Chemical Reactions In Solution Research Articles

Dynamics of bimolecular reactions in solution.

Mechanisms of bimolecular chemical reactions in solution are amenable to study on picosecond timescales, both by transient absorption spectroscopy and by computer simulation. The dynamics of exothermic reactions of CN radicals and of Cl and F atoms with organic solutes in commonly used solvents are contrasted with the corresponding dynamics in the gas phase. Many characteristics of the gas-phase reaction dynamics persist in solution, such as efficient energy release to specific vibrational modes of the products. However, additional complexities associated with the presence of the solvent are open to investigation. These features of liquid-phase reactions include the role of solvent-solute complexes, solvent caging, coupling of the product motions to the solvent bath, thermalization of internally excited reaction products, incipient hydrogen bond formation, and involvement of charge-separated states that arise from proton transfer.

Synthesis and Photo-Response of CuS Thin Films by an In Situ Multi-Deposition Process at Room Temperature: A Facile and Eco-Friendly Approach

Uniform hexagonal covellite CuS thin films were deposited at room temperature by an in situ solution chemical reaction using copper precursor solid films as cationic source and ammonium sulfide ethanol solution as anionic reaction medium. We investigated the influence of both ethanolamine and butanol contents used in copper nitrate/ethylene glycol monomethylether (EGME) cationic solution for the preparation of copper precursor solid films, deposition cycle numbers and annealing treatment of the as-grown thin films by X-ray diffraction (XRD), FESEM, energy dispersive X-ray fluorescence EDX, transmission electron microscopy–Selected area electronic diffraction (TEM–SAED), atomic force microscopy (AFM) and ultraviolet-visible-near-infrared (UV-Vis–NIR) measurements. Photo-response of the CuS thin films was characterized by linear sweep voltammetry. The deposited CuS thin films were used to sensitize TiO 2 anodes for solar cell application. The results showed that the CuS films had two-dimension oriented, half-sheet shaped growing morphology standing disorderly but vertically to substrates, and the calculated texture coefficient TC(102) verified that the half-sheet shaped crystallites had (102) plane orientation. This in situ multi-deposition process had an average deposited rate of 9 nm per cycle, and a self-perfect function to grow smooth, uniform and 2D oriented morphology with increase in the dip-cycle numbers. The photocurrent density was 14.5 Ma/cm2 at 1 V versus Ag / AgCl electrode for the annealed CuS thin films. CuS -sensitized TiO 2 solar cells had a maximum conversion efficiency of 0.224%.

Direct observation of bond formation in solution with femtosecond X-ray scattering.

The making and breaking of atomic bonds are essential processes in chemical reactions. Although the ultrafast dynamics of bond breaking have been studied intensively using time-resolved techniques, it is very difficult to study the structural dynamics of bond making, mainly because of its bimolecular nature. It is especially difficult to initiate and follow diffusion-limited bond formation in solution with ultrahigh time resolution. Here we use femtosecond time-resolved X-ray solution scattering to visualize the formation of a gold trimer complex, [Au(CN)2(-)]3 in real time without the limitation imposed by slow diffusion. This photoexcited gold trimer, which has weakly bound gold atoms in the ground state, undergoes a sequence of structural changes, and our experiments probe the dynamics of individual reaction steps, including covalent bond formation, the bent-to-linear transition, bond contraction and tetramer formation with a time resolution of ∼500femtoseconds. We also determined the three-dimensional structures of reaction intermediates with sub-ångström spatial resolution. This work demonstrates that it is possible to track in detail and in real time the structural changes that occur during a chemical reaction in solution using X-ray free-electron lasers and advanced analysis of time-resolved solution scattering data.

Deposition and characteristics of bismuth sulfide thin films by an in situ chemical reaction process at room temperature: a facile and eco-friendly approach

Uniform, smooth and densely packed Bi2S3 thin films were prepared at room temperature by an in situ solution chemical reaction using bismuth nitrate as precursor in a form of thin solid film which was reacted with ammonium sulfide ethanol solution. Bi2S3 thin films both as-deposited and annealed at different temperatures were characterized by XRD, SEM, EDS, AFM, UV–Vis–NIR and LSV measurements. The thin films growth with deposition cycle numbers was investigated. The results showed that the as-deposited Bi2S3 thin films were almost amorphous and near to chemical stoichiometry. The annealing promoted crystallization to orthorhombic structure as well as crystal growth from very small particles to short-rod shaped nanocrystals. The optical band-gap energy was in the range of 1.34–1.69 eV depended on crystal size on films. The eight dip-cycles Bi2S3 films annealed at 300 °C had a better photoelectrochemical performance with photocurrent density of 5.03 mA/cm2 bias 0.5 V vs. Ag/AgCl reference electrode. This in situ deposition had an average deposited rate of 40 nm per cycle and a self-perfect function to grow smooth with increase of dip-cycle numbers.

Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models.

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting model with a single solvent-independent parameter: the electron density threshold (nc), and a single solvent-dependent parameter: the dispersion scale factor (s6), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s6 parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.

Molecules in motion: chemical reaction and allied dynamics in solution and elsewhere.

After my acceptance of the kind invitation from Todd Martínez and Mark Johnson, Co-Editors of this journal, to write this article, I had to decide just how to actually do this, given the existence of a fairly personal and extended autobiographical account of recent vintage detailing my youth, education, and assorted experiences and activities at the University of Colorado, Boulder, and later also at Ecole Normale Supérieure in Paris ( 1 ). In the end, I settled on a differently styled recounting of the adventures with my students, postdocs, collaborators, and colleagues in trying to unravel, comprehend, describe, and occasionally even predict the manifestations and consequences of the myriad assortment of molecular dances that contribute to and govern the rates and mechanisms of chemical reactions in solution (and elsewhere). The result follows.

Studying the Dynamics of Photochemical Reactions via Ultrafast Time-Resolved Infrared Spectroscopy of the Local Solvent.

Conventional ultrafast spectroscopic studies on the dynamics of chemical reactions in solution directly probe the solute undergoing the reaction. We provide an alternative method for probing reaction dynamics via monitoring of the surrounding solvent. When the reaction exchanges the energy (in form of heat) with the solvent, the absorption cross sections of the solvent's infrared bands are sensitive to the heat transfer, allowing spectral tracking of the reaction dynamics. This spectroscopic technique was demonstrated to be able to distinguish the differing photoisomerization dynamics of the trans and cis isomers of stilbene in acetonitrile solution. We highlight the potential of this spectroscopic approach for studying the dynamics of chemical reactions or other heat transfer processes when probing the solvent is more experimentally feasible than probing the solute directly.

Universal tight binding model for chemical reactions in solution and at surfaces. I. Organic molecules.

As is now well established, a first order expansion of the Hohenberg-Kohn total energy density functional about a trial input density, namely, the Harris-Foulkes functional, can be used to rationalize a non self consistent tight binding model. If the expansion is taken to second order then the energy and electron density matrix need to be calculated self consistently and from this functional one can derive a charge self consistent tight binding theory. In this paper we have used this to describe a polarizable ion tight binding model which has the benefit of treating charge transfer in point multipoles. This admits a ready description of ionic polarizability and crystal field splitting. It is necessary in constructing such a model to find a number of parameters that mimic their more exact counterparts in the density functional theory. We describe in detail how this is done using a combination of intuition, exact analytical fitting, and a genetic optimization algorithm. Having obtained model parameters we show that this constitutes a transferable scheme that can be applied rather universally to small and medium sized organic molecules. We have shown that the model gives a good account of static structural and dynamic vibrational properties of a library of molecules, and finally we demonstrate the model's capability by showing a real time simulation of an enolization reaction in aqueous solution. In two subsequent papers, we show that the model is a great deal more general in that it will describe solvents and solid substrates and that therefore we have created a self consistent quantum mechanical scheme that may be applied to simulations in heterogeneous catalysis.

Universal tight binding model for chemical reactions in solution and at surfaces. II. Water.

A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice--leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point.

Universal tight binding model for chemical reactions in solution and at surfaces. III. Stoichiometric and reduced surfaces of titania and the adsorption of water.

We demonstrate a model for stoichiometric and reduced titanium dioxide intended for use in molecular dynamics and other atomistic simulations and based in the polarizable ion tight binding theory. This extends the model introduced in two previous papers from molecular and liquid applications into the solid state, thus completing the task of providing a comprehensive and unified scheme for studying chemical reactions, particularly aimed at problems in catalysis and electrochemistry. As before, experimental results are given priority over theoretical ones in selecting targets for model fitting, for which we used crystal parameters and band gaps of titania bulk polymorphs, rutile and anatase. The model is applied to six low index titania surfaces, with and without oxygen vacancies and adsorbed water molecules, both in dissociated and non-dissociated states. Finally, we present the results of molecular dynamics simulation of an anatase cluster with a number of adsorbed water molecules and discuss the role of edge and corner atoms of the cluster.

Enhanced structural and morphological properties of Gd-doped CeO2 thin films obtained by polymer-assisted deposition

Gadolinium-doped ceria epitaxial thin films were grown on yttria-stabilized zirconia (YSZ) substrates by polymer-assisted deposition (PAD). PAD utilizes an aqueous polymer to bind a metal or metal complex that serves to encapsulate the metal, in order to prevent chemical reaction in solution and to maintain an even distribution of the metal ions into solution. The structural and morphological properties were investigated by X-ray diffraction (XRD) and atomic force microscopy (AFM). The XRD pattern of the Gd-doped ceria (CGO) films indicated a dramatic improvement of the epitaxial growth with respect to pure CeO2 films. The CGO thin film morphology changes from rounded to plate-like grains when the annealing temperature increases due to an increase of atom mobility.

Yolk-shell ZnO-C microspheres with enhanced electrochemical performance as anode material for lithium ion batteries

Three ZnO-C samples with distinct structures including yolk-shell microspheres, hollow microspheres and solid microspheres are fabricated through a facile chemical solution reaction followed by calcination in argon. When employed as the anode materials for lithium ion batteries, yolk-shell ZnO-C microspheres exhibit the best electrochemical properties than the hollow and solid microspheres. After 150 cycles, yolk-shell ZnO-C microspheres demonstrate a relative high capacity of 520mA h g−1 at a current density of 100mAg−1 with a Coulombic efficiency of about 99.3%. The excellent cycling stability and good rate capability of yolk-shell ZnO-C microspheres stem from the synergistic effect of the unique yolk-shell structures and extra carbon support.

Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation.

From a hypothetical perfect dividing surface, all trajectories commit to opposite basins in forward and backward time without recrossing, transition state theory is exact, the transmission coefficient is one, and the committor distribution is perfectly focused at 1/2. However, chemical reactions in solution and other real systems often have dynamical trajectories that recross the dividing surface. To separate true dynamical effects from effects of a nonoptimal dividing surface, the dividing surface and/or reaction coordinate should be optimized before computing transmission coefficients. For NaCl dissociation in TIP3P water, we show that recrossing persists even when the 1/2-committor surface itself is used as the dividing surface, providing evidence that recrossing cannot be fully eliminated from the dynamics for any configurational coordinate. Consistent with this finding, inertial likelihood maximization finds a combination of ion-pair distance and two solvent coordinates that improves the committor distribution and increases the transmission coefficient relative to those for ion-pair distance alone, but recrossing is not entirely eliminated. Free energy surfaces for the coordinates identified by inertial likelihood maximization show that the intrinsic recrossing stems from anharmonicity and shallow intermediates that remain after dimensionality reduction to the dynamically important variables.

Computational electrochemistry: prediction of liquid-phase reduction potentials.

This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.

化学反応場制御による低次元ナノ構造チタニアの創製と高次機能

化学反応場制御による低次元ナノ構造チタニアの創製と高次機能

Cover Picture: Global Reaction Pathways in the Photodissociation of I3−Ions in Solution at 267 and 400 nm Studied by Picosecond X-ray Liquidography (ChemPhysChem 16/2013)

Time-resolved X-ray liquidography (TRXL) is a powerful tool for revealing the structural dynamics of chemical reactions in solution. By recording the difference scattering pattern at various time delays between ultrashort laser and X-ray pulses this technique allows to collect information on the structural change of the reacting molecules. This is shown by H. Ihee et al. on p. 3687, who elucidate the reaction mechanism of the photodissociation of I3− in solution. In addition to the reaction dynamics of the solute species, the transient structure of the solute/solvent cage and the changes in solvent density and temperature are revealed.

Rough passage across a barrier

The dynamics of chemical reactions in solution are described by Kramers' theory, but the parameters involved have eluded direct measurement. A study of protein folding reveals how this problem can be overcome. See Letter p.685 The kinetics of chemical reactions in solution are best described by a theory developed by Hendrik Kramers in the 1940s that relates Einstein's work on Brownian motion to rate theory. Until now it has not been possible to measure the parameters predicted by Kramers' theory on small molecules. Now Hoi Sung Chung & William Eaton have monitored photons emitted by single molecules during protein folding, and they find a high contribution of internal friction to the Kramers diffusion coefficient. The researchers' measurements of transition path times for protein folding characterize the Kramers diffusion coefficient and free-energy barrier height for the first time in any system.

Tests of an Adaptive QM/MM Calculation on Free Energy Profiles of Chemical Reactions in Solution

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Experimental Evidence of the Relevance of Orientational Correlations in Photoinduced Bimolecular Reactions in Solution

A major problem in the extraction of the reaction probability in bimolecular processes is the disentanglement from the influence of molecular diffusion. One of the strategies to overcome it makes use of reactive solvents in which the reactants do not need to diffuse to encounter each other. However, most of our quantitative understanding of chemical reactions in solution between free partners is based on the assumption that they can be approximated by spheres because rotation averages their mutual orientations. This condition may not be fulfilled when the reaction takes place on time scales faster than that of molecular reorientation. In this work, the fluorescence quenching of two very similar polyaromatic hydrocarbons with different electric dipole moments is measured. The concentration of a liquid electron-donating quencher is varied from very dilute solutions to pure quencher solutions. In both cases, the thermodynamics of the reactions are very similar and, according to the Marcus expression, the kinetics are expected to proceed at similar rates. However, one of them is 10 times faster in the pure quencher solution. This difference starts at relatively low quencher concentrations. An explanation based on the fluorophore-solvent dipole-dipole interaction and the consequent orientational solvent structure is provided. The orientational correlation between fluorophore and quencher is calculated by means of computer simulations. Important differences depending on the fluorophore dipole moment are found. The kinetics can be explained quantitatively with a reaction-diffusion model that incorporates the effects of the presence of the dipole moment and the rotational diffusion, only in the highest quencher concentration case, but not in dilute solutions, most likely due to fundamental limitations of the kinetic theory.

Structural cluster analysis of chemical reactions in solution

We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonstrate that it is possible to automatically resolve as distinct structural clusters the configurations corresponding to reactants, products, and transition states, even in presence of atom-exchanges and of hundreds of solvent molecules. Our approach strongly simplifies the analysis of large trajectories and it opens the way to the construction of kinetic network models of activated processes in solution employing the available efficient schemes developed for proteins conformational ensembles.