Synthetic examination of incorrectly proposed structures of biomolecules

Many incorrect structures of biomolecules have been proposed for natural products. Synthesis of compounds having the proposed structures often enabled us to judge the correctness of the proposals. In some cases, we were able to revise the structures by synthesizing the biomolecules themselves. In other cases, we were able to definitely disprove the proposed structures. Some examples treated in this review include: auxin-a and b; the sex pheromone of Chlamydomonas; sex pheromones of the gypsy moth, the American cockroach, and the pink bollworm moth; Persoons' periplanone-A; orobanchol; naurol A; bifurcarenone; koninginin A; alpha-acoradiene; himachalene-type pheromones of the flea beetle; differolide; blattellastanoside A and B; etc.     

Molecular dynamics (MD) simulations and large-angle X-ray scattering (LAXS) studies of the solid-state structure and assembly of isotactic (R)-poly(2,2'-dioxy-1,1'-binaphthyl-)phosphazene in the bulk state and in the cast film

The intrachain conformation, molecular structure and interchain assembly of isotactic (R)-poly(2,2'-dioxy-1,1'-binaphthyl)phosphazene (P-DBNP) both in the bulk state (I) and in the cast film (II) were studied by molecular dynamics (MD) simulations of models, as implemented by a bias potential for the analysis of the radial distribution function (RDF) obtained from large-angle X-ray scattering (LAXS) data. The microscopic structure and order extension of the polymer changed from I to II, as qualitatively shown in the shapes of their experimentally measured RDF curves. With the use of a bias potential, the MD simulations provided a much more accurate analysis of the models, as seen in the reproduction of the RDFs. The chiral P-DBNP chain was found to be consistent with helix conformations in both the I and the II samples. The predominant interchain clustering motif was best reproduced with a seven-chain model. In the case of I, the maximum chain length was 18 monomeric -R(2)NP- units, while in the case of the cast film II the chain was more elongated, up to distances of approximately 100 A, equivalent to over 48 monomeric -R(2)NP- units. The seven-chain assembly was accounted for in terms of nonbonded interactions favouring the minimum voids area between the seven tubular structures of the material. The results validate our earlier finding that MD analysis with implementation of a biasing potential for the RDFs can provide quantitative information on the structural and conformational features of amorphous solids. The combined theoretical and experimental approach was found to be a useful tool to detect, locate and evaluate the intra- and intermolecular modifications of materials subsequent to their phase transformation and, as in the present case, changes in their microscopic structures or preparation methods.