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Jonathan Yates

Professor Jonathan Yates
Associate Professor of Materials Modelling

Department of Materials
University of Oxford
16 Parks Road
Oxford OX1 3PH
UK

Tel: +44 1865 612797 (Room 271.40.17)
Tel: +44 1865 273777 (reception)
Fax: +44 1865 273764

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Materials Modelling Laboratory

Summary of Interests

My research lies in the field of computational electronic structure theory. In brief, it is the development of new theoretical methods, their implementatio into easy to use computer packages, and finally their application to novel scientific problems.

A major theme of my research has been the development of computational methods to interpret solid-state Nuclear Magnetic Resonance (NMR) experiments. Applications have included pharmaceutical compounds, (bio)minerals and glasses.

Further work has involved the development of techniques to interpret Electron Energy Loss Spectroscopy (EELS) with applications to nano-structured materials and interfaces.

Other work has focused on the use of so-called Wannier functions (www.wannier.org) to describe the properties of metallic systems: Fermi surface properties, transport, phase transitions etc.

This research has led to two publicly available codes: Castep www.castep.org for spectroscopic properties and Wannier90 www.wannier.org to obtain wannier functions.

Current Research Projects

Application of J-Resolved NMR Spectroscopy in Materials Science
T. Green, Dr. J.R. Yates, Dr. S. Cadars*, Dr. P. Florian*, Dr. D Massiot*
The intelligent design of materials requires a detailed understanding of atomic-level structure and dynamics. Acquiring such information is key to harnessing the properties of increasingly complex new materials - one of the major challenges across the physical sciences in the early 21st Century.Solid-State Nuclear Magnetic Resonance (SSNMR) spectroscopy provides extremely detailed insights into ordered and disordered materials at the sub-nanometre scale. Very recently it has become possible to measure in SSNMR a property known as spin-spin (J) coupling. J coupling represents a dialogue between neighbouring atoms in the material and provides important information on the connectivities and spatial arrangement of atoms. To support these experiments a quantum mechanical framework to compute J has been developed (Yates).We are using the combination of solid state NMR experiments and first-principles calculations to provide a deeper understanding of materials structure and properties; specific examples include microporous framework materials such as layer hydroxides and zeolites, and glasses for nuclear waste encapsulation. (*CNRS-CEMHTI - Orleans, France. Supported by EPSRC, The Royal Society)

NMR Crystallography: Exploring the use of J-couplings in Molecular Crystals
Dr. J.R. Yates, Dr. A.L. Webber*, Professor S.P. Brown**
Molecular crystals have a wide range of technological uses, from pharmaceuticals to electronic devices. Unfortunately, X-ray diffraction cannot always determine the structures of such materials. Solid-state NMR is an important technique for materials characterisation and could, in principle, be used for structure solution (so call 'NMR Crystallography'). However, there is no simple theory to link the observed NMR spectrum to the underlying atomic level structure (as Bragg's Law does for XRD).In recent years we have developed computational techniques, based on quantum mechanics, to predict and interpret NMR spectra (see www.gipaw.net). Typically this has focused on the so-call NMR chemical shift, but, excitingly, it has recently become possible to both measure and compute the NMR J-coupling. J-coupling is an indirect interaction of the nuclear magnetic moments mediated by bonding electrons, and provides a direct measure of bonding interactions and a map of the connectivities of a system (hence its importance for crystallography).Calculations of NMR J-coupling are being used to interpret current experiments, understand the microscopic mechanisms, and guide the development of new experiments. (*ENS Lyon; **University of Warwick, UK) Funding: The Royal Society

Developing Solid-State NMR in Materials Science
Dr. J.R. Yates, T. Green, Professor M.E. Smith*, Professor J.V. Hanna*
Solid-State Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful experimental probe of structure and dynamics on an atomic scale. It has been widely applied to problems in chemistry, material science, biology, physics, and geology. By combining first-principles calculations of NMR parameters with state-of-the-art high-field NMR experiments we aim to drive the application of solid-state NMR into challenging areas of materials science: biominerals and their interfaces for medical applications, ionic conductors for energy devices, glasses for electronics and nuclear waste storage to name just few. (*University of Warwick) Support: The Royal Society

Use and Development of Maximally Localised Wannier Functions
Dr. J.R. Yates, Dr. A.A. Mostofi*, Professor I. Souza**, Professor D. Vanderbilt***, Professor N. Marzari
Maximally localized Wannier functions provide a representation of the electronic structure of extended systems in terms of spatially localized functions. Since their introduction, these functions have found numerous applications in solid-state theory and in ab-initio simulation, in physics and in chemistry. In particular wannier functions can provide insight into the nature of chemical bonding in solids, a methodological tool for the study of polarization, a means to study ballistic transport in nanostructures, and an efficient approach to explore Fermi surface properties. An open source code, wannier90, has been developed to compute wannier functions in solids. Current development involves both application and advancement of theory. (*Imperial College London; **Rutgers University, New Jersey, USA ; ***University of California at Berkeley, CA, USA)

CASTEP: A density functional code for the prediction of Material Properties
Dr. J.R. Yates, Dr. K. Refson(1), Prof. S.J. Clark(2), Prof. C.J. Pickard(3), Dr. P.J. Hasnip(4), Dr. M.I.J. Probert(4), Dr. M.D. Segall(5), Prof. M.C. Payne(5)
CASTEP is a software package which uses density functional theory to provide a good atomic-level description of all manner of materials and molecules. CASTEP can give information about total energies, forces and stresses on an atomic system, as well as calculating optimum geometries, band structures, and spectroscopic parameters such as core-level EELS, solid-state NMR, optical properties, IR and Raman spectroscopy. The package is written in modern, modular fortran90 and is designed to run on computer resources ranging from desktop PCs to National level supercomputer facilities. Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire, UK Department of Physics, University of Durham, UK Department of Physics and Astronomy, University College London, UK Department of Physics, University of York, UK Cavendish Laboratory, University of Cambridge, UK In Collaboration with Accelrys Inc. Funding: EPSRC

5 public active projects

Research Publications

Selected publications: full list can be found at http://users.ox.ac.uk/~oums0549/pubs.html

High-Resolution 19F MAS NMR Spectroscopy: Structural Disorder and Unusual J Couplings in a Fluorinated Hydroxy-Silicate
John M. Griffin, Jonathan R. Yates, Andrew J. Berry, Stephen Wimperis, and Sharon E. Ashbrook J. Am. Chem. Soc. (2010)

Structural assignments of NMR chemical shifts in GexSe1-x glasses via first-principles calculations for GeSe2, Ge4Se9, and GeSe crystals
Mikhail Kibalchenko, Jonathan R. Yates, Carlo Massobrio, and Alfredo Pasquarello Phys. Rev. B 82, 020202 (Rapid Comm.) (2010)

Prediction of NMR J-coupling in solids with the planewave pseudopotential approach
Jonathan R. Yates Magn. Reson. Chem (2010)

Time Averaging of NMR Chemical Shifts in the MLF Peptide in the Solid State
Itzam De Gortari, Guillem Portella, Xavier Salvatella, Vikram S. Bajaj, Patrick C. A. van der Wel, Jonathan R. Yates, Matthew D. Segall, Chris J. Pickard, Mike C. Payne and Michele Vendruscolo J. Am. Chem. Soc. 132, 5993 (2010)

Natural Abundance 25Mg Solid-State NMR of Mg Oxyanion Systems: A Combined Experimental and Computational Study 
Lindsay S. Cahill, John V. Hanna, Alan Wong, Jair C. C. Freitas, Jonathan R. Yates, Robin K. Harris, Mark E. Smith Chem. Eur. J. 15, 9785 (2009)

Probing Heteronuclear 15N-17O and 13C-17O Connectivities and Proximities by Solid-State NMR Spectroscopy 
Ivan Hung, Anne-Christine Uldry, Johanna Becker-Baldus, Amy Webber, Alan Wong, Mark Smith, Sian Joyce, Jonathan Yates, Chris Pickard, Ray Dupree, Steven Brown J. Am. Chem. Soc., 131, 1820 (2009)

Density-Functional theory calculations of hydrogen bond mediated NMR J-coupling in the solid-state;
Sian A. Joyce, Jonathan R. Yates, Chris J. Pickard, Steven P. Brown; J. Am. Chem. Soc., 130, 12663 (2008)

Quantifying Weak Hydrogen Bonding in Uracil and 4-cyano-4'-ethynyl-bi-phenyl: A Combined Computational and Experimental Investigation of NMR Chemical Shifts in the Solid State;
Anne-Christine Uldry, John M. Griffin, Jonathan R. Yates, Marta Perez-Torralba, M. Dolores Santa Maria, Amy L. Webber, Max Beaumont, Ago Samoson, Rosa Maria Claramunt, Chris J. Pickard and Steven P. Brown; J. Am. Chem. Soc., 130, 945, (2008)

Wannier90: A Tool for Obtaining Maximally-Localised Wannier Functions;
Arash A. Mostofi, Jonathan R. Yates, Young-Su Lee, Ivo Souza, David Vanderbilt and Nicola Marzari; Computer Physics Communications 178, 685 (2008)

Spectral and Fermi surface properties from Wannier interpolation;
Jonathan R. Yates, Xinjie Wang, David Vanderbilt, and Ivo Souza; Physical Review B 75, 195121 (2007)

Electron-Phonon Interaction via Electronic and Lattice Wannier functions: Superconductivity in Boron-Doped Diamond Reexamined;
Feliciano Giustino, Jonathan R. Yates, Ivo Souza, Marvin L. Cohen, and Steven G. Louie; Physical Review Letters. 98, 047005 (2007)

A First Principles Theory of Nuclear Magnetic Resonance J-Coupling in solid-state systems;
Sian A. Joyce, Jonathan R. Yates, Chris J. Pickard, Francesco Mauri; J. Chem. Phys. 127, 204107 (2007)

Calculation of NMR Chemical Shifts for extended systems using Ultrasoft Pseudopotentials;
Jonathan R. Yates, Chris J. Pickard, and Francesco Mauri; Physical Review B 76, 024401 (2007)

Nonlinear optics of III-V semiconductors in the terahertz regime: an ab-initio study;
Eric Roman, Jonathan R. Yates, Marek Veithen, David Vanderbilt, and Ivo Souza; Physical Review B. 74, 245204 (2006)

Ab-initio calculation of the anomalous Hall conductivity by Wannier interpolation;
Xinjie Wang, Jonathan R. Yates, Ivo Souza, and David Vanderbilt; Physical Review B. 74 195118 (2006)

An Investigation of Weak C–HO Hydrogen Bonds in Maltose Anomers by a Combination of Calculation and Experimental Solid-State NMR Spectroscopy;
Jonathan R. Yates, Tran N. Pham, Chris J. Pickard, Francesco Mauri, Ana M. Amado, Ana M. Gil, and Steven P. Brown; J. Am. Chem. Soc. 127 10216-10220 (2005)

Relativistic nuclear magnetic resonance chemical shifts of heavy nuclei with pseudopotentials and the zeroth-order regular approximation;
Jonathan R. Yates, Chris J. Pickard, Mike C. Payne and Francesco Mauri; J. Chem. Phys. 118, 5746-5743 (2003)

Projects Available

*/**From light to heavy: making predictions of solid-state NMR parameters truly multi-nuclear
Prof J R Yates

TMCS is an EPSRC Centre for Doctoral Training operated by the Universities of Oxford, Bristol and Southampton.

In year one you will be based in Oxford with a cohort of around 12–15 other TMCS students, and will receive in-depth training in fundamental theory, software development, and chemical applications, delivered by academics from all three Universities. Successful completion of the year-one program leads to the award of an Oxford MSc, and progression to the 3-year DPhil project detailed below.

The ability to predict from first-principles NMR parameters for solid-state systems has had a significant impact on the solid-state NMR community (see Chemical Reviews 112 (11), 5733-5779 (2012). Such calculation are often an integral part of any experimental solid-state NMR study. However, a major limitation is the poor description of compounds containing heavier elements (say > Te). This applies not just to the heavy atom itself, but to any light atoms (H, C) directly bonded to the heavier atom (the so called ‘heavy atom - light atom effect)

The reason for this is a neglect of relativistic effects which become important for increasing Z. While scalar relativistic effects are sufficient in some situations, e.g. Journal of chemical physics 140 (23), 234106 (2014), a full treatment including spin-orbit coupling is essential to predict phenomena such as the heavy atom - light atom effect. We have recently extended the CASTEP code to include spin-orbit coupling in the calculation of ground state properties. The aim of this project will be to apply this functionality to the calculation of NMR properties in solids - enabling the accurate prediction of NMR parameters across the periodic table. This will involve the development of new theoretical equations and their implementation into a parallel electronic structure code (CASTEP). Applications of the new methodology will be extensive - and include areas such as catalysis, geominerals and pharmaceuticals, with collaborations in both academia and industry.

Funding will be subject to normal EPSRC rules. UK and EU students will be eligible for full-fee studentships.  In addition, UK students will be eligible for an annual stipend at or above £14,296 each year. 

Applicants would typically be expected to have a first class degree (or overseas equivalent) in chemistry or a closely related discipline. TMCS is committed to promoting equal opportunities in science, and we particularly welcome applications from women. Applications should be made as soon as possible, but will be considered throughout the year until the programme is full. Deadlines for upcoming recruitment rounds and further information on the application process can be found at our website: www.tmcs.ac.uk

Please ensure that you specify clearly that you are making a project-specific application and give the name of the project in your application.  Funding for this project is available through the Theory and Modelling in the Chemical Sciences Doctoral Training Centre (http;//www.tmcs.ac.uk).  Further details can be found at https://www.findaphd.com/search/PhdDetails.aspx?CAID=2278.

Any questions concerning the project can be addressed to Professor Jonathan Yates (jonathan.yates@materials.ox.ac.uk).  General enquiries on how to apply can be made by e mail to graduate.studies@materials.ox.ac.uk.  You must complete the standard Oxford University Application for Graduate Studies.  Further information and an electronic copy of the application form can be found at http://www.ox.ac.uk/admissions/postgraduate_courses/apply/index.html

Also see homepages: Jonathan Yates

*/**Exploring low energy excitations with electron microscopy
Dr R J Nicholls, Prof J R Yates, Prof P D Nellist

Recent advances in electron microscopy mean that a new generation of microscopes have the ability to combine atomic resolution imaging with high resolution spectra showing bond vibrations. The first of these new microscopes in Europe was unveiled at the UK SuperSTEM facility. The high resolution spectra produced by these microscopes are indicative of the bonding within a material and the combination of imaging and spectroscopy is a powerful tool for understanding the chemical, electronic and catalytic properties of a materials. Interpretation of experimental data is not always straightforward and can be aided by computer simulation. In the case of this new spectroscopic data, however, there are still fundamental questions about the interaction between the electron beam and the sample to answer in order to allow us to model experimental data. This project will use data obtained at the new SuperSTEM facility and focus on the formulation of quantum mechanical simulations to aid the interpretation of experimental data.

Candidates are considered in the January 2018 admissions cycle which has an application deadline of 19 January 2018.

This 3.5-year EPSRC DTP studentship will provide full fees and maintenance for a student who has home fee status (this includes an EU student who has spent the previous three years (or more) in the UK undertaking undergraduate study). The stipend will be at least £15,553 per year. Other EU students should read the guidance at http://www.materials.ox.ac.uk/admissions/postgraduate/eu.html for further information about eligibility.

Any questions concerning the project can be addressed to Dr Rebecca Nicholls (rebecca.nicholls@materials.ox.ac.uk) or Professor Pete Nellist (peter.nellist@materials.ox.ac.uk). General enquiries on how to apply can be made by e mail to graduate.studies@materials.ox.ac.uk. You must complete the standard Oxford University Application for Graduate Studies. Further information and an electronic copy of the application form can be found at http://www.ox.ac.uk/admissions/postgraduate_courses/apply/index.html.

Also see homepages: Rebecca Nicholls Jonathan Yates

Quantum crystallography using electron ptychography
Prof P D Nellist, Dr R J Nicholls, Prof J R Yates

Electron ptychography is a newly available mode of imaging in the transmission electron microscope that is somewhat related to holography and can provide very precise measurements of the electrostatic potential in a crystal.  Recent work in Oxford has shown that it can provide a measurement of the charge transfer between boron and nitrogen in a hexagonal boron nitride monolayer. This work demonstrates the potential of ptychography for measuring the effect of bonding on wavefunctions and charge densities in crystals – a field now known as quantum crystallography.  The aim of this work is to develop this method to measure the effects of bonding in a range of different materials, such as compound nanomaterials and transition metal oxides.  It will involve developing the experimental and data processing approaches, and developing methods based on density functional theory modelling to interpret the experimental data.  Projects are available that have either a more experimental emphasis applying the method to a range of materials, or a greater emphasis on developing the theoretical modelling methods to improve how the experimental results can be interpreted.

Also see homepages: Peter Nellist Rebecca Nicholls Jonathan Yates

Probing the atomic scale structure and dynamics of energy materials
J Yates

The aim of this project is to develop and apply computational techniques to interpret solid-state NMR spectra of materials used in solid-oxide fuel cells and battery materials. Determining the local atomic structure and material function of such materials has proved challenging using convention (diffraction based) techniques, due to the presence of long-range disorder and ionic motion.

Solid-state NMR is a powerful probe of atomic scale structure and dynamics. However, there is no simple theory to link the observed NMR spectrum to the underlying atomic level structure (as Bragg's Law does for diffraction). In recent years we have developed computational techniques, based on quantum mechanics, to predict and interpret NMR spectra (see www.gipaw.net).

There are several possible routes for this project, depending on the student's interest - either focusing on applying existing techniques to novel problems, or developing new computational methodologies. There will be close collaboration with experimental NMR groups, both international and within the UK.

Also see homepages: Jonathan Yates

NMR Crystallography: Exploring the use of J-couplings in Molecular Crystals
J Yates

Molecular crystals have a wide range of technological uses, from pharmaceuticals to electronic devices. Unfortunately, X-ray diffraction cannot always determine the structures of such materials. Solid-state NMR is an important technique for materials characterisation and could, in principle, be used for structure solution (so call 'NMR Crystallography'). However, there is no simple theory to link the observed NMR spectrum to the underlying atomic level structure (as Bragg's Law does for XRD).

In recent years we have developed computational techniques, based on quantum mechanics, to predict and interpret NMR spectra (see www.gipaw.net). Typically this has focused on the so-call NMR chemical shift, but, excitingly, it has recently become possible to both measure and compute the NMR J-coupling. J-coupling is an indirect interaction of the nuclear magnetic moments mediated by bonding electrons, and provides a direct measure of bond strength and a map of the connectivities of a system (hence its importance for crystallography).

The aim of this DPhil project is to study the nature of NMR J-coupling in molecular crystals - to interpret current experiments, understand the microscopic mechanisms, and guide the development of new experiments. The project is highly computational and will involve the use of large supercomputers, it may (optionally) include the development of new computational methods. The work will be carried out in close collaboration with experimental solid-state NMR studies performed in the group of Dr Steven Brown (University of Warwick).

Also see homepages: Jonathan Yates

Also see a full listing of New projects available within the Department of Materials.