ChemViz

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 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"

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".

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"

Bridgehead

Carbon on a ring where other carbons are attached in a link across the ring.

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)

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.

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 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.

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

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 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.

GTO

Gaussian Type Orbital, an approximation of the wavefunction using gaussian curves. See also "orbital", "wavefunction", "gaussian"

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 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.

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.

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.

LCAO

Linear Combination of Atomic Orbitals: An approximation which sums atomic orbitals (with certain coefficients) to produce molecular bonding and anti-bonding orbitals.

LUMO

Lowest Unoccupied Molecular Orbital: Orbital with least energy without any electrons in it.

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"

Nanometer

Measure of length, equal to 1x10^-9 meters

Nucleus

Collection of subatomic particles found in the center of an atom. Positively charged.

Orbital

Representation of electron cloud. See "atomic" and "molecular" orbital.

Organic

In chemistry, a compound containing carbon.

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.

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".

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)

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.

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.

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.

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.

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, 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.

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

Unfilled valence

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

Valence

One level of an orbital

Valence electrons

The outermost electrons in an atom

Valence orbital

The outermost orbital containing electrons in an atom

Wavefunction

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

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in cooperation with the
National Center for Supercomputing Applications