Publications

Selected publications from the Stone Lab and collaborators, listed in reverse chronological order.

Full lists: Google Scholar · ORCID 0000-0001-5942-2716

2026

Characterization of Mixed Metal Biogenic Manganese Oxide Materials for Catalysis and Rare Earth Element Sequestration

Elisa Morales, Jeremy Brown, Chloe Runge, Madeline York, Genesis Dennis, Cole Johnson, Anthony Baudino, Norman Paz-Ramírez, Lily Samson, John Rey A. Romal, Kari L. Stone, and Sarah E. Shaner

This work explores biogenic manganese oxides produced by Pseudomonas putida MnB1 for metal cation uptake and rare-earth sequestration. Mixed-metal BMOs were characterized and tested as water-oxidation catalysts, with iron-incorporated materials showing enhanced activity.

Machine Learning Integrated Designing and Screening of 8-Hydroxyquinoline Based Metallo-β-Lactamase Inhibitors

Anthony M. Baudino and Kari L. Stone

A variational autoencoder and XGBoost workflow were used to generate and prioritize 8-hydroxyquinoline-based inhibitors of NDM-1. The approach enriches for zinc-binding compounds likely to perform well in docking while reducing the chemical search space.

Design2Data Faculty Handbook: Networked CURE Implementation Strategies in Undergraduate Chemistry Courses

Anthony M. Baudino, Linda Brzezinski, Sunshine C. Silver, Kari L. Stone, and Ashley Vater

An instructor-facing guide for embedding the Design2Data networked CURE into chemistry and biochemistry laboratories. Worked examples span community-college and four-year institutions and emphasize curriculum-first alignment with enzyme-function data generation.

Developing a Multi-Institutional CURE in Inorganic Chemistry

Madalyn R. Radlauer, Kyle A. Grice, Bryan P. Nell, David A. Quist, and Kari L. Stone

Describes the formation and goals of a multi-institutional inorganic chemistry CURE supported by the IONiC network. The chapter shares implementation experiences, student and faculty outcomes, and an invitation for further collaboration.

2025

Mechanistic Distinction Between Oxidative and Chlorination Transformations of Chloroperoxidase from Caldariomyces fumago Demonstrated by Dye Decolorization

Norman Paz-Ramírez, Jacob Redwinski, Matthew A. Cranswick, Kyle A. Grice, and Kari L. Stone

Chloroperoxidase decolorizes azo dyes preferentially through oxidative C–N bond cleavage rather than chlorination. LC/MS and DFT analyses clarify the dominant pathway and support enzyme-based dye remediation strategies.

2024

Engaging chemistry educators through virtual roundtables: how the COVID-19 pandemic led to a community-wide initiative

M. Taylor Haynes, Justin M. Pratt, Matthew A. Cranswick, Kyle A. Grice, Chip Nataro, Sarah E. Shaner, Kari L. Stone, Meghan Porter, and Jeffrey R. Raker

Reports the development of SLiThEr virtual professional-development roundtables within the IONiC community. The events grew from pandemic needs into a sustained model for interactive teaching support and community building.

Experimental and Theoretical Investigation of the Coordination of 8-Hydroxyquinoline Inhibitors to Biomimetic Zinc Complexes and Histone Deacetylase 8 (HDAC8)

Anthony M. Baudino, Harris F. Ciaccio, Michael J. Turski, Xavier A. Akins, Phoebus Sun Cao, Elisa Morales, Roger D. Sommer, Adam R. Johnson, Donald J. Wink, Kyle A. Grice, and Kari L. Stone

Combines experiment, DFT, crystallography, and docking to examine 8-hydroxyquinoline coordination to model zinc complexes and HDAC8. Results highlight the importance of noncovalent interactions beyond simple zinc-binding models.

Characterizing Biogenic MnOx Produced by Pseudomonas putida MnB1 and Its Catalytic Activity towards Water Oxidation

Elisa Morales, Lauren N. Formanski, Sarah E. Shaner, and Kari L. Stone

Characterizes biogenic manganese oxides formed by MnB1 and evaluates their water-oxidation activity relative to abiotic acid birnessite. Whole-cell and isolated BMO materials show promising catalytic performance.

2023

Buffer Effects in Zirconium-Based UiO Metal−Organic Frameworks (MOFs) That Influence Enzyme Immobilization and Catalytic Activity in Enzyme/MOF Biocatalysts

Raneem Ahmad, Sydnie Rinaldo, Mahnaz Gohari, Jordan Shanahan, Sarah E. Shaner, Kari L. Stone, and Daniel S. Kissel

Demonstrates that phosphate buffers can inhibit enzyme immobilization and activity on UiO MOFs compared with non-coordinating buffers. Characterization reveals differences in loading, surface properties, and catalytic performance.

Determination of Stretching Frequencies by Isotopic Substitution Using Infrared Spectroscopy: An Upper-Level Undergraduate Experiment for an In-Person or Online Laboratory

Sarah E. Shaner and Kari L. Stone

Describes an FTIR laboratory experiment in which students examine protio- and deuterated solvents and apply the harmonic-oscillator model. Computational visualizations reinforce the relationship between reduced mass and vibrational frequency.

2022

Immobilization of a Bienzymatic System via Crosslinking to a Metal-Organic Framework

Raneem Ahmad, Sydnie Rinaldo, Sarah E. Shaner, Daniel S. Kissel, and Kari L. Stone

Reports covalent crosslinking of glucose oxidase and chloroperoxidase to UiO-66-NH₂ using DSG and EDC/NHS. Crosslinked composites show improved activity and recyclability relative to free enzymes.

2020

Co-immobilization of an Enzyme System on a Metal-Organic Framework to Produce a More Effective Biocatalyst

Raneem Ahmad, Jordan Shanahan, Sydnie Rinaldo, Daniel S. Kissel, and Kari L. Stone

Co-immobilizes glucose oxidase and horseradish peroxidase on UiO-66 and UiO-66-NH₂. The amine-functionalized MOF yields higher loading, lower leaching, and greater activity for pyrogallol oxidation.

A Learning Community Involving Collaborative Course-Based Research Experiences for Foundational Chemistry Laboratories

David M. Rubush and Kari L. Stone

Integrates a multi-course learning community with CURE-style laboratory experiences. Students show gains in scientific communication, collaboration, and other essential CURE elements.

Forming a Community of Practice to Support Faculty in Implementing Course-Based Undergraduate Research Experiences

Kari L. Stone, Daniel S. Kissel, Sarah E. Shaner, Kyle A. Grice, and Mary T. van Opstal

Describes formation of a multi-institution Community of Practice to lower barriers for CURE implementation in foundational chemistry laboratories. Emphasizes equitable access and faculty support across PUI, community-college, and high-school settings.

2018

Improving the Success of First Term General Chemistry Students at a Liberal Arts Institution

Kari L. Stone, Sarah E. Shaner, and Carol M. Fendrick

Reports interventions, including a preparatory course and learning-assistant support, that raised pass rates in high-enrollment general chemistry. Focuses on retention of first-year and underrepresented STEM students.

2016

Advances in Engineered Hemoproteins that Promote Biocatalysis

Kari L. Stone and Syeda M. Ahmed

Reviews the use of heme-substituted proteins as scaffolds for non-native cofactors and artificial metalloenzymes. Highlights progress in expanding catalytic reactivity beyond native hemoprotein function.

2015

Manganese-Substituted Myoglobin: Characterization and Reactivity of an Oxidizing Intermediate towards a Weak C-H Bond

Kari L. Stone, Joey Hua, and Humdoon Choudhry

Characterizes a manganese-substituted myoglobin intermediate that performs hydrogen-atom abstraction from weak C–H bonds. Demonstrates oxidative reactivity not observed in native iron myoglobin.

2014

Preparation and properties of an Mn^IV–hydroxide complex: proton and electron transfer at a mononuclear manganese site and its relationship to the oxygen evolving complex within photosystem II

Taketo Taguchi, Kari L. Stone, Rupal Gupta, Benedikt Kaiser-Lassalle, Junko Yano, Michael P. Hendrich, and A. S. Borovik

Reports a mononuclear Mn^IV–OH complex that completes a redox series relevant to the oxygen-evolving complex. Thermodynamic analysis supports stepwise proton-transfer/electron-transfer pathways to high-valent Mn-oxo species.

2013

Thermodynamic Rationale for the Photosynthetic Mn₄Ca Cluster

Andrew Borovik, Kari Stone, Taketo Taguchi, and Trenton Parsell

Provides a thermodynamic framework linking the structure of the photosynthetic Mn₄Ca cluster to its ability to manage high-valent intermediates during water oxidation.

2010

Formation, Structure, and EPR Detection of a High Spin Fe^IV-Oxo Species Derived from Either an Fe^III-Oxo or Fe^II-OH Complex

David C. Lacy, Rupal Gupta, Kari L. Stone, John Greaves, Joseph W. Ziller, Michael P. Hendrich, and A. S. Borovik

Describes a high-spin Fe^IV–oxo complex prepared from both Fe^III–oxo and Fe^III–OH precursors. Parallel-mode EPR and crystallography provide rare structural and spectroscopic characterization of this intermediate.

2009

Lessons from Nature: Unraveling Biological C—H Bond Activation

Kari L. Stone and A. S. Borovik

Reviews how metalloenzymes control highly reactive intermediates for selective C–H bond cleavage. Emphasizes the interplay of redox potential, pKa, and hydrogen-bonding networks in active-site design.

2006

Resonance Raman spectroscopy of chloroperoxidase compound II provides direct evidence for the existence of an iron(IV)–hydroxide

Kari L. Stone, Rachel K. Behan, and Michael T. Green

Reports isotope-sensitive resonance Raman data confirming an Fe^IV–OH unit in chloroperoxidase compound II. The result supports the presence of a protonated ferryl in thiolate-ligated heme enzymes.

2005

Evidence for Two Ferryl Species in Chloroperoxidase Compound II

Kari L. Stone, Lee M. Hoffart, Rachel K. Behan, Carsten Krebs, and Michael T. Green

Mössbauer and DFT studies identify two distinct ferryl species in chloroperoxidase compound II, assigned as Fe^IV–OH and Fe^IV–oxo. The ratio is pH-invariant over the enzyme’s stability range.

X-ray absorption spectroscopy of chloroperoxidase compound I: Insight into the reactive intermediate of P450 chemistry

Kari L. Stone, Rachel K. Behan, and Michael T. Green

Provides the first structural characterization of a thiolate-ligated ferryl radical (chloroperoxidase compound I) by X-ray absorption spectroscopy. Reports an Fe–O distance of 1.65 Å and an unusually long Fe–S bond.