Continued from terms starting with F to M
Newman Projection; Nonbonded Interactions; Optical Activity; Optical Antipodes; Optical Isomerism; Optical Purity; Optical Resolution ; Optical Rotation; Optical Yield; Optically Labile; Out-isomer; P, M; Percent Diastereoisomer Excess; Percent Enantiomer Excess; Periplanar; Perspective Formula; Pitzer Strain; Planar Chirality; Plus, Minus ; Point Group; Polytopal Rearrangement; Primary Structure; Priority; Prochirality; Prochirality Centre; pro-E, pro-Z; Projection Formula; Proprochirality; pro-R, pro-S; Pseudo-asymmetric Carbon Atom; Pseudo-axial; Pseudo-equatorial; Pseudorotation; Pyramidal Inversion; Quasi-axial; Quasi-enantiomers; Quasi-equatorial; Quasi-racemic Compound; Quaternary Structure
A projection formula representing the spatial arrangement of bonds on two adjacent atoms in a molecular entity. The structure appears as viewed along the bond between these two atoms, and the bonds from them to other groups are drawn as projections in the plane of the paper. The bonds from the atom nearer to the observer are drawn so as to meet at the centre of a circle representing that atom. Those from the further atom are drawn as if projecting from behind the circle.
Intramolecular attractions or repulsions between atoms that are not directly linked to each other, affecting the thermodynamic stability of the chemical species concerned. See also eclipsing strain; transannular strain.
A sample of material able to rotate the plane of polarisation of a beam of transmitted plane-polarised light is said to possess optical activity (or to be optically active). This optical rotation is the classical distinguishing characteristic (sufficient but not necessary) of systems containing unequal amounts of corresponding enantiomers. An enantiomer causing rotation in a clockwise direction (when viewed in the direction facing the oncoming light beam) under specified conditions is called dextrorotatory and its chemical name or formula is designated by the prefix (+)-; one causing rotation in the opposite sense is laevorotatory and designated by the prefix (-)-. Materials with optical activity also exhibit other chiroptic phenomena.
Optical Antipodes (usage strongly discouraged)
Obsolete synonym for enantiomers.
Optical Isomerism (usage strongly discouraged)
Obsolescent synonym for stereoisomers with different optical properties. It should be described as diastereoisomerism or enantiomerism.
The ratio of the observed optical rotation of a sample consisting of a mixture of enantiomers to the optical rotation of one pure enantiomer. See enantiomeric excess.
Optical Resolution (usage strongly discouraged) See resolution. Optical Rotation See optical activity.
In a chemical reaction involving chiral reactants and products, the ratio of the optical purity of the product to that of the precursor, reactant or catalyst. This should not be confused with enantiomeric excess.
Optically Labile (usage strongly discouraged)
A term describing a system in which stereoisomerisation results in a change of optical rotation with time.
Out-isomer See in-out isomerism.
P, M See helicity.
Percent Diastereoisomer Excess See diastereoisomer excess.
Percent Enantiomer Excess See enantiomer excess.
Periplanar See torsion angle.
A geometric representation of stereochemical features of a molecule or model which appears as a view from an appropriate direction. See Fischer projection, Newman projection, projection formula, sawhorse projection, wedge projection, zig-zag projection. See also stereochemical formula.
Pitzer Strain See eclipsing strain.
Term used by some authorities to refer to stereoisomerism resulting from the arrangement of out-of-plane groups with respect to a plane (chirality plane). It is exemplified by the atropisomerism of (E)-cyclooctene (chiral plane = double bond and attached atoms) or monosubstituted paracyclophane (chiral plane = substituted ring). The configuration of molecular entities possessing planar chirality is specified by the stereodescriptors Rp and Sp ( or P and M).
See 1. d, l, dl for (+), (-) and ()
2. helicity for P and M.
The classification of the symmetry elements of an object. It is denoted in the Schoenflies notation by an italic symbol, such as C3, D2, Td, etc.
Stereoisomerisation interconverting different or equivalent spatial arrangements of ligands about a central atom or of a cage of atoms, where the ligand or cage defines the vertices of a polyhedron. For example pyramidal inversion of amines, Berry pseudorotation of PF5, rearrangements of polyhedral boranes. See E.L. Muetterties, J. Am. Chem. Soc. 91, 1636-1643 (1969).
In the context of macromolecules such as proteins, the constitutional formula, usually abbreviated to a statement of the sequence and if appropriate cross-linking of chains. See also secondary structure, tertiary structure, quaternary structure.
Priority See CIP priority.
This term is used in different, sometimes contradictory ways; four are listed below.
1. The geometric property of an achiral object (or spatial arrangement of points or atoms) which is capable of becoming chiral in a single desymmetrisation step. An achiral molecular entity, or a part of it considered on its own, is thus called prochiral if it can be made chiral by the replacement of an existing atom (or achiral group) by a different one.
An achiral object which is capable of becoming chiral in two desymmetrisation steps is sometimes described as proprochiral. For example the proprochiral CH3CO2H becomes prochiral as CH2DCO2H and chiral as CHDTCO2H.
2. The term prochirality also applies to an achiral molecule or entity which contains a trigonal system and which can be made chiral by the addition to the trigonal system of a new atom or achiral group. For example addition of hydrogen to one of the enantiotopic faces of the prochiral ketone CH3CH2COCH3 gives one of the enantiomers of the chiral alcohol CH3CH2CHOHCH3; the addition of CN- to one of the diastereotopic faces of the chiral aldehyde shown below converts it into one of the diastereoisomers of the the cyanohydrin. The two faces of the trigonal system may be described as Re and Si.
3. The term prochiral also applies to a tetrahedral atom of an achiral or chiral molecule which is bonded to two stereoheterotopic groups. For example, the prochiral molecule CH3CH2OH can be converted into the chiral molecule CH3CHDOH by the isotopic replacement of one of the two enantiotopic hydrogen atoms of the methylene group. The carbon atom of the methylene group is called prochiral. The prochiral molecule HO2CCH2CHOHCH2CO2H can be converted into a chiral product by esterification of one of the two enantiotopic -CH2CO2H groups. The carbon atom of the CHOH group is called prochiral. The chiral molecule CH3CHOHCH2CH3 can be converted into one of the diastereoisomers of CH3CHOHCHDCH3 by the isotopic replacement of one of the two diastereotopic hydrogen atoms of the methylene group. The carbon atom of the methylene group is called prochiral. The stereoheterotopic groups in these cases may be described as pro-R or pro-S. Reference to the two stereoheterotopic groups themselves as prochiral, although common, is strongly discouraged. See chirality centre.
4. The term prochirality is also applied to the enantiotopic faces of a trigonal system.
An atom of a molecule which becomes a chirality centre by replacing one of the two stereoheterotopic ligands attached to it by a different ligand is said to be a prochirality centre e.g. C-1 of ethanol; C-3 of butan-2-ol.
One of a pair of identical groups c attached to a double bond (as in abC=Cc2) is described as pro-E if, when it is arbitrarily assigned CIP priority over the other group c, the stereodescriptor of the molecule becomes E. The other group c is then described as pro-Z.
A formal two-dimensional representation of a three-dimensional molecular structure obtained by projection of bonds (symbolised as lines) onto a plane with or without the designation of the positions of relevant atoms by their chemical symbols.
A projection formula which indicates the spatial arrangement of bonds is called a stereochemical formula or stereoformula. Examples of stereoformulae are Fischer projection, Newman projection, sawhorse projection, wedge projection and zig-zag projection. See also perspective formula.
Proprochirality See prochirality.
A stereoheterotopic group c (as in tetrahedral Xabc2) is described as pro-R if, when it is arbitrarily assigned CIP priority over the other stereoheterotopic group c, the configuration of the thus generated chiral centre is assigned the stereodescriptor R. The other group c is then described as pro-S. This method for distinguishing between stereoheterotopic groups can be applied to other kinds of prochiral molecular entities or prochiral parts of molecular entities considered on their own. See prochirality centre.
Pseudo-asymmetric Carbon Atom
The traditional name for a tetrahedrally coordinated carbon atom bonded to four different entities, two and only two of which have the same constitution but opposite chirality sense. The r/s descriptors of pseudo-asymmetric carbon atoms are invariant on reflection in a mirror (i.e. r remains r, and s remains s), but are reversed by the exchange of any two entities (i.e. r becomes s, and s becomes r). An example is C-3 of ribaric (C-3 is r), xylaric acid (C-3 is s) or hyoscyamine (C-3 is r). The hyphen in pseudo-asymmetric may be omitted.
Pseudo-axial See axial, equatorial.
Pseudo-equatorial See axial, equatorial.
Stereoisomerisation resulting in a structure that appears to have been produced by rotation of the entire initial molecule and is superposable on the initial one, unless different positions are distinguished by substitution, including isotopic substitution.
One example of pseudorotation is a facile interconversion between the many envelope and twist conformers of a cyclopentane due to the out of plane motion of carbon atoms.
Another example of pseudorotation (Berry pseudorotation) is a polytopal rearrangemnt that provides an intramolecular mechanism for the isomerisation of trigonal bipyramidal compounds (e.g. 5-phosphanes), the five bonds to the central atom E being represented as e1, e2, e3, a1 and a2. Two equatorial bonds move apart and become apical bonds at the same time as the apical bonds move together to become equatorial.
A related conformational change of a trigonal bipyramidal structure is described as turnstile rotation. The process may be visualised as follows. An apical and an equatorial bond rotate as a pair ca. 120o relative to the other three bonds. (Doubts have been expressed about the distinct physical reality of this mechanism.)
A polytopal rearrangement in which the change in bond directions to a three-coordinate central atom having a pyramidal arrangement of bonds (tripodal arrangement) causes the central atom (apex of the pyramid) to appear to move to an equivalent position on the other side of the base of the pyramid. If the three ligands to the central atom are different pyramidal inversion interconverts enantiomers.
Quasi-axial See axial, equatorial.
Constitutionally different yet closely related chemical species MX and MY having the opposite chirality sense of the large common chiral moiety M are called quasi-enantiomers. For example (R)-2-bromobutane is a quasi-enantiomer of (S)-2-chlorobutane. See also quasi-racemic compound.
Quasi-equatorial See axial, equatorial.
The crystalline product of a 1:1 association between quasi-enantiomers.
The defined organisation of two or more macromolecules with tertiary structure such as a protein that are held together by hydrogen bonds and van der Waals and coulombic forces. See also primary structure, secondary structure, tertiary structure.
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