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Making Use of Isotropic Magnetic Shielding to Understand Chemical Bonding and Aromaticity in Different Electronic States


   Department of Chemistry

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  Prof Peter Karadakov  No more applications being accepted  Competition Funded PhD Project (UK Students Only)

About the Project

Background: We have developed an approach based on the analysis of calculated isotropic magnetic shielding isosurfaces and contour plots which reveals how pronounced differences in aromatic character are reflected in chemical bonding and allows very clear distinction between aromaticity and antiaromaticity in the low-lying electronic states of cyclic conjugated systems. Similarly to the Laplacian of the electron density used in Bader’s theory of atoms in molecules (AIM) and the electron localization function (ELF), the isotropic shielding “amplifies” the changes in electron activity within the space encompassing a molecule and, especially, along chemical bonds, making the differences between bonds much easier to visualize. An important advantage of the isotropic shielding is that at atomic positions it is pinned to the experimentally verifiable nuclear shieldings. Recent references include https://doi.org/10.1039/D1CC03701C, https://doi.org/10.1002/anie.202008362, https://doi.org/10.1021/jacs.0c05611, https://doi.org/10.1021/acs.orglett.0c03254, see also the Chemical Word feature https://www.chemistryworld.com/news/magnetic-shielding-maps-reveal-molecules-aromaticity/4012214.article.

Objectives: Our approach is very general and has many potential applications. In this proposal we plan theoretical analyses of

Chemical reactions: These will include excited state aromaticity reversals in twisted internal charge transfers and proton transfers (in collaboration with Brett VanVeller, University of Iowa) and the mechanisms of thermally forbidden and photochemically allowed reactions such as the synchronous cycloaddition or two ethene molecules.

Molecular property changes upon electronic excitation: These will include investigating “flapping” molecules (in collaboration with Shohei Saito, University of Kyoto) and designing molecules with light-controllable behaviour such as molecular photoswitches and molecular motors.

Bonding and aromaticity in polycyclic molecules: This will involve further work on aromatic policyclic hydrocarbons (PAHs), their heteroatom-containing analogues, porphyrins, fullerenes and carbon nanotubes.  

Experimental Approach: We have developed a set of in-house codes which are interfaced with three popular quantum chemical packages, Gaussian, Dalton and CFOUR. The work on the project will involve improving these codes and creating a user-friendly interface to allow other researchers to use our methodology.

Novelty: The ability of calculated isotropic magnetic shielding isosurfaces and contour plots to provide information about chemical bonding and aromaticity in different electronic states is unique in quantum chemistry. Excited state aromaticity reversals have become a “hot” area of experimental and theoretical research and we have very much the best tool for studying these reversals: We obtain aromaticity and antiaromaticity “fingerprints” which are reproduced in various electronic states and allow classification of these states as aromatic, antiaromatic or non-aromatic. Additionally, we have shown that this approach breathes new life into well-known and very popular classical interpretations such as Clar’s sextet theory. Our approach has the potential to become an alternative to Bader’s popular AIM theory; the current project is an important step towards achieving this goal.

Training: The student will learn how to use the ab initio packages Gaussian, Dalton and Molpro to calculate single-point energies, optimize geometries and calculate NMR shielding constants using density functional theory (DFT), Hartree-Fock (HF) and complete-active space self-consistent field (CASSCF) wavefunctions, and post-Hartree-Fock approaches such as 2nd order Møller-Plesser perturbation theory (MP2) and coupled cluster (CC) constructions, all in conjunction with different basis sets. The project involves programming in Fortran and extensive use of the Linux operating system, including shell programming; all required training will be provided. The student will be given extensive training in the processing and analysis of computational results which will involve use of visualisation packages such as GaussView, Molden and VMD (Visual Molecular Dynamics). The student will gain experience in preparing results for publication and writing research papers. All Chemistry research students have access to our innovative Doctoral Training in Chemistry (iDTC): cohort-based training to support the development of scientific, transferable and employability skills: https://www.york.ac.uk/chemistry/postgraduate/cdts/

The Department of Chemistry holds an Athena SWAN Gold Award and is committed to supporting equality and diversity for all staff and students. The Department strives to provide a working environment which allows all staff and students to contribute fully, to flourish, and to excel: https://www.york.ac.uk/chemistry/ed/.

For more information about the project, click on the supervisor's name above to email the supervisor. For more information about the application process or funding, please click on email institution

This PhD will formally start on 1 October 2022. Induction activities may start a few days earlier.

To apply for this project, submit an online PhD in Chemistry application:

https://www.york.ac.uk/study/postgraduate/courses/apply?course=DRPCHESCHE3

You should hold or expect to achieve the equivalent of at least a UK upper second class degree in Chemistry or a related subject.  


Funding Notes

Fully funded for 3 years by the Department of Chemistry and covers: (i) a tax-free annual stipend at the standard Research Council rate (£15,609 for 2021-22), (ii) tuition fees at the Home rate, (iii) funding for consumables. See guidance for further details: https://www.york.ac.uk/chemistry/postgraduate/research/dept-stud/
Studentships are available to any student who is eligible to pay tuition fees at the home rate: https://www.york.ac.uk/study/postgraduate-research/fees/status/
Not all projects will be funded; candidates will be appointed via a competitive process.

References

Candidate selection process:
• You should hold or expect to receive at least an upper second class degree in chemistry or a chemical sciences related subject
• Applicants should submit a PhD application to the University of York by 28 February 2022
• Supervisors may contact candidates either by email, telephone or web-chat
• Supervisors can nominate up to 2 candidates to be interviewed for the project
• The interview panel will shortlist candidates for interview from all those nominated
• Shortlisted candidates will be invited to a panel interview on 30th or 31st March or 1stApril
• The awarding committee will award studentships following the panel interviews
• Candidates will be notified of the outcome of the panel’s decision by email

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