Carbohydrate modeling

Toikka, M. Sipila, J. Teleman, A. Brunow, G. Lignin-carbohydrate model compounds. Formation of lignin-methyl arabinoside and lignin-methyl galactoside benzyl ethers via quinone methide intermediates. J. Chem. Soc., Perkin Trans. 1998, 1, 3813-3818. 

Abstract To understand how membrane-active peptides (MAPs) function in vivo, it is essential to obtain structural information about them in their membrane-bound state. Most biophysical approaches rely on the use of bilayers prepared from synthetic phospholipids, i.e. artificial model membranes. A particularly successful structural method is solid-state NMR, which makes use of macroscopically oriented lipid bilayers to study selectively isotope-labelled peptides. Native biomembranes, however, have a far more complex lipid composition and a significant non-lipidic content (protein and carbohydrate). Model membranes, therefore, are not really adequate to address questions concerning for example the selectivity of these membranolytic peptides against prokaryotic vs eukaryotic cells, their varying activities against different bacterial strains, or other related biological issues. 

Simultaneous to the understanding of some basics of hydrothermal carbonization using pure carbohydrate models, the synthesis of hydrothermal carbon materials using raw biomass was continued. It has been analyzed whether complex biomass - hy-drothermally carbonized - can also be directed to complex structural motifs with distinct surface polarities. Ideally, for this purpose one can use the structures and functionalization components already included in the biomass. We specifically selected waste biomass for material synthesis, starting products which are known to be hard to use otherwise, rich in ternary components, and applied different HTC conditions [29]. That way, one can avoid the food-raw materials competition, a prerequisite we regard as crucial for the development of a fully sustainable chemistry. 

Comparison with Experiment. For carbohydrates, modeling work has often sought to produce a theoretical structure that matches the results from a highly accurate diffraction experiment. This approach is problematic, however, because crystal packing can distort a molecule from the shape that it would have as an isolated molecule. 

J. Although data are available from carbohydrate model compounds... 

Carbonyl groups are not always present in their usual double-bond form, but also exist as the tautomeric enols or as hydrates upon addition of water, which was demonstrated by means of differently oxidized carbohydrate model compounds by NMR [ 102] (Scheme 6). A recent study revealed a much higher percentage of hydrated aldehyde groups compared to the pure acyclic form for all aldohexoses in water [44]. 

The reaction was tested on carbohydrate model compounds and was shown to provide quantitative yields [78,81] (Scheme 18). Following from the reaction mechanism, the carboxyl groups must be present in free form (COOH) for the labeling to proceed. Carboxylates (salts), lactones or esters... 

Alfred D. French and Imre G. Csizmadia, Carbohydrate Modeling, in THEOCHEM, 395-396, Elsevier, Amsterdam, The Netherlands, 1997. 

Sippola, V., Krause, O., and Vuorinen, T., Oxidation of lignin model compounds with cobalt-sulphosalen catalyst in the presence and absence of carbohydrate model compound. Journal Of Wood Chemistry And Technology 2004,24 (4), 323-340. 

Fundamental. Figure 14 illustrates a general scheme for the alkaline degradation of hydrolyzable ether units. The reaction of phenolic units (40) is initiated by the phenoxide ion (41) to yield a quinonemethide intermediate (42) with elimination of the a-ether unit R,. This elimination reaction occurs quite readily for an a-aryl ether unit (in 1 M NaOH at 25°C) [326], whereas the a-ether linkage of a lignin-carbohydrate model was shown to be stable under the same conditions [304]. 

The preparation of four different types of oxaza spirobicyclic systems (143) by 1,6- and 1,7-hydrogen atom transfer promoted by phosphoramidyl radicals in carbohydrate models has been described. The N-radicals are generated by reaction of dibenzyl phosphoramidate derivatives of C-glycosides with (dia-cetoxyiodo)benzene and iodine through a homolytic fragmentation of iodoam-ide intermediates (Scheme 37). 

Tab. 2.1 Complexation free energies (—AC, kJ/mol) . (a) For anions with model amides 1—3 (b) Of these anions with carbohydrate models C and C...

The affinities observed for complexes between amides and anions are remarkably parallel to those found for the interactions between such anions and carbohydrate models. The data in Tab. 2.1 show the same affinity increase in the sequence r
strong acceptor as the result of two geometrically matching hydrogen bonds with vicinal diols. The formation of two almost linear and parallel hydrogen bonds is also responsible for the efficiency of the guanidinium residue for carboxylate complexation in artificial receptors [101] as well as in proteins (cf. Chapter 6) [102]. 

K Li, RF Hehn. Synthesis and rearrangement reactions of ester-linked lignin-carbohydrate model compounds. J Agric Food Chem 43 2098-2103, 1995. 

J Gierer, T Reitberger, E Yang, B-H Yoon. Formation and involvement of radicals in oxygen delignification smdied by the autoxidation of lignin and carbohydrate model compounds. 7 Wood Chem Technol 21 313-341, 2001. 

In a recent paper, the protected a-D-glucofiiranose (1) was selected as a carbohydrate model compound by Oscarson et al. [5] for acetylation, under the action of microwave irradiation, with acetyl chloride (2 equiv.) and pyridine, N,N-(diisopropyl)aminoethylpolystyrene (PS-DIEA), or N-(methylpolystyrene)-4-(methylamino)pyridine (PDS-DMAP) as conventional bases. The acetyl derivative 2 was produced in good to excellent yields in a very short time (Scheme 12.1). 

Solvation is a critical issue in carbohydrate modeling. Both implicit and explicit solvation strategies have been employed. While both a semiempirical quantum mechanical continuum water modeP and a free energy simulation with explicit water have predicted similar values for the free energy difference between the p- and a-anomers of 5 (AGp ), the former approach suggested that the solution free energy (—0.5 kcal/mol) was dominated by gas phase effects, whereas the latter simulation indicated that preferential solvation of the P-anomer was in part responsible for the value (-0.3 kcal/mol) of AGp > . 

Herrera AJ, Rond6n M, Suarez E (2007) Straeocontrolled photocyclization of 1,2-diketones applied to carbohydrate models a new entry to C-ketosides. Synlett 1851-1856... 

Tvaroska, L, Carver, J. P. (1996). Ab Initio Molecular Orbital Calculation of Carbohydrate Model Compounds. 5. Anomeric, xo-Anomeric, and Reverse Anomeric Effects in C-, N-, and S-Glycosyl Compounds. Journal of Physical Chemistry, 100, 11305-11313. 

The HSEA force field is the most historically significant force field for carbohydrate modeling. This force field assumes that the conformation of the oligosaccharide is determined exclusively by van der Waals interactions, with the singular exception of the orientation of the -angle, for which a potential for the exo-anomeric effect is included (equation 1). 

Glennon and co-workers reported an exploration of the influence of intra- and intermolecular interactions in carbohydrate modeling in 1994. On the basis of earlier examinations.> of rotational energy profiles, they concluded that tlje exo-anomeric rotational energies could be adequately repi duced with the default AMBER threefold rotational term for C-0 bonds (equation 14). 

There are numerous force fields and parameter sets available for modeling carbohydrates. Some focus specifically on carbohydrates, while others aim at treating biomolecules in general, and yet others profess to be appropriate for virtually any molecular class. Direct comparisons between force fields are rare and validation of any of the force fields requires extensive and critical comparison with experimental data. Consequently, carbohydrate force fields ate frequently selected on the basis of past familiarity. The advent of convenient graphical modeling interfaces provides a tremendous opportunity to extend carbohydrate modeling to both new users and new molecular systems. Ease of access is not, however, a guarantee of force field suitability. 

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