experiment ◽  
Spun Fibers

Abstract Polycarbonate elastomers were prepared by the addition of phosgene to a pyridine solution of poly (tetramethylene ether) glycol and bisphenols containing norbornane-type groups. These elastomers do not contain the classical “tie-down” points—crosslinks, hydrogen bonding, or crystallinity—which, heretofore, have been considered necessary for good elastomer properties. This work introduces a new concept in elastomer chemistry : bulky, three-dimensional groups are effective tie-down points. Most of the elastomers were prepared with 4,4′- (2-norbornylidene) bis(2,6-dichlorophenol). For comparison, several elastomers with bisphenol-A were also prepared. A statistically designed experiment was carried out to determine the effect of composition variables on the properties of these elastomers. The properties were determined on films cast from methylene chloride and, in many cases, on wet-spun fibers. These elastomers have elongations of 400–600 per cent and instantaneous elastic recoveries up to 100.

The crystal structure of gatehouseite

2011 ◽  
Vol 75 (6) ◽  
pp. 2823-2832
Author(s):  
P. Elliott ◽  
A. Pring
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Direct Methods ◽  
Chemical Analyses ◽  
X Ray Diffraction ◽  
X Ray ◽  
Manganese Phosphate ◽  
Phosphate Mineral ◽  
Unit Formula

AbstractThe crystal structure of the manganese phosphate mineral gatehouseite, ideally Mn52+(PO4)2(OH)4, space group P212121, a = 17.9733(18), b = 5.6916(11), c = 9.130(4) Å, V= 933.9(4) Å3, Z = 4, has been solved by direct methods and refined from single-crystal X-ray diffraction data (T = 293 K) to an R index of 3.76%. Gatehouseite is isostructural with arsenoclasite and with synthetic Mn52+(PO4)2(OH)4. The structure contains five octahedrally coordinated Mn sites, occupied by Mn plus very minor Mg with observed <Mn—O> distances from 2.163 to 2.239 Å. Two tetrahedrally coordinated P sites, occupied by P, Si and As, have <P—O> distances of 1.559 and 1.558 Å. The structure comprises two types of building unit. A strip of edge-sharing Mn(O,OH)6 octahedra, alternately one and two octahedra wide, extends along [010]. Chains of edge- and corner-shared Mn(O,OH)6 octahedra coupled by PO4 tetrahedra extend along [010]. By sharing octahedron and tetrahedron corners, these two units form a dense three-dimensional framework, which is further strengthened by weak hydrogen bonding. Chemical analyses by electron microprobe gave a unit formula of (Mn4.99Mg0.02)Σ5.01(P1.76Si0.07(As0.07)Σ2.03O8(OH)3.97.

scholarly journals Hydrogen bonding inC-methylated nitroanilines: the three-dimensional framework structure of 2-methyl-4-nitroaniline

2001 ◽  
Vol 57 (3) ◽  
pp. 315-316 ◽  
Author(s):  
George Ferguson ◽  
Christopher Glidewell ◽  
John N. Low ◽  
Janet M. S. Skakle ◽  
James L. Wardell
Keyword(s):  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Framework Structure

scholarly journals Bis(nitrilotriacetamide-κ4 N,O,O′,O′′)silver(I) nitrate

IUCrData ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Min Ren ◽  
Ming Yue ◽  
Jingwen Ran
Keyword(s):  
Hydrogen Bonding ◽  
Network Structure ◽  
Title Compound ◽  
Three Dimensional ◽  
Hydrogen Bonding Interactions ◽  
Dimensional Network

In the centrosymmetric cation of the title compound, [Ag(C6H12N4O3)2]NO3, the AgI ion, lying on a threefold rotoinversion axis, is coordinated by two N atoms and six O atoms from two nitrilotriacetamide ligands, forming a distorted dodecahedral environment. In the crystal, cations and anions are linked through N—H...O hydrogen-bonding interactions, leading to a three-dimensional network structure.

scholarly journals Crystal structure of 2-cyano-1-methylpyridinium tetrafluoroborate

2015 ◽  
Vol 71 (10) ◽  
pp. o697-o698 ◽  
Author(s):  
Francesca A. Vaccaro ◽  
Lynn V. Koplitz ◽  
Joel T. Mague
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Solid State ◽  
Three Dimensional ◽  
Asymmetric Unit ◽  
State Structure ◽  
Solid State Structure ◽  
Two Component

The asymmetric unit of the title salt, C7H7N2+·BF4−, comprises two independent but nearly identical formula units. The solid-state structure comprises corrugated layers of cations and anions, formed by C—H...F hydrogen bonding, that are approximately parallel to (010). Further C—H...F hydrogen bonding consolidates the three-dimensional architecture. The sample was refined as a two-component non-merohedral twin.

scholarly journals Crystal structure of trihydrogen bis{[1,1,1-tris(2-oxidoethylaminomethyl)ethane]cobalt(III)} trinitrate

2015 ◽  
Vol 71 (12) ◽  
pp. m275-m276 ◽  
Author(s):  
Waqas Sethi ◽  
Heini V. Johannesen ◽  
Thorbjørn J. Morsing ◽  
Stergios Piligkos ◽  
Høgni Weihe
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Network Structure ◽  
Title Compound ◽  
Rotation Axis ◽  
Three Dimensional ◽  
Rotation Axes ◽  
Dimensional Network ◽  
Nitrate Anions

The title compound, [Co2(L)2]3+·3NO3−[whereL= CH3C(CH2NHCH2CH2OH1/2)3], has been synthesized from the ligand 1,1,1-tris(2-hydroxyethylaminomethyl)ethane. The cobalt(III) dimer has an interesting and uncommon O—H...O hydrogen-bonding motif with the three bridging hydroxy H atoms each being equally disordered over two positions. In the dimeric trication, the octahedrally coordinated CoIIIatoms and the capping C atoms lie on a threefold rotation axis. The N atoms of two crystallographically independent nitrate anions also lie on threefold rotation axes. N—H...O hydrogen bonding between the complex cations and nitrate anions leads to the formation of a three-dimensional network structure. The compound is a racemic conglomerate of crystals containing either D or L molecules. The crystal used for this study is a D crystal.

scholarly journals Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate

2016 ◽  
Vol 72 (5) ◽  
pp. 751-755 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Network Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Arsanilic Acid ◽  
Dimensional Network

In the structure of the brucinium salt of 4-aminophenylarsonic acid (p-arsanilic acid), systematically 2,3-dimethoxy-10-oxostrychnidinium 4-aminophenylarsonate tetrahydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water molecules of solvation are accommodated between the layers and are linked to them through a primary cation N—H...O(anion) hydrogen bond, as well as through water O—H...O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

scholarly journals Poly[bis(μ-4-aminobenzenesulfonato-κ2 N:O)diaquacobalt(II)]

IUCrData ◽  
2018 ◽  
Vol 3 (8) ◽  
Author(s):  
Antoine Blaise Kama ◽  
Mamadou Sidibe ◽  
Cheikh Abdoul Khadre Diop ◽  
Florent Blanchard
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Title Compound ◽  
Three Dimensional ◽  
Water Molecules ◽  
Supramolecular Framework ◽  
Distorted Octahedral Environment ◽  
Octahedral Environment ◽  
Distorted Octahedral

The title compound, [Co(C6H6NO3S)2(H2O)2] n , was obtained from a mixture of Co(NO3)2·6H2O and a previously synthesized salt, namely CyNH3·NH2PhSO3, in a 1:1 ratio (Cy = cyclohexyl; Ph = phenyl). The crystal structure consists of a three-dimensional supramolecular framework, in which polymeric layers are interconnected via N—H...O and O—H...O hydrogen bonding. The polymeric layers are formed by an interconnection of neighbouring cobalt(II) cations via NH2PhSO3 − bridges. Each cobalt(II) cation is surrounded by four NH2PhSO3 − moieties and two water molecules, leading to a distorted octahedral environment.

Ethylenediammonium thiophene-2,5-dicarboxylate dihydrate, an acid–base complex with a three-dimensional hydrogen-bonding system

2006 ◽  
Vol 62 (7) ◽  
pp. o2951-o2952 ◽  
Author(s):  
Si-Min Wu ◽  
Ming Li ◽  
Jiang-Feng Xiang ◽  
Liang-Jie Yuan ◽  
Ju-Tang Sun
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Water Molecules ◽  
Inversion Center ◽  
Acid Base ◽  
Special Position ◽  
Compound C ◽  
Bonding System ◽  
Hydrogen Bonding System

The crystal structure of the title compound, C2H10N2 2+·C6H2O4S2−·2H2O, is built of ethylenediammonium dications, occupying a special position on an inversion center, thiophene-2,5-dicarboxylate dianions, in a special position on the twofold axis, and water molecules in general positions. All residues are involved in an extensive hydrogen-bonding system, which links them into a three-dimensional supramolecular arrangement.

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