Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations employing hybrid density functionals are of great interest as it offers more accurate description of structural and dynamic properties than the GGA functionals. However, computational cost for carrying out calculations using hybrid functionals and plane wave basis set is at least two order of magnitude higher than GGA functionals. Recently, we proposed a strategy that combined the adaptively compressed exchange operator formulation and the multiple time step integration scheme to reduce the computational cost about an order of magnitude [J. Chem. Phys. 151, 151102 (2019)]. In this work, we demonstrate the application of this method to study chemical reactions, in particular, formamide hydrolysis in alkaline aqueous medium. By actuating our implementation with the well-sliced metadynamics scheme, we are able to compute the two-dimensional free energy surface of this reaction at the level of hybrid-DFT. Accuracy of PBE0 (hybrid) and PBE (GGA) functionals in predicting the free energetics of the chemical reaction is investigated here.
Aqueous solutions provide a medium for many important reactions in chemical synthesis, industrial processes, environmental chemistry, and biological functions. It is an accepted fact that aqueous solvents can be direct participants to the reaction process and not act only as simple passive dielectrics. Assisting water molecules and proton wires are thus essential for the efficiency of many reactions. Here we study the decomposition of urea into ammonia and isocyanic acid by means of enhanced ab initio molecular dynamics simulations. We highlight the role of the solvent molecules and their inte…
Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving Fe$^{2+}$/Fe$^{3+}$ ions in water. In most cases, such simulations are performed using density functionals at the level of Generalized Gradient Approximation (GGA). The challenge in modelling ET reactions is the poor quality of GGA functionals in predicting properties of such open-shell systems due to the inevitable self-interaction error (SIE). While hybrid functional…
Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine adaptively compressed exchange (ACE) operator formulation and multiple time step (MTS) integration scheme to reduce the computational cost significantly [J. Chem. Phys. 151, 151102 (2019)]. However, it was found that the construction of the ACE operator, which has to be done at least once in every MD time step, is computationally expensive. In the present work, sy…
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schrödinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of t…
We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear degrees of freedom are coupled to a thermal bath, through a Langevin equation. This method is based on the path integral representation for the stochastic dynamics and yields the time evolution of both nuclear and electronic degrees of freedom, along the most probable reaction pathways, without spending computational time to explore metastable states. This ap…
A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.
We investigate a reaction of boron trichloride (BCl3) with iron(III) hydroxide (Fe(OH)3) by ab initio quantum chemical calculation as a simple model for a reaction of iron impurities in BCl3 gas. We also examine a reaction with water. We find that compounds such as Fe(Cl)(OBCl2)2(OHBCl2) and Fe(Cl)2(OBCl2)(OHBCl2) are formed while producing HCl and reaction paths to them are revealed. We also analyze the stabilization mechanism of these paths using newly-developed interaction energy density derived from electronic stress tensor in the framework of the Regional DFT (Density Functional Theory) a…
The hydrogen oxidation reaction (HOR) and hydrogen evolution reaction (HER) play an important role in hydrogen based energy conversion. Recently, the frustrating performance in alkaline media raised debates on the relevant mechanism, especially on the role of surface hydroxyl (OH*). We present a full pH range electrode/electrolyte kinetics simulation for HER/HOR on Pt(111), with the potential-related rate constants been calculated with density functional theory methods. The polarization curves agree well with the experimental observations. The stability of OH* is found to be unlikely an effect…
Crystal orbital overlap population based on all-electron ab initio simulation with numeric atom-centered orbitals and its application to chemical-bonding analysis in Li-intercalated layered materials
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 investigate the energetics of the atom exchange reaction in the SrF+alkali-metal atom and CaF+alkali-metal atom systems. Such reactions are possible only for collisions of SrF and CaF with the lithium atoms, while they are energetically forbidden for other alkali-metal atoms. Specifically, we focus on SrF interacting with Li, Rb, and Sr atoms and use ab initio methods to demonstrate that the SrF+Li and SrF+Sr reactions are barrierless. We present potential energy surfaces for the interaction of the SrF molecule with the Li, Rb, and Sr atoms in their energetically lowest-lying electronic spi…
The extent of hydrogen coverage of the Si(001)c(4x2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even…
Interactions between molecules and electrode surfaces play a key role in electrochemical processes and are a subject of extensive research, both experimental and theoretical. In this manuscript, we address the water dissociation reaction on a Pd(111) electrode surface, modelled as a slab embedded in an external electric field. We aim at unraveling the relationship between surface charge and zero-point-energy in aiding or hindering this reaction. We calculate energy barriers with dispersion-corrected density-functional theory and an efficient parallel implementation of the nudged-elastic-band m…
Reliable quantum chemical methods for the description of molecules with dense-lying frontier orbitals are needed in the context of many chemical compounds and reactions. Here, we review developments that led to our newcomputational toolbo x which implements the quantum chemical density matrix renormalization group in a second-generation algorithm. We present an overview of the different components of this toolbox.
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab initio (ai) quantum mechanical/molecular mechanics (QM/MM) level is still far too expensive. Semiempirical (SE) method can be hundreds or thousands of times faster than the ai methods. However, the accuracy of SE methods is often unsatisfactory, due to the approximations that have been adopted in these methods. In this work, we proposed a new method termed MBA…
Four cluster models for a copper(I)oxide (111) surface have been designed, of which three were studied with respect to their applicability in density functional calculations in the general gradient approximation. Formic acid adsorption on these systems was modelled and yielded four different adsorption structures, of which two were found to have a high adsorption energy. The energetically most favourable adsorption structure was further investigated with respect to its decomposition and a few reactions with adsorbed H and OH species using synchronous transit methods to estimate reaction barrie…
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We …
Chemical compound space (CCS), the set of all theoretically conceivable combinations of chemical elements and (meta-)stable geometries that make up matter, is colossal. The first principles based virtual sampling of this space, for example in search of novel molecules or materials which exhibit desirable properties, is therefore prohibitive for all but the smallest sub-sets and simplest properties. We review studies aimed at tackling this challenge using modern machine learning techniques based on (i) synthetic data, typically generated using quantum mechanics based methods, and (ii) model arc…
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…
Fingerprints of antiaromaticity in the negative ion (Li$_3$Al$_4$)$^-$, this species being realizable via a laser vaporization technique, are revealed by means of an \emph{ab initio} quantum-chemical investigation. First, the ground-state equilibrium geometry of this ion is predicted. Also, for the corresponding inhomogeneous electron liquid, the characteristics of the HOMO are studied, both for the square and the rectangular Al$_4$ geometry in two low-lying isomers of the negative ion. There is no particular sensitivity to the change in geometry of the Al$_4$ configuration. Therefore, we have…
K+(aq) ion is an integral component of many cellular processes, amongst which the most important, perhaps, is its role in transmitting electrical impulses along the nerve. Understanding its hydration structure and thermodynamics is crucial in dissecting its role in such processes. Her we address these questions using both the statistical mechanical quasi-chemical theory of solutions and ab initio molecular dynamics simulations. Simulations predict an interesting hydration structure for K+(aq): the population of about six (6) water molecules within the initial minimum of the observed g_{KO}(r) …
Computing accurate rate constants for catalytic events occurring at the surface of a given material represents a challenging task with multiple potential applications in chemistry. To address this question, we propose an approach based on a combination of the rare event sampling method called Adaptive Multilevel Splitting (AMS) and ab initio molecular dynamics (AIMD). The AMS method requires a one dimensional reaction coordinate to index the progress of the transition. Identifying a good reaction coordinate is difficult, especially for high dimensional problems such a those encountered in cata…
Accurate predictions of the hydration free energy for anions typically have been more challenging than for cations. Hydrogen bond donation to the anion in hydrated clusters such as $\mathrm{F(H_2O)}_n{}^-$ can lead to delicate structures. Consequently, the energy landscape contains many local minima, even for small clusters, and these minima present a challenge for computational optimization. Utilization of cluster experimental results for the free energies of gas-phase clusters shows that, even though anharmonic effects are interesting, they need not be troublesome magnitudes for careful appl…
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.
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional fre…
The following study investigates the thermodynamic reaction barriers during nitrogen fixation for an inorganic sulfur desorbed photocatalyst Molybdenum disulfide surface. The design space is investigated using an density functional theory (DFT) method within a space bound by MMoS$_2$ M=Mo,Fe,Co. The discussion focuses on Heyrovsky type reactions along both the associative and dissociative pathway. A key insight into the roles of the inorganic and the balance between nitrogen and hydrogen affinity, providing evidence for an optimal material that minimizes the required over-potential. It is foun…
We propose a machine-learning approach based on Bayesian optimization to build global potential energy surfaces (PES) for reactive molecular systems using feedback from quantum scattering calculations. The method is designed to correct for the uncertainties of quantum chemistry calculations and yield potentials that reproduce accurately the reaction probabilities in a wide range of energies. These surfaces are obtained automatically and do not require manual fitting of the {\it ab initio} energies with analytical functions. The PES are built from a small number of {\it ab initio} points by an …
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 …
We use ab initio molecular dynamics as a basis for quasi-chemical theory evaluation of the free energy of water near conventional liquid thermodynamic states. The PW91, PBE, and revised PBE (rPBE) functionals are employed. The oxygen radial density distribution, gOO(r), using the rPBE functional is in reasonable agreement with current experiments, whereas the PW91 and PBE functionals predict a more structured gOO(r). The diffusion coefficient with the rPBE functional is in reasonable accord with experiments. Using a maximum entropy procedure, we obtain x_0 from the coordination number distribu…
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).
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.
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.
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 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.
By judicious use of extrapolations to the 1-particle basis set limit and $n$-particle calibration techniques, total atomization energies of molecules with up to four heavy atoms can be obtained with calibration accuracy (1 kJ/mol or better, on average) without any empirical correction. For the SCF energy a 3-point geometric extrapolation is the method of choice. For the MP2 correlation energy, a 2-point $A+B/(l+1/2)^3$ extrapolation is recommended, while for CCSD and CCSD(T) correlation energies we prefer the 3-point $A+B/(l+1/2)^C$ formula. Addition of high-exponent `inner polarization functi…
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 …
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…
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 …
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.
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…
We present a detailed discussion of self-energy embedding theory (SEET) which is a quantum embedding scheme allowing us to describe a chosen subsystem very accurately while keeping the description of the environment at a lower cost. We apply SEET to molecular examples where commonly our chosen subsystem is made out of a set of strongly correlated orbitals while the weakly correlated orbitals constitute an environment. Such a self-energy separation is very general and to make this procedure applicable to multiple systems a detailed and practical procedure for the evaluation of the system and en…
