Molecular modelling infrared spectroscopy

This comprehensive review of theoretical models and techniques will be invaluable to theorists and experimentalists in the fields of infrared and Raman spectroscopy, nuclear magnetic resonance, electron spin resonance and flame thermometry. It will also be useful to graduate students of molecular dynamics and spectroscopy. 

Novotny et al. [41] used p-polarized reflection and modulated polarization infrared spectroscopy to examine the conformation of 1 -1,000 nm thick liquid polyperfluoropropy-lene oxide (PPFPO) on various solid surfaces, such as gold, silver, and silica surfaces. They found that the peak frequencies and relative intensities in the vibration spectra from thin polymer films were different from those from the bulk, suggesting that the molecular arrangement in the polymer hlms deviated from the bulk conformation. A two-layer model has been proposed where the hlms are composed of interfacial and bulk layers. The interfacial layer, with a thickness of 1-2 monolayers, has the molecular chains preferentially extended along the surface while the second layer above exhibits a normal bulk polymer conformation. 

In earlier literature reports, x-ray data of a-based ceramics, the /3-like phase observed in certain silica minerals was explained by a structural model based on disordered Q -tridymite. However, others have suggested that the structure of the stabilized jS-cristobalite-like ceramics is closer to that of a-cristobalite than that of Q -tridymite, based on the 29Si nuclear magnetic resonance (NMR) chemical shifts (Perrota et al 1989). Therefore, in the absence of ED data it is impossible to determine the microstructure of the stabilized jS-cristobalite-like phase. ED and HRTEM have provided details of the ceramic microstructure and NMR has provided information about the environments of silicon atoms in the structure. Infrared spectroscopy views the structure on a molecular level. 

Even though these approaches are powerful methods for determining functional sites on proteins, they are limited if not coupled with some form of structural determination. As Figure 2 illustrates, molecular biology and synthetic peptide/antibody approaches are not only interdependent, they are tied in with structural determination. Structural determination methods can take many forms, from the classic x-ray crystallography and NMR for three-dimensional determination, to two-dimensional methods such as circular dichroism and Fourier Transformed Infrared Spectroscopy, to predictive methods and modeling. A structural analysis is crucial to the interpretation of experimental results obtained from mutational and synthetic peptide/antibody techniques. 

Moore, D.J., and M.E. Rerek, 2000. Insights into the molecular organisation of lipids in the skin barrier from infrared spectroscopy studies of stratum corneum lipid models. Acta Derm Venereol Suppl Stockh.) 208 16. 

In 1961 a molecular model of a (7/2) helix [Figure 6(a)] was proposed by the author and his coworkers (13.) based on the information from x-ray, infrared, and Raman spectroscopy, but the crystal structure could not be determined at that time. After ten years, owing to the development of methods and apparatus, especially the constrained least-squares method and a vacuum cylindrical camera with a radius of 10 cm, the crystal structure has been determined as shown in Figure 6(c) (22.). The internal rotation angles are considerably distorted from the uniform helix, although the molecular conformation is essentially the (7/2) helix and close to the TTG sequences. 

The most basic information that is needed for constructing a global potential energy surface for gas phase MD simulations is the structures and vibrational frequencies. The earliest information about gas-phase RDX molecular structures was obtained from theoretical calculations [54-58]. In 1984 Karpowicz and Brill [59] reported Fourier transform infrared spectra for vapor-phase (and for the a - and p -phase) RDX in 1984, however, their data precluded a complete description of the molecular conformations and vibrational spectroscopy. More recently, Shishkov et al. [60] presented a more complete description based on electron-scattering data and molecular modeling. They concluded that the data were best reproduced by RDX in the chair conformation with all the nitro groups in axial positions. 

Both X-ray and neutron fiber diffraction (as well as electron microscopy) techniques have been applied to filamentous viruses, for which the prospect of three-dimensional crystals is poor. By combining neutron and X-ray fiber diffraction, NMR, circular dichroism, and Raman and infrared spectroscopies, an atomic model for the filamentous bacteriophage Pfl has been derived (Liu and Day, 1994). Other studies concerning Pfl have relied on purely X-ray fiber diffraction data, together with molecular modeling, to provide detailed filament structures (Pederson et at, 2001 Welsh et at, 1998a,b, 2000). Eiber diffraction was also used to solve the structure of the rodlike helical tobacco mosaic virus (TMV), where all of the coat protein and three genomic nucleotides... 

Menikh A, Nyholm P-G, Boggs JM. Characterization of the inter-achon of Ca with hydroxy and non-hydroxy fatty acid species of cerebroside sulfate by fourier transform infrared spectroscopy and molecular modeling. Biochemistry 1997 36 3438-3447. 

Up to now, infrared spectroscopy has been used mainly to determine the types of hydroxyl groups and the acidity of zeolites (39). The frequencies of the vertical and horizontal vibrations (with respect to the cavity wall) of H2O molecules adsorbed in zeolite A were determined by measurements in the far infrared ( 220 and —75 cm" ) (37). These values are in agreement with a simple theoretical model. A number of ultraviolet and ESR studies are reviewed (33). The difference has been established between the specific molecular interaction of aromatic molecules on zeolites cationized with alkali cations and the more complex interactions involving charge transfer in CaX and deca-tionized X and Y zeolites. These more complex interactions with CaX zeolites containing protonized vacancies and with decationized zeolites are similar. These phenomena are related to the interactions of molecules with acidic centers in zeolites which are stronger, as compared with the molecular adsorption. 

A standard experimental probe of this motion is infrared spectroscopy. We may use the results of Sections 7,5 and 8.2.3 to examine the effect of interaction with the thermal environment on the absorption lineshape. The simplest model for the coupling of a molecular system to the radiation field is expressed by a term —fi S in the Hamiltonian, where is the molecular dipole, and (t) is the oscillating electric field (see Section 3.1). For a one-dimensional oscillator, assuming that /r is proportional to the oscillator displacement from its equilibrium position and taking cos((uZ), we find that the coupling of the oscillator to the thermal environment and the radiation field can be modeled by Eq. (8.31) supplemented by a term (F/ni where F denotes the radiation induced driving force. We can... 

The problems of peak assignment in infrared spectroscopy are probably greater than those faced in analogous NMR experiments. Furthermore, infrared transition probabilities are highly variable owing to symmetry considerations and other molecular properties. In the absence of calibration, relative intensities of infrared absorption bands do not accurately reflect relative concentrations. By characterizing the infrared properties of appropriate model compounds and... 

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