Transition State Modeling for Catalysis

Subject Index

Downloaded by STANFORD UNIV GREEN LIBR on September 30, 2012 | http://pubs.acs.org Publication Date: April 8, 1999 | doi: 10.1021/bk-1999-0721.ix002

A Ab-initio molecular dynamics (AIMD) basis in density functional theory (DFT), 89 Car-Parrinello AIMD, 179-180 Car-Parrinello method, 89 constraints, 90-91 description of molecular dynamics, 178-179 dynamical reaction path (DRP), 93-94 finite-temperature simulations, 94-95 frozen core approximation, 89 homogeneous catalysis, 6-7 hydroamination of alkenes, 95-98 intrinsic reaction coordinate (IRC), 93-94 issues with configurational sampling, 183 locating transition states, 91-93 main characteristics of PAW method, 89-90 methodology, 89-90 projector augmented wave (PAW) CarParrinello AIMD, 180-181 projector-augmented wave (PAW) method, 88 QM/MM calculations for citrate synthase reaction, 457-458 reaction free energy barriers with AIMD, 181-183 useful tool for study of catalytic processes, 88 See also Homogeneous catalysis by QM/MM and ab initio molecular dynamics methods; Largescale ab-initio techniques Ab initio potential energy surface (PES) mapping, homogeneous catalysis, 6 Ab-initio techniques, large-scale. See Large-scale ab-initio techniques Abzymes (antibody enzymes), catalytically active, 61 Acetylene C-H bond activation at cationic iridium center cationic iridium-acetylene complex, 146 compared to ethylene, 147 computational details, 139-140 energy profiles (B3LYP) along oxidative-addition/reductive-elimination (OA/RE) pathway, 147/ optimized geometries (B3LYP) for p-intermediate, oxidative-addition transition state, oxidative-addition intermediate, reductive-elimination transition state, and reductive-elimination product along OA/RE pathway, 146/

relative reaction energies by Lee Yang Parr correlation functional (B3LYP) and (coupled cluster with singles and doubles) CCSD//B3LYP, 142r See also Oxidative-addition/reductive-elimination (OA/RE) at cationic iridium center Acetylene oligomerization with Fe activation of C-C and C-H bonds by density functional theory (DFT), 27 calculated relative energies between Fe(C H ) and Fe(C H4) complexes for various functionals, 29t cyclotrimerization in gas phase induced by transition metal atoms, clusters, and surfaces, 26 equilibrium structures of complexes, 26-27 geometry optimizations, 27, 28/ minima on potential energy surface (PES), 27, 29t optimized geometries of Fe(G$H4) complexes for various functionals, 27, 29t optimized structure and frequencies for transition state connecting two forms of Fe(C H ) complex, 28, 30f optimized structure of transition state connecting metallacycle and cyclobutadiene form of Fe(C H ) complex, 27-28, 30/ Acetylene-vinylidene rearrangement in coordination sphere of transition metal, 114-117 See also Transition metal catalyzed processes iV-Acetylneuraminic acid glycosyltransfer N-acetylneuraminic acid (NeuAc) and possible mechanistic roles for its a-carboxylate group, 412/ aqueous solvation model at RHF/6-31G(d,p) level of theory, 422 calculation at B3LYP/6-31+G(d)/SCRF theory to test intermediacy of cutoff model, 419, 420/ calculation of force constants for potential energy surfaces (PES), 414 comparison of key geometric parameters as function of theory, basis set, and solvation model, 417r experimental and computational approaches applied to NeuAc glycosyltransfer, 413-414 general scheme for specific acid-catalyzed acetal hydrolysis, 413/ hydrogen bonding and transition state stabilization, 418 +

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In Transition State Modeling for Catalysis; Truhlar, D., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1999.

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505 key enzymes for NeuAc glycoside maintenance, 412 key geometric parameters obtained at RHF/631G(d,p) level corresponding to microsolvated structures, 41 It lysozyme mechanism with respect to active-site Asp and Glu carboxyls, 421/ model and methods, 414-415 model structures corresponding to ion-molecule complexes, transition states, and products for reaction of a-H and a-COO-substituted oxocarbenium ions with water, 415/ optimized structures and energetics, 416, 417 relationship to glycosylase catalysis, 420, 422 relative timing of proton transfer and heavy atom motion, 419 self-consistent reaction field (SCRF) solvation model, 414 solvent deuterium isotope effects, 420 two estimates of water/carboxylate interaction energy for transition state stabilization, 419/ See also Enzymes Acidic catalysis by zeolites bond distances and angles of proton jump transition structures, 362, 363/ combined quantum mechanics-empirical valence bond (QM-EVB) studies of proton jumps in zeolites, 359-364 constant temperature molecular dynamics (MD) simulations for C-C bond formation, 364 constraint Car-Parrinello molecular dynamics for C-C bond formation between two methanol molecules in H-chabasite, 364-366 constraint MD simulation of two methanol molecules in H-chabasite, 365/ differences between zeolites, H-chabasite and Hfaujasite, 364 difficulties in localizing transition structures involving solid catalysts, 359 embedded 3T and 4T3 cluster models and free space cluster model, 362/ embedded cluster method, 359-361 fragments of faujasite and chabasite frameworks and topologies around A l site, 361/ increasing complexity in theoretical studies of catalytic activity, 358-359 problem and models for proton jumps in zeolites, 361-362 reaction energies and activation barriers calculated for proton jumps, 363, 364t statistically averaged constrained forces as function of C-C distance, 366/ strategies to overcome difficulties involving solid catalysts, 359 Acid or base catalysis barrier reduction or proton transfer step, 6 transition state theory, 5-6

Adaptive chain method. See Large-scale ab-initio techniques Adsorptive decomposition of nitrous oxide on copper analytical techniques for monitoring course of reaction, 259-260 applying Car-Parrinello approach for ground state configurations, 263 ball and stick illustration of calculated geometry of transition states, 262/ calculated adsorption energy of atomic oxygen, 263, 265 calculated and experimental equilibrium Cu-O distance, 265, 267 calculated GGA "fine" geometric properties of N 0 and atomic oxygen adsorbed in four-fold hollow sites on copper surfaces, 265, 266/ comparison of properties of N 0 and atomic oxygen adsorbed in four-fold hollow site on copper surfaces, 265, 266/ comparison of results from CASTEP calculations on N 0 molecule, 263, 264/ comparison of results from GGA "fine" single point energy calculations on N 0 and atomic oxygen adsorbed on four-fold hollow and twofold bridge sites on copper surfaces, 263, 264/ computational methods, 260-263 highest occupied band calculated from energyminimized structure of N 0 adsorbed in fourfold hollow site on copper, 267, 269/ 270/ 271 mechanism, 271-272 method for quantification of free-copper surface area, 259 modeling on Cu(110) and Cu 2 NM0L3 calculated at B3LYP level, 202/ reliability of B3LYP/DZP method for energy calculations, 205 selected geometric parameters of stationary points on potential energy surface of reaction, 202/ Nickel. See Ethyl to ethylene conversion on nickel and platinum Nickel(II) diimine catalyst. See Brookhart Ni(II) diimine catalyst Nickel ions and butane calculated potential energy surfaces for C-C insertion of Ni , 52, 53/ computational details, 50-51 DFT method B3LYP, 50-51 different multi-center transition states possible, 52-54 methods and basis sets, 50-51 methods for localization of transition states, 51 statistical rate model for reaction, 51-52 structure of one optimized multi-center transition state for Ni + «-C H , 53/ Nicotinamide adenine dinucleotide (NAD ). See Enzymatic hydrolysis of nicotinamide adenine dinucleotide (NAD ); Malate dehydrogenase (MDH) reaction pathway Nitrogen monoxide (NO) dissociation. See Dissociation of N , NO, and CO on transition metal surfaces Nitrogen (N ) dissociation. See Dissociation of N , NO, and CO on transition metal surfaces; N cleavage by three-coordinate group 6 complexes ML Nitrous oxide decomposition on copper. See Adsorptive decomposition of nitrous oxide on copper Norbornadiene calculated relative activation enthalpies of cycloaddition reactions, 195/ reaction with alkylidenes, 193-196 ring-opening metathesis polymerization mechanism, 194-195 stereochemistry of transition structures for reaction with Mo(NH)(CH )(OR') , 195-196 syn and anti addition transition structures, 193-194 transition structures, activation enthalpies and entropies of syn and anti cycloaddition reactions with norbornadiene with Mo(NH)(CH ) (OR') , 194/ See also Metathesis reactions, a-bond; Molybdenum alkylidene catalyzed ring-opening metathesis polymerization 3

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Nose Hoover thermostat, finite temperature simulations, 94 Nose thermostat method, coupling system to heat bath for thermally equilibrated system, 183

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O Olefin polymerization. See Brookhart Ni(II) diimine catalyst; Zirconocene catalysis Organic reaction in solution. See Solvents as catalysts Organometallic reactions, demanding task for theoretical treatment, 21 Osmium tetraoxide addition to ethylene substituent effects on mechanism, 120-122 See also Transition metal catalyzed processes Oxidations, Jacobsen. See Asymmetric epoxidation catalysts Oxidative-addition/reductive-elimination (OA/ RE) at cationic iridium center ab initio and density functional theory (DFT) calculations, 139-140 acetylene C-H bond activation, 145-147 alkane, alkene, and alkyne comparisons, 147-148 computational details, 139-140 ethylene C-H bond activation, 143-145 methane C-H bond activation, 140-143 Oxidative addition to three-coordinate Ir(I) addition of dihydrogen (H ), methane, fluoromethanes, and ethane to Ir(PH ) Cl, 154-157 addition of H to neutral Vaska complexes Ir(PH ) (CO)X, 160-161 calculated addition and activation energies (B3LYP), 154/, 157/ catalytic complexes for organic transformations, 151-152 comparison of computed bond dissociation energies and enthalpies with experimentally determined bond dissociation enthalpies, 153/ computational methods, 152 exothermicity of H addition to Ir(PH ) X, 160 oxidative addition to Ir(PH ) X: X=H, F, and Ph,157-160 reactant and product bond strengths, 152-153 2

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P Palladium(lll) and Pd(2U), dissociation of NO. See Dissociation of N , NO, and CO on transition metal surfaces Palladium-assisted allylation application of asymmetric catalysis modeling, 168-169 proceeding through symmetrically 1,3-disubstituted intermediate, 169/ See also Asymmetric catalysis modeling 2



518 Palladium clusters. See Selective catalytic hydrogenation Palladium complexes a-bond metathesis reaction, 106-107 See also Metathesis reactions, a-bond Parabolic jump model benzene diffusion theory, 302 relating binding energies to modified transition state energies, 303/ Parameterization procedures heavily dependent on quantum mechanical data, 165, 166 transition state parameterization, 166 See also Asymmetric catalysis modeling Pertussis toxin. See Enzymatic hydrolysis of nicotinamide adenine dinucleotide (NAD ) Phosphorylation. See Dephosphorylation by low molecular weight protein tyrosine phosphatase Platinum. See Ethyl to ethylene conversion on nickel and platinum Polarization interaction. See Protein-water interface Polymerization of olefins. See Brookhart Ni(II) diimine catalyst; Molybdenum alkylidene catalyzed ring-opening metathesis polymerization; Zirconocene catalysis Polyoxometallates basis for molecular design of mixed oxide catalysts, 333 See also Methane activation on defects of heteropolyanion structures Potential energy surface (PES) mapping in homogeneous catalysis, 6 transition state theory, 4 Projector-augmented wave (PAW) method ab-initio molecular dynamics (AIMD), 88 Car-Parrinello AIMD program, 180-181 main characteristics, 89-90 QM/MM methodology embedded within PAW code, 183 See also Ab-initio molecular dynamics (AIMD); Homogeneous catalysis by QM/MM and ab initio molecular dynamics methods Propylene polymerization energetics calculated at IMOMO and full-HL levels for propylene incorporation, 216/ optimized geometries of reactants, intermediate, transition state, and product of propylene incorporation, 216/ propylene incorporation calculations for zirconocene catalysis, 215 See also Zirconocene catalysis Protein tyrosine phosphatase. See Dephosphorylation by low molecular weight protein tyrosine phosphatase Protein-water interface alteration of charge distribution within molecule, 445 +

average charge transferred to water by charged/ polar residues of CspA, 442r calculated charge transfer to water molecule as determined using ab initio and semiempirical PM3 Hamiltonian, 443-444 calculated charge transfer to water molecule as determined using semiempirical PM3 Hamiltonian, 444r charge transfer (CT) interaction, 440 charge transfer in experimental systems, 445 contributions of amino acid residues to overall CT, 442-443 decomposition of total interaction energy into polarization, charge transfer (CT), exchange repulsion, and electrostatic contributions, 443f electrostatic potential (ESP) charges and fitting procedure, 440, 442 major cold shock protein of E. coli, CspA, model system, 440 molecular orbital interactions between two molecules giving rise to electrostatic, exchange repulsion, polarization and charge transfer interactions, 441/ polarization interaction, 439-440 total charge on protein over period of simulation, 441/ transfer of charge between protein/water interface, 443 Proton transfer. See Internal proton transfer (IPT) Proton transfer reactions ubiquitous reactions in chemistry, 100,101 See also Metathesis reactions, a-bond

Q Quantum chemistry methods, application to endonuclease V, 430, 432 Quantum mechanical modeling catalytic systems, 3 minimum-size active site model, 3 partitioning of catalytic system, 3 Quantum-mechanical/molecular-mechanical (QM/ MM) method aspartate transcarbamoylase (ATCase)-catalyzed reaction, 463 calculations in homogeneous catalysis, 7 citrate synthase reaction, 455-458 hybrid model, 402-403 simulations for solvation studies, 75 See also Homogeneous catalysis by QM/MM and ab initio molecular dynamics methods

R Reaction free energy barriers with ab initio molecular dynamics (AIMD), 181-183


519 schematic representation of hysteresis in slow growth free energy plot, 182/ See also Ab-initio molecular dynamics (AIMD) Reaction intermediates, characterization by density functional theory (DFT) methods, 20 Rhodium complexes in a-bond metathesis reaction, 101-106 See also Dissociation of N , NO, and CO on transition metal surfaces; Metathesis reactions, abond Ribonucleotide reductase (RNR) substrate reaction computational details, 50, 51 energy diagram for RNA to DNA nucleotide transformation, 58/ important aspects of transition state, 58-59 methods and basis sets, 50-51 methods for localization of transition states, 51 optimized transition state structure for cysteine attach on ribose C3', 59/ transforming RNA nucleotides into DNA nucleotides, 57 Ridge method. See Large-scale ab-initio techniques Ring-opening metathesis polymerization. See Molybdenum alkylidene catalyzedring-openingmetathesis polymerization; Norbornadiene Ruthenium, dissociation of nitrogen. See Dissociation of N , NO, and CO on transition metal surfaces


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Selective catalytic hydrogenation C=C bond hydrogenation on Pd(lll), 229-239 C-H bond activation of substituted ethyl on Pd(lll), 234-239 commercial relevance, 226-227 comparison of transition states for different C - H bond activation reactions, 239-241 computational details, 228-229 density functional theory (DFT) to probe hydrogenation of series of single functional moieties, 227 DFT optimized transition state structures on C - H bond activation processes of ethyl, acetate, formyl, and methane, 239, 240/ 241 di-o- adsorption on Pd(lll), effect of primary substituents, 229-234 effect of direct vinyl substituents on adsorption energy of substituted ethylene on Pd(lll), 231, 233f, 234 frontier orbital interactions for di-o- adsorption mode of ethylene on Pd, 231, 232/ gradient corrected density functional theory (DFT), 228

hydrogenation of CO to form oxygenate intermediates, 241 modeling transition states, 227-228 model studies of a,/3-unsaturated aldehydes on supported metal particles, 227 non-local DFT optimized structures for different substituted ethylene molecules on Pd(lll), 231, 232/ non-local DFT optimized transition state structures for /3-hydride elimination of substituted ethyl on Pd(lll), 236, 237/ normal mode eigenvectors corresponding to reaction coordinate for ethyl /3 C - H bond breaking, 236, 237/ optimized adsorption geometry and binding energy for ethylene on Pd(lll) in IT and di-o-chemisorption modes, 229, 230/ reactant and product structures for /3-hydride elimination of substituted ethyl species, 234, 236 reactive path for C - H bond activation of ethyl on Pd(lll), 234, 235/ substituent effects on /3-hydride elimination of /3substituted ethyl on Pd(lll), 236, 238f, 239 understanding mechanistic pathways, 242 Self-consistent reactionfield(SCRF) calculations, solvents as catalysts, 75 Si(lll) surface, reconstructed. See Dissociative chemisorption of NH on stepped Si(lll) surface Solvation effects. See Zirconocene catalysis Solvents as catalysts alkene epoxidation by DMD promotion by protic solvents, 82 change in solvent-accessible surface area (SASA) for C-C bond formation, 79-80 direct and umbrella sampling, 76 epoxidation of alkenes by dimethyldioxirane (DMD), 78-79 free energy calculations, 76-77 free energy perturbation (FEP) theory, 76-77 hydrogen bonding for cycloaddition reactions, 81-82 hydrophobic effects, 79-80 MC (Monte Carlo)/FEP calculations for dimerization of cyclopentadiene, 80 mixed quantum (QM) and classical (MM) mechanics simulations, 75 molecular dynamics (MD) or Monte Carlo (MC) simulations, 75-76 polarity changes, 77-79 rearrangement of clorismate to prephenate acceleration in water over methanol, 80-81 related MD and MC calculations for various organic reactions, 82-83 self-consistent reactionfield(SCRF) calculations, 75 3


520 solvent effects on reaction rates, 74 solvent polarity for stereomutation of cyclopropanones, 78 transition state theory, 75 variations in hydrogen bonding, 80-82 Subtilisin. See Enzymatic reactions Surface reactions. See Dissociation of N , NO, and CO on transition metal surfaces 2

schematic of planar and nonplanar reaction path for acetylene-vinylidene rearrangement, 115/ Transition metals choice of basis set for catalytic system modeling, 7 geometry optimizations of third-transition-row systems, 7 pitfalls and pathological problems with, 7 role of d orbitals in bonding, 11 See also Dissociation of N , NO, and CO on transition metal surfaces; Metathesis reactions, abond; N cleavage by three-coordinate group 6 complexes ML ; Oxidative-addition/reductiveelimination (OA/RE) at cationic iridium center Transition states analysis of enzymatic reactions, 491, 497 asymmetric Horner Wadsworth Emmons (HWE) reactions, 169-171 characterization by density functional theory (DFT) methods, 20 effects of catalysis on structures and implications for mechanism, 486 energy barrier for linear three-atomic complex, 20 locating using ab-initio molecular dynamics (AIMD), 91-93 methods for determining surface reactions, 246-249 methods for localization of transition states, 51 modeling, 227-228 picture of diffusion for benzene diffusion in zeolite, 301-302 properties for dissociation of N and NO on metal surfaces, 249-252 See also Acidic catalysis by zeolites; Asymmetric catalysis modeling; Asymmetric epoxidation catalysts; Enzymatic hydrolysis of nicotinamide adenine dinucleotide (NAD ); Enzymatic reactions; Large-scale ab-initio techniques; Methane activation over ion-exchanged ZSM-5; Oxidative addition to three-coordinate Ir(I) Transition state simulation. See Zeolites Transition state theory benzene jump dynamics in Na-Y zeolite, 297-298 classifying catalytic effects, 4-5 energetic effects, 5 entropic effects, 5 finding lowest-energy pathways in catalytic systems, 4 frictional/dynamic effects, 5 relationship between transition state structure and kinetic isotope effects (KIEs) in enzymes, 13 solvation effects, 75 theory, 4-6 Tungsten (W) complexes. See N cleavage by three-coordinate group 6 complexes MI^


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Theozymes approach for reaction of amines with esters for peptide bond formation, 62 catalysts development based on theoretical studies of reaction, 61-62 See also Amines with esters, reaction of Titanium compounds. See Hydrosilation reaction; Transition metal catalyzed processes Titanosilicates. See Alkene epoxidation by hydrogen peroxide catalyzed by titanosilicates Transalkylation reactions of aromatics. See Alkylation and transalkylation reactions of aromatics Transition metal catalyzed processes acetylene-vinylidene rearrangement in coordination sphere of transition metal, 114-117 addition of metal oxides to olefins, 122-125 calculated activation barriers and reaction energies for addition of Os0 to olefins, 120/ calculated reaction profile (B3LYP/II) of model pinacolate formation, 118/ calculated relative energies (B3LYP/II) of stationary points for [3+2] and [2+2] addition of metal oxides to ethylene, 122/ CDA partitioning results for transition states of [3+2] addition of Os0 to olefins, 121/ energies for ethylene formation, 118, 119/ mechanism of McMurry reaction, 117-119 mechanism of Os0 addition to ethylene, 120-122 optimized (B3LYP/II) energy minima and transition states on acetylene complex potential energy surface, 116/ optimized transition states (B3LYP/II) of Os0 addition to olefins, 120/ optimized transition states of [3+2] and [2+2] addition and [3+2] reaction product for addition of CpRe0 to ethylene, 124/ optimized transition states of [3+2] and [2+2] addition and [3+2] reaction product for addition of Re0 - and ClRe0 to ethylene, 123/ postulated nucleophilic pathway of McMurry reaction, 117/ reaction profile (B3LYP/II) for formation of cyclic dimetallapinacolate, 119/ reductive coupling of carbonyl compounds in presence of low-valent titanium compounds, 117-120 4

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521 Tyrosine phosphatase. See Dephosphorylation by low molecular weight protein tyrosine phosphatase

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Umbrella sampling, free energy calculations for solution-phase studies, 76

theory; Benzene jump dynamics; Large-scale ab-initio techniques; Methane activation over ion-exchanged ZSM-5 Zirconocene catalysis computation methodologies, 209, 211-213 energetics calculated at IMOMO and full-HL levels for propylene incorporation, 216/ energetics for reaction steps involving [CpCH Cp]ZrR and Cp ZrR , 214/ enthalpy and free energy changes in gas phase and free energy changes in toluene for reaction involving Cp ZrR and [CpCH Cp]ZrR , 218/ features of two specific solvation models for Zr compounds in toluene, 212-213 free energy cycle for developing solvation models, 212/ full high level (full-HL) density functional methodology, 209 full-HL gas-phase energetics of toluene complexation with zirconocenium cations, 214/ gas-phase full-HL calculations ethylene insertion, 214-215 initiation step, relative enthalpies and free energies, 219/ integrated method (IMOMO) calculations for propylene incorporation, 215 optimized geometries of reactants, intermediate, transition state, and product of propylene incorporation, 216/ polymerization reaction steps, 210 propagation step, relative enthalpies and free energies, 219/ solvation effects, 215, 221 solvation models, 209 solvent effects on free energy changes for Zr compound models, 217/ specific binding of toluene to zirconocenium cations, 213-214 standard-state solvation energy calculations, 211-212 structures of stable complexes of toluene with Cp ZrCH , 213/ termination by b-H transfer to metal center, relative enthalpies and free energies, 220/ termination step, relative enthalpies and free energies, 220/ +

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Verlet algorithm, ab-initio molecular dynamics (AIMD) calculations, 91 Vosko-Wilk-Nusair (VWN) approximation, electron correlation in hydrogen abstraction reaction, 22 Voter's Monte Carlo displacement vector approach, benzene jump dynamics in Na-Y zeolite, 298

Z Zeolites benzene adsorption and diffusion modeling in faujasites (Na-X and Na-Y), 296-297 benzene diffusion theory in Na-Y zeolite, 301-304 benzene jump dynamics in Na-Y, 297-301 catalytic systems, 8-9 combination of transition state simulation and analytical theory of activated self-diffusion, 304 electrostatic catalysis, 5 geometry relaxation of cluster geometries, 9 non-reliability of density functional techniques for van der Waals interactions, 9 proton transfer, 8 schematic sites and jumps for benzene in Na-Y, 297/ understanding diffusion in, 296 validity of cluster models, 8 See also Acidic catalysis by zeolites; Alkene epoxidation by hydrogen peroxide catalyzed by titanosilicates; Alkylation and transalkylation reactions of aromatics; Benzene diffusion

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Transition State Modeling for Catalysis

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