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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.

Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1 (2021)
Journal Article
Zhou, J., Wu, S., Lee, B. G., Chen, T., He, Z., Lei, Y., …Hirst, J. D. (2021). Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1. Molecules, 26(24), Article 7492. https://doi.org/10.3390/molecules26247492

A machine learning approach has been applied to virtual screening for lysine specific demethylase 1 (LSD1) inhibitors. LSD1 is an important anti-cancer target. Machine learning models to predict activity were constructed using Morgan molecular finger... Read More about Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1.

Erratum: Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction (Chemical Reviews (2020) 120:15 (7152−7218) DOI: 10.1021/acs.chemrev.9b00813) (2021)
Journal Article
Baiz, C. R., Błasiak, B., Bredenbeck, J., Cho, M., Choi, J. H., Corcelli, S. A., …Zanni, M. T. (2021). Erratum: Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction (Chemical Reviews (2020) 120:15 (7152−7218) DOI: 10.1021/acs.chemrev.9b00813). Chemical Reviews, 121(21), 13698. https://doi.org/10.1021/acs.chemrev.1c00758

The authors make the following additions and corrections to the paper, C. Baiz et al., Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem. Rev. 2020, 120, 7152?7218. 1. The below funding sources should be ad... Read More about Erratum: Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction (Chemical Reviews (2020) 120:15 (7152−7218) DOI: 10.1021/acs.chemrev.9b00813).

Kernel Methods for Predicting Yields of Chemical Reactions (2021)
Journal Article
Haywood, A. L., Redshaw, J., Hanson-Heine, M. W., Taylor, A., Brown, A., Mason, A. M., …Hirst, J. D. (2022). Kernel Methods for Predicting Yields of Chemical Reactions. Journal of Chemical Information and Modeling, 62(9), 2077-2092. https://doi.org/10.1021/acs.jcim.1c00699

The use of machine learning methods for the prediction of reaction yield is an emerging area. We demonstrate the applicability of support vector regression (SVR) for predicting reaction yields, using combinatorial data. Molecular descriptors used in... Read More about Kernel Methods for Predicting Yields of Chemical Reactions.

Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S1 ← S0 Transitions (2021)
Journal Article
Robinson, D., Alarfaji, S. S., & Hirst, J. D. (2021). Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S1 ← S0 Transitions. Journal of Physical Chemistry A, 125(24), 5237–5245. https://doi.org/10.1021/acs.jpca.1c01685

For benzene, toluene, aniline, fluorobenzene, and phenol, even sophisticated treatments of electron correlation, such as MRCI and XMS-CASPT2 calculations, show oscillator strengths typically lower than experiment. Inclusion of a simple pseudo-diabati... Read More about Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S1 ← S0 Transitions.

Near-ultraviolet circular dichroism and two-dimensional spectroscopy of polypeptides (2021)
Journal Article
Segatta, F., Rogers, D. M., Dyer, N. T., Guest, E. E., Li, Z., Do, H., …Hirst, J. D. (2021). Near-ultraviolet circular dichroism and two-dimensional spectroscopy of polypeptides. Molecules, 26(2), Article 396. https://doi.org/10.3390/MOLECULES26020396

A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ul... Read More about Near-ultraviolet circular dichroism and two-dimensional spectroscopy of polypeptides.

Influence of structure and solubility of chain transfer agents on the RAFT control of dispersion polymerisation in scCO2 (2020)
Journal Article
Alves Costa Pacheco, A., Fernandes Da Silva Filho, A., Kortsen, K., Hanson-Heine, M., Taresco, V., Hirst, J. D., …Howdle, S. M. (2021). Influence of structure and solubility of chain transfer agents on the RAFT control of dispersion polymerisation in scCO2. Chemical Science, 12(3), 1016-1030. https://doi.org/10.1039/d0sc05281g

Reversible addition-fragmentation chain transfer (RAFT) dispersion polymerisation of methyl methacrylate (MMA) is performed in supercritical carbon dioxide (scCO2) with 2-(dodecylthiocarbonothioylthio)-2-methylpropionic acid (DDMAT) present as chain... Read More about Influence of structure and solubility of chain transfer agents on the RAFT control of dispersion polymerisation in scCO2.

Origin of Selectivity in Protein Hydrolysis by Zr(IV)-Containing Metal Oxides as Artificial Proteases (2020)
Journal Article
Solé-Daura, A., Rodríguez-Fortea, A., Poblet, J. M., Robinson, D., Hirst, J. D., & Carbó, J. J. (2020). Origin of Selectivity in Protein Hydrolysis by Zr(IV)-Containing Metal Oxides as Artificial Proteases. ACS Catalysis, 10, 13455-13467. https://doi.org/10.1021/acscatal.0c02848

© 2020 American Chemical Society. All rights reserved. The origin of selectivity in protein hydrolysis promoted by Zr(IV)-substituted polyoxometalates (POMs) has been investigated through a variety of computational techniques. Initially, we analyzed... Read More about Origin of Selectivity in Protein Hydrolysis by Zr(IV)-Containing Metal Oxides as Artificial Proteases.

A Machine Learning Protocol for Predicting Protein Infrared Spectra (2020)
Journal Article
Ye, S., Zhong, K., Zhang, J., Hu, W., Hirst, J. D., Zhang, G., …Jiang, J. (2020). A Machine Learning Protocol for Predicting Protein Infrared Spectra. Journal of the American Chemical Society, 142(45), 19071–19077. https://doi.org/10.1021/jacs.0c06530

© 2020 American Chemical Society. Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive... Read More about A Machine Learning Protocol for Predicting Protein Infrared Spectra.

Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid (2020)
Journal Article
Spankie, T. J., Haywood, A. L., Dottorini, T., Barrow, P. A., & Hirst, J. D. (2020). Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid. Journal of Molecular Graphics and Modelling, 101, Article 107723. https://doi.org/10.1016/j.jmgm.2020.107723

© 2020 Elsevier Inc. One promising strategy to combat antimicrobial resistance is to use bacteriophages that attach to the sex pili produced by transmissible antimicrobial resistance (AMR) plasmids, infect AMR bacteria and select for loss of the AMR... Read More about Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid.

Computed optical spectra of SARS-CoV-2 proteins (2020)
Journal Article
Li, Z., & Hirst, J. D. (2020). Computed optical spectra of SARS-CoV-2 proteins. Chemical Physics Letters, 758, Article 137935. https://doi.org/10.1016/j.cplett.2020.137935

© 2020 Elsevier B.V. Treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Covid-19, may well be predicated on knowledge of the structures of protein of this virus. However, often these cannot be determined... Read More about Computed optical spectra of SARS-CoV-2 proteins.

Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene (2020)
Journal Article
Jiang, L., Rogers, D. M., Hirst, J. D., & Do, H. (2020). Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene. Journal of Chemical Theory and Computation, 16(8), 5150-5162. https://doi.org/10.1021/acs.jctc.0c00399

Utilizing a force-matching procedure, we parametrize new force fields systematically for large conjugated systems. We model both conjugated polymers and molecular crystals that contain diketopyrrolopyrrole, thiophene, and thieno[3,2-b]thiophene units... Read More about Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene.