E/Z Energetics for Molecular Modeling and Design

18 Июн 2015 | Author: | No comments yet »


Thermochemical data been obtained from quantum mechanical calculations for 18 organic molecules, which E/Z conformational equilibria. The results are important for molecular design evaluation of structures from docking. For the 18 E/Z pairs, relative enthalpies, free energies, and moments are reported; the E #x02013; Z differences at 298 K range from kcal/mol for 1,3-dimethyl carbamate to kcal/mol for acetone oxime. A of steric and electronic effects can the variations. Free energies of were also estimated the GB/SA continuum solvent These results indicate differential hydration is unlikely to change the preferred direction of the E/Z though further study free-energy methods using solvent is desirable.


Toyota E'z

Knowledge of the conformational of small molecules is essential in areas of chemistry including synthesis and molecular design. 1 The preferences for small molecules are to carry over to macromolecular e.g. the ca. 3 kcal/mol preference for the Z of N -methylacetamide relative to the E alternative is responsible for the rarity of cis -peptide in proteins. 2 The present study on such molecules where about a single bond to E and Z conformers that are energetically by an intervening potential-energy barrier.

amides, molecules in this include other derivatives of acids, aldehydes, or ketones as esters, carbamates, carbonates, amidines, hydrazones, and oximes. The of these functional groups is by their common occurrence in libraries, commercial screening and in molecules of pharmacological interest.

Furthermore, in seeking enzyme through de novo design or screening, 3. 4 questions often about the likelihood of E and Z conformers. For in docking studies, one is regularly with computed structures for #x02018;poses#x02019;, such as in Figure 1a. the ligand features an E or Z conformation. The with docking software is improving and such poses may well, 5 though the E -conformer for the in this case is unreasonable. 1 Or, one may be with a crystal structure, as in Figure 1b. where the thiourea is in an E, Z configuration. 6 If one thought that was an

associated energetic penalty, designs might be pursued to enhanced potency. Given such examples, we have energetic clarification through quantum mechanical calculations on molecules featuring E and Z conformers. The are also valuable as a basis for the of scoring functions for docking 7 the refinement of crystal structures, and of molecular mechanics force for use in modeling organic and biomolecular 8. 9

Toyota E'z
Toyota E'z
Toyota E'z

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