Molecular geometry

Geometry of the water molecule

Molecules have fixed equilibrium geometries--bond lengths and angles--that are dictated by the laws of quantum mechanics. The chemical formula and the structure of a molecule are the two most important factors that determine its properties, particularly its reactivity. Molecules are most often held together with covalent bonds involving single, double, and/or triple bonds (shared electron pairs).

A pure substance is composed of molecules with the same geometrical structure. Isomers share a chemical formula but have different geometries, resulting in very different properties. Stereoisomers, a particular type of isomers, may have very similar physico-chemical properties and at the same time very different biochemical activities.

Protein folding refers to the complex geometries and different isomers that proteins can take.

Hybridization of Orbitals

Bonds in molecules are often the result of hybridization, for two main reasons. First, sometimes electrons from two different orbital types are paired together. A middle ground is needed where both of the electrons can exist with some aspects of their native orbital. Second, sigma bonds are closer to the respective nuclei and thus take less energy to form and maintain. Since reactions tend to occur using the least amount of energy possible, sigma bonds are the most common type of hybrid bond.

Sigma Bonds

Sigma Bonds are those bonds between atoms in a molecule that exhibit hybridization. Sigma bonds are named after the Greek letter "s", as in s orbitals. Sigma bonds require that both atoms give an electron from the s orbital in conjunction with additional electrons from the p and sometimes d (and above) orbitals. Sigma bonds are the strongest type of covalent bonds. They result in a head-to-head orbital overlap - the two combined orbitals meet at the more narrow points. Electrons in sigma bonds are sometimes referred to as sigma electrons.

Pi Bonds

Pi bonds are those bonds between two atoms in a molecule that do not exhibit hybridization. Pi bonds are named after the Greek letter for "p", as in p orbitals. Pi bonds are direct sharing of electrons between two atoms' p orbitals. Pi bonds are weaker than sigma bonds because their orbitals go further from the positive charge of the nucleus, which requires more energy. As a result, sigma bonds are naturally preferred over pi bonds. However, there is a limit of one sigma bond for each pair of atoms. Atoms with double or triple bonds have one sigma bond and the rest are usually pi bonds. Pi bonds result from parallel orbital overlap - the two combined orbitals meet lengthwise and create longer bonds than the sigma bonds. Electrons in Pi Bonds are sometimes referred to as pi electrons.

VSEPR Model

The VSEPR (Valence-Shell Electron-Pair Repulsion) model is one way to generally represent the geometric shape individual molecules will take. It is not perfectly accurate but instead gives a general impression of how atoms and electrons will be arranged. The AXE method is commonly used in formatting molecules to fit the VSEPR model. The A represents the central atom and is always (implied) subscript one. The X represents how many bonds are formed between the central atoms and outside atoms. Multiple covalent bonds (double, triple, etc) count as one X. The E represents the number of lone electron pairs present outside of the central atom. Once the AXE formula has been found, the following table will predict the geometric configuration around the central atom.

See also

atomic orbital, molecular orbital, electron configuration, covalent bond, valence bond theory

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