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Pure Appl. Chem., Vol. 71, No. 10, pp. 1919-1981, 1999

Glossary of terms used in theoretical organic chemistry

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Quantitative structure-activity relationships (QSAR) - Mathematical models designed for the correlation of various types of biological activity, chemical reactivity, equilibria, physical and physicochemical properties with electronic, steric, hydrophobic and other factors of a molecular structure of a given series of compounds such as substituent constants, topological indices as well as with solvent and other physicochemical parameters. IUPAC PHOTOCHEMICAL GLOSSARY (1988). HANSCH (1993).

Quantum mechanical resonance energy (QMRE) - see Resonance energy, various types of.

Radiationless transition - A transition between two states of a system without photon emission or absorption.

Radical - A molecular entity possessing an atomic or molecular orbital occupied by one electron. A radical (free radical) has a net electronic spin experimentally observable in paramagnetic behaviour. Paramagnetic metal ions are not normally regarded as radicals. IUPAC PHYSICAL ORGANIC CHEMISTRY GLOSSARY (1994).

Reaction coordinate - A structural parameter or a certain function of several of these, the variation of which along the reaction path defines the energy profile of a given reaction. In mathematical terms, the arc length along the minimum energy reaction path.

Reaction field - The response field from the induced polarization charges of an outer medium which creates an extra potential at the immersed molecule. The reaction field interacts with the solute molecular system giving rise to a solvent effect (see also solvation energy).

Reaction graph - Topological representation of either all possible reactions that occur (or can occur) in a given chemical system or a subset of these reactions, for which each vertex stands for a component of the system (molecule or ion) and each edge connecting two given vertices stands for the reaction path. Most usable are the reaction graphs for intramolecular rearrangements, with vertices standing for isomers and edges standing for their isomerization paths. BALABAN (1994).

Reaction path - The gradient line (or classic trajectory) in the configurational space interconnecting the reactant and product energy minima on the potential energy surface. BASILEVSKY and SHAMOV (1981); EYRING and POLANYI (1931); MINYAEV (1994); TRUHLAR, STECKLER, and GORDON (1987).
See also Intrinsic reaction coordinate, Minimum energy reaction path.

Reaction path Hamiltonian (RPH) - A Hamiltonian that deals with the dynamics occurring in a small amplitude many-dimensional harmonic valley centered on the reaction path as determined by the intrinsic reaction coordinate. By calculating curvature properties of the reaction path and coupling between the small amplitude degrees of freedom, insight into the mechanism of energy disposal along the reaction path is conveniently gained. MILLER, HANDY, and ADAMS (1980).

Reaction profile - see Energy profile

Relative hardness - The difference between the values of the absolute hardnesses (h) of a given molecule and the corresponding reference structure (ha): hr = h - ha . The values of relative hardnesses correlate well with the resonance energies of cyclic compounds and may be used as an index of aromaticity.

Relativistic effects - Corrections to exact nonrelativistic energy from the fact that inner shell electrons in heavy atoms move with velocities comparable in order of magnitude to the velocity of light.The most important relativistic effect is spin-orbit coupling. See also spin-spin coupling. PYKKÖ (1986)

Renner effect - The dynamic instability of linear molecular species in the degenerate electronic states. The Renner effect is a particular case of the Jahn-Teller effect.

Reorganization energy - The energy (term l in the Marcus equation) required for all structural adjustments (in the reactants and in the surrounding solvent molecules) which are needed in order to arrange the reactants in the reactive configuration. IUPAC: PHYSICAL ORGANIC CHEMISTRY GLOSSARY (1994).

Resonance effect - see Mesomeric effect.

Resonance energy (RE), various types of - Part of the total energy due to electron delocalization. To find the value of the resonance energy (RE), the difference must be calculated between a quantity characterizing experimentally determined energy of a given molecule (such as heat of atomization or heat of formation) and the same characteristic obtained with the aid of an additive scheme, e.g. sum of the bond energies (thermochemical resonance energy). When the total energy or the heat of formation (atomization) is calculated with use of quantum mechanical methods, the RE value is referred to as the quantum mechanical resonance energy (QMRE). Various schemes for the determination of QMRE are distinguished by the choice of the reference structure which should have non-interacting p-bonds. In the framework of the valence bond theory, the reference structure is represented by a single (usually the most stable) resonance structure. Hückel resonance energy, HRE, is equivalent to the delocalization energy, DE. For a conjugated hydrocarbon

HRE = DE = -[Ep - nC=C(2a + 2b)]

where n is the number of p-bonds and Ep is the total p-electron energy.

Dewar resonance energy, DRE, is the quantity which allows one to account for the effects of cyclic electron delocalization and thus serves as a measure of the aromatic stabilization (see aromaticity) of a cyclic molecular entity. The model reference structure is not a system of isolated p-bonds (as is the case for HRE), but a hypothetical cyclic polyene with the number of the p- and s-bonds equal to that in a given molecule. The condition of the additivity of bond energies for cyclic polyenes is adopted.

DRE = DHa - Haadd

where DHa is the calculated heat of atomization of a given conjugated molecule and DHaadd is the heat of atomization for the reference structure.

Topological resonance energy, TRE - The TRE scheme rests on the formalism of graph theory. A characteristic polynomial is constructed for the reference structure with only the acyclic Sachs graphs for the given molecule taken into account. An advantage of the TRE scheme is in the fact that it can be easily extended to radicals and ions and applied to excited states.

For the purposes of comparison of the resonance energies of molecules of different sizes, the normalized quantity resonance energy per electron, REPE, has been introduced. DEWAR (1969); MINKIN, GLUKHOVTSEV, and SIMKIN (1994).

Resonance energy per electron (REPE) - see Resonance energy, various types of.

Resonance hybrid - A localized valence bond representation of a molecule. This describes pictorially an electronic wavefunction that makes some contribution to the state wavefunction of the system. Resonance hybrids are needed to describe the state of a system when that system is not adequately described by a single Lewis structure.

Resonance integral - In the LCAO MO approximation, the energy of the overlap electron density between the atomic orbitals cm and cn due to attraction by the core (see Core approximation). In semiempirical quantum mechanical methods resonance integrals are adjustable parametric functions or parameters designed to achieve better agreement with experimental data.

Restricted Hartree-Fock (RHF) method - see Hartree-Fock method.

Ribbon delocalization - Electron delocalization realized in both acyclic and cyclic p-conjugated, 1, and s-bonded, 2, ribbon-like systems.

For cyclic systems, a variety of linkage fashions between several ribbons (pericyclic, spirocyclic, longicyclic and laticyclic) is possible.

Rice, Ramsperger, Kassel and Marcus (RRKM) theory - A theory of unimolecular and recombination reactions based on the application of transition state theory to a microcanonical ensemble of excited reactant molecules.

Rydberg orbital - For an atom, an orbital whose principal quantum number is greater than that of any occupied orbital of the ground state. For a molecular entity, a molecular orbital which correlates with a Rydberg atomic orbital in an atomic fragment produced by dissociation.

Rydberg state - An electronic state that arises by the excitation of a valence electron to a diffuse atomic-like orbital. For instance, the lowest lying Rydberg state (n, 3S) of NH3 can be described as resulting from the excitation of a nonbonding orbital to a 3S Rydberg orbital. EVLETH and KASSAB (1988).

[A] [B] [C] [D] [E] [F] [G] [H] [I] [J-K] [L] [M]
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> Abstract
> General remarks
> Arrangement

> Fundamental physical constants used in the glossary
> References
> Appendix. Glossary of acronyms of terms used in theoretical organic chemistry

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