Cross-polarization n.m.r. as a tool to investigate solvent-coal molecular interactions

The interaction of pyridine and aniline with an Australian bituminous coal (Liddell) has been studied by cross-polarization ¹³C nuclear magnetic resonance spectroscopy (CP ¹³C n.m.r.). The results show that sorbed aniline or pyridine molecules on coal are sufficiently immobilized to cross polarize. Carbon-proton static dipolar interactions, however, are weak which suggests that sorbed molecules can rotate rapidly about one or more of their axes of symmetry. It is also established that spin diffusion between coal and sorbed molecules is inefficient. Some loss of conformational rigidity of coal molecules is indicated when coal is soaked with pyridine.     

Crystalline molecular machines: a quest toward solid-state dynamics and function

Complex molecular machinery may be envisioned as densely packed, multicomponent, self-assembling systems built with high structural precision to control the dynamics of one or more internal degrees of freedom. With molecular gyroscopes as a test, we describe a general strategy to design crystals capable of supporting structurally programmed molecular motions, a practical approach to their synthesis, convenient strategies to characterize their solid-state dynamics, and potential applications based on polar structures responding collectively to external fields.     

Molecular dynamics simulations as a tool for improving protein stability

Haloalkane dehalogenase (DhlA) was used as a model protein toexplore the possibility to use molecular dynamics (MD) simulationsas a tool to identify flexible regions in proteins that canserve as a target for stability enhancement by introductionof a disulfide bond. DhlA consists of two domains: an     

Heat transfer resistance as a tool to quantify hybridization efficiency of DNA on a nanocrystalline diamond surface

In this article, we report on a label-free real-time method based on heat transfer resistivity for thermal monitoring of DNA denaturation and its potential to quantify DNA fragments with a specific sequence of interest. Probe DNA, consisting of a 36-mer fragment was covalently immobilized on a nanocrystalline diamond surface, created by chemical vapor deposition on a silicon substrate. Various concentrations of full matched 29-mer target DNA fragments were hybridized with this probe DNA. We observed that the change in heat transfer resistance upon denaturation depends on the concentration of target DNA used during the hybridization, which allowed us to determine the dose–response curve. Therefore, these results illustrate the potential of this technique to quantify the concentration of a specific DNA fragment and to quantify the hybridization efficiency to its probe.     

Temperature-programmed desorption of H2 as a tool to determine metal surface areas of Cu catalysts

Temperature-programmed desorption of H₂ (H₂ TPD) is shown to be a useful new tool for the determination of Cu metal surface areas. The technique has been employed in on-line characterization of binary Cu/Al₂O₃ and ternary Cu/ZnO/Al₂O₃ catalysts in a combined TPD-microreactor setup. The catalysts were studied both after reduction and after water gas shift activity tests. A main H₂ TPD peak is observed around 300 K which can be assigned to desorption from Cu metal surface sites. The H₂ TPD method is compared with the N₂O frontal chromatography method which has been extensively used in previous studies for the determination of Cu surface areas. It is found that the dissociative adsorption of N₂O may induce significant changes in the catalyst structure leading to errors in the surface area determination. With the H₂ TPD procedure such irreversible changes can be avoided. A further advantage of the H₂ TPD method is the possibility of providing insight into the nature of the exposed Cu metal surfaces.On leave from Institute of Physics, University of Aarhus, DK-8000 Aarhus C, Denmark.     

Krypton adsorption as a suitable tool for surface characterization of multi-walled CNTs

Multi-walled carbon nanotubes (CNTs), pristine and subjected to treatments, are comparatively characterized from N₂ and Kr (77 K) adsorption measurements. The CNTs are lab-synthesized by in situ chemical vapour deposition of an iron-based organometallic compound at 895 °C. The treatments applied to the CNTs include low temperature gas-phase oxidation, mild temperature annealing and ultrasonic dispersion in ethanol, in an attempt to examine possible changes in adsorption characteristics. N₂ and Kr adsorption measurements give rise to steadily increasing and stepped isotherms, respectively. The former are representative of a multilayer adsorption phenomenon, while the latter indicate successive monolayer condensation. The treatments affect differently gas adsorption capacities of the CNTs. Oxidation leads to CNTs with higher BET specific surface area and increased adsorption capacity, though the effect is more pronounced for Kr adsorption. Ultrasonic dispersion of the CNT brings about a significant reduction only in N₂ adsorption capacity. Modifications in the characteristic steps in Kr adsorption isotherms of the CNTs subjected to annealing can be appreciated, although no remarkable changes are observed in N₂ adsorption isotherms. Present results demonstrate that determination of Kr adsorption isotherms represents a more suitable tool to obtain a more reliable textural characterization of CNTs than does N₂ adsorption.     

Response surface methodology as a tool to study the lipase‐catalyzed synthesis of betulinic acid ester

BACKGROUND: The synthesis of betulinic acid ester using betulinic acid and oleyl alcohol catalyzed by Novozym 435 (immobilized Candida antarctica lipase) was carried out. Response surface methodology (RSM) based on a five‐level, three‐variable, central composite rotatable design (CCRD) was employed to evaluate the interactive effects of various parameters. The parameters were reaction time (8–16 h), temperature (20–60 °C) and enzyme amount (120–160 mg). RESULTS: Simultaneously increasing reaction time, temperature and amount of enzyme increased the yields of betulinic acid ester produced. CONCLUSION: The optimum conditions derived via RSM for the reaction were reaction time of 10.2 h, temperature of 53.1 °C and enzyme amount of 138 mg. The actual experimental yield was 48.5% under optimum conditions, which compared well with the maximum predicted value of 47.6%. Copyright © 2008 Society of Chemical Industry     

Simulation of dynamic behavior of surfactants on a hydrophobic surface using periodic-shell boundary molecular dynamics

The adsorption and aggregation behaviors of sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB) on a hydrophobic graphite surface were examined using a novel molecular dynamics (MD) simulation with the periodic-shell boundary condition (PSBC). Differences in the adsorption behavior of SDS and CTAB molecules were clearly shown on the hydrophobic surface. Unexpectedly, the SDS molecules approached the graphite surface with their hydrophilic head groups. This unexpected approach mode was thought to be due to the aqueous layer on the graphite surface. The hydrophobic moiety of SDS molecules repeatedly adsorbed and desorbed on the graphite surface. In addition, SDS molecules kept moving on the graphite surface; thus, they did not form a stable adsorption layer. In contrast to SDS, the hydrophobic moiety of CTAB molecules approached the graphite surface at the primary step of adsorption. The hydrophobic moieties of CTAB molecules came close to each other, whereas the hydrophilic groups separated from one another. This result suggests that the CTAB molecules form molecular assemblies with a curved structure. The simulation results were consistent with the experimental observations. A clear difference between the adsorption behavior of SDS and CTAB molecules was revealed by MD simulations with PSBC.     

Response surface methodology as a tool to optimize the electrochemical incineration of bromophenol blue on boron-doped diamond anode

This study investigated the electrochemical incineration of bromophenol blue (BPB) at boron-doped diamond (BDD) anode. The individual and interaction effects of three control parameters (applied current density, flow rate and supporting electrolyte concentration) on process efficiency were estimated by central composite rotatable design. Among the independent variables, supporting electrolyte concentration displayed the most interesting roles on BPB degradation. The optimal conditions obtained by response surface methodology were: applied current density of 7.36 mA cm^− 2, 2.6 mM Na₂SO₄ and flow rate of 568 ml min^− 1, which gave a decolorization rate of 91.7% and a mineralization rate of 47.3%, as well as an energy consumption of 3518.89 kWh kg^− 1 TOC (7.0 kWh m^− 3) and a mineralization current efficiency of 15.1% at 120 min of electrolysis. The results presented here demonstrated the high efficiency of BDD technology in mineralizing BPB under mild conditions, as well as the usefulness and capability of the experimental design strategy for successful investigation and modeling of the electrocatalytic processes.     

A molecular dynamics study of 3C-SiC/epoxy nanocomposite as a metal-free friction material

The tribological, mechanical, and thermal properties of an epoxy crosslinking network incorporated with 3C-SiC nanoparticles, serving as a metal-free friction material were investigated by molecular dynamics simulations. The considered models encompass pure epoxy materials with 35%, 50%, 65%, and 80% crosslinking degrees, as well as 3C-SiC/epoxy composite materials at the same crosslinking levels. Glass transition temperature (T_g) of the eight models was analyzed, and the result shows augmenting crosslinking density and addition of 3C-SiC nanofillers improve T_g of all models. Fractional free volume of each model was quantified to reflect the features of epoxy materials and influence the properties at the atomic scale. Frictional force, normal force, and coefficient of friction (COF) were calculated to elucidate the tribological performance of the epoxy-based materials. The introduction of 3C-SiC nanofillers reduces COF. With nanofillers, higher crosslinking degree brings lower COF except 80% crosslinking degree, while without nanofillers, higher COFs are obtained with 35% and 80% crosslinking degrees. 3C-SiC/epoxy composite with heightened crosslinking degree demonstrates superior Young's modulus, elevated tensile stress, and relatively smaller strain. Thermal conductivity analysis highlights the positive impact of both increased crosslinking density and incorporation of 3C-SiC nanofillers on heat transfer. Temperature elevation further enhances thermal conductivity.     

Engineering of human lysozyme as a polyelectrolyte by the alteration of molecular surface charge

The surface positive charges of human lysozyme were either increasedor decreased to alter the electrostatic interaction betweenenzyme and substrate in the lytic action of human lysozyme usingsite-directed mutagenesis. The amino acid substitutions accompanyingeither the addition or the removal of two units of positivecharge have shifted the optimal ionic strength (NaCl concentrationin 10 mM Mes buffer, pH 6.2) for the lysis of Micrococcus lysodeikticuscell from 0.04 M to 0.1 M and from 0.04 M to 0.02 M respectively.In addition to the change in ionic strength–activity profile,the pH–activity profile and the effect of a polycationicelectrolyte, poly-L-Lys-HCl, on the lytic activity were significantlychanged. Owing to the shifts in both ionic strength profilesand pH profiles the Arg⁷⁴/Arg¹²⁶ mutant has become a bettercatalyst than wild-type enzyme under the conditions of highionic strength and high pH, and the Gln⁴¹/Ser¹⁰¹ mutant hasbecome a better catalyst under the conditions of low ionic strengthand low pH.     

Membrane technology as a tool to prevent dangers to human health by water-reuse

The paper gives a discussion of the health risks in reusing domestic sewage water as drinking water after purification.The potential risk of the transmission of viral diseases through a recycling water system can be reduced 5–7 logs by membrane filtration, thus mimimizing the risk of transmission of, for example, hepatitis A, and increasing the safety beyond the level of traditional waterworks.Membrane filtration connected with denitrification will secure the water systems for the transmission of bacterial diseases. Membrane filtration reduces bacterial counts 7–9 logs.Membrane filtration will reduce the need for chlorination, because colloids are removed, and membrane filtration is a safe barrier for eggs of nematodes, helminths, etc.     

Phosphorylation as a tool to modulate aggregation propensity and to predict fibril architecture

Despite the importance of post-translational modifications in controlling the solubility and conformational properties of proteins and peptides, precisely how the aggregation propensity of different peptide sequences is modulated by chemical modification remains unclear. Here we have investigated the effect of phosphorylation on the aggregation propensity of a 13-residue synthetic peptide incorporating one or more phosphate groups at seven different sites at various pH values. Fibril formation was shown to be inhibited when a single phosphate group was introduced at all seven locations in the peptide sequence at pH 7.5, when the phosphate group is fully charged. By contrast, when the same peptides were analysed at pH 1.1, when the phosphate is fully protonated, fibrils from all seven peptide sequences form rapidly. At intermediate pH values (pH 3.6) when the phosphate group is mono-anionic, the aggregation propensity of the peptides was found to be highly dependent on the position of the phosphate group in the peptide sequence. Using this information, combined with molecular dynamics (MD) simulations of the peptide sequence, we provide evidence consistent with the peptide forming amyloid fibrils with a class 7 architecture. The results highlight the potential utility of phosphorylation as a method of reversibly controlling the aggregation kinetics of peptide sequences both during and after synthesis. Moreover, by exploiting the ability of the phosphate group to adopt different charge states as a function of pH, and combining experimental insights with atomistic information calculated from MD simulations as pH is varied, we show how the resulting information can be used to predict fibril structures consistent with both datasets, and use these to rationalise their sensitivity of fibrillation kinetics both to the location of the phosphate group and its charge state.     

Molecular dynamics simulation of fungal cellulose-binding domains: differences in molecular rigidity but a preserved cellulose binding surface

A total of 23 fungal cellulose-binding domain (CBD) sequenceswere aligned. Structural models of the cellulosebinding domainof an exoglucanase (CBHII) and of three endoglucanases (EGI,EGII and EGV) from Trichoderma reesei cellulases were homologymodelled based on the NMR structure of the fungal cellobiohydrolaseCBHI, from the same organism. The completed models and the knownstructure of the CBHI cellulose-binding domain were refinedby molecular dynamics simulations in water. All four modelswere found to be very similar to the structure of the CBHI cellulose-bindingdomain and sequence comparison indicated that in general thethree-dimensional structures of fungal cellulose-binding domainsare very similar. In all the CBDs studied, two disulphide bridgesapparently stabilize the polypeptide fold. From the models,an additional disulphide bridge was predicted in EGI and CBHII,and in eight further CBDs from other organisms. Three highlyconserved aromatic residues on the hydrophilic side of the wedgemake this surface flat This surface is expected to make contactwith the substrate. Three invariant amino acids, Gln7, Asn29and Gln34, on this flat face are in suitable positions for hydrogenbonding with the cellulose surface. Analysis of the differencesin the protein surface properties indicated that the endoglucanasestend to be more hydrophilic than the exoglucanases. The largeststructural variation was found around positions 12-16. The fungalCBD sequences are discussed in relation to variations in functionand pH dependence. Comparison of the modelled structures withexperimental binding data for the CBHI and EGI allowed the formulationof a qualitative relationship to cellulose affinity. This relationshipwas used to predict the cellulose affinities for 21 CBDs.     

Fish erythrocytes as a tool to study temperature-induced responses in plasma membranes

The dorsal aorta of carp (Cyprinus carpio L.) was cannulated, and the fish were kept in thermostated aquaria at 5°C for 24h. The water temperature was then gradually increased to 25°C at a rate of 0.5°C/h, and then decreased to 5°C at the same rate. Blood was withdrawn at five-degree intervals to determine the fluidity of erythrocyte plasma membranes uponex vivo incorporation of the fluorescent dye, 3-[p-(6-phenyl-1,3,5-hexatrienyl)phenyl] propionic acid. Steady-state anisotropy (R_ss) of the plasma membranes increased and decreased with the increase and decrease in water temperature, respectively. The sterol-to-phospholipid ratio remained unchanged throughout the thermal shifts. The fatty acid compositions of the total phospholipids, of phosphatidylcholine and of phosphatidylethanolamine remained virtually unchanged, except for the level of arachidonic acid, which increased in erythrocytes from fish at the higher temperature (25°C). The molecular species compositions of phosphatidylcholines and phosphatidylethanolamines also remained unaffected throughout the thermal shifts. The erythrocyte plasma membranes were more responsive to temperature shiftsin vivo thanin vitro when percent efficacy was compared. Thus, factors other than lipid changes are conceivably involved in the adaptation of erythrocyte plasma membranes to short-term thermal changes.     

In-cell solid-state NMR as a tool to study proteins in large complexes

A major limitation of solution NMR is molecular tumbling, which is often too slow for detection. Here we demonstrate that solid-state NMR spectroscopy in combination with flash freezing of cells can be used to detect proteins in the cellular environment and provides information on backbone chemical shifts.