The Structures of Organic Molecules

Our first three chapters established some fundamental principles concerning the structure of organic molecules and introduced the connection between structure and reactivity with a review of acid-base reactions In this chapter we explore structure and reactivity m more detail by developing two concepts functional groups and reaction mechanisms A functional group is the atom or group m a molecule most respon sible for the reaction the compound undergoes under a prescribed set of conditions How the structure of the reactant is transformed to that of the product is what we mean by the reaction mechanism... 

We contend therefore that introduction of molecular modeling very early into the currieulum need not complicate or eonfuse the learning of organie chemistry, but rather assist the student in visualizing the structures of organic molecules and in learning the intimate connections between molecular structure and molecular properties. 

Dunitz, J. D. (1979) X-Ray Analysis and the Structure of Organic Molecules. Cornell University Press, Ithaca NY [4.2]. 

The results shown in the table provide further evidence of the extraordinary extent to which the tetrahedral carbon atom of van t Hoff and Le Bel determines the structure of organic molecules. 

Chemists, biochemists, biotechnologists, and physicists now routinely use NMR spectroscopy as a powerful research tool. The effective application of ID and 2D NMR expteriments depends largely on the skill and innovation of the user. This book is intended to provide practical knowledge to research workers in the use of NMR spectroscopic techniques to elucidate the structure of organic molecules. Every attempt has been made to prevent the book from becoming too technical, and the underlying principles behind many of the experiments have been described nonmathematically. 

Applications Useful 2D NMR experiments for identification of surfactants are homonuclear proton correlation (COSY, TOCSY) and heteronuclear proton-carbon correlation (HETCOR, HMQC) spectroscopy [200,201]. 2D NMR experiments employing proton detection can be performed in 5 to 20 min for surfactant solutions of more than 50 mM. Van Gorkum and Jensen [238] have described several 2D NMR techniques that are often used for identification and quantification of anionic surfactants. The resonance frequencies of spin-coupled nuclei are correlated and hence give detailed information on the structure of organic molecules. 

Electron dot formulas are useful for deducing the structures of organic molecules, but it is more convenient to use simpler representations—structural or graphic formulas—in which a line is used to denote a shared pair of electrons. Because each pair of electrons shared between two atoms is equivalent to a total bond order of 1, each shared pair can be represented by a line between the symbols of the elements. Unshared electrons on the atoms are usually not shown in this kind of representation. The resulting representations of molecules are called graphic formulas or structural formulas. The structural formulas for the compounds (a) to (e) described in Example 21.1 may be written as follows ... 

During the very first series of studies using single-crystal x-ray crystallography to determine the structures of organic molecules, Robertson reported the structure of resorcinol (1,3-dihydroxybenzene) [25]. This crystalline material corresponded to that ordinarily obtained at room temperature, and was later termed the a-form. Shortly thereafter, it was found that the a-form underwent a transformation into a denser crystalline modification (denoted as the P-form) when heated at about 74°C,... 

Domenicano, A. and Murray-Rust, P. (1979). Tetrahedron Lett. 2283 Dubois, J. E. and Coss6-Barbi, A. (1988). J. Am. Chem. Soc. 110, 1220 Dunitz, J. D. (1979). X-Ray Analysis and the Structure of Organic Molecules. Cornell University Press, Ithaca, NY... 

Dunitz JD (1995) X-ray analysis and the structure of organic molecules. Verlag Helevetica Chlmlca Acta, Basel... 

Wehrli and Kovats (1) introduced the concept of the retention index to help confirm the structure of organic molecules. This method utilizes a series of normal alkanes as a reference base instead of one compound as in the relative retention method. Identification can be assisted with the use of the retention... 

When the reaction product(s) is obtained in pure form, modern instrumental methods of structure determination, rather than traditional wet methods, provide file fastest way to determine the functionality and connectivity present. Today s chemist has a large number of tools available with which to probe the structure of molecules, but for determining the structures of organic molecules the big three are nuclear magnetic resonance (NMR) spectroscopy, infrared (IR) spectroscopy, and mass spectrometry (MS). The frequency of use of these techniques generally falls in the same order (NMR > IR > MS). 

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