Extended structures vibrational analysis

The vibrational analysis of Schlapfer and Nakamoto (2) has been confirmed and extended based on structural and vibrational studies and DFT calculations of [Ni(S2C2Me2)2]01 2 by Holm and co-workers (13). This series is the only one for which high-resolution structural data is available in all three charge states. For the neutral, monoanionic, and dianionic complexes, the mean C=C... 

Although early studies assumed that PG also adopts an APPS structure, electron diffraction studies of single crystals and oriented thin films [94] suggested that extended-chain PG, PGI, has an APRS structure. This was supported by conformational energy calculations [95], and was the basis for a detailed vibrational analysis of the PGI spectra [19, 96], strongly confirming this proposal. (Since the... 

Minimization and vibrational analysis are useful for the determination of force field parameters, system preparation, and the study of many problems of biological interest. A new optimizer based on a truncated Newton method (TNPACK) that is effective for large molecules has been added to CHARMM. All minimizers, excluding TNPACK, support the use of holonomic constraints on selected bonds and angles (SHAKE). Vibrational analysis has been extended via addition of the MOLVIB module (K. Kuczera and J. Wiorkiewicz-Kuczera, unpublished), which allows for the determination of potential energy distributions and the analysis of lattice modes in combination with the CRYSTAL facility. Minimizations may also be performed in the presence of a variety of structural constraints. This allows for atomic positions, internal coordinates, interatomic distances, etc. to be fixed or constrained to specified values. Such constraint methods may be used in molecular dynamics simulations. 

In a large series of studies of non-rigid molecules [6-11], we have omitted the pseudopotential correction on the basis of a previous estimation [12], Since the aim of these papers was the analysis of vibrational structures, the frequencies and intensities, for / = 0, of molecules exhibiting one, two or three large amplitude motions were calculated. However, at the present time, we extend the previous methods to the study... 

Polyethylene has been studied spectroscopically in greater detail than any other polymer. This is primarily a result of its (supposedly) simple structure and the hope that its simple spectrum could be understood in detail. Yet as simple as this structure and spectrum are, a satisfactory analysis had not been made until relatively recently, and even then significant problems of interpretation still remained. The main reason for this is that this polymer in fact generally contains structures other than the simple planar zig-zag implied by (CH2CH2) there are not only impurities of various kinds that differ chemically from the above, but the polymer always contains some amorphous material. In the latter portion of the material the chain no longer assumes an extended planar zig-zag conformation, and as we have noted earlier, such ro-tationally isomeric forms of a molecule usually have different spectra. Furthermore, the molecule has a center of symmetry, which as we have seen implies that some modes will be infrared inactive but Raman active, so that until Raman spectra became available recently it was difficult to be certain of the interpretation of some aspects of the spectrum. As a result of this work, and of detailed studies on the spectra of n-paraffins, it now seems possible to present a quite detailed assignment of bands in the vibrational spectrum of polyethylene. 

Electronic Spectrum. Acetone is the simplest ketone and thus has been one of the most thoroughly studied molecules. The it n absorption spectrum extends from 350 nm and reaches a maximum near 270 nm (125,175). There is some structure observable below 295 nm, but no vibrational and rotational analysis has been possible. The fluorescence emission spectrum starts at about 380 nm and continues to longer wavelengths (149). The overlap between the absorption and the fluorescence spectra is very poor, and the 0-0 band has been estimated to be at - 330 nm (87 kcal/mol). The absorption spectra, emission spectra, and quantum yields of fluorescence of acetone and its symmetrically methylated derivatives in the gas phase havbe been summarized recently (101). The total fluorescence quantum yield from vibrationally relaxed acetone has been measured to be 2.1 x 10 j (105,106), and the measurements for other ketones and aldehydes are based on this fluorescence standard. The phosphorescence quantum yield is -0.019 at 313 nm (105). 

The simplest way to combine electronic stnicture calculations with nuclear dynamics is to use harmonic analysis to estimate both vibrational averaging effects on physico-chemical observables and reaction rates in terms of conventional transition state theory, possibly extended to incorporate tunneling corrections. This requires, at least, the knowledge of the structures, energetics, and harmonic force fields of the relevant stationary points (i.e. energy minima and first order saddle points connecting pairs of minima). Small anq)litude vibrations around stationary points are expressed in terms of normal modes Q, which are linearly related to cartesian coordinates x... 

Polypeptide molecules of course exhibit many more vibrational frequencies than the half-dozen or so amide modes. For example, a molecule as simple as the extended form of polyglycine has about 50 bands in its IR and Raman spectra. It is clear that the information contained in the entire spectrum must therefore be a more sensitive indicator of three-dimensional structure. The only way to utilize this information fully is through a normal-mode analysis, that is, by comparing observed frequencies with those calculated for specific secondary structures. This can provide a powerful method for testing structural hypotheses in great detail. 

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