Atoms dissection

G. A. Kicska, P. C. Tyler, G. B. Evans, R. H. Fumeaux, W. Shi, A. Fedorov, A. Lewandowicz, S. M. Cahill, S. C. Almo, and V. L. Schramm, Atomic dissection of the hydrogen bond network for transition-state analogue binding to purine nucleoside phosphorylase, Biochemistry, 41 (2002) 14489-14498. 

Hansma H G, Vesenka J, Siegerist C, Kelderman G, Morrett H, Sinsheimer R L, Bustamante C, Elings V and Hansma P K 1992 Reproducible imaging and dissection of plasmid DNA under liquid with the atomic force microscope Science 256 1180... 

Substructure searches provide another method of searching for available starting materials. They arc used primarily for planning the synthesis of combinatorial libraries. After the target compound has been dissected into a set of suitable precursors, substructure searches can provide for each of them a series of representatives of a certain class of compounds, Siibsti ucturc searches enable the user to specify attributes such as open sites or atom lists at certain positions of the structure. Figure 10.3-38 shows the possible specification elements for the query in a substructure search. 

MO calculations can provide the minimum-energy structure, total energy, and overall electron density of a given molecule. However, this information is in the form of the sum of the individual MOs and cannot be easily dissected into contributions by specific atoms or groups. How can the properties described by the MOs be related to our concept of molecules as a colleetion of atoms or functional groups held together by chemical bonds ... 

No decomposihon into atom contribuhon is possible, because X not only occurs as the solute, but also as the solvent in (xl. In other words, since the drug is in a dual role of solute and solvent, it is not possible to dissect the contribuhon of individual atoms or groups of atoms in the drug from their role in the solvent state from that in the solute. Reiterahng this important point, log carmot be assumed to be accessible by linear regression with respect to composition descriptors, as is the case for log P . Moreover, it can hardly be - as often assumed - a linear function of log Pow, because the latter is linear with respect to composihon. Thus, any account of log S requires the nonlinear character to be taken into account. 

We have recently characterized the heptacyclic alkaloid chilocorine from the ladybird (coccinellid) beetle Chilocorus cacti (23). In spite of its superficial complexity, this structure is easily dissected into two tricyclic moieties, A and B, each of which can be regarded as an acetogenin which has been elaborated from a straight chain of 13 carbon atoms stitched together at three points by a trivalent nitrogen atom. 

The dissection of a molecular model into those components that are deemed to be essential for the understanding of the stereochemistry of the whole may be termed factorization (9). The first and most important step toward this goal was taken by van t Hoff and Le Bel when they introduced the concept of the asymmetric carbon atom (10a, 1 la) and discussed the achiral stereoisomerism of the olefins (10b,lib). We need such factorization not only for the enumeration and description of possible stereoisomers, important as these objectives are, but also, as we have seen, for the understanding of stereoselective reactions. More subtle differences also giving rise to differences in reactivity with chiral reagents, but referable to products of a different factorization, will be taken up in Sect. IX. 

The chemist John Dalton (of atomic theory fame) was color-blind. He thought it probable that the vitreous humor of his eyes (the fluid that fills the eyeball behind the lens) was tinted blue, unlike the colorless fluid of normal eyes. He proposed that after his death, his eyes should be dissected and the color of the vitreous humor determined. His wish was honored. The day after Dalton s death in July 1844, Joseph Ransome dissected his eyes and found the vitreous humor to be perfectly colorless. Ransome, like many scientists, was reluctant to throw samples away. He placed Dalton s eyes in ajar of preservative (Fig. 1), where they stayed for a century and a half. 

Dissection of the energy into atomic energies with the help of the virial partitioning method. 

The source of this webi-transmission effect and the nature of the 7r-7r excitation process is made apparent by inspection of Figure 3 which schematically gives the electron distribution of the seven molecular orbitals of the benzyl species these seven orbitals are dissected energetically and would, of course, he superimposed on the same sigma framework of the molecule. The electron density per electron at each atom in a particular MO is given adjacent to that atom in Figure 3. 

The simple addition reaction in Scheme 19 illustrates how the notation is used. Ester (1) can be dissected into synthons (2), (3) and (4). Synthons for radical precursors (pro-radicals) possess radical sites ( ) A reagent that is an appropriate radical precursor for the cyclohexyl radical, such as cyclohexyl iodide, is the actual equivalent of synthon (2). By nature, alkene acceptors have one site that reacts with a radical ( ) and one adjacent radical site ( ) that is created upon addition of a radical. Ethyl acrylate is a reagent that is equivalent to synthon (3). Atom or group donors are represented as sites that react with radicals ( ) Tributyltin hydride is a reagent equivalent of (4). In practice, such analysis will usually focus on carbon-carbon bond forming reactions and the atom transfer step may be omitted in the notation for simplicity. 

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