Conformations thermodynamic stability

The thermodynamic stabilities of three possible annular tautomers of the parent 1,2,4,5-thiatriazine 134 were compared using ab initio HF/6-31G calculations (OOJOC931). The 4H isomer 134a appears to be the most stable (it is more stable than 134b by 11.6 kcal/mol and more stable than 134c by 15.5 kcal/mol), presumably because it allows low-energy distortion from planarity and formation of the boat conformation. 

Vinylindoles have been studied extensively and used in the synthesis of carbazoles, alkaloids and other classes of pharmacologically active compounds. MMX force field calculations have shown that coplanar s-cis and. s-trans conformations of 3-vinylindole (84, Figure 2.11) are the most stable conformers they exhibit only slight differences in their thermodynamic stabilities [86]. 

Another concept that may cause confusion is that of stability. Here, the term thermodynamic stability is used in relation to populations, while the term kinetic stability is used in relation to average lifetimes. Thus, the thermodynamically most stable conformer is the most populated one, while the kinetically most stable conformer is the one with the longest average lifetime. Whether these are necessarily the same is discussed on the basis of the examples. 

L. Zheng and J.D. Brennan, Measurement of intrinsic fluorescence to probe the conformational flexibility and thermodynamic stability of a single tryptophan protein entrapped in a sol-gel derived glass matrix. Analyst 123, 1735-1744 (1998). 

In c-Hxn solutions the nucleation behavior is similar to that in EtOH solutions. It is presumed that the concentrations of conformer regarding to the A and B form are competitive and the nucleation process of the polymorph is determined by the supersaturation and the kinetic process. On the other hand in MeCN solutiorrs orrly the stable form nucleates. In MeCN solution it is considered that the thermodynamic stability of the meta-stable form is extremely low due to the large solvent-solute... 

All these methods have found applications in theoretical considerations of numerous problems more or less directly related to solvent extraction. The MM calculated structures and strain energies of cobalt(III) amino acid complexes have been related to the experimental distribution of isomers, their thermodynamic stability, and some kinetic data connected with transition state energies [15]. The influence of steric strain upon chelate stability, the preference of metal ions for ligands forming five- and six-membered chelate rings, the conformational isomerism of macrocyclic ligands, and the size-match selectivity were analyzed [16] as well as the relation between ligand structures, coordination stereochemistry, and the thermodynamic properties of TM complexes [17]. 

The cavitands are essentially synthesized from their resorc[4]arene precursors which are readily obtained by resorcinol condensation with aldehydes. The main feature comes from the different configurations that are expected for this tetrameric species and the relative thermodynamical stability of each isomer, which has been widely investigated by several authors. In addition, the conformational mobility of the resorc[4]arene molecules will depend on substitution at the upper and lower rims [28, 36, 40, 41]. The first attempt to synthesize a phosphorus bridged cavitand was to treat resorc[4]arene la (1, R=CH3) with phenylphosphonic dichloride or phenylphosphonothioic dichloride. Only inseparable isomer mixtures were obtained and isolation of the desired cavitands was not possible [42]. The first isolated phosphorylated resorcinol-based cavitand was described in 1992 by Markovsky et al., who prepared compound D from la and four equivalents of o-phenylenechlorophos-phate in the presence of triethylamine [43, 44]. For this compound, a tautomeric temperature and solvent dependent equilibrium exists between the spirophosphorane structure and the cyclic phosphate form (Scheme 4). 

The approximately 2 1 preference for the p anomer is consistent with our knowledge of conformations in six-membered rings (see Section 3.3.2) this anomer has the variable hydroxyl in a more favourable equatorial position. Note that the difference in thermodynamic stability is not sufficient to force the equilibrium completely in favour of the P anomer, and it is perhaps unexpected that there is quite so much of the a anomer present at equilibrium. We shall return to this topic, the anomeric effect, in Section 12.4. 

Both monensin (24) and nigericin (25) complex Na+ and K+ strongly but not selectively. The crystal structures of the Na+, Tl+ and Ag+ complexes all show the metal ion to be in an O-rich cavity. The carboxylate group is not involved however.97 With the antibiotics (26), (27) and (28) the thermodynamic stabilities (Table 9) are greater for the divalent than for the monovalent metal ions.98 The conformations adopted in these complexes axe very solvent dependent, and the implication of these to the biological transportation of the cations has been discussed.99... 

As a result of the branched chain architecture, TASP molecules exhibit some unique conformational properties)5 12-14 47 75 76 148 For example, the folding to a compact state proceeds via two distinct steps the onset of secondary structure in the attached peptide blocks followed by their template-directed self-assembly to a three-dimensional packing topology. Due to its characteristic branched chain connectivity, the conformational space accessible in the unfolded state is considerably reduced compared to a linear chain of similar size (excluded volume effect), resulting in a smaller chain entropy. Thus, folded TASP molecules are expected to show higher thermodynamic stability compared to unbranched polypeptides of comparable size. 

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