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Organic Chemistry ACCM Journal of Chemical Education Anchoring Concepts Content Map for Organic Chemistry Organic Chemistry Anchoring Concepts Content Map Jeffrey R. Raker,† Thomas Holme†* and Kristen Murphy‡ †Department of Chemistry, Iowa State University, Ames, Iowa 50011 United States; *[email protected] ‡Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53201 United States The outline below delineates the anchoring concepts content map for organic chemistry. I. Atoms: Matter consists of atoms that have internal structures that dictate their chemical and physical behavior. A. Atoms have unique chemical identities based on the number of protons in the nucleus. 1. The atomic number and mass number are used to determine average atomic weight and identify isotopes, which play a part in understanding techniques such as MS, NMR, or IR and rates of reactions via kinetic isotope effects. B. Electrons play the key role for atoms to bond with other atoms. 1. Electrons play a role in understanding the relative stability of resonance structures. a. Stabilization of anions helps to explain pKa values and relative acidities of protons. 2. Some reactions occur because molecules that are electrophilic are prone to react with regions where electron density is high. a. Electron-deficient atoms that seek electron-rich atoms are called electrophiles (meaning “electron seeking”). Electrophiles are commonly neutral or positively charged. b. Alkenes and alkynes are electron-rich and therefore are susceptible to electrophilic addition. Alcohols and alkyl halides are often formed from alkenes via electrophilic addition. 3. Some reactions occur because molecules that are nucleophilic are prone to react with regions where electron density is low. a. Electron-rich atoms that seek electron-deficient atoms are called nucleophiles (meaning “nucleus seeking”). Nucleophiles are commonly neutral or negatively charged. C. Atoms display a periodicity in their structures and observable phenomena that depend on that structure. 1. The valence of the various atoms commonly found in organic molecules shows the periodicity in structure and the phenomena that result from it (e.g., nucleophilicity trends, pKa properties). 2. Organic molecules reflect the periodicity of atoms via bond strengths and bond lengths. D. Most information about atoms is inferred from studies on collections of atoms often involving an interaction with electromagnetic radiation. 1. A discussion of the major historical developments in organic chemistry highlights how organic chemistry discoveries were made. 2. Key techniques for structural elucidation include UV, IR, NMR, and MS. Supporting Information for DOI: 10.1021/ed400175w Page 1 of 15 Journal of Chemical Education Anchoring Concepts Content Map for Organic Chemistry E. Macroscopic samples of matter contain so many atoms that they are counted in moles. 1. Mole-based stoichiometry calculations (i.e., molar equivalents and limiting reagents) are used to determine percentage yield, particularly in the laboratory. F. Atoms maintain their identity, except in nuclear reactions. G. Ions arise when the number of electrons and protons are not equal, and can be formed from atoms. 1. Metal–nonmetal bonds have a large dipole and can function in organic reactions as a strong base or strong nucleophile. II. Bonding: Atoms interact via electrostatic forces to form chemical bonds. A. Because protons and electrons are charged, physical models of bonding are based on electrostatic forces. 1. Organic molecules are held together with covalent bonds that arise from the sharing of electron pairs between nuclei. a. In alkanes, carbons can be labeled as primary, secondary, tertiary, or quaternary, depending on the number of non-hydrogen substituents (i.e., 1, 2, 3, or 4 respectively) on the labeled carbon. 2. An uneven sharing of the electrons in a chemical bond leads to a bond dipole moment. a. Polar bonds (such as cyano groups) result from unequal sharing of electrons (due to electronegativity differences) between two covalently bonded atoms, resulting in a bond dipole moment. b. Carbonyls are an extremely polar functional group; the carbon is partially positive and the oxygen is partially negative. Therefore, the carbon of a carbonyl is very electrophilic. c. Conversion of an alkyl halide to an organomagnesium (or lithium– lithium and copper) results in a partially negative carbon that functions as a nucleophile. Organometallic reagents (e.g., Grignard or Gilman) are strong nucleophiles and participate in a variety of reactions that involve nucleophilic substitution or addition. B. Because chemical bonds arise from sharing of negatively charged electrons between positively charged nuclei, the overall electrostatic interaction is attractive. 1. Chemical bonds result from shared electrons; nuclei involved in the sharing and number of electrons shared results in differences in bond energy. a. Single, double, and triple bonds between atoms give rise to patterns in bond energies and lengths. C. When chemical bonds form, the overall energy of the bonding atoms is lowered relative to free atoms, and therefore energy is released. 1. A chemical bond results in the lowest energy orbitals being filled such that the overall energy change of the system is negative. 2. Chemical bonds can interact in ways to lower the overall energy of the molecule. a. Conjugated alkenes are uniquely stable due to conjugation (p-orbital overlap). Supporting Information for DOI: 10.1021/ed400175w Page 2 of 15 Journal of Chemical Education Anchoring Concepts Content Map for Organic Chemistry b. Benzene is uniquely stable (i.e., aromatic) due to cyclic conjugation of π- bonds. c. Aromatic compounds are flat, continuous cyclic arrays of p-orbitals that contain 4n+2 electrons (anti-aromatic compounds have 4n electrons). D. To break a chemical bond requires an input of energy. 1. The breaking of a bond homolytically requires the input of energy, measured as the bond dissociation energy. E. A theoretical construct that describes chemical bonding utilizes the construction of molecular orbitals for the bond based on overlap of atomic orbitals on the constituent atoms. 1. Hybridization, resonance, and molecular orbital theory provide information about bond formation. a. Molecular orbital theory is based on the wavelike nature of electrons. Atomic orbitals (i.e., s, p, d, f; based on the atomic orbitals of hydrogen) are mathematical probability functions for finding an electron in the circumscribed space for a given atom. Orbitals can be “hybridized” through a process of linear combinations of atomic orbitals’ hybridized orbitals (such as sp or sp3), and are used to better represent actual bond lengths, angles, and energies for molecules. Atomic and hybridized orbitals can be overlapped to form bonding and antibonding molecular orbitals and thus theoretical models of electronic structure and molecular geometry. b. Resonance structures are two or more Lewis structures that differ only in the absolute location of electrons. A weighted linear combination of resonance structures for a given molecule best represents the “actual” electron density of the molecule. c. Allylic radicals, cations, and anions are uniquely stable due to resonance stabilization. 2. The stereochemistry and regiochemistry of cycloaddition reactions is related to the symmetry of the orbitals. a. The products formed in a Diels–Alder reaction retain the stereochemistry of the starting materials. 3. Atomic orbitals mix to form bonding, nonbonding, and antibonding molecular orbitals such that the number of molecular orbitals produced equals the number of atomic orbitals used initially. a. Hybrid orbitals are necessary to describe the geometry of substituents on individual atoms (e.g., the tetrahedral geometry of carbon in methane). b. Orbital diagrams reduced to just p-orbitals are used to understand the differences between aromatic and anti-aromatic compounds. F. Covalent bonds can be categorized based on the number of electrons (pairs) shared. The most common categories are single, double, and triple bonds. 1. Single, double, and triple bonds are discussed in terms of sigma and pi bonds, and the differences in the relative bond lengths and strengths. a. Bonds formed by the overlap of s-orbitals or s-containing hybrid orbitals result in the formation of sigma (σ) bonds; sigma bonds are also formed from the end-to-end overlap of p-orbitals; bonds formed by the side-to- side overlap of p-orbitals result in the formation of pi (π) bonds. Supporting Information for DOI: 10.1021/ed400175w Page 3 of 15 Journal of Chemical Education Anchoring Concepts Content Map for Organic Chemistry b. The “degree(s) of unsaturation” (or index of hydrogen deficiency) is equal to the number of π-bonds or rings in a given molecule. In general, it is the difference between the number of hydrogens in a corresponding fully saturated molecule minus the actual number of hydrogens in the molecule divided by two. Incorporation of heteroatoms (e.g., N or halogens) impacts the way in which unsaturation is calculated. 2. Sigma and pi bonds have effects on geometric structure; in particular, rotation about a single bond occurs readily, while rotation about a double bond is hindered. a. Molecules can adopt conformations based on free rotation around σ- bonds. Relationships between atoms and substituent groups can be described as staggered or eclipsed, gauche or anti using Newman projections. Each conformation has a relative energy; molecules,
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