Atom mapping

Figure 5-26. Reaction query with atom-atom mapping numbers.

The four Build Menus ia REACCS are Stmcture, Query, Top, and HighlightRxn. Stmcture menu contains the basic drawiag commands used to constmct the backbone of the stmcture. Query menu contains the commands used to add flexible stmctural parameters to the query. Top menu contains commands used to build reactions and to store and retrieve reactions, molecules, and graphic queries. HighlightRxn menu contains commands that apply atom/atom mapping and reaction centers to the current reaction. Atom/atom mapping is used to identify the reaction centers and iacrease accuracy and efficiency by letting the searcher specify that a particular atom ia a reactant must correspond to a particular atom ia the product. 

Make sure that symmetry is taken into account when producing the atom mapping between the two conformations. Consider the example given in Fig. 7.17. The molecule - phenyl-cyclohexane - has two independent symmetry axes through the two rings as indicated by dotted lines. This... 

Fig. 3.7. A united-atom PE chain constituted of 100 united atoms mapped around a stream line. The bond angles as well as the bond lengths have been kept fixed. The torsion angles have been subject to a minimization considering a three-fold potential accounting for the simplified chemical structure of the chain. An additional proximity function has been used to force the chain to follow the trajectory of the stream line [114]...

Figure 1.10. This shows a 3DAP atom map across a grain boundary in a neutron irradiated 15KkMFA Russian pressure vessel steel weld. It reveals significant levels of P, Mn, Mo and C segregation, which correlate with poor mechanical properties exhibited by these materials.

Atom-atom mapping, 10 333 Atom economy, 12 803-804 Atom efficiency, 12 810-811 Atomic absorption (AA), 25 370 Atomic absorption spectroscopy, 15 348 of archaeological materials, 5 742 determining trace mercury using, 16 44 5... 

Fig. 9. ISIS/Draw interface used for defining or modify RXN files. The atom-to-atom mapping function in ISIS/Draw is used to define the reaction. In this case the reaction taken out of ISIS/Base (Fig. 8) has been modified to make it more generic.

The second approach is based on the idea of synthesizing bowl-shaped hydrocarbons in which curved networks of trigonal C-atoms map out the same patterns of five- and six-membered rings as those found on the surfaces of Cjq and/or the higher fullerenes [145-152]. An example for such an open geodesic polyarene is circum-trindene (5), generated by flash-vacuum pyrolysis (FVP) of trichlorodecacyclene 4 (Scheme 1.5) [152], Circumtrindene represents 60% of the framework of Cjq. 

Sandstrom, C., el al., Atomic mapping of the interactions between the antiviral agent cyanovirin-N and oligomannosides by saturation-transfer difference NMR. Biochemistry, 2004,43, 13926-13931. 

Chemical reactions are first classified according to the minimal number of valence electrons that must be redistributed during the conversion of the educts into the products this is their minimal chemical distance (MCD). The determination of the MCD of a chemical reaction (ref. 5-7) yields also an atom-by-atom mapping of the educts and the products, and it also identifies the reactive centers whose union is the socalled core of the reaction. 

As the number of equations needed for isotope balances is large, it is important to use a condensed notation to describe the carbon transitions in a reaction. In the case of isotope balancing based on fractional enrichments, the balances can be expressed using so-called atom-mapping matrices [17]. The principle of using atom-mapping matrices is illustrated by considering an example where the carbon transitions in the first reactions in the Krebs cycle are shown (Fig. 3). 

Fignre 18. Potential energy contours for the SFH HOCO surface. The OCO nuclei are fixed, while the H atom maps out the contours, which are spaced by 2500cm". (a) is for the OCO nuclei at the CO2 equilibrium geometry. The system is repulsive except for a shallow well at the C2V positions. In (b), OCO is bent by 15°, resulting in cis and trans wells. In (c), OCO is bent by 30°. The cis and trans wells are more available than in (b), with entrance barriers of 18,000 and 16,000 cm , respectively. In (d), one CO bond is stretched to 2.50 Bohr with OCO bent by 20°. The cis and trans HOCO wells are much deeper than in (b) or (c), and shallow cis and trans wells appear further out. 

Figure 2 Atom mapping in aromatic amino acids. Atoms a-c are biosynthetically equivalent to atoms 1-3 in phosphoenol pyruvate, atoms d-g are equivalent to carbon atoms 1-4 of erythrose 4-phosphate, and atoms i-h are equivalent to carbon atoms 1-2 in ribose 5-phosphate.

Sets of atom properties, such as point charges, atomic lipophilicity parameters or any other atom properties, can be used to describe properties of molecules. However, the use of such single atom properties as descriptors requires an atom-to-atom mapping of all atoms considered of all compounds of the dataset. This is not possible in most cases and, therefore, it is necessary to compute more general descriptors from these parameters ... 

To illustrate the relevance of pharmacophore centers. Fig. 10 shows two ways of superimposing a dihydrofolate and a methotrexate molecule. Both compounds bind to the enzyme dihydrofolate reductase. Dihydrofolate is the natural substrate, methotrexate is a potent inhibitor. Atom-by-atom mapping leads to the first superposition. By looking at pharmacophore centers and the direction of interactions a quite different superposition, in which a part of the molecule is rotated by 180°, is found. Indeed, this is the orientation found by X-ray analyses of the enzyme-ligand complexes [73]. 

Reaction search, including atom mapping and bond-specific search. 

FIGURE 6.5 Pulmonary vein (PV) isolation guided by electroan-atomical mapping. A posteroanterior view of the left atrium is displayed with locations of the PVs indicated by brown tubes. Yellow tags show locations of radiofrequency lesion around the left and right PVs. (From Ref. 182, with permission.)... 

In order to carry out a transformation, it is necessary to know precisely which bonds are to be broken and which are to be made. While this information is implicit in the SMIRKS above and can be understood by any chemist, a more specific set of instructions is necessary in order to make the transformation possible using a computer. Numbering the atoms of the reactants and the corresponding atoms in the products accomplishes this. This produces an atom mapping. Many sketching programs can do this automatically or with some additional input from the user. Using the example shown previously, an atom-mapped SMIRKS would... 

Figure 9.1 Atom-mapped reaction of an amine with an acid or acid chloride.

---