Optimized conformation

Fig. 3. Projections on the (<1>, maps of the CICADA conformational search of the pentasaccharide. The dots indicate the values of all the optimized conformations determined by CICADA at each glycosidic linkange in 8 kcal/mol energy window For comparison, the isocontours, drawn in 1 Kcal/mol steps with an outer limit of 8 kcal/mol, represent the energy level of each disaccharide and calculated with the relaxed grid search approach. Dashed regions represent the locations of the low energy conformation of the pentasaccharide plotted on the potential energy surfaces of the constituting disaccharide segments...

The first step in the DG calculations is the generation of the holonomic distance matrix for aU pairwise atom distances of a molecule [121]. Holonomic constraints are expressed in terms of equations which restrict the atom coordinates of a molecule. For example, hydrogen atoms bound to neighboring carbon atoms have a maximum distance of 3.1 A. As a result, parts of the coordinates become interdependent and the degrees of freedom of the molecular system are confined. The acquisition of these distance restraints is based on the topology of a model structure with an arbitrary, but energetically optimized conformation. 

MP3 optimized conformations of the pyrimido[l,6-c][l,3]oxazine 285 ( = 1) were calculated to see structural similarities with thymidine <1996NN1481>. 

Figure 4.83 Optimized conformers of W2H10, showing (a) staggered (

In the four sets of 324 points calculated, structures failed to optimize properly 37 times. Figure 6e shows the locations and the numbers of those models. All < ), P points that corresponded to improperly optimized conformations, when tested with other starting models, gave optimized energies at least 10 kcal above the minimum. 

FIGURE 23. (a) B3LYP/6-31G optimized conformation for Af-methoxy-W-dimethylaminoform-amide (214) (b) Newman projection along the N—N bond... 

Critical periods are those in which the synaptic circuitry of a given brain region becomes stabilized in a functionally optimized conformation. The cerebral cortex and other brain structures contain functional maps for the activities characteristic of a species. The best example is the ocular dominance columns and other physical and functional characteristics of the circuitry within the visual cortical system that process information derived from the left and right visual fields, producing a map of the visual world. Other internal maps exist for the body (somatosensory, motor corti-... 

It is assumed that the receptor, when complexed with Hsp90, Hsp56 and p23, is fixed in an optimal conformation for hormone binding. The activation of the receptor by the hormone requires the presence of Hsp90, which binds the receptor as a dimer. Hsp90... 

Fig. 9A,B. Space-filling models optimized conformationally A for 8 B for a complex of 8 with Naphthol Yellow S. Two macrocyclic rings of the host are removed for simplicity to show coiiformational change in the binding moieties of 8 (Taken from [44])...

The insertion of a protein within a membrane not only stabilizes the optimal conformation for the enzyme activity, but also limits the possible conformations it may undergo. Thus, assuming a mechanism for the enzymatic activity, where the underlying assumption is that the conformational fluctuation controls the chemical reaction, a decrease in the number of degrees of freedom for the enzyme increases its probability for... 

Saturated six-membered rings are the most common ring systems in nature because they present an optimal conformational situation. As seen in cyclohexane, die molecule adopts a puckered shape called a chair conformation in order to avoid angle strain in the ring bonds. In the chair form, all bond angles are 109° and all the bonds are staggered. 

Scheme 2.8 Optimized conformational geometry of the repeating unit of P4THPMA (From ref. [38])...

Conformational changes during lateral diffusion to the receptor site within the bilayer. In some cases the optimal conformation of the drug may be formed only within the lipid environment. 

Cis diastereoselectivity can be explained by using the Griesbeck rule on the possible triplet biradicals formed in the reaction. Steric interactions are minimized when the biradical assumes the optimal conformation, and this conformation accounts for the formation of the observed stereoisomer [84]. When chiral allylic alcohols were used as substrates in the reaction, cis diastereoisomers were formed. Furthermore, also in this case, a pronounced threo diastereoselectivity was observed, in agreement with a less pronounced hydroxy-directing effect when acetophenone and benzaldehyde were used [79, 84]. Chiral allyl ether gave the corresponding adduct with high diastereoselectivity [85]. 

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