Ab Initio Molecular Orbital Calculation of Carbohydrate Model Compounds. 3. Effect of the Electric Field on Conformations about the Glycosidic Linkage (original) (raw)
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J Mol Struc Theochem, 1997
An ab initio study of the conformational behavior of aglycon OC glycosidic bonds and rotameric distribution in O-methylated carbohydrates has been carried out on axial and equatorial 1,2-, 1,3- and 1,4-dimethoxytetrahydropyran as models. The geometry of the conformers about the C(aglycon)O(glycosidic) bond (Ψ-type) in 12 models was determined by gradient optimization at the SCF level using split valence 6-31G∗ basis sets. The potential of rotation has been calculated using 6-31G∗ and 631 + G∗ basis sets. At all levels of theory, both axial and equatorial forms prefer the GT or TG conformers around the CO glycosidic bond over the GG conformer. Exceptions are models of (1 → 2) linkages with the equatorial anomeric methoxyl group (E2A and E2E), where the TG conformer is not present. Calculated potential energy profiles show high flexibility within a 1.5 kcal mol−1 low energy region that is 180 ° wide. The glycosidic bond angle ClOiCi depends on the torsion angle Ψ and assumes values in the interval from 115 ° to 125 °.
Journal of Molecular Structure: THEOCHEM, 1997
An ab initio study of the conformational behavior of aglycon O-C glycosidic bonds and rotameric distribution in Omethylated carbohydrates has been carried out on axial and equatorial 1,2-, 1,3and 1 $dimethoxytetrahydropyran as models. The geometry of the conformers about the C(aglycon)-O(glycosidic) bond (q-type) in 12 models was determined by gradient optimization at the SCF level using split valence 6-3lG* basis sets. The potential of rotation has been calculated using 6-3 lG* and 63 I + G* basis sets. At all levels of theory, both axial and equatorial forms prefer the GT or TG conformers around the C-O glycosidic bond over the GG conformer. Exceptions are models of (I -2) linkages with the equatorial anomeric methoxyl group (E2A and E2E), where the TG conformer is not present. Calculated potential energy profiles show high flexibility within a 1.5 kcal mol-' low energy region that is 180" wide. The glycosidic bond angle C 1 -Oi-Ci depends on the torsion angle \k and assumes values in the interval from 115" to 125". 0 1997 Elsevier Science B.V.
The Journal of Physical Chemistry B, 1997
An ab initio study of the conformational behavior of Rand -anomeric linkages in C-, N-, and S-glycosyl compounds has been carried out on axially and equatorially 2-substituted derivatives (2-ethyl, 2-methylamino, 2-thiomethyl, and 2-methylammonio) of tetrahydropyran as models. The geometry of the conformers about the anomeric C-X bond was determined by gradient optimization at the SCF level using the 6-31G* basis set. The potential of rotation has been calculated using the 6-31G* and 6-31+G* basis sets. Vibrational frequencies were calculated at the 6-31G* level and used to evaluate zero-point energies, thermal energies, and entropies for minima. Variations in calculated valence geometries for the compounds, display structural changes distinctive for the anomeric and exo-anomeric effects. Differences between bond lengths and bond angles for different conformers correlate with the importance of the lone pair delocalization interactions. The calculated conformational equilibria have been used to estimate the magnitudes of the anomeric, reverse anomeric, and exo-anomeric effects. It was found that the anomeric effect decreases in the following order: chlorine > methoxy ∼ fluorine > thiomethyl > methylamino > ethyl > methylammonio, with the methylamino, ethyl, and methylammonio groups exhibiting reverse anomeric effects. The sc preference of the methyl group over the ap orientation around the C1-C bond in 2-ethyltetrahydropyran is assumed to be entirely on basis of steric interactions. The exo-anomeric effect is expected to be present when the preference for the sc conformation is larger than that for the ethyl group. Thus, the exo-anomeric effect decreases in the order methoxy ∼ methylamino > thiomethyl. The methylammonio group does not show an exo-anomeric effect.
Biophysical Journal, 2007
A range of ab initio calculations were carried out on the axial and equatorial anomers of the model carbohydrate 2-ethoxy tetrahydropyran to evaluate the level of theory required to accurately evaluate the glycosyl dihedral angle and the anomeric ratio. Vacuum CCSD(T)/CBS extrapolations at the global minimum yield DE ¼ E equatorial À E axial ¼ 1.42 kcal/mol. When corrected for solvent (by the IEFPCM model), zero-point vibrations and entropy, DG 298 ¼ 0.49 kcal/mol, in excellent agreement with the experimental value of 0.47 6 0.3 kcal/mol. A new additivity scheme, the layered composite method (LCM), yields DE to within 0.1 kcal/mol of the CCSD(T)/CBS result at a fraction of the computer requirements. Anomeric ratios and onedimensional torsional surfaces generated by LCM and the even more efficient MP2/cc-pVTZ level of theory are in excellent agreement, indicating that the latter is suitable for force-field parameterization of carbohydrates. Hartree-Fock and density functional theory differ from CCSD(T)/CBS for DE by ;1 kcal/mol; they show similar deviations in torsional surfaces evaluated from LCM. A comparison of vacuum and solvent-corrected one-and two-dimensional torsional surfaces indicates the equatorial form of 2-ethoxy tetrahydropyran is more sensitive to solvent than the axial.
Canadian Journal of Chemistry, 1978
The two dimensional conformational spaces available for acetoxymethyl groups in carbohydrates are reported. The studies were performed on two n~olecules differing in their C-4 configurations, i.e. gl~rco and gulucto. The acetoxymethyl group was assigned a mean geometry derived from the computation of 19 equivalent groups as found in pertinent acetylated carbohydrates. The internal energy calculations were performed by including the partitioned contributions arising from the non-bonded energies, electrostatic interactions, and torsion energy. An instability rating of 3 kcal'mol n'as assigned to conformations involving yeri interactions, i.e., trc1n.r-gnrrclre and gnllche-guuche forms in gl~rco and gulncto carbohydrates, respectively. The results ~vhich are best described in term of topology show that several conformatiolls correaponding to the trcms and guc~che states of the C-0 single bond are preferred. However, significant shifts from perfect staggering are observed. The predicted regions of lo\\-energy are found to be in good agreement with experimental data from crystal structures of acetylated carbohydrates. S. PEREZ, J. ST-PIERRE et R. H. MARCHESSAULT. Can. J. Chem. 56.2866 (1978). On presentc l'espace conformationtlel i deux dimensions accessible aux groupes acktoxymkthyles dans les carbohydrates. Les etudes ant port6 sur deux molecules presentant des conformations diflkrentes a I'atome C-4, soit gllrco et gnlircro. On a attribue au groupe acetoxyniethylc une geometrie moyenne deduite de calculs effectues sur 19 groupes semblables se trouvant dans des carbohydrates acktylis appropries. Dans le calcul de 1'Cnergie interne, on a tenu colnpte des contributions respectives des encrgies d'interaction non-liee, des interactions electrostatiques et dc I'energie de torsion. 011 a attribue une instabilite k\aluCe a 3 kca1,mol aux conformations faisant intervenir des interactions ~4 r i , c'est-a-dire les forrnes trcn7s-gurrclle et gurrclli.-gcruclle dans les carbohydrates gllico et galocto respecti~ement. Les resultats, dont on donne une description topologique, montrent une preference pour certaines conformations correspondant aus etats rruirr et galic11~ de la liaisoll simple C-0. Cependant, il y a tles ecarts significatifs au decalage parfait. Les previsions quant aux regions de basses energies sont en bon accord a\,ec les resultats expbrimentaux tires des structures cristalli~tes de carbohqdrates acetyles.
The Journal of Physical Chemistry, 1994
A b initio calculations have been carried out on model compounds for the pyranose halides 2-fluoro-and 2-chlorotetrahydropyran with either an axially or an equatorially oriented halogen atom. Energy minimization has been carried out at the STO-3G. 3-21G, 6-3 lG, 6-3 1G*, 6-31+G*, and MP2/6-3 lG* levels. The optimized geometries were used to calculate the energy difference between the axial and equatorial conformers with STO-3G, 3-21G, 4-31G, 6-31G, 6-31G*, 6-31G**, 6-31+G*, 6-311G*, 6-31+G**, 6-31 l++G**, and MP2/ 6-31G* basis sets. Large differences in C-Hal bond lengths and 0-C-Hal bond angles were found between the axial and equatorial conformers. After including the zero-point energy, thermal energy, entropy, and MP3 electron correlation corrections to energy differences calculated at 6-3 1 1 ++G**//6-3 1 +G* basis set, these calculations favored the axial conformers by 2.4 and 2.5 kcal/mol. Solvent effects considerably reduce this energy difference; in the extreme case, in water, values of 0.5 and 1.5 kcal/mol were obtained for fluoro and chloro derivatives, respectively. The magnitude of the anomeric effect depends on the solvent and was estimated to be in the range 0.9-2.8 kcal/mol for the fluoro and 2.3-3.1 kcal/mol for the chloro forms. On the basis of these results, we suggest that the 6-31+G*//6-31G* procedure is suitable for calculations of the geometry and the conformational energies of carbohydrate molecules. The calculated energies and geometries provide additional data which should prove useful in the reparametrization of existing force fields to better reproduce the behavior of C-O-Hal systems.
Jcc, 1995
The force field previously obtained for both anomers of glucose has been applied to six disaccharides that are molecules of D-glucopyranosyl residues. These six disaccharides have different types of glycosidic linkages-that is, a,a trehalose dihydrate (1-11, sophorose monohydrate ( p, 1-2), laminarabiose ( PI 1-31, maltose monohydrate (a, 1-4) and cellobiose ( p, 1-4), and gentiobiose ( p, 1-6).
Carbohydrate Research, 1995
The calculated ensembles found by a heuristic conformational search algorithm, CICADA, for three small carbohydrates, ethyl fl-lactoside, methyl a-D-galactoside, and methyl fl-D-galactoside, are evaluated in terms of their ability to reproduce time-averaged optical rotation and NMR data. A unique dynamic model for methyl fl-D-galactoside has been obtained by fitting experimental NOESY volumes to the theoretical ones elaborated from the CICADA ensemble internuclear distances with the model-free formalism. In the case of ethyl /3-1actoside, the CICADA ensemble is compared to that of an exhaustive systematic grid-search method. The CICADA algorithm proved to be a very efficient method to find most of the important minima on even very complex potential energy surfaces, and the spectral quality of the CICADA ensemble was found to be of equal quality, if not superior, to that of the exhaustive systematic grid-search method. The CICADA algorithm has several advantages over other conformational search algorithms: (1) It has polynomial dependence of dimensions on computer time in contrast to the grid search, which has exponential dependence, (2) the conformations found are free of artificial harmonic constraint potentials, (3) it passes all barriers amongst families of conformations on conformational hypersurface but spends almost all its time in the essential highly populated areas, (4) the inherent properties of the algorithm make rigorous minimization criteria superfluous and provide good * Corresponding author. 0008-6215/95/$09.50 © 1995 Elsevier Science Ltd. All rights reserved SSDI 0008 -621 5(95)001 52-2 S. B. Engelsen et al. / Carbohydrate Research 276 (1995) 1-29 convergence behavior, and (5) as an important spin-off, it provides low-energy interconversion pathways that can, amongst others, be used for estimating adiabatic rotational barriers.
Journal of Computational Chemistry, 1995
The force field previously obtained for both anomers of glucose has been applied to six disaccharides that are molecules of D‐glucopyranosyl residues. These six disaccharides have different types of glycosidic linkages—that is, α, α trehalose dihydrate (1‐1), sophorose monohydrate (β, 1‐2), laminarabiose (β, 1‐3), maltose monohydrate (α, 1‐4) and cellobiose (β, 1‐4), and gentiobiose (β, 1‐6). From a careful analysis of the infrared and Raman spectra and from harmonic dynamics calculations in the crystalline state, the results show the reliability and the transferability of the set of parameters previously obtained for different carbohydrates. Below 1500 cm−1, observed data and the corresponding calculated frequencies agreed within 5 cm−1 for each of the six disaccharides. The vibrational density of states are well reproduced by these calculations for each molecule, particularly for the fingerprint regions. Moreover, as found by other workers who used sophisticated potential energy f...
Carbohydrate Research, 1998
Carbohydrates are thought to be especially difficult to model because of their highly polar functionality, their flexibility, and their differences in electronic arrangements that occur during conformational and configurational changes, such as the anomeric, exo-anomeric and gauche effects. These issues have been addressed in recent years, yielding several contributions to set up some relevant parameterizations that would account for these specific features of carbohydrates. Within the framework of a workshop involving the participation of 11 research groups active in the field, several commonly used molecular mechanics force fields and special carbohydrate parameter sets have been considered. The application of 20 force fields and/or sets of parameters to a series of seven test cases provided a fairly general picture of the potentiality of these parameter sets for giving a consistent image of structure and energy of carbohydrate molecules. The results derived from a chemometric analysis (principal component analysis, PCA) give a global view of the performances of the force fields and parameter sets for carbohydrates. The present analysis (i) provides an identification of the parameter sets which differ from the bulk, (ii) helps to establish the relationship that