All Outputs (8)

Electronic circular dichroism of proteins computed using a diabatisation scheme (2022)
Journal Article
Rogers, D. M., Do, H., & Hirst, J. D. (2023). Electronic circular dichroism of proteins computed using a diabatisation scheme. Molecular Physics, 121(7-8), Article e2133748. https://doi.org/10.1080/00268976.2022.2133748

Circular dichroism (CD) spectroscopy is a powerful technique employed to study the structure of biomolecules. More accurate calculation of CD from first principles will aid both computational and experimental studies of protein structure and dynamics... Read More about Electronic circular dichroism of proteins computed using a diabatisation scheme.

Machine learning for yield prediction for chemical reactions using in situ sensors (2022)
Journal Article
Davies, J. C., Pattison, D., & Hirst, J. D. (2023). Machine learning for yield prediction for chemical reactions using in situ sensors. Journal of Molecular Graphics and Modelling, 118, Article 108356. https://doi.org/10.1016/j.jmgm.2022.108356

Machine learning models were developed to predict product formation from time-series reaction data for ten Buchwald-Hartwig coupling reactions. The data was provided by DeepMatter and was collected in their DigitalGlassware cloud platform. The reacti... Read More about Machine learning for yield prediction for chemical reactions using in situ sensors.

Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4 (2022)
Journal Article
Silva, A. F., Guest, E. E., Falcone, B. N., Pickett, S. D., Rogers, D. M., & Hirst, J. D. (2023). Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4. Molecular Physics, 121(9-10), Article e2124201. https://doi.org/10.1080/00268976.2022.2124201

Alchemical free energy perturbation (FEP) theory is widely used nowadays to calculate protein–ligand binding energies, often in support of drug discovery endeavours. We assess the accuracy and sensitivity of absolute FEP binding energies with respect... Read More about Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4.

N-Hydroxyethyl acrylamide as a functional eROP initiator for the preparation of nanoparticles under “greener” reaction conditions (2022)
Journal Article
Lentz, J. C., Cavanagh, R., Moloney, C., Falcone Pin, B., Kortsen, K., Fowler, H. R., …Howdle, S. M. (2022). N-Hydroxyethyl acrylamide as a functional eROP initiator for the preparation of nanoparticles under “greener” reaction conditions. Polymer Chemistry, 13(42), 6032-6045. https://doi.org/10.1039/d2py00849a

N-Hydroxyethyl acrylamide was used as a functional initiator for the enzymatic ring-opening polymerisation of ϵ-caprolactone and δ-valerolactone. N-Hydroxyethyl acrylamide was found not to undergo self-reaction in the presence of Lipase B from Candid... Read More about N-Hydroxyethyl acrylamide as a functional eROP initiator for the preparation of nanoparticles under “greener” reaction conditions.

Structure–Property Relationships in Amorphous Thieno[3,2-b]thiophene–Diketopyrrolopyrrole–Thiophene-Containing Polymers (2022)
Journal Article
Jiang, L., Hirst, J. D., & Do, H. (2022). Structure–Property Relationships in Amorphous Thieno[3,2-b]thiophene–Diketopyrrolopyrrole–Thiophene-Containing Polymers. Journal of Physical Chemistry C, 126(26), 10842-10854. https://doi.org/10.1021/acs.jpcc.2c01650

(Figure Presented) We present calculations of electronic structure properties of disordered conducting polymers containing thieno[3,2b]thiophene, diketopyrrolopyrrole, and thiophene. Atomistic force field parameters for the polymer were optimized to... Read More about Structure–Property Relationships in Amorphous Thieno[3,2-b]thiophene–Diketopyrrolopyrrole–Thiophene-Containing Polymers.

Software tools for green and sustainable chemistry (2022)
Journal Article
Derbenev, I. N., Twycross, J., Dowden, J., & Hirst, J. D. (2022). Software tools for green and sustainable chemistry. Current Opinion in Green and Sustainable Chemistry, 35, Article 100623. https://doi.org/10.1016/j.cogsc.2022.100623

In this review, we consider green chemistry metrics, related software tools, and the opportunities and challenges for their use in research laboratories. We provide an overview of state-of-the-art software designed both to aid researchers in planning... Read More about Software tools for green and sustainable chemistry.

Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4 (2022)
Journal Article
Guest, E. E., Cervantes, L. F., Pickett, S. D., Brooks, C. L., & Hirst, J. D. (2022). Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. Journal of Chemical Information and Modeling, 62(6), 1458-1470. https://doi.org/10.1021/acs.jcim.1c01229

Accurate and rapid predictions of the binding affinity of a compound to a target are one of the ultimate goals of computer aided drug design. Alchemical approaches to free energy estimations follow the path from an initial state of the system to the... Read More about Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4.

Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis (2022)
Journal Article
Gaughan, S. J. H., Hirst, J. D., Croft, A. K., & Jäger, C. M. (2022). Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis. Journal of Chemical Information and Modeling, 62(3), 591-601. https://doi.org/10.1021/acs.jcim.1c00791

Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-Adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyo... Read More about Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis.