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Sylvain Robert
Professeur émérite, Dépt de chimie, biochimie et physique

PPH-1003, Modélisation moléculaire - Glossaire

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Glossaire de modélisation moléculaire et de chimie informatique

Sources utilisées pour compiler ce glossaire:

Compilé et édité par Sylvain Robert, Université du Québec à Trois-Rivières, Qc, Canada

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A

Ab initio A quantum mechanical non-parameterised molecular orbital treatment (Latin : from "first principles") for the description of chemical behaviour taking into account nuclei and all electrons. In principle, it is the most accurate of the three computational methodologies: ab initio, semi-empirical all-valence electron methods and molecular mechanics. All results are based on solutions of Schrödinger's Equation and the wavefunction used. No empirical data is used. [biblio]
Acca In the context of molecular modelling or chemical informatics, Acca is a program which assists in conformation searching, by transferring information between related conformation searches.
Accuracy How close a computed value is to the experimental value.
ACID In the context of databases, ACID stands for Atomic, Consistent, Isolated and Durable. The ACID test for a database transaction requires: (i) Atomic - a transaction either succeeds completely, or fails completely, so the database is not left in a half-updated state. (ii) Consistent - a transaction always leaves the database in a correct state. (iii) Isolated - executing transactions do not affect other transactions (iv) Durable - the data should survive.
Activation Energy The amount of energy needed to allow a reaction to proceed. (aka energy hump or energy barrier). Needed to form transition structure.
Active analogue approach In the absence of information regarding the receptor a medicinal chemist may modify known active structures from which one or several pharmacophoric patterns can be deduced. Then a set of possible (low energy) conformations for each compound known to activate the receptor is calculated. For each allowed conformation, the pharmacophoric pattern is determined. The intersection of all generated pharmacophoric patterns may then yield the pharmacophore embedded in all compounds of the set of active analogues. [biblio]
Adiabatic searching Adiabatic (Greek : not passing through) conformational searching in which no strain energy enters or leaves the molecule because at each step during the rotation around a bond all molecular strain energy is relaxed by minimizing all bond stretches and bond angles.
Adiabatic process A chemical process in which the system does not make a transition from one electronic state to another.
AI (artificial intelligence) Computer algorithms that mimic some aspects of how people think.
AIM (atoms in molecules) The molecular structure hypothesis - that a molecule is a collection of atoms linked by a network of bonds - was forged in the crucible of nineteenth century experimental chemistry. It has continued to serve as the principal means of ordering and classifying the observations of chemistry. The difficulty with this hypothesis was that it was not related directly to quantum mechanics, the physics which governs the motions of the nuclei and electrons that make up the atoms and the bonds. Indeed there was, and with some there still is, a prevailing opinion that these fundamental concepts, while unquestionably useful, were beyond theoretical definition. We have in chemistry an understanding based on a classification scheme that is both powerful and at the same time, because of its empirical nature, limited. Richard Feynman and Julian Schwinger have given us a reformulation of physics that enables one to pose and answer the questions "what is an atom in a molecule and how does one predict its properties?" These questions were posed in my laboratory where it was demonstrated that this new formulation of physics, when applied to the observed topology of the distribution of electronic charge in real space, yields a unique partitioning of some total system into a set of bounded spatial regions. The form and properties of the groups so defined faithfully recover the characteristics ascribed to the atoms and functional groups of chemistry. By establishing this association, the molecular structure hypothesis is freed from its empirical constraints and the full predictive power of quantum mechanics can be incorporated into the resulting theory - a theory of atoms in molecules and crystals. The theory recovers the central operational concepts of the molecular structure hypothesis, that of a functional grouping of atoms with an additive and characteristic set of properties, together with a definition of the bonds that links the atoms and impart the structure. Not only does the theory thereby quantify and provide the physical understanding of the existing concepts of chemistry, it makes possible new applications of theory. These new applications will eventually enable one to perform on a computer, in a manner directly paralleling experiment, everything that can now be done in the laboratory, but more quickly and more efficiently, by linking together the functional groups of theory. These applications include the design and synthesis of new molecules and new materials with specific desirable properties. The theory of atoms in molecules enables one to take advantage of the single most important observation of chemistry, that of a functional group with a characteristic set of properties. This document outlines and illustrates the topological basis of the theory and its relation to the quantum mechanics of an open system.
Algorithm Mathematical representation of the application: a mathematical model.
All valence electron methods In contrast to ab initio methods, the semi-empirical molecular orbital methods only consider the valence electrons for the construction of the atomic orbitals. Well-known semi-empirical methods are EHT, CNDO, MNDO, PCILO, AM1 and PM3. These methods are orders of magnitude faster than ab initio calculations. [biblio]
AM1 Austin Model 1. A semi-empirical quantum chemical Hamiltonian originating from the M.J.S. Dewar group. The quality of the AM1 results in most cases is beyond the simpler ab initio results and is superior to the MNDO method especially in the description of hydrogen bonds. [biblio]
AMBER (Assisted Model Building with Energy Refinement) AMBER is a widely used computer programme to build models of molecules and to calculate their interactions using an empirical force field consisting of the usual bond stretch and bond angle deformation terms, a cosine function for the dihedrals and where the non-bonded interactions are represented by a (6-12) Lennard-Jones potential and a Coulomb term. AMBER has been parameterised for proteins and nucleic acids. [biblio]
AMPAC A semi-empirical all valence electron programme dedicated to the study of the chemical behaviour of molecules and ions. Although both AMPAC and MOPAC originate from a set of subroutines developed by M.J.S. Dewar and co-workers at the University of Texas at Austin, the two programmes diverged in 1985 and were called AMPAC and MOPAC. The most obvious difference between MOPAC and AMPAC is the absence of the PM3 Hamiltonian in the latter. AMPAC has a number of excellent techniques for investigating chemical reactions and in particular the location of transition states. [biblio].
AMU Atomic mass unit.
Angstrom Unit of distance. Bohr Radius in these units is a0=.529Å
ANO (atomic natural orbital) A way of deriving basis functions.
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"
Antisymmetric function A function that only changes sign when the identities of two electrons are switched.
AO See atomic orbital.
API (Application Program Interface) Many computer programs (including operating system) are designed so that other programs can access some of their functionality. The specification of how to do this is the API.
Application Scientific situation being represented
APW (augmented plane wave) A band structure computation method.
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"
Arrhenius equation The Arrhenius equation predicts the rate of a chemical reaction at a certain temperature, given the activation energy and chance of successful collision of molecules. It is named after Swedish scientist Svante Arrhenius.
ASP (Application Service Provider) Applications can be delivered over the internet as well as data. Is this the future? Many companies are looking into this evolving delivery model. More information is available from the ASP Industry Consortium. (October 2000).
ASP (Active Server Pages) A web page which contains a script to be which works out what information to send to the user. Typically it is used to process a request for some information from a database. For more information see the ASP toolbox or LearnASP (September 2001).
Atomic orbital (AO) An atomic orbital is a mathematical function which depends on the spatial coordinates of one electron. The expansion of AO's or the linear combination of AO's (LCAO) leads to a molecular orbital. The set of AO's constitute the basis set. It is also the representation of the electron cloud surrounding an atom. Named by primary quantum number and shape, i.e. 1s, 2s, 2p.
Atomic units A system of units convenient for formulating theoretical derivations with a minimum number of constants in the equations. [wikipedia.org]
Azimuthal Quantum Number See Magnetic Quantum Number.

B
B3LYP (Becke 3 term, Lee, Yang Parr) A hybrid DFT method.
B96 (Becke 1996) A gradient corrected DFT method.
Band structure The electronic structure of a crystalline solid.
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.
Beads Individual units in a mesoscale simulation.
BDNR (Block Diagonal Newton Raphson) A minimisation algorithm.
BFGS (Broyden-Fletcher-Goldfarb-Shanno) A minimisation algorithm.
Bioactive conformation The bioactive conformation or the biologically relevant conformation can be defined either as the conformation a molecule must adopt in order to be recognised by the receptor or as the conformation of the ligand at the receptor site after binding. The dual interpretation of bioactive conformation stems from the fact that the environment of the ligand at the stage of recognition of the receptor or when it is fulfilling its biological role is not well understood. [biblio]
BLAST (Basic Local Alignment Search Tool) A set of similarity search programs for DNA and protein sequences, originally published in the Journal of Molecular Biology (1990, 215(3):403-10 Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ). Several web resources are available including the NCBI - NIH and Washington University.
BLYP (Becke, Lee, Yang Parr) A gradient corrected DFT method.
Bohr Atomic unit of length.
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.
Boltzmann distribution Statistical distribution of how many systems will be in various energy states when the system is a a given temperature.
Boltzmann factor In any system of molecules at equilibrium, the number possessing an energy € is proportional to the Boltzmann factor exp (-€/kT) where k and T are the Boltzmann constant and the absolute temperature, respectively. The sum of all the Boltzmann factors for all the energy levels €i is the partition function of that system.
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 angle term The bond angle term in a standard empirical force field describes the molecular potential energy change as a bond angle deviates from an ideal equilibrium bond angle value. In classical force fields the bond angle term is represented by an harmonic function. [biblio]
Bond-angle term The bond angle term is a cross term used in second generation force fields accounting for the mutual influence of bond stretching and bond angle deformation of a bond angle and a bond centered on the same atom. The bond-angle term is the product of a bond stretch and a bond angle term. [biblio]
Bond-bond term The bond-bond term is a cross term used in second generation force fields to account for the fact that bonds are not isolated but do interact during the vibration around their equilibrium value. The bond-bond term is the product of the stretching terms of two adjacent bonds. [biblio]
Bond length Distance between the nuclei of two bonded atoms
Bond stretching The bond stretching term in a standard empirical force field describes the molecular potential energy change as a bond stretches or contracts relative to an equilibrium bond length. In classical force fields the bond stretching term is represented by a harmonic function. [biblio]
Bond-torsion term The bond-torsion term is a cross term used in second generation force fields to account for the fact that the torsional movement around a bond influences the bond length of that bond. The bond-torsion term is a product of a bond angle and a torsional term. [biblio]
Born-Oppenheimer approximation The Born-Oppenheimer approximation consists of separating the motion of nuclei from the electronic motion. The nuclei being so much heavier than electrons may then be treated as stationary as the electrons move around them. The Schrödinger equation can then be solved for the electrons alone at a definite internuclear separation. The Born-Oppenheimer approximation is quite good for the calculation of the quantum chemical behaviour of molecules in the ground-state. [biblio]
Boson A fundamental particle with an integer spin.
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".
BRENDA BRENDA is the comprehensive enzyme information database. It is maintained and developed at the Institute of Biochemistry at the University of Cologne. Data on enzyme functions are extracted directly from the primary literature. Formal and consistency checks are done by computer programs and each data set is checked manually.
Bridgehead Carbon on a ring where other carbons are attached in a link across the ring.
BSSE (Basis Set Superposition Error) An error introduced when using an incomplete basis set. The BSSE in ab initio quantum chemical calculations of intermolecular interactions arises from a minor imbalance between the description given for the complex and its individual constituents. When two molecules approach each other, the description of a given molecule is energetically better within the complex than for the free monomer because orbitals of the partner molecule also become partly available leading to over-estimated stabilisation energies of weakly-bonded complexes. [biblio].
Buckingham potential The Buckingham potential is an alternative to describe van der Waals interactions where the 12th power of the Lennard-Jones potential is replaced by an exponential function which is an alternative description of the repulsive forces arising from overlapping electron clouds. [biblio]

C
CADD (Computer Aided Drug Design) Computer Aided Drug Design in the broadest sense is the science and art of finding molecules of potential therapeutic value that satisfy a whole range of quantitative criteria such as for example, high potency, high specificity, minimal toxic effects, and good bioavailability. CADD relies on computers, information science, statistics, mathematics, chemistry, physics, biology and medicine. In a more narrow sense, CADD implies the use of computer graphics to visualise, manipulate chemical structures, to synthesise "in computro" new molecules, to determine their conformation, to assess the similarities and dissimilarities between series of molecules. CADD further involves the calculation of the interaction energetics between drug molecules and hypothetical or experimentally determined macromolecular structures. It should be noted that CADD only helps in designing ligands, whereas it takes much more disciplines to make a drug. CADD leads to insight in molecular recognition processes and above all stimulates the creativity of all those involved in drug research. [biblio]
CADPAC (Cambridge Analytical Derivatives Package) An ab initio molecular orbital theory package.
CAMM (Computer Assisted Molecular Modelling) See CADD.
CAOS (Computer-Aided Organic Synthesis) A program for predicting a synthesis route
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.
Cartesian coordinates System for locating points in spoace based on three coordinates, which are usually given the symbols x, y, z or i, j, k.
CAS Chemical Abstracts Service. An organisation connected with the American Chemical Society which abstracts the world's chemical literature.
CBS (complete basis set) An ab initio method.
CC (coupled cluster) See coupled cluster.
CCD (Cambridge Crystallographic Database) Also called CCDC for Cambridge Crystallographic Data Centre.
CFF93 A molecular mechanics force field.
CFF (consistent force field) A class of molecular mechanics force fields.
CFMM (continuous fast multipole method) A method for fast DFT calculations on large molecules.
CHAIN A relaxation method for obtaining reaction paths from semiempirical calculations.
Charge density (electron density, number density) Number of electrons per unit volume at a point in space.
CHARMM (Chemistry at Harvard Macromolecular Mechanics) CHARMM is a widely used computer programme which uses empirical energy functions to model macromolecular systems, and ligands with various chemical functionalities. The empirical energy function is made of the harmonic usual bond stretch and bond angle deformation terms, a cosine function for the torsion angles and a harmonic expression for the improper torsion to maintain chirality about a tetrahedral atom. The non-bonded terms are represented by the (6-12) Lennard-Jones potential, the Coulomb term and an angle dependent (10-12) hydrogen bond potential. [biblio]
CHEAT (carbohydrate hydroxyls represented by external atoms) A molecular mechanics force field.
CHelp An electrostatic charge calculation method.
CHelpG An electrostatic charge calculation method.
Chemical Informatics 'Computer-assisted storage, retrieval and analysis of chemical information, from data to chemical knowledge.' (Chem. Inf. Lett. 2003, 6, 14.) This definition is distinct from 'Chemoinformatics' (and the synonymous cheminformatics and chemiinformatics) which focus on drug design.
Chemoinformatics 'The mixing of those information resources [information technology and information management] to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the arena of drug lead identification and optimization.' (Frank K Brown 'Chemoinformatics: what is it and how does it impact drug discovery.' Ann. Rep. Med. Chem. 1998, 33, 375-384.) This article also says that chemometrics is a subset of chemoinformatics. See also Chemical Informatics, which includes chemoinformatics and also encompasses areas of chemistry outside drug design.
Chemometrics Statistical analysis of chemical data.
CI (Configuration interaction) See Configuration interaction.
CIF Crystallographic Information File. A standard format to exchange crystallographic information.
Closed-shell Orbitals contain only paired electrons.
CML (Chemical Markup Language) A SGML for chemistry, designed by Peter Murray-Rust. A browser is available, called JUMBO.
CNDO (Complete Neglect of Differential Overlap) One of the first semi-empirical all valence electron methods formulated by J.A. Pople et al. in the sixties. Because of the drastic simplifications dictated by the speed of the computers in those days, CNDO methods are superseded by more elaborate semi-empirical quantum chemical calculations such as AM1 and PM3. [biblio]
CODATA Committee on Data for Science and Technology.
Combination rule - In molecular mechanics force fields combination rules are used to obtain the well depths €ij and equilibrium distances Rij between dissimilar atoms from the values of the homonuclear pairs. In force fields such as GROMOS and OPLS geometric mean rules are used whereas the arithmetic mean rule is used in MM2, MM3, AMBER, and CHARMM force fields. Other combination rules such as cubic mean, harmonic mean and harmonic mean of the harmonic- and geometric mean often perform much better than the classical combination rules. [biblio]
CoMFA Comparative Molecular Field Analysis. The basic idea of CoMFA developed by R.D. Cramer et al. (Cramer, R. D.; Patterson, D. E.; Bunce, J. D. J. Am. Chem. Soc. 1988, 110, 5959-5967) is that a suitable sampling of the steric and electrostatic field around a ligand molecule may provide all the information necessary for explaining its biological property in a 3D-QSAR. The steric and electrostatic contributions to the total interaction energy between the ligand and a chosen probe are calculated at regularly space grid points of a three-dimensional lattice encompassing the ligand. These contributions are then related to the biological properties in a partial least squares analysis. [biblio]
Computational Chemistry A branch of chemistry that can be defined as computer-assisted simulation of molecular systems and that is used to investigate the chemical behaviour and properties of these systems by means of formalisms based on quantum mechanics, classical mechanics and other mathematical techniques. Because of the ever increasing speed of computers computational chemistry has become and will continue to be a viable alternative to chemical experimentation in cases where experiment is either unfeasible, too dangerous or too costly. According to a recent study the computational chemistry represented a $ 500 million market in 1991 reaching the $ 1 billion level in 1993 and probably $ 2 billion in 1996.
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.
CONCORD Is as computer programme (developed by Robert Pearlman for generating 3D structures from 2D, distributed by Tripos) using tables of standard bond lengths and bond angles in conjunction with expert system techniques and a simplified force field to generate a 3D conformation from a 2D structure representation. CONCORD is used to generate large 3D databases containing tens or hundreds of thousands of structures which can be searched for identifying the presence of pharmacophores and finding new lead compounds. CONCORD accepts SMILES strings as input file formats. [biblio]
Configuration interaction (CI) A variational method for solving the nonrelativistic Schrödinger equation within the Born-Oppenheimer approximation for a multi-electron system. In contrast to the Hartree-Fock method, it uses a variational wave function that is a linear combination of Slater determinants in order to account for electron correlation.
Conformational Analysis The study of the configuration of atoms and the relative molecular energies that result from rotation about any of the single bonds in a molecule. The possible individual arrangements of atoms in space are called conformers, conformational isomers or rotamers. The methods of choice for the characterisation of the conformation of molecules in the three aggregation states viz. solid (crystalline), dissolved and gaseous (isolated state) are X-ray diffraction, NMR and computational methods, respectively. [biblio]
Conformational partition function The conformational partition function Qcon is the summation of the Boltzmann factors exp[-€(ti)/kT] over the conformational energy levels €(ti) of a molecule having ti torsional angles. The conformational partition function can be used when one wants to compare the conformational flexibility of a series of similar molecules.
Conjugate gradients A mathematical procedure to minimise a function such as a potential energy function used in molecular mechanics. The conjugate gradients is the method of choice to energy minimise large molecular systems.
Connectivity index - The molecular connectivity index is a term used to describe molecular structure in terms of the adjacency of each atom in the molecule. A well-known molecular connectivity index is the c-index of Kier and Hall which basically reflects a weighted count (based on the connectivity of each atom) of bonds and connected sets of bonds in a molecule.
Connolly surface The Connolly surface is the molecular surface related to the solvent-accessible-surface-area, but traced by the inward-facing part of a solvent probe model, represented by a sphere with a given radius, free to touch but not to penetrate the van der Waals surface of the solute when the probe is rolled over the van der Waals surface of the solute. The surface combines the contact surface of a solute atom and the probe and the reentrant surface when the probe is in contact with more than one atom. [biblio]
Constitutional descriptors - Constitutional descriptors of molecular structure depend on the composition of the molecule such as molecular weight, number of atoms, bonds and rings.
Constraint A constraint in a target function such as the energy function in molecular mechanics is defined as a degree of freedom that is fixed or not allowed to vary during the molecular simulation.
Conventional integral evaluation Algorithm that stores integrals in a file.
Convergence Criteria for completion of a self-consistent field calculation.
Conversion of units Go directly to www.biocrawler.com for the Conversion of units.
Convex hull A molecular surface that is determined by running a planar probe over a molecule.
COOP (crystal orbital overlap population) A plot analogous to population analysis for band-structure calculations.
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).
CORBA (Common Object Request Broker Architecture) An OMG's open, vendor-independent architecture and infrastructure that computer applications use to work together over networks. Using the standard protocol IIOP, a CORBA-based program from any vendor, on almost any computer, operating system, programming language, and network, can interoperate with a CORBA-based program from the same or another vendor, on almost any other computer, operating system, programming language, and network.
CORINA (COoRdINAtes) The computer programme (from the Gasteiger Group at Erlangen) originally developed to assess the influence of the spatial arrangement of atoms in a molecule on its reactivity, generates 3-D models from 2D information using standard bond lengths and angles. A molecule is fragmented into ring systems subdivided into small rings, rigid and flexible macrocyclic systems and acyclic parts. A pseudo force field is used to optimise geometries. CORINA is documented to have one of the most succesful 2D to 3D conversion rates. CORINA is a rule and data based system, that automatically generates three-dimensional atomic coordinates from the constitution of a molecule as expressed by a connection table or linear code, and which is powerful and reliable to convert large databases of several hundreds of thousand or even millions of compounds. [biblio]
Correlation Name for the statement that there is a higher probability of finding electrons far apart that close to one another, which is reflected by some but not all ab initio calculations.
COSMIC A molecular mechanics force field, and also a molecular modelling program.
COSMO (conductor-like screening model) A method for including solvation effects in orbital-based calculations. [mopac manual]
Coulomb interaction The Coulomb or charge-charge interaction arises from the attraction or repulsion of two charges and is inversely proportional to the distance separating the two charges. Because of this 1/r proportion Coulomb interactions are long-range interactions and therefore are one of the major driving forces governing the recognition process between a ligand and its receptor. The interaction energy of two unit charges at a separation of 10 Å in a dielectric medium of € = 1 amounts to about -332 Kcal/mole.
Coupled cluster (CC) Coupled cluster method is a technique used for description of the many-body systems. The method was initially developed by Fritz Coester and Hermann Kümmel in 1950's for studying nuclear physics phenomena but it became more frequently used after Jiri Cí?ek and Josef Paldus reformulated the method for studying electronic correlation in atoms and molecules in 1960's. It is now one of the most prevalent methods in quantum chemistry that include electronic correlation.
CPHF (coupled perturbed Hartree-Fock) Ab initio method used for computing nonlinear optical properties.
CPK (Corey-Pauling-Koltun) Corey-Pauling-Koltun or space-filling representation of a molecule in which each atom is represented by a sphere the radius of which is proportional to the van der Waals radius of that atom. [biblio]
CPU (central processing unit) The part of a computer that does mathematical and logical operations.
Cross-terms Cross or off - diagonal terms in a force field account for the fact that bonds and angles in a molecule can be interdependent because the energy for a given stretch or bend depends on the actual value of neighbouring bond lengths and bond angles. Cross-terms may increase the accuracy of a force field and may enhance the transferability of the diagonal terms because these are no longer contaminated by these cross-term effects. [biblio].
CSD (Cambridge Structural Database) The Cambridge Structural Database produced by the Cambridge Crystallographic Data Centre contains bibliographic, chemical and numerical data of crystal structures. This machine - readable file is a comprehensive compendium of molecular geometries of organic and organometallic compounds. [biblio]
Cut-off distance In order to improve the computational efficiency in force field calculations non-bonded interaction energy contributions for pairs of atoms separated by distances larger than a predetermined value are neglected. As van der Waals and electrostatic interactions are significant up to 15 Å and for large systems account for more than 90% of the total computational time a given cut-off distance is always a compromise between computational efficiency and accuracy of the calculation.
CVFF (Consistent Valence Force Field) A molecular mechanics force field. See CFF93.
CVT (canonical variational theory) A variational transition state theory technique.

D
3-D Fragment Search Having converted the traditional 2-D databases of chemical structures to a 3-D database, 3-D searching is used to find all molecules in that database that contain a specific pharmacophore or other fragment. Conformationally flexible searching addresses the problem of finding molecules with a conformation different from that which is stored in the primary 3-D database. [biblio].
Debye Unit of dipole moment.
De Novo algorithms Algorithms that apply artificial intelligence or rational techniques to solving chemical problems.
De Novo design Is a ligand design strategy in which the availability of a three-dimensional structure of a therapeutic target (an enzyme or protein) is used to design and predict the affinity of novel ligands. In principle, all de novo design methodologies identify interaction sites within the target followed by various strategies to create molecular fragments that fit on the interaction sites and finally propose molecular links between the fragments to form real ligands that are ranked according to affinity using a scoring function.
Delta Greek symbol, looks like a triangle. Denotes "change in".
Delta bonding Delta bond is a new one in the inorganic compound, it is not appear at organic molecules, because it use d-orbitals to produce it. It have two nodal planes across the center of orbital. Sometimes we call it Up-To-Bottom interaction. It is done by the d-orbital & d-orbital only, it can not be formed by s-orbital & p-orbital. It has a smallest overlap in between two orbitals than sigma & pi bonding. So it is a very weak bond than sigma bond and pi bond, it often seen at metal-metal multiple bonding. Due to the metal-metal d orbital interaction need, the structure of delta bonding orbital compounds have to be eclipsed structure. The good example of delta bonding molecule is Re2Cl82-. [inorganic.chemistry.pu.edu.tw] [www.chembio.uoguelph.ca]
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
Designer Drugs Designer drugs refer to substances of abuse that are structural analogues of substances that are subject to the provisions of the US Controlled Substances Act. By "designing" compounds that produce the euphoria of the controlled substances such as narcotics, antidepressants, stimulants but which are chemically different, laws regulating the controlled substances and the penalties that would be levied for illegally trafficking the controlled substance can be avoided.
Determinant A mathematical procedure for converting a matrix into a function or number.
DFP (Davidson-Fletcher-Powell) A geometry optimization algorithm.
DFT (Density Functional theory) The DFT approach is a calculational procedure according to which all of the electronic properties of a chemical system, including the energy, can be derived from the electronic density. Local DF theory which is steadily gaining popularity in the chemical computational community takes into account electron correlation. It requires considerably less computer time and disk space than ab initio calculations making it feasible to deal with much larger atoms and molecular systems.[biblio]
DHF (Dirac-Hartree-Fock) Relaticistic ab initio method.
DHF (derivative Hartree-Fock) A means for calculating nonlinear optical properties.
Diabatic process (nonadiabatic) A process in which the lowest-energy path is followed, even if it is necessary to change from one electronic state to another.
Diagonal terms Diagonal terms in a force field refer to the terms representing the bond stretch and bond angle deformations, torsion angle and out-of-plane bending contributions. Diagonal force fields do not contain cross-terms (off-diagonal terms). [biblio].
Diffuse functions Basis functions that describe the wave function far from the nucleus.
Dihedral angle Angle between an atom and a plane (formed by three or more other atoms).
DIIS (direct inversion of the iterative subspace) Algorithm used to improve SCF convergence.
DIM (diatomics-in-molecules) A semiempirical method used for representing potential energy surfaces.
Dipole Equal positive and negative charges separated by a distance.
Dipole - dipole force The dipole - dipole force, also called the Keesom force, arises from the interaction of the permanent dipoles of two interacting molecules. The interaction energy is inversely proportional to the sixth power of the distance between the two dipoles. Dipole - dipole interactions are temperature dependent as thermal motion of the molecules competes with the tendency towards favourable dipole orientations. The energy of two interacting dipoles of m = 2 Debye at a distance of 5 Å in vacuum is of the order of -0.25 Kcal/mole.
Dipole - induced dipole force - The dipole - induced dipole force, also called the induction or Debye force, arises when a permanent dipole induces a redistribution of electron density in another polarisable molecule, leading to an induced dipole. This type of interaction is inversely proportional to the sixth power of the distance between the two dipoles and is temperature independent. The average dipole - induced dipole interaction energy of a molecule of m = 1 Debye with e.g. benzene is about -0.2 Kcal/mole at a separation of 3 Å.
Dipole moment Measure of how polarized a molecule is (how large the dipole is).
Dirac equation One-electron relativistic quantum mechanics formulation.
Direct integral evaluation Algorithm that recomputes integrals when needed.
Dispersion force The dispersion or London force arises from the instantaneous transient dipoles that all molecules possess as a result of the changes in the instantaneous positions of electrons. The dispersion force which in fact is an induced dipole - induced dipole interaction depends on the polarisability of the interacting molecules and is inversely proportional to the sixth power of separation. In the case of e.g. two CH4 molecules at a separation of 3Å, the dispersion interaction energy is of the order of -1.1 Kcal/mole.
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.
Distance geometry Distance geometry pioneered by G.M. Crippen is a method for converting a set of distance bounds into a set of coordinates that are consistent with these bounds. In applying distance geometry to conformationally flexible structures upper and lower bounds to the distance between each pair of points (atoms) are used. This approach is useful for molecular model-building, conformational analysis and has been extended to find a common pharmacophore from a set of biologically active molecules. [biblio]
DM (direct minimization) An algorithm for forcing SCF calculations to converge.
DNA Deoxyribonucleic acid.
Docking An operation in which one molecule is brought into the vicinity of another while calculating the interaction energies of the many mutual orientations and conformations of the two interacting species. A docking procedure is used as a guide to identify the preferred orientation of one molecule relative to the other. In docking, the interaction energy is generally calculated by computing the van der Waals and the Coulombic energy contributions between all atoms of the two molecules. [biblio].
DOM Document Object Model.
DOS Disk Operating System. MicroSoft's operating system for PCs which has grown into Windows.
DOS Denial of Service: Computers can be attacked to prevent them providing access to their resources. More information is available from CERT.
Double bond Two pairs of shared electrons. Atoms at either end cannot rotate around bond. Also called pi (p) bond.
DPD (dissipative particle dynamics) A mesoscale algorithm.
DREIDING A molecular mechanics force field.
DTD Document Type Definition. This is an explanation of all the label that may be used in a SGML.
Dublin Core The Dublin Core is a set of core elements which can usefully be used to structure metadata. The name comes from a workshop in Dublin, Ohio.
Dummy atom A dummy atom is a point in space that is treated as an atom for the purpose of a geometry definition. Well-known dummy atoms are the centroids of ring systems, the location of electron lone pairs of heteroatoms and the endpoint of a normal of a plane. [biblio]

E
Eadfrith Eadfrith is a free program which produces high-quality pictures of molecules.
ECEPP (Empirical Conformational Energy Program for Peptides) ECEPP pioneered by H.A. Scheraga et al. is a molecular mechanics programme in which the potential energy is the sum of the electrostatic energy, the non-bonded energy and the torsional energy. ECEPP is thus an approximation of the general force field. [biblio]
ECP (effective core potential) A potential function for representing the core electrons in an ab initio calculation.
EF (eigenvector following) A geometry optimization algorithm.
EFF (empirical force field) A molecular mechanics force field.
EHT (Extended Hückel Theory) One of the first semi-empirical all-valence-electron methods formulated by R. Hoffmann in the early sixties. [biblio]
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 (cherge density, number 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(ic) 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 descriptors The electrostatic descriptors are based on the electronic and electrostatic structure of a molecule such as partial atomic charges, the electronegativity of the atoms, polarisability and molecular electrostatic potential.
Electrostatic potential (f) Derived charges. While net atomic charges qi are not rigorously defined quantum mechanical properties they can be derived by fitting the classical electrostatic potential due to the charges qi to the rigorously defined quantum mechanical electrostatical potential. Also, a function that gives the energy of interaction with an infinitesimal charge at any position in space (if we assume polarizability is negligible).
Electrotopological index The electrotopological index of Hall and Kier combines both the electronic character and the topological characteristics of each atom in a molecule.
EMBL (European Molecular Biology Laboratory) Data Library The main role of the European Molecular Biology Laboratory Data Library is to maintain and distribute a database of nucleotides sequences. This work is collaborative effort with Genbank® and DNA Database of Japan (DDBJ) where each participating group collects a portion of the total reported sequence data. The latest release, (March 1996) contained just under 473 million bases from over 701246 entries. Approximately every 12 months the database doubles in size.
Empirical A procedure not based purely on mathematical theory.
Ensemble When treating systems of interacting particles in a molecular dynamics simulation it is useful to introduce the concept of ensemble which basically means "collection". Taking a closed system with a given volume V, composition N and temperature T and replicating it n times constitutes a canonical ensemble (NVT) in which all the identical closed systems are regarded as being in thermal contact with each other and having the same temperature. In the microcanonical ensemble (NVE) the condition of constant temperature is replaced by the requirement that all the systems should have the same energy. Other ensembles are e.g. the isobaric - isoenthalpic NPH ensemble and the isobaric - isothermal NPT ensemble. Depending on the molecular dynamics simulation experiment an appropriate choice of ensemble has to be made. For example, the NVT ensemble is the appropriate choice when conformational searching of molecules is carried out in in vacuum and no periodic boundary conditions are used.
ESP (electrostatic potential) Normally used to denote charges derived from the electrostatic potential.
Eudismic ratio Is the ratio of activity or affinity of the eutomer (enantiomeric form with higher activity or affinity) to that of the distomer (enantiomeric form with the lower activity or affinity). The eudismic ratio is a measure of stereoselectivity.
Excited state When electrons are not in the lowest possible orbitals.
Excluded volume Is the union of volumes of a set of active ligands that is available to the ligands interacting with the receptor. Subtraction of the volume in common with the volume of the active and inactive ligands from the volume of the inactive ligand leads to the receptor essential volume i.e. the volume required by the receptor.
ExPASy (Expert Protein Analysis System) ExPASy proteomics server of the Swiss Institute of Bioinformatics (SIB).
Extended Basis Set Function A basis set that describes the orbitals in great detail.

F
Fenske-Hall A semiempirical method.
FEP Free Energy Perturbation.
Fermi contact density The electron density at the nucleus of an atom (if we assume that the nucleus is an infinitesimal point with a given mass and charge).
Fermion A fundamental particle with a half-integer spin.
FMM (fast multipole method) A method for fast DFT calculations on large molecules.
Force field A force field is a set of equations and parameters which when evaluated for a molecular system yields an energy. Force fields used in molecular mechanics consider the molecular system as a collection of classical masses held together by classical forces. The contributions to the molecular energy include, bond stretching, angle bending and dihedral angle deformations, van der Waals and electrostatic interactions. [biblio]
FP (Fletcher-Powell) A geometry optimization algorithm.
Free energy perturbation FEP. A statistical mechanical method to derive the free energy difference between two states a and b from an ensemble average of a potential energy difference (DV = Vb - Va) that can be evaluated using molecular dynamics. In the FEP approach the free energy difference between two states of a system is computed by transforming one state into the other by changing a coupling parameter l in small increments such that the system is in equilibrium at all values of l As l increases from l = 0 (state a) to l = 1 the system is transformed into the b state. The free energy difference between the two states a and b is then calculated as the sum of free energy differences between the closely spaced l states. [biblio]
Freely jointed chain (or random flight) A polymer simulation technique.
Free-Wilson model The Free-Wilson model is a mathematical approach for QSAR and is based on the hypothesis that the biological activity within a series of molecules arises from the constant and additive contributions of the various substituents, without determining their physicochemical basis. [biblio]
Frontier orbital Frontier electron theory is based on the idea that a reaction should occur at the position of largest electron density in the frontier orbitals. In the case of an electrophilic reaction, the frontier orbital is the HOMO, and the LUMO in the case of a nucleophilic reaction.
Functional Original meaning - The initial meaning is a function that takes functions as its argument; that is, a function whose domain is a set of functions. This was how the word was used initially, in the calculus of variations, where the integral to be minimized should be a functional, applied to an as-yet unknown function satisfying only some boundary conditions, and differentiability conditions. This usage still applies in that context and in many parts of physics and computer science, where in lambda calculus and functional programming a higher-order function is one that accepts a function and returns some value (or function). [wikipedia.org]

G
G1, G2, G3 (Gaussian thoery) A method for extrapolating from ab initio results to an estimation of the exact energy.
G96 (Gill 96) A DFT method.
G-protein coupled receptors Membrane-bound receptors and effector proteins can communicate via a guanine nucleotide - dependent regulatory protein, the G-protein. The ubiquitous G-protein coupled receptor family has a common structural framework despite a remarkably wide range of structural characteristics of their activating ligands. The common architecture presumably consists of 7 transmembrane a helices of at least 20 residues and intra- and extra cellular loops of varying length. Because of their key role in a variety of physiological processes, many of these receptors are the subject of intense pharmacological and theoretical work including computer - aided molecular modelling.
GAMESS, also MacGAMESS Computational tool run on workstation or desktop computer, performs some of calculations which Gaussian 94 does. Uses ab initio methods only.
GAPT (generalised atomic polar tensor) A charge calculation method.
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.
GB/SA (generalized Bron/surface area) Method for computing solvation effects.
GenBank® Genbank® is the National Institute of Health database of all known nucleotide and protein sequences. Entries in the database include a description of the sequence, scientific name and taxonomy of the source organism. Collaboration with the EMBL Data Library and the DNA Database of Japan enables shared data collection and sequence information.
Genetic Algorithms Genetic Algorithms (GAs) are optimisation methods based on Darwinian evolution and are used for a wide range of global optimisation problems having to do with high-dimensional spaces. As a conformational search method GAs consist of successively transforming one generation of a series of conformers into the next using the operations of selection (conformers with lower energy are "fitter" than those with higher energy), crossover, and mutation. Since the selection process is biased towards conformations with lower energy, the GA method leads to a collection of low energy conformers.
Geometric descriptors The geometric or topographic descriptors reflect the three-dimensional properties of molecules such as molecular volume, solvent accessible surface area, Verloop steric parameters, principal moments of inertia, and torsion angles.
Geometry (of a molecule) Description of bond lengths and angles.
Geometry Optimization Calculation to find a stable (local energy minimum) configuration of a molecule.
GIAO (gauge-independant atomic orbitals) Technique for removing dependance on the coordinate system when computing NMR chemical shifts or optical activity.
Globus The Globus project provides a toolkit, software tools that make it easier to build computational grids and grid-based applications.
GPL ( General Public License) GNUHow can a program be licensed as free software? GPL is one answer.
GRID A program for finding binding sites on biologically important macromolecules, developed by Peter Goodford (J. Med. Chem. 1985, 28, 849-857).
GRID Computational Grids enable computation as well as data to be shared over a network of computers.
GROMACS A molecular dynamics package, primarily designed for biochemical molecules like proteins and lipids.
GROMOS (Groningen Molecular Simulation) The GROMOS suite of programmes uses a classical force field (bond and angle deformations, torsion, van der Waals and Coulomb interactions) and the united-atom approximation. GROMOS is widely known and used for the simulation of the chemical and physical behaviour of systems in solution.
Group additivity An empirical method for computng chemical properties.
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".
GVB (generalized valence bond) An ab initio method.

H
Half-electron approximation An algorithm for open-shell semiempirical calculations.
Hamiltonian The classical Hamiltonian function H = T+V is the sum of the kinetic energy function, T, and the potential energy function, V, representing the total energy, E, of a system. Mathematical operator used in the Schrödinger Equation. The quantum mechanical operator for energy.
Hansch analysis A QSAR method based on extra-thermodynamic principles which expresses the biological activity of a congeneric series of molecules in terms of additive physical quantities as for example lipophilicity (logP, p) electronic effects (pK, s) and steric effects (Es of Taft). [biblio]
Hard sphere Assumption that atoms are like hard billiard balls, which is implemented by having an infinite potential inside the sphere radius and zero potential outside the radius.
Harmonic oscillator A harmonic oscillator is either: a) a mechanical system in which there exists a returning force F directly proportional to the displacement x, i.e. F=-kx,where k > 0 is a constant, or b) any physical system that is analogous to this mechanical system, in which some other quantity behaves in the same way mathematically. Examples of harmonic oscillators include pendulums (in small angles), masses on springs, and RLC circuits.
Hartree Amount of electrostatic repulsion between two electrons held one Bohr radius apart. Used as atomic unit of energy.
Hartree Fock approximation Used to simplify Schrödinger'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.
Hessian matrix The Hessian matrix or the force constant matrix is the second derivative of the energy with respect to the atomic coordinates of a molecular system. Diagonalisation of the Hessian matrix pertaining to a minimum energy conformation leads to all positive eigenvalues. A transition state structure is characterised by one negative eigenvalue; all the others being positive. [biblio]
HFS (Hartree-Fock-Slater) A DFT method.
HOMO (Highest Occupied Molecular Orbital) A molecular orbital calculation yields a set of eigen values or energy levels in which all the available electrons are accommodated. The highest filled energy level is called the HOMO. The next higher energy level which is unoccupied because no more electrons are available is the LUMO or Lowest Unoccupied Molecular Orbital. On the basis of Koopman's theorem the HOMO and LUMO of a molecule can be approximated as its ionisation and electron affinity, respectively.
Homology modelling Homology modelling is the art of building a protein structure knowing only its amino acid sequence and the complete three-dimensional structure of at least one other reference protein. Protein homology building is based on the fact that there are structurally conserved regions in proteins of a particular family that have nearly identical structure. In homology modelling, sequence alignment methods are used in determining which regions of the reference protein(s) and the unknown protein are conserved.
HTML (Hyper Text Mark up Language) This is the language that WWW browsers understand.
Hückel One of the simplest semiempirical methods.
Hybrid orbital An orbital produced by a combination of differently shaped orbitals. Eg, s+p orbitals gives an sp hybrid orbital.
Hybrid QM/MM Is the combination of quantum mechanical (QM) and molecular mechanics (MM) methodologies in Monte Carlo and molecular dynamics calculations where the solute or chemically reacting part of the total system is treated quantum mechanically, whereas the rest of the system is treated in the MM approximation.
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.
Hydrogen bond A hydrogen bond involves the stabilizing interaction, either inter- or intramolecular, between two moieties XH and Y. It is commonly assumed that for a hydrogen bond to be formed that both X and Y should be electronegative elements. Evidence is accumulating that hydrogen bonds can also be formed between e.g. CH.O and OH. p-bonded systems. Hydrogen bonds have specific geometric directionality and properties and therefore give rise to geometrically well-organised structures in biological systems such as DNA and proteins. [biblio]
HyperChem HyperChem Release 7.5 is the newest member of the HyperChem Family. Computational methods include molecular mechanics, molecular dynamics, and semi-empirical and ab-initio molecular orbital methods. HyperChem Data and HyperNMR have been migrated into HyperChem Release 7.5, and new features have been added. The new features include Open GL Rendering, DFT, TNDO, Charmm Protein Simulations, Molecules in Magnetic Fields, and much more.

I

ICSTI International Council for Scientific and Technical Information.
ICVT (improved canonical variational theory) A variational transition state theory technique.
IGAIM (individual gauges for atoms in molecules) Technique for removing dependance on the coordinate system when computing NMR chemical shifts.
IGLO (individual gauge for localized orbitals) Technique for removing dependance on the coordinate system when computing NMR chemical shifts.
Imaginary frequency Vibration which is impossible and would cause molecule to spontaneously break down. Finding EXACTLY ONE indicates that molecule is a transition structure.
In-core integral evaluation Algorithm that stores integrals in memory.
INDO (intermediate neglect of differential overlap) A semiempirical method.
INDO/S (spectroscopic INDO, synonymous to ZINDO) A semiempirical method used for reproducing electronic spectra results.
Initial guess An approximate wave function used at the starting point for an SCF calculation.
Intermediary product See "transition structure".
Internal coordinates The internal coordinates of a molecule define its three-dimensional structure in terms of bond lengths, bond angles and torsion angles. [biblio]
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.
IPCM (isosurface polarized continuum method) An ab initio solvation method.
IRC (Intrinsic reaction coordinate, also known as MEP, minimum-energy path) The lowest-energy route from reactants to products in a chemical process.
Isomer Having the same number of atoms of each element as another molecule.
IUBMB International Union of Biochemistry and Molecular Biology.
IUPAC International Union of Pure and Applied Chemistry.

J
Java A computer language which was designed with World-Wide web-applications particularly in mind.
Javascript A A client-side HTML embedded scripting language for World-Wide Web browsers, which is not closely related to Java.
Journal Abbreviations Chemistry journals have standard abbreviations, which are listed at the University of British Columbia website.
JCAMP The Joint Committee on Atomic and Molecular Physical Data developed standard data formats. The work has now been taken over by IUPAC. JCAMP formats are used for NMR, Mass Spectrometry and other spectral data.

K

KEGG Kyoto Encyclopedia of Genes and Genomes.
Kinetic energy Energy that a particle has due to its motion.
Klein-Gordon Equation for describing relativistic behaviour of spin zero particles.
Kohn-Sham orbitals Functions for describing the electron density in DFT calculations.
Koopman's theorem A means for obtaining the ionization potential from a hartree-Fock calculation.

L

LCAO (Linear Combination of Atomic Orbitals) An approximation which sums atomic orbitals (with certain coefficients) to produce molecular bonding and anti-bonding orbitals.
LDA (Lithium diisopropylamide) A strong, non-nucleophilic base.
LDA (local density approximation) Approximation used in some th the more approximate DFT methods.
LDAP (Lightweight Directory Access Protocol) See, for example, the OpenLDAP project.
Lennard-Jones potential As two atoms approach one another there is the attraction due to London dispersion forces and eventually a van der Waals repulsion as the interatomic distance r gets smaller than the equilibrium distance. A well-known potential energy function to describe this behaviour is the Lennard-Jones (6-12) potential. The LJ (6-12) potential represents the attractive part as r-6-dependent whereas the repulsive part is represented by an r-12 term. Another often used non-bonded interaction potential is the Buckingham potential which uses a similar distance dependence for the attractive part as the LJ (6-12) potential but where the repulsive part is represented by an exponential function. [biblio]
Level shifting Algorithm used to improve SCF convergence.
Lhasa Lhasa is a program to help plan organic syntheses, originally developed by E J Corey at Harvard.
Ligand-receptor interaction The bimolecular reversible association of ligand L and receptor R to form LR entails an unfavourable entropic consequence since both L and R each have three degrees of translational freedom and three degrees of rotational freedom. Those 12 degrees of freedom are reduced to six degrees of freedom for LR. Upon formation of LR free rotation of interacting groups in L and R can be severely restricted or frozen out leading to another unfavourable free energy change. In the case of poor structural complementarity between L and R an enthalpic penalty has to be paid to bring L and R in their binding conformation. If the ligand receptor interaction is to take place these three effects must be counterbalanced by factors favourable for the association of L and R. These are the free energies of interactions between polar functional groups (including the favourable effects of new vibrational modes due to new noncovalent bonds formation upon complexation of L and R), the entropically favourable release of water due to the hydrophobic effect and from the fact that the molecular packing in the LR complex may be more efficient than the packing of solvated L and R. [biblio]
LMP2 (local second-order Møller-Plesset) An ab initio perturbation theory technique.
LORG (localized orbital-local origin) Technique for removing dependence on the coordinate system when computing NMR chemical shifts.
LSDA (local spin-density approximation) Approximation used in more approximate DFT methods for open-shell systems.
LSER (linear solvent energy relationship) Method for computing solvation energy.
LUMO (Lowest Unoccupied Molecular Orbital) Orbital with least energy without any electrons in it.

M

mVT (microcanonical variational theory) A variational transition state theory technique
MacroModel A molecular modelling program (Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. "MacroModel- an Integrated Software System for Modeling Organic and Bioorganic Molecules using Molecular Mechanics" J. Comp. Chem. 1990, 11, 440-467.).
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".
Magnus Magnus is a group of programs for doing chemical calculations and handling chemical information. Most of the programs will run within a web browser.
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
MC (Monte Carlo) Monte Carlo methods are algorithms for solving various kinds of computational problems by using random numbers (or more often pseudo-random numbers), as opposed to deterministic algorithms. Monte Carlo methods are extremely important in computational physics and related applied fields, and have diverse applications from esoteric quantum chromodynamics calculations to designing heat shields and aerodynamic forms. These methods have proven efficient in solving the integro-differential equations defining the radiance field, and thus these methods have been used in global illumination computations which produce photorealistic images of virtual 3D models, with applications in video games, architecture, design, computer generated films, special effects in cinema, business, economics and other fields.
MCSCF (multiconfigurational self-consistent field) A correlated ab initio method.
MD (Molecular Dynamics) See dynamics Molecular Dynamics.
MEP (minimum-energy path, also known as IRC, Intrinsic reaction coordinate) The lowest-energy route from reactants to products in a chemical process.
MIM (molecules-in-molecules) A semiempirical method used for representing potential energy surfaces.
MIME Multipurpose Internet Mail Extension. A MIME-type describes the sort of information that a mail message, or other computer file, contains, and so a computer knows whether to expect an image, a molecule, or a spectrum, for example.
MINDO, MINDO/3 (Modified Intermediate Neglect of Differential Overlap) The MINDO/3 technique representing the third version of MINDO is a semi-empirical all-valence electron self-consistent field molecular orbital approach. MINDO/3 calculations provide fairly accurate values of molecular properties on medium to large organic molecules. [biblio]
Minimal basis set A minimal basis set in quantum chemical calculations is the smallest possible set of orbitals consisting of only that number of functions (Gaussian) necessary to accommodate all the electrons of an atom. The minimal basis set for an atom like carbon is 1s, 2s, 2px, 2py, 2pz. Minimal basis sets cannot adequately describe non-spherical molecular electron distributions. [biblio].
Minimisation Minimisation of the energy of a molecule is a procedure to find configurations for which the molecular energy is a minimum, i.e. finding a point in configuration space where all the forces acting on the atoms are balanced. As there exist several points in large molecules where the atomic forces are balanced, finding the point of the absolute minimum energy is often not a trivial problem. Different minimisation algorithms (e.g. steepest descents, conjugate gradients, Newton-Raphson) and procedures such as simulated annealing are used to find the minimum energy conformation (MEC) of a molecule. [biblio]
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.
Minimum energy conformation MEC. The MEC is that point in configurational space where the energy of the molecule is an absolute minimum and where all the derivatives are zero and the second derivative matrix (Hessian matrix) is positive definite. [biblio].
MK (Mertz-Singh-Kollman) An electrostatic charge calculation method.
MMn (MM1, MM2, MM3, MM4, MMX, MM+) Names of a family of similar molecular mechanics force fields.
MM2* MM2 as implemented in MacroModel.
MMFF (Merck molecular force field) A molecular mechanics force field.
MNDO (Modified Neglect of Diatomic Overlap) A semi-empirical all-valence electron quantum chemical method pioneered by M.J.S. Dewar and coworkers. For the molecular properties investigated such as heats of formation, ionisation potentials, bond lengths and dipole moments MNDO values are quite close to the experimental ones and are superior to the MINDO/3 results, particularly for nitrogen-containing compounds. Taking into account that the computational effort for MNDO is only about 20 % greater than for a MINDO/3 calculation, MNDO is considered to be a significant improvement over MINDO/3. [biblio]
Model A simple way of describing something that is currently more complex than the model.
MOL The MOL file format is defined by MDL (Molecular Design Ltd). A MOL file can describe a chemical structure, but no properties and references. For further detail, see the manual 'MDL CTfile Formats' provided by MDL. MOLFile Structure/Data File is a file format from MDL
Molecular Dynamics (MD) A time-dependant calculation in which a molecular mechanics force field is combined with classical equations of motion. Taking the negative gradient of the potential energy as evaluated from the force field yields the force. Using this force and the mass for each atom, Newton's equation of motion (F = ma) can be numerically integrated to compute the positions of the atoms after a short time interval (typically of the order of one femtosecond, 10-15 sec). By taking successive time steps, a time dependent trajectory of all the atomic motions can be constructed. [biblio]
Molecular Electrostatic Potential The molecular electrostatic potential (MEP) associated with a molecule arises from the distribution of electrical charges of the nuclei and electrons of a molecule. The MEP is quantum mechanically defined in terms of the spatial coordinates of the charges on the nuclei and the electronic density function r(r) of the molecule. As the MEP is the net result of the opposing effects of the nuclei and the electrons, electrophiles will be guided to the regions of a molecule where the MEP is most negative. The MEP is a useful quantity in the study of molecular recognition processes. [biblio]
Molecular Mechanics (MM) An empirical method for predicting molecular shape and interactions. Molecular mechanics is an attempt to formulate a force field that can serve as a computational model for evaluating the potential energy for all degrees of freedom of a molecule. MM calculations are very popular because large structures containing many thousands of atoms can be fully energy minimised at reasonable computational costs. MM methods, however, depend heavily on the parameterisation of the force field. MM is not appropriate for simulating situations where electronic effects such as orbital interactions and bond breaking, are predominant.
Molecular Modelling Molecular modelling of a molecule consists of a computer graphics visualisation and representation of the geometry of a molecule. In addition it involves the manipulation and modification of molecular structures. In combination with X-ray crystallographic or NMR data, molecular modelling implies the use of theoretical methods like ab initio, semi-empirical or molecular mechanics to evaluate and predict the minimum energy conformation and other physical and chemical properties of the molecule. Molecular modelling has become an essential tool for structural molecular biology with applications in drug design, protein engineering and molecular recognition. [biblio]
Molecular orbital Representation of electron cloud surrounding a molecule. May be hybridized.
Molecular recognition The interaction between two molecules, e.g. ligand and receptor is mainly dependent on the drug being able to sterically fit into the active site of the receptor and on the electrostatic complementarity between drug and receptor. The ligand and receptor are at the molecular recognition state when they are separated by more than two van der Waals radii. The contributing interactions for recognition are electrostatic, hydrogen bonding, van der Waals, and hydrophobic in nature.
Molecular similarity The degree of similarity between molecules, although quantitatively measurable, very much depends on what molecular features are used to establish the degree of similarity. One of the many comparators is the electron density of a pair of molecules. Other comparators include electrostatic potentials, reactivity indices, lipophilicity potentials, molecular geometry such as distances and angles between key atoms, solvent accessible surface area, etc. It is an open question as to how much or what part(s) of the molecular structure is to be compared.
Molecule More than one atom bonded together. See also, Bond, Covalent, Bond, Ionic.
Møller-Plesset (MPn, i.e. Møller-Plesset nth order) Corrected ab initio method based on perturbation theory. Møller-Plesset second order perturbation (MP2) theory is a widely used method for electron correlation. The MP2 method yields a large part of the electron correlation energy and considerably improves Hartree-Fock calculations, dispersion interactions, hydrogen bonds and transition state calculations. [biblio]
MOMEC A molecular mechanics force field with a semiempirical term for describing transition metals.
Monte Carlo A simulation technique that incorporates a random movement of atoms or molecules. Straightforward scanning of the complete configuration space of a molecular system containing many degrees of freedom is impossible. In that case, an ensemble of configurations can be generated by the Monte Carlo (MC) method which makes use of random sampling and Boltzmann factors. Given a starting configuration, a new configuration is generated by randomly displacing one or more atoms. The newly generated configuration is either accepted or rejected using an energy criterion involving the change of the potential energy (DV) relative to the previous configuration. The current configuration is accepted only if its potential energy is lower or equal than the previous one (DV ² 0) or for DV > 0 if the Boltzmann factor exp (- DV/RT) is larger than a random number taken from a uniform distribution over the (0,1) interval. MC methods are in general less efficient in sampling configuration space than MD methods. [biblio]
MOPAC A general Molecular Orbital Package based on the semi-empirical all-valence electron approximation for the study of the chemical behaviour of molecules and ions. In its present state of development the user can choose the level of approximation in terms of the MNDO, MINDO/3, AM1 and PM3 Hamiltonians. [biblio]
Morse potential A Morse potential is often used for the bond stretching term in a force field. Instead of the quadratic dependence of a harmonic bond stretching term, a Morse potential describes the bond stretching mode as an exponential function. When a molecule is in a high energy state due to sterically overlapping atoms or at a high temperature in a molecular dynamics simulation, the Morse function may allow the bonded atoms to stretch to unrealistic bond lengths. [biblio]
MP2, MP3, MP4 See Møller-Plesset.
MRCI (multireference configuration interaction) A correlated ab initio method.
mSQL A lightweight database engine developed by David Hughes.
Multiplicity A measure of the number of unpaired electrons in a molecule. Singlet multiplicity means that all the electron spins are paired, a doublet must have one unpaired spin.
MySQL An open-source database management system, available under GPL (Gnu General Public License), developed by Monty Widenius.

N

Nanometer Measure of length, equal to 1x10-9 meters
NCE New Chemical Entity.
NBO (natural bond order) The name of a set of population analysis techniques.
NCI National Cancer Institute: a part of the NIH (qv).
NDO (neglect of differential overlap) The fundamental assumption behind many semiempirical methods.
Neural networks Computer algorithms that simulate how the brain works by having many simple units, analogous to neurons in the brain.
Newton - Raphson A mathematical technique used for the optimisation of a function. In contrast to steepest descents and conjugate gradients methods, where the first derivative or gradient of the function is used, Newton-Raphson (NR) methods also use second derivative information to predict where along the gradient the function will change directions. As the second partial derivative matrix of the energy function (Hessian matrix) is calculated the NR method is much more time consuming than the steepests descents and conjugate gradients methods. NR minimisation becomes unstable when a structure is far from the minimum where the forces are large and the second derivative (the curvature) is small. Because storage requirements scale as 3N2 (N the number of atoms), NR methods are not suitable for large structures such as proteins.
NIH National Institutes of Health, USA.
NIST National Institute of Standards and Technology, USA.
NMR (nuclear magnetic resonance) An analytical chemistry technique.
NOE (Nuclear Overhauser Effect) The origin of the Nuclear Overhauser Effect is dipolar - cross relaxation between protons. Because of the r-6 distance dependence effect, NOEs can only be measured between protons at distances shorter than 5 Å. Using an appropriate distance restraint term in a force field energy function, based on the experimentally derived NOE data is useful in finding theoretical conformations which are consistent with the NMR spectrum.
NPA (natural population analysis) One of the NBO population analysis techniques.
NSF National Science Foundation.
Nucleus Collection of subatomic particles found in the center of an atom. Positively charged.

O

OASIS Organization for the Advancement of Structured Information Standards (OASIS), is a non-profit, international consortium that creates interoperable industry specifications based on public standards such as XML and SGML (See OMG).
OMG (Object Management Group) The Object Management Group (OMG) is an open membership, not-for-profit organisation that produces and maintains computer industry specifications. Its specifications include CORBA and UML.
OPLS (Optimised Potentials for Liquid Simulations) The OPLS force field addresses the classical bond stretches, angle bends and torsions. The non-bonded interactions are represented by Coulomb and Lennard-Jones terms which are parameterised to reproduce experimental thermodynamic and structural data on organic fluids. In the OPLS model no special functions are needed to describe hydrogen bonding nor additional interaction sites for lone pairs. The standard combination rules Aij = (AiiAjj)½ and Cij = (Cii Cjj)½ are used for the parameterisation of the non-bonded dispersion and repulsion interactions, respectively. [biblio]
OPW (orthogonalized plane wave) A band-structure computation method.
Oracle The world's leading supplier of software for information management, and the world's second largest independent software company. The Oracle database, which uses SQL, is being made increasingly internet aware.
Orbital Representation of electron cloud. See "atomic" and "molecular" orbital.
Organic In chemistry, a compound containing carbon.
ORTEP (Oak Ridge Thermal Ellipsoid programme) The Oak Ridge Thermal Ellipsoid programme is still very popular among crystallographers for drawing ball and stick type crystal structure illustrations. The programme can produce stereoscopic pairs which aid in the visualisation of complex packing arrangements of atoms.
Out-of-plane bend The displacement of a trigonal atom above and below the molecular plane is a mode of motion distinguishable from the bond stretching, angle bending and torsional motions. This out-of-plane coordinate is often called improper torsion because it treats the four atoms in the plane as if they were bonded in the usual way as in a proper torsional angle. [biblio]

P

P89 (Perdew 1986) A gradient corrected DFT method.
P2P (Peer-to-peer) A concept for networking computers, used by Gnutella and other applications.
P3P (Platform for Privacy Preferences Project) Platform for Privacy Preferences Project (P3P), not to be confused with P2P, is a simple, automated way for users to gain more control over the use of personal information, developed by the World Wide Web Consortium.
Parachor The parachor is an additive physical property of a substance related to its molar volume. The value of the parachor is determined by the kind and the number of atoms in a molecule as well as their manner of arrangement and binding.
Parallel computer A computer with more than one CPU.
Parameterisation of force fields The reliability of a molecular mechanics calculation depends on the potential energy equations and the numerical values of the parameters. One obstacle is the small amount of experimental data available for parametrizing and testing a force field. The energy, first and second derivatives of the energy with respect to the cartesian coordinate of a molecule obtained from high quality ab initio calculations are used to optimise force field parameters by adjusting the parameters to fit the energy and the energy derivatives by least squares methods. [biblio].
Partial Least Squares PLS is a statistical technique often applied to relate physicochemical properties to one or several measurements of biological activity. The PLS results consist of two sets of computed factors which are, on the one hand, linear combinations of the chemical descriptors and, on the other hand, linear combinations of the biological activities. PLS finds many applications in chemometrics and e.g. in the CoMFA approach.
Partition function The partition function Q is the summation of the Boltzmann factors exp [-€i/kT] over the energy levels €i of a molecule. A large value of Q will result when the energy levels €i are closely spaced. The partition function is a measure of the number of available translational, rotational, vibrational and electronic energy levels. Its value depends on the molecular weight, the temperature, the molecular volume, the internuclear distances, the molecular motions, and the intermolecular forces. Although often the calculation of the energy-level pattern is impossible, reasoning in terms of partition functions may provide a more concrete understanding of the free energy of drug-receptor interactions.
Pattern recognition Pattern recognition (PR) is a branch of artificial intelligence that provides an approach to solve the problem of recognizing an obscure property in a collection of objects from measurements made on the objects. PR techniques can be divided into display, preprocessing, supervised and unsupervised learning. PR methods are used among others in the search for correlations between molecular structure and biological activity. [biblio]
PBC (Periodic Boundary Conditions) PBC refers to the simulation of molecular systems in a periodic 3-D lattice of identical replicates of the molecular system under consideration. Using PBC allows to simulate the influence of bulk solvent in such a way as to minimise edge effects such as diffusion of a solute toward a surface or the evaporation of solvent molecules.
PCA (Principal Component Analysis) A set of variables which may be correlated are transformed to a smaller set of uncorrelated variables.
PCILO (Perturbative Configuration Interaction using Localised Orbitals) The Perturbative Configuration Interaction using Localised Orbitals method is a semi-empirical all-valence electron quantum chemical method where in addition to the ground state, singly and doubly excited configurations are taken into account. The wave function and the ground-state energy are determined by the Rayleigh-Schrödinger perturbation treatment up to the third order. Because of this summation treatment, PCILO is much faster than the Self Consistent Field methods such as MNDO, AM1 and PM3. [biblio]
PCM (polarized continuum method) Method for including solvation effects in ab initio calculations.
PCR Polymerase Chain Reaction.
PCR (Principal Component Regression) A combination of principal component analysis (PCA) with a regression analysis.
PDB (Protein Data Bank) The Protein Data Bank compiled at Brookhaven National Laboratory and distributed from there contains mainly X-ray diffraction and recently also NMR based structural data of macromolecular structures such as proteins, nucleic acids and entire viruses. The PDB file is the primary source for the 3-D coordinates of macromolecular structures and currently available on-line. [biblio]
PDF Portable Document Format.
Penalty function Is a mathematical function added to a target function such as the energy function in molecular mechanics that governs the energy expenditure or the penalty to be paid to force a spatial degree of freedom towards a specific value of a constraint.
Peptidomimetics Peptidomimetics can be described as compounds derived from peptides and proteins and are obtained by structural modification using unnatural amino acids, conformational restraints, isosteric replacement, cyclisation etc. The peptidomimetics bridge the gap between simple peptides and the nonpeptide synthetic structures and as such may be useful in delineating pharmacophores and in helping to translate peptides into small nonpeptide compounds. Peptidomimetic is sometimes used in a broad sense to designate organic molecules mimicking some properties of peptide ligands.
Perl Perl is a interpreted language optimized for scanning text files, extracting information and printing reports.
Perturbation theory An approximation method based on corrections to a solution for a portion of a mathematical problem.
PES (potential energy surface) Space of energies corresponding to locations of nuclei ignoring vibrational motion.
Pharmacophore A pharmacophore is the spatial mutual orientation of atoms or groups of atoms assumed to be recognised by and interact with a receptor or the active site of a receptor. In conjunction with the receptor concept, the notion of a pharmacophore relates directly to the lock-and-key theory proposed by Fischer and Ehrlich around the beginning of this century (Corpora non agunt nisi fixata). [biblio].
Phase One of the three normal states of matter, solid, liquid, or gas, depending on the level of organization between particles.
PHP PHP: Hypertext Preprocessor. A server-side HTML embedded scripting language, closely connected to database access. PHP offers compatibility witha number of SQL database servers. Its syntax is borrowed from C, Java and Perl.
Pi bond See "double bond"
Picometer Measure of length, equal to 1x10-12
PIR (Protein Information Resource) The Protein Information Resource databases are maintained and distributed by an association of macromolecular sequence data collection centers. The Protein Sequence Database is a research tool for the study of protein evolution in which published protein sequences are organised by similarity and evolutionary relationship.
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.
PLS (Partial Least Squares) A fitting algorithm closely related to principal component regression (PCR). Algorithm used for 3D QSAR calculations.
PM3 (Parametrized Model 3) PM3 is a reparameterised version of the AM1 method. A Semi-Empirical Molecular Orbital Theory Hamiltonian, developed by Stewart. On the whole, it seems that PM3 gives better estimates of the heat of formation than AM1. [biblio]
PMF (Potential of Mean Force) A solvation method for molecular dynamics calculations. The thermodynamic quantity needed to estimate equilibrium constants is the DG between reactants and products. By sampling a reaction coordinate r a potential of mean force (pmf) can be obtained. From the frequency of occurrence of different r values a distribution function g(r) is calculated that is related to w(r) the relative free energy or the pmf, by w(r) = -kTlng(r). By using an additional constraining or biasing potential (umbrella) a system can be forced to sample a reaction coordinate region which would be infrequently sampled in the absence of the umbrella potential because of high barriers in w(r).
Point-Group Symmetry See "symmetry".
Poisson-Boltzmann model The PB approximation is one of the more elaborate continuum solvation models that takes into account not only the charge density of the solute but also the mobile charge density within the surrounding continuum. Continuum models of solvation are in general capable of calculating absolute free energies of solvation.
Population analysis A method of partioning the wave function in order to give an understanding of where the electrons are in the molecule.
PostgreSQL PostgreSQL is an open-source object-relational database management system.
Potential energy Energy that a particle has due to its position, particularly because of Coulombic interactions with other particles.
Potential Energy Surface a mathematical relationship between different molecular geometries and their corresponding single point energies.
PPP (Pariser-Parr-Pople) A simple semiempirical method.
PRCG Polak-Ribiere Conjugate Gradient algorithm for minimisation.
PRDDO (partial retention of diatomic differential overlap) A semiempirical method.
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".
PRISM (polymer reference interaction-site model) Method for modelling homopolymer melts.
Probability A number between one and zero which denotes how likely an event is to happen. Multiplied by 100, it becomes a percentage.
Probability amplitude In quantum mechanics, a probability amplitude is a complex number-valued function which describes an uncertain or unknown quantity. For example, each particle has a probability amplitude describing its position.
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).
Protein folding One of the most challenging problems in structural biology is the prediction of the three-dimensional tertiary structure of a protein from its primary structure. Despite many years of experimental and theoretical studies devoted to it, the protein folding problem remains essentially unsolved. There are too many conformations that can occur in both the unfolded and the folded structure to be searched. Present day computational approaches (because of the size of proteins this must necessarily be molecular mechanics) cannot evaluate with sufficient accuracy the relative conformational energies of the folded and unfolded states which differ from one another most probably only by a few Kcal/mol. The problem of protein folding is further compounded by solvent and environmental effects in general that may play an important role in stabilizing particular folded states such as e.g. the a- or the 310-helix. [biblio].
PW91 (Perdew, Wang, 1991) A gradient corrected DFT method.

Q

QCI (quadratic configuration interaction) A correlated ab initio method.
QCPE (Quantum Chemistry Program Exchange) This initiative was undertaken by an organisation committed to the promotion of the concept and practice of computational chemistry initiated by Prof. H. Shull in 1962 at the Department of Chemistry at Indiana University. QCPE till 1970 financially supported by the US Air Force Office of Scientific Research receives software packages and distributes them to other theoretical chemists all over the world at a nominal fee. This organisation has contributed greatly to the dissemination of a number of excellent theoretical chemistry programmes to the scientific chemical community.
QMC (quantum Monte Carlo) An explicitly correlated ab initio method.
QM (Quantum Mechanics) One of the remarkable characteristics of the mathematical formulation of quantum mechanics, which distinguishes it from mathematical formulations of theories developed prior to the early 1900s, is its use of abstract mathematical structures, such as Hilbert spaces and operators on these spaces. Many of these structures had not even been considered before the twentieth century. In a general sense they are drawn from functional analysis, a subject within pure mathematics that developed in parallel with, and was influenced by the needs of quantum mechanics. In brief, physical quantities such as energy and momentum were no longer considered as functions on some phase space, but as operators on such functions.

Quantum mechanics is a fundamental physical theory which extends and corrects Newtonian mechanics, especially at the atomic and subatomic levels. It is the underlying framework of many fields of physics and chemistry, including condensed matter physics, quantum chemistry, and particle physics. The term quantum (Latin, "how much") refers to the discrete units that the theory assigns to certain physical quantities, such as the energy of an atom at rest. Quantum mechanics is a theory of mechanics, a branch of physics that deals with the motion of bodies and associated physical quantities such as energy and momentum. It is believed to be a more fundamental theory than Newtonian mechanics, because it provides accurate and precise descriptions for many phenomena where Newtonian mechanics drastically fails. This includes the behavior of systems at atomic length scales and below — in fact, Newtonian mechanics is unable to account for the existence of stable atoms — as well as special macroscopic systems such as superconductors and superfluids. The predictions of quantum mechanics have never been disproven after a century's worth of experiments. Quantum mechanics incorporates at least three classes of phenomena that classical physics cannot account for: (i) the quantization (discretization) of certain physical quantities, (ii) wave-particle duality, and (iii) quantum entanglement. In certain physical situations, the laws of quantum mechanics approximate the laws of classical mechanics to a high degree of precision; this is often expressed by saying that quantum mechanics reduces to classical mechanics and is known as the correspondence principle. Quantum mechanics can be formulated in either a relativistic or non-relativistic manner. Relativistic quantum mechanics (quantum field theory) provides the framework for some of the most accurate physical theories known, though non-relativistic quantum mechanics is also frequently used for reasons of convenience. We will use the term "quantum mechanics" to refer to both relativistic and non-relativistic quantum mechanics; the terms quantum physics and quantum theory are synonymous. It should be noted, however, that certain authors refer to "quantum mechanics" in the more restricted sense of non-relativistic quantum mechanics. Most physicists believe that quantum mechanics provides a correct description for the physical world under almost all circumstances. It seems likely that quantum mechanics fails in the vicinity of black holes, or when considering the observable Universe as a whole. In these regimes, quantum mechanics conflicts with the predictions of general relativity, the dominant theory of gravity. The question of compatibility between quantum mechanics and general relativity remains an area of active research. The foundations of quantum mechanics were established during the first half of the 20th century by Max Planck, Albert Einstein, Niels Bohr, Werner Heisenberg, Erwin Schrödinger, Max Born, John von Neumann, Paul Dirac, Wolfgang Pauli and others. Some fundamental aspects of the theory are still actively studied. [see also www.biocrawler.com]
QM/MM A technique in which orbital-based calculations and molecular mechanics calculations are combined into one calculation.
QSAR (Quantitative Structure Activity Relationship) QSAR (quantitative structure-activity relationship, sometimes the A stands also for affinity = reactivity) is the quantitative correlation of the biological (ecological, toxicological or pharmacological) activity to the structure of chemical compounds, which allows the prediction of the so-called "drug efficacy" of a structurally related compound. It is thus closely related to the more general field of QSPR and employs many of the latter's methodology. The QSAR approach pioneered by Hansch and co-workers relates biological data of congeneric structures to physical properties such as lipophilicity, electronic and steric effects using linear regression techniques to estimate the relative importance of each of those effects contributing to the biological effect. A statistically sound QSAR regression equation can be used for lead optimisation.
QSPR (Quantitative Structure-Property Relationship) The quantitative structure-property relationship (QSPR) is used in the field of chemistry, and relates bio-physico-chemical properties of chemical compounds to their structures. In biological contexts, these are also called quantitative structure-activity relationships (QSAR).
Quadrupole A general distribution of electric charge may be characterized by its net charge, by its dipole moment, its quadrupole moment and higher order moments. An elementary quadrupole can be represented as two dipoles oriented antiparallel. [hyperphysics.phy-astr.gsu.edu]
Quantum (plural quanta) Separate units of something. For example, money comes in quanta of 1 cent.
Quantum-chemical descriptors The quantum-chemical descriptors are derived from the eigenvalues and eigenvectors. Descriptors based on the eigenvalues are the HOMO and LUMO; atomic charges, dipole moment, bond orders, and frontier orbital indices are derived from the coefficients of the eigenvectors of the atomic orbitals. The superdelocalisability index is based on both the values of the eigenvalues and eigenvectors.
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.
Quantum harmonic oscillator The quantum harmonic oscillator is the quantum mechanical analogue of the classical harmonic oscillator. It is one of the most important model systems in quantum mechanics because, as in classical mechanics, a wide variety of physical situations can be reduced to it either exactly or approximately. In particular, a system near an equilibrium configuration can often be described in terms of one or more harmonic oscillators. Furthermore, it is one of the few quantum mechanical systems for which a simple exact solution is known.
Quantum tunneling Quantum tunneling is the quantum-mechanical effect of transitioning through a classically-forbidden energy state. The classical analogy is for a car on a roller coaster to make it up and over a hill which it does not have enough kinetic energy to surmount.

R

Radius Distance from the center (usually of a circle) to the edge, in chemistry, usually from the nucleus to an electron
RAM (random access memory) Volatile computer memory.
Ramachandran plot A Ramachandran plot (also known as a Ramachandran Map or a Ramachandran diagram), developed by Gopalasamudram Narayana Ramachandran, is a way to visualize dihedral angles f against y of amino acid residues in protein structure. It shows the possible conformations of f and y angles for a polypeptide.
Random flight (or freely jointed chain) A polymer simulation technique.
Rational drug design The majority of drugs on the market today to treat disorders in humans, animals and plants were discovered either by chance observation or by systematic screening of large series of synthetic and natural substances. This traditional method of drug discovery is now supplemented by methods exploiting the increasing knowledge of the molecular targets assumed to participate in some disorder, computer technology, and the physical principles underlying drug - target interactions. Rational drug design - traditional methods were or are not irrational - or better "structure based ligand design" continues to increase in importance in the endeavour of promoting a biologically active ligand towards the status of a drug useful in human and veterinary medicine and the phytopharmaceutical world.
RDBMS Relational Database Management System.
RDF (Radial Distribution Function) Rdf is a term often utilised in analyzing the results of Monte Carlo or MD calculations. The rdf, g(r) gives the probability of occurrence of an atom of type a at a distance r from an atom of type b. Peaks in the g(r) vs r plots can be associated with solvation shells or specific neighbours and can be integrated to yield coordination numbers.
RDF (reaction-data file) RDFile (reaction-data file) is a file format from MDL.
RDF (Resource Description Framework) A foundation for processing metadata providing interoperability between applications that exchange machine-understandable information on the Web.
Receptor A receptor can be envisioned as a macromolecular structure such as a protein, an enzyme or a polynucleotide being an integral part of the complex molecular structure of the cellular membrane in which it is anchored or associated with. The recognition elements or receptor sites are oriented in such a way that recognition of and interaction with ligands can take place, leading to a pharmacological effect.
Receptor mapping Receptor mapping is the topographical feature representation of a receptor based on the SAR and conformational aspects of active and inactive analogs of rigid and flexible molecules all putatively acting on that receptor. Inferences as to a pharmacophore on the basis of molecular interactions such as ionic and hydrogen bonding, dipolar effects, p-p stacking interactions and hydrophobic interactions can be used to construct a hypothetical model of the receptor in which the accessible parts of the amino acids of the receptor protein are delineated.
RECP (relativistic effective core potential) A potential function for representing the core electrons in an ab initio calculation.
Relativity Albert Einstein's theory of relativity is a set of two scientific theories in physics: special relativity and general relativity. These theories were conceived in order to explain the fact that electromagnetic waves do not conform to the Newtonian laws for motion. Electromagnetic waves were shown to move at a constant speed, independent of the motion of an observer. The core idea of both theories is that two observers who move relative to each other will measure different time and space intervals for the same events, but the content of physical law will be observed the same by both.
Resonance structure Different possible structures for the same molecule.
Restraint A restraint biases or forces a target function such as the energy function in molecular mechanics toward a specific value for a degree of freedom. Various restraints are in common use : torsional restraints, distance restraints, and tethering.
Restricted (spin-restricted) Assumption that particles of different spins can be described by the exact same spatial function, rigourously correct for singlet systems.
RFP (request for proposals) The OMG (Object management Group) periodically issues requests for proposals for standards in data exchange and interoperable applications.
RHF (restricted Hartree Fock) Useful approximation in ab initio molecular orbital theory, forcing all electrons to be paired (singlet systems).
RIS (restricted isomeric state) A polymer simulation technique.
ROHF (restricted open-shell Hartree Fock) Useful approximation in ab initio molecular orbital theory, allowing electrons to be unpaired.
RPA (random-phase approximation) Ab initio method used for computing nonlinear optical properties.

S

SAC (symmetry-adapted cluster) A variation on the coupled cluster ab initio method.
SACM (statistical adiabatic channel model) Method for computing reaction rates.
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.
SAM1 (semi-ab initio method one) A semiempirical method. The major difference between SAM1 and AM1 involves the repulsion integrals which are calculated using an STO-3G basis set and then scaled to account for electron correlation.
SASA (solvent accessible surface area) Algorithm for computing solvation effects.
SCF (Self Consistent Field) The self-consistent field method is a numerical approximation algorithm for solving the Schrödinger equation for isolated molecules in the ground state. The interaction of a single electron in a many-body problem with the remaining electrons is approximated by averaging it to resemble a two body interaction. In this way the total energy of a molecule can be obtained. Correlation energy is ignored in this method. Further developments of SCF are CASSCF and configuration interaction. Because this is a form of ab initio quantum chemistry, it can be one of the most CPU intensive computational chemistry algorithms. Calculations of this type are therefore usually reserved for small to medium-sized molecules on typical desktop computers as of 2004. More powerful research workstations are capable of SCF calculations on larger and more complex molecules, however the required time is highly dependent upon the chosen basis set, as with all ab initio methods. Software packages used include GAUSSIAN, Molcas, NWChem, MOLPRO, and GAMESS. Freely available are MPQC and Psi3.
Schrödinger's equation Also called wavefunction. Original equation used to write wavefunctions for particles. In physics, the Schrödinger equation, proposed by the Austrian physicist Erwin Schrödinger in 1925, describes the time-dependence of quantum mechanical systems. It is of central importance to the theory of quantum mechanics, playing a role analogous to Newton's second law in classical mechanics. In the mathematical formulation of quantum mechanics, each system is associated with a complex Hilbert space such that each instantaneous state of the system is described by a unit vector in that space. This state vector encodes the probabilities for the outcomes of all possible measurements applied to the system. As the state of a system generally changes over time, the state vector is a function of time. The Schrödinger equation provides a quantitative description of the rate of change of the state vector.
SCI-PCM (self-consistent isosurface polarized continuum method) An ab initio solvation method.
SCR (structurally conserved regions) Sections of a biopolymer sequence that are identical to that of another sequence, for which there is a known three-dimensional structure.
SCRF (self-consistent reaction field) Method for including solvation effects in ab initio calculations.
SDF The SDF file format is defined by MDL (Molecular Design Ltd). A SDF file can contain multiple compounds together with properties and references. For further detail, see the manual 'MDL CTfile Formats' provided by MDL. SDFile Structure/Data File is a file format from MDL.
SDS (synthesis design system) A program for predicting a synthesis route.
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.
SELF (Standard Electronic Data Files) Developed at a IUCOSPED meeting, a IUPAC task group chaired by Dr Henry Kehiaian.
Semiempirical Method of computational chemistry using some empirical (real-world, from the lab) data to simplify the calculations necessary Within the framework of Hartree-Fock calculations, some pieces of information (such as two-elecron integrals) are sometimes approximated or completely omitted. In order to correct for this loss, semiempirical methods are parametrized, that is their results are fit by a set of parameters in such a way, as to produce results the best agree with experimental data. Semiempirical calcualtions are much faster than their ab initio counterparts. Their results, however, can be very wrong if the molecule being computed is not similar enough to the molecules in the database used to parametrize the method. Semiempirical calculations have been very successful in the description of organic chemistry, where only a few elements are used extensively and molecules are of moderate size.
SGML (Standard Generalised Mark-up language) HTML is an SGML with a particular Document Type Definition (DTD).
SHAKE One approach to reduce the computer time of computationally expensive MD calculations is to increase the time step Dt used for the numerical integration of Newton's equations. For reasons of numerical stability Dt must be small compared to the period of the highest frequency of motions viz. bond stretching vibrations. SHAKE is an algorithm that can constrain bonds (like C-H) to a fixed length during an MD calculation thereby allowing somewhat larger Dt values.
Sigma bond See "single bond"
Simplex A simple, minimisation algorithm which does not require the calculation of derivatives.
Simulated Annealing Simulated annealing is a technique used in locating the global minimum energy structure of polypeptides and proteins. Simulated annealing uses a Monte Carlo search of conformational space starting at high temperature where large changes in conformational energies are allowed. As the temperature is lowered with an appropriate cooling schedule the system is (possibly) trapped into a conformation of lowest energy. [biblio]
SINDO (symmetrically orthogonalized intermediate neglect of differential overlap) A semiempirical method.
Single bond Two shared electron. Atoms at either end can rotate.
Single point energy Calculation of the energy of the molecule at a specific geometry.
Size-consistent A method is size-consistent if the energy obtained for two molecular fragments at large separation will be equal to the sum of the energies of those fragments computed separately.
Size-extensive A method is size-extensive if the energy is a linear function of the number of electrons.
Slow growth The slow growth method for free energy calculations is a free energy perturbation or a thermodynamic integration approach under the assumption that the spacings dl of the coupling parameter l are so small that one needs to sample only one point at any window. This reduces the ensemble average to a single value and allows the derivative to be approximated by a finite difference.
SM1, SM2, SM3, SM4, SM5 Solvation methods for use with semiempirical and ab initio calculations.
SMILES (Simplified Molecular Input Line Entry System) SMILES is a chemical notation system based on the principles of molecular graph theory and denotes a molecular structure as a two-dimensional graph familiar to chemists. It allows a rigourous and unambiguous structure specification representing molecular structures by a linear string of symbols. SMILES is used for chemical structure storage, structural display and substructure searching. [biblio]
SNP (Single Nucleotide Polymorphisms) DNA sequence variations.
Sn1 Substitution, Nucleophilic, Unimolecular.
Sn2 Substitution, Nucleophilic, Bimolecular.
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 effects Changes in the behaviour of a solute due to the presence of the solvent.
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.
Solvent accessible surface The solvent accessible surface is the loci of the center of a solvent probe model, represented by a sphere with a given radius, free to touch but not to penetrate the van der Waals surface of the solute when the probe is rolled over the van der Waals surface of the solute. This surface can be regarded as a surface based on expanded van der Waals radii.
SOMO (Semi-occupied molecular orbital ) Used instead of HOMO or LUMO when the highest occupied orbital contains only one electron.
SOS (sum over states) An algorithm that averages the contributions of various states of the molecule.
Spacer A spacer is a chemical moiety that presumably serves to hold pharmacophoric fragments at a proper distance and in a conformation compatible with optimal binding. Spacers, however, such as double bonds, cyclohexane and phenyl rings probably also provide additional binding at the active site.
Spartan An ab initio molecular orbital theory package. Spartan Essential Edition includes a full range of molecular mechanics and quantum chemical methods, up through and including Hartree-Fock Ab Initio methods, behind the cutting-edge Spartan GUI, putting powerful calculations at your fingertips. This version of Spartan is most commonly used in academic computer labs.

Spartan is the most sophisticated version offered. This program offers all features and methods included in the Essential Edition AND in collaboration with Q-Chem, provides a full range of post-Hartree-Fock methods including Density Functional, Moller Plesset, and an assortment of Advanced Correlated approaches. Spartan is the dominant version used in academic, government, and commercial research.
SPC (Simple Point Charge) In view of the importance of the water-protein interactions it is of utmost interest to have available intermolecular potential functions for the water dimer that yield a good model for liquid water. The SPC (Simple Point Charge) is a three-point charge (on the hydrogen and oxygen positions) model for water with a (6-12) Lennard-Jones potential on the oxygen atom and a charge of 0.41 and -0.82 on the hydrogens and oxygen atoms, respectively.
Spin contamination An error sometimes occuring in unrestricted calculations.
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"
Spin-restricted (restricted) Assumption that particles of different spins can be described by the exact same spatial function, rigourously correct for singlet systems.
Spin-unrestricted (unrestricted) Calculation in which particles of different spins are described by different spatial functions.
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.
SQL Structured query language: a language for interacting with relational databases including Oracle, MySQL, PostgreSQL, and mSQL. There are several dialects of SQL, and a standardisation process. SQL can be used for a variety of tasks including: querying data, updating and deleting rows in a table, altering objects, controlling access to a database and ensuring database consistency.
Statistical mechanics Mathematical theory for computing thermodynamic properties from atomic-scale properties.
Steepest Descents Steepest descents is a minimisation algorithm in which the line search direction is taken as the gradient of the function to be minimised. The Steepest Descents method is very robust in situations where configurations are far from the minimum but converges slowly near the minimum (where the gradient approaches zero).
STO (Slater Type Atomic Orbital) An early basis set for molecular orbital theory describing the wave function of an electron in an atom, which is rigourously correct for atoms with one electron. These are close in shape to atomic orbitals, but much harder to manipulate mathematically than gaussian functions, so the latter are now used almost exclusively.
STO-3G Is an abbreviation employed in ab initio MO calculations indicating the basis set used. The notation STO-n G stands for Slater Type Orbital simulated by n Gaussians functions. This means that each atomic orbital consists of n Gaussian functions. STO-3G is a minimal basis set and is now hardly used any longer. More elaborate basis sets include for example the 6-31 G* basis set whereby six Gaussians are used for the core orbitals, three for the s- and one for the p-valence orbitals and a single set of d-functions are indicated by the asterisk. [biblio]
Stochastic Dynamics The stochastic dynamics (SD) method is a further extension of the original MD method. A space-time trajectory of a molecular system is generated by integration of the stochastic Langevin equation which differs from the simple MD equation by the addition of a stochastic force R and a frictional force proportional to a friction coefficient g. The SD approach is useful for the description of slow processes such as diffusion, the simulation of electrolyte solutions and various solvent effects.
Strain energy Although the first strain theory is due to von Bayer in 1885 there is no generally accepted and unique definition of strain energy. The basic qualitative idea is that simple strainless molecules exist and that larger molecules are strainless if their heats of formation are equal to the summation of the bond energies and other increments from the small strainless molecules. The energy calculated by molecular mechanics is strain energy because the deformation energy occurring in a molecule is equal to the energy of minimised structure relative to the hypothetical reference structure.
Strong acid/base Acid or base which dissociates completely in water. Has a low pKa or pKb.
Superdelocalisability Superdelocalisabilty Sr is defined as the sum of the quotients of the squares of the coefficients Crj of the rth atomic orbital in the jth molecular orbital and the orbital energies. In the case of superdelocalisability for electrophilic attack srE the sum runs over all occupied orbitals, and over all unoccupied orbitals for srN for nucleophilic attack. The superdelocalisability for radical attack is defined as srE + srN.
SVG (Scalable Vector Graphics) A graphics format from Adobe.
SWISS-PROT SWISS-PROT is an annotated protein sequence database maintained by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library. The SWISS-PROT database distinguishes itself from other protein databases by (i) the generous annotation information (ii) a minimal redundancy for a given protein sequence (iii) the cross-reference with twelve other biomolecular databases. A curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.
Switching function In order to avoid discontinuities in derivatives and energies during minimisation calculations a switching function is used in conjunction with a cut-off algorithm ensuring non-bonded interactions to be smoothly reduced from full strength to zero over a predefined interatomic distance range.
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.
Systematic conformational search To a first approximation the conformation of a molecule is defined by the torsional angles about the single bonds of a molecule. The systematic search consists of generating all combinations of the torsion angles through 360_. As the number n of rotable bonds increases and the angular increment Da decreases the total number of conformations N = (360/Da)n fairly rapidly leads to a combinatorial explosion. [biblio]

T

TDGI (time-dependant gauge-invariant) Ab initio method used for computing nonlinear optical properties.
TDHF (time-dependent Hartree-Fock) Ab initio method used for computing nonlinear optical properties.
Temperature conversion formulas Go directly to www.biocrawler.com to the Temperature conversion formulas.
Template forcing Template forcing is a type of restraint useful in the identification of possible biologically relevant conformations of a conformationally flexible molecule. By selecting atoms or groups of atoms belonging to the possible pharmacophoric pattern common to two molecules, the atoms of the flexible molecule are forced to superimpose onto the atoms of the rigid or template molecule. The energy expenditure to force the flexible molecule onto the template molecule is a measure of the similarity between the two molecules.
Theoretical chemistry Theoretical chemistry is the use of non-experimental reasoning to explain or predict chemical phenomena. In recent years, it has consisted primarily of quantum chemistry, i. e., the application of quantum mechanics to problems in chemistry. Much of this has in fact fallen under the heading of computational chemistry, i. e., the application of computation to the solution of problems in chemistry. Chemical theorists have also used the power of statistical mechanics to provide a bridge between the microscopic phenomena of the quantum world and the macroscopic bulk properties of systems. An aspect of theoretical chemistry is covered by mathematical chemistry in which chemical graph theory plays an important role. Theoretical attacks on chemical problems go back to the earliest days, but until the formulation of the Schrödinger equation by the Austrian physicist Erwin Schrödinger, the techniques available were rather crude and speculative. Currently, much more sophisticated theoretical attacks based on quantum mechanics are in vogue.
Thermodynamic Cycle The thermodynamic cycle approach used to calculate relative free energies or binding constants of e.g. drug-receptor interactions is based on the fact that the free energy is a thermodynamic function of state. Thus, as long as a system is changed reversibly the change in free energy is independent of the path and therefore non-chemical processes (paths) can be calculated such as the conversion of one type of atom into another (computational alchemy!).
Thermodynamic Integration (TI) An approach to free energy calculations is thermodynamic integration consisting of numerically integrating the ensemble average of the derivative of the potential energy of a given configuration with respect to a coupling parameter l. Because the free energy is evaluated directly from the ensemble average and not as the logarithm of the average of an exponential function as in the free energy perturbation (FEP), TI is not subject to certain systematic errors inherent to FEP calculations. [biblio]
Thermodynamics Thermodynamics (Greek: thermos = heat and dynamic = change) is the physics of energy, heat, work, entropy and the spontaneity of processes. Thermodynamics is closely related to statistical mechanics from which many thermodynamic relationships can be derived. While dealing with processes in which systems exchange matter or energy, classical thermodynamics is not concerned with the rate at which such processes take place, termed kinetics. For this reason, the use of the term "thermodynamics" usually refers to equilibrium thermodynamics. In this connection, a central concept in thermodynamics is that of quasistatic processes, which are idealized, "infinitely slow" processes. Time-dependent thermodynamic processes are studied by non-equilibrium thermodynamics. Thermodynamic laws are of very general validity, and they do not depend on the details of the interactions or the systems being studied. This means they can be applied to systems about which one knows nothing other than the balance of energy and matter transfer with the environment. Examples of this include Einstein's prediction of spontaneous emission around the turn of the 20th century and the current research into the thermodynamics of black holes.
Time complexity A way of denoting how much additional computational resources, particularly CPU time, will be used as the size of the system being modeled is increased.
Time correlation function Time correlation functions are of great value for the analysis of dynamical processes in condensed phases. A time correlation function C(t) is obtained when a time-dependent quantity A(t) is multiplied by itself (auto-correlation) or by another time-dependent quantity B(t') evaluated at time t' (cross-correlation) and the product is averaged over some equilibrium ensemble. For example, the self-diffusion coefficient can be obtained from the velocity auto-correlated function for the molecular center of mass motion.
TIP (Tranferable Intermolecular Potential) The TIP family of potentials are used for simulating liquid water. The TIP4P potential for water involves a rigid water monomer composed of 3 charge centers and one Lennard-Jones center. Two charge centers (Q = 0.52) are placed on the hydrogen site 0.9572 Å away from the oxygen atom. The third charge center (Q = -1.04) is placed 0.15 Å away from the oxygen atom along the bisector of the HOH angle (104.52°). A Lennard-Jones center is placed on the oxygen atom. The model yields reasonable geometric and energetic results for a linear water dimer and is therefore used in simulations of aqueous solutions.
TIP3P, TIP4P Models for the properties of water molecules (Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. "Comparison of Simple Potential Functions for Simulating Liquid Water" J. Chem. Phys. 1983, 79, 926-935.).
TNDO (typed neglect of differential overlap) A semiempirical method for computing NMR chemical shifts.
Topliss tree The Topliss tree is an empirical decision scheme for a stepwise aromatic substituent selection and lead optimisation that is guided by the supposed influence on potency due to the hydrophobic, electronic and steric effects of the substituents.
Topological descriptors Topological descriptors of molecular structure depend on the molecular topology or connectivity and branching of the molecule. Well-known topological descriptors are the Wiener index, the Randic index and the Kier and Hall connectivity index.
Torsional potential The torsional potential is one of the potential energy terms contributing to the total molecular energy and is represented by an n-fold Fourier series expansion usually truncated up to n = 3. The 1-fold term is an attempt to incorporate dispersion interactions such as dipole-dipole and induced dipole-dipole interactions not accounted for in the explicit non-bonded van der Waals term. The 2-fold term accounts for conjugation effects involving rotation around sp2 bonded atoms. The 3-fold term represents steric effects not accounted for by the other terms in the force field. [biblio]
Trajectory A sequence of geometries produced by a molecular dynamics simulation.
Transition state, transition structure Molecule or group of molecules formed during a reaction. Unstable, containing weak bonds and having high energy: the geometry of a molecular system corresponding to the energy maximum (saddle point) that must be traversed in going from reactants to products. Requires energy of activation to form. Vibrates at imaginary frequencies. See also "activation energy", "imaginary frequency".
Tripos A molecular mechanics force field, also the name of a company that sells coputational chemistry software.
TST (transition state theory) Method for computing rate constants.

U

UFF (universal force field) A molecular mechanics force field.
UHF (Unrestricted Hartee-Fock) Unlike RHF, this permits a system to have any multiplicity. Can lead to spin contamination.
Unfilled valence Valence which has no electrons in it. See also "valence"
United Atom Model For the sake of speeding up an energy calculation the total number of atoms are artificially reduced by lumping together all non-polar hydrogens into the heavy atoms (C atoms) to which they are bonded. Although this approximation may speed up the calculation several-fold, an all hydrogen atom model is preferable for accurate calculations. [biblio]
Unrestricted (spin unrestricted) Calculation in which particles of different spins are described by different spatial functions.
UR (Urey-Bradley term) The Urey-Bradley term in a force field may account for the repulsion between two atoms bonded to a common atom. In essence the U.R term takes into account the 1-3 interaction term and is similar to the bond-bond and bond-angle term. [biblio]
URL (Uniform Resource Locator) The address of a WWW page.

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.
Van der Waals forces The term van der Waals forces denotes the short-range interactions between closed-shell molecules. Van der Waals forces include attractive forces arising from interactions between the partial electric charges and repulsive forces arising from the Pauli exclusion principle and the exclusion of electrons in overlapping orbitals. A very commonly used potential is the so-called Lennard-Jones (6-12) potential to describe the attractive and repulsive components of van der Waals forces. [biblio]
Van der Waals molecule A van der Waals molecule is a weakly bonded cluster of molecules. Because of the weak interactions between the constituting parts there are large zero-point oscillations about the equilibrium leading to large structural changes upon vibrational and rotational excitation. [biblio]
Verlet The Verlet algorithm is a numerical method for the integration of Newton's equations of motion used in MD calculations. Because of its simplicity, the Verlet method is easily adapted to give an algorithm with constraints on internal coordinates such as bond lengths as in the SHAKE algorithm.
VTST (variational transition state theory) Method for predicting rate constants.
VWN (Vosko, Wilks and Nusair) A DFT method.

W

Wavefunction In the most restricted usage in quantum mechanics, the wavefunction associated with a particle such as an electron, is a complex-valued square integrable function defined over a portion of space and normalized. In Max Born's probabilistic interpretation of the wavefunction, the amplitude squared of the wavefunction is the probability density of the particle's position. In the mathematical formulation of quantum mechanics, the state of any system is represented by an object called a ket, which is an element of an abstract mathematical structure called a Hilbert space. For isolated systems, the dynamics (or time evolution) of the system can be described by a one-parameter group of unitary operators. In a wide class of systems this Hilbert space of kets has one or more realizations as a space of complex-valued functions on some space; in this case we refer to these functions as wavefunctions. However, a priori, there is no preferred representation as a Hilbert space of functions. Moreover, in some of these representations the time evolution of the system has the form of a partial differential equation, namely Schrödinger's equation.
WWW World Wide Web.

X

Xa (X alpha) A DFT method.
XED (Extended Electron Distribution) Extended Electron Distribution (Vinter, J. G. Extended electron distributions applied to the molecular mechanics of some intermolecular interactions J Comp.Aided. Mol. Design 1994, 8, 653-668.).
XML (Extensible Markup Language) A unified format for structured documents and data on the web. A less general, and perhaps more useful, SGML.
X-ray structure Single - crystal X-ray diffraction analysis yields the three-dimensional structure of a molecule in the crystalline state. An X-ray structure is likely to be a structure in a minimum energy conformational state or close to an energy minimum. An X-ray structure, therefore may or may not be the biologically relevant conformation. Inspection of the molecular packing arrangement may yield valuable information about intermolecular contacts, and sites of intermolecular hydrogen bonds. Atomic coordinates based on X-ray diffraction data may serve as the primary input data for theoretical conformational analysis calculations. [biblio]

Y

YETI A molecular mechanics force field.

Z

Z-matrix The Z-matrix provides a description of each atom of a molecule in terms of its atomic number, bond length, bond angle and dihedral angle, the so-called internal coordinates. The information from the Z-matrix is used to calculate the Cartesian (X, Y, Z) coordinates of the atoms. [biblio]
Zero-point energy The zero-point energy is the residual energy of a harmonic oscillator at the lowest vibrational state. It arises from the fact that the position of a particle is uncertain and therefore its momentum and hence its kinetic energy cannot be exactly zero. [biblio]
ZINDO (Zerner's intermediate neglect of differential overlap, sinonymous to INDO/S, or spectroscopic INDO) A semiempirical method used for reproducing electronic spectra results.

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      • A.D. Buckingham in Principles of Molecular Recognition. A.D. Buckingham, A.C. Legon and S.M. Roberts, Eds, Blackie Academic & Professional, Chapman & Hall, London, 1993, pp 1-16. Intermolecular Forces.
    • Data bases and structure generation
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      • F.H. Allen and J.E. Davies, Crystallogr. Comput., 2, 271 (1988). File Structures and Search Strategies for the Cambridge Structural Database.
      • Y.C. Martin, E.A. Danaher, C.S. May, and D. Weininger, J. Comput.-Aided Mol. Design, 2, 15 (1988). MENTHOR, a Database System for the Storage and Retrieval of Three-Dimensional Molecular Structures and Associated Data Searchable by Substructural, Biologic, Physical, or Geometric Properties.
      • D. Weininger and A. Weininger, J. Chem. Inf. Comput. Sci., 28, 31 (1988). SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules.
      • A. Rusinko III, J.M. Skell, R. Balducci, C.M. McGarity, and R.S. Pearlman, The University of Texas at Austin and Tripos Associates, St. Louis, Missouri, 1988. CONCORD, A Program for the Rapid Generation of High Quality Approximate 3-Diimensional Molecular Structures.
      • D. Weininger, A. Weininger, and J.L. Weininger, J. Chem. Inf. Comput. Sci., 29, 97 (1989). SMILES. 2. Algorithm for Generation of Unique SMILES Notation.
      • A. Rusinko III, R.P. Sheridan, R. Nilakantan, K.S. Haraki, N. Bauman, and R. Venkataraghavan, J. Chem. Inf. Comput. Sci., 29, 251 (1989). Using CONCORD to Construct a Large Database of Three-Dimensional Coordinates from Connection Tables.
      • R.A. Lewis and P.M. Dean, Proc. R. Soc. London Ser. B, 236, 125 (1989). Automated Site-Directed Drug Design: The Concept of Spacer Skeletons for Primary Structure Generation.
      • R.A. Lewis and P.M. Dean, Proc. R. Soc. London Ser. B, 236, 141 (1989). Automated Site-Directed Drug Design: The Formation of Molecular Templates in Primary Structure Generation.
      • J. Sadowski, J. Gasteiger, and G. Klebe, J. Chem. Inf. Comput. Sci. 34, 1000 (1994). Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures.
    • Pharmacophore and 3-D searching
      • G.R. Marshall, C.D. Barry, H.E. Bosshard, R.A. Dammkoehler, and D.A. Dunn, in Computer-Assisted Drug Design. E. C. Olson and R.E. Christoffersen, Eds., American Chemical Society Symposium, Vol 112, American Chemical Society, Washington DC, 1979, pp. 205-226. The conformational Parameter in Drug Design: The Active Analog Approach.
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      • A.T. Brint and P. Willett, J. Chem. Inf. Comput. Sci., 27, 152 (1987). Algorithms for the Identification of Three-Dimensional Maximal Common Substructures.
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      • R.P. Sheridan, A. Rusinko III, R. Nilakantan, and R. Venkataraghavan, Proc. Natl. Acad. Sci. U.S.A., 86, 8165 (1989). Searching for Pharmacophores in Large Coordinate Databases and Its Use in Drug Design.
      • P.E. Bowen-Jenkins, D.L. Cooper, and W.G. Richards, J. Phys. Chem., 89, 2195 (1985). Ab Initio Computation of Molecular Similarity.
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      • P. Willett, J. Chemometr. 6 (1992) 289-305. A review of three-dimensional chemical structure retrieval systems.
    • Shape, volume, surface, and molecular descriptors
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    • SAR and QSAR
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    • Molecular modeling, CADD and CAMM
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    • Miscellaneous
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The following represents a brief collection of Software tools developed for Molecular modelling and visualisation.

Molecular Visualisation

    • Chem3D Plugin. An alternative browser plugin to Chime. A better option if you want to use it for e.g. measuring bond distances and angles from 3D coordinates. On a Macintosh browser, you can switch between Chime and Chem3D plugins using the Edit/Preferences/Applications menu. On Windows, switching between the two is not trivial (i.e. I don't know how to do it!). Chem3D can also be used as a stand-alone program.
    • ChemApp (all platforms supporting Java). This is an alternative to the Chime Browser plug-in. The latter is written in computer specific code, for which currently the only complete implementation is for Windows NT. Unix, Macintosh and other non-NT users have an alternative based on a language called Java, which ChemApp is implemented in. The Java is interepreted not by the operating system but the Web browser, and hence a measure of platform independence is achieved. ChemApp currently only supports CAChe files and molecular surfaces.
    • ChemSymphony (all platforms supporting Java). Another Java-based molecular visualisation environment.
    • Chime Version 2.0 (Windows NT, 98 and in part Macintosh). This is a Web browser plug-in, developed in 1996 from a stand-alone program called RasMol (written by Roger A. Sayle in the early 1990s at Imperial College). It supports a wide variety of molecule coordinate formats, incouding PDB (Protein databank), Molfile (from ISIS/Draw), MOP (MOPAC input files) and GAU (Gaussian Input files). It also supports the RasMol scripting language developed by Roger Sayle, which allows complex "molecular style sheets" and animations to be developed. Other features include the display of NMR, MS, IR, UV spectra in JCAMP-DX format, and the rendering of 3D volume information in the form of Gaussian Cube files (ie molecular orbitals, surfaces etc).
    • CosmoPlayer: a VRML Browser plug-in (Windows, Macintosh, SGI). VRML (Virtual Reality Modelling Language) is a recent 3D model description language, which allows complex molecular models including surfaces and schematic representations to be created.
    • IMol, a viewing program for MacOS X.
    • Kinemage. A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared in order to better communicate ideas that depend on 3-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations. They are viewed and explored in an open-ended way by the reader using a simple graphics program called MAGE. A utility called PREKIN makes a starting kinemage from a PDB-format coordinate file which can then be modified on-screen in MAGE or off-line in any text editor.
    • MacMolPlt (Macintosh). A molecular and wavefunction visualisation program that also serves as the "front" and "rear" end for the GAMESS program.
    • PovChem. A Ray-tracing program (Mac, Windows, Unix) that renders e.g. PDB files to superb quality. Use this for publications and reports!
    • SwissPdbViewer. Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
    • VEGA, a comprehensive Integrated system running on Windows and Linus. Part of the Drug Design Laboratory.
    • VMD: Visual Molecular Dynamics. VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Unix or Windows, is distributed free of charge, and includes source code.
    • WebLab Viewer, an excellent commercial program with a free "lite" version, which is capable of viewing in many different modes a variety of molecular file formats.

Molecular Mechanics

    • Biomer: online java applet, model builders for polynucleotides (DNA/RNA), polysaccharides and proteins, interactive molecule editor, AMBER force-field based geometry optimization, simulated annealing with molecular dynamics, and the ability to save gif, jpeg, and ppm images
    • CAChe (Macintosh, Windows)
    • Chem3D
    • Ghemical is an open-source Mechanics and visualisation program.
    • HyperChem. HyperChem Release 7.5 is the newest member of the HyperChem Family. Computational methods include molecular mechanics, molecular dynamics, and semi-empirical and ab-initio molecular orbital methods. HyperChem Data and HyperNMR have been migrated into HyperChem Release 7.5, and new features have been added. The new features include Open GL Rendering, DFT, TNDO, Charmm Protein Simulations, Molecules in Magnetic Fields, and much more.
    • MacroModel 6.0/6.5 (SGI Unix).
    • Spartan
    • Tinker: A free suite of programs implementing a number of mechanics force fields and different optimisers. Available for Windows/Mac/Unix versions

Semi-empirical Molecular Orbital

Ab initio Molecular Orbital

Integrated Environments

    • iLab:Compute molecular properties on the ACD site.
    • The Molecular Operating Environment. A very recent collection of modules for performing all modelling operations in chemistry and molecular biology

General Software Compilations