qcscine/readuct: Release 2.0.0

Brunken, Christoph; Steiner, Miguel; Unsleber, Jan P.; Vaucher, Alain C.; Weymuth, Thomas; Reiher, Markus

doi:10.5281/zenodo.3768539

Cited by 2 publications

(2 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…If none of these transition state searches are successful, we attempt a different approach. Using the spline-based reaction path method 49 in the Scine ReaDuct 50,51 software we optimize the minimum energy path between reactant and product and then attempt another TS search at the geometry corresponding to the maximum in the reaction path. There are of course cases where there is no defined barrier to the reaction and in the particular case where the reaction is either an association (two reactants one product)…”

Section: Optimization and Refinement Of The Stationary Points Of Disc...mentioning

confidence: 99%

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

Shannon

Martı́nez-Núñez

Shalashilin

et al. 2021

J. Chem. Theory Comput.

View full text Add to dashboard Cite

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.

show abstract

Section: Optimization and Refinement Of The Stationary Points Of Disc...mentioning

confidence: 99%

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

Shannon

Martı́nez-Núñez

Shalashilin

et al. 2021

J. Chem. Theory Comput.

View full text Add to dashboard Cite

show abstract

“…The final source code used to place the solvent molecules is released with the current version of the SCINE Utilities. 90 For GFN-FF 91 and also GFN2-xTB, 59 their electronic energies and nuclear gradients were forwarded to SCINE Readuct 92,93 for the optimization.…”

Section: Optimization Based Micro-solvation Setupmentioning

confidence: 99%

Solvation Free Energies in Subsystem Density Functional Theory

Bensberg,

Türtscher,

Unsleber

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for the explicit quantum mechanical description of solute-solvent and solvent-solvent interactions based on subsystem density functional theory and continuum solvation schemes. Since explicit solvent molecules may compromise scalability of the model and transferability of the predicted solvent effect, we aim to retain both, for different solutes as well as for different solvents. The key for the transferability is the consistent subsystem decomposition of solute and solvent.The key for the scalability is the performance of subsystem DFT for increasing numbers of subsystems. We investigate molecular dynamics and stationary point sampling of solvent configurations and compare the resulting (Gibbs) free energies to experiment and theoretical methods. We can show that with our hybrid model reaction barriers and reaction energies are accurately reproduced compared to experimental data.

show abstract

qcscine/readuct: Release 2.0.0

Cited by 2 publications

References 0 publications

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

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

Solvation Free Energies in Subsystem Density Functional Theory

Contact Info

Product

Resources

About