Nuclear Overhauser effect dynamic

You can often use experimental data, such as Nuclear Overhauser Effect (NOE) signals from 2D NMR studies, as restraints. NOE signals give distances between pairs of hydrogens in a molecule. Use these distances to limit distances during a molecular mechanics geometry optimization or molecular dynamics calculation. Information on dihedral angles, deduced from NMR, can also limit a conformational search. 

Methods of disturbing the Boltzmann distribution of nuclear spin states were known long before the phenomenon of CIDNP was recognized. All of these involve multiple resonance techniques (e.g. INDOR, the Nuclear Overhauser Effect) and all depend on spin-lattice relaxation processes for the development of polarization. The effect is referred to as dynamic nuclear polarization (DNP) (for a review, see Hausser and Stehlik, 1968). The observed changes in the intensity of lines in the n.m.r. spectrum are small, however, reflecting the small changes induced in the Boltzmann distribution. 

Guichard, G., Briand, J. P., Muller, S., Cung, M. T. Structure of antibody-bound peptides and retro-inverso analogues. A transferred nuclear Overhauser effect spectroscopy and molecular dynamics approach. Biochemistry 2001, 40, 5720-5727. 

Hence, provided that I g is known and that R has been determined by means of an independent experiment, provides the cross-relaxation rate ct. This enhancement is called nuclear Overhauser effect (nOe) (17,19) from Overhauser (20) who was the first to recognize that, by a related method, electron spin polarization could be transferred to nuclear spins (such a method can be worked out whenever EPR lines are relatively sharp it is presently known as DNP for Dynamic Nuclear Polarization). This effect is usually quantified by the so-called nOe factor p... 

No such chemical exchange is observed for NP2—ImH or NP3—ImH, for which WEFT-NOESY spectra have cross peaks due only to through-space nuclear Overhauser effect interactions (91). Interestingly, these two proteins have only one proline in the A-B loop (Fig. 4). However, considerable additional NMR investigation needs to be carried out in order to determine whether the chemical exchange process shown in the NOESY spectra of NPl-ImH is indeed due to the dynamics of the A-Bloop. 

The basis for the determination of solution conformation from NMR data lies in the determination of cross relaxation rates between pairs of protons from cross peak intensities in two-dimensional nuclear Overhauser effect (NOE) experiments. In the event that pairs of protons may be assumed to be rigidly fixed in an isotopically tumbling sphere, a simple inverse sixth power relationship between interproton distances and cross relaxation rates permits the accurate determination of distances. Determination of a sufficient number of interproton distance constraints can lead to the unambiguous determination of solution conformation, as illustrated in the early work of Kuntz, et al. (25). While distance geometry algorithms remain the basis of much structural work done today (1-4), other approaches exist. For instance, those we intend to apply here represent NMR constraints as pseudoenergies for use in molecular dynamics or molecular mechanics programs (5-9). 

The structures of the di- and trimeric profisetinidins from Pithecellobium dulce (Guamii-chil) were rigorously corroborated via synthesis.The synthetic approach was additionally motivated by the precariousness of unequivocally differentiating between 2,3-cis-3,4-trans-and 2,3-c7.s-3,4-c7.s-confugurations of the chain-extension units on the basis of H NMR coupling constants.Furthermore, the powerful nuclear Overhauser effect (NOE) method for differentiating between 2,4-cis- and 2,4-tra i -substitution is less useful at the di- and trimeric levels due to the adverse effects of dynamic rotational isomerism about the interflavanyl bond(s) on NMR spectra at ambient temperatures. 

Nuclear Overhauser Effects. Nuclear Overhauser effects (NOEs) can be used to measure both interactions through space, and chemical exchange (Neuhaus and Williamson, 2000). In a system where a contaminant interacts strongly with NOM, NOEs should be measurable between the NOM and the contaminant. In theory, using such an approach should provide information as to which components in DOM the contaminant is associated, as well as possible information on exchange rates, molecular dynamics, and strength of the interactions. Relatively few studies have used NOEs extensively to study NOM-contaminant interactions directly. The... 

The structure determination of biopolymers using NMR spectroscopy usually involves interactions of protons[216,33. Typically, interactions of protons (nuclear Overhauser effect, NOE) that are close in space but separated by several subunits of the biopolymer are used to establish the folding of the backbone. Distance restraints are then used to compute a structure which is checked by back-calculation of the NOE spectra and comparison with experimental results 361. For large and highly flexible systems molecular dynamics is invaluable for scanning the conformational space. 

A protocol combining molecular dynamics and NMR spectroscopy gave excellent agreement between calculated and experimental nuclear Overhauser effect (NOE) buildup curves of 2,5-oligo(2-thienyl)furans <2002PCA1277>. 

NMR other aspects Two other aspects of the H NMR spectrum of hydrogen bonded aggregates are useful in determining structure. Variable-temperature NMR can reveal dynamic processes that are fast (or slow) on the NMR time scale at room temperature [51]. Nuclear Overhauser effect (nOe) studies can be used to determine relative proximity of the hydrogen bonded protons and the diastereotopic methylene protons [40,43,46]. H NMR competition studies where two different hubs (for example, Hub(M)3 and Flex(M)3) compete for only three equivalents of CA allows direct assessment of the relative stability of the competing aggregates [45,55]. 

The use of NMR in hydration studies is based on two complementary approaches. In one approach, nuclear Overhauser effect (NOE) cross-peaks between DNA protons and hydration water are used to gain insight into the dynamics of localized water... 

The chemical shift is an extremely important NMR parameter but there are many other parameters that can be discerned from NMR spectra. Indeed, NMR is unique among many forms of spectroscopy in that there are so many parameters associated with a spectrum other than just peak intensity and frequency. These include coupling constants, which provide information on local conformations and also on molecular connectivities nuclear Overhauser effects (NOEs), which provide information on internuclear distances and relaxation parameters, which provide information on molecular dynamics. Table 12.1 summarizes the main NMR parameters that may be measured and highlights their applications in the drug discovery process. 

The nuclear Overhauser effect is the most widely measured of the relaxation phenomena in structural studies. The nOe experiments directly measure the dipole-dipole relaxation between nuclei. The great utility of the nOe is its potential to determine internuclear distances. The magnitude of the nOe is proportional to (ris) where rjs is the distance between spins I and S. The nOe effects an increase or decrease in the intensity of a particular signal, based on the spacial proximity of its neighbors and the dynamics of the molecule. For a more rigorous description of the physical basis of the nOe the reader is referred to the excellent text by Neuhaus and Williamson. ... 

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