Glossary for Computational Chemistry Cell

See "spreadsheet"
Computational expense
A Amount of time and platform needed to perform a calculation. eg, a geometry optimization is
more computationally expensive than a single point energy.
ab initio Coordinate Covalent Bond
Latin for "from scratch" or "from first principles". Means that all results are based on solutions of Interatomic attraction resulting from the sharing of a lone pair of electrons from one atom with another
Schroedinger's Equation and the wavefunction(s) used. No empirical data is used. atom
Activation Energy Coordination Compounds
The amount of energy needed to allow a reaction to proceed. (aka energy hump or energy barrier). When an ion of a metal becomes strongly attached to anions or neutral molecules to form more
Needed to form transition structure. complicated ions. In this instance, the metal anion acts as a Lewis acid and the other species acts as a
Algorithm Lewis base. The two form a coordinate covalent bond. (also known as: adduct, complex, complex ion)
Mathematical representation of the application: a mathematical model
Angstrom D
Unit of distance. Bohr Radius in these units is a0=.529A
Anti-Bredt structure Debye
Geometry which does not obey Bredt's rule, ie, has a double bond at a bridgehead position. See related
terms "Bredt's Rule" Unit of dipole moment.
Application Delta
Scientific situation being represented Greek symbol, looks like a triangle. Denotes "change in".
Architecture Delocalization, Delocalized
Computing structure or platform used to execute the algorithm Electrons which do not reside along a single bond, but move from bond to bond, as in an aromatic
Aromatic, Aromaticity carbon bond. See also, aromatic
In organic chemistry, carbon which has bonds that are between single and double bonds. Eg, it has a Dihedral angle
bond with a delocalized electron. See also "delocalization" Angle between an atom and a plane (formed by three or more other atoms).
Atomic orbital Dipole
Representation of the electron cloud surrounding an atom. Named by primary quantum number and Equal positive and negative charges separated by a distance.
shape, i.e. 1s, 2s, 2p Dipole moment
Azimuthal Quantum Number Measure of how polarized a molecule is (how large the dipole is).
See "Magnetic Quantum Number". Dissociation
B When a compound separates into two or more parts. Especially used when an ionic compound breaks
Basis set down into its component ions in solution.
Group of numerical constants used in the wavefunctions. Named by number and type of wavefunctions Dissolve
used to represent an atom. Specific to atom. To distribute particles of one substance throughout another. Especially used with solutions in water. See
Bohr atom also "solution" and related terms.
Idea of the atom with electrons in fixed "orbits". Developed by Niels Bohr in early 20th century. Double bond
Supports idea of ground state and excited state, and explains quantization of photons absorbed and A pair of shared electrons. Atoms at either end cannot rotate around bond. Also called pi bond.
emitted.
Bohr radius E
Distance of the first orbit in the Bohr atom from the nucleus.
Bond, covalent Eigenfunction, Eigenvalue
Connection between two atoms, consisting of a shared orbital Function such that when an operation is performed on it, the result is the same function times a constant.
Bond, ionic That constant is known as the eigenvalue.
Connection between two ions, consisting of an electrostatic attraction (eg, Na+ to OH-) Electron
Bond angle Subatomic particle (with wave-like qualities!), negatively charged. Found in all atoms; balances charge
Angle from a pair of bonded atoms to another atom, one of the bonded pair being the vertex of nucleus.
Bond length Electron Affinity
Distance between the nuclei of two bonded atoms The energy released when an electron is added to an atom.
Born Oppenheimer approximation Electron cloud
Used to simplify Schroedinger's Equation. Assumes that nuclei are massive and slow-moving compared Physical space where the electron's wavefunction indicates it has a high probability of appearing (where
to electrons. it spends almost all of its time).
Bredt's Rule Electron density
Double bonds will not be formed at bridgehead positions. Such structures have too much ring strain to A measure of the "thickness" of the electron cloud in a given place, eg, the probability of the electron's
be stable. Exceptions are known. See related term "Anti-Bredt structure" presence. Function defined over all space; sum over all space gives number of electrons present.
Bridgehead Electron structure
Carbon on a ring where other carbons are attached in a link across the ring. Way of accounting for the shape of an electron cloud. Indicates which orbitals are occupied.
Electronegativity
C An atom's attraction for the electrons in a bond.
Electropositive
Carboxyl group Elements with low electronegativities.
Also called COOH group; functional group consisting of a carbon double bonded to an oxygen and Electrostatic potential (elpot)
single bonded to another oxygen with a hydrogen on the other side. Terminal group on carboxylic acids.
 Attraction between positive and negative charges. Relating to a molecule, it expresses what would Intermediary product
happen to a small positive charge brought near the molecule. See "transition structure"
Energy of activation Ion
see "activation energy" Atom or group of atoms which has a net charge, ie, there are not enough electrons to properly balance
Excited state out the charge of the nuclei.
When electrons are not in the lowest possible orbitals. Ionization energy
Extended Basis Set Function Amount of energy required to remove one electron from an atom.
A basis set that describes the orbitals in great detail Isomer
Having the same number of atoms of each element as another molecule.
G
L
GAMESS, also MacGAMESS
Computational tool run on workstation or desktop computer, performs some of calculations which LCAO
Gaussian 94 does. Uses ab initio methods only. Linear Combination of Atomic Orbitals: An approximation which sums atomic orbitals (with certain
Gaussian coefficients) to produce molecular bonding and anti-bonding orbitals.
Mathematical function shaped like the normal distribution, or bell curve. Used in approximating the LUMO
wavefunction. Lowest Unoccupied Molecular Orbital: Orbital with least energy without any electrons in it.
Gaussian 94
Computational tool for ab initio and other calculations. Must be used in conjunction with a visualization M
tool to produce images, usually run on a high-power platform.
Geometry (of a molecule) Magnetic Quantum Number
Description of bond lengths and angles. Describes the shape of of the orbital. Often described in terms of the x,y,z orientation of the orbital, eg,
Geometry Optimization 2px where the x is the magnetic quantum number. Also called "azimuthal quantum number", written
Calculation to find a stable (local energy minimum) configuration of a molecule. "m".
Ground state Maximum, global (relating to energy, plural maxima)
When electrons are in lowest possible orbitals. Molecular geometry with the largest possible energy.
GTO Maximum, local (relating to energy, plural maxima)
Gaussian Type Orbital, an approximation of the wavefunction using gaussian curves. See also "orbital", Molecular geometry with an energy larger than most, however not the largest energy possible
"wavefunction", "gaussian" Minimal Basis Set Function
A basis set that describes only the most basic aspects of the orbitals
H Minimum, global (relating to energy, plural minima)
Configuration with lowest possible energy.
Hamiltonian Minimum, local (relating to energy, plural minima)
Mathematical operator used in the Schroedinger Equation Configuration such that slight changes produce a more energetic structure, but it is not the lowest
Hartree possible energy.
Amount of electrostatic repulsion between two electrons held one Bohr radius apart. Often used as Molecule
atomic unit of energy. More than one atom bonded together. See also, Bond, Covalent, Bond, Ionic.
Hartree Fock approximation Molecular mechanics
Used to simplify Schroedinger's Equation. Breaks complex orbitals down into a series of one-electron Method of using empirical data to greatly simplify the calculations for very large molecules.
orbitals. Also called self-consistent field (SCF) method. Sometimes called UHF or RHF for unrestricted Molecular orbital
and restricted Hartree Fock approximations. Unrestricted methods allow for lone electrons, while Representation of electron cloud surrounding a molecule. May be hybridized.
restricted methods only deal with paired electrons. Multiple bond
Heat of Formation See "double bond", "triple bond"
Energy which would be required to form a molecule from dissociated atoms. If positive, the structure
will not be formed spontaneously. Lower heats of formation indicate more stable molecules, which are N
formed preferentially. A difference of one kcal/mol means that the more stable geometry will be
approximately 10 times more common. Nanometer
HOMO Measure of length, equal to 1x10-9 meters
Highest Occupied Molecular Orbital: Orbital with the most energy which contains an electron. Nucleus
Hybrid orbital Collection of subatomic particles found in the center of an atom. Positively charged.
An orbital produced by a combination of differently shaped orbitals. Eg, s+p orbitals gives an sp hybrid
orbital. O
Hybridization
When orbitals combine to form bonds which are not exactly one shape or the other. Orbital
Hydrocarbon Representation of electron cloud. See "atomic" and "molecular" orbital.
Molecule which contains only hydrogen and carbon. Type of organic molecule. Organic
In chemistry, a compound containing carbon.
I
P
Imaginary frequency
Vibration which is impossible, ie, would cause molecule to spontaneously break down. Phase
Finding EXACTLY ONE indicates that molecule is a transition structure.
 One of the three normal states of matter, solid, liquid, or gas, depending on the level of organization Spin Quantum Number
between particles. Has values of +1/2 or -1/2, also called "up" and "down" or "alpha" and "beta" spin. Serves to
Pi bond differentiate between two electrons in the same orbital. Written "ms"
See "double bond" Split valence basis set
Picometer Basis set which uses several wavefunctions to represent different valences. Denoted by a star at the end
Measure of length, equal to 1x10-12 of name. See also "basis set", "valence"
pKa, pKb Spreadsheet
Indication of the strength of an acid/base. Higher values correspond to weaker acids or bases. Computational tool which can be set up to hold numerical constants, lists, and labels, and perform
Planck Constant computations on those. Useful for repetitive lists of numbers, usually has graphing capabilities. Divided
Numerical value expressing the amount of uncertainty which must be present in any concurrent into cells.
measurement of a particle's position and momentum. STO
Point-Group Symmetry Slater Type Orbital: Orbital using Slater renormalization factor to approximate wavefunction. See also
See "symmetry". "orbital", "wavefunction"
Potential Energy Surface Solute
a mathematical relationship between different molecular geometries and their corresponding single point Substance dissolved in a solution. See also "solution", "solvent", etc.
energies. Solution
Primary quantum number One substance being evenly distributed throughout another. See also "solute", "solvent", etc.
Number used in electron structure notation, eg 1s, 2s, etc. Corresponds to the orbit in the Bohr atom Solvation energy
where an electron would be found. Written "n". Change in energy when a susbstance is dissolved. See also "solution", "solvent", etc.
Probability Solvent
A number between one and zero which denotes how likely an event is to happen. Multiplied by 100, it Substance in which something is dissolved. See also "solution", "solute", etc.
becomes a percentage. Strong acid/base
Probability density Acid or base which dissociates completely in water. Has a low pKa or pKb.
A mathematical distribution of probability over space or time. Sum of all probabilities must equal one Symmetry, Point-Group Symmetry
(ie, the event has to happen somewhere or sometime) Properties of a molecule describing how it can be transformed and still appear exactly the same. Point-
group symmetry is a method of naming the combination of symmetry elements which a molecule has.
Q
T
Quantum (plural quanta)
Separate units of something. For example, money comes in quanta of 1 cent. Transition state, transition structure
Quantum Numbers Molecule or group of molecules formed during a reaction. Unstable, containing weak bonds and having
Set of numbers used to specify any orbital in a given atom. Consist of Primary, Secondary, Azimuthal, high energy. Requires energy of activation to form. Vibrates at imaginary frequencies. See also
and Spin numbers. See those related terms. "activation energy", "imaginary frequency"
Triple bond
R Three shared electrons

Radius U
Distance from the center (usually of a circle) to the edge, in chemistry, usually from the nucleus to an
electron Unfilled valence
Resonance structure Valence which has no electrons in it. See also "valence"
Different possible structures for the same molecule. V
Valence
S One level of an orbital
Valence electrons
Saddle Point The outermost electrons in an atom
a molecular geometry such that slight changes cause both a maximum in one direction and a minimum Valence orbital
in the other. Saddle points represent a transition structure connecting two equilibrium structures. The outermost orbital containing electrons in an atom
Schrodinger’s equation
Also called wavefunction. Original equation used to write wavefunctions for particles. Incorporates the W
Hamiltonian.
Secondary Quantum Number Wavefunction
Denotes the sub-shell which the orbital occupies. Written "l", but often denoted by a letter, such as Complex mathematical representation of a particle, in compchem, probably an electron.
s,p,d,f.
Semiempirical
Method of computational chemistry using some empirical (real-world, from the lab) data to simplify the
calculations necessary.
Sigma bond
See "single bond"
Single bond
One shared electron. Atoms at either end can rotate.
Single point energy
Calculation of the energy of the molecule at a specific geometry.