Publication: AM1 Parameters for the Prediction of 1H and 13C NMR Chemical Shifts in Proteins

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).