1 - Chemical Naming System
Abstract (TL;DR):
This arc begins by exploring the many rules that molecules follow - starting with their names. The International Union of Pure and Applied Chemistry (IUPAC) names molecules for every culture to follow. Generally, molecules are named based on three criteria: the atoms involved, the structure of the molecule and the kind of bond that forms.
Many molecules are formed with ions, or atoms that have a negative or positive charge. Non-metals, which include the addition of an “-ide” suffix in their name when they have a negative charge, carry their name over when bonded with a metal atom. Molecules themselves can even be ions, producing new names according to the number of oxygen ions present.
Metal atoms, however, have their own rules, according to if they are a regular metal or a transition metal, which has many different potential charges. For transition metals, the name of the molecule has to be changed to reflect the charge (usually by adding a roman numeral corresponding to that charge).
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Glucose Molecule
Image via jonasspil
Atoms dance, lowering their energy as they combine into molecules. These atoms follow rules and hierarchy, behaving predictably, according to the situation. But chemistry and the physics of atoms are a little more complex than just filling valence shells.
We continue our story learning more about the rules that molecules follow, featuring parts within the dreaded field of “organic” chemistry, as we move closer and closer to the vast ocean that is our universe. First, though, we have to consider that, just like atoms, molecules have names - names that provide a lot of information about the molecule itself.
Chemical Structures
The International Union of Pure and Applied Chemistry (IUPAC) is responsible for the formal names of our molecules, which, unlike the metric measuring system, everybody understands and uses (isn’t that nice). This does mean that there are informal names and, further, there isn’t only one formal name for every molecule. Often, one molecule can be represented by two or even three names. In naming a molecule, the most important aspect is that the name refers to a particular molecule, instead of multiple.
The chemical names of our molecules is based on one or more of three parts:
The atoms involved in the molecular bond.
If a molecule contains carbon and hydrogen bonds, it is known as an organic compound, otherwise, it’s an inorganic compound. These organic and inorganic compounds have different naming mechanisms. Moreover, changed atoms, or ions - both cations, positively-charged atoms and anions, negatively-charged atoms - can also inform the naming of a molecule.
The structure of the molecule.
For long chains of molecules - often organic compounds - where certain atoms are bonded on the chain can determine what the name is, even if two molecules have the exact same atoms.
The type of bond that atoms form.
In the last arc, we discussed covalent (and polar covalent) bonds, ionic bonds and metallic bonds. Since each of these involve different types of atoms, naturally, there will also be different names.
Let’s tackle each of these in kind.
Sodium Chloride - Salt
Naming Inorganic Compounds
The names of inorganic compounds depend mostly on the atoms involved and their charges. For example, we’ve spoken at length about elemental oxygen, but what about oxygen ions? You could call it “anionic oxygen”, but that’s very unwieldy. For non-metal anions, we tend to add the suffix “-ide” to the ending. So, O- (oxygen with a negative charge) is called “oxide”, Cl- is chloride, C- is carbide, and so on.
What if a metallic atom bonds with one of these non-metal anions, as is the case in many covalent or ionic bonds?
In these bonds, we start with the name of the metal (cation) and then add the name of the non-metal anion. We refer to common salt, for example, as sodium chloride, an ionic bond between positively-charged sodium and negatively-charged chlorine.
Some metals are more unique cations that can have one, two or even three different charged states. These are the transition metals, which all have an incomplete d-subshell (orbital angular momentum (l) of 2). Some, like iron (Fe) can have a deficit of 2 or 3 electrons (giving it a charge of +2 or +3), while others like vanadium (V) can have a deficit of 2, 3, 4 or 5 electrons (a +2, +3, +4 or +5 charge). Our periodic table, in all of its organizational glory, groups transition metals in the center, between the first two groups of metals and the metalloids and nonmetals.
Image via ScienceNotes
Transition metals in this table are highlighted in yellow. A few transition metals only have one charge, like tungsten (W), with a charge of +6. I encourage you to look up the different charges that different transition metals can have!
Perchlorate
Remember oxygen only needs to form two valence electrons to complete its valence shell. Chlorine, with it’s seven valence electrons, allows three oxygens to complete their shells. If there is another oxygen present, it will bond with the remaining electron that chlorine has, but it has one more valence electron (hence the negative charge that makes it an ion).
These transition metals, when combined with nonmetals anions, we include a roman numeral to represent what the charge of the transition metal is. So, for CuCl, we would call it copper (I) chloride, representing that copper has a charge of +1. Since copper can have a charge of +1 or +2, we need the “(I)” to represent which form of copper it is.
Sodium chloride and copper (I) chloride are examples of molecules with a neutral charge. But there is no reason that a molecule can’t form with a non-neutral charge. These molecules are aptly called molecular ions.
Molecular ions with oxyanions - oxygen ions - in them get special names (because of course oxygen has to steal the spotlight). These ions typically have a core atom that is covalently bonded to one or more oxygen atoms (with one or more of those oxygens being an ion).
3D Perchlorate Molecule
But before we start naming them, there’s one more secret that the periodic table holds. Did you notice the numbers surrounding the table’s rows and columns? The numbers before its rows are called its period numbers, whereas the numbers above the columns of the table are called its group numbers. You also might have noticed that the group numbers come in both Arabic numerals and Roman numerals. In modern times, the IUPAC numbers columns from 1 to 18, however, classically, they used Roman numerals. The system of Roman numerals in the table above, however, is a bit different than the classic IUPAC version. This one, created by the Chemical Abstract Service (CAS), an American organization, separates main elements with the letter “A” and transition metals with “B”.
Whichever you use, the group helps you locate an element based on coordinates. However, they can be helpful in characterizing behavior, as we’ll see when we name molecular ions in a moment.
Overall, when naming molecular ions with oxyanions, there are two prefixes and two suffixes, organized in four different ways. The two prefixes are “hypo-” and “per-”, while the two suffixes are “-ite” and “-ate”.
Usually, if the core atom in the ion is from Groups 7A/B or 8 and it’s bonded to one oxyanion, the name will have a “hypo-” prefix and an “-ite” suffix if it. If it’s bonded to two ions, the name only contains an “-ite” suffix. For three, the name contains an “-ate” suffix. Lastly, four ions adds the prefix “-per” on top of the “-ate” suffix.
| # of Oxyanions | Prefix | Suffix |
|---|---|---|
| 1 | hypo- | -ite |
| 2 | - | -ite |
| 3 | - | -ate |
| 4 | per- | -ate |
Phosphate
For other groups, it’s a lot more complex. While the naming order is the same, the number of oxygen atoms that are bonded to the core is different according to each name. For example, phosphate, a molecular ion with a phosphorus core, contains four oxyanions instead of the three you might expect. This is due to a principle that we will cover in the near future. For now, I would recommend researching the structure and names of molecules with oxyanions in other groups.
Final Thoughts on Inorganic Compounds
3D Phosphate Molecule
These rules on inorganic compounds, despite how they seem, are simpler than those on naming organic compounds. That does make sense, given that living things - which are made almost exclusively of organic compounds - are as complex as they are. Fortunately, once we understand a few organic compounds, the rest fall into place.
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