Molecular force field development for saccharides using the SPASIBA spectroscopic potential. Force field parameters for α-d-glucose

Empirical force fields for biological macromolecules: Overview and issues

“…Other specialized AMBER variants include a united atom model that treats solvent via the Generalized Born/Solvent Accessible Area approach 308 and the SPACIBA force field that is optimized to produce accurate vibrational spectra via the use of Urey-Bradley-Shimanouchi spectroscopic terms that incorporate the effects of vibrational anharmonicity. 309 Again, these models appear to be rather specialized, such that there applicability to a wide range of carbohydrates is questionable. Carbohydrate models have also been developed based on extending the OPLS force field.…”

Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field

“…124,132,133,135,137 Electrostatic effects: Electrostatic effects, mainly intramolecular hydrogen-bonding, are strongly sensitive to the nature and polarity of the solvent. Experimentally, intramolecular hydrogen-bonds in an aqueous environment can be detected only indirectly, for example, via NMR 37,[109][110][111][112]115,[124][125][126][138][139][140][141][142][143][144][145][146][147][148][149] or IR 110,[113][114][115]144,[149][150][151][152][153] spectroscopy. However, most studies to date have investigated model compounds (e.g., monosaccharide analogs) and only provided qualitative information on the existence or absence of a hydrogen-bond.…”

“…Previous simulation studies of mono-and disaccharides were carried out in vacuum or with implicit solvation, 153,237,238,252,262,270,[279][280][281][282] in crystals, 260,275,283 or in water with explicit solvation, either in the finite-concentration 267,268,[284][285][286][287][288][289][290][291][292] or in the dilute regimes. The latter explicit-solvent simulations in the dilute regime were mostly concerned with (i) the validation and refinement of carbohydrate force field parameters; 239,243,[245][246][247][253][254][255][256][257][261][262][263]265,266 (ii) the investigation and rationalization of conformational properties 98,161,164,195,199,200,[214]…”

Vibrational coupling as diagnostic for intramolecular hydrogen bonds of carbohydrates in aqueous solution

“…Many details of carbohydrate vibrational spectra and correlated structures have been given in the literature. Examples of these refer to positions of various types of bands of D-glucopyranose derivatives, [1][2][3][4][5] D-or L-aldopyranoses and their derivatives, 1,3,6,7 and ribose derivatives. 8 -10 However, spectrumstructure correlations regarding intramolecular hydrogen bonds of carbohydrates in aqueous solutions are still lacking.…”

“…8 However, in other works this mode has been reported to be located in the 1400 -1250 cm Ϫ1 region. 5,17 There are two strong arguments for assigning the ␦OH vibration to bands falling in the 1400 -1250 cm Ϫ1 range. First, on deuteration, one would predict that an OH deformation frequency would be lowered by a factor of between 1.3 and 1.4.…”