Force-induced structural changes in non-sulfated carrageenan based oligosaccharides - a theoretical study

Revealing the key structural features promoting the helical conformation in algal polysaccharide carrageenan in solution

Carrageenans are industrially important polysaccharides with tunable viscoelastic and gelation properties. The function of polysaccharide depends on its conformation and chemical composition. However, the solution conformations of carrageenans are highly debated, and the structure-function relationship remains elusive. Here, we have studied the intrinsic conformational behavior of a series of carrageenan hexamers in solution, using extensive all-atom classical MD and enhanced sampling. Our findings comprehensively delineate that carrageenans containing the 3,6-anhydrous bridge (κ-C, ι-C, θ-C, and non-sulfated β-C) adopt compact helical structures as their predominant conformation in solution, whereas carrageenans without the bridge (μ-C, ν-C, and λ-C) remain as extended loosely packed helices; opposing the 'coil-to-helix' paradigm. Glycosidic linkages access a few allowed orientations. We hypothesize that the 3,6-anhydrous bridge, irrespective of carrageenan's sulfation pattern, is essential for stabilizing the helical conformation at the single-chain level. It provides necessary flexibility to the glycosidic linkage to sample conformations close to the experimentally derived helical structure and also prevents the sugar ring flipping. Sulfate groups mainly modify the chain stiffness due to steric and stereo-electronic effects and participate in hydrogen bonding. Such atomistic insights will be helpful for understanding the differential gelation mechanisms of carrageenans and fine-tuning polysaccharide backbone for various industrial applications.

From Cyclo[18]carbon to the Novel Nanostructures-Theoretical Predictions

In this paper, we present a number of novel pure-carbon structures generated from cyclo[18]carbon. Due to the very high reactivity of cyclo[18]carbon, it is possible to link these molecules together to form bigger molecular systems. In our studies, we generated new structures containing 18, 36 and 72 carbon atoms. They are of different shapes including ribbons, sheets and tubes. All these new structures were obtained in virtual reactions driven by external forces. For every reaction, the energy requirement was evaluated exactly when the corresponding transition state was found or it was estimated through our new approach. A small HOMO-LUMO gap in these nanostructures indicates easy excitations and the multiple bonds network indicates their high reactivity. Both of these factors suggest that some potential applications of the new nanostructures are as components of therapeutically active carbon quantum dots, terminal fragments of graphene or carbon nanotubes obtained after fracture or growing in situ in catalytic reactions leading to the formation of carbonaceous materials.

Driving proton transfer reactions in the 2-methylfuran ring with external forces

In this paper we investigate the proton transfer reactions in 2-methylfuran.

Isomerization and Decomposition of 2-Methylfuran with External Forces

The primary goal of this project was to evaluate the performance of the Standard and Enforced Geometry Optimization (SEGO) method which we have recently developed. The SEGO method has been designed for an automatic location of multiple minima on the molecular Potential Energy Surface (PES), and its usefulness has been demonstrated so far for three molecules only. In this project we applied the SEGO method to explore the 2-methylfuran (2MF) PES. Our choice was not accidental: this molecule recently gained a great deal of interest as a potential candidate for biofuel, and therefore its pyrolysis is extensively studied. To understand pyrolysis of 2MF a detailed knowledge about its PES is needed. In these studies we explored the 2MF PES and located a surprisingly large number of local minima corresponding to 2MF isomers and decomposition products. Some of the 2MF isomers and fragments have amazing structures which most likely were previously unknown. All structures presented in this paper were found in an automatic manner as a result of the enforced chemical reactions driven by the SEGO method. Thus, in these studies we have not only proven that the SEGO method is a very efficient tool for exploring molecular potential energy surfaces, but we also obtained very detailed knowledge about the 2MF PES.