Conformational family

Quenched dynamics is a combination of high temperature molecular dynamics and energy minimization. This process determines the energy distribution of conformational families produced during molecular dynamics trajectories. To provide a better estimate of conformations, you should combine quenched dynamics with simulated annealing. 

Table 2 Conformational Families Derived from CICADA...

Figure 22 Positioning of the Tyr8 phenol ring (colored stick structures) relative to the Ni11 (purple sphere) and its chelate ring (ball-and-stick structure). The lowest-energy representatives of conformational families 1-3 are shown in blue, green, and yellow, respectively. The phenol oxygen is a red sphere.1747...

The next linear diamine, 1,3-propanediamine (PDA), was also studied by the same force fields. Four conformational families were considered and defined by the two... 

FIGURE 7. The lowest-energy form of each of the conformational families of perhydroazepine 66 as calculated by MM2 and MM3 (MM2 relative energies in parentheses)... 

Fig. 10 a MD-tar ensembles of conformers for 2-4. The experimental ensemble corresponding to 1 in the free state (reft) is shown for comparison, b Structures representative of the main conformational families present in solution for neomycin-B derivatives 2 (left) and 3 (right) superimposed on the X-Ray structure of paromomycin in the complex with ribosomal RNA, according to X-Ray data. The maximum 4>/ U deviations (for each glycosidic linkage) is shown. Unit IV is omitted for simplicity... 

Medium-sized and large ring systems often show complicated conformational interconversions involving pseudorotations in one or even more conformational families. This makes stereochemical assignments in diastereomers rather difficult. Thus, very few systematic studies have been published. The situation is improved if such rings are embedded in polycyclic systems, or if they contain double bonds, which leads to restricted conformational mobility. An example is the differentiation of diastereomeric 2,3-dihydro-lf/-benzo[6]azepines 1 on the basis of y-gauche effects and on d(13C) and 3/H H values640. 

Having seen that differences between crystal and solution conformations can exist for small molecules, we now turn to the consideration of proteins. First, we must differentiate between those proteins that crystallize and those that do not. Proteins that crystallize are usually globular, whereas those that do not are often nonglobular and are unlikely to conform to a single conformational family. These may be compared to industrial organic polymers such as those used in the plastics industry. 

The absence of Bohlmann bands in the infrared (IR) spectrum indicates that the nitrogen lone pairs of the di-iV-nitroso-l,4-diazepines 23 are delocalized <1995JOC7461>. While the absence of an amide moiety in the ring confers torsional freedom, the m-2,7-di-Ph groups reduce ring flexibility and the 111 NMR data are consistent with major and minor families of four twist chair conformers that project the C-7 Ph and C-6 R -substituents equatorially These interconvert by a pseudorotation that allows the C-2 phenyl and C-3 R substituents to adopt a pseudoaxial orientation in the preferred conformer family. 

The ramifications of the different conformational natures of 166-176 and other similar analogues on biological activity may be a promising area of future exploration. As a preliminary approach, a comparison of the low-energy conformers predicted by molecular mechanics and two-dimensional NMR data are under analysis. A possible correlation with conformational families of these flexible analogues and the antimalarial activity is under examination. 

The racemic mixture of 36 crystallized as a racemic compound in an achiral space group crystal. Analysis of its X-ray crystallographically determined structure shows one of the enantiomers to have a reference,S)-TCBtype33 conformation as depicted in the iconic drawing for 36 (see Fig. 19). Conformational families exist for cis-3 or trans-44 cyclononenes. The various members of a family maintain similar torsion angles for six of the nine bonds compared to those measured for their cyclononane saturated parent.3 Double bonds are formed from either synclinal or antiperiplanar-type bonds in the parent. Conversion of a single bond to a double bond will usually... 

Semi-empirical and molecular mechanics calculations have been widely used in the study of eight-membered heterocycles with three heteroatoms. Theoretical studies have centered on conformations of this class of heterocines, which usually belong to four low-energy conformational families classified as boat-chair, crown, boat, and chair forms (see Section 14.08.4.2). 

Four main low-energy conformational families of eight-membered ring systems, consisting of the boat-chair, crown, boat, and chair forms, were surveyed in CHEC-II(1996). They are discussed in the foregoing sections of this chapter in conjunction with the theoretical and experimental structural studies of triheterocines (see sections 14.08.2 and 14.08.3). 

The monomers exceeding 35 per gram were removed and the 50 highest scoring components from all the conformational families were merged to create the corresponding virtual compounds (g, Fig. 5.30). The compounds were clustered (h. Fig. 

The work described by Deadman et al. [100] considered a subset of the above set of thrombin inhibitors. A training set of 16 homologous nonpeptide inhibitors whose conformations had been generated in continuum solvent (MacroModel) and clustered into conformational families (XCluster) was regressed against this pharmacophore so as to obtain a 3D-QSAR mode. 

The least known conformational family is the boat-boat. It seems that a very special substitution pattern is required to make conformations in this family more stable than those of the crown and boat-chair. Highly fluorinat-ed cyclooctanes possibly exist in the twist-boat or boat-boat conformations however, additional evidence is badly needed to support the conformational assignments which have been made. A boat-boat conformation (in the cyclooctane nomenclature) does occur in [3.3.1]bicyclononane, which contains a 1,5-bridged cyclooctane ring. 3)... 

Fig. 2 Low-energy PF8 conformations (referenced to the Cp isomer). Each symbol corresponds to a single, unique tested conformation. Ca, Cp, and Cy correspond to the conformer families. The inset shows the model of the Cp isomer highlighting side chains. Reprinted with permission from [17]. (2005) by the American Physical Society...

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