Molecular geometry
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Image:Water molecule dimensions.png
Molecular geometry or molecular structure is the three dimensional arrangement of the atoms that constitute a molecule. The molecular geometry affects most properties of a substance including reactivity, polarity, phase of matter, color, magnetism, and biological activity.
A defined molecular geometry at equilibrium can only be expected at temperatures close to absolute zero, because at higher temperatures the atoms will wobble around. The molecular geometry can be measured by X-ray crystallography and computed by quantum mechanical calculations or semi-empirical molecular modeling. Larger molecules often exist in multiple stable conformations which differ in their molecular geometry.
The position of each atom is determined by the chemical bonds through which it is connected to its neighbouring atoms. The molecular geometry can either be described by the positions of the atoms in space or by the bond lengths, the bond angles between two adjacent bonds, and the torsion angles of three consecutive bonds.
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Bonding
Molecules, by definition, are most often held together with covalent bonds involving single, double, and/or triple bonds, where a "bond" is a shared pair of electrons (the other method of bonding between atoms is called ionic bonding and involves a positive cation and a negative anion).
Molecular geometries can be specified in terms of bond lengths, bonds angles and torsional angles. The bond length is defined to be the average distance between the centers of two atoms bonded together in any given molecule. A bond angle is the angle formed by three atoms bonded together. For four atoms bonded together in a straight chain, the torsional angle is the angle between the plane formed by the first three atoms and the plane formed by the last three atoms.
Molecular geometry is determined by the type of bonds between the atoms that make up the molecule. Before atoms interact to form a chemical bond, the atomic orbitals mix in a process called orbital hybridisation. The two most common types of bonds are:
An understanding of these bonds is in the domain of valence bond theory, which relies on an understanding of the wavelike behavior of electrons in atoms and molecules.
Isomers
Isomers are types of molecules that share a chemical formula but have different geometries, resulting in very different properties:
- A pure substance is composed of only one type of isomer of a molecule (all have the same geometrical structure).
- Structural isomers have the same chemical formula but different physical arrangements, often forming alternate molecular geometries with very different properties. The atoms are not bonded (connected) together in the same orders.
- Functional isomers are special kinds of structural isomers, where certain groups of atoms exhibit a special kind of behavior, such as an ether or an alcohol.
- Stereoisomers may have many similar physicochemical properties (melting point, boiling point) and at the same time very different biochemical activities. This is because they exhibit a handedness that is commonly found in living systems. One manifestation of this chirality or handedness is that they have the ability to rotate polarized light in different directions.
- Protein folding concerns the complex geometries and different isomers that proteins can take.
See also
- Atomic orbital
- Covalent bond
- Electron configuration
- Extended Huckel method
- Molecular orbital
- Valence bond theory
- VSEPR
