Lecture 2 - Molecules and Bonds

Proton

A subatomic particle with positive charge found in the nucleus.

Neutron

A subatomic particle with neutral charge found in the nucleus.

Electron

A subatomic particle with negative charge that orbits the nucleus in orbitals.

Nucleus

The central core of an atom containing protons and neutrons.

Valence electrons

The electrons in the outermost orbital that participate in chemical bond formation.

VSEPR

Valence Shell Electron Pair Repulsion theory describing how electron pairs arrange in three-dimensional space.

Orbitals

Regions of space around the nucleus where electrons are likely to be found, each with different energy levels.

Covalent bond

A strong bond formed by shared electrons between two atoms.

Nonpolar covalent bond

A covalent bond in which electrons are shared equally between atoms with similar electronegativity values.

Polar covalent bond

A covalent bond in which electrons are shared unequally between atoms with different electronegativity values, creating partial charges.

Electronegativity

The attraction of an atom for its electrons, unique to each element.

Ionic bond

A weak bond formed between oppositely charged ions through electrostatic attraction.

Hydrogen bond

A weak electrostatic interaction between a lone pair of electrons on an electronegative atom (acceptor) and a hydrogen (donor) bonded covalently to another strongly electronegative atom.

H with N or O, NEVER H with C

hydrogen bond donor

A strongly electronegative atom (nitrogen or oxygen) covalently bonded to hydrogen that participates in hydrogen bonding.

hydrogen bond acceptor

An electronegative atom with a lone pair of electrons that accepts a hydrogen bond.

van der Waals interaction

A weak intermolecular force resulting from induced dipoles when atoms or molecules come within 5 nanometers of each other.

induced dipole

A temporary separation of charge in an atom or molecule caused by a nearby charged particle.

Dipole moment

The measure of separation of positive and negative charge in a molecule.

Cohesion

The tendency of molecules to stick together via hydrogen bonds.

Heat capacity

The amount of energy required to raise the temperature of a substance, high in water due to hydrogen bonding.

Water of hydration

water that is chemically combined with a substance to form a hydrate and can be expelled by heating

hydrophobic effect

The tendency of nonpolar molecules to aggregate and exclude water by forcing water to form hydrogen bonds with itself around the nonpolar material.

amphipathic

Having both hydrophobic and hydrophilic properties, as in molecules with a nonpolar tail and polar head group.

micelle

A spherical structure formed by amphipathic molecules with hydrophobic ends pointing inward and hydrophilic ends pointing outward in water.

membrane

A structure composed of a phospholipid bilayer and proteins that encloses the cell.

autohydration

The self-ionization of water forming hydronium ion and hydroxide ion.

pH

The negative logarithm of hydrogen ion concentration that measures acidity or basicity.

pOH

The negative logarithm of hydroxide ion concentration related to pH by pH + pOH = 14.

acid

A chemical that donates hydrogen ions to a solution, lowering pH.

base

A chemical that donates hydroxide ions to a solution, raising pH.

neutral

A solution with pH 7 where hydrogen ion concentration equals hydroxide ion concentration.

Aufbau principle

The principle that electrons fill lower energy orbitals first when building up the electronic configuration of an atom.

Know the basic structure of the atom.

By identifying that atoms consist of a nucleus containing protons and neutrons, with electrons arranged in orbitals of different energy levels orbiting the nucleus.

Know the subatomic particles.

By recognizing that protons have positive charge, neutrons have neutral charge, and electrons have negative charge.

Understand the Aufbau principle as it pertains to electron distribution.

By applying the principle that electrons fill lower energy orbitals first according to the building up method.

Understand how valence electrons participate in chemical bond formation.

By recognizing that valence electrons are the electrons in the outermost orbital that participate in bonding with other atoms.

Know the different types of chemical bonds.

By distinguishing between covalent bonds (nonpolar and polar), ionic bonds, hydrogen bonds, and van der Waals interactions.

Given the Periodic Table, be able to predict how many bonds an atom can form.

By determining that the number of electrons required to fill the outer orbital equals the number of possible covalent bonds.

Know what types of bonds are considered strong and weak based on electronegativity.

By recognizing that covalent bonds with electronegativity difference 0.0-2.0 are strong and ionic bonds with electronegativity difference 2.0-4.0 can be strong or weak, while hydrogen bonds and van der Waals are weak.

Be able to distinguish strong bonds from weak bonds based on charge interactions.

By identifying that strong bonds involve significant electron sharing or transfer while weak bonds involve electrostatic attractions between partial charges.

Be able to distinguish the types of weak bonds (ionic, hydrogen, hydrophobic / van der Waals).

By recognizing that ionic bonds form between oppositely charged ions, hydrogen bonds form between electronegative atoms and hydrogen, and van der Waals forces result from induced dipoles.

Know what elements can participate in hydrogen bonding.

By identifying that hydrogen bonding occurs when hydrogen is bonded covalently to nitrogen or oxygen, never with carbon.

Understand why dynamic living systems depend on weak bond interactions.

By explaining that many weak bonds together hold molecules in specific configurations while remaining flexible enough to be broken and reformed as needed.

Know how hydrogen bonding influences the properties of water: heat capacity, cohesion, density, hydration.

By describing that hydrogen bonds between water molecules create high heat capacity, cohesion between molecules, make solid ice less dense than liquid water, and allow water to dissolve polar molecules.

Be able to predict the behavior of hydrophilic, hydrophobic and amphipathic substances in water.

By recognizing that hydrophilic substances dissolve in water, hydrophobic substances do not dissolve and are avoided by water, and amphipathic substances have both hydrophobic and hydrophilic properties.

Understand how autohydration of water is related to pH.

By connecting the self-ionization of water producing hydronium ions and hydroxide ions to the pH scale and hydrogen ion concentration.

Be able to approximate the pH of various common materials.

By using the pH scale to estimate the pH of materials such as drain cleaner at pH 14, blood at pH 7.4, pure water at pH 7, and stomach acid at pH 1.