COMPARE-CONFORMER

A cluster analysis requires a measure of the similarity (or dissimilarity) between pairs of objects. When comparing conformations, the RMSD would be an obviou.s measure to use. 

Sources, which compare conformation search algorithms are... 

Schwinefus, J.J., Hammond, R.W., Oana, H., Wang, S.-C., De Carmejane, O., Bonadio, ]., and Morris, M.M., Comparative conformational dynamics of su-percoiled plasmids and linear DNA during capillary electrophoresis, Macromolecules, 32, 4625, 1999. 

Srivastava et al. carried out a complete study of the vibrational spectrum of acetylglycine, and evaluated its relation to the spectrum of acetylcholine [13]. A normal coordinate analysis of acetylglycine was carried out using the Wilson s GF matrix method. Vibrational frequencies were assigned, and the infrared spectra of acetylglycine and acetylcholine compared. Conformation-sensitive modes of acetylcholine were identified, and a transferable Urey-Bradley force field was also obtained. 

Q Use Newman projections to compare conformational energies and predict the most stable conformation. Show how the torsional energy varies as the dihedral angle changes. Problems 3-38,42, 46, and 47... 

There is evidence that the a-cyclodextrin macrocycle can adjust its cavity diameter, within certain limits, to accommodate either two hydrate water molecules in the collapsed or tense form, or a nonaqueous guest molecule in the round or relaxed form. This is the concept of the induced fit [576] which has been applied to comparable conformational changes observed with several enzymes upon substrate binding. 

In conclusion, we were able to design AChE inhibitors based on the docking and GRID/GOLPE study which seems to interact simultaneously with the cation-re subsite of the catalytic site and the peripheral site of the enzyme. Eurther support for our docking study came from the crystal structure of a novel Ach E-inhibitor complex [78]. The crystal structure of AChE complexed with the marketed drug donepezil was solved in 1999. Like donepezil, our most potent inhibitors contain a benzylpiperidine moiety which shows a similar position and orientation when compared with the published crystal structure. The comparison of both AchE-inhibitor complexes revealed that both kind of inhibitors adopt a comparable conformation in the narrow binding pocket [12]. As we predicted for our ami-... 

VIBRATE (normal modes), VOID (protein packing), and mdXvu (visualization of AMBER trajectory files). QCPE has also accepted the responsibility to distribute semicommercial academic software, such as MM2, MM3, MOPAC 93, POLYRATE, PEFF, and COMPARE-CONFORMER. Most programs in library are in FORTRAN and are available as source code. Current catalogs and information are available by anonymous ftp from qcpe6.chem.indiana.edu (129.79.74.206). Many of the programs run on several hardware platforms, including DEC VAX, IBM, Silicon Graphics, Stardent, Sun, Fujitsu, and Cray. 

Verheyden P, De Wolf E, Jaspers H, and Van Binst G. Comparing Conformations at Low Temperature and at High Viscosity. Conformational Study of Somatostatin and Two of its Analogues in Methanol and in Ethylene Glycol. Int J Peptide Protein Res 1994b 44 401—409. 

While nuclear magnetic resonance spectroscopy has become an invaluable tool in lignin analysis, relatively little effort has been directed toward the calculation of such spectra for lignin model compounds. Liptaj et al. [68] compared conformational data for cinnamaldehyde models derived from NMR to calculation, and similar work on quinone methides at both semiempirical and ab initio levels has been reported by Konschin et al. [69]. 

Figure 6 A semi-rigid analog, 13, of isoproterenol is a potent 3-adrenergic agonist. A comparable conformation of 2-F-NE has the hydroxyl group oriented away from fluorine.

Ab initio calculations of rotational barriers of single bonds between elements of group 14 predict a linear relationship between the bond lengths and the barrier, for instance for the series H3SiXH3 with X = C, Si, Ge, Sn and Pb [1]. The barriers decrease from about 6.7kJ/mol for Si-C to about 3.8 for Si-Si and 1.7 kJ/mol for Si-Pb bonds. For the spectroscopist interested in molecular conformations, barriers that lie well above RT at room temperature (2.48 kJ/mol) support the expectation that the interconversion of rotamers will be slow on the time scale typical for Raman vibrational spectroscopy (= lo sec) and that the rotamers can be distinguished by their individual vibrational spectra. It is our objective to compare conformational stabilities of carbosilanes (Si-C bonds) with those of disilanes (Si-Si bonds) bearing identical substituents. Fore this purpose, we have prepared the title compounds 1-4 and investigated their conformational compositions by variable temperature Raman spectroscopy. 

The intrinsic free energy of the solute molecule is dominated by the terms which are included in Equation (2) below. Here we made an implicit assumption that we compare conformations whose rotational entropy differences are not significant. 

A similar situation prevails when we compare conformations of cyclic ethers with those of the corresponding cycloalkanes. For example, tetrahydropyran, the ether analog of cyclohexane, exists in a chair conformation. Following predictions of VSEPR theory, the two oxygen lone pair electrons are shown in positions corresponding to the axial and equatorial C —H bonds of cyclohexane. The conformation of tetrahydropyran is particularly important because many carbohydrates, such as glucose, exist as six-membered tetrahydropyran rings. 

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