Science Fair Project Encyclopedia
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. Structure also plays an important role in determining polarity, phase of matter, color, magnetism, and taste, among several other properties.
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).
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 refers to the complex geometries and different isomers that proteins can take.
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.
The VSEPR model is one way to generally represent the geometric shape individual molecules will take. The AXE method is commonly used in formatting molecules to fit the VSEPR model. It is necessary to construct a valid Lewis structure that shows all of the bonds (bonding pairs of electrons) and the locations of lone pairs of electrons in order to use VSEPR theory properly.
If the connectivity, bond lengths, bond angles and torsional angles are found, a molecules exact geometry is known. For any non-linear molecule with N atoms, 3N - 6 internal coordinates need to be specified in order to know the exact geometry of the molecule.
VSEPR theory is based on the idea that the geometry of a molecule or polyatomic ion is determined primarily by repulsions among the pairs of electrons associated with a central atom. The pairs of electrons may be bonding or nonbonding (also called lone pairs). These electrons are in the valence or outer shell of the atom. The core electrons do not contribute to bonding or to molecular shape in a meaningful way.
For example, the methane molecule (CH4) is tetrahedral because there are four pairs of electrons. The four hydrogen atoms are positioned at the vertices of a tetrahedron, and the bond angle is 109.5°. This is referred to as an AB4 type of molecule. A is the central atom and B represents all of the outer atoms.
The ammonia molecule (NH3) has three pairs of electrons involved in bonding, but there is a lone pair of electrons on the nitrogen atom. It is not bonded with another atom; however, it influences the overall shape through repulsions. As in methane above, there are four regions of electron density. Therefore, the overall orientation of the regions of electron density is tetrahedral. On the other hand, there are only three outer atoms. This is referred to as an AB3E type molecule because the lone pair is represented by an E. The overall shape of the molecule is a trigonal pyramid because the lone pair is not "visible." The shape of a molecule is found from the relationship of the atoms even though it can be influenced by lone pairs of electrons.
VSEPR theory is usually compared and contrasted with valence bond theory, which addresses molecular shape through orbitals that are energentically accessible for bonding. Valence bond theory concerns itself with the formation of sigma and pi bonds. Molecular orbital theory is a more sophisticated model for understanding how atoms and electrons are assembled into molecules and polyatomic ions.
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