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Chemistry Foundations

Alex Payne

CCNY

2025.08.28

https://pdb101.rcsb.org/motm/motm-about

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Goals for Today

  • Review key concepts from Chemistry
    • Electron Orbitals
    • Periodic Trends
    • Chemical Bonds
    • Chemical determinants of molecular shape
  • Analyze a PDB structure

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Chemical Models Are (usually) Approximations of Quantum Physics

  • energies aren’t continuous – they are quantized
  • wave-particle duality
  • scary math
    • eigenvectors and eigenvalues
    • complex numbers
    • multivariable calculus
    • oh my!

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Time-Independent Schrodinger Equation

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Electron Orbitals are Waves of Electron Probability

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Electron orbitals have a set of unique shapes and energy levels

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Ground State Electron Configurations

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Atomic Properties and Periodic Trends

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Electron Shielding and Effective Nuclear Charge

https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/07%3A_Periodic_Properties_of_the_Elements/7.02%3A_Shielding_and_Effective_Nuclear_Charge

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Electronegativity – another wrong model, but a very useful one

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Atomic Radii

https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/07%3A_Periodic_Properties_of_the_Elements/7.03%3A_Sizes_of_Atoms_and_Ions

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Ionic Radii

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Charge density?

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A biophysically relevant aside - hydrated radii are different than ionic radii

Hayamizu, K., Chiba, Y. & Haishi, T. Dynamic ionic radius of alkali metal ions in aqueous solution: a pulsed-field gradient NMR study. RSC Adv. 11, 20252–20257 (2021) https://xlink.rsc.org/?DOI=D1RA02301B

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Charge density!

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A biophysically relevant aside - hydrated radii are different than ionic radii

Hayamizu, K., Chiba, Y. & Haishi, T. Dynamic ionic radius of alkali metal ions in aqueous solution: a pulsed-field gradient NMR study. RSC Adv. 11, 20252–20257 (2021) https://xlink.rsc.org/?DOI=D1RA02301B

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Goals for Today

  • Review key concepts from Chemistry
    • Electron Orbitals
    • Periodic Trends
    • Chemical Bonds
    • Chemical determinants of molecular shape
    • Begin discussing intermolecular forces

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Break

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Chemical Bonds (aren’t real)

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Chemical bonds represent a stable, average position between two atoms with electron orbital overlap

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Hybrid molecular orbitals explain chemical bond shape and order

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Valence-shell electron-pair repulsion (VSEPR)

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Quantum mechanical calculations reveal an even weirder picture, but the simpler models will work pretty well

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electrostatic potential

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Examples of Molecular Shape - Ethane

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Examples of Molecular Shape - Ethylene

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Comparing Ethane with Ethylene

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Molecular Orbitals and Resonance

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Other examples

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Chirality – Non-superimposable mirror images

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The dire consequence of chirality in the case of thalidomide

https://oxbridgeapplications.com/blog/same-but-different-a-story-in-chirality/

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Treats nausea and morning sickness in pregnant women

Highly toxic

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Molecules have preferred conformations

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To think about…

  • what models did we discuss today?
  • Pick one. Consider when it is a relevant model, and when you think it no longer becomes useful.

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Analyze a PDB Structure

  • Download PyMol or ChimeraX
  • Download a PDB Structure
    • 1A3N - DEOXY HUMAN HEMOGLOBIN
    • 6BB5 - Human Oxy-Hemoglobin
  • Compare surface, ball-and-stick, cartoon models
  • Identify Heme molecule
  • Compare deoxy vs oxy hemoglobin

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