Molecules, internal motions

This section will concentrate on the motions of atoms within molecules— internal molecular motions —as comprehended by the revolutionary quantum ideas of the 20th century. Necessarily, limitations of space prevent many topics from being treated in the detail they deserve. Some of these are treated in more detail in... 

As we shall see, in molecules as well as atoms, the interplay between the quantum description of the internal motions and the corresponding classical analogue is a constant theme. However, when referring to the internal motions of molecules, we will be speaking, loosely, of the motion of the atoms in the molecule, rather than of the fiindamental constituents, the electrons and nuclei. This is an extremely fundamental point to which we now turn. 

The result is that, to a very good approxunation, as treated elsewhere in this Encyclopedia, the nuclei move in a mechanical potential created by the much more rapid motion of the electrons. The electron cloud itself is described by the quantum mechanical theory of electronic structure. Since the electronic and nuclear motion are approximately separable, the electron cloud can be described mathematically by the quantum mechanical theory of electronic structure, in a framework where the nuclei are fixed. The resulting Bom-Oppenlieimer potential energy surface (PES) created by the electrons is the mechanical potential in which the nuclei move. Wlien we speak of the internal motion of molecules, we therefore mean essentially the motion of the nuclei, which contain most of the mass, on the molecular potential energy surface, with the electron cloud rapidly adjusting to the relatively slow nuclear motion. 

We will now treat the internal motion on the PES in cases of progressively increasing molecular complexity. We start with the simplest case of all, the diatomic molecule, where the notions of the Bom-Oppenlieimer PES and internal motion are particularly simple. 

It must be pointed out that another type of internal motion is the overall rotation of the molecule. The vibration and rotation of the molecule are shown schematically in figure Al.2.2. 

Flowever, if only the Darling-Deimison conplmg is important for the conpled stretches, what is its importance telling ns about the internal molecnlar motion It turns out that the right kind of analysis of the spectroscopic fitting Flamiltonian reveals a vast amonnt about the dynamics of the molecnle it allows ns to decipher the story encoded in the spectrum of what the molecule is really doing in its internal motion. We will approach this spectral cryptology from two complementary directions ... 

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

Direct experiment-simulation quasielastic neutron scattering comparisons have been perfonned for a variety of small molecule and polymeric systems, as described in detail in Refs. 4 and 18-21. The combination of simulation and neutron scattering in the analysis of internal motions in globular proteins was reviewed in 1991 [3] and 1997 [4]. 

Two physically reasonable but quite different models have been used to describe the internal motions of lipid molecules observed by neutron scattering. In the first the protons are assumed to undergo diffusion in a sphere [63]. The radius of the sphere is allowed to be different for different protons. Although the results do not seem to be sensitive to the details of the variation in the sphere radii, it is necessary to have a range of sphere volumes, with the largest volume for methylene groups near the ends of the hydrocarbon chains in the middle of the bilayer and the smallest for the methylenes at the tops of the chains, closest to the bilayer surface. This is consistent with the behavior of the carbon-deuterium order parameters,. S cd, measured by deuterium NMR ... 

Another way to describe deviations from the simple BPP spectral density is the so-called model-free approach of Lipari and Szabo [10]. This takes account of the reduction of the spectral density usually observed in NMR relaxation experiments. Although the model-free approach was first applied mainly to the interpretation of relaxation data of macromolecules, it is now also used for fast internal dynamics of small and middle-sized molecules. For very fast internal motions the spectral density is given by ... 

Worse was to come. Boltzmann in 1872 made the same weird statistical equality hold for every mode in a dynamical system. It must, for example, apply to any internal motions that molecules might have. Assuming, as most physicists did by then, that the sharp lines seen in the spectra of chemical elements originate in just such internal motions, any calculation now of Cp/C would yield a figure even lower than 1.333. Worse yet, as Maxwell shatteringly remarked to one student, equipartition must apply to solids and liquids as well as gases Boltzmann has proved too much. ... 

Some molecules undergo an internal motion in which one part of the molecule rotates about a bond connecting it with the rest of the molecule. Some examples are... 

This simple relaxation theory becomes invalid, however, if motional anisotropy, or internal motions, or both, are involved. Then, the rotational correlation-time in Eq. 30 is an effective correlation-time, containing contributions from reorientation about the principal axes of the rotational-diffusion tensor. In order to separate these contributions, a physical model to describe the manner by which a molecule tumbles is required. Complete expressions for intramolecular, dipolar relaxation-rates for the three classes of spherical, axially symmetric, and asymmetric top molecules have been evaluated by Werbelow and Grant, in order to incorporate into the relaxation theory the appropriate rotational-diffusion model developed by Woess-ner. Methyl internal motion has been treated in a few instances, by using the equations of Woessner and coworkers to describe internal rotation superimposed on the overall, molecular tumbling. Nevertheless, if motional anisotropy is present, it is wiser not to attempt a quantitative determination of interproton distances from measured, proton relaxation-rates, although semiquantitative conclusions are probably justified by neglecting motional anisotropy, as will be seen in the following Section. 

A water molecule can vibrate by internal motion of its atoms. 

The application of the Bom-Oppenheimer and the adiabatic approximations to separate nuclear and electronic motions is best illustrated by treating the simplest example, a diatomic molecule in its electronic ground state. The diatomic molecule is sufficiently simple that we can also introduce center-of-mass coordinates and show explicitly how the translational motion of the molecule as a whole is separated from the internal motion of the nuclei and electrons. 

Equation (10.28b) describes the internal motions of the two nuclei and the electrons relative to the center of mass. Our next goal is to solve this equation using the method described in Section 10.1. Equation (10.28a), on the other hand, describes the translational motion of the center of mass of the molecule and is not considered any further here. 

For folded proteins, relaxation data are commonly interpreted within the framework of the model-free formalism, in which the dynamics are described by an overall rotational correlation time rm, an internal correlation time xe, and an order parameter. S 2 describing the amplitude of the internal motions (Lipari and Szabo, 1982a,b). Model-free analysis is popular because it describes molecular motions in terms of a set of intuitive physical parameters. However, the underlying assumptions of model-free analysis—that the molecule tumbles with a single isotropic correlation time and that internal motions are very much faster than overall tumbling—are of questionable validity for unfolded or partly folded proteins. Nevertheless, qualitative insights into the dynamics of unfolded states can be obtained by model-free analysis (Alexandrescu and Shortle, 1994 Buck etal., 1996 Farrow etal., 1995a). An extension of the model-free analysis to incorporate a spectral density function that assumes a distribution of correlation times on the nanosecond time scale has recently been reported (Buevich et al., 2001 Buevich and Baum, 1999) and better fits the experimental 15N relaxation data for an unfolded protein than does the conventional model-free approach. 

The previous approach is valid as long as the molecular reorientation can be described by a single correlation time. This excludes molecules involving internal motions and/or molecular shapes which cannot, to a first approximation, be assimilated to a sphere. Due to its shape, the molecule shown in Figure 15 cannot evidently fulfil the latter approximation and is illustrative of the potentiality of HOESY experiments as far as carbon-proton distances and the anisotropy of molecular reorientation are concerned.45 58... 

Figure 15 The model molecule used to demonstrate the possibilities of HOESY experiments in terms of carbon-proton distances and reorientational anisotropy. To a first approximation, the molecule is devoid of internal motions and its symmetry determines the principal axis of the rotation-diffusion tensor. Note that H, H,., H,-, H,/ are non-equivalent. The arrows indicate remote correlations.

When a molecule exhibits large internal motions difficulties arise in using most available techniques for the determination of molecular geometry. In a study of 2,2 -biselenophene it was shown that although internal motion is present, useful structural information can still be obtained in the liquid crystal phase and that, at present, other techniques are not available for obtaining equivalent information, at least not in a liquid-like phase.13 This study also demonstrates the usefulness of the heteroatom satellites, and in particular of Se—H dipolar couplings. 

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