Conformation study of ɛ-cyclodextrin: Replica exchange molecular dynamics simulations

Predicting binding free energies: Frontiers and benchmarks

“…The CDs are computationally tractable [9,16,23,61,73,92,107,108,154,156,190,191,202], and thus can be used for "hard" benchmark sets to test force fields (Section II A 1 c). One complicating feature for calculations, relative to CB7, is that the two entryways to a CD are not equivalent, and asymmetric guest molecules may prefer to bind "head-in" or "head-out".…”

Metadynamics supports molecular dynamics simulation-based binding affinities of eucalyptol and beta-cyclodextrin inclusion complexes

“…The O3 (n) -O2 (n+1) distances of the M2 minima are lengthened, which is connected with the loss of intramolecular hydrogen bond interactions on the secondary rim. 79 This results in the distortion of the CD geometry that can be measured in terms of the structural angle parameter q[C6 (n) -C2 (n+1) -C6 (n+1) ] for a pair with an angle of adjacent glucose subunits (Fig. 1c).…”

Cavity Closure of 2-Hydroxypropyl-β-cyclodextrin: Replica Exchange Molecular Dynamics Simulations

“…The second and third main population were M2 and M3 with d1(i)/d2(i) around 5.5 Å/4.5 Å and 5.0 Å/5.5 Å, respectively. When comparing βCD with a large-ring CD (CD) by the REMD method [33], three important minima were found to be similar with βCD results but the M3 population of CD was higher than that of βCD due to the big size and high flexibility of the macroscopic ring, having a higher probability to flip the glucopyranose units in the large-ring system. Figure 4b and 4c, respectively, in order to compare the conformational minima among the models.…”

“…The REMD simulations were performed by Amber 14 package [30]. The parameters of βCD and HPβCDs were taken from the Glycam06 carbohydrate force field [31,32] with the solvation model based on generalized Born (GB) implicit solvent model, Igb5, which gives a suitable description of cyclodextrin CD as reported by Khuntawee et al [33] and the smaller sizes of CDs (CD-CD, unpublished data) relative to the available crystal structures and MD studies in explicit solvent model. The initial structures of βCD and all HPβCDs were fully minimized with 2000 steps of the steepest descent method, followed by 1000 steps of conjugated gradient method to relax the structures before simulation.…”