Molecular Structure and Dynamics

Robert Carper, Andreas Dolle, Christof G. Hanke, Chris Hardacre, Axel Leuchter, Ruth M. Lynden-Bell, Zhizhong Meng, Gunter Palmer, and Joachim Richter 

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Similar, very detailed studies were made by Ebert [112] on water adsorbed on alumina with similar conclusions. Water adsorbed on zeolites showed a dielectric constant of only 14-21, indicating greatly reduced mobility of the water dipoles [113]. Similar results were found for ammonia adsorbed in Vycor glass [114]. Klier and Zettlemoyer [114a] have reviewed a number of aspects of the molecular structure and dynamics of water at the surface of an inorganic material. 

The above two references are comprehensive and individualistic surveys of symmetry, molecular structure and dynamics. 

Reinhardt W P 1982 Complex coordinates in the theory of atomic and molecular structure and dynamics Ann. Rev. Phys. Chem. 35 223... 

The molecular structure and dynamics of the ice/water interface are of interest, for example, in understanding phenomena like frost heaving, freezing (and the inhibition of freezing) in biological systems, and the growth mechanisms of ice crystals. In a series of simulations, Haymet and coworkers (see Refs. 193-196) studied the density variation, the orientational order and the layer-dependence of the mobilitity of water molecules. The ice/water basal interface is found to be a relatively broad interface of about... 

Models for description of liquids should provide us with an understanding of the dynamic behavior of the molecules, and thus of the routes of chemical reactions in the liquids. While it is often relatively easy to describe the molecular structure and dynamics of the gaseous or the solid state, this is not true for the liquid state. Molecules in liquids can perform vibrations, rotations, and translations. A successful model often used for the description of molecular rotational processes in liquids is the rotational diffusion model, in which it is assumed that the molecules rotate by small angular steps about the molecular rotation axes. One quantity to describe the rotational speed of molecules is the reorientational correlation time T, which is a measure for the average time elapsed when a molecule has rotated through an angle of the order of 1 radian, or approximately 60°. It is indirectly proportional to the velocity of rotational motion. 

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. 

NMR spectroscopy is one of the most widely used analytical tools for the study of molecular structure and dynamics. Spin relaxation and diffusion have been used to characterize protein dynamics [1, 2], polymer systems[3, 4], porous media [5-8], and heterogeneous fluids such as crude oils [9-12]. There has been a growing body of work to extend NMR to other areas of applications, such as material science [13] and the petroleum industry [11, 14—16]. NMR and MRI have been used extensively for research in food science and in production quality control [17-20]. For example, NMR is used to determine moisture content and solid fat fraction [20]. Multi-component analysis techniques, such as chemometrics as used by Brown et al. [21], are often employed to distinguish the components, e.g., oil and water. 

Levine, R. D. (1988), Lie Algebraic Approach to Molecular Structure and Dynamics, in Mathematical Frontiers in Computational Chemical Physics, Springer-Verlag, New York. 

Equation 5.11 is important. It relates the experimentally observed vapor pressure ratio to the theoretically important isotope effects on the free energy differences and/or partition function ratios. This equation encapsulates the essential physics of the vapor pressure isotope effect and, as we shall see, provides a path for its theoretical interpretation in terms of molecular structure and dynamics via the partition function ratios. 

The standard state Helmholtz free energy difference, 8AA°, was introduced in Equations 5.9 and 5.11 to show the connection between VPIE and molecular structure and dynamics. Molecular properties are conveniently expressed using standard state canonical partition functions for the condensed and vapor phases, Qc° and Qv° remember A0 = —RT In Q°. The Q s are 3nN dimensional, n is the number of atoms per molecule and N is Avogadro s number. For convenience we have now dropped the superscript o s on the Q s. The o s specify standard state conditions, now to be implicitly understood. For VPIE and a respectively, not too close to the critical region,... 

W. H. Flygare, Molecular Structure and Dynamics, Prentice-Hall, Englewood Cliffs, 1978. 

These results demonstrated the usefulness of 13C NMR in studies of molecular structure and dynamics for the polymeric constituents of plant cuticle. Although these materials are insoluble and sometimes present as interpenetrating phases, CPMAS and spin relaxation techniques helped identify important carbon types and provided structural clues to the protective functions of cutin and suberin in terrestrial plants. 

Khalil M, Demirdoven N, Tokmakoff A (2003) Coherent 2D IR spectroscopy molecular structure and dynamics in solution. J Phys Chem A 107 5258... 

In PNCs, the details of molecular structure and dynamics in the periphery of the nanoparticles (for example, within the lamellar gallery or at the interface) is quite difficult to establish by regular experimental techniques. The inability to monitor the thermodynamics and kinetics of the molecular interactions between the different constituents that determine the structural evolution and final morphology of the materials hinders progress in this field. This is probably the domain where there is an increasing need for computer modeling and simulations. 

P. H. Vaccaro in H. Hirota, R. W. Field, J. P. Maier, S. Tsuchiya (Eds.), Non-linear Optical Spectroscopy for Molecular Structure and Dynamics, Blackwell Scientific, IUPAC... 

The importance of NMR spectroscopy in determining the polymer molecular structure and dynamics, as well as the rapid development of spectroscopic techniques, resulted in a number of review articles, which have appeared since the late 1950s1 8). The particular types of polymers, as well as the particular NMR Techniques are separately reviewed, such as the characterization of crosslinked polymers by high resolution solid state NMR 9). 

The interpretation of the SL line shapes in terms of molecular structure and dynamics is made with the assumptions that a) the mobility of the crosslink... 

The above experimental developments represent powerful tools for the exploration of molecular structure and dynamics complementary to other techniques. However, as is often the case for spectroscopic techniques, only interactions with effective and reliable computational models allow interpretation in structural and dynamical terms. The tools needed by EPR spectroscopists are from the world of quantum mechanics (QM), as far as the parameters of the spin Hamiltonian are concerned, and from the world of molecular dynamics (MD) and statistical thermodynamics for the simulation of spectral line shapes. The introduction of methods rooted into the Density Functional Theory (DFT) represents a turning point for the calculations of spin-dependent properties [7],... 

B. Molecular Structure and Dynamics of Tricarbonyl-r 4-2,3-dimethyl-1,3-butadiene-bis(ri5-methylcyclopentadienyl)dimolybdenum... 

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