Structural Biochemistry/Strong Intermolecular Forces

Hydrogen Bonding
A property of water is that it has strong intermolecular forces as a result of hydrogen bonding and the dipole moments created by the strong electronegative oxygen and the hydrogen. The electronegativity of oxygen is 3.44 while hydrogen is 2.20. This difference pushes electron density favorably in the direction of oxygen. While the electrons lie closer to the oxygen, the hydrogens molecules surrounding the water molecules start to aggregate together to neutralize the charge imbalance. This aggregation between the hydrogen and the oxygen create the basis for the hydrogen bond.



Due to hydrogen bonding, water contains these distinct characteristics.



A). High melting point - The hydrogen bonds formed between the water molecules in solid water (ice) must be broken before the solid --> liquid phase change can take place. The energy required to break these bonds accounts for the relatively high melting point of water.

B). High boiling point - The hydrogen bonds formed between the water molecules in liquid water must be broken before the liquid --> gas phase change can take place. The energy required to break these bonds accounts for the relatively high boiling point of water.

C). High heat of vaporization - The heat of vaporization is the amount of energy required to convert a specific volume of liquid to a gas. The hydrogen bonds formed between the water molecules must be broken in order for the liquid --> gas phase change to take place. Thus, the breaking of these bonds require energy, therefore accounting for water's the high heat of vaporization.

D). High surface tension. - water molecules interact strongly with one another through hydrogen bonds. These interactions are apparent in the structure of ice. Networks of hydrogen bonds hold the structure together; similar interactions link molecules in liquid water and account for the cohesion of liquid water, although, in the liquid state, approximately one-fourth of the hydrogen bonds present in ice are broken. The polar nature of water is responsible for its high dielectric constant of 80. Molecules in aqueous solution interact with water molecules through the formation of hydrogen bonds and through ionic interactions. These interactions make water a versatile solvent, able to be readily dissolve many species, especially polar and charged compounds that can participate in these interactions.

E). Large Dielectric Constant - The water molecule is bent, not linear, and so the distribution of charge is asymmetric. The oxygen nucleus draws electrons away from the two hydrogen nuclei, which leaves the region around each hydrogen nucleus with a net positive charge. The water molecule is thus an electrically polar structure.

Due to having up to 4 hydrogen bonds for each water molecule and having difficulty breaking these bonds, water has higher melting point, boiling point, and heat of vaporization compared to other liquids. Waters hydrogen bond between the Oδ- and the Hδ+ terminal, and the length of it is known as 0.28±0.01 nm. However, hydrogen bonds are relatively weak in comparison to their covalent bond counterpart. The bond dissociation energy, or the amount of energy that is required to pull apart a hydrogen bond is only 23 kJ/mol while an average covalent bond between an O-H is 470 kJ/mol. This low BDE allows water molecules to dynamically attach and separate spontaneously at room temperature.

Hydrogen bonds are much weaker than covalent bonds such as the carbon-carbon or carbon-nitrogen bonds that define the structures of the bases themselves. Such weak bonds are crucial to biochemical systems; they are weak enough to be reversibly broken in biochemical processes, yet they are strong enough, when many form simultaneously, to help stabilize specific structures such as the double helix.

•	Hydrogen bonds are strongest when the hydrogen when the hydrogen atom and the two atoms that shares it is in a straight line.

hydrophobic interactions •	the stable structures of amphipathic compounds(Amphipathic compounds contain regions that are polar or charged and regions that are nonpolar)in water are called micelles. the forces that hold the nonpolar regions of the molecules together are called hydrophobic interactions. This interaction between nonpolar amino acid also stabilizes the 3D structure of proteins.

Van der waals - When two uncharged atoms are brought very close together, their surrounding electron clouds influence each other. The two dipoles weakly attract each other, bringing the two nuclei closer, and then repel.