Representing Particles

Particles such as ions and molecules can be represented in different ways. One common representation is a 3D model. Below is an example of a Ball-and-Stick Model for methane (CH4). This model provides information about the connectivity and relative locations of the atoms in the particle. Note that hydrogen atoms are typically represented in white and their labels are omitted for simplification.

A Ball-and-Stick Model of methane (CH4).


NoteAtom Color Schemes

Various atom color schemes exist. One common scheme is used by the JMol molecular modelling software. Some common atom colors are provided in the table below.

JMol Atom Colors


The table below provides other examples of particle representations.


NoteKey
  1. Name - the name of the particle
  2. Molecular formula - the number and types of each atom in the particle
  3. Condensed formula - similar to molecular formula but with the order of the atoms arranged in such a way to give information about the structure of the molecule
  4. Structural formula - provides the information necessary to convey how atoms are connected (via bonds) in a particle
  5. Stereochemical formula - similar to structural formula but gives information about the shape of the particle


Bond-Line Structures

While molecular models and structural formulas are useful for showing every atom in a molecule, they can become cumbersome and time-consuming to draw, especially for the larger molecules commonly found in organic chemistry. To draw molecules more efficiently, chemists have developed a widely used convention known as bond-line structures (also called skeletal structures or line-angle formulas).

This notation is a shorthand that simplifies the drawing process by making some assumptions about the atoms present. While it may look abstract at first, reading and drawing skeletal structures is an important skill in chemistry. The zig-zag nature of these drawings also does a better job of representing the true bond angles and overall shape of a molecule compared to a simple condensed formula.

Here are the rules for interpreting skeletal structures:

  1. Vertices and Endpoints Represent Carbon Atoms. Each corner (vertex) and each endpoint of a line represents a carbon atom.

  2. Lines Represent Covalent Bonds. A single line represents a single bond. Double lines represent a double bond, and triple lines represent a triple bond.

  3. Hydrogen Atoms Bonded to Carbon are Implied. This is the most important rule. Hydrogen atoms are not drawn if they are attached to a carbon atom. It is assumed that each carbon has enough hydrogen atoms bonded to it to satisfy carbon’s valence of four. You can determine the number of hydrogens on any carbon by subtracting the number of bonds drawn to that carbon from four.

    • A carbon with one bond showing (an endpoint) has 3 implied hydrogens (CH3).
    • A carbon with two bonds showing (in the middle of a chain) has 2 implied hydrogens (CH2).
    • A carbon with three bonds showing (at a junction or part of a double bond) has 1 implied hydrogen (CH).
    • A carbon with four bonds showing has 0 implied hydrogens (C).

  4. All Other Atoms (Heteroatoms) Are Explicitly Drawn. Any atom that is not carbon or hydrogen (such as oxygen (O), nitrogen (N), sulfur (S), or any halogen (F, Cl, Br, I)) is always written with its chemical symbol.

  5. Hydrogens Bonded to Heteroatoms Are Explicitly Drawn. If a hydrogen atom is attached to any atom other than carbon, it must be drawn. For example, the hydrogen in a hydroxyl group (–OH) or an amine group (–NH2) is always shown.

Consider the molecule butane, which has the condensed structural formula CH3CH2CH2CH3.

A Ball-and-Stick Model of butane (CH3CH2CH2CH3).

The bond-line structure is a simple three-segment zig-zag line.


Bond-line structure of butane shown as a three-segment zig-zag line representing four carbon atoms

Chemical Nomenclature

While a chemical formula or a molecular model provides a precise description of a substance, we also need a way to refer to it by name in writing and conversation. The systematic method for naming chemical substances is called chemical nomenclature. Its purpose is to establish an unambiguous “language” for chemistry, ensuring that a specific name corresponds to exactly one compound.

The international organization that sets these grammatical rules for chemistry is the International Union of Pure and Applied Chemistry (IUPAC). Founded in 1919, IUPAC “is the world authority on digital standards in chemistry; chemical nomenclature and terminology, including the naming of new elements in the periodic table; on standardized methods for measurement; and on atomic weights.” The specific set of rules we will be learning is therefore referred to as IUPAC nomenclature. Four authoritative works provide guidelines on naming (below).

  • Overall summary of chemical nomenclature (PDF)1
  • Inorganic compounds (the Red Book; PDF)2
  • Organic compounds (the Blue Book; PDF)3
  • Polymers (the Purple Book; PDF)4

The following sections will introduce the rules for naming ions, ionic compounds, and covalent compounds (i.e. molecules).

References

(1)
Leigh, G. J. Principles of Chemical Nomenclature: A Guide to IUPAC Recommendations; EBL-schweitzer; Royal Society of Chemistry, 2011.
(2)
Connelly, N. G.; Chemistry (Great Britain), R. S. of; Pure, I. U. of; Chemistry, A. Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005; Royal Society of Chemistry, 2005.
(3)
Favre, H. A.; Powell, W. H. Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013; International Union of Pure and Applied Chemistry; Royal Society of Chemistry, 2014.
(4)
Jones, R. G.; Wilks, E. S.; Metanomski, W. V.; Kahovec, J.; Hess, M.; Stepto, R.; Kitayama, T. Compendium of Polymer Terminology and Nomenclature: IUPAC Recommendations 2008; Royal Society of Chemistry, 2009.