Showing papers on "Transition state published in 2004"

Development of density functionals for thermochemical kinetics

Abstract: A density functional theory exchange-correlation functional for the exploration of reaction mechanisms is proposed. This functional, denoted BMK (Boese-Martin for Kinetics), has an accuracy in the 2 kcal/mol range for transition state barriers but, unlike previous attempts at such a functional, this improved accuracy does not come at the expense of equilibrium properties. This makes it a general-purpose functional whose domain of applicability has been extended to transition states, rather than a specialized functional for kinetics. The improvement in BMK rests on the inclusion of the kinetic energy density together with a large value of the exact exchange mixing coefficient. For this functional, the kinetic energy density appears to correct “back” the excess exact exchange mixing for ground-state properties, possibly simulating variable exchange.

Development of Novel Density Functionals for Thermochemical Kinetics

Abstract: A new density functional theory (DFT) exchange-correlation functional for the exploration of reaction mechanisms is proposed. This new functional, denoted BMK (Boese-Martin for Kinetics), has an accuracy in the 2 kcal/mol range for transition state barriers but, unlike previous attempts at such a functional, this improved accuracy does not come at the expense of equilibrium properties. This makes it a general-purpose functional whose domain of applicability has been extended to transition states, rather than a specialized functional for kinetics. The improvement in BMK rests on the inclusion of the kinetic energy density together with a large value of the exact exchange mixing coefficient. For this functional, the kinetic energy density appears to correct `back' the excess exact exchange mixing for ground-state properties, possibly simulating variable exchange.

Stochastic simulation of chemical reactions with spatial resolution and single molecule detail

Abstract: Methods are presented for simulating chemical reaction networks with a spatial resolution that is accurate to nearly the size scale of individual molecules. Using an intuitive picture of chemical reaction systems, each molecule is treated as a point-like particle that diffuses freely in three-dimensional space. When a pair of reactive molecules collide, such as an enzyme and its substrate, a reaction occurs and the simulated reactants are replaced by products. Achieving accurate bimolecular reaction kinetics is surprisingly difficult, requiring a careful consideration of reaction processes that are often overlooked. This includes whether the rate of a reaction is at steady-state and the probability that multiple reaction products collide with each other to yield a back reaction. Inputs to the simulation are experimental reaction rates, diffusion coefficients and the simulation time step. From these are calculated the simulation parameters, including the 'binding radius' and the 'unbinding radius', where the former defines the separation for a molecular collision and the latter is the initial separation between a pair of reaction products. Analytic solutions are presented for some simulation parameters while others are calculated using look-up tables. Capabilities of these methods are demonstrated with simulations of a simple bimolecular reaction and the Lotka-Volterra system.

Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems.

Abstract: The catalytic reaction pathways in enzymes synthetic systems were investigated. In this regard, the electron transfer, proton transfer, and charge flow to energetics and structural transformations were discussed. The quantum chemical studies of the reaction mechanisms of the metalloenzymes revealed the intermediates and transition states for the enzymes. The mechanisms of protein tyrosine phosphatases (PTPases) and hammerhead ribozyme chemistry were also presented.

Determining the geometries of transition States by use of antihydrophobic additives in water.

Abstract: The quantitative effect of cosolvents on the water solubility of hydrophobic substrates can be correlated with the effect on reaction rates to determine the geometries of transition states for Diels-Alder reactions, the benzoin condensation, and alkylations of phenoxide ions and aniline. Some of these reactions have transition states with packing of hydrophobic surfaces and some do not. Methods were devised to sort out the effect of the cosolvents on solvation of hydrophobic surfaces and the effect on solvation of polar groups. The result is a set of geometries for these reactions that is consistent with theory.

A Comparison of C--F and C--H Bond Activation by Zerovalent Ni and Pt: A Density Functional Study

Abstract: Density functional theory indicates that oxidative addition of the C−F and C−H bonds in C6F6 and C6H6 at zerovalent nickel and platinum fragments, M(H2PCH2CH2PH2), proceeds via initial exothermic formation of an η2-coordinated arene complex. Two distinct transition states have been located on the potential energy surface between the η2-coordinated arene and the oxidative addition product. The first, at relatively low energy, features an η3-coordinated arene and connects two identical η2-arene minima, while the second leads to cleavage of the C−X bond. The absence of intermediate C−F or C−H σ complexes observed in other systems is traced to the ability of the 14-electron metal fragment to accommodate the η3-coordination mode in the first transition state. Oxidative addition of the C−F bond is exothermic at both nickel and platinum, but the barrier is significantly higher for the heavier element as a result of strong 5dπ−pπ repulsions in the transition state. Similar repulsive interactions lead to a relativ...

Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase β's closing

Abstract: Our application of transition path sampling to a complex biomolecular system in explicit solvent, the closing transition of DNA polymerase β, unravels atomic and energetic details of the conformational change that precedes the chemical reaction of nucleotide incorporation. The computed reaction profile offers detailed mechanistic insights into, as well as kinetic information on, the complex process essential for DNA synthesis and repair. The five identified transition states extend available experimental and modeling data by revealing highly cooperative dynamics and critical roles of key residues (Arg-258, Phe-272, Asp-192, and Tyr-271) in the enzyme's function. The collective cascade of these sequential conformational changes brings the DNA/DNA polymerase β system to a state nearly competent for the chemical reaction and suggests how subtle residue motions and conformational rate-limiting steps affect reaction efficiency and fidelity; this complex system of checks and balances directs the system to the chemical reaction and likely helps the enzyme discriminate the correct from the incorrect incoming nucleotide. Together with the chemical reaction, these conformational features may be central to the dual nature of polymerases, requiring specificity (for correct nucleotide selection) as well as versatility (to accommodate different templates at every step) to maintain overall fidelity. Besides leading to these biological findings, our developed protocols open the door to other applications of transition path sampling to long-time, large-scale biomolecular reactions.

CH3O decomposition on PdZn(111), Pd(111), and Cu(111). A theoretical study.

Abstract: Methanol steam re-forming, catalyzed by Pd/ZnO, is a potential hydrogen source for fuel cells, in particular in pollution-free vehicles. To contribute to the understanding of pertinent reaction mechanisms, density functional slab model studies on two competing decomposition pathways of adsorbed methoxide (CH3O) have been carried out, namely, dehydrogenation to formaldehyde and C−O bond breaking to methyl. For the (111) surfaces of Pd, Cu, and 1:1 Pd−Zn alloy, adsorption complexes of various reactants, intermediates, transition states, and products relevant for the decomposition processes were computationally characterized. On the surface of Pd−Zn alloy, H and all studied C-bound species were found to prefer sites with a majority of Pd atoms, whereas O-bound congeners tend to be located on sites with a majority of Zn atoms. Compared to Pd(111), the adsorption energy of O-bound species was calculated to be larger on PdZn(111), whereas C-bound moieties were less strongly adsorbed. C−H scission of CH3O on var...

Theoretical Study of Two-State Reactivity of Transition Metal Cations: The ``Difficult'' Case of Iron Ion Interacting with Water, Ammonia, and Methane

Abstract: The potential energy surfaces corresponding to the dehydrogenation reaction of H 2 O, NH 3 , and CH 4 molecules by Fe + ( 6 D, 4 F) cation have been investigated in the framework of the density functional theory in its B3LYP formulation and employing a new optimized basis set for iron. In all cases, the low-spin ion-dipole complex, which is the most stable species on the respective potential energy hypersurfaces, is initially formed. In the second step, a hydrogen shift process leads to the formation of the insertion products, which are more stable in a low-spin state. From these intermediates, three dissociation channels have been considered. All of the results have been compared with existing experimental and theoretical data. Results show that the three insertion pathways are significantly different, although spin crossings between high- and low-spin surfaces are observed in all cases. The topological analysis of the electron localization function has been used to characterize the nature of the bonds for all of the minima and transition states along the paths.

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.

Abstract: To investigate fundamental features of enzyme catalysis, there is a need for high-level calculations capable of modelling crucial, unstable species such as transition states as they are formed within enzymes. We have modelled an important model enzyme reaction, the Claisen rearrangement of chorismate to prephenate in chorismate mutase, by combined ab initio quantum mechanics/molecular mechanics (QM/MM) methods. The best estimates of the potential energy barrier in the enzyme are 7.4–11.0 kcal mol−1 (MP2/6-31+G(d)//6-31G(d)/CHARMM22) and 12.7–16.1 kcal mol−1 (B3LYP/6-311+G(2d,p)//6-31G(d)/CHARMM22), comparable to the experimental estimate of ΔH‡ = 12.7 ± 0.4 kcal mol−1. The results provide unequivocal evidence of transition state (TS) stabilization by the enzyme, with contributions from residues Arg90, Arg7, and Arg63. Glu78 stabilizes the prephenate product (relative to substrate), and can also stabilize the TS. Examination of the same pathway in solution (with a variety of continuum models), at the same ab initio levels, allows comparison of the catalyzed and uncatalyzed reactions. Calculated barriers in solution are 28.0 kcal mol−1 (MP2/6-31+G(d)/PCM) and 24.6 kcal mol−1 (B3LYP/6-311+G(2d,p)/PCM), comparable to the experimental finding of ΔG‡ = 25.4 kcal mol−1 and consistent with the experimentally-deduced 106-fold rate acceleration by the enzyme. The substrate is found to be significantly distorted in the enzyme, adopting a structure closer to the transition state, although the degree of compression is less than predicted by lower-level calculations. This apparent substrate strain, or compression, is potentially also catalytically relevant. Solution calculations, however, suggest that the catalytic contribution of this compression may be relatively small. Consideration of the same reaction pathway in solution and in the enzyme, involving reaction from a ‘near-attack conformer’ of the substrate, indicates that adoption of this conformation is not in itself a major contribution to catalysis. Transition state stabilization (by electrostatic interactions, including hydrogen bonds) is found to be central to catalysis by the enzyme. Several hydrogen bonds are observed to shorten at the TS. The active site is clearly complementary to the transition state for the reaction, stabilizing it more than the substrate, so reducing the barrier to reaction.

Coupled proton and electron transfer reactions in cytochrome oxidase.

Abstract: Cytochrome oxidase catalyzes the four-electron reduction of O2 to water and conserves the substantial free energy of the reaction in the form of a protonmotive force. For each electron, two full charges are translocated across the membrane, resulting in a voltage. One of the mechanisms to generate the charge separation in cytochrome oxidase is via a proton pump. A single reaction cycle can be monitored over the course of about 1 msec using absorption spectroscopy, revealing distinct intermediates. Thus, the reaction cycle can be studied as a series of steps. Each of the reaction steps in the catalytic cycle involves a sequence of coupled electron and proton transfer reaction, where protons are either consumed in the chemistry of water formation or pumped across the membrane. The pumping mechanism requires consideration of both the thermodynamics of the various species but also the favored kinetic pathways that assure proton pumping is unidirectional. Hence, a knowledge of transition states and transiently, poorly populated intermediates is likely to be important to understand the mechanism of the pump.

A Computational Model Relating Structure and Reactivity in Enantioselective Oxidations of Secondary Alcohols by (−)-Sparteine−Pd^(II) Complexes

Abstract: The key interactions responsible for the unique reactivity of (−)-sparteine−PdX_2 complexes (X = chloride, acetate) in the enantioselective oxidation of secondary alcohols have been elucidated using quantum mechanics (B3LYP DFT with the PBF polarizable continuum solvent model). From examining many possible pathways, we find the mechanism involves: (1) substitution of the alcohol in place of an X-group, (2) deprotonation of the bound alcohol by the deposed anion and free sparteine, (3) β-hydride elimination through a four-coordinate transition state in which the second anion is displaced but tightly associated, (4) replacement of the ketone product with the associated anion. The enantioselectivities observed under base-rich reaction conditions follow directly from calculated energies of diastereomeric β-hydride elimination transition states incorporating (R) and (S) substrates. This relationship reveals an important role of the anion, namely to communicate the steric interaction of the ligand on one side of the PdII square plane and the substrate on the other side. When no anion is included, no enantioselectivity is predicted. Locating these transition states in different solvents shows that higher dielectrics stabilize the charge separation between the anion and metal and draw the anion farther into solution. Thus, the solvent influences the barrier height (rate) and selectivity of the oxidation.

Nucleophilic displacement on 4-nitrophenyl dimethyl phosphinate by ethoxide ion: alkali metal ion catalysis and mechanism.

Abstract: We report on a spectrophotometric kinetic study of the effect of Li+ and K+ cations on the ethanolysis of 4-nitrophenyl dimethylphosphinate (4a) in ethanol at 25 °C. The nucleophilic displacement reaction of 4a with LiOEt and KOEt in the absence and presence of 18-crown-6 ether (18-C-6) furnished observed first-order rate constants which increase in the order EtO− δGip for Li+ and δGts ∼ δGip for K+. These results indicate moderate catalysis by Li+, with 4a manifesting lesser susceptibility to catalysis than other substrates previously studied. Second-order rate constants for the reaction of the aryl dimethylphosphinates 4a–f with free EtO− were obtained from plots of log kobsvs. [KOEt], measured in the presence of excess 18-C-6. Hammett plots with σ and σ° substituent constants give significantly better correlation of rates than σ− and yield a moderately large ρ(ρ°) value; this is interpreted in terms of a stepwise mechanism involving rate-limiting formation of a pentacoordinate intermediate. Comparison of the present results with those of Williams on the aqueous alkaline hydrolysis of Me2P(O)–OPhX and Ph2P(O)–OPhX esters, establishes the rationale for a change in mechanism in the more basic EtO−/EtOH nucleophile/solvent system by a stepwise mechanism instead of a concerted one in aqueous base. Structure–reactivity correlations following Jencks show that the change in mechanism is accounted for by cross interactions between the nucleophile and the leaving group in the transition state. The observed duality of mechanism is rationalized on the basis of the More O'Ferrall–Jencks diagram, as a spectrum of transition states covering a wide range of nucleophile and leaving group basicities.

Exploration of C6H6 Potential Energy Surface: A Computational Effort to Unravel the Relative Stabilities and Synthetic Feasibility of New Benzene Isomers†

Abstract: Ab initio (MP2, CCSD(T)) and hybrid density functional theory (B3LYP) calculations with up to triple-ζ basis set were done to locate all possible minima, where each carbon in the molecule is tetracoordinate, on the C6H6 potential energy surface. The search was initiated with a total of 218 structures, and in few cases, geometrical and stereoisomers were considered. The exhaustive study on all these topological structures resulted in a total of 263 stationary points on the C6H6 potential energy surface. The B3LYP level characterizes 209 as minima, 31 as transition states, 8 as second-order, 7 as third-order, and 1 as fourth-order saddle points. The remaining 7 structures could be located as stationary points only at the MP2 level. The molecules were classified into acyclic, monocyclic, bicyclic, tricyclic, and tetracyclic. The acyclic isomers fall within a range of 60−80 kcal/mol higher in energy compared to benzene. Among the cyclic structures, the range of relative stabilities of minima is larger, viz., ...

Theoretical Investigation of the Dimerization of Linear Alkenes Catalyzed by Acidic Zeolites

Abstract: The zeolite-catalyzed dimerization of ethene, propene, 1-butene, and trans-2-butene has been modeled using quantum chemical methods. Reactants, transition states, and products have been investigated. A cluster model consisting of four tetrahedrally coordinated atoms (T-atoms) has been used to represent the catalyst. Two different mechanism types have been evaluated: concerted and stepwise. In the concerted pathway, protonation and C−C bond formation occur simultaneously. The stepwise mechanism proceeds via alkoxide formation followed by C−C bond formation. The order of reactivity among the different alkene reactants has been assessed. Quantum chemistry predicts that the activation energy of the concerted mechanism lies between the two barriers of the stepwise mechanism. More detailed knowledge concerning the stability of alkoxide species relative to physisorbed alkenes will be necessary for discrimination between the two mechanistic proposals. Implications for the reverse reaction, the β-scission of alke...

Reactivity of Carbon-Centered Radicals toward Acrylate Double Bonds: Relative Contribution of Polar vs Enthalpy Effects

Abstract: The different factors controlling the reactivity of a large series of carbon-centered radicals toward the methyl acrylate monomer unit were examined in detail by using molecular orbital calculations. In agreement with the state correlation diagram, the energy barrier is governed for a large part by the enthalpy term, as supported by an increase of reactivity with increasing exothermicity of the reaction. However, important polar effects, as evidenced by molecular calculations on the transition states, were also highlighted: they dramatically enhance the reactivity of the nucleophilic radicals (aminoalkyl or dialkylketyl radicals) as well as the electrophilic radicals (malonyl radical). Their contribution to the decrease of the barrier was evaluated by using a model based on chemical descriptors. This allows a clear separation of the relative role of the polar and enthalpy effects for 22 radicals.

Activation barriers and rate constants for hydration of platinum and palladium square-planar complexes: an ab initio study.

Abstract: In the present work, an ab initio study on hydration (a metal-ligand replacement by water molecule or OH- group) of cis- and transplatin and their palladium analogs was performed within a neutral pseudomolecule approach (e.g., metal-complex+water as reactant complex). Subsequent replacement of the second ligand was considered. Optimizations were performed at the MP2/6-31+G(d) level with single-point energy evaluation using the CCSD(T)/6-31++G(d,p) approach. For the obtained structures of reactants, transition states (TS's), and products, both thermodynamic (reaction energies and Gibbs energies) and kinetic (rate constants) characteristics were estimated. It was found that all the hydration processes are mildly endothermic reactions-in the first step they require 8.7 and 10.2 kcal/mol for ammonium and chloride replacement in cisplatin and 13.8 and 17.8 kcal/mol in the transplatin case, respectively. Corresponding energies for cispalladium amount to 5.2 and 9.8 kcal/mol, and 11.0 and 17.7 kcal/mol for transpalladium. Based on vibrational analyses at MP2/6-31+G(d) level, transition state theory rate constants were computed for all the hydration reactions. A qualitative agreement between the predicted and known experimental data was achieved. It was also found that the close similarities in reaction thermodynamics of both Pd(II) and Pt(II) complexes (average difference for all the hydration reactions are approximately 1.8 kcal/mol) do not correspond to the TS characteristics. The TS energies for examined Pd(II) complexes are about 9.7 kcal/mol lower in comparison with the Pt analogs. This leads to 10(6) times faster reaction course in the Pd cases. This is by 1 or 2 orders of magnitude more than the results based on experimental measurements.

A wave packet based statistical approach to complex-forming reactions.

Abstract: A wave packet based statistical model is suggested for complex-forming reactions. This model assumes statistical formation and decay of the long-lived reaction complex and computes reaction cross sections and their energy dependence from capture probabilities. This model is very efficient and reasonably accurate for reactions dominated by long-lived resonances, as confirmed by its application to the C(1D)+H2 reaction.

Relationship of Leffler (Brønsted) α values and protein folding Φ values to position of transition-state structures on reaction coordinates

Abstract: The positions of transition states along reaction coordinates (r‡) for simple chemical reactions are often estimated from Leffler α values, the slope of plots of ΔG‡ (activation energy) versus ΔG0 (equilibrium free energy) for a series of structural variants. Protein folding is more complex than simple chemical reactions and has a multitude of reaction coordinates. Φ-Value analysis measures degree of structure formation at individual residues in folding transition states from the ratio ΔΔG‡/ΔΔG0 for mutations. α values are now being used to analyze protein folding by lumping series of Φ values into single plots. But, there are discrepancies in the values of α for folding with more classical measures of the extent of structure formation, which I rationalize here. I show for chemical reactions with just a single reaction coordinate that α = r‡ only for limiting cases, such as for reactants and products being in parabolic energy wells of identical curvature. Otherwise, α can differ radically from r‡, with α being determined just by the angles of intersection of reactant and product energy surfaces. Φ is an index of the progress of a local, energy-based reaction coordinate at the global transition state: Φ 0.5 means >50%. Protein Leffler plots can force different local indexes to a single fit and give skewed underestimates of the extent of global structure formation in transition states that differ from other measures of structure formation.

Atomic Layer Deposition Growth Reactions of Al2O3 on Si(100)-2×1

Abstract: Cluster calculations employing hybrid density functional theory have been carried out to examine the atomistic details and thermochemistry of the early stages of Al2O3 atomic layer deposition (ALD) on the Si(100)-2×1 surface using the gas-phase precursors, trimethylaluminum (TMA) and H2O. The critical point structures and enthalpies characterizing both the Al- and O-deposition half-reactions were investigated. Both sets of ALD half-reactions were found to be thermodynamically favorable and kinetically uninhibited. For all reactions the transition states and reaction products were determined to be lower in energy than the starting reactants. The H2O ALD half-reactions were found to have an overall reaction enthalpy between −1.45 and −1.63 eV, with a transition state energy of −0.13 to −0.21 eV. The TMA ALD half-reactions were found to be exothermic by 1.85−1.88 eV. The transition state energy for the Al deposition half-reactions were determined to be −0.19 to −0.27 eV. Careful comparison of the reaction en...

Basic hydrolysis of formamide in aqueous solution: a reliable theoretical calculation of the activation free energy using the cluster-continuum model

Abstract: The first step of the reaction of the hydroxide ion with formamide in aqueous solution was studied by high level ab initio calculations and including the solvent effect through the cluster-continuum model. This hybrid discrete/continuum solvation model considers the ion explicitly solvated by some solvent molecules and the bulk solvent is described by a dielectric continuum (PCM). Two and three explicit water molecules solvating the hydroxide ion were included to describe the transition states. Our theoretical activation free energy barrier at 25 °C is 23.4 kcal mol−1, only 2.2 kcal mol−1 higher than the experimental value of 21.2 kcal mol−1. We have also investigated a general basic catalysis mechanism, where the hydroxide ion acts as a base and one water molecule in its solvation shell is the nucleophile. Our results indicate that this mechanism does not take place and the real process is the direct nucleophilic attack of the hydroxide ion to the carbonyl carbon.

Thermochemical and Kinetic Analysis on the Reactions of Neopentyl and Hydroperoxy-Neopentyl Radicals with Oxygen: Part I. OH and Initial Stable HC Product Formation

Abstract: Thermochemical properties for reactants, intermediates, products, and transition states in the neopentyl radical + O2 reaction system are analyzed with ab initio and density functional calculations to evaluate reaction paths and kinetics for neopentyl oxidation. Enthalpies of formation (ΔHf°298) are determined using isodesmic reaction analysis at the CBS-Q composite and density functional levels. The entropies (S°298) and heat capacities Cp(T) (0 ≤ T/K ≤ 1500) from vibrational, translational, and external rotational contributions are calculated using statistical mechanics based on the vibrational frequencies and structures obtained from the density functional study. Potential barriers for the internal rotations are calculated at the B3LYP/6-31G(d,p) level, and hindered rotational contributions to S°298 and Cp(T)'s are calculated by using direct integration over energy levels of the internal rotation potentials. The kinetic analysis on reactions of neopentyl with O2 is performed using enthalpies at the CBS...

Entropy considerations in kinetic method experiments

Abstract: In extended kinetic method experiments, relative binding enthalpies ('affinities') and relative entropies are obtained based on unimolecular dissociation kinetics. A series of ion-bound dimers A-X-B(i) is formed, in which the sample (A) and structurally similar reference molecules (B(i)) are bridged by a central cation or anion (X). The branching ratios of the A-X-B(i) set to A-X and B(i)-X are determined at different internal energies, usually by subjecting A-X-B(i) to collisionally activated dissociation at various collision energies. The dependence of the natural logarithm of the branching ratios on the corresponding B(i)-X bond enthalpies (X affinities of B(i)) is evaluated as a function of internal energy to thereby deduce the A-X bond enthalpy (X affinity of A) as well as an apparent relative entropy of the competitive dissociation channels, Delta(DeltaS(app)). Experiments with proton- and Na(+)-bound dimers show that this approach can yield accurate binding enthalpies. In contrast, the derived Delta(DeltaS(app)) values do not correlate with the corresponding thermodynamic entropy differences between the channels leading to A-X and B(i)-X, even after scaling. The observed trends are reconciled by the transition state switching model. According to this model, the kinetics of barrierless dissociations, such as those encountered in kinetic method studies, are dominated by a family of tight transition states ('entropy bottlenecks') lying lower in energy than the corresponding dissociation thresholds. In general, the relative energies of these tight transition states approximately match those of the dissociation products, but their relative entropies tend to be much smaller, as observed experimentally.

Use of DFT-based reactivity descriptors for rationalizing radical reactions: A critical analysis

Abstract: Hydrogen abstraction by C 2 H, OH, CH 3 , CF 3 , C 2 H 3 , and C 2 H 5 radicals from methane and propene and addition reactions of these radicals with substituted propenes have been investigated by using BHandHLYP/6-311G-(d,p) level of theory. Transition states for all these reactions have been located. The reactivity of different radicals and substrates toward hydrogen abstraction and radical addition reactions has been critically analyzed by using density functional theory based reactivity descriptors, namely, local softness and electronegativity. The regiochemistry of the radical addition reaction has also been explained from the local softness values of the potential addition sites.

Isomerizations of Bicyclo[2.1.0]pent-2-ene and Tricyclo[2.1.0.02,5]pentane into Cyclopenta-1,3-diene: A Computational Study by DFT and High-Level ab Initio Methods

Abstract: The thermal isomerizations of bicyclopentene (bcp) and tricyclopentane (tcp) into cyclopentadiene (cp) are investigated by a combination of DFT, CASSCF, CASSCF-MP2, and CR-CCSD(T) methods. Coupled-clusters and B3LYP methods predicted the reaction enthalpies excellently whereas the MCSCF method worked well only when dynamic correlation energy was taken into account. Both processes are concerted, and the reaction paths pass through transition states with high biradical character. Measures of biradical character in DFT and ab initio methods are discussed. The activation enthalpy in the rearrangement of bcp into cp was predicted by the CR-CCSD(T) method to be 25.5 kcal/mol, in good agreement with experiment. The UB3LYP functional also performed well in this case despite the high spin contamination that was present in the singlet biradicaloid transition state. The reaction enthalpy for the conversion of tcp into cp was predicted to be −63.7 kcal/mol. The transition state involved in the isomerization of tcp wa...

The dynamics of the H-atom abstraction reactions between chlorine atoms and the methyl halides

Abstract: The rotational state distributions of nascent HCl( v ′ =0) products of the reactions between ground spin–orbit state Cl( 2 P 3/2 ) atoms and CH 4 and CH 3 X (X=F, Cl, Br, I) molecules are reported. Reactions were initiated by photolysis of molecular chlorine at 355 nm and the nascent HCl( v ′ =0) products were probed using 2 + 1 resonance-enhanced multiphoton ionization in a time-of-flight mass spectrometer. In accord with previous measurements, the HCl( v ′ =0) products for the Cl + CH 4 reaction are rotationally very cold. A much greater degree of rotational excitation is observed in the HCl( v ′ =0) products of the reactions involving the methyl halides, which increases such that CH 3 I 3 Br 3 Cl 3 F, correlating with the magnitudes of the dipole moments of the radical fragment co-products. Ab initio calculations were performed at the G2//MP2/6-311G(d,p) level to characterize molecular complexes and transition states on the reaction pathways for all the reactions studied except Cl + CH 3 I. All proceed over barriers and have weakly bound complexes in the pre- and post-transition state regions of the potential energy surfaces. Comparisons are drawn between the dynamics of these reactions and those of Cl atoms with other organic molecules containing heteroatoms.

Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis.

Abstract: Biological phosphates form the anionic backbone linkage in DNA and RNA and play a central role in the regulation of cellular processes including signaling, respiration, replication, and translation. Consequently, the study of the chemistry of biological phosphates is an area of great importance. Of particular interest are the mechanisms by which RNA can catalyze fairly complicated reactions such as the transphosphorylation and hydrolysis of phosphodiester bonds. A useful experimental strategy to probe the catalytic mechanisms of RNA enzymes is the study of thio effects: changes in the reaction rate that occur upon substitution of key phosphate oxygen atoms with sulfur atoms. Kinetic analysis of thio effects provides insight into the specific role that these oxygen positions play in catalysis. Theoretical methods are powerful tools to aid the interpretation of kinetic data through characterization of the structure and energetics of transition states and intermediates along competing reaction paths. The dominant reaction path for transphosphorylation in RNA (Scheme 1) proceeds via an in-line attack of an activated 2’-hydroxy group of the RNA sugar ring on the reactive phosphate group to produce a pentavalent phosphorane transition state or intermediate, followed by the cleavage of the P-O bond to produce a 2’,3’-cyclic phosphate. Experimental and theoretical data suggest a dianionic oxyphosphorane transphosphorylation intermediate is kinetically indistinguishable from a transition state and is too short-lived to undergo other processes such as protonation or pseudorotation. As the pH is lowered, acid-catalyzed migration products begin to emerge, which result from pseudorotation of a singly or doubly protonated phosphorane intermediate (Scheme 2). The ratio of products resulting from phosphate hydrolysis/ transphosphorylation and isomerization (migration) and their pH dependence involve a balance between the endoand exo-