A review of the theoretical and computational modeling of bimolecular reactions is given. The review is divided into several sections which are as follows: gas-phase thermal reactions; gas-phase state-selected reactions and product state distributions; and condensed-phase bimolecular reactions. The section on gas-phase thermal reactions covers the enthalpies and free energies of reaction, kinetics, saddle points and potential energy surfaces, rate theory for simple barrier reactions and bimolecular reactions over potential wells. The section on gas-phase state-selected reactions focuses on electronically adiabatic reactions and electronically nonadiabatic reactions. Finally, the section on condensed-phase bimolecular reactions covers reactions in liquids, reactions on surfaces and in solids and tunneling at low temperature.

Modeling the Kinetics of Bimolecular Reactions

Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described.

http://faculty.missouri.edu/~glaserr/8330s09/Schlegel_PES.pdf?origin=publication_detail

Exploring potential energy surfaces for chemical reactions: An overview of some practical methods

Publisher Summary This chapter discusses recent advancements and commonly used techniques for exploring potential energy surfaces (PESs) are surveyed in the context of electronic structure methods. Specifically, minimization, transition state optimization, and reaction path following are discussed. In addition to reviewing current progress in these areas, the chapter also deals with a number of practical discussions regarding minimization, transition state optimization, and reaction path following, including suggestions for overcoming common pitfalls. PESs play a central role in computational chemistry. It forms a central concept in the theoretical description of molecular structures, properties, and reactivities. The study of most chemical processes and properties by computational chemists begins with the optimization of one or more structures to find minima on PESs, which correspond to equilibrium geometries. To obtain reaction barriers and calculate reaction rates using transition state theory (TST), it is necessary to locate the first-order saddle points on the PES, which correspond to transition states (TS). Often one needs to confirm that a TS lies on a pathway that actually connects the minima corresponding to reactants and products

Finding minima, transition states, and following reaction pathways on ab initio potential energy surfaces

A single transition state may lead to multiple intermediates or products if there is a post-transition-state reaction pathway bifurcation. These bifurcations arise when there are sequential transition states with no intervening energy minimum. For such systems, the shape of the potential energy surface and dynamic effects, rather than transition-state energetics, control selectivity. This Minireview covers recent investigations of organic reactions exhibiting reaction pathway bifurcations. Such phenomena are surprisingly general and affect experimental observables such as kinetic isotope effects and product distributions.

/pdf/bifurcations-on-potential-energy-surfaces-of-organic-3p04ibnqrg.pdf

Bifurcations on Potential Energy Surfaces of Organic Reactions

Iron(III)-hydroperoxo, [Por(CysS)Fe(III)-OOH](-), a key species in the catalytic cycle of cytochrome P450, was recently identified by EPR/ENDOR spectroscopies (Davydov, R; Makris, T M; Kofman, V; Werst, D E; Sligar, S G; Hoffman, B M J Am Chem Soc 2001, 123, 1403-1415) It constitutes the last station of the preparative steps of the enzyme before oxidation of an organic compound and is implicated as the second oxidant capable of olefin epoxidation (Vaz, A D N; McGinnity, D F; Coon, M J Proc Natl Acad Sci USA 1998, 95, 3555-3560), in addition to the penultimate active species, Compound I (Groves, J T; Han, Y-Z In Cytochrome P450: Structure, Mechanism and Biochemistry, 2nd ed; Ortiz de Montellano, P R, Ed; Plenum Press: New York, 1995; pp 3-48) In response, we present a density functional study of a model species and its ethylene epoxidation pathways The study characterizes a variety of properties of iron(III)-hydroperoxo, such as the O-O bonding, the Fe-S bonding, Fe-O and Fe-S stretching frequencies, its electron attachment, and ionization energies Wherever possible these properties are compared with those of Compound I The proton affinities for protonation on the proximal and distal oxygen atoms of iron(III)-hydroperoxo, and the effect of the thiolate ligand thereof, are determined In accordance with previous results (Harris, D L; Loew, G H J Am Chem Soc 1998, 120, 8941-8948), iron(III)-hydroperoxo is a strong base (as compared with water), and its distal protonation leads to a barrier-free formation of Compound I The origins of this barrier-free process are discussed using a valence bond approach It is shown that the presence of the thiolate is essential for this process, in line with the "push effect" deduced by experimentalists (Sono, M; Roach, M P; Coulter, E D; Dawson, J H Chem Rev 1996, 96, 2841-2887) Finally, four epoxidation pathways of iron(III)-hydroxperoxo are located, in which the species transfers oxygen to ethylene either from the proximal or from the distal sites, in both concerted and stepwise manners The barriers for the four mechanisms are 37-53 kcal/mol, in comparison with 14 kcal/mol for epoxidation by Compound I It is therefore concluded that iron(III)-hydroperoxo, as such, cannot be a second oxidant, in line with its significant basicity and poor electron-accepting capability Possible versions of a second oxidant are discussed

Searching for the second oxidant in the catalytic cycle of cytochrome P450: a theoretical investigation of the iron(III)-hydroperoxo species and its epoxidation pathways.

Molecular dynamics has been used to investigate the reaction of a series of ketyl anion radicals and alkyl halides, CH2O•- + CH3X (X = F, Cl, Br) and NCCHO•- + CH3Cl. In addition to a floppy outer-sphere transition state which leads directly to ET products, there is a strongly bound transition state that yields both electron transfer (ET) and C-alkylated (SUB(C)) products. This common transition state has significant C-- C bonding and gives ET and SUB(C) products via a bifurcation on a single potential energy surface. Branching ratios have been estimated from ab initio classical trajectory calculations. The SUB(C) products are favored for transition states with short C--C bonds and ET for long C--C bonds. ET reactivity can be observed even at short distances of rC-C = ca. 2.4 A as in the transition state for the reaction NCCHO•- + CH3Cl. Therefore, the ET/SUB(C) reactivity is entangled over a significant range of the C--C distance. The mechanistic significance of the molecular dynamics study is discussed.

A Single Transition State Serves Two Mechanisms: An ab Initio Classical Trajectory Study of the Electron Transfer and Substitution Mechanisms in Reactions of Ketyl Radical Anions with Alkyl Halides

Sason Shaik, ,§ and

Papers

A Single Transition State Serves Two Mechanisms: An ab Initio Classical Trajectory Study of the Electron Transfer and Substitution Mechanisms in Reactions of Ketyl Radical Anions with Alkyl Halides