Application Of Transition State Theory Research Articles

Water-in-Salt: Fast Dynamics, Structure, Thermodynamics, and Bulk Properties.

We present concentration-dependent dynamics of highly concentrated LiBr solutions and LiCl temperature-dependent dynamics for two high concentrations and compare the results to those of prior LiCl concentration-dependent data. The dynamical data are obtained using ultrafast optical heterodyne-detected optical Kerr effect (OHD-OKE). The OHD-OKE decays are composed of two pairs of biexponentials, i.e., tetra-exponentials. The fastest decay (t1) is the same as pure water's at all concentrations within error, while the second component (t2) slows slightly with concentration. The slower components (t3 and t4), not present in pure water, slow substantially, and their contributions to the decays increase significantly with increasing concentration, similar to LiCl solutions. Simulations of LiCl solutions from the literature show that the slow components arise from large ion/water clusters, while the fast components are from ion/water structures that are not part of large clusters. Temperature-dependent studies (15-95 °C) of two high LiCl concentrations show that decreasing the temperature is equivalent to increasing the room temperature concentration. The LiBr and LiCl concentration dependences and the two LiCl concentrations' temperature dependences all have bulk viscosities that are linearly dependent on τcslow, the correlation time of the slow dynamics (weighted averages of t3 and t4). Remarkably, all four viscosity vs 1/τCslow plots fall on the same line. Application of transition state theory to the temperature-dependent data yields the activation enthalpies and entropies for the dynamics of the large ion/water clusters, which underpin the bulk viscosity.

Diffusion of Fe3+ Ions in Agar Gel Medium Containing Zinc Sulfate: Obstruction effect and Activation Energy

The paper presents a study on the diffusion behaviour of ferric ions within an agar gel medium containing zinc sulfate electrolyte. Investigations for various aspects, including the obstruction effect introduced by the agar gel, the validation of Wang's diffusion model, and the suitability of applying transition state theory to the diffusion of Fe3+ ions in an agar gel medium with zinc sulfate were made. This investigation involved optimising the gel concentration, electrolyte concentration, and system temperature. The diffusion coefficients are determined by the zone diffusion technique. The results reveal that the activation energy (E) decreases as the electrolyte concentration increases, aligning with Wang's model. This decrease is attributed to the disruption of the water structure induced by ions and agar molecules. Additionally, for a fixed electrolyte concentration, the activation energy decreases with the cubic root of the weight percent of agar (W1/3), while the diffusion coefficient (Do) decreases with the square of the reciprocal of the weight percent of agar (W-2/3). This behaviour is consistent with the principles of the transition state theory of diffusion.

Applicability of Transition State Theory to the (Proton-Coupled) Electron Transfer in Photosynthetic Water Oxidation with Emphasis on the Entropy of Activation

Applicability of Transition State Theory to the (Proton-Coupled) Electron Transfer in Photosynthetic Water Oxidation with Emphasis on the Entropy of Activation

Molecular interactions of glycine and L-alanine + citrate buffer solutions at different temperatures: Volumetric, viscometric, and FTIR approach

Densities,, and viscosities,of glycine/L-alanine in water and in (0.10, 0.50, 1.00) aqueous trisodium citrate buffer (Na 3 CB) solutions of pH 7.40 at T = (298.15 to 318.15) K have been measured by using vibrating tube digital density meter and suspended level Ubbelohde capillary viscometer, respectively, at atmospheric pressure i.e. 101.3 kPa. Thermodynamic parameters, i.e. , , , viscosity B-coefficients, and obtained from density and viscosity measurements have been used to unravel predominant forces among glycine/L-alanine and aqueous Na 3 CB solutions. Activation free energies, for the viscous flow of solutions, have been obtained by applying transition state theory to the viscosity B-coefficients values. The results are further supported by FTIR studies for glycine/L-alanine in water and aqueous Na 3 CB solutions of pH 7.40, revealing the intermolecular hydrogen bonding in these systems. Moreover, the results obtained from volumetric, viscometric, and spectroscopic studies provide valuable information on intermolecular interactions, influencing their efficacy in biological applications.

NO Binding Energies to and Diffusion Barrier on Pd Obtained with Velocity-Resolved Kinetics.

We report nitric oxide (NO) desorption rates from Pd(111) and Pd(332) surfaces measured with velocity-resolved kinetics. The desorption rates at the surface temperatures from 620 to 800 K span more than 3 orders of magnitude, and competing processes, like dissociation, are absent. Applying transition state theory (TST) to model experimental data leads to the NO binding energy E0 = 1.766 ± 0.024 eV and diffusion barrier DT = 0.29 ± 0.11 eV on the (111) terrace and the stabilization energy for (110)-steps ΔEST = 0.060–0.030+0.015 eV. These parameters provide valuable benchmarks for theory.

How Different Electrolytes Can Influence the Aqueous Solution Behavior of 1-Ethyl-3-Methylimidazolium Chloride: A Volumetric, Viscometric, and Infrared Spectroscopy Approach.

The density, sound velocity, and viscosity of 1-ethyl-3-methylimidazolium chloride [C2mim]Cl in pure water and aqueous solutions of some electrolytes such as potassium chloride, potassium carbonate, and potassium phosphate (weight fraction of salt fixed at ws = 0. 11) have been measured over a wide range of temperatures from 298.15 to 318.15 K. The obtained experimental data have been used to compute various volumetric, compressibility, and viscometric parameters, e.g., apparent molar properties, limiting apparent molar and transfer properties. The co-sphere overlap model was employed to describe the dominant intermolecular interactions in the ternary solutions. Additionally, the structure making/breaking nature of the [C2mim]Cl in the ternary solutions has been discussed in terms of Hepler's constant and the temperature derivative of viscosity B-coefficient (dB/dT). The activation free energy of solvent and solute, activation enthalpy, and activation entropy have been calculated by the application of transition state theory. The calculated parameters have been interpreted in the sense of solvent–solute and solute–solute interactions. The Fourier transform infrared (FTIR) studies also have been done for the studied systems. Volumetric, acoustic, viscometric, and spectroscopic studies can render some evidence and help to understand the aqueous solution behavior of ionic liquids.

Degree of rate control and De Donder relations – An interpretation based on transition state theory

We describe sensitivities of elementary steps as salient parameters in determining the rate determining character of elementary steps within a reaction network and develop a formalism wherein the overall composite reaction is described by an apparent rate-determining step that is a sensitivity-weighted average of the elementary steps that comprise the reaction network. Reaction parameters—apparent reaction orders, apparent enthalpy and entropy of activation—of the composite reaction network are determined within the framework we develop by application of transition state theory to the apparent rate-determining step. From this formalism we develop methods for determination of surface coverages by measuring only reaction orders, methods for discrimination between proposed mechanisms, a proof that the kinetic degrees of rate control sum to unity, and a proof for the relationship between fractional coverages and thermodynamic degrees of rate control. Two complementary formalisms for identifying rate-limiting transition states are broadly employed in chemical kinetics—De Donder relations based on assessing the thermodynamic driving forces of elementary steps during reaction and degrees of rate control based on knowledge of the kinetics of elementary reaction steps. The formalism developed herein unifies these two strategies to elucidate in the most general case a relationship between the thermodynamic driving forces of elementary steps captured by the reversibilities and the kinetic and thermodynamic degrees of rate control.

Condensed-phase pyrolysis mechanism of ammonium nitrate based on detailed kinetic model

Ammonium nitrate (AN) is widely used as a fertilizer ingredient and an oxidizer in industrial explosives; however, it can also cause environmental harm through the discharge of nitrogen species such as ammonia and nitrogen oxides to the atmosphere or by catastrophic explosion accidents that injure people and damage surrounding buildings. The purpose of the present work is to fully understand the condensed-phase pyrolysis of AN. Detailed kinetic models for the condensed-phase pyrolysis of AN were developed based on quantum chemistry calculations with the incorporation of solvent effects. Optimized structures for reactants, products, and transition states were obtained at various levels of theory. Rate coefficients were determined to allow the application of transition state theory and variational transition state theory to reactions identified in this study. Models were employed to simulate the pyrolysis of liquid AN under specific heating conditions. The model based on the G4//ωB97XD/SMD method successfully predicted the thermal properties; the shape of the heat flow curve, onset temperature, heat of decomposition, and gases that resulted from condensed-phase pyrolysis. The model also revealed that the condensed-phase pyrolysis mechanism starts with three parallel reactions; NH4+ + HNO3 → NH3NO2+ + H2O, HNO3 + HNO3 → N2O5 + H2O, and HNO3 → NO2 + OH.

Electronic factors determining the methane bond breaking process on small aluminum clusters

AbstractIn order to understand the catalytic activity of small metal clusters as a function of their size, we have studied the interaction of CH4 with Al4 and Al5 neutral and charged clusters, as well as neutral thermally expanded clusters in the two lowest lying spin states, using density functional theory. These calculations, via extended search, are used to determine the stable positions of H and CH3 near the cluster, and the transition state to break the H─CH3 bond. In order to understand the factors underlying the reactivity of the clusters, we have analyzed the electronic structure at the transition state. By an analysis of the change of the electronic density of states close to the transition state, we identify the orbitals involved in the bond breaking process. In conjunction with our previous studies of Al2 and Al3 clusters, we find that the small Al clusters, except for Al5, lower the CH3─H dissociation barrier with respect to the gas‐phase value, although Al lacks occupied d‐orbitals. Still, Al5 does not catalyze methane bond breaking, which is attributed to the required interaction with low‐lying Al sp‐states. Furthermore, in all cases where stable methyl‐aluminum‐hydrides are possible, the recombinative desorption of methane is studied by vibrational analysis and application of transition state theory.

Dynamic Description of the Catalytic Cycle of Malate Enzyme: Stereoselective Recognition of Substrate, Chemical Reaction, and Ligand Release.

In protein engineering, investigations of catalytic cycle facilitate rational design of enzymes. In the present work, deeper analysis on the catalytic cycle of malate enzyme (EC 1.1.1.40), an enzyme involved in cancer metabolic and fatty acid synthesis, was performed. In substrate binding, stereoselective recognition of a substrate originates from distance and angle difference between two chiral substrates and Mn2+ as well as monodentate or coplanar ion reaction with Arg165. In catalytic transformation, the activation barrier for the hydride transfer of d-malate is 20.28 kcal/mol higher than that for l-malate. The activation barrier for β-decarboxylation of oxaloacetate is about 4.59 kcal/mol higher than the activation barrier for the hydride transfer of l-malate. The effective activation barrier is 16.44 kcal/mol, which is in close agreement with the value derived from the application of transition-state theory and the Eyring equation to kcat. In ligand release, l/d-malate needs to overcome a higher barrier than pyruvate to break all bonds in parallel and then to escape from the binding pocket. Leu167 and Asn421 comprise a swinging gate to control the product release. The more open gate is possibly required in the direction of pyruvate to l-malate. Our studies are focused on extending structural knowledge regarding the malate enzyme and provided a powerful strategy for future experimental investigations.

Enzymatic Transition States and Drug Design.

Transition state theory teaches that chemically stable mimics of enzymatic transition states will bind tightly to their cognate enzymes. Kinetic isotope effects combined with computational quantum chemistry provides enzymatic transition state information with sufficient fidelity to design transition state analogues. Examples are selected from various stages of drug development to demonstrate the application of transition state theory, inhibitor design, physicochemical characterization of transition state analogues, and their progress in drug development.

Detailed kinetic model for ammonium dinitramide decomposition

Ammonium dinitramide (ADN; [NH4]+[N(NO2)2]−) is the most promising oxidizer for use with future green solid and liquid propellants for spacecraft applications. To allow the effective development and use of ADN-based propellants, it is important to understand ADN reaction mechanisms. This work presents a detailed chemical kinetics model for the liquid phase reactions of ADN based on quantum chemical calculations. The thermal corrections, entropies, and heat capacities of chemical species were calculated from the partition function using statistical machinery based on the G4 level of theory. Rate coefficients were also determined to allow the application of transition state theory and variational transition state theory to reactions identified in our previous study. The new model employed herein simulates the thermal decomposition of ADN under specific heating conditions and successfully predicts heats of reaction and the gases that result from decomposition under those conditions. The thermal behavior predicted from the new model was an excellent match with the experimental behavior observed from thermal analysis using differential scanning calorimetry and Raman spectroscopy. The new kinetic model reveals the mechanism for the decomposition of ADN.

C4H4 radical cation isomers: Generation, structure, stability, and isomerization reactions

The B3LYP, M06-2X and MP2 methods are used to study the generation, relative stability, structure, charge and spin distributions, along with isomerization reactions, of C4H4+ radical cations in gas phase. The highly endothermic generation of C4H4+ species by ionization of neutral C4H4 precursors is for 7 cases. Stability orders for 10 C4H4+ isomers as derived from the three methods correlate well with one another, where methylenecyclopropene radical cation is the global minimum. Available computational data also agrees well with these orders, and experimental data fairly well. The charge and spin distributions describe one isomer as distonic (with charge and spin separated). Concerted isomerization reactions for the methylenecyclopropene, butatriene, vinylacetylene and methyleneallene radical cations and 2 hypothetical higher energy species proceed via well-defined transition states described with regard to their relative positions along the reaction coordinate in accordance with Hammond’s postulate. These one-step isomerizations are combined to yield five multi-step conversions of various C4H4+ species to the lowest energy methylenecyclopropene isomer. The application of transition state theory and computation of rate coefficients leads to the estimation of activation energies for the concerted isomerizations.

Construction of Darboux coordinates and Poincaré–Birkhoff normal forms in noncanonical Hamiltonian systems

We demonstrate a general method to construct Darboux coordinates via normal form expansions in noncanonical Hamiltonian system obtained from e.g. a variational approach to quantum systems. The procedure serves as a tool to naturally extract canonical coordinates out of the variational parameters and at the same time to transform the energy functional into its Poincaré–Birkhoff normal form. The method is general in the sense that it is applicable for arbitrary degrees of freedom, in arbitrary orders of the local expansion, and it is independent of the precise form of the Hamilton operator. The method presented allows for the general and systematic investigation of quantum systems in the vicinity of fixed points, which e.g. correspond to ground, excited or transition states. Moreover, it directly allows to calculate classical and quantum reaction rates by applying transition state theory.

Drug−Amino Acid Interactions in Aqueous Medium: Volumetric, Compressibility, and Viscometric Studies

Density (ρ), speed of sound (u), and viscosity (η) measurements of amino acids l-glutamine and l-histidine in aqueous solutions of metformin hydrochloride (an antidiabetic drug) (0.01, 0.07, and 0.13 mol·kg–1) were carried out in the concentration range (0.02–0.20 mol·kg–1) at 293.15, 298.15, 303.15, 308.15, and 313.15 K. The experimental data has been meticulously used to enumerate various parameters which assist to procure valuable information regarding the presence of different kinds of intermolecular interactions present in the ternary (metformin hydrochloride + water + amino acids) system. The results were interpreted in terms of various metformin hydrochloride–amino acid intermolecular interactions through a cosphere overlap model. The ion–ion interactions are the key players in ternary system and these interactions are of higher order in the case of histidine as compared to glutamine. Also application of transition state theory has been made to calculate the thermodynamic activation parameters for ...

Unveiling the Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase with QM/MM Calculations

We have determined the catalytic mechanism of the human cytosolic homodimeric isocitrate dehydrogenase (hICDH), an enzyme involved in the regulation of tumorogenesis. Our study constitutes the first theoretical attempt to describe the entire catalytic cycle of hICDH. In agreement with earlier experimental proposals, the catalysis was shown to proceed in three steps: (1) NADP+ reduction by the isocitrate substrate with the help of the Lys212B base, (2) β-decarboxylation of the resulting oxalosuccinate, generating an enolate, and (3) protonation of this intermediate by Tyr139A, giving rise to the α-ketoglutarate product. Our study supports that the β-decarboxylation of oxalosuccinate is the most likely rate-limiting step, with an activation Gibbs free energy of 16.5 kcal mol–1. The calculated values are in close agreement with the 16–17 kcal mol–1 range, derived by the application of transition state theory to the reaction rates determined experimentally (11 to 38 s–1). We emphasize the role of Mg2+ and Asp...

Oxidation of zeolite acid sites in NO/O2 mixtures and the catalytic properties of the new site in NO oxidation

The NO oxidation reaction kinetics over a number of zeolite structures were investigated at temperatures above 423K using plug-flow microreactors and in situ FTIR spectroscopy. Fast catalytic NO oxidation rates (up to 1000×) are observed over H- and Na-exchanged zeolite frameworks (BEA, MFI, and CHA) at temperatures above 423K with respect to the gas-phase reaction. NO oxidation rates increase with temperature over H- and Na-zeolites, while siliceous zeolites display little activity. Activation energies scale in the order of CHA<MFI<BEA (40.8–55.5kJmol−1), and application of transition state theory shows that the formation of the activated complex is an enthalpically controlled process that benefits from smaller zeolite pore size. In all samples, rates are proportional to NO and O2 concentrations, in contrast to low-temperature catalytic rates Loiland et al. [33], which are second order in NO and first order in O2. This difference indicates that a new reaction mechanism is operative above 423K. In-situ FTIR studies reveal that NO+ coordinated at framework sites in the zeolite pores (SiO−(NO+)Al) plays a direct role in the catalysis, and they also reveal that the NO oxidation rate is proportional to the amount of NO+ present in the sample. Furthermore, it is found that NO+ is in equilibrium with gas-phase NO and that desorption of NO+ (as NO) yields an oxidized acid site (SiOAl). No evidence of NO+ formation is observed over the siliceous zeolite samples. A working model of the reaction mechanism for the high-temperature NO oxidation reaction is proposed for acidic zeolites that is consistent with the observed form of the rate equation and the observed NO+ reaction intermediate.

Quantitatively probing propensity for structural transitions in engineered virus nanoparticles by single-molecule mechanical analysis.

Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies.

Diffusion of Oxygen through Cork Stopper: Is It a Knudsen or a Fickian Mechanism?

The aim of this work is to identify which law governs oxygen transfer through cork: Knudsen or Fickian mechanism. This is important to better understand wine oxidation during post-bottling aging. Oxygen transfer through cork wafers is measured at 298 K using a manometric permeation technique. Depending on the mechanism, we can extract the transport coefficients. Increasing the initial pressure of oxygen from 50 to 800 hPa leads to a change in the values of the transport coefficients. This implies that oxygen transport through cork does not obey the Knudsen law. From these results, we conclude that the limiting step of oxygen transport through cork occurs in the cell wall following Fickian law. From the diffusion dependence's coefficients with pressure, we also extract by applying transition state theory an apparent activation volume of 45 ± 4 nm(3). This high value indicates that oxygen molecules also diffuse from one site to another by passing through a gas phase.

The enzymatic reaction catalyzed by lactate dehydrogenase exhibits one dominant reaction path

Enzymes are the most efficient chemical catalysts known, but the exact nature of chemical barrier crossing in enzymes is not fully understood. Application of transition state theory to enzymatic reactions indicates that the rates of all possible reaction paths, weighted by their relative probabilities, must be considered in order to achieve an accurate calculation of the overall rate. Previous studies in our group have shown a single mechanism for enzymatic barrier passage in human heart lactate dehydrogenase (LDH). To ensure that this result was not due to our methodology insufficiently sampling reactive phase space, we implement high-perturbation transition path sampling in both microcanonical and canonical regimes for the reaction catalyzed by human heart LDH. We find that, although multiple, distinct paths through reactive phase space are possible for this enzymatic reaction, one specific reaction path is dominant. Since the frequency of these paths in a canonical ensemble is inversely proportional to the free energy barriers separating them from other regions of phase space, we conclude that the rarer reaction paths are likely to have a negligible contribution. Furthermore, the non-dominate reaction paths correspond to altered reactive conformations and only occur after multiple steps of high perturbation, suggesting that these paths may be the result of non-biologically significant changes to the structure of the enzymatic active site.