Independent Publications

Featured

Efficient Microwave-Enhanced Solid Phase Peptide Synthesis of Secretin Hormones Amenable for Rapid Library Design and Lead Optimization

B. A. Jassim, K. T. Faivre, S. T. Schneebeli, ChemRxiv(Preprint) 2026. DOI: https://doi.org/10.26434/chemrxiv.15003792/v1.

Backmapping of Highly Coarse-Grained Protein Models and Applications to Nanomedicine Designs

Y. Zhu, J. M. Remington, S. Song, B. Yang, B. P. Magee, S. T. Schneebeli, J. Li, J. Chem. Theory Comput. 2026, ASAP, 10.1021/acs.jctc.6c00631.

A General Route to Robust Sequence-Defined Molecular Cavities

K. T. Faivre, K. Xu, K. J. Colston, A. M. Sayed, J. C. Brincken, S. Amagain, L. M. Johnson, M. C. May, S. T. Schneebeli, ChemRxiv (Preprint) 2026. DOI: https://doi.org/10.26434/chemrxiv.15002709/v1.

Permeation Enhancer-Induced Membrane Defects Assist the Oral Absorption of Peptide Drugs

K. J. Colston, K. T. Faivre, S. T. Schneebeli, Nature Commun. 2025, 16, 9512;ChemRxiv (Preprint) 2025, DOI: 10.26434/chemrxiv-2025-n24f8.

A Generalizable Fluorescence Sensor Platform for Sample Preparation-Free Protein Detection

H. D. Wu, T. Trinh, T. Li, S. Thapa, R. B. Lee, T. T. Nguyen, C. F. Petrakian, M. Eisenstein, S. T. Schneebeli, J. Li, H. T. Soh. Adv. Materials 2025, Early View, DOI: 10.1002/adma.202419662.

Challenges and Opportunities in Computational Studies for Lipid Nanoparticle Development

Y. Oh, S. K. Bedingfield, S. T. Schneebeli, J. Li, A. M. Ardekani, K. J. Colston, S. P. Brown. npj Drug Discovery 2025, 2, 23.

Interplay of Hydrophobicity, Charge, and Sequence Length in Oligopeptide Coassembly

S. Thapa, A. Gahlawat, S. T. Schneebeli, J. Li. J. Phys. Chem. B 2025, 129, 4383–4391.

Structure-Based Modeling of Environment-dependent Protonation States Across LNP Formulations with Atomistic CpHMD

K. J. Colston, S. C. Monsalve, S. T. Schneebeli, Mol. Pharmaceutics2025, 22, 7347–7358, Cover Art; ChemRxiv (Preprint) 2025, DOI: 10.26434/chemrxiv-2025-psmd3.

Multiscale Simulations to Discover Self-Assembled Oligopeptides: A Benchmarking Study

S. Thapa, F. Clark, S. T. Schneebeli, J. Li. J. Chem. Theory Comput. 2024, 20, 375–384.

Kinetically Controlled Synthesis of Rotaxane Geometric Isomers

D. R. McCarthy, K. Xu, M. E. Schenkelberg, N. A. Balegamire, H. Liang, S. A. Bellino, J. Li, S. T. Schneebeli, Chem. Sci. 2024, 15, 4860–4870.

Nano-Bio Interactions between DNA Nanocages and Human Serum Albumin

D. R. McCarthy, J. M. Remington, J. B. Ferrel, S. T. Schneebeli, J. Li J. Chem. Theory Comput. 2023, 19, 7873–7881. Cover Art.

Structural and Functional Fine Mapping of Cysteines in Mammalian Glutaredoxin Reveal their Differential Oxidation Susceptibility

E. M. Corteselli, M. Sharafi, R. Hondal, M. MacPherson, S. White, Y.-W. Lam, C. Gold, A. M. Manuel, A. van der Vliet, S. T. Schneebeli, V. Anathy, J. Li, Y. M. W. Janssen-Heininger Nature Commun. 2023, 14, 4550.

Efficient Multigram Procedure for the Synthesis of Large Hydrazone-Linked Molecular Cages

O. Vestrheim, M. E. Schenkelberg, Q. Dai, S. T. Schneebeli Org. Chem. Front. 2023, 10, 3965-3974. Front Cover.

GPCRLigNet: Rapid screening for GPCR Active Ligands using Machine Learning

J. M. Remington, K. T. McKay, N. B. Beckage, J. B. Ferrell, S. T. Schneebeli, J. Li J. Comput. Aid. Mol. Design 2023, 37, 147–156.

Helical Molecular Springs with Varying Spring Constants

K. E. Murphy, K. T. McKay, M. Schenkelberg, M. Sharafi, O. Vestrheim, M. Ivancic, J. Li, S. T. Schneebeli Angew. Chem. Int. Ed. 2022, 61, e202209772. Cover Art.

Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery

K. T. McKay, N. B. Hamilton, J. R. Remington, S. T. Schneebeli, J. Li, Front. Mol. Biosci. 2022, 9, 879212

Concerted Rolling and Penetration of Peptides during Membrane Binding

J. M. Remington, J. B. Ferrell, S. T. Schneebeli, J. Li., J. Chem. Theory Comput., 2022, 18, 3921–3929

NMR-based Quality Assessment of Vermont Grown Saffron (Crocus Sativus L.) — Optimal Drying Conditions and Mechanistic Implications

A. Ghalehgolabbehbahani, O. Vestrheim, M. Skinner, J. Li, S. T. Schneebeli., ACS Food Sci Technol. 2022, 2, 315–320. Cover Art.

Outcome-Based Redesign of Physical Chemistry Laboratories During the COVID-19 Pandemic

N. B. Hamilton, J. M. Remington, S. T. Schneebeli, J. Li.J. Chem. Educ. 2022, 99, 2, 639–645

Molecular Basis for Environment Sensing by a Nucleoid-Structuring Bacterial Protein Filament

X. Zhao, J. Remington, S. T. Schneebeli, S. Arold, J. Li, J. Phys. Chem. Lett. 2021, 12, 32, 7878–7884

Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein

J. M. Remington, K. T. McKay, J. B. Ferrell, S. T. Schneebeli, J. Li, Biophys. J. 2021, 120, 2848-2858

Carbonyl-to-Alkyne Electron Donation Effects in up to 10-nm-Long, Unimolecular Oligo(p-phenylene ethynylenes)

S. C. Rajappan, O. Vestrheim, M. Sharafi, J. Li, S. T. Schneebeli, Org. Materials (Special Issue, Emerging Stars in Organic Materials) 2021, 3(2), 337-345

Iterative Exponential Growth of Oxygen-Linked Aromatic Polymers Driven by Nucleophilic Aromatic Substitution Reactions

. J. Jaynes, M. Sharafi, J. P. Campbell, J. Bocanegra, K. T. McKay, K. Little, R. O. Brown, D. L. Gray, T. J. Woods., J. Li, S. T. Schneebeli, Front. Chem (Special Issue, Rising Stars 2020) 2021

Chiral Auxiliaries for Stereoselective Electrophilic Aromatic Substitutions

M. Sharafi, J. P. Campbell, K. E. Murphy, R. O. Brown, S. T. Schneebeli, Synlett (Synpacts) 2021, 32, 229–234

Aggregation State of Synergistic Antimicrobial Peptides

J. M. Remington, C. Liao, M. Sharafi, E. J. Ste.Marie, J. B. Ferrell, R. J. Hondal, M. J. Wargo, S. T. Schneebeli, J. Li, J. Phys. Chem. Lett. 2020, 11, 9501–9506

Selective Monofunctionalization Enabled by Reaction History-Dependent Communication in Catalytic Rotaxanes

S. C. Rajappan, D. R. McCarthy, J. P. Campbell, J. B. Ferrell, M. Sharafi, O. Ambrozaite, J. Li, S. T. Schneebeli, Angew. Chem. Int. Ed. 2020, 59, 16668–16674

Size-Selective Catalytic Polymer Acylation with a Molecular Tetrahedron

M. Sharafi, K. T. McKay, M. Ivancic, D. R. McCarthy, N. Dudkina, K. E. Murphy, S. C. Rajappan, J. P. Campbell, Y. Shen, A. R. Badireddy, J. Li, S. T. Schneebeli, Chem (Cell Press) 2020, 6, 1469–1494

Machine Learning in a Molecular Modeling Course for Chemistry, Biochemistry, and Biophysics Student

J. M. Remington, J. B. Ferrell, M. Zorman, A. Petrucci, S. T. Schneebeli, J. Li, The Biophysicist 2020, 1, 11

Precise Molecular Shape Control of Linear and Branched Strips with Chirality-Assisted Synthesis

J. P. Campbell, M. Sharafi, K. E. Murphy, J. L. Bocanegra, S. T. Schneebeli, Supramol. Chem. 2019, 80, 565–574, Special Issue, Emerging Supramolecular Chemists in North America.

Chemical Exploration with Virtual Reality in Organic Teaching Laboratories

J. B. Ferrell, J. P. Campbell, D. R. McCarthy, K. T. McKay, M. Hensinger, R. Srinivasan, X. Zhao, A. Wurthmann, J. Li, S. T. Schneebeli, J. Chem. Educ. 2019, 96, 1961–1966

Featured

Controlled Self-Assembly Inside C-Shaped Polyaromatic Strips

M. Sharafi, Z. J. Weinert, I. M. Cohen, C. Liao, M. Ivancic, J. Li, and S. T. Schneebeli, Synlett 2016, 27, 2145–2149, Special Issue. Cluster Report on the 'Synthesis of Non-planar Polyaromatic Compounds'.

Anodic Methods for Covalent Attachment of Ethynylferrocenes to Electrode Surfaces: Comparison of Ethynyl Activation Processes

M. V. Sheridan, K. Lam, M. Sharafi, and S. T. Schneebeli, W. E. Geiger, Langmuir 2016, 32, 1645–1657.

Regulating Molecular Recognition with C-Shaped Strips Attained by Chirality-Assisted Synthesis

X. Liu, Z. J. Weinert, M. Sharafi, C. Liao, J. Li, and S. T. Schneebeli, Angew. Chem. Int. Ed. 2015, 54, 12772–12776.

Melittin Aggregation in Aqueous Solutions: Insight from Molecular Dynamics Simulations

C. Liao, M. E. Selvan, J. Zhao, J. L. Slimovitch, S. T. Schneebeli, M. Shelley, J. C. Shelley, and J. Li, J. Phys. Chem. B 2015, 119, 10390–10398.

Featured

Cooperative Reactivity in an Extended-Viologen-Based Cyclophane

E. J. Dale, D. P. Ferris, N. A. Vermeulen, J. J. Henkelis, I. Popovs, M. Juríček, J. C. Barnes, S. T. Schneebeli*, and J. F. Stoddart*, J. Am. Chem. Soc. 2016, 138, 3667–3670.

Ultrafast Photoinduced Symmetry-Breaking Charge Separation and Electron Sharing in Perylenediimide Molecular Triangles

Y. Wu, R. M. Young, M. Frasconi, S. T. Schneebeli, P. Spenst, D. M. Gardner, K. E. Brown, F. Würthner*, J. F. Stoddart*, and M. R. Wasielewski*, J. Am. Chem. Soc. 2015, 137, 13236–13239.

An Artificial Molecular Pump

C. Cheng, P. R. McGonigal, S. T. Schneebeli, H. Li, N. A. Vermeulen, C. Ke, and J. F. Stoddart*, Nature Nanotech. 2015, 10, 547–553.

Controlling Association Kinetics in the Formation of Donor–Acceptor Pseudorotaxanes

P. R. McGonigal, H. Li, C. Cheng, S. T. Schneebeli, M. Frasconi, L. S. Witus, and J. F. Stoddart*, Tetrahedron Lett. 2015, 56, 3591–3594.

Synthesis and Structural Data of Tetrabenzo[8]circulene

R. W. Miller, A. K. Duncan, S. T. Schneebeli, D. L. Gray, and A. C. Whalley*, Chem. Eur. J. 2014, 20, 3705–3711.

Assembly of Supramolecular Nanotubes from Molecular Triangles and 1,2-Dihalohydrocarbons

Z. Liu, G. Liu, Y. Wu, D. Cao, J. Sun, S. T. Schneebeli, M. S. Nassar, C. A. Mirkin, and J. F. Stoddart*, J. Am. Chem. Soc. 2014, 136, 16651–16660.

Functionalizing Pillar[n]arenes

N. L. Strutt, H. Zhang, S. T. Schneebeli, and J. F. Stoddart*, Acc. Chem. Res. 2014, 47, 2631–2642.

Electron Delocalization in a Rigid Cofacial Naphthalene-1,8:4,5-bis(dicarboximide) Dimer

Y. Wu, M. Frasconi, D. M. Gardner, P. R. McGonigal, S. T. Schneebeli, M. R. Wasielewski*, and J. F. Stoddart*, Angew. Chem. Int. Ed. 2014, 53, 9476–9481.

Amino-Functionalized Pillar[5]arene

N. L. Strutt, H. Zhang, S. T. Schneebeli, and J. F. Stoddart*, Chem. Eur. J. 2014, 20, 10996–11004.

A Square-Planar Tetracoordinate Oxygen-Containing Ti4O17 Cluster Stabilized by Two 1,1′-Ferrocenedicarboxylato Ligands

Z. Liu, J. Lei, M. Frasconi, X. Li, D. Cao, Z. Zhu, S. T. Schneebeli, G. C. Schatz, and J. F. Stoddart*, Angew. Chem. Int. Ed. 2014, 53, 9193–9197.

Redox Switchable Daisy Chain Rotaxanes Driven by Radical–Radical Interactions

C. J. Bruns, M. Frasconi, J. Iehl, K. J. Hartlieb, S. T. Schneebeli, C. Cheng, S. I. Stupp*, and J. F. Stoddart*, J. Am. Chem. Soc. 2014, 136, 4714–4723.

Second-Sphere Coordination Revisited

Z. Liu, S. T. Schneebeli, and J. F. Stoddart*, Chimia 2014, 68, 315–320.

Gated Electron Sharing Within Dynamic Naphthalene Diimide-Based Oligorotaxanes

A.-J. Avestro, D. M. Gardner, N. A. Vermeulen, E. A. Wilson, S. T. Schneebeli, A. C. Whalley, M. E. Belowich, R. Carmieli, M. R. Wasielewski*, and J. F. Stoddart*, Angew. Chem. Int. Ed. 2014, 53, 4442–4449.

An Electrochemically and Thermally Switchable Donor–Acceptor [c2]Daisy Chain Rotaxane

C. J. Bruns, J. Li, M. Frasconi, S. T. Schneebeli, J. Iehl, H.-P. Jacquot de Rouville, S. I. Stupp, G. A. Voth*, and J. F. Stoddart*, Angew. Chem. Int. Ed. 2014, 53, 1953–1958.

Topological isomerism in a chiral handcuff catenane

K. J. Hartlieb, A. K. Blackburn, S. T. Schneebeli, R. S. Forgan, A. A. Sarjeant, C. L. Stern, D. Cao, and J. F. Stoddart*, Chem. Sci. 2014, 5, 90–100.

The topological and chemical implications of introducing oriented rings to [3]catenanes

R. S. Forgan, A. K. Blackburn, M. M. Boyle, S. T. Schneebeli, and J. F. Stoddart*, Supramol. Chem. 2014, 26, 192–201.

Electron Sharing and Anion–π Recognition in Molecular Triangular Prisms†

S. T. Schneebeli, M. Frasconi, Z. Liu, Y. Wu, D. M. Gardner, N. L. Strutt, C. Cheng, R. Carmieli, M. R. Wasielewski, and J. F. Stoddart*, Angew. Chem. Int. Ed. 2013, 52, 13100–13104.

Stereochemical inversion in difunctionalised pillar[5]arenes

N. L. Strutt, S. T. Schneebeli, and J. F. Stoddart*, Supramol. Chem. 2013, 25, 596–608.

Asararenes—A Family of Large Aromatic Macrocycles

S. T. Schneebeli, C. Cheng, K. J. Hartlieb, N. L. Strutt, A. A. Sarjeant, C. L. Stern, and J. Fraser Stoddart*, Chem. Eur. J. 2013, 19, 3860–3868.

Probing the conductance superposition law in single-molecule circuits with parallel paths

H. Vazquez, R. Skouta, S. T. Schneebeli, M. Kamenetska, R. Breslow*, L. Venkataraman*, and M. S. Hybertsen*, Nature Nanotech. 2012, 7, 663–667.

The Chameleonic Nature of Diazaperopyrenium Recognition Processes†

A. N. Basuray, H.-P. Jacquot de Rouville, K. J. Hartlieb, T. Kikuchi, N. L. Strutt, C. J. Bruns, M. W. Ambrogio, A.-J. Avestro, S. T. Schneebeli, A. C. Fahrenbach, and J. F. Stoddart*, Angew. Chem. Int. Ed. 2012, 51, 11872–11877.

High-Contrast Photopatterning of Photoluminescence within Quantum Dot Films through Degradation of a Charge-Transfer Quencher

M. Tagliazucchi, V. A. Amin, S. T. Schneebeli, J. F. Stoddart, and E. A. Weiss*, Adv. Mater. 2012, 24, 3617–3621.

Polarized Raman Spectroscopy of Oligothiophene Crystals To Determine Unit Cell Orientation

J. C. Heckel, A. L. Weisman, S. T. Schneebeli, M. L. Hall, L. J. Sherry, S. M. Stranahan, K. H. DuBay, R. A. Friesner*, and K. A. Willets*, J. Phys. Chem. A 2012, 116, 6804–6816.

Structure–property relationships in molecular wires

R. Breslow* and S. T. Schneebeli, Tetrahedron 2011, 67, 10171–10178.

Highly Conducting π-Conjugated Molecular Junctions Covalently Bonded to Gold Electrodes

W. Chen, J. R. Widawsky, H. Vazquez, S. T. Schneebeli, M. S. Hybertsen*, R. Breslow*, and L. Venkataraman*, J. Am. Chem. Soc. 2011, 133, 17160–17163.

IDSite: An Accurate Approach to Predict P450-Mediated Drug Metabolism

J. Li, S. T. Schneebeli, J. Bylund, R. Farid, and R. A. Friesner*, J. Chem. Theory Comput. 2011, 7, 3829–3845.

In situ formation of highly conducting covalent Au–C contacts for single-molecule junctions

Z. Cheng, R. Skouta, H. Vazquez, J. R. Widawsky, S. T. Schneebeli, W. Chen, M. S. Hybertsen*, R. Breslow*, and L. Venkataraman*, Nature Nanotech. 2011, 6, 353–357.

Parameterization of a B3LYP Specific Correction for Noncovalent Interactions and Basis Set Superposition Error on a Gigantic Data Set of CCSD(T) Quality Noncovalent Interaction Energies

S. T. Schneebeli, A. D. Bochevarov, and R. A. Friesner*, J. Chem. Theory Comput. 2011, 7, 658–668.

Single-Molecule Conductance through Multiple π−π-Stacked Benzene Rings Determined with Direct Electrode-to-Benzene Ring Connections

S. T. Schneebeli, M. Kamenetska, Z. Cheng, R. Skouta, R. A. Friesner, L. Venkataraman*, and R. Breslow*, J. Am. Chem. Soc. 2011, 133, 2136–2139.

The Electrical Properties of Biphenylenes

S. T. Schneebeli, M. Kamenetska, F. Foss, H. Vazquez, R. Skouta, M. S. Hybertsen, L. Venkataraman, and R. Breslow, Org. Lett. 2010, 12, 4114–4117.

Featured

Quantitative DFT Modeling of the Enantiomeric Excess for Dioxirane-Catalyzed Epoxidations

S. T. Schneebeli, M. L. Hall, R. Breslow, and R. A. Friesner, J. Am. Chem. Soc. 2009, 131, 3965–3973.

Patents

Featured

October 26, 2021

Molecular Tetrahedron Nanocage, Its Preparation, and Uses Thereof

October 26, 2021

S. T. Schneebeli, J. Li, M. Sharafi. U.S. Provisional patent application filed on 6/2/2020. U.S. Provisional patent application serial number 63/337,764. PCT application filed on May 28, 2021.

October 26, 2021

Redox Active Triangular Organic Materials

October 26, 2021

J. F. Stoddart, S. T. Schneebeli, M. Frasconi, Z. Liu. U.S. Provisional patent application filed on 9/3/2014. U.S. Patent application filed on 9/3/2015. U.S. Patent number 20160130271.

October 26, 2021

Independent Publications

Postdoctoral and Graduate Publications

Patents

© 2023 — Severin T. Schneebeli, PhD

schneebeli@purdue.edu