41. From Atoms to Molecules

How did life originate on Earth? We have to take the chemistry and biochemistry route to answer this question. In Part 18 I traced the sequence of events which led to the creation of atoms in our universe. From atoms to molecules was the next stage in the cosmic evolution of complexity. And molecular evolution or chemical evolution preceded the emergence and evolution of life.

The chemical symbol H is used for an atom of hydrogen, which is the first element in the periodic table of elements. It has a nucleus, which is just a proton in this case, and there is an electron orbiting around the nucleus. The electron has a negative charge, exactly equal in magnitude to the positive charge of the proton. Taking this quantity as the unit of charge, we say that an H atom has a charge number 1 (Z = 1). Taking the mass of the proton as the unit of mass, we say that H has a mass number 1 (A = 1). The electron is ~2000 times lighter than the proton.

Element number 2 in the periodic table is helium (chemical symbol He). There are two protons in its nucleus, and two electrons orbiting around the nucleus. There are also two neutrons in the nucleus. Neutrons are so called because they are charge-neutral. The mass of a neutron is only slightly greater than that of a proton. So, for the He atom, Z = 2, and A = 4.

Life on Earth is based on organic chemistry, i.e., the chemistry of the carbon atom, denoted by the symbol C. For this atom, Z = 6, and A = 12.

A molecule of hydrogen is denoted by the symbol H₂. It consists of two nuclei of hydrogen, and there are two electrons orbiting around them. Why does hydrogen ‘prefer’ to exist as H₂, rather than as H? Because H₂ is more stable that H. Why? Consider the two electrons of H₂. Quantum mechanics tells that they have no individuality; they are indistinguishable. Let us consider any of them. Since positive and negative charges attract one another, this electron stays close (but not too close) to the two nuclei. [But for the Heisenberg uncertainty principle of quantum mechanics, the electrons of all the atoms would have gone right into their nuclei, and you and I would not be here, discussing chemical evolution of complexity!] Naturally, the positive charges on the two nuclei of H₂ are better than only one positive charge in H, when it comes to exerting an attractive force on the electron. Thus H₂ is more stable (it has a lower internal energy) than H because the former is a more strongly bound entity. Thus H atoms form H₂ molecules spontaneously, because by doing so the overall free energy gets reduced (the second law of thermodynamics demands that the free energy be as small as possible).

http://en.wikipedia.org/wiki/File:Covalent_bond_hydrogen.svg

Formation of H₂ from two atoms of H is an example of 'spontaneous increase of chemical complexity': More information is needed for describing the structure and function of H₂, than of H. An H₂ molecule has a higher degree of complexity than an H atom because more information is needed for describing the molecule than the atom.

What is the nature of the bonding between the two atoms of H₂ or H-H? It is described as covalent bonding. Each of the two H atoms contributes its electron to the chemical bond between them, and the two electrons in the bonding region belong to both the nuclei.

Another kind of chemical bonding is the so-called electrovalent bonding (also called ionic bonding). It is the bonding that occurs between oppositely charged ions. Take sodium chloride (NaCl). For the Na atom, Z = 11, and for the Cl atom, Z = 17. The laws of quantum mechanics are such that an atom of Na is more stable if it is surrounded by only 10 electrons, instead of 11. Similarly, Cl is more stable if it has 18 electrons, rather than 17. They can solve the problem together by getting readily ‘ionized’; i.e., an Na atom can become a positively charged ion Na⁺ by losing an electron (called the valence electron), and a Cl atom can become a negatively charged ion Cl^- by gaining an electron.  The two oppositely charged ions can lower the overall potential energy (and therefore the free energy) by coming close to each other, thus forming an ionic bond between them.

http://www.vfundude.com/definition-ionic-bond-and-formation-of-sodium-chloride/

The third important and generally strong type of bonding is metallic bonding. It occurs in metals like aluminium (Al), copper (Cu), silver (Ag), gold (Au), etc. Take the case of Al. For it, Z = 13. But like an atom of Na considered above, it is more stable if it has just 10 electrons around the nucleus. So Al atoms, when in the close vicinity of many other Al atoms, lose their three valence electrons to a common pool, and these valence electron become the common property of all the Al ions. A lump of Al metal is held together by this cloud of negatively charged electrons, attracted to, and compensating for, the positive charges on the Al ions.

http://www.ndt-ed.org/EducationResources/CommunityCollege/Materials/Structure/metallic.htm

The covalent, electrovalent, and metallic bonds described above are the so-called primary bonds. They are strong bonds. Diamond, for example, consists entirely of covalently bonded carbon atoms, and is an extremely hard material. In metals also the atoms are quite strongly bonded to one another, as are the atoms in a crystal of sodium chloride in which the electrovalent interaction dominates.

There are a number of other types of bonds or interactions which are substantially weaker than the primary bonds, but are very important for biological systems in particular, and 'soft matter' in general. I shall describe them in the next post.