What are Molecules?
Molecules can be described as a group of two or more atoms that combine and form the smallest identifiable unit into which a pure substance can be divided and still retain the composition and chemical properties of that substance.
The process of dividing the sample of a substance into smaller parts gradually leads to no change in both its composition and its chemical properties till the time parts that have single molecules are reached. Furthermore, the process of subdivision of a particular substance creates smaller parts that usually are different from the original substance in the composition and it always varies from it in chemical properties. The chemical bonds that hold the atoms together in the molecule are broken in the latter stage of fragmentation.
Atoms primarily include a single nucleus that has a positive charge and are encircled by a cloud of negatively charged electrons. So, when atoms come close to each other, the electron clouds act together and with the nuclei. If during the interaction, the total energy of the system is gets lowered, then the atoms bond together to create a molecule. Therefore, if we talk from a structural point of view, a molecule comprises an aggregation of atoms that are held together by valence forces. Diatomic molecules have two atoms that are chemically bonded. In a situation where the two atoms are identical, as in, for example, the oxygen molecule (O2), they create a homonuclear diatomic molecule. But if the atoms are different, like in the case of carbon monoxide molecule (CO), they create a heteronuclear diatomic molecule. Molecules have more than two atoms that can be termed polyatomic molecules, e.g., carbon dioxide (CO2) and water (H2O). Polymer molecules include many thousands of component atoms.
Coming to the ratio of the numbers of atoms, they have the potential to be bonded together to form molecules and that is fixed; for example, each water molecule has two atoms of hydrogen and one atom of oxygen. It is because of this feature that chemical compounds can be distinguished from solutions and other mechanical mixtures. So, hydrogen and oxygen could be present in any arbitrary proportions in mechanical mixtures, but when they get electrocuted, they combine only in definite proportions to form the chemical compound water (H2O). It is completely possible for the same types of atoms to get combined in different but definite proportions and form different molecules; let’s say for example, two atoms of hydrogen can bond chemically with one atom of oxygen to yield a water molecule, but two atoms of hydrogen will only chemically bond with two atoms of oxygen to form a molecule of hydrogen peroxide (H2O2). Additionally, atoms can also bond together in identical proportions to form different molecules. These molecules can be termed as isomers and are different only in the arrangement of the atoms within the molecules. Like, ethyl alcohol (CH3CH2OH) and methyl ether (CH3OCH3) have one, two, and six atoms of oxygen, hydrogen, and carbon respectively, but these atoms get bonded in different ways.
It’s crucial to note that all substances comprise distinct molecular units. For example, Sodium chloride (common table salt), has sodium ions and chlorine ions that are put together in a lattice so that each sodium ion is surrounded by six equidistant chlorine ions and each chlorine ion is surrounded by six equidistant sodium ions. The elements that act between any sodium and any adjacent chlorine ion are equal. Therefore, as a molecule of sodium chloride, no distinct aggregate identifiable exists. As a result, the idea of the chemical molecule has no significance in sodium chloride and in all solids of similar type. The formula for these compounds can be explained as the simplest ratio of the atoms, called a formula unit—in the case of sodium chloride, NaCl.
Now this is important information for molecules. Molecules stick to each other with the help of electron pairs, or covalent bonds. These bonds are directional, which means that the atoms take up definite positions that are relative to one another in order to maximize the bond strengths. It can be concluded that every molecule has a specific, spatial distribution of its atoms and reasonably rigid structure. Structural chemistry deals with valence, which estimates how atoms get combined in definite ratios and how this is related to the bond directions and bond lengths. The properties of molecules correlate with their structures; for example, the water molecule is basically bent structurally, so it has a dipole moment; but the carbon dioxide molecule is linear and has no dipole moment. The revelation of how atoms get restructured in the course of chemical reactions is crucial. In a lot of molecules, the structure is not necessarily rigid; like in ethane (H3CCH3), about the carbon-carbon single bond, there is virtually free rotation.
When it comes to nuclear positions in a molecule, they are found out either by neutron diffraction or from microwave vibration-rotation spectra. The electron clouds that surround the nuclei in a molecule can be studied by X-ray diffraction experiments. A lot of advances in electron microscopy have helped produce visual images of individual molecules and atoms accurately. In theory, molecular structure is figured out by finding the quantum mechanical equation for the motion of the electrons in the field of the nuclei (called the Schrödinger equation). When it comes to a molecular structure, the bond lengths and bond angles are those for which the molecular energy is the least. Determining the structures by numerical solution of the Schrödinger equation has now become a highly advanced process and involves the use of computers and supercomputers.
Molecular weight of a molecule can be defined as the sum of the atomic weights of its component atoms. Let’s assume that a substance has molecular weight M, then M grams of the substance are termed one mole. The number of molecules is the same for all substances in one mole, and it is known as Avogadro’s number (6.022140857 × 1023). Molecular weights are also studied by mass spectrometry and using techniques that are based on kinetic transport phenomena or thermodynamics.
Examples of Molecules
Molecules can be simple or complex. Here are some examples of common molecules:
- H2O (water)
- N2 (nitrogen)
- O3 (ozone)
- CaO (calcium oxide)
- C6H12O6 (glucose, a type of sugar)
Molecules versus Compounds
Molecules consist of two or more elements that are called compounds. Water, glucose and calcium oxide are molecules that are compound. All kinds of compounds are molecules, but note that all molecules are not compounds.
What is Not a Molecule?
Single atoms of elements cannot be called as molecules. A single oxygen, O, is not a molecule. When oxygen bonds to itself (e.g., O2, O3) or to another element (e.g., carbon dioxide or CO2), molecules are created.
Representing Molecules: Chemical Formulas
Chemical formulas, which are also known as molecular formulas, are one of the simplest methods to represent molecules. For chemical formulas, the elemental symbols from the periodic table are used to indicate what kind of elements are there, and also subscripts are used to point out how many atoms of each element exist within the molecule. Assuming, a single molecule of NH3, ammonia, contains one nitrogen atom and three hydrogen atoms. On the contrary, a single molecule of N2 H4, hydrazine, contains two nitrogen atoms and four hydrogen atoms.
Concept check: Let us look at the chemical formula for acetic acid, which is a commonly found acid in vinegar: C2 H4 O2 . So, how many oxygen atoms are present in three molecules of acetic acid?
We just told you that the chemical formula for acetic acid is C2 H4 O2 , but we chemist often write it as CH3 COOH. The reason is simple for this second type of formula. The order in which the atoms are written helps in showing the structure of the acetic acid molecule—which is also sometimes known as the condensed structural formula. So, we can think of CH3 COOH as a cross between a chemical formula and a structural formula that we will talk about next.
For you to understand structural formulas better, let us talk about the different ways of depicting a molecule, based on what properties you want to illustrate.
A ball-and-stick model possibly looks like toothpicks and gumdrops. Ideally, carbon atoms are revealed as black balls, nitrogen in blue, oxygen red, and hydrogen white. One can understand these models while studying the exact shape of the molecule and how the atoms connect to each other.
A space-filling model almost looks like blobs that are jammed together and stands for (more or less) the amount of space the atoms and their electron clouds take up. Check out the space-filling model of our friend H2O above. You might come across this kind of model while learning about how molecules interact with each other and fit together.
When you start learning about small molecules, particularly drugs, you will see many line-angle drawings. They represent the structure of a molecule, excluding the details. Carbons practically exist anywhere a line bends or ends. But hydrogens are not generally drawn. The moment you get used to coming across these drawings, you will realize that they are an easy way to understand the shape of a molecule such as a drug.
Many students and scientists quite often build molecules from kits in order to understand the shape of a molecule.
Assume that each gumdrop as an atom and they come in different flavours. Now, these ‘flavors’ of atoms are called elements, as in the Periodic Table of the Elements. You might probably be familiar with some element names, like gold, arsenic and helium.
In biology, molecules that are made of the elements carbon, hydrogen, oxygen, and nitrogen are mostly studied. When a molecule has elements of carbon, it is said that the molecule is organic. The field of organic chemistry has these biological molecules along with others like petroleum (think oil and gasoline) that are mostly carbon and hydrogen.
Representing Molecules: Structural Formulas
Chemical formulas only let us know how many atoms of every element are there in a molecule, but when it comes to structural formulas, they tell us about how the atoms are connected in space. In the case of structural formulas, we, in fact, draw the covalent bonds shared between atoms. As we know, the chemical formula for ammonia is NH3. Now, let’s talk about its structural formula:
Talking about both these structural formulas, can you see that the central nitrogen atom shares a single covalent bond with each hydrogen atom? You need to note the fact that although the atoms and molecules exist in three dimensions—they include the length and width, as well as depth. But for structural formula on the left, there is only a two-dimensional estimate of this molecule. However, when we look at the detailed structural formula on the right, the dashed line indicates that the hydrogen atom on the rightmost is placed behind the plane of the screen, but the bold wedge is indicative of that the center hydrogen is sitting out in front of the plane of the screen. The two dots which are placed above nitrogen are an isolated pair of electrons that are not a part of any covalent bond. For defining three-dimensional shape even more accurately, we can use the space-filling models as well as ball-and-stick models. Let’s talk about both of these models for NH3.
The image on the left depicts the space-filling model for ammonia. The nitrogen atom is the larger, central blue sphere; whereas, the three hydrogen atoms are shown as the smaller white spheres on the sides, which form a kind of tripod. Analyzing the overall shape of the molecule, it can be said that it is a pyramid with nitrogen at the vertex and a triangular base formed by the three hydrogen atoms. This kind of arrangement is also called as trigonal pyramidal. The main benefit of the space-filling model is the fact that it offers an estimate of the relative sizes of the different atoms—nitrogen has a larger atomic radius than hydrogen.
The image on the right shows us ammonia’s ball-and-stick model. As we can guess easily, the balls are nothing but atoms, and the sticks that connect the balls stand for the covalent bonds that are shared between the atoms. The primary plus point of this model is the fact that we can see the covalent bonds, which also let us see the geometry of the molecule.
That’s all for today, folks.
Know more about molar concepts here!