the gomes group @ CMU

chemical {designers | engineers | data scientists} crunching bits into matter since January 2022

publications

‡ = equal authorship
_ = undergrad student

preprints

Krenn, M.; Pollice, R.; Guo, S. Y.; Aldeghi, M.; Cervera-Lierta, A.; Friederich, P.; Gomes, G. dos P.; Häse, F.; Jinich, A.; Nigam, A.; Yao, Z.; Aspuru-Guzik, A. On Scientific Understanding with Artificial Intelligence. arXiv 2022. https://doi.org/10.48550/ARXIV.2204.01467.
Lavigne, C.; Gomes, G. dos P.; Pollice, R.; Aspuru-Guzik, A. Automatic Discovery of Chemical Reactions Using Imposed Activation. 2020. https://doi.org/10.26434/chemrxiv.13008500.v1.
2022

48. Reschützegger, T.; Syphan, T. & dos Passos Gomes, G. Three catalysts tango with olefins. Nat. Synth. 2022 https://doi.org/10.1038/s44160-021-00018-9.
prior to CMU

47. Gensch, T.; Gomes, G. dos P.; Friederich, P.; Peters, E.; Gaudin, T.; Pollice, R.; Jorner, K.; Nigam, A.; D’Addario, M. L.; Sigman, M. S.; Aspuru-Guzik, A. A Comprehensive Discovery Platform for Organophosphorus Ligands for Catalysis. J. Am. Chem. Soc. 2022 https://doi.org/10.1021/jacs.1c09718.
46. Christensen, M.; Yunker, L.; Adedeji, F.; Häse, F.; Roch, L.; Gensch, T.; Gomes, G. dos P.; Zepel, T.; Sigman, M.; Aspuru-Guzik, A.; Hein, J. Data-Science Driven Autonomous Process Optimization. 2020. https://doi.org/10.26434/chemrxiv.13146404.v2.
45. Nigam, A.; Pollice, R.; Krenn, M.; Gomes, G. dos P.; Aspuru-Guzik, A. Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules Using SELFIES. 2021. https://doi.org/10.26434/chemrxiv.13383266.v2.
44. Auhim, H. S.; Grigorenko, B. L.; Harris, T. K.; Aksakal, O. E.; Polyakov, I. V.; Berry, C.; Gomes, G. dos P.; Alabugin, I. V.; Rizkallah, P. J.; Nemukhin, A. V.; Jones, D. D. Stalling Chromophore Synthesis of the Fluorescent Protein Venus Reveals the Molecular Basis of the Final Oxidation Step. Chem. Sci. 2021, 12 (22), 7735–7745. https://doi.org/10.1039/D0SC06693A.
43. R. Pollice, P. Friederich, C. Lavigne, G. P. Gomes, A. Aspuru-Guzik Organic Molecules with Inverted Gaps between First Excited Singlet and Triplet States and Appreciable Oscillator Strengths, Matter 2021 4 (5), 1654. https://doi.org/10.26434/chemrxiv.13087319.
42. dos Passos Gomes, G.; Xu, G.; Zhu, X.; Chamoreau, L.-M.; Zhang, Y.; Bistri-Aslanoff, O.; Roland, S.; Alabugin, I. V.; Sollogoub, M. Mapping C−H⋅⋅⋅M Interactions in Confined Spaces: (α-ICyDMe)Au, Ag, Cu Complexes Reveal “Contra-Electrostatic H Bonds” Masquerading as Anagostic Interactions**. Chemistry – A European Journal 2021, 27 (31), 8127–8142. https://doi.org/10.1002/chem.202100263.
41. Diaz, D. B.; Appavoo, S. D.; Bogdanchikova, A. F.; Lebedev, Y.; McTiernan, T. J.; dos Passos Gomes, G.; Yudin, A. K. Illuminating the Dark Conformational Space of Macrocycles Using Dominant Rotors. Nat. Chem. 2021, 13 (3), 218–225. https://doi.org/10.1038/s41557-020-00620-y.
40. Pollice, R.; dos Passos Gomes, G.; Aldeghi, M.; Hickman, R. J.; Krenn, M.; Lavigne, C.; Lindner-D’Addario, M.; Nigam, A.; Ser, C. T.; Yao, Z.; Aspuru-Guzik, A. Data-Driven Strategies for Accelerated Materials Design. Acc. Chem. Res. 2021, 54 (4), 849–860. https://doi.org/10.1021/acs.accounts.0c00785.
39. Gomes, G. dos P.; Pollice, R.; Aspuru-Guzik, A. Navigating through the Maze of Homogeneous Catalyst Design with Machine Learning. TRECHEM 2021, 3 (2), 96–110. https://doi.org/10.1016/j.trechm.2020.12.006.
38. Kaldas, S. J.; Tien, C.-H.; Gomes, G. dos P.; Meyer, S.; Sirvinskas, M.; Foy, H.; Dudding, T.; Yudin, A. K. Oxidative Rearrangement of MIDA (N-Methyliminodiacetic Acid) Boronates: Mechanistic Insights and Synthetic Applications. Org. Lett. 2021, 23 (2), 324–328. https://doi.org/10.1021/acs.orglett.0c03823.
37. S. C. Davidson, G. P. Gomes, L. R. Kuhn, I. V. Alabugin, A. R. Kennedy, N. C. O. Tomkinson “Organocatalytic sulfoxidation”, Tetrahedron, 2021, 78, 131784, ISSN 0040-4020. https://doi.org/10.1016/j.tet.2020.131784.
36. Mills, L. R.; Monteith, J. J.; dos Passos Gomes, G.; Aspuru-Guzik, A.; Rousseaux, S. A. L. The Cyclopropane Ring as a Reporter of Radical Leaving-Group Reactivity for Ni-Catalyzed C(Sp3)–O Arylation. J. Am. Chem. Soc. 2020, 142 (30), 13246–13254. https://doi.org/10.1021/jacs.0c06904.
35. Friederich, P.; Gomes, G. dos P.; Bin, R. D.; Aspuru-Guzik, A.; Balcells, D. Machine Learning Dihydrogen Activation in the Chemical Space Surrounding Vaska’s Complex. Chem. Sci. 2020, 11 (18), 4584–4601. https://doi.org/10.1039/D0SC00445F.
34. Gonzalez-Rodriguez, E.; Abdo, M. A.; dos Passos Gomes, G.; Ayad, S.; White, F. D.; Tsvetkov, N. P.; Hanson, K.; Alabugin, I. V. Twofold π-Extension of Polyarenes via Double and Triple Radical Alkyne Peri-Annulations: Radical Cascades Converging on the Same Aromatic Core. J. Am. Chem. Soc. 2020, 142 (18), 8352–8366. https://doi.org/10.1021/jacs.0c01856.
33. Elliott, Q.; Gomes, G. dos P.; Evoniuk, C. J.; Alabugin, I. V. Testing the Limits of Radical-Anionic CH-Amination: A 10-Million-Fold Decrease in Basicity Opens a New Path to Hydroxyisoindolines via a Mixed C–N/C–O-Forming Cascade. Chem. Sci. 2020, 11 (25), 6539–6555. https://doi.org/10.1039/C9SC06511C.
32. Lee, R.; Bashrum, B.; Cagle, E. C.; Walters, J.; Massey, J.; Zanghi, M.; Birchfield, C.; French, D.; Joy, J.; dos Passos Gomes, G.; Wiget, P. A. Electronic Donation or Steric Contraction: A Spectroscopic and Structural Analysis of Medium-Sized Constrained Rings for Potential Long-Range Hyperconjugation. J. Org. Chem. 2019, 84 (16), 9897–9906. https://doi.org/10.1021/acs.joc.9b00979.
31. dos Passos Gomes, G.; Wimmer, A.; Smith, J. M.; König, B.; Alabugin, I. V. CO2 or SO2: Should It Stay, or Should It Go? J. Org. Chem. 2019, 84 (10), 6232–6243. https://doi.org/10.1021/acs.joc.9b00503.
30. Hughes, A. M.; dos Passos Gomes, G.; Alabugin, I. V. Stereoelectronic Influence of a “Spectator” Propargylic Substituent Can Override Aromaticity Effects in Radical Peri-Cyclizations En Route to Expanded Polyaromatics. J. Org. Chem. 2019, 84 (4), 1853–1862. https://doi.org/10.1021/acs.joc.8b02779.
29. dos Passos Gomes, G.; Morrison, A. E.; Dudley, G. B.; Alabugin, I. V. Optimizing Amine-Mediated Alkyne–Allene Isomerization to Improve Benzannulation Cascades: Synergy between Theory and Experiments. European Journal of Organic Chemistry 2019, 2019 (2–3), 512–518. https://doi.org/10.1002/ejoc.201801052.
28. Vil’, V. A.; Gomes, G. dos P.; Ekimova, M. V.; Lyssenko, K. A.; Syroeshkin, M. A.; Nikishin, G. I.; Alabugin, I. V.; Terent’ev, A. O. Five Roads That Converge at the Cyclic Peroxy-Criegee Intermediates: BF3-Catalyzed Synthesis of β-Hydroperoxy-β-Peroxylactones. J. Org. Chem. 2018, 83 (21), 13427–13445. https://doi.org/10.1021/acs.joc.8b02218.
27. Gomes, G. dos P.; Loginova, Y.; Vatsadze, S. Z.; Alabugin, I. V. Isocyanides as Stereoelectronic Chameleons: The Donor–Acceptor Dichotomy in Radical Additions. J. Am. Chem. Soc. 2018, 140 (43), 14272–14288. https://doi.org/10.1021/jacs.8b08513.
26. Alabugin, I. V.; dos Passos Gomes, G.; Abdo, M. A. Hyperconjugation. WIREs Computational Molecular Science 2019, 9 (2), e1389. https://doi.org/10.1002/wcms.1389.
25. G. P. Gomes & I. V. Alabugin. Stereoelectronic Effects: Analysis by Computational and Theoretical Methods, chapter 15 for the book “Applied Theoretical Organic Chemistry”, pp. 451-502, 2018, Ed: Dean Tantillohttps://doi.org/10.1021/jacs.8b08513.
24. Y. A. Yaremenko, G. P. Gomes, P. S. Radulov, R. A. Novikov, V. V. Chernyshev, A. A. Korlyukov, G. I. Nikishin, I. V. Alabugin, A. O. Terent’ev. Ozone-free synthesis of ozonides: Assembling bicyclic structures from 1,5-diketones and hydrogen peroxide J. Org. Chem., 2018, 83 (8), 4402. https://doi.org/10.1021/acs.joc.8b00130.
23. Tsvetkov, N. P.; Gonzalez-Rodriguez, E.; Hughes, A.; dos Passos Gomes, G.; White, F. D.; Kuriakose, F.; Alabugin, I. V. Radical Alkyne Peri-Annulation Reactions for the Synthesis of Functionalized Phenalenes, Benzanthrenes, and Olympicene. Angewandte Chemie International Edition 2018, 57 (14), 3651–3655. https://doi.org/10.1002/anie.201712783.
22. Vil’, V. A.; dos Passos Gomes, G.; Bityukov, O. V.; Lyssenko, K. A.; Nikishin, G. I.; Alabugin, I. V.; Terent’ev, A. O. Interrupted Baeyer–Villiger Rearrangement: Building A Stereoelectronic Trap for the Criegee Intermediate. Angewandte Chemie International Edition 2018, 57 (13), 3372–3376. https://doi.org/10.1002/anie.201712651.
21. Sedenkova, K. N.; Averina, E. B.; Grishin, Y. K.; Kolodyazhnaya, J. V.; Rybakov, V. B.; Kuznetsova, T. S.; Hughes, A.; Gomes, G. dos P.; Alabugin, I. V.; Zefirov, N. S. Substituent Effects on Stereoselectivity of Dihalocarbene Reactions with Cyclohexadiene and on the Reactivity of Bis-Dihalocyclopropanes in Electrophilic Nitrations En Route to Pyrimidine N-Oxides. Org. Biomol. Chem. 2017, 15 (44), 9433–9441. https://doi.org/10.1039/C7OB02463K.
20. Evoniuk, C. J.; Gomes, G. dos P.; Hill, S. P.; Fujita, S.; Hanson, K.; Alabugin, I. V. Coupling N–H Deprotonation, C–H Activation, and Oxidation: Metal-Free C(Sp3)–H Aminations with Unprotected Anilines. J. Am. Chem. Soc. 2017, 139 (45), 16210–16221. https://doi.org/10.1021/jacs.7b07519.
19. Harris, T.; Gomes, G. dos P.; Ayad, S.; Clark, R. J.; Lobodin, V. V.; Tuscan, M.; Hanson, K.; Alabugin, I. V. Twisted Cycloalkynes and Remote Activation of “Click” Reactivity. Chem 2017, 3 (4), 629–640. https://doi.org/10.1016/j.chempr.2017.07.011.
18. Park, N. H.; Gomes, G. dos P.; Fevre, M.; Jones, G. O.; Alabugin, I. V.; Hedrick, J. L. Organocatalyzed Synthesis of Fluorinated Poly(Aryl Thioethers). Nat Commun 2017, 8 (1), 166. https://doi.org/10.1038/s41467-017-00186-3.
17. Juaristi, E.; dos Passos Gomes, G.; Terent’ev, A. O.; Notario, R.; Alabugin, I. V. Stereoelectronic Interactions as a Probe for the Existence of the Intramolecular α-Effect. J. Am. Chem. Soc. 2017, 139 (31), 10799–10813. https://doi.org/10.1021/jacs.7b05367.
16. Poonpatana, P.; Gomes, G. dos P.; Hurrle, T.; Chardon, K.; Bräse, S.; Masters, K.-S.; Alabugin, I. Formaldehyde-Extruding Homolytic Aromatic Substitution via C→O Transposition: Selective ‘Traceless-Linker’ Access to Congested Biaryl Bonds. Chemistry – A European Journal 2017, 23 (38), 9091–9097. https://doi.org/10.1002/chem.201700085.
15. Gomes, G. dos P.; Evoniuk, C. J.; Ly, M.; Alabugin, I. V. Changing the Path of Least Resistance, or Access to Endo-Dig Products via a Sequence of Three Exo-Trig Transition States: Electronic Effects in Homoallyic Ring Expansion Cascades of Alkenyl Isonitriles. Org. Biomol. Chem. 2017, 15 (19), 4135–4143. https://doi.org/10.1039/C7OB00527J.
14. Evoniuk, C. J.; Gomes, G. dos P.; Ly, M.; White, F. D.; Alabugin, I. V. Coupling Radical Homoallylic Expansions with C–C Fragmentations for the Synthesis of Heteroaromatics: Quinolines from Reactions of o-Alkenylarylisonitriles with Aryl, Alkyl, and Perfluoroalkyl Radicals. J. Org. Chem. 2017, 82 (8), 4265–4278. https://doi.org/10.1021/acs.joc.7b00262.
13. dos Passos Gomes, G.; Yaremenko, I. A.; Radulov, P. S.; Novikov, R. A.; Chernyshev, V. V.; Korlyukov, A. A.; Nikishin, G. I.; Alabugin, I. V.; Terent’ev, A. O. Stereoelectronic Control in the Ozone-Free Synthesis of Ozonides. Angewandte Chemie International Edition 2017, 56 (18), 4955–4959. https://doi.org/10.1002/anie.201610699.
12. dos Passos Gomes, G.; Alabugin, I. V. Drawing Catalytic Power from Charge Separation: Stereoelectronic and Zwitterionic Assistance in the Au(I)-Catalyzed Bergman Cyclization. J. Am. Chem. Soc. 2017, 139 (9), 3406–3416. https://doi.org/10.1021/jacs.6b11054.
11. Umezu, S.; dos Passos Gomes, G.; Yoshinaga, T.; Sakae, M.; Matsumoto, K.; Iwata, T.; Alabugin, I.; Shindo, M. Regioselective One-Pot Synthesis of Triptycenes via Triple-Cycloadditions of Arynes to Ynolates. Angewandte Chemie International Edition 2017, 56 (5), 1298–1302. https://doi.org/10.1002/anie.201609111.
10. Vatsadze, S. Z.; Loginova, Y. D.; dos Passos Gomes, G.; Alabugin, I. V. Stereoelectronic Chameleons: The Donor–Acceptor Dichotomy of Functional Groups. Chemistry – A European Journal 2017, 23 (14), 3225–3245. https://doi.org/10.1002/chem.201603491.
9. Pati, K.; dos Passos Gomes, G.; Alabugin, I. V. Combining Traceless Directing Groups with Hybridization Control of Radical Reactivity: From Skipped Enynes to Defect-Free Hexagonal Frameworks. Angewandte Chemie 2016, 128 (38), 11805–11809. https://doi.org/10.1002/ange.201605799.
8. Harris, T.; Gomes, G. dos P.; Clark, R. J.; Alabugin, I. V. Domino Fragmentations in Traceless Directing Groups of Radical Cascades: Evidence for the Formation of Alkoxy Radicals via C–O Scission. J. Org. Chem. 2016, 81 (14), 6007–6017. https://doi.org/10.1021/acs.joc.6b01052.
7. Berry, E.; Gomes, G. dos P.; MacLean, A.; Martin, J. R.; Wiget, P. A. Discovery of a Long-Range Perlin Effect in a Conformationally Constrained Oxocane. J. Org. Chem. 2016, 81 (13), 5740–5744. https://doi.org/10.1021/acs.joc.6b00819.
6. Pati, K.; Gomes, G. dos P.; Harris, T.; Alabugin, I. V. Fused Catechol Ethers from Gold(I)-Catalyzed Intramolecular Reaction of Propargyl Ethers with Acetals. Org. Lett. 2016, 18 (5), 928–931. https://doi.org/10.1021/acs.orglett.5b03522.
5. Gomes, G. dos P.; Vil’, V.; Terent’ev, A.; Alabugin, I. V. Stereoelectronic Source of the Anomalous Stability of Bis-Peroxides. Chem. Sci. 2015, 6 (12), 6783–6791. https://doi.org/10.1039/C5SC02402A.
4. Pati, K.; Michas, C.; Allenger, D.; Piskun, I.; Coutros, P. S.; Gomes, G. dos P.; Alabugin, I. V. Synthesis of Functionalized Phenanthrenes via Regioselective Oxidative Radical Cyclization. J. Org. Chem. 2015, 80 (23), 11706–11717. https://doi.org/10.1021/acs.joc.5b01014.
3. Stoyanov, E. S.; Gomes, G. dos P. tert-Butyl Carbocation in Condensed Phases: Stabilization via Hyperconjugation, Polarization, and Hydrogen Bonding The Journal of Physical Chemistry A 2015 119 (32), 8619-8629 https://doi.org/10.1021/acs.jpca.5b04657.
2. Pati, K.; Gomes, G. dos P.; Harris, T.; Hughes, A.; Phan, H.; Banerjee, T.; Hanson, K.; Alabugin, I. V. Traceless Directing Groups in Radical Cascades: From Oligoalkynes to Fused Helicenes without Tethered Initiators Journal of the American Chemical Society 2015 137 (3), 1165-1180 https://doi.org/10.1021/ja510563d.
1. Alabugin, I. V.; Bresch, S.; Gomes, G. dos P. Orbital Hybridization: A Key Electronic Factor in Control of Structure and Reactivity. Journal of Physical Organic Chemistry 2015, 28 (2), 147–162. https://doi.org/10.1002/poc.3382.

Book chapter

1. Gomes, G. dos P.; Alabugin, I. Stereoelectronic Effects: Analysis by Computational and Theoretical Methods. In Applied Theoretical Organic Chemistry; WORLD SCIENTIFIC (EUROPE), 2017; pp 451–502. https://doi.org/10.1142/9781786344090_0015.

PhD thesis

1. Controlling Chemical Reactivity with Stereoelectronic Effects - ProQuest https://www.proquest.com/docview/2174054163 (accessed 2022 -01 -01).
the gomes group at CMU
gabegomes[at]cmu[dot]edu
dev. by thiago reschützegger