Analyzing the Case for Bifunctional Catalysis

Bifunctional coupling of two different catalytic site types has often been invoked to explain experimentally observed enhanced catalytic activities. We scrutinize such claims with generic scaling‐relation‐based microkinetic models that allow exploration of the theoretical limits for such a bifunctional gain for several model reactions. For sites at transition‐metal surfaces, the universality of the scaling relations between adsorption energies largely prevents any improvements through bifunctionality. Only the consideration of systems that involve the combination of different materials, such as metal particles on oxide supports, offers hope for significant bifunctional gains.     

Stereochemistry of transition states and mechanisms of chemical reactions on silica surface

The activation energy of substitution and bond cleavage reactions of siloxane derivatives on silica surfaces is discussed considering the stereochemistry of the transition state. General concepts are developed and utilized in predicting reactivity trends for reactions occurring on the silica surface.     

Optimizing transition states via kernel-based machine learning

We present a method for optimizing transition state theory dividing surfaces with support vector machines. The resulting dividing surfaces require no a priori information or intuition about reaction mechanisms. To generate optimal dividing surfaces, we apply a cycle of machine-learning and refinement of the surface by molecular dynamics sampling. We demonstrate that the machine-learned surfaces contain the relevant low-energy saddle points. The mechanisms of reactions may be extracted from the machine-learned surfaces in order to identify unexpected chemically relevant processes. Furthermore, we show that the machine-learned surfaces significantly increase the transmission coefficient for an adatom exchange involving many coupled degrees of freedom on a (100) surface when compared to a distance-based dividing surface.     

On nonadiabatic transition state theory

A nonseparable semiclassical transition state approximation for reactions involving more than one electronic surface is suggested. The single surface formulation in terms of quasiprobability distributions used by Miller is discussed along with a separable semiclassical approximation for the nonadiabatic rate suggested in the Soviet literature. A thermally averaged nonadiabatic rate is defined, and a semiclassical approximation is presented, wherein the surface through which flux is calculated in the transition state approach is determined by the intersection of adiabatic electronic surfaces viewed as functions of imaginary (or complex) time.     

Sol - gel transition in biopolymers

Rheological measurements have been performed on pectin biopolymers close to the sol-gel transition. From these measurements scaling exponents were determined independently for the viscosity, s = 0.82(5), for the elastic modulus, t = 1.93(8), for the frequency-dependent modulus, Δ = 0.71(2), and for the relaxation times below and above the transition, vz = 2.67(12) and vz' = 2.65(9). The exponents satisfy the scaling relations predicted by the theory and their numerical values agree with those from scalar elasticity percolation.     

Force reversed method for locating transition states

To identify the transition state accurately and efficiently on a high-dimensional potential energy surface is one of the most important topics in kinetic studies on chemical reactions. We present here an algorithm to search the transition state by so-called force reversed method, which only requires a rough reaction direction instead of knowing the initial state and final state. Compared to the nudged elastic band method and the dimer method that require multiple images, the present algorithm with only single image required saves significantly the computational cost. The algorithm was implemented in the first-principle periodic total energy calculation package and applied successfully to several prototype surface processes such as the adsorbate diffusion and dissociation on metal surfaces. The results indicate that the force reversed method is efficient, robust to identify the transition state of various surface processes.     

State-to-state reaction probabilities within the quantum transition state framework

Rigorous quantum dynamics calculations of reaction rates and initial state-selected reaction probabilities of polyatomic reactions can be efficiently performed within the quantum transition state concept employing flux correlation functions and wave packet propagation utilizing the multi-configurational time-dependent Hartree approach. Here, analytical formulas and a numerical scheme extending this approach to the calculation of state-to-state reaction probabilities are presented. The formulas derived facilitate the use of three different dividing surfaces: two dividing surfaces located in the product and reactant asymptotic region facilitate full state resolution while a third dividing surface placed in the transition state region can be used to define an additional flux operator. The eigenstates of the corresponding thermal flux operator then correspond to vibrational states of the activated complex. Transforming these states to reactant and product coordinates and propagating them into the respective asymptotic region, the full scattering matrix can be obtained. To illustrate the new approach, test calculations study the D + H(2)(ν, j) → HD(ν', j') + H reaction for J = 0.     

Optimized spin crossings and transition states for short-range electron transfer in transition metal dimers

Electron-transfer reactions in eight mixed-valence manganese dimers are studied using B3LYP. One of the dimers is a model of the active site of manganese catalase, while another represents a basic building block of the oxygen-evolving complex in photosystem II. The adiabatic reactions are characterized by fully optimized transition states where the single imaginary frequency represents the electron-transfer coordinate. When there is antiferromagnetic coupling between different high-spin centers, electron transfer must be accompanied by a spin transition. Spin transitions are characterized by minimum-energy crossing points between spin surfaces. Three reaction mechanisms have been investigated. First, a single-step reaction where spin flip is concerted with electron transfer. Second, an initial transition to a center with intermediate spin that can be followed by electron transfer. Third, an initial transition to a ferromagnetic state from which the electron can be transferred adiabatically. The complexes prefer the third route with rate-determining barriers ranging from 5.7 kcal/mol to 17.2 kcal/mol for different complexes. The origins of these differences are discussed in terms of oxidation states and ligand environments. Many DFT functionals overestimate charge-transfer interactions, but for the present complexes, the error should be limited because of short Mn-Mn distances.     

A dimensionless reaction coordinate for quantifying the lateness of transition states

The Hammond‐Leffler postulate asserts that transition states of exothermic reactions are reactant‐like (early), whereas transition states of endothermic reactions are product‐like (late). Related postulates have been proposed to describe the sensitivity of activation barriers for reactions occurring on catalytic surfaces to the catalyst structure. To evaluate the validity of these postulates for different chemical reactions, a general method for classifying transition states as either early or late is needed. One can envision a dimensionless reaction coordinate that changes continuously and monotonically from 0 to 1 along a minimum energy reaction pathway. The value of the dimensionless reaction coordinate for the transition state (W_TS) classifies transition states as (a) early when W_TS < 0.5, (b) late when W_TS > 0.5, and (c) equidistant between reactants and products when W_TS = 0.5. In this article, we derive such a dimensionless reaction coordinate and illustrate its usefulness for several different chemical reactions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

First Principles Calculations for Hydrogenation of Acrolein on Pd and Pt: Chemoselectivity Depends on Steric Effects on the Surface

The chemoselective hydrogenation of acrolein on Pt(111) and Pd(111) surfaces is investigated employing density functional theory calculations. The computed potential energy surfaces together with the analysis of reaction mechanisms demonstrate that steric effects are an important factor that governs chemoselectivity. The reactions at the C=O functionality require more space than the reactions at the C=C functionality. Therefore the formation of allyl alcohol is more favorable at low coverage, while the reduction of the C=C bond and the formation of propanal becomes kinetically more favorable at higher coverage. The elementary reaction steps are found to follow different reaction mechanisms, which are identified according to terminology typically used in organometallic catalysis. The transition state scaling (TSS) relationship is demonstrated and the origin of multiple TSS lines is linked to variation of an internal electronic structure of a carbon skeleton.     

Water wetting transition parameters of perfluorinated substrates with periodically distributed flat-top microscale obstacles

Superhydrophobicity is obtained on photolithographically structured silicon surfaces consisting of flat-top pillars after a perfluorosilanization treatment. Systematic static contact angle measurements were carried out on these surfaces as a function of pillar parameters that geometrically determine the surface roughness, including pillar height, diameter, top perimeter, overall filling factor, and disposition. In line with thermodynamics models, two regimes of static contact angles are observed varying each parameter independently: the "Cassie" regime, in which the water drop sits suspended on top of the pillars (referred to as composite), corresponding to experimental contact angles greater than 140-150 degrees, and the "Wenzel" regime, in which water completely wets the asperities (referred to as wetted), corresponding to lower experimental contact angles. A transition between the Cassie and Wenzel regimes corresponds to a set of well-defined parameters. By smoothly depositing water drops on the surfaces, this transition is observed for surface parameter values far from the calculated ones for the thermodynamic transition, therefore offering evidence for the existence of metastable composite states. For all studied parameters, the position of the experimental transition correlates well with a rough estimation of the energy barrier to be overcome from a composite metastable state in order to reach the thermodynamically favored Wenzel state. This energy barrier is estimated as the surface energy variation between the Cassie state and the hypothetical composite state with complete filling of the surface asperities by water, keeping the contact angle constant.     

Electrowetting-based control of droplet transition and morphology on artificially microstructured surfaces

Electrowetting (EW) has recently been demonstrated as a powerful tool for controlling droplet morphology on smooth and artificially structured surfaces. The present work involves a systematic experimental investigation of the influence of electrowetting in determining and altering the state of a static droplet resting on an artificially microstructured surface. Extensive experimentation is carried out to benchmark a previously developed energy-minimization-based model that analyzed the influence of interfacial energies, surface roughness parameters, and electric fields in determining the apparent contact angle of a droplet in the Cassie and Wenzel states under the influence of an EW voltage. The EW voltage required to trigger a transition from the Cassie state to the Wenzel state is experimentally determined for surfaces having a wide range of surface parameters (surface roughness and fraction of surface area covered with pillars). The reversibility of the Cassie-Wenzel transition upon the removal of the EW voltage is also quantified and analyzed. The experimental results from the present work form the basis for the design of surfaces that enable dynamic control of droplet morphology. A significant finding from the present work is that nonconservative dissipative forces have a significant influence in opposing fluid flow inside the microstructured surface that inhibits reversibility of the Cassie-Wenzel transition. The artificially structured surfaces considered in this work have microscale roughness feature sizes that permits direct visual observation of EW-induced Cassie-Wenzel droplet transition; this is the first reported visual confirmation of EW-induced droplet state transition.     

Shifting the scaling relations of single-atom catalysts for facile methane activation by tuning the coordination number

We investigate oxidative methane activation on a wide range of single transition metal atom catalysts embedded on N-doped graphene derivatives using density functional theory calculations. An inverse scaling relationship between *O formation and its hydrogen affinity is observed, consistent with a previous report. However, we find that the latter scaling line can be shifted towards a more reactive region by tuning the coordination number (CN) of the active metal sites. Specifically, we find that lowering the CN plays an important role in increasing the reactivity for methane activation via a radical-like transition state by moving the scaling lines. Thus, in the new design strategy suggested here, different from the conventional efforts focusing mainly on breaking the scaling relations, one maintains the scaling relations but moves them towards more reactive regions by controlling the coordination number of the active sites. With this design principle, we suggest several single atom catalysts with lower C–H activation barriers than some of the most active methane activation catalysts in the literature such as Cu-based zeolites.

The scaling relationship of methane activation via a radical-like transition state shifts toward a more reactive region with decreasing coordination number of the active sites.     

Geometric parameters of the transition state in radical reactions of antioxidants

An algorithm for calculating interatomic distances in a transition state of radical abstraction reactions through the enthalpy of a reaction is developed. The algorithm is based on a combination of quantum-chemical calculations with the calculation by the intersecting-parabolas method. Using this method and experimental data (enthalpies and activation energies of reactions), interatomic distances in a reaction center are calculated for the reactions of antioxidants with a symmetrical transition state of the N...H...N and O...H...O types and a nonsymmetrical transition state of the N...H...C, O...H...C, and O...H...N types. These distances are compared with other characteristics of the reactions and reactants. The influence of such factors as the enthalpy of the reaction, triplet repulsion in the transition state, electronegativity of atoms in the reaction center, and steric repulsion of reactants on the geometric parameters of the transition state is examined. The results obtained are used to calculate the increments characterizing the influence of various factors on interatomic distances of radical reactions considered.Translated from Kinetika i Kataliz, Vol. 45, No. 6, 2004, pp. 877–896.Original Russian Text Copyright © 2004 by Denisova, Denisov.     

Properties of variational transition states for association reactions

The relationships between the structures of microcanonical variational transition states for association reactions and potential energy surface properties are analyzed. The analysis is facilitated by the recent finding that in many cases the vibrational frequencies for the transitional modes in the association reaction vary exponentially with the reaction coordinate. An increase in the attenuation of the transitional mode frequencies results in a tighter transition state. Long-range minimum energy path potentials of the form −c/r″ have only one transition state at each energy. Certain types of association reactions may not have transition states.     

Quantum transition state theory

We derive and discuss upper bound, of transition state form, to the quantum rate constant for bimolecular reactions.     

An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction

The ribosome has an active site comprised of RNA that catalyzes peptide bond formation. To understand how RNA promotes this reaction requires a detailed understanding of the chemical transition state. Here, we report the Br?nsted coefficient of the alpha-amino nucleophile with a series of puromycin derivatives. Both 50S subunit- and 70S ribosome-catalyzed reactions displayed linear free-energy relationships with slopes close to zero under conditions where chemistry is rate limiting. These results indicate that, at the transition state, the nucleophile is neutral in the ribosome-catalyzed reaction, in contrast to the substantial positive charge reported for typical uncatalyzed aminolysis reactions. This suggests that the ribosomal transition state involves deprotonation to a degree commensurate with nitrogen-carbon bond formation. Such a transition state is significantly different from that of uncatalyzed aminolysis reactions in solution.     

Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis

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.