Averaging semiempirical NMR chemical shifts: dynamic effects on the subpicosecond time scale.
The variation of the (1)H and (13)C NMR chemical shifts of heptapeptide ATWLPPR was investigated during a hybrid quantum mechanical (QM)/molecular mechanical (MM = CHARMM) molecular dynamics simulation of the peptide in aqueous solvent. The semiempirical method OM3 was used as the QM method, and the effect of augmenting the OM3 Hamiltonian with an empirical dispersion term (OM3-D) was also explored. The semiempirical MNDO method was used to calculate the chemical shifts of snapshots taken at 50 fs intervals during the 100 ps simulation. The calculated chemical shifts are highly sensitive to fluctuations of the molecular geometry on the time scale of molecular vibrations. However, the time-averaged chemical shift over the full simulation results in reasonable agreement with the experimental NMR chemical shifts and more consistent results compared with the averaged chemical shifts obtained from gas-phase optimized conformations of the peptide. The OM3 and OM3-D methods are stable and reproduce the main features of the experimental geometry during the 100 ps simulation.
Tuttle
Tell
T
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom. tell.tuttle@strath.ac.uk
D000595:Amino Acid Sequence; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D011487:Protein Conformation; D011789:Quantum Theory; D013997:Time Factors
D009842:Oligopeptides