arXiv subjects

Robin J. Shannon

Publications and source records attributed to Robin J. Shannon.

6 recordsLinked to original sources

arXiv2021

AutoMeKin2021: An open-source program for automated reaction discovery

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922-1930). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin

physics.chem-ph↗

arXiv2021

ChemDyME: Kinetically Steered, Automated Mechanism Generation Through Combined Molecular Dynamics and Master Equation Calculations

In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development of automated methods for exploring chemical reactivity or conformational change in a black box manner, harnessing modern computing resources to automate mechanism discovery. In this work we present a new approach to automated mechanism generation implemented which couples molecular dynamics and statistical rate theory to automatically find kinetically important reactions and then solve the time evolution of the species in the evolving network. Key to this ChemDyME approach is the novel concept of kinetic convergence whereby the search for new reactions is constrained to those species which are kinetically favorable at the conditions of interest. We demonstrate the capability of the new approach for two systems, a well-studied combustion system, and a multiple oxygen addition system relevant to atmospheric aerosol formation.

physics.chem-ph↗

arXiv2021

Nonadiabatic kinetics in the intermediate coupling regime: comparing molecular dynamics to an energy grained master equation

Here we outline and test an extension of the energy grained master equation (EGME) for treating nonadiabatic (NA) hopping between different potential energy surfaces, which enables us to model the competition between stepwise collisional relaxation and kinetic processes which transfer population between different potential energy surfaces of the same spin symmetry. By incorporating Zhu-Nakamura theory into the EGME, we are able to treat nonadiabatic passages beyond the simple Landau-Zener approximation, along with corresponding treatments of zero-point energy and tunnelling probability. To evaluate this NA-EGME approach, we carried out detailed studies of the UV photodynamics of the volatile organic compound C6-hydroperoxyaldehyde (C6-HPALD) using on-the-fly ab initio molecular dynamics and trajectory surface hopping. For this multi-chromophore molecule, we show that the EGME is able to quantitatively capture important aspects of the dynamics, including kinetic timescales, and diabatic trapping. Such an approach provides a promising and efficient strategy for treating the long-time dynamics of photo-excited molecules in regimes which are difficult to capture using atomistic on-the-fly molecular dynamics.

physics.chem-ph↗

arXiv2019

Enhancing automated reaction discovery with boxed molecular dynamics in energy space

The rare event acceleration method BXDE is interfaced in the present work with the automated reaction discovery method AutoMeKin. To test the efficiency of the combined AutoMeKin-BXDE procedure, the ozonolysis of a-pinene is studied in comparison with standard AutoMeKin. AutoMeKin-BXDE locates intermediates and transition states that are more densely connected with each other and approximately 50 kcal/mol more stable than those found with standard AutoMeKin. Other than the different density of edges between the nodes, both networks are scale-free and display small-world properties, mimicking the network of organic chemistry. Finally, while AutoMeKin-BXDE finds more transition states than those previously reported for O3 + a-pinene, the standard procedure fails to locate some of the previously published reaction pathways using the same simulation time of 2.5 ns. In summary, the mixed procedure is very promising and clearly outperforms the standard simulation algorithms implemented in AutoMeKin. BXDE will be available in the next release of AutoMekin.

physics.chem-ph↗

arXiv2019

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects, because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often non-intuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline efforts to extend immersive technologies to the molecular sciences, and we introduce 'Narupa', a flexible, open-source, multi-person iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn reactive potential energy surfaces (PESs), biomolecular conformational sampling, protein-ligand binding, reaction discovery using 'on-the-fly' quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances, and how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies like iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.

physics.chem-ph↗

arXiv2014

The fast C(3P) + CH3OH reaction as an efficient loss process for gas-phase interstellar methanol

Rate constants for the C(3P) + CH3OH reaction have been measured in a continuous supersonic flow reactor over the range 50 K to 296 K. C(3P) was created by the in-situ pulsed laser photolysis of CBr4, a multiphoton process which also produced some C(1D), allowing us to investigate simultaneously the low temperature kinetics of the C(1D) + CH3OH reaction. C(1D) atoms were followed by an indirect chemiluminescent tracer method in the presence of excess CH3OH. C(3P) atoms were detected by the same chemiluminescence technique and also by direct vacuum ultra-violet laser induced fluorescence (VUV LIF). Secondary measurements of product H(2S) atom formation have been undertaken allowing absolute H atom yields to be obtained by comparison with a suitable reference reaction. In parallel, statistical calculations have been performed based on ab-initio calculations of the complexes, adducts and transition states (TSs) relevant to the title reaction. By comparison with the experimental H atom yields, the preferred reaction pathways could be determined, placing important constraints on the statistical calculations. The experimental and theoretical work are in excellent agreement, predicting a negative temperature dependence of the rate constant increasing from 2.2 x 10-11 cm3 molecule-1 s-1 at 296 K to 20.0 x 10-11 cm3 molecule-1 s-1 at 50 K. CH3 and HCO are found to be the major products under our experimental conditions. As this reaction is not considered in current astrochemical networks, its influence on interstellar methanol abundances is tested using a model of dense interstellar clouds.

astro-ph.GA↗