Reactant Complex Research Articles

Threshold Collision-Induced Dissociation and Theoretical Studies of Hydrated Fe(II): Binding Energies and Coulombic Barrier Heights

The first experimentally determined bond dissociation energies for losing water from Fe(2+)(H(2)O)(n) complexes, n = 4-11, are measured using threshold collision-induced dissociation (TCID) in a guided ion beam tandem mass spectrometer coupled to an electrospray ionization source that forms thermalized complexes. In this technique, absolute cross-sections for dissociation induced by collisions with Xe at systematically varied kinetic energies are obtained. After accounting for multiple collisions, kinetic shifts, and energy distributions, these cross-sections are analyzed to yield the energy thresholds for losing one, two, or three water ligands at 0 K. The 0 K threshold measurements are converted to 298 K values to give the hydration enthalpies and free energies for sequentially losing water ligands from each complex. Comparisons to previous results for hydration of Zn(2+) indicate that the bond energies are dominated by electrostatic interactions, with no obvious variations associated with the open shell of Fe(2+). Theoretical geometry optimizations and single-point energy calculations are performed using several levels of theory for comparison to experiment, with generally good agreement. In addition to water loss channels, the charge separation process generating hydrated FeOH(+) and protons is observed for multiple reactant complexes. Energies of the rate-limiting transition states are calculated at several levels of theory with density functional approaches (B3LYP and B3P86) disagreeing with MP2(full) results. Comparisons to our kinetic energy dependent cross-sections suggest that the energetics of the MP2(full) level are most accurate.

Why Is the Oxidation State of Iron Crucial for the Activity of Heme-Dependent Aldoxime Dehydratase? A QM/MM Study

Aldoxime dehydratase is a heme-containing enzyme that utilizes the ferrous rather than the ferric ion to catalyze the synthesis of nitriles by dehydration of the substrate. We report a theoretical study of this enzyme aimed at elucidating its catalytic mechanism and understanding this oxidation state preference (Fe(2+) versus Fe(3+)). The uncatalyzed dehydration reaction was modeled by including three and four water molecules to assist in the proton transfer, but the computed barriers were very high at both the DFT (B3LYP) and coupled cluster CCSD(T) levels. The enzymatic dehydration of Z-acetaldoxime was explored through QM/MM calculation using two different QM regions and covering all three possible spin states. The reaction starts by substrate coordination to Fe(2+) via its nitrogen atom to form a six-coordinated singlet reactant complex. The ferrous heme catalyzes the N-O bond cleavage by transferring one electron to the antibond in the singlet state, while His320 functions as a general acid to deliver a proton to the leaving hydroxide, thus facilitating its departure. The key intermediate is identified as an Fe(III)(CH(3)CH═N(•)) species (triplet or open-shell singlet), with the closed-shell singlet Fe(II)(CH(3)CH═N(+)) being about 6 kcal/mol higher. Subsequently, the same His320 residue abstracts the α-proton, coupled with electron transfer back to the iron center. Both steps are calculated to have feasible barriers (14-15 kcal/mol), in agreement with experimental kinetic studies. For the same mode of substrate coordination, the ferric heme does not catalyze the N-O bond cleavage, because the reaction is endothermic by about 40 kcal/mol, mainly due to the energetic penalty for oxidizing the ferric heme. The alternative binding option, in which the anionic aldoxime coordinates to the ferric ion via its oxyanion, also results in a high barrier (around 30 kcal/mol), mainly because of the large endothermicity associated with the generation of a suitable base (neutral His320) for proton abstraction.

Carbonate radical anion as an efficient reactive oxygen species: Its reaction with guanyl radical and formation of 8-oxoguanine

Mechanisms of reactions of four different tautomers (G(-H1)·, G(-H2a)·, G(-H2b)· and G(-H9)·) of guanyl radical with carbonate radical anion (CO3.−) producing the mutagenic product 8-oxoguanine (8-oxoG) have been investigated theoretically using density functional theory and second order Møller–Plesset perturbation (MP2) theory. Geometries of reactant, intermediate and product complexes and those of transition states were optimized in gas phase. Solvent effect of aqueous media was treated by including eight specific water molecules in a hydration cell during optimization and single point energy calculations employing the polarizable continuum model. It is found that the specific water molecules catalyze proton transfer involving the different sites of the guanyl radical during the reaction. Possible roles of aeration, stirring and photoirradiation of reaction media which are employed to facilitate the reaction in experimental studies are explained. The carbonate radical anion is found to be a very effective reactive oxygen species.

Gas-Phase Kinetics Study of Reaction of OH Radical with CH3NHNH2 by Second-Order Multireference Perturbation Theory

The gas-phase kinetics of H-abstraction reactions of monomethylhydrazine (MMH) by OH radical was investigated by second-order multireference perturbation theory and two-transition-state kinetic model. It was found that the abstractions of the central and terminal amine H atoms by the OH radical proceed through the formation of two hydrogen bonded preactivated complexes with energies of 6.16 and 5.90 kcal mol(-1) lower than that of the reactants, whereas the abstraction of methyl H atom is direct. Due to the multireference characters of the transition states, the geometries and ro-vibrational frequencies of the reactant, transition states, reactant complexes, and product complexes were optimized by the multireference CASPT2/aug-cc-pVTZ method, and the energies of the stationary points of the potential energy surface were refined at the QCISD(T)/CBS level via extrapolation of the QCISD(T)/cc-pVTZ and QCISD(T)/cc-pVQZ energies. It was found that the abstraction reactions of the central and two terminal amine H atoms of MMH have the submerged energy barriers with energies of 2.95, 2.12, and 1.24 kcal mol(-1) lower than that that of the reactants respectively, and the abstraction of methyl H atom has a real energy barrier of 3.09 kcal mol(-1). Furthermore, four MMH radical-H(2)O complexes were found to connect with product channels and the corresponding transition states. Consequently, the rate coefficients of MMH + OH for the H-abstraction of the amine H atoms were determined on the basis of a two-transition-state model, with the total energy E and angular momentum J conserved between the two transition-state regions. In units of cm(3) molecule(-1) s(-1), the rate coefficient was found to be k(1) = 3.37 × 10(-16)T(1.295) exp(1126.17/T) for the abstraction of the central amine H to form the CH(3)N(•)NH(2) radical, k(2) = 2.34 × 10(-17)T(1.907) exp(1052.26/T) for the abstraction of the terminal amine H to form the trans-CH(3)NHN(•)H radical, k(3) = 7.41 × 10(-20)T(2.428) exp(1343.20/T) for the abstraction of the terminal amine H to form the cis-CH(3)NHN(•)H radical, and k(4) = 9.13 × 10(-21)T(2.964) exp(-114.09/T) for the abstraction of the methyl H atom to form the C(•)H(2)NHNH(2) radical, respectively. Assuming that the rate coefficients are additive, the total rate coefficient of these theoretical predictions quantitatively agrees with the measured rate constant at temperatures of 200-650 K, with no adjustable parameters.

Can an α-Anomer of the Trinitro Form of d-Glucopyranose Be More Easily Hydrolyzed in Alkaline Environment than the β-Anomer? A Detailed Theoretical Analysis

Comprehensive computational investigations of detailed alkaline hydrolysis reaction pathways of the α-anomeric form of nitrocellulose monomer (2,3,6-trinitro-α-D-glucopyranose) in the (4)C(1) chair conformation within the S(N)2 framework in the gas phase and in bulk water solution are reported. Geometries of reactant complexes, transition states, intermediates, and completely denitrated product were optimized at the density functional theory (DFT) level using the B3LYP functional and the 6-311G(d,p) basis set both in the gas phase and in the bulk water solution. The effect of bulk water was modeled using the polarizable continuum model (PCM) approach. The nature of the potential energy surface of the local minima and transition states was ascertained through vibrational frequency analysis. Intrinsic reaction coordinate (IRC) calculations were also performed to validate the computed transition state structures. Effect of electron correlation on computed energies was considered through a single point energy calculation at the MP2 level using the cc-pVTZ basis set. It was revealed that the presence of hydrogen bonds between the attacking OH(-) ion and various hydrogen bond donating sites (including CH sites) of monomer was necessary for stabilization of the transition state. It was revealed that the α-anomer will be more reactive than the β-anomer with regard to the denitration reaction. The role of entropy and the denitration ability of various sites are also discussed.

Structures and reaction rates of the gaseous oxidation of SO<sub>2</sub> by an O<sub>3</sub><sup>−</sup>(H<sub>2</sub>O)<sub>0-5</sub> cluster – a density functional theory investigation

Abstract. Based on density functional theory calculations we present a study of the gaseous oxidation of SO2 to SO3 by an anionic O3−(H2O)n cluster, n = 0–5. The configurations of the most relevant reactants, transition states, and products are discussed and compared to previous findings. Two different classes of transition states have been identified. One class is characterised by strong networks of hydrogen bonds, very similar to the reactant complexes. The other class is characterised by sparser structures of hydration water and is stabilised by high entropy. At temperatures relevant for atmospheric chemistry, the most energetically favourable class of transition states vary with the number of water molecules attached. A kinetic model is utilised, taking into account the most likely outcomes of the initial SO2 O3−(H2O)n collision complexes. This model shows that the reaction takes place at collision rates regardless of the number of water molecules involved. A lifetime analysis of the collision complexes supports this conclusion. Hereafter, the thermodynamics of water and O2 condensation and evaporation from the product SO3−O2(H2O)n cluster is considered and the final products are predicted to be O2SO3− and O2SO3−(H2O)1. The low degree of hydration is rationalised through a charge analysis of the relevant complexes. Finally, the thermodynamics of a few relevant reactions of the O2SO3− and O2SO3−(H2O)1 complexes are considered.

Isoguanine Formation from Adenine

Several possible mechanisms underlying isoguanine formation when OH radical attacks the C(2) position of adenine (A C 2) are investigated theoretically for the first time. Two steps are involved in this process. In the first step, one of two low-lying A C 2⋅⋅⋅OH reactant complexes is formed, leading to C(2)-H(2) bond cleavage. Between the two reactant complexes there is a small isomerization barrier, which lies well below separated adenine plus OH radical. The complex dissociates to free molecular hydrogen and an isoguanine tautomer (isoG 1 or isoG 2). The local and activation barriers for the two pathways are very similar. This evidence suggests that the two pathways are competitive. After dehydrogenation, there are two possible routes for the second step of the reaction. One is direct hydrogen transfer, via enol-keto tautomerization, which has high local barriers for both tautomers and is not favored. The other option is indirect hydrogen transfer involving microsolvation by one water molecule. The water lowers the reaction barrier by over 20 kcal mol(-1) , indicating that water-mediated hydrogen transfer is much more favorable. Both A+OH(⋅) →isoG+H(⋅) reactions are exothermic and spontaneous. Among four isoguanine tautomers, isoG 1 has the lowest energy. Our findings explain why only the N(1)H and O(2)H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.

ChemInform Abstract: Structure, Bonding, and Reactivity of Reactant Complexes and Key Intermediates

AbstractReview: 160 refs.

Evaluation of the regioselective delactonization of tri-sialic acid lactone by in-solution molecular dynamics simulation

An approximate model for the delactonization of tri-sialic acid lactone is presented with two water-layers that led to neutral hydrolysis of δ-lactone. The hydrolytic reactivity was studied with a 10-ns in-solution molecular dynamics simulation. The initial step of this hydrolysis involves a reactant water nucleophile complex via a proton transfer with another water molecule. Therefore, the probability of water molecules localized at the hydrolytic center correlates to the hydrolysis of δ-lactone. The stepwise delactonization of α2,8-(NeuAc)3 lactone results/resulted from water concentration discrepancy near the carbonyl carbon of lactones in two water oxygen⋯carbonyl carbon shells, and the distances of OC⋯Owater layers were 2.8Å and 5.1Å. Based on in-solution molecular dynamics study, the motion of water molecules over the re-face of the carbonyl groups was used for the quantitative description of the residence probability, p, whose value is 0.11 for lactone I and 0.33 for lactone II. The geometric criteria used to determine the residence statistics are (1) the distance of water–oxygen⋯carbonyl carbon in less than 5.1Å and (2) the cone angle, θ, of carbonyl OC⋯Owater in the range of 85–115°. As expected, a higher residence probability at lactone II led to its faster hydrolysis. Both the radial g(r) and angular p(θ) pair distribution functions of water oxygen and carbonyl groups of lactones ensure a better surrounding hydration encounter for lactone II. In contrast, water molecules around lactone I are deduced due to a steric hindrance by the turn structure of α2,8-(NeuAc)3 lactone.

The fate of branched and linear isomers in the rhodium-catalyzed hydroformylation of 3,4,4-trimethylpent-1-ene

In nonreversible hydroformylations, the computational evaluation of regio- and stereoselectivities from the relative energy barriers of the transition states (TS) for the alkyl-Rh intermediate formation step is possible, provided all low energy conformers are considered. In contrast, in reversible hydroformylations, also the subsequent reaction steps need to be taken into account to shed some light on mechanistic details. Thus, an extensive comparison of branched (B) and linear (L) reaction pathways for the Rh-catalyzed hydroformylation of 3,4,4-trimethylpent-1-ene (a bulky chiral substrate), going from a number of reactant complexes to products, has been carried out to rationalize the experimental result that pointed to reaction reversibility, although the value of the regioselectivity ratio (B:L = 15:85), based on alkyl-Rh TS free energies, computed under the hypothesis of nonreversibility, was in satisfactory agreement with the experimental one (5:95). A density functional theory approach at the B3P86/6-31G* level coupled to effective core potentials for Rh in the LanL2DZ valence basis set has been employed. By comparing the activation free energies involved in the various steps for the different reactant adducts, interestingly a similar behavior along all the linear pathways is found: the alkyl-Rh formation TS presents the highest barrier; thus, the reaction is nonreversible for all the linear isomers that invariably proceed to yield the linear aldehyde. Conversely, the behavior is quite different along the branched pathways. While some branched isomers eventually produce the corresponding aldehydes, two of the others follow distinct competing pathways, because β-hydride elimination occurs (a) to the terminal olefin-Rh complex (the starting material) that reacts again with the original regioselectivity, increasing the linear fraction, when the CO addition and insertion TS are higher than the alkyl-Rh TS and (b) to the internal olefin-Rh complex when the CO addition and insertion TS are higher than the relevant β-hydride elimination TS, but not than the alkyl-Rh TS. The solvent effect on the reversible profile, evaluated either in the supermolecule approach by adding a benzene molecule to the calculations or in the IEF-PCM framework (e = 2.247), does not bring about any substantial change in the profile, leaving unaltered the conclusions reached.

Understanding Product Specificity of Protein Lysine Methyltransferases from QM/MM Molecular Dynamics and Free Energy Simulations: The Effects of Mutation on SET7/9 beyond the Tyr/Phe Switch

The results of hybrid quantum mechanical/molecular mechanical (QM/MM) free energy (potential of mean force) simulations for methyl-transfer processes in SET7/9 and its Y245A mutant are compared to address the question concerning the change of the product specificity as well as catalytic efficiency due to the mutation. One of the key questions is whether or not the free energy profiles of methyl transfers may be used to predict the change of the product specificity as a result of the mutations for the residues that are not located at the Tyr/Phe switch position. The simulations show that while the wild-type SET7/9 is a monomethylase, the Y245→A mutation increases the ability of the enzyme to add more methyl groups on the target lysine (i.e., acting as a trimethylase). However, the first methyl-transfer process seems to become less efficient in the mutant compared to that in wild-type. All these results are consistent with experimental observations concerning the effects of the mutation on the product specificity and catalytic efficiency. Thus, the previous suggestion that the energetics of the methyl-transfer reactions may determine the product specificity, at least in some cases, is confirmed by the present work. Moreover, the dynamic information of the reactant complexes obtained from the QM/MM molecular dynamics simulations shows that the ability of the reactant complexes to form the reactive transition-state-like configurations may be used as an important indicator for the prediction of the product specificity of PKMTs, consistent with previous computational studies.

Large Tunneling Effect on the Hydrogen Transfer in Bis(μ-oxo)dicopper Enzyme: A Theoretical Study

Type-III copper-containing enzymes have dicopper centers in their active sites and exhibit a novel capacity for activating aliphatic C-H bonds in various substrates by taking molecular oxygen. Dicopper enzyme models developed by Tolman and co-workers reveal exceptionally large kinetic isotope effects (KIEs) for the hydrogen transfer process, indicating a significant tunneling effect. In this work, we demonstrate that variational transition state theory allows accurate prediction of the KIEs and Arrhenius parameters for such model systems. This includes multidimensional tunneling based on state-of-the-art quantum-mechanical calculations of the minimum-energy path (MEP). The computational model of bis(μ-oxo)dicopper enzyme consists of 70 atoms, resulting in a 204-dimensional potential energy surface. The calculated values of E(a)(H) - E(a)(D), A(H)/A(D), and the KIE at 233 K are -1.86 kcal/mol, 0.51, and 28.1, respectively, for the isopropyl ligand system. These values agree very well with experimental values within the limits of experimental error. For the representative tunneling path (RTP) at 233 K, the pre- and post-tunneling configurations are 3.3 kcal/mol below the adiabatic energy maximum, where the hydrogen travels 0.54 Å by tunneling. We found that tunneling is very efficient for hydrogen transfer and that the RTP is very different from the MEP. It is mainly heavy atoms that move as the reaction proceeds from the reactant complex to the pretunneling configuration, and the hydrogen atom suddenly hops at that point.

Quantum Mechanical/Molecular Mechanical Study on the Mechanism of the Enzymatic Baeyer–Villiger Reaction

We report a combined quantum mechanical/molecular mechanical (QM/MM) study on the mechanism of the enzymatic Baeyer-Villiger reaction catalyzed by cyclohexanone monooxygenase (CHMO). In QM/MM geometry optimizations and reaction path calculations, density functional theory (B3LYP/TZVP) is used to describe the QM region consisting of the substrate (cyclohexanone), the isoalloxazine ring of C4a-peroxyflavin, the side chain of Arg-329, and the nicotinamide ring and the adjacent ribose of NADP(+), while the remainder of the enzyme is represented by the CHARMM force field. QM/MM molecular dynamics simulations and free energy calculations at the semiempirical OM3/CHARMM level employ the same QM/MM partitioning. According to the QM/MM calculations, the enzyme-reactant complex contains an anionic deprotonated C4a-peroxyflavin that is stabilized by strong hydrogen bonds with the Arg-329 residue and the NADP(+) cofactor. The CHMO-catalyzed reaction proceeds via a Criegee intermediate having pronounced anionic character. The initial addition reaction has to overcome an energy barrier of about 9 kcal/mol. The formed Criegee intermediate occupies a shallow minimum on the QM/MM potential energy surface and can undergo fragmentation to the lactone product by surmounting a second energy barrier of about 7 kcal/mol. The transition state for the latter migration step is the highest point on the QM/MM energy profile. Gas-phase reoptimizations of the QM region lead to higher barriers and confirm the crucial role of the Arg-329 residue and the NADP(+) cofactor for the catalytic efficiency of CHMO. QM/MM calculations for the CHMO-catalyzed oxidation of 4-methylcyclohexanone reproduce and rationalize the experimentally observed (S)-enantioselectivity for this substrate, which is governed by the conformational preferences of the corresponding Criegee intermediate and the subsequent transition state for the migration step.

QCT and QM calculations of the Cl(2P) + NH3 reaction: influence of the reactant well on the dynamics

A detailed dynamics study, using both quasi-classical trajectory (QCT) and reduced-dimensional quantum mechanical (QM) calculations, was carried out to understand the reactivity and mechanism of the Cl((2)P) + NH(3)→ HCl + NH(2) gas-phase reaction, which evolves through deep wells in the entry and exit channels. The calculations were performed on an analytical potential energy surface recently developed by our group, PES-2010 [M. Monge-Palacios, C. Rangel, J. C. Corchado and J. Espinosa-Garcia, Int. J. Quantum. Chem., 2011], together with a simplified model surface, mod-PES, in which the reactant well is removed to analyze its influence. The main finding was that the QCT and QM methods show a change of the reaction probability with collision energy, suggesting a change of the atomic-level mechanism of reaction with energy. This change disappeared when the mod-PES was used, showing that the behaviour at low energies is a direct consequence of the existence of the reactant well. Analysis of the trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (E(coll) > 5 kcal mol(-1)) practically all trajectories are direct, at low energies (E(coll) < 3 kcal mol(-1)) the trajectories are indirect, i.e., with the mediation of a trapping complex in the entry and/or the exit wells. The reactant complex allows repeated encounters between the reactants, increasing the reaction probability at low energies. The differential cross section results reinforce this change of mechanism, showing also the influence of the reactant well on this reaction. Thus, the PES-2010 surface yields a forward-backward symmetry in the scattering, while when the reactant well is removed with the mod-PES the shape is more isotropic.

Density functional investigation on the Reaction Mechanisms of Oxidative Activation of Dihydrogen by Osmium Oxide Cation in Gas Phase

Density functional calculations with UB3LYP functional and an extended ECP basis set are employed to calculate the geometries and energies for all possible reactants, intermediates, transition states and products on sextet, quartet and doublet surfaces in four pathways of addition (oxidative addition and [2+2] cycloaddition)-elimination, abstraction-rebound and oxene-insertion for investigating the mechanisms of oxidative activation of dihydrogen by osmium oxide cation. From the results calculated, the title reaction is spin-forbidden, which starts on the quartet surface and ends on sextet surface, the overall reaction is exothermic by 21.0 kJ•mol. Oxene-insertion process is unfavorable thermodynamically due to more positive Gibbs free energy for the reactant complexes. The other three mechanisms proposed exhibit multiple-state-reactivity (MSR) or two-state-reactivity (TSR). Individually the surfaces in three spin states for the two addition-elimination pathways may cross over three times, while the sextet and quartet surfaces for abstraction-rebound may cross once, respectively. The abstraction-rebound mechanism starts on the 1338 化 学 学 报 Vol. 70, 2012 H-abstraction process with uphill potential surfaces and high endothermicity, followed by a barrierless and highly exothermic rebound of H atom, thus it cannot take place at normal temperature. While the two addition-elimination processes have the same rate-determining step, where each barrier is about 156.9 kJ•mol, which is a little higher than that for the usual reactions in liquid, however it is possible to take place due to coupling with the highly exothermic steps before. Furthermore, the concerted [2+2] cycloaddition step has a lower barrier of only 28.7 kJ•mol, which is 113.7 kJ•mol lower than that for the step of the reductive elimination of the first hydride in oxidative addition-elimination process. Thus, [2+2] cycloaddition process is more favorable than oxidative addition process kinetically.

High linear regioselectivity in the rhodium-catalyzed hydro(deuterio)formylation of 3,4,4-trimethylpent-1-ene: The role of β-hydride elimination

The regioselectivity in the hydroformylation reaction catalyzed by an unmodified Rh catalyst has been investigated for a number of α-methylsubstituted alk-1-enes (3-methylbut-1-ene MB1, 3-methylpent-1-ene MP1, 3,4-dimethylpent-1-ene DMP1, and 3,4,4-trimethylpent-1-ene TMP1) experimentally (at 20°C and 100atm CO/H2 total pressure) and theoretically at the B3P86/6-31G* level with Rh described by effective core potentials in the LanL2DZ valence basis set. For all substrates the formation of the linear aldehyde (L) with respect to the branched one (B) in a prevailing amount has been observed (L/B>62/38); the L isomer was formed as the almost exclusive product in the case of TMP1 (L/B=95/5). 2H NMR investigations of crude reaction mixtures, coming from analogous deuterioformylation experiments interrupted at partial substrate conversion, showed that in the case of TMP1 only the branched alkyl-rhodium intermediate, precursor of the branched aldehyde, via β-hydride elimination mainly generates terminal deuterated olefins and, to a lesser extent, internal ones. The reversibility of the branched alkyl-Rh intermediates accounts for the high regioselectivity in favor of the linear aldehyde. Computational studies confirm the importance of the alkyl-Rh transition state (TS) stability to reproduce the experimental regioselectivity, or even to predict it, when the reaction is nonreversible (i.e. for MB1, MP1, and DMP1). In the case of TMP1, the free energy profiles for further reaction steps along branched and linear pathways have been examined to elucidate the origin of reaction reversibility. The TS for the alkyl migratory insertion onto the CO coordinated to rhodium, higher than that for the alkyl-Rh intermediate formation, explains the reason why in deuterioformylation experiments at partial conversion the monodeuterated terminal olefin TMP1-1-d1 is obtained. This occurs for one out of two most populated reactant conformers of TMP1, although for the Curtin–Hammett principle reactant populations are not particularly important. For the other, the reaction proceeds to the branched aldehyde. Only for a less populated reactant conformer the internal olefin is obtained. Conversely, along the linear pathway the CO addition and alkyl migratory insertion steps occur, respectively, in a practically spontaneous way and with very low TS in any case. Agostic interactions (using the QTAIM theory) and kinetic isotope effects have been evaluated and discussed. The examination of further reaction steps for DMP1 allowed us to demonstrate that the reaction is nonreversible for that substrate, despite the similarity between DMP1 and TMP1. The tert-butyl group exerts its steric hindrance mainly on the very first branched reaction steps, favoring an alkyl-Rh TS arrangement lower in free energy than the alkyl-Rh migratory insertion onto the coordinated CO. In part the branched material returns to the reactant complex, thus enriching the linear fraction.

A study of the atmospherically important reactions of dimethylsulfide (DMS) with I2 and ICl using infrared matrix isolation spectroscopy and electronic structure calculations

The reactions of dimethylsulfide (DMS) with molecular iodine (I(2)) and iodine monochloride (ICl) have been studied by infrared matrix isolation spectroscopy by co-condensation of the reagents in an inert gas matrix. Molecular adducts of DMS + I(2) and DMS + ICl have also been prepared using standard synthetic methods. The vapour above each of these adducts trapped in an inert gas matrix gave the same infrared spectrum as that recorded for the corresponding co-condensation reaction. In each case, the infrared spectrum has been interpreted in terms of a van der Waals adduct, DMS : I(2) and DMS : ICl, with the aid of infrared spectra computed for their minimum energy structures at the MP2 level. Computed relative energies of minima and transition states on the potential energy surfaces of these reactions were used to understand why they do not proceed further than the reactant complexes DMS : I(2) and DMS : ICl. The main findings of this research are compared with results obtained earlier for the DMS + Cl(2) and DMS + Br(2) reactions, and the atmospheric implications of the conclusions are also considered.

Scavenging Mechanism of Curcumin Toward the Hydroxyl Radical: A Theoretical Study of Reactions Producing Ferulic Acid and Vanillin

Curcumin is known to be an antioxidant, as it can scavenge free radicals from biological media. A sequence of H-abstraction and addition reactions involving up to eight OH radicals and curcumin or its degradation products leading to the formation of two other antioxidants, namely, ferulic acid and vanillin, was studied. Single electron transfer from curcumin to an OH radical was also studied. All relevant extrema on the potential energy surfaces were located by optimizing geometries of the reactant and product complexes, as well as those of the transition states, at the BHandHLYP/6-31G(d,p) level of density functional theory in the gas phase. Single-point energy calculations were also performed in the gas phase at the BHandHLYP/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. Solvent effects in aqueous media were treated by performing single-point energy calculations at all of the above-mentioned levels of theory employing the polarizable continuum model and the geometries optimized at the BHandHLYP/6-31G(d,p) level in the gas phase. A few reaction steps were also studied by geometry optimization in aqueous media, and the thus-obtained Gibbs free energy barriers were similar to those obtained by corresponding single-point energy calculations. Our calculations show that the hydrogen atom of the OH group attached to the phenol moiety of curcumin would be most efficiently abstracted by an OH radical, in agreement with experimental observations. Further, our study shows that OH addition would be most favored at the C10 site of the heptadiene chain. It was found that curcumin can serve as an effective antioxidant.

Reductive Elimination of ArCF3 from Bidentate PdII Complexes: A Computational Study

The reductive eliminations of ArCF(3) from Pd(II) complexes bearing small- and large-bite-angle phosphane ligands have been investigated using computational methods. QM/QM' and QM/MM studies were applied and complemented with CP2K molecular dynamics investigations. The ligand substituents were varied and a decomposition analysis was performed to allow us to gain insights into the steric and electronic properties of the ligands. The greater reactivity of Xantphos-derived (Xantphos=4,5-bis(diphenylphosphino)-9,9-dimethylxanthene) complexes in the reductive elimination of ArCF(3) is primarily due to the lower repulsive effect of the phoshine substituents in the transition state than in the reactant complex, combined with the increased electronic interaction in the transition state. For DPPE (1,2-bis(diphenylphosphino)ethane), the steric effect of the ligand substituents is greater in the transition state, leading to a higher reaction barrier overall for reductive elimination. There is no direct correlation of the reactivity with the bite angle of the reactant complexes. Only for complexes with large ligand substituents may the bite angle of the Pd complexes be used as a guide for reactivity.

Theoretical studies of the formation of quaternary ammonium mesylates

The pathway of the reaction between suitable mesylate derivatives and trimethylamine by which quaternary ammonium salts are formed according to the S N2 mechanism was investigated. All calculations were performed at the B3LYP/6-31 + G ** level; activation barriers were also calculated at the MPW1K/6-31 + G ** level. All the structures were fully optimized in the gas phase, whereas single point calculations were done using the Polarizable Continuum Model (PCM) in three solvents: chloroform, ethanol and water. In all four cases studied, the reactions proceed via an initial reactant complex, followed by a transition state leading to an ion pair. In the reaction of methyl mesylate C 3 symmetry an ion pair is formed. The stabilizing exo-anomeric effect observed in compound 4 is lost when the reactant complex is formed. It is shown that the B3LYP/6-31 + G ** activation barrier increases when a hydrogen atom in the methyl group is replaced by a tetrahydrofuran ring. A certain differentiation of barriers relative to the bifurcation occurring at a site more distant from the reaction centre (γ carbon) is observed. MPW1K/6-31 + G ** level calculations show that activation barriers are at least 4 kcal mol −1 higher than those from B3LYP/6-31 + G **. Results from the gas phase, from both the B3LYP and the MPW1K methods, indicate that compound 3 should be the least reactive. In the reaction of methyl mesylate with trimethylamine, transfer from the gas phase to the aqueous solution causes the barrier to decrease by more than 10 kcal mol −1. A decrease in the energy barrier is also observed in the case of the other compounds, though to a considerably smaller degree.