Hydroxyl orientations in cellobiose and other polyhydroxyl compounds: modeling versus experiment

Abstract

Theoretical and experimental gas-phase studies of carbohydrates show that their hydroxyl groups are located in homodromic partial rings that resemble cooperative hydrogen bonds, albeit with long H…O distances and small O-H…O angles. On the other hand, anecdotal experience with disaccharide crystal structures suggested that these clockwise 'c' or counter-clockwise (reverse 'r') sequences are not prevalent in the crystalline state. The situation was clarified with quantum mechanics calculations in vacuum and in continuum solvation, as well as Atoms-In-Molecules analyses. From the experimental side, the Cambridge Structural Database was searched. Geometric criteria for these sequences were developed. A criterion based on 120°ranges of hydroxyl orientations accepted 4% of sequences as having 'c,c' or 'r,r' orientations instead of the 7% expected based on chance. Criteria based on an O-H…O angle [ 90°a nd a 90°lower limit of the absolute value of the H-O-C…H improper torsion accepted 7.0% of the 358 sequences as 'c,c' or 'r,r'. Highly variable orientation of the hydroxyl groups in crystals was seen to depend mostly on strong inter-residue or intermolecular hydrogen bonds. That lack of specific orientation in general for the crystal structures was supported by the solvated calculations that showed very little variation in the energy when one of the hydroxyl groups in 1,2-dihydroxycyclohexane was rotated. The vacuum calculations found the energy to vary with rotation by more than 4 kcal/mol, confirming the gas-phase experiments and calculations on more complicated molecules. Molecules examined in some detail include scyllo inositol and native and methylated cellobiose.

Combining Computational Chemistry and Crystallography for a Better Understanding of the Structure of Cellulose

“…14, the orientations of the exocyclic groups are major factors in the calculated energy. 150 In that project, one of the hydroxyl groups was held fixed as an acceptor, and the other hydroxyl group was rotated in increments, with energies calculated by quantum mechanics. 149 This subject has been explored in greater depth by using 1,2-dihydroxycyclohexane as a model compound.…”

“…158 Figure 16 shows the results from an AIM analysis of the lowest energy structure for the minimum at the bottom of the vacuum QM map in Fig. 150 Other interactions are shown, such as those between the hydrogen atoms on C-3 and C-1 0 . As is typical for computed carbohydrate structures at energy minima, the secondary hydroxyl groups are arranged in counter-(reverse-) clockwise orientations that would appear to form weak hydrogen bonds.…”

Cooperativity in alkane‐1,2‐ and 1,3‐polyols: NMR, QTAIM, and IQA study of O─H…OH and C─H…OH bonding interactions

“…It is generally assumed that in carbohydrates, where there are chains or clusters of OH groups, many features, for example, stability, molecular recognition, and binding with acceptors, are determined by long‐range cooperative effects 24–27 . Spectroscopic studies and theoretical calculations confirm that structures with chains of potentially hydrogen‐bonded OH groups are the most stable 28–44 . However, cooperativity between O─H … OH hydrogen bonds in the 1,2‐diol and 1,3‐diol motifs of pyranoses is irregular and not necessarily reciprocal 45, 46 .…”

In defense of adiabatic ϕ/ψ mapping for cellobiose and other disaccharides

“…The first focuses on their idea that the preferred orientation of the secondary hydroxyl units of their models can predict the hydroxyl orientation in structures determined by experiments done in condensed phases. That paper (French and Csonka 2011) is also within the present issue.…”