Structure of Molecules

Introduction

Molecules are a collection of atoms in a particular way that the overall charge of atoms becomes neutral. These molecules are formed by atomic attractive and repulsive forces. A molecule is also called the smallest identifiable unit of any substance.

Before learning about the structure of molecules, we should be thorough with the structure of atoms. The core element of any material is an atom. And it comprises a nucleus at its center and electrons at its shells. The charge of the neutron is positive as protons are positively charged and neutrons are neutral. However, electrons carry a negative charge making the overall charge of atoms neutral.

Formation of a molecule:

The basic phenomenon of the formation of a molecule is that every atom tries to fill its valence shell. For example, consider the case of the Water molecule. The hydrogen atom contains six electrons in its valence shell and is looking for two more electrons to complete its shell. And Hydrogen contains one electron in its valence shell thus looking for electrons. So, a hydrogen atom combines with an oxygen atom and they both share their electrons to fill their valence shell hence forming a water molecule.

When different atoms combine to form one molecule, that molecule is called a heteronuclear molecule. And when the same atoms combine to form one molecule it is called a homonuclear molecule.

The structure of a molecule is formed by the formation of ionic, covalent or metallic bonds between atoms. And the number of covalent bonds an atom can make is equal to the number of valence electrons if valency is less than or equal to four and if greater than four then the covalent bonds are equal to the number of electrons required to fill the valence shell. Hydrogen can make one covalent bond and oxygen can make two and carbon can make four.

A molecule’s structure can be depicted by valence-shell electron-pair repulsion theory given by Sidgwick and Powell in 1940. Commonly called the VSEPR theory. It is based on the fact that electrons always repel each other, obviously as all electrons have a negative charge. And due to this, the external bonding atoms try to be as far as possible from each other. For example, you can consider a Water molecule. As two hydrogen molecules are 104.50 apart from each other. Not 180o because there are four more electrons in the valence shell of oxygen called lone pair electrons.

A lone pair always influences the molecular structure, such as in NH3 forming 3 single bonds including one lone pair. These lone pairs repel attaching atoms as far as possible from them. According to VSEPR theory, the order of electron pair repulsion is as:

Lone pair-lone pair > lone pair-bond pair > bond pair-bond pair

And the order of space occupied by the lone pairs or attaching atoms bonding is as:

Lone pair > triple bond > double bond > single bond

Another phenomenon affecting the structure of the molecule is the electronegativity of the molecule called polarity or dipole moment. A bond dipole moment is created when two atoms with different electronegativities form a bond, leaving one atom with a partial positive charge and another with a partially negative charge due to which electrons get pulled towards a more electronegative atom. Now, if the molecule contains more than one bond and those are arranged in such a way that their bond moments cancel each other the net dipole moment cancels each other and will be zero and will not affect the molecule’s structure. For example, CO2 [C=O=C]. And when the molecule is asymmetrical such as in the H2O molecule. The dipole doesn’t cancel each other. Hence, having a net dipole which affects the structure of the molecule.

Structure of Organic Compounds

Generally, organic compounds are compounds made up of carbon and hydrogen and are more complex than inorganic compounds. It contains a carbon-hydrogen bond. And there are only three configurations of carbon, Tetrahedral with 4 bonding partners at 109.50 apart, Trigonal with 3 bonding partners at 120o apart, and Linear with 2 bonding partners at 1800 apart. Due to carbon’s unique sizing and bonding capability they can form long chains which are also called carbon skeletons. Which can be straight, cyclic, branched, etc. Due to this property of carbon, a very large number of organic compounds can be formed.

The molecular structure of a carbon-hydrogen bond is always tetrahedral, consisting of a hydrogen-carbon bond unless there is the inclusion of some other organic molecule such as ammonia or cyanide. Methane, or CH4, is the most basic hydrocarbon.

Molecular Structure of Sodium Chloride

Sodium chloride commonly known as rock salt consists of sodium and chloride ions in a 1:1 ratio as Na+ Cl– forming an ionic bond in between them. As sodium and chlorine both have a valency of one, thus they both interact with each other and form Sodium Chloride molecules. It’s a non-organic compound.

                                                         [Na]+ ——————–[Cl]–

When these molecules come together and form a crystal lattice of cubical form which is a face-centered cubic unit cell.

 Conclusion

A molecular structure is the shape of a molecule that is determined and affected by the orientation of covalent bonds formed between atoms.

            VSEPR theory depicts the arrangement of atoms together in 3D space forming a molecule. Which is based on a simple concept that electrons always repel each other. VSEPR theory is used to predict the 3D arrangement but in reality, to find the 3D arrangement spectroscopy is used.