scholarly journals Identification of Structural Motifs Using Networks of Hydrogen-Bonded Base Interactions in RNA Crystallographic Structures

Crystals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 550 ◽  
Author(s):  
Hazrina Yusof Hamdani ◽  
Mohd Firdaus-Raih
Keyword(s):  
Hydrogen Bonds ◽  
Data Bank ◽  
Rna Structures ◽  
Structural Motifs ◽  
Functional Sites ◽  
Network Of Hydrogen Bonds ◽  
Crystallographic Structures ◽  
Rna Structural Motifs ◽  
Large Clusters ◽  
Hydrogen Bonded

RNA structural motifs can be identified using methods that analyze base–base interactions and the conformation of a structure’s backbone; however, these approaches do not necessarily take into consideration the hydrogen bonds that connect the bases or the networks of inter-connected hydrogen-bonded bases that are found in RNA structures. Large clusters of RNA bases that are tightly inter-connected by a network of hydrogen bonds are expected to be stable and relatively rigid substructures. Such base arrangements could therefore be present as structural motifs in RNA structures, especially when there is a requirement for a highly stable support platform or substructure to ensure the correct folding and spatial maintenance of functional sites that partake in catalysis or binding interactions. In order to test this hypothesis, we conducted a search in available RNA crystallographic structures in the Protein Data Bank database using queries that searched for profiles of bases inter-connected by hydrogen bonds. This method of searching does not require to have prior knowledge of the arrangement being searched. Our search results identified two clusters of six bases that are inter-connected by a network of hydrogen bonds. These arrangements of base sextuples have never been previously reported, thus making this the first report that proposes them as novel RNA tertiary motifs.

Polymorphs of phenazine hexacyanoferrate(II) hydrate: supramolecular isomerism in a 2D hydrogen-bonded network

2021 ◽  
Vol 77 (2) ◽  
pp. 211-218
Author(s):  
Ivica Cvrtila ◽  
Vladimir Stilinović
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Two Dimensional ◽  
Structural Motifs ◽  
Supramolecular Isomerism ◽  
Other Hand ◽  
Π Stacking ◽  
Hydrogen Bonded

The crystal structures of two polymorphs of a phenazine hexacyanoferrate(II) salt/cocrystal, with the formula (Hphen)3[H2Fe(CN)6][H3Fe(CN)6]·2(phen)·2H2O, are reported. The polymorphs are comprised of (Hphen)2[H2Fe(CN)6] trimers and (Hphen)[(phen)2(H2O)2][H3Fe(CN)6] hexamers connected into two-dimensional (2D) hydrogen-bonded networks through strong hydrogen bonds between the [H2Fe(CN)6]2− and [H3Fe(CN)6]− anions. The layers are further connected by hydrogen bonds, as well as through π–π stacking of phenazine moieties. Aside from the identical 2D hydrogen-bonded networks, the two polymorphs share phenazine stacks comprising both protonated and neutral phenazine molecules. On the other hand, the polymorphs differ in the conformation, placement and orientation of the hydrogen-bonded trimers and hexamers within the hydrogen-bonded networks, which leads to different packing of the hydrogen-bonded layers, as well as to different hydrogen bonding between the layers. Thus, aside from an exceptional number of symmetry-independent units (nine in total), these two polymorphs show how robust structural motifs, such as charge-assisted hydrogen bonding or π-stacking, allow for different arrangements of the supramolecular units, resulting in polymorphism.

Diaquabis(1,10-phenanthroline-κ2 N,N′)manganese(II) thiodiglycolate bis(1,10-phenanthroline-κ2 N,N′)(thiodiglycolato-κ2 O,O′)manganese(II) tridecahydrate

2003 ◽  
Vol 59 (11) ◽  
pp. m429-m431 ◽  
Author(s):  
Jaromír Marek ◽  
Zdeněk Trávníček ◽  
Pavel Kopel
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Bidentate Ligand ◽  
Membered Ring ◽  
Water Molecules ◽  
Thiodiglycolic Acid ◽  
Network Of Hydrogen Bonds ◽  
Hydrogen Bonded

The title compound, [Mn(C12H8N2)2(H2O)2](C4H4O4S)·[Mn(C4H4O4S)(C12H8N2)2]·13H2O, contains one dianion of thiodiglycolic acid (tdga2−) and two independent manganese(II) moieties, viz. [Mn(phen)2(H2O)2]2+ and [Mn(tdga)(phen)2], where phen is 1,10-phenanthroline. The MnII atoms are octahedrally coordinated by four N atoms of two bidentate phen ligands [Mn—N = 2.240 (2)–2.3222 (19) Å] and either two water O atoms or two tdga carboxyl O atoms [Mn—O = 2.1214 (17)–2.1512 (17) Å]. The tdga ligand chelates as an O,O′-bidentate ligand, forming an eight-membered ring with one Mn atom. The free tdga2− dianion is hydrogen bonded to an [Mn(phen)2(H2O)2]2+ ion, with O...O distances of 2.606 (2) and 2.649 (2) Å. The crystal structure is further stabilized by an extensive network of hydrogen bonds involving 13 water molecules.

scholarly journals The Serological Cross-Detection of Bat-Borne Hantaviruses: A Valid Strategy or Taking Chances?

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1188
Author(s):  
Renata Carvalho de Oliveira ◽  
Jorlan Fernandes ◽  
Elba Regina de Sampaio Lemos ◽  
Fernando de Paiva Conte ◽  
Rodrigo Nunes Rodrigues-da-Silva
Keyword(s):  
Public Health ◽  
In Silico ◽  
Data Bank ◽  
Distinct Species ◽  
Geographic Range ◽  
Ab Initio Methods ◽  
Success Rates ◽  
B Cell Epitopes ◽  
Crystallographic Structures ◽  
A Minor

Bats are hosts of a range of viruses, and their great diversity and unique characteristics that distinguish them from all other mammals have been related to the maintenance, evolution, and dissemination of these pathogens. Recently, very divergent hantaviruses have been discovered in distinct species of bats worldwide, but their association with human disease remains unclear. Considering the low success rates of detecting hantavirus RNA in bat tissues and that to date no hantaviruses have been isolated from bat samples, immunodiagnostic tools could be very helpful to understand pathogenesis, epidemiology, and geographic range of bat-borne hantaviruses. In this sense, we aimed to identify in silico immunogenic B-cell epitopes present on bat-borne hantaviruses nucleoprotein (NP) and verify if they are conserved among them and other selected members of Mammantavirinae, using a combination of (the three most used) different prediction algorithms, ELLIPRO, Discotope 2.0, and PEPITO server. To support our data, we in silico modeled 3D structures of NPs from representative members of bat-borne hantaviruses, using comparative and ab initio methods due to the absence of crystallographic structures of studied proteins or similar models in the Protein Data Bank. Our analysis demonstrated the antigenic complexity of the bat-borne hantaviruses group, showing a low sequence conservation of epitopes among members of its own group and a minor conservation degree in comparison to Orthohantavirus, with a recognized importance to public health. Our data suggest that the use of recombinant rodent-borne hantavirus NPs to cross-detect antibodies against bat- or shrew-borne viruses could underestimate the real impact of this virus in nature.

scholarly journals Taming nitroformate through encapsulation with nitrogen-rich hydrogen-bonded organic frameworks

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jichuan Zhang ◽  
Yongan Feng ◽  
Richard J. Staples ◽  
Jiaheng Zhang ◽  
Jean’ne M. Shreeve
Keyword(s):  
Thermal Stability ◽  
Hydrogen Bonds ◽  
Self Assembly ◽  
Energetic Materials ◽  
Decomposition Temperature ◽  
High Oxygen Content ◽  
The Poor ◽  
Simple Preparation ◽  
First Time ◽  
Hydrogen Bonded

AbstractOwing to its simple preparation and high oxygen content, nitroformate [−C(NO2)3, NF] is an extremely attractive oxidant component for propellants and explosives. However, the poor thermostability of NF-based derivatives has been an unconquerable barrier for more than 150 years, thus hindering its application. In this study, the first example of a nitrogen-rich hydrogen-bonded organic framework (HOF-NF) is designed and constructed through self-assembly in energetic materials, in which NF anions are trapped in pores of the resulting framework via the dual force of ionic and hydrogen bonds from the strengthened framework. These factors lead to the decomposition temperature of the resulting HOF-NF moiety being 200 °C, which exceeds the challenge of thermal stability over 180 °C for the first time among NF-based compounds. A large number of NF-based compounds with high stabilities and excellent properties can be designed and synthesized on the basis of this work.

Relevance of hydrogen bonded associates on the transport properties and nanoscale dynamics of liquid and supercooled 2-propanol

2021 ◽  
Author(s):  
Yanqin Zhai ◽  
Peng Luo ◽  
Michihiro Nagao ◽  
Kenji Nakajima ◽  
Tatsuya Kikuchi ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Transport Properties ◽  
Structural Relaxation ◽  
Model System ◽  
Mesoscale Structures ◽  
Nanoscale Dynamics ◽  
Hydrogen Bonded

2-propanol was investigated, in both the liquid and supercooled states, as a model system to study how hydrogen bonds affect the structural relaxation and the dynamics of mesoscale structures, of...

scholarly journals Spectroscopic, X-ray Diffraction and Density Functional Theory Study of Intra- and Intermolecular Hydrogen Bonds in Ortho-(4-tolylsulfonamido)benzamides

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 926
Author(s):  
Malose J. Mphahlele ◽  
Eugene E. Onwu ◽  
Marole M. Maluleka
Keyword(s):  
Density Functional Theory ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Tetrahedral Geometry ◽  
Hindered Rotation ◽  
Hydrogen Bond Acceptor ◽  
Functional Theory ◽  
Vis Spectroscopy ◽  
Hydrogen Bonded

The conformations of the title compounds were determined in solution (NMR and UV-Vis spectroscopy) and in the solid state (FT-IR and XRD), complemented with density functional theory (DFT) in the gas phase. The nonequivalence of the amide protons of these compounds due to the hindered rotation of the C(O)–NH2 single bond resulted in two distinct resonances of different chemical shift values in the aromatic region of their 1H-NMR spectra. Intramolecular hydrogen bonding interactions between the carbonyl oxygen and the sulfonamide hydrogen atom were observed in the solution phase and solid state. XRD confirmed the ability of the amide moiety of this class of compounds to function as a hydrogen bond acceptor to form a six-membered hydrogen bonded ring and a donor simultaneously to form intermolecular hydrogen bonded complexes of the type N–H···O=S. The distorted tetrahedral geometry of the sulfur atom resulted in a deviation of the sulfonamide moiety from co-planarity of the anthranilamide scaffold, and this geometry enabled oxygen atoms to form hydrogen bonds in higher dimensions.

scholarly journals Cyclooctanaminium hydrogen succinate monohydrate

2012 ◽  
Vol 68 (4) ◽  
pp. o1204-o1204 ◽  
Author(s):  
Sanaz Khorasani ◽  
Manuel A. Fernandes
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Ammonium Cation ◽  
Water Molecules ◽  
Hydrated Salt ◽  
A Chain ◽  
Hydrogen Bonded

In the title hydrated salt, C8H18N+·C4H5O4−·H2O, the cyclooctyl ring of the cation is disordered over two positions in a 0.833 (3):0.167 (3) ratio. The structure contains various O—H.·O and N—H...O interactions, forming a hydrogen-bonded layer of molecules perpendicular to thecaxis. In each layer, the ammonium cation hydrogen bonds to two hydrogen succinate anions and one water molecule. Each hydrogen succinate anion hydrogen bonds to neighbouring anions, forming a chain of molecules along thebaxis. In addition, each hydrogen succinate anion hydrogen bonds to two water molecules and the ammonium cation.

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