hydrogen atoms
Recently Published Documents





Paulina Kalle ◽  
Sergei V. Tatarin ◽  
Marina A. Kiseleva ◽  
Alexander Yu. Zakharov ◽  
Daniil E. Smirnov ◽  

The title compounds, 2-(4-methylphenyl)-1H-perimidine hemihydrate (1, C18H14N2·0.5H2O) and 1-methyl-2-(4-methylphenyl)-1H-perimidine (2, C19H16N2), were prepared and characterized by 1H NMR and single-crystal X-ray diffraction. The organic molecule of the hemihydrate lies on a twofold rotation axis while the water molecule lies on the intersection of three twofold rotation axes (point group symmetry 222). As a consequence, the hydrogen atoms that are part of the N—H group and the water molecule as well as the CH3 group of the p-tolyl ring are disordered over two positions. In compound 1, the perimidine and the 2-aryl rings are slightly twisted while its N-methylated derivative 2 has a more distorted conformation because of the steric repulsion between the N-methyl group and the 2-aryl ring. In the crystal structures, molecules of perimidine 2 are held together only by C—H...π contacts while the parent perimidine 1 does not exhibit this type of interaction. Its crystal packing is established by intermolecular N—H...O hydrogen bonds with the solvent water molecules and additionally stabilized by π–π stacking.

2022 ◽  
Vol 8 (1) ◽  
pp. 8
Vladislav V. Shunaev ◽  
Olga E. Glukhova

Graphene nanomesh (GNM) is one of the most intensively studied materials today. Chemical activity of atoms near GNM’s nanoholes provides favorable adsorption of different atoms and molecules, besides that, GNM is a prospect material for growing carbon nanotubes (CNTs) on its surface. This study calculates the dependence of CNT’s growing parameters on the geometrical form of a nanohole. It was determined by the original methodic that the CNT’s growing from circle nanoholes was the most energetically favorable. Another attractive property of GNM is a tunable gap in its band structure that depends on GNM’s topology. It is found by quantum chemical methods that the passivation of dangling bonds near the hole of hydrogen atoms decreases the conductance of the structure by 2–3.5 times. Controlling the GNM’s conductance may be an important tool for its application in nanoelectronics.

2022 ◽  
Vol 13 (1) ◽  
Lukas Gajdos ◽  
Matthew P. Blakeley ◽  
Michael Haertlein ◽  
V. Trevor Forsyth ◽  
Juliette M. Devos ◽  

AbstractThe opportunistic pathogen Pseudomonas aeruginosa, a major cause of nosocomial infections, uses carbohydrate-binding proteins (lectins) as part of its binding to host cells. The fucose-binding lectin, LecB, displays a unique carbohydrate-binding site that incorporates two closely located calcium ions bridging between the ligand and protein, providing specificity and unusually high affinity. Here, we investigate the mechanisms involved in binding based on neutron crystallography studies of a fully deuterated LecB/fucose/calcium complex. The neutron structure, which includes the positions of all the hydrogen atoms, reveals that the high affinity of binding may be related to the occurrence of a low-barrier hydrogen bond induced by the proximity of the two calcium ions, the presence of coordination rings between the sugar, calcium and LecB, and the dynamic behaviour of bridging water molecules at room temperature. These key structural details may assist in the design of anti-adhesive compounds to combat multi-resistance bacterial infections.

2022 ◽  
Sergei Gavryushov ◽  
Nikolay Kuzmich ◽  
Konstantin Polyakov

Laccases are enzymes catalyzing oxidation of a wide range of organic and inorganic substrates accompanied by molecular oxygen reduction to water. Previously studies of oxygen reduction by laccases have recently been reported. They were based on single-crystal serial X-ray crystallography with increasing absorption doses at subatomic resolution, As a result, coordinates of all non-hydrogen atoms of the active site have been determined with high precision for both oxidized and reduced states of the enzyme. Those data can be used to clarify the mechanism of molecular oxygen reduction by laccases. However, the X-ray data lack information about protonation states of the oxygen ligands involved. Applying quantum mechanical calculations, in the present work protonation of oxygen ligands in the active site of laccase was determined for both reduced and oxidized states of the enzyme (the stable states observed in experiments at reduction of molecular oxygen in laccase). The high precision of X-ray-determined atom coordinates allowed us to simplify preliminary calculations of molecular mechanics for models used in the quantum mechanical calculations.

Atoms ◽  
2022 ◽  
Vol 10 (1) ◽  
pp. 6
Chandra M. Adhikari ◽  
Ulrich D. Jentschura

Pressure shifts inside an atomic beam are among the more theoretically challenging effects in high-precision measurements of atomic transitions. A crucial element in their theoretical analysis is the understanding of long-range interatomic interactions inside the beam. For excited reference states, the presence of quasi-degenerate states leads to additional challenges, due to the necessity to diagonalize large matrices in the quasi-degenerate hyperfine manifolds. Here, we focus on the interactions of hydrogen atoms in reference states composed of an excited nD state (atom A), and in the metastable 2S state (atom B). We devote special attention to the cases n=3 and n=8. For n=3, the main effect is generated by quasi-degenerate virtual P states from both atoms A and B and leads to experimentally relevant second-order long-range (van-der-Waals) interactions proportional to the sixth inverse power of the interatomic distance. For n=8, in addition to virtual states with two states of P symmetry, one needs to take into account combined virtual P and F states from atoms A and B. The numerical value of the so-called C6 coefficients multiplying the interaction energy was found to grow with the principal quantum number of the reference D state; it was found to be of the order of 1011 in atomic units. The result allows for the calculation of the pressure shift inside atomic beams while driving transitions to nD states.

2022 ◽  
Vol 2022 (1) ◽  
Wajahat Ali ◽  
Ali Turab ◽  
Juan J. Nieto

AbstractA branch of mathematical science known as chemical graph theory investigates the implications of connectedness in chemical networks. A few researchers have looked at the solutions of fractional differential equations using the concept of star graphs. Their decision to use star graphs was based on the assumption that their method requires a common point linked to other nodes but not to each other. Our goal is to broaden the scope of the method by defining the idea of a cyclohexane graph, which is a cycloalkane with the molecular formula $C_{6}H_{12}$ C 6 H 12 and CAS number 110-82-7. It consists of a ring of six carbon atoms, each bonded with two hydrogen atoms above and below the plane with multiple junction nodes. This article examines the existence of fractional boundary value problem’ solutions on such graphs in the sense of the Caputo fractional derivative by using the well-known fixed point theorems. In addition, an example is given to support our key findings.

Molecules ◽  
2022 ◽  
Vol 27 (1) ◽  
pp. 278
Martin Jakubec ◽  
Ivana Císařová ◽  
Jindřich Karban ◽  
Jan Sýkora

The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, including two structures of C4-deoxygenated, four C4-deoxyfluorinated and four parent epimino pyranoses. It was found that the substitution of the original hydroxy group by hydrogen or fluorine leads to a weakening of the intermolecular interaction by approximately 4 kcal/mol. The strength of the intermolecular interactions was found to be in the following descending order: hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine and weak electrostatic interactions. The intermolecular interactions that involved fluorine atom were rather weak; however, they were often supported by other weak interactions. The fluorine atom was not able to substitute the role of the hydroxy group in molecular packing and the fluorine atoms interacted only weakly with the hydrogen atoms located at electropositive regions of the carbohydrate molecules. However, the fluorine interaction was not restricted to a single molecule but was spread over at least three other molecules. This feature is a base for similar molecule arrangements in the structures of related compounds, as we found for the C4-Fax and C4-Feq epimines presented here.

10.5006/3901 ◽  
2022 ◽  
Taishi Fujishiro ◽  
Takuya Hara ◽  
Kyono Yasuda ◽  
Daisuke Mizuno ◽  
Nobuyuki Ishikawa ◽  

The severity of sour environments has been determined in accordance with the European Federation of Corrosion 16 and NACE MR0175/ISO 15156-2:2015 standards for carbon and low-alloy steels, based on the experimental results of sulfide stress cracking (SSC). However, the severity map obtained from SSC test results cannot be applicable to the hydrogen-induced cracking (HIC) susceptibility. In this study, the hydrogen permeability and crack area ratio (CAR) of HIC under various pH and H2S partial pressures (pH2S) were measured to establish the link between the sour environmental severity and HIC susceptibility using grades X65 to X80 linepipe steels. In addition, the hydrogen concentration at the location of the HIC was calculated by the finite element analysis. The results showed that the sour environmental severity map obtained from hydrogen permeation tests changes with time, because the hydrogen permeability reached maximum values in the early stage and steady-state values in the later stage. Then, the HIC susceptibility did not correspond to the maximum permeability, but to the steady-state hydrogen permeability. In addition, the hydrogen content at the location of the HIC did not correspond to the maximum hydrogen permeability but corresponded to the steady-state hydrogen permeability, because HIC occurred in the center segregation part and the hydrogen atoms required a certain time to diffuse from the metal surface to the mid-thickness. These results suggest that the HIC susceptibility is dominated by the severity map obtained from the steady-state hydrogen permeability.

2022 ◽  
Vol 64 (1) ◽  
pp. 33
А.А. Валеева ◽  
А.И. Гусев

Possible models of the arrangement of hydrogen atoms at the sites of the cubic lattice of titanium oxyhydride TiOyHp with vacancies in the metallic and nonmetallic sublattices are considered. It was found that titanium oxyhydride retains the B1 type crystal lattice of the initial cubic titanium monoxide TiOy and contains structural vacancies in the metal and oxygen sublattices. Comparison of the found analytical expressions for the intensity of diffraction reflections with experimental X-ray and neutron diffraction data showed that interstitial H atoms in oxyhydrides occupy vacant octahedral positions 4(b) of the oxygen sublattice. No displacement of H atoms in tetrahedral positions 8(c) is observed. A disorder-order phase transition channel associated with the formation of an ordered monoclinic titanium oxyhydride of the Ti5O5 type was found. The distribution functions of Ti, O, and H atoms in the partially ordered monoclinic oxyhydride Ti5.33O5.12H0.74 (Ti0.89O0.85H0.12) with a Ti5O5-type structure are calculated for the first time, and the concentrations of these atoms at the positions of its lattice were found.

Sign in / Sign up

Export Citation Format

Share Document