Molecular dynamics nuclear magnetic resonance

At room temperature, these molecules occupy well-defined locations in their respective crystal lattices. However, they tumble freely and isotropically (equally in all directions) in place at their lattice positions. As a result, their solid phase NMR spectra show features highly reminiscent of liquids. We will see an illustration of this point shortly. Other molecules may reorient anisotropically (as in solid benzene). Polymer segmental motions in the melt may cause rapid reorientation about the chain axis but only relatively slow reorientation of the chain axes themselves. Large molecular aggregates in solution (such as surfactant micelles or protein complexes or nucleic acids) may appear to have solidlike spectra if their tumbling rates are sufficiently slow. There are numerous other instances in which our macroscopic motions of solid and liquid may be at odds with the molecular dynamics. Nuclear magnetic resonance is one of the foremost ways of investigating these situations. 

Anderson, J.E., Barkel, D.J.D., and Parkin, J.E., Conformations and internal rotation of simple 1-alkenylnaphthalenes, studied by dynamic nuclear magnetic resonance spectroscopy, nuclear Over-hauser effects, and molecular mechanics calculation, /. Chem. Soc., Perkin Trans. 2, 955, 1987. 

This comprehensive review of theoretical models and techniques will be invaluable to theorists and experimentalists in the fields of infrared and Raman spectroscopy, nuclear magnetic resonance, electron spin resonance and flame thermometry. It will also be useful to graduate students of molecular dynamics and spectroscopy. 

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. 

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... 

Nuclear magnetic resonance provides means to study molecular dynamics in every state of matter. When going from solid state over liquids to gases, besides mole- cular reorientations, translational diffusion occurs as well. CD4 molecule inserted into a zeolite supercage provides a new specific model system for studies of rotational and translational dynamics by deuteron NMR. 

R. Tycko (ed.) Nuclear Magnetic Resonance Probes of Molecular Dynamics. 

A reevaluation of molecular structure of humic substances based on data obtained primarily from nuclear magnetic resonance spectroscopy, X-ray absorption near-edge structure spectroscopy, electrospray ionization-mass spectrometry, and pyrolysis studies was presented by Sutton and Sposito (2005). The authors consider that humic substances are collections of diverse, relatively low molecular mass components forming dynamic associations stabilized by hydrophobic interactions and hydrogen bonds. These associations are capable of organizing into micellar structures in suitable aqueous environments. Humic components display contrasting molecular motional behavior and may be spatially segregated on a scale of nanometers. Within this new structural context, these components comprise any molecules... 

Carbon-13 nuclear magnetic resonance has become an in ortant tool with which to study the microstructure and molecular dynamics... 

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