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Chemical shakers are active particles with zero propulsion velocity whose activity derives from chemical reactions on portions of their surfaces. Although they do not move, except through Brownian motion, the nonequilibrium concentration and velocity fields that they generate endow them with properties that differ from their equilibrium counterparts. In particular, collections of such shakers can actively move, reorient, and self-assemble into various cluster states, which are the subject of this paper. Elongated chemical shakers constructed from linked catalytic and noncatalytic spheres are considered, and it is shown how hydrodynamic, chemotactic, and shape-dependent interactions give rise to various self-assembled shaker structures. The chemical forces responsible for cluster formation are described in terms of a model based on pair-wise additive contributions. The forms of the self-assembled structures can be varied by changing the chemostat concentrations that control the nonequilibrium state. The resulting structures and their manipulation through chemical means suggest ways to construct a class of active materials for applications. [ABSTRACT FROM AUTHOR]

Based on the relationship between average local ionization energy I ̄ (r) and average local electron affinity A ̄ (r) with the electronic Fukui functions, i.e., f−(r) and f+(r), respectively, in this paper, we establish a connection between nuclear and electronic Fukui functions beyond frontier molecular orbitals. As a consequence of this connection, we obtain expressions of average nuclear Fukui functions interpreted as a variation of average nucleophilicity or electrophilicity (weighted by the electronic orbital Fukui functions) with respect to nuclear displacements, which goes beyond the highest occupied molecular orbital/or lowest unoccupied molecular orbital consideration. Furthermore, from this connection and considering the frontier molecular orbital approximation, we derive expressions of nuclear Fukui functions in terms of the atom-condensed electronic Fukui functions, which imply a locality in the chemical reactivity and could be used to study the variation of local nucleophilicity or electrophilicity with respect to nuclear displacements. Finally, this new way to interpret the nuclear Fukui function could be useful in the future to study the chemical reactivity related to molecular vibrations, internal rotations, bond dissociation, chemical reaction along the model of reaction coordinate, and so on. [ABSTRACT FROM AUTHOR]

Recent experiments of chemical reactions in optical cavities have shown great promise to alter and steer chemical reactions, but still remain poorly understood theoretically. In particular, the origin of resonant effects between the cavity and certain vibrational modes in the collective limit is still subject to active research. In this paper, we study the unimolecular dissociation reactions of many molecules, collectively interacting with an infrared cavity mode, through their vibrational dipole moment. We find that the reaction rate can slow down by increasing the number of aligned molecules, if the cavity mode is resonant with a vibrational mode of the molecules. We also discover a simple scaling relation that scales with the collective Rabi splitting, to estimate the onset of reaction rate modification by collective vibrational strong coupling and numerically demonstrate these effects for up to 104 molecules. [ABSTRACT FROM AUTHOR]

Similar to cells, bacteria, and other micro-organisms, synthetic chemically active colloids can harness the energy from their environment through a surface chemical reaction and use the energy to self-propel in fluidic environments. In this paper, we study the chemo-mechanical coupling that leads to the self-propulsion of chemically active colloids. The coupling between chemical reactions and momentum transport is a consequence of Onsager reciprocal relations. They state that the velocity and the surface reaction rate are related to mechanical and chemical affinities through a symmetric matrix. A consequence of Onsager reciprocal relations is that if a chemical reaction drives the motion of the colloid, then an external force generates a reaction rate. Here, we investigate Onsager reciprocal relations for a spherical active colloid that catalyzes a reversible surface chemical reaction between two species. We solve the relevant transport equations using a perturbation expansion and numerical simulations to demonstrate the validity of reciprocal relations around the equilibrium. Our results are consistent with previous studies and highlight the key role of solute advection in preserving the symmetry of the Onsager matrix. Finally, we show that Onsager reciprocal relations break down around a nonequilibrium steady state, which has implications for the thermal fluctuations of the active colloids used in experiments. [ABSTRACT FROM AUTHOR]

Recently, we proposed a new orbital analysis method, natural reaction orbital (NRO), which automatically extracts orbital pairs that characterize electron transfer in reaction processes by singular value decomposition of the first-order orbital response matrix to the nuclear coordinate displacements [Ebisawa et al., Phys. Chem. Chem. Phys. 24, 3532 (2022)]. NRO analysis along the intrinsic reaction coordinate (IRC) for several typical chemical reactions demonstrated that electron transfer occurs mainly in the vicinity of transition states and in regions where the energy profile along the IRC shows shoulder features, allowing the reaction mechanism to be explained in terms of electron motion. However, its application has been limited to single configuration theories such as Hartree–Fock theory and density functional theory. In this work, the concept of NRO is extended to multiconfigurational wavefunctions and formulated as the multiconfiguration NRO (MC-NRO). The MC-NRO method is applicable to various types of electronic structure theories, including multiconfigurational theory and linear response theory, and is expected to be a practical tool for extracting the essential qualitative features of a broad range of chemical reactions, including covalent bond dissociation and chemical reactions in electronically excited states. In this paper, we calculate the IRC for five basic chemical reaction processes at the level of the complete active space self-consistent field theory and discuss the phenomenon of electron transfer by performing MC-NRO analysis along each IRC. Finally, issues and future prospects of the MC-NRO method are discussed. [ABSTRACT FROM AUTHOR]

We present a methodology for analyzing chemical bonds embedded in the electronic wave function of molecules, especially in terms of spin correlations or so-called "local spin." In this paper, based on biorthogonal second quantization, the spin correlation functions of molecules are naturally introduced, which enables us to extract local singlet and local triplet elements from the wave function. We also clarify the relationship between these spin correlations and traditional chemical concepts, i.e., resonance structures. Several chemical reactions, including the intramolecular radical cyclization and the formation of preoxetane, are demonstrated to verify the analysis method numerically. [ABSTRACT FROM AUTHOR]

The behavior of a particle in a solvent has been framed using stochastic dynamics since the early theory of Kramers. A particle in a chemical reaction reacts slower in a diluted solvent because of the lack of energy transfer via collisions. The flux-over-population reaction rate constant rises with increasing density before falling again for very dense solvents. This Kramers turnover is observed in this paper at intermediate and high temperatures in the backward reaction of the LiNC ⇌ LiCN isomerization via Langevin dynamics and mean first-passage times (MFPTs). It is in good agreement with the Pollak–Grabert–Hänggi (PGH) reaction rates at lower temperatures. Furthermore, we find a square root behavior of the reaction rate at high temperatures and have made direct comparisons of the methods in the intermediate- and high-temperature regimes, all suggesting increased ranges in accuracy of both the PGH and MFPT approaches. [ABSTRACT FROM AUTHOR]

Analysis of electron flux within and in between molecules is crucial in the study of real-time dynamics of molecular electron wavepacket evolution such as those in attosecond laser chemistry and ultrafast chemical reaction dynamics. We here address two mutually correlated issues on the conservation law of molecular electronic flux, which serves as a key consistency condition for electron dynamics. The first one is about a close relation between "weak" nonadiabaticity and the electron dynamics in low-energy chemical reactions. We show that the electronic flux in adiabatic reactions can be consistently reproduced by taking account of nonadiabaticity. Such nonadiabaticity is usually weak in the sense that it does not have a major effect on nuclear dynamics, whereas it plays an important role in electronic dynamics. Our discussion is based on a nonadiabatic extension of the electronic wavefunction similar in idea to the complete adiabatic formalism developed by Nafie [J. Chem. Phys. 79, 4950 (1983)], which has also recently been reformulated by Patchkovskii [J. Chem. Phys. 137, 084109 (2012)]. We give straightforward proof of the theoretical assertion presented by Nafie using a time-dependent mixed quantum–classical framework and a standard perturbation expansion. Explicitly taking account of the flux conservation, we show that the nonadiabatically induced flux realizes the adiabatic time evolution of the electronic density. In other words, the divergence of the nonadiabatic flux equals the time derivative of the electronic density along an adiabatic time evolution of the target molecule. The second issue is about the accurate computationability of the flux. The calculation of flux needs an accurate representation of the (relative) quantum phase, in addition to the amplitude factor, of a total wavefunction and demands special attention for practical calculations. This paper is the first one to approach this issue directly and show how the difficulties arise explicitly. In doing so, we reveal that a number of widely accepted truncation techniques for static property calculations are potential sources of numerical flux non-conservation. We also theoretically propose alternative strategies to realize better flux conservation. [ABSTRACT FROM AUTHOR]

Active colloidal particles that are propelled by a self-diffusiophoretic mechanism are often described by Langevin equations that are either postulated on physical grounds or derived using the methods of fluctuating hydrodynamics. While these descriptions are appropriate for colloids of micrometric and larger size, they will break down for very small active particles. A fully microscopic derivation of Langevin equations for self-diffusiophoretic particles powered by chemical reactions catalyzed asymmetrically by the colloid is given in this paper. The derivation provides microscopic expressions for the translational and rotational friction tensors, as well as reaction rate coefficients appearing in the Langevin equations. The diffusiophoretic force and torque are expressed in terms of nonequilibrium averages of fluid fields that satisfy generalized transport equations. The results provide a description of active motion on small scales where descriptions in terms of coarse grained continuum fluid equations combined with boundary conditions that account for the presence of the colloid may not be appropriate. [ABSTRACT FROM AUTHOR]

The framework of transition state theory relies on the determination of a geometric structure identifying reactivity. It replaces the laborious exercise of following many trajectories for a long time to provide chemical reaction rates and pathways. In this paper, recent advances in constructing this geometry even in time-dependent systems are applied to the LiCN ⇌ LiNC isomerization reaction driven by an external field. We obtain decay rates of the reactant population close to the transition state by exploiting local properties of the dynamics of trajectories in and close to it. We find that the external driving has a large influence on these decay rates when compared to the non-driven isomerization reaction. This, in turn, provides renewed evidence for the possibility of controlling chemical reactions, like this one, through external time-dependent fields. [ABSTRACT FROM AUTHOR]

Suspensions of chemically powered self-propelled colloidal particles are examples of active matter systems with interesting properties. While simple spherical Janus particles are often studied, it is known that geometry is important and recent experiments have shown that chemically active torus-shaped colloids behave differently from spherical colloids. In this paper, coarse-grained microscopic simulations of the dynamics of self-diffusiophoretic torus colloids are carried out in bulk solution in order to study how torus geometric factors influence their active motion. The concentration and velocity fields are key ingredients in self-diffusiophoretic propulsion, and the forms that these fields take in the colloid vicinity are shown to be strong functions of torus geometric parameters such as the torus hole size and thickness of the torus tube. This work utilizes a method where self-diffusiophoretic torus colloids with various geometric and dynamical characteristics can be built and studied in fluid media that include chemical reactions and fluid flows. The model can be used to investigate the collective properties of these colloids and their dynamics in confined systems, topics that are of general importance for applications that use colloidal motors with complex geometries. [ABSTRACT FROM AUTHOR]

We reexamine nonequilibrium thermodynamics of multi-component fluids that undergo chemical reactions and reveal howto describe it in the context ofGENERIC(general equation for the nonequilibrium reversible-irreversible coupling) framework. In the former part of this paper, we study monomer solutions. The independent variables are chosen so that the symmetry in the thermodynamic description of the mixed solution is kept, while avoiding the redundancy in the independent variables that describe the system. In the latter part of this paper, we apply this approach to polymer solutions. One of the species of the solution is the unreactive polymer chain represented by the bead-spring model. The polymer solution is neither dilute nor ideal. We construct the solution entropy so that the contributions from mixing and chain conformation are fully separated. The pressure tensor derived from such entropy with the help of the degeneracy requirement is slightly different from that derived previously for a dilute polymer solution. We discuss how the difference occurs. [ABSTRACT FROM AUTHOR]

The collision between hydrogen and ammonia is a benchmark system to study chemical elementary reactions with five atoms. In this work, we present a description of the system based on mixed Jacobi and Radau coordinates combined with the time-dependent wave packet method to study the H + NH3 reaction. The Radau coordinates are used to describe the reactive moiety NH2. A salient feature of this approach is that the present coordinates have a great advantage that a very small number of basis set functions can be used to describe the NH2 group. Potential-optimized discrete variable representation basis is applied for the vibrational coordinates of the reagent NH3. The reaction probabilities for several initial vibrational states are presented in this paper. The role of the different vibrational excitations on the reactivity is thoroughly described. [ABSTRACT FROM AUTHOR]

This work considers the method of uniformization for continuous-time Markov chains in the context of chemical reaction networks. Previous work in the literature has shown that uniformization can be beneficial in the context of time-inhomogeneous models, such as chemical reaction networks incorporating extrinsic noise. This paper lays focus on the understanding of uniformization from the viewpoint of sample paths of chemical reaction networks. In particular, an efficient pathwise stochastic simulation algorithm for time-homogeneous models is presented which is complexity-wise equal to Gillespie's direct method. This new approach therefore enlarges the class of problems for which the uniformization approach forms a computationally attractive choice. Furthermore, as a new application of the uniformization method, we provide a novel variance reduction method for (raw) moment estimators of chemical reaction networks based upon the combination of stratification and uniformization. [ABSTRACT FROM AUTHOR]

In recent years, moment-closure approximations (MAs) of the chemical master equation have become a popular method for the study of stochastic effects in chemical reaction systems. Several different MA methods have been proposed and applied in the literature, but it remains unclear how they perform with respect to each other. In this paper, we study the normal, Poisson, log-normal, and central-moment-neglect MAs by applying them to understand the stochastic properties of chemical systems whose deterministic rate equations show the properties of bistability, ultrasensitivity, and oscillatory behaviour. Our results suggest that the normal MA is favourable over the other studied MAs. In particular, we found that (i) the size of the region of parameter space where a closure gives physically meaningful results, e.g., positive mean and variance, is considerably larger for the normal closure than for the other three closures, (ii) the accuracy of the predictions of the four closures (relative to simulations using the stochastic simulation algorithm) is comparable in those regions of parameter space where all closures give physically meaningful results, and (iii) the Poisson and log-normal MAs are not uniquely defined for systems involving conservation laws in molecule numbers. We also describe the new software package MOCA which enables the automated numerical analysis of various MA methods in a graphical user interface and which was used to perform the comparative analysis presented in this paper. MOCA allows the user to develop novel closure methods and can treat polynomial, non-polynomial, as well as time-dependent propensity functions, thus being applicable to virtually any chemical reaction system. [ABSTRACT FROM AUTHOR]

The Langevin capture model is often used to describe barrierless reactive collisions. At very low temperatures, quantum effects may alter this simple capture image and dramatically affect the reaction probability. In this paper, we use the trajectory-ensemble reformulation of quantum mechanics, as recently proposed by one of the authors (Poirier) to compute adiabatic-channel capture probabilities and cross-sections for the highly exothermic reaction Li + CaH( v = 0, j = 0) → LiH + Ca, at low and ultra-low temperatures. Each captured quantum trajectory takes full account of tunneling and quantum reflection along the radial collision coordinate. Our approach is found to be very fast and accurate, down to extremely low temperatures. Moreover, it provides an intuitive and practical procedure for determining the capture distance (i.e., where the capture probability is evaluated), which would otherwise be arbitrary. [ABSTRACT FROM AUTHOR]

The formation of atmospheric aerosol particles from condensable gases is a dominant source of particulate matter in the boundary layer, but the mechanism is still ambiguous. During the clustering process, precursors with different reactivities can induce various chemical reactions in addition to the formation of hydrogen bonds. However, the clustering mechanism involving chemical reactions is rarely considered in most of the nucleation process models. Oxocarboxylic acids are common compositions of secondary organic aerosol, but the role of oxocarboxylic acids in secondary organic aerosol formation is still not fully understood. In this paper, glyoxylic acid, the simplest and the most abundant atmospheric oxocarboxylic acid, has been selected as a representative example of oxocarboxylic acids in order to study the clustering mechanism involving hydration reactions using density functional theory combined with the Atmospheric Clusters Dynamic Code. The hydration reaction of glyoxylic acid can occur either in the gas phase or during the clustering process. Under atmospheric conditions, the total conversion ratio of glyoxylic acid to its hydration reaction product (2,2-dihydroxyacetic acid) in both gas phase and clusters can be up to 85%, and the product can further participate in the clustering process. The differences in cluster structures and properties induced by the hydration reaction lead to significant differences in cluster formation rates and pathways at relatively low temperatures. [ABSTRACT FROM AUTHOR]

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes. [ABSTRACT FROM AUTHOR]

The chemical master equation (CME) is frequently used in systems biology to quantify the effects of stochastic fluctuations that arise due to biomolecular species with low copy numbers. The CME is a system of ordinary differential equations that describes the evolution of probability density for each population vector in the state-space of the stochastic reaction dynamics. For many examples of interest, this state-space is infinite, making it difficult to obtain exact solutions of the CME. To deal with this problem, the Finite State Projection (FSP) algorithm was developed by Munsky and Khammash [J. Chem. Phys. 124(4), 044104 (2006)], to provide approximate solutions to the CME by truncating the state-space. The FSP works well for finite time-periods but it cannot be used for estimating the stationary solutions of CMEs, which are often of interest in systems biology. The aim of this paper is to develop a version of FSP which we refer to as the stationary FSP (sFSP) that allows one to obtain accurate approximations of the stationary solutions of a CME by solving a finite linear-algebraic system that yields the stationary distribution of a continuous-time Markov chain over the truncated state-space.We derive bounds for the approximation error incurred by sFSP and we establish that under certain stability conditions, these errors can be made arbitrarily small by appropriately expanding the truncated state-space. We provide several examples to illustrate our sFSP method and demonstrate its efficiency in estimating the stationary distributions. In particular, we show that using a quantized tensor-train implementation of our sFSP method, problems admitting more than 100 x 106 states can be efficiently solved. [ABSTRACT FROM AUTHOR]

Several recent implementations of algorithms for sampling reaction pathways employ a strategy for placing interfaces or milestones across the reaction coordinate manifold. Interfaces can be introduced such that the full feature space describing the dynamics of a macromolecule is divided into Voronoi (or other) cells, and the global kinetics of the molecular motions can be calculated from the set of fluxes through the interfaces between the cells. Although some methods of this type are exact for an arbitrary set of cells, in practice, the calculations will converge fastest when the interfaces are placed in regions where they can best capture transitions between configurations corresponding to local minima. The aim of this paper is to introduce a fully automated machine-learning algorithm for defining a set of cells for use in kinetic sampling methodologies based on subdividing the dynamical feature space; the algorithm requires no intuition about the system or input from the user and scales to high-dimensional systems. [ABSTRACT FROM AUTHOR]

Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = sY between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats sY. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction. [ABSTRACT FROM AUTHOR]

Alkyl combustion models depend on kinetic parameters derived from reliable experimental or theoretical energetics that are often unavailable for larger species. To this end, we have performed a comprehensive investigation of the tert-butyl radical (R· in this paper) autoignition pathways. CCSD(T)/ANO0 geometries and harmonic vibrational frequencies were obtained for key stationary points for the R· + O2 and QOOH + O2 mechanisms. Relative energies were computed to chemical accuracy (±1 kcal mol-1) via extrapolation of RCCSD(T) energies to the complete basis-set limit, or usage of RCCSD(T)-F12 methods. At 0 K, the minimum energy R· +O2 pathway involves direct elimination of HO. 2 (30.3 kcal mol-1 barrier) from the tert-butyl peroxy radical (ROO·) to give isobutene. This pathway lies well below the competing QOOH-forming intramolecular hydrogen abstraction pathway (36.2 kcal mol-1 barrier) and ROO· dissociation (35.9 kcal mol-1 barrier). The most favorable decomposition channel for QOOH radicals leads to isobutene oxide (12.0 kcal mol-1 barrier) over isobutene (18.6 kcal mol-1 barrier). For the QOOH + O2 pathways, we studied the transition states and initial products along three pathways: (1) α-hydrogen abstraction (42.0 kcal mol-1 barrier), (2) γ-hydrogen abstraction (27.0 kcal mol-1 barrier), and (3) hydrogen transfer to the peroxy moiety (24.4 kcal mol-1 barrier). The barrier is an extensive modification to the previous 18.7 kcal mol-1 value andwarrants further study. However, it is still likely that the lowest energy QOOH+O2 pathway corresponds to pathway (3).We found significant spin contamination and/or multireference character in multiple stationary points, especially for transition states stemming from QOOH. Lastly, we provide evidence for an ... surface crossing at a Cs-symmetric, intramolecular hydrogen abstraction structure. [ABSTRACT FROM AUTHOR]

The cage effect is generally invoked when discussing the delay in the decay of time correlation functions of dense fluids. In an attempt to examine the role of caging more closely, we consider the spread of the displacement distributions of Brownian particles. These distributions are necessarily biased by the presence of neighbouring particles. Accommodation of this bias by those neighbours conserves the displacement distribution locally and presents a collective mechanism for exploring configuration space that is more efficient than the intrinsic Brownian motion. Caging of some particles incurs, through the impost of global conservation of the displacement distribution, a delayed, non-local collective process. This non-locality compromises the efficiency with which configuration space is explored. Both collective mechanisms incur delay or stretching of time correlation functions, in particular the particle number and flux densities. This paper identifies and distinguishes these mechanisms in existing data from experiments and computer simulations on systems of particles with hard sphere interactions. [ABSTRACT FROM AUTHOR]

Photoelectron Photoion Coincidence (PEPICO) spectroscopy holds the promise of a universal, isomer-selective, and sensitive analytical technique for time-resolved quantitative analysis of bimolecular chemical reactions. Unfortunately, its low dynamic range of ~103 has largely precluded its use for this purpose, where a dynamic range of at least 105 is generally required. This limitation is due to the false coincidence background common to all coincidence experiments, especially at high count rates. Electron/ion pairs emanating from separate ionization events but arriving within the ion time of flight (TOF) range of interest constitute the false coincidence background. Although this background has uniform intensity at every m/z value, the Poisson scatter in the false coincidence background obscures small signals. In this paper, temporal ion deflection coupled with a position-sensitive ion detector enables suppression of the false coincidence background, increasing the dynamic range in the PEPICO TOF mass spectrum by 2-3 orders of magnitude. The ions experience a time-dependent electric deflection field at a well-defined fraction of their time of flight. This deflection defines an m/zand ionization-time dependent ion impact position for true coincidences, whereas false coincidences appear randomly outside this region and can be efficiently suppressed. When cold argon clusters are ionized, false coincidence suppression allows us to observe species up to Ar9+, whereas Ar9+ is the largest observable cluster under traditional operation. This advance provides mass-selected photoelectron spectra for fast, high sensitivity quantitative analysis of reacting systems. [ABSTRACT FROM AUTHOR]

Accurate methods for excited, ionized, and electron-attached states are critical to the study of many chemical species such as reactive intermediates, radicals, and ionized systems. The equation-of-motion coupled cluster singles, doubles, and triples (EOM-CCSDT) family of methods is very accurate (roughly similar in accuracy as for CCSDT calculations of the ground state), but the computational cost scales iteratively as the eighth power of the system size. Many approximations already exist, although most either correct only the excited state or require an iterative O(n7) procedure which can also be prohibitively expensive. In this paper, new methods, termed EOM-CCSD(T)(a) and EOM-CCSD(T)(a)*, are proposed which correct both the ground and excited states based on a shared effective Hamiltonian, and the latter of which includes only non-iterative corrections to both the CCSD and EOM-CCSD energies. These methods are found to significantly improve the description of excited and ionized potential energy surfaces, equilibrium geometries, and harmonic frequencies; the accuracy is very close to that of full EOM-CCSDT. [ABSTRACT FROM AUTHOR]

In this paper, we describe our efforts to apply rate theories in studies of solvent exchange around Li+ and the kinetics of ion pairings in lithium-ion batteries (LIBs). We report one of the first computer simulations of the exchange dynamics around solvated Li+ in acetonitrile (ACN), which is a common solvent used in LIBs. We also provide details of the ion-pairing kinetics of Li+-[BF4] and Li+-[PF6] in ACN. Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ACN exchange process between the first and second solvation shells around Li+. We calculate exchange rates using transition state theory and weighted them with the transmission coefficients determined by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found the relaxation times changed from 180 ps to 4600 ps and from 30 ps to 280 ps for Li+-[BF4] and Li+-[PF6] ion pairs, respectively. These results confirm that the solvent response to the kinetics of ion pairing is significant. Our results also show that, in addition to affecting the free energy of solvation into ACN, the anion type also should significantly influence the kinetics of ion pairing. These results will increase our understanding of the thermodynamic and kinetic properties of LIB systems. [ABSTRACT FROM AUTHOR]

Instanton rate theory is used to study tunneling events in a wide range of systems including lowtemperature chemical reactions. Despite many successful applications, the method has never been obtained from first principles, relying instead on the "Im F" premise. In this paper, the same expression for the rate of barrier penetration at finite temperature is rederived from quantum scattering theory [W. H. Miller, S. D. Schwartz, and J.W. Tromp, J. Chem. Phys. 79, 4889 (1983)] using a semiclassical Green's function formalism. This justifies the instanton approach and provides a route to deriving the rate of other processes. [ABSTRACT FROM AUTHOR]

We take the golden-rule instanton method derived in the previous paper [J. O. Richardson, R. Bauer, and M. Thoss, J. Chem. Phys. 143, 134115 (2015)] and reformulate it using a ring-polymer instanton approach. This gives equations which can be used to compute the rates of electron-transfer reactions in the nonadiabatic (golden-rule) limit numerically within a semiclassical approximation. The multidimensional ring-polymer instanton trajectories are obtained efficiently by minimization of the action. In this form, comparison with Wolynes' quantum instanton method [P. G. Wolynes, J. Chem. Phys. 87, 6559 (1987)] is possible and we show that our semiclassical approach is the steepest-descent limit of this method. We discuss advantages and disadvantages of both methods and give examples of where the new approach is more accurate. [ABSTRACT FROM AUTHOR]

Stochastic simulation for in silico studies of large biochemical networks requires a great amount of computational time. We recently proposed a new exact simulation algorithm, called the rejectionbased stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)], to improve simulation performance by postponing and collapsing as much as possible the propensity updates. In this paper, we analyze the performance of this algorithm in detail, and improve it for simulating large-scale biochemical reaction networks. We also present a new algorithm, called simultaneous RSSA (SRSSA), which generates many independent trajectories simultaneously for the analysis of the biochemical behavior. SRSSA improves simulation performance by utilizing a single data structure across simulations to select reaction firings and forming trajectories. The memory requirement for building and storing the data structure is thus independent of the number of trajectories. The updating of the data structure when needed is performed collectively in a single operation across the simulations. The trajectories generated by SRSSA are exact and independent of each other by exploiting the rejection-based mechanism. We test our new improvement on real biological systems with a wide range of reaction networks to demonstrate its applicability and efficiency. [ABSTRACT FROM AUTHOR]

Fluoroacetate is a toxic compound whose environmental accumulation may represent an important contamination problem, its elimination is therefore a challenging issue. Fluoroacetate dehalogenase catalyzes its degradation through a two step process initiated by an SN2 reaction in which the aspartate residue performs a nucleophilic attack on the carbon bonded to the fluorine; the second step is hydrolysis that releases the product as glycolate. In this paper, we present a study based on density functional theory calculations of the SN2 initiation reaction modeled through the interaction between the substrate and the propionate anion as the nucleophile. Results are analyzed within the framework of the reaction force and using the reaction electronic flux to identify and characterize the electronic activity that drives the reaction. Our results reveal that the selective protonation of the substrate catalyzes the reaction by decreasing the resistance of the structural and electronic reorganization needed to reach the transition state. Finally, the reaction energy is modulated by the degree of stabilization of the fluoride anion formed after the SN2 reaction. In this way, a site-induced partial protonation acts as a chemical switch in a key process that determines the output of the reaction. [ABSTRACT FROM AUTHOR]

Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give rise to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media. [ABSTRACT FROM AUTHOR]

Stochastic models are often used to help understand the behavior of intracellular biochemical processes. The most common such models are continuous time Markov chains (CTMCs). Parametric sensitivities, which are derivatives of expectations of model output quantities with respect to model parameters, are useful in this setting for a variety of applications. In this paper, we introduce a class of hybrid pathwise differentiation methods for the numerical estimation of parametric sensitivities. The new hybrid methods combine elements from the three main classes of procedures for sensitivity estimation and have a number of desirable qualities. First, the new methods are unbiased for a broad class of problems. Second, the methods are applicable to nearly any physically relevant biochemical CTMC model. Third, and as we demonstrate on several numerical examples, the new methods are quite efficient, particularly if one wishes to estimate the full gradient of parametric sensitivities. The methods are rather intuitive and utilize the multilevel Monte Carlo philosophy of splitting an expectation into separate parts and handling each in an efficient manner. [ABSTRACT FROM AUTHOR]

In this paper we report on the neutral-neutral reaction of the C3 carbon cluster with H2S in solid inert argon at 12 K, conditions that mimic, in part, the surfaces of interstellar grains. In the first step of the reaction, a C3·H2S complex is formed via an almost barrierless entrance addition mechanism. This complex, stabilized by an estimated 7.45 kJ/mol (CCSD(T)/aug-cc-pVTZ//B3LYP/6-311++G(d,p) level), is formed by the interaction of a terminal carbon of C3 with a hydrogen in H2S. This con-covalent complex displays a band at 2044.1 cm-1 observed via Fourier transform infrared absorption spectroscopy. With the help of the MP2/aug-ccpVDZ level method, this band is assigned to the CC asymmetric vibration mode. When the complex is exposed to UV-visible photons (hν < 5.5 eV) the tricarbon sulfur C3S molecule is identified, based on the appearance of a characteristic CC stretching band at 2047.5 cm-1. Calculated ground-state potential energy surfaces also confirm the concomitant formation of molecular H2. This facile reaction pathway involves an attainable transition state of 174.4 kJ/mol. Conversely, competing lower-energy reaction pathways that would lead to the generation of H2C3S (propadienethione), or C2H2 (acetylene) and CS, involve much more complex, multi-stage pathways, and are not observed experimentally. [ABSTRACT FROM AUTHOR]

In this paper, we study a general theoretical framework which allows us to approximate the real space Ewald sum by means of effective force shifted screened potentials, together with a self term. Using this strategy it is possible to generalize the reaction field method, as a means to approximate the real space Ewald sum. We show that this method exhibits faster convergence of the Coulomb energy than several schemes proposed recently in the literature while enjoying a much more sound and clear electrostatic significance. In terms of the damping parameter of the screened potential, we are able to identify two clearly distinct regimes of convergence. First, a reaction field regime corresponding to the limit of small screening, where effective pair potentials converge faster than the Ewald sum. Second, an Ewald regime, where the plain real space Ewald sum converges faster. Tuning the screening parameter for optimal convergence occurs essentially at the crossover. The implication is that effective pair potentials are an alternative to the Ewald sum only in those cases where optimization of the convergence error is not possible. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Biochemical reaction networks often involve reactions that take place on different time scales, giving rise to “slow” and “fast” system variables. This property is widely used in the analysis of systems to obtain dynamical models with reduced dimensions. In this paper, we consider stochastic dynamics of biochemical reaction networks modeled using the Linear Noise Approximation (LNA). Under time-scale separation conditions, we obtain a reduced-order LNA that approximates both the slow and fast variables in the system. We mathematically prove that the first and second moments of this reduced-order model converge to those of the full system as the time-scale separation becomes large. These mathematical results, in particular, provide a rigorous justification to the accuracy of LNA models derived using the stochastic total quasi-steady state approximation (tQSSA). Since, in contrast to the stochastic tQSSA, our reduced-order model also provides approximations for the fast variable stochastic properties, we term our method the “stochastic tQSSA+”. Finally, we demonstrate the application of our approach on two biochemical network motifs found in gene-regulatory and signal transduction networks. [ABSTRACT FROM AUTHOR]