Chemistry for Biochemists II: Molecular Orbitals, Bonding and Hybridization

Week 1, Molecular Orbitals, Bonding and Hybridization

What determines the number of molecular orbitals (MOs) formed?

Number of input atomic orbitals (AOs).

What principle dictates filling orbitals from lowest to highest energy?

Aufbau Principle.

What is the maximum number of electrons per MO/AO?

2 (opposite spins).

How is bond order calculated in MO theory?

(Bonding e⁻ − Antibonding e⁻) / 2.

Why does He₂ not exist?

Bond order = 0 (antibonding orbitals filled).

Which bond is symmetric about the bond axis?

σ-bond (end-on overlap).

Which bond is asymmetric and involves side-on p-orbital overlap?

π-bond.

Why are σ-bonds stronger than π-bonds?

Greater orbital overlap.

What makes double bonds rigid?

1σ + 1π bond (prevents rotation).

Where are π-bonds critical for light absorption?

Conjugated systems (e.g., retinal).

Hund’s Rule & Electron Spin

Q

A

What rule maximizes parallel spins in degenerate orbitals?

Hund’s Rule.

Why is O₂ paramagnetic?

Two unpaired electrons in degenerate orbitals.

How does hemoglobin’s Fe²⁺ bind O₂?

Uses unpaired d-electrons.

What defines atomic orbital shapes/energies?

Hydrogen atom model.

What is the orbital energy order?

1s < 2s < 2p < 3s < 3p < 4s < 3d.

Why do transition metals use d-orbitals?

n=3 includes 5 d-orbitals (e.g., Fe in enzymes).

Which fills first: 4s or 3d?

4s (lower energy).

What hybridization gives tetrahedral geometry?

sp³ (e.g., CH₄).

What shape does sp² hybridization create?

Trigonal planar (e.g., C=C).

Where are lone pairs placed if resonance is possible?

p-orbitals (not hybrids).

How does sp² hybridization affect DNA?

Enables π-stacking in bases.

How does resonance stabilize molecules?

Delocalizes electrons (e.g., ATP).

How is molecular charge calculated?

Valence e⁻ − (bonds + lone pairs).

Why are charged amino acids important?

Mediate enzyme-substrate interactions (e.g., glutamate⁻).

Connections to Biochemistry

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A

How does MO theory explain enzyme redox reactions?

Bond order changes (e.g., electron transport chain).

What determines DNA/protein 3D structure?

Hybridization (e.g., sp³ in α-helices).

What stabilizes DNA base pairing?

Resonance (π-stacking).