Movement Of Hydrogen Atoms Research Articles

Unraveling the friction response from selective hydrogenation of textured amorphous carbon surface

Ultra-low friction of amorphous carbon (a-C) film can be achieved by binding to hydrogen atoms or texturing conformations. However, it remains unclear how selective surface hydrogenation affects the friction behavior of textured a-C film. In particular, the corresponding transformation of interfacial structure and the movement of hydrogen atoms have not yet been reported because of the limitation of in-situ experimental characterization. Here, textured a-C films with selective hydrogenated surfaces were prepared, and the corresponding friction response and the transformation of interfacial structure were investigated systematically using reactive molecular dynamics simulation. Results showed that introducing hydrogen atoms to the selective bump sites of textured a-C surfaces significantly reduced the friction coefficient; however, its efficiency was closely sensitive to the hydrogen content, which was related to the interfacial passivation and the repulsion effect induced by H atoms. Most importantly, the separation of –CH clusters from textured a-C surface during sliding process and their re-bonding with the naked mating a-C surface played a key role in further enhancing the repulsive effect between contacted a-C surfaces, thereby improving the anti-friction behavior, which has not been mentioned in previous studies. These results suggest a new approach to develop the high-efficient a-C friction system for applications.

Barbituric Acid Tautomers: DFT Computations of Keto-Enol Conversions, Frontier Molecular Orbitals and Quadrupole Coupling Constants

In this work, density functional theory (DFT) computations were performed to investigate tautomeric formation processes of barbituric acid (BA). Ten tautomers were totally investigated for the purpose based on the movement of hydrogen atoms among nitrogen and oxygen atoms providing one pure keto form (BA1) and nine other keto-enol forms. The structures were optimized, and BA1 was found to be the most stable one, and both BA3 and BA7 were found to be the most unstable ones. The point was that the ring structure was broken for both BA3 and BA7, but the structure's stability was still approved. Indeed, such serious tautomeric conversion with breaking the structure warns for using such BA bio-organic molecules for further applications, especially in pharmacy-related ones, in which side effects or byproduct synthesis might appear. Further analyses of frontier molecular orbitals features indicated the effects of such tautomerism processes on all model systems, in which more details were obtained by atomic-scale quadrupole coupling constant (Qcc). All obtained results approved significant changes of tautomers regarding molecular and atomic scale features with more or less significant effects regarding the original BA1 reference model.

On the Case of the Misplaced Hydrogens.

Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.

Study confirms ‘hydrogen spillover’

In some industrial processes, flowing hydrogen molecules over solid surfaces containing catalytic metals reduces organic molecules by hydrogenation. On the basis of a mechanism proposed in the 1960s, chemists think such reactions may proceed through the movement of hydrogen atoms in a process called “hydrogen spillover.” But researchers haven’t been able to confirm this mechanism because models of the reaction are difficult to create and analyze. With a new, realistic model system, researchers have shown definitively that hydrogen spillover occurs on two key types of catalytic surfaces, called reducible and nonreducible supports, but to a drastically different extent. The information could help chemists design better catalysts as well as improve hydrogenation processes and hydrogen storage for fuel cells. The approach could also help scientists determine whether hydrogen spillover occurs more generally in important research and industrial reactions. In hydrogen spillover, catalytic platinum nanoparticles ...

Effect of Methylation on the Properties of the H-Bridges in DNA. A Systematic Theoretical Study on the Couples of Base Pairs.

The effects of the addition of one (hemimethylation) or two (methylation) methyl groups on the 10 different couples of base pairs of DNA (three dimers of A-T, three of C-G, and four mixed A-T and C-G complexes) has been studied. Changes in the main static properties (energy, structure, atomic charges) and dynamics (movement of hydrogen atoms from one base to the other) have been considered and analyzed. The results of this study support the idea that the quantitative effects of the methylation of these complexes depend on the specific system under consideration and on the H-bridge studied. In any case, some general behavior can be highlighted. In particular, the relationship between the transfer of hydrogen atoms between the bases (with the possible generation of mutation points) and the methylation can be schematized in the two most important methylated bases: adenine and cytosine. A different behavior has been found in these two cases, and we suggest that this could be related to the different amounts of these methylated systems in prokaryotes and eukaryotes. In particular, this different behavior could explain why adenine methylation is present mainly in the bacteria and cytosine methylation is present in more complex organisms.

Proton nuclear magnetic resonance studies of hydrogen diffusion and electron tunneling in Ni-Nb-Zr-H glassy alloys

Using the Fourier transform of the echo envelope, the proton line shapes, spin-lattice relaxation time, and spin-spin relaxation time have been measured in a (Ni0.36Nb0.24Zr0.40)90H10 glassy alloy at 1.83 T (∼78 MHz) and at temperatures between 1.8 and 300 K. First, the spectral line width decreases abruptly between 1.8 and 2.1 K. Next, it remains almost constant at 13 kHz up to ∼150 K. Finally, the line width decreases as the temperature increases from ∼150 to 300 K. The initial decrease in the spectral line width is ascribed to the distribution of the external field, which is caused by the penetration of vortices in the superconducting state. The subsequent leveling off in the spectral line width is ascribed to the dipole-dipole interaction between protons when hydrogen atoms are trapped into vacancies among the Zr-centered icosahedral Zr5Ni5Nb3 clusters. The final decrease in the spectral line width is ascribed to the motional narrowing of the width that is caused by the movement of hydrogen atoms. The temperature dependences of the spin-lattice and spin-spin relaxation time showed that at temperature above 150 K and the activation energy of 8.7 kJ/mol allowed the hydrogen atoms to migrate among the clusters. The distance between the hydrogen atoms is estimated to be 2.75 Å. Hydrogen occupancies among clusters in the (Ni0.36Nb0.24Zr0.40)90H10 glassy alloy play an important role in the diffusion behavior and in the electronic properties of this alloy.

How Fast a Hydrogen Atom can Move Before Its Proton and Electron Fly Apart?

In this paper we discussed the behavior of a hydrogen atom in moving and found there is a speed threshold for hydrogen atom. As long as the speed of hydrogen reaches or beyond its speed threshold, the proton and electron in hydrogen atom will fly apart. We also discussed the effect of the movement of hydrogen atom on its absorption spectrum which is important in spectrum analysis.

The Lighter Side of a Sweet Reaction

The unique advantage of neutrons as biological probes is the ability to visualize hydrogen atoms in macromolecules. In this issue, Kovalevsky et al. (2010) solved an ensemble of xylose isomerase structures by neutron crystallography, and the determination of hydrogen atom rearrangements during the catalytic cycle provides insight into the enzyme's mechanism.

The Combined Inelastic Neutron Scattering (INS) and Solid-State DFT Study of Hydrogen-Atoms Dynamics in Kaolinite-dimethylsulfoxide Intercalate

AbstractVibrational spectra of two kaolinite-dimethylsulfoxide intercalates, obtained using inelastic neutron scattering (INS), were analyzed with a view to understanding the dynamics of the hydrogen atoms in the structure. The main focus was on the spectral region 0–1700 cm−1, which is difficult to analyze using optical spectroscopy. The experimental vibrational spectra of kaolinite:dimethylsulfoxide and kaolinite:d6-dimethylsulfoxide collected using two different spectrometers were interpreted by means of the solid-state DFT calculations. Calculated spectra were obtained by both normal-mode analysis and molecular dynamics going beyond the harmonic approximation. The Al-O-H bending modes were found to be spread over the large interval 100−1200 cm−1, with the dominant contributions located between 800 and 1200 cm−1. The shape of the individual hydrogen spectrum depends on whether or not the respective hydrogen atom is involved in an O-H⋯O hydrogen bond and on its strength. The modes corresponding to the in-plane movements of the inner-surface hydrogen atoms are well defined and always appear at the top of the intervals of energy transfer. In contrast, the modes generated by the out-of-plane movements of the hydrogen atoms are spread over large energy intervals extending down to the region of external (lattice) modes. The C-H modes are concentrated mainly in the three regions 1200–1450 cm−1, 800–1100 cm−1, and 0–400 cm−1. While the first two regions are typical of the various deformational modes of methyl groups, the low-energy region is populated by the modes corresponding to the movements of the whole dimethylsulfoxide molecule.

Modes of decomposition of n -pentane - II. Kinetic considerations

New or reworked, and in some cases corrected, experimental data confirm that in the decomposition of n -pentane there appear to be, in addition to the radical chain process, two modes of unimolecular reaction. One conforms approximately to the requirements of the classical theory with localization of activation energy in a critical bond (tentatively assumed to be a C—C bond), the non-exponential factor being the same order as a molecular vibration frequency. The other seems to involve a whole series of alternative transition states corresponding to different distributions of a given total energy among degrees of freedom thought to be probably movements of hydrogen atoms. Various possible implications about the gain, loss and redistribution of energy in the molecule are briefly considered.