E/Z Energetics for Molecular Modeling and Design

18 Июн 2015 | Author: | No comments yet »


Abstract

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.

Introduction

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 carboxylic acids, aldehydes, or such as esters, carbamates, ureas, amidines, hydrazones, and The importance of these functional is enhanced by their common in combinatorial libraries, commercial collections, and in molecules of pharmacological

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 pursued energetic through reliable quantum calculations on prototypical molecules E and Z conformers. The findings are also as a basis for the improvement of scoring for docking software, 7 the refinement of structures, and development of molecular force fields for use in modeling and biomolecular systems. 8. 9

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

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