Thermodynamics and kinetics of glyoxal dimer formation: a computational study

Density functional theory (B3LYP//6-311+G) calculations including Poisson-Boltzmann implicit solvent were used to study the hydration of glyoxal and subsequent formation of dimeric species in solution. Our calculations show that the dioxolane ring dimer is the thermodynamic sink among all monomers and dimers with varying degrees of hydration. Although fully hydrated species are thermodynamically favored over their less hydrated counterparts, we find that a preliminary dehydration step precedes dimerization and ring closure. Ring closure of the open dimer monohydrate to the dioxolane ring dimer is kinetically favored over both hydration to the open dimer dihydrate and ring closure to form the dioxane ring dimer. The kinetic barriers for different geometric approaches for dimerization suggest an explanation why oligomerization stops after the formation of a dioxolane ring trimer as observed experimentally.     

Thermodynamics and kinetics of methylboroxine.amine adduct formation: a computational study

Density functional theory (B3LYP//6-311+G*) calculations including Poisson-Boltzmann implicit solvent were applied to study the formation of the trimethylboroxine.amine adduct with respect to methylboronic acid monomers and free amine in solution. Potential intermediates and transition states between intermediates were calculated to assess the thermodynamic and kinetic factors controlling this transformation. Our calculations suggest that the rate-determining steps are condensation reactions to form dimers and trimers, and closure of the boroxine ring. Fast amine exchange is expected throughout the transformation, and the most-stable intermediate is a dimer.amine adduct. Using our calculated barriers for the methyl system as a template, we assess the conversion of phenylboronic acid to the triphenylboroxine.amine adduct and find that the pathway is most likely similar, except that the transformation is thermodynamically and kinetically more favored for the phenyl system in the presence of pyridine.     

Thermodynamics and kinetics of atmospheric aerosol particle formation and growth

In this tutorial review we summarize the standard approaches to describe aerosol formation from atmospheric vapours and subsequent growth - with a particular emphasis on the interplay between equilibrium thermodynamics and non-equilibrium transport. We review the use of thermodynamics in describing phase equilibria and formation of aerosol particles from supersaturated vapour via nucleation. We also discuss the kinetics of cluster formation and transport phenomena, which are used to describe dynamic mass transport between the gaseous and condensed phases in a non-equilibrium system. Finally, we put these theories into the context of atmospheric observations of aerosol formation and growth.     

Mechanism and diastereoselectivity of aziridine formation from sulfur ylides and imines: a computational study

A computational investigation of the title reaction involving semistabilized (R = Ph) and stabilized (R = CO2Me) sulfur ylides has been performed using DFT methods including a continuum model of solvent. Our results provide support for the generally accepted mechanism and are in very good agreement with observed cis/trans selectivities. This study shows that betaine formation is nonreversible, and that selectivity is thereby determined at the initial addition step, in the case of semistabilized ylides. Our analysis indicates moreover that addition TS structures are governed by the steric strain induced by the N-sulfonyl group, which favors the transoid approach in the case of syn betaine formation and the cisoid mode of addition in anti TSs. The observed low trans selectivity is accounted for by the favorable Coulombic interactions and stabilization by C-H...O hydrogen bonding allowed in the cisoid anti addition TS. In the case of stabilized ylides, the endothermicity of betaine formation combined with the high barrier to ring closure render the elimination step rate- and selectivity-determining. Accordingly, the low cis selectivity observed in stabilized ylide reactions is explained by the lower steric strain in the elimination step generated by the formation of the cis aziridine (as compared to the trans case).     

Thermodynamics and kinetics of the formation of the supramolecular complexes bisacetato(5,10,15,20-tetraphenylporphinate)zirconium(IV) with pyridine and imidazole

The equilibria and rates of step reactions for the formation of the supramolecular complexes of bisacetato(5,10,15,20-tetraphenylporphinate)zirconium(IV) (AcO)₂ZrTPP and bioactive bases pyridine (Py) and imidazole (Im) in toluene were studied using UV-Vis and IR spectroscopy. The step stoichiometric mechanism, including the reversible coordination of two Py molecules (K ₁ = 1.8 × 10⁸ l²/mol²), the equilibrium of the displacement of two AcO⁻ into the second coordination sphere by increasing the concentration of the solvent polar component (K ₂ = 2.4), and the coordination of the third and fourth Py molecules in a one step with the formation of [(Py)₄ZrTPP]²⁺ · 2(AcO)⁻ (K ₃ = 2.8 × 10⁴ l²/mol²), was verified. It was established that the spectrophotometric titration is sensible for the two-stage π-π-complexation of [(Py)₄ZrTPP]²⁺ · 2(AcO)⁻ with Py molecules (K ₄ = 29 l/mol and K ₅ = 1.8 l/mol). It was shown that the stronger base Im reacts irreversibly with (AcO)₂ZrTPP. The thermodynamic and optical characteristics of (AcO)₂ZrTPP required for using the complex in the detection of bioactive bases were studied.     

Excited state complex formation between methyl glyoxal and some aromatic bio-molecules: a fluorescence quenching study

Fluorescence quenching of some important aromatic bio-molecules (ABM) such as 3-aminophthalhydrazide (luminol), tryptophan (Try), phenylalanine and tyrosine (Tyr) by methyl glyoxal (MG) has been studied employing different spectroscopic techniques. The interaction of MG with ABM in the excited state has been analysed using Stern-Volmer (S-V) mechanism. In the case of MG-luminol system time correlated single photon counting (TCSPC) technique has also been applied to explain the S-V mechanism. The bimolecular rate constants obtained are found to be higher than the rate constant for diffusion controlled process. A plausible explanation of the quenching mechanism has been discussed on the basis of hydrogen bonding, charge transfer and energy transfer interaction between the colliding species.     

Thermodynamics, kinetics, and mechanism of the reversible formation of oxorhenium(VII) catecholate complexes

Mononuclear Re(V) compounds MeReO(mtp)NC(5)H(4)X, 3, where mtpH(2) is 2-(mercaptomethyl)thiophenol have been prepared from the monomerization of [MeReO(mtp)](2) by pyridines with electron-donating substituents in the para or meta position; X = 4-Me, 4-Bu(t), 3-Me, 4-Ph, and H. Analogous compounds, MeReO(edt)N(5)H(4)X, 4, edtH(2) = 1,2-ethanedithiol, were prepared similarly. The equilibrium constants for the reaction, dimer + 2Py = 2M-Py, are in the range (2.5-31.6) x 10(2) L mol(-1). Both groups of monomeric compounds react with quinones (phenanthrenequinone, PQ, and 3,5-tert-butyl-1,2-benzoquinone, DBQ), displacing the pyridine ligand and forming Re(VII) catecholate complexes MeReO(dithiolate)PCat and MeReO(dithiolate)DBCat. With PQ, the reaction MeReO(dithiolate)Py + PQ = MeReO(dithiolate)PCat + Py is an equilibrium; values of K(Q) for different Py ligands lie in the ranges 9.2-42.7 (mtp) and 3.2-11.2 (edt) at 298 K. These second-order rate constants (L mol(-1) s(-1)) at 25 degrees C in benzene were obtained for the PQ reactions: k(f) = (5.3-15.5) x 10(-2) (mtp), (6.6-16.4) x 10(-2) (edt); k(r) = (3.63-5.71) x 10(-3) (mtp), (14.7-22.0) x 10(-3) (edt). The ranges in each case refer to the series of pyridine ligands, the forward rate constant being the largest for C(5)H(5)N, with the lowest Lewis basicity. The reactions of MeReO(dithiolate)Py with DBQ proceed to completion. Values of k(f)/L mol(-1) s(-1) fall in a narrow range, 4.02 (X = Bu(t)) to 8.4 (X = H) with the dithiolate being mtp.     

A study on the kinetics of condensation reaction of cardanol and formaldehyde,part I

Novolac resins having cardanol‐to‐formaldehyde mole ratios of 1:0.4, 1:0.5, and 1:0.6 were prepared by using aromatic sulphonic acid as the catalyst at four different temperatures ranging between 90°C and 120°C, with an interval of 10°C. Free formaldehyde and free phenol contents were determined at regular time intervals to check the completion of the reaction. The synthesized novolacs were characterized by Fourier‐transform infrared spectroscopic analysis, nuclear magnetic resonance, and gel permeation chromatography. The reaction between cardanol and formaldehyde was found to follow second‐order kinetics. The overall rate constant (k) increased with the increase of temperature. On the basis of the value of k, various other activation parameters such as activation energy (E_a), change in enthalpy (ΔH), entropy (ΔS), and free energy (ΔG) of the reaction were also evaluated. It was found that the condensation reaction of cardanol and formaldehyde with aromatic sulphonic acid was nonspontaneous and irreversible. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 559–572, 2009     

Antioxidant activity of trans-resveratrol toward hydroxyl and hydroperoxyl radicals: a quantum chemical and computational kinetics study

In this work, we have carried out a systematic study of the antioxidant activity of trans-resveratrol toward hydroxyl ((?)OH) and hydroperoxyl ((?)OOH) radicals in aqueous simulated media using density functional quantum chemistry and computational kinetics methods. All possible mechanisms have been considered: hydrogen atom transfer (HAT), proton-coupled electron transfer (PCET), sequential electron proton transfer (SEPT), and radical adduct formation (RAF). Rate constants have been calculated using conventional transition state theory in conjunction with the Collins-Kimball theory. Branching ratios for the different paths contributing to the overall reaction, at 298 K, are reported. For the global reactivity of trans-resveratrol toward (?)OH radicals, in water at physiological pH, the main mechanism of reaction is proposed to be the sequential electron proton transfer (SEPT). However, we show that trans-resveratrol always reacts with (?)OH radicals at a rate that is diffusion-controlled, independent of the reaction pathway. This explains why trans-resveratrol is an excellent but very unselective (?)OH radical scavenger that provides antioxidant protection to the cell. Reaction between trans-resveratrol and the hydroperoxyl radical occurs only by phenolic hydrogen abstraction. The total rate coefficient is predicted to be 1.42 × 10(5) M(-1) s(-1), which is much smaller than the ones for reactions of trans-resveratrol with (?)OH radicals, but still important. Since the (?)OOH half-life time is several orders larger than the one of the (?)OH radical, it should contribute significantly to trans-resveratrol oxidation in aqueous biological media. Thus, trans-resveratrol may act as an efficient (?)OOH, and also presumably (?)OOR, radical scavenger.     

The association reaction between C2H and 1-butyne: a computational chemical kinetics study

The potential energy surfaces (PES) for the reaction of the C(2)H radical with 1-butyne (C(4)H(6)) have been studied using the CBS-QB3 method. Density functional B3LYP/cc-pVTZ and M06-2X/6-311++G(d,p) calculations have also been performed to analyze the reaction energetics. For detailed theoretical calculation on the total reaction mechanism, the initial association reactions on more and less substituted C atoms of 1-butyne are treated separately followed by a variational transition state theory (VTST) calculation to obtain reaction rates. The successive unimolecular reactions from the association reaction complexes are subjected to Rice-Ramsperger-Kassel-Marcus (RRKM) calculations for reaction rate constants and product branching ratios. The calculated rate constants in the temperature range 70-295 K for both the association reactions are found to be highly temperature dependent at low temperatures, which is contrary to the experimental findings of temperature independent association rates. We have explained this observation with the help of variational nature of the transition states, and we found a "loose" transition state at low temperatures. The calculated product branching ratios for the unimolecular reactions generally agree with the available experimental data, although some channels show a significant method dependency and therefore the correlation with experiment is lost to some extent. Our detailed reaction energetics calculations confirm that the C(2)H + C(4)H(6) reaction proceeds without an entrance barrier and leads to the important products ethynylallene + CH(3), 1,3-hexadiyne + H, 3,4-hexadiene-1-yne + H, 2-ethynyl-1,3-butadiene + H, 3,4-dimethylenecyclobut-1-ene + H and fulvene + H exothermic by 25-75 kcal mol(-1), with strong dependence of the product distribution on the association mode of C(2)H with C(4)H(6), making these reactions fast under low temperature conditions of Titan's atmosphere. Therefore this study can provide a detailed picture of the complex hydrocarbon formation mechanism in the upper atmosphere.     

Favoring heterotrimeric boroxine formation using an internal Lewis base: a computational study

Heterotrimeric arylboroxines can be favorably formed by designing one of the arylboronic acid monomers to contain a pendant Lewis base. Using density functional theory (B3LYP//6-311+G*) calculations including Poisson-Boltzmann implicit solvent, we found that AB2 trimeric arylboroxines were thermodynamically favored over A2B, A3, or B3, where A and B are monomeric arylboronic acids with and without a pendant Lewis base, respectively. The most stable AB2 trimers were formed when the B monomer contained electron-withdrawing substituents, particularly halogens in the para-position or pi-acceptors in the meta-position. On the other hand, adding different para-substituents to the A monomer did not significantly change the energetics. Our calculations also suggest that ABC trimers with three different monomers will not be significantly favored over AB2 trimers when making small electronic perturbations, by changing the substituents on each monomer.     

Thermodynamics and kinetics of bubble nucleation: Simulation methodology

The simulation of homogeneous liquid to vapor nucleation is investigated using three rare-event algorithms, boxed molecular dynamics, hybrid umbrella sampling Monte Carlo, and forward flux sampling. Using novel implementations of these methods for efficient use in the isothermal-isobaric ensemble, the free energy barrier to nucleation and the kinetic rate are obtained for a Lennard-Jones fluid at stretched and at superheated conditions. From the free energy surface mapped as a function of two order parameters, the global density and largest bubble volume, we find that the free energy barrier height is larger when projected over bubble volume. Using a regression analysis of forward flux sampling results, we show that bubble volume is a more ideal reaction coordinate than global density to quantify the progression of the metastable liquid toward the stable vapor phase and the intervening free energy barrier. Contrary to the assumptions of theoretical approaches, we find that the bubble takes on cohesive non-spherical shapes with irregular and (sometimes highly) undulating surfaces. Overall, the resulting free energy barriers and rates agree well between the methods, providing a set of complementary algorithms useful for studies of different types of nucleation events.     

The di-(2-alkyl-2-nitroethyl)-methylamines from reactions of nitroalkanes with formaldehyde and methylamine

Di-(2-alkyl-2-nitroethyl)-methylamines obtained from reactions of nitroalkanes with formaldehyde and methylamine were separated in diastereoisomers. NMR assignments of meso and racemic forms, and conformations are discussed. Partial separation of racemates into enantiomers was carried out by liquid-solid chromatography, on an optically-active adsorbent.     

Mechanism of rhodium‐catalyzed hydroacylation of propylene using formaldehyde: A computational study

Density functional theory was used to study Rh(I)‐catalyzed hydroacylation of propylene and formaldehyde. All the intermediates and the transition states were optimized completely at the B3LYP/6‐311++G(d,p) level (LANL2DZ(d) for Rh, P). Calculation results confirm that Rh(I)‐catalyzed hydroacylation of propylene and formaldehyde is exothermic, and the total released Gibbs free energy is about ?33 kJ mol^?1. This hydroacylation have eight possible pathways, and pathways (1), (2), (3), and (4) are the dominant reaction channels. The dominant product predicted theoretically is butyl aldehyde, and it is a linear product, which agrees well with these experiments. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Thermodynamics, kinetics, and dynamics of the two alternative aniomesolytic fragmentations of C-O bonds: an electrochemical and theoretical study

Fragmentation reactions of radical anions (mesolytic cleavages) of cyanobenzyl alkyl ethers (intramolecular dissociative electron transfer, heterolytic cleavages) have been studied electrochemically. The intrinsic barriers for the processes have been established from the experimental thermodynamic and kinetic parameters. These values are more than 3 kcal/mol lower as an average than the related homolytic mesolytic fragmentations of radical anions of 4-cyanophenyl ethers. In the particular case of isomers 4-cyanobenzyl phenyl ether and 4-cyanophenyl benzyl ether, the difference in intrinsic barriers amounts to 5.5 kcal/mol, and this produces an energetic crossing where the thermodynamically more favorable process (homolytic) is the kinetically slower one. The fundamental reasons for this behavior have been established by means of theoretical calculations within the density functional theory framework, showing that, in this case, the factors that determine the kinetics are clearly different (mainly present in the transition state) from those that determine the thermodynamics and they are not related to the regioconservation of the spin density ("spin regioconservation principle"). Our theoretical results reproduce quite well the experimental energetic difference of barriers and demonstrate the main structural origin of the difference.     

Thermodynamics of crystalline nanonucleus formation from liquid phase

The energy of crystal nucleation from liquid phase was considered, with the following two stages taken into account: (1) the formation of metastable supercooled melt (solution), containing pre-nuclei with intermediate amorphous (quasicrystalline) structure, and (2) the transformation of amorphous clusters into solid crystalline nuclei having different structures. With growth of a nucleus the nucleation energy profile manifests 2–3 maxima corresponding to these stages, and the kinetics of the non-stationary nucleation has five characteristic variations.     

Spectrophotometric determination of formaldehyde,glycollic and glyoxalic acids in the presence of glyoxal and some carboxylic acids

A spectrophotometric procedure is described for determining glycollic acid, glyoxalic acid and formaldehyde in the presence of high concentrations of oxalic acid and ammonium oxalate, and in the presence of glyoxal, formic acid, tartaric acid, and dihydroxytartaric acid. Three known spectrophotometric methods required modification. The experimental error under the specified conditions does not exceed ±5%.     

On the mechanism of peripentacene formation from pentacene: computational studies of a prototype for graphene formation from smaller acenes

The formation of peripentacene during the high-temperature vacuum sublimation of pentacene (P) in the presence of trace amounts of 6,13-dihydropentacene (DHP) has been studied computationally with density functional theory. Computational and kinetic analyses indicate that competing mechanisms involving a series of H atom transfers initiated by hydrogen transfer from DHP to P can account for the formation of peripentacene. The overall reaction is predicted to proceed with a free energy barrier of 36.1 kcal/mol and to be autocatalytic. Kinetic modeling supports the proposed mechanism.