Structural Biochemistry/Chemical Bonding/Noncovalent bonds

Background Information
A noncovalent bond is a type of chemical bond that typically bond between macromolecules. They do not involve sharing a pair of electrons. Noncovalent bonds are used to bond large molecules such as proteins and nucleic acids. Noncovalent bonds are weaker than covalent bonds but they are crucial for biochemical processes such as the formation of double helix. There are four commonly mentioned fundamental noncovalent bond types. They include electrostatic interactions, hydrogen bonds, van der Waals interactions, and hydrophobic interactions. Each type differs in geometry, strength, and specificity.

Electrostatic interactions
The energy of an electrostatic interaction is given by Coulomb’s Law: E = kq1q2 / Dr2 where E is the energy, q1 and q2 are the charges of two atoms, r is the distance between the two atoms, D is the dielectric constant, and k is a proportionality constant. k = 1389 for energy that’s measured in kilojoules/mol or k = 332 for energy that’s measured in kcal/mol. A charged group on a molecule can attract an oppositely charged group from another molecule. By contrast, an attractive interaction has a negative energy. The dielectric constant is important for the medium.

Hydrogen bonds
A hydrogen bond is the interaction of a hydrogen atom with an electronegative atom. The electronegative atom can be nitrogen, oxygen, fluorine that comes from another chemical group. Hydrogen bonds are responsible for specific base-pair formation in the DNA double helix. The hydrogen atom in a hydrogen bond is shared by two electronegative atoms such as nitrogen or oxygen. A hydrogen-bond donor is the group that includes an electronegative atom where the hydrogen atom is more tightly bound to and a hydrogen-bond acceptor is when an electronegative atom is less tightly bound to the hydrogen atom. The electronegative atom where the hydrogen atom covalently bonds can pull electron density away from the hydrogen atom creating a positive electronegativity charge. The hydrogen atom can also interact with an atom that has negative electronegativity charge.

van der Waals interactions
Van der Waals interaction is the distribution of electronic charge around an atom that fluctuates with time. It is the sum of the attractive or repulsive forces between molecules. The charge distribution is not perfectly symmetric. The attraction increases as two atoms come closer to each other, until they are separated by the van der Waals contact distance. When the distance of the energy is shorter than the van der Waals contact distance, a very strong repulsive force becomes dominant.

Hydrophobic interactions
Hydrophobic interaction is the physical property of a molecule that is repelled from a mass of water. They are also called hydrophobic exclusions. It is the tendency of hydrocarbons to form intermolecular aggregates in an aqueous medium, and analogous intramolecular interactions.

Ion Induced Dipole
An ion induced dipole is a noncovalent bond interaction that results when the approach of an ion induced a dipole in an atom or in a nonpolar molecule by distributing the arrangement of electrons in the nonpolar species.

Dipole Induced Dipole
A dipole-induced dipole interactions results a nonpolar molecule has it's electron density shifted by a charged molecule. If a negatively charged species described by its electron density (for example, in water electron density is centralized on the oxygen atom) is brought near a species with an evenly distributed charged molecule, the electrons go towards the side where the positive species is, and away from the opposite side, creating an artificial dipole.

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