Extension of the GROMOS 56a6 Force Field for Charged, Protonated, and Esterified Uronates.

An extension of the GROMOS 56a6 force field for hexopyranose-based carbohydrates is presented. The additional parameters describe the conformational properties of uronate residues. The three distinct chemical states of the carboxyl group are considered: deprotonated (negatively charged), protonated (neutral), and esterified (neutral).

Acyclic forms of aldohexoses and ketohexoses in aqueous and DMSO solutions: conformational features studied using molecular dynamics simulations.

The molecular properties of aldohexoses and ketohexoses are usually studied in the context of their cyclic, furanose or pyranose structures which is due to the abundance of related tautomeric forms in aqueous solution. We studied the conformational features of a complete series of D-aldohexoses (D-allose, D-altrose, D-glucose, D-mannose, D-gulose, d-idose, D-galactose and D-talose) and D-ketohexoses (D-psicose, D-fructose, D-sorbose and D-tagatose) as well as of L-psicose by using microsecond-timescale molecular dynamics in explicit water and DMSO with the use of enhanced sampling methods. In each of the studied cases the preferred conformation corresponded to an extended chain structure; the less populated conformers included the quasi-cyclic structures, close to furanose rings and common for both aldo- and ketohexoses.

Ring inversion properties of 1→2, 1→3 and 1→6-linked hexopyranoses and their correlation with the conformation of glycosidic linkages.

Enhanced-sampling molecular dynamics simulations performed within the GROMOS 56a6CARBO_R force field were applied in order to elucidate ring-inversion properties of hexopyranose residues in a chain for the case of α(1→n) and β(1→n) glycosidic linkages (n = 2, 3 or 6). The results indicate that ring-inversion free energies calculated for residues in a chain are weakly correlated with those of corresponding monomers, except of the case of 1→6 linkages. This, in combination with the results for O1-methyl-hexopyranosides (Plazinski et al, 2016), suggests that both the type of functionalization (glycolysation vs.

Kinetic characteristics of conformational changes in the hexopyranose rings.

The shape of the hexopyranose ring is an important factor which can influence the properties of carbohydrate molecules and affect their biological activity. Due to a limited availability of the experimental data, the conformational rearrangements (puckering) which occur within the pyranose rings are studied extensively by using various computational approaches. Contrary to the basic structural and energetic features characterizing the process of ring flexing, the kinetic and dynamics properties of puckering remain less recognized.

The influence of the hexopyranose ring geometry on the conformation of glycosidic linkages investigated using molecular dynamics simulations.

The conformation of the carbohydrate molecules is a subject of many theoretical and experimental studies. The different timescales associated with the particular degrees of freedom hinder the progress in both those fields. The present paper reports the results of computational studies aimed at elucidating and characterizing the potential correlations between the two main structural determinants of the carbohydrate structure, i.

The water-catalyzed mechanism of the ring-opening reaction of glucose.

The hexopyranose mutarotation is an important focus for carbohydrate chemistry for more than 150 years. The paper describes the results of advanced computational studies aimed at elucidating the ring-opening reaction of glucose. Molecular simulations based on the combination of the DFT method with the molecular dynamics formalism allowed for a detailed insight into the mechanism of the process accompanied by the information of the kinetic and dynamic nature.

Alkane separation using nanoporous graphene membranes.

We studied the permeability of graphene sheets with designed nanopores using the classical molecular dynamics. To characterize the energy profile for transmission we calculated the potential of the mean force. A high selectivity for methane + butane mixture with the hydrogen-passivated pore diameter of 0.

Calcium-α-L-guluronate complexes: Ca2+ binding modes from DFT-MD simulations.

The interactions of divalent calcium ions with a single α-L-guluronate anion and oligo(α-L-guluronate) chain have been studied in terms of the 'hybrid' molecular dynamics technique in which the selected parts of the system are treated with different level of theory (DFT-MD). The simulations were focused on obtaining the free energy profiles designed to clarify the possible calcium binding modes. In all considered cases, the calcium ion is coordinated by carboxyl oxygen atoms and water molecules exclusively.

Supramolecular assembly of interfacial nanoporous networks with simultaneous expression of metal-organic and organic-bonding motifs.

The formation of 2D surface-confined supramolecular porous networks is scientifically and technologically appealing, notably for hosting guest species and confinement phenomena. In this study, we report a scanning tunneling microscopy (STM) study of the self-assembly of a tripod molecule specifically equipped with pyridyl functional groups to steer a simultaneous expression of lateral pyridyl-pyridyl interactions and Cu-pyridyl coordination bonds. The assembly protocols yield a new class of porous open assemblies, the formation of which is driven by multiple interactions.

Implicit solvent model for effective molecular dynamics simulations of systems composed of colloid nanoparticles and carbon nanotubes.

In this paper we propose an implicit solvent model which can be used in molecular dynamics simulations of systems comprising colloid nanoparticles and carbon nanotubes. Such systems, due to finite nanometer sizes of both components cannot be accurately approximated by a smaller slab geometry and thus represent a particularly difficult case in terms of computer simulations. In particular, nanoparticle sizes of a few tens of nanometers lead to billions of solvent molecules in a simulation box and require very long cut-off distances which drastically increases computation time.

The dynamics of the calcium-induced chain-chain association in the polyuronate systems.

The calcium-induced formation of strong, hydrophilic gels is the important feature of polyuronates, connected with most of their practical applications. The insight into the molecular details of gelling process dynamics is hardly feasible for both experimental and theoretical methods. Here, the application of the transition path sampling method for studying this problem is reported; the focus was on the poly(α-L-guluronate) systems, treated as the representative for all polyuronate-containing systems.

Computer simulation of chiral nanoporous networks on solid surfaces.

A lattice Monte Carlo (MC) model was proposed with the aim of understanding the factors affecting the chiral self-assembly of tripod-shaped molecules in two dimensions. To that end a system of flat symmetric molecules adsorbed on a triangular lattice was simulated by using the canonical ensemble method. Special attention was paid to the influence of size and composition of the building block on the morphology of the adsorbed overlayer.

Monte Carlo modeling of chiral adsorption on nanostructured chiral surfaces and slit pores.

Adsorptive separation of chiral molecules is a powerful technique that has long been used in the chemical and pharmaceutical industries. An important challenge in this field is to design and optimize new adsorbents to provide selective discrimination of enantiomers. In this article, we introduce an off-lattice model of chiral adsorption on nanostructured surfaces and slit pores with the aim of predicting their enantioslective properties.

Modeling of binary adsorption on heterogeneous surfaces characterized by a quasi-gaussian adsorption energy distribution.

The integral equation (IE) approach coupled with a quasi-Gaussian adsorption energy distribution is used to model the adsorption of single gases and their binary mixture on a heterogeneous solid surface. The adsorbing surface is assumed to be characterized by two, generally different in width, quasi-Gaussian distribution functions, each of them related to a single component of the mixture. The influence of correlations between the distribution functions associated with different components on the corresponding adsorption isotherms and phase diagrams is discussed.