Conformation comparing

Fig. 7.5 Illustration of how dispersion forces affect gauche (G) conformations. Compared to structures with gauche forms devoid of dispersion forces (i.e., HF-optimized), structures with gauche forms subject to dispersion forces (MP2 optimized) contract in such a way that the 1. ..5 nonbonded interactions in an attractive part of the van der Waals potential are shortened. Thus, in GG-pentane (shown above), MP2-optimized torsional angles are contracted by several degrees compared to the HF-optimized geometry, causing a reduction in the 1...5 nonbonded distances by several tenths of an A. For additional details and the numerical values see R. F. Frey, M. Cao, S. Q. Newton, and L. Schafer, J. Mol. Struct. 285 (1993) 99.

The planar Haworth projection formulae bear little resemblance to the shape of the six-membered pyranoses that actually adopt a non-planar ring conformation comparable to that of cyclohexane. The chair form is the most... 

ATP binds to the inhibitor site only when the protein is in the T form. In occupying the inhibitor site, ATP locks the enzyme in the inactive conformation, preventing binding of F6P (Figure 3.10). Overall, the cytosolic ratio of ATP-to-AMP ratio determines the proportion of PFK-1 in the R conformation. Compare with the effect of the ATP-to-ADP ratio on HK above (Section 3.3.1.1)... 

It is difficult to prepare stretched oriented fibres and such fibres may differ in their polymer chain conformation compared with the unstretched materials. Furthermore the quality of the single crystal X-ray data is poor and difficult to interpret. In contrast power X-ray data of relatively high quality may be obtained from polycrystalline polymer films. Lightfoot, Mehta and Bruce (1992) have obtained the first crystal structure of a polymer-salt complex, PEOjiNaClQ from powder X-ray data. Fig. 5.11(h). The structure is similar to the corresponding PEOjiNal structure, the PEO chains are wrapped around the Na ions with each Na ... 

Spherical polar coordinates are used for conformational representation of pyranose rings in the C-P system. Unlike the free pseudorotation of cyclopentane, the stable conformations of cyclohexane conformers are in deeper energy wells. Even simong the (less stable) equatorial (6 = 90 ) forms, pseudorotation is somewhat hindered. Substitutions of heteroatoms in the ring and additions of hydroxylic or other exocyclic substituents further stabilize or destabilize other conformers compared to cyclohexane. A conformational analysis of an iduronate ring has been reported based on variation of < ) and 0 (28), and a study of the glucopyranose ring... 

The polarographic oxidation potentials of some methyl-substituted hexahelicenes were determined to investigate whether the more facile oxidation of 1,16-dimethyl-hexahelicene is due to the change in conformation compared to hexahelicene or to the electronic effect of the methyl groups 138). It was found that both 3,14-dimethyl-and 1,14-dimethylhexahelicene have the same oxidation potentials (e1/2 (1st wave) = 1.23 V e1/2 (2nd wave) = 1.45 V), whereas their conformations are different24). 

Biopharmaceuticals based on natural proteins and peptides are often called by the same name as the biologic natural material despite differences in one or more amino-acid residues. For example, insulin, which regulates blood glucose and is used clinically to treat type 1 diabetes and some cases of type 2 diabetes, has several variants that are approved for human use. Insulin contains two polypeptides, A and B chains (Figure 1.2), that are linked together by two disulfide bridges to assume a biologically active conformation. Compared with human insulin, insulin extracted from beef tissue exhibits threonine alanine and isoleucine valine substitutions at posi-... 

Three cytotoxic peptides, patellamide D (31) and lissoclinamides 4-5 (32-33) were isolated from a Great Barrier Reef specimen of L. patella and identified by interpretation of spectral data. The peptides were found within the obligate algal symbiont of the genus Prochloron [65]. Another study of the same Australian L. patella reported lissoclinamide 6 (34), in addition to lissoclinamides 4-5 (32-33) and patellamide D (31). The structure of patellamide D (31) was obtained by X-ray crystallography and its conformation compared with those obtained by molecular modelling [66]. Patellamide D (31) has been reported to be a... 

An acyclic molecule has more entropy than a similar cyclic molecule because there are more conformations (compare hexane and cyclohexane). Ring opening therefore means a gain in entropy and ring closing a loss. 

The deoxyribose moiety of the 5 guanine has adopted an almost pure N-type conformation, compared to the S-conformation in free d(GpG). 

Begin by writing each of the compounds in its most stable conformation. Compare them by examining their conformations for sources of strain, particularly van der Waals strain arising from groups located too close together in space. 

A conformational comparative study has been performed on a penem, a carbapenem, and a 1/3-methylcarbapenem, bearing the same C-2 and C-6 side chains, using both NMR and theoretical tools. The corresponding calculations have been performed at the 3-21G level using the ab initio MO method, while 111 NMR measurements and nuclear Overhauser effect (NOE) enhancements were carried out in DzO solution. It arose from this study that there are conformational differences in the side chains of these three compounds in the physiological environment in particular, the conformation of the C-6 side chain in the penem appears to be different from that in the carbapenem <1998BMC367>. 

More recently, additional 2H "I J REDOR measurements on new PTX derivatives bound to MT provided three new interatomic distances that helped to define more precisely the bound conformation of PTX [87], The two PTX analogues labeled with fluorine and deuterium were designed to determine the three key distances based on the measurement of 2II— "I distances, as indicated in Fig. 9 (compounds 4 and 5). These interatomic distances rule out the polar and nonpolar conformers and further support the T-taxol conformation (Tablel). The polar conformation is rejected on the basis of distance IV, as the 4.5 A is much shorter than the > 8 A determined by REDOR. The nonpolar conformation can be ruled out on the basis of distances I and II, that are too short in the nonpolar conformer compared to the experimental ones (1.8 and 3.6 A short). Besides, bridged taxanes resembling the nonpolar conformation displayed no activity in the tubulin assembly assay [88], PTX-NY closely matches the REDOR distances. Nevertheless, it is discarded as the bioactive form of PTX due to its poor fit to the EC density [87],... 

Draw alkane conformations, compare their energies, and predict the most stable conformations. 

In this case, the endo-254 product is formed. The authors explain the stereochemistry through a transition state 255 that has a boat conformation. Comparing transition states 251 and 255, it is clear that, besides allowing complexation of the lithium atom with the 7i-system, the coordination of the lithium atom with the non-bonded electrons of the N is also favored. In both states, the N is located on the same side of the it-system. It could be presumed that the isomer which gives the more favorable transition state is mainly determined by the position of the N in the bicyclic ring. 

Procyanidin oligomers [(4a) n = 0 to 10] apparently possess mainly linear conformations, compared with the proven angularity of profisetinidin and prorobinetinidin analogues (2) and (3). 

Thermodynamic calculations, based on integrated intensity measurements, show that the crown form has the lower enthalpy, and also the lower entropy (.dS =8.5 ) or 6 2 eu ). The low entropy of the crown finds an explanation in the high symmetry of this conformation, compared to the low symmetry of the boat-chair. The best boat-chair for tetroxocane appears to be the BC-1,3,5,7 conformation. However, the ether functions at positions 3 and 7 have their dipoles close together in an unfavorable orientation but... 

The staggered conformations (1, 3, and 5) are lower in energy than the eclipsed conformations (2, 4, and 6), but how do the energies of the individual staggered and eclipsed conformations compare to each other The relative energies of the individual staggered conformations (or the individual eclipsed conformations) depend on their steric strain. 

---