Hydration of cellobiose: Structure and dynamics of cellobiose –(H2O)n, n=5–25

Gas phase dynamics, conformational transitions and spectroscopy of charged saccharides: the oxocarbenium ion, protonated anhydrogalactose and protonated methyl galactopyranoside

Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a d-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl d-galactopyranoside-H+. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ∼300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.

Conformational Behavior of d-Lyxose in Gas and Solution Phases by Rotational and NMR Spectroscopies

Understanding the conformational preferences of carbohydrates is crucial to explain the interactions with their biological targets and to improve their use as therapeutic agents. We present experimental data resolving the conformational landscape of the monosaccharide d-lyxose, for which quantum mechanical (QM) calculations offer model-dependent results. This study compares the structural preferences in the gas phase, determined by rotational spectroscopy, with those in solution, resolved by nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations. In contrast to QM calculations, d-lyxose adopts only pyranose forms in the gas phase, with the α-anomer exhibiting both the ⁴C₁ and ¹C₄ chairs (60:40). The predominantly populated β-anomer shows the ⁴C₁ form exclusively, as determined experimentally by isotopic substitution. In aqueous solution, the pyranose forms are also dominant. However, in contrast to the gas phase, the α-anomer as ¹C₄ chair is the most populated, and its solvation is more effective than for the β derivative. Markedly, the main conformers found in the gas phase and solution are characterized by the lack of the stabilizing anomeric effect. From a mechanistic perspective, both rotational spectroscopy and solid-state nuclear magnetic resonance (NMR) corroborate that α ↔ β or furanose ↔ pyranose interconversions are prevented in the gas phase. Combining microwave (MW) and NMR results provides a powerful method for unraveling the water role in the conformational preferences of challenging molecules, such as flexible monosaccharides.

How Cellulose Elongates--A QM/MM Study of the Molecular Mechanism of Cellulose Polymerization in Bacterial CESA

The catalytic mechanism of bacterial cellulose synthase was investigated by using a hybrid quantum mechanics and molecular mechanics (QM/MM) approach. The Michaelis complex model was built based on the X-ray crystal structure of the cellulose synthase subunits BcsA and BcsB containing a uridine diphosphate molecule and a translocating glucan. Our study identified an SN2-type transition structure corresponding to the nucleophilic attack of the nonreducing end O4 on the anomeric carbon C1, the breaking of the glycosidic bond C1-O1, and the transfer of proton from the nonreducing end O4 to the general base D343. The activation barrier found for this SN2-type transition state is 68 kJ/mol. The rate constant of polymerization is estimated to be ∼8.0 s(-1) via transition state theory. A similar SN2-type transition structure was also identified for a second glucose molecule added to the growing polysaccharide chain, which aligned with the polymer 180° rotated compared to the initially added unit. This study provides detailed insights into how cellulose is extended by one glucose molecule at a time and how the individual glucose units align into cellobiose repeating units.

Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study

Interactions determining the dissolution of a monomer of β-cellulose, i.e., cellobiose in a room temperature ionic liquid, [Emim][OAc], have been studied using ab initio molecular dynamics simulations. Although anions are the predominant species in the first coordination shell of cellobiose, cations too are present to a minor extent around it. The presence of low concentration of water in the solution does not significantly alter the nature of the coordination environment of cellobiose. All intra-molecular hydrogen bonds of anti-syn cellobiose are replaced by inter-molecular hydrogen bonds formed with the anions, whereas the anti-anti conformer retains an intramolecular hydrogen bond.

Proton transfer rates in ionized water clusters (H2O)n (n = 2–4)

A proton transfer process is usually dominant in several biological phenomena such as the energy relaxation of photo-excited DNA base pairs and a charge relay process in Ser-His-Glu.

Carbohydrates

Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).