Transition-state-theory calculations for reactions of O(3P) with halogenated olefins

The potential energy surfaces for the reactions of atomic oxygen in its ground electronic state, O(P-3), with the olefins: CF2=CCl2 and CF2=CF - CF3, have been characterized using ab initio molecular orbital calculations. Geometry optimization and vibrational frequency calculations were performed for reactants, transition states and products at the MP2 and QCISD levels of theory using the 6-31G(d) basis set. This database was then used to calculate the rate constants by means of Transition-State-Theory. To obtain a better reference and to test the reliability of the activation barriers we have also carried out computations using the CCSD(T)(fc)/6-311Gdagger, MP4(SDQ)(fc)/CBSB4 and MP2(fc)/CBSB3 single point energy calculations at both of the above levels of theory, as well as with the composite CBS-RAD procedure ( P. M. Mayer, C. J. Parkinson, D. M. Smith and L. Radom, J. Chem. Phys., 1998, 108, 604) and a modi. cation of this approach, called: CBS-RAD( MP2, MP2). It was found that the kinetic parameters obtained in this work particularly with the CBS-RAD ( MP2, MP2) procedure are in reasonable agreement with the experimental values. For both reactions it is found that the channels leading to the olefin double-bond addition predominates with respect to any other reaction pathway. However, on account of the different substituents in the alkenes we have located, at all levels of theory, two transition states for each reaction. Moreover, we have found that, for the reactions studied, a correlation exists between the activation energies and the electronic structure of the transition states which can explain the influence of the substituent effect on the reactivity of the halo-olefins.

Quantum transition state theory and solving a first order master equation for complex reactions numerically

The field of chemical kinetics is an exciting and active field. The prevailing theories make a number of simplifying assumptions that do not always hold in actual cases. Another current problem concerns a development of efficient numerical algorithms for solving the master equations that arise in the description of complex reactions. The objective of the present work is to furnish a completely general and exact theory of reaction rates, in a form reminiscent of transition state theory, valid for all fluid phases and also to develop a computer program that can solve complex reactions by finding the concentrations of all participating substances as a function of time. To do so, the full quantum scattering theory is used for deriving the exact rate law, and then the resulting cumulative reaction probability is put into several equivalent forms that take into account all relativistic effects if applicable, including one that is strongly reminiscent of transition state theory, but includes corrections from scattering theory. Then two programs, one for solving complex reactions, the other for solving first order linear kinetic master equations to solve them, have been developed and tested for simple applications.

Investigations into the mechanism of orotidine 5'-monophosphate decarboxylase: Sources of substrate destabilization and transition state stabilization

Orotidine 5′-monophosphate decarboxylase (OMPDC) achieves a rarely paralleled rate acceleration, yet the catalytic basis prompting this enhancement have yet to be fully elucidated. To accomplish decarboxylation, OMPDC must overcome the high energy barrier due to the localized anionic charge of the intermediate. Mechanistic studies employing enzyme mutagenesis and product or intermediate analogues were used to investigate possible transition state stabilization by a carbene resonance structure. Viability of the carbene structure depends upon a key hydrogen bond between O4 of the substrate and the amide backbone of a conserved serine or threonine. Substitution of the conserved residue with Pro resulted in a kcat/KM of 1 M-1s-1; deletion of the FUMP O4 resulted in a product analogue that does not undergo H6 exchange or inhibit decarboxylation. Hence, indirect evidence reveals the O4-backbone interaction plays an important role for binding and catalysis. OMPDC likely has honed multiple mechanisms to attain its remarkable catalysis. The successful crystallizations of OMPDC a decade ago sparked hypotheses that structure and sequence conserved residues induced productive strain on the substrate-enzyme complex. Here, we demonstrate a new source of stress: a hydrophobic pocket adjacent to the OMP carboxylate that exhibits kinetic parameters characteristic of substrate destabilization. Substitution of these residues with hydrophilic side-chains, by providing hydrogen-bonding partners, decreased kcat by 10 to 10^4–fold. The same substitutions display very little change in the rate of product H6 exchange, supporting that this hydrophobic pocket affects the substrate-enzyme complex before the transition state. We also provide evidence that hydrophilic residues can insert water molecules into the pocket with detrimental effects to catalysis.

Buckled nano rod - a two state system: quantum effects on its dynamics

We consider a suspended elastic rod under longitudinal compression. The compression can be used to adjust potential energy for transverse displacements from the harmonic to the double well regime. The two minima in potential energy curve describe two possible buckled states. Using transition state theory (TST) we have calculated the rate of conversion from one state to other. If the strain epsilon = 4 epsilon c the simple TST rate diverges. We suggest a method to correct this divergence for quantum calculations. We also find that zero point energy contributions can be quite large so that single mode calculations can lead to large errors in the rate.

Folding of Protein L with Implications for Collapse in the Denatured State Ensemble

A fundamental question in protein folding is whether the coil to globule collapse transition occurs during the initial stages of folding (burst phase) or simultaneously with the protein folding transition. Single molecule fluorescence resonance energy transfer (FRET) and small-angle X-ray scattering (SAXS) experiments disagree on whether Protein L collapse transition occurs during the burst phase of folding. We study Protein L folding using a coarse-grained model and molecular dynamics simulations. The collapse transition in Protein L is found to be concomitant with the folding transition. In the burst phase of folding, we find that FRET experiments overestimate radius of gyration, R-g, of the protein due to the application of Gaussian polymer chain end-to-end distribution to extract R-g from the FRET efficiency. FRET experiments estimate approximate to 6 angstrom decrease in R-g when the actual decrease is approximate to 3 angstrom on guanidinium chloride denaturant dilution from 7.5 to 1 M, thereby suggesting pronounced compaction in the protein dimensions in the burst phase. The approximate to 3 angstrom decrease is close to the statistical uncertainties of the R-g data measured from SAXS experiments, which suggest no compaction, leading to a disagreement with the FRET experiments. The transition-state ensemble (TSE) structures in Protein L folding are globular and extensive in agreement with the Psi-analysis experiments. The results support the hypothesis that the TSE of single domain proteins depends on protein topology and is not stabilized by local interactions alone.

Investigations of group IVA transition metal mediated carbon-carbon bond forming reactions

Zirconocene aldehyde and ketone complexes were synthesized in high yield by treatment of zirconocene acyl complexes with trimethylaluminum or diisobutylaluminum hydride. These complexes, which are activated by dialkylaluminum chloride ligands, inserted unsaturated substrates such as alkynes, allenes, ethylene, nitriles, ketenes, aldehydes, ketones, lactones, and acid chlorides with moderate to high conversion. Insertion of aldehyde substrates yielded zirconocene diolate complexes with up to 20:1 (anti:syn) diastereoselectivity. The zirconocene diolates were hydrolyzed to afford unsymmetrical 1,2-diols in 40-80% isolated yield. Unsymmetrical ketones gave similar insertion yields with little or no diastereoselectivity. A high yielding one-pot method was developed that coupled carbonyl substrates with zirconocene aldehyde complexes that were derived from olefins by hydrozirconation and carbonylation. The zirconocene aldehyde complexes also inserted carbon monoxide and gave acyloins in 50% yield after hydrolysis.

The insertion reaction of aryl epoxides with the trimethylphoshine adduct of titanocene methylidene was examined. The resulting oxytitanacyclopentanes were carbonylated and oxidatively cleaved with dioxygen to afford y-lactones in moderate yields. Due to the instability and difficult isolation of titanocene methylidene trimethylphoshine adducts, a one-pot method involving the addition of catalytic amounts of trimethylphosphine to β,β-dimethyltitanacyclobutane was developed. A series of disubstituted aryl epoxides were examined which gave mixtures of diastereomeric insertion products. Based on these results, as well as earlier Hammett studies and labeling experiments, a biradical transition state intermediate is proposed. The method is limited to aryl substituted epoxide substrates with aliphatic examples showing no insertion reactivity.

The third study involved the use of magnesium chloride supported titanium catalysts for the Lewis acid catalyzed silyl group transfer condensation of enol silanes with aldehydes. The reaction resulted in silylated aldol products with as many as 140 catalytic turnovers before catalyst inactivation. Low diastereoselectivities favoring the anti-isomer were consistent with an open transition state involving a titanium atom bound to the catalyst surface. The catalysts were also used for the aldol group transfer polymerization of t-butyldimethylsilyloxy-1-ethene resulting in polymers with molecular weights of 5000-31,000 and molar mass dispersities of 1.5-2.8. Attempts to polymerize methylmethacrylate using GTP proved unsuccessful with these catalysts.

State-to-state dynamics of elementary chemical reactions using Rydberg H-atom translational spectroscopy

In this review, a few examples of state-to-state dynamics studies of both unimolecular and bimolecular reactions using the H-atom Rydberg tagging TOF technique were presented. From the H2O photodissociation at 157 nm, a direction dissociation example is provided, while photodissociation of H2O at 121.6 has provided an excellent dynamical case of complicated, yet direct dissociation process through conical intersections. The studies of the O(D-1) + H-2 --> OH+H reaction has also been reviewed here. A prototype example of state-to-state dynamics of pure insertion chemical reaction is provided. Effect of the reagent rotational excitation and the isotope effect on the dynamics of this reaction have also been investigated. The detailed mechanism for abstraction channel in this reaction has also been closely studied. The experimental investigations of the simplest chemical reaction, the H-3 system, have also been described here. Through extensive collaborations between theory and experiment, the mechanism for forward scattering product at high collision energies for the H+HD reaction was clarified, which is attributed to a slow down mechanism on the top of a quantized barrier transition state. Oscillations in the product quantum state resolved different cross sections have also been observed in the H+D-2 reaction, and were attributed to the interference of adiabatic transition state pathways from detailed theoretical analysis. The results reviewed here clearly show the significant advances we have made in the studies of the state-to-state molecular reaction dynamics.

The near-edge structure in energy-loss spectroscopy: many-electron and magnetic effects in transition metal nitrides and carbides

We investigate the ability of the local density approximation (LDA) in density functional theory to predict the near-edge structure in electron energy-loss spectroscopy in the dipole approximation. We include screening of the core hole within the LDA using Slater's transition state theory. We find that anion K-edge threshold energies are systematically overestimated by 4.22 +/- 0.44 eV in twelve transition metal carbides and nitrides in the rock-salt (B1) structure. When we apply this 'universal' many-electron correction to energy-loss spectra calculated within the transition state approximation to LDA, we find quantitative agreement with experiment to within one or two eV for TiC, TiN and VN. We compare our calculations to a simpler approach using a projected Mulliken density which honours the dipole selection rule, in place of the dipole matrix element itself. We find remarkably close agreement between these two approaches. Finally, we show an anomaly in the near-edge structure in CrN to be due to magnetic structure. In particular, we find that the N K edge in fact probes the magnetic moments and alignments of ther sublattice.

Trends in C-O and C-N bond formations over transition metal surfaces: An insight into kinetic sensitivity in catalytic reactions

Transition metal catalyzed bond formation is a fundamental process in catalysis and is of general interest throughout chemistry. To date, however, the knowledge of association reactions is rather limited, relative to what is known about dissociative processes. For example, surprisingly little is known about how the bond-forming ability of a metal, in general, varies across the Periodic Table. In particular, the effect of reactant valency on such trends is poorly understood. Herein, the authors examine these key issues by using density functional theory calculations to study CO and CN formations over the 4d metals. The calculations reveal that the chemistries differ in a fundamental way. In the case of CO formation, the reaction enthalpies span a much greater range than those of CN formation. Moreover, CO formation is found to be kinetically sensitive to the metal; here the reaction barriers (E-a) are found to be influenced by the reaction enthalpy. CN formation, conversely, is found to be relatively kinetically insensitive to the metal, and there is no correlation found between the reaction barriers and the reaction enthalpy. Analysis has shown that at the final adsorbed state, the interaction between N and the surface is relatively greater than that of O. Furthermore, in comparison with O, relatively less bonding between the surface and N is observed to be lost during transition state formation. These greater interactions between N and the surface, which can be related to the larger valency of N, are found to be responsible for the relatively smaller enthalpy range and limited variation in E-a for CN formation. (C) 2007 American Institute of Physics.

Importance of electronegativity differences and surface structure in molecular dissociation reactions at transition metal surfaces

The dissociative adsorption of N-2 has been studied at both monatomic steps and flat regions on the surfaces of the 4d transition metals from Zr to Pd. Using density functional theory (DFT) calculations, we have determined and analyzed the trends in both straight reactivity and structure sensitivity across the periodic table. With regards to reactivity, we find that the trend in activation energy (Ea) is determined mainly by a charge transfer from the surface metal atoms to the N atoms during transition state formation, namely, the degree of ionicity of the N-surface bond at the transition state. Indeed, we find that the strength of the metal-N bond at the transition state (and therefore the trend in Ea) can be predicted by the difference in Mulliken electronegativity between the metal and N. Structure sensitivity is analyzed in terms of geometric and electronic effects. We find that the lowering of Ea due to steps is more pronounced on the right-hand side of the periodic table. It is found that for the early transition metals the geometric and electronic effects work in opposition when going from terrace to step active site. In the case of the late 4d metals, however, these effects work in combination, producing a more marked reduction in Ea.

Reactivity of the 4d transition metals toward N hydrogenation and NH dissociation: A DFT-based HSAB analysis

The density functional theory (DFT) based hard-soft acid-base (HSAB) reactivity indices, including the electrophilicity index, have been successfully applied to many areas of molecular chemistry. In this work we test the applicability of such an approach to fundamental surface chemistry. We have considered, as prototypical surface reactions, both the hydrogenation of atomic nitrogen and the dissociative adsorption of the NH molecular radical. By use of a DFT methodology, the minimum energy reaction pathways, and corresponding reaction barriers, of the above reactions over Zr(001), Nb(110), Mo(110), Tc(001), Ru(001), Rh(111), and Pd(111) have been determined. By consideration of the chemical potential and chemical hardness of the surface metal atoms, and the principle of electronegativity equalization, it is found that the charge transferred to the NH radical during the process of dissociative adsorption correlates very well with that determined by Mulliken population analysis. Furthermore, it is found that the stability of the NH/surface transition state complex relates directly to this charge transfer and that the trend in transition state stability predicted by a HSAB; treatment correlates very strongly with that determined by DFT calculations. With regards to N hydrogenation, we find that during the course of the reaction, H loses cohesion to the surface, as it must migrate from a 3-fold hollow site to either a bridge or top site, to react with N. Partial density of states (PDOS) and Mulliken population analysis reveal that this loss of bonding is accompanied by charge transfer from H to the surface metal atoms. Moreover, by simple modeling, we show that the reaction barriers are directly proportional to this mandatory charge transfer. Indeed, it is found that the reaction barriers correlate very well with the electrophilicity index of the metal atoms.

Insights into the Staggered Nature of Hydrogenation Reactivity over the 4d Transition Metals

Hydrogenation reactions at transition metal surfaces comprise a key set of reactions in heterogeneous catalysis. In this paper, density functional theory methods are employed to take an in-depth look at this fundamental reaction type. The energetics of hydrogenation of atomic C, N, and O have been studied in some detail over low index Zr, Nb, Mo, Tc, Ru, Rh, and Pd surfaces. Detailed bonding analysis has also been employed to track carefully the chemical changes taking place during reaction. A number of interesting horizontal and vertical trends have been uncovered relating to reactant valency and metal d-band filling. A general correlation has also been found between the reaction barriers and the reaction potential energies. Moreover, when each reaction is considered independently, correlation has been found to improve with decreasing reactant valency. Bonding analysis has pointed to this being related to the relative position of the transition state along the reaction coordinate and has shown that as reactant valency decreases, the transition states become progressively later.

Femtosecond real-time probing of reactions. 12. Vectorial dynamics of transition states

Femtosecond time-resolved techniques with KETOF (kinetic energy time-of-flight) detection in a molecular beam are developed for studies of the vectorial dynamics of transition states. Application to the dissociation reaction of IHgI is presented. For this system, the complex [I---Hg---I](++)* is unstable and, through the symmetric and asymmetric stretch motions, yields different product fragments: [I---Hg---I](++)* -> HgI(X^2/sigma^+) + I(^2P_3/2) [or I*(^2P_l/2)] (1a); [I---Hg---I](++)* -> Hg(^1S_0) + I(^2P_3/2) + I(^2P_3/2) [or I* (^2P_1/2)] (1 b). These two channels, (1a) and (1b), lead to different kinetic energy distributions in the products. It is shown that the motion of the wave packet in the transition-state region can be observed by MPI mass detection; the transient time ranges from 120 to 300 fs depending on the available energy. With polarized pulses, the vectorial properties (transition moments alignment relative to recoil direction) are studied for fragment separations on the femtosecond time scale. The results indicate the nature of the structure (symmetry properties) and the correlation to final products. For 311-nm excitation, no evidence of crossing between the I and I* potentials is found at the internuclear separations studied. (Results for 287-nm excitation are also presented.) Molecular dynamics simulations and studies by laser-induced fluorescence support these findings.

A potential energy surface for the ground state of formaldehyde, H2CO(1A1)

A model potential energy function for the ground state of H2CO has been derived which covers the whole space of the six internal coordinates. This potential reproduces the experimental energy, geometry and quadratic force field of formaldehyde, and dissociates correctly to all possible atom, diatom and triatom fragments. Thus there are good reasons for believing it to be close to the true potential energy surface except in regions where both hydrogen atoms are close to the oxygen. It leads to the prediction that there should be a metastable singlet hydroxycarbene HCOH which has a planar trans structure and an energy of 2•31 eV above that of equilibrium formaldehyde. The reaction path for dissociation into H2 + CO is predicted to pass through a low symmetry transition state with an activation energy of 4•8 eV. Both of these predictions are in good agreement with recently published ab initio calculations.

Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)