Carbohydrates molecular complexes

Easily available advanced synthons, such as the carbohydrates, amino acids, hydroxyacids, and terpenoids, make the synthetic task easier than the complexity metrics of the target suggests this is especially true for the glycosides, if the carbohydrate portion can be introduced intactly. It must also be borne in mind that the S metric is counted in a linearly additive hion, neglecting interactions between the functional groups (Whitlock 1998) such interactions are not treated adequately by any method so far proposed to calculate the molecular complexity. Moreover, no attention was paid here to the graphic analysis of the synthesis plan based on the molecular complexity of the intermediates these aspects have recently been reviewed (Bertz 1993 Whitlock 1998 Chanon 1998). 

For the carbohydrates especially, the amount of available crystal structural data decreases sharply with molecular complexity [479]. With the exception of the cyclodextrins, discussed in Part III, Chapter 18, there are less than 40 crystal structure analyses of oligosaccharides, of which less than 10 are trisaccharides, one is a tetrasaccharide, and one a hexasaccharide (Part III, Chap. 18). The majority of the basic monosaccharides that are the subunits of the polysaccharides that occur naturally have been studied for example, the pyranose forms of /7-arabinose, a-xylose, a- and -glucose, / fructose, a-sorbose, a-mannose, a- and -galactose, a-fucose, a-rhamnose, N-acetyl glucosamine, and mannosamine (Box 13.2). How-... 

Sometimes smaller porphyrin assemblies could be reversibly dissolved via molecular complex formation. The protoporphyrin-bis-amide 17 with two w-phenylboronic substituents dissolves in 1 30 DMSO/water mixtures, but is heavily aggregated in this medium. The Soret band s intensity was only the half of that in pure DMSO solution and the fluorescence was almost nil. However, upon addition of 10 M fructose the carbohydrate was bound as a molecular complex and the porphyrin became more water-soluble whereby the fluo-recence increased drastically. Other monosaccharides had lesser effects. 

Lipids form membranes inside and around the cell. Carbohydrates form complex tree-like molecules that become attached to the surface of proteins and cellular membranes. In both cases, the three-dimensional molecular structure is not unique, but the molecular assemblies are highly flexible. Thus, analyzing the molecular structure involves the inspection of a process in time. Molecular dynamics is the only available computer-based method for doing so. Compared with protein structures there are relatively few results on lipids and carbohydrates. The book does not detail this topic. 

Despite the success of proton nuclear magnetic resonance ( H n.m.r.) spectroscopy as a tool for studying the structures of organic compounds in solution, the technique nevertheless suffers from a number of limitations. These limitations become increasingly serious with increase in the size and molecular complexity of the system of interest. In particular, when attention is directed to studies of polymeric materials, especially those of biochemical relevance, much of the incisive power of the H n.m.r. technique has, to date, been lost. The outcome of this situation is clearly exemplified in the carbohydrate area, where H n.m.r. spectroscopy is generally the tool preferred for structural studies of mono-... 

Abstract In this chapter we review recent advances in theoretical methods to understand and rationalize anharmonic vibrational spectroscopy (IR-MPD and IR-PD) and collision induced dissociations (CID) in the gas phase. We focused our attention on the application of molecular dynamics-based methods. DFT-based molecular dynamics was shown to be able to reproduce InfraRed Multi-Photon Dissociation (IR-MPD) and InfraRed Pre-Dissociation (IR-PD) action spectroscopy experiments, and help assign the vibrational bands, taking into account finite temperature, conformational dynamics, and various anharmonicities. Crucial examples of dynamical vibrational spectroscopy are given on the protonated AlanH" series (related to IR-MPD in the 800-4,0(X) cm domain), ionic clusters (related to IR-PD in the 3,000-4,(XX) cm region), and neutral peptides (related to IR-MPD in the far-lR). We give examples from simple (e.g., cationized urea) to more complex (e.g., peptides and carbohydrates) molecular systems where molecular dynamics was particularly suited to understanding CID experiments. 

Infrared MultiPhoton Dissociation (IRMPD) spectroscopy coupled to ElectroSpray Ionization (ESI) sources have also been applied to CBHs [60-66]. So far, the study of CBHs by ESI has focused on relatively simple mono- or disaccharides bound to metal atoms carrying the charge. This is because stabilizing the protonated forms of non-substituted carbohydrates with this ionization technique is difficult, although probably not impossible. However, it has recently been possible to observe the formation of a protonated monosaccharide (aMeGal-H" ) produced by UV photo-ionization of phenol bound to the CBH within a molecular complex [67]. 

Molecular recognition and noncovalent complexes are at the core of reaction networks in biology. Molecular complexes are often associated with the proliferation of disease (see, for example, the Tax-associated complexes in human T-cell leukemia type 1, HTLV-1 [33]). Along with other competing techniques (e.g., surface plasmon resonance), mass spectrometry can be successfully used to detect noncovalent complex formation. The corresponding ions can be present in both MALDl [34] and ESI [35] spectra, although the latter is used more often. A wide variety of protein-protein interactions as well as protein interactions with other species (nucleotides, carbohydrates, etc.) have been studied. The spectra can reveal the components of the complex and in some cases the association constant. 

Aldolases constitute attractive tools in the asymmetric construction of molecular frameworks as well as in the synthesis of chiral bioactive compoxmds, such as carbohydrates, amino acids, and their analogues. Indeed, molecular complexity through enz3unatic C—C cormection can be built up xmder mild conditions, without a need for iterative steps of protection and deprotection of sensitive or reactive functional groups, increasing the atom economy of the transformation. Moreover, the same or different aldolase types can be applied independently in consecutive... 

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