*"The Stereochemistry of the Ketonization Reaction of Enols," Zimmerman, H. E. J. Org. Chem., 1955, 20, 549-557. 
*"The Stereochemistry of the Ivanov and Reformatsky Reactions. I," Zimmerman, H. E.; Traxler, M. D. J. Am. Chem. Soc., 1957, 79, 1920-1923. 
*"The Photochemical Rearrangement of 4,4-Diphenylcyclohexadienone. Paper I on a General Theory of Photochemical Reactions," Zimmerman, H. E.; Schuster, D. I. J. Am. Chem. Soc., 1961, 83, 4486-4487. 
*"On Molecular Orbital Correlation Diagrams, the Occurrence of Möbius Systems in Cyclization Reactions, and Factors Controlling Ground and Excited State Reactions. I," Zimmerman, H. E. J. Am. Chem. Soc., 1966, 88, 1564-1565. 
*"Photochemical Migratory Aptitudes in Cyclohexenones. Mechanistic and Exploratory Organic Photochemistry. XXIII," Zimmerman, H. E.; Rieke, R. D.; Scheffer, J. R. J. Am. Chem. Soc., 1967, 89, 2033-2047. 
*"The Di-π-Methane Rearrangement. Interaction of Electronically Excited Vinyl Chromophores. Zimmerman, H. E.; Mariano, P. S. J. Am. Chem. Soc., 1969, 91, 1718-1727. 
*"The Barrelene to Semibullvalene Transformation. Correlation of Excited State Potential Energy Surfaces With Reactivity. Mechanistic and Exploratory Organic Photochemistry. XLIV," Zimmerman, H. E.; Binkley, R. W.; Givens, R. S.; Sherwin, M. A.; Grunewald, G. L.; J. Am. Chem. Soc., 1969, 91, 3316-3323.  .
*"The Möbius-Hückel Concept in Organic Chemistry. Application to Organic Molecules and Reactions," Zimmerman, H. E. Acc. Chem. Res., 1971, 4, 272-280. 
*"Quantum Mechanics for Organic Chemists," Zimmerman, H. E. Academic Press, New York, 1975. 
*"Some Theoretical Aspects of Organic Photochemistry," Zimmerman, H. E. Accts. of Chem. Research, 1982, 10, 312-317. 
*"Kinetic Protonation of Enols, Enolates and Analogs; The Stereochemistry of Ketonization," Zimmerman, H. E.. Accounts of Chem. Res.', 1987, 20, 263-268. 
*"Regioselectivity of the Birch Reduction", Zimmerman, H. E.; Wang, P. A., J. Am. Chem. Soc., 1993, 115, 2205-2216. 
*"The Meta Effect in Organic Photochemistry; Mechanistic and Exploratory Organic Photochemistry", Zimmerman, H. E., J. Am. Chem. Soc. 1995, 117, 8988-8991. 
*"Synthetic Aspects of the Di-π-methane Rearrangement", Zimmerman, H. E.; Armesto, D. Chem. Revs, 1996, 96, 3065-3112.  
*"Energy Distribution and Redistribution and Chemical Reactivity. The Generalized Delta Overlap-Density Method for Ground State and Electron Transfer Reactions; A new Quantitative Counterpart of Electron Pushing”, Zimmerman, H. E.; Alabugin, I. V. J. Am. Chem. Soc. 2001, 121, 2265-2270  
*“Inter and Intramolecular Stereoselective Protonation of Enols”, Zimmerman, H. E.; Wang, P., J. Org. Chem. 2002, 69, 9216-9226. 
*"Triplet Photochemistry of Vinyl Cyclopropenes; Mechanistic and Exploratory Organic Photochemistry",  Zimmerman, H. E., J Org. Chem. 2009, 73, 1247-1251. .