A quantum mechanical approach to the oxidation mechanism of graphene oxide (GO).

Elucidation of the reaction mechanism concerning the oxidation above the face and at the edge of a large, oxidized graphene (GO) cluster, namely CHO, by molecular oxygen in the first excited state (Δ) was achieved with quantum mechanical calculations using the ONIOM two-layer method. Oxidation on the face of the aforementioned cluster leads to the formation of an ozone molecule, whereas oxygen molecule attack at the edge of the oxidized graphene surface either launches an ozonide -a five-membered ring species- formation during its outward approach or an 1,3-dioxetane -a four-membered ring species- production along its inward invasion. A detailed examination of the proposed pathways suggests that the ozonide formation should overcome almost one and a half times an adiabatic energy barrier with respect to the ozone production and is strongly exergonic by up to -50.

Switching of Protonation Sites in Hydrated Nicotine via a Grotthuss Mechanism.

The switching of the protonation sites in hydrated nicotine, probed by experimental infrared (IR) spectroscopy and theoretical calculations, is facilitated via a Grotthuss instead of a bimolecular proton transfer (vehicle) mechanism at the experimental temperature ( = 130 K) as unambiguously confirmed by experiments with deuterated water. In contrast, the bimolecular vehicle mechanism is preferred at higher temperatures ( = 300 K) as determined by theory. The Grotthuss mechanism for the concerted proton transfer results in the production of nicotine's bioactive and addictive pyrrolidine-protonated (Pyrro-H) protomer with just 5 water molecules.

Statistical Inference of Rate Constants in Chemical and Biochemical Reaction Networks Using an "Inverse" Event-Driven Kinetic Monte Carlo Method.

The use of rate models for networks of stochastic reactions is frequently used to comprehend the macroscopically observed dynamic properties of finite size reactive systems as well as their relationship to the underlying molecular events. Τhis particular approach usually stumbles on parameter derivation associated with stochastic kinetics, a quite demanding procedure. The present study incorporates a novel algorithm, which infers kinetic parameters from the system's time evolution, manifested as changes in molecular species populations.

OH Radical and Chlorine Atom Kinetics of Substituted Aromatic Compounds: 4-chlorobenzotrifluoride (-ClCHCF).

The mechanisms for the OH radical and Cl atom gas-phase reaction kinetics of substituted aromatic compounds remain a topic of atmospheric and combustion chemistry research. 4-Chlorobenzotrifluoride (-chlorobenzotrifluoride, -ClCHCF, PCBTF) is a commonly used substituted aromatic volatile organic compound (VOC) in solvent-based coatings. As such, PCBTF is classified as a volatile chemical product (VCP) whose release into the atmosphere potentially impacts air quality.

Unscrambling micro-solvation of -COOH and -NH groups in neat dimethyl sulfoxide: insights from H-NMR spectroscopy and computational studies.

Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO viaH NMR studies along with extensive theoretical approaches, i.

Probing micro-solvation in "numbers": the case of neutral dipeptides in water.

How many solvent molecules and in what way do they interact directly with biomolecules? This is one of the most challenging questions regarding a deep understanding of biomolecular functionalism and solvation. We herein present a novel NMR spectroscopic study, achieving for the first time the quantification of the directly interacting water molecules with several neutral dipeptides. Our proposed method is supported by both molecular dynamics simulations and density functional theory calculations, advanced analysis of which allowed the identification of the direct interactions between solute-solvent molecules in the zwitterionic L-alanyl-L-alanine dipeptide-water system.

A two-dimensional magnetic hybrid material based on intercalation of a cationic Prussian blue analog in montmorillonite nanoclay.

A highly ordered two-dimensional hybrid magnetic nanocomposite has been prepared by synthesizing and intercalating a new cationic aluminum-hydroxy ferric ferrocyanide compound into a cation-adsorbing nanoclay (montmorillonite). Chemical and structural properties were investigated by X-ray diffraction, transmission electron microscopy, thermogravimetric and differential thermal analyses, Fourier transform infrared, X-ray photoemission, and Mössbauer spectroscopies. Elemental analysis was based on proton-induced gamma ray emission and X-ray fluorescence spectroscopy data, N/C elemental ratios, and cation-exchange capacity measurements.

An experimental and theoretical study of the S(1)<--S0 transition of p-ethynyltoluene.

The one photon and the two photon S(1)<--S(0) spectra of jet-cooled p-ethynyltoluene have been measured for the first time, and a detailed vibronic analysis for both spectra has been attained. Mass analyzed resonance enhanced multiphoton ionization spectroscopy is the employed technique. In the one photon spectrum, the allowed component (origin and Franck-Condon bands) is much weaker than the forbidden component, and the same mechanisms as in the one photon spectrum of phenylacetylene are observed.

A DFT study of the nitric oxide and tyrosyl radical interaction: a proposed radical mechanism.

The present study employs a complete theoretical investigation, at the B3LYP/cc-pVTZ level of theory, of the interactions between the tyrosyl radical and nitric oxide, exploring in detail the nitrotyrosine formation radical mechanism. Tyrosyl radicals play an essential role in catalytic reactions of numerous enzymes and biological systems have regulated appropriate mechanisms for their formation. Nitric oxide reacts with the tyrosyl radical and affords a weak intermediate complex which, through a sequence of non-ionic water catalyzed and biologically feasible intermediate reactions, yields the iminoxyl radical.

Force field development for poly(dimethylsilylenemethylene) with the aid of ab initio calculations.

The molecular geometries, conformational energies, and zero-point energies of di(trimethylsilylene)methylene have been determined from high-level quantum chemistry calculations. The results are further used in the parametrization of a classical potential energy function suitable for performing simulations of the corresponding polymer, namely, poly(dimethylsilylenemethylene). Di(trimethylsilylene)methylene geometrical parameter optimizations for a proper location of the global minimum and other local minima, constrained at certain dihedral and bond angles, were performed at both the B3LYP/6-311G and MP2(full)/6-311G levels of theory.

An extremely stable Ni(II) complex derived from the hydrolytic cleavage of the C-terminal tail of histone H2A.

The C-terminal blocked tetrapeptides SHHK- and SAHK-, which represent the fragments produced from the hydrolysis of the hexapeptides' -TASHHK-, -TESHHK-, and -TESAHK- complexes with Ni(II), were synthesized and their interactions with Ni(II) ions were studied potentiometrically and spectroscopically. Both tetrapeptides interact strongly with Ni(II) ions leading to square-planar complexes with 4N {NH(2),2N(-),N(im)} coordination. The stability of the Ni-SHHK- complex is about 2 orders of magnitude higher than the Ni-SAHK- complex.