Short Story ⬡ Biochemistry

Why Bond Angles Are Determined

Learning molecular geometry and shape prediction using VSEPR theory.

  • #molecular geometry
  • #VSEPR theory
  • #bond angle
  • #molecular shape

"Why is the water molecule bent?"

Kana asked while looking at a molecular model.

Rei answered thoughtfully. "Electron pair repulsion. Can be explained by VSEPR theory."

"VSEPR?"

"Valence Shell Electron Pair Repulsion theory. Electron pairs repel each other, so they take positions as far apart as possible."

Milia began drawing a diagram. Oxygen at the center, electron pairs around it.

"There are four electron pairs around oxygen. Two are bonding pairs, two are lone pairs."

"With four, tetrahedral arrangement is most separated," Rei continued.

"But," Kana objected, "water molecules are bent, not linear, right?"

"Yes. Because lone pairs and bonding pairs differ in repulsion strength."

Milia illustrated in detail. Electron pairs of different sizes.

"Lone pairs are attracted to one atom," Rei explained.

"But bonding pairs are attracted to two atoms, confined to narrower space."

"So lone pairs occupy wider space."

Kana began to understand. "Lone pairs push bonding pairs away?"

"More precisely, they repel more strongly. As a result, the H-O-H angle becomes smaller than 109.5 degrees."

"104.5 degrees."

"Yes. Because lone pairs' space is wider."

Milia wrote another example. "NH₃: 107 degrees, CH₄: 109.5 degrees."

"Ammonia also has one lone pair, so the angle becomes smaller."

"Methane has all bonding pairs, so it's tetrahedral."

Kana asked questions in succession. "Why is CO₂ linear?"

"Only two electron pairs around carbon. With two, 180 degrees is most separated."

"Two C=O double bonds point in opposite directions."

Rei supplemented. "In VSEPR theory, double bonds are also treated as one electron pair group."

"Triple bonds too."

Milia made a table. Correspondence between number of electron pairs and basic shapes.

"Two: linear, three: trigonal planar, four: tetrahedral, five: trigonal bipyramidal, six: octahedral."

"From the basic shape, actual shape is determined by lone pair positions."

Kana gave a difficult example. "What about SF₆?"

"Six fluorines arrange octahedrally around sulfur," Rei answered.

"Only six bonding pairs, no lone pairs."

"So perfect octahedron."

Toma entered and joined the conversation. "XeF₄ is interesting."

"Six electron pairs around xenon. Four bonding pairs, two lone pairs."

Milia assembled a model. "Lone pairs at opposite positions of octahedron."

"Then the four fluorines become square planar arrangement."

Kana was moved. "Lone pair positions are also determined by repulsion minimization."

"Yes. Lone pairs take the most distant positions from each other."

Rei gave biomolecule examples. "Protein structure follows the same principle."

"Peptide bonds are planar. Because of partial double bond character."

"Amino acid side chain arrangement avoids steric hindrance."

Milia supplemented. "Hydrogen bonding also depends on angles."

"Linear hydrogen bonds are strongest."

"Protein α-helices and β-sheets have optimized hydrogen bond angles."

Kana asked seriously. "Does molecular shape determine function?"

"Yes," Rei emphasized. "Enzyme active sites, receptor-ligand binding, all are shape complementarity."

"Lock and key relationship."

Toma gave an example. "Hemoglobin's oxygen binding curve. Cooperativity is due to structural changes."

"When one oxygen binds, structure changes making the next oxygen easier to bind."

Milia said quietly. "Shape is function's language."

Rei nodded. "Molecular shape determines chemical properties."

"Same composition but different shapes means different properties. The essence of isomers."

Kana summarized in her notebook. "Bond angles are determined by electron pair repulsion. And angles determine molecular properties and functions."

Milia wrote finally. "Geometry is destiny."

"Geometry is destiny."

Outside the window, snow began falling. Hexagonal crystals. Ice structure is also determined by hydrogen bond angles. Bond angles create the beauty and function of matter.