# Department of Chemistry

The self-assembly of complex mesoscopic structures, the folding of proteins, and the complicated phenomenology of glasses are all manifestations of the underlying potential energy surface (PES). In each of these fields related ideas have emerged to explain and predict chemical and physical properties in terms of the PES. In studies of clusters and glasses the PES itself is often investigated directly, whereas for proteins and other biomolecules it is also common to define free energy surfaces, as the figure below illustrates for lysozyme.

Applications of energy landscape theory in my group range from studies of tunnelling splitting patterns in small molecules to computer simulation of protein folding and misfolding, including aggregation of misfolded proteins. Other active research topics include global optimisation and investigation of how the thermodynamic and dynamic properties of glasses are related to the underlying PES.

Two recent advances are now providing new insight into larger systems. Discrete path sampling enables dynamical properties to be obtained efficiently, and is being used to calculate folding rates for proteins. Unexpected connections between dynamics and thermodynamics have also been revealed by the application of catastrophe theory to energy landscapes, and new results are now being obtained to characterize phase transitions.

## Publications

Affinity-selected bicyclic peptide G-quadruplex ligands mimic a protein-like binding mechanism
KC Liu, K Röder, C Mayer, S Adhikari, DJ Wales, S Balasubramanian
– J Am Chem Soc
(2020)
142,
8367
From sticky-hard-sphere to Lennard-Jones-type clusters.
L Trombach, RS Hoy, DJ Wales, P Schwerdtfeger
– Phys Rev E
(2018)
97,
043309
Defining, Calculating, and Converging Observables of a Kinetic Transition Network
TD Swinburne, DJ Wales
– J Chem Theory Comput
(2020)
16,
2661
A multifunnel energy landscape encodes the competing $\alpha$-helix and $\beta$-hairpin conformations for a designed peptide
D Chakraborty, Y Chebaro, DJ Wales
– Physical chemistry chemical physics : PCCP
(2020)
22,
1359
Counterion‐Trapped‐Molecules: From High Polarity and Enriched IR Spectra to Induced Isomerization
FY Naumkin, DJ Wales
– ChemPhysChem
(2020)
21,
348
Multifunnel Energy Landscapes for Phosphorylated Translation Repressor 4E-BP2 and Its Mutants.
W Kang, F Jiang, Y-D Wu, DJ Wales
– J Chem Theory Comput
(2020)
16,
800
Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding.
K Röder, G Stirnemann, A-C Dock-Bregeon, DJ Wales, S Pasquali
– Nucleic Acids Research
(2020)
48,
373
Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers.
DJ Sharpe, K Röder, DJ Wales
– J Phys Chem B
(2020)
124,
4062
Flip rearrangement in the water pentamer: Analysis of electronic structure
T Xu, X Bin, SR Kirk, DJ Wales, S Jenkins
– International Journal of Quantum Chemistry
(2020)
120,
ARTN e26124
Transforming the Accuracy and Numerical Stability of ReaxFF Reactive Force Fields
D Furman, DJ Wales
– The journal of physical chemistry letters
(2019)
10,
7215
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