Publications | Kulik Research Group

P. N. Johnson, Y. Yao, Xiao Huang, Ilia Kevlishvili, S. Schrettl, C. Weder, Heather J. Kulik, S. L. Craig. Metal Identity Effects in the Fracture Behavior of Coordinatively Crosslinked Elastomers. submitted.

Husain Adamji, Aditya Nandy, Ilia Kevlishvili, Yuriy Roman-Leshkov, Heather J. Kulik. Computational Discovery of Stable Metal-Organic Frameworks for Methane-to-Methanol Catalysis. submitted.

H. Wakefield IV, Ilia Kevlishvili, K. E. Wentz, Y. Yao, T. B. Kouznetsova, S. J. Melvin, E. G. Ambrosius, A. Herzog-Arbeitman, M. A. Siegler, J. A. Johnson, S. L. Craig, Heather J. Kulik, R. S. Klausen. Synthesis and Ring-opening Metathesis Polymerization of a Strained trans-Silacycloheptene and Single Molecule Mechanics of its Polymer. J. Am. Chem. Soc., in press.

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. submitted.

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).

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. submitted.

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).

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. submitted.

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., advance article (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).