Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence

Cooperative Catalysis Mechanism of Brønsted and Lewis Acids from Al(OTf)3 with Methanol for β-Cellobiose-to-Fructose Conversion: An Experimental and Theoretical Study

Al-containing catalysts, e.g., Al(OTf)3, show good catalytic performance toward the conversion of cellulose to fructose in methanol solution. Here, we report the catalytic isomerization and alcoholysis mechanisms for the conversion of cellobiose to fructose at the PBE0/6-311++G(d,p), aug-cc-pVTZ theoretical level, combining the relevant experimental verifications of electrospray ionization mass spectrometry (ESI-MS), high-performance liquid chromatography (HPLC), and the attenuated total reflection-infrared (ATR-IR) spectra. From the alcoholysis of Al(OTf)3 in methanol solution, the catalytically active species involves both the [CH3OH2]+ Brønsted acid and the [Al(CH3O)(OTf)(CH3OH)4]+ Lewis acid. There are two reaction pathways, i.e., one through glucose (glycosidic bond cleavage followed by isomerization, w-G) and another through cellobiulose (isomerization followed by glycosidic bond cleavage, w-L). The Lewis acid ([Al(CH3O)(OTf)(CH3OH)4]+) is responsible for the aldose-ketose tautomerization, while the Brønsted acid ([CH3OH2]+) is in charge of ring-opening, ring-closure, and glycosidic bond cleavage. For both w-G and w-L, the rate-determining steps are related to the intramolecular [1,2]-H shift between C1-C2 for the aldose-ketose tautomerization catalyzed by the [Al(CH3O)(OTf)(CH3OH)4]+ species. The Lewis acid ([Al(CH3O)(OTf)(CH3OH)4]+) exhibits higher catalytic activity toward the aldose-ketose tautomerization of glycosyl-chain-glucose to glycosyl-chain-fructose than that of chain-glucose to chain-fructose. Besides, the Brønsted acid ([CH3OH2]+) shows higher catalytic activity toward the glycosidic bond cleavage of cellobiulose than that of cellobiose. Kinetically, the w-L pathway is predominant, whereas the w-G pathway is minor. The theoretically proposed mechanism has been experimentally testified. These insights may advance on the novel design of the catalytic system toward the conversion of cellulose to fructose.

Boron Adsorption Kinetics of Microcrystalline Cellulose and Polymer Resin

Tailoring boron-polysaccharide interactions is an important strategy for developing functional soft materials such as hydrogels, fire retardants, and sorbents for environmental remediation, for example, using lignocellulosic biomass. For such applications to be realized, it is paramount to understand the adsorption kinetics of borate anions on cellulose and their local structures. Here, the kinetic aspects of boron adsorption by microcrystalline cellulose, lignin, and polymeric resin are investigated and compared. Borate anions interact with the vicinal diols in the glucopyranoside moieties of cellulose to yield chemisorbed boron chelate complexes. In contrast to cellulose, technical lignin contains fewer cis-vicinal diols, and it does not have a tendency to form such chelate complexes upon treatment with the aqueous boric acid solution. The formation kinetics and stability of these chelate complexes strongly depend on nanoscale structures, as well as reaction conditions such as pH and concentration of the sorbate and sorbent. Specifically, insights into the distinct boron adsorption sites were obtained by solid-state one-dimensional (1D) ¹¹B magic-angle spinning NMR and the local structures and intermolecular interactions in the vicinities of boron chelate complexes are elucidated by analyzing two-dimensional (2D) ¹H-¹³C and ¹¹B-¹H heteronuclear correlation NMR spectra. The total boron adsorption capacity of cellulose is estimated to be in the 1.3-3.0 mg range per gram of sorbent, which is lower than the boron adsorption capacity of a polystyrene-based resin, ∼17.2 mg of boron per gram of Amberlite IRA 743. Our study demonstrates that the local backbone and side chain flexibility as well as the structures of polyol groups play a significant role in determining the kinetic and thermodynamic stability of chelate complexes, yielding to different boron adsorption capabilities of lignocellulosic polymers.

Role and importance of solvents for the fractionation of lignocellulosic biomass

Lignocellulosic biomass is one of the most important renewable materials to replace carbon-based fossil resources. Solvent-based fractionation is a promising route for fractionation of biomass into its major components. Processing is governed by the employed solvent-systems properties. This review sheds light on the factors governing both dissolution and potential reactivities of the chemical structures present in lignocellulose, highlighting how proper understanding of the underlying mechanisms and interactions between solute and solvent help to choose proper systems for specific fractionation needs. Structural and chemical differences between the carbohydrate-based structural polymers and lignin require very different solvents capabilities in terms of causing and eventually stabilizing conformational changes and consequent activation of bonds to be cleaved by other active components in the. A consideration of potential depolymerization events during dissolution and energetic aspects of the dissolution process considering the contribution of polymer functionalities allow for a mapping of solvent suitability for biomass fractionation.

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

The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially, the molecular shape is inferred from the crystal structures of many small molecules that have β-(1→4) linkages. Then, conformational analyses with potential energy calculations of cellobiose are covered, followed by the use of Atoms-In-Molecules theory to learn about interactions in experimental and theoretical structures. The last section covers models of cellulose nanoparticles. Controversies addressed include the stability of twofold screw-axis conformations, the influence of different computational methods, the predictability of crystalline conformations by studies of isolated molecules, and the twisting of model cellulose crystals.

O-Methylation in Carbohydrates: An NMR and MD Simulation Study with Application to Methylcellulose

Methylated carbohydrates are important from both biological and technical perspectives. Specifically, methylcellulose is an interesting cellulose derivative that has applications in foods, materials, cosmetics, and many other fields. While the molecular dynamics simulation technique has the potential for both advancing the fundamental understanding of this polymer and aiding in the development of specific applications, a general drawback is the lack of experimentally validated interaction potentials for the methylated moieties. In the present study, simulations using the GROMOS 56 carbohydrate force field are compared to NMR spin–spin coupling constants related to the conformation of the exocyclic torsion angle ω in d-glucopyranose and derivatives containing a 6-O-methyl substituent and a ¹³C-isotopologue thereof. A ³J_CC Karplus-type relationship is proposed for the C5–C6–O6–C_Me torsion angle. Moreover, solvation free energies are compared to experimental data for small model compounds. Alkylation in the form of 6-O-methylation affects exocyclic torsion only marginally. Computed solvation free energies between nonmethylated and methylated molecules were internally consistent, which validates the application of these interaction potentials for more specialized purposes.

Self-assembly of cellulose for creating green materials with tailor-made nanostructures

Inspired by living systems, biomolecules have been employed in vitro as building blocks for creating advanced nanostructured materials. In regard to nucleic acids, peptides, and lipids, their self-assembly pathways and resulting assembled structures are mostly encoded in their molecular structures. On the other hand, outside of its chain length, cellulose, a polysaccharide, lacks structural diversity; therefore, it is challenging to direct this homopolymer to controllably assemble into ordered nanostructures. Nevertheless, the properties of cellulose assemblies are outstanding in terms of their robustness and inertness, and these assemblies are attractive for constructing versatile materials. In this review article, we summarize recent research progress on the self-assembly of cellulose and the applications of assembled cellulose materials, especially for biomedical use. Given that cellulose is the most abundant biopolymer on Earth, gaining control over cellulose assembly represents a promising route for producing green materials with tailor-made nanostructures.

Dynamical Water Ingress and Dissolution at the Amorphous-Crystalline Cellulose Interface

The use of cellulose has considerable promise in a wide range of industrial applications but is hampered by degradation in mechanical properties due to ambient moisture uptake. Existing models of equilibrium moisture content can predict the impact of these effects, but at present, the dynamical, atomic-scale picture of water ingress into cellulose is lacking. The present work reports nonequilibrium molecular simulations of the interface between cellulose and water aimed at capturing the initial stages of two simultaneous dynamical processes, water ingress into cellulose and cellulose dissolution into water. These simulations demonstrate that the process depends on the temperature and chain length in the amorphous region, where high temperatures can induce more mass exchange and short chains can easily detach from amorphous cellulose. A cooperative mechanism that involves both chemical and physical aspects, namely, hydrogen bonding and chain intertwining, respectively, is proposed to interpret the incipient dual ingress/dissolution process. Outcomes of this work will provide a foundation for cellulose functionalization strategies to impede moisture uptake and preserve the mechanical properties of nanocellulose in applications.

Self-assembly in biobased nanocomposites for multifunctionality and improved performance

Concerns of petroleum dependence and environmental pollution prompt an urgent need for new sustainable approaches in developing polymeric products. Biobased polymers provide a potential solution, and biobased nanocomposites further enhance the performance and functionality of biobased polymers. Here we summarize the unique challenges and review recent progress in this field with an emphasis on self-assembly of inorganic nanoparticles. The conventional wisdom is to fully disperse nanoparticles in the polymer matrix to optimize the performance. However, self-assembly of the nanoparticles into clusters, networks, and layered structures provides an opportunity to address performance challenges and create new functionality in biobased polymers. We introduce basic assembly principles through both blending and in situ synthesis, and identify key technologies that benefit from the nanoparticle assembly in the polymer matrix. The fundamental forces and biobased polymer conformations are discussed in detail to correlate the nanoscale interactions and morphology with the macroscale properties. Different types of nanoparticles, their assembly structures and corresponding applications are surveyed. Through this review we hope to inspire the community to consider utilizing self-assembly to elevate functionality and performance of biobased materials. Development in this area sets the foundation for a new era of designing sustainable polymers in many applications including packaging, construction chemicals, adhesives, foams, coatings, personal care products, and advanced manufacturing.

Biobased superhydrophobic coating enabled by nanoparticle assembly

Understanding biobased nanocomposites is critical in fabricating high performing sustainable materials. In this study, fundamental nanoparticle assembly structures at the nanoscale are examined and correlated with the macroscale properties of coatings formulated with these structures. Nanoparticle assembly mechanisms within biobased polymer matrices were probed using in situ liquid-phase atomic force microscopy (AFM) and computational simulation. Furthermore, coatings formulated using these nanoparticle assemblies with biobased polymers were evaluated with regard to the hydrophobicity and adhesion after water immersion. Two biobased glycopolymers, hydroxyethyl cellulose (HEC) and hydroxyethyl starch (HES), were investigated. Their repeating units share the same chemical composition and only differ in monomer conformations (α- and β-anomeric glycosides). Unique fractal structures of silica nanoparticle assemblies were observed with HEC, while compact clusters were observed with HES. Simulation and AFM measurement suggest that strong attraction between silica surfaces in the HEC matrix induces diffusion-limited-aggregation, leading to large-scale, fractal assembly structures. By contrast, weak attraction in HES only produces reaction-limited-aggregation and small compact cluster structures. With high particle loading, the fractal structures in HEC formed a network, which enabled a waterborne formulation of superhydrophobic coating after silane treatment. The silica nanoparticle assembly in HEC was demonstrated to significantly improve adhesion, which showed minimum adhesion loss even after extended water immersion. The superior performance was only observed with HEC, not HES. The results bridge the assembly structures at the nanoscale, influenced by molecular conformation of biobased polymers, to the coating performance at the macroscopic level. Through this study we unveil new opportunities in economical and sustainable development of high-performance biobased materials.

Comparison of cellooligosaccharide conformations in complexes with proteins with energy maps for cellobiose

Shapes (conformations) of cellulose molecules are described by their glycosidic linkage torsion angles ϕ and ψ. Although the torsions are known for cellulose in crystals, amorphous shapes are also interesting for understanding reactivity and physical properties. ϕ and ψ determination for unorganized matter is difficult; one approach is to study their range in many related molecules. For example, linkage torsions of cellulose should be similar to those in cellobiose. Herein, torsions were measured for cellooligosaccharides and lactose moieties complexed with proteins in the Protein Data Bank (PDB). These torsions were compared with ϕ/ψ maps based on quantum mechanics energies for solvated cellobiose and analogs lacking hydroxyl groups. Most PDB conformations corresponded to low map energies. Amorphous cellulose should be generally extended with individual linkages that would give 2- to 3-fold helices. The map for an analog lacking hydrogen bonding ability was more predictive for PDB linkages than the cellobiose map.

Relation between glycosidic linkage, structure and dynamics of α- and β-glucans in water

In a molecular dynamics simulation study of several oligosaccharides comprising of the very basic building block of carbohydrate, the α- or β-d glucopyranose units, linked by any one of the 1-3/1-4 or 1-6 glycosidic linkages, we compare and contrast their structural and dynamical properties. Results indicate that the litheness of the oligosaccharide chain is noticeably controlled by the composition, anomeric nature and glycosidic linkage type of the units. In mixed β 1-4/1-3 d-glucopyranosides, as those found in oats and barley, the ratio of the β 1-4 and β 1-3 linked residues is crucial in determining the structural and dynamical attributes. Principal component analysis (PCA) using the internal coordinates of torsion angles subtended by glycosidic oxygen atoms and subsequent K-means clustering of the dynamical space spanned by PC1 to PC2 point to the dynamical and structural disparity in the various types of oligosaccharides studied. The properties simulated in this work are meant to provide a systematic yet comparative understanding of the importance of linkage and anomericity on the oligosaccharide chain properties and are in line with some experimental structural attributes.

Computerized Molecular Modeling of Carbohydrates

Computerized molecular modeling continues to increase in capability and applicability to carbohydrates. This chapter covers nomenclature and conformational aspects of carbohydrates, perhaps of greater use to computational chemists who do not have a strong background in carbohydrates, and its comments on various methods and studies might be of more use to carbohydrate chemists who are inexperienced with computation. Work on the intrinsic variability of glucose, an overall theme, is described. Other areas of the authors' emphasis, including evaluation of hydrogen bonding by the atoms-in-molecules approach, and validation of modeling methods with crystallographic results are also presented.

Modeling of the morphological change of cellulose microfibrils caused with aqueous NaOH solution: the longitudinal contraction and laterally swelling during decrystallization

The conformation of cellulose microfibrils treated with aqueous NaOH was modeled as partially decrystallized cellulose chains before completing conversion to cellulose II, in order to elucidate the change in morphology of ramie fiber caused by NaOH treatment. Equations for the relative length and width of the microfibrils were derived on the basis of partially decrystallized microfibrils modeling. Each equation contains four parameters, n, β, w _c , and c _r , which correspond to the number of glucose residues between periodic defects along the untreated ramie cellulose microfibrils, the extension ratio of amorphous cellulose chain along length, the cross-section crystallinity, and the correction term of crystallinity, respectively. The validity of the derived equations was confirmed by two types of simulations. One is performed using experimental data L/L ₀ and W/W ₀ as a function of crystallinity, while the other is done using the relationship between the relative length and width obtained from the experimental data, which is independent of crystallinity, was performed. The best-fit simulation was obtained under n = 277, β = 2.813, and c _r w _c  = 0.671 for the former and under n = 301 and β = 2.792 for the latter. These values of n and β correspond closely to the values reported in references for ramie microfibrils. Both simulation results show that macroscopic changes in the morphology of ramie fibers is attributable to the changes in cellulose chain conformation in the decrystallized regions created along the microfibrils upon NaOH treatment.

Replica exchange molecular dynamics simulations reveal the structural and molecular properties of levan-type fructo-oligosaccharides of various chain lengths

Background

Levan and levan-type fructo-oligosaccharides (LFOs) have various potential applications in pharmaceutical and food industries due to their beneficial properties such as their low intrinsic viscosity and high water solubility. Previous studies showed that they exhibited prebiotic effects, anti-inflammatory and anti-tumor activities against Sarcoma-180 tumor cells of human. Despite their various potential applications, the structural and molecular properties of LFOs of various chain lengths are not well understood.

Results

We employed the replica-exchange molecular dynamics simulations method (REMD) in AMBER14 to elucidate structural and molecular properties of LFOs with chain lengths of 5 (LFO₅), 10 (LFO₁₀) and 15 (LFO₁₅) residues in two models of generalized Born implicit solvent (GB_HCT and GB_OBC1). For LFO₁₀ and LFO₁₅, four distinct conformations (helix-like, partial helix, zig-zag and random structures) were characterized by their upper-middle and lower-middle torsions. For LFO₅, two distinct conformations (partial helix and random structures) were characterized by their middle torsion and molecular angle of residues 1, 3 and 5. To determine hydrogen bonds important for the formation of helix-like structures of LFO₁₀ and LFO₁₅, occurrence frequencies of hydrogen bonds were analyzed, and the O6_(i)--H3O_(i+1) hydrogen bond was found with the highest frequency, suggesting its importance in helix formation. Among three dihedral angles between two fructosyl units [ϕ (O5’-C2’-O6-C6), ψ (C2’-O6-C6-C5) and ω (O6-C6-C5-C4)], dihedral angle distributions showed that ω was the most flexible dihedral angle and probably responsible for conformational differences of LFOs.

Conclusions

Our study provides important insights into the structural and molecular properties of LFOs, which tend to form helical structures as the chain length increases from 5 to 15 residues. This information could be beneficial for the selection of LFOs with appropriate lengths and properties for pharmaceutical and biological applications.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-1182-7) contains supplementary material, which is available to authorized users.

Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM)

Oligosaccharides and polysaccharides exert numerous functional roles in biology through their structural diversity and conformational properties. To investigate their conformational properties using computational methods, Hamiltonian replica exchange (H-REX) combined with two-dimensional grid-based correction maps as biasing potentials (bpCMAP) significantly improves the sampling efficiency about glycosidic linkages. In the current study, we extend the application of H-REX with bpCMAP to complex saccharides and establish systematic procedures for bpCMAP construction, determination of replica distribution, and data analysis. Our main findings are that (1) the bpCMAP for each type of glycosidic linkage can be constructed from the corresponding disaccharide using gas-phase umbrella sampling simulations, (2) the replica distribution can be conveniently determined following the exact definition of the average acceptance ratio based on the assigned distribution of biasing potentials, and (3) the extracted free energy surface (or potential of mean force (PMF)) can be improved using the weighted histogram analysis method (WHAM) allowing for the inclusion of data from the excited state replicas in the calculated probability distribution. The method is applied to a branched N-glycan found on the HIV gp120 protein, and a linear N-glycan. Considering the general importance of N-glycans and the wide appreciation of the sampling problem, the present method represents an efficient procedure for the conformational sampling of complex oligo- and polysaccharides under explicit solvent conditions. More generally, the use of WHAM is anticipated to be of general utility for the calculation of PMFs from H-REX simulations in a wide range of macromolecular systems.

Energy maps for glycosidic linkage conformations

Glycosidic linkage conformations are the main factors in determining the shapes of disaccharide, oligosaccharide, and polysaccharide molecules. The conformations are expressed in terms of the torsion angles about the bonds from each ring of the disaccharide moiety to its glycosidic oxygen atom, and the probability of a given conformation is often expressed in terms of its free or potential energy. The energy surface or map for a disaccharide is a display of the energy plotted against the two torsion angles. Successful mapping allows a particular kind of energy calculation to provide the energy values for each conformation and avoids possible pitfalls. Although different methods are discussed, the main emphasis of this chapter is on the technical production of the maps and their exploitation in further understanding the shape of the molecule in question.

Surface-Sensitive Approach to Interpreting Supramolecular Rearrangements in Cellulose by Synchrotron Grazing Incidence Small-Angle X-ray Scattering

The supramolecular rearrangements of biopolymers have remained difficult to discern. Here, we present a versatile approach that allows for an in situ investigation of two major types of rearrangements typically observed with cellulose, the most abundant biopolymer on earth. Model thin films were employed to study time-resolved pore size changes using in situ grazing incidence small-angle X-ray scattering (GISAXS) during regeneration and drying.

A bioinspired polymer-bound Mn-porphyrin as an artificial active center of catalase

The complex comprising a cationic Mn-porphyrin and carboxymethyl poly(1-vinylimidazole) (CM-PVIm) was prepared as an artificial active center of catalase. Interestingly, the catalase activity of the complex depends on the chain length of the polymer and the chemical structure of Mn-porphyrin. This study is one step forward in the development of a new class of water-soluble catalase mimics.

Unique aspects of the structure and dynamics of elementary Iβ cellulose microfibrils revealed by computational simulations

The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Iβ cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18- and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18- and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains.

Investigation of Carbohydrate Recognition via Computer Simulation

Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Recently, interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. We focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We review the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.

Spectral and thermal characterization of halogen-bonded novel crystalline oligo(p-bromoacetophenone formaldehyde)

A novel oligomer p-bromoacetophenone-formaldehyde (OPBAF) was prepared by condensation polymerization in the presence of an acid as catalyst. It was characterized by FT-IR, NMR, pyrolysis GC/MS, XRD, GPC, and TG-DTG. The crystallographic parameters and space group for hexagonal OPBAF were a = b = 2.0810 Å and c = 9.2340 Å and P3̅m1, respectively. The degradation activation energy of the oligomer was studied by the Kissinger method. The kinetic parameters were also obtained. Halogen bonding interactions in the crystalline oligomers are identified between halogen···carbonyl and halogen···halogen. Little correlation was found in the halogen bonding motifs exhibited as a function of bromine present in this oligomer, and a unique bifurcated Br···Br/Br···O═C halogen bonding synthon was identified. This newly developed oligomer may be used as an interesting material for the development of 3D-designed structural products.

Dissolution of cellulose in room temperature ionic liquids: anion dependence

The dissolution of cellulosic biomass in room temperature ionic liquids (RTILs) is studied through free energy calculations of its monomer, viz., cellobiose, within a molecular dynamics simulation approach. The solvation free energy (SFE) of cellobiose in ionic liquids containing any of seven different anions has been calculated. The ranking of these liquids based on SFE compares well with experimental data on the solubility of cellulose. The dissolution is shown to be enthalpically dominated, which is correlated with the strength of intermolecular hydrogen bonding between cellobiose and the anions of the IL. Large entropic changes upon solvation in [CF3SO3](-) and [OAc](-) based ionic liquids have been explained in terms of the solvent-aided conformational flexibility of cellobiose.

Elucidating the conformational energetics of glucose and cellobiose in ionic liquids

The energetics driving the conformational preference of the ω dihedral of glucose and the φ–ψ dihedrals of cellobiose solvated in imidazolium acetate ionic liquids and water are elucidated and compared.

Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride

Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H'···O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures.

Detecting low-level flexibility using residual dipolar couplings: a study of the conformation of cellobiose

We have developed novel NMR methods for the measurement of heteronuclear residual dipolar couplings (RDCs) in molecules with severely overlapping NMR resonances. These and other methods enabled us to obtain 31 RDCs for α-D-cellobiose and 24 RDCs for β-D-cellobiose. The interpretation of the data in the approximation of a rigid disaccharide structure, using RDCs and interglycosidic (3)J coupling constants, yielded conformation that is very close to that determined using X-ray crystallography. However, depending on which ring was used to calculate the order parameters, the dihedral angle ψH varied up to 30° or 40°, while the φH angle was always the same. This indicates residual flexibility of the glycosidic linkage between the two monosaccharide rings and was observed for both α- and β-D-cellobiose. The RDC analysis using rigid fragments rather than a complete molecule has thus shown that the glycosidic bond of cellobiose is not completely rigid and exhibits low-level flexibility. The sources of this flexibility are discussed and evidence presented to support a hypothesis that it is associated with the ψ more than the φ angle.

Conformational flexibility of N-glycans in solution studied by REMD simulations

Protein-glycan recognition regulates a wide range of biological and pathogenic processes. Conformational diversity of glycans in solution is apparently incompatible with specific binding to their receptor proteins. One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein. However, the labile nature of glycans makes characterizing their conformational states a challenging issue. All-atom molecular dynamics (MD) simulations provide the atomic details of glycan structures in solution, but fairly extensive sampling is required for simulating the transitions between rotameric states. This difficulty limits application of conventional MD simulations to small fragments like di- and tri-saccharides. Replica-exchange molecular dynamics (REMD) simulation, with extensive sampling of structures in solution, provides a valuable way to identify a family of glycan conformers. This article reviews recent REMD simulations of glycans carried out by us or other research groups and provides new insights into the conformational equilibria of N-glycans and their alteration by chemical modification. We also emphasize the importance of statistical averaging over the multiple conformers of glycans for comparing simulation results with experimental observables. The results support the concept of "conformer selection" in protein-glycan recognition.