Sequencing Intermediate Form

Sequencing Intermediate Form (SIF) A hierarchical sequencing graph is used to capture both control-flow and data-flow at the structural synthesis level. 

Recently, the cyclopenta[c]pyran (122) was obtained as a secondary product along with 1,2,3-tribenzoylcyclopropane from phenacyl-trimethylammonium hydroxide a complicated sequence was proposed involving a Michael addition to 1,2-dibenzoylethylene intermediately formed. 

The sequence of decomposition intermediates formed varies with the particular preparation of reactant being studied. Gillibrand and Halliwell... 

By the time the concentration of monomer is low, the back-skip of the polymer chain to the less-hindered site is faster than the formation of the high-energy alkene coordinated intermediate (IV). For this reason, at low propene concentrations and elevated temperatures isotactic sequences are formed. The probability of monomer coordination at the aspecific site (IV) is enhanced when the propene concentration increases. The consequence is that single stereoerrors [mrrm] are introduced in the isotactic polymer chain. 13C-NMR was able to prove the mechanism because a... 

Oscillations of concentrations of intermediates can occur when one substance in a sequence of reactions is either an activator or an inhibitor for a reaction step that occurs earlier in the sequence. Such activation or inhibition can control intermediate forming steps and will be responsible for producing oscillation in the concentration of the intermediate. The important conditions required to generate oscillations in a chemical system are ... 

Nonelementary reactions are explained by assuming that what we observe as a single reaction is in reality the overall effect of a sequence of elementary reactions. The reason for observing only a single reaction rather than two or more elementary reactions is that the amount of intermediates formed is negligibly small and, therefore, escapes detection. We take up these explanations later. 

To explain the kinetics of nonelementary reactions we assume that a sequence of elementary reactions is actually occurring but that we cannot measure or observe the intermediates formed because they are only present in very minute quantities. Thus, we observe only the initial reactants and final products, or what appears to be a single reaction. For example, if the kinetics of the reaction... 

Since then, there have been a number of studies of this reaction, which have been summarized by Hatakeyama and Akimoto (1994). The mechanism appears to involve formation of an adduct that can either decompose to S02 and an isomerization product of the Criegee intermediate or, alternatively, react with a second S02 molecule to generate other products. For the Criegee intermediate formed in the ethene-ozone reaction, for example, the proposed reaction sequence is the following ... 

Much the same activity is retained when the nitrogen atoms in the heterocyclic nucleus are shifted around. The convergent scheme to this related compound starts with the acylation of alanine (35-1) with butyryl chloride (35-2). The thus-produced amide (35-3) is then again acylated, this time with the half-acid chloride from ethyl oxalate in the presence of DMAP and pyridine to afford the intermediate (35-4). In the second arm of the scheme, the benzonitrile (35-5) is reacted with the aluminate (35-6), itself prepared from trimethyl aluminum and ammonium chloride, to form the imidate (35-7). Treatment of this intermediate with hydrazine leads to the replacement of one of the imidate nitrogen atoms by the reagent by an addition-elimination sequence to form (35-8). Condensation of this product with (35-4) leads to the formation of the triazine (35-9). Phosphorus oxychloride then closes the second ring... 

Imines, ethyl acetylenedicarboxylate and benzoyl chloride were combined in the presence of carbon monoxide and a palladium-tri-o-tolylphosphine catalyst system to pyrrole derivatives (3.90.). Although the carbon monoxide is formally oxidized to carbon dioxide, during the catalytic cycle it is inserted into the intermediates formed and is extruded in a retro-Diels-Alder reaction only in the concluding step of the reaction sequence.114... 

So far, except for the iron(III)/iron(II) couple [reaction (6) in Table 14.2], we have considered reduction potentials of half reactions with an overall transfer of an even number of electrons (i.e., 2, 4, 6, etc.). However, in many abiotic multielectron redox processes, particularly if organic compounds are involved, the actual electron transfer frequently occurs by a sequence of one-electron transfer steps (Eberson, 1987). The resulting intermediates formed are often very reactive, and they are not stable under environmental conditions. In our benzoquinone example, BQ is first reduced to the corresponding semiquinone (SQ), which is then reduced to HQ ... 

Vinyl ethers and amines disclose little tendency to revert to type thus, the intermediate formed by reaction with an electrophilic reagent reacts further by adding a nucleophilic species to yield an addition compound cf the sequence (8) — (11). Thiophene and pyrrole have a high degree of aromatic character consequently the initial product formed by reaction of thiophene or pyrrole with an electrophilic species subsequently loses a proton to give a substituted compound cf the reaction sequence (12) — (15). Furan has less aromatic character and often reacts by overall addition as well as by substitution. In electrophilic addition, the first step is the same as for substitution, i.e. the formation of a tr-complex (e.g. 13), but instead of losing a proton this now adds a nucleophile. 

In nonelementary reactions, the reaction order and stoichiometric coefficients are different. A single reaction is observed, but in reality a sequence of elementary reactions occurs. The amount of intermediates formed is negligible and, therefore, not detectable. One famous example is the reaction between hydrogen and bromine. The overall reaction can be described as ... 

The oxidation of one functional group of a molecule by an adjacent group in the same molecule is a feature of many metabolic sequences. In most cases an enolic intermediate, formed either from a ketone as in Eq. 13-25 or by a dehydration reaction (see Eq. 13-32), is postulated. 

Mechanisms of catalase and peroxidase catalysis. Attention has been focused on a series of strikingly colored intermediates formed in the presence of substrates. When a slight excess of H202 is added to a solution of horseradish peroxidase, the dark brown enzyme first turns olive green as compound I is formed, and then pale red as it turns into compound II. The latter reacts slowly with substrate AH2 or with another H202 molecule to regenerate the original enzyme. This sequence of reactions is indicated by the colored arrows in Fig. 16-14, steps a-d. 

Unsaturated fatty acids. Mitochondrial P oxidation of such unsaturated acids as the A9-oleic acid begins with removal of two molecules of acetyl-CoA to form a A5-acyl-CoA. However, further metabolism is slow. Two pathways have been identified (Eq. 17-l).26 29b The first step for both is a normal dehydrogenation to a 2-fraus-5-czs-dienoyl-CoA. In pathway I this intermediate reacts slowly by the normal p oxidation sequence to form a 3-czs-enoyl-CoA intermediate which must then be acted upon by an auxiliary enzyme, a ds-AMra s-A2-enoyl-CoA isomerase (Eq. 17-1, step c), before P oxidation can continue. 

When the enone chromophore of the diketone (148) is excited selectively using 2537 A-light, a smooth conversion to the two stereoisomeric cyclopropyl diketones (149) and (150) takes place exclusively.27,28,44 Experiments with the 4a-deuteriomethyl analog of (148) establish a stepwise reaction sequence with the diradicals (151) [- (149)] and (152) [-> (150)] as the most likely intermediates formed in the primary photoprocess. Total quenching with naphthalene indicates the triplet nature of the reaction. 

A similar sequence of reactions occurs with LiBu, although in this instance methylation or protonation of the intermediates formed after addition of either two or three equivalents of alkyllithium reagent, respectively, allow the corresponding acyl - or hydroxyalkyl-vinylidene complexes to be isolated (26) ... 

The process of coacervation is finely tuned to the physiological conditions of the extracellular matrix. Optimal coacervation of human tropo-elastin occurs at 37 °G, 150 mM NaCl, and pH 7-8 (Vrhovski et al, 1997). The arrangement of sequences in tropoelastin is critical to this process of coacervation, where association through hydrophobic domains depends on their contextual location in the molecule (Toonkool et al., 2001b). Tropoelastin association rapidly proceeds through a monomer to tuner transition, with little evidence of intermediate forms (Toonkool et al, 2001a). 

---