Molecules structure, spectrometric determination

The set of energy levels associated with a particular substance is a unique characteristic of that substance and determines the frequencies at which electromagnetic radiation can be absorbed or emitted. Qualitative information regarding the composition and structure of a sample is obtained through a study of the positions and relative intensities of spectral lines or bands. Quantitative analysis is possible because of the direct proportionality between the intensity of a particular line or band and the number of atoms or molecules undergoing the transition. The various spectrometric techniques commonly used for analytical purposes and the type of information they provide are given in Table 7.1. 

Mass spectrometry (MS) is based on the generation of gaseous ions from an analyte molecule, the subsequent separation of those ions according to their mass-to-charge (m/z) ratio, and the detection of those ions [23]. The resulting mass spectrum is a plot of the (relative) abundance of the produced ions as a function of the m/z ratio. MS is important in determining the molecular mass, molecular fonnula and elemental composition and in elucidating the structure of the compound. Moreover, MS is the most sensitive spectrometric method for molecular analysis. Now, on-line... 

Mulliken attributed the strong absorption band of the system to the excitation of the ground-state complex to the CT state with the aromatic molecule acting as the electron donor and the iodine as the acceptor, that is, Bz+ I2. Several spectroscopic and theoretical studies have predicted that the Bz I2 ground state has a C(,v axial structure with the 1—I bond being perpendicular to the benzene molecular plane. The heat of formation of this complex in the gas phase was determined by spectrometric methods to be on the order of 2-3 kcal/mol and our ab initio calculations support these values. 

Modern mass spectrometers make it possible for substances in the femtomole range (10-15M) to be analyzed, and for high molecular masses of complex molecules well over 100 kDa to be obtained. Mass spectrometers allow molecular mass determination, and the generation of fragmentation data to allow sequencing and structure elucidation, generally in tandem mass-spectrometric experiments. 

The scan mode determines the extent and quality of mass spectrometric data and has thus to be chosen with respect to the analytical requirements. Detection of unknown compounds, identification of unknown structures and confirmation of known molecules as well as quantification of distinct target analytes require different scan modes for reliable optimum analytical acuity. 

Although molecules cannot be identified as the building blocks of ionic crystals, the free molecules of some compounds may be considered as if they were taken out of the crystal. A nice example is sodium chloride whose main vapor components are monomeric and dimeric molecules. They are indicated in the crystal structure in Figure 9-56, as is a tetrameric species. Mass spectrometric studies of cluster formation determined a great relative abundance of a species with 27 atoms in the cluster. The corresponding 3x3x3 cube may, again, be considered as a small crystal [106],... 

Unfortunately, from the point of view of the physical organic chemist, the mass-spectrometric approach suffers from certain intrinsic limitations. In the first place, the range of pressures accessible to the investigator is severely limited, and most of the available data refer to experiments carried out at pressures well below one torr. In the second place, the mass spectrometer detects only charged species, and the neutral molecules, which represent the final products of the carbonium-ion reactions and are of prime concern to the physical organic chemist, cannot be determined at all. Finally, since the structure of the ionic species, that are analysed exclusively according to their m/e ratio, cannot be directly deduced from mass spectra, it is difficult to discriminate isomeric ions, and to study the isomerization reactions of the carbonium ions, which play such an important role in their solution chemistry. 

Mass spectrometry is an important method in determining carbohydrate structures, and there are excellent reviews of the most recent mass spectrometric methods for complex carbohydrates [16,17]. Among many useful techniques, classical ionization of volatile molecules through electron impact (El) or chemical ionization (Cl) [18,19], electrospray ionization (ESI) [20], and field desorption techniques (ED) [21] are frequently employed in structural analysis. 

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