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chem.tut
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1.0 Atomic Orbitals
Atoms are composed of a nucleus and electrons that surround the
nucleus. The electrons tend to stay in specific locations around
the atom called Atomic Orbitals. An Atomic Orbital may contain
at most two electrons.
1.1 Types of Atomic Orbitals
The Atomic Orbitals included in most chemical bonding are the s,
p, and d type. Each Atom has only one s type orbital. An s
orbital can bond in any direction. Each Atom has three p type
orbitals (Px,Py,Pz). In 3-dimensional space one p orbital
is parallel to each of the 3 axis: X,Y,Z. The direction
that a p orbital will bond is determined by the axis it is
parallel with. Each Atom has five d type orbitals Dxy, Dyz,
Dxz, Dxx-yy, and Dzz (CHEMICAL numbers these a,b,c,d,e).
1.2 Atomic Orbital Hybrids
The s, p, and d Atomic Orbitals can be combined to form a
veriety of hybrids such as sp, dsp, sp2, etc. The number of
hybrids formed matches the number of Atomic Orbitals that
combined to form the hybrid. The directional characteristics
taken by a hybrid are determined by the directional tendancies
of the Atomic Orbitals that are combined. However, bonding atoms
will tend to spread out evenly in 3 dimensional space. The
hybrids formed are numbered with the symbols ' ` ^ ~ + : in
CHEMICAL.
CHEMICAL includes some special versions of the sp2 and sp3
hybrids to make ring structures easier to generate. The
sp2_5 and the sp3_5 hybrids should be selected if a 5 atom
ring is desired. The sp2 and sp3_6 hybrids should be
selected if a six atom ring is desired.
2.0 Molecular Orbitals
Atomic Orbitals from two atoms can combine to form Molecular
Orbitals, the electrons shared (covalently) between the two
Atoms. Molecular Orbitals replace the Atomic Orbitals. Molecular
orbitals are either Bonding or Anti-Bonding. The Bonding
Orbitals are lower energy and are more commonly used for
bonding. Each Molecular Orbital can hold at most two electons.
2.1 Types of Molecular Orbitals
There are only three types of Molecular orbitals: sigma, pi, and
delta. Sigma orbitals are formed when the "ends" of Atomic
Orbitals bond, and thus are free to rotate after bonding. Pi and
delta Molecular Orbitals are by side by side bonding and thus
are not free to rotate. (CHEMICAL Version 2.0 does not include
delta bonds)
3.0 Bonding
Atomic and Molecular orbitals have energy states associated with
them. Bonding occures when a lower energy state occures by
sharing electrons. No more than two electrons may occupy any
orbital. When many possible bondings exist the lowest energy one
will dominate and determine the 3 dimensional configuration.
3.1 Bonding Electrons
Typically each atom donates an electron for bonding. Sometimes
one atom will donate both electrons, this is called a Dative
bond. Sometimes bonding can only occure by using the higher
energy anti-bonding orbitals.
3.2 Bond Order
The bond order is determined by the number of pairs of electrons
in bonding orbitals minus the number of pairs of electrons in
anti-bonding orbitals. The higher the bond order the stronger the
bond.
4.0 Size of Atoms
Atoms for higher numbered elements are generally larger. The
size also varies with the type of hybrid and bonding. CHEMICAL
has a built in table of atom sizes according to the orbital
type and bond order. This information was taken from the Van
Nostrand's Scientific Encyclopedia.
5.0 Ionic Bonding
Some atoms have strong electrostatic charge and tend to bond to
atoms of opposite charge by Ionic Bonding. CHEMICAL has a built
in table of atoms with strong electrostatic charge to construct
chemicals with Ionic Bonding. Negative ions are large because
they hae gained an additional electron. Positive ions are small
due to the loss of an electron.