The images above are a collage of photos taken from a workshop on the structure of molecules at an event called Skirting Science, aimed at engaging year 9 girls with Science, Technology, Engineering and Mathematics (STEM) subjects. As you can see, the workshop involved a variety of materials, including molecular model kits (used by undergraduate chemists), food and playdough, to make different molecules. The idea was to show the participants that they could do this chemistry at home with items they have in their houses. The photo on the bottom right shows the girls trying to get the playdough structure to stand up with the correct bond angles, a difficult task!
What are molecules?
[Editor’s note: Chemists like to debate fundamental definitions, including what exactly is a molecule (see, for example, this link). We will try not to stray into these finer philosophical points here.]
Molecules are made up of atoms. While there are several different definitions of atoms, for the purposes of this blog post we will go with assuming that it is the key part of elements and compounds which can’t be broken by chemical means (adapted from this link). In terms of chemistry, you can think of atoms as your basic building block, and, like bricks, these come in a range of different sizes and can be arranged in different ways.
Atoms are linked together by bonds to make molecules. For example, 2 oxygen atoms bonded together make an oxygen molecule. 1 carbon atom and 4 hydrogen atoms make up a methane molecule, and it has the formula CH4. A methane molecule is an example of a compound because it contains 2 different elements, whereas an element consists only of atoms of one type (the oxygen mentioned above, for example). There are philosphical issues around how you define elements, but we will leave it to Philip Ball to explain that in the January 2019 edition of Chemistry World.
To help scientists think about molecules, we tend to use simple models, such as the ball and stick model of methane in Fig. 1. The grey sphere in Fig. 1 represents a carbon atom and the white spheres represent the hydrogen atoms. Each white line represents a carbon-hydrogen bond; a carbon-hydrogen bond shares 2 electrons, one from a carbon atom and one from a hydrogen atom. A carbon atom is a larger atom than a hydrogen atom because it has a larger atomic mass. Based on its mass and properties, carbon is placed in group 4 of the periodic table; this also means that it normally forms 4 bonds (shares 4 of its electrons to form bonds). Hydrogen is placed in group 1 of the periodic table, so forms 1 bond.
All carbon atoms are the same, regardless of which molecule they are in, again, a bit like bricks. So, the carbon atoms in ethane and methane are the same. The same applies for all other atoms, so the hydrogens in methane are the same as the hydrogens in ethane (Fig. 2). As noted above, they cannot be changed by chemical means, and when you think about a chemical reaction, you can’t create or destroy atoms, so they all need to be accounted for.
Shapes of molecules
Methane has a tetrahedral shape with the 4 carbon-hydrogen bonds placed equally far away from each other. Bonds can be thought of as the sharing of electron pairs; electrons are negatively charged and, since like charges repel, tend to avoid other electrons. The shape of a molecule is then determined by the arrangement in 3 dimensions which minimises interactions, placing bonds (and electron pairs) as far apart from each other as possible.
Figure 4 below is a molecule of borane, with the larger pink atom being boron and the white atoms being hydrogens.
Borane has a trigonal planar shape. Boron is placed in group 3 in the periodic table so forms 3 bonds. Hydrogen is in group 1 in the periodic table so forms 1 bond. The boron-hydrogen bonds contain negatively charged electrons which repel each other; for three bonds, the trigonal planar arrangement minimises their interactions.
How do we know that molecules exist?
Atoms and molecules are very, very small so require atomic force microscopes to view them. These microscope images give direct proof that molecules exist. There are many other experiments which provide further, indirect proof of molecules and their structures.
This image below taken from an atomic force microscope shows the change in molecular structure after a reaction takes place.
Before we had the tools to view atoms and molecules, a botanist called Robert Brown noticed that the pollen grains suspended in water, which he was viewing under a microscope, were moving. It was Einstein who came to explain this phenomenon (usually referred to as “Brownian motion”, describing how it was water molecules which were moving the pollen grains.
Why do molecules matter?
The molecular structure of a compound determines its properties. Even very small changes in molecular structure can lead to different chemical and physical properties. In Figure 4 below we have 2 different enantiomers of the molecule of carvone. The carbon atom labelled 4 is a chiral carbon, and R-(-)- and S-(+)-carvone have groups in a different order around this carbon atom. The thick wedged bond indicates that the group is coming towards you, whilst the dashed bond is going away from you. While these changes do not affect the chemical and physical properties, they matter when carvones encounter a chiral environment, such as your nose. This causes S-(+)-carvone to smell like spearmint and R-(-)-carvone to smell like caraway. See our post on Spearmint (Mentha spicata) for more details.
Molecules have different properties depending on the atoms of which they are composed. Chemistry is the study of molecules and their interactions, as well as their manipulation to make other molecules. We can’t live without water, oxygen or DNA; all three of these are molecules. Chemistry is fundamentally about observing, analysing, making and changing molecules, so it’s important to be able to visualise their structure.