Publications
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84. Bimolecular Sandwich Aggregates of Porphyrin Nanorings
H. Gotfredsen*, J. Hergenhahn, F. Duarte. T. D. W. Claridge, H. L. Anderson*, J. Am. Chem. Soc. 2024, XXX, XX, XXXXX
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83. Modeling Chemical Processes in Explicit Solvents with Machine Learning Potentials
H. Zhang, V. Juraskova, F. Duarte.* Nat Commun 2024, 15, 6114. ChemRxiv 2023 Prep
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82. Modelling ligand exchange in metal complexes with machine learning potentials
V Juraskova, G Tusha, H Zhang, L Schäfer,* F Duarte*, ChemRxiv 2024 Preprint. Faraday Discuss., 2024 ASAP
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81. Origins of High-Activity Cage-Catalyzed Michael Addition
P. J. Boaler, T. K. Piskorz, L. E. Bickerton, J. Wang,DOI: 10.1021/jacs.4c05160 F. Duarte,* G. C. Lloyd-Jones,* P. J. Lusby.* J. Am. Chem. Soc., 2024, 146, 28, 19317
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80. metallicious: Automated force-field parametrization of covalently bound metals for supramolecular structures
T. K. Piskorz, B. Lee, S. Zhan, F. Duarte.* ChemRxiv 2024 Preprint
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79. PythiaCHEM : a user-friendly machine learning toolkit for chemistry
Stamatia Zavitsanou, Zonghua Bo, Emanuele Casali, Matthew Langton, and Fernanda Duarte*, ChemRxiv 2024 Preprint
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78. Transfer learning for Heterocycle Synthesis Prediction
E. Wieczorek, J. W. Sin, M. T. O. Holland, L. Wilbraham, V. S. Perez, A. Bradley, D. Miketa, P. E. Brennan, F. Duarte*, ChemRxiv 2024 Preprint
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77. CageCavityCalc (C3): A computational tool for calculating and visualizing cavities in Molecular Cages
V. Martí-Centelles,* T. K. Piskorz, F. Duarte* ChemRxiv 2024 Preprint. J. Chem. Inf. Model. 2024, ASAP
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76. Responsive Anionophores with AND Logic Multi‐stimuli activation
M. Ahmad, TG Johnson, M. Flerin, F. Duarte,* M. J. Langton*, Angew. Chem. Int. Ed. 2024, e202403314
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75. Beyond Strain Release: Delocalization-Enabled Organic Reactivity
A. J. Sterling,* R. C. Smith, E. A. Anderson,* F. Duarte, J. Org. Chem., 2024, Article ASAP DOI: 10.1021/acs.joc.4c00857
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74. α-Amino bicycloalkylation through organophotoredox catalysis
J. Nugent, A. López-Francé, A. J. Sterling, M. Y. Tay, N. Frank, J. J. Mousseauc, F. Duarte,* E. A. Anderson. Chem. Sci., 2024, Advance Article
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73. Template-Directed Synthesis of Strained meso-meso-Linked Porphyrin Nanorings
J. Van Raden, J. Deng, H. Gotfredsen, J. Hergenhahn, M. Clarke, M. Edmondson, J. Hart, J. O'Shea, F. Duarte, A. Saywell, H. L. Anderson*, Angew. Chem. Int. Ed. 2024 Accepted
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72. Mutate and Conjugate: A Method to Enable Rapid In-Cell Target Validation
A. M. Thomas, M. Serafini, E. K. Grant, E. A. J. Coombs, J. P. Bluck, M. Schiedel, M. A. McDonough, J. K. Reynolds, B. Lee, M. Platt, V. Sharlandjieva, P. C. Biggin, F. Duarte, T. A. Milne, J. T. Bush and S. J. Conway, ACS Chem. Biol., , DOI:10.1021/acschembio.3c00437.
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71. Mass spectrometric assays monitoring the deubiquitinase activity of the SARS-CoV-2 papain-like protease inform on the basis of substrate selectivity and have utility for substrate identification
1L. Brewitz, H. T. Henry Chan, P. Lukacik, C. Strain-Damerell, M. A. Walsh, F. Duarte* and C. J. Schofield,* Bioorg. Med. Chem. 2023, 95, 117498.
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70. Picking the Lock of Coordination Cage Catalysis
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69. Redox Reorganization: Aluminium Promoted 1,5-Hydride Shifts Allow the Controlled Synthesis of Multisubstituted Cyclohexenes
L. B. Smith, R. J. Armstrong, J. Hou, E. Smith, Ming Sze, A. J. Sterling, A. Smith, F. Duarte,* T. J. Donohoe.* Angew. Chem. Int. Ed. 2023, e202307424.
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68. Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2' proline of the viral polyprotein
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67. Dynamical nonequilibrium molecular dynamics simulations identify allosteric sites and positions associated with drug resistance in the SARS-CoV-2 main protease
H. T. H. Chan, A. S. F. Oliveira, C. J. Schofield, A. J. Mulholland,* F. Duarte,* JACS Au 2023, 3, 6, 1767–1774. BioRxiv 2022 Preprint.
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66. Taming non-classical carbocations to control small ring reactivity
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65. Mobile Molecules: Reactivity Profiling Guides Faster Movement on a Cysteine Track
Z. Bo, Z. H. Lim, F. Duarte,* H. Bayley,* Y. Qing,* Angew. Chem. Int. Ed. 2023, e20
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64. Visible Light Photoredox-Catalyzed Decarboxylative Alkylation of 3-Aryl-Oxetanes and Azetidines via Benzylic Tertiary Radicals and Implications of Benzylic Radical Stability
M. A. Dubois, J. J. Rojas, A. J. Sterling, H. C. Broderick, M. A. Smith, A. J. P. White, P. W. Miller, C. Choi, J. J. Mousseau, F. Duarte,* J. A. Bull,* J. Org. Chem. 2023, 88, 6476–6488.
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63. Reaction dynamics of Diels-Alder reactions from machine learned potentials
T. A. Young, T. Johnston-Wood, H. Zhang, F. Duarte*, Phys. Chem. Chem. Phys. 2022, 24, 20820. ChemRxiv 2022 Preprint.
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62. Synthesis of meta-substituted arene bioisosteres from [3.1.1]propellane
N. Frank, J. Nugent, B. Shire, H. Pickford, P. Rabe, A. Sterling, T. Zarganes-Tzitzikas, T. Grimes, A. Thompson, R. Smith, C. Schofield, P. Brennan, F. Duarte and E. Anderson, Nature 2022, 611, 721. ChemRxiv 2022 Preprint.
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61. Collective Synthesis of Illudalane Sesquiterpenes via Cascade Inverse Electron Demand (4 + 2) Cycloadditions of Thiophene S,S-Dioxides
K. H. K. Park, N. Frank, F. Duarte,* E. Anderson.* J. Am. Chem. Soc., 2022, 144, 10017–10024.
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60. Computational Modeling of Supramolecular Metallo-organic Cages – Challenges and Opportunities
T. K. Piskorz, V. Martí-Centelles, T. A. Young, P. J. Lusby*, F. Duarte*, ACS Catal. 2022, 12, 5806–5826
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59. Identification of Histone Peptide Binding Specificity and Small-Molecule Ligands for the TRIM33α and TRIM33β Bromodomains
A. R. Sekirnik, J. K. Reynolds, L. See, J. P. Bluck, A. R. Scorah, C. Tallant, B. Lee, K. B. Leszczynska, R. L. Grimley, R. I. Storer, M. Malattia, S. Crespillo, S. Caria, S. Duclos, E. M. Hammond, S. Knapp, G. M. Morris, F. Duarte, P. C. Biggin, S. J. Conway, ACS Chem. Biol. 2022, 17, 2753–2768. ChemRxiv 2022 Preprint.
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58. Bending a Photonic Wire into a Ring
H. Gotfredsen, J-R Deng, J. Van Raden,M. Righetto, J. Hergenhahn, M. Clarke,A. Bellamy-Carter, J. Hart, J. O’Shea, T. D. W. Claridge, F. Duarte, A. Saywell, L. M. Herz, H. L. Anderson.*, Nat. Chem. 2022. ChemRxiv 2021 Preprint.
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57. Amino-oxetanes as amide isosteres by an alternative defluorosulfonylative coupling of sulfonyl fluorides
J. J. Rojas, R. A. Croft, A. J. Sterling, E. L. Briggs, D. Antermite, D. C. Schmitt, L. Blagojevic, P.Haycock, A. J. P. White, F. Duarte, C. Choi, J. J Mousseau, J. A Bull, Nat. Chem. 2022, 14, 160-169.
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56. Electrophilic Activation of [1.1.1] Propellane for the Synthesis of Nitrogen‐Substituted bicyclo[1.1.1]pentanes
S. Livesley, A. J. Sterling, C. M. Robertson, W. R. F. Goundry, J. A. Morris, F. Duarte,* C. Aïssa,* Angew. Chem. Int. Ed. 2022, 60, 4266.
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55. Red-shifted tetra-ortho-halo-azobenzenes for photo-regulated transmembrane anion transport
A. Kerckhoffs, Z. Bo, S. Penty, F. Duarte,* M. Langton,* Org. Biomol. Chem. 2021, 19, 9058.
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54. Catalytic Enantioselective Nucleophilic Desymmetrisation of Phosphonate Esters
M. Formica , T. Rogova , H. Shi , N. Sahara , A. J. M. Farley , K. E. Christensen, F. Duarte* & D. J. Dixon,* ChemRxiv 2021 Preprint.
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53. A Transferable Active-Learning Strategy for Reactive Molecular Force Fields
T. A. Young, T. Johnston-Wood, V. Deringer,* F. Duarte,* Chem. Sci. 2021, 12, 10944. ChemRxiv 2021 Preprint.
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52. Discovery of SARS-CoV-2 Mpro Peptide Inhibitors from Modelling Substrate and Ligand Binding
H. T. H. Chan, M. A. Moesser, R. K. Walters, T. R. Malla, R. M. Twidale, Tobias John, H. M. Deeks, T. Johnston-Wood, V. Mikhailov, R. B. Sessions, W. Dawson, E. Salah, P. Lukacik, C. Strain-Damerell, C. D. Owen, T. Nakajima, K. Świderek, A. Lodola, V. Moliner, D.R. Glowacki, M. A. Walsh, C. J. Schofield,* L. Genovese,* D. K. Shoemark,* A. J. Mulholland,* F. Duarte,* G. M. Morris,* Chem. Sci. 2021, 12, 13686. BioRxiv 2021
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51. Highly Active Halogen Bonding and Chalcogen Bonding Chloride Transporters with Non‐Protonophoric Activity
L.E. Bickerton, A. Docker, A.J. Sterling, H. Kuhn, F. Duarte,* P. D. Beer,* M. Langton,* Chem. Eur. J. 2021, 27, 11738.
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50. Direct catalytic asymmetric synthesis of α-chiral bicyclo [1.1. 1] pentanes
M. L. J. Wong, A. J. Sterling, J. J Mousseau, F. Duarte,* E. A. Anderson,* Nat. Commun. 2021, 12, 1644.
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49. Mass spectrometry reveals potential of β-lactams as SARS-CoV-2 Mpro inhibitors
T.R Malla, A. Tumber, T. John, L. Brewitz, C. Strain-Damerell, C. D. Owen, P. Lukacik, H.T.H Chan, P. Maheswaran, E. Salah, F. Duarte, H. Yang, Z. Rao, M. A. Walsh, C. J Schofield, Chem. Commun. 2021, 57, 1430.
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48. Selectivity in organocatalysis—From qualitative to quantitative predictive models
A. J. Sterling, S. Zavitsanou, J. Ford, F. Duarte,* WIREs Comput Mol Sci. 2021, e1518.
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47. autodE: Automated Calculation of Reaction Energy Profiles – Application to Organic and Organometallic Reactions
T. A. Young, J. J. Silcock, A. J. Sterling, F. Duarte,* Angew. Chem. Int. Ed. 2021, 60, 4266. ChemRxiv 2020.
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46. trans-Hydroboration–oxidation products in Δ5-steroids via a hydroboration-retro-hydroboration mechanism
J. C. Hilario-Martinez, F. Murillo, J. Garcia-Mendez, E. Dzib, J. Sandoval-Ramirez, M.A Muñoz-Hernandez, S. Bernes, Laszlo Kürti, F. Duarte, G. Merino, M. A. Fernández-Herrera, Chem. Sci. 2020, 11, 12764.
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45. Synergistic Non-Covalent Catalysis Facilitates Base-Free Michael Addition
J. Wang, T. A. Young, F.Duarte,* P. J. Lusby,* J. Am. Chem. Soc. 2020, 142, 17743.
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44. Reverse Polarity Reductive Functionalization of Tertiary Amides via a Dual Iridium Catalyzed Hydrosilylation & SET Strategy
T. Rogova, P. Gabriel, S. Zavitsanou, J. A. Leitch, F. Duarte,* D.J. Dixon,* ACS Catal. 2020, 10, 11438.
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43. Harnessing Sulfinyl Nitrenes: A Unified One-Pot Synthesis of Sulfoximines and Sulfonimidamides
T. Q. Davies, M. J. Tilby, J Ren, N. A. Parker, D. Skolc, A. Hall, F. Duarte, M. C. Willis,* J. Am. Chem. Soc. 2020, 142, 15445.
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42. Atropisomerism in diarylamines: structural requirements and mechanisms of conformational interconnection
R. Costil, A. J. Sterling, F. Duarte, J. Clayden, Angew. Chem. Int. Ed. 2020, 59 ,18670.
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41. cgbind: A Python Module and Web App for Automated Metallocage Construction and Host-Guest Characterization
T. A. Young, R. Gheorghe, F. Duarte,* J. Chem. Inf. Model. 2020, 60, 354. ChemRxiv 2020 Preprint.
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40. Characterization of the Zwitterionic Intermediate in 1,1-Carboboration of Alkynes
A. Bismuto, G. S. Nichol, F. Duarte,* M. J. Cowley,* and S. P. Thomas,* Angew. Chem. Int. Ed. 2020, 59, 12731.
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39. Transmembrane anion transport mediated by halogen bonding and hydrogen bonding triazole anionophores
L.E Bickerton, A.J. Sterling, P.D. Beer, F Duarte,* M.J. Langton,* Chem. Sci. 2020, 11, 4722.
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38. Rationalizing the diverse reactivity of [1.1.1]propellane through sigma-pi-delocalization
A.J. Sterling, A. Durr, R.C Smith, E. Anderson,* F. Duarte,* Chem. Sci. 2020, 11, 4895. ChemRxiv 2019 Preprint.
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37. Tuning the anion binding properties of lanthanide receptors to discriminate nucleoside phosphates in a sensing array
S.H. Hewitt, G. Macey, R. Mailhot, M.R.J. Elsegood, F. Duarte, A.M. Kenwright, S. J. Butler,* Chem. Sci. 2020, 11, 3619.
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36. Double and Triple Ionisation of Isocyanic Acid
J. H. D. Eland, R. J. Squibb, A. J. Sterling, M. Wallner, A. Hult Roos, J. Andersson, V. Axelsson, E. Johansson, A. Teichter, S. Stranges, B. Brunetti, J. M. Dyke, F. Duarte & R. Feifel, Sci. Rep. 2020, 10, 2288.
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35. Host-Guest Induced Electron Transfer Triggers Radical-Cation Catalysis
R. L. Spicer, A. Stergiou, T. A. Young, F. Duarte,* M. D Symes,* P. J. Lusby,* J. Am. Chem. Soc. 2020, 142, 2134.
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34. Dearomative Photocatalytic Construction of Bridged 1,3-Diazepanes
J. A. Leitch, T. Rogova, F. Duarte,* D. J. Dixon,* Angew. Chem. Int. Ed. 2020, 59, 2. ChemRxiv 2019, Preprint.
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33. Rationalizing the Activity of an “Artificial Diels-Alderase”: Establishing Efficient and Accurate Protocols for Calculating Supramolecular Catalysis
T. A. Young, V. Martí-Centelles, J. Wang, P. J. Lusby,* F. Duarte,* J. Am. Chem. Soc. 2020, 142, 1300. ChemRxiv 2019, Preprint.
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32. The Energetic Significance of Metallophilic Interactions
Q. Zheng, S. Borsley, G.S Nichol, F. Duarte, S. L. Cockroft, Angew. Chem. Int. Ed. 2019, 58, 12617.
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31. Catalytic Asymmetric Synthesis of Cyclohexanes by Hydrogen Borrowing Annulations
R. Armstrong, W. Akhtar, T. Young, F. Duarte,* T. J. Donohoe,* Angew. Chem. Int. Ed. 2019, 58, 12558.
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30. Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds
N. Tatum, F. Duarte, S. C. L. Kamerlin, E. Pohl, J. Phys. Chem. Lett. 2019, 10, 2244.
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29. A General Route to Bicyclo[1.1.1] pentanes through Photoredox Catalysis
J. Nugent, C. Arroniz, B. Shire, A. J. Sterling, H. D. Pickford, M. L. J. Wong, S. J. Mansfield, D. F. J. Caputo, B. Owen, J. J. Mousseau, F. Duarte,* E. Anderson,* ACS Catal. 2019, 9, 9568. ChemRxiv 2019, Preprint.
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28. Stereospecific 1,3-H Transfer of Indenols Proceeds via Persistent Ion-Pairs Anchored By NH···π Interactions
D. M. H. Ascough, F. Duarte, and R. S. Paton, J. Am. Chem. Soc. 2018, 140, 16740.
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27. Host-Guest chemistry of self-assembled hemi-cage systems: The dramatic effect of lost pre-organization
V. Martí-Centelles, F. Duarte,* P. J. Lusby,* Isr. J. Chem. 2018, 58, 1.
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26. Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset
C. M. Miton, S. Jonas, G. Fischer, F. Duarte, M. F. Mohamed, B. van Loo, B. Kintses, S. C. L. Kamerlin, N. Tokuriki, M. Hyvönen, and F. Hollfelder, Proc. Natl. Acad. Sci. U.S.A 2018, 115, E7293.
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25. Bio‐inspired Domino oxa‐Michael/Diels–Alder/oxa‐Michael Dimerization of para‐Quinols
N. J. Green, C. A. Connolly, K. PW Rietdijk, G. S. Nichol, F. Duarte,* A. L. Lawrence,* Angew. Chem. Int. Ed. 2018, 57, 6198.
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24. Cation–π interactions in protein-ligand binding: theory and data-mining reveal different roles for lysine and arginine
K. Kumar, S. M. Woo, T. Siu, W. A. Cortopassi, F. Duarte,* and R. S. Paton,* Chem. Sci. 2018, 9, 2655.
Empirical Valence Bond Book
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Theory and Applications of the Empirical Valence Bond Approach: From Physical Chemistry to Chemical Biology
Description. Over the past couple of decades, Empirical Valence Bond (EVB) approaches have become one of the key tools for studying chemical processes in condensed phases and proteins. This book provides a comprehensive overview of these advances, highlighting how they have shaped our current understanding of enzyme catalysis and chemical processes in general. Written by leading scientists in the field, the book focuses on the applications and extension of the original EVB approach to a variety of different areas of research, including reaction dynamics, design of artificial catalysts, and the study of complex biological problems.
The book begins with concise yet comprehensive introduction to the basic concepts and historical background of valence bond theory, and EVB specifically. Subsequent chapters discuss the application of EVB models to a broad range of molecular systems of chemical and biological interest, and highlight the effectiveness of EVB to study chemical processes in the condensed phase and in enzymes.
