Positive fragments

Ion-pair formation. An ionization process in which a positive fragment ion and a negative fragment ion are the only products. 

Some examples of addition followed by loss of a positive fragment are shown below. The decomposition of the diazonium salt XXXVI is... 

The method used in drawing the ionic species in these two equations and throughout this chapter is meant to show that the ionic species usually do not exist as free ions but as ion pairs. The parentheses around the anionic fragment is used to indicate that the negative counterion remains close to the positive fragment. (Even when the counterion is not shown, one should understand it is present.) However, keep in mind that free ions coexist with the ion pairs, and it is the relative concentrations that determine the overall polymerization rate. 

Termination occurs by transfer of a positive fragment, usually a proton, from the solvent or some transfer agent (often deliberately added), although other modes of termination are also known. Many anionic polymerizations are living polymerizations when the reaction components are appropriately chosen. 

The formation of a multiply charged ion following the ejection of a core electron often leads to decay of the molecule into several positive fragments, and, in the end, gives different final products than in photochemistry. An ion with a core hole can also make transitions into the highly excited states that cannot be occupied spectroscopically (for instance, into the C2S + state of the ion5 ). 

In the other type of fragmentation, a bond is cleaved so that the positive charge remains with one fragment and the odd electron goes with the other. Only the positive fragment is detected and appears in the mass spectrum. The stability of the product cation and radical determine the favorableness of this type of cleavage. You are already quite familiar with the factors that affect the stability of cations, especially carbocations. Although radicals are inherently more stable than carbocations because they are less electron deficient, they are stabilized by the same factors that stabilize carbocations. Thus, tertiary radicals are more stable than secondary radicals, and secondary radicals are more stable than primary radicals. Resonance stabilization is also important. 

Arrhenius is a Swedish chemist. In 1903 he won the Nobel Prize for his work with solutions. He explained why some solutions conduct electricity. In his theory, Arrhenius concluded that the molecule breaks apart into a positive fragment and negative fragment, called ions. He also explained weak and strong electrolytes according to the ratio of the ions in solutions. 

As seen with cationic polymerization, there is also no formal termination step with anionic-initiated systems. Dead chains are produced by transfer of a proton (or other positive fragment), usually from the solvent to the anion. When this happens with this particular example, it regenerates amide ion again, the primary initiating species (Eq. 22.35). 

Fit of fragments onto the interaction sites two different modes of operation are possible standard mode unconstrained positioning in the protein binding site, link-mode fragments are attached onto already positioned fragments. 

Figure 3. Basic steps of a calculation with LUDI. First, the interaction sites are generated (donor and acceptor interaction sites are depicted as bars, lipophilic interaction sites are depicted as circles). The next step is the fit of fragments onto the interaction sites. Finally, LUDI appends further fragments onto an already positioned fragment or lead compound...

A further requirement for a successfully positioned fragment is that it does not overlap with the protein. However, small overlaps of up to 0.5 A are tolerated, in order to account for induced fit effects. 

Figure 6.15. Positive fragmentation pathways of the monomer catechin retro-Diels-Alder fission (RDA), heterocychc ring fission (HRF), benzofuran-forming fission (BFF), and loss of water molecule. (Reprinted from Li and Deinzer, 2007, Tandem Mass Spectrometry for Sequencing Proanthocyanidins, Analytical Chemistry, 79, p. 1740, with permission from American Chemical Society.)...

NOTE Ortho-position fragments(s) on Phenyl ring(s) are NOT CONSIDERED ... 

Pre- or user-defined fragments are called up by pressing the respective function key. The size and the orientation of the fragment on the screen is defined by positioning fragment atoms 1 and 2 with the mouse cursor. 

Acrylate homopolymers behave similarly, except that the repeat unit ions are much less stable. The characteristic common positive fragment is the acryloyl ion at m/z 55. Common negative ions appear at m z 65, 67, 71, and 81, whilst specific ions are [M-H]", [M-Fl3] , [M-F27]-, [M-F39], and [M-F53] . 

Similarly, the enthalpy of formation of a positive fragment ion A+ with appearance energy AE formed by dissociative ionization of precursor molecule AB is given by... 

Acrylate homopolymers hehave similarly, except that the repeat unit ions are much less stable. The characteristic common positive fragment is the acryloyl ion at miz 55 ... 

Fragment connection methods Start with previously positioned fragments and find linkers or scaffolds to connect those fragments and hold them in a desirable orientation. 

As shown in the third column of Table II, we also obtained a hydroxa-mate positive fragment which seemed to contain Asp, Thr, Ser, ... 

Figure 3 Basic steps in the de novo ligand design using the program LUDI. First, die interaction sites are generated according to a rule-based approach (top). Then small fragments are fitted onto the interaction sites (center). Finally, positioned fragments are linked together or extended by additional groups (bottom)...

In the LIMA technique, the surface of the sample is subjected to a pulsed UV laser which is sufficiently energetic to volatilise a small volume (about 1 im cube) of material. The ionised fragments in this volume are then separated and identified by means of a time of flight mass spectrometer. Both negative and positive fragment data can be obtained. 

---