Publication: AM1 Parameters for the Prediction of 1H and 13C NMR Chemical Shifts in Proteins
October 02, 2009
Abstract: The semiempirical quantum mechanical description of NMR chemical shifts has been
implemented at the AM1 level with NMR-specific parameters to reproduce
experimental 1H and 13C NMR chemical shifts. The methodology adopted here is
formally the same as that of the previously published finite perturbation theory
GIAO-MNDO-NMR approach [Wang, B.; et al. J. Chem. Phys. 2004, 120, 24.]. The
primary impetus for this parametrization was the accurate capture of chemical
environments of atoms in biological systems. Protein-specific parameters were
developed on a training set that comprised five globular protein systems with
varied secondary structure and a range in size from 46−61 amino acid residues. A
separate set of parameters was developed using a training set of small organic
compounds with an emphasis on functional groups that are relevant to biological
studies. Our approach can be employed using semiempirical (AM1) geometries and
can be executed at a fraction of the cost of ab initio and DFT methods, thus
providing an attractive option for the computational NMR studies of much larger
protein systems. Analysis carried out on 3340 1H and 2233 13C chemical shifts
for protein systems shows significant improvement over the standard AM1
parameters. Using 1H and 13C specific parameters, the rms errors are from 1.05
and 21.28 ppm to 0.62 and 4.83 ppm for hydrogen and carbon, respectively.
Authors: Duane E. Williams, Martin B. Peters, Bing Wang, Adrian E. Roitberg and Kenneth M. Merz, Jr.
Reference: J. Phys. Chem. A, 2009, 113 (43), pp 11550–11559. (see
link for full paper).