Scalable Quantum Chemistry with Flexible Embedding Stage 2
Lead Research Organisation:
Science and Technology Facilities Council
Department Name: Computational Science & Engineering
Abstract
In stage two of the "Scalable Quantum Chemistry with Flexible Embedding" project we propose to refine the software we have developed in stage one for molecular modelling of reactivity in complex systems, in particular surface chemistry and heterogeneous catalysis in the presence of a solvent such as water. This software combines quantum chemistry (also known as first principles) techniques, which can treat the chemically reacting centres, embedded in an empirical (molecular mechanics) model for the rest of the system, i.e. the slab of material which models the surface and the solvent layers on top of it.
In stage one we are extending our embedding model to include new treatments for spin-polarised systems such as magnetically ordered materials, an implementation of a low-cost quantum method to describe anisotropic and spin-polarised environments and periodic boundary conditions in order to perform calculations on solvated surfaces. Examples of the science this software targets includes metal oxide catalysis that work in the presence or water; the binding of pollutant species (heavy metals or toxic organics) to natural minerals in the environment, or specially designed inorganic materials that could potentially remove them from the environment; catalysis by more complex minerals, not well treated by existing treatments but of great industrial importance; and the design of sensors and photoelectric materials by organic layers on inorganic surfaces.
The aim of stage two is to make it is as straightforward as possible for new users to set up and run flexible embedding calculations based on the methods developed in stage one, and for advanced users to adapt the code to their own needs. We will achieve this by replacing the user interface the stage one code, which is able to achieve the scientific goals of stage one but is many-layered and relies on a legacy software package, with a new direct user interface written in the popular scripting language Python. The new interface will radically simplify use and development of the code without compromising on the primary goal of stage one, namely achieving high performance for the new embedding models on large-scale parallel machines.
We will incorporate all the key functionality from our legacy codebase into the new version of the code, including utilities to set up embedded cluster calculations, an advanced geometry optimisation library, and the ability to interface to multiple quantum mechanical and molecular mechanical software packages, in particular the FHI-AIMS package which will be coupled to the code in collaboration with the FHI-AIMS developers. We also aim to make the new code as user-friendly as possible through the development of comprehensive documentation, tutorials and case studies from the demonstration applications program began in stage one.
By the end of stage two we will have a new version of the code that is ready for release to the community, with all the key functionality of the legacy version implemented, and we will be in a position to transition users to the new code and use it as our platform for all future QM/MM and multiscale developments.
In stage one we are extending our embedding model to include new treatments for spin-polarised systems such as magnetically ordered materials, an implementation of a low-cost quantum method to describe anisotropic and spin-polarised environments and periodic boundary conditions in order to perform calculations on solvated surfaces. Examples of the science this software targets includes metal oxide catalysis that work in the presence or water; the binding of pollutant species (heavy metals or toxic organics) to natural minerals in the environment, or specially designed inorganic materials that could potentially remove them from the environment; catalysis by more complex minerals, not well treated by existing treatments but of great industrial importance; and the design of sensors and photoelectric materials by organic layers on inorganic surfaces.
The aim of stage two is to make it is as straightforward as possible for new users to set up and run flexible embedding calculations based on the methods developed in stage one, and for advanced users to adapt the code to their own needs. We will achieve this by replacing the user interface the stage one code, which is able to achieve the scientific goals of stage one but is many-layered and relies on a legacy software package, with a new direct user interface written in the popular scripting language Python. The new interface will radically simplify use and development of the code without compromising on the primary goal of stage one, namely achieving high performance for the new embedding models on large-scale parallel machines.
We will incorporate all the key functionality from our legacy codebase into the new version of the code, including utilities to set up embedded cluster calculations, an advanced geometry optimisation library, and the ability to interface to multiple quantum mechanical and molecular mechanical software packages, in particular the FHI-AIMS package which will be coupled to the code in collaboration with the FHI-AIMS developers. We also aim to make the new code as user-friendly as possible through the development of comprehensive documentation, tutorials and case studies from the demonstration applications program began in stage one.
By the end of stage two we will have a new version of the code that is ready for release to the community, with all the key functionality of the legacy version implemented, and we will be in a position to transition users to the new code and use it as our platform for all future QM/MM and multiscale developments.
Planned Impact
Materials research is an underpinning technology for a wide range of UK industries. In the chemicals industry economic and environmental sustainability of processes depends on innovation in the area of catalysis. The emerging area of supported nanoparticulate catalysts depends on the construction of specific metal/support combinations with the particle size and interface with the oxide playing an important role in catalyst performance. Advances in this field will require fundamental understanding of the connection between catalyst structure and activity for which modelling at the quantum level is an indispensible tool. The new software package developed as a result of stage 2 will help improve the range of problems that can be addressed by both academic and industrial researchers in this area, without needing the intimate knowledge of the methods and codes required to operate the transitional workflow in stage 1.
For systems of interest, new fundamental insights will be obtained. Materials are widely used in industrial context, including electronics, catalysis, energy materials, environmentally friendly materials and materials used as filters and sorbents tackling chemical and or radioactive waste. New classes of minerals will be addressed along with their interfaces with water thus impacting on our knowledge in earth sciences (calcite and water cycles) and biominerals (apatite in tooth enamel and bones etc.)
The partners are all active participants in the Collaborative Computational Projects, in particular CCP5 (SCP is chair and CRAC is a past chair). The developments described here are believed to be highly relevant to the use of condensed phase simulation techniques for systems of technological and commercial interest, and it is anticipated that many within the CCP5 network will be able to exploit the software within their own commercial interactions.
STFC and UCL have worked together on an earlier embedding scheme for solids and implemented it in ChemShell. Commercial interest in the model was the main motivation for Accelrys to licence ChemShell as the basis of their QMERA product, which they are now selling commercially. Once the ability of the stage 2 package to interface to multiple QM packages has been demonstrated, it should be straightforward to introduce the required additional functionality into the Accelrys QM code, DMol3, so that the new methods can be exploited by users of Materials Studio, which is widely used in industry.
For systems of interest, new fundamental insights will be obtained. Materials are widely used in industrial context, including electronics, catalysis, energy materials, environmentally friendly materials and materials used as filters and sorbents tackling chemical and or radioactive waste. New classes of minerals will be addressed along with their interfaces with water thus impacting on our knowledge in earth sciences (calcite and water cycles) and biominerals (apatite in tooth enamel and bones etc.)
The partners are all active participants in the Collaborative Computational Projects, in particular CCP5 (SCP is chair and CRAC is a past chair). The developments described here are believed to be highly relevant to the use of condensed phase simulation techniques for systems of technological and commercial interest, and it is anticipated that many within the CCP5 network will be able to exploit the software within their own commercial interactions.
STFC and UCL have worked together on an earlier embedding scheme for solids and implemented it in ChemShell. Commercial interest in the model was the main motivation for Accelrys to licence ChemShell as the basis of their QMERA product, which they are now selling commercially. Once the ability of the stage 2 package to interface to multiple QM packages has been demonstrated, it should be straightforward to introduce the required additional functionality into the Accelrys QM code, DMol3, so that the new methods can be exploited by users of Materials Studio, which is widely used in industry.
Publications
Abdul Nasir J
(2023)
Influence of Solvent on Selective Catalytic Reduction of Nitrogen Oxides with Ammonia over Cu-CHA Zeolite.
in Journal of the American Chemical Society
Aprà E
(2020)
NWChem: Past, present, and future
in The Journal of Chemical Physics
Berger D
(2014)
Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework.
in The Journal of chemical physics
Buckeridge J
(2015)
Determination of the nitrogen vacancy as a shallow compensating center in GaN doped with divalent metals.
in Physical review letters
Buckeridge J
(2018)
Deep vs shallow nature of oxygen vacancies and consequent n -type carrier concentrations in transparent conducting oxides
in Physical Review Materials
Deng W
(2021)
Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations
in Journal of Chemical Information and Modeling
Farrow M
(2014)
From Stable ZnO and GaN Clusters to Novel Double Bubbles and Frameworks
in Inorganics
Gould A
(2015)
Influence of Composition and Chemical Arrangement on the Kinetic Stability of 147-Atom Au-Ag Bimetallic Nanoclusters
in The Journal of Physical Chemistry C
Gould A
(2015)
Understanding the Thermal Stability of Silver Nanoparticles Embedded in a-Si
in The Journal of Physical Chemistry C
Gould A
(2014)
Segregation effects on the properties of (AuAg) 147
in Phys. Chem. Chem. Phys.
Description | The scientific developments from stage 1 of the Scalable Quantum Chemistry with Flexible Embedding project ( EP/I030662/1) have been taken forward into a new python-based computational chemistry environment for QM/MM calculations, the objective of which was to make the stage 1 models accessible to other researchers through the development of a robust, easy-to-use and flexible user interface. Key functionality from the old Tcl-based version of ChemShell to the new python version, such that the legacy code is no longer required to perform materials chemistry QM/MM simulations. The python-based version of ChemShell is now in beta testing by our collaborators and an initial release to the scientific community was made in December 2017. |
Exploitation Route | The python-based version of ChemShell will be of general applicability to all scientific projects involving solid state QM/MM calculations and we expect a quick uptake based on the existing ChemShell user community and the appeal of the open-source licencing model to new users outside the UK. Future work will include porting of features from the legacy code and new developments to support biomolecular QM/MM modelling and other multiscale methods. |
Sectors | Chemicals Digital/Communication/Information Technologies (including Software) Energy Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
URL | http://www.chemshell.org |
Description | This project resulted in the creation of a new piece of software, the Python-based version of the ChemShell computational chemistry environment, initially in alpha form and subsequently through several beta releases with increasing functionality for multiscale modelling. We expect impacts from this project over a long timescale, hopefully 20 years or more, but it is already being used for fundamental research particularly in catalysis and enzymatic modelling, in partnership with leading experimental groups, which will contribute to the development of new technologies in these areas with a wide societal impact, notably in energy materials, green technologies, quantum computing and biotechnology, through work in both academia and industry. Apart from the technological impacts, the software will also be used in STFC's public engagement programme to encourage a new generation of scientists. |
First Year Of Impact | 2021 |
Sector | Chemicals,Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology |
Impact Types | Economic |
Description | BEORHN: Bacterial Enzymatic Oxidation of Reactive Hydroxylamine in Nitrification via Combined Structural Biology and Molecular Simulation |
Amount | £368,451 (GBP) |
Funding ID | BB/V016660/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2022 |
End | 06/2025 |
Description | Particles At eXascale on High Performance Computers (PAX-HPC) |
Amount | £3,041,190 (GBP) |
Funding ID | EP/W026775/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 12/2021 |
End | 11/2024 |
Description | Quantum Enhanced Computing Platform for Pharmaceutical R&D - QuPharma |
Amount | £4,700,000 (GBP) |
Funding ID | TS/W006286/1 |
Organisation | Innovate UK |
Sector | Public |
Country | United Kingdom |
Start | 03/2022 |
End | 02/2025 |
Description | Transition metal controlled nitrogen chemistry in zeolite and protein environments using a unified quantum embedding model |
Amount | £1,022,120 (GBP) |
Funding ID | EP/R001847/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2018 |
End | 04/2022 |
Description | Collaboration with Karsten Reuter, Technical University of Munich, Germany |
Organisation | Technical University of Munich |
Department | Faculty of Medicine |
Country | Germany |
Sector | Academic/University |
PI Contribution | Development of an FHI-aims interface in Python-ChemShell |
Collaborator Contribution | In-depth experience of the FHI-aims package and the modelling of surface catalytic reactions in general, and resources from the SUPER-MUC HPC machine at the Leibniz Rechenzentrum in Garching |
Impact | Development of the FHI-aims interface in Python-ChemShell |
Start Year | 2014 |
Description | Collaboration with Volker Blum, Fritz Haber Institute, Berlin |
Organisation | Max Planck Society |
Department | Fritz Haber Institute |
Country | Germany |
Sector | Academic/University |
PI Contribution | Development of an interface to FHI-aims in Python ChemShell |
Collaborator Contribution | Time and computational resources at the Fritz Haber Institute and the Garching Computing Centre of the Max Planck Society |
Impact | Development of an interface to FHI-aims in Python-ChemShell |
Start Year | 2014 |
Description | Dalton development team |
Organisation | University of Oslo |
Country | Norway |
Sector | Academic/University |
PI Contribution | We develop an interface to the Dalton and LSDalton electronic structure packages in our ChemShell software for QM/MM calculations |
Collaborator Contribution | They have made a number of modifications to the Dalton and LSDalton codes in order to facilitate interface development. |
Impact | The Dalton & LSDalton interfaces in Tcl & Py-ChemShell |
Start Year | 2011 |
Title | Py-ChemShell alpha release |
Description | Py-ChemShell is the python-based version of the ChemShell multiscale computational chemistry environment, a leading package for combined quantum mechanical/molecular mechanical simulations. |
Type Of Technology | Software |
Year Produced | 2017 |
Open Source License? | Yes |
Impact | An initial alpha release of Py-ChemShell was made in December 2017 and is now being tested in preparation for the first full release. |
URL | http://www.chemshell.org |
Description | Bristol Chemshell training Feb 2019 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Tom Keal and You Lu gave a 2-day training course in the use of ChemShell for materials and biomolecular modelling to a group of 15 researchers at the University of Bristol |
Year(s) Of Engagement Activity | 2019 |
Description | ChemShell presentation at DL_SOFTWARE training workshop, Guangzhou, China |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Tom Keal and You Lu gave a presentation on recent developments in ChemShell to over 50 students at the DL_SOFTWARE traininng workshop, Guangzhou, China on 27 October 2015. |
Year(s) Of Engagement Activity | 2015 |
Description | ChemShell presentation at MCC conference, Lincoln, September 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Tom Keal gave a presentation on recent ChemShell developments at the Materials Chemistry Consortium conference at the University of Lincoln on 4 September 2018. |
Year(s) Of Engagement Activity | 2018 |
Description | ChemShell presentation at MCC meeting, December 2016 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Tom Keal gave a presentation on recent developments in ChemShell at the Materials Chemistry Consortium meeting at UCL, 21 December 2016. |
Year(s) Of Engagement Activity | 2016 |
Description | ChemShell presentation at MCC meeting, July 2015 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Tom Keal gave a presentation on recent ChemShell developments at the Materials Chemistry Consortium meeting at UCL on 6 July 2015 |
Year(s) Of Engagement Activity | 2015 |
Description | ChemShell training at Imperial College (DL_SOFTWARE workshop) - December 2019 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Tom Keal and You Lu gave ChemShell training as part of the DL_SOFTWARE workshop held at Imperial College, and discussed plans for future research with the trainees. |
Year(s) Of Engagement Activity | 2019 |
Description | ChemShell training workshop at PRACE Autumn School 2021: Fundamentals of Biomolecular Simulations and Virtual Drug Development |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | A ChemShell biomolecular QM/MM training day was held online as part of the PRACE Autumn School 2021: Fundamentals of Biomolecular Simulations and Virtual Drug Development (20-24 Sep 2021), featuring an introduction to the DL_Software suite by Ilian Todorov, and talks and demonstrations of the ChemShell QM/MM package by Tom Keal, Kakali Sen and You Lu. |
Year(s) Of Engagement Activity | 2021 |
URL | https://events.prace-ri.eu/event/1222/ |
Description | ChemShell training workshop at the CCPBioSim training week, September 2021 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | As part of the CCPBioSim training week 2021, a training session on ChemShell for biomolecular QM/MM calculations was held, with talks and demonstrations from Tom Keal, Kakali Sen, You Lu and Sarah Fegan of STFC. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.ccpbiosim.ac.uk/events/workshop-course-material/eventdetail/135/-/ccpbiosim-training-wee... |
Description | DL ChemShell training January 2019 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Tom Keal and You Lu gave ChemShell training to a group of 6 researchers from UCL |
Year(s) Of Engagement Activity | 2019 |
Description | PRACE Winter School: Catalysis for Europe's Green Transition - ChemShell talks, Nov 2022 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | As part of the PRACE Winter School on Catalysis for Europe's Green Transition, Tom Keal and Kakali Sen of STFC Scientific Computing presented talks on "Introduction to QM/MM modelling of catalytic systems with ChemShell" and "Modelling Enzyme Reactivity by Combining QM/MM with Serial Crystallography". |
Year(s) Of Engagement Activity | 2022 |
Description | Presentation at UK Catalysis Hub Summer Conference, July 2015 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Matthew Farrow gave a presentation on "An introduction to ChemShell: A hybrid QM/MM embedded cluster approach for the computational modelling of heterogeneous catalysis" at the UK Catalysis Hub Summer Conference on 2 July 2015 to an audience of postgraduates and senior researchers, with questions and discussion afterwards. |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.ukcatalysishub.co.uk/events/highlights |
Description | Presentation at the Cardiff University, Cardiff, December 2017 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | You Lu gave a talk on "Python-Based Redevelopment of ChemShell" at the Computational Chemistry Seminar of Cardiff University on 05/12/2017. More than twenty academic staff and students attended and raised questions after the talk. Tom Keal and You Lu visited Prof. David Willock and Dr. Andrew Logsdail of Cardiff University to discuss the future plan for collaboration and tutored a postdoctoral researcher Sachin Nanavati to set up and use Py-ChemShell. |
Year(s) Of Engagement Activity | 2017 |
Description | Presentation at the University of Limpopo, South Africa, January 2016 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | 30 mainly undergraduate students attended a talk given by Matthew Farrow on ChemShell entitled "Computational Modelling of Heterogeneous Catalysis" at the University of Limpopo, South Africa, 28 January 2016. A question and answer session followed and there was a great deal of interest among the students in using the code in future. |
Year(s) Of Engagement Activity | 2016 |
Description | Royce Industrial Engagement Workshop - Combining Ab Initio and Atomistic Methods |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | As part of the CCP5/Royce Industrial Engagement Event, Thomas Keal chaired a session and presented on "Predictive Power and Capability: Combining Ab Initio and Atomistic Modelling" |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.royce.ac.uk/events/the-power-of-materials-modelling-for-industrial-applications-an-indus... |
Description | STFC Seminar talk on DL_PY2F |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | You Lu gave an STFC seminar on DL_PY2F--A general-purpose Python/FORTRAN interoperability library, and its use to couple codes within the ChemShell computational chemistry environment |
Year(s) Of Engagement Activity | 2021 |
Description | UCL Embedding Day workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Tom Keal was invited to speak at the UCL Embedding Workshop on the topic of recent developments in ChemShell. Alexey Sokol, Andrew Logsdail and You Lu also participated in the meeting. |
Year(s) Of Engagement Activity | 2014 |