Mark Sims | research

Computational chemistry group at Northumbria University

I am currently a Senior Lecturer in Computational Chemistry in the Department of Applied Sciences at Northumbria University.

I obtained my PhD from the University of York in 2015 where I was subsequently appointed a Postdoctoral Research Associate with the groups of Dr. John Moore and Prof. John Goodby in 2015, working on combining experimental and computational studies of ordered systems in order to develop design methods to aid in identifying synthetic targets. I was appointed to my current role at Northumbria University in 2017.

Current and previous research

Modelling de Vries behaviour in liquid crystals

Contributors: Kristian Poll

Ferroelectric SmC* liquid crystals have the potential to be used widely in future display technologies, but the shrinkage they typically exhibit on tilting at the SmA/SmC transition is particularly problematic. A sub-class of these materials exhibit “de Vries” behaviour, in which no such shrinkage is observed, but the behaviour is poorly understood. We have used fully atomistic molecular dynamics simulations to gain an understanding of these intriguing materials.

Papers Sub-layer rationale of anomalous layer-shrinkage from atomistic simulations of a fluorinated mesogen
Mater. Adv., 2022, 3, 1212-1223

An insight into de Vries behaviour of smectic liquid crystals from atomistic molecular dynamics simulations
J. Mater. Chem. C, 2020 ,8 , 13040-13052

Rationalising reactivity of bioorthogonal reagents

In collaboration with Dr Valery Kozhevnikov

Contributors: Connor Atess, Numair Zaman, Aminah Shafiq

Bioorthogonal reactions are those that take place in-vivo without interfering with biological processes. Designing such reagents and understanding trends in reactivity can be aided by the use of ab-initio methods to calculate transition state energies, transition state conformations, frontier orbital energies etc.

Papers Catching up with tetrazines: coordination of Re(i) to 1,2,4-triazine facilitates an inverse electron demand Diels–Alder reaction with strained alkynes to a greater extent than in corresponding 1,2,4,5-tetrazines
Dalton Trans., 2023, 52 , 10927-10932

Iridium(iii) complexes of 1,2,4-triazines as potential bioorthogonal reagents: metal coordination facilitates luminogenic reaction with strained cyclooctynes
Chem. Commun., 2019, 55 , 14283-14286

Calculating ligand binding in lanthanide extraction

In collaboration with Dr Frank Lewis

Contributors: Anthony Sayer, Anya Nelson, Sam Taylor, Lauren Gardiner

Design of ligands that selectively bind actinides over lanthanides is a challenging problem. Use of ab-initio methods to calculate binding energies can aid sythetic chemists in understanding ligand behaviour and in designing new, improved materials.

Papers Exploring the Subtle Effect of Aliphatic Ring Size on Minor Actinide-Extraction Properties and Metal Ion Speciation in Bis-1,2,4-Triazine Ligands
Chem. Eur. J., 2020, 26 , 428-437

Elucidating structure-property relationships in dye-doped liquid crystals

Liquid-crystal dye mixtures have many potential applications including smart windows, privacy glass, and low-power displays. However, the understanding of dye behaviour is such mixtures and rational design of systems with desirable characteristics is an area that has received relatively little attention from a computational perspective. Combining classical methods with ab-initio approaches enables experimental alignment behaviour to be understood, and provides a route by which improved systems can be designed.

Papers Dyes for guest–host liquid crystal applications: a general approach to the rapid computational assessment of useful molecular designs
Phys. Chem. Chem. Phys., 2023, 25, 10367-10383

Guest–host systems containing anthraquinone dyes with multiple visible transitions giving positive and negative dichroic order parameters: an assessment of principal molecular axes and computational methods
Liq. Cryst., 2017, 44, 2029-2045

Photoswitching of Dihydroazulene Derivatives in Liquid-Crystalline Host Systems
Chem. Eur. J., 2017, 23 , 5090-5103

Principal molecular axis and transition dipole moment orientations in liquid crystal systems: an assessment based on studies of guest anthraquinone dyes in a nematic host
Phys. Chem. Chem. Phys., 2017, 19, 813-827

Dyes as guests in ordered systems: current understanding and future directions
Liq. Cryst., 2016, 43, 2363-2374

Experimental and molecular dynamics studies of anthraquinone dyes in a nematic liquid-crystal host: a rationale for observed alignment trends
Phys. Chem. Chem. Phys., 2016, 18 , 20651-20663

Molecular Design Parameters of Anthraquinone Dyes for Guest–Host Liquid-Crystal Applications: Experimental and Computational Studies of Spectroscopy, Structure, and Stability
J. Phys. Chem. C, 2016, 120, 11151–11162

Dyes in Liquid Crystals: Experimental and Computational Studies of a Guest–Host System Based on a Combined DFT and MD Approach
Chem. Eur. J., 2015, 21 , 10123-10130

Quantifying and understanding self-organisation using x-ray scattering

The quantification of alignment in self-organising systems is often not straightforward. X-ray scattering theoretically provides significantly more information than many other methods, but data processing can lead to significant errors that some of our work has addressed. Subtle changes in molecular structure can heavily influence the molecular organisation in liquid crystals; a combinination of x-ray scattering experiments with classical simulations is a powerful tool with which such influences can be quantified and understood at a molecular and sub-molecular level.

Papers Shape segregation in molecular organisation: a combined X-ray scattering and molecular dynamics study of smectic liquid crystals
Soft Matter, 2019, 15, 7722-7732

Considerations in the determination of orientational order parameters from X-ray scattering experiments
Liq. Cryst., 2017, 46, 11-24