Why does it matter what shape a molecule has - Essay Example

?SIGNIFICANCE OF THE SHAPE OF MOLECULES Introduction The world is composed of atoms which are the smallest indivisible particles of matter “made up of negatively charged electrons in orbitals around positively charged nuclei” (RBI 1988, p.53). Atoms integrate through interactions between electrons to form units termed as molecules. These are the contexts in which the manner in which materials behave are described, whether they are simple gases, or complex biological structures. The bonds between atoms have distinct lengths, energy and direction which distinguish the atomic structure of materials. The shape of a molecule is formed by the spatial relationships of chemically bonded atoms, and this feature contributes significantly to understanding how molecules react with each other. Ionic bonds are formed by the electrostatic attraction between a cation and an anion. The electric field of an ion has spherical symmetry, hence ionic bonds have no directional character. Contrastingly, covalent bonds are formed by the overlap of atomic orbitals. Since the overlap is such that the atomic orbitals can attain maximum overlap, a covalent bond has a directional character. Therefore, “the shape of a molecule is determined by the angle between two bonds, which in turn is determined by the atomic orbitals that form the bond” (Iwanami 2006, p.1). Thesis Statement: The purpose of this paper is to investigate why the shape of a molecule is significant in the study of chemistry. The Importance of Molecular Shape in Medicinal Drugs “The shape and size of a molecule are very important in determining its affinity for a biomolecular target” (Corey, Czako & Kurti 2012, p.55). Among the forces of attraction between nonpolar molecules such as straight-chain hydrocarbons are van der Waal’s forces, which are much weaker than covalent bonds, ionic bonds, or even hydrogen bonds. At the same time, however, van der Waal’s attractions between molecules can become significant when two nonpolar molecular surfaces are complementary in shape, and of sizable area. These forces determine the specificity of drug action in the case of medicinal products. It is because of the interaction of such forces that it is possible for gecko lizards to walk across smooth ceilings or vertical walls. The attraction between two adjacent non-polar molecules increases in proportion to the area of contact. Generally, the closeness of the tie between the two increases with greater area of van der Waal’s contact attraction and also with the degree of hydrogen bonding. The higher the level of molecular fit, the stronger is the affinity between a molecule and the biomolecular target in therapeutic agents. A therapeutic agent or medicine in aqueous solution is stablized by hydrogen bonding to water and dipolar solvation. It is evident that in medicines, there is a trade-off; they must be sufficiently well solvated to be soluble in water, “but not so strongly solvated that they cannot be pulled from solution by the target biomolecule” (Corey et al 2012, p.55). Noncyclic organic molecules are usually flexible because the barrier to rotation about single bonds having low energy. Therefore, most medicines’ structures have cyclic subunits with a few preferred conformations, sometimes just one. Fig.1a. and 1b. show the conformation of prednisone, a significant anti-inflammatory and immunosuppressive drug, along with the preferred conformation of glucose. Fig.1a. Chemical Structure of Glucose Molecule (Corey et al 2012, p.56) Fig.1b. Prednisone Chemical Structure (Corey et al 2012, p.56) While the molecular formula for glucose is C5H12O6, the formula for prednisone is C21H26O5. “The polycyclic framework of prednisone is quite rigid and gives the molecule a characteristic shape” (Corey et al 2012, p.56). Concurrently, several polar functional groups are situated at specific sites in space, facilitating their optimal binding to the target molecule. The Different Shapes of Molecules Based on Structure There are compounds with a divalent central atom. According to the theory of Valence shell electron pair repulsion (VSEPR), two electron pairs belonging to a divalent central atom will be separated to the maximum width when the bond angle is 180 degrees. This means the molecule will have a linear structure. For example, Beryllium chloride BdCl2 with a divalent central atom is a linear molecule. Some compounds such as carbon dioxide CO2 and allene H2C=C=CH2 are also linear, similar to having a divalent central atom (Iwanami 2006). For compounds with a trivalent central atom such as boron trichloride BCl3, when the Valence shell electron pair repulsion (VSEPR) theory is applied, the bond angle Read More