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We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis–Menten mechanism, which exemplifies an out-of-equilibrium process in the living system. Our theoretical approach begins with the principle of equal a priori probabilities and defines the reaction path entropy to construct a new nonequilibrium ensemble as a collection of possible chemical reaction paths. As a result, we evaluate a variety of path-based partition functions and free energies by using the formalism of statistical mechanics. They allow us to calculate the timescales of a given enzymatic reaction, even in the absence of an explicit boundary condition that is necessary for the equilibrium ensemble. We also consider the large deviation theory under a closed-boundary condition of the fixed observation time to quantify the enzyme–substrate unbinding rates. The result demonstrates the presence of a phase-separation-like, bimodal behavior in unbinding events at a finite timescale, and the behavior vanishes as its rate function converges to a single phase in the long-time limit. [ABSTRACT FROM AUTHOR]

We present a coarse-graining strategy for reducing the number of particle species in mixtures to achieve a simpler system with higher diffusion while preserving the total particle number and characteristic dynamic features. As a system of application, we chose the bidisperse Lennard-Jones-like mixture, discovered by Kob and Andersen [Phys. Rev. Lett. 73, 1376 (1994)], possessing a slow dynamics due to the fluid's multi-component character with its apparently unconventional choice for the pair potential of the type-A–type-B arrangement. We further established in a so-formed coarse-grained and temperature-independent monodisperse system an equilibrium structure with a radial distribution function resembling its mixture counterpart. This one-component system further possesses similar dynamic features such as glass transition temperature and critical exponents while subjected to Newtonian mechanics. This strategy may finally lead to the manufacturing of new nanoparticle/colloidal fluids by experimentally modeling only the outcoming effective pair potential(s) and no other macroscopic quantity. [ABSTRACT FROM AUTHOR]

The locally heterogeneous dynamics of the glass‐forming liquids is an unusual and distinct phenomenon that is not observed in a typical liquid system above the melting temperature. Room‐temperature ionic liquids (RTILs) are usually good glass formers, exhibiting various interesting features of glassy materials such as nonexponential and non‐Arrenhius relaxations and transport decoupling behaviors. In this study, we propose a minimal model that represents the general structural features of RTILs to study their dynamics by extending the restricted primitive model. We mainly focus on the heterogeneous dynamics of the RTIL as a glass former and investigate how the charge symmetry of each ion affects the structural relaxation, diffusive behavior, and the dynamic heterogeneity lifetime of the system. [ABSTRACT FROM AUTHOR]

Recent advances in machine learning technologies and their applications have led to the development of diverse structure–property relationship models for crucial chemical properties. The solvation free energy is one of them. Here, we introduce a novel ML-based solvation model, which calculates the solvation energy from pairwise atomistic interactions. The novelty of the proposed model consists of a simple architecture: two encoding functions extract atomic feature vectors from the given chemical structure, while the inner product between the two atomistic feature vectors calculates their interactions. The results of 6239 experimental measurements achieve outstanding performance and transferability for enlarging training data owing to its solvent-non-specific nature. An analysis of the interaction map shows that our model has significant potential for producing group contributions on the solvation energy, which indicates that the model provides not only predictions of target properties but also more detailed physicochemical insights. [ABSTRACT FROM AUTHOR]

We investigate statistics of dynamical exchange events in coarse-grained models of supercooled liquids in spatial dimensions d=1, 2, and 3. The models, based upon the concept of dynamical facilitation, capture generic features of statistics of exchange times and persistence times. Here, distributions for both times are related and calculated for cases of strong and fragile glass formers over a range of temperatures. Exchange-time distributions are shown to be particularly sensitive to the model parameters and dimensions, and exhibit more structured and richer behavior than persistence-time distributions. Mean exchange times are shown to be Arrhenius, regardless of models and spatial dimensions. Specifically, 〈tx〉∼c-2, with c being the excitation concentration. Different dynamical exchange processes are identified and characterized from the underlying trajectories. We discuss experimental possibilities to test some of our theoretical findings. [ABSTRACT FROM AUTHOR]

We survey the current status of single-molecule spectroscopy in the view point of theoretical aspects. After an explanation of basic concepts in single-molecule spectroscopy, we focus on the following topics: (1) line shape phenomena in disordered media, (2) photon counting statistics for time-dependent fluctuations in single-molecule spectroscopy, (3) fluorescence intensity fluctuations for nonergodic systems, (4) time-resolved single-molecule fluorescence for conformational dynamics of single biomolecules, (5) single-molecule reaction dynamics at room temperature, and (6) quantum jump method of single quantum system. We conclude this paper with some open questions and perspectives of single-molecule spectroscopy. [ABSTRACT FROM AUTHOR]

Electron transfer processes in Debye solvents are studied using a spectral analysis method recently proposed. Spectral structure of a nonadiabatic two-state diffusion equation is investigated to reveal various kinetic regimes characterized by a broad range of physical parameters; electronic coupling, energy bias, reorganization energy, and solvent relaxation rate. Within this unified framework, several kinetic behaviors of the electron transfer kinetics, including adiabatic Rabi oscillation, crossover from the nonadiabatic to adiabatic limits, transition from the incoherent to coherent kinetic limits, and dynamic bath effect, are demonstrated and compared with results from previous theoretical models. Dynamics of the electron transfer system is also calculated with the spectral analysis method. It is pointed out that in the large reorganization energy case the nonadiabatic diffusion equation exhibits a nonphysical behavior, yielding a negative eigenvalue. [ABSTRACT FROM AUTHOR]

The recombination reaction of radicals photolytically produced in solution proceeds via two distinguishable kinetic phases. At short times recombination between geminate radicals predominates, while at long times recombination between nongeminate radicals that have diffused away from their geminate counterparts to the bulk solution takes place. In most previous theories dealing with the effect of added scavenger molecules on the radical recombination reaction, only the geminate recombination phase has been considered. However, if the concentration of radical pairs generated is high, the interplay of bulk recombination in the dynamics needs to be considered. In the present paper, we formulate a theory that deals with the scavenging effect in both the geminate and bulk recombination phases within a unified framework. We show that the scavenger concentration CS and the scavenging rate coefficient kS have independent effects on the reaction, in general. In contrast, conventional theories involve these two quantities only as a product kSCS, usually in the form of a Laplace transformation variable. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Motivated by recent experimental observations of power-law statistics both in spectral diffusion process and fluorescence intermittency of individual semiconductor nanocrystals (quantum dots), we consider two different but related problems: (a) a stochastic lineshape theory for the Kubo–Anderson oscillator whose frequency modulation follows power-law statistics and (b) photon counting statistics of quantum dots whose intensity fluctuation is characterized by power-law kinetics. In the first problem, we derive an analytical expression for the lineshape formula and find rich type of behaviors when compared with the standard theory. For example, new type of resonances and narrowing behavior have been found. We show that the lineshape is extremely sensitive to the way the system is prepared at time t=0 and discuss the problem of stationarity. In the second problem, we use semiclassical photon counting statistics to characterize the fluctuation of the photon counts emitted from quantum dots. We show that the photon counting statistics problem can be mapped onto a Le´vy walk process. We find unusually large fluctuations in the photon counts that have not been encountered previously. In particular, we show that Mandel’s Q parameter may increase in time even in the long time limit. [Copyright &y& Elsevier]

Fo¨rster–Dexter theory for excitation energy transfer (EET) is generalized for the account of short time nonequilibrium kinetics due to the nonstationary bath relaxation. The final rate expression is presented as a spectral overlap between the time dependent stimulated emission and the stationary absorption profiles, which allows experimental determination of the time dependent rate. For a harmonic oscillator bath model, an explicit rate expression is derived and model calculations are performed in order to examine the dependence of the nonequilibrium kinetics on the excitation–bath coupling strength and the temperature. Relevance of the present theory with recent experimental findings and possible future theoretical directions are discussed. [Copyright &y& Elsevier]

Abnormally slower diffusional processes than its internal structure relaxation have been observed in ring polymeric melt systems recently. A key structural feature in ring polymer melts is topological constraints which allow rings to assume a threading configuration in the melt phase. In this work, we constructed a lattice model under the assumption of asymmetric diffusivity between two threading rings, and investigated a link between the structural correlation and its dynamic behavior via Monte Carlo simulations. We discovered that the hierarchical threading configurations render the whole system to exhibit abnormally slow dynamics. By analyzing statistical distributions of timescales of threading configurations, we found that the decoupling between internal structure relaxation and diffusion is crucial to understand the threading effects on the dynamics of a ring melt. In particular, in the limit of small but threaded rings, scaling exponents of the diffusion coefficient D and timescale τ diff with respect to the degree of polymerization N agree well with that of the annealed tree model as well as our mean-field analysis. As N increases, however, the ring diffusion abruptly slows down to the glassy behavior, which is supported by a breakdown of the Stokes–Einstein relation. [ABSTRACT FROM AUTHOR]

Herein, the self‐reinforced inductive effect derived from coexistence of both p‐ and n‐type redox‐active motifs in a single organic molecule is presented. Molecular orbital energy levels of each motif are dramatically tuned, which leads to the higher oxidation and the lower reduction potentials. The self‐reinforced inductive effect of the symmetric bipolar organic molecule, N,N'‐dimethylquinacridone (DMQA), is corroborated, by both experimental and theoretical methods. Furthermore, its redox mechanism and reaction pathway in the Li+‐battery system are scrutinized. DMQA shows excellent capacity retention at the operating voltage of 3.85 and 2.09 V (vs Li+/Li) when used as the cathode and anode, respectively. Successful operation of DMQA electrodes in a symmetric all‐organic battery is also demonstrated. The comprehensive insight into the energy storage capability of the symmetric bipolar organic molecule and its self‐reinforced inductive effect is provided. Thus, a new class of organic electrode materials for symmetric all‐organic batteries as well as conventional rechargeable batteries can be conceived. [ABSTRACT FROM AUTHOR]

A stochastic lineshape theory is formulated for the non-Markovian and multistate frequency modulation model. The frequency of the stochastic oscillator undergoes non-Markovian modulations between multiple states, and the transition processes are described by arbitrary waiting-time distributions. By incorporating stationarity into the stochastic process in a proper way, we calculate the propagator and the relaxation function. It is shown that a stationary distribution among the oscillator states satisfies a generalized detailed balance condition even in the non-Markovian case. We find an exact expression for the lineshape function, which contains the Markovian case as a special limit. [ABSTRACT FROM AUTHOR]

The nature of hydrated protons formed at water/metal interfaces is one of the most intriguing research questions in the field of interfacial chemistry. We prepared coadsorption layers of hydrogen and water on a Pt(111) surface in ultrahigh vacuum and studied the ionization of adsorbed hydrogen atoms to H+ ions by employing a combined experimental and theoretical approach. Spectroscopic evidence obtained by mass spectrometry and reflection absorption infrared spectroscopy as well as corresponding density functional theory calculations consistently show that adsorbed hydrogen atoms ionize into multiply hydrated proton species (H5O2+, H7O3+, and H9O4+) on the surface, rather than H3O+. Then, upon addition of a water overlayer, the metal-bound hydrated protons spontaneously evolve into three-dimensional fully hydrated proton structures through proton transfer along the water overlayer. The stability of hydrated protons on the Pt surface and their bulk dissolution behavior suggest the possibility that surface hydrated protons are a key intermediate in electrochemical interconversion between adsorbed H atoms and H+(aq) in water electrolysis and hydrogen evolution reactions. [ABSTRACT FROM AUTHOR]

Diffusion of long ring polymers in a melt is much slower than the reorganization of their internal structures. While direct evidence for entanglements has not been observed in the long ring polymers unlike linear polymer melts, threading between the rings is suspected to be the main reason for slowing down of ring polymer diffusion. It is, however, difficult to define the threading configuration between two rings because the rings have no chain end. In this work, evidence for threading dynamics of ring polymers is presented by using molecular dynamics simulation and applying a novel analysis method. The simulation results are analyzed in terms of the statistics of persistence and exchange times that have proved useful in studying heterogeneous dynamics of glassy systems. It is found that the threading time of ring polymer melts increases more rapidly with the degree of polymerization than that of linear polymer melts. This indicates that threaded ring polymers cannot diffuse until an unthreading event occurs, which results in the slowing down of ring polymer diffusion. [ABSTRACT FROM AUTHOR]

Nicotinamide adenine dinucleotide (NAD+) is one of the most well‐known redox cofactors carrying electrons. Now, it is reported that the intrinsically charged NAD+ motif can serve as an active electrode in electrochemical lithium cells. By anchoring the NAD+ motif by the anion incorporation, redox activity of the NAD+ is successfully implemented in conventional batteries, exhibiting the average voltage of 2.3 V. The operating voltage and capacity are tunable by altering the anchoring anion species without modifying the redox center itself. This work not only demonstrates the redox capability of NAD+, but also suggests that anchoring the charged molecules with anion incorporation is a viable new approach to exploit various charged biological cofactors in rechargeable battery systems. [ABSTRACT FROM AUTHOR]

Nicotinamide adenine dinucleotide (NAD+) is one of the most well‐known redox cofactors carrying electrons. Now, it is reported that the intrinsically charged NAD+ motif can serve as an active electrode in electrochemical lithium cells. By anchoring the NAD+ motif by the anion incorporation, redox activity of the NAD+ is successfully implemented in conventional batteries, exhibiting the average voltage of 2.3 V. The operating voltage and capacity are tunable by altering the anchoring anion species without modifying the redox center itself. This work not only demonstrates the redox capability of NAD+, but also suggests that anchoring the charged molecules with anion incorporation is a viable new approach to exploit various charged biological cofactors in rechargeable battery systems. [ABSTRACT FROM AUTHOR]

A spectral analysis method is proposed to characterize multiple time scales in electron transfer processes, including vibrational relaxation, electronic coherence, activated curve crossing, or barrier crossing. Within this unified framework, observed rate behavior, biexponential and multiexponential decay, and population recurrences and oscillations are different components of the same kinetic spectrum; thus, several existing theoretical models, developed for limiting cases of electron transfer, can be analyzed, tested, and extended. In particular, the rate constant extracted from the analysis does not saturate as the electronic coupling increases but shows a crossover from the nonadiabatic to adiabatic limits, and the kinetic spectrum in the large coupling regime reveals the nature of the localization-delocalization transition as the consequence of two competing mechanisms. Though the analysis is presented in the context of electron transfer, this approach provides a different perspective for understanding dissipative dynamics and hence can be applied to study condensed-phase laser spectroscopy, quantum coherence control, energy transfer, and other charge transfer processes. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulation is employed to study graphene supercapacitors. Four different ionic liquids are considered as an electrolyte, each of which is combination of the same cation 1-ethyl-3-methylimidazolium([emim] + ), and different, cyano-containing anions, thiocyanate ([SCN] – ), dicyanamide ([N(CN) 2 ] – ), tricyanomethanide ([C(CN) 3 ] – ), and tetracyanoborate ([B(CN) 4 ] – ), respectively. In particular we investigate how electric double layer structure and electrical properties are affected by the structure of cyano containing anions. Cations and anions make alternating structure near charged electrode. Differential capacitances in four ionic liquids are found to have a maximum value at negative potential. The maximum capacitances are comparable to each other, but the corresponding potential shifts to the negative side as more cyano groups are attached to the anion. Starting from the interfacial layer, the effects of the further ionic layers on differential capacitance are systematically investigated. Comparing charges of the electrode and those of ionic layers, we find that differential capacitance behavior mainly stems from the ion exchange between electric double layer and bulk region. The ion exchange behaviors are decomposed into cation and anion contributions. The differential charging mechanisms of the system are strongly dependent on the electric potential. The maximum capacitances are consequence of rapid desorption of respective anions. [ABSTRACT FROM AUTHOR]

Supercapacitors with graphene electrodes are studied via molecular dynamics simulation. As an electrolyte, we consider three different room-temperature ionic liquids (RTILs), each of which is made up of the same anion BF 4 − , and different cations, 1-C n (n = 2,4,6)-3-methylimidazolium, respectively. We investigate how the alkyl chain length of the cation affects their interfacial structure and electrical properties for electric double layer capacitors. As a whole, cations and anions make layering structures between two parallel electrodes. Cations in the nearest layer orient predominantly in parallel to the electrode. Imidazolium rings of cations form π-stacking with graphene, then the alkyl chains of cations align parallel to the electrode. Differential capacitances in three RTILs are found to decrease with an increase of the magnitude of electrode potentials. The ion size and orientation affect both structure and capacitance behavior. The parallel orientations of cations become stronger with an increase of the alkyl chain length for the considered RTILs. The differential capacitance tends to decrease with raising the alkyl chain length over a wide range of the electrode potential. This is ascribed to a steric effect caused by larger cation size. It is also found that anodic capacitance is higher than cathodic one due to a higher screening efficiency by small anions, and an asymmetry in the peak of capacitance biased to the cathodic side becomes weaker as the alkyl chain length increases. Comparing electrode charge with ion numbers near the electrodes, with respect to their changes in response to the electrode potential, we find that the interfacial layer of the electrolyte mainly governs capacitive behavior of the systems. [ABSTRACT FROM AUTHOR]

Frontispiz: Biological Nicotinamide Cofactor as a Redox-Active Motif for Reversible Electrochemical Energy Storage Keywords: Bioenergetik; Cofaktoren; Energiespeicherung; Organische Elektroden; Redoxchemie B Energiespeicherung b Das biologisch aktive Nicotinamid-Adenin-Dinukleotid-Motiv ermöglicht eine reversible Energiespeicherung in Lithiumionenbatterien, wie C. B. Park, K. Kang et al. in ihrer Zuschrift auf S. 16920 zeigen. [Extracted from the article]