Normal modes structure

The influence of solvent can be incorporated in an implicit fashion to yield so-called langevin modes. Although NMA has been applied to allosteric proteins previously, the predictive power of normal mode analysis is intrinsically limited to the regime of fast structural fluctuations. Slow conformational transitions are dominantly found in the regime of anharmonic protein motion. 

An interesting approach has recently been chosen in the MBO(N)D program ([Moldyn 1997]). Structural elements of different size varying from individual peptide planes up to protein domains can be defined to be rigid. During an atomistic molecular dynamics simulation, all fast motion orthogonal to the lowest normal modes is removed. This allows use of ca. 20 times longer time steps than in standard simulations. 

One type of single point calculation, that of calculating vibrational properties, is distinguished as a vibrations calculation in HyperChem. A vibrations calculation predicts fundamental vibrational frequencies, infrared absorption intensities, and normal modes for a geometry optimized molecular structure. 

Evidence exists that some of the softest normal modes can be associated with experimentally determined functional motions, and most studies apply normal mode analysis to this purpose. Owing to the veracity of the concept of the normal mode important subspace, normal mode analysis can be used in structural refinement methods to gain dynamic information that is beyond the capability of conventional refinement techniques. 

In this paper, we review progress in the experimental detection and theoretical modeling of the normal modes of vibration of carbon nanotubes. Insofar as the theoretical calculations are concerned, a carbon nanotube is assumed to be an infinitely long cylinder with a mono-layer of hexagonally ordered carbon atoms in the tube wall. A carbon nanotube is, therefore, a one-dimensional system in which the cyclic boundary condition around the tube wall, as well as the periodic structure along the tube axis, determine the degeneracies and symmetry classes of the one-dimensional vibrational branches [1-3] and the electronic energy bands[4-12]. 

One way to do so is to look at the normal mode corresponding to the imaginary frequency and determine whether the displacements that compose it tend to lead in the directions of the structures that you think the transition structure connects. The symmetry of the normal mode is also relevant in some cases (see the following example). Animating the vibrations with a chemical visualization package is often very useful. Another, more accurate way to determine what reactants and products the transition structure coimects is to perform an IRC calculation to follow the reaction path and thereby determine the reactants and products explicity this technique is discussed in Chapter 8. 

A minimum > 1 imaginary frequencies The structure is a saddle point, not a minimum. Continue searching for a minimum (try unconstraining the molecular symmetry or distorting the molecule along the normal mode corresponding to the imaginary frequency). 

A transition state 1 imaginary frequency The structure is a true transition state. Determine if the structure connects the correct reactants and products by examining the imaginary frequency s normal mode or by-performing an IRC calculation. 

A transition state > 1 imaginary frequency The structure is a higher-order saddle point, but is not a transition structure that connects two minima. QST2 may again be of use. Otherwise, examine the normal modes corresponding to the imaginary frequencies. One of them will (hopefully) point toward the reactants and products. Modify the geometry based on the displacements in the other mode(s), and rerun the optimization. 

The 180° trans structure is only about 2.5 kcal/mol higher in energy than the 0° conformation, a barrier which is quite a bit less than one would expect for rotation about the double bond. We note that this structure is a member of the point group. Its normal modes of vibration, therefore, will be of two types the symmetrical A and the non-symmetrical A" (point-group symmetry is maintained in the course of symmetrical vibrations). 

We must look further in order to locate the transition structure linking the cis and trans forms of 1-propene. Since we are looking for a normal mode which su esis... 

The transition state optimization (Opt=(TS,CakFC)) of the structure on the right converges in 12 steps. The UHF frequency calculation finds one imaginary frequency. Here is the associated normal mode ... 

In many of the normal modes of vibration of a molecule the main participants in the vibration will be two atoms held together by a chemical bond. These vibrations have frequencies which depend primarily on the masses of the two vibrating atoms and on the force constant of the bond between them. The frequencies are also slightly affected by other atoms attached to the two atoms concerned. These vibrational modes are characteristic of the groups in the molecule and are useful in the identification of a compound, particularly in establishing the structure of an unknown substance. 

Exercise 4.4. Take the minimized structure of the three-carbon ring of Exercise 4.1 and evaluate its normal modes. 

The first-principles calculation of NIS spectra has several important aspects. First of all, they greatly assist the assignment of NIS spectra. Secondly, the elucidation of the vibrational frequencies and normal mode compositions by means of quantum chemical calculations allows for the interpretation of the observed NIS patterns in terms of geometric and electronic structure and consequently provide a means of critically testing proposals for species of unknown structure. The first-principles calculation also provides an unambiguous way to perform consistent quantitative parameterization of experimental NIS data. Finally, there is another methodological aspect concerning the accuracy of the quantum chemically calculated force fields. Such calculations typically use only the experimental frequencies as reference values. However, apart from the frequencies, NIS probes the shapes of the normal modes for which the iron composition factors are a direct quantitative measure. Thus, by comparison with experimental data, one can assess the quality of the calculated normal mode compositions. 

How can one hope to extract the contributions of the different normal modes from the relaxation behavior of the dynamic structure factor The capability of neutron scattering to directly observe molecular motions on their natural time and length scale enables the determination of the mode contributions to the relaxation of S(Q, t). Different relaxation modes influence the scattering function in different Q-ranges. Since the dynamic structure factor is not simply broken down into a sum or product of more contributions, the Q-dependence is not easy to represent. In order to make the effects more transparent, we consider the maximum possible contribution of a given mode p to the relaxation of the dynamic structure factor. This maximum contribution is reached when the correlator in Eq. (32) has fallen to zero. For simplicity, we retain all the other relaxation modes = 1 for s p. 

---