Stereochemistry, atom numbering

Note. In these compounds carbon atom number 1 has become chiral. When known, the stereochemistry at this new chiral centre is indicated using the R,S system ([13], Section E). 

We have designed PBUILD, a new CHEMLAB module, for easy construction of random copolymers. A library of monomers has been developed from which the chemists can select a particular sequence to generate a polymeric model. PBUILD takes care of all the atom numbering, three dimensional coordinates, and knows about stereochemistry (tacticity) as well as positional isomerism (head to tail versus head to head attachment). The result is a model of the selected polymer (or more likely a polymer fragment) in an all trans conformation, inserted into the CHEMLAB molecular workspace in literally a few minutes. 

It is known that plots of the formation constants /3/versus the atomic number Z for a series of complexes ML/of the same stereochemistry reflect such phenomena as the ligand field stabilization (1) and the nephelauxetic effect (2). 

The [2 + 2] cycloreversion reaction proceeds stereospecifically with retention at carbon atoms, its rate obeys first-order kinetics and it depends on the stereochemistry and number of substituents at the ring carbon atoms. It is therefore concluded that the reaction mechanism is a concerted [2S + 2a] cycloreversion. 

The stereochemical designation of a tetrahedral chiral centre is determined by the priorities of the four substituents. The convention applies to all tetrahedral centres, not just carbon. Priorities in the first instance are determined by atomic weight (not atomic number the convention works for molecules chiral by isotopic substitution). The chiral centre is viewed along the line of the bond from the central atom to the substituent of lowest priority, with the central atom in front. If the priorities of the three remaining substituents decrease clockwise the stereochemistry is R (for rectus, right in Latin), otherwise it is S (for sinister, left). 

Many of the exciting scientific theories of a hundred years ago originated with chemists such as Stoney, who postulated the existence of electrons, and those who formulated the periodic law of the elements. Van t Hoff, the father of stereochemistry, was also the first Nobel laureate. A chemist named van den Broek introduced the concept of atomic number, and another chemist named Harkins postulated the neutron and first mooted the idea of a mass defect as the origin of nuclear binding energy. Not only the chemists of the era but also the subject area of chemistry produced spectacular theoretical advances. The physicist Lord Rutherford, who is purported to have stated... 

During the optimisation of the structure against the distance constraints it is usual to incorporate chiral consiraints. These are used to ensure that the final conformation is the desired stereoisomer. Chiral constraints are necessary because the interatomic distances in two enantiomeric conformations are identical and as a consequence the wrong isomer may quite legitimately be generated. Chiral constraints are usually incorporated into the error function as a chiral volume, calculated as a scalar triple product. For example, to maintain the correct stereochemistry about the tetrahedral atom number 4 in Figure 9,16, the following scalar triple product must be positive ... 

Edge-coalesced icosahedra eleven-coordinate compounds, 99 repulsion energy coefficients, 33, 34 Effective atomic number concept, 16 Effective bond length ratios non-bonding electron pairs, 37 Effective Eight-coordinate compounds stereochemistry, 86-94 Electrochemistry, 475-477 aqueous solution, 479-490 multimetallic systems, 485 non-aqueous solutions, 493 Electrodes... 

Another approach, which lends itself particularly to forms of stereochemistry involving non-tetrahedral geometries e.g. in coordination compounds) is the stereovertex list. Here, the atom numbers around the stereocentre are mapped as an n-tuple onto the corners of a standard polyhedron representing the geometry in question, and stored separately from the main connection table. ... 

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