Publications

Numbers follow the CV (P = preprint, B = book or chapter, T = thesis, IP = patent or invention disclosure). Bold: J. L. Mendoza-Cortés; underlined: students and postdocs of the group; * corresponding author; ‡ equal contribution.

2026

1. 69

   Projected Hessian Learning: Fast Curvature Supervision for Accurate Machine-Learning Interatomic Potentials

   A. Rodriguez, J. S. Smith, S. Matin, N. Lubbers^*, K. Barros^*, J. L. Mendoza-Cortes^*

   Machine Learning: Science and Technology 2026, 7, 055037

   Training machine-learning interatomic potentials on Hessians, the second derivatives that describe the curvature of a potential energy surface, improves accuracy, but full Hessians are costly to compute and store. We introduce Projected Hessian Learning, which supervises curvature using only Hessian-vector products along random probe directions, and benchmark it on reactants, products, transition states and reaction paths. It matches full-Hessian training accuracy for energies, forces and Hessians while training more than 24 times faster per epoch.

   DOI arXiv PDF PHL OpenREACT-CHON-EFH Copy citationMachine learning and AIInteratomic potentialsQuantum mechanics
2. 68

   How Does Intercalation Reshape Layered Structures? A First-Principles Study of Sodium Insertion in Layered Potassium Birnessite

   A. Lee Punaro, D. Maldonado-Lopez, J. L. Cholula-Diaz, M. Videa^*, J. L. Mendoza-Cortes^*

   The Journal of Chemical Physics 2026, 165, 084703

   Layered manganese oxides such as birnessite can host ions between their sheets, but how intercalation reshapes their structure and electronic properties is not well understood. Using hybrid density functional theory, we follow sodium insertion into potassium birnessite through formation energies, simulated Raman and X-ray diffraction patterns, diffusion barriers and binding energies. Intercalation shifts manganese oxidation states and distorts the lattice, and some intercalated structures behave as bipolar magnetic semiconductors, suggesting uses in spintronics.

   DOI arXiv PDF Copy citationEnergy storage2D materials
3. 67

   Ferrocene-functionalized covalent organic framework exceeding the ultimate hydrogen storage targets: a first-principles multiscale computational study

   M. Djokic, J. L. Mendoza-Cortes^*

   npj Energy Materials 2026, 1, 18

   Storing enough hydrogen in a compact, lightweight tank is a key hurdle for hydrogen-powered vehicles, for which the Department of Energy sets targets of 6.5 wt% and 50 g/L. Following our multi-binding-sites strategy for covalent organic frameworks (COFs), we design MSUCOF-4-FeCp by adding ferrocene groups to the IRCOF-102 framework and evaluate it with first-principles multiscale simulations. At room temperature and 700 bar it stores 18.0 wt% and 72.6 g/L, a lower-cost alternative to precious-metal COFs.

   DOI arXiv PDF Copy citationEnergy storagePorous materials
4. 66

   Leveraging Polymorphism in YbCuBi to Map Transport and Elastic Properties

   A. K. M. A. Shawon, G. Yumnam, H. Wang, Q. Zhang, D. L. Abernathy, M. E. Manley, J. L. Mendoza-Cortes^*, R. P. Hermann^*, A. Zevalkink^*

   Chemistry of Materials 2026, 38, 3, 1425–1434

   Zintl compounds with honeycomb layers, such as YbCuBi, combine vacancy tolerance with low thermal conductivity, but how their structure controls heat transport is unclear. Below 410 K, YbCuBi changes from flat to corrugated copper–bismuth layers, and we exploit this polymorphism using inelastic neutron scattering, resonant ultrasound spectroscopy, thermal conductivity measurements and first-principles calculations. The results tie honeycomb corrugation directly to elastic and thermal transport properties, guiding the design of materials with tailored thermal behavior.

   DOI PDF Copy citationCrystals and polymorphismEnergy conversionQuantum mechanics
5. 65

   A first-principles theoretical study on two-dimensional MX and MX₂ metal halides: bandgap engineering, magnetism, and catalytic descriptors

   Y.-H. Lin, D. Maldonado-Lopez, J. L. Mendoza-Cortes^*

   Physical Chemistry Chemical Physics 2026, 28, 6, 3832–3840 Front cover PCCP Emerging Investigators 2025

   Metal halides with MX and MX₂ formulas can be thinned from bulk crystals into two-dimensional sheets, but how this changes their electronic behavior is poorly understood. Using hybrid density functional theory, we build a database of 60 compounds in bulk and slab forms and evaluate their bandgaps, magnetism and catalytic descriptors. Most are semiconductors, with bandgaps from 0 to 9 eV, and nine switch from indirect to direct bandgaps when thinned, which could benefit energy conversion.

   DOI arXiv PDF Copy citation2D materialsQuantum materialsCatalysis
6. P7

   Can Strain or Anion Interchange Make an Unstable Structure Stable? Energetics, Lattice Dynamics and Strain-Tunable Band Gaps of Lithium Chalcohalide Antiperovskites (Li₃BA) and their Anion Interchange Variants (Li₃AB)

   I. A. Buliyaminu, E. Gowdini, P. Duxbury, J. L. Mendoza-Cortes^*

   arXiv preprint 2026, arXiv:2608.23815

   Lithium chalcohalide antiperovskites are non-toxic alternatives to lead halide perovskites and candidate solid electrolytes for lithium-ion batteries. We computationally map their energetics, lattice dynamics and electronic structure, and test whether swapping the two anions or applying strain can stabilize the cubic structures. Placing the smaller anion inside the octahedron favors stability, compression makes Li₃FS and Li₃FSe dynamically stable, and a few percent strain tunes the band gap within the electrochemical stability window.

   arXiv Copy citationCrystals and polymorphismEnergy storageMaterials discovery
7. P6

   CheMLFlow: An Open-Source Platform for Cheminformatics and Materials Informatics Applications

   B. Smith, S. Lopez-Moreno, E. Dolores-Cuenca, S. Kim, J. L. Mendoza-Cortes^*, N. Abdulrahiman^*

   arXiv preprint 2026, arXiv:2608.04942

   Scientific machine learning often forces researchers to assemble a full pipeline, from data acquisition to reporting, even when they contribute to only one step. We present CheMLFlow, an open-source platform of modular components and ready-to-run reference pipelines for reproducible, high-throughput and agent-assisted workflows in cheminformatics and materials informatics. Benchmarks reach literature-level performance for quantum-mechanical, physicochemical and bioactivity property prediction, and time-series examples show that the platform extends beyond molecular data.

   arXiv CheMLFlow Copy citationMachine learning and AIMaterials discovery
8. B3

   Quantum Computing Live Book

   F. Velasquez, W. Comaskey, E. Dolores-Cuenca, J. L. Mendoza-Cortes^*

   Open-access e-book 2026

   Quantum computing is easiest to learn by running it. This open, executable textbook introduces quantum computing through examples that readers can run and modify, and grew out of our courses on machine learning and quantum computing. It was written with an undergraduate researcher and two former members of the group and is archived on Zenodo.

   DOI Read online Copy citationQuantum computing
9. IP5

   Metallocene-functionalized covalent organic frameworks for exceeding ultimate volumetric and gravimetric hydrogen storage targets

   J. L. Mendoza-Cortes, M. Djokic

   U.S. provisional patent application 2026

   Protects the design of framework materials with metallocene binding sites for room-temperature hydrogen storage; see the related npj Energy Materials article.

   Copy citationEnergy storagePorous materials
10. IP4

    Two-dimensional MX/MX₂-enes utilized for optoelectronic, catalytic and magnetic applications

    J. L. Mendoza-Cortes, Y.-H. Lin, D. Maldonado-Lopez

    U.S. provisional patent application 2026

    Covers two-dimensional metal halides identified in our PCCP study for optoelectronic, catalytic and magnetic uses.

    Copy citation2D materialsCatalysis
11. IP3

    Enhanced antibacterial efficacy of copper single-atom catalysts on a two-dimensional boron nitride platform

    J. L. Mendoza-Cortes, Y. Lei, D. Maldonado-Lopez, W. Li

    U.S. provisional patent application (invention disclosure) 2026

    Covers antibacterial copper single-atom catalysts on boron nitride described in our ACS Nano article.

    Copy citationBio-inspired and healthCatalysis
12. Property Modulation in Two-Dimensional Materials

    D. Maldonado-Lopez

    Ph.D. dissertation, Chemical Engineering and Materials Science, Michigan State University (advisor: J. L. Mendoza-Cortes) 2026 Directed in the Mendoza Lab

    DOI MSU Libraries Copy citation2D materialsQuantum materials
13. Integrating Machine Learning and Density Functional Theory to Unravel and Optimize Catalytic Reaction Mechanisms

    A. R. Rodriguez

    Ph.D. dissertation, Chemical Engineering and Materials Science, Michigan State University (advisor: J. L. Mendoza-Cortes) 2026 Directed in the Mendoza Lab

    DOI MSU Libraries Copy citationMachine learning and AICatalysis

2025

1. 64

   Enhanced Antibacterial Efficacy of Copper Single-Atom Catalysts on a Two-Dimensional Boron Nitride Platform

   W.-B. Li, D. Maldonado-Lopez, Y.-C. Zhao, C. Wang, J.-X. Gao, B. Sun, Y.-C. Bai, L.-X. Sun, M.-C. Zhao, H.-Q. He, J. Lou, Q. Yu, X. Zhang, V. K. Pandey, …, J. L. Mendoza-Cortes^*, Y. Lei^* (18 authors)

   ACS Nano 2025, 19, 50, 42198

   Copper-based antibacterial materials kill microbes with reactive oxygen species, but released copper ions can harm human cells and promote bacterial resistance. We anchor copper single atoms at defect sites of biocompatible boron nitride nanosheets and combine experiments with density functional theory (DFT) to explain how copper–boron nitride bonding boosts light-driven production of reactive oxygen species. Under sunlight the single-atom catalyst inactivates E. coli within 30 minutes and offers the best balance of safety and efficacy.

   DOI Correction (ACS Nano 2026) PDF MSUToday story MSU Engineering Copy citationBio-inspired and healthCatalysis2D materials
2. 63

   Enhanced Activity in Layered Metal-Oxide-Based Oxygen Evolution Catalysts by Layer-by-Layer Modulation of Metal-Ion Identity

   R. Ding, D. Maldonado-Lopez, J. E. Henebry, J. L. Mendoza-Cortes^*, M. J. Zdilla^*

   ACS Catalysis 2025, 15, 20204

   Producing hydrogen by splitting water requires efficient, earth-abundant catalysts for the oxygen evolution reaction, and layered cobalt and nickel oxides are promising candidates. We compare few-layer potassium cobalt and nickel oxides with uniform, randomly mixed and layer-by-layer alternating metal arrangements, combining electrochemical experiments with density functional theory (DFT). Alternating cobalt and nickel oxide sheets lowers the overpotential by roughly 200–400 mV, showing that the atomic-level arrangement of metal ions matters more than overall composition.

   DOI arXiv PDF Copy citationCatalysisEnergy conversion
3. 62

   Impact of Grain Size on Low-Temperature Carrier Phase Coherence Length in Polycrystalline Halide Perovskite Films

   A. Sen, L. J. Scanlon, A. M. Gaona Carranza, J. L. Mendoza-Cortes^*, J. Pollanen^*, R. R. Lunt^*, W. J. Gannon^*

   Advanced Materials Interfaces 2025, 13, 1, e00567 Cover

   Halide perovskites are promising for quantum devices, but how grain boundaries affect the quantum-coherent motion of charge carriers at low temperature is unclear. We compare polycrystalline cesium tin iodide (CsSnI₃) films of different grain sizes with epitaxial films using low-temperature magnetoresistance measurements and density functional theory (DFT). The coherence length does not depend on grain size; crystal structure and strain dominate instead, and calculations indicate weaker electron–phonon scattering in single-domain epitaxial films.

   DOI PDF Copy citationQuantum materials
4. 61

   Terahertz field control of surface topology probed with subatomic resolution

   V. Jelic, S. Adams, D. Maldonado-Lopez, I. A. Buliyaminu, M. A. Hassan, J. L. Mendoza-Cortes^*, T. L. Cocker^*

   Nature Photonics 2025, 19, 1048-1055

   Using light to switch topological states in quantum materials could enable nanoscale devices with precise local control of electronic properties. Combining terahertz scanning tunneling microscopy with hybrid density functional theory, we show that ultrafast terahertz pulses focused at an atomically sharp tip drive a shear motion of the top atomic layer of the Weyl semimetal candidate WTe₂. Subatomic-resolution imaging and tunneling spectroscopy reveal a reversible, light-induced suppression of topologically protected surface states in that layer.

   DOI arXiv MSUToday story WILX TV Copy citationQuantum materials2D materials
5. 60

   Does Hessian Data Improve the Performance of Machine Learning Potentials?

   A. Rodriguez, J. S. Smith, J. L. Mendoza-Cortes^*

   Journal of Chemical Theory and Computation 2025, 21, 14, 6698

   Machine-learning interatomic potentials predict energies and forces at near quantum-chemical accuracy and far lower cost, but models trained only on stable geometries may extrapolate poorly. We test whether adding Hessian data, the second derivatives that capture the curvature of the potential energy surface, improves training on a small-molecule reactive dataset. Hessian-trained models better predict non-equilibrium structures, reaction pathways, transition states and vibrational spectra, and need less training data, at a higher computational cost.

   DOI arXiv PDF MLFFwithHessians OpenREACT-CHON-EFH Copy citationMachine learning and AIInteratomic potentialsQuantum mechanics
6. 59

   How Can We Engineer Electronic Transitions Through Twisting and Stacking in TMDC Bilayers and Heterostructures? A First-Principles Approach

   Y.-H. Lin, W. P. Comaskey, J. L. Mendoza-Cortes^*

   Nanoscale Advances 2025, 7, 2047

   Stacking and twisting layers of transition metal dichalcogenides (TMDCs) such as MoS₂ and WSe₂ can create properties absent in single layers, including moiré patterns at critical twist angles. Using hybrid density functional theory (DFT), we examine 30 heterostructures built from six TMDCs and twisted homobilayers under relaxed and low-strain conditions. Stacking and twist angle tune the size and character of the band gap and band flatness, offering a toolkit for designing electronic transitions.

   DOI arXiv PDF Copy citation2D materials
7. B2

   Machine Learning and Quantum Computing Guide for Humans

   J. L. Mendoza-Cortes^*, E. Dolores-Cuenca, C. Aguirre, Y.-Y. Tzeng, G. Xu, N. Crock, A. Aduenko

   Open-access e-book 2025

   Students in science and engineering increasingly need machine learning but rarely take computer-science courses. This open textbook combines short explanations with executable notebooks on regression, decision trees, neural networks, quantum algorithms and variational methods, with examples from art, materials discovery, medicine and physics. The course behind it was preserved in the GitHub Arctic Code Vault in 2020.

   Read online Copy citationMachine learning and AIQuantum computing
8. IP2

   Terahertz field control of surface topology probed with subatomic resolution

   J. L. Mendoza-Cortes, T. L. Cocker, V. Jelic, S. Adams, D. Maldonado-Lopez

   U.S. provisional patent application 2025

   Based on the terahertz control of surface topology reported in Nature Photonics.

   Copy citationQuantum materials2D materials
9. IP1

   Reaction-driven restructuring of defective PtSe₂ into ultrastable catalyst for the oxygen reduction reaction

   J. L. Mendoza-Cortes, B. E. Koel, W. Niu

   U.S. provisional patent application 2025

   Based on the ultrastable fuel-cell catalyst reported in Nature Materials.

   Copy citationEnergy conversionCatalysis
10. Quantum-Enabled High-Throughput Discovery of 2D Materials for Sustainable Energy

    Y.-H. Lin

    Ph.D. dissertation, Chemical Engineering and Materials Science, Michigan State University (advisor: J. L. Mendoza-Cortes) 2025 Directed in the Mendoza Lab

    DOI MSU Libraries Copy citation2D materialsMaterials discovery

2024

1. 58

   Reaction-driven restructuring of defective PtSe₂ into ultrastable catalyst for the oxygen reduction reaction

   W. Niu^‡, S. Pakhira^‡, G. Cheng, F. Zhao, N. Yao, J. L. Mendoza-Cortes^*, B. E. Koel^*

   Nature Materials 2024, 23, 1704

   Platinum dichalcogenides are promising two-dimensional materials, but their potential as catalysts for the oxygen reduction reaction in fuel cells has been underestimated because they are semiconducting and stack tightly. We restructure defective platinum diselenide (PtSe₂) by electrochemical cycling in oxygen-saturated electrolyte and use hybrid density functional theory to explain its activity. The catalyst outperforms commercial platinum on carbon even after 126,000 cycles, owing to synergy between platinum nanoparticles and active sites on the PtSe₂ surface.

   DOI MSUToday story Copy citationEnergy conversionCatalysis2D materials
2. 57

   Nitrogen-Containing Surface Ligands Lead to False Positives for Photofixation of N₂ on Metal Oxide Nanocrystals: An Experimental and Theoretical Study

   D. Maldonado-Lopez, P.-W. Huang, K. R. Sanchez-Lievanos, G. Jana, J. L. Mendoza-Cortes^*, K. E. Knowles^*, M. C. Hatzell^*

   Advanced Functional Materials 2024, 35 (3), 2413319

   Photocatalytic nitrogen fixation, using light to turn nitrogen gas into ammonia, is widely studied on metal oxide nanoparticles, yet many synthesis recipes use nitrogen-containing ligands. Combining photocatalysis experiments with hybrid density functional theory (DFT), we show that leftover ligands such as oleylamine produce false positives for nitrogen photofixation. Nitrogen-free synthesis routes avoid the artifact, and synthesis protocols need careful scrutiny because such contamination often goes undetected.

   DOI arXiv PDF Copy citationClean energyCatalysis
3. 56

   Beyond lithium-ion batteries: Are effective electrodes possible for alkaline and other alkali elements? Exploring ion intercalation in surface-modified few-layer graphene and examining layer quantity and stages

   Y.-H. Lin, J. L. Mendoza-Cortes^*

   Journal of Applied Physics 2024, 136 (7), 075001

   Earth-abundant sodium and potassium could replace lithium in batteries, but how ions insert in stages into layered carbon electrodes is poorly understood. Using hybrid density functional theory (DFT), we study staged intercalation of lithium, sodium, potassium, beryllium, magnesium and calcium into few-layer graphene with a fluorinated surface modifier. We find a previously unknown, most favorable binding site and show that the number of graphene layers strongly affects binding, guiding alternatives to lithium-ion batteries.

   DOI arXiv PDF Copy citationEnergy storage2D materials
4. 55

   Rare isotope-containing diamond colour centres for fundamental symmetry tests

   I. M. Morris, K. Klink, J. T. Singh, J. L. Mendoza-Cortes^*, S. S. Nicley, J. N. Becker^*

   Philosophical Transactions of the Royal Society A 2024, 382, 2265 Front cover

   Detecting an electric dipole moment in a nucleus would reveal physics beyond the Standard Model, and rare pear-shaped isotopes such as protactinium-229 amplify this signal but are scarce. We propose embedding such isotopes in synthetic diamond, where they form color centers that can be probed repeatedly, and use density functional theory to study protactinium-229 defects and lanthanide proxies. The results suggest such defects may exist and could support a quantum-information-inspired toolbox for rare isotopes.

   DOI arXiv PDF Copy citationFundamental physicsRelativistic quantum mechanics
5. 53

   MultiBinding Sites United in Covalent-Organic Frameworks (MSUCOF) for H₂ Storage and Delivery at Room Temperature

   M. Djokic, J. L. Mendoza-Cortes^*

   Energy & Fuels 2024, 38, 5, 4711 Front cover

   Hydrogen fuel needs materials that store large amounts of gas at room temperature, yet many porous frameworks bind hydrogen too weakly. We design 24 covalent organic frameworks (COFs) whose linkers chelate transition metals and simulate hydrogen uptake at 298 K and up to 700 bar using quantum-derived force fields and Monte Carlo methods. Several designs can meet the Department of Energy's 2025 targets, and cheaper first-row metals often outperform precious palladium and platinum.

   DOI arXiv PDF Copy citationEnergy storagePorous materials
6. P5

   Order Theory in the Context of Machine Learning

   E. Dolores-Cuenca, A. Guzman-Saenz, S. Kim, S. Lopez-Moreno, J. L. Mendoza-Cortes^*

   arXiv preprint 2024, arXiv:2412.06097

   Order theory, the mathematics of partially ordered sets (posets), may offer interpretable, geometry-aware building blocks for deep learning. Building on links between neural networks and tropical geometry, we study networks whose associated polytopes are order polytopes and show that four-point posets give "poset filters" that act like 2×2 convolutional filters. Used for pooling, these filters update network weights more precisely than average, max or mixed pooling without adding trainable parameters.

   arXiv Poset-Filters Copy citationMathematics of AIMachine learning and AI
7. Modelling and investigation of new one dimensional porous materials for various applications

   L. Nascimento Santos

   M.S. thesis, Materials Science, Michigan State University (advisor: J. L. Mendoza-Cortes) 2024 Directed in the Mendoza Lab

   DOI MSU Libraries Copy citationPorous materials

2023

1. 54

   Transforming Materials Discovery for Artificial Photosynthesis: High-Throughput Screening of Earth-Abundant Semiconductors

   S. M. Stafford, A. Aduenko, M. Djokic, Y.-H. Lin, J. L. Mendoza-Cortes^*

   Journal of Applied Physics 2023, 134, 235706

   Artificial photosynthesis, using sunlight to make fuels by splitting water, needs semiconductors made of earth-abundant elements that absorb light well, produce hydrogen or oxygen efficiently and resist corrosion in water. We present a high-throughput workflow in which a model trained on a crystal structure database proposes over 30,000 new compositions, followed by redox-stability screening, crystal structure generation and accurate bandgap calculations. The workflow identifies dozens of promising semiconductors for solar fuel production.

   DOI arXiv PDF SALSA Copy citationMaterials discoveryEnergy conversion
2. 52

   Exquisite Control of Electronic and Spintronic Properties on Highly Porous Covalent Organic Frameworks (COFs): Transition Metal Intercalation in Bilayers

   D. Maldonado-Lopez, J. L. Mendoza-Cortes^*

   Physica Scripta 2023, 98, 10, 105926

   Two-dimensional covalent organic frameworks (COFs) are porous, highly tunable layered materials, but weak electron delocalization limits their use in electronics. Using hybrid density functional theory, we study a bilayer COF built from benzene, boroxine and triazine rings and insert first-row transition metals between its layers, examining 63 intercalated bilayers. The concentration and position of the metals strongly change electronic, magnetic and spintronic properties, yielding candidate water-splitting catalysts, visible-light semiconductors, half metals and bipolar magnetic semiconductors.

   DOI PDF Copy citationPorous materialsQuantum materials
3. 51

   Unveiling the mechanisms of epoxide polymerization with N–Al adduct catalysts: a comprehensive experimental and theoretical investigation

   N. Safaie^‡, A. Rodriguez^‡, G. Jana^‡, J. Smak, J. L. Mendoza-Cortes^*, R. C. Ferrier Jr.^*

   Polymer Chemistry 2023, 14, 3213

   Polyethers made by ring-opening polymerization of epoxides are used in adhesives, elastomers and biomedical devices, and earth-abundant aluminum catalysts are attractive, but their mechanisms have remained unclear. Combining experiments with density functional theory (DFT), we determine the complete polymerization mechanism of functional epoxides with nitrogen–aluminum adduct catalysts. The results establish these adducts as a customizable platform for controlled epoxide polymerization and guide the design of sustainable aluminum-based catalysts.

   DOI PDF Copy citationPolymersCatalysisClean energy
4. 50

   NMR Magnetic Shielding in Transition Metal Compounds Containing Cadmium, Platinum, and Mercury

   A. D. Zapata-Escobar, A. F. Maldonado, J. L. Mendoza-Cortes^*, G. A. Aucar

   Magnetochemistry 2023, 9, 7, 165

   Interpreting nuclear magnetic resonance (NMR) signals from molecules that contain heavy atoms requires accounting for relativistic effects. We apply LRESC-Loc, a relativistic linear-response method built on chemically intuitive localized molecular orbitals, to platinum halides and to cadmium and mercury complexes. We separate ligand-independent and ligand-dependent contributions to magnetic shielding and explain their electronic origins, showing for example that spin–orbit effects dominate in four-coordinate platinum halides while mass-velocity and Darwin terms dominate in six-coordinate ones.

   DOI PDF Copy citationRelativistic quantum mechanics
5. 49

   Recent Advances in 2D Material Theory,Synthesis, Properties, and Applications

   Y.-C. Lin, R. Torsi, R. Younas, C. Hinkle, A. Rigosi, H. Hill, K. Zhang, S.-X. Huang, C. Shuck, C. Chen, Y.-H. Lin, D. Maldonado-Lopez, J. L. Mendoza-Cortes, J. P. Ferrier, …, J. A. Robinson^* (48 authors)

   ACS Nano 2023, 17, 11, 9694

   Research on two-dimensional (2D) materials now spans theory, synthesis, characterization, devices and quantum physics. This multi-group review surveys recent advances, including modeling of defects and intercalants, machine learning for synthesis and sensing, growth of MXenes, magnetic and low-symmetry crystals, optical and phonon properties, mixed-dimensional heterostructure devices for logic and memory, and quantum transport in twisted homojunctions. It closes with perspectives on future directions for the field.

   DOI PDF Copy citation2D materials
6. 48

   Polychrony as Chinampas

   E. Dolores-Cuenca, J. A. Arciniega-Nevarez^*, A. Nguyen, A. Y. Zou, L. Van Popering, N. Crock, G. Erlebacher, J. L. Mendoza-Cortes^*

   Algorithms 2023, 16, 4, 193

   Polychronization, a concept from computational neuroscience, describes networks whose nodes fire in precisely timed patterns when two incoming signals coincide. We build a graph-theoretic framework for these dynamics, giving an efficient algorithm to reconstruct signal cascades and naming the graph of a cascade a chinampa, after the interlinked farm islets of pre-Hispanic Mexico. Counting one family of chinampas turns out to be equivalent to computing Stanley order polynomials of partially ordered sets.

   DOI arXiv PDF CHINAMPAS Copy citationMathematics of AIMachine learning and AI
7. 47

   Thermodynamics, Kinetics, and Optical Properties of Rotaxane: A First-Principles Molecular Dynamics Study

   G. Jana, J. L. Mendoza-Cortes^*

   The Journal of Physical Chemistry A 2023, 127, 12, 2671

   Rotaxanes are mechanically interlocked molecules, a ring threaded onto a dumbbell-shaped axle, that serve as building blocks for molecular machines. We combine ab initio molecular dynamics from 300 to 2500 K with noncovalent-interaction analyses and time-dependent density functional theory to study a prototypical rotaxane. It remains stable at high temperatures, shows strong linear and nonlinear optical responses and absorbs broadly across ultraviolet and visible light, suggesting uses in optical materials and solar energy harvesting.

   DOI PDF Copy citationMolecular machinesInteratomic potentials
8. 46

   Synergistic Steric and Electronic Effects on the Photoredox Catalysis by a Multivariate Library of Titania Metal--Organic Frameworks

   J. T. Bryant, M. W. Logan, Z. Chen, M. Djokic, D. R. Cairnie, D. A. Vazquez-Molina, A. Nijamudheen, K. R. Langlois, M. J. Markley, G. Pombar, A. A. Holland, J. D. Caranto, J. K. Harper, A. J. Morris^*, …, J. L. Mendoza-Cortes^*, F. J. Uribe-Romo^* (18 authors)

   Journal of the American Chemical Society 2023, 145, 8, 4589

   Metal–organic frameworks (MOFs) that drive light-powered redox reactions are promising for sustainable photocatalysis because their pore size and electronic structure can be tuned. We build a library of eleven titanium-based MOFs whose linker length and amine electron-donating groups separate steric (pore size) and electronic (HOMO–LUMO gap) effects on the photo-oxidation of benzyl alcohol. Longer linkers and more donor groups give rates almost 20 times faster than the benchmark framework MIL-125.

   DOI PDF Copy citationPorous materialsCatalysis
9. 45

   Relativistic Quantum Calculations to Understand the Contribution of f-type Atomic Orbitals and Chemical Bonding of Actinides with Organic Ligands

   A. D. Zapata-Escobar, S. Pakhira, J. Barroso-Flores, G. A. Aucar^*, J. L. Mendoza-Cortes^*

   Physical Chemistry Chemical Physics 2023, 25, 5592

   Understanding how actinides bond to organic ligands matters for nuclear waste chemistry, but these heavy elements require relativistic quantum methods that are costly for large molecules. We compare scalar and spin–orbit relativistic DFT with all-electron four-component Dirac–Hartree–Fock calculations for plutonium, americium, berkelium and californium complexes of the redox-active ligand DOPO, with up to 421 electrons. Relativistic effects control how 5f orbitals contribute to bonding, and the cheaper DFT approach gives a useful first approximation.

   DOI arXiv PDF Copy citationRelativistic quantum mechanicsNuclear-waste separation and recovery

2022

1. 44

   Role of spin currents on electron-electron interaction in the quantum spin Hall phase

   W. P. Comaskey, F. Bodo, A. Erba^*, J. L. Mendoza-Cortes^*, J. K. Desmarais^*

   Physical Review B 2022, 106, 20, L201109

   Quantum spin Hall materials, two-dimensional topological insulators, are hard to model because standard density functional theory captures spin–orbit coupling only partially. We apply spin-current density functional theory, in which the electron–electron potential depends on spin currents, to a strained bismuth bilayer that changes from an ordinary to a topological insulator. Including spin currents qualitatively improves the electronic structure and is essential for the Dirac cone that appears at the onset of the topological transition.

   DOI arXiv PDF Copy citationQuantum materialsQuantum mechanics
2. 43

   A Surface Modification Strategy Towards Reversible Na-ion Intercalation on Graphitic Carbon Using Fluorinated Few-Layer Graphene

   D. Sarbapalli, Y.-H. Lin, S. Stafford, J. Son, A. Mishra, J. Hui, A. Nijamudheen, A. I. B. Romo, Z. T. Gossage, A. M. van der Zande, J. L. Mendoza-Cortes^*, J. Rodriguez-Lopez^*

   Journal of The Electrochemical Society 2022, 169, 10, 106522

   Sodium-ion batteries are an attractive alternative to lithium-ion technology, but graphite anodes generally fail to take up sodium because sodium-intercalated graphite is unstable. Building on our calculations predicting that fluorine surface modification stabilizes sodium between graphene layers, we test fluorinated few-layer graphene using cyclic voltammetry, ion-sensitive scanning electrochemical microscopy and in situ Raman spectroscopy. Reversible sodium intercalation occurs, but only with both surface fluorination and a pre-formed lithium-based solid electrolyte interphase.

   DOI PDF Copy citationEnergy storage2D materials
3. 42

   Multi-dimensional designer catalysts for negative emissions science (NES): bridging the gap between synthesis, simulations, and analysis

   C. M. Hill^*, J. L. Mendoza-Cortes^*, J. M. Velazquez^*, L. Whittaker-Brooks^*

   iScience 2022, 25, 1, 103700

   Negative emissions technologies, which remove carbon dioxide from the atmosphere, will likely be needed to limit global warming, and catalytic CO₂ reduction could play a central role. In this perspective, we examine the gap between catalysts that can be made and probed experimentally and those that can be modeled with adequate rigor. We outline how materials design, synthesis, characterization and theory can be integrated to accelerate the development of catalysts for negative emissions science.

   DOI PDF Copy citationClean energyCatalysis
4. 41

   Ubiquity of cubanes in bioinorganic relevant compounds

   A. Bigness, S. Vaddypally, M. J. Zdilla^*, J. L. Mendoza-Cortes^*

   Coordination Chemistry Reviews 2022, 450, 214168

   Cube-shaped heterocubane clusters of metal and oxygen or sulfur atoms sit at the heart of key enzymes, enabling biological water splitting, nitrogen fixation and the citric acid cycle. This review surveys synthetic cubane chemistry in terms of coordination environment and geometry, and connects these synthetic systems with their natural counterparts across different core metals and ligands. Linking biology with synthetic chemistry, it presents heterocubanes as a unifying scaffold for understanding and emulating demanding redox transformations.

   DOI PDF Copy citationBio-inspired and healthCatalysis
5. P4

   Obtaining transferable chemical insight from solving machine-learning classification problems: Thermodynamical properties prediction, atomic composition as good as Coulomb matrix

   L. Alday-Toledo, R. Bernal-Jaquez, S. Zapotecas-Martinez, J. L. Mendoza-Cortes^*

   arXiv preprint 2022, arXiv:2212.01420

   Machine-learning surrogate models predict chemical properties much faster than calculations or experiments, but choosing a good descriptor and training setup is difficult. We cast property prediction as classification problems to gauge task difficulty and test molecular representations, using enthalpy, Gibbs free energy, zero-point energy and heat capacity across the 133,885-molecule QM9 database. A simple atomic-composition descriptor classifies nearly as well as the detailed sorted Coulomb matrix when a suitable optimizer is used.

   arXiv Copy citationMachine learning and AI
6. P3

   A poset version of Ramanujan results on Eulerian numbers and zeta values

   E. Dolores-Cuenca, J. L. Mendoza-Cortes^*

   arXiv preprint 2022, arXiv:2205.05208

   Partially ordered sets (posets) link combinatorics, number theory and our work on the mathematical foundations of machine learning. We study the operad of finite posets and its algebras, using order polytopes to analyze zeta values and generalize a family of zeta-value identities. We also re-prove Ramanujan's results on Eulerian numbers by showing that his series carry the structure of disjoint unions of points, and relate the results to the linear independence of zeta values.

   arXiv Copy citationMathematics of AI

2021

1. 40

   Low temperature activation of inert hexagonal boron nitride for metal deposition and single atom catalysis

   Y. Lei^‡, S. Pakhira^‡, K. Fujisawa, H. Liu, C. Guerrero-Bermea, T. Zhang, A. Dasgupta, L. M. Martinez, S. R. Singamaneni, K. Wang, J. Shallenberger, A. L. Elías, R. Cruz-Silva, M. Endo, J. L. Mendoza-Cortes^*, M. Terrones^*

   Materials Today 2021, 51, 108-116

   Hexagonal boron nitride is usually considered chemically inert because of its wide bandgap and strong bonds, which makes it hard to use as a catalyst support. We introduce vacancies by cryomilling in liquid nitrogen and combine photoluminescence and electron spin resonance spectroscopy with density functional theory (DFT) to show that they create mid-gap states and localized radicals. The defective material spontaneously reduces metal cations into single atoms and clusters, which improve hydrogen evolution catalysis.

   DOI PDF Phys.org story Copy citation2D materialsCatalysis
2. 39

   Helical Covalent Polymers with Unidirectional Ion Channels as Single Lithium-Ion Conducting Electrolytes

   Y. Hu, N. Dunlap, H. Long, H. Chen, L. J. Wayment, M. Ortiz, Y. Jin, A. Nijamudheen, J. L. Mendoza-Cortes, S.-H. Lee, W. Zhang

   CCS Chemistry 2021, 3, 2762

   Solid polymer electrolytes that conduct only lithium ions could make batteries safer than flammable liquid electrolytes, but most suffer from low room-temperature conductivity. We report the first crystalline anionic helical polymer used as such an electrolyte, whose double helices bundle into one-directional, negatively charged channels for lithium transport. Without added salt it conducts 1.2 × 10⁻³ S cm⁻¹ at room temperature, and with an ionic liquid it enables reversible cycling of a solid-state cell.

   DOI PDF Copy citationEnergy storagePorous materialsPolymers
3. 38

   Multi-objective parametrization of interatomic potentials for large deformation pathways and fracture of two-dimensional materials

   X. Zhang, H. Nguyen, J. T. Paci, S. K. R. S. Sankaranarayanan, J. L. Mendoza-Cortes, H. D. Espinosa^*

   npj Computational Materials 2021, 7, 113

   Simulating how two-dimensional materials stretch and fracture depends on interatomic potentials, which are hard to parameterize for large deformations. We develop a framework that combines a multi-objective genetic algorithm with correlation and principal component analyses to select training properties and optimize parameters, testing Buckingham, Stillinger–Weber, Tersoff and modified REBO potentials on MoSe₂. The Tersoff potential performs best, and the approach guides parameterization for mechanical and phonon properties of many 2D and bulk materials.

   DOI PDF Copy citationInteratomic potentialsMachine learning and AI2D materials
4. 37

   Rapidly Reversible Organic Crystalline Switch for Conversion of Heat into Mechanical Energy

   M. Dharmarwardana^‡, S. Pakhira^‡, R. P. Welch, C. Caicedo-Narvaez, M. A. Luzuriaga, B. S. Arimilli, G. T. McCandless, B. Fahimi, J. L. Mendoza-Cortes^*, J. J. Gassensmith^*

   Journal of the American Chemical Society 2021, 143, 15, 5951

   Solids that abruptly expand or contract when heated could serve as actuators, but organic crystals with this behavior are rare and usually degrade or reverse slowly. We report an organic crystalline switch that, near ambient temperature, contracts to 90% of its length almost instantly when heated above 45 °C and re-expands on cooling. It stays stable for years, survives more than 200 cycles and enables a real-time thermal fuse, converting heat into mechanical work.

   DOI PDF Copy citationCrystals and polymorphismEnergy conversionMolecular machines
5. 36

   Nernstian Li+ intercalation into few-layer graphene and its use for the determination of K+ co-intercalation processes

   J. Hui, A. Nijamudheen, D. Sarbapalli, C. Xia, Z. Qu, J. L. Mendoza-Cortes^*, J. Rodriguez-Lopez^*

   Chemical Science 2021, 12, 559

   Lithium-ion batteries rely on ions slipping between carbon layers, yet whether this charge transfer follows the textbook Nernst equation, and how two different alkali ions insert together, had not been examined. Using few-layer graphene electrodes, we combine voltammetry, chronoamperometry, intermittent titration and density functional theory (DFT). Lithium intercalation follows Nernstian behavior, the response shifts with the potassium-to-lithium ratio, and calculations show that lithium and potassium can favorably co-intercalate within the same graphene layer.

   DOI PDF Copy citationEnergy storage2D materials

2020

1. 35

   Understanding Disorder in 2D Materials: The Case of Carbon Doping of Silicene

   R. Pablo-Pedro, M. A. Magana-Fuentes, M. Videa, J. Kong, M.-D. Li, J. L. Mendoza-Cortes^*, T. Van Voorhis^*

   Nano Letters 2020, 20, 9, 6336

   Silicene, the silicon analogue of graphene, is compatible with silicon electronics but lacks a natural band gap. Using first-principles calculations on finite and periodic structures, we study how carbon dopants create lattice disorder and local electron correlation in silicene. Changing where the dopants sit drives a Mott–Anderson transition and sets the band gap, while the doped structures remain ferromagnetic despite disorder, suggesting uses in silicon-based nanoelectronics such as field-effect transistors.

   DOI arXiv Supporting information Copy citation2D materialsQuantum materials
2. 34

   Impact of Surface Modification on the Lithium, Sodium, and Potassium Intercalation Efficiency and Capacity of Few-Layer Graphene Electrodes

   A. Nijamudheen, D. Sarbapalli, J. Hui, J. Rodriguez-Lopez^*, J. L. Mendoza-Cortes^*

   ACS Applied Materials & Interfaces 2020, 12, 17, 19393

   Graphite is the standard lithium-ion battery anode, but it cannot reversibly store sodium at ambient conditions, so better carbon anodes are needed for sodium batteries. Using first-principles calculations, we test three surface modifications of few-layer graphene: heteroatom doping of the top layer, a single-side fluorinated graphene overlayer and a Janus hydrofluorographene monolayer. With a suitable two-dimensional modifier, lithium, sodium and potassium intercalation becomes thermodynamically favorable, enabling reversible sodium binding and a large sodium storage capacity.

   DOI PDF Copy citationEnergy storage2D materials
3. 33

   Quantum Nature in the Interaction of Molecular Hydrogen with Porous Materials: Implications for Practical Hydrogen Storage

   S. Pakhira, J. L. Mendoza-Cortes^*

   The Journal of Physical Chemistry C 2020, 124, 11, 6454

   Storing hydrogen in porous materials under mild conditions could help replace petroleum fuels, yet the quantum nature of hydrogen binding in these materials is little studied. We use quantum calculations on 240 complexes that vary the transition metal, chelating ligand, spin state, oxidation state and geometry of porous-material building units. Dispersion and electrostatics dominate the interaction, and several complexes bind hydrogen at 10 kJ/mol or more, a key requirement for practical storage.

   DOI arXiv PDF Copy citationEnergy storagePorous materialsQuantum mechanics

2019

1. 32

   Raman and electrical transport properties of few-layered arsenic-doped black phosphorus

   N. R. Pradhan, C. Garcia, M. C. Lucking, S. Pakhira, J. Martinez, D. Rosenmann, R. Divan, A. V. Sumant, H. Terrones^*, J. L. Mendoza-Cortes^*, S. A. McGill, N. D. Zhigadlo, L. Balicas

   Nanoscale 2019, 11, 39, 18449–18463

   Black phosphorus is a layered semiconductor whose properties can be tuned by the number of layers, but its alloys remain little explored. Combining Raman spectroscopy, transport measurements on few-layer transistors, and density functional theory (DFT), the study examines black phosphorus with a quarter of its atoms replaced by arsenic. DFT explains the split Raman modes and the hole conduction, and the doped material keeps high mobility and strong anisotropy, promising for optoelectronics.

   DOI PDF Copy citation2D materials
2. 31

   Stabilizing polymer electrolytes in high-voltage lithium batteries

   S. Choudhury^‡, Z. Tu^‡, A. Nijamudheen^‡, M. J. Zachman, S. Stalin, Y. Deng, Q. Zhao, D. Vu, L. F. Kourkoutis, J. L. Mendoza-Cortes^*, L. A. Archer^*

   Nature Communications 2019, 10, 3091

   Ether-based liquid and polymer electrolytes are promising for high-energy lithium and sodium batteries, but they polymerize uncontrollably at the anode and break down at the high voltages of the most attractive cathodes. In a joint experimental and computational study, we show that cationic chain-transfer agents stop this runaway polymer growth, while cathode interphases made of preformed polymers protect the electrolyte. Together, these strategies extend ether electrolytes well beyond their accepted voltage limits.

   DOI PDF MagLab story Copy citationEnergy storagePolymers
3. 30

   Intercalation of First Row Transition Metals inside Covalent-Organic Frameworks (COFs): A Strategy to Fine Tune the Electronic Properties of Porous Crystalline Materials

   S. Pakhira, J. L. Mendoza-Cortes^*

   Physical Chemistry Chemical Physics 2019, 21, 17, 8785–8796

   Covalent-organic frameworks (COFs) are porous crystals whose structures are easy to tailor but whose electronic properties are hard to control, which limits their use in electronics. Using first-principles calculations, we design 31 new materials by intercalating each first-row transition metal, from scandium to zinc, into boroxine- and triazine-linked COFs. The band gap and density of states can be tuned by the choice and amount of metal, pointing toward porous electronic materials.

   DOI PDF Copy citationPorous materials2D materials
4. 29

   Online Measurement of Glucose Consumption from HepG2 Cells Using an Integrated Bioreactor and Enzymatic Assay

   A. G. Adams, R. K. M. Bulusu, N. Mukhitov, J. L. Mendoza-Cortes, M. G. Roper^*

   Analytical Chemistry 2019, 91, 8, 5184–5190

   Liver cells help regulate blood sugar in response to hormones such as insulin, but how the changing timing of insulin release affects liver metabolism is not well understood. The study builds a modular microfluidic system that couples a bioreactor of human liver-derived HepG2 cells to a droplet-based enzymatic assay that reads glucose levels by fluorescence. The device detects rapid insulin-induced changes in glucose consumption and could be extended to other liver metabolites.

   DOI PDF Copy citationBio-inspired and health
5. 28

   Synthesis and Characterization of Tris-chelate Complexes for Understanding f-Orbital Bonding in Later Actinides

   S. S. Galley, S. A. Pattenaude, C. A. Gaggioli, Y. Qiao, J. M. Sperling, M. Zeller, S. Pakhira, J. L. Mendoza-Cortes, E. J. Schelter, T. E. Albrecht-Schmitt, L. Gagliardi, S. C. Bart^*

   Journal of the American Chemical Society 2019, 141, 6, 2356–2366

   How much the f-orbitals of the later actinides take part in chemical bonding is still debated, partly because few well-defined molecular examples exist. The study prepares the first nonaqueous matching series of complexes spanning lanthanides and the later actinides americium, berkelium, and californium, combining crystallography and spectroscopy with multireference (CASSCF) and relativistic DFT calculations. The bonding is mostly ionic, and the combined computational approach offers a practical first route to hard-to-handle f-elements.

   DOI PDF Copy citationRelativistic quantum mechanicsNuclear-waste separation and recovery
6. 24

   S-Doped MoP Nanoporous Layer Toward High-Efficiency Hydrogen Evolution in pH-Universal Electrolyte

   K. Liang, S. Pakhira, Z. Yang, A. Nijamudheen, L. Ju, M. Wang, C. I. Aguirre-Velez, G. E. Sterbinsky, Y. Du, Z. Feng, J. L. Mendoza-Cortes^*, Y. Yang^*

   ACS Catalysis 2019, 9, 1, 651–659

   Producing hydrogen by splitting water requires efficient catalysts made from abundant elements instead of platinum. Combining experiments with density functional theory (DFT), the work makes a self-organized, sulfur-doped molybdenum phosphide nanoporous layer that serves directly as a binder-free hydrogen-evolution catalyst in acidic, neutral, and basic electrolytes. DFT shows that hydrogen forms more readily on this material than on molybdenum disulfide, indicating that sulfur doping boosts both activity and stability.

   DOI PDF Copy citationCatalysisEnergy conversion
7. P2

   Designing a path towards superconductivity through magnetic exchange in transition-metal intercalated bilayer graphene

   K. P. Lucht, A. D. Mahabir, A. Alcantara, A. V. Balatsky, J. L. Mendoza-Cortes^*, J. T. Haraldsen^*

   arXiv preprint 2019, arXiv:1903.10112

   Inserting alkali or alkaline-earth metals between carbon layers can induce superconductivity, which raises the question of whether transition metals could do the same in bilayer graphene. Using density functional theory (DFT), we compute the electronic structure, induced magnetic moments and exchange coupling for every first-row transition metal intercalated between two graphene layers. Carbon p-bands hybridize with metal d-bands below the Fermi level, suggesting a path to magnetically mediated superconductivity and to tunable magneto-electric Dirac materials.

   arXiv Copy citationQuantum materials2D materials

2018

1. 27

   Achieving Fast and Efficient K+ Intercalation on Ultrathin Graphene Electrodes Modified by a Li+ Based Solid-Electrolyte Interphase

   J. Hui^‡, N. B. Schorr^‡, S. Pakhira^‡, Z. Qu, J. L. Mendoza-Cortes^*, J. Rodríguez-López^*

   Journal of the American Chemical Society 2018, 140, 42, 13599–13603

   Potassium-ion batteries could offer a lower-cost alternative to lithium-ion technology, but potassium tends to plate on carbon electrodes rather than slipping between their layers. Using ultrathin few-layer graphene as a model electrode, experiments supported by theory show that first forming a solid-electrolyte interphase in a lithium-containing electrolyte enables fast, efficient potassium intercalation. The treated electrodes charge rapidly and cycle stably, a simple strategy toward practical potassium-ion batteries.

   DOI Copy citationEnergy storage2D materials
2. 26

   Apically Dominant Mechanism for Improving Catalytic Activities of N-Doped Carbon Nanotube Arrays in Rechargeable Zinc-Air Battery

   W. Niu^‡, S. Pakhira^‡, K. Marcus, Z. Li, J. L. Mendoza-Cortes^*, Y. Yang^*

   Advanced Energy Materials 2018, 8, 20, 1800480

   Rechargeable zinc-air batteries need low-cost, durable catalysts for oxygen reduction and oxygen evolution that can replace scarce platinum-group metals. Combining synthesis, electrochemical tests, and density functional theory (DFT), the work places cobalt-nickel nanoparticles at the tips of nitrogen-doped carbon nanotubes grown on nickel foam. This apically dominant design outperforms conventional nanotube arrays and precious-metal catalysts in zinc-air cells, and DFT traces the activity to sites near the embedded particles.

   DOI Copy citationEnergy storageCatalysis
3. 25

   Reaction Mechanism of the Selective Reduction of CO₂ to CO by a Tetraaza [Co(II)N₄H]²⁺ Complex in the Presence of Protons

   A. J. Garza, S. Pakhira, A. T. Bell, J. L. Mendoza-Cortes^*, M. Head-Gordon^*

   Physical Chemistry Chemical Physics 2018, 20, 37, 24058–24064

   Turning carbon dioxide into carbon monoxide is a key step toward recycling carbon, but many molecular catalysts waste electrons by making hydrogen instead. Using density functional theory (DFT), we identify the most likely mechanism by which a cobalt tetraaza complex selectively reduces CO₂ to CO. The catalyst's ligand preferences favor CO₂ over protons, a second CO₂ molecule helps break the C–O bond, and high barriers block formic acid, consistent with experiments.

   DOI arXiv Supporting information Copy citationCatalysisClean energyQuantum mechanics
4. 23

   Exploring Low Internal Reorganization Energies for Silicene Nanoclusters

   R. Pablo-Pedro, H. Lopez-Rios, J. L. Mendoza-Cortes, J. Kong, S. Fomine, T. Van Voorhis, M. S. Dresselhaus

   Physical Review Applied 2018, 9, 5, 054012

   Materials for efficient electronics need small reorganization energies, the energy cost of reshaping a structure when it gains or loses charge, because this favors charge separation and transport. Using density functional theory (DFT), the study predicts small reorganization energies for rectangular silicene nanoclusters with hydrogen-capped edges. Their large electron affinities and stable negative ions suggest they could serve as size-tunable n-type materials for electronics and spintronics.

   DOI arXiv Copy citation2D materialsQuantum mechanics
5. 22

   Framework vs. side-chain amphidynamic behaviour in oligo-(ethylene oxide) functionalised covalent-organic frameworks

   D. A. Vazquez-Molina, G. M. Pope, A. A. Ezazi, J. L. Mendoza-Cortes^*, J. K. Harper^*, F. J. Uribe-Romo^*

   Chemical Communications 2018, 54, 50, 6947–6950 RSC Emerging Investigators 2018

   Crystals that combine a rigid lattice with moving molecular parts, known as amphidynamic crystals, are hard to design because flexible groups can disrupt crystallization. The work builds a family of covalent-organic frameworks bearing flexible ethylene oxide side chains of different lengths and probes their motion with solid-state nuclear magnetic resonance (NMR) relaxation and computer simulations. The open frameworks still crystallize predictably, showing that complex organic crystals with designed internal motion can be made.

   DOI Copy citationCrystals and polymorphismPorous materialsMolecular machines
6. 21

   General Theory of Absorption in Porous Materials: The Restricted Multilayer Theory

   A. A. Aduenko, A. Murray, J. L. Mendoza-Cortes^*

   ACS Applied Materials & Interfaces 2018, 10, 15, 13244–13251

   Classic models of gas adsorption, the Langmuir and Brunauer–Emmett–Teller (BET) theories, make unphysical assumptions about how many layers of gas can stack inside the pores of crystalline materials. We derive a restricted multilayer theory that predicts gas uptake from only the pore geometry and the gas–framework interaction energy. Validated against experiments on seven metal-organic frameworks, it yields optimal binding strengths and a universal formula for the best linker length for hydrogen storage.

   DOI arXiv Supporting information Copy citationPorous materialsEnergy storage
7. 20

   Demystifying the Mechanism of Regio- and Isoselective Epoxide Polymerization Using the Vandenberg Catalyst

   R. C. Ferrier^‡, S. Pakhira^‡, S. E. Palmon, C. G. Rodriguez, D. E. Goldfeld, O. O. Iyiola, M. Chwatko, J. L. Mendoza-Cortes^*, N. A. Lynd^*

   Macromolecules 2018, 51, 5, 1777–1786

   For half a century the aluminum-based Vandenberg catalyst has made polyethers with a regular, isotactic structure, but the origin of its selectivity has remained unclear. Combining spectroscopy, kinetics, and density functional theory (DFT), the work identifies the active species as a rigid dialuminum complex bridged by oxygen atoms that grips the growing chain so that monomers of one configuration insert preferentially. This picture guides the design of new aluminum catalysts for stereoregular polyethers.

   DOI Copy citationPolymersCatalysis
8. 19

   Modulating Electrocatalysis on Graphene Heterostructures: Physically Impermeable Yet Electronically Transparent Electrodes

   J. Hui^‡, S. Pakhira^‡, R. Bhargava, Z. J. Barton, X. Zhou, A. J. Chinderle, J. L. Mendoza-Cortes^*, J. Rodríguez-López^*

   ACS Nano 2018, 12, 3, 2980–2990

   Graphene is only one atom thick yet blocks molecules, raising the question of whether a metal buried beneath it can still influence reactions on its outer surface. Combining electrochemical experiments with quantum mechanical calculations, the work builds graphene electrodes with metal underlayers and molecular catalyst adlayers to tune the oxygen reduction reaction. The buried metal shapes the activity through the graphene while staying protected, showing graphene to be physically impermeable yet electronically transparent.

   DOI Copy citationCatalysis2D materials
9. 18

   Dirac cone in two dimensional bilayer graphene by intercalation with V, Nb, and Ta transition metals

   S. Pakhira, K. P. Lucht, J. L. Mendoza-Cortes^*

   The Journal of Chemical Physics 2018, 148, 6, 064707

   Bilayer graphene is a semiconductor whose properties can be adjusted by doping or applied voltage, but recreating the Dirac cone that gives monolayer graphene its fast electrons is a challenge. Using dispersion-corrected density functional theory (DFT), we insert vanadium, niobium, and tantalum atoms between two graphene sheets. Symmetry, spin, and metal concentration emerge as key controls: a single vanadium atom yields a Dirac cone, while other arrangements give metallic, semimetallic, or semiconducting behavior.

   DOI arXiv PDF Copy citationQuantum materials2D materials
10. 17

    Tuning the Dirac Cone of Bilayer and Bulk Structure Graphene by Intercalating First Row Transition Metals Using First-Principles Calculations

    S. Pakhira, J. L. Mendoza-Cortes^*

    The Journal of Physical Chemistry C 2018, 122, 9, 4768–4782

    Inserting metal atoms between graphene sheets offers a way to tailor carbon materials for electronics. Using first-principles density functional theory (DFT), we design 20 new materials by intercalating each first-row transition metal, from scandium to zinc, into bilayer graphene and its bulk analogue. Mixing between carbon and metal orbitals sets the electronic states near the Fermi level, and the choice of metal shifts the Dirac point, giving tunable properties for future devices.

    DOI arXiv Supporting information Copy citationQuantum materials2D materials
11. P1

    Using a High-Throughput Screening Algorithm and relativistic Density Functional Theory to Find Chelating Agents for Separation of Radioactive Waste

    A. Gannon, S. Marxsen, K. Mueller, B. D. Quaife, J. L. Mendoza-Cortes^*

    arXiv preprint 2018, arXiv:1806.09733

    Radioactive waste from Cold War-era weapons production still contaminates sixteen sites in the United States, and cleanup requires separating actinides from complex mixtures. We combine relativistic density functional theory (DFT) with a high-throughput screening algorithm to design chelating ligands for thorium, protactinium and uranium. Covalent linkers joining two catecholamide ligands increase complex stability, non-covalent interactions between ligands improve selectivity, and several of the linkers identified could be used with other ligands.

    arXiv Copy citationNuclear-waste separation and recoveryRelativistic quantum mechanicsMaterials discovery

2017

1. 16

   Iron Intercalation in Covalent-Organic Frameworks: A Promising Approach for Semiconductors

   S. Pakhira, K. P. Lucht, J. L. Mendoza-Cortes^*

   The Journal of Physical Chemistry C 2017, 121, 39, 21160–21170

   Covalent-organic frameworks (COFs) are attractive platforms for functional materials, but they are usually electrical insulators. Using dispersion-corrected hybrid density functional theory (DFT), we design seven new boroxine- and triazine-linked COFs with iron atoms placed between their organic layers and study their structures and electronic properties. Iron intercalation fine-tunes the band structure and density of states, making these frameworks promising porous semiconductors.

   DOI arXiv Supporting information Copy citationPorous materials2D materials
2. 15

   Low-temperature Synthesis of Heterostructures of Transition Metal Dichalcogenide Alloys (W_xMo_1−xS₂) and Graphene with Superior Catalytic Performance for Hydrogen Evolution

   Y. Lei^‡, S. Pakhira^‡, K. Fujisawa, X. Wang, O. O. Iyiola, N. Perea-López, A. L. Elías, L. P. Rajukumar, C. Zhou, B. Kabius, N. Alem, M. Endo, R. Lv^*, J. L. Mendoza-Cortes^*, M. Terrones^*

   ACS Nano 2017, 11, 5, 5103–5112

   Splitting water to make hydrogen requires catalysts that can replace costly platinum. The work makes centimeter-scale films that alternate graphene with layers of tungsten–molybdenum disulfide alloys, using wet chemistry and low-temperature heating, and tests them for hydrogen evolution, with density functional theory (DFT) explaining the activity. The best alloy outperforms the pure sulfides because alloying lowers the energy barrier for hydrogen formation, giving a scalable, low-cost, platinum-free catalyst.

   DOI arXiv Penn State News FSU News Copy citationCatalysisEnergy conversion2D materials

2016

1. 14

   Design Principles for High H₂ Storage Using Chelation of Abundant Transition Metals in Covalent Organic Frameworks for 0–700 bar at 298 K

   Y. Pramudya, J. L. Mendoza-Cortes^*

   Journal of the American Chemical Society 2016, 138, 46, 15204–15213

   Storing hydrogen fuel by adsorbing it in porous materials is promising, but most materials bind hydrogen too weakly to reach volumetric storage targets at room temperature. Using quantum mechanical calculations, we study five linkers chelated with 11 transition metals, then design 30 new covalent-organic frameworks and estimate their hydrogen uptake with grand canonical Monte Carlo simulations. Frameworks based on abundant cobalt, nickel, and iron give high uptake and delivery from 0 to 700 bar.

   DOI Preprint (PDF) Supporting information MRS Bulletin highlight Materials Today Copy citationEnergy storagePorous materials

2015

1. 13

   Birnessite: A Layered Manganese Oxide To Capture Sunlight for Water-Splitting Catalysis

   K. P. Lucht, J. L. Mendoza-Cortes^*

   The Journal of Physical Chemistry C 2015, 119, 40, 22838–22846

   Birnessite, a natural layered manganese oxide, is an earth-abundant analogue of the water-oxidizing center of photosynthesis, but its electronic structure must be tuned to harvest visible light for water splitting. Using first-principles calculations, we model thirteen different metal ions inserted between its manganese oxide sheets. The guest ions narrow the band gap and shift the band edges, several compositions suit sunlight-driven water splitting, and isolating single layers further improves light absorption.

   DOI Preprint (PDF) Forbes CNBC FSU release (Phys.org) ScienceAlert Christian Science Monitor Copy citationEnergy conversionCatalysis2D materials
2. 12

   Visible Light Sensitized CO₂ Activation by the Tetraaza [Co^IIN₄H(MeCN)]²⁺ Complex Investigated by FT-IR Spectroscopy and DFT Calculations

   M. Zhang^‡, M. El-Roz^‡, H. Frei^*, J. L. Mendoza-Cortes^‡, M. Head-Gordon^*, D. C. Lacy, J. C. Peters^*

   The Journal of Physical Chemistry C 2015, 119, 9, 4645–4654

   Using sunlight to turn carbon dioxide into fuels requires understanding how molecular catalysts bind and activate CO₂. Combining infrared (FT-IR) spectroscopy under visible-light sensitization with density functional theory (DFT), the study follows a cobalt macrocycle catalyst through its one- and two-electron reduced states. Calculations show that the ligand itself takes up an electron in the doubly reduced state, which binds CO₂ strongly, and experiments close the catalytic cycle by detecting CO.

   DOI Copy citationClean energyCatalysisQuantum mechanics
3. 11

   Prediction of the crystal packing of di-tetrazine-tetroxide (DTTO) energetic material

   J. L. Mendoza-Cortes^‡, Q. An^‡, W. A. Goddard III^*, C. Ye, S. Zybin

   Journal of Computational Chemistry 2015, 37, 2, 163–167

   How molecules pack in a crystal sets the density, and with it the performance, of an energetic material. Earlier calculations had suggested that di-tetrazine-tetroxide (DTTO), not yet synthesized, could be unusually dense. We compare 20 possible isomers with density functional theory and, for the two most stable, search for the best crystal packings among the ten space groups most common for organic crystals, using force fields with Monte Carlo sampling followed by DFT optimization. The predicted crystals (space groups P2₁2₁2₁ and Pbca, 1.96 and 1.98 g/cm³) would be among the densest energetic materials, compared with 1.81 g/cm³ for RDX and 2.01 g/cm³ for CL-20, and the more stable polymorphs are denser and less planar.

   DOI PDF Copy citationCrystals and polymorphism
4. B1

   The oxygen-evolving complex of Photosystem II: insights from computation and synthetic models

   J. S. Kanady^‡, J. L. Mendoza-Cortes^‡, W. A. Goddard III, T. Agapie

   Metalloproteins: Theory, Calculations, and Experiments (CRC Press) 2015, 165–204

   Plants split water with a manganese–calcium cluster in Photosystem II, a reaction that artificial photosynthesis tries to copy. This book chapter reviews what quantum-mechanical calculations and synthetic model clusters reveal about the structure of the oxygen-evolving complex and how it forms the oxygen–oxygen bond.

   DOI Copy citationBio-inspired and healthEnergy conversion

2013

1. 10

   1,3-Sigmatropic fluorine migration to boron in McLafferty type of rearrangements: Observation of tetrafluorobenzyne radical cation and trifluorobenzyne cation by CID-mass spectrometry

   N. G. Nair^‡, J. L. Mendoza-Cortes^‡, R. Abrol, W. A. Goddard III^*, V. P. Reddy^*

   Journal of Organometallic Chemistry 2013, 747, 133–139

   Collision-induced dissociation (CID) mass spectrometry breaks ions into fragments, and understanding the rearrangements behind those fragments helps chemists interpret spectra and detect unusual reactive species. The study examines McLafferty-type rearrangements in which a fluorine atom migrates to boron through a 1,3-sigmatropic shift. These rearrangements lead to the observation of the tetrafluorobenzyne radical cation and the trifluorobenzyne cation, highly reactive fragments formed in the gas phase.

   DOI PDF Copy citationQuantum mechanics
2. 9

   Oxygen atom transfer and oxidative water incorporation in cuboidal Mn₃MO_n complexes based on synthetic, isotopic labeling, and computational studies

   J. S. Kanady^‡, J. L. Mendoza-Cortes^‡, E. Y. Tsui, R. J. Nielsen, W. A. Goddard III^*, T. Agapie^*

   Journal of the American Chemical Society 2013, 135, 3, 1073–1082 Models of Metalloenzymes virtual issue

   In photosynthesis, a manganese-calcium-oxygen cluster splits water, and how its bridging oxygen atoms react is central to how it works. Combining synthesis, isotopic labeling, and quantum mechanical calculations, the study examines cube-shaped manganese-oxygen model complexes that transfer oxygen atoms or take up oxygen from water. Oxygen transfer is controlled by how easily the surrounding ligands detach, and labeling shows oxygen atoms migrating within the cluster, supporting recent proposals for the natural catalyst's mechanism.

   DOI Copy citationBio-inspired and healthCatalysis

2012

1. 8

   A Covalent Organic Framework that Exceeds the DOE 2015 Volumetric Target for H₂ Uptake at 298 K

   J. L. Mendoza-Cortes, W. A. Goddard III^*, H. Furukawa, O. M. Yaghi

   The Journal of Physical Chemistry Letters 2012, 3, 18, 2671–2675

   Storing hydrogen in porous materials is attractive for vehicles, but most materials bind hydrogen too weakly to reach volumetric targets at room temperature. Using accurate quantum mechanical calculations, we evaluate hydrogen binding in 48 metal-containing versions of five common covalent-organic framework (COF) linkers. The new framework COF-301-PdCl₂ is predicted to store 60 grams of hydrogen per liter at 298 K and 100 bar, 1.5 times the 2015 Department of Energy target.

   DOI Supporting information Copy citationEnergy storagePorous materials
2. 7

   High H₂ Uptake in Li-, Na-, K-Metalated Covalent Organic Frameworks and Metal Organic Frameworks at 298 K

   J. L. Mendoza-Cortes, S. S. Han, W. A. Goddard III^*

   The Journal of Physical Chemistry A 2012, 116, 6, 1621–1631

   Highly porous frameworks store large amounts of hydrogen at 77 K, but room-temperature storage remains a challenge. Using grand canonical Monte Carlo simulations with a force field derived from accurate quantum mechanics, we compute hydrogen uptake at 298 K in leading covalent-organic and metal-organic frameworks and their lithium-, sodium-, and potassium-doped versions. Eleven compounds reach the 2010 Department of Energy weight target, showing that alkali-metal doping of simple, low-cost frameworks strongly boosts hydrogen storage.

   DOI Copy citationEnergy storagePorous materialsInteratomic potentials
3. T2

   Design of molecules and materials for applications in clean energy, catalysis and molecular machines through quantum mechanics, molecular dynamics and Monte Carlo simulations

   J. L. Mendoza-Cortes

   Ph.D. thesis, California Institute of Technology (advisor: W. A. Goddard III) 2012

   The doctoral thesis combines quantum mechanics, molecular dynamics and Monte Carlo simulations to design covalent and metal-organic frameworks for storing hydrogen and methane, models of the oxygen-evolving complex for water oxidation, and molecular machines.

   DOI PDF Copy citationInteratomic potentialsPorous materialsEnergy storageCatalysisPolymersMolecular machines

2011

1. 6

   Design of Covalent Organic Frameworks for Methane Storage

   J. L. Mendoza-Cortes, T. A. Pascal, W. A. Goddard III^*

   The Journal of Physical Chemistry A 2011, 115, 47, 13852–13857

   Methane-fueled vehicles need storage materials that deliver large amounts of gas at moderate pressures. Using grand canonical Monte Carlo simulations to compute methane delivery and molecular dynamics to test stability, we design 14 new covalent-organic frameworks (COFs). Two of them exceed the U.S. Department of Energy target at 35 bar, rivaling the best known materials and showing that frameworks made only of light elements can compete with metal-containing ones.

   DOI Copy citationEnergy storagePorous materialsInteratomic potentials
2. Topology in the solid-state sciences: rotaxanes, crystal engineering, topological insulators

   J. L. Mendoza-Cortes

   Lecture, Caltech 2011

   A lecture on how topology connects mechanically interlocked molecules, the design of crystals and topological insulators.

   PDF Copy citationQuantum materialsCrystals and polymorphismMolecular machines

2010

1. 5

   Adsorption Mechanism and Uptake of Methane in Covalent Organic Frameworks: Theory and Experiment

   J. L. Mendoza-Cortes, S. S. Han, H. Furukawa, O. M. Yaghi^*, W. A. Goddard III^*

   The Journal of Physical Chemistry A 2010, 114, 40, 10824–10833

   Storing natural gas (methane) on board vehicles requires porous materials that pack the gas densely at moderate pressures. We measure methane uptake in covalent-organic frameworks (COFs) and model it with grand canonical Monte Carlo simulations using force fields fitted to high-level quantum calculations, matching experiments within 2%. The simulations reveal multilayer adsorption coexisting with pore filling and identify COF-1 as exceeding the U.S. Department of Energy volumetric storage target.

   DOI Copy citationEnergy storagePorous materialsInteratomic potentials

2009

1. 4

   Recent advances on simulation and theory of hydrogen storage in metal-organic frameworks and covalent organic frameworks

   S. S. Han^‡, J. L. Mendoza-Cortes^‡, W. A. Goddard III^*

   Chemical Society Reviews 2009, 38, 5, 1460–1476

   Storing hydrogen in porous materials is a promising route to clean transportation fuel, and computer simulation helps explain and predict how much gas a material can hold. This review surveys how quantum calculations, grand canonical Monte Carlo, and molecular dynamics are applied to hydrogen storage in metal-organic and covalent-organic frameworks. It then discusses strategies to improve storage, including tuning pore size, open metal sites, alkali-metal doping, lighter metals, functionalized linkers, and hydrogen spillover.

   DOI Copy citationEnergy storagePorous materialsInteratomic potentials
2. 3

   Secondary building units, nets and bonding in the chemistry of metal-organic frameworks

   D. J. Tranchemontagne^‡, J. L. Mendoza-Cortes^‡, M. O'Keeffe, O. M. Yaghi^*

   Chemical Society Reviews 2009, 38, 5, 1257–1283 Top 10 most accessed, 2009

   Metal-organic frameworks (MOFs) are built by linking metal-containing clusters with organic molecules, and the shape of these clusters, called secondary building units (SBUs), determines which frameworks can form. This review describes the geometry, connectivity, and composition of 131 metal carboxylate SBUs collected from the Cambridge Structural Database. It also lists the many frameworks in which these units appear, providing a reference for designing and synthesizing new MOFs.

   DOI Secondary building units Copy citationPorous materials

2008

1. T1

   Ab initio based grand canonical Monte Carlo simulations of CH₄ uptake in covalent organic frameworks (COFs)

   J. L. Mendoza-Cortes

   B.Sc. thesis, Tecnológico de Monterrey, UCLA and Caltech 2008

   The undergraduate thesis develops a first-principles force field for methane and uses grand canonical Monte Carlo simulations to predict methane uptake in covalent organic frameworks.

   PDF Copy citationInteratomic potentialsPorous materialsEnergy storage
2. Secondary building units (SBU): 279 examples

   J. L. Mendoza-Cortes

   Compendium; published as part of Chemical Society Reviews 2009, 38, 1257 2008

   Drawings, connectivity and composition of 279 metal carboxylate clusters that serve as secondary building units of metal-organic frameworks, compiled for the 2009 review.

   PDF Copy citationPorous materials

2007

1. 2

   Designed synthesis of 3D covalent organic frameworks

   H. M. El-Kaderi^‡, J. R. Hunt^‡, J. L. Mendoza-Cortes^‡, A. P. Côté, R. E. Taylor, M. O'Keeffe, O. M. Yaghi^*

   Science 2007, 316, 5822, 268–272 AAAS Newcomb Cleveland Prize

   Covalent-organic frameworks (COFs) are porous crystals built from light elements, and extending them into three dimensions requires building blocks that connect into a targeted network. By targeting two network topologies built from triangular and tetrahedral nodes, the work synthesizes crystalline three-dimensional COFs held together entirely by strong covalent bonds. The frameworks are thermally stable to about 400–500 °C, with very high surface areas and an extremely low density.

   DOI PDF AAAS Newcomb Cleveland Prize Copy citationPorous materialsDynamic bonding

2005

1. 1

   A high-yield, one-step synthesis of o-phenylene ethynylene cyclic trimer via precipitation-driven alkyne metathesis

   W. Zhang, S. M. Brombosz, J. L. Mendoza, J. S. Moore^*

   The Journal of Organic Chemistry 2005, 70, 24, 10198–10201

   Rigid, ring-shaped molecules built from conjugated units are of interest in materials chemistry, but making them efficiently can be difficult. The work uses alkyne metathesis, a reversible reaction that reshuffles carbon–carbon triple bonds, with the product precipitating from solution, to make an ortho-phenylene ethynylene cyclic trimer in one step and 86% yield. This molecular triangle forms selectively without a template under thermodynamic control, and the same dynamic chemistry yields a new tetrameric ring.

   DOI PDF Supporting information Copy citationDynamic bonding