Quantum nonadiabatic dynamics of hydrogen exchange reactions

In continuation of our earlier effort to understand the nonadiabatic coupling effects in the prototypical H + H₂ exchange reaction [Jayachander Rao et al. Chem. Phys. 333 (2007) 135], we present here further quantum dynamical investigations on its isotopic variants. The present work also corrects a technical scaling error occurred in our previous studies on the H + HD reaction. Initial state-selected total reaction cross sections and Boltzmann averaged thermal rate constants are calculated with the aid of a time-dependent wave packet approach employing the double many body expansion potential energy surfaces of the system. The theoretical results are compared with the experimental and other theoretical data whenever available. The results re-establish our earlier conclusion, on a more general perspective, that the electronic nonadiabatic effects are negligible on the important quantum dynamical observables of these reactive systems reported here.     

Quantum mechanical calculations on phosphate hydrolysis reactions

Multiple biological processes are regulated by kinases and phosphatases. This study aims to provide nonenzymatic models for phosphorylation and dephosphorylation of serine, threonine, and tyrosine phosphate using ab initio guantum mechanical calculations. We reduce the problem to methyl phosphate hydrolysis to model serine/threonine, and the hydrolysis of phenyl phosphate to model the tyrosine. HF, B3LYP, and MP2 calculations with a 6‐31+G(d) basis set were employed. The effect of water as a catalyst was also analyzed. As expected, the activation energy barrier is lowered. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 43–51, 2000     

Oscillatory reactions involving hydrogen peroxide and thiosulfate-kinetics of the oxidation of tetrathionate by hydrogen peroxide

The reaction between tetrathionate and hydrogen peroxide forms an important part of several pH oscillators based on the oxidation of thiosulfate. The kinetics of this reaction were examined in a batch reactor by measurement of the initial pH values in the range from 8 to 10.5. Experimental data were evaluated by the method of initial reaction rates combined with the assumption of instantaneously equilibrated acid-base reactions. The rate-determining step was found to be of the first order with respect to tetrathionate, hydrogen peroxide, and OH- ions with the value of rate constant k = (1.50 +/- 0.03) x 10(2) (M2 s)(-1) at 25 degrees C. In the alkaline solution, no distinct catalytic effect of Cu2+ was observed in contrast to earlier assumptions. The waveform of measured pH over the course of the reaction indicates that thiosulfate is probably an intermediate because characteristics of the curves are very similar to those for the oxidation of thiosulfate. We also measured the time evolution of concentrations of major components by the attenuated total internal reflectance infrared spectroscopy to further elucidate the underlying reaction mechanism. These measurements confirm the suspected role of thiosulfate as an intermediate in the studied reaction and provide valuable detailed information on the time evolution of thiosulfate, sulfite, sulfate, tetrathionate, and trithionate. These experimental observations are included in a simple mechanism that accurately simulates the reaction course in an alkaline solution. The results provide considerable new insights into the nature of autocatalysis in the hydrogen peroxide-thiosulfate-Cu2+ reaction and suggest that a new role for Cu2+ in the oscillatory dynamics observed in a flow-through reactor needs to be found.     

Quantum chemical investigation of low-temperature intramolecular hydrogen transfer reactions of hydrocarbons

The B3LYP functional was evaluated as a method to calculate reaction barriers and structure-reactivity relationships for intramolecular hydrogen transfer reactions involving peroxy radicals. Nine different basis sets as well as five other MO/DFT and hybrid methods were used in comparing three reactions to available experimental data. It was shown that B3LYP/6-311+G(d,p) offers a good compromise between speed and accuracy for studies in which thermodynamic and kinetic data of many reactions are required. Sixteen reactions were studied to develop structure-reactivity relationships to correlate the activation energy with the heat of reaction. As long as no structural heterogeneities were present in the transition state ring, a simple Evans-Polanyí relationship was shown to capture the activation energy as a function of heat of reaction for reactions in the 1,5-hydrogen shift family. For peroxy radicals undergoing self-abstraction of a hydrogen atom in the 1,5-position, the activation energy was calculated as E(a) (kcal mol(-1)) = 6.3 + Delta H(rxn) (kcal mol(-1)). For reactions with a carbonyl group embedded in the ring of the transition state, the activation energy of peroxy radicals undergoing self-abstraction was correlated as E(a) (kcal mol(-1)) = 18.1 + 0.74 Delta H(rxn) (kcal mol(-1)). The impact of the size of the transition state ring on the activation energy and pre-exponential factor was also probed, and it was shown that these effects can be described using simple nonlinear and linear fits, respectively.     

Quantum mechanical analysis of 1,2-ethanediol conformational energetics and hydrogen bonding

A proper understanding of the conformational energetics of 1,2-ethanediol (ethylene glycol) is important to the construction of molecular mechanics force fields for the treatment of carbohydrates since these biologically important molecules have a prevalence of vicinal hydroxyl groups. In the present study, quantum mechanical analysis of the 10 unique minimum-energy conformations of ethylene glycol is performed by using 10 model chemistries ranging from HF/6-311++G(d,p) up to a hybrid method that approximates CCSD(T)/cc-pVQZ. In addition, natural bond orbital (NBO) analysis of these conformations with deletion of pairings of CO bond/antibonding and lone pair/antibonding orbitals is used to investigate contributions from the "gauche" effect to ethylene glycol conformational energetics. MP2 with the "correlation consistent" basis sets and DFT/6-311++G(d,p) do the best job of matching the approximate CCSD(T)/cc-pVQZ energies while MP2/6-31G(d) and Hartree-Fock both fare poorly. NBO analysis shows the conformational energies to be independent of the deletion of matrix elements associated with (i) CO bonding and antibonding orbital interactions and (ii) lone pair and antibonding orbital interactions, whereas the energetic ordering correlates with geometric parameters consistent with internal hydrogen bonds. Thus, the present results suggest that standard molecular mechanics potential energy functional forms, which lack explicit terms to account for stereoelectronic effects, are appropriate for carbohydrates.     

Isotope heat effect in reactions involving hydrogen evolution on palladium catalyst particles

The heat effect in the reduction of copper(II) by formaldehyde on palladium catalyst particles accompanied by hydrogen evolution depends on the presence of deuterium in the system. In the case of 80% substitution of hydrogen in the system by deuterium the heat effect increases 1·5 times. This fact can not be attributed only to the difference in the energies of the bonds of hydrogen and deuterium in compounds participating in the reaction.     

Quantum mechanical predictions of the stereoselectivities of proline-catalyzed asymmetric intermolecular aldol reactions

Quantum mechanical calculations were employed to predict the ratio of four stereoisomeric products expected from two complex reactions involving the aldol reactions of cyclohexanone with benzaldehyde or with isobutyraldehyde catalyzed by (S)-proline. Experimental tests of these predictions provide an assessment of the state-of-the-art in quantum mechanical prediction of products of complex organic reactions in solution.     

Quantum mechanical reaction dynamics in collisions of chlorine atom with hydrogen molecule

We report the accurate determinations of quantum mechanical state-to-state probabilities tor reactions Cl H2 - HCl H and H' HCl - H'Cl H by the generalized Newton variational principle, on the most accurate available potential energy surface. We compare the results for three versions of realistic potential energy surfaces, and to those from hyperspherical close-coupling calculations.     

Heterocyclization reactions involving thiols

Information on the syntheses of sulfur-containing heterocycles involving thiols is systematized and generalized. Data on biological action of some among these systems are mentioned.     

Transmetallation reactions involving phenylenemercurials

When heated with Group V and Group VI elements, the phenylenemercurials (C₆H₄Hg)₃, (C₆F₄Hg)₃ and (C₆Cl₄Hg)₃ form heterocycles of formulae (M₂(C₆X₄)₃ and M′₂(C₆X₄)₂ where M = As, Sb, Bi and M′ = S, Se, Te. The compounds Te₂(C₆Cl₄)₂ and M₂(C₆Cl₄)₃ (M = As, Sb, Bi) were also obtained by heating the elements with 1,2-I₂C₆Cl₄, which was prepared by mercuration of 1,2-H₂C₆Cl₄ followed by iododemercuration. Octachlorothianthrene has been obtained by heating sulphur with Te₂(C₆Cl₄)₂, C₆Cl₆ or C₆Cl₅I, and from the reaction between 1,2-H₂C₆Cl₄, AlCl₃, and S₂Cl₂.     

Organocatalytic reactions involving nitrogen-ylides

Nitrogen ylides represent an important class of nucleophilic or bifunctional reagents. This digest summarizes the application of diverse nitrogen ylides for the construction of important and interesting carbo- or heterocycles in the reactions with a variety of electrophiles, especially under the catalysis of an organic compound.     

Quantum mechanical approach to the chemisorption of molecular hydrogen on defect magnesium oxide surfaces

Quantum mechanical theoretical calculations have been performed on the linear atomic chain in order to simulate the interaction of molecular hydrogen with the defects present at the surface of activated MgO. The total energy of the system, the relative energy of the various molecular orbitals, and the electronic charge distribution have been computed for various lattice parameters (d _O-O = 4.0–4.8 Å) as a function of the H-H (or O-H) separation. A symmetrical motion of the hydrogen nuclei with respect to the central Mg²⁺ vacancy was assumed. It is shown that chemisorption of hydrogen on surface O^–ions sites results in the formation of pseudo-hydroxyl groups. For a small lattice parameter (4.0 Å), no stable state of molecular hydrogen has been found while an increase in the lattice parameter results in a uniform increase of the calculated activation energy for the molecular hydrogen activation process. A mechanism is proposed which is not so different from that put forward for the hydrogen activation by transition metal complexes. Molecular hydrogen is found to act as an electron donor.     

Benzindoles. 18. Some electrophilic substitution reactions involving the hydrogen atoms in 4,5,6,7-dibenzindole

The principal electrophilic substitution reactions involving the hydrogen atom of 4,5,6,7-dibenzindole — the Vilsmeier reaction, the Mannich reaction, diazo coupling, and acylation — were studied, and a qualitative comparison of its reactivities with indole and 4,5- and 6,7-benzindoles was made. It was established that 4,5,6,7-dibenzindole has the most clearly expressed electron-donor properties. The structures of the synthesized compounds were proved by data from the IR, UV, PMR, and mass spectra.See [1] for communication 17.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 366–370, March, 1979.     

OH hydrogen abstraction reactions from alanine and glycine: A quantum mechanical approach

Density functional theory (B3LYP and BHandHLYP) and unrestricted second‐order Møller–Plesset (MP2) calculations have been performed using 3‐21G, 6‐31G(d,p), and 6‐311 G(2d,2p) basis sets, to study the OH hydrogen abstraction reaction from alanine and glycine. The structures of the different stationary points are discussed. Ring‐like structures are found for all the transition states. Reaction profiles are modeled including the formation of prereactive complexes, and very low or negative net energy barriers are obtained depending on the method and on the reacting site. ZPE and thermal corrections to the energy for all the species, and BSSE corrections for B3LYP activation energies are included. A complex mechanism involving the formation of a prereactive complex is proposed, and the rate coefficients for the overall reactions are calculated using classical transition state theory. The predicted values of the rate coefficients are 3.54×10⁸ L?mol^?1?s^?1 for glycine and 1.38×10⁹ L?mol^?1?s^?1 for alanine. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1138–1153, 2001