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Dihydroazulene/vinylheptafulvene pairs are known as molecular dipole switches that undergo a ring-opening/-closure reaction by UV irradiation or thermal excitation. Herein, we show that the ring-closure reaction of a single vinylheptafulvene adsorbed on the Au(111) surface can be induced by voltage pulses from the tip of a scanning tunneling microscope. This cyclization is accompanied by the elimination of HCN, as confirmed by simulations. When inducing lateral movements by applying voltage pulses with the STM tip, we observe that the response of the single molecules changes with the ring closing reaction. This behaviour is discussed by comparing the dipole moment and the charge distribution of the open and closed forms on the surface.

Native cellulose is insoluble in water, despite the high number of hydrogen bonding sites per chain, as molecules preferably hydrogen bond to each other, preventing its use in industrial applications. The modification of cellulose has received considerable recent attention, motivated by the move away from conventional petroleum-based, water-soluble polymers, however, a systematic analysis of the effects of modification is rare. Herein a detailed study of hydroxypropyl (HP)- and (2-hydroxypropyl) trimethylammonium chloride-modified cellulose, with degrees of substitution (DS) determined by NMR, establishes modification-property relationships. TEM, small-angle X-ray scattering and rheology demonstrated that increasing DS gradually changes the aqueous solubility, resulting in the formation of different morphologies, including micron-sized aggregates, needle-like cellulose nanoparticles (CNPs) and solvated molecules. It was found that aqueous dispersions with DSHP of 50%, assigned to a ‘sweet spot’ in cellulose modification, are suitable for fiber formation. It is shown that this state of the material can be easily detected by rheo-optical methods based on birefringence. Using structural analysis, molecular dynamics simulation and fiber-spinning results, it is proposed that co-existing CNPs and cellulose molecules, interacting via H-bonding, form a network which orients under shear, acting as a precursor for fiber formation from aqueous solutions.

Alternating block copolymers consisting of diketopyrrolopyrrole and benzothiadiazole electron acceptor units linked together via aromatic five-membered donor heterocycles are studied using a combination of computer simulation techniques and experiments. Four copolymers are modeled starting from their monomers to stacked macromolecules: with two different linkers—thiophene or furan, connecting electron-withdrawing core units—and two different alkyl substituents at lactam nitrogens of diketopyrrolopyrrole—linear dodecyl and branched 2-octyldodecyl chains. In our experiments, we aim at characterization of the optical and electrochemical properties of two copolymers with branched side chains differing in the linker, since as the literature survey shows the data published on these copolymers are very sparse. These properties can be easily interpreted and later compared with theoretical predictions. The results of simulations supported by experiments show that monomers of these polymers have very similar electr...

Objective Several studies suggest that psychological factors including anxiety are associated with negative outcomes and in particular higher mortality rates among heart failure (HF) patients. However, the impact of anxiety on mortality in patients with implanted cardiac devices has not been fully appreciated. The aim of this study was to assess the association between state (SA) and trait (TA) anxiety and all-cause mortality in patients with HF after cardiac electronic devices implantation. Methods The monocentric prospective study enrolled 265 patients (215 men and 50 women) aged 23 to 84 years (mean age 57.1 ± 10.0), who received cardiac resynchronization therapy or cardioverter-defibrillator implantation. Mean duration of prospective follow-up was 62.3 ± 36.6 months. State-Trait Anxiety Inventory (STAI) was used to measure anxiety symptoms. Cox proportional hazards multivariate regression model was used to calculate hazard ratio (HR) of all-cause mortality with 95% confidence interval (95% CI). Results During the prospective follow-up period, 45 (17.0%) patients died due to all causes. According to quantitative analysis, HR for death used for SA scale was 1.04 (95% CI 1.00–1.07, p = 0.07) and for the TA scale 1.02 (95% CI 0.99–1.05, p = 0.21). Analysis of categorical indicators found statistically significant higher HR of mortality in patients with severe SA (2.35, 95% CI 1.17–4.71, p = 0.02), and TA (2.02, 95% CI 1.04–3.94, p = 0.04). Conclusion High levels of SA and TA was significantly and independently associated with a high risk of all-cause mortality in patients, who underwent implantation of cardiac electronic devices.

In this paper, we elucidate a generic mechanism behind strain-induced phase transition in aqueous solutions of silk-inspired biomimetics by atomistic molecular dynamics simulations. We show the results of modeling of homopeptides polyglycine Gly30 and polyalanine Ala30 and a heteropeptide (Gly-Ala-Gly-Ala-Gly-Ser)5, i.e., the simplest and yet relevant sequences that could mimic the behavior of natural silk under stress conditions. First, we analyze hydrophobicities of the sequences by calculating the Gibbs free energy of hydration and inspecting the interchain hydrogen bonding and hydration by water. Second, the force-extension profiles are scanned and compared with the results for poly(ethylene oxide), the synthetic polymer for which the aquamelt behavior has been proved recently. Additionally, the conformational transitions of oligopeptides from coiled to extended states are characterized by a generalized order parameter and by the dependence of the solvent-accessible surface area of the chains on applied stretching. Fibrillation itself is surveyed using both the two-dimensional interchain pair correlation function and the SAXS/WAXS patterns for the aggregates formed under stress. These are compared with experimental data found in the literature on fibril structure of silk composite materials doped with oligoalanine peptides. Our results show that tensile stress introduced into aqueous oligopeptide solutions facilitates interchain interactions. The oligopeptides display both a greater resistance to extension as compared to poly(ethylene oxide) and a reduced ability for hydrogen bonding of the stretched chains between oligomers and with water. Fiber formation is proved for all simulated objects, but the most structured one is made of a heteropeptide (Gly-Ala-Gly-Ala-Gly-Ser)5: For this sequence, we obtain the highest degree of the secondary structure motifs in the fiber. We conclude that this is the most promising candidate among considered sequences to find the aquamelt behavior in further experimental studies.

Recently, we have shown that a tensile stress applied to chains of poly(ethylene oxide) (PEO) in water reduces the solubility and leads to phase separation of PEO chains from water with the formation of a two-phase region. In this work, we further elucidate the generic mechanism behind strain-induced phase transitions in aqueous PEO solutions with concentrations of 50-60 wt % by performing all-atom molecular dynamics simulations. In particular, we study the stability of oriented PEO fibers after removing stretching forces. We found that the size of the PEO bundle increased with time, which is associated with the dissolution of PEO chains on the fiber surface due to the reformation of hydrogen bonds between the outer PEO molecules and water. For precise characterization of the fibers, the scattering patterns (small- and wide-angle X-ray spectra) for configurations taken at different relaxation times are calculated. The tendency of the oligomer chains to be peeled off from the surface of the bundle eventually might lead to a complete dissolution of the PEO fiber. We conclude that either entanglement constraints or a quick drying process are necessary to conserve the fiber structure in a quiescent state. The scattering results show that external strain induced a liquid-liquid phase separation first. On long time scales, this can be a precursor for crystallization of the fiber.

Bio-engineered surfaces that aim to induce normal cell behaviour in vitro need to ‘mimic’ the extracellular matrix in a way that allows cell adhesion. In this computational work, several model cell...

We report on light-induced deformation of colloidal spheres consisting of azobenzene-containing polymers. The colloids of the size between 60 nm and 2 μm in diameter were drop casted on a glass surface and irradiated with linearly polarized light. It was found that colloidal particles can be deformed up to ca. 6 times of their initial diameter. The maximum degree of deformation depends on the irradiation wavelength and intensity, as well as on colloidal particles size. On the basis of recently proposed theory by Toshchevikov et al. [ J. Phys. Chem. Lett. 2017 , 8 , 1094 ], we calculated the opto-mechanical stresses (ca. 100 MPa) needed for such giant deformations and compared them with the experimental results.

This study focuses on comparing physical properties of photoisomers of an azobenzene star with benzene-1,3,5-tricarboxamide core. Three azobenzene arms of the molecule undergo a reversible trans-cis isomerization upon UV-vis light illumination giving rise to multiple states from the planar all-trans one, via two mixed states to the kinked all-cis isomer. Employing density functional theory, we characterize the structural and photophysical properties of each state indicating a role the planar core plays in the coupling between azobenzene chromophores. To characterize the light-triggered switching of solvophilicity/solvophobicity of the star, the difference in solvation free energy is calculated for the transfer of an azobenzene star from its gas phase to implicit or explicit solvents. For the latter case, classical all-atom molecular dynamics simulations of aqueous solutions of azobenzene star are performed employing the polymer consistent force field to shed light on the thermodynamics of explicit hydration as a function of the isomerization state and on the structuring of water around the star. From the analysis of two contributions to the free energy of hydration, the nonpolar van der Waals and the electrostatic terms, it is concluded that isomerization specificity largely determines the polarity of the molecule and the solute-solvent electrostatic interactions. This convertible hydrophilicity/hydrophobicity together with readjustable occupied volume and the surface area accessible to water, affects the self-assembly/disassembly of the azobenzene star with a flat core triggered by light.

Herein we present a molecular doping of a high mobility diketopyrrolopyrrole–dithienylthieno[3,2-b]thiophene donor–acceptor copolymer poly[3,6-(dithiophene-2-yl)-2,5-di(6-dodecyloctadecyl)pyrrolo[3,4-c]pyrrole-1,4-dione-alt-thieno[3,2-b]thiophene], PDPP(6-DO)2TT, with the electron-deficient compound hexafluorotetracyanonaphthoquinodimethane (F6TCNNQ). Despite a slightly negative HOMOdonor–LUMOacceptor offset of −0.12 eV which may suggest a reduced driving force for the charge transfer (CT), a partial charge CT was experimentally observed in PDPP(6-DO)2TT:F6TCNNQ by absorption, vibrational, and electron paramagnetic resonance spectroscopies and predicted by density functional theory calculations. Despite the modest CT, PDPP(6-DO)2TT:F6TCNNQ films possess unexpectedly high conductivities up to 2 S/cm (comparable with the conductivities of the benchmark doped polymer system P3HT:F4TCNQ having a large positive offset). The observation of the high conductivity in doped PDPP(6-DO)2TT films can be explained by a...

A theoretical study is applied to gain insight into the microscopic electron and hole transport in benzothiadiazole-cored molecular semiconductors either with furan or thiophene flanks arranged in π-stacks. For the characterization of the energetics of the reduction and oxidation processes and their impact on the molecular geometry, the internal reorganization energy is defined for isolated molecules in the gas phase. The outer-shell reorganization energy is evaluated within the frequency-resolved cavity model and as an electrostatic contribution within the polarizable continuum model. The intermolecular electronic coupling interaction for the Marcus charge hopping is calculated using the energy splitting in dimer method, the generalized Mulliken-Hush approach and the fragment charge difference scheme. In order to probe the relation between the charge hopping rate/charge carrier mobility and the molecular organization within the π-stacks, different stacking modes are investigated: (i) dimers with a perfect registry, i.e. segregated stacking motif, when molecules are placed face-to-face, and (ii) dimers forming slipped cofacial orientations with longitudinal and transverse shifts, i.e. mixed stacking motif. Besides, the effects of molecular planarity and rigidity, influencing internal molecular relaxation upon charging, the effects of non-covalent interactions within stacks and the heteroatom replacement on the charge carrier mobility are studied. The results obtained in the simulations of one-dimensional aligned π-stacks of molecular semiconductors are compared with available experimental data for small conjugated benzothiadiazole-cored molecules with thiophene flanks and benzothiadiazole-quaterthiophene-based copolymers.

Symmetrical benzothiadiazole-cored (BTZ) oligomers with aromatic flanks are widely used in experiments as structural blocks for organic electronic materials. Along with chemical composition, the molecular conformation plays a crucial role in crystal packing/self-assembly of these building blocks in thin films. In this study, we perform an extensive theoretical comparison of conformational preferences, electronic and optical properties of small π-conjugated molecules having BTZ central unit symmetrically decorated with thiophene (Th) or furan (Fu) rings using DFT calculations. In addition to the conformational screening of small molecules, the torsion potentials of the internal rotation and the energetics of weak intramolecular S⋯N, O⋯N, O⋯H and N⋯H nonbonded interactions stabilizing certain conformations are evaluated. The conformational properties of –[BTZ-Fu]n– and –[BTZ-Th]n– chains are predicted applying the hindered rotation model. Our calculation shows that substitution of one atom, here sulphur by oxygen, leads to huge stiffening of the resulting polymer as estimated by the Kuhn length based on the rotational isomeric model. On the other hand, the calculation of the band gaps and the UV–vis spectra shows that the electronic and optical properties of both compounds are almost identical. This offers the possibility to decouple the intramolecular electronic properties from the intermolecular arrangement and the morphology of the materials since the latter properties are sensitive to the local stiffness of oligomers and polymers.

The clustering properties of star-shaped molecules comprising three photochromic azobenzene-containing arms are investigated with specific focus on the influence of light on these structures. Previous experimental works report self-assembly of azobenzene stars in aqueous solution into long columnar clusters that are detectable using optical microscopy. These clusters appear to vanish under UV irradiation, which is known to induce trans-to-cis photoisomerization of the azobenzene groups. We have performed MD simulations, density functional theory, and density functional tight binding calculations to determine conformational properties and binding energies of these clusters. Our simulation data suggest that the binding strength of the clusters is large enough to prevent a breaking along their main axis. We conclude that very likely other mechanisms lead to the apparent disappearance of the clusters.

π-Conjugated small molecules containing diketopyrrolopyrrole (DPP) and thiophene moieties represent a modern class of functional materials that exhibit promising charge transport properties and therefore have great potential as building blocks of active elements of electronic devices. As a starting point of this computational study, the molecular structure, electronic characteristics, and reorganization energies associated with electron or hole transfer are considered. Prediction of molecular crystal packing is followed by the calculation of couplings between adjacent molecules and detection of the effective charge transfer pathways. Finally, the rates of charge transfer process are evaluated. The obtained results shed light not only on the properties of materials containing low-molecular species but also serve as a benchmark for further classical force-field simulations of DPP-based polymers.

In this paper, the columnar supramolecular aggregates of photosensitive star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core and azobenzene arms are analyzed theoretically by applying a combination of computer simulation techniques. Without a light stimulus, the azobenzene arms adopt the trans-state and build one-dimensional columns of stacked molecules during the first stage of the noncovalent association. These columnar aggregates represent the structural elements of more complex experimentally observed morphologies&mdash, fibers, spheres, gels, and others. Here, we determine the most favorable mutual orientations of the trans-stars in the stack in terms of (i) the &pi, &ndash, &pi, distance between the cores lengthwise the aggregate, (ii) the lateral displacements due to slippage and (iii) the rotation promoting the helical twist and chirality of the aggregate. To this end, we calculate the binding energy diagrams using density functional theory. The model predictions are further compared with available experimental data. The intermolecular forces responsible for the stability of the stacks in crystals are quantified using Hirshfeld surface analysis. Finally, to characterize the self-assembly mechanism of the stars in solution, we calculate the hydrogen bond lengths, the normalized dipole moments and the binding energies as functions of the columnar length. For this, molecular dynamics trajectories are analyzed. Finally, we conclude about the cooperative nature of the self-assembly of star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core in aqueous solution.

In this computational work, we investigate the photosensitive cationic surfactants with the trimethylammonium or polyamine hydrophilic head and the azobenzene-containing hydrophobic tail. The azobenzene-based molecules are known to undergo a reversible trans-cis-trans isomerization reaction when subjected to UV-visible light irradiation. Combining the density functional theory and the all-atom molecular dynamics simulations, the structural and the hydration properties of the trans- and the cis-isomers and their interaction with the oppositely charged poly(methacrylic acid) in aqueous solution are investigated. We establish and quantify the correlations of the molecular structure and the isomerization state of the surfactants and their hydrophilicity/hydrophobicity and the self-assembling altered by light. For this reason, we compare the hydration free energies of the trans- and the cis-isomers. Moreover, the investigations of the interaction strength between the azobenzene molecules and the polyanion provide additional elucidations of the recent experimental and theoretical studies on the light triggered reversible deformation behavior of the microgels and the polymer brushes loaded with azobenzene surfactants.

We studied the formation of hydrogen-bonded supramolecular polymers of Ethyl Hexyl Urea Toluene (EHUT) on a gold (111) surface by low temperature scanning tunneling microscopy. Tunneling spectroscopy performed along an individual molecule embedded in a self-assembled layer revealed strong changes in the value of the HOMO-LUMO gap. A variation of the LUMO state is attributed to the effect of space charge accumulation resulting from anisotropic adhesion of the molecule. In addition, for specific tunneling conditions, changes induced through the formation of hydrogen bonds became visible in the differential conductance (dI/dV) maps; isolated molecules, hydrogen bonded dimers and supramolecular polymers of EHUT were distinguishable through their electronic properties.

In this work we apply a joint experimental and theoretical approach to investigate thin films of side chain substituted dicyanovinyl quaterthiophenes (DCV4T-Et2) and DCV4T-Et2:C60 blends, prototypic absorbers for small molecule organic solar cells. Structural characterization of the morphology of thin films thermally deposited at different substrate temperatures on a silica surface was performed by variable angle spectroscopic ellipsometry, grazing incidence X-ray diffraction, and atomic force microscopy measurements. These methods, combined with full-atomistic molecular dynamic (MD) simulation, provide detailed information about thin film morphology, namely about molecular orientation, absorption, phase separation, and crystallinity, i.e., factors that affect the efficiency of organic solar cells. Using molecular dynamics simulation, we can constitute why the DCV4T-Et2 molecules arrange strongly tilted in pristine (69° to 70° tilt angle to the substrate normal) and DCV4T-Et2:C60 blend films (tilt angle o...

A wide variety of peptides and their natural ability to self-assemble makes them very promising candidates for the fabrication of solid-state devices based on nano- and mesocrystals. In this work, we demonstrate an approach to form peptide composite layers with gold nanoparticles through in situ reduction of chloroauric acid trihydrate by dipeptide and/or dipeptide/formaldehyde mixture in the presence of potassium carbonate at different ratios of components. Appropriate composition of components for the synthesis of highly stable gold colloidal dispersion with particle size of 34–36 nm in dipeptide/formaldehyde solution is formulated. Infrared spectroscopy results indicate that dipeptide participates in the reduction process, conjugation with gold nanoparticles and the self-assembly in 2D, which accompanied by changing peptide chain conformations. The structure and morphology of the peptide composite solid layers with gold nanoparticles on gold, mica and silica surfaces are characterized by atomic force microscopy. In these experiments, the flat particles, dendrites, chains, mesocrystals and Janus particles are observed depending on the solution composition and the substrate/interface used. The latter aspect is studied on the molecular level using computer simulations of individual peptide chains on gold, mica and silica surfaces.

Using coarse-grained DPD simulations, we study the morphology of AB diblock copolymer brushes in selective solvents which are good for the anchored A blocks but poor (of varying degrees measured by...

An atomistic molecular dynamics (MD) simulation of the adsorption of biantennary oligoglycine [H-Gly4-NH(CH2)5]2 onto a graphite and mica surface is described. The structure of the resultant adsorption layers is analyzed. The secondary structure motifs of peptide blocks are studied by the STRIDE (structural identification) and DSSP (dictionary of the secondary structure of proteins) methods. The results of the study confirm the possibility of forming a polyglycine-II (PGII) structure in the monolayers of biantennary oligoglycines (BAOG) on a graphite surface previously supposed from the data of atomic force microscopy.

The development of bioengineered surface coatings with stimuli-responsive properties is beneficial for a number of biomedical applications. Environmentally responsive and switchable polymer brush systems have a great potential to create such smart biointerfaces. This study focuses on the bioconjugation of cell-instructive peptides, containing the arginine-glycine-aspartic acid tripeptide sequence (RGD motif), onto well-defined polymer brush films. Herein, the highly tailored end-grafted homo polymer brushes are either composed of the polyelectrolyte poly(acrylic) acid (PAA), providing the reactive carboxyl functionalities, or of the temperature-responsive poly(N-isopropylacrylamide) (PNIPAAm). Of particular interest is the preparation of grafted-to binary brushes using both polymers and their subsequent conversion to RGD-biofunctionalized PNIPAAm-PAA binary brushes by a carbodiimide conjugation method. The bioconjugation process of two linear RGD-peptides Gly-Arg-Gly-Asp-Ser and Gly-Arg-Gly-Asp-Ser-Pro-Lys and one cyclic RGD-peptide cyclo(Arg-Gly-Asp-D-Tyr-Lys) is comparatively investigated by complementary analysis methods. Both techniques, in situ attenuated total reflectance Fourier transform infrared spectroscopy measurements and the in situ spectroscopic ellipsometric analysis, describe changes of the brush surface properties due to biofunctionalization. Besides, the bound RGD-peptide amount is quantitatively evaluated by ellipsometry in comparison to high performance liquid chromatography analysis data. Additionally, molecular dynamic simulations of the RGD-peptides themselves allow a better understanding of the bioconjugation process depending on the peptide properties. The significant influence on the bioconjugation result can be derived, on the one hand, of the polymer brush composition, especially from the PNIPAAm content, and, on the other hand, of the peptide dimension and its reactivity.

This review highlights recent advances achieved by different groups with various molecular simulation approaches for the prediction and fine-tuning of the supramolecular organization of thiophene derivatives, oligo- and polythiophenes. The focus is on functionalized oligo- and polythiophenes, including bio-inspired thiophene/ peptide copolymers ("molecular chimeras"). The subject matter of the article is divided up into subsections covering electronic and structural properties of single molecules, solution and solid-state self-assembly, amorphous polythiophene and polymer blends, thiophene-based nanomechanical devices, self-organization on substrates and applications. A number of examples are used to provide experimental data with which to compare the theoretical predictions.

This review presents the results of atomistic molecular dynamic simulation during the adsorption of hybrid molecules, which are co-oligomers of thiophene and peptide (biomimetic) segments. A surface of highly ordered pyrolitic graphite (HOPG) is used as an adsorbent. The processes of self-organization are investigated as a function of the temperature and adsorption intensity for two types of hybrids, such as diblock and triblock cooligomers (with a central thiophene block). The structure of the formed adsorption layers is studied in detail. In the self-organizing associates, the emergence of possible π stacking in the thiophene segment is considered. The motifs of the secondary structure in the peptide blocks and their evolution with increasing adsorption intensity are examined.

We study the effect of comonomer sequence distributions in random copolymers (RCPs) on RCP adsorption on flat impenetrable surfaces. RCP poly(styrene-co-4-bromostyrene) (PBrxS), where x denotes the mole fraction of 4-bromostryrene (4-BrS), is prepared by bromination of parent homopolystyrene. By varying the solvent quality during the bromination, either “truly random” (good solvent) or “random-blocky” (poor solvent) PBrxS RCPs are prepared. Adsorption studies of PBrxS from various solvents at silica surfaces reveal that the adsorption of PBrxS increases with (1) increasing blockiness of the macromolecule, (2) increasing content of 4-BrS in PBrxS, and (3) decreasing solvent quality. Additionally, the effect of comonomer sequence distribution on RCP adsorption is modeled in detail using a coarse-grained statistical mechanical model and fully atomistic simulations based on configurational-biased grand-canonical Monte Carlo (CB-GCMC) technique. The main result from the simulations can be summarized as follows...

We present the results of an extensive molecular dynamics simulation aimed at investigating the structural organization of bioinspired copolymers consisting of thiophene and silk-forming peptide blocks. These ‘molecular chimeras’ are studied, apparently for the first time, both in adsorbed state (on the surface of graphite) and in dilute solution. It is shown that the attachment of the terminal peptide blocks to the oligothiophene fragments can lead to the formation of various stable supramolecular structures, including bilayers and fibrils, which can be promising for nanoelectronic applications.

Natural and synthetic polymers have a number of common traits; however, each class of compounds demonstrates specific properties. The design of hybrid copolymers based on such different macromolecules is a unique strategy for constructing smart materials. The review deals with two aspects: state-of-the-art studies in bioinspired hybrid systems, including those based on oligopeptides and oligothiophenes, and achievements in the computer modeling of this new class of molecular chimeras.

The results of computer simulation of adsorption layers composed of α-tetrathiophene derivatives via the molecular dynamics method are described. The structural organization of systems and the conformational behavior of molecules have been studied as a function of temperature and length of alkyl chains linked to β-carbon atoms of end thiophene rings.

The results of molecular dynamics simulation of solutions of highly charged rigid-chain polymers in the presence of multivalent counterions are presented. The processes of self-assembly of macromolecules that occur during the condensation of counterions and depend on temperature, the dielectric permittivity of the medium, and the charge of counterions were studied. Various conformational rearrangements induced by changing the parameters of the medium were examined. The conditions that lead to the formation of network superstructures composed of aggregating polymer chains were found. Size distribution functions for free-volume holes were constructed and the average dimensions of voids in the network structures formed were calculated.

By combining atomic force microscopy experiments and full-atomistic computer simulations, we compared the two-dimensional ordering dynamics of two variants of supramolecular polymers of bis-urea molecules which differed only by a single cis-double bond in their side groups. At early stages of ordering, the double bonds favored kinks at the level of individual molecules, which induced transient steric constraints hindering the spontaneous formation of long supramolecular polymers. In addition, due to these kinks, molecule–substrate interactions were disturbed. At later stages, however, due to a progressively increasing number of established directional hydrogen bonds between molecules, the self-assembly process improved and thereby increased the length of the supramolecular polymers. Large domains of micrometer-long and aligned supramolecular polymers were formed, epitaxially guided by the graphite substrate and having a constant width consistent with the length of the molecule. Thus, introducing flexible ...

Fullerene C60 sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C60 fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientational correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the “dangling” –OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some “dry” regions of C60 are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.

Azobenzene-containing side chain polymers [1,2] and molecular glasses based on propeller-like C3-symmetric azobenzene mesogenes [3] are investigated in classical molecular dynamics simulations. Two length scales are considered: (i) the molecular level with atomistic resolution, where reversible conformational changes of azobenzene chromophores upon light illumination lead to contractions/extensions of low amplitudes due to a limited size of mesogene groups, and (ii) the mesoscopic level, where light-induced molecular movements are observed over larger distances, comparable with the gyration radius of polymer chains. The influence of isomerization and orientation mechanisms on molecular structure and light-induced deformation is elucidated. [1] J. Ilnytskyi et al., J. Chem. Phys. 135, 044901 (2011). [2] M Saphiannikova et al., Proceedings of SPIE "Optical Materials and Biomaterials in Security and Defence Systems Technology X", 8901, 890138 (2013). [3] N.S. Jadavalli et al., Appl. Phys. Lett. 105, 051601 (2014).

Complexation in solutions of strongly charged polyelectrolytes and diblock copolymers composed of oppositely charged and neutral blocks were studied via the molecular dynamics method. Stoichiometric micellar complexes formed in a dilute solution represent cylindrical brushes whose conformation is determined by the linear charge density on the polyelectrolyte and by temperature. As the concentration of macromolecules increases, the orientational ordering of anisotropic ionic micelles takes place. The complexation can induce the stiffening of the polyelectrolyte chain.

The structure and stability of complexes formed by oppositely charged rigid-chain macromolecules, as well as their response to variation in external conditions, were studied using the molecular dynamics method. The conditions of conformational transitions depending on the chain length and configuration, temperature, and dielectric permittivity of the medium were considered. It was shown that the chains involved in a complex may take various conformations of the torus, tennis racket, etc., types.

An integral equation theory has been used as the basis for studying the structure of dispersions containing charged colloidal particles: globular protein molecules with a nonzero dipole moment, a polyelectrolyte and a low-molecular salt. It is demonstrated that there is an effective attraction between charged colloidal particles, which increases in the presence of charged polymer chains. The influence of the length of polyelectrolyte chains and of salt concentration on the partial structure factor of colloidal particles was studied.

Using a coarse-grained model, we performed molecular dynamics simulations of the electrostatically driven self-assembly of strongly charged polyelectrolytes and diblock copolymers composed of oppositely charged and neutral blocks. Stoichiometric micelle-like complexes formed in a dilute solution represent cylindrical brushes whose conformation is determined by the linear charge density on the polyelectrolyte and by temperature. The core-shell morphology of the cylindrical brushes is proven. The core of these anisotropic micelles consists of an insoluble complex coacervate formed by the ionic chains and a shell made up of the neutral solvophilic blocks. As the concentration of macromolecules increases, the orientational ordering of ionic micelles takes place. The complexation can induce effective steric stiffening of the polyelectrolyte chains.

Extensive full-atomistic molecular dynamics simulations are performed to study the self-organization of C60-fullerene dyad molecules in water, namely phenyl-C61-butyric acid methyl ester and fulleropyrrolidines, which have two elements of ordering, the hydrophobic fullerene cage and the hydrophilic/ionic group. While pristine fullerene or phenyl-C61-butyric acid methyl ester forms spherical droplets in order to minimize the surface tension, the amphiphilic nature of charged solute molecules leads to the formation of supramolecular assemblies having cylindrical shape driven by charge repulsion between the ionic groups located on the surface of the aggregates. We show that formation of non-spherical micelles is the geometrical consequence if the fullerene derivatives are considered as surfactants where the ionized groups are only hydrophilic unit. The agglomeration behavior of fullerenes is evaluated by determining sizes of the clusters, solvent accessible surface areas, and shape parameters. By changing the size of the counterions from chloride over iodide to perchlorate we find a thickening of the cylinder-like structures which can be explained by stronger condensation of larger ions and thus partial screening of the charge repulsion on the cluster surface. The reason for the size dependence of counterion condensation is the formation of a stronger hydration shell in case of small ions which in turn are repelled from the fullerene aggregates. Simulations are also in good agreement with the experimentally observed morphologies of decorated C60-nanoparticles.

We have studied the self-assembly of nano-particles (NPs) at the surface of microphase-separated AB diblock copolymer brushes in a selective solvent by means of dissipative particle dynamics (DPD) simulations. The structure of such nano-composites depends both on the morphology of the underlying brush which is basically determined by chain composition fB and solvent selectivity τB, and on specific parameters of the NPs added such as polymer compatibility aBP, solvophobicity aPS, and concentration φ, where aij are the DPD interaction parameters. The immense parameter space is explored within a coarse-grained model that contains polymer A and B beads, solvent (S), nano-particle (P), and wall (W) beads. For composites with B-like nano-particles, i.e., NPs that are covered by polymer B ligands, we construct the phase diagram in the fB − φ space. For B-unlike NPs, it is found that the solvophobicity of the particles set by aPS is crucial for the spreading of nano-droplets. We show that in principle microphase-separated diblock copolymer brushes can be used to create ordered nano-dots as well as nano-wires and deduce some rules which should facilitate the design of such novel polymer nano-composites. Finally we suggest a new mechanism to move nano-objects on the surface of diblock copolymer brushes.

We investigate the organization of nanosized particles in a polymer brush by DPD simulations. The brush is composed of flexible chains grafted by one end to a solid substrate. The polymer-insoluble nanoparticles are treated as rather rigid aggregates of almost spherical form. Varying either the strength of interaction between polymer and nanoparticle beads or the concentration of nanoparticles (i.e., the load by nanoparticles) we observe particle cluster formation in the distal brush region. For low load, in agreement with theoretical predictions we demonstrate that the nanodroplet formed is vertically oriented and exhibits cylinder shape. With increasing concentration the aggregate at the rim of the brush becomes a flattened sphere. For high load, when the droplet-droplet interaction is significant, the cluster becomes highly anisotropic and the horizontally oriented nanodroplet adopts a cylinder (or baguette-like) shape.