Appendix A — Periodic Table and Atomic Data

Reference data for the elements most important in organic chemistry, plus the orbital and geometric primitives that everything else builds on. Use this alongside Chs 1-3 (atoms, bonds, structure) and Ch 9 (NMR).

Periodic table — organic-relevant block

The elements you will actually meet in this book live in rows 1-4, plus Br and I. Transition metals appear as catalysts (Pd, Pt, Ni, Cu, Rh, Ru, Os, Hg) but their detailed electronic structure is not exam material here.

H                                                                He
Li Be                                          B  C  N  O  F   Ne
Na Mg                                          Al Si P  S  Cl  Ar
K  Ca  Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br  Kr
                                                       I (row 5)

Second-row elements (the backbone of organic chemistry)

Third-row and halogens

Reading the trends — EN rises right and falls down. Covalent radius falls right and rises down. Polarizability rises down (large diffuse electron clouds). These three trends explain most of organic reactivity (Ch 3).

Electronegativity scale (Pauling) — discussion

Electronegativity is an atom's pull on bonding electrons. The numbers are unitless and calibrated such that F = 3.98 and Cs ≈ 0.79. For organic chemistry, four practical thresholds matter:

Two consequences run through the whole book — bond dipoles (Ch 2), and the direction of nucleophile/electrophile flow (Chs 3, 10). When you draw a curved arrow, the electrons leave the less electronegative atom for the more electronegative one.

Bond dissociation energies — comprehensive (kcal/mol, homolytic)

BDE = energy to break A-B into A• + B•. Use for radical chemistry (Ch 18) and for thermochemical estimates (Ch 8).

C-H bonds by hybridization and environment

Trend — 3° < 2° < 1° < methyl (radical stability mirrors cation stability). Allylic and benzylic are even weaker due to resonance delocalization of the radical (Ch 18).

C-C bonds

C-X (halogen)

C-F is the strongest C-X bond — relevant for medicinal chemistry and ¹⁹F NMR. C-I is the weakest, hence iodides are the best leaving groups (Ch 10).

C-heteroatom (single bonds)

C=heteroatom (multiple bonds)

X-H and X-X reference

Bond lengths (Å)

Shorter = stronger, for a given pair of atoms. A C≡C bond is shorter and stronger than C=C, which is shorter and stronger than C-C.

Bond angles — VSEPR for organic-relevant geometries

Lone pairs occupy more space than bonding pairs, compressing bond angles (107° in NH₃, 104.5° in H₂O).

Atomic orbitals — shapes and signs

The sign (phase) of an orbital matters because bonding combinations require matching phases (constructive overlap) and antibonding combinations have mismatched phases. This is the entire basis for MO theory (Ch 2, Ch 19).

Hybrid orbitals — summary

Higher s character → shorter, stronger bond, and the electrons are held more tightly. Hence sp C-H (pKa ~25) is more acidic than sp² C-H (pKa ~44) is more acidic than sp³ C-H (pKa ~50). See Appendix B and Ch 3.

Dipole moments of common functional groups (D)

Molecular dipoles measured in debye (D). 1 D = 3.336 × 10⁻³⁰ C·m. A pure C-H bond is ~0.4 D; C=O is huge.

Nitriles and amides have surprisingly large dipoles — relevant to polar aprotic solvent strength (Ch 10) and to crystal packing in pharmaceuticals.

Polarizability — halogens and chalcogens

Polarizability (α, in 10⁻²⁴ cm³) measures how easily an electron cloud distorts. Larger atoms = more polarizable = better nucleophiles in protic solvents and better leaving groups.

Consequence — in protic solvents, nucleophilicity follows I⁻ > Br⁻ > Cl⁻ > F⁻ (opposite of basicity). In aprotic solvents, the order flips (Ch 10).

Ionic vs covalent radii (Å)

Cations are smaller than their neutral atoms; anions are larger. This explains why countercations matter in enolate chemistry (Li⁺ tight, K⁺ loose; Ch 27).

Isotopes used in organic chemistry

Magnetic properties / NMR-active nuclei

A nucleus is NMR-active if its spin I ≠ 0. Cross-reference Ch 9.

¹²C and ¹⁶O have I = 0 and are invisible to NMR. This is why ¹H NMR rarely shows direct C-H coupling — most carbons are ¹²C.

Formal charge — cheat sheet

Formula — formal charge = (valence e⁻ of neutral atom) − (lone pair e⁻) − (½ bonding e⁻)

Memorize the neutral patterns — C(4,0), N(3,1), O(2,2), X(1,3) — and reason away from those.

Oxidation states of carbon

Carbon's oxidation state ranges from −4 to +4 depending on what it's bound to. More bonds to O, N, X = higher (more oxidized); more bonds to H = lower (more reduced). Useful for tracking redox in reactions (Ch 36).

The oxidation-state ladder for a single carbon — alkane (−3 to −4) → alcohol (−2) → aldehyde/ketone (0) → carboxylic acid (+2) → CO₂ (+4) — is the spine of functional group interconversion (Ch 36).

Oxidation states of nitrogen, oxygen, sulfur

Print this. The atomic primitives — radii, EN, BDEs, hybridization, geometry — recur everywhere. Knowing them cold lets you reason about any reaction.