Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle.

Effect of Tricarboxylic Acids on the Formation of Hydrogels with Melem or Melamine: Morphological, Structural and Rheological Investigations

Herein, aggregation behaviors of melem or melamine in the presence of three symmetric carboxylic acids (1,3,5-tris(4-carboxyphenyl)benzene (TPCA), 1,3,5-benzene-tri-carboxylic acid (BTA) and 1,3,5-cyclohexane-tri-carboxylic acid (CHTA)) have been performed to check the influence of acid on the formation of aggregated structures which have been investigated by optical microscopy, FESEM, FTIR, XRD and viscoelastic properties have been explored with rheological studies. Interestingly, melem, that has limited solubility in aqueous medium, forms aggregation that leads to the formation of hydrogels with TPCA. More significantly, hydrogel is formed here by matching the size selectivity. Melem forms hydrogel with only large tricarboxylic acid, whereas melamine produces hydrogel with any kind of its counterpart from small to large tricarboxylic acid derivatives. Present investigations and results provide the strategy of design of organic self-assembled materials having two component systems.

One-step synthesis of sequence-controlled multiblock polymers with up to 11 segments from monomer mixture

Switchable polymerization holds considerable potential for the synthesis of highly sequence-controlled multiblock. To date, this method has been limited to three-component systems, which enables the straightforward synthesis of multiblock polymers with less than five blocks. Herein, we report a self-switchable polymerization enabled by simple alkali metal carboxylate catalysts that directly polymerize six-component mixtures into multiblock polymers consisting of up to 11 blocks. Without an external trigger, the catalyst polymerization spontaneously connects five catalytic cycles in an orderly manner, involving four anhydride/epoxide ring-opening copolymerizations and one L-lactide ring-opening polymerization, creating a one-step synthetic pathway. Following this autotandem catalysis, reasonable combinations of different catalytic cycles allow the direct preparation of diverse, sequence-controlled, multiblock copolymers even containing various hyperbranched architectures. This method shows considerable promise in the synthesis of sequentially and architecturally complex polymers, with high monomer sequence control that provides the potential for designing materials.

Sorption of Fulvic Acids and Their Compounds with Heavy Metal Ions on Clay Minerals

In real soils the interaction of humic substances with clay minerals often occurs with the participation of metal cations. The adsorption of fulvic acids (FA) solution and their solutions in the presence of heavy metal ions (Pb or Zn) on two clay minerals (kaolinite and bentonite) was investigated by measurement of the optical density changes in the of equilibrium solutions. The FA adsorption by bentonite at the concentrations 0.05–1 g/L proceeds according to the polymolecular mechanism and has a stepwise character. The adsorption of FA on kaolinite can be described by the mechanism of monomolecular adsorption. In three-component systems, including FA, trace element ions and a clay mineral, complex processes occur, including the formation of complexes and salts and their adsorption. The sorption of colored complexes of FA with Pb on the surface of kaolinite and bentonite increases with increasing metal concentrations (0.5–2 mmol/L). The interaction of the FA-Zn2+ compounds with bentonite is a more complicated process—adsorption takes place at the lowest concentration used only. Thus, binding of FA by clay minerals in the presence of metal cations is a complex phenomenon due to the chemical heterogeneity of FA, different properties of metals, characteristics of mineral surfaces and the variability of environmental conditions.

Revealing the Toxicity of Chlorate Through the Analysis of Molecular Interaction using Viscosity Measurements and Apparent Molar Volumes

While chlorate has the ability to induce flowering in longan, it also has adverse impacts on the crop. Revealing the toxicity of chlorate in the environment is more than just about the environment and about human health, as well.Because of the large introduction of this chemical into the environment from the paper processing industry, there is indeed a lot of concern about its toxicity. Chlorate toxicology in the longan plant has been thoroughly investigated in solutions using viscosities and apparent molar volumes. The hydration of molecules and volume changes are involved in various chemical and biological processes in plant tissues, and their complete understanding demands a good idea for volumetric and viscometric study. It offers good data acquisition techniques for solute, solvent and solvent-solvent interactions. Multi-component systems containing KClO3+ water + ionic solid (ionic solids = KCl, KNO3 ,NH4NO3 and KH2PO4, are currently being worked out to study the dependence of transport properties of potassium chlorate in aqueous electrolyte solutions, with concentrations and temperature of solutions. The assessed kd values are used to predict whether the solvolysis of KClO3 in the presence of other electrolytes is a quick or slow process.

Structural study of anhydrous and hydrated 5-fluorouracil co-crystals with nicotinamide and isonicotinamide

5-Fluorouracil is a widely used anti-cancer drug which exhibits diverse polymorphic and co-crystalline behavior. Here we report two new solvent-free co-crystals of 5-fluorouracil with model co-formers nicotinamide and isonicotinamide, along with the redetermination of their hydrated analogues. Selected co-formers are categorized as safe and therefore suitable for pharmaceutical applications. Differences and similarities in supramolecular topology of the given structures are discussed. A special emphasis is set on the influence of fluorine moieties on the overall packing and synthetic accessibility of the presented multi-component systems.

Checkpoints That Regulate Balanced Biosynthesis of Lipopolysaccharide and Its Essentiality in Escherichia coli

The outer membrane (OM) of Gram-negative bacteria, such as Escherichia coli, is essential for their viability. Lipopolysaccharide (LPS) constitutes the major component of OM, providing the permeability barrier, and a tight balance exists between LPS and phospholipids amounts as both of these essential components use a common metabolic precursor. Hence, checkpoints are in place, right from the regulation of the first committed step in LPS biosynthesis mediated by LpxC through its turnover by FtsH and HslUV proteases in coordination with LPS assembly factors LapB and LapC. After the synthesis of LPS on the inner leaflet of the inner membrane (IM), LPS is flipped by the IM-located essential ATP-dependent transporter to the periplasmic face of IM, where it is picked up by the LPS transport complex spanning all three components of the cell envelope for its delivery to OM. MsbA exerts its intrinsic hydrocarbon ruler function as another checkpoint to transport hexa-acylated LPS as compared to underacylated LPS. Additional checkpoints in LPS assembly are: LapB-assisted coupling of LPS synthesis and translocation; cardiolipin presence when LPS is underacylated; the recruitment of RfaH transcriptional factor ensuring the transcription of LPS core biosynthetic genes; and the regulated incorporation of non-stoichiometric modifications, controlled by the stress-responsive RpoE sigma factor, small RNAs and two-component systems.