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 the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.
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…
We here apply the recently developed initiator density matrix quantum Monte Carlo (i-DMQMC) to a wide range of chemical environments using atoms and molecules in vacuum. i-DMQMC samples the exact density matrix of a Hamiltonian at finite temperature and combines the accuracy of full configuration interaction quantum Monte Carlo (FCIQMC) - full configuration interaction (FCI) or exact energies in a finite basis set - with finite temperature. By way of exploring the applicability of i-DMQMC for molecular systems, we choose to study a recently developed test set by Rubenstein and coworkers: Be, H…
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…
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 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…
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…
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…
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…
The energetics of the gas-phase S$_N$2 reactions Y$^-$ + CH$_3$X $\longrightarrow$ CH$_3$Y + X$^-$ (where X,Y = F, Cl, Br), were studied using (variants on) the recent W1 and W2 {\em ab initio} computational thermochemistry methods. Our computed benchmark data (including cases for which experimental data are unavailable altogether) are used to assess the quality of a number of semiempirical compound thermochemistry schemes such as G2 theory, G3 theory, and CBS-QB3, as well as a variety of density functional theory methods. Upon applying some modifications to the level of theory used for the re…
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 …
The discovery of effective hydrogen storage materials is fundamental for the progress of a clean energy economy. Ammonia borane ($\mathrm{H_3BNH_3}$) has attracted great interest as a promising candidate but the reaction path that leads from its solid phase to hydrogen release is not yet fully understood. To address the need for insights in the atomistic details of such a complex solid state process, in this work we use \textit{ab-initio} molecular dynamics and metadynamics to study the early stages of AB dehydrogenation. We show that the formation of ammonia diborane ($\mathrm{H_3NBH_2(}$$μ$$…
The temperature dependence of the rate of the reaction CH_4+H \to CH_3+H_2 is studied using classical collision theory with a temperature-dependent effective potential derived from a path integral analysis. Analytical expressions are obtained for the effective potential and for the rate constant. The rate constant expressions use a temperature-dependent activation energy. They give better agreement with the available experimental results than do previous empirical fits. Since all but one of the parameters in the present expressions are obtained from theory, rather than by fitting to experiment…
In modeling the interior of cells by simulating a reaction-diffusion master equation over a grid of compartments, one employs the assumption that the copy numbers of various chemical species are small, discrete quantities. We show that in this case, textbook expressions for the change in Gibbs free energy accompanying a chemical reaction or diffusion between adjacent compartments become inaccurate. We derive exact expressions for these free energy changes under the assumption of discrete copy numbers and illustrate how these expressions reduce to the textbook expressions under a series of succ…
It is demonstrated that the reaction path for a polyatomic molecule (applied to the HCO molecule) is easily calculated via ab-initio configuration interaction (CI) total energies. This Hamiltonian not only reproduces the CI calculations accurately and efficiently, but also effectively corrects any CI energies happening to erroneously converge to excited states.
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 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…
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…
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 …
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…
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…
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…
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.
In order to obtain a comprehensive understanding of both thermodynamics and kinetics of water dissociation on TiO2, the reactions between liquid water and perfect and defective rutile TiO2 (110) surfaces were investigated using ab initio molecular dynamics simulations. The results showed that the free-energy barrier (~ 4.4 kcal/mol) is too high for a spontaneous dissociation of water on the perfect rutile (110) surface at a low temperature. The most stable oxygen vacancy (Vo1) on the rutile (110) surface cannot promote the dissociation of water, while other unstable oxygen vacancies can signif…
A theoretical rate constant for the associative detachment reaction Rb($^{2}S$)$+$OH$^{-}$($^{1}Σ^{+}$)$\rightarrow \,$ RbOH($^{1}Σ^{+}$)$+\,e^{-}$ of 4$\,\times$10$^{-10}$cm$^{3}$s$^{-1}$ at 300 K has been calculated. This result agrees with the experimental rate constant of 2$^{+2}_{-1}\,\times10^{-10}$cm$^{3}$s$^{-1}$ obtained by Deiglmayr \textit{et al.} (Phys. Rev. A 86, 2012) for a temperature between 200 K and 600 K. A Langevin-based dynamics which depends on the crossing point between the anion (RbOH$^{-}$) and neutral (RbOH) potential energy surfaces has been used. The calculation wer…
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen pe…
In conventional chemisorption model, the d-band center theory (augmented sometimes with the upper edge of d-band for imporved accuarcy) plays a central role in predicting adsorption energies and catalytic activity as a function of d-band center of the solid surfaces, but it requires density functional calculations that can be quite costly for large scale screening purposes of materials. In this work, we propose to use the d-band width of the muffin-tin orbital theory (to account for local coordination environment) plus electronegativity (to account for adsorbate renormalization) as a simple se…
The cross section and rate constants for the title reaction are calculated for all the spin-orbit states of N$^+$($^3P_{J_A}$) using two statistical approaches, one purely adiabatic and the other one mixing quantum capture for the entrance channel and adiabatic treatment for the products channel. This is made by using a symmetry adapted basis set combining electronic (spin and orbital) and nuclear angular momenta in the reactants channel. To this aim, accurate {\it ab initio} calculations are performed separately for reactants and products. In the reactants channel, the three lowest electronic…
Calculating dipole moments with high-order basis sets is generally only possible for the light molecules, such as water. A simple, yet highly effective strategy of obtaining high-order dipoles with small, computationally less expensive basis sets is described. Using the finite field method for computing dipoles, energies calculated with small basis sets can be extrapolated to produce dipoles that are comparable to those obtained in high order calculations. The method reduces computational resources by approximately 50% (allowing the calculation of reliable dipole moments for larger molecules) …
The time-dependent rate coefficients for the charge exchange reaction C+ + Si -> C + Si+ for doublet and quartet states have been determined with ab initio quantum calculations coupled with a non-adiabatic transition model based on a simple Landau-Zener picture. This reaction plays a key role in determining the abundances of C, Si, and their ions, in the ISM since these abundances affect the fine structure cooling and hence the star formation rates. We also provide additional calculations to evaluate the differences between the gas evolution as obtained by using the empirical rate estimates fo…
Water dissociation is a rate limiting step in many industrially important chemical reactions. In this investigation, climbing image nudged elastic band (CINEB) method, within the framework of density functional theory, is used to report the activation energies (E a ) of water dissociation on Cu(111) surface with a vacancy. Introduction of vacancy results in a reduced coordination of the dissociated products, which facilitates their availability for reactions that involve water dissociation as an intermediate step. Activation energy for dissociation of water reduces by nearly 0.2 eV on Cu(111) …
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (Delta G(hyd)) within a few kcal/mol, or better than 4%, of Tissandier 's [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E wa…
Chemical networks used for models of interstellar clouds contain many reactions, some of them with poorly determined rate coefficients and/or products. In this work, we report a method for improving the predictions of molecular abundances using sensitivity methods and ab initio calculations. Based on the chemical network osu.2003, we used two different sensitivity methods to determine the most important reactions as a function of time for models of dense cold clouds. Of these reactions, we concentrated on those between C and C3 and between C and C5, both for their effect on specific important …
Experimental studies of the oxygen reduction reaction (ORR) at nitrogen doped graphene electrodes have reported a remarkably low overpotential, on the order of 0.5 V, similar to Pt based electrodes. Theoretical calculations using density functional theory have lent support for this claim. However, other measurements have indicated that transition metal impurities are actually responsible for the ORR activity, thereby raising questions about the reliability of both the experiments and the calculations. In order to assess the accuracy of the theoretical calculations, various generalized gradient…
In this work we characterize an initial van der Waals adduct in the potential energy surface of reaction between cyanoacetylene HC3N and the cyano radical. The geometry of the CN-HC3N adduct has been optimized through calculations employing ab initio methods. Results show that the energy of the adduct lays below the reactants. Additionally, a saddle point that connects the adduct to an important intermediate of the PES has been localized, with energy below the reactants. Calculations of the intermolecular potential have been performed and results show that the energy of the van der Waals adduc…
Synthesis routes of novel piperidine-containing diacetylene are presented. The new molecules are expected to exhibit plant growth stimulation properties. In particular, the yield in a situation of drought is expected to increase. The synthesis makes use of the Favorskii reaction between cycloketones/piperidone and triple-bond containing glycols. The geometries of the obtained molecules were determined using nuclear magnetic resonance (NMR). The electronic structure and geometries of the molecules were studied theoretically using first-principles calculations based on density functional theory.…
We develop a spectral formulation and a stationary WKB approximation for calculating the probabilities of rare events (large deviations from the mean) in systems of reacting particles with infinite-range interaction, describable by a master equation. We compare the stationary WKB approximation with a recent time-dependent semiclassical approximation developed, for the same class of problems, by Elgart and Kamenev. As a benchmark we use an exactly solvable problem of the binary annihilation reaction 2A -> 0.
