Our group is primarily interested in the characterization of short-lived (μs to ns range) organic intermediates that exist during reactions in aqueous solution.  In recent years we have focused on cationic intermediates, including aryl- and heteroarylnitrenium ions and aryloxenium ions (Scheme).  The nitrenium ions are of interest because they have been implicated as the reactive intermediates responsible for the genetic damage caused by carcinogenic metabolites of aromatic and heteroaromatic amines.  The carbocyclic amines are largely industrial products, but the heterocyclic amines are produced during the cooking of protein containing foods. The oxenium ions are thought to be involved in synthetically useful phenol oxidation reactions and in the formation of commercially important polymers of phenols. We apply the techniques of physical organic chemistry, including kinetics measurements, trapping experiments, isotopic labeling experiments, and direct spectroscopic observation following laser flash photolysis to characterize these species.

 Major scientific contributions made by our research group since 1993 include: 

1)       The demonstration of the long lifetime of nitrenium ions derived from metabolites of carcinogenic amines by azide clock methodology.  This finding showed that these ions are sufficiently long-lived in an aqueous environment to be attacked by biological and other non-solvent nucleophiles. J. Am. Chem. Soc. 1993,  J. Org. Chem. 1998.

2)       The direct spectroscopic observation of nitrenium ions derived from carcinogenic amines (collaboration with R. A. McClelland).  This work confirmed the results of our trapping studies, and provided directly measured rate constants for a number of ions. J. Am. Chem. Soc. 1994, J. Chem. Soc., Perkin Trans. 2 1999.

3)       The demonstration that nitrenium ions are responsible for the formation of the d-G adduct that apparently initiates carcinogenesis. This work showed for the first time that nitrenium ions have the requisite chemical properties to be the reactive intermediates responsible for aromatic amine induced carcinogenesis.  J. Am. Chem. Soc. 1995, J. Am. Chem. Soc. 1997.

4)       The demonstration that glutathione trapping of nitrenium ions from carcinogenic amines is inefficient at physiological concentrations. Glutathione, and other small biological nucleophiles, are not present in sufficient concentrations in the cell to trap a significant fraction of the nitrenium ions derived from carcinogenic amines.   J. Am. Chem. Soc. 1996.

5)       The demonstration that heteroarylnitrenium ions are generated from metabolites of food-derived heterocyclic amine carcinogens. A second class of carcinogenic aromatic amines, generated from cooking protein-containing foods, also produce selective nitrenium ions after metabolic activation.  J. Am. Chem. Soc. 1998, J. Am. Chem. Soc. 2000, J. Am. Chem. Soc. 2002.

6)       The development of a quantitative understanding of the factors that control nitrenium ion reactivity/selectivity.  These ions are significantly more stabilized by π-interactions than their carbenium ion analogues. J. Am. Chem. Soc. 1994, J. Org. Chem. 1995, J. Org. Chem. 1999.

7)       The demonstration of a correlation of nitrenium ion selectivity with mutagenicty of the corresponding amine. A major factor in determining the mutagenicity of aromatic and heteroaromatic amines appears to be the chemical selectivity of the nitrenium ion. J. Org. Chem. 1999, Chem. Res. Toxicol. 2002.

8)       The demonstration that the 4-biphenylyloxenium ion has a significant lifetime in an aqueous environment. Although oxenium ions have been invoked in many reaction schemes, this is the first demonstration that a reactive sterically unhindered oxenium ion, albeit one stabilized by a π-interaction, is sufficiently selective to be trapped by azide in water.  J. Am. Chem Soc. 2004.

9)       The demonstration that aryloxenium ion chemistry in nucleophilic solvents is limited by the short lifetimes of many of these species. Aryloxenium ions not stabilized by π-interactions may be too unstable to react with non-solvent nucleophiles. Apparent “oxenium ion” reactions of precursors to these species occur via alternative mechanisms.  J. Am. Chem. Soc. 2005, J. Org. Chem. 2006.

10)   The direct observation and kinetic characterization of an aryloxenium ion generated by laser flash photolysis. J. Am. Chem. Soc. 2007.

Undergraduate Research Opportunities

Since 1979, 55 undergraduate students have performed research in our laboratory for at least one semester or one summer. Most students have worked in the laboratory for multiple semesters/summers. Summer support for undergraduate researchers in our lab can be provided by grant funds, Miami’s Undergraduate Summer Scholars Program, or other sources such as the HHMI summer fellowships.

Over 60% of undergraduate research students in our lab have gone on to earn a Ph.D, M.D., or D.D.S.. As of early 2008, 37 of these students have appeared as co-authors on 30 individual peer-reviewed publications, primarily in the Journal of the American Chemical Society and the Journal of Organic Chemistry. Some of these publications are cited in the Recent Publications list on this webpage. Several more students from this group will appear as co-authors over the next few years. These students have also been listed as co-authors on many papers presented at scientific meetings, and some students have been able to travel to meetings to present their papers.
 

Undergraduates Sam Leopold and Andrew Vollman, shown with graduate student Yue-Ting Wang are co-authors on Journal of Organic Chemistry 2007, 72, 9954-9962.

Current undergraduate projects in the group include the characterization of oxenium ion-like reactions of 4-acyloxy-4-alkyl-2,5-cyclohexadienones, the attempted generation and characterization of 4-alkoxyphenyloxenium ions, and the photochemical generation of reactive intermediates including oxenium ions. Additional projects are developed as our research program evolves. All undergraduate research students in the Novak group are given responsibility for projects that are separate from, but related to, those of graduate students in the group. Research work includes some organic synthesis, but the primary focus of the group is the study of organic reaction mechanisms using kinetics, trapping experiments, isotopic labeling, kinetic isotope effects, and similar experiments. These experiments require students to become proficient in NMR, mass spectrometry, UV-vis spectroscopy, HPLC, and a number of other modern spectroscopic and analytical methods.

Instructional Projects

Organic Laboratory for Majors, 2^nd semester (CHM 255), 2006-2008

This project is part of a major modification to both semesters of the majors’ laboratory course meant to increase student use of technology and improve critical thinking skills. For spring 2006 the course included a traditional component that stressed laboratory skills development, spectroscopic interpretation, and notebook keeping (375/500 points) and a critical thinking component that stressed written communication skills (125/500 points).

The traditional component consisted of 7 experiments with individually generated data, limited data sharing, short write-ups (150 points), 2 spectroscopy problem sets, including 2D NMR (COSY, HMQC, HMBC) (55 points), 2 quizzes (70 points), and a two-hour final (100 points). Tools used in the traditional component included a standard lab manual, handouts (on Blackboard), an emphasis on keeping accurate and up-to-date laboratory notebooks, the use of chemical drawing and molecular mechanics software (ACD Chemsketch, HyperChem Lite), the use of library searching software (SciFinder Scholar, minimal usage mostly to look up properties of known compounds), spectroscopy websites (sdbs and NIST webbook), spectroscopy instrumentation (NMR, IR, GC/MS), and standard laboratory instrumentation.  Although this component of the course would be recognizable to any organic student/instructor it was organized to make maximum use of modern technology currently available to organic chemists.

The writing/critical thinking component consisted of an individual formal journal-style write-up of one laboratory experiment (40 points), a group literature project (CIITN (Chemistry is in the News) based) (35 points), and a group independent laboratory research project (50 points).

The individual journal-style write-up occurred in the first third of the course. It was a kinetics experiment involving basic catalysis of a nucleophilic aromatic substitution. Students generated a shared data set from individual kinetics experiments. A literature search was conducted by each student to find appropriate kinetic models for analysis of the data set. Students were individually responsible for application of the analysis to the data set and for making mechanistic conclusions based upon the data analysis. A number of tools were utilized by the students in this experiment including NMR, IR, UV-vis spectrophotometry for characterization of reactants and products and collection of kinetic data, SciFinder Scholar to find the kinetic models, Plotting and curve-fitting software to analyze the data, and the LabWrite website/software and ChemSketch to generate the write-up.

The group literature project required an analysis of the scientific basis of news stories in the popular press. Groups consisting of 5 to 6 students were chosen by the Instructor. Topics were chosen by the student groups with approval of the instructor. Individual students were responsible for searches of the scientific literature and annotated bibliographies turned in before the group project was due. The written analyses turned in by the group included an evaluation of the scientific validity of conclusions made by popular press articles. The grade for each student was determined by the quality of the individual searches and by the quality of the group analyses. Tools used for the group literature project included the CIITN website, LexisNexis News and other news websites, SciFinder Scholar, and ChemSketch.

For the group research project, students were given background, leading references, and guidelines for a research project based on the Suzuki coupling reaction in the first third of the course. Students were divided into the same groups that performed the literature project. Groups prepared a research proposal, including budget ($200 limit per group) about mid-course. Proposals were reviewed by the instructor and returned for resubmission. After resubmission, chemicals were purchased by the instructor. The groups performed the proposed research (12 laboratory hours, last three weeks of course), and generated a final written, journal-style report. Tools used in the research project included SciFinder Scholar, NMR, IR, LabWrite website/software, and ChemSketch.

During both semesters ChemSketch, HyperChem Lite, SciFinder Scholar software packages were used frequently, and with increasing sophistication throughout the year. Spectroscopy websites were utilized frequently, especially in the 2^nd semester. The group literature assignments allowed the students to develop the ability to read scientific and popular literature critically, although the assignments revealed considerable student confusion about what constituted popular and scientific literature. Student performance on formal written laboratory assignments improved over time: they were better able to follow the standard format as they gained experience. Students did obtain positive results in the Suzuki coupling project, although they needed more time than was allotted.  As a result, some products were not completely characterized. Another round of proposal resubmission/evaluation is needed to improve the proposals. LabWrite was not significantly utilized by students. It may be more useful in a non-majors’ lab course. The density of writing assignments was too high. Students did not have sufficient time to concentrate adequately on each assignment.

There is a need to provide time and space for collaborative work. Students avoid doing this work if in-class time is not provided At least some students needed help in using technology. They were surprisingly not very ‘adventurous’ in using software. One needs to emphasize that these are professional tools, not just instructional aids. Students need tools to evaluate whether references meet the qualifications of primary scientific literature. Students are allergic to proofreading even when using software packages that assist in this endeavor.

Recent Publications: 1998-2007 (*undergraduate co-author) 
 

45.      “Inhibitory Effect of DNA Structure on the Efficiency of Reaction of Guanosine Moieties with a Nitrenium Ion”, Novak, M.; Kennedy, S. A.  Journal of Physical Organic Chemistry 1998, 11, 71-76.

46.      “Synthesis and Characterization of the Food Derived Carcinogens 2-Hydroxylamino-α-carboline and 2-Hydroxylamino-3-methyl-α-carboline”, Kazerani. S.; Novak, M. Journal of Organic Chemistry 1998, 63, 895-897.

47.      “Nitrenium Ions from Food-Derived Heterocyclic Arylamine Mutagens”, Novak, M.; Xu, L.; Wolf*, R. A.  Journal of the American Chemical Society 1998, 120, 1643-1644.

48.      “Azide and Solvent Trapping of Electrophilic Intermediates Generated during the Hydrolysis of N-(Sulfonatooxy)-N-acetyl-4-aminostilbene”, Novak, M.; Kayser, K. J.; Brooks, M. E. Journal of Organic Chemistry 1998, 63, 5489-5496.

49.      “Hydrolysis Reactions of N-Sulfonatooxy-N-acetyl-1-aminonaphthalene and N-Sulfonatooxy-N-acetyl-2-aminonaphthalene: Limited Correlations of Nitrenium Ion Azide/Solvent Selectivities with Mutagenicities of the Corresponding Amines”, Novak, M.; VandeWater*, A. J.; Brown*, A. J.; Sanzenbacher*, S. A.; Hunt*, L. A.; Kolb*, B. A.; Brooks, M. E.  Journal of Organic Chemistry 1999, 64, 6023-6031.

50.      “Correlation of Azide/Solvent Selectivities for Nitrenium Ions with Ab Initio Hydration Energies: Understanding the Kinetic Lability of Nitrenium Ions in Aqueous Solution”, Novak, M.; Lin, J. Journal of Organic Chemistry 1999, 64, 6032-6040.

51.      “Spectroscopic Characterization by Laser Flash Photolysis of Electrophilic Intermediates Derived from 4-Aminostilbenes.  Stilbene “Nitrenium” Ions and Quinone Methide Imines”, Bose, R.; Ahmad, A. R.; Dicks, A. P.; Novak, M.; Kayser, K. J.; McClelland, R. A. Journal of the Chemical Society, Perkin Transactions 2 1999, 1591-1599.

52.      “Characterization of the 2-(α-Carbolinyl)nitrenium Ion and Its Conjugate Base Produced during the  Decomposition of the Model Carcinogen 2-N-(Pivaloyloxy)-2-amino-α-carboline in Aqueous Solution”, Novak, M.; Kazerani, S. Journal of the American Chemical Society 2000, 122, 3606-3616.

53.      “N-Arylnitrenium Ions”, Novak, M; Rajagopal, S. in Advances in Physical Organic Chemistry, Vol. 36; Tidwell, T. T.; Richard, J. P. Eds.; Academic Press: New York, 2001; pp 167-253.

54.      “Kinetics of Hydrolysis of 8-(Arylamino)-2´-deoxyguanosines”, Novak, M.; Ruenz, M.; Kazerani, S.; Toth, K.; Nguyen, T.-M.; Heinrich,* B. Journal of Organic Chemistry 2002, 67, 2303-2308.

55.      “Reactivity and Selectivity of the N-Acetyl-Glu-P-1, N-Acetyl-Glu-P-2, N-Acetyl-MeIQx, and N-Acetyl-IQx Nitrenium Ions: Comparison to Carbocyclic N-Arylnitrenium Ions”, Novak, M.; Toth, K.; Rajagopal, S.; Brooks, M.; Hott*, L. L.;  Moslener*, M. Journal of the American Chemical Society 2002, 124, 7972-7981.

56.      “Correlations of Nitrenium Ion Selectivities with Quantitative Mutagenicity and Carcinogenicity of the Corresponding Amines”, Novak, M.; Rajagopal, S. Chemical Research in Toxicology 2002, 15, 1495-1503.

57.      “Unusual Reactions of the Model Carcinogen N-Acetoxy-N-acetyl-2-amino-α-carboline”, Novak, M.; Nguyen, T.-M.  Journal of Organic Chemistry 2003, 68, 9875-9881.

58.      “Synthesis and Characterization of the Aqueous Solution Chemistry of the Food-Derived Carcinogen Model N-Acetoxy-N-(1-methyl-5H-pyrido[4,5-b]indol-3yl)acetamide and its N-Pivaloyloxy Analogue”, Rajagopal, S.; Brooks, M. E.; Nguyen, T.-M.; Novak, M. Tetrahedron 2003, 59, 8003-8010.

59.      “Chemistry of Carcinogenic and Mutagenic Metabolites of Heterocyclic Aromatic Amines” Novak, M.; Rajagopal, S.; Xu, L.; Kazerani, S.; Toth, K.; Brooks, M. E.; Nguyen, T.-M. Journal of Physical Organic Chemistry 2004, 17, 615-624.

60.      “Generation and Trapping of the 4-Biphenylyloxenium Ion by Water and Azide: Comparisons with the 4-Biphenylylnitrenium Ion”, Novak, M.; Glover, S. A. Journal of the American Chemical Society 2004, 126, 7748-7749.

61.      “The Hydrolysis of 4-Acyloxy-4-substituted-2,5-cyclohexadienones: Limitations of Aryloxenium Ion Chemistry”, Novak, M.; Glover, S. A.  Journal of the American Chemical Society 2005, 127, 8090-8097.

62.      “Computational Study of the Properties of Phenyloxenium Ions: A Comparison with Phenylnitrenium and Phenylcarbenium Ions”, Glover, S. A.; Novak, M. Canadian Journal of Chemistry 2005, 83, 1372-1381.

63.      “4´-Substituted-4-biphenylyloxenium Ions: Reactivity and Selectivity In Aqueous Solution”, Novak, M.;  Poturalski*, M. J.;  Johnson*, W. L.; Jones*, M. P.; Wang, Y.; Glover, S. A. Journal of Organic Chemistry 2006, 71, 3778-3785.

64.      “Synthesis and Decomposition of an Ester Derivative of the Procarcinogen and Promutagen, PhIP, 2-Amino-1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridine: Unusual Nitrenium Ion Chemistry” Nguyen, T.-M.; Novak, M. Journal of Organic Chemistry 2007, 72, 4698-4706.

65.      “A Research Project in the Organic Instructional Laboratory Involving the Suzuki-Miyaura Cross Coupling Reaction Novak, M.; Wang, Y.-T.; Ambrogio*, M. W.; Chan*, C. A.; Davis*, H. E.; Goodwin*, K. S.; Hadley*, M. A.; Hall*, C. M.; Herrick*, A. M.; Ivanov*, A. S.; Mueller*, C. M.; Oh*, J. J.; Soukup*, R. J.; Sullivan*, T. J.; Todd*, A. M. The Chemical Educator 2007, 12, 414-418.

66.      “Chemistry of 4-Alkylaryloxenium Ion “Precursors”: Sound and Fury Signifying Something?” Novak, M.; Brinster*, A. M.; Dickhoff*, J. N.; Erb*, J. M.; Jones*, M. P.; Leopold*, S. H.; Vollman*, A. T.; Wang, Y.-T.; Glover, S. A. Journal of Organic Chemistry 2007, 72, 9954-9962.

67.  “Direct Detection of a Transient Oxenium Ion in Water Generated by Laser Flash Photolysis” Wang, Y.-T.; Wang, J.; Platz, M. S.; Novak, M. Journal of the American Chemical Society 2007, 129, 14566-14567.