Atoms, Ions, Molecules, and Naming Compounds, CHM 11100 Ch. 2 – Study Notes
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Difficulty: Introductory to Intermediate | Prerequisites: Chapter 1 (metric units, classifications of matter)

Big Picture

Chapter 2 introduces the building blocks: what atoms are made of, how the periodic table organises them, and the rules for naming the compounds they form. This is the chapter where you learn the vocabulary of chemistry. If you cannot write a correct formula from a compound name (or vice versa), every later topic, from stoichiometry to reactions, becomes much harder. Naming compounds is one of the most heavily tested skills on Exam 1.

TL;DR

Atoms consist of protons, neutrons, and electrons. The periodic table groups elements by similar properties. Elements combine as ions (charge transfer) or molecules (electron sharing). Naming compounds follows a set of systematic rules that differ for ionic compounds, molecular compounds, and acids. Memorise the seven diatomic molecules, the common polyatomic ions, and the naming conventions.


Key Terms

Proton

A positively charged subatomic particle found in the nucleus. Its charge is +1, and its mass is approximately 1 amu. The number of protons defines which element an atom is.

Neutron

A neutral subatomic particle found in the nucleus, with a mass of approximately 1 amu. Changing the neutron count gives you a different isotope of the same element.

Electron

A negatively charged subatomic particle found outside the nucleus in electron clouds. Its mass is negligible compared to protons and neutrons. Electrons are what get gained, lost, or shared when atoms bond.

Atomic number (Z)

The number of protons in the nucleus of an atom. It defines the element and determines its position on the periodic table. In simple terms, Z is the element's identity card.

Mass number (A)

The total number of protons plus neutrons in the nucleus. A = Z + number of neutrons. Think of it as the "weight tag" for a specific isotope.

Isotope

Atoms of the same element (same number of protons) that have different numbers of neutrons. Isotopic symbols are written as ᴬ_Z X, where A is the mass number and Z is the atomic number. In simple terms, isotopes are versions of the same element that differ in mass.

Ion

An atom or group of atoms that has gained or lost electrons, giving it a net electrical charge. Positive ions are cations; negative ions are anions.

Cation

A positively charged ion, formed when an atom loses one or more electrons. Metals typically form cations. Think of "cat" as positive (a cat has paws, paws sounds like "pos").

Anion

A negatively charged ion, formed when an atom gains one or more electrons. Nonmetals typically form anions.

Diatomic molecule

A molecule consisting of exactly two atoms bonded together. Seven elements exist naturally as diatomic molecules: H₂, O₂, N₂, F₂, Cl₂, Br₂, I₂. The mnemonic "HONClBrIF" (or "Have No Fear Of Ice Cold Beer") helps you remember them.

Monoatomic ion

An ion formed from a single atom (e.g. Na⁺, Cl⁻). Main group metals and nonmetals form predictable monoatomic ions based on their group number.

Polyatomic ion

A charged group of two or more covalently bonded atoms that acts as a single unit (e.g. SO₄²⁻, NO₃⁻, NH₄⁺). These must be memorised; they appear repeatedly in naming problems.

Ionic compound

A compound formed by the electrostatic attraction between cations and anions. Typically a metal combined with a nonmetal or polyatomic ion. Formulas are written so that total positive charge equals total negative charge.

Molecular compound

A compound formed by nonmetals sharing electrons through covalent bonds. Named using Greek prefixes (mono-, di-, tri-, tetra-, penta-, hexa-, etc.) to indicate the number of each atom.

Stock system

A naming convention for ionic compounds containing metals that can have more than one charge. The metal's charge is indicated by a Roman numeral in parentheses, e.g. iron(II) chloride for FeCl₂.

Binary acid

An acid that contains hydrogen and one other element. Named with the prefix "hydro-" and the suffix "-ic acid" (e.g. HCl = hydrochloric acid).

Oxoacid (oxyacid)

An acid containing hydrogen, oxygen, and one other element. The name depends on the polyatomic ion it is related to: "-ate" ions become "-ic acid," "-ite" ions become "-ous acid" (e.g. H₂SO₄ = sulfuric acid from sulfate; H₂SO₃ = sulfurous acid from sulfite).


Core Content

Atomic Structure (Section 2.2)

  • The nuclear model: a dense, positively charged nucleus (protons + neutrons) surrounded by a cloud of electrons.

  • Proton: charge +1, mass ~1 amu, in the nucleus.

  • Neutron: charge 0, mass ~1 amu, in the nucleus.

  • Electron: charge -1, mass ~0 amu (1/1836 of a proton), outside the nucleus.

Atomic Number, Mass Number, and Isotopes (Section 2.3)

  • Atomic number (Z) = number of protons. This never changes for a given element.

  • Mass number (A) = protons + neutrons.

  • Number of neutrons = A - Z.

  • In a neutral atom, the number of electrons equals the number of protons.

  • Isotopes have the same Z but different A. Written as ᴬ_Z X or as element-A (e.g. carbon-14).

The Periodic Table (Section 2.4)

  • Alkali metals: Group 1 (Li, Na, K, etc.), highly reactive, form +1 ions.

  • Alkaline earth metals: Group 2 (Be, Mg, Ca, etc.), form +2 ions.

  • Halogens: Group 17 (F, Cl, Br, I, etc.), highly reactive nonmetals, form -1 ions.

  • Noble gases: Group 18 (He, Ne, Ar, etc.), generally unreactive, full valence shells.

  • Main group elements: Groups 1, 2, and 13 through 18.

  • Transition metals: Groups 3 through 12, can form multiple charges.

Molecules and Ions (Section 2.5)

  • Noble gases exist as single (monoatomic) atoms.

  • Seven diatomic molecules to memorise: H₂, O₂, N₂, F₂, Cl₂, Br₂, I₂.

  • Monoatomic ions form when atoms gain or lose electrons to achieve a noble-gas electron configuration.

    • Main group metals lose electrons: Na → Na⁺, Mg → Mg²⁺, Al → Al³⁺.

    • Main group nonmetals gain electrons: Cl → Cl⁻, O → O²⁻, N → N³⁻.

  • Transition metals can form more than one ion (e.g. Fe²⁺ and Fe³⁺). You do not need to memorise which charges they take, but you must be able to work out the charge from the compound's formula.

Chemical Formulas (Section 2.6)

  • Structural formulas show which atoms are bonded to which.

  • Ball-and-stick models show spatial arrangement and bond connections.

  • Space-filling models show relative atomic sizes and the overall shape.

  • A molecular formula tells you the exact number of each type of atom in one molecule (e.g. C₆H₁₂O₆).

Naming Compounds (Section 2.7)

Ionic compounds (metal + nonmetal or polyatomic ion):

  • Name the cation first, then the anion.

  • Monatomic cations: use the element name (e.g. sodium, calcium).

  • Monatomic anions: change the ending to "-ide" (chlorine → chloride, oxygen → oxide).

  • If the metal can have multiple charges, use the Stock system: metal name + (Roman numeral). FeCl₂ = iron(II) chloride, FeCl₃ = iron(III) chloride.

  • For polyatomic ions, use the ion name directly: NaNO₃ = sodium nitrate, CaSO₄ = calcium sulfate.

  • Writing formulas: balance the charges so the compound is neutral. Ca²⁺ and Cl⁻ → CaCl₂.

Molecular compounds (nonmetal + nonmetal):

  • Use Greek prefixes for both elements: mono- (1), di- (2), tri- (3), tetra- (4), penta- (5), hexa- (6), hepta- (7), octa- (8), nona- (9), deca- (10).

  • Drop "mono-" on the first element. CO₂ = carbon dioxide (not monocarbon dioxide).

  • The second element gets the "-ide" ending.

  • Trivial names to know: H₂O = water, NH₃ = ammonia, H₂O₂ = hydrogen peroxide.

Acids:

  • Binary acids (H + one nonmetal): hydro____ic acid. HCl(aq) = hydrochloric acid.

  • Oxoacids from "-ate" polyatomic ions: ____ic acid. HNO₃ = nitric acid (from nitrate).

  • Oxoacids from "-ite" polyatomic ions: ____ous acid. HNO₂ = nitrous acid (from nitrite).

  • Acids dissociate in water to produce H⁺ ions. Bases produce OH⁻ ions.


Formulas and Reference Tables

The seven diatomic molecules

H₂, O₂, N₂, F₂, Cl₂, Br₂, I₂

Mnemonic: Have No Fear Of Ice Cold Beer (H, N, F, O, I, Cl, Br)

Common polyatomic ions to memorise

Ion

Formula

Ion

Formula

Ammonium

NH₄⁺

Nitrate

NO₃⁻

Hydroxide

OH⁻

Nitrite

NO₂⁻

Sulfate

SO₄²⁻

Carbonate

CO₃²⁻

Sulfite

SO₃²⁻

Bicarbonate

HCO₃⁻

Phosphate

PO₄³⁻

Acetate

C₂H₃O₂⁻

Perchlorate

ClO₄⁻

Permanganate

MnO₄⁻

Chlorate

ClO₃⁻

Chromate

CrO₄²⁻

Chlorite

ClO₂⁻

Dichromate

Cr₂O₇²⁻

Hypochlorite

ClO⁻

Cyanide

CN⁻

Greek prefixes for molecular compounds

Number

Prefix

1

mono-

2

di-

3

tri-

4

tetra-

5

penta-

6

hexa-

7

hepta-

8

octa-

9

nona-

10

deca-

Predicting monoatomic ion charges from the periodic table

  • Group 1 metals → +1

  • Group 2 metals → +2

  • Aluminium (Group 13) → +3

  • Group 15 nonmetals → -3

  • Group 16 nonmetals → -2

  • Group 17 nonmetals (halogens) → -1


Real-World Applications

Isotopes are the basis of radiocarbon dating (carbon-14) and medical imaging (technetium-99m in bone scans). The naming system for ionic and molecular compounds is the same one pharmacists and chemical engineers use daily: knowing that "sodium chloride" is NaCl or that "dinitrogen monoxide" is N₂O (laughing gas) is the shared language of the field.


Common Misconceptions

  • Students often forget that the seven diatomic elements exist as molecules, not lone atoms. If a question asks for the formula of elemental oxygen, the answer is O₂, not O.

  • Students often apply Greek prefixes to ionic compounds. Ionic compounds never use prefixes. NaCl is "sodium chloride," not "monosodium monochloride."

  • Students often confuse atomic mass (the weighted average on the periodic table) with mass number (the integer count of protons + neutrons for a specific isotope).

  • Students often forget to balance charges when writing ionic formulas. The total positive charge must exactly equal the total negative charge.


Why It Matters / Exam Flags

⚠️ Naming compounds from formulas and writing formulas from names is the single most tested skill from Chapter 2. Practise both directions.

⚠️ Expect questions where you are given a transition metal compound (e.g. CuO or CuO₂-type formulas) and must determine the metal's charge and name the compound using the Stock system.

⚠️ Polyatomic ions (especially sulfate, nitrate, carbonate, phosphate, hydroxide, ammonium) appear in many naming and formula-writing questions.

⚠️ The seven diatomic molecules are tested directly and also show up indirectly: any question involving elemental chlorine, for instance, expects you to write Cl₂.

⚠️ Acid naming (binary acids vs oxoacids) is a common exam topic. Know the "-ate → -ic acid" and "-ite → -ous acid" pattern cold.


Quick Self-Test

  1. True or False: An atom of carbon-14 has 6 protons and 8 neutrons. (True)

  1. Fill in the blank: The charge on a monoatomic ion formed by a Group 16 nonmetal is ______. (-2)

  1. True or False: N₂O₅ is named "nitrogen pentoxide." (False; it is dinitrogen pentoxide)

  1. Fill in the blank: The polyatomic ion SO₄²⁻ is called ______. (sulfate)

  1. True or False: FeBr₃ is named iron tribromide. (False; it is iron(III) bromide, because ionic compounds use the Stock system, not Greek prefixes)


Practice Q&A

Q: Write the formula for aluminium sulfate.

A: Al³⁺ and SO₄²⁻. To balance: 2(Al³⁺) = +6 and 3(SO₄²⁻) = -6. Formula: Al₂(SO₄)₃.

Q: Name the compound CuCl₂.

A: Copper(II) chloride. Each Cl is -1, so two Cl⁻ ions give -2 total. Cu must be +2 to balance.

Q: What is the name of H₂SO₃(aq)?

A: Sulfurous acid. SO₃²⁻ is sulfite ("-ite"), so the acid is "-ous acid."

Q: Write the formula for dinitrogen tetroxide.

A: N₂O₄. "Di-" = 2 nitrogens, "tetra-" = 4 oxygens.

Q: How many protons, neutrons, and electrons are in ³⁷Cl⁻?

A: Protons = 17 (atomic number of Cl). Neutrons = 37 - 17 = 20. Electrons = 17 + 1 = 18 (the -1 charge means one extra electron).

Q: Distinguish between molecular and ionic compounds by formula. Is PCl₃ ionic or molecular?

A: Molecular. Both phosphorus and chlorine are nonmetals. Nonmetal + nonmetal = molecular (covalent) compound.


Connections to Other Topics

The periodic table groups introduced here (alkali metals, halogens, etc.) reappear in Chapters 7 and 8 when you study electron configurations and periodic trends. The concept of ions is the foundation for Chapter 9's discussion of ionic bonding. Naming compounds is a prerequisite for writing and balancing chemical equations later in the course.


Related Terms / Search Tags

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