Crystal molecular, normal vibrational modes

Polymer films were produced by surface catalysis on clean Ni(100) and Ni(lll) single crystals in a standard UHV vacuum system H2.131. The surfaces were atomically clean as determined from low energy electron diffraction (LEED) and Auger electron spectroscopy (AES). Monomer was adsorbed on the nickel surfaces circa 150 K and reaction was induced by raising the temperature. Surface species were characterized by temperature programmed reaction (TPR), reflection infrared spectroscopy, and AES. Molecular orientations were inferred from the surface dipole selection rule of reflection infrared spectroscopy. The selection rule indicates that only molecular vibrations with a dynamic dipole normal to the surface will be infrared active [14.], thus for aromatic molecules the absence of a C=C stretch or a ring vibration mode indicates the ring must be parallel the surface. 

Figure 7. Projections of double six ring modes in siliceous faujasite on modes of molecular double six rings [14], is the square of the projection of the normalized vibrational displacement vector of the crystal on the normalized displacement vector of the molecule.

As pointed out in Section IIB, it is possible to approach the lattice dynamics problem of a molecular crystal by choosing the cartesian displacement coordinates of the atoms as dynamical variables (Pawley, 1967). In this case, all vibrational degrees of freedom of the system are included, i.e., translational and librational lattice modes (external modes) as well as intramolecular vibrations perturbed by the solid (internal modes). It is then obviously necessary to include all intermolecular and intramolecular interactions in the potential function O. For the intramolecular part a force field derived from a molecular normal coordinate analysis is used. The force constants in such a case are calculated from the measured vibrational frequencies, The intermolecular part of O is usually expressed as a sum of terms, each representing the interaction between a pair of atoms on different molecules, as discussed in Section IIA. 

But if we examine the localized near the donor or the acceptor crystal vibrations or intra-molecular vibrations, the electron transition may induce much larger changes in such modes. It may be the substantial shifts of the equilibrium positions, the frequencies, or at last, the change of the set of normal modes due to violation of the space structure of the centers. The local vibrations at electron transitions between the atomic centers in the polar medium are the oscillations of the rigid solvation spheres near the centers. Such vibrations are denoted by the inner-sphere vibrations in contrast to the outer-sphere vibrations of the medium. The expressions for the rate constant cited above are based on the smallness of the shift of the equilibrium position or the frequency in each mode (see Eqs. (11) and (13)). They may be useless for the case of local vibrations that are, as a rule, high-frequency ones. The general formal approach to the description of the electron transitions in such systems based on the method of density function was developed by Kubo and Toyozawa [7] within the bounds of the conception of the harmonic vibrations in the initial and final states. 

In Eq. (10), E nt s(u) and Es(in) are the s=x,y,z components of the internal electric field and the field in the dielectric, respectively, and p u is the Boltzmann density matrix for the set of initial states m. The parameter tmn is a measure of the line-width. While small molecules, N<pure solid show well-defined lattice-vibrational spectra, arising from intermolecular vibrations in the crystal, overlap among the vastly larger number of normal modes for large, polymeric systems, produces broad bands, even in the crystalline state. When the polymeric molecule experiences the molecular interactions operative in aqueous solution, a second feature further broadens the vibrational bands, since the line-width parameters, xmn, Eq. (10), reflect the increased molecular collisional effects in solution, as compared to those in the solid. These general considerations are borne out by experiment. The low-frequency Raman spectrum of the amino acid cystine (94) shows a line at 8.7 cm- -, in the crystalline solid, with a half-width of several cm-- -. In contrast, a careful study of the low frequency Raman spectra of lysozyme (92) shows a broad band (half-width 10 cm- -) at 25 cm- -,... 

The treatment thus far has been for isolated molecules, either small or one-dimensional infinite helices. In some instances crystalline intermolecular interactions are important, and it is therefore necessary to be able to compute the normal modes of a molecular crystal. The general theory of crystal dynamics has been presented by Born and Huang (1954), and the theory of molecular vibrations in solids has been discussed by a number of authors (Fanconi, 1972a,b Zak, 1975 Neto et al., 1976 Decius and Hexter, 1977 Califano, 1977 Schrader, 1978). 

In the regions intermediate between these limiting cases, normal modes of vibration "erode" at different rates and product distributions become sensitive to the precise conditions of the experiment. Intramolecular motions in different product molecules may remain coupled by "long-range forces even as the products are already otherwise quite separated" (Remade Levine, 1996, p. 51). These circumstances make possible a kind of temporal supramolecular chemistry. Its fundamental entities are "mobile structures that exist within certain temporal, energetic and concentration limits." When subjected to perturbations, these systems exhibit restorative behavior, as do traditional molecules, but unlike those molecules there is no single reference state—a single molecular structure, for example—for these systems. What we observe instead is a series of states that recur cyclically. "Crystals have extension because unit cells combine to fill space networks of interaction that define [dissipative structures] fill time in a quite... 

Occasionally molecular crystals of suitable size are found that have all of their molecules aligned mutually parallel [8], It is worth investigating how the scattering law of one particular atom, vibrating in the normal mode, v, would change as a function of the relative... 

The band at 1338 cm was identified in Ref [16] to be a Bjg band based on its frequency and intensity in the crystal spectra, while a band at 1292 cm is likely to be a shifted variant of the C-H deformation Ag mode at 1303 cm in the single crystal [17]. The other bands correspond to modes which normally show infrared activity (see Figure 13.4). Considering that all the modes occurring upon In and Ag deposition are normal modes of the PTCDA molecule, the observed break-down of the Raman-infrared selection rules was proposed to originate from a weak charge transfer between the molecules and the metal surface mediated by molecular vibrations [9]. 

In collaboration with experimental groups, we have recently studied some chlorinated-benzene crystals, 1,2,4,5-tetrachlorobenzene (TCB) [59] and 1,4-dichlorobenzene (DCB) [60], as well as solid tetracyanoethene (TCNE) [58]. In these studies we have used empirical atom-atom potentials, of exp-6 type [see Eq. (6)], which we have supplemented with the Coulomb interactions between fractional atomic charges. Lattice dynamics calculations have been performed by the harmonic method, with inclusion of intramolecular vibrations [70], see Eqs. (17) to (24). The normal modes of the free molecules have been calculated from empirical Valence Force Fields, using the standard CF-matrix method [101, 102]. The results of these calculations are used here to illustrate some phenomena occurring in more complex molecular crystals. These phenomena are well known the numerical results show their quantitative importance, in some specific systems. 

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