Entropy Of Transition State Research Articles

(Invited) Computational Predictions of Site-Dependent Reactivities for Complex Reactions in Confinement

It is well known that the relatively high overpotentials for oxygen evolution reactions arise from similar binding energies for HO* and HOO* intermediates that tend to move in lockstep on different catalysts. A strategy to break this scaling limitation is through differential stabilization of the two intermediates by engineering the reaction environment. Nanoporous materials such as zeolites and metal-organic frameworks provide such a possibility through their well-defined pore space that presents microscopically tunable reaction environments. Yet the predictive understanding of catalytic actions in these heterogeneous catalysts requires the ability to describe not only the electronic structure at the active site, but also how the extended environment interacts with the reacting species through individually weak yet collectively significant non-covalent interactions. In this talk, we present a new computational procedure that couples quantum-chemical methods and forcefield-based sampling to enable a consistent calculation of local activation energies for articulated reactants. As a first application, we studied hydrocarbon reactions in four different zeolites and showed how the method allows for the estimation of transition-state entropy and for the systematic calculation of site-dependent activation energies. The latter can be used to derive rigorous ensemble-averaged barriers for comparison with experiments, as well as guiding future strategies for controlling Al distributions during zeolite synthesis.

Mutation at the entrance of the quinone cavity severely disrupts quinone binding in respiratory complex I

In all resolved structures of complex I, there exists a tunnel-like Q-chamber for ubiquinone binding and reduction. The entrance to the Q-chamber in ND1 subunit forms a narrow bottleneck, which is rather tight and requires thermal conformational changes for ubiquinone to get in and out of the binding chamber. The substitution of alanine with threonine at the bottleneck (AlaThr MUT), associated with 3460/ND1 mtDNA mutation in human complex I, is implicated in Leber's Hereditary Optic Neuropathy (LHON). Here, we show the AlaThr MUT further narrows the Q-chamber entrance cross-section area by almost 30%, increasing the activation free energy barrier of quinone passage by approximately 5 kJ mol−1. This severely disrupts quinone binding and reduction as quinone passage through the bottleneck is slowed down almost tenfold. Our estimate of the increase in free energy barrier is entirely due to the bottleneck narrowing, leading to a reduction of the transition state entropy between WT and MUT, and thus more difficult quinone passage. Additionally, we investigate details of possible water exchange between the Q-chamber and membrane. We find water exchange is dynamic in WT but may be severely slowed in MUT. We propose that LHON symptoms caused by 3460/ND1 mtDNA mutation are due to slowed quinone binding. This leads to an increased production of reactive oxidative species due to upstream electron backup at the FMN site of complex I, thus resulting in a mt bioenergetic defect.

Synergic Heterodinuclear Catalysts for the Ring-Opening Copolymerization (ROCOP) of Epoxides, Carbon Dioxide, and Anhydrides.

ConspectusThe development of sustainable plastic materials is an essential target of chemistry in the 21st century. Key objectives toward this goal include utilizing sustainable monomers and the development of polymers that can be chemically recycled/degraded. Polycarbonates synthesized from the ring-opening copolymerization (ROCOP) of epoxides and CO2, and polyesters synthesized from the ROCOP of epoxides and anhydrides, meet these criteria. Despite this, designing efficient catalysts for these processes remains challenging. Typical issues include the requirement for high catalyst loading; low catalytic activities in comparison with other commercialized polymerizations; and the requirement of costly, toxic cocatalysts. The development of efficient catalysts for both types of ROCOP is highly desirable. This Account details our work on the development of catalysts for these two related polymerizations and, in particular, focuses on dinuclear complexes, which are typically applied without any cocatalyst. We have developed mechanistic hypotheses in tandem with our catalysts, and throughout the Account, we describe the kinetic, computational, and structure–activity studies that underpin the performance of these catalysts. Our initial research on homodinuclear M(II)M(II) complexes for cyclohexene oxide (CHO)/CO2 ROCOP provided data to support a chain shuttling catalytic mechanism, which implied different roles for the two metals in the catalysis. This mechanistic hypothesis inspired the development of mixed-metal, heterodinuclear catalysts. The first of this class of catalysts was a heterodinuclear Zn(II)Mg(II) complex, which showed higher rates than either of the homodinuclear [Zn(II)Zn(II) and Mg(II)Mg(II)] analogues for CHO/CO2 ROCOP. Expanding on this finding, we subsequently developed a Co(II)Mg(II) complex that showed field leading rates for CHO/CO2 ROCOP and allowed for unique insight into the role of the two metals in this complex, where it was established that the Mg(II) center reduced transition state entropy and the Co(II) center reduced transition state enthalpy. Following these discoveries, we subsequently developed a range of heterodinuclear M(III)M(I) catalysts that were capable of catalyzing a broad range of copolymerizations, including the ring-opening copolymerization of CHO/CO2, propylene oxide (PO)/CO2, and CHO/phthalic anhydride (PA). Catalysts featuring Co(III)K(I) and Al(III)K(I) were found to be exceptionally effective for PO/CO2 and CHO/PA ROCOP, respectively. Such M(III)M(I) complexes operate through a dinuclear metalate mechanism, where the M(III) binds and activates monomers while the M(I) species binds the polymer change in close proximity to allow for insertion into the activated monomer. Our research illustrates how careful catalyst design can yield highly efficient systems and how the development of mechanistic understanding aids this process. Avenues of future research are also discussed, including the applicability of these heterodinuclear catalysts in the synthesis of sustainable materials.

Impact of dimensionality and confinement on reaction dynamics and thermodynamics within 1D and 2D nanostructures.

Confinement has been shown to contribute to the dynamics of small molecules within nanoscale hydrophobic or hydrophilic cavities. Enclosure within a confined space can also influence energy transfer pathways, such as the enhancement of fluorescence over thermal relaxation. In this paper, the effect of confinement on the thermodynamic properties and reaction kinetics of small hydrophobic molecules confined in a soft polymeric template is detailed. A quasi-elastic neutron scattering experiment identified a substantial decrease in translational diffusion of pyrrole after solubilization within a hydrophobic cavity. This decrease in mobility is due to pyrrole's closer packing and increased density under confinement vs the bulk liquid. The decreased mobility and increased density explain the spontaneous polymerization reaction of pyrrole observed within the cavity. The precise characterization of the polymerization kinetics under confinement found that the reaction is independent of pyrrole concentration, consistent with the close packing density. Kinetic data also show that confinement dimensionality finds a thermodynamic expression in the transition state entropy. The dynamics and kinetics experiments reported here offer rare empirical insight into the important influence that cavity geometry places on the reactions they host.

Thermodynamic mechanism evaluate the feasibility of oil shale pyrolysis by topochemical heat

Topochemical heat in-situ pyrolysis of oil shale is achieved by injecting high temperature nitrogen to promote oil shale pyrolysis and release heat, and then injecting air to trigger oil shale combustion in the early stage of oil shale pyrolysis, and then by injecting normal temperature air continuously to promote local oxidation of oil shale in the later stage. In order to verify the oil and gas recovery by topochemical heat method, Jilin University has chosen Fuyu City, Jilin Province, to carry out pilot project of oil shale in-situ pyrolysis by topochemical heat method. Besides, in order to infer the spontaneity, feasibility and difficulty of continuous pyrolysis of oil shale based on topochemical heat, this paper, the mechanism of solid-state pyrolysis and the thermodynamic analysis of transition state of oil shale in Fuyu area are discussed. Because the second stage of oil shale pyrolysis is the main stage of oil production. Therefore, the characteristics of Gibbs free energy, free enthalpy and free entropy of transition state in the main oil production stage of oil shale pyrolysis are obtained by calculation. The results show that in situ pyrolysis of oil shale topochemical heat can be carried out spontaneously and continuously, and the release characteristics of volatiles during pyrolysis of oil shale are described.

Understanding metal synergy in heterodinuclear catalysts for the copolymerization of CO2 and epoxides.

Carbon dioxide and epoxide copolymerization is an industrially relevant means to valorize waste and improve sustainability in polymer manufacturing. Given the value of the polymer products-polycarbonates or polyether carbonates-it could provide an economic stimulus to capture and storage technologies. The process efficiency depends upon the catalyst, and previously Zn(II)Mg(II) heterodinuclear catalysts showed good performances at low carbon dioxide pressures, attributed to synergic interactions between the metals. Now, a Mg(II)Co(II) catalyst is reported that exhibits significantly better activity (turnover frequency > 12,000 h-1) and high selectivity (>99% CO2 utilization and polycarbonate selectivity) for carbon dioxide and cyclohexene oxide copolymerization. Detailed kinetic investigations show a second-order rate law, independent of CO2 pressure from 1-40 bar, to produce polyols. Kinetic data also reveal that synergy arises from differentiated roles for the metals in the mechanism: epoxide coordination occurs at Mg(II), with reduced transition state entropy, while the Co(II) centre accelerates carbonate attack by lowering the transition state enthalpy. This rare insight into intermetallic synergy rationalizes the outstanding catalytic performance and provides a new feature to exploit in other homogeneous catalyses.

Dehydra-Decyclization of Tetrahydrofuran on H-ZSM5: Mechanisms, Pathways, and Transition State Entropy

Butadiene is an important monomer for rubbery and hard polymeric materials, and it can be produced efficiently from biomass-derived tetrahydrofuran (THF) using solid-acid zeolite catalysts. In this...

Statistical derivation of basic equations of diffusional kinetics in alloys with application to the description of diffusion of carbon in austenite

Basic equations of diffusional kinetics in alloys are statistically derived using the master equation approach. To describe diffusional transformations in substitution alloys, we derive the “quasi-equilibrium” kinetic equation that generalizes its earlier versions by taking possible “interaction renormalization” effects into account. For the interstitial alloys Me-X, we derive an explicit expression for the diffusivity D of an interstitial atom X. This expression notably differs from those used in previous phenomenological treatments. This microscopic expression for D is applied to describe the diffusion of carbon in austenite based on some simple models of carbon-carbon interaction. The results obtained enable us to make certain conclusions about the real form of these interactions and about the scale of the “transition state entropy” for diffusion of carbon in austenite.

Hydroxyalkylation of Cyclic Imides with Oxiranes. Part II. The Mechanism of Reaction in Presence of Triethylamine

The mechanism of reaction of cyclic monoimides with oxiranes was established based upon kinetic studies and product analysis. It has been established that the reaction proceeds through initial formation of an adduct of imide and triethylamine. The crucial bond in adduct has ionic character; in non-aqueous solvents it is present as ion pair, while in water the adduct dissociate and free ions are present. The adduct enables the proton transfer from imide to oxirane. The rate determining step is reaction of imide and this adduct. Different values of entropy of transition states obtained from thermodynamic calculations suggest slightly different structure of transition state of rate determining step.

Grafting of 4-aminoantipyrine from guar gum substrates using graft atom transfer radical polymerization (ATRP) process

ATRP graft copolymerization of 4-aminoantipyrine (AAP) was carried out successfully at 50°C from a guar gum based macroinitiator (GGBr), Cu(I)Br and 2,2′-bipyridyl(bpy) as initiator, catalyst and ligand, respectively, in water. Factors affecting the conversion and rate of graft copolymerization such as temperature, concentration of monomer, catalyst, ligand and initiator were studied. The best initial molar concentration ratio of [AAP]:[GGBr]:[Cu(I)Br]:[bpy] was found 100:1:1:2 for controlled graft copolymerization. The plot ln[M]0/[M]t vs. time showed first order kinetics with respect to 4-aminoantipyrine. The activation energy (Ea=25.15kJmol−1), enthalpy of activation (ΔH‡=22.42kJmol−1) and negative value of entropy of transition state (ΔS‡=−233.82Jmol−1K−1) support the progress of polymerization reaction. The % grafting ratio was found to be 5184% and the graft copolymer was characterised by 1H NMR, FTIR, UV, GPC, XRD, TGA and DSC analyses.

Kinetics study of the substitution reaction of fac-[Fe II(CN) 2(CO) 3I] − with PPh 3

Substitution reaction of fac-[Fe II(CN) 2(CO) 3I] − with triphenylphosphine (PPh 3) produced mono phosphine substituted complex cis- cis-[Fe II(CN) 2(CO) 2(PPh 3)I] −. Crystal structure of the product showed that carbonyl positioned trans- to iodide was replaced by PPh 3. The substitution reaction was monitored by quantitative infrared spectroscopic method, and the rate law for the substitution reaction was determined to be rate = k[[Fe II(CN) 2(CO) 2(PPh 3)I] −][PPh 3]. Transition state enthalpy and entropy changes were obtained from Eyring equation k = ( k BT / h)exp(−Δ H ≠/ RT + Δ S ≠/ R) with Δ H ≠ = 119(4) kJ mol −1 and Δ S ≠ = 102(10) J mol −1 K −1. Positive transition state entropy change suggests that the substitution reaction went through a dissociative pathway.

Determination of the Transition-State Entropy for Aggregation Suggests How the Growth of Sickle Cell Hemoglobin Polymers can be Slowed

Sickle cell anemia is associated with the mutant hemoglobin HbS, which forms polymers in red blood cells of patients. The growth rate of the polymers is several micrometers per second, ensuring that a polymer fiber reaches the walls of an erythrocyte (which has a 7-μm diameter) within a few seconds after its nucleation. To understand the factors that determine this unusually fast rate, we analyze data on the growth rate of the polymer fibers. We show that the fiber growth follows a first-order Kramers-type kinetics model. The entropy of the transition state for incorporation into a fiber is 95 J mol−1 K−1, very close to the known entropy of polymerization. This agrees with a recent theoretical estimate for the hydrophobic interaction and suggests that the gain of entropy in the transition state is due to the release of the last layer of water molecules structured around contact sites on the surface of the HbS molecules. As a result of this entropy gain, the free-energy barrier for incorporation of HbS molecules into a fiber is negligible and fiber growth is unprecedentedly fast. This finding suggests that fiber growth can be slowed by components of the red cell cytosol, native or intentionally introduced, which restructure the hydration layer around the HbS molecules and thus lower the transition state entropy for incorporation of an incoming molecule into the growing fiber.

Reaction Pathway of the Trans-Acting Hepatitis Delta Virus Ribozyme: A Conformational Change Accompanies Catalysis

The hepatitis delta virus (HDV), an infectious human pathogen and satellite of hepatitis B virus, leads to intensified disease symptoms, including progression to liver cirrhosis. Both the circular RNA genome of HDV and its complementary antigenome contain the same cis-cleaving catalytic RNA motif that plays a crucial role in virus replication. Previously, the high-resolution crystal structure of the product form of a cis-acting genomic HDV ribozyme has been determined, while a trans-acting version of the ribozyme was used to dissect the cleavage reaction pathway. Using fluorescence resonance energy transfer (FRET) on a synthetic trans-cleaving form of the ribozyme, we are able to directly observe substrate binding (at a rate constant k(on) of 7.8 x 10(6) M(-1) min(-1) at pH 7.5, 11 mM MgCl(2), and 25 degrees C) and dissociation (at 0.34 min(-1)). Steady-state and time-resolved FRET experiments in solution and in nondenaturing gels reveal that the substrate (precursor) complex is slightly more compact (by approximately 3 A) than the free ribozyme, yet becomes significantly extended (by approximately 15 A) upon cleavage and product complex formation. We also find that trans cleavage is characterized by a high transition-state entropy (-26 eu). We propose that the significant global conformational change that we observe between the precursor and product structures occurs on the reaction trajectory into a constrained product complex-like transition state. Our observations may present the structural basis of the recently described utilization of intrinsic substrate binding energy to the overall catalytic rate enhancement by the trans-acting HDV ribozyme.

Gas-phase basicity of (CH3)3N+-C6H4-COO- zwitterions: a new class of organic super bases.

Gas-phase basicity of (CH3)3N+-C6H4-COO- zwitterions: a new class of organic super bases.

Thermodynamics and Kinetics of a Folded-Folded′ Transition at Valine-9 of a GCN4-Like Leucine Zipper

Spin inversion transfer (SIT) NMR experiments are reported probing the thermodynamics and kinetics of interconversion of two folded forms of a GCN4-like leucine zipper near room temperature. The peptide is 13C α -labeled at position V9( a) and results are compared with prior findings for position L13( e). The SIT data are interpreted via a Bayesian analysis, yielding local values of T 1a, T 1b, k ab, k ba, and K eq as functions of temperature for the transition F a V 9 ⇄ F b V 9 between locally folded dimeric forms. Equilibrium constants, determined from relative spin counts at spin equilibrium, agree well with the ratios k ab/ k ba from the dynamic SIT experiments. Thermodynamic and kinetic parameters are similar for V9( a) and L13( e), but not the same, confirming that the molecular conformational population is not two-state. The energetic parameters determined for both sites are examined, yielding conclusions that apply to both and are robust to uncertainties in the preexponential factor ( kT/ h) of the Eyring equation. These conclusions are 1) the activation free energy is substantial, requiring a sparsely populated transition state; 2) the transition state's enthalpy far exceeds that of either F a or F b; 3) the transition state's entropy far exceeds that of F a, but is comparable to that of F b; 4) “Arrhenius kinetics” characterize the temperature dependence of both k ab and k ba, indicating that the temperatures of slow interconversion are not below that of the glass transition. Any postulated free energy surface for these coiled coils must satisfy these constraints.

Is Arginine a Zwitterion in the Gas Phase?

Is Arginine a Zwitterion in the Gas Phase?

Activation of Peptide ions by blackbody radiation: factors that lead to dissociation kinetics in the rapid energy exchange limit.

Unimolecular rate constants for blackbody infrared radiative dissociation (BIRD) were calculated for the model protonated peptide (AlaGly)(n) (n = 2-32) using a variety of dissociation parameters. Combinations of dissociation threshold energies ranging from 0.8 to 1.7 eV and transition entropies corresponding to Arrhenius preexponential factors ranging from very "tight" (A(infinity) = 10(9.9) s(-1)) to "loose" (A(infinity) = 10(16.8) s(-1)) were selected to represent dissociation parameters within the experimental temperature range (300-520 K) and kinetic window (k(uni) = 0.001-0.20 s(-1)) typically used in the BIRD experiment. Arrhenius parameters were determined from the temperature dependence of these values and compared to those in the rapid energy exchange (REX) limit. In this limit, the internal energy of a population of ions is given by a Boltzmann distribution, and kinetics are the same as those in the traditional high-pressure limit. For a dissociation process to be in this limit, the rate of photon exchange between an ion and the vacuum chamber walls must be significantly greater than the dissociation rate. Kinetics rapidly approach the REX limit either as the molecular size or threshold dissociation energy increases or as the transition-state entropy or experimental temperature decreases. Under typical experimental conditions, peptide ions larger than 1.6 kDa should be in the REX limit. Smaller ions may also be in the REX limit depending on the value of the threshold dissociation energy and transition-state entropy. Either modeling or information about the dissociation mechanism must be known in order to confirm REX limit kinetics for these smaller ions. Three principal factors that lead to the size dependence of REX limit kinetics are identified. With increasing molecular size, rates of radiative absorption and emission increase, internal energy distributions become relatively narrower, and the microcanonical dissociation rate constants increase more slowly over the energy distribution of ions. Guidelines established here should make BIRD an even more reliable method to obtain information about dissociation energetics and mechanisms for intermediate size molecules.

The role of entropy in the discrimination between CO and O2 in myoglobin.

Using stopped-flow rapid mixing and flash photolysis techniques, the dissociation rate coefficients of horse carbonmonoxy myoglobin (hMbCO) and oxygenated myoglobin (hMbO2) in aqueous solution have been determined as a function of temperature between 274 and 342 K. From the Arrhenius plot, an activation enthalpy for dissociation of 74 kJ/mol was obtained for both ligands. The pronounced kinetic differences arise from markedly different pre-exponentials. We compare the Arrhenius parameters with those of the association reaction, as measured at cryogenic temperatures. In our analysis we conclude that the entropy loss upon binding of O2 is twice as large as that for CO. Taking reasonable estimates for the frequency factor, the transition state entropy in hMbO2 is located roughly half way in between the entropies of the bound and unbound states. By contrast, the entropy of the transition state in hMbCO appears to be identical to that of the bound state. Possible structural reasons for the different behavior are discussed.

Charge transfer in polar media. Transition-state entropy

Abstract The theory of charge (electron, proton and other ions) transfer chemical reactions in polar media is considered. Within the semiclassical approximation the transition-state entropy is derived for an arbitrarily large term splitting. The dependence of entropy on dielectric medium properties and the heat of reaction is obtained. It is pointed out that the dependence of the transition probability on the heat of the reaction results in a compensation effect. In the limiting case of the exchange integral β being small (β ⪡ k B T ) an expression for the activated-complex entropy is derived in agreement with that found in the literature. The validity condition of this approximation is given. Water is chosen as a typical example of a polar medium: the pre-exponent is estimated to be larger by a factor of 10 3 than the one in the Einstein model of a medium vibronic spectrum. The activation energy of the charge transfer is shown to be less than Marcus'.