Selected Publications

Hinz, D. J.; Krajewski, A. E.; Lee, J. K. “Carbon−Fluorine Activation in the Gas Phase: The Reactions of Benzyl C−F Bonds and Silyl Cations,” J. Org. Chem., 2024, 89, 13595−13600.

Zhang, L.; Kiruba, G. S. M.; Lee, J. K. “Gas Phase Studies of Hypoxanthine-Guanine-(Xanthine) Phosphoribosyltransferase (HG(X)PRT) Substrates,” J. Org. Chem., 2023, 88, 6816-6826.

Krajewski, A. E.; Lee, J. K.  “Nucleophilicity and Electrophilicity in the Gas Phase: Silane Hydricity,” J. Org. Chem., special issue, “Solvation Effects in Organic Chemistry,”  2022, 87, 1840-1849.

Zhang, L.; Hinz, D. J.; Kiruba, G. S. M.; Ding, X.; Lee, J. K.  “Gas-Phase Experimental and Computational Studies of Human Hypoxanthine-Guanine Phosphoribosyltransferase Substrates: Intrinsic Properties and Biological Implications,” J. Phys. Org, special issue honoring Barry Carpenter, 2022, e4343.

Hinz, D. J.; Zhang, L.; Lee, J. K. “Mass Spectrometry in Organic and Bio-organic Catalysis: Using Thermochemical Properties to Lend Insight into Mechanism,” Mass Spectrom. Rev., 2022, 1-19.

Lotsof, E. R.; Krajewski, A. E.; Anderson-Steele, B.; Rogers, J. P.; Zhang, L.; Yeo, J.; Conlon, S.; Manlove, A. H.; Lee, J. K.; David, S. S. “NEIL1 Recoding due to RNA Editing Impacts Lesion-Specific Recognition and Excision,”  J. Am. Chem. Soc., 2022, 144, 14578-14589.

Krajewski, A. E.; Lee, J. K.  “Gas-Phase Experimental and Computational Studies of 5-Halouracils: Intrinsic Properties and Biological Implications,” J. Org. Chem., 2021, 86, 6361-6370.

Lee, J. K. “Gas Phase Models for Biocatalysis,” in “Gas Phase Models for Catalysis: Atoms, Molecules, Clusters, and Complexes/Physical Chemistry in Action,” Lang, S.; Berhardt, T.. Eds. Springer, 2021, in press.

Majumdar, C.; McKibbin, P. L.; Krajewski, A. E.; Manlove, A. H.; Lee, J. K.; David, S. S. “Unique Hydrogen Bonding of Adenine with the Oxidatively Damaged Base 8-Oxoguanine Enables Specific Recognition and Repair by DNA Glycosylase MutY,” J. Am. Chem. Soc., 2020, 142, 20340-20350.

Wang, N.; Lee, J. K. “Gas-Phase and Ionic Liquid Experimental and Computational Studies of Imidazole Acidity and Carbon Dioxide Capture,” J. Org. Chem., 2019, 84, 14593-14601.

Xu, J.; Krajewski, A. E.; Niu, Y.; Kiruba, G. S. M.; Lee, J. K.  “Kinetic Hydricity of Silane Hydrides in the Gas Phase,”  Chemical Science, 2019, 10, 8002-8008.

Xu, J.; Mieres-Perez, J.; Sanchez-Garcia, E.; Lee, J.K. “Gas-Phase Deprotonation of Benzhydryl Cations: Carbene Basicity, Multiplicity, and Rearrangements,” J. Org. Chem., 2019, 84, 7685-7693. Also highlighted as journal issue cover.

Wang, N.; Xu, J.; Lee, J. K. “The Importance of N-Heterocyclic Carbene Basicity in Organocatalysis,” Org. Biomol. Chem., 2018, 16, 6852-6866.

Lee, J. K.; Niu, Y. “pK_a Prediction,” in “Applied Theoretical Organic Chemistry,” World Scientific, 2018, 503-518.

Niu, Y.; Wang, N.; Munoz, A.; Xu, J.; Zeng, H.; Rovis. T.; Lee, J. K.  “Experimental and Computational Gas Phase Acidities of Conjugate Acids of Triazolylidene Carbenes:  Rationalizing Subtle Electronic Effects,” J. Am. Chem. Soc., 2017, 139, 14917-14930.

Bird, J. G.; Zhang, Y.; Tian, Y.; Greene, L.; Liu, M.; Buckley, B.; Lee, J. K.; Kaplan, C. D.; Ebright, R. H.; Nickels, B. E. “The Mechanism of RNA 5′ Capping with NAD+, NADH, and CoA,” Nature, 2016, 535, 444-447.

Kiruba, G. S. M.; Xu, J.; Zelikson, V.; Lee, J. K. “Gas Phase Studies of Formamidopyrimidine Glycosylase (Fpg) Substrates,” Chem. Eur. J., 2016, 22, 3881-3890 (special issue “Women in Chemistry“)

Tian, Y.; Lee, J. K.  “Gas Phase Studies of N-Heterocyclic Carbene-Catalyzed Condensation Reactions,” J. Org. Chem., 2015, 80, 6831-6838. Selected by “Organic Process Research & Development” as a “Highlight from the Literature”

Teator, A. J.; Tian, Y.; Chen, M.; Lee, J. K.; Bielawski, C. W.  “An Isolable, Photoswitchable N-Heterocyclic Carbene: On-Demand Reversible Ammonia Activation,”  Angew. Chemie Int. Ed., 2015, 54, 11559-11563.

Chen, M.; Lee, J. K. “Computational Studies of the Gas-Phase Thermochemical Properties of Modified Nucleobases,” J. Org. Chem., 2014, 79, 11295-1130. Selected as “Highlighted Article”

Zeng, H.; Wang, K.; Tian, Y.; Niu, Y.; Greene, L.; Hu, Z.; Lee, J. K. “The Benzoin Condensation: Charge Tagging of the Catalyst Allows for Tracking by Mass Spectrometry,” Int. J. Mass. Spectrom., 2014, 369, 92-97.

Wang, K.; Chen, M.; Wang, Q.; Shi, X.; Lee, J. K. “1,2,3-Triazoles: Gas Phase Properties,” J. Org. Chem., 2013, 78, 7249-7258.

Chen, M.; Moerdyk, J. P.; Blake, G. A.; Bielawski, C. W.; Lee, J. K. “Assessing the Proton Affinities of N,N’-Diamidocarbenes,” J. Org. Chem., 2013, 78, 10452–10458 (“Highlighted Article”)

Maiti, A.; Michelson, A. Z.; Hwang, B.-J.; Armwood, C. J.; Lu, A.-L.; Lee, J. K.; Drohat, A. C. “Divergent Mechanisms for TDG Excision of 5-Formylcytosine and 5-Carboxylcytosine from DNA,” J. Am. Chem. Soc., 2013, 135, 15813-15822.

Michelson, A. Z.; Rozenberg, A.; Tian, Y.; Sun, X.; Davis, J.; Francis, A. W.; O’Shea, V. L.; Halasyam, M.: Manlove, A. H.; David, S. S.; Lee, J. K. “Gas-Phase Studies of Substrates for the DNA Mismatch Repair Enzyme MutY,” J. Am. Chem. Soc., 2012, 134, 19839-19850.

Michelson, A. Z.; Chen, M.; Wang, K.; Lee, J. K. “Gas-Phase Studies of Purine 3-Methyladenine DNA Glycosylase II (AlkA) Substrates,” J. Am. Chem. Soc., 2012, 134, 9622-9633.

Michelson, A. Z.; Petronico, A.; Lee, J. K. “2-Pyridone and Derivatives: Gas Phase Acidity, Proton Affinity, Tautomer Preference and Leaving Group Ability,” J. Org. Chem., 2012, 77, 1623-1631.

Liu, M.; Chen, M.; Zhang, S.; Yang, I.; Buckley, B.; Lee, J. K. “Reactivity of Carbene•Phosphine Dimers: Proton Affinity Revisited,” J. Phys. Org. Chem. 2011, 24, 929-936.

Lee, J. K.; Tantillo, D. J. “Reaction Mechanisms: Pericyclic Reactions,” Annu. Rep. Prog. Chem., Sect. B 2011, 107, 266-286.

Liu, M.; Tran, N. T.; Franz, A. K.; Lee, J. K. “Gas-Phase Acidity Studies of Dual Hydrogen-Bonding Organic Silanols and Organocatalysts,” J. Org. Chem. 2011, 76, 7186-7194.

Liu, M.; Yang, I.; Buckley, B.; Lee, J. K. “Proton Affinities of Phosphines versus N-Heterocyclic Carbenes,” Org. Lett. 2010, 21, pp 4764–4767.

Lee, J. K.; Tantillo, D. J. “Reaction Mechanisms: Pericyclic Reactions,” Annu. Rep. Prog. Chem., Sect. B 2010, 106, 283-303.

Sun, X.; Lee, J. K. “The Stability of DNA Duplexes Containing Hypoxanthine (Inosine): Gas versus Solution Phase and Biological Implications,” J. Org. Chem., 2010, 75, 1848-1854.

Zhachkina, A.; Lee, J. K. “Uracil and Thymine Reactivity in the Gas Phase: The SN2 Reaction and Implications for Electron Delocalization in Leaving Groups,” J. Am. Chem. Soc. 2009, 131, 18376-18385.

Zhachkina, A.; Liu, M.; Sun, X.; Amegayibor, F. S.; Lee, J. K. “Gas-Phase Thermochemical Properties of the Damaged Base O-Methylguanine versus Adenine and Guanine,” J. Org. Chem. 2009, 74, 7429-7440.

Tantillo, D. J.; Lee, J. K. “Reaction Mechanisms: Pericyclic Reactions,” Annu. Rep. Prog. Chem., Sect. B, 2009, 105, 285-309.

Liu, M; Li, T.; Amegayibor, F. S.; Cardoso, D. S.; Fu, Y.; Lee, J. K. “Gas-Phase Thermochemical Properties of Pyrimidine Nucleobases,” J. Org. Chem. 2008, 73, 9283-9291.

Rozenberg, A; Lee, J. K. “Theoretical Studies of the Quinolinic Acid to Nicotinic Acid Mononucleotide Transformation,” J. Org. Chem. 2008, 73, 9314-9319.

Wepukhulu, W. O.; Smiley, V. L.; Vemulapalli, B.; Smiley, J. A.; Phillips, L. M.; Lee, J. K. “Evidence for Pre-Protonation in the Catalytic Reaction of OMP Decarboxylase: Kinetic Isotope Effects using the Remote Double Label Method,” Organic and Biomolecular Chemistry 2008, 6, 4533-4541 (ALSO FEATURED ON COVER).

Tantillo, D. J.; Lee, J. K. “Reaction Mechanisms: Pericyclic Reactions,” Annu. Rep. Prog. Chem., Sect. B. 2008, 104, 260-283.

Liu, M.; Xu, M.; Lee, J. K. “The Intrinsic Reactivity of Ethenoadenine and Mechanism for Excision from DNA,” J. Org. Chem. 2008, 73, 5907-5914.

Sun, X.; Lee, J. K. “The Acidity and Proton Affinity of Hypoxanthine in the Gas Phase versus in Solution: Intrinsic Reactivity and Biological Implications,” J. Org. Chem. 2007, 72, 6548-6555.

Tantillo, D. J.; Lee, J. K. “Reaction Mechanisms: Pericyclic Reactions,” Annu. Rep. Prog. Chem., Sect. B. 2007, 103, 272-293.

Pan, S.; Sun, X.; Lee, J. K. “DNA Stability in the Gas versus Solution Phases: A Systematic Study of Thirty-One Duplexes with Varying Length, Sequence, and Charge Level,” J. Am. Soc. Mass Spectrom. 2006, 17, 1383-1395.

Pan, S.; Sun, X.; Lee, J. K. “Stability of Complementary and Mismatched DNA Duplexes: Comparison and Contrast in Gas versus Solution Phases,” Int. J. Mass Spectrom. 2006, 253, 238-248.

Pan, S.; Verhoeven, K.; Lee, J. K. “Investigation of the Initial Fragmentation of Oligodeoxynucleotides in a Quadrupole Ion Trap: Charge Level-Related Base Loss,” J. Am. Soc. Mass Spectrom. 2005, 16, 1863-1865.

Phillips, L. M; Lee, J. K. “Theoretical Studies of the Effect of Thio Substitution on Orotidine Monophosphate Decarboxylase Substrates,” J. Org. Chem. 2005, 70, 1211-1221.

Lee, J. K. “Insights into Nucleic Acid Reactivity through Gas Phase Studies,” Int. J. Mass Spectrom. 2005, 240, 261-272.

Sharma, S.; Lee, J. K. “Gas Phase Acidity Studies of Multiple Sites of Adenine and Adenine Derivatives,” J. Org. Chem. 2004, 69, 7018-7025.

Lee, J. K., Editor. “Orotidine Monophosphate Decarboxylase: A Mechanistic Dialogue,” Topics in Current Chemistry 2004.

Lee, J. K.; Tantillo, D. J. “Computational Studies on the Mechanism of Action of Orotidine Monophosphate Decarboxylase,” Adv. Phys. Org. Chem. 2003, 38, 183-218.

Haeffner, F.; Houk, K. N.; Schulze, S. M.; Lee, J. K. “Concerted Rearrangement versus Heterolytic Cleavage in Anionic [2,3]- and [3,3]-Sigmatropic Shifts. A DFT Study of Relationships Between Anion Stabilities and Mechanisms and Rates,” J. Org. Chem. 2003, 68 2310-2316.

Kurinovich, M. A.; Phillips, L. M.; Sharma, S.; Lee, J. K. “The Gas Phase Proton Affinity of Uracil: Measuring Multiple Basic Sites and Implications for the Enzyme Mechanism of Orotidine 5-Monophosphate Decarboxylase,” Chem. Commun. 2002, 2354-2355.

Sharma, S.; Lee, J. K. “The Acidity of Adenine and Adenine Derivatives and Biological Implications. A Computational and Experimental Gas Phase Study,” J. Org. Chem. 2002, 67, 8360-8365.

Kurinovich, M. A.; Lee, J. K. “The Acidity of Uracil and Uracil Analogs in the Gas Phase: Four Surprisingly Acidic Sites and Biological Implications” J. Am. Soc. Mass. Spectrom. 2002, 13, 985-995.

Phillips, L. M.; Lee, J. K. “Theoretical Studies of Mechanisms and Kinetic Isotope Effects on the Decarboxylation of Orotic Acid and Derivatives,” J. Am. Chem. Soc. 2001, 123, 12067-12073.

Schulze, S. M.; Santella, N.; Grabowski, J. J., Lee, J. K. “The Secondary and Tertiary Anionic Oxy-Cope Alkoxides Rearrange in the Gas Phase,” J. Org. Chem. 2001, 66, 7247-7253.

Houk, K. N.; Lee, J. K.; Tantillo, D. J.; Bahmanyar, S.; Hietbrink, B. N. “Crystal Structures of Orotidine Monophosphate Decarboxylase: Does the Structure Reveal the Mechanism of Natures Most Proficient Enzyme?,” ChemBioChem 2001, 2, 113-118.

Kurinovich, M.A.; Lee, J, K. “The Acidity of Uracil from the Gas Phase to Solution: The Coalescence of the N1 and N3 Sites and Implications for Biological Glycosylation,” J. Am. Chem. Soc. 2000,122, 6258-6262.

Singleton, D. A.; Merrigan, S. R.; Kim, B. J.; Beak, P.; Phillips, L. M.; Lee, J. K. “¹³C Kinetic Isotope Effects and the Mechanism of the Uncatalyzed Decarboxylation of Orotic Acid,” J. Am. Chem. Soc. 2000, 122, 3296-3300.

Chen, J.; McAllister, M. A., Lee, J. K., Houk, K. N. “Short, Strong Hydrogen Bonds in the Gas Phase and in Solution: Theoretical Exploration of pK_a Matching and Environmental Effects on the Strengths of Hydrogen Bonds, and their Potential Roles in Enzymatic Catalysis,” J. Org. Chem. 1998, 63, 4611-4619.

Yoo, H. Y.; Houk, K. N.; Lee, J. K.; Scialdone, M. A.; Meyers, A. I. “A New Paradigm for Anionic Heteroatom Cope Rearrangements,” J. Am. Chem. Soc. 1998, 120, 205-206.

Lee, J. K.; Houk, K. N. “A Proficient Enzyme Revisited: The Predicted Mechanism for Orotidine Monophosphate Decarboxylase,” Science 1997, 276, 942-945. Reported in “News of the Week“: Rouhi, A. M. “Carbenes May Be Key to Enzymes Power,” Chemical and Engineering News 1997, 75, 12.

Lee, J. K.; Houk, K. N. “Cation Cyclization Selectivity: Variable Structures of Protonated Cyclopropanes and Selectivity Control by Catalytic Antibodies,” Angew. Chem. Int. Ed. Engl. 1997, 36, 1003-1005.

Houk, K. N.; Lee, J. K. “Physical Organic in the 21st Century: Evanescent or Transcendent?,” Pure Appl. Chem. 1997, 69, 237-239.

Houk, K. N.; Beno, B. R.; Nendel, M.; Black, K.; Yoo, H. Y.; Wilsey, S.; Lee, J. K. “Exploration of Pericyclic Reaction Transition Structures with Quantum Mechanical Methods: Competing Concerted and Stepwise Mechanisms,” J. Mol. Struct. (Theochem.) 1997, 398-399, 169-179.

Lee, J. K.; Grabowski, J. J. “Anion Structure Determination in the Gas Phase: Chemical Reactivity as a Probe,” J. Org. Chem. 1996, 61, 9422-9429.

Wu, Y.-D.; Lee, J. K.; Houk, K. N.; Dondoni, A. “Theoretical Study of a Termolecular Mechanism for the Reaction of (Trimethyl)silylthiazole with Carbonyl Compounds,” J. Org. Chem. 1996, 61, 1922-1926.