Molecular Biology Protein Structure

Interactions of Molecules

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Molecular Interactions are attractive or repulsive forces between molecules and between non-bonded atoms. Molecular interactions are also known as non-covalent interactions or intermolecular interactions.

Uses

  • In protein folding
  • In drug design
  • In material science
  • In sensors
  • In nanotechnology
  • In separations
  • In origins of life

The potential energy of interaction of a molecule near a solid surface can be constructed as a sum of terms for the molecule interacting with unit cells for a periodic lattice or with atom groups for amorphous surfaces. 

Molecular interactions are not bonds. Bonds hold atoms together within molecules. A molecule is a set of atoms that associates tightly enough that it does not dissociate or lose its structure when it interacts with its environment. At room temperature two nitrogen atoms are bonded (N2). Two argon atoms not bonded. Bonds break and form during chemical reactions. 

Bonds remain intact when 

  • ice melts
  • water boils
  • carbon dioxide sublimes
  • proteins unfold
  • RNA unfolds
  • DNA strands separate 
  • membranes disassemble

Hydrogen bonding

A hydrogen bond is the attraction between the lone pair of an electronegative atom and a hydrogen atom that is bonded to an electronegative atom, usually nitrogen, oxygen, or fluorine. The hydrogen bond is often known as a strong electrostatic dipole–dipole interaction. However, it also has some features of covalent bonding: it is directional, stronger than a van der Waals force interaction, produces interatomic distances shorter than the sum of their van der Waals radii, and usually involves a limited number of interaction partners, which can be interpreted as a kind of valence. 

Ionic bonding

The attraction between cationic and anionic sites is a non-covalent, or intermolecular interaction which is usually referred to as ion pairing or salt bridge. It is essentially due to electrostatic forces, although in aqueous medium the association is driven by entropy and often even endothermic. 

Dipole–dipole and similar interactions 

Dipole–dipole interactions are electrostatic interactions between molecules which have permanent dipoles. This interaction is stronger than the London forces but is weaker than ion-ion interaction because only partial charges are involved. These interactions tend to align the molecules to increase attraction (reducing potential energy). Often molecules have dipolar groups of atoms, but have no overall dipole moment on the molecule as a whole. 

Ion–dipole and ion–induced dipole forces

Ion–dipole and ion–induced dipole forces are similar to dipole–dipole and dipole–induced dipole interactions but involves ions, instead of only polar and nonpolar molecules. Ion–dipole and ion–induced dipole forces are stronger than dipole–dipole interactions because the charge of any ion is much greater than the charge of a dipole moment. Ion–dipole bonding is stronger than hydrogen bonding. 

Van der Waals forces

The van der Waals forces arise from interaction between uncharged atoms or molecules, leading not only to such phenomena as the cohesion of condensed phases and physical absorption of gases, but also to a universal force of attraction between macroscopic bodies. 

London dispersion force 

The dominant contribution is the dispersion or London force, which arises due to the non-zero instantaneous dipole moments of all atoms and molecules. Such polarization can be induced either by a polar molecule or by the repulsion of negatively charged electron clouds in non-polar molecules. Thus, London interactions are caused by random fluctuations of electron density in an electron cloud. 

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