Jump to main content
Jump to site search

Issue 33, 2011
Previous Article Next Article

Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances

Author affiliations

Abstract

Molecular dynamics simulations describing the solvation process of native and modified cyclodextrins (per-substituted α-, β-, and γ-cyclodextrins, as well as an amino-acid derived β-cyclodextrin) have been performed. A homogeneous force field, namely “q4md-CD”, has been built from the development of a new force field topology database and from a combination of the GLYCAM04 and Amber99SB force fields to correctly describe the geometrical, structural, dynamical and hydrogen bonding aspects of heterogeneous cyclodextrin based systems. These include native, organo- and peptidic-linked cyclodextrins. q4md-CD features: (i) geometrical parameters from Amber99SB to describe the protein parts, (ii) geometrical parameters from GLYCAM04 for the carbohydrate and organic parts when available or those of Amber99SB otherwise, (iii) partial atomic charges, embedded in force field libraries for the carbohydrate and organic fragments, were derived using the R.E.D. tools according to the “Amber” strategy and (iv) scaling factors of 1.2 and 2.0 were imposed for the 1–4 electrostatic and 1–4 van der Waals interactions, respectively. Results given by q4md-CD on native cyclodextrins have been compared to those obtained with reference to force fields like GLYCAM04, GLYCAM06 and Amber99SB as well as with experimental data. This work not only gives a global view of the performances of the aforementioned force fields towards a correct description of solvated cyclodextrins, but also extends the capabilities of current force fields by addressing some issues concerning hydrogen bonding and opens new possibilities towards studies of glycoconjugates by molecular dynamics.

Graphical abstract: Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances

Back to tab navigation

Supplementary files

Publication details

The article was received on 21 Mar 2011, accepted on 02 Jun 2011 and first published on 26 Jul 2011


Article type: Paper
DOI: 10.1039/C1CP20854C
Citation: Phys. Chem. Chem. Phys., 2011,13, 15103-15121
  •   Request permissions

    Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances

    C. Cézard, X. Trivelli, F. Aubry, F. Djedaïni-Pilard and F. Dupradeau, Phys. Chem. Chem. Phys., 2011, 13, 15103
    DOI: 10.1039/C1CP20854C

Search articles by author

Spotlight

Advertisements