KEVIN NAIDOO

KEVIN J NAIDOO Associate Professor: BSc Honours (1987), MSc. (1989) University of Cape Town, PhD (1994) University of Michigan, Post-doctoral Fellow Cornell University (1994-1995), African representative on the United Nations Industrial Development Organisation (UNIDO) project on Computer-Aided Molecular Design (1997-2003). South African Chemical Institute Raikes Research Medal (1999). Member of the American Chemical Society.

E-mail: Kevin.Naidoo@uct.ac.za

 

RESEARCH INTERESTS 

My purpose is to balance the time consuming but important method’s development aspect of computational chemistry research with the application of methods developed by us and other groups to problems in solution structure and reactivity of macromolecules.  Computational techniques offer a useful complement to particularly solution phase experimental techniques and are used in systems that are hard to probe experimentally. My research group uses computational methods to calculate physical properties of carbohydrates (glycobiology), dendrimers (polymers) and Platinum Group Metal complexes that are inaccessible from experiments.  In the process of doing this I have developed methods not available in computational chemistry to investigate the condensed phase behavior of macromolecules and transition metal complexes.  More recently I have developed methods for calculating chemical reaction surfaces in condensed phases (solution and enzymes, etc.) More details of my research are outlined below:
 

Solvation and Conformation  My research group continues to  investigate the solution properties of carbohydrates. Of particular interest to me is the effect of the glycosidic linkage on macromolecular solubility and reactivity.  The combination of computer simulations and NMR spectroscopy constitutes an extremely powerful tool for studies of carbohydrates at the molecular level. In particular, we have studied maltose, isomaltose, panose and Cyclodextrins in solution and measured relaxation parameters: T1, T2 and NOEs (e.g., see ref [3]). 
 We developed a Carbohydrate Solution Force Field (CSFF, ref [4]) which has now been used by various groups for carbohydrate computer simulations. Recently we investigated the electronic factors governing glycosidic linkage conformation preferences using density functional theory and Bader’s Atoms In Molecules methods. In the process we established a procedure that allows for the determination of the strength of intramolecular hydrogen bonds in bio molecules such as oligosaccharides.
 

  

 

Reaction surface from QM/MD simulation of ammonia proton exchange in solution .
 

Evaluating Intramolecular Hydrogen Bond Strengths in (1-4) linked Disaccharides from Electron Density

 

Mechanical Properties of Carbohydrates
We have developed protocols for the simulation of single polysaccharide strands that are subjected to a stretching force leading to  force-extension curves are remarkably similar to that obtained from Atomic Force Microscopy experiments. This allows us to describe the unfolding of polysaccharides and oligosaccharide macromolecules.

Chemical Reactions and Transition State Modelling Whenever a computer simulation has been performed the issue of whether there has been sufficient sampling is often not resolved.  To this end we developed methods based on umbrella sampling to address this question and so obtained the free energy surface as a function of glycosidic linkages (see ref [1]) and rotational groups in saccharides (see ref [4]).  More recently we developed a similar procedure for the calculation of multidimensional free energy reaction surfaces that are similar to More O’Ferral-Jencks diagrams (see ref [6]).  This method has been shown to work well for proton exchange reactions. 

 
  Separation Processes for Platinum Group Metals
We have developed protocols for the simulation anion cation association mechanisms for platinum group metals in organic and aqueous solvents (e.g., ref [5]). We are able to calculate the association constants for the PGM chloroanion complexes within the accuracy of experimental measurements.
 		    

 

REPRESENTATIVE PUBLICATIONS

  1. Calculation of the Ramachandran Potential of Mean Force for a Disaccharide in Aqueous Solution. Kevin J. Naidoo and J. W. Brady,  1999, J. Am. Chem. Soc., 121, 2244

  2. Computational predictions of structural and physical properties of poly(benzyl phenyl ether) dendrimers; Kevin J Naidoo, John R. Moss and S. Hughes; 1999, Macromolecules, 32, 331-341.

  3. Molecular Dynamics and NMR Study of the a(1-4) and a(1-6) Glycosidic linkages: Maltose and Isomaltose; Robert B. Best, Graham E. Jackson and Kevin J. Naidoo, 2001, J. Phys. Chem. B., 105(20), 4742-4751.

  4. Carbohydrate Solution Simulations: Producing a Force Field with Experimentally-Consistent Hydroxyl Rotational Frequencies; Michelle Kuttel,  J. W. Brady, Kevin J. Naidoo, 2002.   J. Comput. Chem. 23(13): 1236-1243.

  5. Contact Ion Pair between Na+ and PtCl62- Favoured in Methanol; Kevin J Naidoo, Anton S. Lopis, Arjan N. Westra, David J Robinson and Klaus R Koch, 2003 J. Am. Chem. Soc. (Communication) 125, 13330-13331.

  6. Implementation of an Adaptive Umbrella Sampling Method for the Calculation of Multidimensional Potential of Mean Force of Chemical Reactions  in Solution; Ramkumar Rajamani, Kevin J. Naidoo, and Jiali Gao, 2003, J. Comput. Chem .24, 1775-1781. 

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