Physisorption-induced C-H bond elongation in methane

Mapping Hydrogen Positions along the Proton Transfer Pathway in an Organic Crystal by Computational X-ray Spectra

Understanding proton transfer (PT) dynamics in condensed phases is crucial in chemistry. We computed a 2D map of N 1s X-ray photoelectron/absorption spectroscopy (XPS/XAS) for an organic donor-acceptor salt crystal against two varying N-H distances to track proton motions. Our results provide a continuous spectroscopic mapping of O-H···N↔O-··· H+-N processes via hydrogen bonds at both nitrogens, demonstrating the sensitivity of N 1s transient XPS/XAS to hydrogen positions and PT. By reducing the O-H length at N1 by only 0.2 Å, we achieved excellent theory-experiment agreement in both XPS and XAS. Our study highlights the challenge in refining proton positions in experimental crystal structures by periodic geometry optimizations and proposes an alternative scaled snapshot protocol as a more effective approach. This work provides valuable insights into X-ray spectra for correlated PT dynamics in complex crystals, benefiting future experimental studies.

Simulations of x-ray absorption spectra for CO desorbing from Ru(0001) with transition-potential and time-dependent density functional theory approaches

The desorption of a carbon monoxide molecule from a Ru(0001) surface was studied by means of X-ray Absorption Spectra (XAS) computed with Transition Potential (TP-DFT) and Time Dependent (TD-DFT) DFT methods. By unraveling the evolution of the CO electronic structure upon desorption, we observed that at 2.3 Å from the surface, the CO molecule has already predominantly gas-phase character. While C 1s XAS is quite insensitive to changes in the C-O bond length, the O 1s excitation is very sensitive with the π* coming down in energy upon CO bond stretching, which competes with the increase in orbital energy due to the repulsive interaction with the metallic surface. We show in a systematic way that the TP-DFT method can describe the XAS rather well at the endpoints (chemisorbed and gas phase) but is affected by artificial charge transfer and/or incorrect spin treatment in the transition region in cases like CO, where there are low-lying π* orbitals and large exchange interactions between the core 1s and valence-acceptor π* orbitals. As an alternative, we demonstrate by comparing with experimental data that a linear response approach using TD-DFT employing common exchange-correlation functionals and finite-size clusters can yield a good description of the spectral evolution of the 1s → π* transition with correct spin and gas-to-chemisorbed chemical shifts in good agreement with experiment.

Methane storage in nanoporous material at supercritical temperature over a wide range of pressures

The methane storage behavior in nanoporous material is significantly different from that of a bulk phase, and has a fundamental role in methane extraction from shale and its storage for vehicular applications. Here we show that the behavior and mechanisms of the methane storage are mainly dominated by the ratio of the interaction between methane molecules and nanopores walls to the methane intermolecular interaction, and a geometric constraint. By linking the macroscopic properties of the methane storage to the microscopic properties of a system of methane molecules-nanopores walls, we develop an equation of state for methane at supercritical temperature over a wide range of pressures. Molecular dynamic simulation data demonstrates that this equation is able to relate very well the methane storage behavior with each of the key physical parameters, including a pore size and shape and wall chemistry and roughness. Moreover, this equation only requires one fitted parameter, and is simple, reliable and powerful in application.

X-ray absorption from large molecules at metal surfaces: theoretical and experimental results for Co-OEP on Ni(100)

Metal octaethylporphyrins (M-OEP), M-N(4)C(20)H(4)(C(2)H(5))(8), adsorbed at a metallic substrate are promising candidates to provide spin dependent electric transport. Despite these systems having been studied extensively by experiment, details of the adsorbate geometry and surface binding are still unclear. We have carried out density functional theory calculations for cobalt octaethyl porphyrin (Co-OEP) adsorbate at clean and oxygen-covered Ni(100) surfaces as well as for the free Co-OEP molecule where equilibrium structures were obtained by corresponding energy optimizations. These geometries were then used in calculations of Co-OEP carbon and nitrogen 1s core excitations yielding theoretical excitation spectra to be compared with corresponding K-edge x-ray absorption fine structure (NEXAFS) measurements. The experimental NEXAFS spectra near the carbon K-edge of Co-OEP bulk material show large intensity close to the ionization threshold and a triple-peak structure at lower energies, which can be reproduced by the calculations on free Co-OEP. The experimental nitrogen K-edge spectra of adsorbed Co-OEP layers exhibit always a double-peak structure below ionization threshold, independent of the layer thickness. The peaks are shifted slightly and their separation varies with adsorbate-substrate distance. This can be explained by hybridization of N 2p with corresponding 3d contributions of the Ni substrate in the excited final state orbitals as a result of adsorbate-substrate binding via N-Ni bond formation.

Two-dimensional superstructures and softened C-H stretching vibrations of cyclohexane on Rh(111): effects of preadsorbed hydrogen

Adsorption structures and interaction of cyclohexane molecules on the clean and hydrogen-preadsorbed Rh(111) surfaces were investigated using scanning tunneling microscopy, spot-profile-analysis low-energy electron diffraction, temperature-programmed desorption, and infrared reflection absorption spectroscopy (IRAS). Various ordered structures of adsorbed cyclohexane were observed as a function of hydrogen and cyclohexane coverages. When the fractional coverage (θ(H)) of preadsorbed hydrogen was below 0.8, four different commensurate or higher-order commensurate superstructures were found as a function of θ(H); whereas more densely packed incommensurate overlayers became dominant at higher θ(H). IRAS measurements showed sharp softened C-H vibrational peaks at 20 K, which originate from the electronic interaction between adsorbed cyclohexane and the Rh surface. The multiple softened C-H stretching peaks in each phase are due to the variation in the adsorption distance from the substrate. At high hydrogen coverages they became attenuated in intensity and eventually diminished at θ(H) = 1. The gradual disappearance of the soft mode correlates well with the structural phase transition from commensurate structures to incommensurate structures with increasing hydrogen coverage. The superstructure of adsorbed cyclohexane is controlled by the delicate balance between adsorbate-adsorbate and adsorbate-substrate interactions which are affected by preadsorbed hydrogen.

On the mechanism of anion desorption from DNA induced by low energy electrons

Our knowledge of the mechanisms of radiation damage to DNA induced by secondary electrons is still very limited, mainly due to the large sizes of the system involved and the complexity of the interactions. To reduce the problem to its simplest form, we investigated specific electron interactions with one of the most simple model system of DNA, an oligonucleotide tetrameter compound of the four bases. We report anion desorption yields from a thin solid film of the oligonucleotide GCAT induced by the impact of 3-15 eV electrons. All observed anions (H-, O-, OH-, CN-, and OCN-) are produced by dissociative electron attachment to the molecule, which results in desorption peaks between 6 and 12 eV. Above 14 eV nonresonant dipolar dissociation dominates the desorption yields. By comparing the shapes and relative intensities of the anion yield functions from GCAT physisorbed on a tantalum substrate with those obtained from isolated DNA basic subunits (i.e., bases, deoxyribose, and phosphate groups) from either the gas phase or condensed phase experiments, it is possible to obtain more details on the mechanisms involved in low energy electron damage to DNA, particularly on those producing single strand breaks.