The intermolecular NOE is strongly influenced by dynamics

Abstract

The intermolecular NOE in NMR spectroscopy is analyzed theoretically via computer simulation. Our test case is the homonuclear NOE between hydrogens in the ionic liquid 1-ethyl-3-methylimidazolium trifluoromethanesulfonate. A coarse-grained model of this system is developed and simulated in a 3 microseconds molecular dynamics run, subsequently used for analysis. Our findings are the following: Spin pair specific dynamics has a strong influence on the spectrum. As a consequence, structural information cannot be read off directly. Instead, different contributions to the signals must be disentangled before one can gain information about structure. We show that the extent of signal distortion through dynamics correlates with the spins' distance to their respective molecular centers of mass. Since we deal with pair distributions of spins, the extracted structure does not represent average distances between two spins but the sum of the influence of surrounding spins. In fact, we find that this influence is long-ranged. Our data explicitly shows that the usual 1/r(6) dependence is replaced by a distance dependence between 1/r(3) and 1/r. However, structural information consists of a spin pair specific short-ranged contribution and a uniform long-ranged contribution. The transition from specific to uniform is sensitive to the behavior of the underlying pair distribution functions.

Synthetic Evolution of the Multifarene Cavity from Planar Predecessors

“…Through‐space correlations are attributed to the anti ‐ 12 (blue) and syn ‐ 12 (red) conformers. Through‐bond and weak intermolecular NOEs are also detectable but were not assigned for clarity …”

“…Accordingly, we examined the solid-state structure of all compounds along the synthetic voyage from 2-dimensional build- T hroughspace correlationsa re attributed to the anti-12 (blue)a nd syn-12 (red) conformers.Through-bond and weak intermolecular NOEs are also detectable but were not assignedf or clarity. [31] .…”

Examination of ethanol interactions with Trp‐cage peptide through MD simulations and intermolecular nuclear Overhauser effects

“… Although the conformations of Trp‐cage appear to oscillate near its starting structure during a simulation, excursions to other conformations take place once or twice every 0.1 μs (Figures and SI‐1). It may be that the frequency or magnitude of these transitions is not correctly reproduced by the simulations, thus biasing the calculated away from the experimental value. The intermolecular NOE is influenced by local dynamics; the dynamics of ethanol aggregation or interaction with water molecules and the interaction of these solvent components with peptide may be incorrectly reproduced in the simulations. However, while local diffusion of the water and ethanol components of the solvent near a peptide hydrogen are slowed a factor of 2 to 3 relative to diffusion in the bulk solvent, calculations done with Equation indicate that, at the RF used for our experiments (500 MHz), calculated are relatively insensitive to diffusion and that a 3‐fold change in bulk diffusion coefficient could not produce the overestimates of that are obtained from calculations with the MD trajectories.…”

Determination of inter‐ionic and intra‐ionic interactions in a monofluorinated imidazolium ionic liquid by a combination of X‐ray crystallography and NOE NMR spectroscopy

“…Some of the ‘distances’ reported there seemed reasonable while others did not. One possible reason for these findings was delivered by Weingärtner and Steinhauser shortly after in a series of publications utilizing our own published NMR data . Essentially, by reinvestigating the fundamental mathematics of the NOE theory, they stated that for our ILs the so‐called ‘extreme narrowing limit’ condition was not met.…”