Low Kinetic Barrier Research Articles

Experimental and Theoretical Examination of C−CN and C−H Bond Activations of Acetonitrile Using Zerovalent Nickel

Experimental and density functional theory show that the reaction of acetonitrile with a zerovalent nickel bis(dialkylphosphino)ethane fragment (alkyl = methyl, isopropyl) proceeds via initial exothermic formation of an eta(2)-nitrile complex. Three well-defined transition states have been found on the potential energy surface between the eta(2)-nitrile complex and the activation products. The lowest energy transition state is an eta(3)-acetonitrile complex, which connects the eta(2)-nitrile to a higher energy eta(3)-acetonitrile intermediate with an agostic C-H bond, while the other two lead to cleavage of either the C-H or the C-CN bonds. Gas-phase calculations show C-CN bond activation to be endothermic, which contradicts the observation of thermal C-CN activation in THF. Therefore, the effect of solvent was taken into consideration by using the polarizable continuum model (PCM), whereupon the activation of the C-CN bond was found to be exothermic. Furthermore the C-CN bond activation was found to be favored exclusively over C-H bond activation due to the strong thermodynamic driving force and slightly lower kinetic barrier.

Esters with Ease

CHEMISTRY Organic esters are widely used as fragrances and in the synthesis of pharmaceutical compounds. Among the many synthetic routes to esters, the oxidative dimerization of alcohols is direct and involves the endothermic liberation of a dihydrogen equivalent from each alcohol; efficient reactivity therefore requires another component, a stoichiometric H2 acceptor. Zhang et al. have developed a homogeneous ruthenium catalyst to couple primary alcohols into esters in the absence of any extra reagents. The reaction occurs in toluene (115°C) at 0.1 mole % catalyst loading; continuous purging of H2 from the system drives the equilibrium to >90% yield of the ester for butanol, hexanol, and benzyl alcohol. The key component of the catalyst is a tridentate ligand, consisting of diethyl-amino and di- tert -butylphosphino coordinating groups appended to a pyridine ring, and the low kinetic barrier may be due to lability of the diethylamino arm at the Ru center. Preliminary studies of the mechanism support the initial oxidation of one alcohol to the aldehyde, followed by addition of the second alcohol to form a hemiacetal, which in turn loses H2 to give the ester. — JSY J. Am. Chem. Soc. 10.1021/ja052862b (2005).

In memory of our authors

The mass spectra of gases liberated from single-walled carbon nanotubes saturated with deuterium under a pressure of 5 GPa at temperatures up to 50°C (10.8 wt % D) have been measured at different steps of heating to 550°C in a vacuum. Hydrocarbons were found to dominate in the spectra at temperatures up to 400°C, whereas the D2 and HD molecules became the main components of the spectra at 500–550°C. Changes in the spectra with temperature are consistent with the hypothesis that the major portion of hydrogen in the single-walled carbon nanotubes hydrogenated under pressure and reverted to normal conditions was present in the molecular form. The low temperatures of the hydrocarbon liberation are indicative of lower kinetic barriers in the reaction paths of the hydrocarbon liberation as compared with the liberation of D2 molecules. Spectral-peak-shape analysis demonstrates the high hydrophilicity of hydrogenated single-walled carbon nanotubes, whereas the sorption of atmospheric oxygen is insignificant as compared with the sorption of water.

A comparison of C-F and C-H bond activation by zerovalent ni and pt: a density functional study.

Density functional theory indicates that oxidative addition of the C-F and C-H bonds in C6F6 and C6H6 at zerovalent nickel and platinum fragments, M(H2PCH2CH2PH2), proceeds via initial exothermic formation of an eta2-coordinated arene complex. Two distinct transition states have been located on the potential energy surface between the eta2-coordinated arene and the oxidative addition product. The first, at relatively low energy, features an eta3-coordinated arene and connects two identical eta2-arene minima, while the second leads to cleavage of the C-X bond. The absence of intermediate C-F or C-H sigma complexes observed in other systems is traced to the ability of the 14-electron metal fragment to accommodate the eta3-coordination mode in the first transition state. Oxidative addition of the C-F bond is exothermic at both nickel and platinum, but the barrier is significantly higher for the heavier element as a result of strong 5dpi-ppi repulsions in the transition state. Similar repulsive interactions lead to a relatively long Pt-F bond with a lower stretching frequency in the oxidative addition product. Activation of the C-H bond is, in contrast, exothermic only for the platinum complex. We conclude that the nickel system is better suited to selective C-F bond activation than its platinum analogue for two reasons: the strong thermodynamic preference for C-F over C-H bond activation and the relatively low kinetic barrier.

Kinetic and Thermodynamic Barriers to Carbon and Oxygen Alkylation of Phenol and Phenoxide Ion by the 1-(4-Methoxyphenyl)ethyl Carbocation

Rate constant ratios for addition of the three nucleophilic sites of phenol to the 1-(4-methoxyphenyl)ethyl carbocation (1+) in 50/50 (v/v) trifluoroethanol/water were determined from the relative yields of the three phenol adducts, and absolute rate constants were determined from product rate constant ratios for addition of phenol and azide ion to 1+ using k(az) = 5 x 10(9) M(-1) s(-1) for the diffusion-limited reaction of azide ion. A selectivity of 230:20:1 was determined for alkylation of phenol at oxygen, C-4 and C-2 to form 1-OPh and biphenyls 1-(4-C6H4OH) and 1-(2-C6H4OH), respectively, and of 2:2:1 for alkylation of the corresponding nucleophilic sites of phenoxide ion in diffusion-limited reactions. The Mayr nucleophilicity parameter for C-4 of phenol is N = 2.0. Encounter-limited addition of phenoxide ion to 1+ to form 1-OPh is faster than encounter-limited addition of oxygen anions that are either more or less basic than phenoxide ion. Only the products of solvolysis are observed from acid-catalyzed cleavage of 1-OPh in 50/50 (v/v) trifluoroethanol/water, but a 50% yield of biphenyls 1-(4-C6H4OH) and 1-(2-C6H4OH) are observed from spontaneous cleavage of 1-OPh, where the leaving group is phenoxide ion, because of the very low kinetic barriers to collapse of the ion pair intermediate 1+.PhO-. The 230-fold larger rate constant for O-compared to C-2-alkylation of phenol is due primarily to the larger thermodynamic driving force for oxygen addition. There are similar Marcus intrinsic barriers for these two reactions.

Buffed energy landscapes: another solution to the kinetic paradoxes of protein folding.

The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological temperatures leads to energy landscapes having a single dominant basin and an overall funnel topography. We show here that, although such a landscape topography is indeed a sufficient condition for folding, another possibility also exists, giving a previously undescribed class of foldable sequences. These sequences have landscapes that are only weakly funneled in the conventional thermodynamic sense but have unusually low kinetic barriers for reconfigurational motion. Traps have been specifically removed by selection. Here we examine the possibility of folding on these "buffed" landscapes by mapping the determination of statistics of pathways for the heterogeneous nucleation processes involved in escaping from traps to the solution of an imaginary time Schroedinger equation. This equation is solved analytically in adiabatic and "soft-wall" approximations, and numerical results are shown for the general case. The fraction of funneled vs. buffed proteins in sequence space is estimated, suggesting the statistical dominance of the funneling mechanism for achieving foldability.

The competing crystalline and amorphous solid solutions in the Ag–Cu system

Upon nonequilibrium processing using vapor quenching or mechanical alloying, the supersaturated fcc solid solution predominates over the amorphous solution in the Ag–Cu system. The thermodynamic and kinetic origins of this phase selection are explored. The enthalpy of formation of both solutions has been determined as a function of composition using calorimetry measurements and molecular dynamics (MD) simulations. The enthalpy of the fcc solution is found to be lower than that of the competing amorphous phase. The preference for the fcc crystalline state is enhanced by the low kinetic barrier to crystallization of the amorphous solution, which occurred during quenching even when high cooling rates were employed or during annealing at low temperatures. Consequently, the retention of an amorphous Ag–Cu solution required kinetic trapping using ultrahigh quenching rates achievable only under stringent vapor deposition conditions or in MD simulations. However, transmission electron microscopy revealed the presence of local regions of amorphous Ag–Cu after cold rolling of multilayers of elemental Ag and Cu foils at room temperature. This result of partial amorphization demonstrates the possibility of mechanically driven solid-state amorphization in a system with a positive heat of mixing.

The protonation of gaseous cyclopropane.

The protonation of cyclopropane by gaseous Brønsted acids of varying strength in radiolytic experiments at atmospheric pressure leads to two distinct C3H7- isomers that have been sampled by their reaction with benzene. The neutral end products, nC3H7-C6H5 and iC3H7-C6H5, arise from the electrophilic aromatic substitution reaction with the cC3H7+ and iC3H7+ ions, respectively. Their relative abundance was studied as a function of pressure, temperature, and the presence of additives in the gaseous systems; the results indicate a large extent of isomerization to the thermodynamically favored iC3H7+ from the protonation by strong acids. The presence of a kinetic barrier prevents any thermal isomerization from taking place in the time frame of 10(-8) s. In the peculiar case in which protonated benzene is the Brønsted acid, C3H7+ ions are formed in the presence of neutral benzene within the same ion - molecule complex. The ensuing reaction shows that cC3H7+ ions are formed exclusively and react in the 10(-10) s(-1) estimated lifetime of the complex. Still, such cC3H7+ ions undergo complete randomization of their hydrogen atoms; this points to a low kinetic barrier for the process. Agreement is found between the reported experimental results and updated computations of the relevant species in the C3H7+ potential energy surface.

The Mechanism of Carbon−Carbon Bond Activation in Cationic 6-Alkylcyclohexadienyl Ruthenium Hydride Complexes

Carbon−carbon bond activation in cationic 6-endo-methyl-η5-cyclohexadienyl and 6-exo-methyl-η5-cyclohexadienyl ruthenium hydride complexes has been investigated. Contrary to expectations, it is the 6-exo-methyl complex and not the stereoisomeric 6-endo-methyl complex that undergoes selective carbon−carbon bond activation under exceptionally mild conditions, quantitatively converting the 6-exo-methyl substituent and the hydride ligand to methane. The mechanism of the activation reaction involves dissociation of protic acid from the agostic starting complex by reaction with a weak base (typically water), followed by protolytic activation of the alkyl group, with “back-side” assistance from the nucleophilic metal center. Under the same conditions, the corresponding 6-endo-methyl isomer undergoes selective dehydrogenation rather than demethylation, despite the proximity of the endo-methyl substituent to the metal center. For both exo and endo isomers, the cationic ruthenium hydride intermediates were determined by spectroscopic analysis to adopt fluxional agostic structures. The agostic complexes are kinetically stable at room temperature under rigorously anhydrous conditions but convert quantitatively to cationic η6-arene products in the presence of a Brønsted base. The rates of both carbon−carbon bond activation and dehydrogenation are dependent on the identity and concentration of the base and suppressed in the presence of excess acid. The protolytic mechanism for carbon−carbon bond activation is supported by deuterium-labeling studies and by the reactivity of the neutral complexes toward Lewis acids and one-electron oxidants. This mechanism is shown to be relevant to carbon−carbon bond activation reactions observed in less-substituted 6-exo-methyl-η5-cyclohexadienyl complexes and in a steroid-derived 6,6-disubstituted-η5-cyclohexadienyl complex, representative of previously reported cases of dealkylative ligand aromatization. The low kinetic barrier for the protolytic dealkylation mechanism is contrasted to the comparatively high activation barriers reported for carbon−carbon bond activation reactions that occur in structurally related systems that cannot access a protolytic pathway. This investigation provides a consistent basis for rationalizing this potentially important but poorly understood class of metal-mediated reactions.

Influence of kinetic barriers on the structures of non-covalently bonded states

The dissociation of two similar bimolecular complexes, of comparable thermodynamic stabilities, but different kinetic stabilities, is considered. Relative to the complex with the lower kinetic barrier to dissociation, it is concluded from proton NMR data that the complex with the higher kinetic barrier to dissociation has, at a defined point, a tighter interface and a less dynamic structure. The work illustrates how high kinetic barriers to dissociation of non-covalently bonded states can improve bonding at parts of the non-covalently bonded interface. The conclusions drawn should be of general relevance to the non-covalent complexes that are involved in biological functions.

Clay gouge

Clays are a common component of fault gouge, but their genesis and importance in fault evolution is poorly understood. We present preliminary evidence that clays participate in extensive mineral reactions and microfabric changes during faulting. Rather than thinking of clay reactions as a consequence of mechanical processes or fault localization following diagenetically altered horizons, we see the interplay between clay mineral reactions and mechanical processes as a single, integrated process. Furthermore, faulting may lower kinetic barriers to low-temperature (∼100°C) mineral reactions that are common in sedimentary rocks. Our most striking example of fault diagenesis-deformation is a profile of %illite in mixed-layer illite/smectite in shales beneath the Lewis Thrust, Canada. Whereas burial diagenesis caused minimal smectite-to-illite reaction, shales within meters of the thrust are almost completely converted to illite. The consequences of these changes are manifested in geochemical, geochronologic and microfabric characteristics of clay gouge. In this example, faulting has helped overcome a kinetic barrier in the smectite-to-illite reaction without appreciable addition of heat. In another example we infer that dissolution–precipitation reactions continue during faulting even when smectite has already been completely transformed to illite. If mineral reactions intimately interact with mechanical processes in shallow-crustal faults, then our current understanding of the mechanical and hydraulic properties of fault zones may be incomplete. Syndeformational mineral reactions and associated fabric changes could make faults much weaker than would be expected from evaluation of the static mineral assemblage of gouge and single crystal properties. Syndeformational mineral reactions may promote fault slip (affecting earthquake activity) in gouge-bearing faults under stress conditions considerably lower than predicted from static mineral properties. In addition, fault-induced dissolution-precipitation reactions may contribute to fault localization.

Intermolecular proton transfer in catalysis by carbonic anhydrase V

The dehydration of bicarbonate catalyzed by carbonic anhydrase is accompanied by the transfer of a proton from solution to the zinc-bound hydroxide. We have investigated the properties of proton transfer from donors in solution, mostly derivatives of imidazole and pyridine, to a truncated mutant of carbonic anhydrase V with replacements that render the active site cavity less sterically constrained, Tyr 64 →> Ala and Phe 65 →> Ala. Catalysis was measured by determining the rate of exchange of 18O between the CO2-HCO3- system and water, and rate constants for proton transfer were estimated as the rate-limiting step in the release of H218O from the enzyme to solution. Each proton donor enhanced catalytic activity in a saturable manner. The resulting rate constants for proton transfer when compared with the values of pKa of the donor and acceptor gave a Brønsted plot of high curvature. These data could also be described by Marcus theory which showed an intrinsic barrier for intermolecular proton transfer near 0.8 kcal/mol and a work term or thermodynamic contribution to the free energy of reaction near 10 kcal/mol. This low intrinsic kinetic barrier for proton transfer is very similar to nonenzymic bimolecular proton transfer between nitrogen and oxygen acids and bases in solution. However, the significant thermodynamic contribution suggests appreciable involvement of solvent and active-site organization prior to proton transfer. These Marcus parameters are very similar to those describing intramolecular proton transfer from His 64 in carbonic anhydrase, suggesting similarities in the intra- and intermolecular proton transfer processes.Key words: carbonic anhydrase, proton transfer, Marcus theory, carbon dioxide.

Intermolecular proton transfer in catalysis by carbonic anhydrase V

The dehydration of bicarbonate catalyzed by carbonic anhydrase is accompanied by the transfer of a proton from solution to the zinc-bound hydroxide. We have investigated the properties of proton transfer from donors in solution, mostly derivatives of imidazole and pyridine, to a truncated mutant of carbonic anhydrase V with replacements that render the active site cavity less sterically constrained, Tyr 64 →> Ala and Phe 65 →> Ala. Catalysis was measured by determining the rate of exchange of 18O between the CO2-HCO3- system and water, and rate constants for proton transfer were estimated as the rate-limiting step in the release of H218O from the enzyme to solution. Each proton donor enhanced catalytic activity in a saturable manner. The resulting rate constants for proton transfer when compared with the values of pKa of the donor and acceptor gave a Brønsted plot of high curvature. These data could also be described by Marcus theory which showed an intrinsic barrier for intermolecular proton transfer near 0.8 kcal/mol and a work term or thermodynamic contribution to the free energy of reaction near 10 kcal/mol. This low intrinsic kinetic barrier for proton transfer is very similar to nonenzymic bimolecular proton transfer between nitrogen and oxygen acids and bases in solution. However, the significant thermodynamic contribution suggests appreciable involvement of solvent and active-site organization prior to proton transfer. These Marcus parameters are very similar to those describing intramolecular proton transfer from His 64 in carbonic anhydrase, suggesting similarities in the intra- and intermolecular proton transfer processes.Key words: carbonic anhydrase, proton transfer, Marcus theory, carbon dioxide.

Preferential island nucleation at the elbows of the Au(111) herringbone reconstruction through place exchange

It has previously been shown that deposition of Fe, Co or Ni on Au(111) results in island formation preferentially at the elbows of the herringbone reconstruction, while other metals such as Al, Cu, Ag, and Au do not exhibit such behaviour. Here, new results of the Ni Au(111) system are presented which suggest an explanation for this disparity. STM images show a two-step process for the preferential nucleation of islands at certain points in the Au(111) reconstructed unit cell: first, place exchange of Ni adatoms with Au surface atoms, followed by nucleation of Ni islands on top of substitutional Ni atoms. It is argued that the preferential nucleation of islands results from a lower kinetic barrier to place exchange at these specific sites rather than slower (hopping) diffusion.

Degree of supersaturation and precipitation of organogenic dolomite

Research Article| April 01, 1988 Degree of supersaturation and precipitation of organogenic dolomite John S. Compton John S. Compton 1Department of Marine Science, University of South Florida, St. Petersburg, Florida 33701 Search for other works by this author on: GSW Google Scholar Geology (1988) 16 (4): 318–321. https://doi.org/10.1130/0091-7613(1988)016<0318:DOSAPO>2.3.CO;2 Article history first online: 02 Jun 2017 Cite View This Citation Add to Citation Manager Share Icon Share MailTo Twitter LinkedIn Tools Icon Tools Get Permissions Search Site Citation John S. Compton; Degree of supersaturation and precipitation of organogenic dolomite. Geology 1988;; 16 (4): 318–321. doi: https://doi.org/10.1130/0091-7613(1988)016<0318:DOSAPO>2.3.CO;2 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyGeology Search Advanced Search Abstract This paper integrates the degree of carbonate saturation into a general model for the origin of dolomite in organic-rich marine sediments. Degradation of organic matter by sulfate-reducing bacteria promotes early dolomite precipitation by simultaneously increasing the carbonate alkalinity and lowering the sulfate ion concentration to near zero. The interstitial water in organic-rich sediments of several Deep Sea Drilling Project sites where dolomite is believed to be precipitating is up to 103 times supersaturated with respect to near-ideal dolomite and up to 10 times supersaturated with respect to calcite. The highly supersaturated interstitial waters appear to overcome low temperature kinetic barriers to precipitate a nonideal, fine-grained calcian dolomite. The degree of supersaturation with respect to dolomite decreases, and the interstitial water approaches carbonate equilibrium with increasing burial depth at several of these sites. Removal of sulfate ion is important because sulfate ion may inhibit dolomite precipitation. A calcareous sediment is not required, but the presence of calcite or aragonite appears to greatly enhance dolomitization by providing an additional source of Ca and carbonate ions. This content is PDF only. Please click on the PDF icon to access. First Page Preview Close Modal You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

Thermal stability and growth kinetics of Co2Si and CoSi in thin-film reactions

We have investigated the growth of Co2Si and CoSi around 400 °C in samples of Si/Co and Si/CoSi/Co. We selected the Co-Si system because CoSi is known to have a larger heat of formation than Co2Si, hence the former should be favorable for formation from the viewpoint of free energy change or driving force. However, we found that Co2Si is the one which always grows first. This leads us to conclude that it is not the driving force but rather the kinetics which governs the selective growth of thin-film intermetallic compounds. Thus, we propose here that the first phase formation is selected by the one with the lowest kinetic barrier.

Elasticity of some mantle crystal structures: 1. Pleonaste and hercynite spinel

The elasticity of high-pressure mantle phases can be characterized by using data for chemically similar crystal compounds. The single-crystal elastic constants are determined as a function of pressure and temperature for pleonaste spinel and at room conditions for hercynite spinel. The bulk modulus increases from 1.95 Mb for pleonaste spinel to 2.10 Mb for hercynite spinel. Low or negative values of the pressure derivatives of shear constants are characteristic of the spinel structure and imply a low kinetic barrier to phase transformations and diffusion. Compressional and shear velocities of the spinel phase of olivine are estimated as a function of mean atomic weight by using the pleonaste and hercynite data.