Introduction to Organic Chemistry, Structural Formulas, and Chemical Bonding, and Formal Charge

Organic chemistry is considered the heart of science, particularly as one advances to higher-level studies where branches such as biology, chemistry, and physics begin to intermingle.
It is a foundational component for biological concepts, which is why it is heavily emphasized on professional exams like the Medical College Admission Test (MCAT) and dental school entrance exams.
Organic molecules are pervasive in daily life: for example, roasted coffee beans contain over $1,000$ chemical compounds. - The distinct aromas of coffee are caused by various organic compounds. - Nitrogen-based organic compounds, known as amines, often have very distinct and typically unpleasant (smelly) odors.

Organic chemistry is defined as the study of all carbon compounds.
Carbon is unique because it can form long chains and rings, a property that gives rise to a vast array of chemical properties.
Common elements found alongside carbon (heteroatoms) in organic molecules include: - Halogens: Bromine ( $Br$ ), Chlorine ( $Cl$ ), Fluorine ( $F$ ), and Iodine ( $I$ ). - Sulfur ( $S$ ). - Oxygen ( $O$ ). - Nitrogen ( $N$ ).
Molecule stability depends on the specific atoms present. Compounds consisting mostly of carbon and hydrogen are generally very stable, while the introduction of heteroatoms provides new sets of properties and varying levels of stability.

For every functional group covered in the course (and in 2262), students must mast four core themes: - Nomenclature: How to name the compounds. - Structure: The physical arrangement and stability of the molecule. - Reactions: Identifying the chemical transformations the group participates in. - Mechanisms: The step-by-step process of how a reaction proceeds from starting material (reactants) to final material (products).

While General Chemistry focuses on Lewis structures, Organic Chemistry utilizes skeletal structures (also called bond-line formulas).
Rules for Bond-Line Formulas: - Carbon and hydrogen symbols are typically omitted. - A zig-zag format is used; each vertex represents a carbon atom, and the end of every line represents a carbon atom. - Exceptions where hydrogen must be drawn: - When hydrogen is bonded to a carbon involved in a carbon-carbon triple bond. - When hydrogen is attached to the carbon in an aldehyde functional group. - Heteroatoms: Atoms like halogens ( $O, N, S$ ) must be explicitly written out. Additionally, any hydrogen atoms bonded to these heteroatoms (e.g., the $H$ in an $OH$ or $NH_2$ group) must be shown.
Determining Hydrogen Counts: To determine the number of omitted hydrogens, remember that carbon must have $4$ bonds to be neutral. If a carbon vertex shows $2$ bonds, there are $2$ implied hydrogens ( $4 - 2 = 2$ ). If it shows only $1$ bond, there are $3$ implied hydrogens.

Periodic Table Trends: - Elements in the same row have similar sizes. - Elements in the same column share similar electronic and chemical properties because they have the same number of valence electrons.
Atomic Structure and Electrons: - Principal Quantum Number ( $n$ ): Defines the shell ( $n = 1, 2, 3...$ ). - Orbitals: - $s$ orbitals are spherical; as $n$ increases, the orbital size increases (e.g., $3s$ is larger than $1s$ ). - $p$ orbitals are dumbbell-shaped with two lobes (top and bottom) and exist in three orientations: $p_x$ , $p_y$ , and $p_z$ . - Aufbau Principle: Electrons fill orbitals in order of increasing energy (lowest energy first). - Valence Electrons: Found in the outermost shell; these are the only electrons involved in chemical bonding.

Ionic Bonds: Characterized by the electrostatic force holding ions together. It involves the transfer of electrons from an atom of low electronegativity (metal) to an atom of high electronegativity (nonmetal). This results in a cation (positive charge) and an anion (negative charge).
Covalent Bonds: Formed by the sharing of electrons between two nonmetals. For example, in $Cl_2$ , each chlorine atom shares its seventh valence electron to achieve an octet.
The Octet Rule: Atoms gain, lose, or share electrons to be surrounded by $8$ valence electrons, mimicking noble gas configurations.
Electronegativity: The ability of an atom to attract electrons to itself. This creates dipole moments. In Hydrogen Fluoride ( $HF$ ), electrons spend more time near the more electronegative Fluorine, creating a partial negative charge ( $\delta^-$ ) on $F$ and a partial positive charge ( $\delta^+$ ) on $H$ .
Determining Bond Type by Electronegativity Difference ( $\Delta EN$ ): - Nonpolar Covalent: $\Delta EN < 0.5$ - Polar Covalent: $0.5 \le \Delta EN \le 1.9$ - Ionic: $\Delta EN > 1.9$

Formal Charge Formula: $\text{Formal Charge} = \text{Group Number} - [\text{Number of Lone Pair Electrons} + \frac{1}{2}(\text{Number of Bonding Electrons})]$
Heuristics for Neutral Atoms: - Hydrogen: $1$ bond. - Carbon: $4$ bonds, $0$ lone pairs. - Nitrogen: $3$ bonds, $1$ lone pair. - Oxygen: $2$ bonds, $2$ lone pairs. - Halogens: $1$ bond, $3$ lone pairs.
Exceptions to the Octet Rule: - Expanded Octet: Sulfur and Phosphorus can accommodate $10$ or $12$ electrons. - Incomplete Octet: Aluminum, Beryllium, and Boron often have only $6$ electrons around them.
Constitutional Isomers: Molecules with the same molecular formula but different structural connectivity. Examples include Ethanol (an alcohol) and Dimethyl Ether (an ether), both with the formula $C_2H_6O$ .

Carbocation: A carbon atom with an overall positive ( $+1$ ) formal charge. It typically has $3$ bonds and $0$ lone pairs, failing the octet rule.
Carbanion: A carbon atom with an overall negative ( $-1$ ) formal charge. It typically has $3$ bonds and $1$ lone pair of electrons.
Free Radical: An atom with an unpaired electron. A carbon free radical has $3$ bonds and one single unpaired electron; its formal charge is calculated as $4 - 1 - 3 = 0$ .
Oxygen Cations: When oxygen has $3$ bonds and $1$ lone pair, it carries a $+1$ formal charge (e.g., hydronium-type environments in organic molecules).
Preferred Structures: If multiple elements can carry a negative formal charge, the structure with the negative charge on the more electronegative atom is preferred.

Question: When drawing bond-line structures, how do we handle aldehydes?
Answer: In an aldehyde, we typically do draw the hydrogen atom attached to the carbonyl carbon, though there are specific conventions we will cover later.
Question: Why do we ignore math like stoichiometry and gas laws in this course?
Answer: Organic chemistry is more conceptual and focuses on what is happening at the molecular level rather than quantitative calculations like moles or equilibrium constants from General Chemistry.
Question: Do we need to know the specific names for all charged carbons?
Answer: Yes. You must commit the terms "carbocation" and "carbanion" to memory, as they are fundamental to understanding reactions in later chapters.
Question: Will the slides with written notes be posted?
Answer: No, only the clean slides are posted. Students are encouraged to take pictures or notes during the lecture as updating annotated slides is too cumbersome.