4.  Performance of Methods Used For the Methyl Orange Structure Modelling

Authors: S. Funar-Timofei


Abstract:

Methyl orange (MO) structure obtained by experimental X-ray crystallography data was previously compared by statistical analysis to the conformations of minimal energy obtained by molecular mechanics calculations using the MM2 force field and by the AM1, PM3 and DFT quantum chemical methods. Good performance was obtained by molecular mechanics, as well as by the DFT approach. This paper presents a comparison of MO structure obtained by additional molecular mechanics methods, which use the MMFF94s, MMFF and AMBER force fields, with the previously studied ones. The conformations of minimal energy thus obtained were then compared by superposition on the heavy atoms by a least-square procedure with the experimental X-ray crystallography data and, also, with the conformations obtained by the previously studied methods. Comparison of these structures was performed by the RMS value thus obtained and by the torsion angle between the phenyl rings of the MO structure. Better RMS value was noticed by the superposition of X-ray structure with the conformation obtained by DFT. The conformations derived from the AM1 semiempirical approach and from the molecular mechanics methods employing the MM, MMFF and MMFF94s force fields gave still reasonable accurate superposition results, as compared to the X-ray structure.


Keywords: methyl orange, Omega, Hyperchem, MMFF94s, MMFF, Amber

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