Publications

Publications from ChemEd Group:

Xia, K.T.; Toste, F.D.; Francis, M.B.; Baranger, A.M. “Integrating Social Responsibility and Diversity, Equity, and Inclusion into the Graduate Chemistry Curriculum” Chemical Science Journal, 2025, advance article.

Coté, L. E.; Van Doren, S.; Zamora, A. N.; Jaramillo Salcido, J.; Law, E. W.; Otero Munoz, G.; Manocha, A.; Flood, C. L.; Baranger, A. M. “When I talk about it, my eyes light up!” Impacts of a national laboratory internship on community college student success” PLOS One, 2025, 20(1): e0317403. https://doi.org/10.1371/journal.pone.0317403.

Xia, K.T.; Bumann, S.; Yates, B.; Toste, F.D.; Francis, M.B.; Baranger, A.M. “Impacts of Value Alignment for Pursuing Graduate Chemistry Research” Journal of Chemical Education, 2024, 101, 5160–5172.

Armstrong, L.B.; Rivas, M.; Zhou, Z.; Douskey, M.C.; Baranger, A.M. “Behind the Scenes of Teaching Green: An Iterative Approach to Curriculum Design and Implementation in the General Chemistry Laboratory” Journal of Chemical Education 2024, 101, 3264-3275.

Armstrong, L.B.; Irie, L.; Chou, K.; Rivas, M.; Douskey, M.C.; Baranger, A.M. “What’s in a word? Student beliefs and understanding about green chemistry.” Chemistry Education Research and Practice 2024, 25, 115-132.

Blackford, K.A.; Greenbaum, J.C.; Redkar, N.S.; Gaillard, N.T.; Helix, M.R.; Baranger, A.M. “Metacognitive Regulation in Organic Chemistry Students: How and Why Students Use Metacognitive Strategies When Predicting Reactivity” Chemistry Education Research and Practice, 2023, 24, 828-851.

Clune, R.; Cohen, O.; Das, A.; Jasrasaria, D.; Rossomme, E.; Baranger, A.M. “Competence and confidence: addressing inequity among incoming chemistry graduate students through a week-long mathematics intervention.” Journal of Chemical Education 2023, 100, 3291–3301.

Reeves, A.G.; Bischoff, A.J.; Yates, B.; Brauer, D.D.; Baranger, A.M. “A Pilot Graduate Student-Led Near-Peer Mentorship Program for Transfer Students Provides a Supportive Network at an R1 Institution”. Journal of Chemical Education 2023, 100, 1, 134–142.

Porter, I.; Zuerch, M.; Baranger, A.M.; Leone, S. "Coherent Phonons in Antimony: an Undergraduate Physical Chemistry Solid-State Ultrafast Laser Spectroscopy Experiment."
Journal of Chemical Education, 2023, 100, 1, 342–349.

Helix, M.R.; Blackford, K.A.; Firestein, Z.M.; Greenbaum, J.C.; Gibson, K.; Baranger, A.M. “Characterization of Student Problem Solving and Development of a General Workflow for Predicting Organic Reactivity.” Chemistry Education Research and Practice, 2022, 23, 844-875.

Calvin, J. J.; Ondry, J.C.; Dahl, J.C., Sedlak, A.B.; McKeown-Green, A.; Wang, X; Crook, M.F. Gleason, S.P.; Hauwiller, M.R.; Baranger, A.M., and Alivisatos, A.P.“Research Group-Led Undergraduate Research Program: Analyzing and Improving a Versatile Springboard for First-Year Undergraduates.” Journal of Chemical Education 2022, 99, 799–809.

Blackford, K. A.; Calderon, A.A.; Gaillard, N.T.; Zera, A.;  Droege, D.; Pitch, S.G.; Binder, C.M.; Marsden, P.C.; Fredriksen, L.L.; Shusterman, A.A.; Douskey, M.C.; Baranger, A.M. “Design and Evaluation of the BeArS@home and Slugs@home Choose-Your-Own-Adventure-Style Online Laboratory Experiments.” Journal of Chemical Education 2022, 99, 2351–63.

Brauer, D.D.; Mizuno, H.; Stachl, C.N.; Gleason, J.M.; Bumann, S.; Yates, B.; Francis, M.B.; Baranger, A.M. "Mismatch in Perceptions of Success: Investigating Academic Values among Faculty and Doctoral Students" The Journal of Chemical Education, 2022, 99, 338-345  

Helix, M.; Coté, L.; Stachl, C.N.; Linn, M.; Stone, E.M.; Baranger, A.M. “Measuring integrated understanding of undergraduate chemistry research experiences: Assessing oral and written research artifacts” Chemical Education Research Practice, 2022, 23, 313-334.

Stachl, C.N.; Brauer, D.D.; Mizun, H.; Gleason, J.M.; Francis, M.B.; Baranger, A.M. “Improving the Academic Climate of an R1 STEM Department: Quantified Positive Shifts in Perception” ACS Omega, 2021, 6, 14410. 

Stachl, C.N.; Brauer, D.D.; Mizun, H.; Gleason, J.M.; Julie E. Rorre; Francis, M.B.; Baranger, A.M. “Shaping the future of higher education: Practical community-driven initiatives to improve academic climate” ACS Central Science, Invited editorial: 2021, 7, 910.

Bourne, S.M.; Limfat, S.; Dilip, S.; Han, S.; Robak, M.T.; Marsden, P.; Baranger, A.M. “The Undergraduate Teacher-Scholar Program: Comparing Near-Peer and Non Near-Peer Instructors in Laboratory Courses” Journal of College Science Teaching, 2021, 50, 10.  

Stachl, C.N.; Baranger, A.M. "Sense of Belonging within the Graduate Community of a Research-Focused STEM
Department: Quantitative Assessment Using a Visual Narrative and Item Response Theory" PLoS ONE, 2020, 15(5),e0233431.

Armstrong, L.B.; Rivas, M.C.; Zhou, Z; Irie, L.M.; Kerstiens, G.A.; MaryAnn T. Robak, M.T.; Douskey, M.C.; Baranger, A.M. “Developing a Green-Chemistry Focused General Chemistry Laboratory Curriculum: What Do Students Understand and Value About Green Chemistry?” Journal of Chemical Education, 2019, 96, 2410.

Hauwiller, M.R.; Ondry, J.C.; Calvin, J.J.; Baranger, A.M.; Alivisatos, A.P. "Translatable Research Group-Based Undergraduate Research Program for Lower-Division Students" Journal of Chemical Education, 2019, 969, 1881.

Armstrong, L.B.; Rivas, M.C.; Douskey, M.C.; Baranger, A.M. "Teaching students the complexity of green chemistry and assessing growth in attitudes and understanding" Current Opinion in Green and Sustainable Chemistry, 2018, 13, 61

Purcell, S. C.; Pande, P.; Lin,Y.; Rivera,E.J.; LatishaPawU, L.; Smallwood, L.M.; Kerstiens, G.A.; Armstrong, L.B.; Robak, M.T.; Baranger, A.M.; Douskey, M.C. “Extraction and Antibacterial Properties of Thyme Leaf Extracts: Authentic Practice of Green Chemistry” J. Chem. Ed. 2016, 93, 1422

Linn, M.L., Palmer, E., Baranger, A., Gerard, E., Stone, E. "Undergraduate research experiences: Impacts and opportunities" Science, 2015, 347, 627

Publications from work previous to Berkeley:

2010-2015

1. Ramisetty, R.R.; Baranger, A.M. “Cooperative Binding of a Quinoline Derivative to an RNA Stem Loop Containing a Dangling End”, Bioorg. Med. Chem. Lett. 2010 3134.

2. Benitex, Y.; Baranger, A.M. “Control of the Stability of a Protein-RNA Complex by the Position of Fluorine in a Base Analog”, J. Am. Chem. Soc. 2011, 133, 3687.

3. Kormos, B.L.; Pieniazek, S.N.; Beveridge, D.L.; Baranger, A.M. “U1A Protein – Stem Loop 2 RNA Recognition: Prediction of Structural Differences from Protein Mutations ”, Biopolymers, 2011, 95, 591.

4. Anunciado, D.; Dhar, A.; Gruebele, M;  Baranger, A.M. "Multistep Kinetics of the U1A-SL2 RNA Complex Dissociation", J. Mol. Biol. 2011, 408, 896.

5. Wong, C.-H.; Fu, Y.; Ramisetty, S.R.; Baranger, A.M.; Zimmerman, S.C. “Selective inhibition of MBNL1–CCUG interaction by small molecules toward potential therapeutic agents for myotonic dystrophy type 2 (DM2)”, Nucleic Acids Res. 2011, 39, 8881.

6. Warui, D.M.; Baranger, A.M. “Identification of Small Molecule Inhibitors of the HIV-1 Nucleocapsid-SL3 RNA Complex”, J. Med. Chem. 2012, 55, 4132.

7. Fu, Y.; Ramisetty, S.R.; Hussain, N.; Baranger, A.M. “MBNL1–RNA Recognition: Contributions of MBNL1 Sequence and RNA Conformation”, ChemBioChem 2012, 13, 112.

8. Wong, C.-H.; Richardson, S.L.; Ho, Y.-J.; Lucas, A.M.H.; Tuccinardi, T.; Baranger, A.M.; Zimmerman, S.C. “Investigating the Binding Mode of an Inhibitor of the MBNL1-RNA Complex in Myotonic Dystrophy Type 1 (DM1) Leads to the Unexpected Discovery of a DNA-Selective Binder”, ChemBioChem, 2012, 13, 2505.

9. Jahromi, A.H.; Nguyen, L.;  Fu, Y.; Miller, K.A., Anne M. Baranger, A.M.; Zimmerman, S.C. “A Novel CUGexp·MBNL1 Inhibitor with Therapeutic Potential for Myotonic Dystrophy Type 1”, ACS Chem. Biol., 2013, 8, 1037

10. Jahromi, A.H.; Fu, Y.; Nguyen, L.; Miller, K.; Baranger, A.M.; Zimmerman, S.C. “Developing Bivalent Ligands to Target CUG Triplet Repeats, the Causative Agent of Myotonic Dystrophy Type 1" J. Med. Chem. 2013, 56, 9471.

11. Wong, C.-H.; Nguyen, L.; Peh, J.; Luu, L.M.; Sanchez, J.S.; Richardson, S.L.; Tuccinardi, T.; Tsoi, H.; Chan, W.Y.; Chan, H.Y.E.; Baranger, A.M.; Hergenrother, P.J.; Zimmerman, S.C.  “Targeting Toxic RNAs that Cause Myotonic Dystrophy Type 1 (DM1) with a Bisamidinium Inhibitor”, J. Am. Chem. Soc. 2014, 136, 6355.

12. Guzman, I.; Ghaemi, Z.; Baranger, A.; Luthey-Schulten, Z.; Gruebele, M. “Native Conformational Dynamics of the Spliceosomal U1A Protein” J. Phys. Chem. B 2015, 119, 3651.

13. Linn, M.C.; Palmer, E.; Baranger, A.; Gerard, E.; Stone, E. “Undergraduate Research Experiences: Impacts and Opportunities” Science 2015, 347, 627.

2000-2010

1. Luchansky, S.; Nolan, S.J.; Baranger, A.M. “Contribution of RNA Conformation to the Stability of a High-Affinity RNA-Protein Complex”, J. Am. Chem. Soc. 2000, 122, 7130.

2. Blakaj, D.M.; McConnell, K.J.; Beveridge, D.L.; Baranger, A.M. "Molecular Dynamics and Thermodynamics of a Protein-RNA Complex: Mutation of a Conserved Aromatic Residue Modifies Stacking Interactions and Structural Adaptation in the U1A-stem Loop 2 RNA Complex", J. Am. Chem. Soc. 2001, 123, 2548.

3. Shiels, J.C.; Jerkovic, B.; Baranger, A.M.; Bolton, P.H. “RNA-DNA Hybrids Containing Damaged DNA are Substrates for RNase H”, Bioorg. Med. Chem. Lett. 2001, 11, 2623.

4. Shiels, J.C.; Tuite, J.B.; Nolan, S.J.; Baranger, A.M. "Investigation of a Conserved Stacking Interaction in Target Site Recognition by the U1A Protein", Nucleic Acids Res. 2002, 30, 550.

5. Pitici, F.; Baranger, A.M., Beveridge, D.L. “Molecular Dynamics Simulation Studies of Induced Fit and Conformational Capture in U1A-RNA Binding: Do Molecular Substates Code for Specificity?”, Biopolymers 2002, 65, 424.

6. Gayle, A.Y.; Baranger, A.M. “Inhibition of the U1A-RNA Complex by an Aminoacridine Derivative”, Bioorg. Med. Chem. Lett. 2002, 12, 2839.

7. Tuite, J.B.; Shiels, J.C.; Baranger, A.M. “Substitution of an Essential Adenine in the U1A-RNA Complex with a Non-polar Isostere”, Nucleic Acids Res. 2002, 30, 5269, cover article.

8. Zhao, Y.; Baranger, A.M. “Design of an Adenosine Analog that Selectively Improves the Affinity of a Mutant U1A Protein for RNA”, J. Am. Chem. Soc. 2003, 125, 2480.

9. Yan, Z.; Baranger, A.M. “Binding of an Aminoacridine Derivative to a Tetraloop RNA”, Bioorg. Med. Chem. Lett. 2004, 14, 5889.

10. Zhao, Y.; Kormos, B.L.; Beveridge, D.L.; Baranger, A.M. “Molecular Dynamics Simulation Studies of a Protein-RNA Complex with a Selectively Modified Binding Interface”, Biopolymers 2006, 81, 256.

11. Kormos, B.L; Baranger, A.M.; Beveridge, D.L. “Do Collective Atomic fluctuations Account for Cooperative Effects? Molecular Dynamics Studies of the U1A-RNA Complex”, J. Am. Chem. Soc. 2006, 128, 8992.

12. Beveridge, D.L.; Dixit, S.B.; Kormos, B.L.; Baranger, A.M.; Jayaram, B.. "Molecular Dynamics Simulations and Free Energy Calculations on Protein-Nucleic Acid Complexes." In Computational Studies of DNA and RNA. Eds., J. Sponer and F. Lankas. Springer: New York. 2006.

13. Kormos, B.L; Baranger, A.M.; Beveridge, D.L. “A Study of Collective Atomic Fluctuations and Cooperativity in a U1A-RNA Complex Based on Molecular Dynamics Simulations”, J. Struct. Biol. 2007, 157, 500.

14. Kormos, B.L.; Benitex, Y.; Baranger, A.M.; Beveridge, D.L. “Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model”, J. Mol. Biol. 2007, 371, 1405.

15. Yan, Z.; Sikri, S.: Beveridge, D.L.; Baranger, A.M. “Identification of an Aminoacridine Derivative that Binds to RNA Tetraloops”, J. Med. Chem.2007, 50, 4096

16. Yan, Z.; Ramisetty, S.R.; Bolton, P.H.; Baranger, A.M. “Selective Recognition of RNA Helices Containing Dangling Ends by a Quinoline Derivative”, ChemBioChem 2007, 8, 1658.

17. Benitex, Y.; Baranger, A.M., “Recognition of Essential Purines by the U1A Protein”, BMC Biochemistry 2007, 8, 22.

18. Anunciado, D.; Agumeh, M.; Kormos, B.L.; Beveridge, D.L.; Knee, J.L.; Baranger, A.M. “Characterization of the Dynamics of an Essential Helix in the U1A Protein By Time-Resolved Fluorescence Measurements”, J. Phys. Chem. B., 2008, 112, 6122.

19. Zhao, Y.; Knee, J.L.; Baranger, A.M. “Characterization of Two Adenosine Analogs as Fluorescence Probes in RNA” Bioorg. Chem., 2008, 36, 271.

20. Ong, H.C.; Arambula, J.F.; Ramisetty, S.R., Baranger, A.M.; Zimmerman, S.C. “Molecular Recognition of a Thymine Bulge by a High Affinity, Deazaguanine-based (DAD) Hydrogen Bonding Ligand”, Chem. Comm. 2009, 668.

21. Warui, D.M.; Baranger, A.M. “Using Computational Docking to Identify Specific Small Molecule Ligands That Bind SL3 RNA of the y-Recognition Element of HIV-1”, J. Med. Chem., 2009, 52, 5462.

22. Arambula, J.F.; Ramisetty, R.R.; Baranger, A.M.; Zimmerman, S.C. “A Simple Ligand that Selectively Targets CUG Trinucleotide Repeats and Inhibits MBNL Protein Binding”, Proc. Natl. Acad. Sci., 2009, 106, 16068.

1988-2000

1. Becker, M.; Lesser, D.; Kurpiewski, M.; Baranger, A.; Jen-Jacobson, L. "'Ultraviolet Footprinting' Accurately Maps Sequence-Specific Contacts and DNA Kinking in the EcoRI Endonuclease DNA Complex", Proc. Natl. Acad. Sci. 1988, 85, 6247.

2.    Walsh, P.J.; Baranger, A.M.; Bergman, R.G. "Stoichiometric and Catalytic Hydroamination of Alkynes and Allene by Zirconium Bisamides Cp2Zr(NHR)2", J. Am. Chem. Soc. 1992, 114, 1708.

3.    Baranger, A.M.; Walsh, P.J.; Bergman, R.G. "Variable Regiochemistry in the Stoichiometric and Catalytic Hydroamination of Alkynes by Imidozirconium Complexes Caused by an Unusual Dependence of Rate Law on Alkyne Structure and Temperature", J. Am. Chem. Soc. 1993, 115, 2753.

4.    Baranger, A.M.; Hollander, F.J.; Bergman, R.G. "Synthesis of an Early-Late Heterobimetallic Imido Complex: Cooperative Reactivity with N-H, O-H, and S-H Bonds and Formation of a Novel Aminophosphine Complex", J. Am. Chem. Soc. 1993, 115, 7890.

5.    Baranger, A.M.; Bergman, R.G. "Cooperative Reactivity in the Interactions of X-H Bonds with a Zirconium-Iridium Bridging Imido Complex", J. Am. Chem. Soc. 1994, 116, 3822.

6.    Hanna, T.A.; Baranger, A.M.; Walsh, P.J.; Bergman, R.G. "Formation of a,b-Unsaturated Imines and Successful Trapping of an Oxozirconocene in a [4+2] Azaoxametallacyclohexene Retrocycloaddition", J. Am. Chem. Soc. 1995, 117, 3292.

7.    Baranger, A.M.; Palmer, C.R.; Hamm, M.K.; Giebler, H.A.; Brauweiler, A.; Nyborg, J.K.; Schepartz, A. "Mechanism of DNA Binding Enhancement by the Human T-Cell Leukaemia Virus Transactivator Tax", Nature 1995, 376, 606.

8.    Baranger, A.M.; Hanna, T.A.; Bergman, R.G. "Transfer of Oxygen and Sulfur from Organic Molecules to a Zr-Ir Bond. Evidence for an Unusually Rapid Atom Abstraction Reaction", J. Am. Chem. Soc. 1995, 117, 10041.

9.    Hanna, T.A.; Baranger, A.M.; Bergman, R.G. "Reaction of Carbon Dioxide and Heterocumulenes with an Unsymmetrical Metal-Metal Bond. Direct Addition of CO2 across a Zr-Ir Bond and Stoichiometric Reduction of CO2 to Formate", J. Am. Chem. Soc. 1995, 117, 11363.

10. Hanna, T.A.; Baranger, A.M.; Bergman, R.G. "Addition of Organic 1,3-Dipolar Compounds across an Early-Late Heterobinuclear (Zr-Ir) Bond. Mechanism of Nitrogen Loss from an Organoazido Complex", Angew. Chem. 1996, 35, 653.

11. Hanna, T.A.; Baranger, A.M.; Bergman, R.G. "Reactivity of Zirconocene Azametallacyclobutenes: Insertion of Aldehydes, Carbon Monoxide, and Formation of a,b-Unsaturated Imines. Formation and Trapping of [Cp2Zr=O] in a [4+2] Retrocycloaddition", J. Org. Chem. 1996, 61, 4532.

12. Baranger, A.M. “Accessory Factor-bZIP-DNA Interactions”, Curr. Opin. Chem. Biol. 1998, 2, 18.

13. Nolan, S.J.; Shiels, J.C.; Tuite, J.B.; Cecere, K.L.; Baranger, A.M. “Recognition of an Essential Adenine at a Protein-RNA Interface: Comparison of the Contributions of Hydrogen Bonds and a Stacking Interaction”, J. Am. Chem. Soc. 1999, 121, 8951