Bond Lengths and Energies
1) In macromolecules (DNA and proteins) covalent bond length ranges between 1.0 and 1.8 Angstroms.(using CHNOS atoms)
The typical energy for a covalent bond is 50 to 200 kCal/mol (200 to 800 kJoule/mol).A typical carbon-carbon (C-C) covalent bond has a bond length of 1.54 Angstroms and bond energy of 85 kcal/mol (356 kJoule/mol).
The bases in DNA have even stronger covalent bonds, the carbon-oxygen (C=O) double bonds have bond energies near 175 kcal/mol (732 kJoule/mol).
2) In macromolecules, at least five types of noncovalent bonds may be distinguished: electrostatic, hydrogen, van der Waals, pi aromatic, and hydrophobic.
Electrostatic Bonds: Also called "salt bridges" in proteins is a dipole interaction between 2 charged particles.
At neutral pH and both glutamic and aspartic acids normally carry a negative charge, and histidine, lysine and arginine each have a positive charge.
Typical energies for electrostatic bonds range between 1.4 to 3 kCal/mol ( 5.9 to 12 kJoule/mol).
Typical "salt bridges" have lengths of around 3.0 Angstroms.
Hydrogen Bonds: A dipole formed when a hydrogen atom covalently bonded to an electronegative atom is shared with a second electronegative atom (typically an oxygen or nitrogen atom), such that the proton may be approached very closely by an unshared pair of electrons.
DNA double-helical and protein alpha-helical and beta-structure conformations are extensively hydrogen bonded.
Typical energies for hydrogen bonds range between 1 to 3 kCal/mol ( 4 to 13 kJoule/mol)
and bond lengths range between 2.6 and 3.5 Angstroms separating the two nonhydrogen atoms.
Van der Waals:
There is an attractive component due to the induction of complementary partial charges or dipoles in the electron density of adjacent atoms when the electron orbitals of two atoms approach to a close distance. There is also a strongly repulsive component at shorter distances, when the electron orbitals of the adjacent atoms begin to overlap, commonly called steric hindrance.
Typical energies for Van de Waals interactions are very small around 0.5 to 1 kCal/mol (2 to 4 kJoule/mol) and bond lengths range beteen 2.5 and 4.6 Angstroms, averaging 3.6 Angstroms.
PI Aromatic bond:
PI interaction (pi electron to pi electron), called "aromatic" or "pi" bonding, occurs when two aromatic rings (conjugated p systems) approach each other with the plane of their aromatic rings overlapping, with successive p-bonded systems stacked like layers in a cake. PI bond stacking forces contribute to nucleic acid stability at least as much as the hydrogen bonds between bases.
Typical energy for PI interactions is around 10 kCal/mol ( 40 kJoule/mol) and bond lengths 3.8 Angstroms.
When two nonpolar residues approach each other, the surface area exposed to solvent is reduced, increasing the entropy of all the water present and decreasing the entropy of the residues. The hydrophobic energy is roughly 5 kCal for every 100 Angstroms**2 of contact surface area that was formerly exposed to water.