Efficient conformational sampling of multiconformational cyclic molecules: application to 1,4,7,10,13-Pentaoxacyclopentadecane.
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.
Jagannadh
Bulusu
B
Division of Organic Chemistry III, Indian Institute of Chemical Technology, Hyderabad, India. jagan@iict.res.in
Dharshna Priya
Kondalu R
KR
Chandini Devi
Laveti
L
Kranthi Sri
Gopiparthi
G
D043844:Crown Ethers / Q000737:chemistry*; D047028:Macrocyclic Compounds / Q000737:chemistry*; D008722:Methods; D008958:Models, Molecular; D008968:Molecular Conformation; D013816:Thermodynamics
D043844:Crown Ethers; D047028:Macrocyclic Compounds