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Aristolochic acid II

OK I am back, I have done some molecular mechanics and I have calculated the shape of the molecule. For those of you at home with copies of ORTEP at the bottom of this post is an XYZ file.

When I looked at the results I noticed something interesting. The aromatic system was not flat. The steric repulsion between the nitro and carboxylic acid groups distorts the molecule away from being flat. This is a well known effect which can be seen in some other aromatic compounds.

I also wondered about how the compound formed by the reaction of the DNA base (plus sugar) and aristolochic acid formed. I made a check of the literature and I found that the formation of C-N bonds by the nucleophilic attack of hydroxylamine on 9-nitrophenanthrene has been reported by J. W.Barton, A. R. Grinham and K. E. Whitaker in the Journal of the Chemical Society, section C, 1971, page 1384. In this paper the authors describe the reaction of hydroxylamine with 9-nitrophenanthrene followed by loss of water. In the diagram below I have shown how the paper indicates how the reaction occurs.

How hydroxylamine reacts with a nitroarene

XYZ file : Aristolochic acid as calculated by MM (Mark Foreman 19Feb2010)
C   -0.814703    0.435274   -0.098342
C   -0.684474   -0.920933   -0.056728
C    0.528218   -1.493506   -0.234232
C    1.538614   -0.684211   -0.583191
C    1.405758    0.648962   -0.667176
C    0.272160    1.252860   -0.234820
C    0.174434    2.595703    0.012909
C   -1.042522    3.173359    0.017731
C   -2.119454    2.395795   -0.039860
C   -2.009560    1.063943   -0.030705
C   -1.691892   -1.792026    0.170843
C   -1.521458   -3.119866    0.210166
C   -0.302041   -3.631921    0.033563
C    0.758851   -2.827985   -0.146062
O   -3.282052    2.783860    0.005411
C   -4.101593    1.627484   -0.006198
O   -3.138568    0.576964    0.040095
C    1.206352    3.457775    0.311288
O    0.961644    4.636928    0.476418
O    2.472838    3.081429    0.637229
O    1.979071   -3.414490   -0.392711
C    2.786354   -3.545812    0.756370
N    2.361659    1.275470   -1.193000
O    2.181942    2.479651   -1.681695
O    3.520910    0.764647   -1.527219
H    2.498407   -1.140575   -0.871539
H   -1.230829    4.251921    0.147644
H   -2.736169   -1.510929    0.341012
H   -2.377937   -3.795286    0.379390
H   -0.170100   -4.727122    0.040240
H   -4.697020    1.572014   -0.947062
H   -4.773178    1.603757    0.883451
H    2.626845    2.135364    0.510446
H    2.288814   -4.214908    1.493778
H    3.756722   -3.996352    0.450245
H    2.976109   -2.548670    1.212039


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