Evaluation of Computational Chemistry Methods: Crystallographic and Cheminformatics Analysis of Aminothiazole Methoximes.

Exploration of the Conformational Space of a Polymeric Material that Inhibits Human Immunodeficiency Virus

“…We built the initial structure of the trimer by appropriately linking three monomer units of the ATMO model from our previous work. 21 The amide was placed in a trans configuration and the oxime in an E configuration. 38 In future work, we would like to examine other configurational possibilities for the polymer model.…”

“…Since all the new dihedral angles in the pentamer structure showed a large variation, we put constraints on the torsions according to the tetramer distribution analysis. Fifteen rotatable bonds (1,4,5,7,9,(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) were marked for exploration. Distribution analysis results from JMP revealed that most of the conformers had dihedral angle 18 near 87°, dihedral angle 19 near 74°, dihedral angle 20 near -48°, dihedral angle 21 near 157°, dihedral angle 22 near -85°, dihedral angle 24 near 84°, dihedral angle 25 near 4°, dihedral angle 26 near 143°, and dihedral angle 27 near 170° (Figure 7).…”

“…21 The two force fields performed about equally well. We selected the MMFF94 force field as Other molecular modeling programs including SYBYL, Spartan, Cerius2, and InsightII/Discover were also examined but were not as useful for meeting our needs of (1) running conformational searches of organic molecules with up to 400 atoms and many rotatable bonds, (2) using the MMFF94 force field, (3) selecting some torsional angles to be free to rotate but constraining others, and (4) analyzing the results from the conformational searches and being able to export the results to other programs for further analysis.…”

A curious conformational property of 2-amino-4-thiazolyl-methoxyimino polymers exhibiting activity against HIV-1 reverse transcriptase

“…This force field was developed from ab initio calculations on model systems and was designed to treat pharmaceutically interesting molecules. Earlier work showed that this force field performs well on the ATMO system, yielding optimized bond lengths and bond angles in good agreement with crystallographic data for ATMOcontaining cephalosporins [28,41]. To help ensure that the structures in our buildup procedure were as close as possible to an equilibrium geometry, energy minimizations were run twice on each structure.…”