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.

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.

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

This study investigates the interactions of –COOH and –NH groups in neat DMSO solutions, with special focus on their thermodynamics and kinetics.

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.

Ab initio and density functional theory studies for the explanation of the antioxidant activity of certain phenolic acids

Ab initio and density functional theory molecular orbital calculations were carried out at both the HF/6-31 +G(d) and B3LYP/6-31+G(d) levels for the four antioxidants, p-hydroxycinnamic acid derivatives, namely, the p-coumaric, caffeic, ferulic, and sinapinic acid and the corresponding radicals, in an attempt to explain the structural dependency of the antioxidant activity of these compounds. Optimized resulting geometries, vibrational frequencies, absolute infrared intensities, and electron-donating ability are discussed. Both the high degree of conjugation and the extended spin delocalization in the phenoxyl radicals offer explanation for the scavenging activity of the four acids. In structurally related compounds, the calculated heat of formation value in radical formation appears as a meaningful molecular descriptor of antioxidant activity in accordance with experimental data. This becomes more clear at the B3LYP level.