Global Reaction Route Mapping on Potential Energy Surfaces of Formaldehyde, Formic Acid, and Their Metal-Substituted Analogues

Finding Minimum Structures on the Seam of Crossing in Reactions of Type A + B → X: Exploration of Nonadiabatic Ignition Pathways of Unsaturated Hydrocarbons

A new theoretical approach is proposed for finding automatically minimum structures on the seam of crossing (MSX) in reactions of type A + B → X, where the artificial-force-induced reaction (AFIR) method is combined with the seam model function (SMF) approach. Its application to reactions between triplet dioxygen and unsaturated hydrocarbons provided many MSX structures. In addition to known ignition pathways, we discovered a pathway through a new type of MSX in the reaction of dioxygen with aromatic hydrocarbons; for benzene, this new pathway requires a lower energy than those of three known ignition pathways and is likely to be the most important. This demonstrates that the AFIR-SMF approach has the ability to discover unknown/unexpected MSX structures without prejudice for presumed pathways or mechanisms.

Rapid and quantitative disulfide bond formation for a polypeptide chain using a cyclic selenoxide reagent in an aqueous medium

To elucidate the reaction mechanism of the disulfide (SS) bond formation reaction of a polypeptide molecule with a water-soluble selenoxide reagent, trans-3,4-dihydroxyselenolane oxide (DHS(ox)), short-term oxidation experiments were carried out for the reduced state (R) of a recombinant hirudin CX-397 variant at pH 7.0 and 25 °C. In the reaction, R was oxidized sequentially to one-SS, two-SS, and three-SS intermediate ensembles within 1 min. The kinetic analysis revealed that the three second-order rate constants for the SS formation are proportional to the number of thiol groups existing in the reactant SS intermediates, indicating the stochastic nature of the SS formation. Ab initio calculation at the HF/6-31++G(d,p) level in water by using the polarizable continuum model suggested that the SS formation reaction is highly exothermic and proceeds via a reactive thioselenurane intermediate with a distorted linear O-Se-S linkage. The results clearly demonstrated that the rate-determining step of the SS formation reaction is the first bimolecular process between a thiol substrate and DHS(ox) rather than the subsequent process to release a SS product.

Quantum chemistry of C(3)H(6)O molecules: structure and stability, isomerization pathways, and chirality changing mechanisms

Electronic structure calculations were carried out to study the various isomers of formula C(3)H(6)O, as a part of our current quantum chemical and dynamical approaches to intra- and intermolecular kinetics for the C(n)H(2n)O (n = 1, 2, 3) molecules. The usefulness of the GRRM (global reaction route mapping) program developed by Ohno and Maeda in predicting the structure of all isomers and of the transition states connecting them is fully exploited. All the isomers are identified as local minima on the MP2/CC-PVDZ potential energy surface. Acetone is the most stable isomer. In increasing order of stability the others are propanal, 2-propenol, 1-propenol, allyl alcohol, methyl vinyl ether, cyclopropanol, propylene oxide, and oxetane. Various isomerization paths connecting them are identified. All the transition states are fully characterized using intrinsic reaction coordinate calculations. The isomerization reactions may proceed through a single step or involve an intermediate species which is either a carbene or a diradical. Special attention is devoted to propylene oxide, a favorite molecule in current photochemical and stereodynamical studies because of its chiral nature. It is a rigid molecule, and chirality switching is found to be supported by its isomers. Two different chirality switching mechanisms which are assisted by propanal and allyl alcohol are presented.

Experimental and theoretical study of the reaction of POCl(3) (-) with O(2)

The oxidation of the trichlorooxyphosphorus anion (POCl(3) (-)), which takes place in combustion flames, has been examined experimentally at a variety of temperatures and theoretically via ab initio and density functional methods. The reaction was examined in a turbulent ion flow tube and kinetics was measured between 300 and 626 K, estimating an overall reaction barrier of 1.23 kcal/mol. Calculations at the density functional, Moller-Plesset second order perturbation, and coupled cluster levels of theory with basis sets up to augmented triple-zeta quality point to a multistep reaction mechanism involving an initial [OP(Cl)(3)(OO)](-) intermediate, an adduct between triplet O(2) with POCl(3) (-), subsequent formation of a four-membered nonplanar P-O-O-Cl ring transition state, with concomitant breaking of the P-Cl and O-O bonds to provide a transient intermediate [OP(Cl)(2)OO...Cl](-), which, in turn, converts to the product complex (POCl(2) (-))(ClO) upon formation of the Cl-O bond without barrier. The calculated energy of the four-membered transition state is considered to be in good agreement with the small overall barrier found by experiment. The final step is responsible for the large exothermicity of the reaction.

Quantum Chemistry Study of H+(H2O)8: A Global Search for Its Isomers by the Scaled Hypersphere Search Method, and Its Thermal Behavior

The structures of the protonated water cluster H+(H2O)8 have been globally explored by the scaled hypersphere search method. On the Hartree-Fock potential energy surface 174 isomers were found, among which 168 were computed to be minima at the B3LYP/6-31+G** level, and their energies were further refined at the level of MP2/6-311++G(3df,2p). The global minimum on the potential energy surface computed at the B3LYP/6-31+G** level shows a cagelike structure with the "Eigen" motif, while the lowest-free-energy isomer has a five-membered-ring structure at 170 K and a chain form at 273 K. The present results are well in line with previous experimental findings. In addition, the ADMP (atom-centered density matrix propagation) simulation indicates that the extra proton in the lowest-free-energy isomer (170 K), which has a five-membered ring and the "Zundel" feature, is often in an asymmetrical hydrogen bond.

Temperature, composition, and hydrogen isotope effect in the hydrogenation of CO on amorphous ice surface at 10–20K

An experiment on the addition reaction of a D atom (deuteration) to CO on a cold ice surface is performed by deuterium atom exposure of three types of samples (pure solid CO, CO-capped H2O ice, and CO-H2O mixed ice) at 10-20 K. The variation of IR absorption spectra for the samples was measured by a Fourier transform infrared spectrometer during exposure to deuterium atoms. Reactions on pure solid CO were observed only at 10 K, while reactions on CO-capped H2O ice and CO-H2O mixed ice were observed to proceed even at 20 K. This indicates that the coexistence of H2O at the surface raises the reactive temperature. In addition, the experiment on H atom exposure was also carried out at 15 K to compare the reaction rate constant between the H and D atoms. The ratio of reaction rate constant kD/kH obtained is about 0.08 at 15 K. The authors provide information on the potential energy for the H+CO reaction at the surface by using the ratio kD/kH and by a model calculation of the potential tunneling with the asymmetric Eckart potential.

Insight into Global Reaction Mechanism of [C2, H4, O] System from ab Initio Calculations by the Scaled Hypersphere Search Method

A detailed computational study is performed on the singlet potential energy surface (PES) for possible isomerization and dissociation reactions of CH(3)CHO at the DFT (B3LYP/6-311++G(d,p)) and CCSD(T)/cc-pVTZ//B3LYP/6-311++G(d,p) levels. The pathways around the equilibrium structures can be discovered by the scaled hypersphere search (SHS) method, which enables us to make a global analysis of the PES for a given chemical composition. Fourteen isomers inclusive of 11 single-molecules and three "non-stabilized" oxygen-based ylides, 5 energetically favored complexes, and 79 interconversion transition states have been found on the singlet PES. Four lowest lying isomers with thermodynamic stability are also kinetically stable with respect to metastable intermediates. It was revealed that vinyl alcohols, which could be generated by the tautomerization of acetaldehyde, could undergo dissociation to form acetylene and water. In addition, recombination channels between some fragments, such as H(2)CO + (1)CH(2) and (1)CHOH + (1)CH(2), are energetically accessible via collision complex or oxygen-based ylides. Most of available unimolecular decompositions are found to be responsible for favorable hydrogen abstraction processes.

Structures of Water Octamers (H2O)8: Exploration on Ab Initio Potential Energy Surfaces by the Scaled Hypersphere Search Method

The potential energy surface (PES) of water octamers has been explored by the scaled hypersphere search method. Among 164 minima on the PES (based on MP2/6-311++G(3df,2p)//B3LYP/6-311+G(d,p) calculations), the cubic structure with D2d symmetry has been confirmed to be the global minimum. In a thermodynamic simulation using these 164 structures, the cubic structure with S4 symmetry has the highest population at low temperature, though double rings can become dominant as temperature going up, in good accord with a recent Monte Carlo simulation using an empirical potential. A transition temperature from cubic to noncubic has significantly been underestimated when potential energy data of B3LYP/6-311+G(d,p) calculations are employed in the simulation. This serious discrepancy between the MP2 and the B3LYP results suggests an importance of dispersion interactions for discussions on thermodynamics of water octamers.