Organic reactions are usually assigned to classes containing reactions with similar reagents and mechanisms. Reaction classes facilitate the communication of complex concepts and efficient navigation through chemical reaction space. However, the classification process is a tedious task. It requires the identification of the corresponding reaction class template via annotation of the number of molecules in the reactions, the reaction center, and the distinction between reactants and reagents. This work shows that transformer-based models can infer reaction classes from non-annotated, simple text-based representations of chemical reactions. Our best model reaches a classification accuracy of 98.2%. We also show that the learned representations can be used as reaction fingerprints that capture fine-grained differences between reaction classes better than traditional reaction fingerprints. The insights into chemical reaction space enabled by our learned fingerprints are illustrated by an interactive reaction atlas providing visual clustering and similarity searching.
In this letter we analyse an amazing variational approach to chemical reactions. Our results clearly show that the variational expressions are unsuitable for the analysis of empirical data obtained from chemical reactions.
School of Information and Computer Sciences, University of California, Irvine（加州大学尔湾分校信息与计算机科学学院）
It is fundamental for science and technology to be able to predict chemical reactions and their properties. To achieve such skills, it is important to develop good representations of chemical reactions, or good deep learning architectures that can learn such representations automatically from the data. There is currently no universal and widely adopted method for robustly representing chemical reactions. Most existing methods suffer from one or more drawbacks, such as: (1) lacking universality; (2) lacking robustness; (3) lacking interpretability; or (4) requiring excessive manual pre-processi…
Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet, revealing the reaction pathways for complex systems and processes is still challenging due to the lack of knowledge of the involved species and reactions. Here, we present a neural network approach that autonomously discovers reaction pathways from the time-resolved species concentration data. The proposed Chemical Reaction Neural Network (CRNN), by design, sa…
Centre of New Technologies, University of Warsaw（华沙大学新技术中心）；Institute of Organic Chemistry, Polish Academy of Sciences（波兰科学院有机化学研究所）
The central challenge in automated synthesis planning is to be able to generate and predict outcomes of a diverse set of chemical reactions. In particular, in many cases, the most likely synthesis pathway cannot be applied due to additional constraints, which requires proposing alternative chemical reactions. With this in mind, we present Molecule Edit Graph Attention Network (MEGAN), an end-to-end encoder-decoder neural model. MEGAN is inspired by models that express a chemical reaction as a sequence of graph edits, akin to the arrow pushing formalism. We extend this model to retrosynthesis p…
Dynamic properties of chemical reactions and appropriate relationships for open chemical equilibrium are discussed in approach of the chemical dynamics. New way to calculate composition of chemical systems in open equilibrium, based on the amended equation for the change of Gibbs' free energy, was exemplified using reactions of cobalt double oxides with sulfur. Evaluated this way equilibrium reaction extents had a good match with values found by direct thermodynamic simulation. The developed method allows us to perform analysis of complex chemical systems without coefficients of thermodynamic …
van't Hoff equation relates equilibrium constant $K$ of a chemical reaction to temperature $T$. Though the van't Hoff plot ($\ln K$ vs $1/T$) is linear, it is nonlinear for certain chemical reactions. In this work we attribute such observations to virial coefficients.
This perspective on laser control provides a quick overview over different schemes for coherent control of chemical reactions and photophysical processes. It originally appeared in Bunsen Magazin 1, 13 - 23 (2012).
We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent. Our theory reveals the existence of an intermediate situation between ionic and covalent which may be almost barrierless and isoenegetic and which should be of high interest for understanding biochemistry.
The use of optical cavities to control chemical reactions has been of great interest recently, following demonstrations of enhancement, suppression, and negligible effects on chemical reaction rates depending on the specific reaction and cavity frequency. In this work, we study the reaction rate inside imperfect cavities, where we introduce a broadening parameter in the spectral density to mimic Fabry-Pérot cavities. We investigate cavity modifications to reaction rates using non-Markovian Langevin dynamics with frictional and random forces to account for the presence of imperfect optical cavi…
The highly-sensitive method is proposed for the real-time diagnostics of the von Neumann peak at detonation of brisant high explosives. The absence of the direct link between the pressure and the course of chemical reactions was shown. For TNT (trinitrotoluene), the influence of the structure of charge on the kinetics of chemical peak was demonstrated.
Earlier it has been supposed that the law of conservation of energy in chemical reactions has the following form: DU=DQ-PDV+SUM(muiDN) In the present paper it has been proved by means of the theory of ordinary differential equations that in the biggest part of the chemical reactions it must have the following form: DU=DQ+PDV+SUM(muiDN) The result obtained allows to explain a paradox in chemical thermodynamics: the heat of chemical processes measured by calorimetry and by the Vant-Hoff equation differs very much from each other. The result is confirmed by many experiments.
The nonlinear dynamics of resistive flow with a chemical reaction is studied. Proceeding from the Lagrangian description, the influence of a chemical reaction on the development of fluid singularities is considered.
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…
Simple bimolecular reactions $A_1+A_2\rightleftharpoons A_3+A_4$ are analyzed within the framework of the Boltzmann equation in the initial stage of a chemical reaction with the system far from chemical equilibrium. The Chapman-Enskog methodology is applied to determine the coefficients of the expansion of the distribution functions in terms of Sonine polynomials for peculiar molecular velocities. The results are applied to the reaction $H_2+Cl\rightleftharpoons HCl+H$, and the influence of the non-Maxwellian distribution and of the activation-energy dependent reactive cross sections upon the …
We present numerical results for a chemical reaction of colloidal particles which are transported by a laminar fluid and are focused by periodic obstacles in such a way that the two components are well mixed and consequently the chemical reaction is speeded up. The roles of the various system parameters (diffusion coefficients, reaction rate, obstacles sizes) are studied. We show that focusing speeds up the reaction from the diffusion limited rate (t to the power -1/2) to very close to the perfect mixing rate, (t to the power -1).
While attaining external field control of bimolecular chemical reactions has long been a coveted goal of physics and chemistry, the role of hyperfine interactions and dc magnetic fields in achieving such control has remained elusive. We develop an extended coupled-channel statistical theory of barrierless atom-diatom chemical reactions, and apply it to elucidate the effects of magnetic fields and hyperfine interactions on the ultracold chemical reaction Li($^2\text{S}_{1/2}$) + CaH($^2Σ^+$) $\to$ LiH($^1Σ^+$) + Ca($^1\text{S}_{0}$) on a newly developed set of ab initio potential energy surface…
In nonequilibrium chemical reaction systems, a fundamental relationship between unbalanced kinetic one-way fluxes and thermodynamic chemical driving forces is believed to exists. However this relation has been rigorously demonstrated only in a few cases in which one-way fluxes are well defined. In terms of its stochastic kinetic representation, we formulate the one-way fluxes for a general chemical reaction far from equilibrium, with arbitrary complex mechanisms, multiple intermediates, and internal kinetic cycles. For each kinetic cycle, the logarithm of the ratio of the steady-state forward …
In the previous papers of the author it has been shown that the 1st law of thermodynamics in chemical reactions is the following one: dU=dQ+PdV+SUM In the present paper this theory was developed and it has been shown that the 1st law of thermodynamics in chemical reactions has the following form: dC=-dU+dA and -dU=dQ where dC is the change in the chemical energy, dU is the change in the internal energy. Internal energy is the energy of thermal motion of molecules.
We derive the Hessian geometric structure of nonequilibrium chemical reaction networks (CRN) on the flux and force spaces induced by the Legendre duality of convex dissipation functions and characterize their dynamics as a generalized flow. With this structure, we can extend theories of nonequilibrium systems with quadratic dissipation functions to more general ones with nonquadratic ones, which are pivotal for studying chemical reaction networks. By applying generalized notions of orthogonality in Hessian geometry to chemical reaction networks, we obtain two generalized decompositions of the …
This paper summarizes the recent theoretical works on inelastic collisions and chemical reactions at cold and ultracold temperatures involving neutral or ionic systems of atoms and molecules. Tables of zero-temperature rate constants of various molecules are provided.
We present a theoretical investigation of the chemical reaction SrF + SrF $\rightarrow$ products, focusing on reactions at ultralow temperatures. We find that bond swapping, SrF + SrF $\rightarrow$ Sr$_2$ + F$_2$, is energetically forbidden at these temperatures. Rather, the only energetically allowed reaction is SrF + SrF $\rightarrow$ SrF$_2$ + Sr, and even then only singlet states of the SrF$_2$ trimer can form. A calculation along a reduced reaction path demonstrates that this abstraction reaction is barrierless, and proceeds by one SrF molecule "handing off" a fluorine atom to the other m…
A natural condition on the structure of the underlying chemical reaction network, namely weak reversibility, is shown to guarantee the existence of an equilibrium (steady state) in each positive stoichiometric compatibility class for the associated mass-action system. Furthermore, an index formula is given for the set of equilibria in a given stoichiometric compatibility class.
Fueled by advances in hardware and algorithm design, large-scale automated explorations of chemical reaction space have become possible. Here, we present our approach to an open-source, extensible framework for explorations of chemical reaction mechanisms based on the first principles of quantum mechanics. It is intended to facilitate reaction network explorations for diverse chemical problems with a wide range of goals such as mechanism elucidation, reaction path optimization, retrosynthetic path validation, reagent design, and microkinetic modeling. The stringent first-principles basis of al…
Coupling and decoupling of chemical reactions are explored through a modified heat balance equation. Reaction enthalpies are found to play crucial role; the sign of their product for a pair of consecutive chemical reactions determine whether they couple or not. The possibility of a coupling-uncoupling transition for such reactions is thus introduced for the first time. The present work resolves a paradox concerning negative efficiency of coupled consecutive chemical reactions. Enthalpy is also shown to be a "constant of motion" along the reaction coordinate as long as the mass action ratio var…
We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation single- and double-ended transition-state optimization algorithms - the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unkn…
Chemical reactions on metal surfaces are important in various processes such as heterogeneous catalysis and nanostructure growth. At moderate or lower temperatures, these reactions generally follow the minimum energy path and temperature effects can be reasonably described by a harmonic oscillator model. At a high temperature approaching the melting point of the substrate, general behaviors of surface reactions remain elusive. In this study, by taking hydrocarbon species adsorbed on Cu(111) as a model system and performing extensive molecular dynamics simulations powered by machine learning po…
We show that the interaction of polar alkali dimers in the quintet spin state leads to the formation of a deeply bound reaction complex. The reaction complex can decompose adiabatically into homonuclear alkali dimers (for all molecules except KRb) and into alkali trimers (for all molecules). We show that there are no barriers for these chemical reactions. This means that all alkali dimers in the $a^3Σ^+$ state are chemically unstable at ultracold temperature, and the use of an optical lattice to segregate the molecules and suppress losses may be necessary. In addition, we calculate the minimum…
We present results that compare the accuracy of the AM05 density functional to a set of chemical reaction energies. The reactions were generated from the singlet species in the well-known G2 test suite. Our results show that, in general, the AM05 functional performs nearly as well as the other "pure" density functionals, but none of these perform as well as the hybrid B3LYP functional. These results are nonetheless encouraging because the AM05 functional arises from very simple assumptions, and does not require the calculation of the Hartree-Fock exchange integrals.
We present some qualitative aspects concerning the solution to the mathematical model describing the dynamical behavior of the reversible chemical reaction SO2(g)+1/2O2(g)<=>SO3(g) carried out in a catalytic reactor used in the process of sulfuric acid production.
Using the mass balance equations for chemical reactions, we show how the system relaxes towards a steady state in and out of the Onsager region. In the chemical affinities space, after fast transients, the relaxation process is a straight line when operating in the Onsager region, while out of this regime, the evolution of the system is such that the projections of the evolution equations for the forces and the shortest path on the flows coincide. For spatially-extended systems, similar results are valid for the evolution of the thermodynamic mode (i.e., the mode with wave-number k = 0). These…
Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms using Molecular Configuration Transformer
Peking University（北京大学）；Shenzhen Bay Laboratory（深圳湾实验室）；Changping Laboratory（昌平实验室）
We use the formalism of Geometrothermodynamics to describe chemical reactions in the context of equilibrium thermodynamics. Any chemical reaction in a closed system is shown to be described by a geodesic in a $2-$dimensional manifold that can be interpreted as the equilibrium space of the reaction. We first show this in the particular cases of a reaction with only two species corresponding to either two ideal gases or two van der Waals gases. We then consider the case of a reaction with an arbitrary number of species. The initial equilibrium state of the geodesic is determined by the initial c…
The asymptotic limit-cycle analysis of mathematical models for oscillating chemical reactions is presented. In this work, after a brief presentation of mathematical preliminaries applied to the biased Van der Pol oscillator, we consider a two-dimensional model of the Chlorine dioxide Iodine Malonic-Acid (CIMA) reactions and the three-dimensional and two-dimensional Oregonator models of the Belousov-Zhabotinsky (BZ) reactions. Explicit analytical expressions are given for the relaxation-oscillation periods of these chemical reactions that are accurate within 5\% of their numerical values. In th…
Michigan State University（密歇根州立大学）；Peking University（北京大学）；Tsinghua University（清华大学）
In this paper, we propose a data-driven method to discover multiscale chemical reactions governed by the law of mass action. First, we use a single matrix to represent the stoichiometric coefficients for both the reactants and products in a system without catalysis reactions. The negative entries in the matrix denote the stoichiometric coefficients for the reactants and the positive ones for the products. Second, we find that the conventional optimization methods usually get stuck in the local minima and could not find the true solution in learning the multiscale chemical reactions. To overcom…
The molecular energies of chemical systems have been successfully calculated on quantum computers, however, more attention has been paid to the dynamic process of chemical reactions in practical application, especially in catalyst design, material synthesis. Due to the limited the capabilities of the noisy intermediate scale quantum (NISQ) devices, directly simulating the reaction dynamics and determining reaction pathway still remain a challenge. Here we develop the ab initio molecular dynamics based on quantum computing to simulate reaction dynamics by extending correlated sampling approach.…
For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.
We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical potentials, and makes use of the topological properties of the network (conservation laws and cycles). Our approach is proven to be exact if the network results from a bigger network of elementary reactions where the fast-evolving species have been coarse grained. Our work should be particularly relevant for energetic considerations in biosystems where the char…
In this paper we present a difference algebraic technique for the evaluation of the Einstein's strength of a system of partial difference equations and apply this technique to the comparative analysis of difference schemes for chemical reaction-diffusion equations. In particular, we analyze finite-difference schemes for the Murray, Fisher, Burgers and some other reaction-diffusion equations, as well as mass balance PDEs of chromatography from the point of view of their strength.
The theory of chemical kinetics form the basis to describe the dynamics of chemical systems. Owing to physical and thermodynamic constraints, chemical reaction systems possess various structures, which can be utilized to characterize important physical properties of the systems. In this work, we reveal the Hessian geometry which underlies chemical reaction systems and demonstrate how it originates from the interplay of stoichiometric and thermodynamic constraints. Our derivation is based on kinetics, we assume the law of mass action and characterize the equilibrium states by the detailed balan…
Reaction paths and classical and quantum trajectories are studied within a generalized Hamilton-Jacobi framework, which allows to put on equal footing topology and dynamics in chemical reactivity problems. In doing so, we show how high-dimensional problems could be dealt with by means of Caratheodory plots or how trajectory-based quantum-classical analyses reveal unexpected discrepancies. As a working model, we consider the reaction dynamics associated with a Mueller-Brown potential energy surface, where we focus on the relationship between reaction paths and trajectories as well as on reactio…
In this paper, a topological classification of molecules and their chemical reactions is proposed on a single particle level . We consider zero-dimensional electronic Hamiltonians in a real-space tight-binding basis with spinless time-reversal symmetry and an additional spatial reflection symmetry. The symmetry gives rise to a perplectic structure and suggests a $\mathbb{Z}_2$ invariant in form of a pfaffian, which can be captured by an entanglement cut. We apply our findings to a class of chemical reactions studied by Woodward and Hoffmann, where a reflection symmetry is preserved along a one…
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph containing 14.4 million molecules and 8.2 million binary reactions, which represents the bulk of all chemical reactions ever published in the scientific literature. Our model outperforms a rule-based expert system in the reaction prediction task for 180,000 randomly selected binary …
Physical kinetic roughening processes are well known to exhibit universal scaling of observables that fluctuate in space and time. Are there analogous dynamic scaling laws that are unique to the chemical reaction mechanisms available synthetically and occurring naturally? Here, we formulate two complementary approaches to the dynamic scaling of stochastic fluctuations in thermodynamic observables at and away from equilibrium. Both analytical expressions and numerical simulations confirm our dynamic scaling ans{ä}tze with their associated exponents, functions, and laws. A survey of common chemi…
The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit approximations of eigenvalues and eigenvectors of kinetic matrix. Accuracy of estimates is proven. Performance of the algorithms is demonstrated on simple examples. Application of algorithms to nonlinear systems is discussed.
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many reactants or highly reactive species), the size of such network may grow rapidly. Here, we present a computational protocol that constructs such reaction networks in a fully automated fashion steered in an intuitive, graph-based fashion through a single graphical user interface. Starting from a set of initial reagents new intermediates are explored through …
Predicting the outcome of a chemical reaction using efficient computational models can be used to develop high-throughput screening techniques. This can significantly reduce the number of experiments needed to be performed in a huge search space, which saves time, effort and expense. Recently, machine learning methods have been bolstering conventional structure-activity relationships used to advance understanding of chemical reactions. We have developed a model to predict the products of catalytic reactions on the surface of oxygen-covered and bare gold using machine learning. Using experiment…
We consider stochastic models of chemical reaction networks with time dependent input rates and several types of molecules. We prove that, in despite of strong time dependence of input rates, there is a kind of homeostasis phenomenon: far away from input nodes the mean numbers of molecules of each type become approximately constant (do not depend on time).
I propose a novel approach to balancing equations that is applicable to all chemical-reaction equations; it is readily accessible to students via scientific calculators and basic computer spreadsheets that have a matrix-inversion application. The new approach utilizes the familiar matrix-inversion operation in an unfamiliar and innovative way; its purpose is not to identify undetermined coefficients as usual, but, instead, to compute a matrix null space (or matrix kernel). The null space then provides the coefficients that balance the equation. Indeed, the null space contains everything there …
We present an embedding technique for metallic systems that makes it possible to model energy dissipation into substrate phonons during surface chemical reactions from first principles. The separation of chemical and elastic contributions to the interaction potential provides a quantitative description of both electronic and phononic band structure. Application to the dissociation of O$_2$ at Pd(100) predicts translationally "hot" oxygen adsorbates as a consequence of the released adsorption energy (ca. 2.6 eV). This finding questions the instant thermalization of reaction enthalpies generally…
