Examination of the Conformational Properties of the Prymnesin System: A Computational Chemistry Approach

Bulletin of the Chemical Society of Japan

Volumn 69, Issue 8, 1996, Pages 2253-2263

  Glendenning, Lionel ^a   Igarashi, Tomoji ^a,b   Yasumoto, Takeshi ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b JAPAN FOOD RESEARCH LABORATORIES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000334827     PISSN: 00092673     EISSN: None     Source Type: Journal    
DOI: 10.1246/bcsj.69.2253     Document Type: Article

References (35)

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13. For a paper which describes a similar method to the random torsional searching technique used in this study see: D. M. Ferguson and D. J. Raber, J. Am. Chem. Soc., 111, 4371 (1989).
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16. Parameters apply to the "D" ring random torsionally searched in this study as part of the fragments "C/D/E" and "A/B/C/D/E" as described in the text.
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20. A variety of conformational searching techniques for cyclic systems have been examined and compared in: a) M. Saunders, K. N. Houk, Y.-D. Wu, W. C. Still, M. Lipton, G. Chang, and W. C. Guida, J. Am. Chem. Soc., 112, 1419 (1990); and b) H. Goto and E. Osawa, J. Chem. Soc., Perkin Trans. 2, 1993, 187 c) A. 'R. Leach, in "Reviews in Computational Chemistry," ed by K. B. Lipkowitz and D. B. Boyd, VCH Publishers, New York (1991), Vol. 2, Chap. 1, pp. 1-55.
21. A variety of conformational searching techniques for cyclic systems have been examined and compared in: a) M. Saunders, K. N. Houk, Y.-D. Wu, W. C. Still, M. Lipton, G. Chang, and W. C. Guida, J. Am. Chem. Soc., 112, 1419 (1990); and b) H. Goto and E. Osawa, J. Chem. Soc., Perkin Trans. 2, 1993, 187 c) A. 'R. Leach, in "Reviews in Computational Chemistry," ed by K. B. Lipkowitz and D. B. Boyd, VCH Publishers, New York (1991), Vol. 2, Chap. 1, pp. 1-55.
22. A variety of conformational searching techniques for cyclic systems have been examined and compared in: a) M. Saunders, K. N. Houk, Y.-D. Wu, W. C. Still, M. Lipton, G. Chang, and W. C. Guida, J. Am. Chem. Soc., 112, 1419 (1990); and b) H. Goto and E. Osawa, J. Chem. Soc., Perkin Trans. 2, 1993, 187 c) A. 'R. Leach, in "Reviews in Computational Chemistry," ed by K. B. Lipkowitz and D. B. Boyd, VCH Publishers, New York (1991), Vol. 2, Chap. 1, pp. 1-55.
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24. -1 (Tripos force field).
25. 5 = 243 low energy conformers for the "E to N" backbone.
26. -1 barrier to rotation between the +G and -G conformers, clearly indicating that there is a lower energy pathway between the +G and A conformers (and vice versa).
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31. 5N, the pyridine component of which may serve to destabilize the intramolecular π-stacking interaction of the lowest energy conformations found in vacuo.
32. The mathematical formulae which describe the planes discussed in the text to this paper and referred to in Table 5 and Ref. 24 are as follows: The plane which passes through the "seat" section of the "A" ring and is defined by the atoms C20, C21, C23 and C24, can be described by the equation: 7.133e-02x -8.805e-01y -4.687e-01z -2.275e+01 = 0 (RMS distance of defining atoms from plane =±0.01 Å) for the "A to N" energy minimized fragment. The plane which passes through the "seat" section of the "E" ring and is defined by the atoms C33, C34, C36, and C37, can be described by the equation: 5.917e-01x -6.610e-01y -4.616e-01z -2.268e+01 = 0 (RMS distance of defining atoms from plane = ±0.004 Å) for the "E to N" energy minimized fragment. The plane which passes through the "seat" section of the "N" ring and is defined by the atoms C70, C71, C73, and C74, can be described by the equations: -8.653e-01x -4.746e-01y -1.612e-01z -1.462e+01 = 0 (RMS distance of defining atoms from plane = ±0.0008 Å) for the "A to N" energy minimized fragment. -8.667e-01x-4.740e-01y-1.553e-01z-1.449e+01 =0 (RMS distance of defining atoms from plane = ±0.0009 Å) for the "E to N" energy minimized fragment.
33. Similarly, describing a plane which passes through the C70, C71, C73, and C74 atoms (ring "N") and measuring a normal to this plane which intersects the C20 atom at the "A" ring terminus of the prymnesin system suggests that the axial twist of the backbone, when viewed along the axis from ring "N" to ring "A", has deviated by approximately 17.0 Å from the "N" ring plane, implying the angular twist along the backbone is not uniform in two dimensions, i.e. the resultant "screw" secondary structure of the backbone has deviated from the true "cylindrical" axis of rotation along the prymnesin backbone "A to N" to a "conical" axis of rotation.
34. L. Stryer in, "Biochemistry", 3rd ed, W. H. Freeman and Co. (Pub.), New York (1988).
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