Showing papers on "Transition state published in 2006"
TL;DR: Two distinct reaction pathways are explored toward the formation of the Michael product that differ in the mode of electrophile activation, and both reaction channels are shown to be consistent with the notion of noncovalent organocatalysis in that the transition states leading to the Michael adduct are stabilized by extensive H-bonded networks.
Abstract: The mechanism of enantioselective Michael addition of acetylacetone to a nitroolefin catalyzed by a thiourea-based chiral bifunctional organocatalyst is investigated using density functional theory calculations. A systematic conformational analysis is presented for the catalyst, and it is shown that both substrates coordinate preferentially via bidentate hydrogen bonds. The deprotonation of the enol form of acetylacetone by the amine of the catalyst is found to occur easily, leading to an ion pair characterized by multiple H-bonds involving the thiourea unit as well. Two distinct reaction pathways are explored toward the formation of the Michael product that differ in the mode of electrophile activation. Both reaction channels are shown to be consistent with the notion of noncovalent organocatalysis in that the transition states leading to the Michael adduct are stabilized by extensive H-bonded networks. The comparison of the obtained energetics for the two pathways allows us to propose an alternative mec...
367 citations
TL;DR: In this article, a computational study with the Becke3LYP DFT functional is carried out on the cross-coupling reaction of vinyl bromide H2CCHBr and vinylboronic acid H 2CCHB(OH)2 catalyzed by palladium diphosphine [Pd(PH3)2] in the presence of an excess of base OH-.
336 citations
TL;DR: Quantum-mechanical tunneling in CH(4) dissociative adsorption and associative desorption is estimated to be important below 200 K and is, therefore, not expected to play an important role under typical conditions.
Abstract: The results of theoretical calculations of associative desorption of CH(4) and H(2) from the Ni(111) surface are presented. Both minimum-energy paths and classical dynamics trajectories were generated using density-functional theory to estimate the energy and atomic forces. In particular, the recombination of a subsurface H atom with adsorbed CH(3) (methyl) or H at the surface was studied. The calculations do not show any evidence for enhanced CH(4) formation as the H atom emerges from the subsurface site. In fact, there is no minimum-energy path for such a concerted process on the energy surface. Dynamical trajectories started at the transition state for the H-atom hop from subsurface to surface site also did not lead to direct formation of a methane molecule but rather led to the formation of a thermally excited H atom and CH(3) group bound to the surface. The formation (as well as rupture) of the H-H and C-H bonds only occurs on the exposed side of a surface Ni atom. The transition states are quite similar for the two molecules, except that in the case of the C-H bond, the underlying Ni atom rises out of the surface plane by 0.25 A. Classical dynamics trajectories started at the transition state for desorption of CH(4) show that 15% of the barrier energy, 0.8 eV, is taken up by Ni atom vibrations, while about 60% goes into translation and 20% into vibration of a desorbing CH(4) molecule. The most important vibrational modes, accounting for 90% of the vibrational energy, are the four high-frequency CH(4) stretches. By time reversibility of the classical trajectories, this means that translational energy is most effective for dissociative adsorption at low-energy characteristic of thermal excitations but energy in stretching modes is also important. Quantum-mechanical tunneling in CH(4) dissociative adsorption and associative desorption is estimated to be important below 200 K and is, therefore, not expected to play an important role under typical conditions. An unexpected mechanism for the rotation of the adsorbed methyl group was discovered and illustrated a strong three-center C-H-Ni contribution to the methyl-surface bonding.
160 citations
TL;DR: A general experimental protocol is described that is capable of studying conformational isomerization in such circumstances, measuring the product quantum yields following conformation-specific infrared excitation, and measuring energy thresholds for isomership of specific X --> Y reactant-product isomer pairs following excitation via stimulated emission pumping (SEP).
Abstract: Molecules with several flexible coordinates have potential energy surfaces with a large number of minima and many transition states separating them. A general experimental protocol is described that is capable of studying conformational isomerization in such circumstances, measuring the product quantum yields following conformation-specific infrared excitation, and measuring energy thresholds for isomerization of specific X --> Y reactant-product isomer pairs following excitation via stimulated emission pumping (SEP). These methods have been applied to a series of molecules of varying size and conformational complexity, including 3-indolepropionic acid (IPA), meta-ethynylstyrene, N-acetyltryptophan methyl amide (NATMA), N-acetyltryptophan amide (NATA), and melatonin. Studies of isomerization in solute-solvent complexes are also described, including a measurement of the barrier to isomerization in the IPA-H2O complex, and a unique isomerization reaction in which a single water molecule is shuttled between H-bonding sites on the trans-formanilide (TFA) molecule.
154 citations
TL;DR: The values of beta(lg) and additional data suggest that the transition state for AP-catalyzed phosphate diester hydrolysis is indistinguishable from that in solution, and the AP active site has the ability to recognize different transition states, a property that could assist in the evolutionary optimization of promiscuous activities.
Abstract: Enzyme-catalyzed phosphoryl transfer reactions have frequently been suggested to proceed through transition states that are altered from their solution counterparts. Previous work with Escherichia coli alkaline phosphatase (AP), however, suggests that this enzyme catalyzes the hydrolysis of phosphate monoesters through a loose, dissociative transition state, similar to that in solution. AP also exhibits catalytic promiscuity, with a low level of phosphodiesterase activity, despite the tighter, more associative transition state for phosphate diester hydrolysis in solution. Because AP is evolutionarily optimized for phosphate monoester hydrolysis, it is possible that the active site environment alters the transition state for diester hydrolysis to be looser in its bonding to the incoming and outgoing groups. To test this possibility, we have measured the nonenzymatic and AP-catalyzed rate of reaction for a series of substituted methyl phenyl phosphate diesters. The values of beta(lg) and additional data suggest that the transition state for AP-catalyzed phosphate diester hydrolysis is indistinguishable from that in solution. Instead of altering transition state structure, AP catalyzes phosphoryl transfer reactions by recognizing and stabilizing transition states similar to those in aqueous solution. The AP active site therefore has the ability to recognize different transition states, a property that could assist in the evolutionary optimization of promiscuous activities.
141 citations
TL;DR: The topology of the hypersurfaces and the state properties explain the absence of secondary decay in 9-substituted adenines in water in terms of the higher position of the 1(npi*) state and also that the 1 (pipi* Lb) state of 7H-adenine is responsible for the observed fluorescence in water.
Abstract: An ab initio theoretical study at the CASPT2 level is reported on minimum energy reaction paths, state minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of two tautomers of adenine: 9H- and 7H-adenine. The obtained results led to a complete interpretation of the photophysics of adenine and derivatives, both under jet-cooled conditions and in solution, within a three-state model. The ultrafast subpicosecond fluorescence decay measured in adenine is attributed to the low-lying conical intersection (gs/pipi* La)(CI), reached from the initially populated 1(pipi* La) state along a path which is found to be barrierless only in 9H-adenine, while for the 7H tautomer the presence of an intermediate plateau corresponding to an NH2-twisted conformation may explain the absence of ultrafast decay in 7-substituted compounds. A secondary picosecond decay is assigned to a path involving switches towards two other states, 1(pipi* Lb) and 1(npi*), ultimately leading to another conical intersection with the ground state, (gs/npi*), with a perpendicular disposition of the amino group. The topology of the hypersurfaces and the state properties explain the absence of secondary decay in 9-substituted adenines in water in terms of the higher position of the 1(npi*) state and also that the 1(pipi* Lb) state of 7H-adenine is responsible for the observed fluorescence in water. A detailed discussion comparing recent experimental and theoretical findings is given. As for other nucleobases, the predominant role of a pipi*-type state in the ultrafast deactivation of adenine is confirmed.
138 citations
TL;DR: It is proposed that geometrical complementarity between theOxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and it is suggested that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.
Abstract: A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing p K a models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50–0.76 ppm/p K a unit, suggesting a bond shortening of ˜0.02 A/p K a unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (ΔΔG = −0.2 kcal/mol/p K a unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (ΔΔH = −2.0 kcal/mol/p K a unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of ˜300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.
130 citations
Book•
08 Nov 2006
TL;DR: In this paper, the authors proposed a method for determining the energy of activation and Arrhenius Factor of a chemical reaction in order to determine the half-life of a reaction.
Abstract: Preface 1. Elementary 1.1. Rate of Reaction 1.2. Rate Constant 1.3. Order and Molecularity 1.4. Rate Equations 1.5. Half-life of a Reaction 1.6. Zero Order Reactions 1.7. First Order Reactions 1.8. Radioactive Decay as a First Order Phenomenon 1.9. Second Order Reactions 1.10. Third Order Reactions 1.11. Determination of Order of Reaction 1.12. Experimental Methods of Chemical Kinetics Exercises 2. Temperature Effect on Reaction Rate 2.1. Derivation of Arrhenius Equation 2.2. Experimental Determination of Energy of Activation and Arrhenius Factor 2.3. Potential Energy Surface 2.4. Significance of Energy of Activation Exercises 3. Complex Reactions 3.1. Reversible Reactions 3.2. Parallel Reactions 3.3. Consecutive Reactions 3.4. Steady-State Treatment 3.5. Chain Reactions Reactions Exercises 4. Theories of Reaction Rate 4.1. Equilibrium and Rate of Reaction 4.2. Partition Functions and Statistical Mechanics of Chemical Equilibrium 4.3. Partition Functions and Activated Complex 4.4. Collision Theory 4.5. Transition State Theory 4.6. Unimolecular Reactions and the Collision Theory 4.7. Kinetic and Thermodynamic Control 4.8. Hammond's Postulate 4.9. Probing of the Transition State Exercises 5. Kinetics of Some Special Reactions 5.1. Kinetics of Photochemical Reactions 5.2. Oscillatory Reactions 5.3. Kinetics of Polymerization 5.4. Kinetics of Solid State Reactions 5.5. Electron Transfer Reactions Exercises 6. Kinetics of Catalyzed Reactions 6.1. Catalysis 6.2. Theories of Catalysis 6.3. Characteristics of Catalytic Reactions 6.4. Mechanism of Catalysis 6.5. Activation Energies of Catalyzed Reactions 6.6. Acid Base Catalysis 6.7. Enzyme Catalysis 6.8. Influence of pH 6.9. Heterogeneous Catalysis 6.10. Micellar Catalysis 6.11. Phase Transfer Catalysis 6.12. Kinetics of Inhibition Exercises 7. Fast Reactions 7.1. Introduction 7.2. Flow Techniques 7.3. Relaxation Method 7.4. Shock Tubes 7.5. Flash Photolysis 7.6. ESR Spectroscopic Technique 7.7. NMR Spectroscopic Techniques Exercises 8. Reactions in Solutions 8.1. Introduction 8.2. Theory of Absolute Reaction Rate 8.3. Influence of Internal Pressure 8.4. Influence of Solvation 8.5. Reactions between Ions 8.6. Entropy Change 8.7. Influence of Ionic Strength (Salt Effect) 8.8. Secondary Salt Effect 8.9. Reactions between the Dipoles 8.10. Kinetic Isotope Effect 8.11. Solvent Isotope Effect 8.12. Hemmett Equation 8.13. Linear Free Energy Relationship 8.14. The Taft Equation 8.15. Compensation Effect Exercises 9. Reaction Dynamics 9.1. Molecular Reaction Dynamics 9.2. Microscopic-Macroscopic Relation 9.3. Reaction Rate and Rate Constant 9.4. Distribution of Velocities of Molecules 9.5. Rate of Reaction for Collisions with a Distribution of Relative Speeds 9.6. Collision Cross Sections 9.7. Activation Energy 9.8. Potential Energy Surface 9.9. Classical Trajectory Calculations 9.10. Potential Energy Surface and Classical Dynamics 9.11. Disposal of Excess Energy 9.12. Influence of Rotational Energy 9.13. Experimental Chemical Dynamics Suggested Readings Index
122 citations
TL;DR: In this article, the role of adsorbed atomic oxygen and adorbed OH in the oxidation of ammonia on Pt{1, 1, 1} has been investigated by means of density functional theory calculations.
120 citations
TL;DR: The calculations show that this spin state selectivity is the result of geometric orientation of the transition state structures, whereby the triplet ones are destabilized by electrostatic repulsions between the substrate and the ligand while the quintet spin transition states are aligned along the ideal axis.
Abstract: Density functional calculations on a nonheme biomimetic (Fe=O(TMCS+) have been performed and its catalytic properties versus propene investigated Our studies show that this catalyst is able to chemoselectively hydroxylate C=H bonds even in the presence of C=C double bonds This phenomenon has been analyzed and found to occur due to Pauli repusions between protons on the TMCS ligand with protons attached to the approaching substrate The geometries of the rate determining transition states indicate that the steric hindrance is larger in the epoxidation transition states than in the hydroxylation ones with much shorter distances; hence the hydroxylation pathway is favored over the epoxidation Although, the reactant experiences close lying triplet and quintet spin states, the dominant reaction mechanism takes place on the quintet spin state surface; ie, Fe=O(TMCS)+ reacts via single-state reactivity Our calculations show that this spin state selectivity is the result of geometric orientation of the transition state structures, whereby the triplet ones are destabilized by electrostatic repulsions between the substrate and the ligand while the quintet spin transition states are aligned along the ideal axis The reactivity patterns and geometries are compared with oxoiron species of dioxygenase and monoxygenase enzymes Thus, Fe=O(TMCS)+ shows some similarities with P450 enzyme reactivity: it chemoselectively hydroxylates C=H bonds even in the presence of a C=C double bond and therefore is an acceptable P450 biomimetic However, the absolute barriers of substrate oxidation by Fe=O(TMCS)+ are higher than the ones obtained with heme enzymes, but the chemoselectivity is lesser affected by external perturbations such as hydrogen bonding of a methanol molecule toward the thiolate sulfur or a dielectric constant This is the first oxoiron complex whereby we calculated a chemoselective hydroxylation over epoxidation in the gas phase
120 citations
TL;DR: The first total synthesis of (R)-convolutamydine A has been achieved by the organocatalytic addition of acetone to 4,6-dibromoisatin this paper.
TL;DR: It is proposed that the enzyme has evolved a network of relatively short hydrogen bonds that collectively stabilize the transition states and a short ionic hydrogen bond (SIHB) between His57 Nepsilon2 and the substrate's leaving group may promote forward progression of the TI1-to-acylenzyme reaction.
Abstract: To address questions regarding the mechanism of serine protease catalysis, we have solved two X-ray crystal structures of α-lytic protease (αLP) that mimic aspects of the transition states: αLP at pH 5 (0.82 A resolution) and αLP bound to the peptidyl boronic acid inhibitor, MeOSuc-Ala-Ala-Pro-boroVal (0.90 A resolution). Based on these structures, there is no evidence of, or requirement for, histidine-flipping during the acylation step of the reaction. Rather, our data suggests that upon protonation of His57, Ser195 undergoes a conformational change that destabilizes the His57-Ser195 hydrogen bond, preventing the back-reaction. In both structures the His57-Asp102 hydrogen bond in the catalytic triad is a normal ionic hydrogen bond, and not a low-barrier hydrogen bond (LBHB) as previously hypothesized. We propose that the enzyme has evolved a network of relatively short hydrogen bonds that collectively stabilize the transition states. In particular, a short ionic hydrogen bond (SIHB) between His57 Ne2 an...
TL;DR: Conclusions of the modeling lead to a better understanding of the anticatalytic effect of cancer causing mutation of Gln61 from Ras, which has been debated in recent years.
Abstract: The hydrolysis reaction of guanosine triphosphate (GTP) by p21(ras) (Ras) has been modeled by using the ab initio type quantum mechanical-molecular mechanical simulations. Initial geometry configurations have been prompted by atomic coordinates of the crystal structure (PDBID: 1QRA) corresponding to the prehydrolysis state of Ras in complex with GTP. Multiple searches of minimum energy geometry configurations consistent with the hydrogen bond networks have been performed, resulting in a series of stationary points on the potential energy surface for reaction intermediates and transition states. It is shown that the minimum energy reaction path is consistent with an assumption of a two-step mechanism of GTP hydrolysis. At the first stage, a unified action of the nearest residues of Ras and the nearest water molecules results in a substantial spatial separation of the gamma-phosphate group of GTP from the rest of the molecule (GDP). This phase of hydrolysis process proceeds through the low barrier (16.7 kcal/mol) transition state TS1. At the second stage, the inorganic phosphate is formed in consequence of proton transfers mediated by two water molecules and assisted by the Gln61 residue from Ras. The highest transition state at this segment, TS3, is estimated to have an energy 7.5 kcal/mol above the enzyme-substrate complex. The results of simulations are compared to the previous findings for the GTP hydrolysis in the Ras-GAP (p21(ras)-p120(GAP)) protein complex. Conclusions of the modeling lead to a better understanding of the anticatalytic effect of cancer causing mutation of Gln61 from Ras, which has been debated in recent years.
TL;DR: Results show that the presence of Mg(II) monocoordinated to thymine activates the hydrogenic motion by inducing structural and electronic changes in the molecular backbone.
Abstract: The 1,3 intramolecular hydrogen transfer reaction in free thymine and in Mg(II)-thymine have been studied at the density functional theory level. The mechanism of intramolecular proton transfer in these systems emerges from the analysis of the reaction force profile along the reaction path; it is rationalized in terms of structural and electronic reorganizations that take place during the chemical transformation. Results show that the presence of Mg(II) monocoordinated to thymine activates the hydrogenic motion by inducing structural and electronic changes in the molecular backbone. In the metallic complex, it is found that the hydrogen transfer is followed by a relaxation process that facilitates the metal cation migration to form a bicoordinated complex.
TL;DR: Compared with this third-row transition metal system with the first-row and second-row congeners, Cu+ and Ag+.
Abstract: The potential energy surface for activation of methane by the third-row transition metal cation, Au+, is studied experimentally by examining the kinetic energy dependence of this reaction using guided ion beam tandem mass spectrometry. A flow tube ion source produces Au+ primarily in its 1S0 (5d10) electronic ground state level but with some 3D (and perhaps higher lying) excited states that can be completely removed by a suitable quenching gas (N2O). Au+ (1S0) reacts with methane by endothermic dehydrogenation to form AuCH2+ as well as C-H bond cleavage to yield AuH+ and AuCH3+. The kinetic energy dependences of the cross sections for these endothermic reactions are analyzed to give 0 K bond dissociation energies (in eV) of D0(Au+ - CH2) = 3.70 +/- 0.07 and D0(Au+ -CH3) = 2.17 +/- 0.24. Ab initio calculations at the B3LYPHW + /6-311++G(3df,3p) level performed here show good agreement with the experimental bond energies and previous theoretical values available. Theory also provides the electronic structures of the product species as well as intermediates and transition states along the reactive potential energy surface. Surprisingly, the dehydrogenation reaction does not appear to involve an oxidative addition mechanism. We also compare this third-row transition metal system with the first-row and second-row congeners, Cu+ and Ag+. Differences in thermochemistry can be explained by the lanthanide contraction and relativistic effects that alter the relative size of the valence s and d orbitals.
TL;DR: In this paper, the potential energy surface for activation of methane by the third-row transition metal cation, Ir+, is studied experimentally by examining the kinetic energy dependence of reactions of Ir+ with methane, IrCH2+ with H2 and D2, and collision-induced dissociation of IrCH 2+ with Xe using guided ion beam tandem mass spectrometry.
TL;DR: In this paper, a density functional study on the mechanism of the asymmetric alpha-alkylation of aldehydes has been conducted and the authors provide an explanation for the remarkable and unexpected increase in enantioselectivity that is observed when using 2-methylproline instead of proline as the catalyst.
Abstract: [structure: see text] An organocatalytic asymmetric alpha-alkylation of aldehydes has recently been shown to provide cyclic aldehydes in high yields and enantioselectivities upon treating substituted acyclic halo-aldehydes with a catalytic amount of 2-methylproline in the presence of 1 equiv of triethylamine. Here, we report a density functional study on the mechanism of this reaction. The crucial step is an intramolecular nucleophilic substitution in the enamine intermediate. The added base accelerates the reaction through the electrostatic activation of the leaving group and affects the stereoselectivity by stabilizing anti and syn transition states to a different extent. On the basis of the computed barriers and transition states, we provide an explanation for the remarkable and unexpected increase in enantioselectivity that is observed when using 2-methylproline instead of proline as the catalyst. Calculated and observed enantiomeric excess values are in good agreement.
TL;DR: In this article, the authors focus on the use of kinetic isotope effects (KIEs) as a method of determining the mechanism and transition state structures of SN2 reactions.
Abstract: Publisher Summary This chapter focuses on the use of kinetic isotope effects (KIEs) as a method of determining the mechanism and transition state structures of SN2 reactions. A primary KIE is found when the bond to the isotopically labeled atom is breaking or forming in the transition state of the slow step of the reaction. Three basic relationships indicate how the magnitude of a primary KIE varies with transition state structure in SN2 reactions. Because the smallest α-carbon KIE reported for an SN2 reaction is 80% of the largest-observed KIE, the qualitative conclusion would be that all these SN2 reactions have symmetric or almost symmetric transition states. A secondary KIE is observed when the bond to the isotopically substituted atom is not being broken or formed in the transition state of the rate-determining step of the reaction. KIEs still remain one of the most convincing probes of transition state structure and reaction mechanism, especially when applied at several positions in a reaction.
Abstract: The Baeyer-Villiger reactions of acetone and 3-pentanone, including their fluorinated and chlorinated derivatives, with performic acid have been studied by ab initio and DFT calculations. Results are compared with experimental findings for the Baeyer-Villiger oxidation of aliphatic fluoro and chloroketones. According to theoretical results, the first transition state is rate-determining for all substrates even in the presence of acid catalyst. Although the introduction of acid into the reaction pathway leads to a dramatic decrease in the activation energy for the first transition state (TS), once entropy is included in the calculations, the enthalpic gain is lost. Of all substrates examined, pentanone reacts with performic acid via the lowest energy transition state. The second transition state is also lowest for pentanone, illustrating the accelerating effect of the additional alkyl group. Interestingly, there is only a small energetic difference in the transition states leading to migration of the fluorinated substituent versus the alkyl substituent in fluoropentanone and fluoroacetone. These differences match remarkably well with the experimentally obtained ratios of oxidation at the fluorinated and nonfluorinated carbons in a series of aliphatic ketones (calculated, 0.3 kcal/mol, observed, 0.5 kcal/mol), which are reported herein. The migration of the chlorinated substituent is significantly more difficult than that of the alkyl, with a difference in the second transition state of approximately 2.6 kcal/mol.
TL;DR: The transition states for anomerization are found, and it is concluded that it is forbidden for the water molecule to form a hydrogen bond bridge to both OH1 and O5 of glucose simultaneously in either transition state.
Abstract: Glucose is a central molecule in biology and chemistry, and the anomerization reaction has been studied for more than 150 years. Transition-state structure is the last impediment to an in-depth understanding of its solution chemistry. We have measured kinetic isotope effects on the rate constants for approach of R-glucopyranose to its equilibrium with ‚-glucopyranose, and these were converted into unidirectional kinetic isotope effects using equilibrium isotope effects. Saturation transfer 13 C NMR spectroscopy has yielded the relative free energies of the transition states for the ring-opening and ring- closing reactions, and both transition states contribute to the experimental kinetic isotope effects. Both transition states of the anomerization process have been modeled with high-level computational theory with constraints from the primary, secondary, and solvent kinetic isotope effects. We have found the transition states for anomerization, and we have also concluded that it is forbidden for the water molecule to form a hydrogen bond bridge to both OH1 and O5 of glucose simultaneously in either transition state.
TL;DR: These data provide powerful evidence that structural isomerism, and not different spin states, is responsible for the observed biexponential reaction kinetics.
Abstract: The structure, energetics, and interconversion of isomers of Rh(6) and Rh(6)(+) are studied by using density functional theory with Gaussian basis sets, using guess structures derived from basin-hopping simulations, and obtained by using the Sutton-Chen potential. A large range of spin multiplicities is considered for each isomer. Our calculations suggest two low-lying structures as possible structural isomers: a square bipyramid and a trigonal prism. The reactivity of these two candidate structural isomers with respect to adsorption of nitric oxide is studied via location of reaction transition states and calculation of reaction barriers. Similarities and differences with surface reaction studies are highlighted. These data provide powerful evidence that structural isomerism, and not different spin states, is responsible for the observed biexponential reaction kinetics.
TL;DR: Primary and secondary kinetic and equilibrium isotope effects are calculated with density-functional methods for the in-line dianionic methanolysis of the native and thio-substituted cyclic phosphates, and the structures and bond orders of the rate-controlling transition states are characterized.
Abstract: Primary and secondary kinetic and equilibrium isotope effects are calculated with density-functional methods for the in-line dianionic methanolysis of the native (unsubstituted) and thio-substituted cyclic phosphates. These reactions represent reverse reaction models for RNA transesterification under alkaline conditions. The effect of solvent is treated with explicit (single and double) water molecules and self-consistently with an implicit (continuum) solvation model. Singly substituted reactions at the nonbridging OP1 position and bridging O2‘, O3‘, and O5‘ positions and a doubly substituted reaction at the OP1 and OP2 positions were considered. Aqueous free energy barriers are calculated, and the structures and bond orders of the rate-controlling transition states are characterized. The results are consistent with available experimental data and provide useful information for the interpretation of measured isotope and thio effects used to probe mechanism in phosphoryl transfer reactions catalyzed by en...
TL;DR: Though the direct dynamics simulations are classical, better agreement is obtained using quantum instead of classical harmonic RRKM theory, and correlations are found between the stretching motions of molozonide, indicative of nonchaotic and non-RRKM dynamics.
Abstract: A direct chemical dynamics simulation, at the B3LYP∕6-31G(d) level of theory, was used to study the post-transition state intramolecular and unimolecular dynamics for the O3+propene reaction. Comparisons of B3LYP∕6-31G(d) with CCSD(T)/cc-pVTZ and other levels of theory show that the former gives accurate structures and energies for the reaction’s stationary points. The direct dynamics simulations are initiated at the anti and syn O3+propene transition states (TSs) and the TS symmetries are preserved in forming the molozonide intermediates. Anti↔syn molozonide isomerization has a very low barrier of 2–3kcal∕mol and its Rice-Ramsperger-Kassel-Marcus (RRKM) lifetime is 0.3ps. However, the trajectory isomerization is slower and it is unclear whether this anti↔syn equilibration is complete when the trajectories are terminated at 1.6ps. The syn (anti) molozonides dissociate to CH3CHO+H2COO and H2CO+syn (anti) CH3CHOO. The kinetics for the latter reactions are in overall good agreement with RRKM theory, but ther...
TL;DR: Analysis based on the natural bond orbital (NBO) and the topological analysis of the electron localization function (ELF) at the transition structures and intermediates explains correctly the polar nature of these reactions.
Abstract: The reactions of electrophilically activated benzonitrile N-oxides (BNOs) toward 3-methylenephthalimidines (MPIs) have been studied using density functional theory (DFT) at the B3LYP/6-31G* level For these reactions, two different channels allowing the formation of the [3 + 2] cycloadducts and two isomeric (E)- and (Z)-oximes have been characterized The 1,3-dipolar cycloadditions take place along concerted but highly asynchronous transition states, while formation of the oximes is achieved through a stepwise mechanism involving zwitterionic intermediates Both reactions are initiated by the nucleophilic attack of the methylene carbon of the MPIs to the carbon atom of the electrophilically activated BNOs The analysis based on the natural bond orbital (NBO) and the topological analysis of the electron localization function (ELF) at the transition structures and intermediates explains correctly the polar nature of these reactions Solvent effects considered by the PCM model allow explaining the low incide
TL;DR: In this paper, the deamination reaction of cytosine with H2O and OH- to produce uracil was investigated using ab initio calculations using optimized geometries of reactants, transition states, intermediates, and products.
Abstract: The mechanism for the deamination reaction of cytosine with H2O and OH- to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H2O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer fo...
TL;DR: In this paper, the formation of DMC from MeOH and CO2 under [Nb(OMe)5]2 catalysis follows a different route (acid-plus-base activation of methanol) with respect to other known catalytic systems such as Sn(IV) and dicyclohexyl carbodiimide (DCC) that promote a double base activation.
Abstract: The formation of dimethylcarbonate (DMC) from MeOH and CO2 under [Nb(OMe)5]2 catalysis follows a different route (“acid-plus-base activation” of methanol) with respect to other known catalytic systems such as Sn(IV) and dicyclohexylcarbodiimide (DCC) that promote a “double-base activation”. The reaction intermediates and related transition states obtained from density functional (DFT) calculations are presented. Experimental data also feature a different reaction mechanism.
TL;DR: Calculation of the reaction path for the enzymatic hydrolysis of the substrate by dUTPase for an active-site model with 85 atoms, including several loosely bound water molecules, indicates that the method is feasible for the study of enzyme mechanisms.
Abstract: We present a generalization of the reaction coordinate driven method to find reaction paths and transition states for complicated chemical processes, especially enzymatic reactions. The method is based on the definition of a subset of chemical coordinates; it is simple, robust, and suitable to calculate one or more alternative pathways, intermediate minima, and transition-state geometries. Though the results are approximate and the computational cost is relatively high, the method works for large systems, where others often fail. It also works when a certain reaction path competes with others having a lower energy barrier. Accordingly, the procedure is appropriate to test hypothetical reaction mechanisms for complicated systems and provides good initial guesses for more accurate methods. We present tests on a number of simple reactions and on several complicated chemical transformations and compare the results with those obtained by other methods. Calculation of the reaction path for the enzymatic hydrolysis of the substrate by dUTPase for an active-site model with 85 atoms, including several loosely bound water molecules, indicates that the method is feasible for the study of enzyme mechanisms.
TL;DR: In this paper, density functional theory calculations at the B3LYP/6-31+G** level were employed to characterize the critical points for adducts, isomers, products, and intervening transition states for the reactions between benzene and the C2H or cyano (CN) radicals.
TL;DR: The transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical.
Abstract: We have studied the performance of local and semilocal exchange-correlation functionals [meta-generalized-gradient-approximation (GGA)-TPSS, GGA–Perdew-Burke-Ernzerhof (PBE), and local density approximation (LDA)] in the calculation of transition states, reaction energies, and barriers for several molecular and one surface reaction, using the plane-wave pseudopotential approach. For molecular reactions, these results have been compared to all-electron Gaussian calculations using the B3LYP hybrid functional, as well as to experiment and high level quantum chemistry calculations, when available. We have found that the transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical. Both the meta-GGA-TPSS and the GGA-PBE functionals improve significantly the calculated LDA barrier heights. The meta-GGA-TPSS further improves systematically, albeit not always sufficiently, the GGA-PBE barriers. We have also found that, on the Si(001) surface, the meta-GGA-TPSS barriers for hydrogen adsorption agree significantly better than the corresponding GGA-PBE barriers with quantum Monte Carlo cluster results and experimental estimates.
TL;DR: The experimental observations of the lack of reaction of the non-fluorinated dienophile, the stereochemical outcomes, and the rate acceleration accompanying furan methylation are all well predicted by the calculations, supporting a reaction mechanism in which zwitterionic character is developed strongly.
Abstract: Difluorinated alkenoate ethyl 3,3-difluoro-2-(N,N-diethylcarbamoyloxy)-2-propenoate reacts rapidly and in high yield with furan and a range of substituted furans in the presence of a tin(IV) catalyst. Non-fluorinated congener 2-(N,N-diethylcarbamoyloxy)-2-propenoate fails to react at all under the same conditions. These reactions have been explored using density functional theory (DFT) calculations. They reveal a highly polar transition state, which is stabilized by the Lewis acid catalyst SnCl4 and by polar solvents. In the presence of both catalyst and solvent, a two-step reaction is predicted, corresponding to the stepwise formation of the two new carbon−carbon bonds via transition states which have similar energies in all cases. Our experimental observations of the lack of reaction of the non-fluorinated dienophile, the stereochemical outcomes, and the rate acceleration accompanying furan methylation are all well predicted by our calculations. The calculated free energy barriers generally correlate we...