Femtosecond infrared study of the dynamics of solvation and solvent caging.

The ultrafast reaction dynamics following 295-nm photodissociation of Re2CO10 were studied experimentally with 300-fs time resolution in the reactive, strongly coordinating CCl4 solution and in the inert, weakly coordinating hexane solution. Density-functional theoretical (DFT) and ab initio calculations were used to further characterize the transient intermediates seen in the experiments. It was found that the quantum yield of the Re-Re bond dissociation is governed by geminate recombination on two time scales in CCl4, approximately 50 and approximately 500 ps. The recombination dynamics are discussed in terms of solvent caging in which the geminate Re(CO)5 pair has a low probability to escape the first solvent shell in the first few picoseconds after femtosecond photolysis. The other photofragmentation channel resulted in the equatorially solvated dirhenium nonacarbonyl eq-Re2(CO)9(solvent). Theoretical calculations indicated that a structural reorganization energy cost on the order of 6-7 kcal/mol might be required for the unsolvated nonacarbonyl to coordinate to a solvent molecule. These results suggest that for Re(CO)5 the solvent can be treated as a viscous continuum, whereas for the Re2(CO)9 the solvent is best described in molecular terms.     

Exploring the dynamics of dimer crossing over a Kramers type potential

We explore the escape rate of a dimer crossing a potential barrier using both analytical and numerical approaches. We find that for small coupling strength k, the barrier hopping can be well approximated by a two step reaction scheme where one monomer hops over the barrier and is then followed by the other. In this regime the escape rate increases with k showing that the cooperativity between monomers enhances the crossing rate. However, in the limit of large coupling strength, applying the method of adiabatic elimination, we find that the escape rate is a decreasing function of k. Thus, we find that the escape rate is a non-monotonic function of the spring constant which is peaked at an optimal coupling strength. Furthermore, in the presence of a weak periodic signal, we show that the system response to the periodic signal is pronounced at a particular spring constant showing the dimer can be transported rapidly across the reaction coordinate in a half period.     

Picosecond fluorescence decays from electronic excited states of 2,2′-bipyridine solutions

The photophysics of 2,2′-bipyridine in solution has been studied using picosecond excitation and single photon counting detection technique. Excited state relaxations could occur through non reactive (internal conversion, radiative decay) and reactive (photoisomerization) channels. The solvent influences the decay both indirectly (energy ordering of states) or directly through the friction exerted on the isomerization coordinate.     

Transient free radicals in viscous solvents

The majority of free radicals are highly reactive species which participate in bimolecular reactions with each other. Validation of the theory of molecular diffusion and reactivity in the liquid state requires knowledge of rate constants of radical–radical reactions (recombination, disproportionation) and their viscosity dependencies. An accurate comparison of theory and experiment has become available due to experimentally measured diffusion coefficients of reactive radicals by transient grating technique. Initial distribution of radicals in solution can be not random but pair-wise as in photo- or thermoinitiation of free radical polymerization reactions. Probability of a radical escape of a partner (cage escape) characterizes the initiator efficiency. Despite decades of measurement of cage effect values, cage effect dynamics with free radicals have only been investigated quite recently. The present tutorial review considers the effect of viscosity of Newtonian liquid on two types of recombination—in the solvent bulk and in a cage. Further, since radicals are paramagnetic species, external magnetic field affects probability of their reactions in pairs. These effects are also observed in viscous liquids, and reasons for such observations are explained. The recently discovered low magnetic field effect is also observed on radical pairs in viscous liquids.     

一种计算Feshbach共振态寿命的新方法

在自然碰撞坐标下构建偏分势能面, 利用数值传播方法求解沿反应坐标的核运动方程, 然后用过渡态波函数的相移因子构造反应体系共振态寿命矩阵. 这是一种直接计算化学反应散射共振寿命的量子散射方法. 用此方法计算了I+HI(υ)→IH(υ’)+I体系的第一散射共振态寿命, 所得数值与Neumark 的高分辨阈值光分离光谱实验的结果相一致.     

Dynamic reaction coordinate in thermally fluctuating environment in the framework of the multidimensional generalized Langevin equations

A framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in a multidimensional Langevin equation is extended to the generalized Langevin equations without a priori assumption of the forms of the potential (in general, nonlinearly coupled systems) and the friction kernel. The equation of motion with memory effect can be transformed into an equation without memory at the cost of an increase in the dimensionality of the system, and hence the theoretical framework developed for the (nonlinear) Langevin formulation can be generalized to the non-Markovian process with colored noise. It is found that the increased dimension can be physically interpreted as effective modes of the fluctuating environment. As an illustrative example, we apply this theory to a multidimensional generalized Langevin equation for motion on the Müller-Brown potential surface with an exponential friction kernel. Numerical simulations find a boundary between the highly reactive region and the less reactive region in the space of initial conditions. The location of the boundary is found to depend significantly on both the memory kernel and the nonlinear couplings. The theory extracts a reaction coordinate whose sign determines the fate of the reaction taking into account thermally fluctuating environments, memory effect, and nonlinearities. It is found that the location of the boundary of reactivity is satisfactorily reproduced as the zero of the statistical average of the new reaction coordinate, which is an analytical functional of both the original position coordinates and velocities of the system, and of the properties of the environment.     

Friction dependence of reaction rates in simple barrierless reactions

We have investigated the dynamics of simple chemical reactions which proceed without an activation barrier along the reaction coordinate. In the absence of the barrier the solvent friction is the only impediment to the reactive motion. By numerical simulation we show that in the low-friction limit the reaction rate increases as a fractional power of the friction coefficient. The power law dependence is sensitive to the initial conditions of the reactive coordinate. After exhibiting a maximum, the behaviour crosses over to that of inverse friction dependence in the high-friction limit. We have compared our results with earlier approximate analytical treatments and differences are pointed out.     

Revisiting roaming trajectories in ketene isomerization at higher dimensionality

Roaming dynamics have been observed in a three-dimensional model of the ketene isomerization reaction. The roaming trajectories sample the region between the outer potential barriers closest to the respective ketene isomers and involve turning points along the reaction coordinate in a polar representation. These roaming trajectories avoid the intrinsic reaction coordinate and the intermediates to which it is associated. Thus, one-dimensional transition state theory (TST) is generally insufficient as has been confirmed through an analysis of the reactive flux along the dividing surface (DS). A global representation of the DS, however, leads to accurate TST rate constants. The exact and TST microcanonical rates of isomerization have been obtained for the three-dimensional model and compare well to experiment. The global DS is therefore particularly important for obtaining rates in reactions that exhibit roaming. This work thus confirms the findings of our previous two-dimensional treatment of ketene isomerization (Ulusoy et al. in J. Phys. Chem. A 117:7553–7560, 2013).     

A general treatment of vibration-rotation coordinates for triatomic molecules

An exact, within the Born–Oppenheimer approximation, body-fixed Hamiltonian for the nuclear motions of a triatomic system is presented. This Hamiltonian is expressed in terms of two arbitrarily defined internal distances and the angle between them. The body-fixed axis system is related to these coordinates in a general fashion. Problems with singularities and the domain of the Hamiltonian are discussed using specific examples of axis embedding. A number of commonly used coordinate systems including Jacobi, bond-length-bond-angle, and Radau coordinates are special cases of this Hamiltonian. Sample calculations on the H₂S molecule are presented using all these and other coordinate systems. The possibility of using this Hamiltonian for reactive scattering calculations is also discussed.     

Detecting Reaction Pathways and Computing Reaction Rates in Condensed Phase

Methods for the computation of rate constants that characterize classical reactions occurring in the condensed phase are discussed. While microscopic expressions for these transport properties are well known, their computation presents challenges for simulation since reactive events often occur rarely, and the long time scales that are typical for reactive processes are not accessible using simple molecular dynamics methods. Furthermore, the underlying free energy surface is very complex with many saddle points that prevent sampling of possible reaction pathways. As a result, the reaction coordinate may be a complex many-body function of the system’s degrees of freedom. Since there is not an a priori way to define a “good” reaction coordinate, methods are being developed to assist in a systematic construction of a reaction coordinate. These methods are reviewed and examples of non-trivial reaction coordinates are presented.     

Kramers problem for nonequilibrium current-induced chemical reactions

We discuss the use of tunneling electron current to control and catalyze chemical reactions. Assuming the separation of time scales for electronic and nuclear dynamics we employ Langevin equation for a reaction coordinate. The Langevin equation contains nonconservative current-induced forces and gives nonequilibrium, effective potential energy surface for current-carrying molecular systems. The current-induced forces are computed via Keldysh nonequilibrium Green's functions. Once a nonequilibrium, current-depended potential energy surface is defined, the chemical reaction is modeled as an escape of a Brownian particle from the potential well. We demonstrate that the barrier between the reactant and the product states can be controlled by the bias voltage. When the molecule is asymmetrically coupled to the electrodes, the reaction can be catalyzed or stopped depending on the polarity of the tunneling current.     

Momentum representation of the solute/bath interaction in the dynamic theory of chemical processes in condensed phase

For the system consisting of the chemically reactive solute immersed in the oscillator bath, we consider an approach based on the solute/medium interaction expressed in terms of momenta rather than coordinates. In the adiabatic representation the medium reorganization effects are suppressed, being hidden in the solute renormalized potential and new spectral density function. The advantage proposed by the bilinear interaction in momentum representation is its spatial uniformity important for approximate dynamical treatments. The procedure of explicit transforming a standard spectral density (coordinate representation of interaction) into the spectral density in adiabatic representation (momentum representation of interaction) is the main new result of the present study. Illustrative calculations for several types of spectral functions are performed. Special discussion is devoted to clarifying the nature of the slow diffusion coordinate, to which the present approach is mainly addressed.     

Synthesis and antioxidant efficiency of a new copolymer containing phosphorylated myo-inositol

New data are constantly gathered to show the role of oxidative stress and the involvement of reactive oxygen species in the pathogenesis of degenerative diseases. InsP6 is able to coordinate iron metal in order to prevent iron-catalyzed free radical formation. The aim of the present paper is to describe a new synthetic strategy in order to prepare a polymeric structure containing chemical functions able to coordinate iron ions. Here, we report the synthesis of a copolymer containing phosphorylated myo-inositol groups and we evaluate its antioxidant efficiency. Such a system was synthesized by binding chemical groups susceptible of radical polymerization to myo-inositol. The synthesized monomer was copolymerized with N,N-dimethylacrylamide (DMAA) (molar ratio 1:3) and submitted to exhaustive phosphorylation. The reaction was proved by an assay specific for phosphate groups. Finally, we evaluated the copolymer's ability in inhibiting lipid peroxidation in rat liver microsomal membranes. This study showed that the designed macromolecular system is particularly effective as antioxidant.     

Multidimensional reactive scattering with quantum trajectories: dynamics with 50-200 vibrational modes

The dynamics of ensembles containing thousands of quantum trajectories are studied for multidimensional systems undergoing reactive scattering. The Hamiltonian and equations of motion are formulated in curvilinear reaction path coordinates, for the case of a planar (zero-torsion) reaction path. In order to enhance the computational efficiency, an improved least squares fitting procedure is introduced. This scheme involves contracted basis sets and the use of inner and outer stencils around points where fitting is performed. This method is applied to reactive systems with 50-200 harmonic vibrational modes which are coupled to motion along the reaction coordinate. Dynamical results, including trajectory evolution and time-dependent reaction probabilities, are presented and power law scaling of computation time with the number of vibrational modes is described.     

Transition state theory for laser-driven reactions

Recent developments in transition state theory brought about by dynamical systems theory are extended to time-dependent systems such as laser-driven reactions. Using time-dependent normal form theory, the authors construct a reaction coordinate with regular dynamics inside the transition region. The conservation of the associated action enables one to extract time-dependent invariant manifolds that act as separatrices between reactive and nonreactive trajectories and thus make it possible to predict the ultimate fate of a trajectory. They illustrate the power of our approach on a driven Henon-Heiles system, which serves as a simple example of a reactive system with several open channels. The present generalization of transition state theory to driven systems will allow one to study processes such as the control of chemical reactions through laser pulses.     

Unexpected copper(II) catalysis: catalytic amine base promoted β-borylation of α,β-unsaturated carbonyl compounds in water

Using bis(pinacolato)diboron, catalytic amounts of Cu(II), and various amine bases in water under atmospheric conditions at rt, acyclic and cyclic α,β-unsaturated ketones and esters are β-borylated in up to 98% yield. Mechanistic investigations using UV-vis spectroscopy, (11)B NMR, and solvent kinetic isotope effect suggest that the role of the amine is not only to coordinate to Cu(II) but also to activate a nucleophilic water molecule to form the reactive sp(2)-sp(3) diboron complex.     

The synthesis and application of polyamino polycarboxylic bifunctional chelating agents

Bifunctional chelating agents (BFCAs) are molecules which contain two different moieties: a strong metal chelating unit and a reactive functional group. The latter is directed to react with amines, thiols, alcohols or other reactive molecules to form stable covalent bonds while the chelating moiety is able to strongly coordinate a metal ion. In this way, it is possible to label a molecule of interest (e.g. an antibody or a peptide) with a metal or a radioactive metal ion. Of all the ligands reported so far, those based on a polyamino polycarboxylic structure are most efficient and are widely employed for the chelation of metal ions. The resulting metal complexes have found a broad range of applications in chemistry, biology and medicine. Diagnostic imaging (MRI, SPECT, PET), molecular imaging, tumour therapy and luminescent materials are only a few examples. The present critical review gives an overview of the syntheses and most important applications of polyamino polycarboxylic BFCAs (334 references).     

The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction

BACKGROUND: The 2'-hydroxyl of U preceding the cleavage site, U(-1), in the Tetrahymena ribozyme reaction contributes 10(3)-fold to catalysis relative to a 2'-hydrogen atom. Previously proposed models for the catalytic role of this 2'-OH involve coordination of a catalytic metal ion and hydrogen-bond donation to the 3'-bridging oxygen. An additional model, hydrogen-bond donation by the 2'-OH to a nonbridging reactive phosphoryl oxygen, is also consistent with previous results. We have tested these models using atomic-level substrate modifications and kinetic and thermodynamic analyses. RESULTS: Replacing the 2'-OH with -NH(3)(+) increases the reaction rate approximately 60-fold, despite the absence of lone-pair electrons on the 2'-NH(3)(+) group to coordinate a metal ion. Binding and reaction of a modified oligonucleotide substrate with 2'-NH(2) at U(-1) are unaffected by soft-metal ions. These results suggest that the 2'-OH of U(-1) does not interact with a metal ion. The contribution of the 2'-moiety of U(-1) is unperturbed by thio substitution at either of the nonbridging oxygens of the reactive phosphoryl group, providing no indication of a hydrogen bond between the 2'-OH and the nonbridging phosphoryl oxygens. In contrast, the 10(3)-fold catalytic advantage of 2'-OH relative to 2'-H is eliminated when the 3'-bridging oxygen is replaced by sulfur. As sulfur is a weaker hydrogen-bond acceptor than oxygen, this effect suggests a hydrogen-bonding interaction between the 2'-OH and the 3'-bridging oxygen. CONCLUSIONS: These results provide the first experimental support for the model in which the 2'-OH of U(-1) donates a hydrogen bond to the neighboring 3'-bridging oxygen, thereby stabilizing the developing negative charge on the 3'-oxygen in the transition state.