Publications | Kulik Research Group

Heather J. Kulik. Using experimental data in computationally-guided rational design of inorganic materials with machine learning. J. Mater. Res., in press.

Heather J. Kulik. Incorporating anionic ligands in chemical space exploration with new ligand additivity relationships. submitted.

Clorice Reinhardt, David Kastner, Heather J. Kulik. Role of Active Site Residues and Weak Noncovalent Interactions In Substrate Positioning in N,N-Dimethylformamidase. submitted.

Allison Keys, David Kastner, Laura L. Kiessling, Heather J. Kulik. CH-π Interactions Confer Orientational Flexibility in Protein–Carbohydrate Binding Sites. submitted.

Lauren Hendricks, Clorice Reinhardt, Tierani Green, Lily Kunczynski, August Jaunzarins Roberts, Naomi Miller, Noga Rafalin, Heather J. Kulik, John T. Groves, Rachel N. Austin. Fontimonas thermophila Alkane Monooxygenase (FtAlkB) Is an Alkyl Fluoride Dehalogenase. J. Am. Chem. Soc., 147, 9085–9090 (2025).

Akash K. Ball, Gianmarco Terrones, Shuwen Yue, Heather J. Kulik. Data-driven discovery of water-stable metal-organic frameworks with high water uptake capacity. submitted.

Yeongsu Cho, Jakob Teetz, Heather J. Kulik. Assessing UFF and DFT-Tuned Force Fields for Predicting Experimental Isotherms of MOFs. J. Chem. Inf. Model., in press.

Sophia J. Melvin, Yunxin Yao, Xiao Huang, Rowina C. Bell, Ryann E. Kemmerling, Ilia Kevlishvili, Angus C. Berg, Ana P. K. Vasconcelos, Alshakim Nelson, Heather J. Kulik, Stephen L. Craig, Rebekka S. Klausen. Enabling Selective Mechanochemical Scission of Network Crosslinks by Exchanging Single Carbon Atoms for Silicon. J. Am. Chem. Soc., 147, 6006–6015 (2025).

Heejung Roh, Tyler J. Quill, Gan Chen, Huaxin Gong, Yeongsu Cho, Heather J. Kulik, Zhenan, Alberto Salleo, Aristide Gumyusenge. Copper-Based Two-Dimensional Conductive Metal–Organic Framework Thin Films for Ultrasensitive Detection of Perfluoroalkyls in Drinking Water. ACS Nano, 19, 6332–6341 (2025).

Vyshnavi Vennelakanti, Mugyeom Jeon, Heather J. Kulik. Computational Investigation of the Role of Metal Center Identity in Cytochrome P450 Enzyme Model Reactivity. Biochemistry, 64, 678–691 (2025).

C. H. Ng, E. R. Wearing, D. E. Blackmun, Gianmarco Terrones, J. Toigo, K-M Tong, K. C. Harper, J. C. Donovan, M. A. Gonley, E. A. Voight, B. D. Bergstrom, M. O. Wolf, Heather J. Kulik, Corinna S. Schindler. Monocyclic Azetidines via a Visible-Light-Mediated Aza Paternò-Büchi Reaction of Ketone-Derived Sulfonylimines. submitted.

Haojun Jia, Chenru Duan, Gianmarco Terrones, Ilia Kevlishvili, Heather J. Kulik. Computational Exploration of Codoped Fe and Ru Single-Atom Catalysts for the Oxygen Reduction Reaction. submitted.

Allison Keys, David Kastner, Laura L. Kiessling, Heather J. Kulik. The Energetic Landscape of CH–π Interactions in Protein–Carbohydrate Binding. Chem. Sci., 16, 1746–1761 (2025).

Clorice Reinhardt, Juliet A. Lee, Lauren Hendricks, Tierani Green, Lily Kunczynski, August Jaunzarins Roberts, Naomi Miller, Noga Rafalin, Heather J. Kulik, Christopher J. Pollock, Rachel N. Austin. No Bridge between Us: EXAFS and Computations Confirm Two Distant Iron Ions Comprise the Active Site of Alkane Monooxygenase (AlkB). J. Am. Chem. Soc., 147, 2432–2443 (2025).

Xiao Huang, Ilia Kevlishvili, Stephen L. Craig, Heather J. Kulik. Force-Activated Spin-Crossover in Fe²⁺ and Co²⁺ Transition Metal Mechanophores. Inorg. Chem., 64, 380–392 (2025).

Camille Violet, Makenna Parkinson, Akash K. Ball, Heather J. Kulik, John D. Fortner, Menachem Elimelech. Tuning Metal-Organic Framework Linker Chemistry for Transition Metal Ion Separations. ACS Appl. Mater. Interfaces, 17, 1911–1921 (2025).

Ralf Meyer, Daniel B. K. Chu, Heather J. Kulik. Many-body expansion based machine learning models for octahedral transition metal complexes. Mach. Learn.: Sci. Technol., 5, 045080 (2024).

Colin Y. Kim, David Kastner, Andrew J. Mitchell, Michael A. Gutierrez, Jocelyn S. Yao, Edwin N. Neumann, Heather J. Kulik, Jing-Ke Weng. Tracing the stepwise Darwinian evolution of a plant halogenase. submitted.

Chenru Duan, Guan-Horng Liu, Yuanqi Du, Tianrong Chen, Qiyuan Zhao, Haojun Jia, Carla P. Gomes, Evangelos A. Theodorou, Heather J. Kulik. React-OT: Optimal Transport for Generating Transition State in Chemical Reactions. Nat. Mach. Intell., in press.

Ilia Kevlishvili, Roland St. Michel, Aaron Garrison, Jacob W. Toney, Husain Adamji, Haojun Jia, Yuriy Roman-Leshkov, Heather J. Kulik. Leveraging natural language processing to curate the tmCAT, tmPHOTO, tmBIO, and tmSCO datasets of functional transition metal complexes. Faraday Discuss., 256, 275–303 (2025).

Jacob W. Toney, Roland St. Michel, Aaron Garrison, Ilia Kevlishvili, Heather J. Kulik. Graph neural networks for predicting metal–ligand coordination of transition metal complexes. PNAS, in press.

Andy S. Anker, Alán Aspuru-Guzik, Tim Bechtel, Filippo Bigi, Ksenia R. Briling, Basita Das, Nicholas David, Graeme M. Day, Volker L. Deringer, Matthew Dyer, Annabel Eardley-Brunt, Matthew L. Evans, Rob Evans, Barnabas A. Franklin, Alex M. Ganose, Janine George, Mark Goulding, Niamh Hickey, Gillian James, Adarsh V. Kalikadien, Venkat Kapil, Heather J. Kulik, Vishank Kumar, Christian Kuttner, Erwin Lam, Magdalena Lederbauer, Yuchen Lou, Jennie Martin, Andres Marulanda Bran, Miriam Mathea, Chris J. Pickard, Branko Ruscic, Matthew R. Ryder, Victor Sabanza Gil, Philippe Schwaller, Marwin H. S. Segler, Wenhao Sun, Sara Tanovic, Wojtek Treyde, Aron Walsh, Ruiqi Wu. Discovering synthesis targets: general discussion. Faraday Discuss., 256, 639–663 (2025).

Andy S. Anker, Alán Aspuru-Guzik, Chiheb Ben Mahmoud, Sophie Bennett, Ksenia R. Briling, Arya Changiarath, Sanggyu Chong, Christopher M. Collins, Andrew I. Cooper, Daniel Crusius, Kevion K. Darmawan, Basita Das, Nicholas David, Graeme M. Day, Volker L. Deringer, Fernanda Duarte, Annabel Eardley-Brunt, Matthew L. Evans, Rob Evans, Ian Fairlamb, Barnabas A. Franklin, Jeremy Frey, Alex M. Ganose, Mark Goulding, Roohollah Hafizi, Matthijs Hakkennes, Niamh Hickey, Gillian James, Kim E. Jelfs, Adarsh V. Kalikadien, Venkat Kapil, Zsuzsanna Koczor-Benda, Ferdinand Krammer, Heather J. Kulik, Vishank Kumar, Christian Kuttner, Erwin Lam, Yuchen Lou, Eltjo Mante, Jennie Martin, Austin M. Mroz, Tahereh Nematiaram, Charles W. P. Pare, Sarbani Patra, James Proudfoot, Branko Ruscic, Matthew R. Ryder, Ken Sakaushi, Jörg Saßmannshausen, Brett M. Savoie, Nadine Schneider, Philippe Schwaller, Bastian Bjerkem Skjelstad, Wenhao Sun, Filip T. Szczypiński, Steven Torrisi, Katharina Ueltzen, Shubham Vishnoi, Aron Walsh, Xinwei Wang, Chloe Wilson, Ruiqi Wu, Jakob Zeitler. Discovering structure–property correlations: general discussion. Faraday Discuss., 256, 373–412 (2025).

Alán Aspuru-Guzik, Tim Bechtel, Varinia Bernales, Philip C. Biggin, Filippo Bigi, Itamar Borges, Ksenia R. Briling, Joshua Cheung, Christopher M. Collins, Kevion K. Darmawan, Nicholas David, Graeme M. Day, Volker L. Deringer, Claudia Draxl, Matthew Dyer, Annabel Eardley-Brunt, Rob Evans, Ian Fairlamb, Barnabas A. Franklin, Janine George, Mark Goulding, Joanna Grundy, Roohollah Hafizi, Matthijs Hakkennes, Niamh Hickey, Gillian James, Veronika Juraskova, Adarsh V. Kalikadien, Venkat Kapil, Heather J. Kulik, Vishank Kumar, Christian Kuttner, Magdalena Lederbauer, Yuchen Lou, Eltjo Mante, Liam Marsh, Jennie Martin, Clelia Middleton, Tahereh Nematiaram, Charles W. P. Pare, Bianca Pasca, Chris J. Pickard, Branko Ruscic, Matthew R. Ryder, Brett M. Savoie, Wenhao Sun, Filip T. Szczypiński, Takuya Taniguchi, Steven Torrisi, Shubham Vishnoi, Aron Walsh, Shirui Wang. Discovering chemical structure: general discussion. Faraday Discuss., 256, 177–220 (2025).

Craig S. Day, Niklas Grabicki, Daniel B. K. Chu, Allison Keys, Avni Singhal, Vyshnavi Vennelakanti, Ilia Kevlishvili, Rafael Gómez-Bombarelli, Heather J. Kulik, Jeremiah A. Johnson. Blueprints for the Geometric Control of NHC-CDI Isomers. submitted.

Woo Seok Lee, Yeongsu Cho, Watcharaphol Paritmongkol, Tomoaki Sakurada, Seung Kyun Ha, Heather J. Kulik, William A. Tisdale. Mixed-Chalcogen 2D Silver Phenylchalcogenides (Ag₁₋ₓEₓPh; E = S, Se, Te). ACS Nano, 18, 35066–35074 (2024).

Daniel B. K. Chu, David A. Gonzalez-Narvaez, Ralf Meyer, Aditya Nandy, Heather J. Kulik. Ligand Many-Body Expansion as a General Approach for Accelerating Transition Metal Complex Discovery. J. Chem. Inf. Model, 64, 9397–9412 (2024).

Bayu I. Z. Ahmad, Ronald T. Jerozal, Sijing Meng, Changhwan Oh, Yeongsu Cho, Heather J. Kulik, Tristan H. Lambert, Phillip J. Milner. Defect-Engineered Metal–Organic Frameworks as Bioinspired Heterogeneous Catalysts for Amide Bond Formation. J. Am. Chem. Soc., 146, 34743–34752 (2024).

Mariya Aleksich, Yeongsu Cho, Daniel W. Paley, Maggie C. Wilson, Hawi N. Nyiera, Patience A. Kotei, Vanessa Oklejas, David W. Mittan-Moreau, Elyse A. Schriber, Kara Christensen, Ichiro Inoue, Shigeki Owada, Kensuke Tono, Michihiro Sugahara, Satomi Inaba-Inoue, Mohammad Vaikili, Christopher J. Milne, Fabio Dall'Antonia, Dmitry Khakhulin, Fernando Ardana-Lamas, Frederico Lima, Joana Valerio, Huijong Han, Tamires Gallo, Hazem Yousef, Oleksii Turkot, Ivette J. Bermudez Macias, Thomas Kluyver, Philipp Schmidt, Luca Gelisio, Adam R. Round, Yifeng Jiang, Doriana Vinci, Yohei Uemura, Marco Kloos, Adrian P. Mancuso, Mark Warren, Nicholas K. Sauter, Jing Zhao, Tess Smidt, Heather J. Kulik, Sahar Sharifzadeh, Aaron S. Brewster, J. Nathan Hohman. Ligand-Mediated Quantum Yield Enhancement in 1-D Silver Organothiolate Metal–Organic Chalcogenolates. Adv. Funct. Mater., 2414914 (2024).

Antonio Del Rio Flores, Rui Zhai, David Kastner, Kaushik Seshadri, Siyue Yang, Kyle De Matias, Yuanbo Shen, Wenlong Cai, Maanasa Narayanamoorthy, Nicholas B. Do, Zhaoqiang Xue, Dunya Al Marzooqi, Heather J. Kulik, Wenjun Zhang. Enzymatic synthesis of azide by a promiscuous N-nitrosylase. Nat. Chem., 16, 2066–2075 (2024).

Michael P. Torrens-Spence, Jason O. Matos, Tianjie Li, David Kastner, Colin Y. Kim, Ziqi Wang, Christopher M. Glinkerman, Jennifer Sherk, Heather J. Kulik, Yi Wang, Jing-Ke Weng. Mechanistic basis for the emergence of EPS1 as a catalyst in salicylic acid biosynthesis of Brassicaceae. Nat. Commun., 15, 10356 (2024).

Matt Rivera, Gianmarco Terrones, Tae Hoon Lee, Zachary P. Smith, Heather J. Kulik. Data-driven Screening and Discovery of Metal-organic Frameworks as C₂ Adsorbents from Over 900 Experimental Isotherms. ACS Appl. Mater. Interfaces, 16, 64759–64773 (2024).

Herbert Wakefield IV, Nicholas J. Frommel, Jennifer Jiang, Ilia Kevlishvili, Yunxin Yao, Stephen L. Craig, Heather J. Kulik, Rebekka S. Klausen. Isomer-driven polymerization, depolymerization, and reconstruction. Polym. Chem., 15, 5016–5022 (2024).

Abraham Herzog-Arbeitman, Ilia Kevlishvili, Devosmita Sen, Julianna Lian, Joshika Chakraverty, Shu Wang, Bradley D. Olsen, Heather J. Kulik, Stephen L. Craig, Jeremiah A. Johnson. Controlled Gel Toughening with Tetrafunctional Cyclobutane Mechanophores. submitted.

Sangeeta Rajpurohit, Vyshnavi Vennelakanti, Heather J. Kulik. Improving Predictions of Spin-Crossover Complex Properties through DFT Calculations with a Local Hybrid Functional. J. Phys. Chem. A, 128, 9082–9089 (2024).

Changhwan Oh, Aditya Nandy, Shuwen Yue, Heather J. Kulik. MOFs with the Stability for Practical Gas Adsorption Applications Require New Design Rules. ACS Appl. Mater. Interfaces, 16, 55541–55554 (2024).

Yunyan Sun, Kecheng Wang, Xiao Huang, Shixuan Wei, Enrique Contreras, Prashant K. Jain, Luis M. Campos, Heather J. Kulik, Jeffrey S. Moore. Caged AIEgens: Multicolor and White Emission Triggered by Mechanical Activation. J. Am. Chem. Soc., 146, 27117–27126 (2024).

Roger C. Diehl, Rajeev S. Chorghade, Allison Keys, Mohammad M. Alam, Stephen A. Early, Amanda E. Dugan, Miri Krupkin, Katharina Ribbeck, Heather J. Kulik, Laura L. Kiessling. CH−π Interactions Are Required for Human Galectin-3 Function. JACS Au, 4, 3028–3037 (2024).

Camille Violet, Akash K. Ball, Mohammad Heiranian, Luis Francisco Villalobos, Junwei Zhang, Betul Uralcan, Heather J. Kulik, Amir Haji-Akbari, Menachem Elimelech. Designing membranes with specific binding sites for selective ion separations. Nature Water, 2, 706–718 (2024).

Heather J. Kulik. Reaction: The Challenge of Open-Shell Transition Metal Catalysis in "Systems Chemistry". Chem, 8, 2338–2339 (2024).

Clorice Reinhardt, Melissa Manetsch, Wan-Lu Li, Yuriy Roman-Leshkov, Teresa Head-Gordon, Heather J. Kulik. Computational Screening of Putative Catalyst Transition Metal Complexes as Guests in a Ga₄L₆⁻¹² Nanocage. Inorg. Chem., 63, 14609–14622 (2024).

Gianmarco Terrones, Shih-Peng Huang, Matt Rivera, Shuwen Yue, Alondra Hernandez, Heather J. Kulik. Metal–Organic Framework Stability in Water and Harsh Environments from Data-Driven Models Trained on the Diverse WS24 Data Set. J. Am. Chem. Soc., 146, 20333–20348 (2024).

Ilia Kevlishvili, Jafer Vakiil, David Kastner, Xiao Huang, Stephen L. Craig, Heather J. Kulik. High-Throughput Discovery of Ferrocene Mechanophores with Enhanced Reactivity and Network Toughening. submitted.

Heejung Roh, Dong-Ha Kim, Yeongsu Cho, Young-Moo Jo, Jesús A. del Alamo, Heather J. Kulik, Mircea Dinca, Aristide Gumyusenge. Robust Chemiresistive Behavior in Conductive Polymer/MOF Composites. Adv. Mater., 36, 2312382 (2024).

Emily R. Wearing, Yu-Cheng Yeh, Gianmarco Terrones, Seren G. Parikh, Ilia Kevlishvili, Heather J. Kulik, Corinna S. Schindler. Visible light–mediated aza Paternò–Büchi reaction of acyclic oximes and alkenes to azetidines. Science, 384, 1468–1476 (2024).

Yunyan Sun, Ilia Kevlishvili, Tatiana B. Kouznetsova, Zach P. Burke, Stephen L. Craig, Heather J. Kulik, Jeffrey S. Moore. The tension-activated carbon–carbon bond. Chem, 10, 3055–3066 (2024).

David Kastner, Clorice Reinhardt, Husain Adamji, Melissa Manetsch, Yuriy Roman-Leshkov, Heather J. Kulik. Dynamic Charge Distribution as a Key Driver of Catalytic Reactivity in an Artificial Metalloenzyme. submitted.

Vivian Zhang, Carrie Ou, Ilia Kevlishvili, Christina M. Hemmingsen, Joseph V. Accardo, Heather J. Kulik, Julia A. Kalow. Internal Catalysis in Dynamic Hydrogels with Associative Thioester Cross-links. ACS Macro Lett., 13, 621–626 (2024).

Aditya Nandy, Heather J. Kulik. Learning Design Rules for Catalysts through Computational Chemistry and Machine Learning. in Exploring Chemical Concepts through Theory and Computation, ed. Shubin Liu, p. 513–558 (2024).

Y. Du, Chenru Duan, A.M. Bran, A. Sotnikova, AY. Qu, Heather J. Kulik, A. Bosselut, J. Hu, P. Schwaller. Large Language Models are Catalyzing Chemistry Education. submitted.

David J. Lundberg, Christopher M. Brown, Eduard O. Bobylev, Nathan J. Oldenhuis, Yasmeen S. Alfaraj, Julia Zaho, Ilia Kevlishvili, Heather J. Kulik, Jeremiah A. Johnson. Nested Non-covalent Interactions Expand the Functions of Supramolecular Polymer Networks. Nat. Commun, 15, 3951 (2024).

Ran Zhu, Husain Adamji, Zachariah Berkson, Jie Zhu, Ashley Head, Heather J. Kulik, Christophe Copéret, Yuriy Roman-Leshkov. Insights into the catalytic promotion of propylene self-metathesis over silica-supported molybdenum oxide using substituted olefins. submitted.

Timothy Kench, Arielle Rahardjo, Gianmarco Terrones, Adinarayana Bellamkonda, Thomas E. Maher, Marko Storch, Heather J. Kulik, Ramon Vilar. A semi-automated, high-throughput approach for the synthesis and identification of highly photo-cytotoxic iridium complexes. Angew. Chemie., 63, e202401808 (2024).

Yunyan Sun, William H. Neary, Xiao Huang, Tatiana B. Kouznetsova, Tetsu Ouchi, Ilia Kevlishvili, Kecheng Wang, Yingying Chen, Heather J. Kulik, Stephen L. Craig, Jeffrey S. Moore. A Thermally Stable SO₂ Releasing Mechanophore: Facile Activation, Single-Event Spectroscopy, and Molecular Dynamic Simulations. J. Am. Chem. Soc., 146, 10943–10952 (2024).

Yeongsu Cho, Heather J. Kulik. Improving Gas Adsorption Modeling for MOFs by Local Calibration of Hubbard U Parameters. J. Chem. Phys., 160, 154101 (2024).

Yixin Hu, Liqi Wang, Ilia Kevlishvili, Shu Wang, Chun-Yun Chiou, Peyton Shieh, Yangju Lin, Heather J. Kulik, Jeremiah A. Johnson, Stephen L. Craig. Self-Amplified HF Release and Polymer Deconstruction Cascades Triggered by Mechanical Force. J. Am. Chem. Soc., 146, 10115–10123 (2024).

Herbert Wakefield IV, Sophia J. Melvin, Jennifer Jiang, Ilia Kevlishvili, Maxime A. Siegler, Stephen L. Craig, Heather J. Kulik, Rebekka S. Klausen. Angle-strained sila-cycloalkynes. Chem. Commun., 60, 4842–4845 (2024).

Vyshnavi Vennelakanti, Mugyeom Jeon, Heather J. Kulik. How Do Differences in Electronic Structure Affect the Use of Vanadium Intermediates as Mimics in Nonheme Iron Hydroxylases?. Inorg. Chem., 63, 4997–5011 (2024).

Cody H. Ng, Scott L. Kim, Ilia Kevlishvili, Gianmarco Terrones, Emily R. Wearing, Heather J. Kulik, Corinna S. Schindler. Visible-Light-Mediated Macrocyclization for the Formation of Azetine-Based Dimers. ACS Catalysis, 14, 4175–4185 (2024).

Freya Edholm, Aditya Nandy, Clorice Reinhardt, David Kastner, Heather J. Kulik. Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify. J. Comput. Chem., 45, 352–361 (2024).

Husain Adamji, Ilia Kevlishvili, Aditya Nandy, Yuriy Roman-Leshkov, Heather J. Kulik. Large-scale Comparison of Fe and Ru Polyolefin C–H Activation Catalysts. J. Catal., 431, 115631 (2024).

Haojun Jia, Chenru Duan, Ilia Kevlishvili, Aditya Nandy, Mingjie Liu, Heather J. Kulik. Computational Discovery of Codoped Single-Atom Catalysts for Methane-to-Methanol Conversion. ACS Catalysis, 14, 2992–3005 (2024).

Tristan Pitt, Haojun Jia, Tyler Azbell, Mary Zick, Aditya Nandy, Heather J. Kulik, Phillip Milner. Benchmarking Nitrous Oxide Adsorption and Activation in Metal-Organic Frameworks Bearing Coordinatively Unsaturated Metal Centers. J. Mater. Chem. C, 12, 3164–3174 (2024).

Vyshnavi Vennelakanti, Irem B. Kilic, Gianmarco Terrones, Chenru Duan, Heather J. Kulik. Machine Learning Prediction of the Experimental Transition Temperature of Fe(II) Spin-Crossover Complexes. J. Phys. Chem. A, 128, 204–216 (2024).

Heather J. Kulik. Section Introduction: Molecular Interactions and Catalysis. in Comprehensive Computational Chemistry, eds. Russell Boyd and M. Yanez, 4, 449–453 (2024).

Maria H. Rasmussen, Chenru Duan, Heather J. Kulik, Jan Halborg Jensen. Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets. J. Cheminform., 15, 121 (2023).

Chenru Duan, Yuanqi Du, Haojun Jia, Heather J. Kulik. Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model. Nature Computational Science, 3, 1045–1055 (2023).

Ilia Kevlishvili, Chenru Duan, Heather J. Kulik. Classification of Hemilabile Ligands Using Machine Learning. J. Phys. Chem. Lett., 14, 11100–11109 (2023).

Shuwen Yue, Aditya Nandy, Heather J. Kulik. Discovering Molecular Coordination Environment Trends for Selective Ion Binding to Molecular Complexes Using Machine Learning. J. Phys. Chem. B, 127, 10592–10600 (2023).

Vyshnavi Vennelakanti, Grace Li, Heather J. Kulik. Why Nonheme Iron Halogenases Do Not Fluorinate C–H Bonds: A Computational Investigation. Inorg. Chem., 62, 19758–19770 (2023).

Julia Zhao, Eduard O. Bobylev, David J. Lundberg, Nathan J. Oldenhuis, Heng Wang, Ilia Kevlishvili, Stephen L. Craig, Heather J. Kulik, Xiaopeng Li, Jeremiah A. Johnson. Polymer Networks with Cubic, Mixed Pd(II) and Pt(II) M₆L₁₂ Metal–Organic Cage Junctions: Synthesis and Stress Relaxation Behavior. J. Am. Chem. Soc., 45, 21879–21885 (2023).

Isuru Ariyarathna, Yeongsu Cho, Chenru Duan, Heather J. Kulik. Gas-Phase and Solid-State Electronic Structure Analysis and DFT Benchmarking of HfCO. Phys. Chem. Chem. Phys., 25, 26632–26639 (2023).

Patricia N. Johnson, Yunxin Yao, Xiao Huang, Ilia Kevlishvili, Stephen Schrettl, Christoph Weder, Heather J. Kulik, Stephen L. Craig. Metal Identity Effects in the Fracture Behavior of Coordinatively Crosslinked Elastomers. Polymer, 285, 126337 (2023).

Kelsie E. Wentz, Yunxin Yao, Ilia Kevlishvili, Tatiana B. Kouznetsova, Braden A. Mediavilla, Heather J. Kulik, Stephen L. Craig, Rebekka S. Klausen. Systematic Investigation of Silicon Substitution on Single Macromolecule Mechanics. Macromolecules, 56, 6776–6782 (2023).

Vivian Zhang, Joseph V. Accardo, Ilia Kevlishvili, Eliot F. Woods, Steven J. Chapman, Christopher T. Eckdahl, Heather J. Kulik, Julia A. Kalow. Tailoring Dynamic Hydrogels by Controlling Associative Exchange Rates. Chem, 9, 2298–2317 (2023).

Xin He, Tzuhsiung Yang, Andrei Iliescu, Maxx Arguilla, Tianyang Chen, Heather J. Kulik, Mircea Dinca. Reversible O–O Bond Scission and O₂ Evolution at MOF-supported Tetramanganese Clusters. J. Am. Chem. Soc., 145, 16872–16878 (2023).

Heejung Roh, Shuwen Yue, Hang Hu, Ke Chen, Heather J. Kulik, Aristide Gumyusenge. Unraveling Polymer–Ion Interactions in Electrochromic Polymers for their Implementation in Organic Electrochemical Synaptic Devices. Adv. Funct. Mater., 2304893 (2023).

Aditya Nandy, Michael G. Taylor, Heather J. Kulik. Identifying Underexplored and Untapped Regions in the Chemical Space of Transition Metal Complexes. J. Phys. Chem. Lett., 14, 5798-5804 (2023).

Husain Adamji, Aditya Nandy, Ilia Kevlishvili, Yuriy Roman-Leshkov, Heather J. Kulik. Computational Discovery of Stable Metal-Organic Frameworks for Methane-to-Methanol Catalysis. J. Am. Chem. Soc., 145, 14365–14378 (2023).

Vyshnavi Vennelakanti, Michael G. Taylor, Heather J. Kulik. Assessing the Performance of Approximate Density Functional Theory on 95 Experimentally Characterized Fe(II) Spin Crossover Complexes. J. Chem. Phys., 159, 024120 (2023).

Gianmarco Terrones, Y. Chen, A. Datar, L.-C. Lin, Heather J. Kulik, Y. G. Chung. SESAMI APP: An Accessible Interface for Surface Area Calculation of Materials from Adsorption Isotherms. J. Open Source Softw., 8, 5429 (2023).

Herbert Wakefield IV, Ilia Kevlishvili, Kelsie E. Wentz, Yunxin Yao, Tatiana B. Kouznetsova, Sophia J. Melvin, Em G. Ambrosius, Abraham Herzog-Arbeitman, Maxime A. Siegler, Jeremiah A. Johnson, Stephen L. Craig, Heather J. Kulik, Rebekka S. Klausen. Synthesis and Ring-opening Metathesis Polymerization of a Strained trans-Silacycloheptene and Single Molecule Mechanics of its Polymer. J. Am. Chem. Soc., 145, 10187-10196 (2023).

Aditya Nandy, Shuwen Yue, Changhwan Oh, Chenru Duan, Gianmarco Terrones, Yongchul G Chung, Heather J. Kulik. A Database of Ultrastable MOFs Reassembled from Stable Fragments with Machine Learning Models. Matter, 6, 1585-1603 (2023).

Tomoaki Sakurada, Yeongsu Cho, Watcharaphol Paritmongkol, Woo Seok Lee, Ruomeng Wan, Annlin Su, Wenbi Shcherbakov-Wu, Peter Müller, Heather J. Kulik, William A. Tisdale. 1D Hybrid Semiconductor Silver 2,6-Difluorophenylselenolate. J. Am. Chem. Soc., 145, 5183-5190 (2023).

David Kastner, Aditya Nandy, Rimsha Mehmood, Heather J. Kulik. Mechanistic Insights Into Substrate Positioning Across Non-heme Fe(II)/Alpha-Ketoglutarate-Dependent Halogenases and Hydroxylases. ACS Catal., 13, 2489-2501 (2023).

Colin Y. Kim, Andrew J. Mitchell, David Kastner, Claire E. Albright, Michael Gutierrez, Christopher M. Glinkerman, Heather J. Kulik, Jing-Ke Weng. Emergence of a Proton Exchange-Based Isomerization and Lactonization Mechanism in the Plant Coumarin Synthase COSY. Nat. Commun., 14, 597 (2023).

Chenru Duan, Aditya Nandy, Ralf Meyer, Naveen Arunachalam, Heather J. Kulik. A Transferable Recommender Approach for Selecting the Best Density Functional Approximations in Chemical Discovery. Nat. Comput. Sci., 3, 38-47 (2023).

Keith E. L. Husted, Christopher M. Brown, Peyton Shieh, Ilia Kevlishvili, Samantha L. Kristufek, Hadiqa Zafar, Joseph V. Accardo, Julian C. Cooper, Rebekka S. Klausen, Heather J. Kulik, Jeffrey S. Moore, Nancy R. Sottos, Julia A. Kalow, Jeremiah A. Johnson. Remolding and Deconstruction of Industrial Thermosets via Carboxylic Acid-Catalyzed Bifunctional Silyl Ether Exchange. J. Am. Chem. Soc., 145, 1916-1923 (2023).

Yael Cytter, Aditya Nandy, Chenru Duan, Heather J. Kulik. Insights into the deviation from piecewise linearity in transition metal complexes from supervised machine learning models. Phys. Chem. Chem. Phys., 25, 8103-8116 (2023).

Yeongsu Cho, Aditya Nandy, Chenru Duan, Heather J. Kulik. DFT-based Multireference Diagnostics in the Solid State: Application to Metal-organic Frameworks. J. Chem. Theory Comput., 19, 190-197 (2023).

Gianmarco Terrones, Chenru Duan, Aditya Nandy, Heather J. Kulik. Low-cost machine learning prediction of excited state properties of iridium-centered phosphors. Chem. Sci., 14, 1419-1433 (2023).

Chenru Duan, Aditya Nandy, Gianmarco Terrones, David Kastner, Heather J. Kulik. Active Learning Exploration of Transition Metal Complexes to Discover Method-Insensitive and Synthetically Accessible Chromophores. JACS Au, 3, 391-401 (2023).

Narayana Aluru, Fikret Aydin, Martin Z. Bazant, Daniel Blankschtein, Alexandra H. Brozena, J. Pedro de Souza, Menachem Elimelech, Samuel Faucher, John T. Fourkas, Volodymyr B. Koman, Matthias Kuehne, Heather J. Kulik, Hao-Kun Li, Zhongwu Li, Arun Majumdar, Joel Martis, Rahul Prasanna Misra, Aleksandr Noy, Tuan Anh Pham, Haoran Qu, Archith Rayabharam, Mark A. Reed, Cody L. Ritt, Zuzanna Siwy, Michael S. Strano, Yuhuang Wang, Cheng Zhan, Ze Zhang. Fluids and Electrolytes under Confinement in Single-Digit Nanopores. Chem. Rev., 123 2737-2831 (2023).

Shuwen Yue, Changhwan Oh, Aditya Nandy, Gianmarco Terrones, Heather J. Kulik. Effects of MOF Linker Rotation and Functionalization on Methane Uptake and Diffusion. Mol. Sys. Des. Eng., 8, 527-537 (2023).

Woo Seok Lee, Yeongsu Cho, Eric R. Powers, Watcharaphol Paritmongkol, Tomoaki Sakurada, Heather J. Kulik, William A. Tisdale. Light Emission in 2D Silver Phenylchalcogenolates. ACS Nano, 16, 20318-20328 (2022).

Naveen Arunachalam, Stefan Gugler, Michael G. Taylor, Chenru Duan, Aditya Nandy, Jon Paul Janet, Ralf Meyer, Jonas Oldenstaedt, Daniel B. K. Chu, Heather J. Kulik. Ligand Additivity Relationships Enable Efficient Exploration of Transition Metal Chemical Space. J. Chem. Phys., 157, 184112 (2022).

Sunggyu Lee, Ilia Kevlishvili, Heather J. Kulik, Hee-Tak Kim, Yongchul G. Chung, Dong-Yeun Koh. Highly Efficient Bromine Capture and Storage Using N-containing Porous Organic Cages. J. Mater. Chem. A, 10, 24802-24812 (2022).

Natalie H. Chan, Christian A. Gomez, Vyshnavi Vennelakanti, Qian Du, Heather J. Kulik, Jared C. Lewis. Non-Native Anionic Ligand Binding and Reactivity in Engineered Variants of the Fe(II)- and α-Ketoglutarate-Dependent Oxygenase, SadA. Inorg. Chem., 61, 14477-14485 (2022).

Adam H Steeves, Heather J. Kulik. Insights into the Stability of Engineered Mini-Proteins from Their Dynamic Electronic Properties. Electron. Struct., 4, 034005 (2022).

Daniel H. Ess, Kim E. Jelfs, Heather J. Kulik. Chemical Design by Artificial Intelligence. J. Chem. Phys., 157, 120401, (2022).

Aditya Nandy, Husain Adamji, David Kastner, Vyshnavi Vennelakanti, Azadeh Nazemi, Mingjie Liu, Heather J. Kulik. Using Computational Chemistry to Reveal Nature's Blueprints for Single-Site Catalysis of C–H Activation. ACS Catal., 12, 9281–9306 (2022).

Christopher M. Brown, David J. Lundberg, Jessica R. Lamb, Ilia Kevlishvili, Denise Kleinschmidt, Yasmeen S. Alfaraj, Heather J. Kulik, Maria Francesca Ottaviani, Nathan J. Oldenhuis, Jeremiah A. Johnson. Endohedrally Functionalized Metal–Organic Cage-Cross-Linked Polymer Gels as Modular Heterogeneous Catalysts. J. Am. Chem. Soc., 144, 13276–13284 (2022).

Beverly Fu, Azadeh Nazemi, Benjamin J. Levin, Zhongyue Yang, Heather J. Kulik, Emily P. Balskus. Mechanistic Studies of a Skatole-Forming Glycyl Radical Enzyme Suggest Reaction Initiation via Hydrogen Atom Transfer. J. Am. Chem. Soc., 144, 11110–11119 (2022).

Chenru Duan, Aditya Nandy, Husain Adamji, Yuriy Roman-Leshkov, Heather J. Kulik. Machine learning models predict calculation outcomes with the transferability necessary for computational catalysis. J. Chem. Theory Comput., 18, 4282–4292 (2022).

Chenru Duan, Adriana J. Ladera, Julian C.-L. Liu, Michael G. Taylor, Isuru Ariyarathna, Heather J. Kulik. Exploiting Ligand Additivity for Transferable Machine Learning of Multireference Character Across Known Transition Metal Complex Ligands. J. Chem. Theory Comput., 18, 4836–4845 (2022).

Heather J. Kulik, Thomas Hammerschmidt, Jonathan Schmidt, Silvana Botti, Miguel A. L. Marques, Mario Boley, Matthias Scheffler, Milica Todorović, Patrick Rinke, Corey Oses, Andriy Smolyanyuk, Stefano Curtarolo, Alexandre Tkatchenko, Albert Bartok, Sergei Manzhos, Manabu Ihara, Tucker Carrington, Jörg Behler, Olexandr Isayev, Max Veit, Andrea Grisafi, Jigyasa Nigam, Michele Ceriotti, Kristoff T Schütt, Julia Westermayr, Michael Gastegger, Reinhard Maurer, Bhupalee Kalita, Kieron Burke, Ryo Nagai, Ryosuke Akashi, Osamu Sugino, Jan Hermann, Frank Noé, Sebastiano Pilati, Claudia Draxl, Martin Kuban, Santiago Rigamonti, Markus Scheidgen, Marco Esters, David Hicks, Cormac Toher, Prasanna Balachandran, Isaac Tamblyn, Stephen Whitelam, Colin Bellinger, Luca M. Ghiringhelli. Roadmap on Machine Learning in Electronic Structure. Electron. Struct., 4, 023004 (2022).

Azadeh Nazemi, Adam H. Steeves, David Kastner, Heather J. Kulik. Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: The Case of Formate Dehydrogenase. The Journal of Physical Chemistry B, 126, 4069–4079 (2022).

Heather J. Kulik. What's Left for a Computational Chemist To Do in the Age of Machine Learning?. Israel J. Chem., 62, e202100016 (2022).

Isuru Ariyarathna, Chenru Duan, Heather J. Kulik. Understanding the chemical bonding of ground and excited states of HfO and HfB with correlated wavefunction theory and density functional approximations. J. Chem. Phys., 156, 184113 (2022).

Vyshnavi Vennelakanti, Aditya Nandy, Heather J. Kulik. The Effect of Hartree-Fock Exchange on Scaling Relations and Reaction Energetics for C–H Activation Catalysts. Top. Catal., 65, 296-311 (2022).

Daniel R. Harper, Aditya Nandy, Naveen Arunachalam, Chenru Duan, Jon Paul Janet, Heather J. Kulik. Representations and Strategies for Transferable Machine Learning Improve Model Performance in Chemical Discovery. J. Chem. Phys., 156, 074101 (2022).

Rimsha Mehmood, Heather J. Kulik. Quantum-Mechanical/Molecular-Mechanical (QM/MM) Simulations for Understanding Enzyme Dynamics. Enzyme Engineering: Methods and Protocols, 227-248 (2022).

Antonio Del Rio Flores, David Kastner, Y. Du, Maanasa Narayanamoorthy, Y. Shen, Wenlong Cai, Vyshnavi Vennelakanti, N. A. Zill, L. B. Dell, Heather J. Kulik, Wenjun Zhang. Probing the mechanism of isonitrile formation by a non-heme iron(II)-dependent oxidase/decarboxylase. J. Am. Chem. Soc., 144, 5893-5901 (2022).

Aditya Nandy, Chenru Duan, Conrad Goffinet, Heather J. Kulik. New Strategies for Direct Methane-to-Methanol Conversion from Active Learning Exploration of 16 Million Catalysts. JACS Au, 2, 1200-1213 (2022).

Akash Bajaj, Chenru Duan, Aditya Nandy, Michael G Taylor, Heather J. Kulik. Molecular orbital projectors in non-empirical jmDFT recover exact conditions in transition-metal chemistry. J. Chem. Phys., 156 184112 (2022).

Aditya Nandy, Gianmarco Terrones, Naveen Arunachalam, Chenru Duan, David Kastner, Heather J. Kulik. MOFSimplify, machine learning models with extracted stability data of three thousand metal–organic frameworks. Sci. Data, 9, 74 (2022).

Haojun Jia, Aditya Nandy, Mingjie Liu, Heather J. Kulik. Modeling the roles of rigidity and dopants in single-atom methane-to-methanol catalysts. J. Mater. Chem. A, 10, 6193-6203 (2022).

Cody L. Ritt, Mingjie Liu, Tuan Anh Pham, Razi Epsztein, Heather J. Kulik, Menachem Elimelech. Machine Learning Reveals Key Ion Selectivity Mechanisms in Polymeric Membranes. Sci. Adv., 8, eabl5771 (2022).

Chenru Duan, Aditya Nandy, Heather J. Kulik. Machine Learning for the Discovery, Design, and Engineering of Materials. Annu. Rev. Chem. Biomol. Eng., 13, 18.1-18.25 (2022).

Yael Cytter, Aditya Nandy, Akash Bajaj, Heather J. Kulik. Ligand Additivity and Divergent Trends in Two Types of Delocalization Errors from Approximate Density Functional Theory. J. Phys. Chem. Lett., 13, 4549-4555 (2022).

Mingjie Liu, Azadeh Nazemi, Michael G. Taylor, Aditya Nandy, Chenru Duan, Adam H. Steeves, Heather J. Kulik. Large-scale Screening Reveals Geometric Structure Matters More than Electronic Structure in Bioinspired Catalyst Design of Formate Dehydrogenase Mimics. ACS Catal., 12, 383-396 (2022).

Vyshnavi Vennelakanti, Azadeh Nazemi, Rimsha Mehmood, Adam H. Steeves, Heather J. Kulik. Harder, better, faster, stronger: large-scale QM and QM/MM for predictive modeling in enzymes and proteins. Curr. Opin. Struct. Biol., 72, 9-17 (2022).

Akash Bajaj, Heather J. Kulik. Eliminating Delocalization Error to Improve Heterogeneous Catalysis Predictions with Molecular DFT+U. J. Chem. Theory Comput., 18, 1142-1155 (2022).

Chenru Duan, Daniel B. K. Chu, Aditya Nandy, Heather J. Kulik. Detection of multi-reference character imbalances enables a transfer learning approach for chemical discovery with coupled cluster accuracy at DFT cost. Chem. Sci., 13, 4962-4971 (2022).

Daniel R. Harper, Heather J. Kulik. Computational Scaling Relationships Predict Experimental Activity and Rate Limiting Behavior in Homogenous Water Oxidation. Inorg. Chem., 61, 2186-2197 (2022).

Zhongyue Yang, Natalia Hajlasz, Heather J. Kulik. Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch. J. Phys. Chem. B, 126, 3398-3406 (2022).

Aditya Nandy, Chenru Duan, Heather J. Kulik. Audacity of huge: overcoming challenges of data scarcity and data quality for machine learning in computational materials discovery. Curr. Opin. Chem. Eng., 36, 100778 (2022).

Vyshnavi Vennelakanti, Rimsha Mehmood, Heather J. Kulik. Are Vanadium Intermediates Suitable Mimics in Non-Heme Iron Enzymes? An Electronic Structure Analysis. ACS Catal., 12, 5489-5501 (2022).

Heather J. Kulik, Matthew S. Sigman. Advancing Discovery in Chemistry with Artificial Intelligence: From Reaction Outcomes to New Materials and Catalysts. Acc. Chem. Res., 54, 2335-2336 (2021).

Zhongyue Yang, Heather J. Kulik. Protein Dynamics and Substrate Protonation State Mediate the Catalytic Action of Trans-4-Hydroxy-L-Proline Dehydratase. J. Phys. Chem. B., 125, 7774-7784 (2021).

Akash Bajaj, Heather J. Kulik. Molecular DFT+U: A Transferable, Low-Cost Approach to Eliminate Delocalization Error. J. Phys. Chem. Lett., 12, 3633-3640 (2021).

Christopher D. Dawson, Stephania M. Irwin, Lindsey R. F. Backman, Chip Le, Jennifer X. Wang, Vyshnavi Vennelakanti, Zhongyue Yang, Heather J. Kulik, Catherine L. Drennan, Emily P. Balskus. Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase. Cell Chem. Biol., 28, 1333-1346 (2021).

Jon Paul Janet, Chenru Duan, Aditya Nandy, Fang Liu, Heather J. Kulik. Navigating Transition-Metal Chemical Space: Artificial Intelligence for First-Principles Design. Acc. Chem. Res., 54, 532-545 (2021).

Vyshnavi Vennelakanti, Helena W. Qi, Rimsha Mehmood, Heather J. Kulik. When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins. Chem. Sci., 12, 1147-1162 (2021).

Aditya Nandy, Chenru Duan, Heather J. Kulik. Using Machine Learning and Data Mining to Leverage Community Knowledge for the Engineering of Stable Metal-Organic Frameworks. J. Am. Chem. Soc., 143, 17535-17547 (2021).

Rimsha Mehmood, Vyshnavi Vennelakanti, Heather J. Kulik. Spectroscopically Guided Simulations Reveal Distinct Strategies for Positioning Substrates to Achieve Selectivity in Nonheme Fe(II)/α-Ketoglutarate-Dependent Halogenases. ACS Catal., 11, 12394-12408 (2021).

Daniel G. A. Smith, Annabelle T. Lolinco, Zachary L. Glick, Jiyoung Lee, Asem Alenaizan, Taylor A. Barnes, Carlos H. Borca, Roberto Di Remigio, David L. Dotson, Sebastian Ehlert, Alexander G. Heide, Michael F. Herbst, Jan Hermann, Colton B. Hicks, Joshua T. Horton, Adrian G. Hurtado, Peter Kraus, Holger Kruse, Sebastian J. R. Lee, Jonathon P. Misiewicz, Levi N. Naden, Farhad Ramezanghorbani, Maximilian Scheurer, Jeffrey B. Schriber, Andrew C. Simmonett, Johannes Steinmetzer, Jeffrey R. Wagner, Logan Ward, Matthew Welborn, Doaa Altarawy, Jamshed Anwar, John D. Chodera, Andreas Dreuw, Heather J. Kulik, Fang Liu, Todd J. Martínez, Devin A. Matthews, Henry F. Schaefer, Jiří Šponer, Justin M. Turney, Lee-Ping Wang, Nuwan De Silva, Rollin A. King, John F. Stanton, Mark S. Gordon, Theresa L. Windus, C. David Sherrill, Lori A. Burns. Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. J. Chem. Phys., 155, 204801 (2021).

Zhongyue Yang, Natalia Hajlasz, Adam H. Steeves, Heather J. Kulik. Quantifying the Long-Range Coupling of Electronic Properties in Proteins with Ab Initio Molecular Dynamics. Chem. Methods, 1, 362-373 (2021).

Chenru Duan, Fang Liu, Aditya Nandy, Heather J. Kulik. Putting Density Functional Theory to the Test in Machine-Learning-Accelerated Materials Discovery. J. Phys. Chem. Lett., 12, 4628-4637 (2021).

Michael G. Taylor, Heather J. Kulik. Mapping the Origins of Surface- and Chemistry-Dependent Doping Trends in III-V Quantum Dots with Density Functional Theory. Chem. Mater., 33, 7113-7123 (2021).

Chenru Duan, Shuxin Chen, Michael G. Taylor, Fang Liu, Heather J. Kulik. Machine learning to tame divergent density functional approximations a new path to consensus materials design principles. Chem. Sci., 12, 13021-13036 (2021).

Michael G. Taylor, Aditya Nandy, Connie C. Lu, Heather J. Kulik. Deciphering Cryptic Behavior in Bimetallic Transition Metal Complexes with Machine Learning. J. Phys. Chem. Lett., 12, 9812-9820 (2021).

Aditya Nandy, Chenru Duan, Michael G. Taylor, Fang Liu, Adam H. Steeves, Heather J. Kulik. Computational Discovery of Transition-Metal Complexes: From High-throughput Screening to Machine Learning. Chem. Rev., 121, 9927-10000 (2021).

Rohan Jonnalagadda, Antonio Del Rio Flores, Wenlong Cai, Rimsha Mehmood, Maanasa Narayanamoorthy, Chaoxiang Ren, Jan Paulo T. Zaragoza, Heather J. Kulik, Wenjun Zhang, Catherine L. Drennan. Biochemical and crystallographic investigations into isonitrile formation by a nonheme iron-dependent oxidase/decarboxylase. J. Biol. Chem., 296, 100231 (2021).

Aditya Nandy, Heather J. Kulik. Why Conventional Design Rules for C–H Activation Fail for Open-Shell Transition-Metal Catalysts. ACS Catal., 10, 15033-15047 (2020).

Cody L. Ritt, Jay R. Werber, Mengyi Wang, Zhongyue Yang, Yumeng Zhao, Heather J. Kulik, Menachem Elimelech. Ionization behavior of nanoporous polyamide membranes. Proc. Natl. Acad. Soc., 117, 30191-30200 (2020).

Fang Liu, Chenru Duan, Heather J. Kulik. Rapid Detection of Strong Correlation with Machine Learning for Transition-Metal Complex High-Throughput Screening. J. Phys. Chem. Lett., 11, 8067-8076 (2020).

Seyed Mohamad Moosavi, Aditya Nandy, Kevin Maik Jablonka, Daniele Ongari, Jon Paul Janet, Peter G. Boyd, Yongjin Lee, Berend Smit, Heather J. Kulik. Understanding the diversity of the metal-organic framework ecosystem. Nat. Commun., 11, 4068 (2020).

Chenru Duan, Fang Liu, Aditya Nandy, Heather J. Kulik. Semi-supervised Machine Learning Enables the Robust Detection of Multireference Character at Low Cost. J. Phys. Chem. Lett., 11, 6640-6648 (2020).

Akash Bajaj, Fang Liu, Heather J. Kulik. Uncovering Alternate Pathways to Nafion Membrane Degradation in Fuel Cells with First-Principles Modeling. J. Phys. Chem. C, 124, 15094-15106 (2020).

Chenru Duan, Fang Liu, Aditya Nandy, Heather J. Kulik. Data-Driven Approaches Can Overcome the Cost–Accuracy Trade-Off in Multireference Diagnostics. J. Chem. Theory Comput., 16, 4373-4387 (2020).

Jon Paul Janet, Heather J. Kulik. Machine Learning in Chemistry. Machine Learning in Chemistry, ACS InFocus (2020).

Rimsha Mehmood, Heather J. Kulik. Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase. J. Chem. Theory Comput., 16, 3121-3134 (2020).

Michael G. Taylor, Tzuhsiung Yang, Sean Lin, Aditya Nandy, Jon Paul Janet, Chenru Duan, Heather J. Kulik. Seeing Is Believing: Experimental Spin States from Machine Learning Model Structure Predictions. J. Phys. Chem. A, 124, 3286-3299 (2020).

Jon Paul Janet, Sahasrajit Ramesh, Chenru Duan, Heather J. Kulik. Accurate Multiobjective Design in a Space of Millions of Transition Metal Complexes with Neural-Network-Driven Efficient Global Optimization. ACS Cent. Sci., 6, 513-524 (2020).

Heather J. Kulik. Making machine learning a useful tool in the accelerated discovery of transition metal complexes. Wiley Interdiscip. Rev.: Comput. Mol. Sci., 10, e1439 (2020).

Aditya Nandy, Daniel B. K. Chu, Daniel R. Harper, Chenru Duan, Naveen Arunachalam, Yael Cytter, Heather J. Kulik. Large-scale comparison of 3d and 4d transition metal complexes illuminates the reduced effect of exchange on second-row spin-state energetics. Phys. Chem. Chem. Phys., 22, 19326-19341 (2020).

Fang Liu, Heather J. Kulik. Impact of Approximate DFT Density Delocalization Error on Potential Energy Surfaces in Transition Metal Chemistry. J. Chem. Theory Comput., 16, 264-277 (2020).

Stefan Gugler, Jon Paul Janet, Heather J. Kulik. Enumeration of de novo inorganic complexes for chemical discovery and machine learning. Mol. Sys. Des. Eng., 5, 139-152 (2020).

Qing Zhao, Heather J. Kulik. Stable Surfaces That Bind Too Tightly: Can Range-Separated Hybrids or DFT+U Improve Paradoxical Descriptions of Surface Chemistry?. J. Phys. Chem. Lett., 10, 5090-5098 (2019).

Helena W. Qi, Heather J. Kulik. Reply to “Comment on ‘Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis’”. J. Chem. Inf. Model., 59, 3609-3610 (2019).

Aditya Nandy, Jiazhou Zhu, Jon Paul Janet, Chenru Duan, Rachel B. Getman, Heather J. Kulik. Machine Learning Accelerates the Discovery of Design Rules and Exceptions in Stable Metal–Oxo Intermediate Formation. ACS Catal., 9, 8243-8255 (2019).

Jon Paul Janet, Fang Liu, Aditya Nandy, Chenru Duan, Tzuhsiung Yang, Sean Lin, Heather J. Kulik. Designing in the Face of Uncertainty: Exploiting Electronic Structure and Machine Learning Models for Discovery in Inorganic Chemistry. Inorg. Chem., 58, 10592-10606 (2019).

Zhongyue Yang, Fang Liu, Adam H. Steeves, Heather J. Kulik. Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases. J. Phys. Chem. Lett., 10, 3779-3787 (2019).

Rimsha Mehmood, Helena W. Qi, Adam H. Steeves, Heather J. Kulik. The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: The Case of SyrB2/SyrB1. ACS Catal., 9, 4930-4943 (2019).

Helena W. Qi, Heather J. Kulik. Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis. J. Chem. Inf. Model., 59, 2199-2211 (2019).

Akash Bajaj, Fang Liu, Heather J. Kulik. Non-empirical, low-cost recovery of exact conditions with model-Hamiltonian inspired expressions in jmDFT. J. Chem. Phys., 150, 154115 (2019).

Chenru Duan, Jon Paul Janet, Fang Liu, Aditya Nandy, Heather J. Kulik. Learning from Failure: Predicting Electronic Structure Calculation Outcomes with Machine Learning Models. J. Chem. Theory Comput., 15, 2331-2345 (2019).

Zhongyue Yang, Rimsha Mehmood, Mengyi Wang, Helena W. Qi, Adam H. Steeves, Heather J. Kulik. Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation. React. Chem. Eng., 4, 298-315 (2019).

Fang Liu, David M. Sanchez, Heather J. Kulik, Todd J. Martínez. Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor-like polarizable continuum models. Int. J. Quantum Chem., 119, e25760 (2019).

Luca Frediani, Oliviero Andreussi, Heather J. Kulik. Coding solvation: challenges and opportunities. Int. J. Quantum Chem., 119, e25839 (2019).

Fang Liu, Tzuhsiung Yang, Jing Yang, Eve Xu, Akash Bajaj, Heather J. Kulik. Bridging the Homogeneous-Heterogeneous Divide: Modeling Spin for Reactivity in Single Atom Catalysis. Front. Chem., 7, 219 (2019).

Wesley J. Transue, Matthew Nava, Maxwell W. Terban, Jing Yang, Matthew W. Greenberg, Gang Wu, Elizabeth S. Foreman, Chantal L. Mustoe, Pierre Kennepohl, Jonathan S. Owen, Simon J. L. Billinge, Heather J. Kulik, Christopher C. Cummins. Anthracene as a Launchpad for a Phosphinidene Sulfide and for Generation of a Phosphorus–Sulfur Material Having the Composition P2S, a Vulcanized Red Phosphorus That Is Yellow. J. Am. Chem. Soc., 141, 431-440 (2019).

Jon Paul Janet, Chenru Duan, Tzuhsiung Yang, Aditya Nandy, Heather J. Kulik. A quantitative uncertainty metric controls error in neural network-driven chemical discovery. Chem. Sci., 10, 7913-7922 (2019).

Aditya Nandy, Chenru Duan, Jon Paul Janet, Stefan Gugler, Heather J. Kulik. Strategies and Software for Machine Learning Accelerated Discovery in Transition Metal Chemistry. Ind. Eng. Chem. Res., 57, 13973-13986 (2018).

Qing Zhao, Heather J. Kulik. Electronic Structure Origins of Surface-Dependent Growth in III–V Quantum Dots. Chem. Mater., 30, 7154-7165 (2018).

Jeong Yun Kim, Heather J. Kulik. When Is Ligand pKa a Good Descriptor for Catalyst Energetics? In Search of Optimal CO2 Hydration Catalysts. J. Phys. Chem. A, 122, 4579-4590 (2018).

Jon Paul Janet, Lydia Chan, Heather J. Kulik. Accelerating Chemical Discovery with Machine Learning: Simulated Evolution of Spin Crossover Complexes with an Artificial Neural Network. J. Phys. Chem. Lett., 9, 1064-1071 (2018).

Qing Zhao, Heather J. Kulik. Where Does the Density Localize in the Solid State? Divergent Behavior for Hybrids and DFT+U. J. Chem. Theory Comput., 14, 670-683 (2018).

Terry Z. H. Gani, Heather J. Kulik. Understanding and Breaking Scaling Relations in Single-Site Catalysis: Methane to Methanol Conversion by FeIV═O. ACS Catal., 8, 975-986 (2018).

Heather J. Kulik. Modeling Mechanochemistry from First Principles. Rev. Comput. Chem., 31, 265-311 (2018).

Heather J. Kulik. Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer. Phys. Chem. Chem. Phys., 20, 20650-20660 (2018).

Terry Z. H. Gani, Heather J. Kulik. Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics. J. Chem. Theory Comput., 13, 5443-5457 (2017).

Jon Paul Janet, Heather J. Kulik. Resolving Transition Metal Chemical Space: Feature Selection for Machine Learning and Structure–Property Relationships. J. Phys. Chem. A, 121, 8939-8954 (2017).

Helena W. Qi, Maria Karelina, Heather J. Kulik. Quantifying Electronic Effects in QM and QM/MM Biomolecular Modeling with the Fukui Function. Acta Phys. -Chim. Sin., 34, 81-91 (2018).

Akash Bajaj, Jon Paul Janet, Heather J. Kulik. Communication: Recovering the flat-plane condition in electronic structure theory at semi-local DFT cost. J. Chem. Phys., 147, 191101 (2017).

Jon Paul Janet, Terry Z. H. Gani, Adam H. Steeves, Efthymios I. Ioannidis, Heather J. Kulik. Leveraging Cheminformatics Strategies for Inorganic Discovery: Application to Redox Potential Design. Ind. Eng. Chem. Res., 56, 4898-4910 (2017).

Jeong Yun Kim, Adam H. Steeves, Heather J. Kulik. Harnessing Organic Ligand Libraries for First-Principles Inorganic Discovery: Indium Phosphide Quantum Dot Precursor Design Strategies. Chem. Mater., 29, 3632-3643 (2017).

Jon Paul Janet, Qing Zhao, Efthymios I. Ioannidis, Heather J. Kulik. Density functional theory for modelling large molecular adsorbate–surface interactions: a mini-review and worked example. Mol. Simul., 43, 327-345 (2017).

Maria Karelina, Heather J. Kulik. Systematic Quantum Mechanical Region Determination in QM/MM Simulation. J. Chem. Theory Comput., 13, 563-576 (2017).

Efthymios I. Ioannidis, Heather J. Kulik. Ligand-Field-Dependent Behavior of Meta-GGA Exchange in Transition-Metal Complex Spin-State Ordering. J. Phys. Chem. A, 121, 874-884 (2017).

Jon Paul Janet, Heather J. Kulik. Predicting electronic structure properties of transition metal complexes with neural networks. Chem. Sci., 8, 5137-5152 (2017).

Brendan D. Mar, Heather J. Kulik. Depolymerization Pathways for Branching Lignin Spirodienone Units Revealed with ab Initio Steered Molecular Dynamics. J. Phys. Chem. A, 121, 532-543 (2017).

Terry Z. H. Gani, Heather J. Kulik. Where Does the Density Localize? Convergent Behavior for Global Hybrids, Range Separation, and DFT+U. J. Chem. Theory Comput., 12, 5931-5945 (2016).

Heather J. Kulik, Jianyu Zhang, Judith P. Klinman, Todd J. Martínez. How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase. J. Phys. Chem. B, 120, 11381-11394 (2016).

Terry Z. H. Gani, Efthymios I. Ioannidis, Heather J. Kulik. Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion Separation. Chem. Mater., 28, 6207-6218 (2016).

Qing Zhao, Stanley S. H. Ng, Heather J. Kulik. Predicting the Stability of Fullerene Allotropes Throughout the Periodic Table. J. Phys. Chem. C, 120, 17035-17045 (2016).

Qing Zhao, Efthymios I. Ioannidis, Heather J. Kulik. Global and local curvature in density functional theory. J. Chem. Phys., 145, 054109 (2016).

Niladri Patra, Efthymios I. Ioannidis, Heather J. Kulik. Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase. PLoS One, 11, e0161868 (2016).

Heather J. Kulik, Natasha Seelam, Brendan D. Mar, Todd J. Martínez. Adapting DFT+U for the Chemically Motivated Correction of Minimal Basis Set Incompleteness. J. Phys. Chem. A, 120, 5939-5949 (2016).

Lisi Xie, Qing Zhao, Klavs F. Jensen, Heather J. Kulik. Direct Observation of Early-Stage Quantum Dot Growth Mechanisms with High-Temperature Ab Initio Molecular Dynamics. J. Phys. Chem. C, 120, 2472-2483 (2016).

Efthymios I. Ioannidis, Terry Z. H. Gani, Heather J. Kulik. molSimplify: A toolkit for automating discovery in inorganic chemistry. J. Comput. Chem., 37, 2106-2117 (2016).

Xiao Su, Heather J. Kulik, Timothy F. Jamison, T. Alan Hatton. Anion-Selective Redox Electrodes: Electrochemically Mediated Separation with Heterogeneous Organometallic Interfaces. Adv. Funct. Mater., 26, 3394-3404 (2016).

Qing Zhao, Lisi Xie, Heather J. Kulik. Discovering Amorphous Indium Phosphide Nanostructures with High-Temperature ab Initio Molecular Dynamics. J. Phys. Chem. C, 119, 23238-23249 (2015).

Efthymios I. Ioannidis, Heather J. Kulik. Towards quantifying the role of exact exchange in predictions of transition metal complex properties. J. Chem. Phys., 143, 034104 (2015).

Fang Liu, Nathan Luehr, Heather J. Kulik, Todd J. Martínez. Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models. J. Chem. Theory Comput., 11, 3131-3144 (2015).

Heather J. Kulik. Perspective: Treating electron over-delocalization with the DFT+U method. J. Chem. Phys., 142, 240901 (2015).

Jianyu Zhang, Heather J. Kulik, Todd J. Martínez, Judith P. Klinman. Mediation of donor–acceptor distance in an enzymatic methyl transfer reaction. Proc. Natl. Acad. Sci., 112, 7954-7959 (2015).

Brendan D. Mar, Helena W. Qi, Fang Liu, Heather J. Kulik. Ab Initio Screening Approach for the Discovery of Lignin Polymer Breaking Pathways. J. Phys. Chem. A, 119, 6551-6562 (2015).

Charles E. Diesendruck, Gregory I. Peterson, Heather J. Kulik, Joshua A. Kaitz, Brendan D. Mar, Preston A. May, Scott R. White, Todd J. Martínez, Andrew J. Boydston, Jeffrey S. Moore. Mechanically triggered heterolytic unzipping of a low-ceiling-temperature polymer. Nat. Chem., 6, 623-628 (2014).

Heather J. Kulik, S. E. Wong, S. E. Baker, C. A. Valdez, J. H. Satcher, Roger. D. Aines, Felice C. Lightstone. Developing an approach for first-principles catalyst design: application to carbon-capture catalysis. Acta Crystallogr., Sect. C, 70, 123-131 (2014).

Heather J. Kulik, Catherine L. Drennan. Substrate Placement Influences Reactivity in Non-heme Fe(II) Halogenases and Hydroxylases. J. Biol. Chem., 288, 11233-11241 (2013).

Heather J. Kulik, Nathan Luehr, Ivan S. Ufimtsev, Todd J. Martínez. Ab Initio Quantum Chemistry for Protein Structures. J. Phys. Chem. B, 116, 12501-12509 (2012).

Heather J. Kulik, Eric Schwegler, Giulia Galli. Probing the Structure of Salt Water under Confinement with First-Principles Molecular Dynamics and Theoretical X-ray Absorption Spectroscopy. J. Phys. Chem. Lett., 3, 2653-2658 (2012).

Heather J. Kulik, Nicola Marzari. Accurate potential energy surfaces with a DFT+U(R) approach. J. Chem. Phys., 19, 194105 (2011).

Heather J. Kulik, Nicola Marzari. Transition-metal dioxides: A case for the intersite term in Hubbard-model functionals. J. Chem. Phys., 134, 094103 (2011).

J. H. Satcher, S. E. Baker, Heather J. Kulik, C. A. Valdez, R. L. Krueger, Felice C. Lightstone, Roger D. Aines. Modeling, synthesis and characterization of zinc containing carbonic anhydrase active site mimics. Energy Procedia, 4, 2090-2095 (2011).

Sergio E. Wong, Edmond Y. Lau, Heather J. Kulik, Joseph H. Satcher, Carlos Valdez, Marcus Worsely, Felice C. Lightstone, Roger D. Aines. Designing small-molecule catalysts for CO2 capture. Energy Procedia, 4, 817-823 (2011).

Heather J. Kulik, Nicola Marzari. Systematic study of first-row transition-metal diatomic molecules: A self-consistent DFT+U approach. J. Chem. Phys., 133, 114103 (2010).

U. G. E. Perera, Heather J. Kulik, V. Iancu, L. G. G. V. Dias da Silva, S. E. Ulloa, Nicola Marzari, S.-W. Hla. Spatially Extended Kondo State in Magnetic Molecules Induced by Interfacial Charge Transfer. Phys. Rev. Lett., 105, 106601 (2010).

Heather J. Kulik, Nicola Marzari, Alfredo A. Correa, David Prendergast, Eric Schwegler, Giulia Galli. Local Effects in the X-ray Absorption Spectrum of Salt Water. J. Phys. Chem. B, 114, 9594-9601 (2010).

Heather J. Kulik, Nicola Marzari. Electronic Structure and Reactivity of Transition Metal Complexes. Fuel Cell Science: Theory, Fundamentals, and Bio-Catalysis, 433-455 (2010).

Heather J. Kulik, Adam H. Steeves, Robert W. Field. Ab initio investigation of high multiplicity Σ+–Σ+ optical transitions in the spectra of CN and isoelectronic species. Journal of Molecular Spectroscopy, 258, 6-12 (2009).

Heather J. Kulik, Leah C. Blasiak, Nicola Marzari, Catherine L. Drennan. First-Principles Study of Non-heme Fe(II) Halogenase SyrB2 Reactivity. J. Am. Chem. Soc., 131, 14426-14433 (2009).

Heather J. Kulik, Nicola Marzari. A self-consistent Hubbard U density-functional theory approach to the addition-elimination reactions of hydrocarbons on bare FeO+. J. Chem. Phys., 129, 134314 (2008).

Heather J. Kulik, Matteo Cococcioni, Damian A. Scherlis, Nicola Marzari. Density Functional Theory in Transition-Metal Chemistry: A Self-Consistent Hubbard U Approach. Phys. Rev. Lett., 97, 103001 (2006).