Notes: Atoms, Bonds, Water, pH, Ocean Acidification

Nature of Atoms and Elements

  • Matter is composed of atoms; atoms have a nucleus (protons + neutrons) and electrons in orbitals.

  • Atomic number ZZ equals the number of protons (and, in a neutral atom, the number of electrons).

  • All atoms of an element share the same ZZ; mass number A=Z+NA = Z + N (where NN = neutrons).

  • Isotopes: same ZZ, different NN; some are radioactive with a half-life, t1/2t_{1/2}.

Atomic Structure and Energy Levels

  • Electrons occupy energy levels; levels labeled as K, L, M, N; each orbital holds up to two electrons.

  • Bohr model vs modern: orbitals are regions where electrons are likely found; energy levels increase with distance from the nucleus.

  • Electrons farther from the nucleus have higher potential energy.

  • Redox: oxidation = loss of electrons; reduction = gain of electrons.

Chemical Bonds and Electronegativity

  • Ionic bonds: transfer of electrons -> cations and anions; bonds arise from electrical attraction between ions.

  • Covalent bonds: atoms share electrons; bond strength depends on number of shared electrons; single, double, triple bonds exist.

  • Polar covalent vs nonpolar covalent: electronegativity differences cause unequal (polar) or equal (nonpolar) sharing of electrons.

Water: Structure and Hydrogen Bonding

  • Water is a polar molecule; partial charges: δ− on oxygen, δ+ on hydrogens.

  • Hydrogen bonds form between water molecules; individual bonds are weak but collectively strong.

  • Cohesion (water–water) and adhesion (water to polar surfaces) arise from hydrogen bonding.

Properties of Water

  • Emergent properties due to hydrogen bonding:

    • High specific heat: large energy required to change temperature.

    • High heat of vaporization: evaporation cools surfaces.

    • Ice is less dense than liquid water; ice floats.

    • Excellent solvent for polar molecules and ions; hydrophilic vs hydrophobic behavior.

pH, Acids, Bases, and Buffers

  • pH = −<br>log⁡[H+]-<br>\log [\mathrm{H^+}]; neutral water ~ pH 7.

  • Acids donate H+\mathrm{H^+}; bases accept H+\mathrm{H^+}.

  • Autoionization of water: H2O⇌H++OH−\mathrm{H_2O \rightleftharpoons H^+ + OH^-}

  • Buffers resist pH changes by releasing or absorbing H+\mathrm{H^+}; common biological buffer pairs include carbonic acid / bicarbonate.

Carbonate-Bicarbonate System and Ocean Acidification

  • Dissolved CO₂ forms carbonic acid: CO<em>2+H</em>2O⇌H<em>2CO</em>3\mathrm{CO<em>2 + H</em>2O \rightleftharpoons H<em>2CO</em>3}

  • Carbonic acid dissociates: H<em>2CO</em>3⇌H++HCO3−\mathrm{H<em>2CO</em>3 \rightleftharpoons H^+ + HCO_3^-}

  • Bicarbonate can dissociate: HCO<em>3−⇌H++CO</em>32−\mathrm{HCO<em>3^- \rightleftharpoons H^+ + CO</em>3^{2-}}

  • Increasing atmospheric CO₂ lowers ocean pH; carbonate ions decrease, reducing calcification for marine organisms; bicarbonate acts as a buffer but alters carbonate availability for CaCO₃ formation.

Quick Takeaways

  • Water’s polarity and hydrogen bonding drive its properties.

  • Four emergent properties support life (high specific heat, high heat of vaporization, density of ice, solvent abilities).

  • Ocean acidification poses risks to marine calcifiers and food webs.

Key Equations (recap)

  • Mass relation: A=Z+NA = Z + N

  • Ion charge (net): q=Z−Neq = Z - N_e

  • pH definition: pH=−log⁡[H+]\text{pH} = -\log [\mathrm{H^+}]

  • Water autoionization: H2O⇌H++OH−\mathrm{H_2O \rightleftharpoons H^+ + OH^-}

  • Covalent vs ionic bonding (conceptual).

  • Carbonate-bicarbonate system:

    • CO<em>2+H</em>2O⇌H<em>2CO</em>3CO<em>2 + H</em>2O \rightleftharpoons H<em>2CO</em>3

    • H<em>2CO</em>3⇌H++HCO3−H<em>2CO</em>3 \rightleftharpoons H^+ + HCO_3^-

    • HCO<em>3−⇌H++CO</em>32−HCO<em>3^- \rightleftharpoons H^+ + CO</em>3^{2-}