the gomes group @ CMU

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

publications

§ = Equal Contribution
_ = Undergrad Student

Preprints

Latest

  1. D. A. Boiko, R. Pollice, B. Kline, G. P. Gomes "Autonomous chemical research with large language models", Nature 624, 570–578 (2023), GitHub | doi: 10.1038/s41586-023-06792-0

  2. A. G. Garrison, J. Heras-Domingo, J. R. Kitchin, G. P. Gomes, Z. W. Ulissi, & S. M. Blau (2023). Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Data Set. Journal of Chemical Information and Modeling, 63(24), 7642-7654. | doi: 10.1021/acs.jcim.3c01226

  3. C. Lavigne, G. P. Gomes§, R. Pollice§, A. Aspuru-Guzik "Automatic discovery of chemical reactions using imposed activation", Preprint on ChemRxiv, 2020, GitHub | doi: 10.26434/chemrxiv.13008500.v1

  4. M. Krenn, R. Pollice, S. Y. Guo, M. Aldeghi, A. Cervera-Lierta, P. Friederich, G. P. Gomes, F. Häse, A. Jinich, A. Nigam, Z. Yao, A. Aspuru-Guzik On Scientific Understanding with Artificial Intelligence. Nature Reviews Physics, 2022, doi: 10.1038/s42254-022-00518-3.

  5. J. Law§, D. Callen§, E. L. Paola, G. P. Gomes*, J. Frederich* "A Stereoselective Photoinduced Cycloisomerization Inspired by Ophiobolin A", Org Lett 2022, in print, doi: 10.1021/acs.orglett.2c02272 | preprint on ChemRxiv: 10.26434/chemrxiv-2022-wjsd9.

  6. T. Reschützegger, T. Syphan, G. P. Gomes* "Three catalysts tango with olefins", Nat Synth 2, 1, 13 (News Views) | doi: 10.1038/s44160-021-00018-9

prior to CMU

  1. T. Gensch§, G. P. Gomes§, P. Friederich§, E. Peters, T. Gaudin, R. Pollice, K. Jorner, A. Nigam, M. L. D'Addario, M. S. Sigman, A. Aspuru-Guzik "A comprehensive platform for the discovery and understanding of organophosphorus ligands in catalysis", J. Am. Chem. Soc. 2022, 144 (3), 1205 | doi: 10.1021/jacs.1c09718.

  2. M. Christensen, L. Yunker, F. Adedeji, F. Häse, L. Roch, T. Gensch, G. P. Gomes, T. Zepel, M. S. Sigman, A. Aspuru-Guzik, J. Hein "Data-science driven autonomous process optimization", NPG's Commun. Chem. 2021, 4, 112 | doi: 10.1038/s42004-021-00550-x.

    • Preprint on ChemRxiv, 2020
    • A collaboration with Merck, UBC and U of Utah

  3. A. Nigam, R. Pollice, M. Krenn, G. P. Gomes, A. Aspuru-Guzik "Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES", Chem. Sci. 2021, 12, 7079 | doi: 10.26434/chemrxiv.13383266.v2.

    • Preprint on ChemRxiv, 2020
    • Featured in Iwatobi Pen's chemoinformatics blog

  4. H. S. Auhim, B. L. Grigorenko, T. Harris, I. V. Polyakov, G. P. Gomes, I. V. Alabugin, P. J. Rizkallah, A. V. Nemukhin, D. D. Jones "Stalling chromophore maturation of the fluorescent protein Venus reveals the molecular basis of the final oxidation step", Chem. Sci. 2021, 12, 7735 | doi: 10.1039/D0SC06693A.

  5. 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 | doi: 10.26434/chemrxiv.13087319.

    • Preprint on ChemRxiv, 2020 (patent pending)

  6. G. P. Gomes, G. Xu, X. Zhu, L.-M. Chamoreau, O. Bistri-Aslanoff, S. Roland, I. V. Alabugin, M. Sollogoub "Mapping C–; H∙∙∙M interactions in confined spaces: (α-ICyDMe) Au, Ag, Cu complexes reveal "contra-electrostatic H-bonds" masquerading as anagostic interactions", Chem. Eur. J. 2021, 27, 8127 | doi: 10.1002/chem.202100263.

  7. D. Diaz, S. D. Appavoo, A. F. Bogdanchikova, Y. Lebedev, T. J. McTiernan, G. P. Gomes, A. K. Yudin "Illuminating the dark conformational space of ring structures with dominant rotors", Nature Chemistry, 2021, 13, 218 | doi: 10.1038/s41557-020-00620-y.

  8. R. Pollice, G. P. Gomes, M. Aldeghi§, R. J. Hickman§, M. Krenn§, C. Lavigne§, M. L. D'Addario§, A. Nigam§, C.-T. Ser§, Z. Yao§, A. Aspuru-Guzik "Data-driven Strategies for Accelerated Materials Design", Acc. Chem. Res. 2021, 54(4), 849 | doi: 10.1021/acs.accounts.0c00785.

  9. G. P. Gomes§, R. Pollice§, A. Aspuru-Guzik "Navigating through the Maze of Homogeneous Catalyst Design with Machine Learning", Trends in Chemistry 2021, 3(2), 96 special issue: "Machine Learning for Molecules and Materials" Guest editors: Rafael Gomez-Bombarelli (MIT) Alexander Wiltschko (Google Brain) | doi: 10.1016/j.trechm.2020.12.006.

  10. S. Kaldas, C.-H. Tien, G. P. Gomes, S. Meyer, M. Sirvinskas, H. Foy, T. Dudding, A. K. Yudin "Oxidative Rearrangement of MIDA (N-Methyliminodiacetic Acid) Boronates: Mechanistic Insights and Synthetic Applications", Org. Lett. 2021, 23(2), 324 | doi: 10.1021/acs.orglett.0c03823.

  11. 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 | doi: 10.1016/j.tet.2020.131784.

  12. L. R. Mills, J. J. Monteith, G. P. Gomes, A. Aspuru-Guzik, S. A. L. Rousseaux "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 | doi: 10.1021/jacs.0c06904.

    • Preprint on ChemRxiv
    • Featured on OPRD as interesting reaction to process RD chemists: Zhao et. al.
    • Org. Process Res. Dev. 2020, acs.oprd.0c00419

  13. P. Friederich, G. P. Gomes, R. D. Bin, A. Aspuru-Guzik, D. Balcells "Machine Learning Dihydrogen Activation in the Chemical Space Surrounding Vaska's Complex", Chem. Sci. 2020, 11, 4584 | doi: 10.1039/D0SC00445F.

  14. E. Gonzalez-Rodriguez, M. Abdo, G. P. Gomes, S. Ayad, N. P. Tsvetkov, F. D. White, K. Hanson, I. V. Alabugin "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 | doi: 10.1021/jacs.0c01856.

    • Preprint on ChemRxiv
    • Highlighted on: Synfacts 2020, 16, 794 "Peri-Peri: Spicy Radical Double Annulations"

  15. Q. Elliott, G. P. Gomes, C. J. Evoniuk, I. V. Alabugin "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, 5, 369 | doi: 10.1039/C9SC06511C.

  16. R. Lee, E. Cagle, B. Bashrum, E. Walters, J. Massey, M. Zanghi, C. Birchfield, D. French, J. Joy, G. P. Gomes, P. A. Wiget, "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 | doi: 10.1021/acs.joc.9b00979.

  17. G. P. Gomes, A. Wimmer, J. M. Smith, B. Koenig, I. V. Alabugin "CO2 or SO2: Should it stay, or should it go?", J. Org. Chem., 2019, 84 (10), 6232 | doi: 10.1021/acs.joc.9b00503.

  18. A. Hughes, G. P. Gomes, I. V. Alabugin, "Stereoelectronic Influence of a "Spectator" Propargylic Substituent Can Override Aromaticity Effects in Radical Peri-cyclizations on Route to Expanded Polyaromatics", J. Org. Chem., 2019, 84 (4), 1853 | doi: 10.1021/acs.joc.8b02779.

  19. G. P. Gomes, A. E. Morrison, G. B. Dudley, I. V. Alabugin "Optimizing amine-mediated alkyne-allene isomerization to improve benzannulation cascades: synergy between theory and experiments", Eur. J. Org. Chem., 2019, 512, Special Issue: Catalyst Design | doi: 10.1002/ejoc.201801052.

  20. V. A. Vil', G. P. Gomes, M. V. Ekimova, K. A. Lyssenko, G. I. Nikishin, I. V. Alabugin, A. O. Terent'ev "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 | doi: 10.1021/acs.joc.8b02218.

  21. G. P. Gomes, Y. Loginova, S. Z. Vatsadze, I. V. Alabugin "Isocyanides as Stereoelectronic Chameleons: The Donor-Acceptor Dichotomy in Radical Additions", J. Am. Chem. Soc., 2018, 140 (43), 14272.

  22. I. V. Alabugin, G. P. Gomes, M. Abdo, "Hyperconjugation", WIREs Comput Mol Sci., 2018 | doi: 10.1002/wcms.1389.

  23. 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 | doi: 10.1021/acs.joc.8b00130.

  24. N. P. Tsvetkov, E. Gonzalez-Rodriguez, A. Hughes, G. P. Gomes, F. D. White, I. V. Alabugin "Radical Alkyne Peri-annulations for Synthesis of Functionalized Phenalenes, Benzanthrenes, and Olympicene", Angew. Chem. Int. Ed., 2018, 57, 3651 | doi: 10.1002/anie.201712783.

  25. V. A. Vil', G. P. Gomes, O. V. Bityukov, M. A. Syroeshkin, K. A. Lyssenko, G. I. Nikishin, I. V. Alabugin. A. O. Terent'ev "Interrupted Baeyer-Villiger Rearrangement: Building A Stereoelectronic Trap for the Criegee Intermediate", Angew. Chem. Int. Ed., 2018, 57, 3372 | doi: 10.1002/anie.201712651.

  26. K. N. Sedenkova, E. B. Averina, Y. K. Grishin, J. V. Kolodyazhnaya, V. B. Rybakov, T. S. Kuznetsova, A. Hughes, G. P. Gomes, I. V. Alabugin, N. S. Zefirov "Substituent effects on stereoselectivity of dihalocarbene reactions with cyclohexadiene and on the reactivity of bis-dihalocyclopropanes in electrophilic nitrations on route to pyrimidine N-oxides" Org. Biom. Chem., 2017, 15, 9433 | doi: 10.1039/C7OB02463K.

  27. C. J. Evoniuk, G. P. Gomes, S. Hill, F. Satoshi, I. V. Alabugin "Coupling C-H activation, N-H deprotonation and Oxidation: metal-free C(sp3)-H aminations with unprotected anilines" J. Am. Chem. Soc., 2017, 139 (45), 16210 | doi: 10.1021/jacs.7b07519.

    • Featured on: Synfacts 2018, 14 (02), 144 "Expanded N-Heterocycles through C(sp3)–H Amination"
    • In the top 20 most-read JACS papers in Oct-Nov 2017

  28. T. Harris, G. P. Gomes, R. Clark, S. Ayad, V. V. Lobodin, K. Hanson, I. V. Alabugin "Twisted chiral cyclodecynes and remote activation of click reactivity" Chem, 2017, 3 (4), 629.

  29. N. H. Park, G. P. Gomes, M. Fevre, G. O. Jones, I. V. Alabugin, J. L. Hedrick, "Organocatalyzed Synthesis of Fluorinated Poly(aryl thioethers)" Nature Communications, 2017, 8, 166.

    • A collaboration with IBM Research, San Jose, CA
    • Featured on: Plastic News
    • Synfacts 2017, 13 (10), 1035 "Salt-Free Polymerization Yields Fluorinated Poly(aryl thioether)s"

  30. E. Juaristi, G. P. Gomes, A. O. Terent'ev, R. Notario, I. V. Alabugin "Stereoelectronic Interactions as a Probe for the Existence of the Intramolecular α-Effect", J. Am. Chem. Soc., 2017 , 139 (31), 10799 | doi: 10.1021/jacs.7b05367.

  31. P. Poonptana, G. P. Gomes, T. Hurrle, K. Chardon, S. Bräse, K-S. Masters, I. V. Alabugin "Formaldehyde-Extruding Homolytic Aromatic Substitution via C→O Transposition: Evolution of a Contaminating Side-Reaction to 'Traceless-Linker' access to Congested Biaryl Bonds" Chem. Eur. J., 2017, 23, 9091 | doi: 10.1002/chem.201700085.

  32. G. P. Gomes§, C. J. Evoniuk§, M. Ly, I. V. Alabugin "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. Biom. Chem., 2017, 15, 4135 | doi: 10.1039/C7OB00527J.

  33. C. J. Evoniuk§, G. P. Gomes§, M. Ly, F. D. White, I. V. Alabugin "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 | doi: 10.1021/acs.joc.7b00262.

  34. G. P. Gomes§, Y. A. Yaremenko§, P. S. Radulov, R. A. Novikov, V. V. Chernyshev, A. A. Korlyukov, G. I. Nikishin, A. O. Terent'ev, I. V. Alabugin "Stereoelectronic Control in the Ozone-Free Synthesis of Ozonides" Angew. Chem. Int. Ed., 2017, 56, 4955 | doi: 10.1002/anie.201610699.

  35. G. P. Gomes, I. V. Alabugin "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 | doi: 10.1021/jacs.6b11054.

  36. S. Umedu, G. P. Gomes, M. Sakae, T. Yoshinaga, K. Matsumoto, T. Iwata, I. Alabugin, M. Shindo "Regioselective One-pot Synthesis of Triptycenes via Triple-Cycloadditions of Arynes to Ynolates" Angew. Chem. Int. Ed., 2016, 56, 1298 | doi: 10.1002/anie.201609111.

    • Featured on: Synfacts2017, 13 (03), 253 "Three Benzynes and the Ynolate"

  37. S. Z. Vatsadze, Y. Loginova, G. P. Gomes, I. V. Alabugin "Stereoelectronic Chameleons: The Reversal of Donor-Acceptor Properties of Common Functional Groups by a Geometric Change" Chem. Eur. J., 2016, 23, 3225 | doi: 10.1002/chem.201603491.

  38. K. Pati, G. P. Gomes, I. V. Alabugin "Combining Traceless Directing Groups with Hybridization Control of Radical Reactivity: from Skipped Enynes to Defect-Free Hexagonal Frameworks" Angew. Chem. Int. Ed., 2016, 55, 11633.

  39. T. Harris, G. P. Gomes, R. Clark, I. V. Alabugin, "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 | doi: 10.1021/acs.joc.6b01052.

  40. E. Berry§, G. P. Gomes§, A. MacLean, J. R. Martin, P. A. Wiget, "Discovery of a new type of Perlin effect in a conformationally constrained oxocane" J. Org. Chem., 2016, 81 (13), 5740 | doi: 10.1021/acs.joc.6b00819.

  41. K. Pati, G. P. Gomes, T. Harris, I. V. Alabugin "Fused Catechol Ethers from Gold (I)-Catalyzed Intramolecular Reaction of Propargyl Ethers with Acetals" Org. Lett., 2016, 18 (5), 928 | doi: 10.1021/acs.orglett.5b03522.

  42. G. P. Gomes, V. A. Vil', A. Terent'ev and I. V. Alabugin, "Stereoelectronic Source of the Anomalous Stability of Bis-peroxides" Chem. Sci., 2015, 6, 6783 | doi: 10.1039/C5SC02402A.

  43. S. Umedu, G. P. Gomes, M. Sakae, T. Yoshinaga, K. Matsumoto, T. Iwata, I. Alabugin, M. Shindo "Regioselective One-pot Synthesis of Triptycenes via Triple-Cycloadditions of Arynes to Ynolates" Angew. Chem. Int. Ed., 2016, 56, 1298 | doi: 10.1021/acs.joc.5b01014.

    • Featured on: Synfacts, 2017, 13 (03), 253 "Three Benzynes and the Ynolate")

  44. E. Stoyanov G. P. Gomes "Tert-Butyl Carbocation in Condensed Phases: Stabilization via Hyperconjugation, Polarization and Hydrogen Bonding" J. Phys. Chem. A, 2015, 119, 8619 | doi: 10.1021/acs.jpca.5b04657.

  45. K. Pati, G. P. Gomes, T. Harris, A. Hughes, H. Phan, T. Banerjee, K. Hanson, I. V. Alabugin "Traceless Directing Groups in Radical Cascades: From Oligoalkynes to Fused Helicenes without Tethered Initiators" J. Am. Chem. Soc., 2015, 137, 1165 | doi: 10.1021/ja510563d.

  46. I. V. Alabugin, S. Bresch, G. P. Gomes "Orbital Hybridization: A Key Electronic Factor in Control ofStructure And Reactivity" J. Phys. Org. Chem. 2014, 28 147 | doi: 10.1002/poc.3382.

    • One of the most accessed papers on JPOC between 10/2015-09/2016 & 02/2016-08/2017
    • Department's most read paper on ResearchGate in October-November 2017
    • Featured on: amphoteros.com

Book chapter


PhD thesis

Controlling Chemical Reactivity with Stereoelectronic Effects - ProQuest https://www.proquest.com/docview/2174054163 (accessed 2022 -01 -01).

the gomes group at CMU
dev. by thiago reschützegger