IR and Structure Determination

Since its introduction, IR spectroscopy has proven to be a valuable tool for determining the functional groups in organic molecules. 

IR spectroscopy is often used to determine the outcome of a chemical reaction. For example, oxidation of the hydroxy group in C to form the carbonyl group in periplanone B (Section 9.5C) is accompanied by the disappearance of the OH absorption (3600-3200 cm ) and the appearance of a carbonyl absorption near 1700 cm in the IR spectrum of the product. 

The combination of IR and mass spectral data provides key information on the structure of an unknown compound. The mass spectrum reveals the molecular weight of the unknown (and the molecular formula if an exact mass is available), and the IR spectrum helps to identify the important functional groups. 

Example What information is obtained from the mass spectrum and IR spectrum of an unknown compound X Assume X contains the elements C, H, and O. 

Step [1] Use the molecular ion to determine possible molecular formulas. Use an exact mass (when available) to determine a molecular formula. 

Problem 13.17 What functional groups are responsible for the absorptions above 1500 cm in the IR spectra for compounds A and B  

Problem 13.18 What are the major IR absorptions in the functional group region for each compound  

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Wilson et al. [662-665] have described various prototype systems for total organic analysis devices. It has proved technically feasible to obtain UV, IR, NMR and MS spectra (together with atomic composition based on accurate mass determination) following RPLC separation. The fully integrated approach offers the benefit that one chromatographic run is required, thus ensuring that all of the spectrometers observe the same separation. Such multiple hyphenations might favour the analysis of complex mixtures for both confirmation of identity and structure determination (should this represent a cost-effective approach). Table 7.72 illustrates the main features of on-flow multiple LC hyphenation. 

Fourier-transformed infrared spectroscopy (FT1R), either in the transmission mode(70), the grazing incidence reflection (GI) mode(7,5) or the attenuated total reflection (ATR) mode(7,2), has been the most widely used experimental tool for the characterization and structure determination of SA monolayers. GI-IR is especially useful in determining the molecular orientation in the film structures because it senses only the vibrational component perpendicular to the substrate surface(7,5). Polarized ATR-IR can also be used to study molecular orientation(7,77). McKeigue and Gula-ri(72) have used ATR-IR to quantitatively study the adsorption of the surfactant Aerosol-OT. 

Use MS and IR for Structure Determination 484 Nuclear Magnetic Resonance Spectroscopy... 

Vedadi M, Niesen PH, Allali-Hassani A, Pedorov OY, Pinerty PI Ir, Wasney GA, Yeung R, Arrowsmith C, Ball LI, Berglund H, et al. Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc. Natl. Acad. Sci. U.S.A. 2006 103 15835-15840. 

Qualitative Analyses and Structural Determination by Mid-IR Absorption Spectroscopy... 

M02X4(LL)2 3.5 X = Cl, L = dppe, arphos, dpae. IR spectra and structural determination (X = Br, L = arphos) show deviations of about 30° from eclipsed ligand configuration. 25-27... 

When the structure of a newly synthesized compound has to be established, first the probable molecular fragments are detected using their characteristic features in spectra of different nature (IR, NMR, MS, etc.) and then an attempt to build all feasible structures is made. For this purpose, currently available expert systems are used (see Infrared Data Correlations with Chemical Structure NMR Data Correlation with Chemical Structure and Structure Determination by Computer-based Spectrum Interpretation). 

Organic NLO materials have been intensively studied recently due to their potential application in various fields, such as telecommunications and optical information processes. A series of dicyanoisophorones have been synthesized and structurally determined by single-crystal X-ray diffraction by Kolev and coauthors [421-428] on the basis of Lemke s [444] pioneering studies. Experimental and computational studies on the vibrational spectra of 2-[5,5-dimethyl-3-(2-phenyl-vinil)-cyclohex-2-enylidene]-malononitrile have been reported [445]. However, the presence of aromatic and conjugated systems in the structures of these compounds makes the assignment of individual bands difficult using IR spectra. Therefore, this chapter deals with the solid-state IR-LD analysis of 2-[5,5-dimethyl-3-(2-phenyl-vinyl)-cyclohex-2-enylidene]-malononitrile (/), 2- 5,5-dimethyl-3-[2-(2-methoxyphenyl) vinyl]cyclo-hex-2-enylidene malononitrile (2), and 2-[3-[2-(2,4-dimethoxyphenyl)... 

As diverse as these techniques are all of them are based on the absorption of energy by a molecule and all measure how a molecule responds to that absorption In describing these techniques our emphasis will be on then application to structure determination We 11 start with a brief discussion of electromagnetic radiation which is the source of the energy that a molecule absorbs m NMR IR and UV VIS spectroscopy... 

GW Carter Ir. Entropy, likelihood and phase determination. Structure 3 147-150, 1995. RL Dunbrack Ir, EE Cohen. Bayesian statistical analysis of protein sidecham rotamer preferences. Protein Sci 6 1661-1681, 1997. 

The tetramethylammonium salt [Me4N][NSO] is obtained by cation exchange between M[NSO] (M = Rb, Cs) and tetramethylammonium chloride in liquid ammonia. An X-ray structural determination reveals approximately equal bond lengths of 1.43 and 1.44 A for the S-N and S-O bonds, respectively, and a bond angle characteristic bands in the IR spectrum at ca. 1270-1280, 985-1000 and 505-530 cm , corresponding to o(S-N), o(S-O) and (5(NSO), respectively. Ab initio molecular orbital calculations, including a correlation energy correction, indicate that the [NSO] anion is more stable than the isomer [SNO] by at least 9.1 kcal mol . ... 

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