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Identification of Active Sites of Biomolecules II: Saccharide and Transition Metal ion in Aqueous Solution



Orkid Coskuner, Denis E. Bergeron, Luis C. Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez


We discuss the coordination mechanism of FeIII and methyl-a-mannopyranoside in aqueous solution using a recently presented integrated approach comprising ab initio electronic structure calculations, molecular dynamics simulations, and mass spectrometric measurements. First principles Car-Parrinello molecular dynamics (CPMD) simulations find that a single FeIII ion interacts with specific hydroxyl groups of the saccharide in aqueous solution. Specifically, we find that one FeIII ion complexed to methyl-a-mannopyranoside also associates with two water molecules. These simulations are in accord with electrospray ionization mass spectrometry measurements involving guided ion beam hydration measurements, which reveal an optimal coordination number of four about the FeIII ion. CPMD simulations identified specific intra-molecular and inter-molecular hydrogen bonding interactions that have an impact on the conformation of the saccharide and on the coordination with FeIII; in contrast, classical molecular dynamics simulations were insensitive to these effects. This study illustrates the strenght of ab initio molecular dynamics simulations, chemical reactivity calculations, and natural partial charge analysis coupled with mass spectrometric measurements in identifying the active sites of biomolecules toward ligands and for studying the complexation and coordination chemistry associated with substrate and ligand interactions relevant to the design of biochemical syntheses, drugs, and biomarkers in medicine.
Journal of Physical Chemistry A


Car-Parrinello molecular dynamics simulations, classical molecular dynamics simulations, chemical reactivity, carbohydrate, metal ion, water, electrospray ionization mass spectrometry


Coskuner, O. , Bergeron, D. , Rincon, L. , Hudgens, J. and Gonzalez, C. (2009), Identification of Active Sites of Biomolecules II: Saccharide and Transition Metal ion in Aqueous Solution, Journal of Physical Chemistry A (Accessed May 28, 2024)


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Created February 23, 2009, Updated February 19, 2017