Publications

Vibrationally Assisted Tunneling through the Bread of a Proton Sandwich — Connections to Dynamic Matching

Y. G. Ahmed, G. Gomes*, D. Tantillo*

Journal of the American Chemical Society 2025, 147 (7), 5971

Transferable Machine Learning Interatomic Potential for Pd-Catalyzed Cross-Coupling Reactions

R. Zubatyuk, D. M. Anstine, L. C. Gallegos, R. S. Paton, O. Wiest, B. Nebgen, T. Jones, G. Gomes, S. Tretiak, O. Isayev*

ChemRxiv 2025, doi: 10.26434/chemrxiv-2025-n36r6

Generation of connections between protein sequence space and chemical space to enable a predictive model for biocatalysis

A. Golliher, D. Boiko, J. Perkins, N. Cemalovic, D. Yang, C.-H. Chiang, T. Reschützegger, G. Gomes*, A. R. H. Narayan*

ChemRxiv 2024, doi: 10.26434/chemrxiv-2024-w4dtr

Advancing Molecular Machine Learned Representations with Stereoelectronics-Infused Molecular Graphs

D. Boiko, T. Reschützegger, B. Sanchez-Lengeling, S. Blau*, G. Gomes*

arXiv 2024, doi: 10.48550/arXiv.2408.04520

Prioritizing High-Consequence Biological Capabilities in Evaluations of Artificial Intelligence Models

J. Pannu*, D. Bloomfield, A. Zhu, R. MacKnight, M. Hanke, G. Gomes, A. Cicero, T. Inglesby*

SSRN 2024, doi: 10.2139/ssrn.4873106

Organic Molecule Light Emitters with High Internal Quantum Efficiency, Low Triplet Population and Fast Reverse Intersystem Crossing for Optoelectronic Applications

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

2024 • granted

Autonomous chemical research with large language models

D. Boiko, R. MacKnight, B. Kline, G. Gomes*

Nature 2023, 624, 570

Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Data Set

A. Garrison, J. Heras-Domingo, J. Kitchin, G. Gomes, Z. Ulissi*, S. Blau*

Journal of Chemical Information and Modeling 2023, 63, 24, 7642

Guided discovery of chemical reaction pathways with imposed activation

C. Lavigne, G. Gomes*§, R. Pollice*§, A. Aspuru-Guzik*

Chemical Science 2022, 13, 13857

On scientific understanding with artificial intelligence

M. Krenn, R. Pollice, S.-Y. Guo, M. Aldeghi, A. Cervera-Lierta, P. Friederich, G. Gomes, F. Häse, A. Jinich, A. Nigam, Z. Yao, A. Aspuru-Guzik

Nature Reviews Physics 2022, 4, 761

A Stereoselective Photoinduced Cycloisomerization Inspired by Ophiobolin A

J. Law§, D. Callen§, E. L. Paola, G. Gomes*, J. Frederich*

Organic Letters 2022, 24, 36, 6499

Three catalysts tango with olefins

T. Reschützegger, T. Syphan, G. P. Gomes*

Nature Synthesis 2022, 1, 13

A comprehensive platform for the discovery and understanding of organophosphorus ligands in catalysis

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

Journal of the American Chemical Society 2022, 144, 3, 1205

Data-science driven autonomous process optimization

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

Communications Chemistry 2021, 4, 112

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

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

Chemical Science 2021, 12, 7079

Stalling chromophore maturation of the fluorescent protein Venus reveals the molecular basis of the final oxidation step

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

Chemical Science 2021, 12, 7735

Organic Molecules with Inverted Gaps between First Excited Singlet and Triplet States and Appreciable Oscillator Strengths

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

Matter 2021, 4, 5, 1654

Mapping C–H⋯M interactions in confined spaces: (α-ICyDMe)Au

Ag, Cu complexes reveal "contra-electrostatic H-bonds" masquerading as anagostic interactions

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

Chemistry - A European Journal 2021, 8127

Illuminating the dark conformational space of ring structures with dominant rotors

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

Nature Chemistry 2021, 13, 218

Data-driven Strategies for Accelerated Materials Design

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

Accounts of Chemical Research 2021, 54, 4, 849

Navigating through the Maze of Homogeneous Catalyst Design with Machine Learning

G. P. Gomes§, R. Pollice§, A. Aspuru-Guzik

Trends in Chemistry 2021, 3, 2, 96

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

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

Organic Letters 2021, 23, 2, 324

Organocatalytic sulfoxidation

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

Tetrahedron 2021, 78, 131784

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

L. R. Mills, J. J. Monteith, G. P. Gomes, A. Aspuru-Guzik, S. A. L. Rousseaux

Journal of the American Chemical Society 2020, 142, 30, 13246

Machine Learning Dihydrogen Activation in the Chemical Space Surrounding Vaska's Complex

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

Chemical Science 2020, 11, 4584

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

E. Gonzalez-Rodriguez, M. Abdo, G. P. Gomes, S. Ayad, N. P. Tsvetkov, F. D. White, K. Hanson, I. V. Alabugin

Journal of the American Chemical Society 2020, 142, 18, 8352

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

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

Chemical Science 2020, 5, 369

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

R. Lee, E. Cagle, B. Bashrum, E. Walters, J. Massey, M. Zanghi, C. Birchfield, D. French, J. Joy, G. P. Gomes, P. A. Wiget

Journal of Organic Chemistry 2019, 84, 16, 9897

CO₂ or SO₂: Should it stay, or should it go?

G. P. Gomes, A. Wimmer, J. M. Smith, B. Koenig, I. V. Alabugin

Journal of Organic Chemistry 2019, 84, 10, 6232

Stereoelectronic Influence of a "Spectator" Propargylic Substituent Can Override Aromaticity Effects in Radical Peri-cyclizations on Route to Expanded Polyaromatics

A. Hughes, G. P. Gomes, I. V. Alabugin

Journal of Organic Chemistry 2019, 84, 4, 1853

Optimizing amine-mediated alkyne-allene isomerization to improve benzannulation cascades: synergy between theory and experiments

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

European Journal of Organic Chemistry 2019, , 512

Five roads that converge at the cyclic peroxy-Criegee intermediates: BF3‑catalyzed synthesis of β-hydroperoxy-β-peroxylactones

V. A. Vil', G. P. Gomes, M. V. Ekimova, K. A. Lyssenko, G. I. Nikishin, I. V. Alabugin, A. O. Terent'ev

Journal of Organic Chemistry 2018, 83, 21, 13427

Isocyanides as Stereoelectronic Chameleons: The Donor-Acceptor Dichotomy in Radical Additions

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

Journal of the American Chemical Society 2018, 140, 43, 14272

Hyperconjugation

I. V. Alabugin, G. P. Gomes, M. Abdo

WIREs Computational Molecular Science 2018, , e1389

Ozone-free synthesis of ozonides: Assembling bicyclic structures from 1,5-diketones and hydrogen peroxide

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

Journal of Organic Chemistry 2018, 83, 8, 4402

Radical Alkyne Peri-annulations for Synthesis of Functionalized Phenalenes

Benzanthrenes, and Olympicene

N. P. Tsvetkov, E. Gonzalez-Rodriguez, A. Hughes, G. P. Gomes, F. D. White, I. V. Alabugin

Angewandte Chemie International Edition 2018, 3651

Interrupted Baeyer-Villiger Rearrangement: Building A Stereoelectronic Trap for the Criegee Intermediate

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

Angewandte Chemie International Edition 2018, 57, 3372

Stereoelectronic Effects: Analysis by Computational and Theoretical Methods

Chapter 15, Applied Theoretical Organic Chemistry

G. P. Gomes, I. V. Alabugin

Editor: Dean Tantillo 2018, 451-502

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

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

Organic & Biomolecular Chemistry 2017, 15, 9433

Coupling C-H activation, N-H deprotonation and Oxidation: metal-free C(sp3)-H aminations with unprotected anilines

C. J. Evoniuk, G. P. Gomes, S. Hill, F. Satoshi, I. V. Alabugin

Journal of the American Chemical Society 2017, 139, 45, 16210

Twisted chiral cyclodecynes and remote activation of click reactivity

T. Harris, G. P. Gomes, R. Clark, S. Ayad, V. V. Lobodin, K. Hanson, I. V. Alabugin

Chem 2017, 3, 4, 629

Organocatalyzed Synthesis of Fluorinated Poly(aryl thioethers)

N. H. Park, G. P. Gomes, M. Fevre, G. O. Jones, I. V. Alabugin, J. L. Hedrick

Nature Communications 2017, 8, 166

Stereoelectronic Interactions as a Probe for the Existence of the Intramolecular α-Effect

E. Juaristi, G. P. Gomes, A. O. Terent'ev, R. Notario, I. V. Alabugin

Journal of the American Chemical Society 2017, 139, 31, 10799

Formaldehyde-Extruding Homolytic Aromatic Substitution via C→O Transposition: Evolution of a Contaminating Side-Reaction to 'Traceless-Linker' access to Congested Biaryl Bonds

P. Poonptana, G. P. Gomes, T. Hurrle, K. Chardon, S. Bräse, K-S. Masters, I. V. Alabugin

Chemistry - A European Journal 2017, 23, 9091

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

G. P. Gomes§, C. J. Evoniuk§, M. Ly, I. V. Alabugin

Organic & Biomolecular Chemistry 2017, 15, 4135

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

C. J. Evoniuk§, G. P. Gomes§, M. Ly, F. D. White, I. V. Alabugin

Journal of Organic Chemistry 2017, 82, 8, 4265

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

Angewandte Chemie International Edition 2017, 56, 4955

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

G. P. Gomes, I. V. Alabugin

Journal of the American Chemical Society 2017, 139, 9, 3406

Regioselective One-pot Synthesis of Triptycenes via Triple-Cycloadditions of Arynes to Ynolates

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

Angewandte Chemie International Edition 2016, 56, 1298

Stereoelectronic Chameleons: The Reversal of Donor-Acceptor Properties of Common Functional Groups by a Geometric Change

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

Chemistry - A European Journal 2016, 23, 3225

Combining Traceless Directing Groups with Hybridization Control of Radical Reactivity: from Skipped Enynes to Defect-Free Hexagonal Frameworks

K. Pati, G. P. Gomes, I. V. Alabugin

Angewandte Chemie International Edition 2016, 55, 11633

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

T. Harris, G. P. Gomes, R. Clark, I. V. Alabugin

Journal of Organic Chemistry 2016, 81, 14, 6007

Discovery of a new type of Perlin effect in a conformationally constrained oxocane

E. Berry§, G. P. Gomes§, A. MacLean, J. R. Martin, P. A. Wiget

Journal of Organic Chemistry 2016, 81, 13, 5740

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

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

Organic Letters 2016, 18, 5, 928

Stereoelectronic Source of the Anomalous Stability of Bis-peroxides

G. P. Gomes, V. A. Vil', A. Terent'ev, I. V. Alabugin

Chemical Science 2015, 6, 6783

Synthesis of Functionalized Phenanthrenes via Regioselective Oxidative Radical Cyclization

K. Pati, C. Michas, D. Allenger, I. Piskun, P. S. Coutros, G. P. Gomes, I. V. Alabugin

Journal of Organic Chemistry 2015, 80, 23, 11706

Tert-Butyl Carbocation in Condensed Phases: Stabilization via Hyperconjugation, Polarization and Hydrogen Bonding

E. Stoyanov, G. P. Gomes

Journal of Physical Chemistry A 2015, 119, 8619

Traceless Directing Groups in Radical Cascades: From Oligoalkynes to Fused Helicenes without Tethered Initiators

K. Pati, G. P. Gomes, T. Harris, A. Hughes, H. Phan, T. Banerjee, K. Hanson, I. V. Alabugin

Journal of the American Chemical Society 2015, 137, 1165

Orbital Hybridization: A Key Electronic Factor in Control of Structure And Reactivity

I. V. Alabugin, S. Bresch, G. P. Gomes

Journal of Physical Organic Chemistry 2014, 28, 147