Compound models

Many compounds have been synthesized, characterized, and studied as models for the proposed intermediates in various homogeneous catalytic reactions. Here we discuss a few typical examples. Complex 331 is proposed as a model that shows the mode of interaction between an organic hydroperoxide and high-valent metal ions such as 11 % and Mo. Ibis type of interaction is considered to be necessary for the oxygen atom transfer from the hydroperoxide to an alkene to give an epoxide. 

Anions of the type 332 arc excellent models that provide strong support for the proposed intermediales in Heck reaction (also see 3.28). These anions have been made with diffaimt countercations and characterized by single-crystal X-ray diffiaction. Onreaction with styrene, they produce HiCH=CHF1i by a mechanism discussed in greater detail later (see Section 7.4.2). 

In asymmetric hydrogenation reactions (see Section 5.1.2) where 333 is used as the precatalyst, structure 3.34 is proposed to be a model for one of the catalytic intermediates. Crystals of 334 are obtained from deuterated methanol solution of 333. This means that in the catalytic system, where methanol is used as the solvent, 333 must first undergo conversion to a structure like 334. 

In a series of papers, Aulin-Erdtman et al. [15-17] compiled extensive data on UV-visible spectra of lignin model phenols and the corresponding phenolate ions. A selection of these is presented in Table 3.4. 

The hypothesis of Doub and Vandenbelt that the spectra of substituted benzenes can be understood as a shifting of the three basic bands of benzene seems sufficient to understand qualitatively the spectra of these lignin model compounds. Absorptions below about 260 nm are B transitions, while those above are due to and transitions. Depending on the exact substitution pattern, the band may be obscured under the more intense band. 

For the series of p-hydroxybenzyl alcohols a single absorption maximum is observed above 260 nm, which is probably due largely to the transition. This band is hardly shifted from its position in phenol (see Table 3.4) because all the substituents are of the same character, electron donating. Similarly, in the series of coumaryl [15], coniferyl [17] and sinapyl [15] alcohols the longest wavelength band is only slightly shifted relative to that observed for the most shifted mono-substituted compound, cinnamyl alcohol, = 292 nm [195], 

The benzaldehyde and acetophenone series follow the pattern observed by Doub and Vandenbelt for benzenes with one electron-withdrawing and two electron-donating substituents. Thus, in p-hydroxybenzaldehyde the band is shifted to 285 nm, and obscures the band, which is little affected by p-disubstitution. The additional m-methoxy groups in vanillin and syringaldehyde intensify and red-shift the Lb band, which becomes visible as a discrete maximum at 310 nm. 

UV-Visible Data for Selected Lignin Model Phenols and Phenolate Anions  

The crystal structure of tran.r-stilbene is well-known from the study by Finder et al. [275]. Bond lengths and bond angles derived from these data have been used to construct single-chain geometries for quantum chemical modelling. Another feature that is relevant for the 

Macrocyclic polyethers, synthesized by Pedersen,form complexes with various metal salts in the metal-ether ratio of 1 1 whatever the oxidation state of the metal. Other ratios were later obtained, depending upon the relative size of ether and metal. Effective compounds contained groups of two oxygen atoms separated by two carbon atoms, as in (11)—(16). Portions of the monobasic acids (4)—(9) are of this type but the neutral antibiotics are quite different. Replacement of two oxygen atoms in (15) by NH groups 

Proceedings of the Xlllth International Conference on Co-ordination Chemistry, 1970, Vol. II, p. 185. 

So far, no synthetic compounds have been reported which change their hydrogen-bonding to form complexes as do valinomycin and monensin. 

Herceg and R. Weiss, Inorg. Nuclear Chem. Letters, 1970, 6, 437. 

In Sect. B.l.a) we have summarized some previous results obtained from the study of the interaction of triene (I) with AIBN performed with the aim to test the reactivity of the conjupted function present in (I) toward r anoisobutyric radicals. 

The results obtained for the model compound of triene (ID), named (lll,a), are shown in Fig. 6. It is evidmt that BPO is more reactive than AIBN, and that in the first 30 minutes the H abstractirm mechanism is by far predominant. However, at high conversions the addition mechanism is still imprnrtant. Ctm rsely, the conversion curves obtained with AIBN by VPC and UV analysis are very close, and this means that the addition mechanism is prevalrat in this case. 

When the conjupted function is l ear, as in the case of (Vn,a) (Fig. 7), AIBN displays a reactivity simikr or higher than that of BPO, but the latter initiator acts through the allylic H abstractitm, whereas the former adds the conjupted double bonds. 

The model compound (2-ethylidene-norbornane, NB) of the reference dienic termonomer ENB is less reactiw toward BPO than compounds (III,a) or (VII,a) because AIBN attacks NB only after proltmged reaction times (Fig. 8). This result explains the experimental observation described by Meredith according to which 04B-EPDM cannot be palled by SAN in the presence of AIBN. In contrast, Hp. 6 and 7 allow us to predict that EPTMs omtaining linear conjupted unsaturatitms can be pafted even in the pre ce of the less favorable AIBN. 

Properties (Type of elastomer) ABS (Polybutadiene ) ATS (ENB - EPDM ) (IID-EPTM )  

Isolation and purification of the metalloprotein. For instance, Hb was first crystallized in 1849, its physiological purpose of oxygen transport was recognized by 1864, and its molecular weight and primary amino acid sequence was known by 1930. 

Characterization of structural, spectroscopic, and reactivity properties of model compounds—that is, metal cofactor small molecule analogs. 

Comparisons between the protein and the analogs to reveal new structure-function relationships. 

Quantitative data are available in the literature only for methyl radical addition to conjugated dienes relative to the hydrogen abstraction reaction. According to the results obtained by Szwarc et al.so-s2 methyl substitution on the terminal carbon atom of the diene system decreases reactivity, whereas methyl substitution elsewhere 

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There is quite a large body of literature on films of biological substances and related model compounds, much of it made possible by the sophisticated microscopic techniques discussed in Section IV-3E. There is considerable interest in biomembranes and how they can be modeled by lipid monolayers [35]. In this section we briefly discuss lipid monolayers, lipolytic enzyme reactions, and model systems for studies of biological recognition. The related subjects of membranes and vesicles are covered in the following section. 

Figure C3.2.7. A series of electron transfer model compounds with the donor and acceptor moieties linked by (from top to bottom) (a) a hydrogen bond bridge (b) all sigma-bond bridge (c) partially unsaturated bridge. Studies with these compounds showed that hydrogen bonds can provide efficient donor-acceptor interactions. From Piotrowiak P 1999 Photoinduced electron transfer in molecular systems recent developments Chem. Soc. Rev. 28 143-50.

It can be seen from Table 2 that the intrinsic values of the pK s are close to the model compound value that we use for Cys(8.3), and that interactions with surrounding titratable residues are responsible for the final apparent values of the ionization constants. It can also be seen that the best agreement with the experimental value is obtained for the YPT structure suplemented with the 27 N-terminal amino acids, although both the original YPT structure and the one with the crystal water molecule give values close to the experimentally determined one. Minimization, however, makes the agreement worse, probably because it w s done without the presence of any solvent molecules, which are important for the residues on the surface of the protein. For the YTS structure, which refers to the protein crystallized with an SO4 ion, the results with and without the ion included in the calculations, arc far from the experimental value. This may indicate that con-... 

As mentioned, we also carried out IR studies (a fast vibrational spectroscopy) early in our work on carbocations. In our studies of the norbornyl cation we obtained Raman spectra as well, although at the time it was not possible to theoretically calculate the spectra. Comparison with model compounds (the 2-norbornyl system and nortri-cyclane, respectively) indicated the symmetrical, bridged nature of the ion. In recent years, Sunko and Schleyer were able, using the since-developed Fourier transform-infrared (FT-IR) method, to obtain the spectrum of the norbornyl cation and to compare it with the theoretically calculated one. Again, it was rewarding that their data were in excellent accord with our earlier work. 

CIS calculations from the semiempirical wave function can be used for computing electronic excited states. Some software packages allow Cl calculations other than CIS to be performed from the semiempirical reference space. This is a good technique for modeling compounds that are not described properly by a single-determinant wave function (see Chapter 26). Semiempirical Cl... 

Backbone generation is the first step in building a three-dimensional model of the protein. First, it is necessary to find structurally conserved regions (SCR) in the backbone. Next, place them in space with an orientation and conformation best matching those of the template. Single amino acid exchanges are assumed not to affect the tertiary structure. This often results in having sections of the model compound that are unconnected. 

As described in the chapter on band structures, these calculations reproduce the electronic structure of inhnite solids. This is important for a number of types of studies, such as modeling compounds for use in solar cells, in which it is important to know whether the band gap is a direct or indirect gap. Band structure calculations are ideal for modeling an inhnite regular crystal, but not for modeling surface chemistry or defect sites. 

The continued effectiveness of the nitronium ion in relatively dilute solutions has been indicated by comparing the dependence of the rates on the concentration of sulphuric acid, with the acidity-dependence of the ionisation of model compounds. The (formerly or Cq) acidity... 

In the reaction of Q,/3-unsaturated ketones and esters, sometimes simple Michael-type addition (insertion and hydrogenolysis, or hydroarylation, and hydroalkenylation) of alkenes is observed[53,54]. For example, a simple addition product 56 to methyl vinyl ketone was obtained by the reaction of the heteroaromatic iodide 55[S5]. The corresponding bromide affords the usual insertion-elimination product. Saturated ketones are obtained cleanly by hydroarylation of o,/3l-unsaturated ketones with aryl halides in the presence of sodium formate, which hydrogenolyses the R—Pd—I intermediate to R— Pd—H[56]. Intramolecular hydroarylation is a useful reaction. The diiodide 57 reacts smoothly with sodium formate to give a model compound for the afla-toxin 58. (see Section 1.1.6)[57]. Use of triethylammonium formate and BU4NCI gives better results. 

The intramolecular version for synthesizing cyclic and polycyclic compounds offers a powerful synthetic method for naturally occurring macrocyclic and polycyclic compounds, and novel total syntheses of many naturally occurring complex molecules have been achieved by synthetic designs based on this methodology. Cyclization by the coupling of an enone and alkenyl iodide has been applied to the synthesis of a model compound of l6-membered car-bomycin B 162 in 55% yield. A stoichiometric amount of the catalyst was used because the reaction was carried out under high dilution conditions[132]. 

Both 2-hydroxythiazoie and 2-mercaptothiazoIe have been studied to determine the position of the protomeric equilibrium 43 7 43a 43b (Scheme 17). Most studies indicate that form 43a is largely predominant in neutral solution for X = 0 and X=S (52-56, 887, 891). The basic principle is to compare a physical property of the investigated product with that of a model representative of each protomeric form. The similarity of physicochemical properties between the product and one of the model compounds is taken as evidence for the position of the protomeric equilibrium. The limits of such an approach have been discussed in detail elsewhere (57). 

X-ray analysis of 2-phenylmethylaraino-5-phenyl-A-2-thiazoline-4-one (176), which exists in the keto form in the solid state (420), and of 4,4 -diacetoxy-5,5 -dimethy]-2,2 bithiazolyl (177) (419) are available as model compounds for theoretical calculations (Scheme 92). 

The structural unit associated with an electronic transition m UV VIS spectroscopy IS called a chromophore Chemists often refer to model compounds to help interpret UV VIS spectra An appropriate model is a simple compound of known structure that mcor porates the chromophore suspected of being present m the sample Because remote sub stituents do not affect Xmax of the chromophore a strong similarity between the spectrum of the model compound and that of the unknown can serve to identify the kind of rr electron system present m the sample There is a substantial body of data concerning the UV VIS spectra of a great many chromophores as well as empirical correlations of sub stituent effects on k Such data are helpful when using UV VIS spectroscopy as a tool for structure determination... 

The molecules used in the study described in Fig. 2.15 were model compounds characterized by a high degree of uniformity. When branching is encountered, it is generally in a far less uniform way. As a matter of fact, traces of impurities or random chain transfer during polymer preparation may result in a small amount of unsuspected branching in samples of ostensibly linear molecules. Such adventitious branched molecules can have an effect on viscosity which far exceeds their numerical abundance. It is quite possible that anomalous experimental results may be due to such effects. 

One of the most sensitive tests of the dependence of chemical reactivity on the size of the reacting molecules is the comparison of the rates of reaction for compounds which are members of a homologous series with different chain lengths. Studies by Flory and others on the rates of esterification and saponification of esters were the first investigations conducted to clarify the dependence of reactivity on molecular size. The rate constants for these reactions are observed to converge quite rapidly to a constant value which is independent of molecular size, after an initial dependence on molecular size for small molecules. The effect is reminiscent of the discussion on the uniqueness of end groups in connection with Example 1.1. In the esterification of carboxylic acids, for example, the rate constants are different for acetic, propionic, and butyric acids, but constant for carboxyUc acids with 4-18 carbon atoms. This observation on nonpolymeric compounds has been generalized to apply to polymerization reactions as well. The latter are subject to several complications which are not involved in the study of simple model compounds, but when these complications are properly considered, the independence of reactivity on molecular size has been repeatedly verified. 

It is proposed to polymerize the vinyl group of the hemin molecule with other vinyl comonomers to prepare model compounds to be used in hemoglobin research. Considering hemin and styrene to be species 1 and 2, respectively, use the resonance concept to rank the reactivity ratios rj and X2. 

The spectrum shown in Fig. 7.5 shows the appropriate portion of the spectrum for a copolymer prepared from a feedstock for which fj = 0.153 It turns out that each polyene produces a set of three bands The dyad is identified with the peaks at X = 298, 312, and 327 nm the triad, with X = 347 367, and 388 nm and the tetrad with X = 412 and 437 nm. Apparently one of the tetrad bands overlaps that of the triad and is not resolved. Likewise only one band (at 473 nm) is observed for the pentad. The identification ol these features can be confirmed with model compounds and the location and relative intensities of the peaks has been shown to be independent of copolymer composition. 

The effect of the conformation of amic acid on the imidi2ation rate is also consistent with the observation that the thermal cycli2ation of model compounds, N-substituted phthalamic acids, is strongly influenced by the steric effect imposed by N-substituents (18). 

AijAT-dicyclohexylcarhodiimide (DCC) also leads to essentially quantitative conversion of amic acids to isoimides, rather than imides (30,31). Combinations of trifluoroacetic anhydride—triethjlarnine and ethyl chi oroform a te—triethyl amine also result in high yields of isoimides (30). A kinetic study on model compounds has revealed that isoimides and imides are formed via a mixed anhydride intermediate (12) that is formed by the acylation of the carboxylic group of amic acid (8). 

Chemistry ofDelig niiic tion. The chemistry of delignification is complex and, despite the extensive Hterature, not completely understood. A variety of lignin model compounds have been studied and the results compared with the observed behavior of lignin during pulping (1,10—12,16). 

Delignification Chemistty. The chemical mechanism of sulfite delignification is not fully understood. However, the chemistry of model compounds has been studied extensively, and attempts have been made to correlate the results with observations on the rates and conditions of delignification (61). The initial reaction is sulfonation of the aUphatic side chain, which occurs almost exclusively at the a-carbon by a nucleophilic substitution. The substitution displaces either a hydroxy or alkoxy group ... 

Of special importance is the complex problem of nitrogen addition as related to the dmg dopamine, where even model compounds lead to extremely complex chemistry and difficult analytical problems (65). 

Early studies of the condensation reaction on the monomer level did not give the full picture of this process and only in the 1980s was polycondensation of siloxanols studied by using oligomeric model compounds (76,77). These studies revealed that in the presence of strong protic acids three processes must be considered linear condensation (eq. 14), cyclization (eq. 15), and disproportionation (eq. 16). 

One development involves the use of vitamin B 2 to cataly2e chemical, in addition to biochemical processes. Vitamin B 2 derivatives and B 2 model compounds (41,42) cataly2e the electrochemical reduction of alkyl haUdes and formation of C—C bonds (43,44), as well as the 2inc—acetic acid-promoted reduction of nitriles (45), alpha, beta-unsaturated nitriles (46), alpha, beta-unsaturated carbonyl derivatives and esters (47,48), and olefins (49). It is assumed that these reactions proceed through intermediates containing a Co—C bond which is then reductively cleaved. 

Discrimination between exposed and unexposed areas in this process requires the selection of thia zolidine compounds that do not readily undergo alkaline hydrolysis in the absence of silver ions. In a study of model compounds, the rates of hydrolysis of model /V-methyl thia zolidine and A/-octadecyl thiazolidine compounds were compared (47). An alkaline hydrolysis half-life of 33 min was reported for the /V-methyl compound, a half-life of 5525 min (3.8 days) was reported for the corresponding V/-octadecyl compound. Other factors affecting the kinetics include the particular silver ligand chosen and its concentration (48). Polaroid Spectra film introduced silver-assisted thiazolidine cleavage to produce the yellow dye image (49), a system subsequentiy used in 600 Plus and Polacolor Pro 100 films. 

Polyanilines. Initial preparations of polyaniline (PANI) led to insoluble materials that were difficult to characterize. Use of model compounds and polymers (124,125) allowed for definitive stmctural analysis. Poly( phenylene amineimine) (PPAI) was synthesized directiy to demonstrate that PANI is purely para-linked (126). The synthesis was designed so as to allow linkage through the nitrogen atoms only (eq. 9). Comparison of the properties of PPAI and PANI showed PPAI to be an excellent model both stmcturaHy and electronically. 

Resonance energies of ca. 90, 182 and 330 kJ moF have been estimated for pyrrole, indole and carbazole respectively by comparing their protonation constants with those for selected model compounds (72C1(L)335, 72TL5019). 

The acetyl transfer reactions of acetylated pyrazolones (acylotropy) have been carefully studied by Arakawa and Miyasaka (74CPB207,74CPB214) (Section 4.04.2.1.3(x)). Methylation of 3-methyl-l-phenyl-4-phenylazo-5-pyrazolone (402) yields, depending on the experimental conditions, the N- and the O-methylated derivatives (483) and (484) (66BSF2990). These derivatives have been used as model compounds in a study of the tautomerism of (402) (structure 139 Section 4.04.1.5.2). 

Presented in Table 1 is a list of the parameters in Eqs. (2) and (3) and the type of target data used for their optimization. The infonnation in Table 1 is separated into categories associated with those parameters. It should be noted that separation into the different categories represents a simplification in practice there is extensive correlation between the different parameters, as discussed above for example, changes in bond parameters that affect the geometry may also have an influence on AGsoivation for a given model compound. These correlations require that parameter optimization protocols include iterative approaches, as will be discussed below. 

Internal parameters are generally optimized with respect to the geometries, vibrational spectra, and confonnational energetics of selected model compounds. The equilib-... 

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