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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]


    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.
    Mathematical representation of the application: a mathematical model
    Unit of distance. Bohr Radius in these units is a0=.529A
    Anti-Bredt structure
    Geometry which does not obey Bredt's rule, ie, has a double bond at a bridgehead position. See related terms "Bredt's Rule"
    Scientific situation being represented
    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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    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 slow-moving 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 "Anti-Bredt structure"
    Carbon on a ring where other carbons are attached in a link across the ring.

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    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.
    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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    Unit of dipole moment.
    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).
    Equal positive and negative charges separated by a distance.
    Dipole moment
    Measure of how polarized a molecule is (how large the dipole is).
    When a compound separates into two or more parts. Especially used when an ionic compound breaks down into its component ions in solution.
    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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    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.
    Subatomic particle (with wave-like 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.
    An atom's attraction for the electrons in a bond.
    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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    GAMESS, also MacGAMESS
    Computational tool run on workstation or desktop computer, performs some of calculations which Gaussian 94 does. Uses ab initio methods only.
    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 high-power 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.
    Gaussian Type Orbital, an approximation of the wavefunction using gaussian curves. See also "orbital", "wavefunction", "gaussian"

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    Mathematical operator used in the Schroedinger Equation
    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 one-electron orbitals. Also called self-consistent 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.
    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.
    When orbitals combine to form bonds which are not exactly one shape or the other.
    Molecule which contains only hydrogen and carbon. Type of organic molecule.

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    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"
    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.
    Having the same number of atoms of each element as another molecule.

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    Linear Combination of Atomic Orbitals: An approximation which sums atomic orbitals (with certain coefficients) to produce molecular bonding and anti-bonding orbitals.
    Lowest Unoccupied Molecular Orbital: Orbital with least energy without any electrons in it.

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    Magnetic Quantum Number
    Describes the shape of of the orbital. Often described in terms of the x,y,z orientation of the orbital, eg, 2px 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.
    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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    Measure of length, equal to 1x10-9 meters
    Collection of subatomic particles found in the center of an atom. Positively charged.

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    Representation of electron cloud. See "atomic" and "molecular" orbital.
    In chemistry, a compound containing carbon.

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    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"
    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.
    Point-Group 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".
    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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    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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    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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    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 sub-shell which the orbital occupies. Written "l", but often denoted by a letter, such as s,p,d,f.
    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.
    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 "ms"
    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"
    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.
    Slater Type Orbital: Orbital using Slater renormalization factor to approximate wavefunction. See also "orbital", "wavefunction"
    Substance dissolved in a solution. See also "solution", "solvent", etc.
    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.
    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, Point-Group Symmetry
    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.

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    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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    Unfilled valence
    Valence which has no electrons in it. See also "valence"

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    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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    Complex mathematical representation of a particle, in compchem, probably an electron.

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