Mass spectrometry determining structures using

Mass spectrometers use the difference in mass-to-charge ratio (m/z) of ionized atoms, molecular fragments, or whole molecules to differentiate between them. Mass spectrometry is therefore useful for quantitation of atoms or molecules and also for determining chemical and structural information about them [329, 531-533]. Molecules have distinctive fragmentation patterns which provide information to identify structural components. The general operation of a mass spectrometer is to (1) create gas-phase ions, (2) separate the ions in space or time based on their mass-to-charge ratio, and (3) measure the quantity of ions of each mass-to-charge ratio. The ion separation power of a mass spectrometer is described by the resolution, which is defined as ... 

Once an assessment on a particular impurity has been made all process-related compounds will be examined to confirm that the impurity of interest is indeed an unknown. An easy way of doing this is to compare the retention times of known process-related compounds to that in question. If this analysis confirms that the compound is an unknown, the next step would be to obtain an LC-MS on the compound. Mass spectrometry provides structural information which aids in determining structure. In some cases, mass spectrometry will be enough to identify the compound. In other cases, more complicated methods like LC-NMR are needed or the impurity will need to be isolated in order to obtain additional information. Compounds that are not purified often contain high levels of by-products and can be used for this purpose. Alternatively, mother liquors from crystallizations also contain levels of by-products. Other ways of obtaining larger quantities of impurities include flash chromatography which is typically used for normal phase separations or preparative HPLC which is more common for reversed phase methods. Once a suitable quantity of the compound in question has been obtained a full characterization can be carried out to identify it. 

Mass spectrometry has been used to determine the structures of isomeric monocyclic... 

Structure determination for new GAs. Mass spectrometry is a useful tool for identifying GAs whose structures have been previously determined, in which case comparison of mass spectra is sufficient. In contrast, the characterization of GAs of unknown structure is a much more difficult and time-consuming task. In these cases mass spectrometry can give information such as molecular weight and some indications of structure. 

Mass spectrometry has been used for the structural determination of isomeric I -methyl-3(5)-nitro-4-pyrazolcarbonitriles [302], l,5-dimethyl-3,4-dinitropyrazole [279], 4,4-dinitro-l,l-methylenedipyrazole [1291], 3-amino-5-bcnzylamino-4-nitro-yrazole [317], amino derivatives of 4-nitropyrazole [1292], antibacterial compounds 3-(3-mcthyl-4-nitro- lf/-pyrazole-5-yl)- and 3-(3-methyl-4-nitro-l-alkylpyrazole-5-yl)-5-methyl-4-nitroisoxazoles [500], some l-heteroaryl-4-nitropyrazoles [311]. 

In an investigation of another alkaloid of the dimeric type, vinblastine, high-resolution mass spectrometry was extensively used to determine the molecular formulas of the molecule ion and its cleavage products.117 This was veiy helpful in the structure determination.118 The structure elucidation of villastonine, also an indole alkaloid of the... 

II. Use of Stable Isotopes for Structure Elucidation - Mass spectrometry is commonly used in medicinal chemistry to determine the structure of therapeutic agents and their metabolites. The unequivocal interpretation of the mass spectrum for most classes of compounds requires the use of derivatives which are labeled specifically with stable isotopes. For example, the loss of 16 mass units from hydroxamic acids was shown to be due to the loss of the hydroxylamino oxygen by specific labeling with... 

Because of these powerful qualitative capabilities, FTICR mass spectrometry is especially useful for characterization of DCLs. Because the composition of the DCL cannot be statically defined, except when in equilibrium with the receptor, it is essential to be able to identify the components at this stage. Using FTICR MS, identification can be done by a combination of exact mass determination and tandem-in-time mass spectrometry to yield par-ent/daughter ion structural information. Although FTICR is an expensive option for combinatorial library characterization, it can provide the most direct information for ligand identification in libraries. 

Mass spectra of a great variety of monocyclic and condensed 1,2,3-triazines have been published. Since all monocyclic 1,2,3-triazines show the same fragmentation pattern, mass spectrometry can be used to determine the structure of isomeric monocyclic 1,2,3-triazines and their V-oxides. In general, the mass spectrum of monocyclic 1,2,3-triazines show peaks for M+, [M+ -N2], for one or two nitriles and one or two acetylenes. This indicates the following fragmentation pattern.1,17,79,8( 89... 

Mass spectrometry was also used to confirm the structure of burnamicine (222), which gives also fragments mainly by rupture of bonds in ring C, and another 2-acylindole alkaloid, picraphylline. Mass spectrometry aided also in the structure determination of apparicine (223), vallesamine (224), and o-acetylvallesamine. The spectrum of uleine (225) aided in the identification of naturally occurring derivatives thereof. ... 

High resolution mass spectrometry has been used as an additional tool for structural elucidation since this method provides exact mass determinations and therefore the possibility of the determination of elemental composition. 

Mass spectrometry can be used for peak identification, with fragmentation patterns showing the presence of specific chemical groups. Infrared and NMR detection are useful for this because they also give information about the chemical functionaHty of the peaks detected. This can be used either to determine the stmc-ture of unknown peaks or to monitor specific chemical structures such as methyl groups, a carbonyl group, or an ether Hnkage. 

Organic stractures can be determined accurately and quickly by spectroscopic methods. Mass spectrometry determines mass of a molecule and its atomic composition. NMR spectroscopy reveals the carbon skeleton of the molecule, whereas IR spectroscopy determines functional groups in the molecules. UV-visible spectroscopy tells us about the conjugation present in a molecule. Spectroscopic methods have also provided valuable evidence for the intermediacy of transient species. Most of the common spectroscopic techniques are not appropriate for examining reactive intermediates. The exceptions are visible and ultraviolet spectroscopy, whose inherent sensitivity allows them to be used to detect very low concentrations for example, particularly where combined with flash photolysis when high concentrations of the intermediate can be built up for UV detection, or by using matrix isolation techniques when species such as ortho-benzyne can be detected and their IR spectra obtained. Unfortunately, UV and visible spectroscopy do not provide the rich structural detail afforded by IR and especially H and NMR spectroscopy. Current mechanistic studies use mostly stable isotopes such as H, and 0. Their presence and position in a molecule can... 

Spectroscopic methods are mainly useful to identify the elements, functional groups, and chemical structures close to the biomaterial surface. Techniques like X-ray photoelectron spectroscopy, attenuated total reflection fourier transform infrared spectroscopy, and secondary ion mass spectrometry have been used widely in determining the elemental composition and charged species at biomaterial surface. Other important characteristics obtained from the biomaterial surface are surface energy and relative wettability using thermodynamic method such as contact angle experiments. 

Since the 1960s, mass spectrometry has played a pivotal role in the field of structure elucidation and identification of organic compounds. Over the years, a wealth of knowledge has been gained on reactions of gas-phase ions from the use of a variety of mass spectrometric techniques. Mass spectrometry can be used to identify unknown compounds or to perform de nova stmcture determination. The former is relatively easy if one knows accurate mass and a reference spectrum. The latter is much more difficult and requires detailed knowledge of the rules for interpretation of a mass spectrum. Providing this knowledge is the focus of this chapter. 

Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) are useful techniques for structural elucidation of unknown compounds but the results obtained are difficult to quantify. Liquid chromatography (LC) methods have been used extensively for the determination of highly intense sweeteners because in many instances the sample... 

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