Activation Barrier Height Research Articles

Adsorption and activation of CO2 molecule on subnanometer-sized anionic vanadium carbide clusters VnC4− (n = 1–6): A theoretical study

Adsorption and activation of CO2 onto small-sized transition metal clusters is of practical importance for the conversion of this molecule to value-added products. We study the efficacy of small anionic vanadium carbide clusters, VnC4− with n = 1–6 towards the aforementioned key step by employing density functional theory based method. One of such clusters has been shown to perform very well in activating N2 molecule as revealed in a recent experiment. The results of our calculations suggest that the binding of CO2 molecule with the anionic vanadium carbide clusters becomes stronger with increase in number of vanadium atoms in the cluster. This adsorption energy trend can be properly rationalized by using the d-band center model. The strong adsorption of CO2 molecule is also accompanied with its high degree of activation. The high activation of CO2 is characterized by a significant amount of charge transfer from the anionic clusters to the molecule. We further find that the activation barrier heights for the dissociation of CO2 to CO and O fragments are considerably small for V4C4− and V5C4− clusters. In particular, V5C4− cluster with an activation barrier of 0.83 eV may serve as a good candidate for activation and dissociation of a CO2 molecule.

Metadynamics Study of the Crystallization of Supercooled Lennard-Jones Liquids

Results are presented from molecular dynamics modeling of the crystallization of a supercooled Lennard-Jones liquid. Calculations are made for three isobars at positive and negative pressures. The height of the crystallization activation barrier is determined via metadynamics, and the size dependence is calculated for the effective surface free energy at the liquid–critical crystal nucleus interface.

Finding Reactive Configurations: A Machine Learning Approach for Estimating Energy Barriers Applied to Sirtuin 5.

Sirtuin 5 is a class III histone deacetylase that, unlike its classification, mainly catalyzes desuccinylation and demanoylation reactions. It is an interesting drug target that we use here to test new ideas for calculating reaction pathways of large molecular systems such as enzymes. A major issue with most schemes (e.g., adiabatic mapping) is that the resulting activation barrier height heavily depends on the chosen educt conformation. This makes the selection of the initial structure decisive for the success of the characterization. Here, we apply machine learning to a large number of molecular dynamics frames and potential energy barriers obtained by quantum mechanics/molecular mechanics calculations in order to identify (1) suitable start-conformations for reaction path calculations and (2) structural features relevant for the first step of the desuccinylation reaction catalyzed by Sirtuin 5. The latter generally aids the understanding of reaction mechanisms and important interactions in active centers. Using our novel approach, we found eleven key features that govern the reactivity. We were able to estimate reaction barriers with a mean absolute error of 3.6 kcal/mol and identified reactive configurations.

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.

Analysis of plastic strain-enhanced diffusivity in nanocrystalline iron by atomistic simulation

Plastic deformation may affect bulk diffusion in nanocrystalline materials by altering the rates of point defect production and annihilation. In the present work, a detailed analysis of this phenomenon is given by a series of molecular dynamics (MD) simulations to clarify the effect of preplastic strain on the diffusivity of iron atoms. The embedded atom method interatomic potential was used to perform MD simulations. The self-diffusion coefficient of iron atoms in unstrained and prestrained samples was measured over temperatures ranging from 600 to 1000 K and at total strains of 5%–20%. The results reveal that the diffusivity is indeed enhanced as a result of plastic straining, especially at low temperatures. The calculated diffusion coefficient of iron atoms in the prestrained samples is 10–80 times higher than that in the unstrained samples. The atomic structure analysis results indicated that the generation of excess vacancies and unstructured region by preplastic deformation contributes to the enhancement of self-diffusion under plastic straining conditions. At low temperatures, preplastic straining has a considerable effect in the peak shifting and broadening of the radial distribution function, which probably lowers the activation barrier height for diffusion.

Electrophilic Impact of High-Oxidation State Main-Group Metal and Ligands on Alkane C–H Activation and Functionalization Reactions

High-oxidation state main-group metal complexes are potential alternatives to transition metals for electrophilic alkane C–H functionalization reactions. However, there is little known about how selection of the p-block, main-group metal and ligand impact alkane C–H activation and functionalization thermodynamics and reactivity. This work reports density functional theory calculations used to determine qualitative and quantitative features of C–H activation and metal-methyl functionalization energy landscapes for reaction between high-oxidation state d10s0 InIII, TlIII, SnIV, and PbIV carboxylate complexes with methane. While the main-group metal influences the C–H activation barrier height in a periodic manner, the carboxylate ligand has a much larger quantitative impact on C–H activation with stabilized carboxylate anions inducing the lowest barriers. For metal-methyl reductive functionalization reactions, the main-group metal dramatically influences the barrier heights, which are correlated to reaction...

QM/MM Molecular Dynamics Investigations of the Substrate Binding of Leucotriene A4 Hydrolase: Implication for the Catalytic Mechanism.

LTA4H is a monozinc bifunctional enzyme which exhibits both aminopeptidase and epoxide hydrolase activities. Its dual functions in anti- and pro-inflammatory roles have attracted wide attention to the inhibitor design. In this work, we tried to construct Michaelis complexes of LTA4H with both a native peptide substrate and LTA4 molecule using combined quantum mechanics and molecular mechanics molecular dynamics simulations. First of all, the zinc ion is coordinated by H295, H299, and E318. For its aminopeptidase activity, similar to conventional peptidases, the fourth ligand to the zinc ion is suggested to be an active site water, which is further hydrogen bonded with a downstream glutamic acid, E296. For the epoxide hydrolase activity, the fourth ligand to the zinc ion is found to be an epoxy oxygen atom. The potential of mean force calculation indicates about an 8.5 kcal/mol activation barrier height for the ring-opening reaction, which will generate a metastable carbenium intermediate. Subsequent frontier molecular orbital analyses suggest that the next step would be the nucleophilic attacking reaction at the C12 atom by a water molecule activated by D375. Our simulations also analyzed functions of several important residues like R563, K565, E271, Y383, and Y378 in the binding of peptide and LTA4.

Diffusion of One-Dimensional Crystals in Channels of Single-Walled Carbon Nanotubes

The transport of one-dimensional CuI crystals in channels of single-walled carbon nanotubes (SWCNTs) has been studied by high resolution electron microscopy. The diffusion kinetics has been investigated by counting the number of CuI atoms escaping from the nanotube channel. The diffusivity is calculated to be 6.8 × 10–21 m2/s, which corresponds to an activation-barrier height of ~1 eV/atom. A comparison with the theoretically estimated height of the energy barrier for molecular transport through a graphene layer is indicative of mass transfer through vacancy defects in graphene.

Methane dissociation on the steps and terraces of Pt(211) resolved by quantum state and impact site.

Methane dissociation on the step and terrace sites of a Pt(211) single crystal was studied by reflection absorption infrared spectroscopy (RAIRS) at a surface temperature of 120 K. The C-H stretch RAIRS signal of the chemisorbed methyl product species was used to distinguish between adsorption on step and terrace sites allowing methyl uptake to be monitored as a function of incident kinetic energy for both sites. Our results indicate a direct dissociation mechanism on both sites with higher reactivity on steps than on terraces consistent with a difference in an activation barrier height of at least 30 kJ/mol. State-specific preparation of incident CH4 with one quantum of antisymmetric (ν3) stretch vibration further increases the CH4 reactivity enabling comparison between translational and vibrational activation on both steps and terraces. The reaction is modeled with first principles quantum theory that accurately describes dissociative chemisorption at different sites on the surface.

Mass Transport through Defects in Graphene Layers

The paper reports an experimental study of ZnTe and CuI transport through graphene wall of SWNTs by high resolution transmission electron microscopy. It is shown that encapsulated material evacuates the tube through the defects in the nanotube walls, while in-tube diffusion appears high enough to provide matter intake from the nanotube volume. Diffusion kinetics was studied by “atoms count” resulting in ZnTe and CuI diffusivities of 7.67 × 10–21 and 1.99 × 10–20 m2/s through single defects in SWNT wall. Semiempirical and DFT modeling of potential energy profiles for different types of defects was utilized to propose minimal structural disturbances in a graphene layer to make possible cross-plane transport of matter. The comparison of experimentally observed diffusivities with calculated activation barrier heights was carried out taking into account an effective temperature of substance under electron beam. Neither of the defects including framework disturbance with 5–7 defects or sp3-bound carbon atomic p...

The Nature of Plasmonically Assisted Hot-Electron Transfer in a Donor–Bridge–Acceptor Complex

This work provides a mechanistic understanding of hot-electron-based catalysis on Au nanoparticles (NPs) induced under plasmonic excitation. Plasmon excitation-induced hot-electron transfer from an Au NP (donor) to a ferricyanide anion (acceptor) was studied as a function of the donor–acceptor distance set by a thiolate-based self-assembled monolayer (SAM). Hot-electron-transfer rates and activation barrier heights were measured as a function of the donor–acceptor distance, up to 20 A. Hot-electron transfer was found to be longer range than anticipated. The distance-dependent kinetics reveal that the hot-electron transfer takes place via multistep hopping in a “wire-like” manner across the insulating ligands, quite unlike the tunneling-dominated electron transfer known to take place across SAMs in the absence of plasmonic excitation. Field-assisted electron hopping may play a crucial role in hot-electron extraction and catalysis involving plasmon-excited NPs.

Accuracy of Substrate Selection by Enzymes Is Controlled by Kinetic Discrimination.

Enzymes have the remarkable ability to select the correct substrate from the pool of chemically similar molecules. The accuracy of such a selection is determined by differences in the free-energy profiles for the right and wrong reaction pathways. Here, we investigate which features of the free-energy landscape govern the variation and minimization of selectivity error. It is generally believed that minimal error is affected by both kinetic (activation barrier heights) and thermodynamic (binding stability) factors. In contrast, using first-passage theoretical analysis, we show that the steady-state selectivity error is determined only by the differences in transition-state energies between the pathways and is independent of the energies of the stable complexes. The results are illustrated for two common catalytic mechanisms: (i) the Michaelis-Menten scheme and (ii) an error-correcting kinetic proofreading scheme with tRNA selection and DNA replication as guiding biological examples. Our theoretical analysis therefore suggests that the selectivity mechanisms are always kinetically controlled.

Non-isothermal kinetics of spin crossover.

Non-isothermal magnetic studies can be used to estimate the activation energy of cooperative spin transition. Model-free isoconversional integral methods give reliable estimates of the activation barrier height for highly cooperative spin crossover systems with wide thermal hysteresis.

Glass-like dynamics of the strain-induced coil/helix transition on a permanent polymer network.

We study the stress response to a step strain of covalently bonded gelatin gels in the temperature range where triple helix reversible crosslink formation is prohibited. We observe slow stress relaxation towards a T-dependent finite asymptotic level. We show that this is assignable to the strain-induced coil → helix transition, previously evidenced by Courty et al. [Proc. Natl. Acad. Sci. U. S. A. 102, 13457 (2005)], of a fraction of the polymer strands. Relaxation proceeds, in a first stage, according to a stretched exponential dynamics, then crosses over to a terminal simple exponential decay. The respective characteristic times τK and τf exhibit an Arrhenius-like T-dependence with an associated energy E incompatibly larger than the activation barrier height for the isomerisation process which sets the clock for an elementary coil → helix transformation event. We tentatively assign this glass-like slowing down of the dynamics to the long-range couplings due to the mechanical noise generated by the local elementary events in this random elastic medium.

Accessing and predicting the kinetic profiles of homogeneous catalysts from volcano plots.

Volcano plots are frequently used as aids in the search for new heterogeneous and electrochemical catalysts. These tools successfully predict catalytic processes based solely on thermodynamic descriptions, which also capably describe many aspects of the catalytic cycles of homogeneous species. However, homogeneous catalysts also frequently depend upon the kinetic influences brought about by steric interactions to promote or prevent specific chemical reactions. Here, a prototypical transformation facilitated by a homogeneous catalysis, the hydroformylation of an olefin using CO and H2, is examined to establish the viability of creating kinetic volcano plots and to determine their ability to ascertain the influences steric bulk plays on catalytic cycle energetics. Similar to their thermodynamic counterparts, kinetic volcanoes successfully reproduce many experimentally known facets of the hydroformylation reaction. In contrast to thermodynamic volcanoes, kinetic volcanoes emphasize changes in the height of the different activation barriers brought about by steric interactions. This crucial information, however, comes with considerable computational cost, since the transition states of catalysts bearing large bulky ligands must be identified and characterized. To overcome this drawback, a procedure is proposed that relates a simple steric parameter, the Tolman cone angle, with the descriptors used to create the kinetic volcano plots. In this way, the activation barriers of bulky catalysts can be estimated without requiring expensive transition state computations. These newly derived structure-activity relationship volcano plots represent useful tools for identifying new homogeneous catalysts.

Theoretical studies on the reaction of mono- and ditriflate derivatives of 1,4:3,6-dianhydro-D-mannitol with trimethylamine--Can a quaternary ammonium salt be a source of the methyl group?

DFT studies on the mechanism of the formation of "gemini" quaternary ammonium salts in the reaction of 1,4:3,6-dianhydro-D-mannitol ditriflate derivative with trimethylamine and its subsequent conversion to tertiary amine through the methyl-transfer reaction are discussed. Two alternative reaction pathways are presented in the gas phase and in ethanol. Additionally, the transformation of the monotriflate derivative of 1,4:3,6-dianhydro-D-mannitol into the single quaternary ammonium salt is presented. Two functionals (B3LYP, M062X) and two basis sets (6-31+G** and 6-311++G**) were used for the calculations. The effect of the substituent attached to the five-membered rings at the C2 (and/or C5) carbon atom on the activation barrier is described. The trimethylammonium group bond to the five-membered ring greatly reduces the activation barrier height. The preferred reaction pathway for the conversions was established. Including the London dispersion in the calculations increases the stabilization of all the points on the potential energy surface in relation to individual reactants.

Methane C–H bond activation by niobium oxides: Theoretical analyses of the bonding and reactivity properties of [formula omitted] (m = 1, 2; n = 0, 1, 2)

The catalytic properties of NbOmn+ (m = 1, 2; n = 0, 1, 2) on the methane C–H bond activation were investigated using B3LYP and CCSD(T) calculations. The spin–orbit relativistic effects were evaluated by means of ZORA approximations. The main results indicate that in agreement with the previous experimental findings only the neutral NbO monoxide is kinetically and thermodynamically feasible via the oxidative addition, whereas the remaining oxides and dioxides show better theoretical predictions in the hydrogen abstraction pathways. In these reactions, a known mechanism described as “Oxidative Hydrogen Migration (OHM)” was found to be more stable for the neutral and singly charged niobium-oxo species, while competitive direct H abstraction (DHA) and OHM pathways were obtained for the doubly charged niobium oxides, with slightly preferential conditions observed in DHA. Overall, the increase of charge on the metal center and the presence of the oxo ligands favors the initial electrostatic interaction between niobium oxides and methane, decreasing the activation barrier heights in the H abstraction pathways due to the electron acceptor nature of oxo ligands. Among the investigated oxides, NbO2+ and NbO22+ show the best performances in the methane activation process, with activation barriers computed to be around 1.5–5.9 kcal mol−1.

Addition Rate Constants of Phosphorus- and Carbon-Centered Radicals to Double Bond of Monomers as Studied by a Pulsed Electron Paramagnetic Resonance Method.

Addition reaction of a radical to the double bond of a monomer, which is important at early stage of photopolymerization, has been studied by time-resolved (TR-) and pulsed electron paramagnetic resonance (EPR) spectroscopic methods. Reactions of one phosphorus-centered and three carbon-centered radicals attacking to several monomers have been employed. Intermediate radicals were identified by analyzing the recorded TR-EPR spectra, and the reaction rate constants were determined by the electron spin-echo detection method proposed by Weber and Turro [J. Phys. Chem. A, 2003, 107 (18), 3326 - 3334]. The quantum chemical calculation shows that the rate constants for the addition reactions are well-explained by introducing two factors of "enthalpy effect" and "polar effect" to control the activation barrier height. It was observed that the rate constants of the phosphorus-centered radical were larger than those of carbon-centered radicals for some monomers. The difference in the rate constants was argued on the basis of frequency factor and activation barrier both of which are influenced by an atom of radical center.

Functional role of R462 in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae.

Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding mode, we in this work further investigate the functional role of active site arginine residue, R462, in the degradation of hyaluronan. The site directed mutagenesis simulation of R462A and R462Q were modeled using a combined quantum mechanical and molecular mechanical method. The overall substrate binding features upon mutations do not have significant changes. The energetic profiles for the reaction processes are essentially the same as that in wild type enzyme, but significant activation barrier height changes can be observed. Both mutants were shown to accelerate the overall enzymatic activity, e.g., R462A can reduce the barrier height by about 2.8 kcal mol(-1), while R462Q reduces the activation energy by about 2.9 kcal mol(-1). Consistent with the active site model calculated using density functional theory, our results can support that the positive charge on R462 guanidino side chain group plays a negative role in the catalysis. Finally, the functional role of R462 was proposed to facilitate the formation of initial enzyme-substrate complex, but not in the subsequent catalytic degradation reaction. Graphical Abstract Degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae.

Investigation of the CH3Cl + CN(-) reaction in water: Multilevel quantum mechanics/molecular mechanics study.

The CH3Cl + CN(-) reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.