Transition State Activation Research Articles

Origin of norbornene-mediated selective meta-C–H arylation of anisole derivatives overcoming the “ortho constraint” in Pd/S,O-ligand catalysis

Bridgehead-modified norbornene has a significant impact on the geometries of meta-C–H activation transition states and main factors regulating mono- and di-meta-selectivity.

Evidence for a kinetic FLP reaction pathway in the activation of benzyl chlorides by alkali metal-phosphine pairs.

Kinetic frustrated Lewis pairs (FLP) allow facile cleavage of a number of E-H bonds (E = H, Si, C, B) where both the Lewis base and Lewis acid are involved in the bond activation transition state. More recently, kinetic FLP systems have been extended to the cleavage of C-X (X = F, Cl, Br) bonds. We report on the role of sodium tetrakis(pentafluorophenyl)borate in the benzylation of triarylphosphines, where the sodium cation and phosphine support a kinetic FLP type transition state.

QM evaluation of the intramolecular aromatic π-π interactions of Ir(I) complex transition states

Major π-π interactions within Ir(I) complex Cp*Ir(I)PPh3 were quantum mechanically characterized using the major hybrid DFT, MP2 and CCSD(T) methods. Almost all the neighborhood π-π interactions are found to be slightly repulsive, and MP2 interaction energies range from -0.49 to 19.16 kcal/mol. The representative A-B π-π pair (See Figure 2) is further addressed using DFT methods. Interaction energies of the A-B π-π pair calculated from 6 hybrid DFT methods ranges from 0.52 kcal/mol by the SVWN method to 8.23 kcal/mol by the O3LYP method. The interaction energies calculated with unrestricted open shell MP2 theory can be up to 25% higher than those computed using restricted open shell MP2 method. Comparison between the DFT results and the benchmark CCSD(T) results shows that the DFT calculations of π-π interaction are reasonable but still need to be interpreted with caution. This study helps to pinpoint intramolecular aromatic π-π interactions of transition state for alkyl CH bond activation of saturated hydrocarbons and rational molecular design.

Theoretical study to gain fundamental insight into reaction mechanism of N-S acyl transfer of N-sulfanylethylanilide-based protein labeling reagent on protein surface.

Elucidation of protein function is one of the central issues in the field of life sciences. To study the function of proteins not in isolation, but in a cell or its lysate, thus, it is necessary to selectively label the target protein in a mixture. Affinity labeling is one of several widely used methods for selective labeling; however, this method has the disadvantage that the labeling reagent is always activated, albeit weakly. Therefore, fine-tuning of the reactivity and/or reaction conditions is generally required for successful target-selective labeling. We previously developed a new affinity labeling reagent with N-sulfanylethylanilide (SEAlide) as a key reactive unit. It was designed based on the following hypotheses. SEAlide is less reactive and does not label in the absence of a target protein. Upon target binding, amino acid side-chain functional groups on the target surface convert SEAlide into a thioester form via N-S acyl transfer, allowing the target to be labeled. However, no evidence has been obtained so far to directly prove the hypothesis. In this study, we examine whether amino acid side-chain functional groups can activate SEAlide from the viewpoint of theoretical chemistry. The theoretical studies show that the activation free energy and enthalpy of the acyl transfer of SEAlide are reduced in the presence of methylammonium, which is a model for the protonated side chain of Lys, and acetate, which is a model for the deprotonated side chain of Asp/Glu. It suggests that Lys and Asp/Glu side chains could potentially stabilize the activation transition states to accelerate the thioester formation. Furthermore, the significant decrease in the activation enthalpy indicates that the contribution of entropy to the transition state is large. This result supports the original hypothesis that the SEAlide-based labeling reagent is efficiently activated by binding to the target protein.

A Leucyl-tRNA Synthetase Urzyme: Authenticity of tRNA Synthetase Catalytic Activities and Promiscuous Phosphorylation of Leucyl-5'AMP.

Aminoacyl-tRNA synthetase (aaRS)/tRNA cognate pairs translate the genetic code by synthesizing specific aminoacyl-tRNAs that are assembled on messenger RNA by the ribosome. Deconstruction of the two distinct aaRS superfamilies (Classes) has provided conceptual and experimental models for their early evolution. Urzymes, containing ~120–130 amino acids excerpted from regions where genetic coding sequence complementarities have been identified, are key experimental models motivated by the proposal of a single bidirectional ancestral gene. Previous reports that Class I and Class II urzymes accelerate both amino acid activation and tRNA aminoacylation have not been extended to other synthetases. We describe a third urzyme (LeuAC) prepared from the Class IA Pyrococcus horikoshii leucyl-tRNA synthetase. We adduce multiple lines of evidence for the authenticity of its catalysis of both canonical reactions, amino acid activation and tRNALeu aminoacylation. Mutation of the three active-site lysine residues to alanine causes significant, but modest reduction in both amino acid activation and aminoacylation. LeuAC also catalyzes production of ADP, a non-canonical enzymatic function that has been overlooked since it first was described for several full-length aaRS in the 1970s. Structural data suggest that the LeuAC active site accommodates two ATP conformations that are prominent in water but rarely seen bound to proteins, accounting for successive, in situ phosphorylation of the bound leucyl-5′AMP phosphate, accounting for ADP production. This unusual ATP consumption regenerates the transition state for amino acid activation and suggests, in turn, that in the absence of the editing and anticodon-binding domains, LeuAC releases leu-5′AMP unusually slowly, relative to the two phosphorylation reactions.

Hot atom chemistry: Oxygen at stepped platinum surfaces

It is a paradigm in chemistry that chemical reactions are mainly governed by thermodynamics. Within this assumption, reaction rates can be derived from transition state theory which requires a quasi-equilibrium between reactants and activated transition state complexes that is achieved through friction. However, to reach thermal equilibrium through friction takes some time. Here we show, based on ab initio molecular dynamics simulations of the interaction of molecular oxygen with stepped Pt surfaces, that chemical reactions in heterogeneous catalysis can occur in a non-equilibrium fashion when the excess kinetic energy upon entering the potential well of a reaction intermediate is large enough.

An Exception to the Carothers Equation Caused by the Accelerated Chain Extension in a Pd/Ag Cocatalyzed Cross Dehydrogenative Coupling Polymerization.

The Carothers equation is often used to predict the utility of a small molecule reaction in a polymerization. In this study, we present the mechanistic study of Pd/Ag cocatalyzed cross dehydrogenative coupling (CDC) polymerization to synthesize a donor-acceptor (D-A) polymer of 3,3'-dihexyl-2,2'-bithiophene and 2,2',3,3',5,5',6,6'-octafluorobiphenyl, which go counter to the Carothers equation. It is uncovered that the second chain extension cross-coupling proceeds much more efficiently than the first cross-coupling and the homocoupling side reaction (at least 1 order of magnitude faster) leading to unexpectedly low homocoupling defects and high molecular weight polymers. Kinetic analyses show that C-H bond activation is rate-determining in the first cross-coupling but not in the second cross-coupling. Based on DFT calculations, the high cross-coupling rate in the second cross-coupling was ascribed to the strong Pd-thiophene interaction in the Pd-mediated C-H bond activation transition state, which decreases the energy barrier of the Pd-mediated C-H bond activation. These results have implications beyond polymerizations and can be used to ease the synthesis of a wide range of molecules where C-H bond activation may be the limiting factor.

Unconventional mechanism and selectivity of the Pd-catalyzed C\u2013H bond lactonization in aromatic carboxylic acid

The search for more effective and highly selective C–H bond oxidation of accessible hydrocarbons and biomolecules is a greatly attractive research mission. The elucidating of mechanism and controlling factors will, undoubtedly, help to broaden scope of these synthetic protocols, and enable discovery of more efficient, environmentally benign, and highly practical new C–H oxidation reactions. Here, we reveal the stepwise intramolecular SN2 nucleophilic substitution mechanism with the rate-limiting C–O bond formation step for the Pd(II)-catalyzed C(sp3)–H lactonization in aromatic 2,6-dimethylbenzoic acid. We show that for this reaction, the direct C–O reductive elimination from both Pd(II) and Pd(IV) (oxidized by O2 oxidant) intermediates is unfavorable. Critical factors controlling the outcome of this reaction are the presence of the η3-(π-benzylic)–Pd and K+–O(carboxylic) interactions. The controlling factors of the benzylic vs ortho site-selectivity of this reaction are the: (a) difference in the strains of the generated lactone rings; (b) difference in the strengths of the η3-(π-benzylic)–Pd and η2-(π-phenyl)–Pd interactions, and (c) more pronounced electrostatic interaction between the nucleophilic oxygen and K+ cation in the ortho-C–H activation transition state. The presented data indicate the utmost importance of base, substrate, and ligand in the selective C(sp3)–H bond lactonization in the presence of C(sp2)–H.

Automated Construction and Optimization Combined with Machine Learning to Generate Pt(II) Methane C–H Activation Transition States

Automated Construction and Optimization Combined with Machine Learning to Generate Pt(II) Methane C–H Activation Transition States

Partitioning Entropy with Action Mechanics: Predicting Chemical Reaction Rates and Gaseous Equilibria of Reactions of Hydrogen from Molecular Properties.

Our intention is to provide easy methods for estimating entropy and chemical potentials for gas phase reactions. Clausius’ virial theorem set a basis for relating kinetic energy in a body of independent material particles to its potential energy, pointing to their complementary role with respect to the second law of maximum entropy. Based on this partitioning of thermal energy as sensible heat and also as a latent heat or field potential energy, in action mechanics we express the entropy of ideal gases as a capacity factor for enthalpy plus the configurational work to sustain the relative translational, rotational, and vibrational action. This yields algorithms for estimating chemical reaction rates and positions of equilibrium. All properties of state including entropy, work potential as Helmholtz and Gibbs energies, and activated transition state reaction rates can be estimated, using easily accessible molecular properties, such as atomic weights, bond lengths, moments of inertia, and vibrational frequencies. We conclude that the large molecular size of many enzymes may catalyze reaction rates because of their large radial inertia as colloidal particles, maximising action states by impulsive collisions. Understanding how Clausius’ virial theorem justifies partitioning between thermal and statistical properties of entropy, yielding a more complete view of the second law’s evolutionary nature and the principle of maximum entropy. The ease of performing these operations is illustrated with three important chemical gas phase reactions: the reversible dissociation of hydrogen molecules, lysis of water to hydrogen and oxygen, and the reversible formation of ammonia from nitrogen and hydrogen. Employing the ergal also introduced by Clausius to define the reversible internal work overcoming molecular interactions plus the configurational work of change in Gibbs energy, often neglected; this may provide a practical guide for managing industrial processes and risk in climate change at the global scale. The concepts developed should also have value as novel methods for the instruction of senior students.

Toward the design of chemical reactions: Machine learning barriers of competing mechanisms in reactant space.

The interplay of kinetics and thermodynamics governs reactive processes, and their control is key in synthesis efforts. While sophisticated numerical methods for studying equilibrium states have well advanced, quantitative predictions of kinetic behavior remain challenging. We introduce a reactant-to-barrier (R2B) machine learning model that rapidly and accurately infers activation energies and transition state geometries throughout the chemical compound space. R2B exhibits improving accuracy as training set sizes grow and requires as input solely the molecular graph of the reactant and the information of the reaction type. We provide numerical evidence for the applicability of R2B for two competing text-book reactions relevant to organic synthesis, E2 and SN2, trained and tested on chemically diverse quantum data from the literature. After training on 1-1.8k examples, R2B predicts activation energies on average within less than 2.5 kcal/mol with respect to the coupled-cluster singles doubles reference within milliseconds. Principal component analysis of kernel matrices reveals the hierarchy of the multiple scales underpinning reactivity in chemical space: Nucleophiles and leaving groups, substituents, and pairwise substituent combinations correspond to systematic lowering of eigenvalues. Analysis of R2B based predictions of ∼11.5k E2 and SN2 barriers in the gas-phase for previously undocumented reactants indicates that on average, E2 is favored in 75% of all cases and that SN2 becomes likely for chlorine as nucleophile/leaving group and for substituents consisting of hydrogen or electron-withdrawing groups. Experimental reaction design from first principles is enabled due to R2B, which is demonstrated by the construction of decision trees. Numerical R2B based results for interatomic distances and angles of reactant and transition state geometries suggest that Hammond's postulate is applicable to SN2, but not to E2.

Supported Molybdenum Carbide Nanoparticles as an Excellent Catalyst for CO2 Hydrogenation

Experiments under controlled conditions show that MoCx nanoclusters supported on an inert Au(111) support are efficient catalysts for CO2 conversion, although with a prominent role of stoichiometry. In particular, C-deficient nanoparticles directly dissociate CO2 and rapidly become deactivated. On the contrary, nearly stoichiometric nanoparticles reversibly adsorb/desorb CO2 and, after exposure to hydrogen, CO2 converts predominantly to CO with a significant amount of methanol and no methane or other alkanes as reaction products. The apparent activation energy for this process (14 kcal/mol) is smaller than that corresponding to bulk δ-MoC (17 kcal/mol) or a Cu(111) benchmark system (25 kcal/mol). This trend reflects the superior ability of MoC1.1/Au(111) to bind and dissociate CO2. Model calculations carried out in the framework of density functional theory provide insights into the underlying mechanism suggesting that CO2 hydrogenation on the hydrogen-covered stoichiometric MoCx nanoparticles supported on Au(111) proceeds mostly under an Eley–Rideal mechanism. The influence of the Au(111) is also analyzed and proven to have a role on the final reaction energy but almost no effect on the activation energy and transition state structure of the analyzed reaction pathways.

First-Principles Modeling of the Electrochemical Kinetics at Solid-Water Interface

Kinetic information, such as the activation energy and transition state, is critical to understanding the reaction. However, the kinetic information of electrochemistry at solid-water interface is challenging to obtain from conventional models of density functional theory (DFT), as they often neglect the presence and/or the dynamics of the surface charge [1] and the solvent configuration, which are further coupled. Here we present a new model that accounts for these effects, by combining hybrid solvation, constant-electron-potential, and slow-growth sampling techniques together. We then apply this model to elucidate the active site structure and the mechanism of electrochemical carbon dioxide reduction catalyzed by single-nickel-atom embedded in graphene, which shows high performance in experiments while is not well understood [2].[1] D. Kim, J. Shi, Y. Liu, J. Am. Chem. Soc. 2018, DOI: 10.1021/jacs.8b03002[2] X. Zhao, Y. Liu, J. Am. Chem. Soc. 2020, DOI: 10.1021/jacs.9b13872

Highly Z-Selective Double Bond Transposition in Simple Alkenes and Allylarenes through a Spin-Accelerated Allyl Mechanism.

Double-bond transposition in alkenes (isomerization) offers opportunities for the synthesis of bioactive molecules, but requires high selectivity to avoid mixtures of products. Generation of Z-alkenes, which are present in many natural products and pharmaceuticals, is particularly challenging because it is usually less thermodynamically favorable than generation of the E isomers. We report a β-dialdiminate-supported, high-spin cobalt(I) complex that can convert terminal alkenes, including previously recalcitrant allylbenzenes, to Z-2-alkenes with unprecedentedly high regioselectivity and stereoselectivity. Deuterium labeling studies indicate that the catalyst operates through a π-allyl mechanism, which is different from the alkyl mechanism that is followed by other Z-selective catalysts. Computations indicate that the triplet cobalt(I) alkene complex undergoes a spin state change from the resting-state triplet to a singlet in the lowest-energy C-H activation transition state, which leads to the Z product. This suggests that this change in spin state enables the catalyst to differentiate the stereodefining barriers in this system, and more generally that spin-state changes may offer a route toward novel stereocontrol methods for first-row transition metals.

Phosphodianion Activation of Enzymes for Catalysis of Central Metabolic Reactions.

The activation barriers ΔG⧧ for kcat/Km for the reactions of whole substrates catalyzed by 6-phosphogluconate dehydrogenase, glucose 6-phosphate dehydrogenase, and glucose 6-phosphate isomerase are reduced by 11–13 kcal/mol by interactions between the protein and the substrate phosphodianion. Between 4 and 6 kcal/mol of this dianion binding energy is expressed at the transition state for phosphite dianion activation of the respective enzyme-catalyzed reactions of truncated substrates d-xylonate or d-xylose. These and earlier results from studies on β-phosphoglucomutase, triosephosphate isomerase, and glycerol 3-phosphate dehydrogenase define a cluster of six enzymes that catalyze reactions in glycolysis or of glycolytic intermediates, and which utilize substrate dianion binding energy for enzyme activation. Dianion-driven conformational changes, which convert flexible open proteins to tight protein cages for the phosphorylated substrate, have been thoroughly documented for five of these six enzymes. The clustering of metabolic enzymes which couple phosphodianion-driven conformational changes to enzyme activation suggests that this catalytic motif has been widely propagated in the proteome.

Theoretical Study to Predict the Ability to Use Different Organic Substituents as Carrier Linkages for Diclofenac

The research includes unrestricted (UDFT) and (UPM3) quantum mechanical calculations for studying the reaction path of bonds rupture energies of (O-R) and (C-OAr) in twelve diclofenac derivatives containing different substituted organic groups. All the calculations were performed at the optimize geometries in vacuum phase by using Gaussian 09 program. Comparison was done between the studied diclofenac derivatives and the standard ionic diclofenac of sodium and potassium included geometrical structures, physical properties, total energies of the reactants and products, activation energies and transition states. The results showed that some substituted organic groups could be used to form good carrier bonds for the acidic drug diclofenac, while others were less efficient depending on the nature of the substituted carrier, and that there is a preference for carriers of the type (–R) over the carriers of the type (–Ar).

Mechanical contribution to muscle thin filament activation

Vertebrate striated muscle thin filaments are thought to be thermodynamically activated in response to an increase in Ca2+ concentration. We tested this hypothesis by measuring time intervals for gliding runs and pauses of individual skeletal muscle thin filaments in cycling myosin motility assays. A classic thermodynamic mechanism predicts that if chemical potential is constant, transitions between runs and pauses of gliding thin filaments will occur at constant rate as given by a Poisson distribution. In this scenario, rate is given by the odds of a pause, and hence, run times between pauses fit an exponential distribution that slopes negatively for all observable run times. However, we determined that relative density of observed run times fits an exponential only at low Ca2+ levels that activate filament gliding. Further titration with Ca2+, or adding excess regulatory proteins tropomyosin and troponin, shifted the relative density of short run times to fit the positive slope of a gamma distribution, which derives from waiting times between Poisson events. Events that arise during a run and prevent the chance of ending a run for a random interval of time account for the observed run time distributions, suggesting that the events originate with cycling myosin. We propose that regulatory proteins of the thin filament require the mechanical force of cycling myosin to achieve the transition state for activation. During activation, combinations of cycling myosin that contribute insufficient activation energy delay deactivation.

Bioengineering of Cytochrome P450 OleTJE: How Does Substrate Positioning Affect the Product Distributions?

The cytochromes P450 are versatile enzymes found in all forms of life. Most P450s use dioxygen on a heme center to activate substrates, but one class of P450s utilizes hydrogen peroxide instead. Within the class of P450 peroxygenases, the P450 OleTJE isozyme binds fatty acid substrates and converts them into a range of products through the α-hydroxylation, β-hydroxylation and decarboxylation of the substrate. The latter produces hydrocarbon products and hence can be used as biofuels. The origin of these product distributions is unclear, and, as such, we decided to investigate substrate positioning in the active site and find out what the effect is on the chemoselectivity of the reaction. In this work we present a detailed computational study on the wild-type and engineered structures of P450 OleTJE using a combination of density functional theory and quantum mechanics/molecular mechanics methods. We initially explore the wild-type structure with a variety of methods and models and show that various substrate activation transition states are close in energy and hence small perturbations as through the protein may affect product distributions. We then engineered the protein by generating an in silico model of the double mutant Asn242Arg/Arg245Asn that moves the position of an active site Arg residue in the substrate-binding pocket that is known to form a salt-bridge with the substrate. The substrate activation by the iron(IV)-oxo heme cation radical species (Compound I) was again studied using quantum mechanics/molecular mechanics (QM/MM) methods. Dramatic differences in reactivity patterns, barrier heights and structure are seen, which shows the importance of correct substrate positioning in the protein and the effect of the second-coordination sphere on the selectivity and activity of enzymes.

Theoretical Investigation on Reaction Pathway, Biological Activity, Toxicity and NLO Properties of Diclofenac Drug and Its Ionic Carriers

The present study included the use of the approximate semi-experimental method, the time-independent density function theory (unrestricted), the time-dependent density function theory, and Hartree-Fock method to calculate the reaction pathway of the anti-inflammatory drug diclofenac with its common ionic carriers (sodium and potassium). The basis sets used were STO-3G, 3-21G, 6-31G, and 6-311G. The drug was studied with two new proposed carrier ions (lithium and calcium) which were compared with common carriers. The calculations included the optimized geometrical structure and some physical properties such as standard heat of formation, dipole moment, total energies, and analytical spectra of IR, UV-VIS and 1H NMR. The biological and toxicological activities and the nonlinear optical (NLO) properties were also studied theoretically for the drug and for its proposed and common carriers. All calculations were performed using Gaussian-09 program. The results of the proposed carriers were compared with the common carriers in terms of activation energies, transition states, and products. This study is considered as a step to develop diclofenac prodrugs and find new carriers for diclofenac. The proposed lithium showed a good result and a potential for use as a drug carrier. The results also showed the convergence of the values of the common carriers (Na, K) and those of the proposed carrier (Ca), with their preference over it.

Selecting between two transition states by which water oxidation intermediates decay on an oxide surface

Although catalytic mechanisms on electrode surfaces have been proposed for decades, the pathways by which the product’s chemical bonds evolve from the initial charge-trapping intermediates have not been resolved. Here, we discover a reactive intermediate population with states in the middle of a semiconductor’s bandgap that reveal the dynamics of two parallel transition state pathways for their decay. After phototriggering the water oxidation reaction from the n-SrTiO3 surface, the microsecond decay of the intermediates affirms transition state theory through two distinct time constants, the primary kinetic salt and H/D kinetic isotope effects, realistic activation barrier heights and transition state theory pre-factors. Furthermore, we show that the reaction conditions can be adjusted to allow selection between the two pathways, one characterized by a labile intermediate facing the electrolyte (the oxyl), and the other by a lattice oxygen (the bridge). In summary, we experimentally isolate an important activation barrier in multi-electron transfer water oxidation and, in doing so, identify competing mechanisms for O2 evolution at surfaces. Elucidating reaction mechanisms on electrode surfaces is of utmost importance. Now, using canonical transition state theory, Cuk and colleagues show the competing pathways by which the charge-trapping intermediates of the water oxidation reaction on n-SrTiO3 decay towards the next step in the reaction.