Communication pubs.acs.org/jchemeduc
Transition-Structure Catalog of Organic Reactions Daniel H. Ess* Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States S Supporting Information *
ABSTRACT: Modern organic chemistry textbooks contain qualitative Lewis-structure drawings of transition structures. Missing from these drawings are estimates of partial bond lengths. A catalog of accurate density functional ground and transition structures for radical abstraction, substitution, elimination, oxidation, and pericyclic reactions is provided in the Supporting Information and discussed here. These xyz transition-structure coordinates can be conveniently and easily viewed in a variety of free and commercial viewers and provide the ability to quantitatively discuss bonding changes in organic reactions. In addition to the lowest-energy-pathway transition structures, this catalog also provides higher-energy-pathway transition structures, for example, backside and frontside SN2 transition structures as well as anti and syn E2 transition structures. KEYWORDS: Second-Year Undergraduate, Organic Chemistry, Computer-Based Learning, Computational Chemistry, Molecular Modeling
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for all reactions except OsO4 addition to ethylene that utilized the M06 method with the LANL2DZ effective core potential for Os and the 6-311+G(2df,2p) basis set for all other atoms. For open-shell species, unrestricted-type calculations were carried out. All calculations used an ultrafine integration grid. These structures can be viewed by opening the xyz coordinate files in a variety of free or commercial programs. A list of popular programs is given in a README file in the Supporting Information.
lthough undergraduate organic textbooks do not derive transition-state theory, these books use it to rationalize reactivity and selectivity in organic reactions.1 This often occurs in the form of drawing a reaction coordinate energy diagram with valleys and peaks along with sketching out the minima and transition structures (TSs).2 Missing from these Lewis-structure drawings is an estimation of partial bond lengths that would provide quantitative and additional qualitative insight into how much bonding has reorganized. In addition, these Lewisstructure drawings often do not convey the correct threedimensional (3D) structure. To combat this 3D downfall, it has become popular to animate reaction pathways.3 Although these animations are appealing, many are done with no precise quantum mechanical definition of the transition structure or done with low-level or semiempirical quantum mechanics.4 In addition, extracting transition-structure data is either impossible or difficult. A density-functional transition-structure catalog is introduced that provides convenient xyz coordinates in the Supporting Information for five reaction types: (i) halogen radical hydrogen atom abstraction, (ii) bimolecular substitution, (iii) bimolecular elimination, (iv) alkene oxidation, and (v) pericyclic reactions. By providing the computed xyz coordinate files that can be viewed in a variety of free or commercial viewers, instructors will have immediate access to quantitative information about transition structures such as bond lengths, angles, and dihedral angles.
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Halogen Radical Hydrogen Atom Transfer
The hydrogen atom transfer reaction between C−H bonds and bromine or chlorine atoms is the first propagation step in the radical halogenation of alkanes. The catalog contains TSs for methane, ethane, and propane hydrogen atom transfer. Figure 1 showcases how the transition structures for ethane hydrogen atom transfer can be presented in a Lewis-type drawing.
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Figure 1. Bromine and chlorine radical hydrogen atom transfer transition structures depicted in Lewis-structure representation. The bond lengths are in Å.
CHOICE OF THEORETICAL METHOD The structures presented in the TS catalog are based on the M06 set of density functional methods. The M06 and M06-2X methods are hybrid meta functionals designed for broad applicability including transition metals, main group thermochemistry, and medium-range correlation energy and are the most generally accurate functionals currently available.5 The Hessian was computed for each structure to confirm it as a minimum or first-order saddle point in the gas phase. The M06-2X method with the 6-311+G(2df,2p) basis set was used © 2012 American Chemical Society and Division of Chemical Education, Inc.
REACTION TYPES
Substitution Reactions
The bimolecular substitution transition state involves bond formation between a nucleophile and electrophile with simultaneous ejection of a leaving group. Figure 2 shows the Published: April 5, 2012 817
dx.doi.org/10.1021/ed2005856 | J. Chem. Educ. 2012, 89, 817−818
Journal of Chemical Education
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Communication
AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected].
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ACKNOWLEDGMENTS BYU and the Fulton Supercomputing Lab are acknowledged for computational support.
Figure 2. SN2 backside (top) and frontside (bottom) transition structures for bromide with methyl bromide. The bond lengths are in angstroms (Å).
SN 2 6 backside and frontside 7 transition structures for degenerate halide exchange between bromide and methyl bromide. The transition-structure catalog also contains coordinates for SN2 reactions between bromide, chloride, and fluoride nucleophiles with methyl and ethyl alkyl halide electrophiles. Also included is the transition structure for the reaction of cyanide with methyl bromide. Elimination Reactions
Bimolecular elimination (E2) TSs have also been cataloged. Included are both the lower energy anti and the higher energy syn TSs. Figure 3 shows Lewis-type depictions of these TSs for
Figure 3. Anti and syn E2 transition structures for reaction of bromide with ethyl bromide.
bromide with ethyl bromide. The TS catalog also provides elimination TSs for ethyl chloride. Alkene Oxidation Reactions
The catalog contains well-established TSs for OsO4 addition to ethylene,8 concerted 1,3-dipolar cycloaddition of ozone with ethylene,9 and epoxidation of ethylene by performic acid.10 Pericyclic Reactions
The TS catalog also includes concerted hydrocarbon pericyclic reactions for the Diels−Alder reaction between butadiene and ethylene, cyclopentadiene and ethylene, and the Cope and Claisen rearrangements.11
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CONCLUSION The TS catalog presented here is a collection of structures intended as an aid for instructors teaching undergraduate organic chemistry. The computed structures are advantageous because they provide quantitative and additional qualitative insight into bonding reorganization. The catalog is given as an easily useable set of xyz coordinate files in the Supporting Information that can be opened and viewed in a variety of free or commercial software programs.
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REFERENCES
(1) (a) Eyring, H. J. Chem. Phys. 1935, 3, 107−115. (b) Eyring, H. Chem. Rev. 1935, 17, 65−77. (c) Laidler, K. J.; King, M. C. J. Phys. Chem. 1983, 87, 2657−2664. (d) Truhlar, D. G.; Hase, W. L.; Haynes, J. T. J. Phys. Chem. 1982, 87, 2664−2682. For textbook discussion on transition state theory see: (e) Anslyn, E. V.; Dougherty, D. A. Modern Physical Organic Chemistry; University Science Books: Sausalito, CA, 2006; pp 363−369. (2) A transition structure is a quantum mechanical stationary point on a potential energy surface. A transition state requires the free energy surface. However, in most cases the transition structure and transition state are expected to be similar. For a nice discussion on this topic see: Leach, A. R. Molecular Modelling Principles and Applications, 2nd ed.; Pearson Education Limited: Harlow, England, 2001; pp 279− 283. (3) (a) Fleming, S. A.; Savage, P. B.; Hart, G. R. J. Chem. Educ. 2000, 77, 790−793. For the current version see: Fleming, S. A.; Savage, P. B.; Hart, G. R. Organic Reaction Animations [CD-ROM], Version 2.3 published with Jones, M., Jr.; Fleming, S. A. Organic Chemistry, 4th ed.; W.W. Norton & Company, Inc.: New York, 2010. (b) Interactive Organic Reaction Animation Online. http://www.chemtube3d.com/ (accessed Feb 2012). (4) Mol4D provides a Web-based environment to calculate and then animate a limited number of organic reactions using low-level quantum mechanics. See: Stueker, O.; Brunberg, I.; Fels, G.; Borkent, H.; Rooij, J. v. J. Chem. Educ. 2003, 80, 583. http:// wetche.cmbi.ru.nl//organic/mopjob.html (accessed Feb 2012). (5) (a) Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157−167. (b) Xu, X.; Alecu, I. M.; Truhlar, D. G. J. Chem. Theory Comput. 2011, 7, 1667−1676. (6) M06-2X performs very well for SN2 and E2 activation barriers. See (a) Bento, A. P.; Solà, M.; Bickelhuapt, F. M. J. Chem. Theory Comput. 2008, 4, 929−940. (b) Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2010, 6, 1104−1108. (7) Several textbooks have adopted a frontier orbital explanation for preferential backside attack because of the location of the lowest unoccupied molecular orbital (LUMO) on the electrophile. However, energy decomposition analysis, although not a rigorously unique way to dissect energy, suggests that the classic explanation of charge and steric repulsion is also important. See: Bento, A. P.; Bickelhuapt, F. M. J. Org. Chem. 2008, 73, 7290−7299 and references therein. (8) (a) Veldkamp, A.; Frenking, G. J. Am. Chem. Soc. 1994, 116, 4937−4946. (b) Dapprich, S.; Ujaque, G.; Maseras, F.; Lledos, A.; Musaev, D. G.; Morokuma, K. J. Am. Chem. Soc. 1996, 118, 11660− 11661. (c) Pidun, U.; Boehme, C.; Frenking, G. Angew. Chem., Int. Ed. Engl. 1996, 35, 2817−2820. (d) Torrent, M.; Deng, L.; Duran, M.; Sola, M.; Ziegler, T. Organometallics 1997, 16, 13−19. (e) DelMonte, A. J.; Haller, J.; Houk, K. N.; Sharpless, K. B.; Singleton, D. A.; Strassner, T.; Thomas, A. A. J. Am. Chem. Soc. 1997, 119, 9907−9908. (f) Deubel, D. V.; Frenking, G. J. Am. Chem. Soc. 1999, 121, 2021− 2031. (g) Ess, D. H. J. Org. Chem. 2009, 74, 1498−1508. (9) Wheeler, S. E.; Ess, D. H.; Houk, K. N. J. Phys. Chem. A 2008, 112, 1798−1807 and references therein. (10) Bach, R. D.; Owensby, A. L.; Gonzalez, C.; Schlegel, H. B. J. Am. Chem. Soc. 1991, 113, 2338−2339. (11) (a) Guner, V.; Khuong, K. S.; Leach, A. G.; Lee, P. S.; Bartberger, M. D.; Houk, K. N. J. Phys. Chem. A 2003, 107, 11445− 11459. (b) Ess, D. H.; Houk, K. N. J. Phys. Chem. A 2005, 109, 9542− 9553.
ASSOCIATED CONTENT
S Supporting Information *
Transition-structure catalog. This material is available via the Internet at http://pubs.acs.org. 818
dx.doi.org/10.1021/ed2005856 | J. Chem. Educ. 2012, 89, 817−818
