Understanding Reaction Dynamics in Coordination Chemistry—Application of High Pressure Techniques

In order to understand the dynamics of chemical reactions in general, detailed information on electronic, structural and kinetic properties is required. The key questions on how chemical reactions actually occur can in many cases only be answered in terms of information obtained from kinetic studies. In conventional kinetic studies of chemical reactions in solution, the variables usually selected include concentration, acidity, solvent, and temperature. In recent years, pressure has become an additional selected variable in such studies. It enables the measurement of the volume of activation and the construction of reaction volume profiles and thus assists in the elucidation of the underlying mechanism; it also completes the comprehension of reaction kinetics by adding another kinetic parameter that the suggested reaction mechanism must account for. Furthermore, the volume of activation is the only transition state property that can be correlated with the corresponding ground state property in an experimentally simple manner. In this paper, the insights so gained in our understanding of the dynamics of reactions involving coordination complexes will be presented. Such reactions are of fundamental interest to chemists since they often form the basis of catalytic, biological, environmental and energy related processes. Any additional information that will add to the understanding of the reaction dynamics is therefore of exceptional importance.     

Constraining molecules at the closest approach: chemistry at high pressure

The purpose of this tutorial review is to illustrate the effects that the application of high pressures can have on chemical reactions involving highly compressible molecular materials. The essentials of the high-pressure technology (generation and in situ control of high pressures) are described with particular attention to the versatile diamond anvil cell (DAC) apparatus. The general effects of pressure on chemical equilibrium, reaction rate and reaction mechanism are discussed. The motivation for application of high-pressure methods (in the 1-300 MPa range) to chemical synthesis and in biochemistry are illustrated focusing the attention on environmental effects and with an excursus on developing biotechnological applications. The peculiarities and the unexpected outcomes of chemical reactions occurring at very high pressures (>or=300 MPa) are discussed considering the extraordinary results obtained in polymerization and amorphization of simple molecules and of unsaturated hydrocarbons. The possible connection of the high temperature-high pressure thresholds for chemical reactions with microscopic counterparts (intermolecular distances, molecular orientations) is also discussed.     

Sonochemistry and sonoluminescence in ionic liquids, molten salts, and concentrated electrolyte solutions

Ionic liquids have favorable intrinsic properties that make them of interest as solvents for various chemical reactions. The same properties that make the liquids effective solvents also make them interesting liquids for studies involving sonochemistry, acoustic cavitation, and sonoluminescence. Recent interest in using ultrasound to accelerate chemical reactions conducted in ionic liquids necessitates an understanding of the effects of acoustic cavitation on these solvents. Here, we review our previous results on the effects of cavitation on some room-temperature ionic liquids, including the sonoluminescence spectra of molten salt eutectics and concentrated aqueous electrolyte solutions. In all cases, regardless of the essentially nonexistent vapor pressure of the solution atomic and small molecule emitters are observed in the spectra which arise from sonolysis of the ionic liquids.     

Equilibrium shapes of liquid bridges under gravity: Symmetry breaking and imperfect bifurcations of two-dimensional bridges

The equilibrium shapes of a two-dimensional liquid bridge are constructed via a shooting and continuation numerical solution of the Laplace—Young equation which focuses on the bifurcation points of the solution branches. For the neutrally buoyant case, two new asymmetric shapes bifurcate from the point of maximum excess pressure where circular profiles with reflective symmetry have been shown to be unstable with respect to constant pressure disturbances. This occurs when the profile is exactly at right angles to the support. With the introduction of gravitational effects, this codimension 5 singularity is retained although the critical contact angle decreases slightly below 90° as one increases the difference between the interior and the exterior densities. However, when a slight tilt angle is introduced to the bridge, the maximum pressure singularity degenerates into two turning points (folds) and the solution branches are isolated from each other. This indicates that hysteretic jumps in the surface curvature and excess pressure exist with respect to changes in diameter/length ratio or liquid volume. Our numerical solution also reveals the existence of a maximum bridge volume that can be sustained by a nonneutrally buoyant bridge. No equilibrium shapes, symmetric or asymmetric, exist for bridge volumes beyond this critical value.     

Scherzonen

Within so‐called shear zones, along which variably sized units of the earth crust are subject to a displacement, numerous chemical reactions result in the re‐structuring of the rock mineralogy. This metamorphic transformation is continuously intensified from the rim to the centre of the shear zone and is chiefly controlled by pressure, temperature, and the existence of a fluid phase. As documented with the help of a concrete example chemical mass balancing in a given shear zone requires both the chemical analysis of educt and product and the documentation of eventual changes of rock density and rock volume. The latter changes allow a final distinction between isochemical and anisochemical transformation processes.     

Dielectric effects of step-increased pressure on the mass- and diffusion-controlled linear chain and network macromolecules growth

The dielectric properties of four stoichiometric liquid mixtures of a diepoxide with two monoamines and two diamines have been studied in real time during the mixture's polymerization isothermally to a linear-chain polymer in two cases and a network polymer in the other two cases, at 1 and 200 bar. The pressure was applied: (a) at the beginning of polymerization, (b) after a small extent of polymerization when the viscosity was low, and (c) after a relatively large extent of polymerization when the viscosity was high. For a fixed polymerization period, pressure increased the dielectric relaxation time much more than any other quantity in all cases, without a change in the distribution of relaxation times. Contributions to the dielectric permittivity and loss from physical and chemical effects have been considered and related to the changes in the dielectric relaxation time, viscosity and polymerization-rate constant as the extent of polymerization increased with time. Pressure is expected to decrease the polymerization rate for all conditions, but the decrease is relatively insignificant at the early stage, when polymerization is mass-controlled. Here other effects override the effect of viscosity increase, and the polymerization rate instead increases. The decrease in the rate becomes significant and predominates only when polymerization becomes diffusion-controlled. Since theories of diffusion-controlled reactions do not consider the mutual slowing of the molecular diffusion and the rate of chemical reactions leading to a macromolecule's growth until its vitrification isothermally, a method for determining the onset of diffusion control was needed. It is shown that this onset can be determined from plotting the rate of polymerization against the dielectric relaxation time. Expressed in terms of the dielectric loss, these plots cross each other. The cross-over point indicates the onset of diffusion control. Thus, the effect of pressure on the dielectric behaviour can be used to determine the change from mass-controlled to diffusion-controlled kinetics.     

Solution properties of ion-containing polymers in polar solvents

The placement of ionic groups within the molecular structure of a polymer produces marked modification in physical properties. A large number of studies have been performed on these ion-containing polymers, but few have focused on the effects of anion–cation interactions (i.e., counterion binding or ionization) on hydrodynamic volume, especially as the molecular structure of the solvent and nature of counterion are varied. In this study changes in hydrodynamic volume are followed through reduced viscosity measurements as a function of the abovementioned molecular parameters. The dilute solution properties of various polyelectrolytes that contain sulfonate and carboxylate groups were investigated as a function of the counterion structure, charge density, molecular weight, and solvent structure. The polymeric materials were selected because of their specific chemical structure and physical properties. In the first instance a (2-acrylamide-2 methylpropanesulfonic acid)-acrylamide-sodium vinyl sulfonate terpolymer was synthesized and subsequently neutralized with a series of bases. Viscometric measurements on these materials indicate that the nature of the cation affects the ability of the polyelectrolyte to expand its hydrodynamic volume at low polymer levels. The magnitude of the molecular expansion is shown to be due in part to the ability of the counterion to dissociate from the backbone chain, which, in turn, is directly related to the solvent structure. The changes in solution behaviour of these inomers lend support for the existence of ion pairs (i.e., site binding) and ionized moieties on the polymer chains. Measurements performed in a variety of solvent systems further confirm this interpretation. In addition, and acrylamide-sodium vinyl sulfonate copolymer was partially hydrolyzed with sodium hydroxide to study the effect of varying the charge density at a constant degree of polymerization and counterion structure. The results show that the charge density has a significant effect on the magnitude of the reduced viscosity and dilute solution behaviour. These observations, made in aqueous and nonaqueous solvents, are related to the interrelation of hydrodynamic volume, counterion concentration, and site binding. Again the controlling factor is the degree of site binding of the counterion onto the polymer backbone. Finally, we observe that the increased hydrodynamic volume affects viscosity behavior beyond the polyelectrolyte effect regime. If the average charge density on the macromolecule is relative high and/or the molecular weight is large (≥ 10⁶) sufficient intermolecular interactions will occur to produce rapid changes in reduced viscosity.     

Silicon clusters: chemistry and structure

The chemical reactions of size selected silicon cluster ions (containing up to 70 atoms) have been studied with a number of different reagents using injected ion drift tube techniques. Both kinetic and equilibrium measurements have been performed as a function of temperature, and the influence of cluster annealing on chemical reactivity explored. Unlike metal clusters, where bulk behavior appears to be approached with around 30 atoms, large silicon clusters (n up to 70) are much less reactive than bulk silicon surfaces. These results suggest that the clusters in the size range examined here are not small crystals of bulk silicon, but have compact, high coordination number structures with few dangling bonds.     

On the role of free volume in pick-off annihilation and positronium chemical reactions

Free volume effects are important for positronium formation, pick-off annihilation and chemical reactions. The relation between the long-lived component intensity and the number of defects is considered for the case of selective localization of positrons and positronium in ordered and disordered sites of plymers. Positronium lifetimes for the large pores (r1 nm) are discussed. In positronium chemical reactions recent results show crucial role of the bubble parameters in liquids.     

Global sensitivity analysis of nonlinear chemical kinetic equations using lie groups: I. Determination of one-parameter groups

We introduce one-parameter groups of transformations that effect wide-ranging changes in the rate constants and input/output fluxes of homogeneous chemical reactions involving an arbitrary number of species in reactions of zero, first and second order. Each one-parameter group is required to convert every solution of such elementary rate equations into corresponding solutions of a one-parameter family of altered elementary rate equations. The generators of all allowed one-parameter groups are obtained for systems withN species using an algorithm which exactly determines their action on the rate constants, and either exactly determines or systematically approximates their action on the concentrations. Compounding the one-parameter groups yields all many-parameter groups of smooth time-independent transformations that interconvert elementary rate equations and their solutions.     

Numerical Simulation of Nonequilibrium Species Diffusion in a Low-Power Nitrogen–Hydrogen Arcjet Thruster

Species distributions in a low-power arcjet thruster are investigated using a two-dimensional thermal and chemical nonequilibrium numerical model that incorporates the self-consistent effective binary diffusion coefficient approximation treatment of diffusion. Plasma flows in arcjet thruster with different input mole ratios of nitrogen to hydrogen are modelled. It is found that species separation due to nonequilibrium chemical kinetic processes occurs mainly in the regions where the dissociation and ionization of nitrogen and hydrogen species take place. The enrichment of nitrogen molecules at the fringes of the arc and hydrogen molecules near the anode wall of the thruster occurs mainly because the recombination processes of these two gases occur in different temperature ranges. In the expansion portion of the thruster nozzle, the gas residence times are of the same order as some chemical kinetic processes. Comparison between the nitrogen and hydrogen species profiles at the constrictor and thruster exit shows that the recombination of hydrogen ions and atoms are dominant kinetic processes near the thruster centreline, while the chemical reactions of nitrogen species are almost frozen in the high speed flow. The effects of temperature and pressure gradients on the species diffusion inside the arcjet thruster are also presented, with thermal diffusion found to have a much larger influence than pressure diffusion.     

Effects of Vibrational Nonequilibrium on the Chemistry of Two-Temperature Nitrogen Plasmas

A new two-temperature chemical kinetics model for nitrogen plasmas is presented. The model is used together with the vibrationally-specific collisional-radiative model to study the effects of vibrational nonequilibrium distributions on the chemical composition of two-temperature atmospheric pressure nitrogen plasmas. It is found that over a wide range of conditions the vibrational levels follow Boltzmann distributions and that the vibrational temperature T_v is well approximated by gas temperature T_g at low electron number densities and by electron temperature T_e at high electron number densities. This result suggests that simple kinetic models with two-temperature rate coefficients can be used to reliably model nonthermal plasmas. The calculation also yields a surprising result that, for a given constant gas temperature, the steady-state electron number density exhibits an S-shaped dependence on the electron temperature. This S-shaped behavior is caused by competing ionization, charge transfer reactions, two-body dissociative recombination, and three-body electron recombination reactions, and therefore is characteristic of molecular plasmas.     

Reprogramming DNA-directed reactions on the basis of a DNA conformational change

A strategy has been developed for switching chemical reactions between two identical reagents on the basis of DNA duplex-triplex transition. In response to the change of solution pH, a DNA complex changes its conformation and repositions chemical reagents that are conjugated with DNA strands. As a result, chemical reactions are reprogrammed. This strategy is expected to be applicable to sophisticated chemical syntheses.     

Reverse Spin‐Crossover and High‐Pressure Kinetics of the Heme Iron Center Relevant for the Operation of Heme Proteins under Deep‐Sea Conditions

By design of a heme model complex with a binding pocket of appropriate size and flexibility, and by elucidating its kinetics and thermodynamics under elevated pressures, some of the pressure effects are demonstrated relevant for operation of heme‐proteins under deep‐sea conditions. Opposite from classical paradigms of the spin‐crossover and reaction kinetics, a pressure increase can cause deceleration of the small‐molecule binding to the vacant coordination site of the heme‐center in a confined space and stabilize a high‐spin state of its Fe center. This reverse high‐pressure behavior can be achieved only if the volume changes related to the conformational transformation of the cavity can offset the volume changes caused by the substrate binding. It is speculated that based on these criteria nature could make a selection of structures of heme pockets that assist in reducing metabolic activity and enzymatic side reactions under extreme pressure conditions.     

Cosolvent and Crowding Effects on the Temperature- and Pressure-Dependent Dissociation Process of the α/β-Tubulin Heterodimer

Tubulin is one of the main components of the cytoskeleton of eukaryotic cells. The formation of microtubules depends strongly on environmental and solution conditions, and has been found to be among the most pressure sensitive processes in vivo. We explored the effects of different types of cosolvents, such as trimethylamine-N-oxide (TMAO), sucrose and urea, and crowding agents to mimic cell-like conditions, on the temperature and pressure stability of the building block of microtubules, i. e. the α/β-tubulin heterodimer. To this end, fluorescence and FTIR spectroscopy, differential scanning and pressure perturbation calorimetry as well as fluorescence anisotropy and correlation spectroscopies were applied. The pressure and temperature of dissociation of α/β-tubulin as well as the underlying thermodynamic parameters upon dissociation, such as volume and enthalpy changes, have been determined for the different solution conditions. The temperature and pressure of dissociation of the α/β-tubulin heterodimer and hence its stability increases dramatically in the presence of TMAO and the nanocrowder sucrose. We show that by adjusting the levels of compatible cosolutes and crowders, cells are able to withstand deteriorating effects of pressure even up to the kbar-range.     

Direct monitoring of protein-chemical reactions utilising nanoelectrospray mass spectrometry

The feasibility of nanoelectrospray mass spectrometry (nanoESI) for the direct analysis of protein chemical reactions and structural changes of proteins has been evaluated. Taking advantage of the long spraying time and the capability of nanoESI for employing a wide range of solvent conditions such as buffers and detergents, applications of monitoring reaction pathways, and dynamics have been carried out with several peptides and proteins. The time course of proteolytic digestions with trypsin and pepsin was investigated for several model polypeptides, and nanoESI showed to provide an efficient tool for optimising digestion conditions for the mass spectrometric peptide mapping analysis. Examples of specific protein chemical modification reactions at arginine and tyrosine residues illustrate the feasibility of nanoESI to monitoring reaction yields and modification sites for more than 180 min. Furthermore, changes of the pattern of protonated molecules caused by temperature effects and by protein unfolding due to disulfide bond reduction have been studied with the model proteins cytochrome c and hen eggwhite lysozyme. The results indicate that nanoESI is an efficient technique for the direct, molecular characterisation of protein-chemical reactions in solution.     

A Genetic Algorithm‐Based Method for the Automatic Reduction of Reaction Mechanisms

An automatic method for the reduction of chemical kinetic mechanisms under specific physical or thermodynamic conditions is presented. The method relies on the genetic algorithm search logic to gradually reduce the number of reactions from the detailed mechanism while still preserving its ability to describe the overall chemistry at an acceptable error. Accuracy of the reduced mechanism is determined by comparing its solution to the solution obtained with the full mechanism under the same initial and/or physical conditions. However, not only the chemical accuracy and the size of the mechanism are considered but also the time for its solution which helps to avoid stiff and slow converging mechanisms, thus preferring the fast solutions. The reduction method is demonstrated for a detailed mechanism for methane combustion, GRI‐Mech 3.0, which was reduced from 325 reactions and 53 species to 58 reactions and 26 species, and for an iron oxide formation mechanism from iron pentacarbonyl doped flames by Wlokas et al. (Int J Chem Kinet 2013, 45(8), 487–498),  originally consisting of 144 reactions and 34 species, which was reduced to 37 reactions and 24 species. The performance of the reduced mechanisms is shown for homogeneous constant pressure reactors and for burner‐stabilized flames. The results show a good agreement between reduced and full mechanisms for both the reactor and flame cases. The presented method is flexible and can be easily adjusted to either yield more accurate (but bigger) or smaller (but less accurate) reduced mechanisms, depending on the user's preference.     

Morphology and etching processes on macroscopic metal catalysts

Changes in the morphology of catalysts during their preparation and use are probably important to the stability of most catalyst systems, but, in spite of extensive investigations of these phenomena, the rates of these changes and the structures formed are typically characterized only qualitatively and no consensus exists as to the mechanisms of morphology changes.In this paper experiments on the morphology of macroscopic unsupported metal catalysts in unreactive gases (thermal etching) and in reactive gases (catalytic etching) are reviewed, and a number of mechanisms which may be responsible for etching are summarized.In both thermal and catalytic etching a variety of structures such as faceting to form specific crystal planes, grooving of grain boundaries, pit and hillock formation, undercutting, and crystallite growth are observed. All studies indicate strong dependences of morphological features and etching rates on temperature, pressure, gas composition, impurities, flow velocities, and time. Most studies have been for exothermic reactions on Group VIII transition metals, but even for similar reactions and similar metals, correlations are frequently elusive.Morphology changes have frequently been interpreted through equilibrium considerations, the driving force assumed to be the reduction in surface free energy which accompanies faceting. The mechanisms of mass transport in many systems are probably capillarity—induced surface and volume diffusion and evaporation-condensation processes. These considerations may be adequate to explain simple morphological features especially in thermal etching under certain simplified conditions. Additional complexities arise in catalytic etching, where the superposition of chemical reactions onto a process driven by capillarity can significantly alter mass transport. Moreover, the undercutting and crystallite growths, which occur when catalyst material is being continuously lost (e.g. in the form of volatile compounds), produces nonequilibrium processes requiring a detailed specification of the boundary layer at the catalyst surface.