Publications

Preprints and Submitted Manuscripts

‡ = equal authorship

(48) “A Comprehensive Discovery Platform for Organophosphorus Ligands for Catalysis”

  • 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

Preprint on ChemRxiV, 2021, doi: 10.26434/chemrxiv.12996665.v1

  • the kraken web app.
  • Featured on: UofT Chemistry website.
  • A collaboration with University of Utah (Sigman group), TU Berlin (Tobias Gensch), KIT (Pascal Friederich), IBM Research Zurich (Theophile Gaudin), and AstraZeneca UK (Kjell Jorner).

 

(47) “Data-science driven autonomous process optimization”

  • Christensen, L. Yunker, F. Adedeji, F. Häse, L. Roch, T. Gensch, G. P. Gomes, T. Zepel, M. S. Sigman, A. Aspuru-Guzik, J. Hein

Preprint on ChemRxiV, 2020, doi.org/10.26434/chemrxiv.13146404

  • A collaboration with Merck, University of British Columbia (Hein group), and University of Utah (Sigman group).

 

(46) “Automatic discovery of chemical reactions using imposed activation”

  • Lavigne, G. P. Gomes‡, R. Pollice‡, A. Aspuru-Guzik

Preprint on ChemRxiV, 2020, doi.org/10.26434/chemrxiv.13008500.v1

  • GitHub page: coming soon

 

Just Accepted

(45) “Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES”

  • Nigam, M. Krenn, R. Pollice, G. P. Gomes, A. Aspuru-Guzik

Chem. Sci, 2021, in print, doi: 10.1039/D1SC00231G

Preprint on ChemRxiV, 2020, https://doi.org/10.26434/chemrxiv.13383266

 

(44) “Stalling chromophore maturation of the fluorescent protein Venus reveals the molecular basis of the final oxidation step” 

  • 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

Chem. Sci, 2021, in print, doi: 10.1039/D0SC06693A

Preprint on bioRxiv, 2020, doi.org/10.1101/2020.10.13.337386

 

(43) “Organic Molecules with Inverted Gaps between First Excited Singlet and Triplet States and Appreciable Oscillator Strengths”

  • Pollice, P. Friederich, C. Lavigne, G. P. Gomes, A. Aspuru-Guzik

Matter, 2021, in print, doi: 10.1016/j.matt.2021.02.017

Preprint on ChemRxiV, 2020, doi.org/10.26434/chemrxiv.13087319

 

(42) “Mapping C-H•••M interactions in confined spaces: (α-ICyDᴹᵉ)Au, Ag, Cu complexes reveal “contra-electrostatic H-bonds” masquerading as anagostic interactions”

  • P. Gomes, G. Xu, X. Zhu, L.-M. Chamoreau, O. Bistri-Aslanoff, S. Roland, I. V. Alabugin, M. Sollogoub

Chem. Eur. J., 2021, in print, doi: 10.1002/chem.202100263

Preprint on ChemRxiV, 2020, Version 1, doi: 10.26434/chemrxiv.12167916

 

Published

(41) “Illuminating the dark conformational space using dominant rotors”

  • Diaz, S. D. Appavoo, A. F. Bogdanchikova, Y. Lebedev, T. J. McTiernan, G. P. Gomes, A. K. Yudin

Nature Chemistry, 2021, 13, 218 doi: 10.1038/s41557-020-00620-y

 

(40) “Data-driven Strategies for Materials Design”

  • 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

Accounts of Chemical Research, 2021, 54(4), 849 doi: 10.1021/acs.accounts.0c00785

 

(39) “Navigating through the Maze of Homogeneous Catalyst Design with Machine Learning”

  • P. Gomes‡, R. Pollice‡, A. Aspuru-Guzik

Trends in Chemistry 2021, 3(2), 96–110 doi: 10.1016/j.trechm.2020.12.006

 

(38) “Oxidative Rearrangement of MIDA (N-Methyliminodiacetic Acid) Boronates: Mechanistic Insights and Synthetic Applications”

  • Kaldas, C.-H. Tien, G. P. Gomes, S. Meyer, M. Sirvinskas, H. Foy, T. Dudding, A. K. Yudin

Org. Lett. 2021, 23(2), 324 doi.org/10.1021/acs.orglett.0c03823

 

(37) “Organocatalytic sulfoxidation”

  • C. Davidson, G. P. Gomes, L. R. Kuhn, I. V. Alabugin, A. R. Kennedy, N. C. O. Tomkinson

Tetrahedron, 2021, 78, 131784, ISSN 0040-4020 doi: 10.1016/j.tet.2020.131784

 

(36) “The cyclopropane ring as a reporter of radical leaving-group reactivity for Ni-catalyzed C(sp3)–O arylation”

  • R. Mills, J. J. Monteith, G. P. Gomes, A. Aspuru-Guzik, S. A. L. Rousseaux
  1. Am. Chem. Soc., 2020, 142 (30), 13246 doi: 110.1021/jacs.0c06904

 

(35) “Machine Learning Chemical Reactivity Surrounding Vaska’s Complexes Chemical Space”

  • Friederich, G. P. Gomes, R. D. Bin, A. Aspuru-Guzik, D. Balcells

Chem. Sci., 2020, 11, 4584 doi: 10.1039/D0SC00445F

 

(34) “Twofold π-Extension of Polyarenes via Double and Triple Radical Alkyne peri-Annulations: Radical Cascades Converging on the Same Aromatic Core”

  • Gonzalez-Rodriguez, M. Abdo, G. P. Gomes, S. Ayad, N. P. Tsvetkov, F. D. White, K. Hanson, I. V. Alabugin
  1. Am. Chem. Soc., 2020, 142 (18), 8352 doi: 10.1021/jacs.0c01856

(Highlighted on: • Synfacts 2020, 16, 0794 “Peri-Peri: Spicy Radical Double Annulations”, doi: 10.1055/s-0040-1707043)

 

(33) “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”

  • Elliott, G. P. Gomes, C. J. Evoniuk, I. V. Alabugin

Chem. Sci., 2020, 5, 369 doi: 10.1039/C9SC06511C

 

(32) “Electronic donation or steric contraction: a spectroscopic and structural analysis of medium-sized constrained rings for potential long-range hyperconjugation”

  • Lee, E. Cagle, B. Bashrum, E. Walters, J. Massey, M. Zanghi, C. Birchfield, D. French, J. Joy, G. P. Gomes, P. A. Wiget
  1. Org. Chem., 2019, 84 (16), 9867, doi: 10.1021/acs.joc.9b00979

 

(31) “CO2 or SO2: Should it stay, or should it go?”

  • P. Gomes, A. Wimmer, J. Smith, B. König, I. V. Alabugin
  1. Org. Chem., 2019, 84 (10), 6232, doi: 10.1021/acs.joc.9b00503

 

(30) “Stereoelectronic Influence of a “Spectator” Propargylic Substituent Can Override Aromaticity Effects in Radical Peri-cyclizations on Route to Expanded Polyaromatics”

  • Hughes, G. P. Gomes, I. V. Alabugin
  1. Org. Chem., 2019, 84 (4), 1853, doi: 10.1021/acs.joc.8b02779

 

(29) “Optimizing amine-mediated alkyne-allene isomerization to improve benzannulation cascades: synergy between theory and experiments”

  • P. Gomes, A. E. Morrison, G. B. Dudley, I. V. Alabugin

Eur. J. Org. Chem., 2019, 512, Special Issue: Catalyst Design, doi.org/10.1002/ejoc.201801052

 

(28) “Five roads that converge at the cyclic peroxy-Criegee intermediates: BF3-catalyzed synthesis of β-hydroperoxy-β-peroxylactones”

  • A. Vil’, G. P. Gomes, M. V. Ekimova, K. A. Lyssenko, G. I. Nikishin, I. V. Alabugin, A. O. Terent’ev
  1. Org. Chem., 2018, 83 (21), 13427, doi: 10.1021/acs.joc.8b02218

 

(27) “Isonitriles as Stereoelectronic Chameleons: The Donor-Acceptor Dichotomy in Radical Additions”

  • P. Gomes, Y. D. Loginova, S. Z. Vatsadze, I. V. Alabugin
  1. Am. Chem. Soc., 2018, 140 (43), 14272, doi: 10.1021/jacs.8b08513

(Highlighted on: • ACS Axial; • Colorblind Chemist)

 

(26) “Hyperconjugation”

  • V. Alabugin, G. P. Gomes, M. Abdo
  • WIREs Comput. Mol. Sci., 2018;e1389, org/10.1002/wcms.1389

(• Featured as one of the top 10% most downloaded papers in WIREs Comput. Mol. Sci. between 2018 and 2019.)

(25) “Stereoelectronic Effects: Analysis by Computational and Theoretical Methods”
    • P. Gomes & I. V. Alabugin
  • Chapter 15: “Stereoelectronic Effects: Analysis by Computational and Theoretical Methods”, Applied Theoretical Organic Chemistry. Editor: Dean Tantillo, Wiley, pp. 451–502, May, 2018, doi:10.1142/9781786344090_0015 link


(24) “Ozone-free synthesis of ozonides: Assembling bicyclic structures from 1,5-diketones and hydrogen peroxide”
  • 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
  • Org. Chem., 2018, 83 (8), 4402, doi: 10.1021/acs.joc.8b00130


(23) “Radical Alkyne Peri-annulations for Synthesis of Functionalized Phenalenes, Benzanthrenes, and Olympicene”
  • P. Tsvetkov, E. Gonzalez-Rodriguez, A. Hughes, G. P. Gomes, F. D. White, I. V. Alabugin
  • Chem. Int. Ed., 2018, 57, 3651, doi: 10.1002/anie.201712783

• Featured on FSU News and reproduced on: phys.org; sciencedaily.com; EurekAlert!)

(22) “Interrupted Baeyer-Villiger Rearrangement: Building A Stereoelectronic Trap for the Criegee Intermediate”
  • A. Vil’, G. P. Gomes, O. V. Bityukov, M. A. Syroeshkin, K. A. Lyssenko, G. I. Nikishin, I. V. Alabugin. A. O. Terent’ev
  • Chem. Int. Ed., 2018, 57, 3372, doi: 10.1002/anie.201712651

• Featured on Chemical & Engineering News)

(21) “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”
  • 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
  • Biom. Chem., 2017, 15, 9433, doi: 10.1039/C7OB02463K


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


(19) “Twisted chiral cyclodecynes and remote activation of click reactivity”
  • Harris, G. P. Gomes, S. Ayad, V. V. Lobodin, K. Hanson, I. V. Alabugin
  • Chem, 2017, 3 (4), 629, doi: 10.1016/j.chempr.2017.07.011,
 Video-summary of the paper
  • This paper was featured on FSU News.

(18) “Organocatalyzed Synthesis of Fluorinated Poly(aryl thioethers)”
  • H. Park, G. P. Gomes, M. Fevre, G. O. Jones, I. V. Alabugin, J. L. Hedrick
  • Nature Communications, 2017, 8, 166, doi: 10.1038/s41467-017-00186-3 
a collaboration with IBM Research, CA

Fig.2: here
(This paper was featured on: • Plastic News; • Synfacts 2017, 13 (10), 1035 “Salt-Free Polymerization Yields Fluorinated Poly(aryl thioether)s”, doi: 10.1055/s-0036-1591247; • IBM Research Blog, “New discovery: Rapid preparation of high performance materials and coatings”

(17) “Stereoelectronic Interactions as a Probe for the Existence of the Intramolecular α-Effect”
  • Juaristi, G. P. Gomes, A. O. Terent’ev, R. Notario, I. V. Alabugin
  • Am. Chem. Soc., 2017, 139 (9), 3406, doi: 10.1021/jacs.7b05367


(16) “Formaldehyde-Extruding Homolytic Aromatic Substitution via C->O Transposition: Evolution of a Contaminating Side-Reaction to ‘Traceless-Linker’ access to Congested Biaryl Bonds”
  • Poonptana, G. P. Gomes, T. Hurrle, K. Chardon, S. Bräse, K-S. Masters, I. V. Alabugin
  • Eur. J., 2017, 23, 9091, doi: 10.1002/chem.201700085

• Featured as Hot Paper on _Chemistry – A European Journal_

(15) “Changing the path of least resistance, or access to endo-dig products via a sequence of three exo-trigtransition states: electronic effects in homoallyic ring expansion cascades of alkenyl isonitriles”
    • P. Gomes‡, C. J. Evoniuk‡, M. Ly, I. V. Alabugin
  • Biom. Chem., 2017, 15, 4135, doi: 10.1039/C7OB00527J


(14) “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. Evoniuk‡, G. P. Gomes‡, M. Ly, F. D. White, I. V. Alabugin
  • Org. Chem., 2017, 82 (8), 4265, doi: 10.1021/acs.joc.7b00262

Featured on: • Synfacts 2017, 13 (06), 253 “Synthesis of Quinolines From o-Alkenylaryl Isonitriles”, doi: 10.1055/s-0036-1590439; • on
organic-chemistry.org

(13) “Stereoelectronic Control in the Ozone-Free Synthesis of Ozonides“
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

Angew. Chem. Int. Ed., 2017, 56, 4955, doi: 10.1002/anie.201610699

 

(12) “Drawing Catalytic Power from Charge Separation: Stereoelectronic and Zwitterionic Assistance in the Au(I)-Catalyzed Bergman Cyclization”

  • P. Gomes & I. V. Alabugin
  1. Am. Chem. Soc., 2017, 139 (9), 3406, doi: 10.1021/jacs.6b11054

 

(11) “Regioselective One-pot Synthesis of Triptycenes via Triple-Cycloadditions of Arynes to Ynolates”

  • Umedu, G. P. Gomes, M. Sakae, T. Yoshinaga, K. Matsumoto, T. Iwata, I. V. Alabugin, M. Shindo

Angew. Chem. Int. Ed., 2016, 56, 1298, doi: 10.1002/anie.201609111

 

(10) “Stereoelectronic Chameleons: The Donor–Acceptor Dichotomy of Functional Groups”

  • Z. Vatsadze, Y. D. Loginova, G. P. Gomes, I. V. Alabugin

Chem. Eur. J., 2016, 23, 3225, doi: 10.1002/chem.201603491

(• Featured as a Web of Science’s top 1% Chemistry highly cited papers for Nov/Dec 2017; Frontspiece of Chemistry – A European Journal, doi: 10.1002/chem.201781461

 

(09) “Combining Traceless Directing Groups with Hybridization Control of Radical Reactivity: From Skipped Enynes to Defect-Free Hexagonal Frameworks”

  • Pati, G. P. Gomes, I. V. Alabugin

Angew. Chem. Int. Ed., 2016, 128, 11805, doi: 10.1002/ange.201605799

 

(08) “Domino Fragmentations in Traceless Directing Groups of Radical Cascades: Evidence for the Formation of Alkoxy Radicals via C-O Scission”

  • Harris, G. P. Gomes, R. Clark, I. V. Alabugin
  1. Org. Chem., 2016, 81 (14), 6007, doi: 10.1021/acs.joc.6b01052

 

(07) “Discovery of a new type of Perlin effect in a conformationally constrained oxocane”

  • Berry‡, G. P. Gomes‡, A. MacLean, J. R. Martin, P. A. Wiget
  1. Org. Chem., 2016, 81 (13), 5740, doi: 10.1021/acs.joc.6b00819

 

(06) “Fused Catechol Ethers from Gold (I)-Catalyzed Intramolecular Reaction of Propargyl Ethers with Acetals”

  • Pati, G. P. Gomes, T. Harris, I. V. Alabugin

Org. Lett., 2016, 18 (5), 928, doi: 10.1021/acs.orglett.5b03522

 

(05) “Stereoelectronic source of the anomalous stability of bis-peroxides”

  • P. Gomes, V. A. Vil’, A. Terent’ev and I. Alabugin

Chem. Sci., 2015, 6, 6783, doi: 10.1039/C5SC02402A.

This paper was featured on: • RSC’s Chemistry World; • on NBO’s features website.

Behind the scenes on: medium.com.

 

(04) “Synthesis of Functionalized Phenanthrenes via Regioselective Oxidative Radical Cyclization”

  • Pati, C. Michas, D. Allenger, I. Piskun, P. Spiro Coutros, G. P. Gomes, I. V Alabugin
  1. Org. Chem., 2015, 80 (23), 11706, doi: 10.1021/acs.joc.5b01014

 

(03) “tert-Butyl Carbocation in Condensed Phases: Stabilization via Hyperconjugation, Polarization and Hydrogen Bonding”

  • Stoyanov & G. P. Gomes
  • Phys. Chem. A, 2015, 119, 8619, doi: 10.1021/acs.jpca.5b04657


(02) “Traceless Directing Groups in Radical Cascades: From Oligoalkynes to Fused Helicenes without Tethered Initiators”
  • Pati, G. P. Gomes, T. Harris, A. Hughes, H. Phan, T. Banerjee, K. Hanson, I. V. Alabugin
  • Am. Chem. Soc., 2014, 137, 1165; doi: 10.1021/ja510563d


(01) “Orbital Hybridization: a Key Electronic Factor in Control of Structure and Reactivity”
  • V. Alabugin, S. Bresch, G. P. Gomes
  1. Phys. Org. Chem., 2014, 28, 147, doi: 10.1002/poc.3382.

• This paper was featured on amphoteros.com

PhD dissertation
G. P. Gomes “Controlling chemical reactivity with stereoelectronic effects.” Ann Arbor: The Florida State University; 2018. 326 p. link