Oligomers conformers

Isomer ratios for oligomers Conformer ratios in oligomers... 

Raman spectra were taken of duplex oligomers with the sequences, 15 -d(TN(CG)8AN)J2 in aqueous 6M NaCl solutions. These oligomers showed the presence of two B/Z junctions. Molecular modeling was used to show that the oligomer conformation went abruptly from the B to the Z form and from the Z back to the B form inside die (CG)g tract. 

The specific effects of hydration on monomer dynamics and oligomer conformational energies have been determined for several different carbohydrates. In addition, the structuring effects of these molecules upon water have also been explored in some detail, which has not yet been done for peptides or other types of solutes. From the carbohydrate simulations... 

Oligomer conformation was evaluated by force field and semiempirical molecular orbital calculations using MM3 [83], MMFF94s [84], and COMPASS [85] force fields and a semiempirical PM5 [51] method. 

In order to obtain information on the poly(PDBF) molecular structure, molecular dynamics (MD) simulations were performed for a PDBF 20-mer model created on the basis of the DBF oligomer conformation in crystal (see X-ray Crystal Analyses section) under a constant NVT condition with COMPASS force field at 300 K for 8.6 ns. The simulation afforded the structure shown in Fig. 40 in which the neighboring fluorene moieties stack on top of each other in a chiral, slightly twisted arrangement. The entire chain formed a relatively long-pitched helical structure in the simulation. Hence, the local twist and the helix may contribute to the CD spectra. 

Ah initio calculations of polymer properties are either simulations of oligomers or band-structure calculations. Properties often computed with ah initio methods are conformational energies, polarizability, hyperpolarizability, optical properties, dielectric properties, and charge distributions. Ah initio calculations are also used as a spot check to verify the accuracy of molecular mechanics methods for the polymer of interest. Such calculations are used to parameterize molecular mechanics force fields when existing methods are insulficient, which does not happen too often. 

Polymers can be crystalline, but may not be easy to crystallize. Computational studies can be used to predict whether a polymer is likely to crystallize readily. One reason polymers fail to crystallize is that there may be many conformers with similar energies and thus little thermodynamic driving force toward an ordered conformation. Calculations of possible conformations of a short oligomer can be used to determine the difference in energy between the most stable conformer and other low-energy conformers. 

In 1965, Jacques Monod, Jeffries Wyman, and Jean-Pierre Changeux proposed a theoretical model of allosteric transitions based on the observation that allosteric proteins are oligomers. They suggested that allosteric proteins can exist in (at least) two conformational states, designated R, signifying relaxed, and T, or taut, and that, in each protein molecule, all of the subunits have the same conformation (either R or T). That is, molecular symmetry is conserved. Molecules of mixed conformation (having subunits of both R and T states) are not allowed by this model. 

Starting from the assumption that the geometry relaxation after excitation is of primary importance with respect to the luminescence response, we decided to employ a solid polymer matrix to suppress conformational changes of the oligomers. For the measurements, dilute blends with polysulfone as the transparent host matrix were prepared. In Figure 16-13, the PL decay curves for the two cyano compounds in both chloroform and polysulfone are presented, as are the PL spectra of Ooct-OPV5-CN in chloroform and polysulfone [69J. 

Alzheimer s Disease. Figure 1 A(3 monomers can self-associate to form dimers, trimers and higher oligomers. Globular structures of synthetic A(342 are known as A(3-derived diffusible ligands (ADDLs) (3-12-mers of A(3). These structures are similar to the smallest protofibrils and represent the earliest macromolecular assembly of synthetic A(3. The characteristic amyloid fiber exhibits a high beta-sheet content and is derived in vitro by a nucleation-dependent self-association and an associated conformational transition from random to beta-sheet conformation of the A(3 molecule. Intermediate protofibrils in turn self-associate to form mature fibers. 

The cyclic dimer, tetramer, and hexamer can be crystallized in acetonitrile, and also in chloroform (the former two oligomers). X-ray analysis of the crystals of the cyclic dimer47 disclosed that it consisted of a pair of different enantiomers of 53 and that all of the four substituents attached to the two tetrahydropyran rings occupied the axial position as illustrated in Fig. 54s). Such a conformation is in... 

Patch, ).A., Wu, C.W., Sanborn, T.J., Huang, K., Zuckermann, R.N., Barron, A. E., and Radhakrishnan, I. A peptoid oligomer with a unique, cyclic folded structure and a solvent-depend conformational switch. (Manuscript in preparation). 

Fig. 2.45 Preferential conformation ofa-ami-noxy peptide oligomers. (A) Formulae of oli-go(a-aminoxy acid) 170 and 171 studied by the combination of NMR and CD as well as a summary of key NOEs in 171 observed by ROESY in CDCI3. (B) Theoretical model generated by ab-initio quantum-mechanical calcula-...

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