Impact of third-grade nanofluid flow across a convective surface in the presence of inclined Lorentz force: an approach to entropy optimization

Journal of Thermal Analysis and Calorimetry - The current article deals with heat transfer and entropy generation analysis using Cattaneo–Christov heat flux (CCHF) for a flow of third grade...     

SURFCOMP: a novel graph-based approach to molecular surface comparison

Analysis of the distributions of physicochemical properties mapped onto molecular surfaces can highlight important similarities or differences between compound classes, contributing to rational drug design efforts. Here we present an approach that uses maximal common subgraph comparison and harmonic shape image matching to detect locally similar regions between two molecular surfaces augmented with properties such as the electrostatic potential or lipophilicity. The complexity of the problem is reduced by a set of filters that implement various geometric and physicochemical heuristics. The approach was tested on dihydrofolate reductase and thermolysin inhibitors and was shown to recover the correct alignments of the compounds bound in the active sites.     

Interfacial surface properties of thiol-protected gold nanoparticles: a molecular probe EPR approach

We present a molecular probe technique for accessing interfacial surface electrostatics of ligand-protected gold nanoparticles. A series of ligands with variable length of the hydrocarbon bridge between the anchoring sulfur and the reporting pH-sensitive nitroxide is described. The protonation state of this probe is directly observed by EPR spectroscopy. For tiopronin-protected Au nanoparticles, we observed an increase in pKa of up to ca. 1.1 pH units that was affected by the position of the reporter moiety with respect to the monolayer interface.     

New approach for representation of molecular surface

A new algorithm is proposed for approximation to the molecular surface. It starts with a triangular mesh built on an ellipsoid embracing the whole molecular surface. The triangular mesh is obtained from an icosahedron subdivision sphere with highly uniform vertex distribution, and the embracing surface is deflated stepwise to the best adherence of its triangles onto the surface of the molecule. The deflating direction of each vertex of a triangle is defined by the vector normal at this point to the previous deflated embracing surface. Our results show that the speed of the triangulation embracing ellipsoid method and the quality of the surface obtained by the method are faster and better than the method that starts with a quadrilateral mesh built from meridian and parallel representations on an embracing sphere to get the molecular surface. Furthermore, the surface obtained by the method can be used directly to approximate the molecular surface by spherical harmonic expansions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1805–1815, 1998     

Novel surface acoustic wave-interdigitated array electrode gas sensor for dissolved ammonia

A novel surface acoustic wave-interdigitated array electrode (SAW-IDA) ammonia gas sensor is proposed. A gas-permeable membrane is employed to separate the buffer solution in the inner cell of the gas-sensing probe from the sample solution in the detection cell. The response of the IDA conductive electrodes is based on the impedance change of the buffer solution during ammonia adsorption. Therefore, this gas sensor overcomes the influence of water vapour in the conventional film-coated SAW gas sensor and can be used for the detection of gases in aqueous solutions. The ammonia sensor exhibits a favourable frequency response to 5 × 10⁻⁷−1 × 10⁻³ mol/1 ammonia. The optimal buffer composition and probe parameters have been determined. Dynamic range, response time, selectivity, and temperature drift are discussed. The ammonia sensor was also applied to the determination of serum ammonia. Results were in good agreement with those from the conventional enzymatic-spectro-photometric method.     

Novel surface acoustic wave-interdigitated array electrode gas sensor for dissolved ammonia

 A novel surface acoustic wave-interdigitated array electrode (SAW-IDA) ammonia gas sensor is proposed. A gas-permeable membrane is employed to separate the buffer solution in the inner cell of the gas-sensing probe from the sample solution in the detection cell. The response of the IDA conductive electrodes is based on the impedance change of the buffer solution during ammonia adsorption. Therefore, this gas sensor overcomes the influence of water vapour in the conventional film-coated SAW gas sensor and can be used for the detection of gases in aqueous solutions. The ammonia sensor exhibits a favourable frequency response to 5×10^-7–1×10^-3 mol/l ammonia. The optimal buffer composition and probe parameters have been determined. Dynamic range, response time, selectivity, and temperature drift are discussed. The ammonia sensor was also applied to the determination of serum ammonia. Results were in good agreement with those from the conventional enzymatic-spectrophotometric method. Received: 1 December 1995/Revised: 9 April 1996/Accepted: 14 April 1996     

Self-assembled enzymatic monolayer directly bound to a gold surface: activity and molecular recognition force spectroscopy studies

Escherichia coli dihydrofolate reductase (ecDHFR) has one surface cysteine, C152, located opposite and distal to the active site. Here, we show that the enzyme spontaneously assembles on an ultraflat gold surface as a homogeneous, covalently bound monolayer. Surprisingly, the activity of the gold-immobilized ecDHFR as measured by radiographic analysis was found to be similar to that of the free enzyme in solution. Molecular recognition force spectroscopy was used to study the dissociation forces involved in the rupture of AFM probe-tethered methotrexate (MTX, a tight-binding inhibitor of DHFR) from the gold-immobilized enzyme. Treatment of the ecDHFR monolayer with free MTX diminished the interaction of the functionalized tip with the surface, suggesting that the interaction was indeed active-site specific. These findings demonstrate the viability of a simple and direct enzymatic surface-functionalization without the use of spacers, thus, opening the door to further applications in the area of biomacromolecular force spectroscopy.     

Evidence supporting the presence of dissolved dimethylarsinate in the marine environment

Experiments have been carried out to test the commonly held belief that the dissolved dimethylarsenic species present in marine waters is dimethylarsinate. By employing a novel combination of HPLC and cryogenic‐trap hydride generation atomic absorption spectroscopy (HG AA), the sensitivity limitations of conventional in‐line HPLC instrumentation can be overcome, permitting dimethylarsinate to be measured by HPLC at levels below 200 pg cm⁻³. A comparison of results obtained by this procedure with those obtained by direct cryogenic‐trap HG AA demonstrated that much of the dissolved dimethylarsenic present in the mouth of the Beaulieu River estuary (Hampshire, UK) had HPLC retention characteristics consistent with the presence of dimethylarsinate. Copyright © 1999 John Wiley & Sons, Ltd.     

Charge-transfer complex study by chemical force spectroscopy: a dynamic force spectroscopic approach

Charge-transfer interaction, as a reversible and rapid phenomenon, was evidenced by force microscopy. Pull-off forces were measured between a tip grafted with a trinitrofluorenone derivative and a surface functionalized with an electron-rich aromatic anthracene compound in a dodecane environment. The effect of the sweep time on the measured interaction forces is described, together with an extensive study of a competitive influence of free aromatic molecules in dodecane diluted solutions. These forces depend on the nature of the competitor and its concentration as well as on the velocity of tip/sample separation.     

Soluble molecular compounds with the Mg-O-Al structural motif: a model approach for the fixation of organometallics on a MgO surface

We report a facile route to the molecular compounds with the Mg-O-Al structural motif. The reaction of Mg[N(SiMe3)2]2 (1) with a stoichiometric amount of LAlOH(Me) (2) [L = CH{(CMe)(2,6-iPr2C6H3N)}2] in THF/n-hexane at 0 degrees C results in the formation of the heterobimetallic compound (Me3Si)2NMg(THF)2-O-Al(Me)L (3) in high yield. The similar reaction of 1 equiv of Mg[N(SiMe3)2]2 and 2 equiv of LAlOH(Me) results in the formation of trimetallic compound L(Me)Al-O-Mg(THF)2-O-Al(Me)L (4). Structural analyses of 3 and 4 have been carried out, revealing the presence of the Mg-O-Al motif. A tentative assignment of the Mg-O-Al vibrations has been made and was supported by calculations.     

Determination of the surface characteristics of particulate fillers by inverse gas chromatography at infinite dilution: a critical approach

CaCO3 fillers were investigated by inverse gas chromatography (IGC) to determine the dispersion component of their surface tension as well as their acid-base character. Because of the high energy of the filler surface, it readily adsorbs water, thus the parameters measured by IGC depend on the conditioning temperature, as well as on the measurement conditions. As a consequence, the determined surface characteristics are not material constants; different fillers or the effect of coating can be compared only under standard conditions. The use of the same conditioning and measurement temperature eliminates the effect of measurement time. Under appropriate standard conditions the acid-base characteristics of the filler can be determined reliably. However, the accuracy of the determination and the value of the derived parameters depend very much on the selected approach and on the acid-base constants used for the probe molecules. A critical analysis of the approaches used in the current literature pointed out those that yield the most reasonable and accurate values. The results prove that the surface of CaCO3 is strongly basic in character. Coating significantly reduces basicity. Surprisingly, the filler coated with an amount of stearic acid resulting in minimum surface tension showed relatively strong acidity, which indicates a coating exceeding monolayer coverage and/or the uneven distribution of the surfactant on the surface.     

Hydration of calcium oxide surface predicted by reactive force field molecular dynamics

In this work, we present the parametrization of Ca-O/H interactions within the reactive force field ReaxFF, and its application to study the hydration of calcium oxide surface. The force field has been fitted using density functional theory calculations on gas phase calcium-water clusters, calcium oxide bulk and surface properties, calcium hydroxide, bcc and fcc Ca, and proton transfer reactions in the presence of calcium. Then, the reactive force field has been used to study the hydration of the calcium oxide {001} surface with different water contents. Calcium oxide is used as a catalyzer in many applications such as CO(2) sequestration and biodiesel production, and the degree of surface hydroxylation is a key factor in its catalytic performance. The results show that the water dissociates very fast on CaO {001} bare surfaces without any defect or vacancy. The surface structure is maintained up to a certain amount of water, after which the surface undergoes a structural rearrangement, becoming a disordered calcium hydroxyl layer. This transformation is the most probable reason for the CaO catalytic activity decrease.     

Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals

The electrostatic interaction among molecules solvated in ionic solution is governed by the Poisson-Boltzmann equation (PBE). Here the hypersingular integral technique is used in a boundary element method (BEM) for the three-dimensional (3D) linear PBE to calculate the Maxwell stress tensor on the solvated molecular surface, and then the PB forces and torques can be obtained from the stress tensor. Compared with the variational method (also in a BEM frame) that we proposed recently, this method provides an even more efficient way to calculate the full intermolecular electrostatic interaction force, especially for macromolecular systems. Thus, it may be more suitable for the application of Brownian dynamics methods to study the dynamics of protein/protein docking as well as the assembly of large 3D architectures involving many diffusing subunits. The method has been tested on two simple cases to demonstrate its reliability and efficiency, and also compared with our previous variational method used in BEM.     

Oscillatory molecular driving force for protein folding at high concentration: a molecular simulation

This paper presents a Langevin dynamics simulation that suggests a novel way to fold protein at high concentration, a fundamental issue in neurodegenerative diseases in vivo and the production of recombinant proteins in vitro. The simulation indicates that the folding of a coarse-grained beta-barrel protein at high concentration follows the "collapse-rearrangement" mechanism but it yields products of various forms, including single proteins in the native, misfolded, and uncollapsed forms and protein aggregates. Misfolded and uncollapased proteins are the "nucleus" of the aggregates that also encapsulate some correctly folded proteins (native proteins). An optimum hydrophobic interaction strength (epsilon*(p)) between the hydrophobic beads of the model protein, which results from a compromise between the kinetics of collapse and rearrangement, is identified for use in increasing the rate of folding over aggregating. Increased protein concentration hinders the structural transitions in both collapse and rearrangement and thus favors aggregation. A new method for protein folding at high concentration is proposed, which uses an oscillatory molecular driving force (epsilon*(p)) to promote the dissociation of aggregates in the low epsilon*(p) regime while promoting folding at a high epsilon*(p). The advantage of this method in enhancing protein folding while depressing aggregation is illustrated by a comparison with the methods based on direct dilution or applying a denaturant gradient.     

Probing protein-peptide-protein molecular architecture by atomic force microscopy and surface plasmon resonance

We demonstrate the creation of a protein multilayer which utilises the high affinity interaction between streptavidin and biotin and incorporates a peptidic spacer. Surface plasmon resonance measurements enabled us to monitor the construction of the multilayer in real time. Atomic force microscopy was utilised to determine surface functionality at each stage of the multilayer construction, allowing us to investigate the associated mechanical properties. In this context we observed an increase in biomolecular stretching on the formation of the multilayer. We demonstrate, utilising circular dichroism, that variations in the solvent can affect the secondary structure of the peptide linker and hence its mechanical properties. Trifluoroethanol titrations on the assembled system indicate that the multilayer properties are also stimuli responsive with regard to solvent conditions. These results indicate that the multilayer stretch before cleavage is increased in the presence of trifluoroethanol. This was not expected from the study of the individual linker alone, indicating the need to study the system as a whole as opposed to the isolated components.     

A modular approach to mechanically gated photoswitching with color-tunable molecular force probes

Molecular force probes conveniently report on mechanical stress and/or strain in polymers through straightforward visual cues. Unlike conventional mechanochromic mechanophores, the mechanically gated photoswitching strategy decouples mechanochemical activation from the ultimate chromogenic response, enabling the mechanical history of a material to be recorded and read on-demand using light. Here we report a completely redesigned, highly modular mechanophore platform for mechanically gated photoswitching that offers a robust, accessible synthesis and late stage diversification through Pd-catalyzed cross-coupling reactions to precisely tune the photophysical properties of the masked diarylethene (DAE) photoswitch. Using solution-phase ultrasonication, the reactivity of a small library of functionally diverse mechanophores is demonstrated to be exceptionally selective, producing a chromogenic response under UV irradiation only after mechanochemical activation, revealing colored DAE isomers with absorption spectra that span the visible region of the electromagnetic spectrum. Notably, mechanically gated photoswitching is successfully translated to solid polymeric materials for the first time, demonstrating the potential of the masked diarylethene mechanophore for a variety of applications in force-responsive polymeric materials.

A highly modular and synthetically accessible mechanophore platform enables mechanically gated photoswitching in solution and in solid polymeric materials.     

Polymer-clay nanocomposites: a multiscale molecular modeling approach

A hierarchical procedure bridging the gap between atomistic and mesoscopic simulation for polymer-clay nanocomposite (PCN) design is presented. The dissipative particle dynamics (DPD) is adopted as the mesoscopic simulation technique, and the interaction parameters of the mesoscopic model are estimated by mapping the corresponding energy values obtained from atomistic molecular dynamics (MD) simulations. The predicted structure of the nylon 6 PCN system considered is in excellent agreement with previous experimental and atomistic simulation results.     

RRS-PBC: a molecular approach for periodic systems

Technically, when dealing with a perfect crystal, methods in k-(reciprocal) space that impose periodic boundary conditions(PBC) in conjunction with plane-wave basis sets are widely used. Chemists, however, tend to think of a solid as a giant molecule, which offers a molecular way to describe a solid by using a finite cluster model(FCM). However, FCM may fail to simulate a perfect crystal due to its inevitable boundary effects. We propose an RRS-PBC method that extracts the k-space information of a perfect crystalline solid out of a reduced real space(RRS) of an FCM. We show that the inevitable boundary effects in an FCM are eliminated naturally to achieve converged high-quality band structures.     

Toward the supramolecular structure of collagen: a molecular dynamics approach

The structure, stability, and conformational dynamics of an assembly of two pentameric bundles made of collagen-like triple helical segments are explored using 1.2 ns molecular dynamics simulations in three environments: 8.0% (v/v) formaldehyde/water solution, 1.4% (v/v) gallic acid/water solution, and pure water. Stable supramolecular arrangements, where the two collagen units are very close to each other at interacting distances, are identified via docking and energy minimization procedures. Analysis of the interaction with formaldehyde and gallic acid suggests that they perturb the protein in a similar way depending on hydrogen-bonding capability, hydrophobic association properties, and the size and concentration of the compound.