Large molecules in the gas phase

Finally, from the point of view of the organic chemist, obtaining amino acids from proteins, which is done by either acid or base hydrolysis (after cleaving the sulfur-sulfur bonds) rather than by structural analysis, is of concern. Indeed, at this writing, a significant amount of structural analysis is accomphshed by specialized computer-coupled mass spectrometric (Chapter 2) techniques. The special nature of these techniques derives from the need to put the very large molecules in the gas phase and so desorption from various materials— without decomposition— becomes important and exotic technology, such as matrix-assisted laser desorption ionization (MALDI) MS becomes necessary. 

Very fast energy dissipation after vibrational excitation in the electronic ground state, however, has been inferred from picosecond relaxation measurements on large molecules in the gas phase. Moreover the view has been adopted that in solids even at low temperature rapid energy dissipation prevents multiphoton excitation and vibrational ladder climbing in matrix isolated molecules. On the other hand, in recent experiments surface reactions, such as desorption, evaporation and molecular decomposition, stimulated by vibrational multi-quantum excitation with resonant laser infrared have been observed at moderate threshold laser intensity and with high frequency selectivity. 

Here we see clearly the large concentration of density around the oxygen nucleus, and the very small concentration around each hydrogen nucleus. The outer contour is an arbitrary choice because the density of a hypothetical isolated molecule extends to infinity. However, it has been found that the O.OOlau contour corresponds rather well to the size of the molecule in the gas phase, as measured by its van der Waal s radius, and the corresponding isodensity surface in three dimensions usually encloses more than 98% of the total electron population of the molecule (Bader, 1990). Thus this outer contour shows the shape of the molecule in the chosen plane. In a condensed phase the effective size of a molecule is a little smaller. Contour maps of some period 2 and 3 chlorides are shown in Figure 8. We see that the electron densities of the atoms in the LiCl molecule are only very little distorted from the spherical shape of free ions consistent with the large ionic character of this molecule. In... 

The first systematic measurements of the reactions of ions with molecules in the gas phase were initiated largely by workers associated with analytical mass spectrometry.4-6 It was the rapidly expanding area of ion-molecule reactions which led to the origin of Gas-Phase Ion Chemistry as a distinct field.7 The discovery that ion-molecule equilibria in the gas phase can be determined by mass spectrometric techniques8 led to an explosion of thermochemical measurements based on determination of equilibria by a variety of techniques.9 Significantly, for the first time, information could be obtained on the thermochemistry of reactions which had solution counterparts of paramount importance such as acidities and basicities. These were obtained from proton transfer equilibria such as,... 

In all of these applications, the emphasis to date has been on the use of lasers to study chemically and physically well characterized systems, that is, simple molecules in the gas phase, or in ordered phases such as molecular crystals, or in cryogenic matrices. There are exceptions to this statement, but the basic fact is that the great strides in chemical applications of lasers have been made by the chemical physics and analytical chemistry communities and largely ignored by inorganic, organic, and biological chemists. 

A popular misconception says a molecule in the gas phase travels faster than when in a liquid. In fact, the molecular velocities will be the same in the gas and liquid phases if the temperatures are the same. Molecules only appear to travel slower in a liquid because of the large number of collisions between its particles, causing the overall distance travelled per unit time to be quite short. 

In 1988-1989, two processes were discovered that allowed the transfer of large molecules into the gas phase matrix-assisted laser desorption and ionization (MALDI) and electrospray ionization (Karas and Hillenkamp, 1988 Fenn et al., 1989). 

The semiempirical molecular orbital (MO) methods of quantum chemistry [1-12] are widely used in computational studies of large molecules. A number of such methods are available for calculating thermochemical properties of ground state molecules in the gas phase, including MNDO [13], MNDOC [14], MNDO/d [15-18], AMI [19], PM3 [20], SAMI [21,22], OM1 [23], OM2 [24,25] MINDO/3 [26], SINDOl [27,28], and MSINDO [29-31]. MNDO, AMI, and PM3 are widely distributed in a number of software packages, and they are probably the most popular semiempirical methods for thermochemical calculations. We shall therefore concentrate on these methods, but shall also address other NDDO-based approaches with orthogonalization corrections [23-25],... 

It thus appears that, in general, the rates of electronic relaxation processes in dense media are of the same order of magnitude as those found for isolated molecules in the gas phase, assuming that the molecule has a sufficiently large number of vibrational degrees of freedom. Therefore it may be concluded that the mechanism which operates in isolated molecules must be responsible for the gross features of the phenomena observed in dense media. 

Recent mass spectral studies confirm the presence of CsAu molecules in the gas phase. From the appearance potentials and the slope of the ionization curve, a dissociation energy of 460 kJ mol-1 was deduced, which agrees well with predicted values for a largely ionic bond. It is also very similar to the value arrived at for CsCl, 444 kJ mol-1 (19a). 

Comparing FTMS with Fourier transform nuclear magnetic resonance (FTNMR), we first notice how the frequency range to be covered here is very large. Second, relaxation in NMR is invariably linked with the interaction among liquid-phase or solid-phase molecules. In the gas phase, relaxation depends on the vacuum and on the stability of the ions being observed. If the vacuum is not sufficient, collisions slow the ions and their movement becomes incoherent. The observation of an ion is also limited to its lifetime. 

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