Extensions and improvements of empirical force fields are discussed in view of applications to computational vibrational spectroscopy and reactive molecular dynamics simulations. Particular focus is on quantitative studies which make contact with experiments and provide complementary information for a molecular-level understanding of processes in the gas phase and in solution. Methods range from including multipolar charge distributions to reproducing kernel Hilbert space approaches and machine learned energy functions based on neural networks.
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).
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.
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…
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 …
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.
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…
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 …
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…
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…
Qualitative Aspects of the Solutions of a Mathematical Model for the Dynamic Analysis of the Reversible Chemical Reaction SO2(g)+1/2O2(g)<=>SO3(g) in a Catalytic Reactor
我们提出了有关描述硫酸生产过程中催化反应器中进行的可逆化学反应SO2（g）+1/2O2（g）<=> SO 3（g）动力学行为的数学模型解的一些定性方面。
IBM Research – Zurich（IBM苏黎世研究院）；University of Bern（伯尔尼大学）
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 tex…
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.…
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…
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…
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…
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…
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）
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…
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…
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…
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.
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 …
This paper studies a mathematical formalism of nonequilibrium thermodynamics for chemical reaction models with $N$ species, $M$ reactions, and general rate law. We establish a mathematical basis for J. W. Gibbs' macroscopic chemical thermodynamics under G. N. Lewis' kinetic law of entire equilibrium (detailed balance in nonlinear chemistry kinetics). In doing so, the equilibrium thermodynamics is then naturally generalized to nonequilibrium settings without detailed balance. The kinetic models are represented by a Markovian jumping process. A generalized macroscopic chemical free energy functi…
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…
