A Model Glycosidic Linkage: An ab Initio Geometry Optimization Study of 2-Cyclohexoxytetrahydropyran (original) (raw)
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The Journal of Physical Chemistry, 1995
An ab initio study of the conformational behavior of aand ,!%glycosidic linkages has been carried out on axial and equatorial 2-methoxytetrahydropyrans as models. The geometry of the conformers about the glycosidic C-0 bond was determined by gradient optimization at the SCF level using the 4-21G and 6-31G* basis sets and at the second-order Moller-Plesset level using the MP2/6-31G* basis set. The potential of rotation has been calculated using 4-21G, 6-31G*, 6-31+G*, MP2/6-31G*, and 6-31 l++G** basis sets. At all levels of theory, both axial and equatorial forms prefer the GT conformation around the C-0 glycosidic bond. Conformational changes in bond lengths and angles at the anomeric center also display significant variations with computational methods, but structural trends are in fair agreement with experiment. The correction for the effect of zero-point energy, thermal energy, and entropy on the axial-equatorial energy difference at the 6-31G* level is-0.63 kcal/mol. After these corrections to the energy difference calculated at the 6-31G* level, the axial form is favored by 0.84 kcaymol, in reasonable agreement with experimental values of AG = 0.7-0.9 kcaymol estimated for nonpolar solvents. Solvent effects reduce this energy difference; in the extreme case of water, a value of 0.24 kcal/mol was obtained. Complete torsional profiles have been obtained for rotation about the glycosidic C-0 bond in eleven solvents, and the calculated energy differences are in fair agreement with experimental data on 2-alkoxytetrahydropyrans in solutions. The MM3 (6 = 1.5) force field reproduces the 6-31G* a b initio energy difference reasonably well, but barrier heights are in poor agreement with the ab initio data. The calculated energies and geometries provide an essential set of data for the parametrization of the behavior of acetal fragments in molecular mechanical force fields for carbohydrates.
Journal of the American Chemical Society, 1992
Two suggestions are made to increase the efficiency and accuracy of ab initio optimization of molecular geometries. To improve the convergence of the optimization, a set of internal coordinates, the natural valence coordinates, is suggested. These coordinates originate from vibrational spectroscopy and reduce both harmonic and anharmonic coupling terms in the potential function as much as possible in a purely geometrical definition. The natural valence coordinates are local, eliminate most redundancies, and conform to local pseudosymmetry. Special attention has been paid to ring systems. A computer program has been included in our program system TX90 to generate the natural internal coordinates automatically. The usefulness of these coordinates is demonstrated by numerous examples of ab initio geometry optimization. Starting with a geometry preoptimized by molecular mechanics and using a simple diagonal estimate of the Hessian in conjunction with the GDIIS optimization technique, we usually achieved convergence in 8-15 steps, even for large molecules. It is demonstrated that, due to the reduction in anharmonic couplings, natural coordinates are superior to Cartesian or other simple internal coordinates, even when an accurate initial Hessian is available. Constrained optimization and the location of transition states are also discussed. The gradient optimization method has been generalized to handle redundancies; this is necessary in some complex polycyclic molecules and is illustrated on, among others, the porphine molecule. To increase the accuracy of relatively low-level calculations, empirical corrections to ab initio SCF geometries are suggested in the form of "offset forces" acting along bonds. We recommend offset forces for the most important bonds, to be used with the 4-21G(*) and the 6-31G* basis sets. Based on 130 comparisons, the mean absolute error between theoretical and experimental bond lengths is reduced this way from 0.014 to 0.005 A.
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.
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 °.
A comparison of conformational energies calculated by several molecular mechanics methods
Journal of Computational Chemistry, 1996
Several commonly used molecular mechanics force fields have been tested for accuracy in conformational energy calculations. Differences in performance between the force fields are discussed for different classes of structures. MMFF93 and force fields based on the MM2 or MM3 functional form are found to perform significantly better than other force fields in the test, with average conformational energy errors around 0.5 kcal/mol. CFF91 also reaches this accuracy for the subset in which fully determined parameters are used, but it doubles the overall error due to use of estimated parameters. Harmonic force fields generally have average errors exceeding 1 kcal/mol. Factors influencing accuracy are identified and discussed. 0 1996 by John Wiley & Sons, Inc. different programs can be run on personal computers or small workstations. The problem today in routine work is not so much how to perform the calculation as what force field to use. A few years ago, two of us participated in a compafison of some of the most popular force fields at that time.' However, the last few years have seen the advent
Ab Initio Study of Lowest-Energy Conformers of Lewis X (Le x ) Trisaccharide
The Journal of Physical Chemistry A, 2000
This paper presents the first ab initio conformational study of the Gal--1,4-[Fuc-R-1,3]-GlcNAc--OCH3 and Gal--1,4-[Fuc-R-1,3]-GlcNAc--OH trisaccharides (Lewis x) in the gas phase. Their lowest-energy conformers were selected first by the MM2*-SUMM conformational search technique. MM2* relative energies do not follow the same order for the two similar compounds. The molecular geometries and energies of the lowest-energy rotamers (7 of the acetal and 11 of the hemiacetal) were further analyzed at the HF/6-31G(d) level of theory. The ab initio method yields the same energetic order for the rotamers of the two molecules with considerably larger energetic differences for the first 7 rotamers: the MM2* method provides 0.3-0.5 kcal/mol, whereas the HF/6-31G(d) method provides 4.5 kcal/mol. In the most stable MM2* structures the hydrogen-bonded chains of galactose (in counterclockwise direction) and fucose (in clockwise direction) are not connected. The Gal(O6H) is a hydrogen bond donor (in clockwise direction) to the O3 glycosidic oxygen of GlcNAc. The Fuc(O2H)f(OdC)GlcNAc interaction connects the fucose and GlcNAc. In contrast, the most stable HF/6-31G(d) structure has a long chain of seven ordered hydrogen bonds including a Gal(O6H)f(O3)Fuc interaction (with clockwise hydrogen-bonded chain in galactose and fucose). The torsion angles for Fuc-R-1,3-GlcNAc and Gal--1,4-GlcNAc glycosidic bonds agree well in the solid, liquid, and gas phases. For example there is a rather good overlap between the GlcNAc moiety of one of the X-ray structures and the most similar HF/6-31G(d) structure. The stacking of the fucose and galactose moieties is similar. The orientations of the hydroxyl groups are usually different, as they are influenced by intramolecular hydrogen bonding in the gas-phase Hartree-Fock structure versus intermolecular hydrogen bonding in the solid-phase X-ray structure.
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.
Journal of The American Chemical Society, 1992
Equation 5 offers a simple way to determine the Madelung energy of the zeolite lattice from experimental data, provided the binding energy of the corresponding neutral atom is known. The N12, Si 2: , and 01: energies are roughly approached by the values in Me4NC1 (402.0 eV), Si (98.5 eV), and PhOCOOPh (535.0 eV)' compounds, respectively. The calculated AV values and also the measured constant k values are listed in . The X zeolites possess slightly larger AV values than Y zeolites, which is consistent with the fact that higher A1 content in zeolites produces more negative charges on the framework. Hence the contribution from Coulombic interaction between framework and extraframework cations increases, which will result in an increase of the total Madelung energy. The Madelung energy of the potassium zeolite X was calculated theoretically using a PLUTO program.l* The average Madelung energy calculated using this method is about -14.7 eV for cations located at site 11. This value is higher than our results but still comparable. The high value obtained by the PLUTO method might be due to the ionic crystal model for the zeolite lattice employed in the calculation, since the real zeolite lattice is only partially ionic.'