Caracal: A Versatile Ring Polymer Molecular Dynamics Simulation Package

A new open-source program package named Caracal covering simulations of molecular systems with ring polymer molecular dynamics (RPMD) is presented. It combines a powerful RPMD implementation including chemical reaction rate calculations and biased periodic and nonperiodic samplings with a collection of easy to set up potential energy surface (PES) methodologies, thus delivering an all-inclusive approach. Most implemented PESs are based on the QMDFF and EVB-QMDFF methods. Where the quantum mechanically derived force field (QMDFF) can be set up for an arbitrary molecular system in a black-box fashion, the empirical valence bond (EVB)-QMDFF connects two QMDFFs and is able to represent the PES of a chemical reaction. With our previously published flavors of this composite method, PESs for almost arbitrary gas phase thermal ground state reactions can be set up. Given an optimized reaction path, the mechanism of the reaction can be classified and RPMD rate constants can be obtained via umbrella sampling and recrossing calculations on an EVB-QMDFF PES. Further, QMDFFs can be polymerized for the description of liquid systems. In this paper, the internal structure as well as the handling philosophy of Caracal are outlined. Further, examples of the different possible kinds of calculations are given.

Gas Phase Formation of Methylgermylene (HGeCH3)

The methylgermylene species (HGeCH₃ ; X¹ A') has been synthesized via the bimolecular gas phase reaction of ground state methylidyne radicals (CH) with germane (GeH₄ ) under single collision conditions in crossed molecular beams experiments. Augmented by electronic structure calculations, this elementary reaction was found to proceed through barrierless insertion of the methylidyne radical in one of the four germanium-hydrogen bonds on the doublet potential energy surface yielding the germylmethyl (CH₂ GeH₃ ; X² A') collision complex. This insertion is followed by a hydrogen shift from germanium to carbon and unimolecular decomposition of the methylgermyl (GeH₂ CH₃ ; X² A') intermediate by atomic hydrogen elimination leading to singlet methylgermylene (HGeCH₃ ; X¹ A'). Our investigation provides a glimpse at the largely unknown reaction dynamics and isomerization processes of the carbon-germanium system, which are quite distinct from those of the isovalent carbon system thus providing insights into the intriguing chemical bonding of organo germanium species on the most fundamental, microscopic level.

Kinetics and dynamics study of the OH + C2H6 → H2O + C2H5 reaction based on an analytical global potential energy surface

To describe the gas-phase hydrogen abstraction reaction between the hydroxyl radical and the ethane molecule, an analytical full-dimensional potential energy surface was developed within the Born-Oppenheimer approximation. This reactive process is a ten-body system with 24 degrees of freedom, which represents a theoretical challenge. The new surface, named PES-2020, presents low barrier, 3.76 kcal mol-1, high exothermicity, -16.20 kcal mol-1, and intermediate complexes in the entrance and exit channels. To test the quality and accuracy of the analytical surface several stringent tests were performed and, in general, PES-2020 reasonably simulates the theoretical information used as input, it is a continuous and smooth potential, without spurious minima, it presents great versatility and a reasonable description of this ten-body reaction. Based on this surface, an exhaustive kinetics and dynamics study was performed with a double objective: to analyze the capacity of the new surface to simulate the experimental evidence, and to help understand the mechanism of reaction and the role of the ethyl group in the reaction. In the kinetics study, three approaches were used: variational transition-state theory with multidimensional tunnelling (VTST/MT), ring polymer molecular dynamics (RPMD) and quasi-classical trajectory (QCT) results, in the temperature range 200-2000 K. There is general agreement between the three approaches and they reasonably simulate the experimental behaviour, which gives confidence to the fitness of the new surface to describe the system. In the dynamics study, QCT calculations were performed at 298 K for a direct comparison with the only experimental result reported. We found that ethyl fragment presents a noticeable internal energy (∼20%) and so cannot be considered as a spectator. The water product vibrational energy is reasonably reproduced, though when a level-by-level distribution is analyzed the agreement is only qualitative.

Mechanism study of ammonium nitrate decomposition with chloride impurity using experimental and molecular simulation approach

Fire/explosion due to ammonium nitrate (AN) decomposition poses significant safety hazards which are exacerbated in the presence of salts including potassium chloride (KCl). In this work, key thermal parameters of AN decomposition over a range of KCl mass fraction were experimentally measured using advanced reactive chemical screening tool (ARSST). Based on experimental findings and past literature review, AN/KCl decomposition mechanism was proposed consisting of four separate pathways, specifically, (i) direct AN main decomposition pathway, (ii) indirect AN main decomposition pathway via chlorine radical, (iii) direct pure AN side decomposition pathway and (iv) indirect AN side decomposition pathway via chlorine radical. Gaussian software was used to estimate activation energies for each reaction step involved in the proposed mechanism via density function theory (DFT). The computational chemistry model explained experimental data with good agreement. Both computational and experimental findings confirm that chlorine radical reduce reaction barrier of AN decomposition via indirect pathways (ii) and (iv). As these indirect decomposition pathways are more exothermic than the primary paths (i), (iii), KCl addition not only accelerates AN decomposition but also increases reaction heat release.

Chemical Kinetics Approves the Occurrence of C (3Pj) Reaction with H2O

Although both atomic carbon and water are omnipresent in human life, there is a debate about the possibility of carbon reaction with water. Some low-temperature spectroscopic investigations have rejected the reaction, whereas some room-temperature experiments and theoretical studies have accepted the possibility of the reaction by reporting rate coefficients ranging from 10⁵ to 10⁹ L mol^-1 s^-1. This study provides new lines of evidence about the reaction through exploration of the reaction mechanism using the CCSD(T) method and solving the corresponding master equation by following two main approaches. According to the results, the rate coefficient of the reaction is significantly influenced by the tunneling and hindered rotation effects, in addition to the selected total angular momentum (J). Furthermore, the total rate coefficient of the reaction increases dramatically (from 10⁷ to 10¹¹ L mol^-1 s^-1) with the rise of temperature from 100 to 4000 K, while the total rate coefficient is insensitive to pressure (0.1-10 atm). Despite some differences between the results of the two approaches, the rate coefficients of both methods are consistent with the previously reported rate coefficients. Also, in agreement with the previous studies, the major products are ²HOC + ²H and ²HCO + ²H. In general, the findings approve the occurrence of the title reaction and indicate that the mentioned conflict is due to the sensitivity of the reaction to the investigated temperature and J level. The sensitivity does not permit low-temperature spectroscopic studies to detect any products and varies the measured and calculated rate coefficients.

F(2P) + C2H6 → HF + C2H5 kinetics study based on a new analytical potential energy surface

An exhaustive kinetics study was performed for the title reaction using two theoretical approaches: variational transition-state theory and quasi-classical trajectory calculations, based on an original new analytical full-dimensional potential energy surface, named PES-2018, which has been fitted to high-level ab initio calculations.

QCT dynamics study of OH/OD + GeH4 reactions. The problem of water bending excitation

The difficulties in the description of the water bending population could be related to the zero-point violation problem in QCT calculations.

Kinetics study of the CN + CH4 hydrogen abstraction reaction based on a new ab initio analytical full-dimensional potential energy surface

We have developed an analytical full-dimensional potential energy surface, named PES-2017, for the gas-phase hydrogen abstraction reaction between the cyano radical and methane.

Variational transition state theory: theoretical framework and recent developments

This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications.