Fragment ion formation

Energy is added to molecules during ionization. The distribution of the energy may result in the breaking of chemical bonds and> consequently, in fragment ion formation. The fragmentation may be so extensive that no molecular ion is observed. 

FD-MS has been shown to be an excellent method for recording the mass spectra of compounds showing both molecular and fragment-ion formation (1, 76, 88, 95, 108, 161, 372). Compounds that do not produce good mass spectra due to instability even under field desorption conditions - such as zwitterions - can be... 

Comparison of basic El and Cl processes showing different types of molecular ions and the formation of fragment ions in El. 

The formation of a simple El mass spectrum from a number (p) of molecules (M) interacting with electrons (ep. Peak 1 represents M , the molecular ion, the ion of greatest mass (abundance q). Peaks 2, 3 represent A+, B. two fragment ions (abundances r, s). Peak 2 is also the largest and, therefore, the base peak. 

Formation of normal ions in an ion source. In this example, some initially formed ions (m,+) dissociate (fragment) to give smaller ions (mj ) and a neutral particle (iio). Unchanged ions (m +) and the fragment ions (mj" ) are drawn out of the source as beams moving with velocities v, V2, respectively. 

Ion-pair formation. An ionization process in which a positive fragment ion and a negative fragment ion are the only products. 

Physical Chemical Characterization. Thiamine, its derivatives, and its degradation products have been fully characterized by spectroscopic methods (9,10). The ultraviolet spectmm of thiamine shows pH-dependent maxima (11). H, and nuclear magnetic resonance spectra show protonation occurs at the 1-nitrogen, and not the 4-amino position (12—14). The H spectmm in D2O shows no resonance for the thiazole 2-hydrogen, as this is acidic and readily exchanged via formation of the thiazole yUd (13) an important intermediate in the biochemical functions of thiamine. Recent work has revised the piC values for the two ionization reactions to 4.8 and 18 respectively (9,10,15). The mass spectmm of thiamine hydrochloride shows no molecular ion under standard electron impact ionization conditions, but fast atom bombardment and chemical ionization allow observation of both an intense peak for the patent cation and its major fragmentation ion, the pyrimidinylmethyl cation (16). 

The limitations of SIMS - some inherent in secondary ion formation, some because of the physics of ion beams, and some because of the nature of sputtering - have been mentioned in Sect. 3.1. Sputtering produces predominantly neutral atoms for most of the elements in the periodic table the typical secondary ion yield is between 10 and 10 . This leads to a serious sensitivity limitation when extremely small volumes must be probed, or when high lateral and depth resolution analyses are needed. Another problem arises because the secondary ion yield can vary by many orders of magnitude as a function of surface contamination and matrix composition this hampers quantification. Quantification can also be hampered by interferences from molecules, molecular fragments, and isotopes of other elements with the same mass as the analyte. Very high mass-resolution can reject such interferences but only at the expense of detection sensitivity. 

Cluster ions are also emitted from organic materials their identity and yield depend on the chemical structure of the materials. Molecular or quasi-molecular ions may be observed as well as other ions that are formed by fragmentation, rearrangement, decomposition, or reaction [52], Several typical ion formation processes are summarized in Table 3 [40]. 

The advantages of SIMS are its high sensitivity (detection limit of ppms for certain elements), its ability to detect hydrogen and the emission of molecular fragments that often bear tractable relationships with the parent structure on the surface. Disadvantages are that secondary ion formation is a poorly understood phenomenon and that quantification is often difficult. A major drawback is the matrix effect secondary ion yields of one element can vary tremendously with chemical environment. This matrix effect and the elemental sensitivity variation of five orders of magmtude across the periodic table make quantitative interpretation of SIMS spectra oftechmcal catalysts extremely difficult. 

Potzinger and coworkers determined ionisation and appearance energies for the molecular and major fragment ions of several dialkylsulfoxides, R SOR (R =Me R = Me, Et, i-Pr, and i-pentyland R = R = Et or i-Pr). In addition to the evaluation of dissociation energies in the ions and their enthalpies of formation, a value of 280 + 30kJmol" for the C—S dissociation energy in neutral dialkyl sulfoxides was derived. 

A triple-quadrupole mass spectrometer with an electrospray interface is recommended for achieving the best sensitivity and selectivity in the quantitative determination of sulfonylurea herbicides. Ion trap mass spectrometers may also be used, but reduced sensitivity may be observed, in addition to more severe matrix suppression due to the increased need for sample concentration or to the space charge effect. Also, we have observed that two parent to daughter transitions cannot be obtained for some of the sulfonylurea compounds when ion traps are used in the MS/MS mode. Most electrospray LC/MS and LC/MS/MS analyses of sulfonylureas have been done in the positive ion mode with acidic HPLC mobile phases. The formation of (M - - H)+ ions in solution and in the gas phase under these conditions is favorable, and fragmentation or formation of undesirable adducts can easily be minimized. Owing to the acid-base nature of these molecules, negative ionization can also be used, with the formation of (M - H) ions at mobile phase pH values of approximately 5-7, but the sensitivity is often reduced as compared with the positive ion mode. 

The process of ion formation is extremely soft usually no fragmentation occurs. Mass spectra in ESI+ mode are dominated by pseudo-molecular ions (M+, [M + H] + or [M + Na]+) and cluster ions formed by the addition of one or more solvent molecules. For samples with molecular masses up to ca. 1000 Da (as in case of polymer additives), the ions produced from ESI are similar to those formed by other soft ionisation techniques, namely a protonated molecular ion (MH+) in the positive ionisation mode for basic compounds such... 

The crystal structure of a CODH/ACS enzyme was reported only in 2002.43,44 It reveals a trio of Fe, Ni, and Cu at the active site (6). The Cu is linked to the Ni atom through two cysteine-S, the Ni being square planar with two terminal amide ligands. Planarity and amide coordination bear some resemblance to the Ni porphinoid in MCR. A two-metal ion mechanism is likely for acetyl CoA synthesis, in which a Ni-bound methyl group attacks an adjacent Cu—CO fragment with formation of a Cu-acyl intermediate. A methylnickel species in CODH/ACS has been identified by resonance Raman spectroscopy.45... 

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