Averaging semiempirical NMR chemical shifts: dynamic effects on the subpicosecond time scale

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

The variation of the 1H and 13C 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.
LanguageEnglish
Pages11723-11733
Number of pages10
JournalJournal of Physical Chemistry A
Volume113
Issue number43
DOIs
Publication statusPublished - 29 Oct 2009

Fingerprint

Chemical shift
chemical equilibrium
Nuclear magnetic resonance
nuclear magnetic resonance
peptides
simulation
Molecular vibrations
Hamiltonians
Peptides
Geometry
geometry
Conformations
Molecular dynamics
Gases
vapor phases
molecular dynamics
intervals
vibration
Computer simulation

Keywords

  • semiempirical
  • NMR chemical shifts
  • subpicosecond time scale
  • nuclear magnetic resonance

Cite this

@article{d86adbbe37b94ab0bfeeef730aa4d8d4,
title = "Averaging semiempirical NMR chemical shifts: dynamic effects on the subpicosecond time scale",
abstract = "The variation of the 1H and 13C 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.",
keywords = "semiempirical, NMR chemical shifts, subpicosecond time scale, nuclear magnetic resonance",
author = "T. Tuttle",
year = "2009",
month = "10",
day = "29",
doi = "10.1021/jp902875d",
language = "English",
volume = "113",
pages = "11723--11733",
journal = "Journal of Physical Chemistry A",
issn = "1089-5639",
publisher = "American Chemical Society",
number = "43",

}

Averaging semiempirical NMR chemical shifts: dynamic effects on the subpicosecond time scale. / Tuttle, T.

In: Journal of Physical Chemistry A, Vol. 113, No. 43, 29.10.2009, p. 11723-11733.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Averaging semiempirical NMR chemical shifts: dynamic effects on the subpicosecond time scale

AU - Tuttle, T.

PY - 2009/10/29

Y1 - 2009/10/29

N2 - The variation of the 1H and 13C 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.

AB - The variation of the 1H and 13C 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.

KW - semiempirical

KW - NMR chemical shifts

KW - subpicosecond time scale

KW - nuclear magnetic resonance

UR - http://dx.doi.org/10.1021/jp902875d

U2 - 10.1021/jp902875d

DO - 10.1021/jp902875d

M3 - Article

VL - 113

SP - 11723

EP - 11733

JO - Journal of Physical Chemistry A

T2 - Journal of Physical Chemistry A

JF - Journal of Physical Chemistry A

SN - 1089-5639

IS - 43

ER -