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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