{"id":521,"date":"2024-08-22T20:20:37","date_gmt":"2024-08-22T20:20:37","guid":{"rendered":"https:\/\/sites.rutgers.edu\/jklee-lab\/?page_id=521"},"modified":"2025-10-02T17:39:41","modified_gmt":"2025-10-02T17:39:41","slug":"selected-publications","status":"publish","type":"page","link":"https:\/\/sites.rutgers.edu\/jklee-lab\/selected-publications\/","title":{"rendered":"Selected Publications"},"content":{"rendered":"

Hinz, D. J.; Cao, Z.; Lipke, M. C.; Lee, J. K. “Apparent Gas-Phase Nucleophilic Aromatic Substitution Reactions of Dimethyl(phenyl)silyl Cations,”\u00a0J. Org. Chem.,\u00a0<\/em>2025<\/strong>,\u00a090<\/em>, 12860\u221212865.<\/p>\n

Hinz, D. J.; Krajewski, A. E.; Lee, J. K. “Carbon\u2212Fluorine Activation in the Gas Phase: The Reactions of Benzyl C\u2212F Bonds and Silyl Cations,” J. Org. Chem.<\/em>, 2024<\/strong>, 89<\/em>, 13595\u221213600.<\/p>\n

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<\/strong>, 88, 6816-6826.<\/p>\n

Krajewski, A. E.; Lee, J. K.\u00a0 “Nucleophilicity and Electrophilicity in the Gas Phase: Silane Hydricity,” J. Org. Chem., special issue, “Solvation Effects in Organic Chemistry,”\u00a0<\/em> 2022<\/strong>, 87<\/em>, 1840-1849.<\/p>\n

Zhang, L.; Hinz, D. J.; Kiruba, G. S. M.; Ding, X.; Lee, J. K.\u00a0 “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, <\/em>2022<\/strong>, e4343.<\/p>\n

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.<\/em>, 2022<\/strong>, 1-19.<\/p>\n

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,” \u00a0J. Am. Chem. Soc.<\/em>, 2022<\/strong>, 144, 14578-14589.<\/p>\n

Krajewski, A. E.; Lee, J. K.\u00a0 “Gas-Phase Experimental and Computational Studies of 5-Halouracils: Intrinsic Properties and Biological Implications,” J. Org. Chem.<\/em>, 2021<\/strong>, 86<\/em>, 6361-6370.<\/p>\n

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<\/em>, 2021<\/strong>, in press.<\/p>\n

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<\/strong>, 142<\/em>, 20340-20350.<\/p>\n

Wang, N.; Lee, J. K. “Gas-Phase and Ionic Liquid Experimental and Computational Studies of Imidazole Acidity and Carbon Dioxide Capture,” J. Org. Chem.<\/em>, 2019<\/strong>, 84<\/em>, 14593-14601.<\/p>\n

Xu, J.; Krajewski, A. E.; Niu, Y.; Kiruba, G. S. M.; Lee, J. K.\u00a0 “Kinetic Hydricity of Silane Hydrides in the Gas Phase,”\u00a0 Chemical Science<\/em>, 2019<\/strong>, 10<\/em>, 8002-8008.<\/p>\n

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.<\/em>, 2019<\/strong>, 84, 7685-7693. Also highlighted as journal issue cover.<\/em><\/p>\n

Wang, N.; Xu, J.; Lee, J. K. \u201cThe Importance of N-Heterocyclic Carbene Basicity in Organocatalysis,\u201d Org. Biomol. Chem.,<\/em> 2018<\/strong>, 16, 6852-6866.<\/p>\n

Lee, J. K.; Niu, Y. “pKa<\/sub> Prediction,” in “Applied Theoretical Organic Chemistry,” World Scientific<\/em>, 2018<\/strong>, 503-518.<\/p>\n

Niu, Y.; Wang, N.; Munoz, A.; Xu, J.; Zeng, H.; Rovis. T.; Lee, J. K.\u00a0 “Experimental and Computational Gas Phase Acidities of Conjugate Acids of Triazolylidene Carbenes:\u00a0 Rationalizing Subtle Electronic Effects,” J. Am. Chem. Soc.,<\/em> 2017<\/strong>, 139, <\/em>14917-14930.<\/p>\n

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<\/em>, 2016<\/strong>, 535, 444-447.<\/p>\n

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

Tian, Y.; Lee, J. K.\u00a0 “Gas Phase Studies of N-Heterocyclic Carbene-Catalyzed Condensation Reactions,” J. Org. Chem.<\/em>, 2015<\/strong>, 80, 6831-6838. Selected by “Organic Process Research & Development” as a “Highlight from the Literature”<\/p>\n

Teator, A. J.; Tian, Y.; Chen, M.; Lee, J. K.; Bielawski, C. W.\u00a0 “An Isolable, Photoswitchable N-Heterocyclic Carbene: On-Demand Reversible Ammonia Activation,”\u00a0 Angew. Chemie Int. Ed.<\/em>, 2015<\/strong>, 54, 11559-11563.<\/p>\n

Chen, M.; Lee, J. K. “Computational Studies of the Gas-Phase Thermochemical Properties of Modified Nucleobases,” J. Org. Chem.<\/em>, 2014<\/strong>, 79, 11295-1130. Selected as “Highlighted Article”<\/p>\n

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.<\/em>, 2014<\/strong>, 369<\/em>, 92-97.<\/p>\n

Wang, K.; Chen, M.; Wang, Q.; Shi, X.; Lee, J. K. “1,2,3-Triazoles: Gas Phase Properties,” J. Org. Chem.<\/em>, 2013<\/strong>, 78<\/em>, 7249-7258.<\/p>\n

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.,<\/em> 2013<\/strong>, 78<\/em>, 10452\u201310458 (“Highlighted Article”)<\/p>\n

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.<\/em>, 2013<\/strong>, 135<\/em>, 15813-15822.<\/p>\n

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.<\/em>, 2012<\/strong>, 134<\/em>, 19839-19850.<\/p>\n

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.<\/em>, 2012<\/strong>, 134<\/em>, 9622-9633.<\/p>\n

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.<\/em>, 2012<\/strong>, 77<\/em>, 1623-1631.<\/p>\n

Liu, M.; Chen, M.; Zhang, S.; Yang, I.; Buckley, B.; Lee, J. K. “Reactivity of Carbene\u2022Phosphine Dimers: Proton Affinity Revisited,” J. Phys. Org. Chem.<\/em> 2011<\/strong>, 24<\/em>, 929-936.<\/p>\n

Lee, J. K.; Tantillo, D. J. “Reaction Mechanisms: Pericyclic Reactions,” Annu. Rep. Prog. Chem., Sect. B<\/em> 2011<\/strong>, 107<\/em>, 266-286.<\/p>\n

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.<\/em> 2011<\/strong>, 76<\/em>, 7186-7194.<\/p>\n

Liu, M.; Yang, I.; Buckley, B.; Lee, J. K. “Proton Affinities of Phosphines versus N-Heterocyclic Carbenes,” Org. Lett.<\/em> 2010<\/strong>, 21<\/em>, pp 4764\u20134767.<\/p>\n

Lee, J. K.; Tantillo, D. J. “Reaction Mechanisms: Pericyclic Reactions,” Annu. Rep. Prog. Chem., Sect. B<\/em> 2010<\/strong>, 106<\/em>, 283-303.<\/p>\n

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

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.<\/em> 2009<\/strong>, 131<\/em>, 18376-18385.<\/p>\n

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.<\/em> 2009<\/strong>, 74<\/em>, 7429-7440.<\/p>\n

Tantillo, D. J.; Lee, J. K. “Reaction Mechanisms: Pericyclic Reactions,” Annu. Rep. Prog. Chem.<\/em>, Sect. B, 2009<\/strong>, 105<\/em>, 285-309.<\/p>\n

Liu, M; Li, T.; Amegayibor, F. S.; Cardoso, D. S.; Fu, Y.; Lee, J. K. \u201cGas-Phase Thermochemical Properties of Pyrimidine Nucleobases,\u201d J. Org. Chem.<\/em> 2008<\/strong>, 73<\/em>, 9283-9291.<\/p>\n

Rozenberg, A; Lee, J. K. \u201cTheoretical Studies of the Quinolinic Acid to Nicotinic Acid Mononucleotide Transformation,\u201d J. Org. Chem.<\/em> 2008<\/strong>, 73<\/em>, 9314-9319.<\/p>\n

Wepukhulu, W. O.; Smiley, V. L.; Vemulapalli, B.; Smiley, J. A.; Phillips, L. M.; Lee, J. K. \u201cEvidence for Pre-Protonation in the Catalytic Reaction of OMP Decarboxylase: Kinetic Isotope Effects using the Remote Double Label Method,\u201d Organic and Biomolecular Chemistry<\/em> 2008<\/strong>, 6<\/em>, 4533-4541 (ALSO FEATURED ON COVER).<\/p>\n

Tantillo, D. J.; Lee, J. K. \u201cReaction Mechanisms: Pericyclic Reactions,\u201d Annu. Rep. Prog. Chem., Sect. B.<\/em> 2008<\/strong>, 104<\/em>, 260-283.<\/p>\n

Liu, M.; Xu, M.; Lee, J. K. \u201cThe Intrinsic Reactivity of Ethenoadenine and Mechanism for Excision from DNA,\u201d J. Org. Chem.<\/em> 2008<\/strong>, 73<\/em>, 5907-5914.<\/p>\n

Sun, X.; Lee, J. K. \u201cThe Acidity and Proton Affinity of Hypoxanthine in the Gas Phase versus in Solution: Intrinsic Reactivity and Biological Implications,\u201d J. Org. Chem.<\/em> 2007<\/strong>, 72<\/em>, 6548-6555.<\/p>\n

Tantillo, D. J.; Lee, J. K. \u201cReaction Mechanisms: Pericyclic Reactions,\u201d Annu. Rep. Prog. Chem., Sect. B.<\/em> 2007<\/strong>, 103<\/em>, 272-293.<\/p>\n

Pan, S.; Sun, X.; Lee, J. K. \u201cDNA Stability in the Gas versus Solution Phases: A Systematic Study of Thirty-One Duplexes with Varying Length, Sequence, and Charge Level,\u201d J. Am. Soc. Mass Spectrom.<\/em> 2006<\/strong>, 17<\/em>, 1383-1395.<\/p>\n

Pan, S.; Sun, X.; Lee, J. K. \u201cStability of Complementary and Mismatched DNA Duplexes: Comparison and Contrast in Gas versus Solution Phases,\u201d Int. J. Mass Spectrom.<\/em> 2006<\/strong>, 253<\/em>, 238-248.<\/p>\n

Pan, S.; Verhoeven, K.; Lee, J. K. \u201cInvestigation of the Initial Fragmentation of Oligodeoxynucleotides in a Quadrupole Ion Trap: Charge Level-Related Base Loss,\u201d J. Am. Soc. Mass Spectrom.<\/em> 2005<\/strong>, 16<\/em>, 1863-1865.<\/p>\n

Phillips, L. M; Lee, J. K. \u201cTheoretical Studies of the Effect of Thio Substitution on Orotidine Monophosphate Decarboxylase Substrates,\u201d J. Org. Chem.<\/em> 2005<\/strong>, 70<\/em>, 1211-1221.<\/p>\n

Lee, J. K. \u201cInsights into Nucleic Acid Reactivity through Gas Phase Studies,\u201d Int. J. Mass Spectrom.<\/em> 2005<\/strong>, 240<\/em>, 261-272.<\/p>\n

Sharma, S.; Lee, J. K. \u201cGas Phase Acidity Studies of Multiple Sites of Adenine and Adenine Derivatives,\u201d J. Org. Chem.<\/em> 2004<\/strong>, 69<\/em>, 7018-7025.<\/p>\n

Lee, J. K., Editor. \u201cOrotidine Monophosphate Decarboxylase: A Mechanistic Dialogue,\u201d Topics in Current Chemistry<\/em> 2004<\/strong>.<\/p>\n

Lee, J. K.; Tantillo, D. J. \u201cComputational Studies on the Mechanism of Action of Orotidine Monophosphate Decarboxylase,\u201d Adv. Phys. Org. Chem.<\/em> 2003<\/strong>, 38<\/em>, 183-218.<\/p>\n

Haeffner, F.; Houk, K. N.; Schulze, S. M.; Lee, J. K. \u201cConcerted 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,\u201d J. Org. Chem.<\/em> 2003<\/strong>, 68<\/em> 2310-2316.<\/p>\n

Kurinovich, M. A.; Phillips, L. M.; Sharma, S.; Lee, J. K. \u201cThe Gas Phase Proton Affinity of Uracil: Measuring Multiple Basic Sites and Implications for the Enzyme Mechanism of Orotidine 5-Monophosphate Decarboxylase,\u201d Chem. Commun.<\/em> 2002<\/strong>, 2354-2355.<\/p>\n

Sharma, S.; Lee, J. K. \u201cThe Acidity of Adenine and Adenine Derivatives and Biological Implications. A Computational and Experimental Gas Phase Study,\u201d J. Org. Chem. <\/em>2002<\/strong>, 67<\/em>, 8360-8365.<\/p>\n

Kurinovich, M. A.; Lee, J. K. \u201cThe Acidity of Uracil and Uracil Analogs in the Gas Phase: Four Surprisingly Acidic Sites and Biological Implications\u201d J. Am. Soc. Mass. Spectrom. <\/em>2002<\/strong>, 13<\/em>, 985-995.<\/p>\n

Phillips, L. M.; Lee, J. K. \u201cTheoretical Studies of Mechanisms and Kinetic Isotope Effects on the Decarboxylation of Orotic Acid and Derivatives,\u201d J. Am. Chem. Soc.<\/em> 2001<\/strong>, 123<\/em>, 12067-12073.<\/p>\n

Schulze, S. M.; Santella, N.; Grabowski, J. J., Lee, J. K. \u201cThe Secondary and Tertiary Anionic Oxy-Cope Alkoxides Rearrange in the Gas Phase,\u201d J. Org. Chem.<\/em> 2001<\/strong>, 66<\/em>, 7247-7253.<\/p>\n

Houk, K. N.; Lee, J. K.; Tantillo, D. J.; Bahmanyar, S.; Hietbrink, B. N. \u201cCrystal Structures of Orotidine Monophosphate Decarboxylase: Does the Structure Reveal the Mechanism of Natures Most Proficient Enzyme?,\u201d ChemBioChem<\/em> 2001<\/strong>, 2<\/em>, 113-118.<\/p>\n

Kurinovich, M.A.; Lee, J, K. \u201cThe Acidity of Uracil from the Gas Phase to Solution: The Coalescence of the N1 and N3 Sites and Implications for Biological Glycosylation,\u201d J. Am. Chem. Soc.<\/em> 2000<\/strong>,122<\/em>, 6258-6262.<\/p>\n

Singleton, D. A.; Merrigan, S. R.; Kim, B. J.; Beak, P.; Phillips, L. M.; Lee, J. K. \u201c13<\/sup>C Kinetic Isotope Effects and the Mechanism of the Uncatalyzed Decarboxylation of Orotic Acid,\u201d J. Am. Chem. Soc.<\/em> 2000<\/strong>, 122<\/em>, 3296-3300.<\/p>\n

Chen, J.; McAllister, M. A., Lee, J. K., Houk, K. N. \u201cShort, Strong Hydrogen Bonds in the Gas Phase and in Solution: Theoretical Exploration of pKa<\/sub> Matching and Environmental Effects on the Strengths of Hydrogen Bonds, and their Potential Roles in Enzymatic Catalysis,\u201d J. Org. Chem. <\/em>1998<\/strong>, 63<\/em>, 4611-4619.<\/p>\n

Yoo, H. Y.; Houk, K. N.; Lee, J. K.; Scialdone, M. A.; Meyers, A. I. \u201cA New Paradigm for Anionic Heteroatom Cope Rearrangements,\u201d J. Am. Chem. Soc.<\/em> 1998<\/strong>, 120<\/em>, 205-206.<\/p>\n

Lee, J. K.; Houk, K. N. \u201cA Proficient Enzyme Revisited: The Predicted Mechanism for Orotidine Monophosphate Decarboxylase,\u201d Science<\/em> 1997<\/strong>, 276<\/em>, 942-945. Reported in \u201cNews of the Week\u201c: Rouhi, A. M. \u201cCarbenes May Be Key to Enzymes Power,\u201d Chemical and Engineering News 1997<\/strong>, 75<\/em>, 12.<\/p>\n

Lee, J. K.; Houk, K. N. \u201cCation Cyclization Selectivity: Variable Structures of Protonated Cyclopropanes and Selectivity Control by Catalytic Antibodies,\u201d Angew. Chem. Int. Ed. Engl.<\/em> 1997<\/strong>, 36<\/em>, 1003-1005.<\/p>\n

Houk, K. N.; Lee, J. K. \u201cPhysical Organic in the 21st Century: Evanescent or Transcendent?,\u201d Pure Appl. Chem.<\/em> 1997<\/strong>, 69<\/em>, 237-239.<\/p>\n

Houk, K. N.; Beno, B. R.; Nendel, M.; Black, K.; Yoo, H. Y.; Wilsey, S.; Lee, J. K. \u201cExploration of Pericyclic Reaction Transition Structures with Quantum Mechanical Methods: Competing Concerted and Stepwise Mechanisms,\u201d J. Mol. Struct. (Theochem.)<\/em> 1997<\/strong>, 398-399<\/em>, 169-179.<\/p>\n

Lee, J. K.; Grabowski, J. J. \u201cAnion Structure Determination in the Gas Phase: Chemical Reactivity as a Probe,\u201d J. Org. Chem.<\/em> 1996<\/strong>, 61<\/em>, 9422-9429.<\/p>\n

Wu, Y.-D.; Lee, J. K.; Houk, K. N.; Dondoni, A. \u201cTheoretical Study of a Termolecular Mechanism for the Reaction of (Trimethyl)silylthiazole with Carbonyl Compounds,\u201d J. Org. Chem.<\/em> 1996<\/strong>, 61<\/em>, 1922-1926.<\/p>\n","protected":false},"excerpt":{"rendered":"

Hinz, D. J.; Cao, Z.; Lipke, M. C.; Lee, J. K. “Apparent Gas-Phase Nucleophilic Aromatic Substitution Reactions of Dimethyl(phenyl)silyl Cations,”\u00a0J. Org. Chem.,\u00a02025,\u00a090, 12860\u221212865. Hinz, D. J.; Krajewski, A. E.; Lee, … Read More<\/a><\/p>\n","protected":false},"author":3628,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-521","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"\nSelected Publications - The JKLee Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sites.rutgers.edu\/jklee-lab\/selected-publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Selected Publications - The JKLee Lab\" \/>\n<meta property=\"og:description\" content=\"Hinz, D. J.; Cao, Z.; Lipke, M. C.; Lee, J. K. “Apparent Gas-Phase Nucleophilic Aromatic Substitution Reactions of Dimethyl(phenyl)silyl Cations,”\u00a0J. Org. Chem.,\u00a02025,\u00a090, 12860\u221212865. Hinz, D. J.; Krajewski, A. 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