Mateusz Drach

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., β, γ, and δ). Phases β 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.

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.

ADSORPTION OF CATIONIC SURFACTANTS ON HYDROPHILIC SILICA : EFFECTS OF SURFACE ENERGETIC HETEROGENEITY

Abstract The thermodynamics of adsorption of cationic surfactants on a hydrophilic silica surface is discussed. The adsorption isotherms of these surfactants on negatively charged silica surfaces exhibit a two-step character, as a rule. The heights of these steps and the concentration at which the second step begins depend strongly on the surface charge determined by the pH and indifferent electrolyte concentration in the equilibrium bulk solution. In our previous publication we have developed a theoretical description based on the model of the adsorbed phase being a mixture of monolayered and bilayered aggregates of different sizes. Only the “excluded area” interactions were taken into account. The potential energy per molecule was assumed to decrease linearly with the aggregate size. The theoretical expressions obtained for adsorption isotherms and heats of adsorption were next fitted to experimental data of cationic surfactants adsorption on precipitated silica. Although our model was able to reproduce well the two steps observed on the adsorption isotherms of these surfactants, it failed to predict the behavior of isosteric heats of adsorption at low surface coverages. In this paper our model is extended by taking into account the effects of surface heterogeneity on single monomer adsorption. This leads to a much better description of entropic effects accompanying surfactant adsorption in the low coverage region. It is therefore concluded that individual adsorption of surfactant ions, which is determined primarily by the specific solid–surfactant interactions, is strongly affected by the surface heterogeneity effects.

The dynamics of the conformational changes in the hexopyranose ring: a transition path sampling approach

The ring conformation of the hexopyranose-based carbohydrate molecules is one of the central issues in glycobiology. We report the results of the transition path sampling simulations aimed at the detailed description of the dynamic features of these conformational changes. We focused on the α-D- and β-D-glucopyranose molecules (GlcA and GlcB, respectively), treated as model systems. A large number of unbiased dynamic trajectories leading from the 4C1 conformation to the 1C4 one has been collected and subjected to analysis. The results allowed for: (i) identifying the distinct local minima of the free energy corresponding to the states intermediate for the 4C1 → 1C4 transitions; (ii) assigning the time-characteristics to these transitions and intermediate states; (iii) searching for the optimal reaction coordinate based on the Peters–Trout approach (likelihood maximization, LM). Additionally, the structures corresponding to the 4C1 → 1C4 transition states (TS) have been found; surprisingly, in the case of GlcA, the water dynamics has very little influence on the probability of the TS evolution either to 4C1 or to 1C4. The differing result obtained for GlcB (large influence of water dynamics on the behavior of TS as well as the poor applicability of the LM approach for calculation of the reaction coordinate) speaks for slightly different mechanisms of the 4C1 → 1C4 puckering in the molecules of GlcB and GlcA.

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 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.

Molecular dynamics study of Congo red interaction with carbon nanotubes

This work deals with molecular dynamics simulations of Congo red (CR) interaction with carbon nanotubes (CNT). We studied several combinations of systems parameters in order to assess how the nanotube diameter and Congo red density affect the structure and stability of CNT–CR conjugates at various pH conditions. We found that, at the considered conditions, the CR binds strongly to the CNT surfaces and the CNT–CR conjugates are thermodynamically stable according to the determined values of the free energies. Adsorption on wider nanotubes is stronger than on the narrow ones and larger densities of CR on the CNT surfaces lead to weakening of binding energy per single CR molecule. Changes of pH, that is varying concentration of protonated and deprotonated forms of CR, lead to significant changes in binding energies as well as to qualitative changes of the structure of the adsorbed CR. It was found that at pH > 5.5 the CR molecules readily occupy inner cavities of the nanotubes. Upon lowering pH the occupation of the inner space of CNTs is strongly reduced and the preferred configuration is formation of a densely packed CR layer on the sidewalls of the CNT. This effect can potentially be utilized in pH controlled corking/uncorking of carbon nanotubes in water solutions.

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 β-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.

Binding of bivalent metal cations by α-L-guluronate: insights from the DFT-MD simulations

The negatively charged polyuronates exhibit a high affinity for binding the bivalent metal cations. This feature is used for the removal of heavy metals from aqueous solutions. The aim of the present paper is to: (i) present the computational strategy, helpful in simulating the metal ion–uronate complexes; (ii) illustrate its applicability to the example of the α-L-guluronate anion (the monomeric unit of alginates) interacting with bivalent metal ions: Zn2+, Cu2+, Cd2+, Mn2+ and Co2+. The study was carried out on the basis of the ‘hybrid’ molecular dynamics simulations in which the selected part of the system (uronate anions and metal cations) is treated with the ab initio level of accuracy, whereas the interactions within the rest of the system are approximated by the classical force fields. The results allowed for determining the basic structural and energetic (for example, the free energy profiles associated with the cation binding–unbinding process) characteristics related to the metal ion–guluronate complexes. Most of the studied ions exhibited the preference for monodentate binding. Bidentate binding can be observed for Mn2+ and Co2+ (dominant binding mode) and Cd2+ (secondary binding mode). The calculated binding free energy order (Cu > Co > Zn ∼ Mn > Cd) follows both the experimentally determined order of transition metal ion–alginate affinities and the metal–uronate interaction energies. The efficiency of the calculations and the general characteristics of the method allow for its potential use in simulations of other uronate–metal ion systems, increasing the range of methods which can be used for studying the metal biosorption processes.

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.