THE SECOND STEP ON THE PATH TO MATTER: MOLECULES


What is it that makes the objects you see in your surroundings different from each other? What is it that discriminates their colours, shapes, smells, and tastes? Why is one substance soft, another hard, and yet another fluid? From what you have read so far, you may answer these questions saying, "The differences between their atoms do this". Yet, this answer is not sufficient, because if the atoms were the cause for these differences, then there would have to be billions of atoms bearing different properties from each other. In practice, this is not so. Many materials look different and bear different properties although they contain the same atoms. The reason for this is the different chemical bonds the atoms form among them to become molecules.

On the way to matter, molecules are the second step after atoms. Molecules are the smallest units determining the chemical properties of matter. These small bodies are made up of two or more atoms and some, of thousands of groups of atoms. Atoms are held together inside molecules by chemical bonds determined by the electromagnetic force of attraction, which means that these bonds are formed on the basis of the electrical charges of the atoms. The electrical charges of atoms, in turn, are determined by the electrons on their outermost shell. The arrangements of molecules in different combinations give rise to the diversity of matter we see around us. The importance of the chemical bonds that lie at the heart of the diversity of matter come forward at this very point.

 
Chemical Bonds

As explained above, chemical bonds are formed through the motion of electrons in the outermost electron shells of the atoms. Each atom has a tendency to fill up its outermost shell with the maximum number of electrons it may shelter. The maximum number of electrons the atoms can hold in their outermost shells is 8. To do this, atoms either receive electrons from other atoms to complete the electrons in their outermost shells to eight, or if they have lesser electrons in their outermost shells, then they give these to another atom, making a sub-shell that had previously been completed in their outermost orbits. The tendency of the atoms to exchange electrons constitutes the basic inciting force of the chemical bonds they form between each other.

This driving force, that is, the objective of the atoms to raise the number of electrons in their outermost shells to maximum, causes an atom to form three types of bonds with other atoms. These are the ionic bond, covalent bond and metallic bond.

Commonly, special bonds categorised under the general title of "weak bonds" act between molecules. These bonds are weaker than the bonds formed by atoms to constitute molecules because molecules need more flexible structures to form matter.

Let us now, in brief, see the properties of these bonds and how they are formed.

Ionic Bonds

Atoms combined by this bond swap electrons to complete the number of electrons in their outermost shells to eight. Atoms having up to four electrons in their outermost shells give these electrons to the atom with which they are going to combine, that is, with which they will bond. Atoms having more than four electrons in their outermost shells receive electrons from the atoms with which they will bond. Molecules formed by this type of bond have crystal (cubic) structures. Familiar table salt (NaCl) molecules are among substances formed by this bond. Why do atoms have such a tendency? What would happen if they did not have it?



The sodium atom gives its outermost electron to a chlorine atom and becomes positively charged. Receiving the electron, the chlorine atom becomes negatively charged. The two form an ionic bond through these two opposite charges attracting each other.24

Until today, the bonds formed by atoms could be defined only in very general terms. It has not yet been understood why atoms adhere to this principle. Could it be that atoms decide by themselves that the number of electrons in their outermost shells should be eight? Definitely not. This is such decisive behaviour that it goes beyond the atom, because it has no intellect, will, or consciousness. This number is the key in the combination of atoms as molecules that constitute the first step in the creation of the matter, and eventually, the universe. If atoms did not have such a tendency based on this principle, molecules, and in turn, matter would not exist. Yet, from the first moment they were created, atoms have been serving in the formation of molecules and matter in a perfect manner thanks to this tendency.

Covalent Bonds


Scientists who studied the bonds between atoms faced an interesting situation. While some atoms swap electrons for bonding, some of them share the electrons in their outermost shells. Further research revealed that many molecules that are of critical importance for life owe their existence to these 'covalent' bonds.



Some atoms form new molecules by covalent bonding, sharing the electrons in their outer orbits.25

Let us give a simple example to explain covalent bonds better. As we mentioned previously on the subject of electron shells, atoms can carry a maximum of two electrons in their innermost electron shells. The hydrogen atom has a single electron and it has the tendency to increase the number of its electrons to two to become a stable atom. Therefore, the hydrogen atom forms a covalent bond with a second hydrogen atom. That is, the two hydrogen atoms share each other's single electron as a second electron. Thus, the H2 molecule is formed.


Metallic Bonds

If a large number of atoms come together by sharing each others' electrons, this is called a "metallic bond". Metals like iron, copper, zinc, aluminium, etc., that form the raw material of many tools and instruments we see around us or use in daily life, have acquired a substantial and tangible body as a result of the metallic bonds formed by the atoms constituting them.



The bonds between metal atoms are very different from other forms of chemical bonding – each metal atom contributes its outer electrons to a common pool. This "sea of electrons" explains a key property of metals – their ability to conduct electricity.26

Scientists are not able to answer the question as to why electrons in the electron shells of the atoms have such a tendency. Living organisms, most interestingly, owe their existence to this tendency.

The Next Step: Compounds

Do you wonder how many different compounds these bonds can form?
In laboratories, new compounds are produced everyday. Currently, it is possible to talk about almost two million compounds. The simplest chemical compound can be as small as the hydrogen molecule, while there are also compounds made up of millions of atoms. . L. Vlasov, D. Trifonov, 107 Stories About Chemistry, 1977, p. 117



The Raw Materials of the Universe and the Periodic Table: 92 elements found freely in nature and 17 elements formed artificially in laboratories or in nuclear reactions are arranged in a table called the "Periodic Table" according to the number of their protons. At first look, the Periodic Table may appear to be a bunch of boxes containing one or two letters with numbers at the top and bottom corners. Most interestingly, however, this table accommodates the elements of the entire universe including the air we breathe, as well as of our bodies.

How many different compounds can an element form at most? The answer to this question is quite interesting because, on the one hand, there are certain elements that do not interact with any others (inert gases), while, on the other hand, there is the carbon atom that is able to form 1,700,000 compounds. As stated above, the total number of compounds is about two million. 108 elements out of the total of 109 form 300,000 compounds. Carbon, however, forms 1,700,000 compounds all by itself in a most amazing fashion.

The Building Block of Life: the "Carbon" Atom



Carbon atom

Carbon is the most vital element for living beings, because all living organisms are constructed from compounds of carbon. Numerous pages would not be enough to describe the properties of the carbon atom, which is extremely important for our existence. Nor has the science of chemistry yet been able to discover all of its properties. Here we will mention only a few of the very important properties of carbon.

Structures as diverse as the cell membrane, the horns of an elk, the trunk of a redwood, the lens of the eye, and the venom of a spider are composed of carbon compounds. Carbon, combined with hydrogen, oxygen, and nitrogen in many different quantities and geometric arrangements, results in a vast assortment of materials with vastly different properties. So, what is the reason for carbon's ability to form approximately 1.7 million compounds?

One of the most significant properties of carbon is its ability to form chains very easily by lining carbon atoms up one after another. The shortest carbon chain is made up of two carbon atoms. Despite the unavailability of an exact figure on the number of carbons that make up the longest carbon chain, we can talk about a chain with seventy links. If we consider that the atom that can form the longest chain after the carbon atom is the silicon atom forming six links, the exceptional position of the carbon atom will be better understood. . L. Vlasov, D. Trifonov, 107 Stories About Chemistry, 1977, p. 118

The reason for carbon's ability to form chains with so many links is because its chains are not exclusively linear. Chains may be branched, as they may also form polygons.

At this point, the form of the chain plays a very important role. In two carbon compounds, for example, if the carbon atoms are the same in number yet combined in different forms of chains, two different substances are formed. The abovementioned characteristics of the carbon atom produce molecules that are critical for life.
Some carbon compounds' molecules consist of just a few atoms; others contain thousands or even millions. Also, no other element is as versatile as carbon in forming molecules with such durability and stability. To quote David Burnie in his book Life:


THREE SIMILAR MOLECULES

RESULT: THREE VERY DIFFERENT SUBSTANCES

Even a difference in a few atoms between molecules leads to very different results. For instance, look carefully at the two molecules written below. They both seem very similar except for very small differences in their carbon and hydrogen components. The result is two totally opposite substances:

C18H24O2 and C19H28O2

Can you guess what these molecules are? Let us tell you immediately: the first is oestrogen, the other is testosterone. That is, the former is the hormone responsible for female characteristics and the latter is the hormone responsible for male characteristics. Most interestingly, even a difference of a few atoms can cause sexual differences.
Now take a look at the formula below.

C6H12O2

Doesn't this molecule look very much alike the oestrogen and testosterone hormone molecules? So, what is this molecule, is it another hormone? Let us answer right away: this is the sugar molecule.
From the examples of these three molecules made up of elements of the same type, it is very clear how diverse the substances are that the difference in the number of atoms may produce. On the one hand, there are the hormones responsible for sexual characteristics, while on the other hand, there is sugar, a basic food.

Diamond, which is a very valuable stone, is a derivative of carbon, which is otherwise commonly found in nature as graphite.

Carbon is a very unusual element. Without the presence of carbon and its unusual properties, it is unlikely that there would be life on Earth. David Burnie, Life, Eyewitness Science, London: Dorling Kindersley, 1996, p.8
Concerning the importance of carbon for living beings, the British chemist Nevil Sidgwick writes in Chemical Elements and Their Compounds:

Carbon is unique among the elements in the number and variety of the compounds which it can form. Over a quarter of a million have already been isolated and described, but this gives a very imperfect idea of its powers, since it is the basis of all forms of living matter. . Nevil V. Sidgwick, The Chemical Elements and Their Compounds, vol.1, Oxford: Oxford University Press, 1950, p.490

The class of compounds formed exclusively from carbon and hydrogen are called "hydrocarbons". This is a huge family of compounds that include natural gas, liquid petroleum, kerosene, and lubricating oils. The hydrocarbons ethylene and propylene form the basis of the petrochemical industry. Hydrocarbons like benzene, toluene, and turpentine are familiar to anyone who's worked with paints. The naphthalene that protects our clothes from moths is another hydrocarbon. Hydrocarbons combined with chlorine or fluorine form anaesthetics, the chemicals used in fire extinguishers and the Freons used in refrigeration.

As the chemist Sidgwick stated above, the human mind is insufficient to fully understand the potential of this atom that has only six protons, six neutrons and six electrons. It is impossible for even a single property of this atom, which is vital for life, to form by chance. The carbon atom, like everything else, has been created by Allah perfectly adapted for the bodies of living beings, which Allah encompasses down to their very atoms.
What is in the heavens and in the earth belongs to Allah. Allah encompasses all things. (Surat an-Nisa': 126)

What Would Happen If Every Atom That
Stood Close Together Immediately Reacted?


We just said that the whole universe is formed by the interaction of the atoms of 109 different elements. Here, there is a point that needs to be mentioned, which is that a very important condition must be fulfilled for the reaction to start.

For instance, water does not form whenever oxygen and hydrogen come together and iron does not rust away as soon as it comes in contact with air. If it did so, iron, which is a hard and shiny metal, would be transformed into ferrous oxide, which is a soft powder, in a few minutes. No such thing as a metal would be left on earth and the order of the world would be greatly disturbed. If atoms that happened to be placed close to each other at a certain distance had united immediately without the fulfilment of certain conditions, atoms of two different substances would have interacted right away. In that case, it would be impossible even for you to sit on a chair, because the atoms forming the chair would immediate react with the atoms forming your body and you would become a being between chair and human (!). Of course, in such a world, life would be out of the question. How is such an end avoided?

To give an example, hydrogen and oxygen molecules react very slowly at room temperature. That means that water forms very slowly at room temperature. Yet, as the temperature of the environment rises, the energies of molecules also increase and reaction is accelerated, and thus water is formed more rapidly.

The minimum amount of energy required for molecules to react with each other is called the "activation energy". For instance, in order for hydrogen and oxygen molecules to react with each other to form water, their energy has to be higher than the activation energy.

Just consider. If the temperature on earth were a little higher, the atoms would react too rapidly, which would destroy the equilibrium in nature. If the opposite were true, that is the temperature on earth were lower, then atoms would react too slowly, which would again disturb the equilibrium in nature. As this clarifies, the distance of the earth from the sun is just appropriate to support life on earth. Certainly, the delicate balances required for life do not end there. The inclination in the axis of the earth, its mass, surface area, the proportion of the gases in its atmosphere, the distance between the earth and its satellite, the moon, and many other factors have to be precisely at their present values so that living beings can survive. This points to the fact that all these factors could not have formed progressively by chance and that they were all created by Allah, the Owner of Supreme power, Who knows all the properties of living beings.

Typically, the role of science during these processes is just to name the laws of physics that it observes. As we explained in the beginning, in the case of such phenomena, questions like "what?", "how?", and "in what way?" fade into insignificance. What we can reach by these questions are only the details of an already existing law. The main questions that should be asked are "why?" and "by whom was this law created"? The answer to these questions remains an enigma for scientists who blindly adhere to their materialist dogmas.

At this point, where materialists reach a deadlock, the picture is very clear for a person who looks at events by using his mind and conscience. The flawless balances in the universe, which cannot be explained as coincidences, have been brought about at the bidding of a supreme mind and will, as stated in the verse, "Allah takes account of everything." (Surat an-Nisa: 86), and He created everything according to a very precise calculation, order and equilibrium.

Intermolecular Bonds: Weak Bonds


The bonds combining the atoms in molecules are much stronger than these weak intermolecular bonds. These bonds can help the formation of millions, and even billions of kinds of molecules.

Well, how do molecules combine to form matter?

Since molecules become stable after their formation, they no longer swap atoms.

So, what holds them together?


The sequence of the amino acids and the three-dimensional shape determine the function of the protein in the body. Weak bonds between molecules form these structures.

In an effort to answer this question, chemists produced different theories. Research showed that molecules are able to combine in different ways depending on the properties of the atoms in their composition.

These bonds are very important for organic chemistry, which is the chemistry of living beings, because the most important molecules constituting life are formed due to their ability to form these bonds. Let us take the example of proteins. The complex three-dimensional shapes of proteins, which are the building blocks of living things, are formed thanks to these bonds. This means that the weak chemical bond between molecules is at least as necessary as the strong chemical bond between atoms for the formation of life. Certainly, the strength of these bonds must be of a certain measure.

We can continue with the protein example. Molecules called amino acids combine to form proteins, which are much larger molecules. The atoms forming amino acids are combined by covalent bonds. Weak bonds combine these amino acids in such a way as to produce three-dimensional patterns. Proteins can function in living organisms only if they have these three dimensional patterns. Therefore, if these bonds did not exist, neither would the proteins or therefore, life exist.

The "hydrogen" bond, a type of weak bond, plays a major role in the formation of materials that bear great importance in our lives. For instance, the molecules forming water, which is the basis of life, are combined by hydrogen bonds.