Extension of the GROMOS 56a6CARBO/CARBO_R Force Field for Charged, Protonated, and Esterified Uronates.

An extension of the GROMOS 56a6CARBO/CARBO_R 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). The parametrization procedure was based on quantum-chemical calculations, and the resulting parameters were tested in the context of (i) flexibility of the pyranose rings under different pH conditions, (ii) conformation of the glycosidic linkage of the (1 → 4)-type for uronates with different chemical states of carboxyl moieties, (iii) conformation of the exocyclic (i.e., carboxylate and lactol) moieties, and (iv) structure of the Ca2+-linked chain-chain complexes of uronates. The presently proposed parameters in combination with the 56a6CARBO/CARBO_R set can be used to describe the naturally occurring polyuronates, composed either of homogeneous (e.g., glucuronans) or heterogeneous (e.g., pectins, alginates) segments. The results of simulations relying on the new set of parameters indicate that the conformation of glycosidic linkage is nearly unaffected by the chemical state of the carboxyl group, in contrary to the ring conformational equilibria. The calculations for the poly(α-d-galacturonate)-Ca2+ and poly(α-l-guluronate)-Ca2+ complexes show that both parallel and anitiparallel arrangements of uronate chains are possible but differ in several structural aspects.

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. The orientational preferences of the aldehyde or ketone groups are correlated with the relative populations of anomers characteristic of cyclic aldo- and ketohexoses, respectively, thus indicating that basic features of anomeric equilibria are preserved even if hexose molecules are not in their cyclic forms. No analogous relationship is observed in the case of other structural characteristics, such as the preferences of acyclic molecules to form either the furanose-or pyranose-like structures or maintaining the chair-like geometry of pseudo-pyranose rings.

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 ß(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. methylation) and the topology of glycosidic linkage play an important role in possible alterations of the hexopyranose ring flexibility. Additionally, the correlation of the ring shape with the preferred geometry of glycosidic linkages was investigated. The linkages of the 1→2, 1→3 and 1→6 types do not follow the trend found in the case of the 1→4 linkages, i.e. there is no correlation between the range of changes in the glycosidic linkage conformation and the topological orientation of the glycosidic oxygen atoms. Overall, the ring shape affects the glycosidic linkages of the 1→6 type to the least extent in comparison to the remaining ones.

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. We performed the first, molecular dynamics-based, systematic calculations aimed at description of the kinetic characteristics of the conformational changes in the rings of α-d- and ß-d-glucopyranose molecules. The rate constants representing particular molecular events which comprise the chair-chair inversion are determined and analyzed in the context of the available experimental data. Furthermore, several various variables (e.g. transmission coefficients) and issues (e.g. memorylessness of the puckering process) are investigated and discussed. As several different parameter sets were used during the study (GROMOS 56A6CARBO, GLYCAM, GROMOS 53A6GLYC), the results provide the conclusion on the capability of the carbohydrate-dedicated force fields to describe the kinetic properties of pyranose ring flexing.

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.e. the ring conformation and the orientation of the glycosidic bonds (expressed in terms of the ϕ and ψ glycosidic dihedral angles). The free energy landscapes computed for 16 different oligomers composed of unsubstituted, 1,4-linked hexopyranose residues allowed for a detailed insight into how the ring geometry affects the glycosidic linkage conformation. The factor of main importance appeared to be the local changes of the chain length induced by the ring conformational rearrangements. This effect is important mainly for the carbohydrate chains exploiting the glycosidic bonds of uniform orientation with respect to the ring (i.e. either exclusively axially or exclusively equatorially oriented). The shape of the ring may affect the (ϕ,ψ) free energy maps but only if the population of the alternative ring conformers is relatively high and (at the same time) the presence of such conformers is associated with the significant shifts of the favorable ϕ and ψ values.

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. The results indicate that the process is initiated by deprotonation of the anomeric hydroxyl group by water molecules and the subsequent proton transfer to the ring oxygen atom. The latter event has been identified as a 'bottleneck' of the process triggering the ring cleavage. The most time-consuming steps of the ring-opening reaction are the orientational rearrangements of water molecule(s) participating in the proton transfer(s) and the final extension of the newly-formed aldehyde chain. The orientational preferences of the aldehyde group present in the acyclic form of D-hexopyranoses are responsible for the anomeric equilibrium characteristics.

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 0.32 nm was found where the volume exclusion mechanism governs the separation process. In the case of a slightly larger pore diameter of 0.64 nm the same alkane mixture separates completely unexpectedly: a larger butane molecule permeates much faster than a small methane one. The blocking effect of the permeation path by a larger mixture component when it worked like a cork was also observed. This is a promising perspective for using graphene to design intelligent membranes which can maintain a constant composition of mixtures in the permeable area.

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. The tripod forms a purely porous organic network on Ag(111), phase α, in which the presence of the pyridyl groups is crucial for porosity, as confirmed by molecular dynamics and Monte Carlo simulations. Additional deposition of Cu dramatically alters this scenario. For submonolayer coverage, three different porous phases coexist (i.e., ß, γ, and δ). Phases ß and γ are chiral and exhibit a simultaneous expression of lateral pyridyl-pyridyl interactions and twofold Cu-pyridyl linkages, whereas phase δ is just stabilized by twofold Cu-pyridyl bonds. An increase in the lateral molecular coverage results in a rise in molecular pressure, which leads to the formation of a new porous phase (ε), only coexisting with phase α and stabilized by a simultaneous expression of lateral pyridyl-pyridyl interactions and threefold Cu-pyridyl bonds. Our results will open new avenues to create complex porous networks on surfaces by exploiting components specifically designed for molecular recognition through multiple interactions.

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. The results allowed for (i) determining the dentacy of calcium binding; (ii) estimating the calcium binding/unbinding-related free energy profiles; and (iii) positive verification of the previously [J. Comput. Chem. 2011, 32, 2988] proposed modification of the egg-box model describing the calcium alginate/guluronate structure. Additionally, the findings indicate that the polarization of the carboxyl group induced by the presence of Ca(2+) ion causes the increase of the free energy barrier separating the 'free' and 'bound' states of Ca(2+), in comparison to the classical biomolecular force fields (GROMOS/SPC and GLYCAM/TIP3P).

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. To overcome this difficulty we develop an implicit solvent model based on Hamaker theory of dispersive interactions. The predictions of our model are verified by comparison with the exact model, involving all atoms and full description of pair interactions. The proposed model correctly predicts the work of adhesion and average configuration in colloid - carbon nanotube systems. Moreover, application of the Langevin dynamics reproduces the dynamic behaviour of the exact model either.

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. The results allowed for identifying several distinct local minima of the free energy lying on the transition paths and visited by the system during the process of chain-chain association. These minima usually correspond to the intermediate structures in which the water molecules bridge calcium ion and carboxyl groups. This work emphasizes the importance of water and provides more complete understanding of the calcium binding by the polyuronate chains.

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. The obtained results demonstrated a spontaneous self-assembly into extended chiral networks with hexagonal cavities, highlighting the ability of the model to reproduce basic structural features of the corresponding experimental systems. The simulated assemblies were analyzed with respect to their structural and energetic properties resulting in quantitative estimates of the unit cell parameters and mean potential energy of the adsorbed layer. The predictive potential of the model was additionally illustrated by comparison of the obtained superstructures with the recent STM images that have been recorded for different organic tripod-shaped molecules adsorbed at the liquid/pyrolytic graphite interface.

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. The concept presented here involves finding the optimal chiral pattern of active sites on the pore walls that maximizes the difference between the binding energies of the enantiomers. Our initial effort focuses on chiral molecules that do not have specific interactions with the pore surface. One candidate meeting this requirement is 1,2-dimethylcyclopropane (DMCP), a chiral hydrocarbon whose interaction with a model pore surface was described using the Lennard-Jones potential. To model the adsorption of DMCP, we used the Monte Carlo simulation method. It was demonstrated that the separation of the enantiomers of DMCP is hardly obtainable because of the smoothness of the potential energy surface for molecules physisorbed in the pore. However, the simulated results allowed the identification of key factors that influence the binding of the enantiomers of DMCP to the pore walls with a special distribution of active sites. This information will be useful in future considerations of the adsorption of more complex chiral molecules.

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. In particular, it is demonstrated that a lack of microscopic correlations between the adsorption energies of the components may lead to the formation of an azeotropic mixture. The predictions of the theory are also compared with the results of the grand canonical Monte Carlo (GCMC) simulations carried out for the system studied.