Research

The Stone Lab organizes its work into three collaborative teams: Team Mn (biogenic manganese oxides), Team Zn (zinc-binding inhibitors), and Team Biocat (enzyme biocatalysis and remediation). Each team combines undergraduate research with synthetic, computational, and biochemical approaches.

Team Mn — Biogenic Manganese Oxides

Team Mn studies biogenic manganese oxides (BMOs) produced by Pseudomonas putida MnB1. These materials are characterized structurally and compositionally and evaluated for water-oxidation catalysis and for the sequestration of rare-earth elements (La, Ce, Eu, Nd). Mixed-metal BMOs, including iron- and cerium-incorporated forms, are compared with abiotic birnessite to understand how biological templating influences reactivity and ion uptake.

Selected publications

• Characterization of Mixed Metal Biogenic Manganese Oxide Materials for Catalysis and Rare Earth Element Sequestration (2026)
• Characterizing Biogenic MnOx Produced by Pseudomonas putida MnB1 and Its Catalytic Activity towards Water Oxidation (2024)

Team Zn — Zinc-Binding Inhibitors

Team Zn develops machine-learning workflows to design and prioritize 8-hydroxyquinoline (8HQ) based inhibitors of zinc-dependent enzymes, particularly NDM-1 metallo-β-lactamases. A variational autoencoder generates novel 8HQ analogues in SMILES space; these candidates are then ranked with an XGBoost classifier trained on molecular fingerprints and descriptors. Complementary experimental and computational studies examine how 8HQ ligands coordinate to biomimetic zinc complexes and to HDAC8.

Selected publications

• Machine Learning Integrated Designing and Screening of 8-Hydroxyquinoline Based Metallo-β-Lactamase Inhibitors (2026)
• Experimental and Theoretical Investigation of the Coordination of 8-Hydroxyquinoline Inhibitors to Biomimetic Zinc Complexes and Histone Deacetylase 8 (HDAC8) (2024)

Team Biocat — Biocatalysis and Enzyme Remediation

Team Biocat investigates the catalytic mechanisms and engineering of heme enzymes, with a focus on chloroperoxidase from Caldariomyces fumago. Recent work distinguishes oxidative C–N bond cleavage from chlorination pathways in azo-dye decolorization, supporting enzyme-based remediation strategies. The team also develops enzyme–MOF biocatalysts by immobilizing multi-enzyme systems on zirconium-based frameworks for improved stability and recyclability.

Selected publications

• Mechanistic Distinction Between Oxidative and Chlorination Transformations of Chloroperoxidase from Caldariomyces fumago Demonstrated by Dye Decolorization (2025)
• Immobilization of a Bienzymatic System via Crosslinking to a Metal-Organic Framework (2022)
• Buffer Effects in Zirconium-Based UiO Metal−Organic Frameworks (MOFs) That Influence Enzyme Immobilization and Catalytic Activity in Enzyme/MOF Biocatalysts (2023)
• Co-immobilization of an Enzyme System on a Metal-Organic Framework to Produce a More Effective Biocatalyst (2020)
• Advances in Engineered Hemoproteins that Promote Biocatalysis (2016)

See the full Publications page for the complete list.