Showing papers on "Transition state published in 2011"

Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes.

Abstract: Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein's...

Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of Reaction Mechanisms.

Abstract: In these five decades, many useful tools have been developed for exploring quantum chemical potential energy surfaces. The success in theoretical studies of chemical reaction mechanisms has been greatly supported by these tools. However, systematic prediction of reaction mechanisms starting only from given reactants and catalysts is still very difficult. Toward this goal, we describe the artificial force induced reaction (AFIR) method for automatically finding reaction paths of type A + B → X (+ Y). By imposing an artificial force to given reactants and catalysts, the method can find the reactive sites very efficiently. Further pressing by the artificial force provides approximate transition states and product structures, which can be easily reoptimized to the corresponding true ones. This procedure can be executed very efficiently just by minimizing a single function called the AFIR function. All important reaction paths can be found by repeating this cycle starting from many initial orientations. We also discuss perspectives of automated reaction path search methods toward the above goal.

Efficient exploration of reaction paths via a freezing string method.

Abstract: The ability to efficiently locate transition states is critically important to the widespread adoption of theoretical chemistry techniques for their ability to accurately predict kinetic constants. Existing surface walking techniques to locate such transition states typically require an extremely good initial guess that is often beyond human intuition to estimate. To alleviate this problem, automated techniques to locate transition state guesses have been created that take the known reactant and product endpoint structures as inputs. In this work, we present a simple method to build an approximate reaction path through a combination of interpolation and optimization. Starting from the known reactant and product structures, new nodes are interpolated inwards towards the transition state, partially optimized orthogonally to the reaction path, and then frozen before a new pair of nodes is added. The algorithm is stopped once the string ends connect. For the practical user, this method provides a quick and convenient way to generate transition state structure guesses. Tests on three reactions (cyclization of cis,cis-2,4-hexadiene, alanine dipeptide conformation transition, and ethylene dimerization in a Ni-exchanged zeolite) show that this “freezing string” method is an efficient way to identify complex transition states with significant cost savings over existing methods, particularly when high quality linear synchronous transit interpolation is employed.

Glutathione: mechanism and kinetics of its non-enzymatic defense action against free radicals

Abstract: Glutathione, which is the most abundant cytosolic thiol, plays important roles in the non-enzymatic antioxidant defence system. Its free radical scavenging activity towards radicals of different nature (·OH, ·OOH, ·OCH3, ·OOCH3, ·OOCHCH2 and ·OOCCl3) have been studied in aqueous solution, using the Density Functional Theory. It was found that the rate constants range from 2.02 × 104 M−1s−1 to diffusion limit (7.68 × 109 M−1s−1). Therefore it can be stated that glutathione is an excellent free radical scavenger, able of efficiently scavenging a wide variety of free radicals. It reacts exclusively by H transfer, and with the exception of its reaction with ·OH there is only one important channel of reaction, yielding to the S-centered radical. For the reaction with ·OH, on the other hand, a wide product distribution is expected, which explains the formation of C-centered radicals experimentally observed. Glutathione was found to be exceptionally good as a OOH radical scavenger, comparable to 2-propenesulfenic acid. This has been explained based on the strong H bonding interactions found in the transition states, which involves the carboxylate moiety. Therefore this might have implications for other biological systems where this group is present.

Roaming-mediated isomerization in the photodissociation of nitrobenzene

Abstract: Roaming reactions comprise a new class of reaction in which a molecule undergoes frustrated dissociation to radicals, followed by an intramolecular abstraction reaction. Nitro compounds have long been known to dissociate to give NO as a major product. However, rates based upon isomerization via calculated tight transition states are implausibly slow, so the key dissociation pathway for this important class of molecules remains obscure. Here, we present an imaging study of the photodissociation of nitrobenzene with state-specific detection of the resulting NO products. We observe a bimodal translational energy distribution in which the slow products are formed with low NO rotational excitation, and the fast component is associated with high rotational excitation. High-level ab initio calculations identified a 'roaming-type' saddle point on the ground state. Branching ratio calculations then show that thermal dissociation of nitrobenzene is dominated by 'roaming-mediated isomerization' to phenyl nitrite, which subsequently decomposes to give C(6)H(5)O + NO.

Development and application of a ReaxFF reactive force field for hydrogen combustion.

Abstract: To investigate the reaction kinetics of hydrogen combustion at high-pressure and high-temperature conditions, we constructed a ReaxFF training set to include reaction energies and transition states relevant to hydrogen combustion and optimized the ReaxFF force field parameters against training data obtained from quantum mechanical calculations and experimental values. The optimized ReaxFF potential functions were used to run NVT MD (i.e., molecular dynamics simulation with fixed number of atoms, volume, and temperature) simulations for various H2/O2 mixtures. We observed that the hydroperoxyl (HO2) radical plays a key role in the reaction kinetics at our input conditions (T ≥ 3000 K, P > 400 atm). The reaction mechanism observed is in good agreement with predictions of existing continuum-scale kinetic models for hydrogen combustion, and a transition of reaction mechanism is observed as we move from high pressure, low temperature to low pressure, high temperature. Since ReaxFF derives its parameters from q...

Ab initio calculations of the reaction pathways for methane decomposition over the Cu (111) surface

Abstract: Growth of large-area, few-layer graphene has been reported recently through the catalytic decomposition of methane (CH4) over a Cusurface at high temperature. In this study, we used ab initio calculations to investigate the minimum energy pathways of successive dehydrogenation reactions of CH4 over the Cu (111) surface. The geometries and energies of all the reaction intermediates and transition states were identified using the climbing image nudged elastic band method. The activation barriers for CH4 decomposition over this Cusurface are much lower than those in the gas phase; furthermore, analysis of electron density differences revealed significant degrees of charge transfer between the adsorbates and the Cu atoms along the reaction path; these features reveal the role of Cu as the catalytic material for graphene growth. All the dehydrogenation reactions are endothermic, except for carbon dimer (C2) formation, which is, therefore, the most critical step for subsequent graphene growth, in particular, on Cu (111) surface.

A Computational Study of the Oxidation of SO2 to SO3 by Gas-Phase Organic Oxidants

Abstract: We have studied the oxidation of SO(2) to SO(3) by four peroxyradicals and two carbonyl oxides (Criegee intermediates) using both density functional theory, B3LYP, and explicitly correlated coupled cluster theory, CCSD(T)-F12. All the studied peroxyradicals react very slowly with SO(2) due to energy barriers (activation energies) of around 10 kcal/mol or more. We find that water molecules are not able to catalyze these reactions. The reaction of stabilized Criegee intermediates with SO(2) is predicted to be fast, as the transition states for these oxidation reactions are below the free reactants in energy. The atmospheric relevance of these reactions depends on the lifetimes of the Criegee intermediates, which, at present, is highly uncertain.

Mechanism of the living lactide polymerization mediated by robust zinc guanidine complexes.

Abstract: Zinc bis(chelate) guanidine complexes promote living lactide polymerization at elevated temperatures By means of kinetic and spectroscopic analyses the mechanism has been elucidated for these special initiators that make use of neutral N-donor ligands The neutral guanidine function initiates the polymerization by a nucleophilic ring-opening attack on the lactide molecule DFT calculations on the first ring-opening step show that the guanidine is able to act as a nucleophile Three transition states were located for ligand rearrangement, nucleophilic attack, and ring-opening The second ring-opening step was modeled as a representation for the chain growth because here, the lactate alcoholate opens the second lactide molecule via two transition states (nucleophilic attack and ring-opening) Additionally, the resulting reaction profile proceeds overall exothermically, which is the driving force for the reaction The experimental and calculated data are in good agreement and the presented mechanism explains why the polymerization proceeds without co-initiators

Mechanistic Insights into the Decomposition of Fructose to Hydroxy Methyl Furfural in Neutral and Acidic Environments Using High-Level Quantum Chemical Methods

Abstract: Efficient catalytic chemical transformation of fructose to hydroxy methyl furfural (HMF) is one of the key steps for attaining industrial level conversion of biomass to useful chemicals. We report an investigation of the reaction mechanisms for the decomposition of fructose to HMF in both neutral and acidic environments at the Gaussian-4 level of theory including calculation of enthalpies, free energies, and effective solvation interactions. In neutral water solvent, the transformation of fructose to HMF involves a four step reaction sequence with four transition states. The effective activation energy relative to fructose in neutral water at 298 K is very large, about 74 kcal/mol, so that transformation in neutral media around this temperature is unlikely. In contrast, the computed potential energy surface is much more favorable for the transformation in acidic media at 498 K, as the effective activation barrier is about 39 kcal/mol. The transformation in acidic media is a much more complex mechanism involving dehydration and hydrogen transfer steps, which are more favorable when protonated intermediates are involved.

Transition States and Energetics of Nucleophilic Additions of Thiols to Substituted α,β-Unsaturated Ketones: Substituent Effects Involve Enone Stabilization, Product Branching, and Solvation

Abstract: CBS-QB3 enthalpies of reaction have been computed for the conjugate additions of MeSH to six α,β-unsaturated ketones. Compared with addition to methyl vinyl ketone, the reaction becomes 1–3 kcal mol–1 less exothermic when an α-Me, β-Me, or β-Ph substituent is present on the C═C bond. The lower exothermicity for the substituted enones occurs because the substituted reactant is stabilized more by hyperconjugation or conjugation than the product is stabilized by branching. Substituent effects on the activation energies for the rate-determining step of the thiol addition (reaction of the enone with MeS–) were also computed. Loss of reactant stabilization, and not steric hindrance, is the main factor responsible for controlling the relative activation energies in the gas phase. The substituent effects are further magnified in solution; in water (simulated by CPCM calculations), the addition of MeS– to an enone is disfavored by 2–6 kcal mol–1 when one or two methyl groups are present on the C═C bond (ΔΔG⧧). The...

Different substrate-dependent transition states in the active site of the ribosome

Abstract: Two reactions occur in the ribosome catalytic centre: peptide bond formation and peptide release. Previous modelling has suggested that the hydrolysis reaction during release involves a concerted proton shuttle in the transition state. Kuhlenkoetter et al. have conducted proton inventories of the reaction and find that one hydrogen bond is formed during the rate-limiting step, rather than the three produced during peptide bond formation. They conclude that the peptidyl transferase centre is able to support two different transition states. The active site of the ribosome, the peptidyl transferase centre, catalyses two reactions, namely, peptide bond formation between peptidyl-tRNA and aminoacyl-tRNA as well as the release-factor-dependent hydrolysis of peptidyl-tRNA. Unlike peptide bond formation, peptide release is strongly impaired by mutations of nucleotides within the active site, in particular by base exchanges at position A2602 (refs 1, 2). The 2′-OH group of A76 of the peptidyl - tRNA substrate seems to have a key role in peptide release3. According to computational analysis4 , the 2′-OH may take part in a concerted ‘proton shuttle’ by which the leaving group is protonated, in analogy to similar current models of peptide bond formation4,5,6. Here we report kinetic solvent isotope effects and proton inventories (reaction rates measured in buffers with increasing content of deuterated water, D2O) of the two reactions catalysed by the active site of the Escherichia coli ribosome. The transition state of the release factor 2 (RF2)-dependent hydrolysis reaction is characterized by the rate-limiting formation of a single strong hydrogen bond. This finding argues against a concerted proton shuttle in the transition state of the hydrolysis reaction. In comparison, the proton inventory for peptide bond formation indicates the rate-limiting formation of three hydrogen bonds with about equal contributions, consistent with a concerted eight-membered proton shuttle in the transition state5. Thus, the ribosome supports different rate-limiting transition states for the two reactions that take place in the peptidyl transferase centre.

Mechanistic insights on N-heterocyclic carbene-catalyzed annulations: the role of base-assisted proton transfers.

Abstract: The density functional theory investigation on the mechanism of NHC-catalyzed cycloannulation reaction of the homoenolate derived from butenal with pentenone is studied. The M06-2X/6-31+G** and B3LYP/6-31+G** levels of theory, including the effect of continuum solvation in dichloromethane and tetrahydrofuran, are employed. Several mechanistic scenarios are examined for each elementary step by identifying the key intermediates and the corresponding transition states interconnecting them on the respective potential energy surfaces. Both assisted and unassisted pathways for important proton transfer steps are considered, respectively, with and without the explicit inclusion of base (DBU) in the corresponding transition states. The barrier for the crucial proton transfer steps involved in the formation of the Breslow intermediate as well as in the subsequent steps is found to be significantly lowered by explicit inclusion of DBU. The energetic comparison between two key pathways, depicted as path A and path B...

Mechanism of silver- and copper-catalyzed decarboxylation reactions of aryl carboxylic acids

Abstract: Silver- and copper-catalyzed decarboxylation reactions of aryl carboxylic acids were investigated with the aid of density functional theory calculations. The reaction mechanism starts with a carboxylate complex of silver or copper. Decarboxylation occurs via ejecting CO2 from the carboxylate complex followed by protodemetallation with an aryl carboxylic acid molecule to regenerate the starting complex. Our results indicated that the primary factor to affect the overall reaction barriers is the ortho steric destabilization effect on the starting carboxylate complexes for most cases. Certain ortho substituents that are capable of coordinating with the catalyst metal center without causing significant ring strain stabilize the decarboxylation transition states and reduce the overall reaction barriers. However, the coordination effect is found to be the secondary factor when compared with the ortho effect.

Reaction kinetics of ethylene glycol reforming over platinum in the vapor versus aqueous phases

Abstract: First-principles, periodic, density functional theory (DFT) calculations are carried out on Pt(111) to investigate the structure and energetics of dehydrogenated ethylene glycol species and transition states for the cleavage of C−H/O−H and C−C bonds. Additionally, reaction kinetics studies are carried out for the vapor phase reforming of ethylene glycol (C2H6O2) over Pt/Al2O3 at various temperatures, pressures, and feed concentrations. These results are compared to data for aqueous phase reforming of ethylene glycol on this Pt catalyst, as reported in a previous publication (Shabaker, J. W.; et al. J. Catal. 2003, 215, 344). Microkinetic models were developed to describe the reaction kinetics data obtained for both the vapor-phase and aqueous-phase reforming processes. The results suggest that C−C bond scission in ethylene glycol occurs at an intermediate value of x (3 or 4) in C2HxO2. It is also found that similar values of kinetic parameters can be used to describe the vapor and aqueous phase reforming ...

A density functional theory study on CO2 capture and activation by graphene-like boron nitride with boron vacancy

Abstract: First principle calculations for a hexagonal (graphene-like) boron nitride (g-BN) monolayer sheet in the presence of a boron-atom vacancy show promising properties for capture and activation of carbon dioxide. CO2 is found to decompose to produce an oxygen molecule via an intermediate chemisorption state on the defect g-BN sheet. The three stationary states and two transition states in the reaction pathway are confirmed by minimum energy pathway search and frequency analysis. The values computed for the two energy barriers involved in this catalytic reaction after enthalpy correction indicate that the catalytic reaction should proceed readily at room temperature.

Potential Energy Surface for (Retro-)Cyclopropanation: Metathesis with a Cationic Gold Complex

Abstract: The gas-phase cyclopropanation and apparent metathesis reactivity of ligand-supported gold arylidenes with electron-rich olefins is explained by quantum-chemical calculations. A deep potential minimum corresponding to a metal-bound cyclopropane adduct is in agreement with the measured absolute energies of the cyclopropanation and metathesis channels and is also consistent with previously reported electronic effects of arylidenes and supporting phosphorus ylid ligands on the product ratios. In the gas phase, the rate-determining step for the cyclopropanation is dissociation of the Lewis-acidic metal fragment, whereas the metathesis pathway features several rate-limiting transition states that are close in energy to the final product dissociation and hence contribute to the overall reaction rate. Importantly, the presented potential energy surface also accounts for the recently reported gold-catalyzed solution-phase retro-cyclopropanation reactivity.

Electrocatalytic oxygen evolution from water on a Mn(III–V) dimer model catalyst—A DFT perspective

Abstract: A complete water oxidation and oxygen evolution reaction (OER) cycle is monitored by means of density functional theory (DFT). A biomimetic model catalyst, comprising a μ-OH bridged Mn(III–V) dimer truncated by acetylacetonate ligand analogs and hydroxides is employed. The reaction cycle is divided into four electrochemical hydrogen abstraction steps followed by a series of chemical steps. The former employ the tyrosine/tyrosyl redox couple acting as electron and proton sink, thus determining the reference potential. Stripping hydrogen from water leads to the formation of two highly unstable Mn(V)O/Mn(IV)–O˙ moieties, which subsequently combine to form a μ-peroxy O–O bond. O2 evolution results from subsequent consecutive replacement of the remaining Mn–O bonds by water. A Zener “spintronic” type mechanism for virtually barrierless O2 evolution is found. The applicability of DFT is discussed and extended to include the rate-limiting steps in the OER. Rather than attempting to compute transition states where KS-DFT is unreliable, an upper bound for the activation barrier of the O–O bond formation step is estimated from the hessians of the relevant intermediates.

Scavenging mechanism of curcumin toward the hydroxyl radical: a theoretical study of reactions producing ferulic acid and vanillin.

Abstract: Curcumin is known to be an antioxidant, as it can scavenge free radicals from biological media. A sequence of H-abstraction and addition reactions involving up to eight OH radicals and curcumin or its degradation products leading to the formation of two other antioxidants, namely, ferulic acid and vanillin, was studied. Single electron transfer from curcumin to an OH radical was also studied. All relevant extrema on the potential energy surfaces were located by optimizing geometries of the reactant and product complexes, as well as those of the transition states, at the BHandHLYP/6-31G(d,p) level of density functional theory in the gas phase. Single-point energy calculations were also performed in the gas phase at the BHandHLYP/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. Solvent effects in aqueous media were treated by performing single-point energy calculations at all of the above-mentioned levels of theory employing the polarizable continuum model and the geometries optimized at the BHandHLYP/6-31G(d,p) level in the gas phase. A few reaction steps were also studied by geometry optimization in aqueous media, and the thus-obtained Gibbs free energy barriers were similar to those obtained by corresponding single-point energy calculations. Our calculations show that the hydrogen atom of the OH group attached to the phenol moiety of curcumin would be most efficiently abstracted by an OH radical, in agreement with experimental observations. Further, our study shows that OH addition would be most favored at the C10 site of the heptadiene chain. It was found that curcumin can serve as an effective antioxidant.

DFT Study of Chiral‐Phosphoric‐Acid‐Catalyzed Enantioselective Friedel–Crafts Reaction of Indole with Nitroalkene: Bifunctionality and Substituent Effect of Phosphoric Acid

Abstract: The enantioselective Friedel-Crafts reaction of indoles with nitroalkenes proceeds catalytically by means of a chiral-phosphoric-acid catalyst to afford products with high enantioselectivities (up to 91% ee). The use of a 3,3'-SiPh(3)-substituted (R)-binol-derived (binol=1,1'-binaphthyl-2,2'-diol) catalyst and a free indole that bears an N-H moiety is essential to achieving high enantioselectivity as well as high yield. To elucidate the reaction mechanism and the origin of the high enantioselectivity, DFT calculations were carried out. The reaction proceeded through a cyclic transition state formed by the two-point binding of both substrates to the conjugated O-P-O moiety of the catalyst, in which indoles and nitroalkenes could be simultaneously activated by Bronsted acidic (proton) and basic (phosphoryl oxygen) sites, respectively. The enantioselectivity was entirely controlled by the steric effect between the 3,3'-substituent group on the (R)-binol-derived phosphoric acid catalyst and the indole ring. When the sterically demanding SiPh(3) group was used as the 3,3'-substituent group, the energy difference between the most-stable diastereomeric transition states that afforded the S and R products was increased to lead to the high enantioselectivity in agreement with the experimental results.

Energetics and dynamics of proton transfer reactions along short water wires.

Abstract: Proton transfer (pT) reactions in biochemical processes are often mediated by chains of hydrogen-bonded water molecules. We use hybrid density functional calculations to study pT along quasi one-dimensional water arrays that connect an imidazolium–imidazole proton donor–acceptor pair. We characterize the structures of intermediates and transition states, the energetics, and the dynamics of the pT reactions, including vibrational contributions to kinetic isotope effects. In molecular dynamics simulations of pT transition paths, we find that for short water chains with four water molecules, the pT reactions are semi-concerted. The formation of a high-energy hydronium intermediate next to the proton-donating group is avoided by a simultaneous transfer of a proton from the donor to the first water molecule, and from the first water molecule into the water chain. Lowering the dielectric constant of the environment and increasing the water chain length both reduce the barrier for pT. We study the effect of the driving force on the energetics of the pT reaction by changing the proton affinity of the donor and acceptor groups through halogen and methyl substitutions. We find that the barrier of the pT reaction depends linearly on the proton affinity of the donor but is nearly independent of the proton affinity of the acceptor, corresponding to Bronsted slopes of one and zero, respectively.

Product energy deposition of CN + alkane H abstraction reactions in gas and solution phases.

Abstract: In this work, we report the first theoretical studies of post-transition state dynamics for reaction of CN with polyatomic organic species. Using electronic structure theory, a newly developed analytic reactive PES, a recently implemented rare-event acceleration algorithm, and a normal mode projection scheme, we carried out and analyzed quasi-classical and classical non-equilibrium molecular dynamics simulations of the reactions CN + propane (R1) and CN + cyclohexane (R2). For (R2), we carried out simulations in both the gas phase and in a CH2Cl2 solvent. Analysis of the results suggests that the solvent perturbations to the (R2) reactive free energy surface are small, leading to product energy partitioning in the solvent that is similar to the gas phase. The distribution of molecular geometries at the respective gas and solution phase variational association transition states is very similar, leading to nascent HCN which is vibrationally excited in both its CH stretching and HCN bending coordinates. This...

Acrolein hydrogenation on Pt(211) and Au(211) surfaces: a density functional theory study

Abstract: Partial hydrogenation of acrolein, the simplest α,β-unsaturated aldehyde, is not only a model system to understand the selectivity in heterogeneous catalysis, but also technologically an important reaction. In this work, the reaction on Pt(211) and Au(211) surfaces is thoroughly investigated using density functional theory calculations. The formation routes of three partial hydrogenation products, namely propenol, propanal and enol, on both metals are studied. It is found that the pathway to produce enol is kinetically favoured on Pt while on Au the route of forming propenol is preferred. Our calculations also show that the propanal formation follows an indirect pathway on Pt(211). An energy decomposition method to analyze the barrier is utilized to understand the selectivities at Pt(211) and Au(211), which reveals that the interaction energies between the reactants involved in the transition states play a key role in determining the selectivity difference.

Calculation of multiple initial state selected reaction probabilities from Chebyshev flux-flux correlation functions: influence of reactant internal excitations on H + H2O → OH + H2.

Abstract: A Chebyshev-based flux-flux correlation function approach is introduced for calculating multiple initial state selected reaction probabilities for bimolecular reactions. Based on the quantum transition-state theory, this approach propagates, with the exact Chebyshev propagator, transition-state wave packets towards the reactant asymptote. It is accurate and efficient if many initial state selected reaction probabilities are needed. This approach is applied to the title reaction to elucidate the influence of the H2O ro-vibrational states on its reactivity. Results from several potential energy surfaces are compared.