Multi-level Protocol for Mechanistic Reaction Studies Using Semi-local Fitted Potential Energy Surfaces

In this work, we propose a multi-scale protocol for routine theoretical studies of chemical reaction mechanisms. The initial reaction paths of our investigated systems are sampled using the Nudged-Elastic Band (NEB) method driven by a cheap electronic structure method. Forces recalculated at the more accurate electronic structure theory for a set of points on the path are fitted with a machine-learning technique (in our case symmetric gradient domain machine learning or sGDML) to produce a semi-local reactive Potential Energy Surface (PES), embracing reactants, products and transition state (TS) regions. This approach has been successfully applied to a unimolecular (Bergman cyclization of enediyne) and a bimolecular (S$_\text{N}$2 substitution) reaction. In particular, we demonstrate that with only 50 to 150 energy-force evaluations with the accurate reference methods (here CASSCF and CCSD) it is possible to construct a semi-local PES giving qualitative agreement for stationary-point geometries, intrinsic reaction-coordinates and barriers. Furthermore, we find a qualitative agreement in vibrational frequencies and reaction rate coefficients. The key aspect of the method's performance is its multi-scale nature, which not only saves computational effort but also allows extracting meaningful information along the reaction path, characterized by zero gradients in all but one direction. Agnostic to the nature of the TS and computationally economic, the protocol can be readily automated and routinely used for mechanistic reaction studies

Shallow and deep trap states of solvated electrons in methanol and their formation, electronic excitation, and relaxation dynamics

We present condensed-phase first-principles molecular dynamics simulations to elucidate the presence of different electron trapping sites in liquid methanol and their roles in the formation, electronic transitions, and relaxation of solvated electrons (emet−) in methanol. Excess electrons injected into liquid methanol are most likely trapped by methyl groups, but rapidly diffuse to more stable trapping sites with dangling OH bonds. After localization at the sites with one free OH bond (1OH trapping sites), reorientation of other methanol molecules increases the OH coordination number and the trap depth, and ultimately four OH bonds become coordinated with the excess electrons under thermal conditions. The simulation identified four distinct trapping states with different OH coordination numbers. The simulation results also revealed that electronic transitions of emet− are primarily due to charge transfer between electron trapping sites (cavities) formed by OH and methyl groups, and that these transitions differ from hydrogenic electronic transitions involving aqueous solvated electrons (eaq−). Such charge transfer also explains the alkyl-chain-length dependence of the photoabsorption peak wavelength and the excited-state lifetime of solvated electrons in primary alcohols

Dynamics of the Bulk Hydrated Electron from Many‐Body Wave‐Function Theory

The structure of the hydrated electron is a matter of debate as it evades direct experimental observation owing to the short life time and low concentrations of the species. Herein, the first molecular dynamics simulation of the bulk hydrated electron based on correlated wave‐function theory provides conclusive evidence in favor of a persistent tetrahedral cavity made up by four water molecules, and against the existence of stable non‐cavity structures. Such a cavity is formed within less than a picosecond after the addition of an excess electron to neat liquid water, with less regular cavities appearing as intermediates. The cavities are bound together by weak H−H bonds, the number of which correlates well with the number of coordinated water molecules, each type of cavity leaving a distinct spectroscopic signature. Simulations predict regions of negative spin density and a gyration radius that are both in agreement with experimental data

Application of classical simulations for the computation of vibrational properties of free molecules

In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS2, benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I2-1,2-closo-C2B10H10. The MD sampling of NVT ensembles was performed using chains of Nose–Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post–Hartree–Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension

Franck–Condon theory of quantum mechanochemistry

The spectroscopic Franck-Condon (FC) principle is extended to mechanochemistry. If the external force is applied rapidly (the sudden-force regime), then the transition between the potential energy surface and the force-modified potential energy surface is analogous to the optical electronic transition. Such a transition produces a nonequilibrium ensemble of vibrationally excited molecules. This excess of vibrational energy is another activation source in addition to the well-known reaction barrier modulation by the external force. In the same time, the nonequilibrium vibrational distribution implies nonstatistical kinetics of a mechanochemical transformation. Mechanochemical FC principle thus provides a conceptual picture for the sudden-force mechanochemistry and opens possibilities for quantitative calculations of the mechanochemical rates and mechanisms. Here we use it to compute the dissociation rates of a model diatomic molecule and to explain the selectivity in mechanochemical bond breaking in n-butane. The approach is predicted to be relevant for large-magnitude external forces, applied instantaneously. Otherwise, the excess vibrational energy will dissipate due to intramolecular vibrational redistribution and interaction with environment

Development of Direct Born–Oppenheimer Molecular Dynamics with Applications to Water Clusters and Mechanochemistry

New methods for Born-Oppenheimer molecular dynamics simulations have been developed and used to study protonated water clusters and mechanochemistry of alkanes. The novel algorithms are an efficient coordinate transformation and sampling microcanonical ensembles of trajectories used for generating starting conditions for simulations. In combination with existing techniques as well as with electronic structure methods within DALTON program, they make it a powerful tool to study reaction dynamics, free of charge. This has been demonstrated by investigation of protonated water clusters relevant for water nucleation in atmospheric chemistry. The structure of the proton salvation shell and evaporation kinetics have been revealed. Another application is the dynamics of alkanes under mechanical stress. Short-chain alkanes – butane and octane – are model compounds for polymers. Their dynamical behavior was simulated and analyzed under two scenarios mimicking the modes ofmechanochemical activation: slow stretching in the atomic-force microscope and violent action of ultrasound

Mechanism of Aqueous Carbon Dioxide Reduction by the Solvated Electron

Aqueous solvated electron (eaq–), a key species in radiation and plasma chemistry, can efficiently reduce CO2 in a potential green chemistry application. Here, the mechanism of this reaction is unravelled by condensed-phase molecular dynamics based on the correlated wave function and an accurate density functional theory (DFT) approximation. Here, we design and apply the holistic protocol for solvated electron’s reactions encompassing all relevant reaction stages starting from diffusion. The carbon dioxide reduction proceeds via a cavity intermediate, which is separated from the product (CO2–) by an energy barrier due to the bending of CO2 and the corresponding solvent reorganization energy. The formation of the intermediate is caused by solvated electron’s diffusion, whereas the intermediate transformation to CO2– is triggered by hydrogen bond breaking in the second solvation shell of the solvated electron. This picture of an activation-controlled eaq– reaction is very different from both rapid barrierless electron transfer and proton-coupled electron transfer, where key transformations are caused by proton migration

Double-Hybrid DFT Functionals for the Condensed Phase: Gaussian and Plane Waves Implementation and Evaluation

Intermolecular interactions play an important role for the understanding of catalysis, biochemistry and pharmacy. Double-hybrid density functionals (DHDFs) combine the proper treatment of short-range interactions of common density functionals with the correct description of long-range interactions of wave-function correlation methods. Up to now, there are only a few benchmark studies available examining the performance of DHDFs in condensed phase. We studied the performance of a small but diverse selection of DHDFs implemented within Gaussian and plane waves formalism on cohesive energies of four representative dispersion interaction dominated crystal structures. We found that the PWRB95 and ωB97X-2 functionals provide an excellent description of long-ranged interactions in solids. In addition, we identified numerical issues due to the extreme grid dependence of the underlying density functional for PWRB95. The basis set superposition error (BSSE) and convergence with respect to the super cell size are discussed for two different large basis sets