The mean hydration of carbohydrates as studied by normalized two-dimensional radial pair distributions

The liydration of carbohydrates plays a key role in many biological processes. Molecular dynamics simulations provide an effective tool for investigating the liydration of complex solutes such as carbohydrates. In this article we devise an algorithm for the calculation of two-dimensional radial pair distributions describing the probability of finding a water molecule in a site defined by two reference atoms. The normalized 2D radial pair distribution is proposed as an effective tool for investigating and comparing localized or ordered water sites around flexible molecules such as carbohydrates when analyzing molecular dynamics simulations and the utility of 2D radial pair distributions is demonstrated using sucrose as an example. In this relatively simple structure, 2D radial pair distributions were able to characterize and quantify the importance of two unique interresidue liydration sites in which a water molecule is forming a bridge between the glycopyranosyl and fructofuranosyl residues. The approach is proposed to be a valuable tool for comparing and understanding the liydration of flexible biomolecules such as carbohydrates. ©2000 by Elsevier Science Inc.