Self-assembly in systems based on L-cysteine-silver-nitrate aqueous solution: multiscale computer simulation.

We use fully atomistic, quantum mechanics and mesoscopic simulations to investigate multiscale structure formation in a supramolecular system based on aqueous solutions of silver nitrate with L-cysteine (CSS). Fully atomistic modeling reveals that silver mercaptide clusters are formed in solution at the stage of aging, which has a pronounced "core-shell" structure. The core is formed due to the bonding of SAg groups of silver mercaptide (SM) zwitterions while the shell consists of NH3+ and C(O)O- groups. Self-assembly of large-scale aggregates in CSS occurs due to the interaction of SM functional groups located on the surface of the clusters, which allows them to be considered supramonomers. Quantum-mechanical calculations reveal additional insight into the intermolecular interaction of L-cysteine with the components of the system. The data on the structure and properties of supramonomers are used to develop and parameterize a mesoscopic CSS model supplemented with allowance for salt concentration. In the mesoscopic model, supramonomers are presented as "sticky spheres", the interaction between which is determined by short-range and screened Coulomb potentials. Depending on the salt concentration, all structural transitions typical of CSS are observed: the formation of a stabilized colloidal dispersion, the filamentary aggregates of a gel network, the formation of large-scale unbound aggregates, and precipitation. These stages qualitatively reproduce the experimentally observed behavior of a real solution.

Additive-induced ordered structures formed by PC71BM fullerene derivatives.

We report the results of an experimental and theoretical study of structure formation in mixtures of phenyl-C71-butyric acid methyl ester (PC71BM) with high boiling octane based solvent additives 1,8-octanedithiol (ODT), 1,8-dibromooctane, and 1,8-diiodooctane obtained by evaporation of a host-solvent (chlorobenzene). Experimental studies by DSC, SAXS and WAXS methods found evidence of crystallization of fullerenes in the presence of the high boiling additives in the mixtures. A molecular dynamics simulation of a PC71BM/ODT mixture revealed the self-assembly of fullerenes into sponge-like network structures.

Mechanism of gelation in low-concentration aqueous solutions of silver nitrate with l-cysteine and its derivatives.

We discuss the results of experimental studies of the processes of gelation in aqueous solutions of silver nitrate with l-cysteine and its derivatives. We focus on understanding what determines if these small molecules will self-assemble in water at their extremely low concentration to form a gel. A mechanism of gel formation in a cysteine-silver solution (CSS) is proposed. The analysis of the results indicates that filamentary aggregates of a gel network are formed via interaction of NH3+ and C(O)O- groups that belong to neighboring silver mercaptide (SM) aggregates. In turn, formation of sulphur-silver bonds between silver mercaptide molecules is responsible for self-assembling these molecules into SM aggregates which can be considered as supramonomers. Free polar groups located on the surfaces of the aggregates can form hydrogen bonds with water molecules, which explains the unique ability of CSS hydrogels to trap water at low concentrations of low-molecular-weight hydrogelators.

A new concept for molecular engineering of artificial enzymes: a multiscale simulation.

We propose a new concept for the design of artificial enzymes from synthetic protein-like copolymers and non-natural functional monomers which in terms of their affinity for water can be divided into two categories: hydrophobic and hydrophilic. Hydrophilic monomers comprise catalytically active groups similar to those in the corresponding amino acid residues. A key ingredient of our approach is that the target globular conformation of protein-like, core-shell morphology with multiple catalytic groups appears spontaneously in the course of controlled radical polymerization in a selective solvent. As a proof of concept, we construct a fully synthetic analog of serine hydrolase, e.g.α-chymotrypsin, using the conformation-dependent sequence design approach and multiscale simulation that combines the methods of "mesoscale chemistry" and atomistic molecular dynamics (MD). A 100 ns GPU-accelerated MD simulation of the designed polymer-supported catalyst in the aqueous environment provides valuable information on the structural organization of this system that has been synthesized in our Lab.

Structure simulation of ultrathin dichloromethane layer on a solid substrate by density functional theory and molecular dynamics simulations.

The method for prediction of structural properties of ultrathin liquid layers has been developed on the base of the atomistic molecular dynamics (AMD) and the density functional theory (DFT). A comparative analysis of ultrathin dichloromethane layer density profiles on three types of solid flat substrates showed that these approaches can be effectively used as mutually complementary procedures to describe the structural properties of nanometer scale surface layers. We used AMD calculations to predict the dichloromethane layer density profile on a solid substrate. However, it is difficult and computationally expensive to calculate structural and thermodynamic layers properties. At the same time, DFT can retain the microscopic details of macroscopic systems at the calculative cost significantly lower than that used in AMD. Therefore, in context of DFT, the substrate potential parameters are adjusted to reproduce AMD data. Thus, the obtained potential allows us to compute structural characteristics and, further, can be used to predict other physical properties of ultrathin films within the DFT framework. For instance, we calculated the coefficient of thermal expansion of dichloromethane in the case of three different substrates such as graphite, silicon oxide, and gold.

Effect of Nanoparticles Surface Bonding and Aspect Ratio on Mechanical Properties of Highly Cross-Linked Epoxy Nanocomposites: Mesoscopic Simulations.

The paper aims to study the mechanical properties of epoxy resin filled with clay nanoparticles (NPs), depending on their shapes and content on the surface of a modifying agent capable of forming covalent bonds with a polymer. The cylindrical clay nanoparticles with equal volume and different aspects ratios (disks, barrel, and stick) are addressed. The NPs' bonding ratio with the polymer (RGC) is determined by the fraction of reactive groups and conversion time and varies from RGC = 0 (non-bonded nanoparticles) to RGC = 0.65 (more than half of the surface groups are linked with the polymer matrix). The performed simulations show the so-called load-bearing chains (LBCs) of chemically cross-linked monomers and modified nanoparticles to determine the mechanical properties of the simulated composites. The introduction of nanoparticles leads to the breaking of such chains, and the chemical cross-linking of NPs with the polymer matrix restores the LBCs and strengthens the composite. At small values of RGC, the largest value of the elastic modulus is found for systems filled with nanoparticles having the smallest surface area, and at high values of RGC, on the contrary, the systems containing disk-shaped particles with the largest surface area have a larger elastic modulus than the others. All calculations are performed within the framework of a mesoscopic model based on accurate mapping of the atomistic structures of the polymer matrix and nanoparticles into coarse-grained representations, which, if necessary, allow reverse data mapping and quantitative assessment of the state of the filled epoxy resin. On the other hand, the obtained data can be used to design the functional materials with specified mechanical properties based on other practically significant polymer matrices and nanofillers.

Dynamic and Static Mechanical Properties of Crosslinked Polymer Matrices: Multiscale Simulations and Experiments.

We studied the static and dynamic mechanical properties of crosslinked polymer matrices using multiscale simulations and experiments. We continued to develop the multiscale methodology for generating atomistic polymer networks, and applied it to the case of phthalonitrile resin. The mechanical properties of the resulting networks were analyzed using atomistic molecular dynamics (MD) and dissipative particle dynamics (DPD). The Young's and storage moduli increased with conversion, due both to the appearance of a network of covalent bonds, and to freezing of degrees of freedom and lowering of the glass transition temperature during crosslinking. The simulations' data showed good quantitative agreement with experimental dynamic mechanical analysis measurements at temperatures below the glass transition. The data obtained in MD and DPD simulations at elevated temperatures were conformable. This makes it possible to use the suggested approach for the prediction of mechanical properties of a broad range of polymer matrices, including ones with high structural heterogeneity.

Self-Assembly of Lecithin and Bile Salt in the Presence of Inorganic Salt in Water: Mesoscale Computer Simulation.

The influence of inorganic salt on the structure of lecithin/bile salt mixtures in aqueous solution is studied by means of dissipative particle dynamics simulations. We propose a coarse-grained model of phosphatidylcholine and two types of bile salts (sodium cholate and sodium deoxycholate) and also take into account the presence of low molecular weight salt. This model allows us to study the system on rather large time and length scales (up to about ∼20 µs and 50 nm) and to reveal mechanisms of experimentally observed increasing viscosity upon increasing the low molecular weight salt concentration in this system. We show that increasing the low molecular weight salt concentration induces the growth of cylinder-like micelles formed in lecithin/bile salt mixtures in water. These wormlike micelles can entangle into transient networks displaying perceptible viscoelastic properties. Computer simulation results are in good qualitative agreement with experimental observations.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport.

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25-50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

Computer simulation of the assembly of gold nanoparticles on DNA fragments via electrostatic interaction.

Using Monte Carlo simulation, we study the metallization of DNA fragments via the templating of gold nanoparticles. To represent the interaction between metal entities, a nanoparticle-nanoparticle interaction potential was derived on the basis of the many-body Gupta potential. The aggregation of the nanoparticles on the template surface is due to the additive effect of electrostatic attraction between the positive charges on the Au particles and the negative charges of the phosphate groups of DNA molecule and the short-range attraction between the metallic nanoparticles. As a result, the assembly of a continuous nanowire can be templated. Depending on the nanoparticle size and charge, the metallic covering can be both continuous and discontinuous. The question of how size and charge of Au nanoparticles influence the structure of metallic coat is discussed in detail. Both monodisperse and polydisperse nanoparticles are considered. Dispersion in the nanoparticle size was found to have little effect on the calculated characteristics of the aggregate.

The formation of planar ribbonlike aggregates from stiff polyanions in the presence of anisotropic cations.

A dilute salt-free solution of rodlike polyanions in the presence of anisotropic (chain) cations consisting of neutral tails and charged heads is studied. Using Monte Carlo simulation within the framework of the primitive model, different Coulomb coupling regimes were considered. While aggregation in the strong coupling limit is expected, we report new morphology, namely, the formation of ribbonlike nanostructures. At strong electrostatic interaction, the system is found to undergo the self-organization resulting in the formation of planar aggregates that look like a "ladder" of polyanions sandwiched between cationic chains. We investigate the stability of different morphologies and find that these aggregates are thermodynamically stable. Focus has been made on how the chemical structure of anisotropic cations affects the morphology of the aggregates.