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 C80H22O, by molecular oxygen in the first excited state (1Δg) 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 -50.1 kcal mol-1, supporting the experimental findings that both compounds are critically involved in the explosive deoxygenation of GO. On the other hand, the 1,3-dioxetane alternative pathway is considered even more exergonic, although it requires an overwhelming adiabatic energy barrier of 29.8 kcal mol-1 to accomplish its target.

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 ab initio calculations, is facilitated via a Grotthuss instead of a bimolecular proton transfer (vehicle) mechanism at the experimental temperature (T = 130 K) as unambiguously confirmed by experiments with deuterated water. In contrast, the bimolecular vehicle mechanism is preferred at higher temperatures (T = 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. Theoretical analysis suggests that the concerted proton transfer occurs via hydrogen-bonded bridges consisting of a 3 water molecule "core" that connects the pyridine protonated (Pyri-H+) with the pyrrolidine-protonated (Pyrro-H+) protomers. Additional water molecules attached as acceptors to the hydrogen-bonded "core" bridge result in lowering the reaction barrier of the concerted proton transfer down to less than 6 kcal/mol, which is consistent with the experimental observations.

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. The proposed methodology reconstructs distributions required to infer kinetic parameters of a stochastic process pertaining to either a simulation or experimental data. The suggested approach accurately replicates rate constants of the stochastic reaction networks, which have evolved over time by event-driven Monte Carlo (MC) simulations using the Gillespie algorithm. Furthermore, our approach has been successfully used to estimate rate constants of association and dissociation events between molecular species developing during molecular dynamics (MD) simulations. We certainly believe that our method will be remarkably helpful for considering the macroscopic characteristic molecular roots related to stochastic physical and biological processes.

OH Radical and Chlorine Atom Kinetics of Substituted Aromatic Compounds: 4-chlorobenzotrifluoride (p-ClC6H4CF3).

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 (p-chlorobenzotrifluoride, p-ClC6H4CF3, 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. In this study, rate coefficients, k1, for the OH + PCBTF reaction were measured over the temperature ranges 275-340 and 385-940 K using low-pressure discharge flow-tube reactors coupled with a mass spectrometer detector in the ICARE/CNRS (Orléans, France) laboratory. k1(298-353 K) was also measured using a relative rate method in the thermally regulated atmospheric simulation chamber (THALAMOS; Douai, France). k1(T) displayed a non-Arrhenius temperature dependence with a negative temperature dependence between 275 and 385 K given by k1(275-385 K) = (1.50 ± 0.15) × 10-14 exp((705 ± 30)/T) cm3 molecule-1 s-1, where k1(298 K) = (1.63 ± 0.03) × 10-13 cm3 molecule-1 s-1 and a positive temperature dependence at elevated temperatures given by k1(470-950 K) = (5.42 ± 0.40) × 10-12 exp(-(2507 ± 45) /T) cm3 molecule-1 s-1. The present k1(298 K) results are in reasonable agreement with two previous 296 K (760 Torr, syn. air) relative rate measurements. The rate coefficient for the Cl-atom + PCBTF reaction, k2, was also measured in THALAMOS using a relative rate technique that yielded k2(298 K) = (7.8 ± 2) × 10-16 cm3 molecule-1 s-1. As part of this work, the UV and infrared absorption spectra of PCBTF were measured (NOAA; Boulder, CO, USA). On the basis of the UV absorption spectrum, the atmospheric instantaneous UV photolysis lifetime of PCBTF (ground level, midlatitude, Summer) was estimated to be 3-4 days, assuming a unit photolysis quantum yield. The non-Arrhenius behavior of the OH + PCBTF reaction over the temperature range 275 to 950 K is interpreted using a mechanism for the formation of an OH-PCBTF adduct and its thermochemical stability. The results from this study are included in a discussion of the OH radical and Cl atom kinetics of halogen substituted aromatic compounds for which only limited temperature-dependent kinetic data are available.

Unscrambling micro-solvation of -COOH and -NH groups in neat dimethyl sulfoxide: insights from 1H-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 via1H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i.e. acetic and benzoic acid, ethyl acetamidocyanoacetate). Both experimental and theoretical results show excellent agreement, thereby permitting the calculation of the association constants between the studied compounds and DMSO molecules. Our coupled MD simulations, DFT and ab initio calculations, and NMR spectroscopy results indicated that complex formation is entropically driven and DMSO molecules undergo multiple strong interactions with the studied molecules, particularly with the -COOH groups. The combined experimental and theoretical techniques unraveled the interactions of DMSO with the most abundant functional groups of peptides (i.e. peptide bonds, side chain and terminal carboxyl groups) in high detail, providing significant insights on the underlying thermodynamics driving these interactions. Moreover, the developed methodology for the analysis of the simulation results could serve as a template for future thermodynamic and kinetic studies of similar systems.

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. Beyond the quantification of dipeptide-water molecule direct interactions, this NMR technique could be useful for the determination and elucidation of small to moderate bio-organic molecular groups' direct interactions with various polar solvent molecules, shedding light on the biomolecular micro-solvation processes and behaviour in various solvents.

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. Magnetic properties were studied by SQUID magnetometry. The results suggest: (i) that the cationic Prussian blue analog comprises Al-hydroxy cations embedded into a monolayer thick two-dimensional ferric ferrocyanide array; and (ii) that the clay-Prussian blue nanohybrid consists of such arrays stacked between the clay layers. The latter material orders ferromagnetically at approximately 5K showing a hundred times higher remanence than that of the starting material, soluble Prussian blue (ammonium ferric ferrocyanide).

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. The methyl torsional transitions are active. The 0(0) (0) band is at 35 483 cm(-1). The two photon spectrum is very strong and bears a resemblance to the two photon spectrum of phenylacetylene. The potential barrier of the methyl rotor in the S(1) state has been determined as V(6)=-12 cm(-1) with B(CH(3) )=5.55 cm(-1). Ab initio calculations, MP2(full)/cc-pVTZ and CAS/cc-pVTZ, have been implemented for the geometry optimization and the normal mode vibration computation in the S(0) and S(1) states.

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. The iminoxyl radical further combines with hydroxyl radical, a species present in pathophysiological conditions, to yield nitrotyrosine.

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. The global minimum configuration is slightly displaced from a perfectly staggered geometry, approximately by 16.0 degrees, at both levels of theory. Molecular mechanics and Monte Carlo calculations for isolated polymer chains together with molecular dynamics runs for the modeled dimer provide very good results in terms of conformational and thermodynamic properties.

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. Spectroscopic evidence and theoretical predictions suggest the positioning of the free imidazole ring, in the Ni-SHHK- complex, above the coordination plane, explaining the extra stability of the complex.