Scalable Quantum Chemistry with Flexible Embedding

Lead Research Organisation: STFC - Laboratories
Department Name: Scientific Computing Department

Abstract

We propose to develop and a new piece of software for molecular modelling of reactivity in complex systems, in particular, surface chemistry and heterogeneous catalysis in the presence of solvent such as water.Examples of the science we are targetting are * 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 * design of sensors and photoelectric materials by organic layers on inorganic surfacesWe will do this by combining quantum chemistry (also known as first principles) techniques, which can treat the chemically reacting centres with classical (or empirical) models for the rest of the system (the slab of material which is modelling a surgfae, and the solvent layers on top of it.The novelty in our approach is that we are extending the quality of the interaction between the classically modelled environment and the quantum mechanical calculation in a number of significant respects. We are combining some of our own ideas, such as adapting existing models to include spin polarisation effects with ideas (frozen electron density models for water molecules) that have been developed and tested by others.We are choosing an Open Source quantum chemistry program, NWChem as the basis for the new features because it has been designed from scratch for use on high-performance computers, and is modular in design which will help support the changes we need to make. The MM code (GULP) is already used in our existing work, and works well on parallel machines. Parallel efficiency is a key driver for the design of the interfaced code and will inform the way we implement the new methods.In the long run, it is intended the code developed here will form the nucleus of a modelling framework for a wider range of systems (including biological ones) building on experience we have had in past software projects (www.chemshell.org).

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. As such this project will help improve the range of problems that can be addressed by both academic and industrial researchers in this area. 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 (appatite 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. This was the main motivations for Accelrys to licence ChemShell as the basis of their QMERA product, which they are now selling commercially. Once the scientific capabilities of the new code have 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 within Materials Studio (which incorporates GULP already) by a wider, less computationally expert, modelling community.

Publications

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Dutta G (2012) Activation of carbon dioxide over zinc oxide by localised electrons. in Chemphyschem : a European journal of chemical physics and physical chemistry

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Gould A (2015) Understanding the Thermal Stability of Silver Nanoparticles Embedded in a-Si in The Journal of Physical Chemistry C

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Logsdail AJ (2016) Modelling the chemistry of Mn-doped MgO for bulk and (100) surfaces. in Physical chemistry chemical physics : PCCP

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Lu Y (2019) Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment. in Journal of chemical theory and computation

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Metz S (2013) C hem S hell-a modular software package for QM / MM simulations in Wiley Interdisciplinary Reviews: Computational Molecular Science

 
Description A new QM/MM driver module has been implemented in NWChem with a directly linked interface to GULP to perform QM/MM calculations with an emphasis on parallel efficiency. This module fully supports embedded cluster calculations and supersedes the current QM/MM driver in ChemShell for materials simulations.

The embedded cluster QM/MM model has been enhanced through the implementation of spin-polarised effective core potentials (ECPs) in NWChem, enabling the investigation of spin-polarised systems such as manganese oxide. A standalone program for optimising these ECPs has been written with support for a variety of local and global minimisation algorithms. The ChemShell/NWChem interface has been extended to support a more flexible description of the embedding potential, with analogous improvements made to the interfaces to GAMESS-UK and FHI-AIMS, including development of the requisite pseudopotential infrastructure in FHI-AIMS.

The developments in stage 1 can be controlled directly through NWChem input files, but will be taken further to form the core of the new modelling framework to be developed in our Stage 2 grant EP/K038419/1. The aim of the follow-on project is to make the code developments in stage 1 easy to use by the ChemShell user and developer communities through the development of a new python-based user interface.
Exploitation Route The developments are highly relevant to industrial molecular modelling as evidenced by our own industrially-relevant work on surface catalysis. The new code will be applicable to problems in catalysis, energy materials, and more widely to biomolecular modelling, for example in understanding the behaviour of enzymatic reactions, with relevance to drug discovery. The developments in this project are by their nature applicable to a wide range of problems in materials chemistry. We have used the embedded cluster model to investigate why mixed-phase TiO2 outperforms pure phases in catalysing the photolysis of water, and in the calculation of the reduction potentials of iron in iron-substituted zeolites. Future work using the code will include further applications of the model in the context of spin-polarised systems, the mechanism of alcohol oxidation on metal oxide surfaces, methane oxidation in iron-doped zeolites, and oxidative catalysis reactions on mineral surfaces including the introduction of a solvent environment.
Sectors Chemicals,Digital/Communication/Information Technologies (including Software),Energy

 
Description Scalable Quantum Chemistry with Flexible Embedding Stage 2
Amount £474,549 (GBP)
Funding ID EP/K038419/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 08/2014 
End 07/2016
 
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 Academic/University
Country United Kingdom
Start 01/2018 
End 04/2021
 
Description FHI-AIMS development collaboration 
Organisation Max Planck Society
Department Fritz Haber Institute
Country Germany 
Sector Academic/University 
PI Contribution FHI-AIMS developments are carried out in collaboration with the core FHI-AIMS development team
Start Year 2012
 
Description NWChem development team 
Organisation U.S. Department of Energy
Department Pacific Northwest National Laboratory
Country United States 
Sector Public 
PI Contribution The stage 1 project was carried out in collaboration with the NWChem development team at Pacific Northwest National Laboratories
Start Year 2012
 
Title Py-ChemShell 
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
 
Title Stage 1 software developments 
Description The software developments in stage 1 of the project comprise: - A new driver for QM/MM calculations linking NWChem and GULP - An implementation of spin-polarised effective core potentials in NWChem - Implementation of pseudopotentials in FHI-AIMS - A standalone code for optimisation of ECP parameters - Improvements to ECP handling in the NWChem, GAMESS-UK and FHI-AIMS interfaces in ChemShell 
Type Of Technology Software 
Year Produced 2014 
Impact These developments provided the foundation for the redeveloped python-based version of ChemShell. 
 
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 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 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