We present Monte Carlo simulations on Eley-Rideal abstraction reactions of atomic hydrogen chemisorbed on graphite. The results are obtained via a hybrid approach where energy barriers derived from density functional theory calculations are used as input to Monte Carlo simulations. By comparing with experimental data, we discriminate between contributions from different Eley-Rideal mechanisms. A combination of two different mechanisms yields good quantitative and qualitative agreement between the experimentally derived and the simulated Eley-Rideal abstraction cross sections and surface configurations. These two mechanisms include a direct Eley-Rideal reaction with fast diffusing H atoms and a dimer mediated Eley-Rideal mechanism with increased cross section at low coverage. Such a dimer mediated Eley-Rideal mechanism has not previously been proposed and serves as an alternative explanation to the steering behavior often given as the cause of the coverage dependence observed in Eley-Rideal reaction cross sections.
The hydrogenation and deuteration of graphite with potassium intercalation compounds (GICs) as starting materials was investigated. Characterization of the reactions products (hydrogenated and deuterated graphene) was carried out by thermogravimetric analysis coupled with mass spectrometry (TG-MS) and Raman spectroscopy including statistical Raman spectroscopy (SRS) and -microscopy (SRM). The results reveal that the choice of the hydrogen/deuterium source, the nature of the graphite (used as starting material), the potassium concentration in the intercalation compound as well as the choice of …
We studied, by scanning tunneling microscopy, the morphology of nanopits of monolayer depth created at graphite surfaces by hydrogen plasma etching under various conditions such as H$_2$ pressure, temperature, etching time, and RF power of the plasma generation. In addition to the known pressure-induced transition of the nanopit morphology, we found a sharp temperature-induced transition from many small rather round nanopits of ~150 nm size to few large hexagonal ones of 300-600 nm within a narrow temperature range. The remote and direct plasma modes switching mechanism, which was proposed to …
This account presents author's opinion on the mechanism of the H-abstraction from methane by the [FeO](2+) group. In the course of reaction with hydrogen, the Fe-O bond in the ferryl configuration becomes elongated causing transfer of the spin-up electron from one of doubly occupied bonding orbitals leaving behind single spin-down electron on oxygen. This oxygen in so-formed oxyl configuration of the [FeO](2+) moiety then easily accept the spin-up hydrogen atom from methane in the same way as the radical-localized oxygen does. This mechanism is compared with the scheme in which the hydrogen is…
The interaction energy between a water molecule and graphitic structured clusters terminated by hydrogen atoms is analyzed by ab initio methods and decomposed into electrostatic, induction, Pauli repulsion, and correlation energy contributions. Contributions to the energy which are due solely to the perimeter of the clusters are identified. These can be isolated and discarded which greatly simplifies the problem of extrapolation to the large cluster limit. The remaining terms are intrinsic to the interaction of a water molecule with real graphitic layers and an explicit analytical form is give…
H-abstraction reactions occurring on electron ionization mass spectrometry (EI-MS) are a long-standing and crucial topic in MS research. Yet some critical relevant mechanisms are controversial and ambiguous, and information about the EI-induced H-abstraction reactions of halogenated organic compounds (HOCs) is completely in the dark. This study provides a systematic investigation of H-abstraction reactions of HOCs taking place on EI source using 13C6-hexachlorobenzene (13C6-HCB) and 13C6-hexabromobenzene (13C6-HBB) as exemplary compounds by gas chromatography high resolution mass spectrometry …
The recently proposed natural orbital functional second-order Møller-Plesset (NOF-MP2) method is capableof achieving both dynamic and static correlation even for those systems with significant multiconfigurational character. We test its reliability to describe the electron correlation in radical formation reactions, namely, in the homolytic X-H bond cleavage of LiH, BH, CH4, NH3, H2O and HF molecules. Our results are compared with CASSCF and CASPT2 wavefunction calculations and the experimental data. For a dataset of 20 organic molecules, the thermodynamics of C-H homolytic bond cleavage, in w…
The hydrogen abstraction reaction between H and H$_2$S, yielding HS and H$_2$ as products, has been studied within the framework of interstellar surface chemistry. High-temperature rate constants up to 2000 K are calculated in the gas phase and are in agreement with previously reported values. Subsequently low-temperature rate constants down to 55 K are presented for the first time that are of interest to astrochemistry, i.e., covering both bimolecular and unimolecular reaction mechanisms. For this, a so-called implicit surface model is used. Strictly speaking, this is a structural gas-phase m…
Hydrogen addition and abstraction reactions play an important role as surface reactions in the buildup of complex organic molecules in the dense interstellar medium. Addition reactions allow unsaturated bonds to be fully hydrogenated, while abstraction reactions recreate radicals that may undergo radical-radical recombination reactions. Previous experimental work has indicated that double and triple C--C bonds are easily hydrogenated, but aldehyde -C=O bonds are not. Here, we investigate a total of 29 reactions of the hydrogen atom with propynal, propargyl alcohol, propenal, allyl alcohol, and…
Reactivity of the [FeO]2+ group in the abstraction of hydrogen from methane is determined by metastable oxyl state FeIII-O* causing the negative spin polarization of the methyl moiety as was shown by quantum-chemical means with the use of model iron hydroxide species FeO(OH)2, Fe2O(OH)5, and Fe4O5(OH)3 as an example.
Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to reveal the effect of hydroxyl radicals produced by the secondary effect of radiation. Previous studies address the problem with truncated DNA bases as ab-initio quantum simulation required to study such electronic spin dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid Quantum-Mechanical-Molecular-Mechanical simulation to study the interaction of OH radicals with guanine-deoxyribose-phosphate DNA molecular unit in the pre…
Radical recombination has been proposed to lead to the formation of complex organic molecules (COMs) in CO-rich ices in the early stages of star formation. These COMs can then undergo hydrogen addition and abstraction reactions leading to a higher or lower degree of saturation. Here, we have studied 14 hydrogen transfer reactions for the molecules glyoxal, glycoaldehyde, ethylene glycol, and methylformate and an additional three reactions where \ce{CH_nO} fragments are involved. Over-the-barrier reactions are possible only if tunneling is invoked in the description at low temperature. Therefor…
The results of a detailed kinetic study of the main plasma chemical processes in non-equilibrium ethanol/argon plasma are presented. It is shown that at the beginning of the discharge the molecular hydrogen is mainly generated in the reaction of ethanol H-abstraction. Later hydrogen is formed from active H, CH2OH and CH3CHOH and formaldehyde. Comparison with experimental data has shown that the used kinetic mechanism predicts well the concentrations of main species at the reactor outlet.
We present a combined experimental and theoretical study focussing on the quantum tunneling of atoms in the reaction between CH4 and OH. The importance of this reaction pathway is derived by investigating isotope substituted analogs. Quantitative reaction rates needed for astrochemical models at low temperature are currently unavailable both in the solid state and in the gas phase. Here, we study tunneling effects upon hydrogen abstraction in CH4 + OH by focusing on two reactions: CH4 + OD -> CH3 + HDO and CD4 + OH -> CD3 + HDO. The experimental study shows that the solid-state reaction rate R…
We present a first temperature dependence and kinetic isotope effect study on the reaction of C_2(a^3Pi_u) with methanol. The bimolecular rate constants for a series of methanol isotopomers have been measured as a function of temperature between 293 and 673 K. The observed positive temperature dependences as well as deuterium kinetic isotope effects permit determination of the reaction mechanism as a site-specific hydrogen abstraction from the methyl site rather than from the hydroxyl site.
In the coldest (10--20 K) regions of the interstellar medium, the icy surfaces of interstellar grains serve as solid-state supports for chemical reactions. Among their plausible roles, that of third body is advocated, in which the reaction energies of surface reactions dissipate throughout the grain, stabilizing the product. This energy dissipation process is poorly understood at the atomic scale, although it can have a high impact on Astrochemistry. Here, we study, by means of quantum mechanical simulations, the formation of NH3 via successive H-additions to atomic N on water ice surfaces, pa…
The lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes that can enhance polysaccharide depolymerization through an oxidative mechanism and hence boost generation of biofuel from e.g. cellulose. By employing density functional theory in a combination of quantum mechanics and molecular mechanics (QM/MM), we report a complete description of the molecular mechanism of LPMOs. The QM/MM scheme allows us to describe all reaction steps with a detailed protein environment and we show that this is necessary. Several active species capable of abstracting a hydrogen from the substrate h…
Here we describe a computational study undertaken in an effort to elucidate the reaction mechanisms behind the experimentally observed oxidations and hydrations catalyzed by graphene oxide (GO). Using the oxidation of benzyl alcohol to benzaldehyde as a model reaction, density functional theory (DFT) calculations revealed that this reactivity stemmed from the transfer of hydrogen atoms from the organic molecule to the GO surface. In particular, neighbouring epoxide groups decorating GO's basal plane were ring-opened, resulting in the formation of diols, followed by dehydration. Consistent with…
The exact and phaseless variants of Auxiliary-Field Quantum Monte Carlo (AFQMC) have been shown to be capable of producing accurate ground-state energies for a wide variety of systems including those which exhibit substantial electron correlation effects. The computational cost of performing these calculations has to date been relatively high, impeding many important applications of these approaches. Here we present a correlated sampling methodology for AFQMC which relies on error cancellation to dramatically accelerate the calculation of energy differences of relevance to chemical transformat…
