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Glossary for Computational Chemistry
Click on the first letter of the term.
[a][b][c][d][e][f][g][h][i][j][k][l][m][n][o][p][q][r][s][t][u][v][w][x][y][z]
A
 ab initio
 Latin for "from scratch" or "from first principles". Means that all
results are based on solutions of Schroedinger's Equation and the
wavefunction(s) used. No empirical data is used.
 Activation Energy
 The amount of energy needed to allow a reaction to proceed. (aka energy
hump or energy barrier). Needed to form transition structure.
 Algorithm
 Mathematical representation of the application: a mathematical model
 Angstrom
 Unit of distance. Bohr Radius in these units is a_{0}=.529A
 AntiBredt structure
 Geometry which does not obey Bredt's rule, ie, has a double bond at a
bridgehead position. See related terms "Bredt's Rule"
 Application
 Scientific situation being represented
 Architecture
 Computing structure or platform used to execute the algorithm
 Aromatic, Aromaticity
 In organic chemistry, carbon which has bonds that are between single and
double bonds. Eg, it has a bond with a delocalized electron. See also
"delocalization"
 Atomic orbital
 Representation of the electron cloud surrounding an atom. Named by primary
quantum number and shape, i.e. 1s, 2s, 2p
 Azimuthal Quantum Number
 See "Magnetic Quantum Number".
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B
 Basis set
 Group of numerical constants used in the wavefunctions. Named by number
and type of wavefunctions used to represent an atom. Specific to atom.
 Bohr atom
 Idea of the atom with electrons in fixed "orbits". Developed by Niels Bohr
in early 20th century. Supports idea of ground state and excited state, and
explains quantization of photons absorbed and emitted.
 Bohr radius
 Distance of the first orbit in the Bohr atom from the nucleus.
 Bond, covalent
 Connection between two atoms, consisting of a shared orbital
 Bond, ionic
 Connection between two ions, consisting of an electrostatic attraction
(eg, Na+ to OH)
 Bond angle
 Angle from a pair of bonded atoms to another atom, one of the bonded pair
being the vertex
 Bond length
 Distance between the nuclei of two bonded atoms
 Born Oppenheimer approximation
 Used to simplify Schroedinger's Equation. Assumes that nuclei are massive
and slowmoving compared to electrons.
 Bredt's Rule
 Double bonds will not be formed at bridgehead positions. Such structures
have too much ring strain to be stable. Exceptions are known. See related term
"AntiBredt structure"
 Bridgehead
 Carbon on a ring where other carbons are attached in a link across the ring.
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C
 Carboxyl group
 Also called COOH group; functional group consisting of a carbon double
bonded to an oxygen and single bonded to another oxygen with a hydrogen on the
other side. Terminal group on carboxylic acids.
 Cell
 See "spreadsheet"
 Computational expense
 Amount of time and platform needed to perform a calculation. eg, a
geometry optimization is more computationally expensive than a single
point energy.
 Coordinate Covalent Bond
 Interatomic attraction resulting from the sharing of a lone pair of
electrons from one atom with another atom
 Coordination Compounds
 When an ion of a metal becomes strongly attached to anions or neutral
molecules to form more complicated ions. In this instance, the metal anion
acts as a Lewis acid and the other species acts as a Lewis base. The two form
a coordinate covalent bond. (also known as: adduct, complex, complex ion)
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D
 Debye
 Unit of dipole moment.
 Delta
 Greek symbol, looks like a triangle. Denotes "change in".
 Delocalization, Delocalized
 Electrons which do not reside along a single bond, but move from bond to
bond, as in an aromatic carbon bond. See also, aromatic
 Dihedral angle
 Angle between an atom and a plane (formed by three or more other atoms).
 Dipole
 Equal positive and negative charges separated by a distance.
 Dipole moment
 Measure of how polarized a molecule is (how large the dipole is).
 Dissociation
 When a compound separates into two or more parts. Especially used when an
ionic compound breaks down into its component ions in solution.
 Dissolve
 To distribute particles of one substance throughout another. Especially
used with solutions in water. See also "solution" and related terms.
 Double bond
 A pair of shared electrons. Atoms at either end cannot rotate around
bond. Also called pi bond.
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E
 Eigenfunction, Eigenvalue
 Function such that when an operation is performed on it, the result is the
same function times a constant. That constant is known as the eigenvalue.
 Electron
 Subatomic particle (with wavelike qualities!), negatively charged. Found
in all atoms; balances charge of nucleus.
 Electron Affinity
 The energy released when an electron is added to an atom.
 Electron cloud
 Physical space where the electron's wavefunction indicates it has a high
probability of appearing (where it spends almost all of its time).
 Electron density
 A measure of the "thickness" of the electron cloud in a given place, eg,
the probability of the electron's presence. Function defined over all space;
sum over all space gives number of electrons present.
 Electron structure
 Way of accounting for the shape of an electron cloud. Indicates which
orbitals are occupied.
 Electronegativity
 An atom's attraction for the electrons in a bond.
 Electropositive
 Elements with low electronegativities.
 Electrostatic potential (elpot)
 Attraction between positive and negative charges. Relating to a molecule,
it expresses what would happen to a small positive charge brought near the
molecule.
 Energy of activation
 see "activation energy"
 Excited state
 When electrons are not in the lowest possible orbitals.
 Extended Basis Set Function
 A basis set that describes the orbitals in great detail
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G
 GAMESS, also MacGAMESS
 Computational tool run on workstation or desktop computer, performs some
of calculations which Gaussian 94 does. Uses ab initio methods only.
 Gaussian
 Mathematical function shaped like the normal distribution, or bell
curve. Used in approximating the wavefunction.
 Gaussian 94
 Computational tool for ab initio and other calculations. Must be
used in conjunction with a visualization tool to produce images, usually run
on a highpower platform.
 Geometry (of a molecule)
 Description of bond lengths and angles.
 Geometry Optimization
 Calculation to find a stable (local energy minimum) configuration of a
molecule.
 Ground state
 When electrons are in lowest possible orbitals.
 GTO
 Gaussian Type Orbital, an approximation of the wavefunction using gaussian
curves. See also "orbital", "wavefunction", "gaussian"
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H
 Hamiltonian
 Mathematical operator used in the Schroedinger Equation
 Hartree
 Amount of electrostatic repulsion between two electrons held one Bohr
radius apart. Often used as atomic unit of energy.
 Hartree Fock approximation
 Used to simplify Schroedinger's Equation. Breaks complex orbitals down
into a series of oneelectron orbitals. Also called selfconsistent field
(SCF) method. Sometimes called UHF or RHF for unrestricted and restricted
Hartree Fock approximations. Unrestricted methods allow for lone electrons,
while restricted methods only deal with paired electrons.
 Heat of Formation
 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 formed
preferentially. A difference of one kcal/mol means that the more stable
geometry will be approximately 10 times more common.
 HOMO
 Highest Occupied Molecular Orbital: Orbital with the most energy which
contains an electron.
 Hybrid orbital
 An orbital produced by a combination of differently shaped orbitals. Eg,
s+p orbitals gives an sp hybrid orbital.
 Hybridization
 When orbitals combine to form bonds which are not exactly one shape or the
other.
 Hydrocarbon
 Molecule which contains only hydrogen and carbon. Type of organic molecule.
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I
 Imaginary frequency
 Vibration which is impossible, ie, would cause molecule to spontaneously
break down. Finding EXACTLY ONE indicates that molecule is a
transition structure.
 Intermediary product
 See "transition structure"
 Ion
 Atom or group of atoms which has a net charge, ie, there are not enough
electrons to properly balance out the charge of the nuclei.
 Ionization energy
 Amount of energy required to remove one electron from an atom.
 Isomer
 Having the same number of atoms of each element as another molecule.
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L
 LCAO
 Linear Combination of Atomic Orbitals: An approximation which sums atomic
orbitals (with certain coefficients) to produce molecular bonding and
antibonding orbitals.
 LUMO
 Lowest Unoccupied Molecular Orbital: Orbital with least energy without any
electrons in it.
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M
 Magnetic Quantum Number
 Describes the shape of of the orbital. Often described in terms of the
x,y,z orientation of the orbital, eg, 2p_{x} where the x is the
magnetic quantum number. Also called "azimuthal quantum number", written "m".
 Maximum, global(relating to energy, plural maxima)
 Molecular geometry with the largest possible energy.
 Maximum, local(relating to energy, plural maxima)
 Molecular geometry with an energy larger than most, however not the
largest energy possible
 Minimal Basis Set Function
 A basis set that describes only the most basic aspects of the orbitals
 Minimum, global (relating to energy, plural minima)
 Configuration with lowest possible energy.
 Minimum, local (relating to energy, plural minima)
 Configuration such that slight changes produce a more energetic structure,
but it is not the lowest possible energy.
 Molecule
 More than one atom bonded together. See also, Bond, Covalent, Bond, Ionic.
 Molecular mechanics
 Method of using empirical data to greatly simplify the calculations for
very large molecules.
 Molecular orbital
 Representation of electron cloud surrounding a molecule. May be hybridized.
 Multiple bond
 See "double bond", "triple bond"
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N
 Nanometer
 Measure of length, equal to 1x10^{9} meters
 Nucleus
 Collection of subatomic particles found in the center of an
atom. Positively charged.
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O
 Orbital
 Representation of electron cloud. See "atomic" and "molecular" orbital.
 Organic
 In chemistry, a compound containing carbon.
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P
 Phase
 One of the three normal states of matter, solid, liquid, or gas, depending
on the level of organization between particles.
 Pi bond
 See "double bond"
 Picometer
 Measure of length, equal to 1x10^{12}
 pKa, pKb
 Indication of the strength of an acid/base. Higher values correspond to
weaker acids or bases.
 Planck Constant
 Numerical value expressing the amount of uncertainty which must be present
in any concurrent measurement of a particle's position and momentum.
 PointGroup Symmetry
 See "symmetry".
 Potential Energy Surface
 a mathematical relationship between different molecular geometries and
their corresponding single point energies.
 Primary quantum number
 Number used in electron structure notation, eg 1s, 2s, etc. Corresponds to
the orbit in the Bohr atom where an electon would be found. Written "n".
 Probability
 A number between one and zero which denotes how likely an event is to
happen. Multiplied by 100, it becomes a percentage.
 Probability density
 A mathematical distribution of probability over space or time. Sum of all
probabilities must equal one (ie, the event has to happen somewhere or
sometime)
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Q
 Quantum (plural quanta)
 Separate units of something. For example, money comes in quanta of 1 cent.
 Quantum Numbers
 Set of numbers used to specify any orbital in a given atom. Consist of
Primary, Secondary, Azimuthal, and Spin numbers. See those related
terms.
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R
 Radius
 Distance from the center (usually of a circle) to the edge, in chemistry,
usually from the nucleus to an electron
 Resonance structure
 Different possible structures for the same molecule.
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S
 Saddle Point
 a molecular geometry such that slight changes cause both a maximum in one
direction and a minimum in the other. Saddle points represent a transition
structure connecting two equilibrium structures.
 Schroedinger's equation
 Also called wavefunction. Original equation used to write wavefunctions
for particles. Incorporates the Hamiltonian.
 Secondary Quantum Number
 Denotes the subshell which the orbital occupies. Written "l", but often
denoted by a letter, such as s,p,d,f.
 Semiempirical
 Method of computational chemistry using some empirical (realworld, 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.
 Spin Quantum Number
 Has values of +1/2 or 1/2, also called "up" and "down" or "alpha" and
"beta" spin. Serves to differentiate between two electrons in the same
orbital. Written "m_{s}"
 Split valence basis set
 Basis set which uses several wavefunctions to represent different
valences. Denoted by a star at the end of name. See also "basis set",
"valence"
 Spreadsheet
 Computational tool which can be set up to hold numerical constants, lists,
and labels, and perform computations on those. Useful for repetitive lists of
numbers, usually has graphing capabilities. Divided into cells.
 STO
 Slater Type Orbital: Orbital using Slater renormalization factor to
approximate wavefunction. See also "orbital", "wavefunction"
 Solute
 Substance dissolved in a solution. See also "solution", "solvent", etc.
 Solution
 One substance being evenly distributed throughout another. See also
"solute", "solvent", etc.
 Solvation energy
 Change in energy when a susbstance is dissolved. See also "solution",
"solvent", etc.
 Solvent
 Substance in which something is dissolved. See also "solution", "solute",
etc.
 Strong acid/base
 Acid or base which dissociates completely in water. Has a low pKa or pKb.
 Symmetry, PointGroup Symmetry
 Properties of a molecule describing how it can be transformed and still
appear exactly the same. Pointgroup symmetry is a method of naming the
combination of symmetry elements which a molecule has.
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T
 Transition state, transition structure
 Molecule or group of molecules formed during a reaction. Unstable,
containing weak bonds and having high energy. Requires energy of activation to
form. Vibrates at imaginary frequencies. See also "activation energy",
"imaginary frequency"
 Triple bond
 Three shared electrons
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U
 Unfilled valence
 Valence which has no electrons in it. See also "valence"
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V
 Valence
 One level of an orbital
 Valence electrons
 The outermost electrons in an atom
 Valence orbital
 The outermost orbital containing electrons in an atom
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W
 Wavefunction
 Complex mathematical representation of a particle, in compchem, probably
an electron.
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