Nuclear magnetic resonance simulation

Figure Bl.13.7. Simulated NOESY peak intensities in a homoniielear two-spin system as a fiinetion of the mixing time for two different motional regimes. (Reprodiieed by pennission of Wiley from Neiihaiis D 1996 Encyclopedia of Nuclear Magnetic Resonance ed D M Grant and R K Harris (Chiehester Wiley) pp 3290-301.)...

M Vasquez, ElA Scheraga. Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. J Biomol Struct Dyn 5 705-755, 1988. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

A review is given of the application of Molecular Dynamics (MD) computer simulation to complex molecular systems. Three topics are treated in particular the computation of free energy from simulations, applied to the prediction of the binding constant of an inhibitor to the enzyme dihydrofolate reductase the use of MD simulations in structural refinements based on two-dimensional high-resolution nuclear magnetic resonance data, applied to the lac repressor headpiece the simulation of a hydrated lipid bilayer in atomic detail. The latter shows a rather diffuse structure of the hydrophilic head group layer with considerable local compensation of charge density. 

Jurs PC, Ball JW, Anker LS. Carbon-13 nuclear magnetic resonance spectrum simulation. / Chem Inf Comput Sci 1992 32(4) 272-8. 

Finally, Burkhard Luy, Andreas Frank and Horst Kessler discuss Conformational Analysis of Drugs by Nuclear Magnetic Resonance Spectroscopy . The determination and refinement of molecular conformations comprehends three main methods distance geometry (DG), molecular dynamics (MD) and simulated anneahng (SA). In principle, it is possible to exclusively make use of DG, MD or... 

Dynamics of Poly(oxyethylene) Melts Comparison of 13C Nuclear Magnetic Resonance Spin-Lattice Relaxation and Dielectric Relaxation as Determined from Simulations and Experiments. 

Simulation of Dynamic Nuclear Magnetic Resonance Spectra for Systems with Many Spins or Exchange Sites. 

Crystal reaction study mechanistic tools, 296 computer simulation, 297 electronic spectroscopy, 298 electron microscopy, 298 electron paramagnetic resonance (EPR), 299 nuclear magnetic resonance (NMR), 298 Raman spectroscopy, 299 Crystal reaction study techniques crystal mounting, 308 decomposition limiting, 309 polarized IR spectroscopy, 309 temperature control, 308 Cycloreversions, adiabatic photochemical involving anthracenes, 203 excited state properties of lepidopterenes, 206... 

The simulated distillation data (Table V and Figures 2, 4, 6) and the FIA analyses of the distillates (Table II) were obtained by standard ASTM methods D2887 and D1319, respectively. The mass spectrometric analyses (MS) of the saturates fractions (Table VI) were obtained by an in-house method similar to that of Hood and O Neal (44). The aromatic fractions were analyzed by the proton nuclear magnetic resonance (NMR) method of Clutter et al. (45), and the results are reported in Tables VII and VIII. 

The term DNMR, Dynamic Nuclear Magnetic Resonance, refers to the process of recording and usually computer simulating exchange broadened NMR spectra at a number of temperatures in order to determine mechanistic and/or kinetic information. b The terms fast and slow are used rather than the more familiar labile and nonlabile because the latter imply an intermolecular reaction. 

Abstract We use Nuclear Magnetic Resonance relaxometry (i.e. the frequency variation of the NMR relaxation rates) of quadrupolar nucleus ( Na) and H Pulsed Gradient Spin Echo NMR to determine the mobility of the counterions and the water molecules within aqueous dispersions of clays. The local ordering of isotropic dilute clay dispersions is investigated by NMR relaxometry. In contrast, the NMR spectra of the quadrupolar nucleus and the anisotropy of the water self-diffusion tensor clearly exhibit the occurrence of nematic ordering in dense aqueous dispersions. Multi-scale numerical models exploiting molecular orbital quantum calculations, Grand Canonical Monte Carlo simulations, Molecular and Brownian Dynamics are used to interpret the measured water mobility and the ionic quadrupolar relaxation measurements. 

Molecular dynamics (MD) simulations fill a significant niche in the study of chemical structure. While nuclear magnetic resonance (NMR) yields the structure of a molecule in atomic detail, this structure is the time-averaged composite of several conformations. Electronic and vibrational circular dichroism spectroscopy and more general ultraviolet/visible and infrared (IR) spectroscopy yield the secondary structure of the molecule, but at low resolution. MD simulations, on the other hand, yield a large set of individual structures in high detail and can describe the dynamic properties of these structures in solution. Movement and energy details of individual atoms can then be easily obtained from these studies. 

For the investigation of the molecular dynamics in polymers, deuteron solid-state nuclear magnetic resonance (2D-NMR) spectroscopy has been shown to be a powerful method [1]. In the field of viscoelastic polymers, segmental dynamics of poly(urethanes) has been studied intensively by 2D-NMR [78, 79]. In addition to ID NMR spectroscopy, 2D NMR exchange spectroscopy was used to extend the time scale of molecular dynamics up to the order of milliseconds or even seconds. In combination with line-shape simulation, this technique allows one to obtain correlation times and correlation-time distributions of the molecular mobility as well as detailed information about the geometry of the motional process [1]. 

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