Use of IR Spectroscopy for Structure Determination

The very strongly H-bound carboxylic acid dimer has a very broad absorption at 2500 cm 1 for the OH bond. Because H bonding is dependent on concentration and on the polarity and H-bonding properties of the solvent, frequency shifts due to H bonding are quite variable. 

While other structural effects on absorption frequencies are known, the above factors are the ones most commonly encountered in routine organic structure determination. 

As seen above, IR spectroscopy is most commonly used to identify functional groups and bonding patterns in molecules from the higher energy portion of the spectrum (1200-4000 cm ) where absorptions are primarily due to bondstretching vibrations. Some information on atom connectivity in the molecule can also be deduced from the frequency shifts caused by structural factors. In general, however, it is not possible to completely deduce the structure of a molecule by examination of its IR spectrum. However, IR spectroscopy is a powerful complement to NMR spectroscopy for structure determination. 

For example, the reaction of 3-chlorocyclohexanone with DBU in toluene gives a product which is seen to have two vinyl protons by NMR and thus is an elimination product, probably either A or B. Now while one might rationalize by both chemical intuition and by the splitting pattern that conjugated isomer A is the product, examination of the IR spectrum shows a carbonyl group (at 1680 cm-1) and an olefin band (at 1630 cm-1). A typical cyclohexanone comes at 1710 cm-1 and cyclohexene comes at 1643 cm-1. 

Clearly the observed frequencies of the product are at lower frequencies than a simple ketone or olefin and are indicative of a conjugative interaction between these two functions. Thus A and not B is the product. 

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We will concentrate upon the most commonly used techniques in organic structure determination nuclear magnetic resonance (NMR), infrared (IR) and ultraviolet-visible (UV-Vis) spectroscopy, and mass spectrometry (MS). The amount of space devoted to each technique in this text is meant to be representative of their current usage for structure determination. 

In the preceding example several types of spectroscopy are brought to bear. While the product structure could probably be deduced from IR spectroscopy or NMR (either 1II or 13C), the use of all three methods confirms the assignment. It is often prudent to use more than a single technique for structure determination so that the results reinforce each other. If a structure assignment is not consistent with all the data, the structure is probably incorrect. 

When X-radiography studies are not possible, theoretical calculations and spectroscopic studies can help in the structural characterization of C02 complexes. The most largely used as a diagnostic tool is infrared (IR) spectroscopy, both for the quantitative determination of C02 and for structural analysis. 

The benefits of using recycle in the analytical mode can be illustrated by referring to the chromatogram in Figure 6-8. The reacted mixture is separated into the parent compound (rubrene), its oxide, and the ozone complex. It was desired that both the ozone complex and the oxide be isolated as individual peaks for structure determination. Therefore, before each peak was collected and identified by an analytical technique such as IR, NMR, or mass spectroscopy, the peaks were recycled to attain high peak purity. 

The information derived from NMR spectroscopy is extraordinarily useful for structure determination. Not only can we count the number of nonec]uiva-lent carbon atoms in a molecule, we can also get information about tbe electronic environment of each carbon and can even find how many protons each is attached to. As a result, we can answ er mani structural questions that go unanswered by IR spectroscopy or mass spectrometry. 

Considerations of this kind do not apply to labeling with deuterium, which is available cheaply as the almost pure isotope and is not dangerous. Deuterium-labeled compounds are, for instance, used in analysis, in studies of reaction mechanism, for investigation of isotope effects, and for research on the metabolism of biochemically important substances. They are of particular value for the determination of the structure of chemical substances both by means of chemical reactions and by means of mass spectroscopy or IR or NMR spectroscopy. Moreover, the perdeuterated compounds are important solvents for use in these physical measurements. 

Modern IR spectrometry is a versatile tool that is applied to the qualitative and quantitative determination of molecular speries of all types. In this chapter we first focus on the. uses of mid-IR absorption and reflection spectrometry for structural investigations of molecular compounds, particularly organic compounds and species of interest in biochemistry. We then examine in less detail several of the other cqtplications of IR spectroscopy. 

The biosynthesis and chemistry of alkaloids have been discussed in a recent book on natural products (Hendrickson, 1965). Hendrickson has pointed out the important contributions made to structural chemistry by instrumental methods of analysis such as UV, IR, NMR, and ORD spectroscopy. One of the alkaloids discussed in which reference to the use of infrared spectroscopy was made was vindoline (CIII) (a compound isolated from periwinkles Vinca rosea in a search for anticancer agents). Dihydrovindoline hydrochloride on mild pyrolysis yielded a ketone C21H28-N2O2. The infrared spectrum of this compound showed absorption at 1709cm", which indicated a cyclohexanone. This result was used, together with other information, in determining the total structure. 

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