title: Computational protocols for prediction of solute NMR relative chemical shifts. a case study of L-tryptophan in aqueous solution.
abstract: In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.
authors: Department of Chemistry, Center for Computational Molecular Sciences, H. C. Ørsted Institute, University of Copenhagen, Copenhagen Ø DK-2100, Denmark.
authors: Janus J
authors: JJ
authors: Eriksen
authors: Jógvan Magnus H
authors: JM
authors: Olsen
authors: Kęstutis
authors: K
authors: Aidas
authors: Hans
authors: H
authors: Ågren
authors: Kurt V
authors: KV
authors: Mikkelsen
authors: Jacob
authors: J
authors: Kongsted
mesh_terms: D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D056004:Molecular Dynamics Simulation; D012996:Solutions; D014364:Tryptophan / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D012996:Solutions; D014867:Water; D014364:Tryptophan