Ring polymer molecular dynamics (RPMD) is an accurate method for calculating thermal chemical reaction rates. It has recently been discovered that low-temperature calculations are strongly affected by the simulation parameters. Here, for the thermally activated reaction DH + H -> D + H2, we calculate the RPMD rate constants at T = 50, 100, and 300 K and demonstrate that for T >= 100 K the standard input parameters yield accurate results, but at low temperatures (e.g., 50 K) one must increase the asymptotic distance and force constant, and decrease the umbrella integration step.
This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical applications to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rate coefficients in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a…
The ring-polymer molecular dynamics (RPMD) was used to calculate the thermal rate coefficients of the two-channel roaming reaction H + MgH. Both reaction channels, tight and roaming, are explicitly considered. This is a pioneering attempt of exerting RPMD method to multi-channel reactions. With the help of a newly developed optimization-interpolation protocol for preparing the initial structures and adaptive protocol for choosing the force constants, we have successfully obtained the thermal rate coefficients. The results are consistent with those from other theoretical methods, such as variat…
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to rigorous Quantum Transition-State Theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H+H$_2$, D+MuH and F+H$_2$, and the prototypical polyatomic reaction H+CH$_4$. Above the crossover temperature, the TRPMD rat…
Accurately modeling gas-surface collision dynamics presents a great challenge for theory, especially in the low energy (or temperature) regime where quantum effects are important. Here, a path integral based non-equilibrium ring polymer molecular dynamics (NE-RPMD) approach is adapted to calculate dissociative initial sticking probabilities (S0) of H2 on Cu(111) and D2O on Ni(111), revealing distinct quantum nature in the two benchmark surface reactions. NE-RPMD successfully captures quantum tunneling in H2 dissociation at very low energies, where the quasi-classical trajectory (QCT) method su…
Artificial Thermalization in Ring-Polymer Molecular Dynamics: The Breakdown of RPMD for Gas-Phase Reactions with Pre-Reactive Complexes and How to Fix It
By employing an analytically solvable model including the Duschinsky rotation effect, we investigated the applicability of the commonly used Born-Oppenheimer (BO) approximation for separating the proton and proton donor-acceptor motions in theories of proton coupled electron transfer (PCET) reactions. Comparison with theories based on the BO approximation shows that, the BO approximation for the proton coordinate is generally valid while some further approximations may become inaccurate in certain range of parameters. We have also investigated the effect of vibrationally coherent tunneling in …
The accurate and efficient calculation of the rate coefficients of chemical reactions is a key issue in the research of chemical dynamics. In this work, by applying the dimension-free ultra-stable Cayley propagator, the thermal rate coefficients of a prototypic high dimensional chemical reaction OH + CH4 -> H2O + CH3 in the temperature range of 200 K to 1500 K are investigated with ring polymer molecular dynamics (RPMD), on a highly accurate full-dimensional potential energy surface. Kinetic isotope effects (KIEs) for three isotopologues of the title reaction are also studied. The results demo…
Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in nucleic acids or polypeptides, is complicated by the structural dynamics of their chains. Although both intramolecular reactions, such as cyclization, and intermolecular reactions have been studied extensively, both experimentally and theoretically, there is to date no exact explicit analytical treatment of transport-limited polymer reaction kinetics, even in the case of the simplest (Rouse) model of monomers connected by linear springs. We introduce a new analytical approach to calculate the mean reac…
Liquid states theories have emerged as a numerically efficient alternative to costly molecular dynamics simulations of electron transfer reactions in solution. In a recent paper [Chem. Sci., 2019, 10, 2130], we introduced the framework to compute energy gap, free energy profile and reorganization free energy using molecular density functional theory. However, this technique, as other molecular liquid state theories, overestimates the bulk pressure of the fluids. Because of the too high pressure, the predicted free energy is dramatically exaggerated. Several attempts were made to fix this issue…
Thermal rate coefficients for the astrochemical reaction C + CH$^+$ $\to$ C$_2^+$ + H were computed in the temperature range 20-300 K by using novel rate theory based on ring polymer molecular dynamics (RPMD) on a recently published bond-order based potential energy surface and compared with previous Langevin capture model (LCM) and quasi-classical trajectory (QCT) calculations. Results show that there is a significant discrepancy between the RPMD rate coefficients and the previous theoretical results which can lead to overestimation of the rate coefficients for the title reaction by several o…
The reaction between D$^+$ and H$_2$ plays an important role in astrochemistry at low temperatures and also serves as a prototype for simple ion-molecule reaction. Its ground $\tilde{X}~^1A^{\prime}$ state has a very small thermodynamic barrier (up to 1.8$\times 10^{-2}$ eV) and the reaction proceeds through the formation of an intermediate complex lying within the potential well of depth of at least 0.2 eV thus representing a challenge for dynamical studies. In the present work, we analyze the title reaction within the temperature range of 20 $-$ 100 K by means of ring polymer molecular dynam…
Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying full-dimensional potential energy surfaces (PESs) and the corresponding energy gradients are required. Recently, we have proposed a fully automated procedure based on combining the original RPMDrate code with active learning for PES on-the-fly using moment tensor potential and successfully applied it to two representative thermally activated chemical reactions [I…
A general technique to investigate charge storage characteristics of conducting polymer films has been developed. A redox reaction is conducted on a polymer film on a rotating disk electrode under potentiostatic condition so that the rate of charging of the film equals the rate of removal of the charge by the reaction. In an experiment on polyaniline film deposited on platinum substrate, using Fe2+/Fe3+ in HCl as the redox system, the voltammogram shows five distinct linear segments (bands) with discontinuity in the slope at specific transition potentials. These bands are the same as those ind…
Mean-Field Ring Polymer Molecular Dynamics (MF-RPMD) is a powerful, efficient, and accurate method for approximate quantum dynamic simulations of multi-level system dynamics. Initial efforts to compute nonadiabatic reaction rates using MF-RPMD were not successful; recent work showed that this can be remedied by including a simple, if adhoc, correction term that accounts for the formation of `kinked' or mixed electronic state ring polymer configurations. Here, we build on this idea, introducing a electronic state population based reaction coordinate and novel skew dividing surface that constrai…
Metallic nanoparticles embedded in stimuli-responsive polymers can be regarded as nanoreactors since their catalytic activity can be changed within wide limits: the physicochemical properties of the polymer network can be tuned and switched by external parameters, e.g. temperature or pH, and thus allows a selective control of reactant mobility and concentration close to the reaction site. Based on a combination of Debye's model of diffusion through an energy landscape and a two-state model for the polymer, here we develop an analytical expression for the observed reaction rate constant $k_{\rm…
We present two multistate ring polymer instanton (RPI) formulations, both obtained from an exact path integral representation of the quantum canonical partition function for multistate systems. The two RPIs differ in their treatment of the electronic degrees of freedom; whereas the Mean-Field (MF)-RPI averages over the electronic state contributions, the Mapping Variable (MV)-RPI employs explicit continuous Cartesian variables to represent the electronic states. We compute both RPIs for a series of model two-state systems coupled to a single nuclear mode with electronic coupling values chosen …
We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral representation in the set of nuclear coordinates and electronic states to provide continuous equations of motion that describe the quantized, electronically non-adiabatic dynamics of the system. KC-RPMD preserves the favorable properties of the usual RPMD formulation in the position representation, including rigorous detailed balance, time-reversal symmetry, and invaria…
A mathematical model to describe the emulsion polymerization kinetics of co- and ter-polymerizations is developed. The model is based on the classical Smith-Ewart (SE) equations, within the pseudo-homopolymerization approach, with state-of-the-art models for radical entry and desorption. For co- and ter-polymerizations there are unknown parameters in the model which are related to monomer-specific gel-effect coefficients, that are needed to compute the bimolecular termination reaction rates. The unknown parameters are determined through extensive calibration of the model on literature data for…
We devise a novel technique to control the shape of polymer molecular weight distributions (MWDs) in atom transfer radical polymerization (ATRP). This technique makes use of recent advances in both simulation-based, model-free reinforcement learning (RL) and the numerical simulation of ATRP. A simulation of ATRP is built that allows an RL controller to add chemical reagents throughout the course of the reaction. The RL controller incorporates fully-connected and convolutional neural network architectures and bases its decision upon the current status of the ATRP reaction. The initial, untraine…
We investigate theoretically a diffusion-limited reaction between a reactant attached to a Rouse polymer and an external fixed reactive site in confinement. The present work completes and goes beyond a previous study [T. Guérin, O. Bénichou and R. Voituriez, Nat. Chem., 4, 268 (2012)] that showed that the distribution of the polymer conformations at the very instant of reaction plays a key role in the reaction kinetics, and that its determination enables the inclusion of non-Markovian effects in the theory. Here, we describe in detail this non-Markovian theory and we compare it with numerical …
A fundamental paradigm in polymer physics is that macromolecular conformations in equilibrium can be described by universal scaling laws, being key for structure, dynamics, and function of soft (biological) matter and in the materials sciences. Here, we reveal that during diffusion-influenced, nonequilibrium chain-growth polymerization, scaling laws change qualitatively, in particular, the growing polymers exhibit a surprising self-avoiding walk (SAW) behavior in poor and theta-solvents. Our analysis, based on monomer-resolved reaction-diffusion computer simulations, demonstrates that this phe…
Redox flow batteries (RFBs) are potential solutions for grid-scale energy storage, and deeper understanding of the effect of flow rate on RFB performance is needed to develop efficient, low-cost designs. In this study we highlight the importance of modeling tanks, which can limit the charge/discharge capacity of redox-active polymer (RAP) based RFBs. The losses due to tank mixing dominate over the polarization-induced capacity losses that arise due to resistive processes in the reactor. A porous electrode model is used to separate these effects by predicting the time variation of active specie…
We address the calculation of microcanonical reaction rates for processes involving significant nuclear quantum effects using ring-polymer molecular dynamics (RPMD), both with and without electronically non-adiabatic transitions. After illustrating the shortcomings of the naive free-particle direct-shooting method, in which the temperature of the internal ring-polymer modes is set to the translational energy scale, we investigate alternative strategies based on the expression for the microcanonical rate in terms of the inverse Laplace transform of the thermal reaction rate. It is shown that si…
Ring-polymer instanton theory has been developed to simulate the quantum dynamics of molecular systems at low temperatures. Chemical reaction rates can be obtained by locating the dominant tunneling pathway and analyzing fluctuations around it. In the standard method, calculating the fluctuation terms involves the diagonalization of a large matrix, which can be unfeasible for large systems with a high number of ring-polymer beads. Here we present a method for computing the instanton fluctuations with a large reduction in computational scaling. This method is applied to three reactions describe…
We investigate theoretically the physics of diffusion-limited intramolecular polymer reactions. The present work completes and goes beyond a previous study [Nat. Chem. 4, 268 (2012)] that showed that the distribution of the polymer conformations at the very instant of reaction plays a key role in the cyclization kinetics, and takes explicitly into account the non-Markovian nature of the reactant motion. Here, we present in detail this non-Markovian theory, and compare it explicitly with existing Markovian theories and with numerical stochastic simulations. A large focus is made on the descript…
We propose a methodology for fully automated calculation of thermal rate coefficients of gas phase chemical reactions, which is based on combining the ring polymer molecular dynamics (RPMD) with the machine-learning interatomic potentials actively learning on-the-fly. Based on the original computational procedure implemented in the RPMDrate code, our methodology gradually and automatically constructs the potential energy surfaces (PESs) from scratch with the data set points being selected and accumulated during the RPMDrate simulation. Such an approach ensures that our final machine-learning m…
We take the golden-rule instanton method derived in the previous paper [arXiv:1509.04919] and reformulate it using a ring-polymer 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 approac…
We present a quantum mechanical / molecular mechanics (QM/MM) to tackle chemical reactions with substantial molecular reorganization. For this, molecular dynamics simulations with smoothly switched interaction models are used to suggest suitable product states, whilst a Monte Carlo algorithm is employed to assess the reaction likeliness subject to energetic feasibility. As a demonstrator, we study the cross-linking of bisphenol F diglycidyl ether (BFDGE) and 4,6-diethyl-2-methylbenzene-1,3-diamine (DETDA). The modeling of epoxy curing was supplemented by Differential Scanning Calorimetry (DSC)…
The use of ring polymer molecular dynamics (RPMD) for the direct simulation of electron transfer (ET) reaction dynamics is analyzed in the context of Marcus theory, semiclassical instanton theory, and exact quantum dynamics approaches. For both fully atomistic and system-bath representations of condensed-phase ET, we demonstrate that RPMD accurately predicts both ET reaction rates and mechanisms throughout the normal and activationless regimes of the thermodynamic driving force. Analysis of the ensemble of reactive RPMD trajectories reveals the solvent reorganization mechanism for ET that is a…
In Part I [J. Chem. Phys. 138, 084108 (2013)] we derived a quantum transition-state theory by taking the t->0+ (short-time) limit of a new form of quantum flux-side time-correlation function containing a ring-polymer dividing surface. This t->0+ limit appears to be unique in giving positive-definite Boltzmann statistics, and is identical to ring-polymer molecular dynamics (RPMD) TST. Here, we show that quantum TST (i.e. RPMD-TST) is exact if there is no recrossing (by the real-time quantum dynamics) of the ring-polymer dividing surface, nor of any surface orthogonal to it in the space describi…
The gel point of end-linked model networks is determined from computer simulation data. It is shown that the difference between the true gel point conversion, $p_{\text{c}}$, and the ideal mean field prediction for the gel point, $p_{\text{c,id}}$, is a function of the average number of cross-links per pervaded volume of a network strand, $P$, and thus, contains an explicit dependence on junction functionality $f$. On the contrary, the amount of intra-molecular reactions at the gel point is independent of $f$ in a first approximation and exhibits a different power law dependence on the overlap…
We present a theoretical study of degradation mechanisms for photoinduced oxidation in organic polymers in the condensed phase, using poly(3-hexylthiophene)(P3HT) as an example. Applying density functional theory with a hybrid density functional and periodic boundary conditions that account for steric effects and permit the modeling of interchain chemical reactions, we investigate reaction pathways that may lead to the oxidation of thiophene backbone as a critical step toward disrupting the polymer conjugation. We calculate energy barriers for reactions of the P3HT backbone with oxidizing agen…
Understanding of degradation mechanisms in polymer:fullerene bulk-heterojunctions on the microscopic level aimed at improving their intrinsic stability is crucial for the breakthrough of organic photovoltaics. These materials are vulnerable to exposure to light and/or oxygen, hence they involve electronic excitations. To unambiguously probe the excited states of various multiplicities and their reactions with oxygen, we applied combined magneto-optical methods based on multifrequency (9 and 275 GHz) electron paramagnetic resonance (EPR), photoluminescence (PL), and PL-detected magnetic resonan…
Assemblies of nanocrystals with complex morphologies have solicited great scientific interest. Controlling the formation of these self-assembled structures has proved difficult. Here we present a novel transformation reaction for transforming a single crystal of minerals into assemblies of nanocrystals of substances with lower solubility without changing the overall morphology. This study focusses on the transformation of rhombohedral calcite crystals to assemblies of hydroxyapatite nanocrystals to control the transformation process. This yielded particle assemblies of HAP nanoparticles grossl…
The yardstick of new first-principles approaches to key points on reaction paths at metal surfaces is chemical accuracy compared to reliable experiment. By this we mean that such values as the activation barrier are required to within 1 kcal/mol. Quantum Monte Carlo (QMC) is a promising (albeit lengthy) first-principles method for this and we are now beyond the dawn of QMC benchmarks for these systems, since hydrogen dissociation on Cu(111) has been studied with quite adequate accuracy in two improving QMC studies \cite{hog0, kdd2}. Pt and Cu require the use of pseudo-potentials in these calcu…
Silver nanocrystals have been prepared by reacting silver nitrate with ascorbic acid in aqueous solution containing a low concentration of a commercial polynaphtalene sulphonate polymer (Daxad 19). Various crystalline morphologies have been obtained simply by tuning the reaction temperature. We have investigated the nanoparticle formation mechanism at three different temperatures by in situ and time resolved Small Angle X ray Scattering measurements. By modeling the scattering intensity with interacting spherical particles in a fractal-like polymer-Ag matrix, we found signatures of nucleation,…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory focuses on two competing effects: polymer shape fluctuations, which speed up association, and the hydrodynamic coupling between the diffusing particle and the chain, which slows down association. Polymer bending fluctuations are described using a mean field dynamical theory, while the hydrodynamic coupling between polymer and particle is incorporated through a si…
