ChemShell News and Highlights

Understanding how oxygen vacancies affect conductivity in transparent conducting oxides

Thursday, 18 April, 2019

The role of oxygen vacancies in the transparent conducting oxides (TCOs) In2O3, SnO2 and ZnO has remained controversial, with some studies indicating that they act as shallow donors, but many computational studies using plane-wave supercell techniques claiming that they act as deep traps. Using the hybrid QM/MM embedded cluster technique via the ChemShell code, we calculated the formation and thermal ionisation energies of oxygen vacancies in the three TCOs.

We found that, in In2O3 vacancies acted as shallow donors and accounted for the large n-type carrier concentrations observed experimentally in undoped samples. Furthermore, we computed equilibrium defect and carrier concentrations, showing that, even in ZnO and SnO2, where the vacancies formed deep centres, they contributed significantly to intrinsic carrier concentrations.

Citation: 

J. Buckeridge, C. R. A. Catlow, M. R. Farrow, A. J. Logsdail, D. O. Scanlon, T. W. Keal, P. Sherwood, S. M. Woodley, A. A. Sokol, and A. Walsh, "Deep vs shallow nature of oxygen vacancies and consequent n-type carrier concentrations in transparent conducting oxides", Phys. Rev. Materials, 2018, 2, 054604.

 


Water formation in the interstellar medium

Tuesday, 16 April, 2019

Chemical reactions in the interstellar medium occur at low temperature, often on ice surfaces. Those are found to enhance chemical reactivity. In combination with atom tunnelling, reactions with a significant activation barrier can take place even at the cryogenic temperatures of outer space.

To model the chemical environment of water formation, we calculated rate constants with semiclassical instanton theory and the QM/MM approach. For that, ChemShell was a crucial tool enabling easy setup and communication between the electronic structure calculations, the force field, and the DL-FIND geometry optimisation library.

We found that atom tunnelling is responsible for this reaction to proceed with a rate constant more than three orders of magnitude higher than classically expected at a temperature of 150 K. These reaction rate constants are currently used to model the chemical kinetics in interstellar objects, ranging from molecular clouds to protoplanetary disks.

Citation: 

J. Meisner, T. Lamberts, and J. Kästner, "Atom Tunneling in the Water Formation Reaction H2 + OH → H2O + H on an Ice Surface", ACS Earth Space Chem., 2017, 1, 399-410.

 


Unravelling of the reaction mechanism and tunnelling contributions in Taurine Dioxygenase

Thursday, 28 March, 2019

The biochemical turnover of taurin is catalysed by taurine dioxygenase, aided by molecular oxygen and alpha-ketogluterate. The rate-limiting step is a hydrogen atom transfer for which a significant kinetic isotope effect was found experimentally. To study it with high predictive power, quantum mechanics is needed for the chemical transformations at the catalytic centre, but the protein environment also needs to be taken into account. Since a full quantum description is computationally infeasible, a QM/MM approach was used.

"ChemShell was invaluable for this project as it took over the coupling of the quantum mechanics program and the force field, as well as the geometry optimisations and rate calculations", says Sonia Álvarez-Barcia from the University of Stuttgart, Germany, who conducted the study. The simulations found that atom tunnelling increases the efficiency of the enzyme by a factor of 40 and explains the strong kinetic isotope effect.

 


Highlight your research on this site!

Tuesday, 26 March, 2019

If you've used ChemShell in published research, we would like to highlight it on this page and on our Twitter feed to help publicise your work and demonstrate the capabilities of the program.

If you would like to highlight your research here please email Tom Keal (thomas.keal [at] stfc.ac.uk) with the subject "chemshell.org research highlight", including the following in your email:

    Headline: a one-sentence description of your research.
    Text: a brief summary of your research focussing on results obtained with ChemShell (maximum 150 words). Include researcher names, affiliations etc. as appropriate.
    Image (optional): a small "table of contents" style image (no larger than 500x250) to illustrate the research.
    Citation: the full citation of your publication including DOI.

NB: By submitting this information you consent to it being published on this website and on social media. Please ensure you hold the copyright for all the information you submit (or it is licenced in a way that permits sharing). Submissions may be edited for clarity.

 


Py-ChemShell 2019 released

Monday, 25 March, 2019

We are pleased to announce Py-ChemShell 2019 (v19.0), the first beta release of the Python-based version of ChemShell.

Py-ChemShell 2019 offers new interfaces to ORCA and DL_POLY 4, a complete task-farmed parallelisation framework (including parallel finite difference gradients), RESP charge fitting procedures, and case studies for problems in materials modelling.

The new version represents a major advance on the alpha release with substantial improvements to every part of the underlying code base. We now regard Py-ChemShell as suitable for production calculations on materials systems, although you may find some features from Tcl-ChemShell are still missing (we're working on it...). If you are a biomolecular modeller we recommend continuing to use Tcl-ChemShell for now but automated import of biomolecular forcefields is coming soon.

Py-ChemShell can be downloaded free of charge under the open source GNU LGPL v3 licence from this site. If you have any questions about the code, please get in touch via the user forums.

 


ChemShell redevelopment work published

Thursday, 3 January, 2019

The project to redevelop ChemShell as a python-based program has been published in the Journal of Chemical Theory and Computation.

The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, and new interfaces to high performance QM and MM programs. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate in the article with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.

Citation: 

Y. Lu, M. R. Farrow, P. Fayon, A. J. Logsdail, A. A. Sokol, C. R. A. Catlow, P. Sherwood, and T. W. Keal, "Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment", J. Chem. Theory Comput., 2019, 15, 1317-1328.

 
 

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