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Efficient conformational sampling of multiconformational cyclic molecules: application to 1,4,7,10,13-Pentaoxacyclopentadecane

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Abstract

The result of an exhaustive search of low-energy conformers of 1,4,7,10,13-Pentaoxacyclopentadecane is presented. The search method combines the generation of large number of trial conformers using local nonstochastic deformations known as the Conflex method, which is coupled to AMBER force field as the minimizer. The extent of the conformational space sampled was evaluated from the view point of the number of duplicates of each conformer, generation of inclusion type structures without considering the substrate and the spread of the allowed torsion angles visited during the search. It is shown that the conformational search is exhaustive and efficient as conformers, which the metal coordinated crown ether complexes adopt, were generated. Free energies using the AMBER structures were calculated using the model of Cramer and Truhlar. The study suggests that 1,4,7,10,13-Pentaoxacyclopentadecane exists as a mixture of conformers in solution. The results show the efficiency of the method and could be the method of choice in the design of synthetic macrocyclic receptors.

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Acknowledgments

R. P. Thangavelu of CMMACS (Centre for Mathematical Modelling and Computer Simulation, Bangalore) for his help in programming.

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Authors and Affiliations

  1. Division of Organic Chemistry III, Indian Institute of Chemical Technology, Hyderabad, 500 007, India

    Bulusu Jagannadh, Kondalu R. Dharshna Priya, Laveti Chandini Devi & Gopiparthi Kranthi Sri

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  1. Bulusu Jagannadh
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  2. Kondalu R. Dharshna Priya
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  3. Laveti Chandini Devi
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  4. Gopiparthi Kranthi Sri
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Correspondence to Bulusu Jagannadh.

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Jagannadh, B., Dharshna Priya, K.R., Chandini Devi, L. et al. Efficient conformational sampling of multiconformational cyclic molecules: application to 1,4,7,10,13-Pentaoxacyclopentadecane. J Mol Model 16, 285–290 (2010). https://doi.org/10.1007/s00894-009-0550-x

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  • DOI: https://doi.org/10.1007/s00894-009-0550-x

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