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This paper reports the structural behavior and thermodynamics of the complexation of siRNA with poly(amidoamine) (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) through fully atomistic molecular dynamics (MD) simulations accompanied by free energy calculations and inherent structure determination. We have also done simulation with one siRNA and two dendrimers (2×G3 or 2×G4) to get the microscopic picture of various binding modes. Our simulation results reveal the formation of stable siRNA−dendrimer complex over nanosecond time scale. With the increase in dendrimer generation, the charge ratio increases and hence the binding energy between siRNA and dendrimer also increases in accordance with available experimental measurements. Calculated radial distribution functions of amines groups of various subgenerations in a given generation of dendrimer and phosphate in backbone of siRNA reveals that one dendrimer of generation 4 shows better binding with siRNA almost wrapping the dendrimer when compared to the binding with lower generation dendrimer like G3. In contrast, two dendrimers of generation 4 show binding without siRNA wrapping the dendrimer because of repulsion between two dendrimers. The counterion distribution around the complex and the water molecules in the hydration shell of siRNA give microscopic picture of the binding dynamics. We see a clear correlation between water, counterions motions and the complexation i.e. the water molecules and counterions which condensed around siRNA are moved away from the siRNA backbone when dendrimer start binding to the siRNA backbone. As siRNA wraps/bind to the dendrimer counterions originally condensed onto siRNA (Na) and dendrimer (Cl−) get released. We give a quantitative estimate of the entropy of counterions and show that there is gain in entropy due to counterions release during the complexation. Furthermore, the free energy of complexation of 1G3 and 1G4 at two different salt concentrations shows that increase in salt concentration leads to the weakening of the binding affinity of siRNA and dendrimer. [ABSTRACT FROM AUTHOR]

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nfdegrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor−liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations. [ABSTRACT FROM AUTHOR]

We used molecular dynamics (MD) simulations to study the reorientational dynamics of water molecules confined inside narrow carbon nanotubes immersed in a bath of water. Our simulations show that the confined water molecules exhibit bistability in their reorientational relaxation, which proceeds by angular jumps between the two stable states. The angular jump of a water molecule in the bulk involves the breaking of a hydrogen bond with one of its neighbors and the formation of a hydrogen bond with a different neighbor. In contrast, the angular jump of a confined water molecule corresponds to an interchange of the two hydrogen atoms that can form a hydrogen bond with the same neighbor. The free energy barrier between these two states is a few kBT. The analytic solution of a simplified two-state jump model that qualitatively explains the reorientational behavior observed in simulations is also presented. [ABSTRACT FROM AUTHOR]

Using several hundred nanosecond long fully atomistic molecular dynamics simulations, we investigate the monomer and counterion local concentrations in poly amido amide (PAMAM) dendrimer systems for various generations at neutral pH. We also calculate the ζ potential as a function of dendrimer generation. It is found that the ζ potential increases with dendrimer generation, but slowlyat high generation. The ζ potential behavior is remarkably well reproduced when employing Monte Carlo simulations and the Poisson−Boltzmann theory for colloidalparticles with size and effective charge of the dendrimer as relevant input parameters from the fully atomistic simulations. [ABSTRACT FROM AUTHOR]

We study sequence-dependent complexation between oligonucleotides (single-strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by free energy calculations and inherent structure determination. Simulations reveal formation of a stable complex and provide a detailed molecular level understanding of the structure and dynamics of such a complexation. The reaction free energy surface in the initial stage is found to be funnel-like, with a significantbarrier arising in the late stage due to the occurrence of misfolded states of DNA. Complexation shows surprisingly strong sensitivity to the ssDNA sequence, which is found to arise from a competition between enthalpic versus entropic rigidity of ssDNA. [ABSTRACT FROM AUTHOR]

Phosphate is a major nonpoint source pollutant in both the Louisiana local streams as well as in the Gulf of Mexico coastal waters. Phosphates from agricultural run-off have contributed to the eutrophication of global surface waters. Phosphate environmental dissemination and eutrophication problems are not yet well understood. Thus, this study aimed to monitor phosphate in the local watershed to help identify potential hot spots in the local community (Mississippi River, Louisiana) that may contribute to nutrient loading downstream (in the Gulf of Mexico). An electrochemical method using a physical vapor deposited cobalt microelectrode was utilized for phosphate detection using cyclic voltammetry and amperometry. The testing results were utilized to evaluate the phosphate distribution in river water and characterize the performance of the microsensor. Various characterizations, including the limit of detection, sensitivity, and reliability, were conducted by measuring the effect of interferences, including dissolved oxygen, pH, and common ions. The electrochemical sensor performance was validated by comparing the results with the standard colorimetry phosphate detection method. X-ray photoelectron spectroscopy (XPS) measurements were performed to understand the phosphate sensing mechanism on the cobalt electrode. This proof-of-concept sensor chip could be utilized for on-field monitoring using a portable, hand-held potentiostat., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

A unique and novel structural morphology with high specific surface area, highly synergistic, remarkable porous conductive networks with outstanding catalytic performance, and durability of oxygen reduction electrocatalyst are typical promising properties in fuel cell application; however, exploring and interpreting this fundamental topic is still a challenging task in the whole world. Herein, we have demonstrated a simple and inexpensive synthesis strategy to design three-dimensional (3D) iron tungsten oxide nanoflower-anchored nitrogen-doped graphene (3D Fe-WO 3 NF/NG) hybrid for a highly efficient synergistic catalyst for oxygen reduction reaction (ORR). The construction of flowerlike Fe-WO 3 nanostructures, based on synthesis parameters, and their ORR performances are systematically investigated. Although pristine 3D Fe-WO 3 NF or reduced graphene oxides show poor catalytic performance and even their hybrid shows unsatisfactory results, impressively, the excellent ORR activity and its outstanding durability are further improved by N doping, especially due to pyridinic and graphitic nitrogen moieties into a graphene sheet. Remarkably, 3D Fe-WO 3 NF/NG hybrid nanoarchitecture reveals an outstanding electrocatalytic performance with a remarkable onset potential value (∼0.98 V), a half-wave potential (∼0.85 V) versus relative hydrogen electrode, significant methanol tolerance, and extraordinary durability of ∼95% current retention, even after 15 000 potential cycles, which is superior to a commercial Pt/C. The exclusive porous architecture, excellent electrical conductivity, and the high synergistic interaction between 3D Fe-WO 3 NF and NG sheets are the beneficial phenomena for such admirable catalytic performance. Therefore, this finding endows design of a highly efficient and durable nonprecious metal-based electrocatalyst for high-performance ORR in alkaline media.

A new cyclic pentasaccharide comprising an oxymethylene glycosidic bond connecting the individual α-d-glycopyranoside monomers is synthesized through cycloglycosylation of a linear pentasaccharide precursor, which, in turn, is synthesized through the block glycosylation method. Molecular modeling shows that the 30-membered macrocyclic pentasaccharide is a distorted ellipsoid structure, with the lower and upper rims occupied by secondary and primary hydroxyl groups, respectively. Following the synthesis, the microenvironment of the cyclic pentasaccharide is assessed through thermodynamic evaluation upon complexation with 1-aminoadamantane in an aqueous solution, which shows the formation of ∼1:2 host-to-guest complex and a binding affinity of 10 500 (±425) M -1 . Synthesis and assessment of the host-guest binding property of the new glycosidic bond expanded cyclic pentasaccharide are presented., Competing Interests: The authors declare no competing financial interest.

The oxidation of l-serine by chloro and chlorohydroxo complexes of gold(III) was spectrophotometrically investigated in acidic buffer media in the absence and presence of the anionic surfactant sodium dodecyl sulfate (SDS). The oxidation rate decreases with increase in either [H + ] or [Cl - ]. Gold(III) complex species react with the zwitterionic form of serine to yield acetaldehyde (principal reaction product) through oxidative decarboxylation and subsequent deamination processes. A reaction pathway involving one electron transfer from serine to Au(III) followed by homolytic cleavage of α-C-C bond with the concomitant formation of iminic cation intermediate has been proposed where Au(III) is initially reduced to Au(II). The surfactant in the submicellar region exhibits a catalytic effect on the reaction rate at [SDS] ≤ 4 mM; however, in the postmicellar region an inhibitory effect was prominent at [SDS] ≥ 4 mM. The catalytic effect below the critical micelle concentration (cmc) may be attributable to the electrostatic attraction between serine and SDS that, in turn, enhances the nucleophilicity of the carboxylate ion of the amino acid. The inhibition effect beyond cmc has been explained by considering the distribution of the reactant species between the aqueous and the micellar pseudophases that restricts the close association of the reactant species. The thermodynamic parameters Δ H 0 and Δ S 0 associated with the binding between serine and SDS micelle were calculated to be -14.4 ± 2 kJ mol -1 and -6.3 ± 0.5 J K -1 mol -1 , respectively. Water structure rearrangement and micelle-substrate binding play instrumental roles during the transfer of the reactant species from aqueous to micellar pseudophase.

Development of highly active and durable catalysts for oxygen reduction reaction (ORR) alternative to Pt-based catalyst is an essential topic of interest in the research community but a challenging task. Here, we have developed a new type of face-centered tetragonal (fct) PdFe-alloy nanoparticle-encapsulated Pd (fct-PdFe@Pd) anchored onto nitrogen-doped graphene (NG). This core-shell fct-PdFe@Pd@NG hybrid is fabricated by a facile and cost-effective technique. The effect of temperature on the transformation of face-centered cubic (fcc) to fct structure and their effect on ORR activity are systematically investigated. The core-shell fct-PdFe@Pd@NG hybrid exerts high synergistic interaction between fct-PdFe@Pd NPs and NG shell, beneficial to enhance the catalytic ORR activity and excellent durability. Impressively, core-shell fct-PdFe@Pd@NG hybrid exhibits an excellent catalytic activity for ORR with an onset potential of ∼0.97 V and a half-wave potential of ∼0.83 V versus relative hydrogen electrode, ultrahigh current density, and decent durability after 10 000 potential cycles, which is significantly higher than that of marketable Pt/C catalyst. Furthermore, the core-shell fct-PdFe@Pd@NG hybrid also shows excellent tolerance to methanol, unlike the commercial Pt/C catalyst. Thus, these findings open a new protocol for fabricating another core-shell hybrid by facile and cost-effective techniques, emphasizing great prospect in next-generation energy conversion and storage applications.

Remedial cancer therapy deals with a large number of theranostic applications. However, systems, so far known, are only capable of single surveillance for both diagnostic and therapeutic modes of action. A nanosystem, which can be localized to the cancer and deliver the chemotherapeutic agent on demand, will provide effective therapeutic activity. Herein, we designed a single component nanoprodrug ANPD-X (Activatable Nano Pro-Drug-X) which indentified the tumor sites by fluorescent color change (signal 1, blue to green fluorescence) using H 2 O 2 -mediated oxidation of boronate fluorophore. In the next step, precise spatiotemporal irradiation of light only on identified tumor sites resulted in the release of anticancer drug chlorambucil. The real time information on drug release was achieved by a second fluorescence color change (signal 2, green to blue fluorescence). Thus, nanoprodrug ANPD-X provided overall two-step surveillance in the anticancer drug delivery. Activation of the ANPD-X after addition of H 2 O 2 and drug release upon photoirradiation was investigated in vitro by monitoring its fluorescence in the HeLa cell line.

A bisthiocarbonohydrazone-based chemosensor molecule ( R1 ) containing a tetrahydro-8-hydroxyquinolizine-9-carboxaldehyde moiety has been synthesized and characterized as a new ratiometric fluorescent probe for picric acid (PA). The ratiometric probe R1 is a highly selective and sensitive colorimetric chemosensor for PA. The association between the chemosensor and PA and the ratiometric performance enabled by the key role of excited state intramolecular proton transfer in the detection process are demonstrated. Selectivity experiments proved that R1 has excellent selectivity to PA over other nitroaromatic chemicals. Importantly, the ratiometric probe exhibited a noteworthy change in both colorimetric and emission color, and this key feature enables R1 to be employed for detection of PA by simple visual inspection in silica-gel-coated thin-layer chromatography plates. Probe R1 has been shown to detect PA up to 3.2 nM at pH 7.4. Microstructural features of R1 and its PA complex have been measured by a field emission scanning electron microscope, and it clearly proves that their morphological features differ dramatically both in shape and size. Density function theory and time-dependent density function theory calculations were performed to establish the sensing mechanism and the electronic properties of probe R1 . Furthermore, we have demonstrated the utility of probe R1 for the detection of PA in live Vero cells for ratiometric fluorescence imaging., Competing Interests: The authors declare no competing financial interest.

A new cyclic trisaccharide is synthesized by cycloglycosylation of a linear trisaccharide, modified with hydroxymethyl moiety at C4 of glucopyranose moiety. The cyclic trisaccharide possesses a rarely observed perfect trigonal symmetry in the P3 space group, in a narrow cone shape, and a brick-wall type arrangement of molecules in the solid state, and exhibits a significantly enhanced binding affinity to 1-aminoadamantane in aqueous solution.

The characteristics of fluorescent components of dissolved organic matter (DOM) were examined using excitation emission matrix (EEM) fluorescence spectroscopy combined with parallel-factor analysis (PARAFAC) for seawater samples obtained from the northern Gulf of Mexico (NGoM) before, during, and after the 2010 Deepwater Horizon (DwH) oil spill. An EEMs PARAFAC modeling of samples collected within 16 km of the wellhead during the oil spill in May 2010, which included one typical subsurface sample with a PAH concentration of 1.09 μg/L, identified two humic-like and two previously reported oil-like components. Compared to prespill levels, however, there were order-of-magnitude higher fluorescence intensities associated with these components that are consistent with an oil-spill source. The spectral decomposition of the EEMs data using individual and combined data sets from coastal and offshore waters impacted by the DwH spill further revealed the changing nature of fluorescent DOM composition. Although the PAHs concentrations were at prespill conditions after the spill in 2012 and 2013 near the DwH site, the variable and anomalous levels of fluorescence intensities and DOC concentrations three years after the spill suggest the potential long-term persistence of the oil in the DOC pool in the NGoM.

We investigate the structural, electronic, and transport properties of substitutional defects in SiC-graphene by means of scanning tunneling microscopy and magnetotransport experiments. Using ion incorporation via ultralow energy ion implantation, the influence of different ion species (boron, nitrogen, and carbon) can directly be compared. While boron and nitrogen atoms lead to an effective doping of the graphene sheet and can reduce or raise the position of the Fermi level, respectively, (12)C(+) carbon ions are used to study possible defect creation by the bombardment. For low-temperature transport, the implantation leads to an increase in resistance and a decrease in mobility in contrast to undoped samples. For undoped samples, we observe in high magnetic fields a positive magnetoresistance that changes to negative for the doped samples, especially for (11)B(+)- and (12)C(+)-ions. We conclude that the conductivity of the graphene sheet is lowered by impurity atoms and especially by lattice defects, because they result in weak localization effects at low temperatures.

Bolaforms B(1), B(2), and B(3) of the formulas, Br(-)Me(3)N(+)(CH(2))(10)N(+)Me(3)Br(-), Br(-)Me(3)N(+)(CH(2))(10)OH, and Br(-)Me(3)N(+)(CH(2))(10)COO(-)Na(+), respectively, were synthesized, and their properties in the bulk as well as at the air/aqueous NaBr (10 mM) solution interface have been studied. Their interactions with sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB) also have been investigated. Tensiometry, conductometry, spectrophotometry, and microcalorimetry techniques were used for characterization and estimation. Both pure bolaforms and their mixtures with SDS and CTAB have been found to self-aggregate, forming micelles in solution. The mixed systems of bolaform and SDS have been observed to form both micelles and vesicles. Their mutual interactions were synergistic, which at the interface was more spontaneous than in the bulk. The interfacial and bulk compositions of the mixed binary systems (bolaform and SDS or CTAB) with their associated interaction parameters have been estimated from the Rosen interaction model and the regular solution theory of Rubingh, respectively. The formed vesicles have been found to entrap the water-soluble dye, bromophenol blue, and the dye solubilized vesicles of B(1)-SDS and B(2)-SDS completely eluted out of the sephadex column proving their formation. A rough estimation of the size and polydispersity index of the formed micelles and vesicles has been made from DLS measurements.

Ellagic acid (EA) has been reported as a potent antioxidant from natural resources with several nutritional benefits. The major disadvantage of this phytoconstituent is its rapid elimination from the body after administration. To overcome this limitation, a novel dietary formulation of EA with phospholipid was developed to investigate the effect of this complex on carbon tetrachloride induced liver damage in rats. The antioxidant activity of the complex (equivalent of EA = 25 and 50 mg/kg of body weight) and free EA (25 and 50 mg/kg of body weight) was evaluated by measuring various enzymes in oxidative stress condition. The complex significantly protected the liver by restoring the activity of superoxide dismutase, catalase and liver glutathione, and thiobarbituric acid reactive substances with respect to the carbon tetrachloride treated group (P < 0.05 and < 0.01). The complex provided better protection to rat liver than free EA at the same dose. The serum concentration of EA obtained from the complex (equivalent to 80 mg/kg of EA) was higher (C(max) = 0.54 microg/mL) than that of pure EA (80 mg/kg) (C(max) = 0.21 microg/mL), and the complex maintained effective concentration for a longer period of time in serum. The experimental outcome highlighted better hepatoprotective activity of the EA complex due to its potential antioxidant property compared with the free EA tested at the same dose level.

Octadecyl-trimethyl-ammonium bromide (C18TAB) is a much less studied representative in the alkyltrimethylammonium halide surfactant series. A comprehensive study of its normal and reverse micelle (microemulsion) formation has been herein conducted by the methods of conductometry, tensiometry, fluorimetry, and microcalorimetry. The energetics of its air/liquid interfacial adsorption and self-association in aqueous solution have been examined. The phase behavior of its combinations with water, n-butanol, and n-heptane in the formation of microemulsions have been investigated with identification of a variety of phases. The energetics of formation of water dispersion in oil (w/o) has been evaluated from dilution experiments conducted at different temperatures. From the results, structural parameters of the droplets have been determined at different [water]/[surfactant] mole ratios (omega) and temperatures. The w/o dispersions have evidenced both volume- and temperature-induced conductance percolation. The results have been treated in light of the Scaling equations, and the associated parameters for the process have been determined. The activation energies for the temperature-induced percolation process of the w/o dispersion have been evaluated and assessed.