Probing the imine silylenoid HN=SiNaF and its insertions reaction with R–H (R=F,OH, NH<Subscript>2</Subscript>, CH<Subscript>3</Subscript>) using DFT

The geometries and isomerization of the imine silylenoid HN=SiNaF as well as its insertion reactions with some R–H molecules have been systematically investigated theoretically, where R=F, OH, NH₂, and CH₃, respectively. The barrier heights for the four insertion reactions are 67.7, 115.6, 153.5, and 271.5 kJ/mol at the B3LYP/6-311+G* level of theory, respectively. Here, all the mechanisms of the four reactions are identical to each other, i.e., a stable intermediate has been formed during the insertion reaction. Then, the intermediate could dissociate into the substituted silylene (HN=SiHR) and NaF with a barrier corresponding to their respective dissociation energies. Correspondingly, the reaction energies for the four reactions are 71.8, 95.5, 123.3, and 207.6 kJ/mol, respectively, which are linearly correlated with the calculated barrier heights. Furthermore, the effects of halogen substitutions (F, Cl, and Br) on the reaction activity have also been discussed. As a result, the relative reactivity among the four insertion reactions should be as follows: H–F > H–OH > H–NH₂ > H–CH₃.     

DFT studies of the phosphinidene derivative HPNaF and its insertion reaction with R–H(R=F,OH, NH<Subscript>2</Subscript>, CH<Subscript>3</Subscript>)

The formations of the phosphinidene derivative HPNaF and its insertion reactions with R–H (R=F, OH, NH₂, CH₃) have been systematically investigated employing the density functional theory (DFT), such as the B3LYP and MPW1PW91 methods. A comparison with the results of MP2 calculations shows that MPW1PW91 underestimates the barrier heights for the four reactions considered. Similarly, the same is also true for the B3LYP method depending on the selected reactions, but by much less than MPW1PW91, where the barrier heights of the four reactions are 25.2, 85.7, 119.0, and 142.4 kJ/mol at the B3LYP/6-311+G* level of theory, respectively. All the mechanisms of the four reactions are identical to each other, i.e., an intermediate has been located during the insertion reaction. Then, the intermediate could dissociate to substituted phosphinidane(H₂RP) and NaF with a barrier corresponding to their respective dissociation energies. Correspondingly, the reaction energies for the four reactions are −92.2, −68.1, −57.2, and −44.3 kJ/mol at the B3LYP/6-311+G* level of theory, respectively, where both the B3LYP and MPW1PW91 methods underestimate the reaction energies compared with the MP2 results. The linear correlations between the calculated barrier heights and the reaction energies have also been observed. As a result, the relative reactivity among the four insertion reactions should be as follows: H–F > H–OH > H–NH₂ > H–CH₃.     

Finding the possible mechanisms for a given type of overall reaction

A systematic way to derive all thea priori possible mechanisms classified according to the numbers, ϱ, of elementary or molecular reaction steps was presented recently. The method is now applied to overall reactions of the type A +B ⇒ C+D. The “laminar” (elementary steps' stoichiometric coefficients unity) mechanisms that turn out possible are derived and listed for the important ϱ = 2 case. The ϱ = 3 three step mechanisms were reported in another paper. Many examples from actual chemical, biochemical mechanisms, such as S_E1, S_N1, S_E2, S_N2, activated complex theory of abstraction reactions, free radical chain propagation and biochemical electron transport chains are given. By far most mechanisms usually encountered are of the laminar type, although the method also gives the “turbulent” ones, i.e. with some stoichiometric coefficients in elementary steps larger than one or some species occurring in many of the steps. Alexander von Humboldt Senior Scientist Awardee, West Germany. Predoctoral Research Assistant, Yale University 1973–74. Then at the Roswell Park Memorial Institute, Department of Experimental Therapeutics, Buffalo, New York 14203.     

About the Secondary Electron Emission Yield, δ, from e−-Irradiated Insulators

 To account for the published yield curves, δ = f ( E ₀), of some insulators such as diamond, an elementary theory of secondary electron emission (s.e.e) is used. This theory permits the estimation of the effective attenuation lengths of the emitted electrons during their transport and to explain the significant differences between the s.e.e. from metals and that from insulators. Some practical consequences related for instance to the lack of topographic contrast in LVSEM and to charging mechanisms in electron beam techniques are then deduced.     

A theoretical study on the mechanism of the addition reaction between carbene and epoxyethane

The mechanism of addition reaction between carbene and epoxyethane has been investigated employing the MP2 and B3LYP/6-311+G* levels of theory. Geometry optimization, vibrational analysis, and energy property for the involved stationary points on the potential energy surface have been calculated. Based on the calculated results at the MP2/6-311+G* level of theory, it can be predicted that there are two reaction mechanisms (1) and (2). In the first reaction carbene attacks the atom O of epoxyethane to form an intermediate 1a (IM1a), which is a barrier-free exothermic reaction. Then, IM1a can isomerize to IM1b via a transition state 1a (TS1a), where the potential barrier is 48.6 kJ/mol. Subsequently, IM1b isomerizes to a product epoxypropane (Pro1) via TS1b with a potential barrier of 14.2 kJ/mol. In the second carbene attacks the atom C of epoxyethane firstly to form IM2 via TS2a. Then IM2 isomerizes to a product allyl alcohol (Pro2) via TS2b with a potential barrier of 101.6 kJ/mol. Correspondingly, the reaction energies for the reactions (1) and (2) are −448.4 and −501.6 kJ/mol, respectively. Additionally, the orbital interactions are also discussed for the leading intermediate. The results based on the B3LYP/6-311+G* level of theory are paralleled to those on the MP2/6-311+G* level of theory. Furthermore, the halogen and methyl substituent effects of H₂C: on the two reaction mechanisms have been investigated. The calculated results indicate that the introductions of halogen or methyl make the addition reaction difficult to proceed.     

Rationalizing cellulose (in)solubility: reviewing basic physicochemical aspects and role of hydrophobic interactions

Despite being the world’s most abundant natural polymer and one of the most studied, cellulose is still challenging researchers. Cellulose is known to be insoluble in water and in many organic solvents, but can be dissolved in a number of solvents of intermediate properties, like N-methylmorpholine N-oxide and ionic liquids which, apparently, are not related. It can also be dissolved in water at extreme pHs, in particular if a cosolute of intermediate polarity is added. The insolubility in water is often referred to strong intermolecular hydrogen bonding between cellulose molecules. Revisiting some fundamental polymer physicochemical aspects (i.e. intermolecular interactions) a different picture is now revealed: cellulose is significantly amphiphilic and hydrophobic interactions are important to understand its solubility pattern. In this paper we try to provide a basis for developing novel solvents for cellulose based on a critical analysis of the intermolecular interactions involved and mechanisms of dissolution.     

Theoretical studies on the mechanisms of NCCO + O2 reaction

The mechanisms of the reaction of NCCO with molecular oxygen are investigated at the G3MP2//B3LYP/6-311G(d,p) levels for the first time. The calculation results show that two mechanisms are involved, namely, O attack on α atom mechanism and O attack on β atom mechanism, with six products yielded. The most feasible channel is the addition of O₂ to β atom in NCCO radical leading to the energy-rich intermediate IM1, NCC(O)OO, which can isomerize to a four-center-structure IM3, and then undergoes C–C and O–C bond fission to form P1(NCO + CO₂) finally. The barriers are 27.3 and 25.4 kcal/mol, respectively. For other channels involved in the two mechanisms, with less stable initial adducts and higher barrier, they are less conceivable dynamically and thermochemically.     

Recent advances in quantum mechanical/molecular mechanical calculations of enzyme catalysis: hydrogen tunnelling in liver alcohol dehydrogenase and inhibition of elastase by α-ketoheterocycles

 Hybrid quantum mechanical (QM)/molecular mechanical (MM) calculations are used to study two aspects of enzyme catalysis, Kinetic isotope effects associated with the hydride ion transfer step in the reduction of benzyl alcohol by liver alcohol dehydrogenase are studied by employing variational transition-state theory and optimised multidimensional tunnelling. With the smaller QM region, described at the Hartree–Fock ab initio level, together with a parameterised zinc atom charge, good agreement with experiment is obtained. A comparison is made with the proton transfer in methylamine dehydrogenase. The origin of the large range in pharmacological activity shown by a series of α-ketoheterocycle inhibitors of the serine protease, elastase, is investigated by both force field and QM/MM calculations. Both models point to two different inhibition mechanisms being operative. Initial QM/MM calculations suggest that these are binding, and reaction to form a tetrahedral intermediate, the latter process occurring for only the more potent set of inhibitors. Recieved 3 October 2001 / Accepted: 6 September 2002 / Published online: 31 January 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: I. H. Hillier Acknowledgements. We thank EPSRC and BBSRC for support of the research and D.G. Truhlar for the use of the POLYRATE code.     

Characterisation of two novel cyclodextrinases using on-line microdialysis sampling with high-performance anion exchange chromatography

In this work, a real-time sampling/analytical method for on-line measurements of two newly discovered cyclomaltodextrinases (CDases) has been developed and evaluated. This novel methodology not only allows the final products to be investigated, but it also reveals enzyme-specific differences in the degradation pathways during the hydrolysis of different substrates, which is a great advantage in the important tasks of investigating the mechanisms of and classifying new hydrolases, and is an advantage that conventional techniques cannot offer. Two different enzymes, one CDase from Laceyella sacchari (LsCda13) and one from Anoxybacillus flavithermus (AfCda13), were investigated during the hydrolysis of α-, β- and γ-cyclodextrin, and the hydrolysis products were sampled via a microdialysis probe and injected on-line every 30 min into a high-performance anion exchange chromatography system equipped with a pulsed amperometric detector (HPAEC–PAD), where they were identified. The enzymes yielded the same end-products, maltose and glucose, in an approximate molar ratio of 2:1, but they exhibited distinctly different patterns of intermediate product formation before reaching the end-point. LsCda13 had a more random distribution of the intermediate products, whereas AfCda13 showed the distinct intermediate production of maltotriose, which in some cases accumulated.     

Modeling the H5+ potential-energy surface: a first attempt

 Ab initio molecular electronic structure calculations are performed for H₅ ⁺ at the QCISD(T) level of theory, using a correlation-consistent quadruple-zeta basis set. Structures, vibrational frequencies and thermochemical properties are evaluated for ten stationary points of the H₅ ⁺ hypersurface and are compared with previous calculations. The features of the H₃ ⁺…H₂ interaction at intermediate and large intermolecular distances are also investigated. Furthermore, an analytical functional form for the potential-energy surface of H₅ ⁺ is derived using a first-order diatomics-in-molecule perturbation theory approach. Its topology is found to be qualitatively correct for the short-range interaction region. Received: 15 March 2001 / Accepted: 5 July 2001 / Published online: 11 October 2001     

Calculation of correlation energy by many-body diagrammatic perturbation theory

The many-body diagrammatic perturbation theory is used for calculation of the correlation energy of closed-shell molecular systems. We apply Brueckner's concept of the two-particle renormalized interaction defined by a non-linear diagrammatic expression containing all possible (diagonal and/or non-diagonal) particle-particle, hole-hole and particle-hole intermediate elementary processes. Then, a “second-order” simple diagrammatic expression for the correlation energy can be formed, where the correlation energy is approximated by all the diagrams with biexcited intermediate states. An illustrative numerical application for the LiH molecule is presented. This article is dedicated to the memory of our friends and colleagues Dr. Jarka Surá and Dr. Marta Černayová, who tragically died in July 1976.     

Distribution of the products from the alkylation of isobutane with butenes at a zeolite catalyst and the reaction mechanism

The mechanisms of formation are proposed on the basis of the distribution of the intermediate and final products of zeolite alkylation of isobutane with butenes. The mechanisms are based on activation of the isobutane molecule at the methyl groups, simultaneous intermolecular and intramolecular hydride transfer, and β dissociation during skeletal isomerization of the carbonium ions.     

Potential surface topology of a butene—gold atom system in the ground state

Quantum chemical modeling of but-1-ene isomerization to cis-but-2-ene and trans-but-2-ene in the presence of a gold atom has been carried out in the framework of the density functional theory with an extended basis set, the PBE functional, and a pseudopotential with relativistic corrections included. Two possible mechanisms have been considered, viz., with the formation of an intermediate σ-complex with one C(sp²)—Au bond and with gold insertion into the C—H bond. In the former case, the calculated energy barriers to two isomerization stages are higher than 30 kcal mol⁻¹. In the latter case, the reaction involves three stages and proceeds via a metal hydride complex with low barriers. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1330–1337, July, 2008.     

Kinetics for tautomerizations and dissociations of triglycine radical cations

Fragmentations of tautomers of the α-centered radical triglycine radical cation, [GGG^•]⁺, [GG^•G]⁺, and [G^•GG]⁺, are charge-driven, giving b-type ions; these are processes that are facilitated by a mobile proton, as in the fragmentation of protonated triglycine (Rodriquez, C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006–3012). By contrast, radical centers are less mobile. Two mechanisms have been examined theoretically utilizing density functional theory and Rice-Ramsperger-Kassel-Marcus modeling: (1) a direct hydrogen-atom migration between two α-carbons, and (2) a two-step proton migration involving canonical [GGG]^•+ as an intermediate. Predictions employing the latter mechanism are in good agreement with results of recent CID experiments (Chu, I. K. et al. J. Am. Chem. Soc. 2008, 130, 7862–7872).     

Mechanism of singlet oxygen generation during catalytic decomposition of methyl(trifluoromethyl)dioxirane by chloride ions

The mechanism of the chloride ion-induced catalytic decomposition of methyl(trifluoromethyl)dioxirane in trifluoroacetone was studied at the MP4//MP2/6-31+G(d) level of theory. The solvated chloride ion interacts with dioxirane to form an ion-dipole pair, which is transformed into the key intermediate ClO—C(Me)(CF₃)—O⁻ acting as a chain carrier in the catalytic decomposition of dioxirane. The generation of singlet oxygen occurs during the transformations of this intermediate on the singlet potential energy surface.     

Second-order energy components in basis-set-superposition-error-free intermolecular perturbation theory

 Recently a basis-set-superposition-error-free second-order perturbation theory was introduced based on the “chemical Hamiltonian approach” providing the full antisymmetry of all wave functions by using second quantization. Subsequently, the “Heitler–London” interaction energy corresponding to the sum of the zero- and first-order perturbational energy terms was decomposed into different physically meaningful components, like electrostatics, exchange and overlap effects. The first-order wave function obtained in the framework of this perturbation theory also consists of terms having clear physical significance: intramolecular correlation, polarization, charge transfer, dispersion and combined polarization–charge transfer excitations. The second-order energy, however, does not represent a simple sum of the respective contributions, owing to the intermolecular overlap. Here we propose an approximate energy decomposition scheme by defining some “partial Hylleraas functionals” corresponding to the different physically meaningful terms of the first-order wave functions. The sample calculations show that at large and intermediate intermolecular distances the total second-order intermolecular interaction energy contribution is practically equal to the sum of these “physical” terms, while at shorter distances the overlap-caused interferences become of increasing importance. Received: 18 June 2001 / Accepted: 28 August 2001 / Published online: 16 November 2001     

Ab initio correlation corrections to the Hartree-Fock quasi band-structure of periodic systems employing Wannier-type orbitals

A size-consistent ab initio formalism to calculate correlation corrections to ionization potentials as well as electron affinities of periodic systems is presented. Our approach is based on a Hartree-Fock scheme which directly yields local orbitals without any a posteriori localization step. The use of local orbitals implies non-zero off-diagonal matrix elements of the Fock operator, which are treated as an additional perturbation and give rise to localization diagrams. Based on the obtained local orbitals, an effective Bloch Hamiltonian is constructed to second order of perturbation theory with all third-order localization diagrams included. In addition, the summation of certain classes of diagrams up to infinite order in the off-diagonal Fock elements as well as the Epstein-Nesbet partitioning of the full Hamiltonian are discussed. The problem of intruder states, frequently encountered in many-body perturbation theory, is dealt with by employing the theory of intermediate Hamiltonians. As model systems we have chosen cyclic periodic structures up to an oligoethylene ring in double-zeta basis; however, the theory presented here straightforwardly carries over to infinite periodic systems. Received: 30 April 1998 / Accepted: 27 July 1998 /  Published online: 7 October 1998     

Ab initio MD simulations of a prototype of methyl chloride hydrolysis with explicit consideration of three water molecules: a comparison of MD trajectories with the IRC path

Ab initio molecular dynamics simulations at the Hartree-Fock/6-31G level of theory are performed on methyl chloride hydrolysis with explicit consideration of one solute and two solvent water molecules at a temperature of 298 K. The reaction involves the formation of a reactant complex and the energy surface to the transition state is found to be simple. Two types of trajectories toward the product are observed. In the first type, the system reaches an intermediate complex (complex-P1) region after two nearly concerted proton transfers involving the attacking water molecule and the solvent water molecules. These trajectories resemble the intrinsic reaction coordinate trajectory. The thermal motion of the atoms leads the system to another intermediate complex (complex-P2) region. A second type of trajectory is found in which the system reaches the complex-P2 region directly after the proton transfers. In both of these forward trajectories, back proton transfers lead the system to a final complex-F region which resembles protonated methanol. Received: 3 July 1998 / Accepted: 2 September 1998 / Published online: 15 February 1999     

Mechanistic possibilities for oxetane formation in the biosynthesis of Taxol’s D ring

Three mechanistic possibilities for the formation of the oxetane (D ring) of Taxol were examined at various levels of theory [B3LYP/6-31+G(d,p), mPW1PW91/6-31+G(d,p), and MP2/6-31+G(d,p)] including one mechanism involving an unusual oxabicyclobutonium ion intermediate. The mechanisms examined differ considerably in terms of their predicted inherent activation barriers, and the requirements for acceleration of each by an enzyme active site are outlined. Our calculations provide an important starting point for future studies in this area. Also examined were previously published calculations on simple oxabicyclobutonium ions, as well as the all-carbon analog of the pathway involving the oxabicyclobutonium ion. Published in Rossiiskii Khimicheskii Zhurnal, 2007, Vol. 51, No. 5, pp. 49–55.     

Controversy and complementarity in mechanistic organic chemistry. The transition state and structural theories reexamined

It is proposed that molecular phenomena may only be described within the framework of the Complementarity Principle (‘CP’), and that scientific controversy may originate in the essential incompatibility of complementary representations. Complementarity based on the temporal Uncertainty Principle leads to new insights into transition state theory, microscopic reversibility and the Curtin-Hammett Principle. An empirical application of the ‘CP’ to the structural theory leads to a revision of present concepts of ‘reaction dynamics’, with the Principle of Least Nuclear Motion (‘PLNM’) emerging as a general alternative to electronic theories of reactivity. In fact, it is argued that the ‘PLNM’ is a better basis for the Woodward-Hoffmann rules than is orbital symmetry. A more flexible approach to organic reaction mechanisms is thus indicated. Also, as the basis of the structural theory is fundamentally uncertain, and the present theory of X-ray diffraction apparently incompatible with the ‘UP’, a reinterpretation of the Bragg equation has been attempted.