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The study of chemical reactions in aqueous media is very important for its implications in several fields of science, from biology to industrial processes. However, modeling these reactions is difficult when water directly participates in the reaction, since it requires a fully quantum mechanical description of the system. Ab-initio molecular dynamics is the ideal candidate to shed light on these processes. However, its scope is limited by a high computational cost. A popular alternative is to perform molecular dynamics simulations powered by machine learning potentials, trained on an extensive set of quantum mechanical calculations. Doing so reliably for reactive processes is difficult because it requires including very many intermediate and transition state configurations. In this study we used an active learning procedure accelerated by enhanced sampling to harvest such structures and to build a neural-network potential to study the urea decomposition process in water. This allowed us to obtain the free energy profiles of this important reaction in a wide range of temperatures, to discover several novel metastable states, and improve the accuracy of the kinetic rates calculations. Furthermore, we found that the formation of the zwitterionic intermediate has the same probability of occurring via an acidic or a basic pathway, which could be the cause of the insensitivity of reaction rates to the solution pH.

The cleavage of the N2 triple bond on the Fe(111) surface is believed to be the rate limiting step of the famed Haber-Bosch ammonia catalysis. Using a combination of machine learning potentials and advanced simulation techniques, we study this important catalytic step as a function of temperature. We find that at low temperatures our results agree with the well-established picture. However, if we increase the temperature to reach operando conditions the surface undergoes a global dynamical change and the step structure of the Fe(111) surface is destroyed. The catalytic sites, traditionally associated with the Fe(111) surface appear and disappear continuously. Our simulations illuminate the danger of extrapolating low-temperature results to operando conditions and indicate that the catalytic activity can only be inferred from calculations that take dynamics fully into account. More than that, they show that it is the transition to this highly fluctuating interfacial environment that drives the catalytic process.

It is known that metal nanoparticles (NPs) may be dynamic and atoms may move within them even at fairly low temperatures. Characterizing such complex dynamics is key for understanding NPs’ properties in realistic regimes, but detailed information on, e.g., the stability, survival, and interconversion rates of the atomic environments (AEs) populating them are non-trivial to attain. Here we show a machine learning approach that allows us to reconstruct the complex atomic dynamics of metal NPs from high-dimensional data extracted from molecular dynamics simulations. Using different-shape gold NPs as a representative example, an AEs’ dictionary allows us to label step-by-step the individual atoms in the NPs, identifying the native and non-native AEs and populating them along the MD simulations at various temperatures. Tracking the emergence, annihilation, lifetime, and dynamic interconversion of the AEs, our approach permits estimating a “statistical equivalent identity” for metal NPs based on the intrinsic atomic dynamics present within them.

Metals are traditionally considered hard matter. However, it is well known that their atomic lattices may become dynamic and undergo reconfigurations even well below the melting temperature. The innate atomic dynamics of metals is directly related to their bulk and surface properties. Understanding their complex structural dynamics is, thus, important for many applications but is not easy. Here, we report deep-potential molecular dynamics simulations allowing to resolve at an atomic resolution the complex dynamics of various types of copper (Cu) surfaces, used as an example, near the Hüttig ([Formula: see text] of melting) temperature. The development of deep neural network potential trained on density functional theory calculations provides a dynamically accurate force field that we use to simulate large atomistic models of different Cu surface types. A combination of high-dimensional structural descriptors and unsupervized machine learning allows identifying and tracking all the atomic environments (AEs) emerging in the surfaces at finite temperatures. We can directly observe how AEs that are non-native in a specific (ideal) surface, but that are, instead, typical of other surface types, continuously emerge/disappear in that surface in relevant regimes in dynamic equilibrium with the native ones. Our analyses allow estimating the lifetime of all the AEs populating these Cu surfaces and to reconstruct their dynamic interconversions networks. This reveals the elusive identity of these metal surfaces, which preserve their identity only in part and in part transform into something else under relevant conditions. This also proposes a concept of “statistical identity” for metal surfaces, which is key to understanding their behaviors and properties.

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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 in 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 interactions with the reactants providing a proper description of the reaction mechanism and how the water hydrogen-bond network affects the reaction dynamics. Reaction free energy and rates have been calculated taking into account this important effect.

The present work suggests the use of a mixed water-based electrolyte containing sulfuric and phosphoric acid for both negative and positive electrolytes of a vanadium redox flow battery. Computational and experimental investigations reveal insights on the possible interactions between the vanadium ions in all oxidation states and sulphate, bisulphate, dihydrogen phosphate ions and phosphoric acid. In situ cycling experiments and ion-specific electrochemical impedance measurements confirmed a significant lowering of the charge-transfer resistance for the reduction of V(iii) ions and, consequently, an increase of the voltaic efficiency associated with the negative side of the battery. This increase of performance is attributable to the complexation of this oxidation state by phosphoric acid. So far, mixed acids have mainly been discussed with the focus on V(v) solubility. In this work we rationalize the impact of the mixed acids on the electrochemical efficiency opening new strategies on how to improve the cycling performance with ionic additives.

Large polycyclic aromatic hydrocarbons (PAHs) are thought to be responsible for the formation of soot particles in combustion processes. However, there are still uncertainties on the course that leads small molecules to form PAHs. This is largely due to the high number of reactions and intermediates involved. Metadynamics combined with ab initio molecular dynamics can provide a very precious contribution because offers the possibility to explore new possible pathways and suggest new mechanisms. Here, we adopt this method to investigate the chemical evolution of the benzyl radical, whose role is very important in PAHs growth. This species has been intensely studied, and though most of its chemistry is known, there are still open questions regarding its decomposition. The simulation reproduces the most commonly accepted decomposition pathway and it suggests also a new one which can explain recent experimental data that are in contradiction with the old mechanism. In addition, quantitative free energy evaluation of some key reaction steps sheds light on the role of entropy.

The possibility that the reaction between two cyclopentadienyl radicals (cC 5 H 5 ) may lead to the production of naphthalene has been the subject of considerable theoretical and experimental studies. Though it has been proposed that this reaction may be the main channel for the formation of naphthalene in many combustion environments, the elementary mechanism leading from the initial adduct (C 5 H 5 _C 5 H 5 ) to naphthalene is still not clear. In this study the portion of the C 10 H 10 PES accessible to C 5 H 5 _C 5 H 5 has been theoretically re-examined using density functional theory to locate stationary points and the CBS-QB3 computational protocol to determine energies. A new reaction pathway leading to the formation of a set of azulyl radicals was identified. Since it is known that azulyl radicals can easily decompose to naphthalene and atomic H, the proposed pathway provides an effective route for the formation of naphthalene. Channel specific kinetic constants were determined between 1100 K and 2000 K integrating the master equation for a PES comprising both this reaction pathway and the literature reaction pathway, which main product is the fulvalenyl radical. It was found that the main reaction channel is decomposition to reactants in the whole temperature range investigated and that the azulyl reaction channel is dominant over the fulvalenyl pathway up to 1450 K. The rate constants calculated at 1 bar for the azulyl and fulvalenyl reaction channels are 10 14.72 T (K) −0.853 exp(−3650/ T (K)) and 10 10.30 T (K) 0.951 exp(−7948/ T (K)) cm 3 /mol/s, respectively. The rate constant for the formation of naphthalene through the azulyl channel is consistent with recent estimates based on the kinetic simulation of the pyrolysis and oxidation of cyclopentadiene.

While the decomposition kinetics of the benzyl radical has been studied in depth both from the experimental and the theoretical standpoint, much less is known about the reactivity of what is likely to be its main decomposition product, fulvenallene. In this work the high temperature reactivity of fulvenallene was investigated on a Potential Energy Surface (PES) consisting of 10 wells interconnected through 11 transition states using a 1 D Master Equation (ME). Rate constants were calculated using RRKM theory and the ME was integrated using a stochastic kinetic Monte Carlo code. It was found that two main decomposition channels are possible, the first is active on the singlet PES and leads to the formation of the fulvenallenyl radical and atomic hydrogen. The second requires intersystem crossing to the triplet PES and leads to acetylene and cyclopentadienylidene. ME simulations were performed calculating the microcanonical intersystem crossing frequency using Landau-Zener theory convoluting the crossing probability with RRKM rates evaluated at the conical intersection. It was found that the reaction channel leading to the cyclopentadienylidene diradical is only slightly faster than that leading to the fulvenallenyl radical, so that it can be concluded that both reactions are likely to be active in the investigated temperature (1500-2000 K) and pressure (0.05-50 bar) ranges. However, the simulations show that intersystem crossing is rate limiting for the first reaction channel, as the removal of this barrier leads to an increase of the rate constant by a factor of 2-3. Channel specific rate constants are reported as a function of temperature and pressure.

Though the unimolecular decompositions of SiH4 and GeH4 are important reaction steps for the CVD of Si and Ge, only few studies are available in the literature on their kinetics. In this work we investigated the decomposition of SiH4 and GeH4, as well as the reactions between SiH3 and GeH3 and H adopting a combined ab initio-RRKMmaster equation approach. Structures of reactants and transition states were determined at the B3LYP/aug-ccpVTZ level, while energies were calculated using coupled cluster theory with single and double excitations and perturbational estimate of triple excitations and extrapolated to infinite basis set using cc-pVTZ and ccpVQZ basis sets. The first reaction investigated was Silane decomposition, which can take place through two different reaction channels

The reactions of singlet methylene, (1)CH2, with unsaturated hydrocarbons are of considerable significance to the formation and growth of polycyclic aromatic hydrocarbons (PAHs). In this work, we employ high level ab initio transition state theory to predict the high pressure rate coefficient for singlet methylene reacting with acetylene (C2H2), ethylene (C2H4), propyne (CH3CCH), propene (CH3CHCH2), allene (CH2CCH2), 1,3-butadiene (CH2CHCHCH2), 2-butyne (CH3CCCH3), and benzene (C6H6). Both addition and insertion channels are found to contribute significantly to the kinetics, with the insertion kinetics of increasing importance for larger hydrocarbons due to the increasing number of CH bonds and increasingly attractive interactions. We treat the addition kinetics with direct CASPT2 based variable-reaction-coordinate transition state theory. One-dimensional corrections to the CASPT2 interaction energies are obtained from geometry relaxation calculations and CCSD(T)/CBS evaluations. The insertion kinetics is treated with traditional variational TST methods employing CCSD(T)/CBS energies obtained along the CASPT2/cc-pVTZ distinguished coordinate reaction paths. The overall rate constant and branching fractions are obtained from a multiple transition state model that accounts for the physical distinction between tight inner and loose outer transition states. The predicted rate constants, which cover the range from 200 to 2000 K, are found to be in excellent agreement with the available experimental data, with a maximum observed discrepancy of about 40%.

The cyclopentadienyl radical (cC(5)H(5)) is among the most stable radical species that can be generated during the combustion and pyrolysis of hydrocarbons and it is generally agreed that its contribution to the gas phase reactivity is significant. In this study the kinetics of one key cC(5)H(5) reaction channel, namely the reaction between cC(5)H(5) and cyclopentadiene (cC(5)H(6)), was investigated using ab initio calculations and RRKM/Master Equation theory. It was found that most of the excited C(5)H(5)_C(5)H(6) adducts formed by the addition of cC(5)H(5) to cC(5)H(6) decompose back to reactants and that the major reaction products are, in order of importance, indene, vinylfulvene (a most probable styrene precursor), phenylbutadiene, and benzene. The preferred reaction pathway of the C(5)H(5)_C(5)H(6) adduct is started by the migration of the tertiary hydrogen of the C(5)H(5) ring to a vicinal carbon and followed by the β-opening of the C(5)H(6) ring, which is the rate determining step. Successive molecular rearrangements lead to decomposition to the four possible products. The kinetic constants for the four reaction channels, calculated at atmospheric pressure and interpolated in cm(3) mol(-1) s(-1) between 900 and 2000 K, are k(indene) = 10(25.197)T(-3.935) exp(-11630/T(K)), k(vinylfulvene) = 10(65.077)T(-14.20) exp(-37567/T(K)), k(benzene) = 10(29.172)T(-4.515) exp(-20570/T(K)), and k(phenylbutadiene) = 10(16.743)T(-1.407) exp(-11804/T(K)). The predictive capability of the reaction set so determined was tested through the simulations of recent cC(5)H(6) pyrolysis and combustion experiments using a detailed kinetic mechanism. A quantitative agreement with experimental data was obtained by assuming that vinylfulvene converts rapidly to stryrene, increasing its reaction channel by a factor of 2, and assuming that phenylbutadiene rapidly decomposes with equal probability to styrene and benzene.

The high temperature decomposition kinetics of toluene and benzyl were investigated by combining a kinetic analysis with the ab initio/master equation study of new reaction channels. It was found that similarly to toluene, which decomposes to benzyl and phenyl losing atomic hydrogen and methyl, also benzyl decomposition proceeds through two channels with similar products. The first leads to the formation of fulvenallene and hydrogen and has already been investigated in detail in recent publications. In this work it is proposed that benzyl can decompose also through a second decomposition channel to form benzyne and methyl. The channel specific kinetic constants of benzyl decomposition were determined by integrating the RRKM/master equation over the C(7)H(7) potential energy surface. The energies of wells and saddle points were determined at the CCSD(T) level on B3LYP/6-31+G(d,p) structures. A kinetic mechanism was then formulated, which comprises the benzyl and toluene decomposition reactions together with a recently proposed fulvenallene decomposition mechanism, the decomposition kinetics of the fulvenallenyl radical, and some reactions describing the secondary chemistry originated by the decomposition products. The kinetic mechanism so obtained was used to simulate the production of H atoms measured in a wide pressure and temperature range using different experimental setups. The calculated and experimental data are in good agreement. Kinetic constants of the new reaction channels here examined are reported as a function of temperature at different pressures. The mechanism here proposed is not compatible with the assumption often used in literature kinetic mechanisms that benzyl decomposition can be effectively described through a lumped reaction whose products are the cyclopentadienyl radical and acetylene.

The dissociation kinetics of germane and its decomposition products were studied determining microcanonical kinetic constants with RRKM theory and integrating the master equation using a stochastic approach. Relevant reaction parameters were calculated through first principles calculations. Structures of reactants and transition states were determined at the B3LYP/aug-cc-pvtz level while energies were computed at the CCSD(T) level and extended to the complete basis set limit. Though similar for many aspects to the kinetics of decomposition of SiH(4), GeH(4) has some peculiar features that indicate a different chemical reactivity. It was found that the main decomposition channel leads to the formation of germylene, GeH(2), which rapidly decomposes to atomic Ge and H(2). The dissociation of GeH(2) to Ge and H(2) is a formally spin forbidden reaction characterized by an activation energy of 160.3 kJ mol(-1) calculated at the minimum energy crossing point between the singlet and triplet states. The intersystem crossing probability was explicitly included in the microcanonical simulations through Landau-Zener theory. It was found that its effect on the reaction rate is almost negligible, both because of the large spin-orbit coupling between the singlet and triplet states and for the fall off conditions prevailing in the examined pressure and temperature ranges. Kinetic constants of the main decomposition channels were determined as a function of pressure and temperature between 0.0013 and 10 bar and 1100 and 1700 K. The high and low pressure kinetic constants for GeH(4) decomposition are 6.4 x 10(13) (T/K)(0.272) exp(-26 700 K/T) and 2.7 x 10(48) (T/K)(-9.05) exp(-31 600 K/T), while those for GeH(2) are 6.02 x 10(12) (T/K)(0.203) exp(-19 660 K/T) and 1.6 x 10(26) (T/K)(-3.06) exp(-21 121 K/T), respectively. A quantitative agreement with experimental data for GeH(4) decomposition could be obtained adopting a downward energy transfer parameter of 340 x (T/298 K)(0.85) cm(-1) in the collisional model, and assuming that atomic Ge can react fast with GeH(4) to form Ge(2)H(2) and H(2), thus enhancing the germane decomposition rate and suggesting that a fast kinetic route leading to the Ge(2)H(2) production can be active in the gas phase.

CO2 has attracted considerable attention in recent years due to its role in the greenhouse effect and environmental management. While its reaction with water has been studied extensively, the same cannot be said for reactivity in the supercritical CO2 phase, where the conjugate acid/base equilibria proceed through different mechanisms and activation barriers. In spite of the apparent simplicity of the CO2 + H2O reaction, the collective effect of different environments has a drastic influence on the free energy profile. Enhanced sampling techniques and well-tailored collective variables provide a detailed picture of the enthalpic and entropic drivers underscoring the differences in the formation mechanism of carbonic acid in the gas, aqueous, and supercritical CO2 phases.

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(}$$\mu$$\mathrm{-H)BH_3}$) leads to the release of $\mathrm{NH_4^+}$, which in turn triggers an autocatalytic $\mathrm{H_2}$ production cycle. Our calculations provide a model for how complex solid state reactions can be theoretically investigated and rely upon the presence of multiple ammonia borane molecules, as substantiated by standard quantum-mechanical simulations on a cluster.

We have studied the cyclization reaction of deprotonated 4-chloro-1-butanethiol to tetrahydrothiophene by means of well-tempered metadynamics. To properly select the collective variables, we used the recently proposed variational approach to conformational dynamics within the framework of metadyanmics. This allowed us to select the appropriate linear combinations from a set of collective variables representing the slow degrees of freedom that best describe the slow modes of the reaction. We performed our calculations at three different temperatures, namely, 300, 350, and 400 K. We show that the choice of such collective variables allows one to easily interpret the complex free-energy surface of such a reaction by univocal identification of the conformers belonging to reactants and product states playing a fundamental role in the reaction mechanism.