Chemical Model Systems Research Articles

Amoeba-like motion of an oil droplet

In this paper, we demonstrate our recent attempt to construct a chemical model system of amoeboid motion. The system is intended to mimic biological motility based on the generation and collapse of an elastic aggregate; it is composed of oil, water, and surfactants. In this chemical system, the oil–water interface shows extension and retreat of spherical extrusions accompanied by the generation of aggregate on the interface. This instability of the oil–water interface can cause autonomous splitting and motion of a floating oil droplet. The current mathematical model based on the generation of a passive elastic gel is explained, as well as the discrepancy between the model and the experiments. We further describe recently observed microscopic characteristics of the aggregate formation process that might cause the interfacial instability. Finally, we discuss the disadvantage of a chemical model system compared with active colloid and in vitro biological systems, and also mention its potential advantages.

Effects of antioxidants of bamboo leaves and flavonoids on 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) formation in chemical model systems.

The inhibitory effects of antioxidants of bamboo leaves (AOB) and flavonoids against 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) formation were investigated in creatinine and phenylalanine model systems. AOB and the tested flavonoids (orientin, homoorientin, vitexin, isovitex, apigenin, luteolin, isorhamnetin, fisetin, and hesperetin) had significant dose-dependent inhibition effects on PhIP formation with different IC50 values. The superoxide anion (O2(•-)) scavenging activities of these nine flavonoids were evaluated using the pyrogallol autoxidation system. The EC50 values of compounds that showed antioxidant activity were found to correlate well (R(2) = 0.8003) with the corresponding IC50 values representing their inhibition of PhIP formation. It was assumed that the inhibitory effects of flavonoids on PhIP formation were probably achieved by scavenging free radicals generated in the reaction system. These findings provide valuable information for the development of effective strategies to minimize heterocyclic amine content in thermally processed food.

Exchange–correlation functionals from the strong interaction limit of DFT: applications to model chemical systems

The strong-interaction limit of DFT provides an exchange–correlation potential that is able to describe strong correlation in 1D model chemical systems.

Modeling of temporal patterns and sources of atmospherically transported and deposited pesticides in ecosystems of concern: A case study of toxaphene in the Great Lakes

AbstractPesticides have adverse effects on human health and the environment and can be transported through the atmosphere from application sites and deposited to sensitive ecosystems. This study applies a comprehensive multimedia regional pesticide fate and chemical transport modeling system that we developed to investigate the atmospheric transport and deposition of toxaphene to the Great Lakes. Simulated results predict a significant amount of toxaphene (~350 kg) being transported through the atmosphere and deposited into the Great Lakes in the simulation year. Results also show that U.S. residues and global background are major sources to toxaphene deposition into the Great Lakes and atmospheric concentrations in the region. While the U.S. residues are the dominant source in warm months, the background dominates during winter months. In addition, different sources have different influences on the individual Great Lakes due to their proximity and relative geographical positions to the sources; U.S. residues are the dominant source to Lakes Ontario, Erie, Huron, and Michigan, but they are a much less important source to Lake Superior. These results shed light on the mystery that observed toxaphene concentrations in Great Lakes' lake trout and smelt declined between 1982 and 1992 in four of the Great Lakes except Lake Superior. While monthly total depositions to Lakes Ontario, Erie, Huron, and Michigan have clear seasonal variability with much greater values in April, May, and June, monthly total depositions to Lake Superior are more uniformly distributed over the year with comparatively greater levels in cold months.

Simulated air quality and pollutant budgets over Europe in 2008

Major gaseous and particulate pollutant levels over Europe in 2008 have been simulated using the offline-coupled WRFCMAQ chemistry and transport modeling system. The simulations are compared with surface observations from the EMEP stations, ozone (O3) soundings, ship-borne O3 and nitrogen dioxide (NO2) observations in the western Mediterranean, tropospheric NO2 vertical column densities from the SCIAMACHY instrument, and aerosol optical depths (AOD) from the AERONET. The results show that on average, surface O3 levels are underestimated by 4 to 7% over the northern European EMEP stations while they are overestimated by 7–10% over the southern European EMEP stations and underestimated in the tropospheric column (by 10–20%). Particulate matter (PM) mass concentrations are underestimated by up to 60%, particularly in southern and eastern Europe, suggesting underestimated PM sources. Larger differences are calculated for individual aerosol components, particularly for organic and elemental carbon than for the total PM mass, indicating uncertainty in the combustion sources. Better agreement has been obtained for aerosol species over urban areas of the eastern Mediterranean, particularly for nss-SO42, attributed to the implementation of higher quality emission inventories for that area. Simulated AOD levels are lower than the AERONET observations by 10% on average, with average underestimations of 3% north of 40°N, attributed to the low anthropogenic emissions in the model and 22% south of 40°N, suggesting underestimated natural and resuspended dust emissions. Overall, the results reveal differences in the model performance between northern and southern Europe, suggesting significant differences in the representation of both anthropogenic and natural emissions in these regions. Budget analyses indicate that O3 and peroxyacetyl nitrate (PAN) are transported from the free troposphere (FT) to the planetary boundary layer over Europe, while other species follow the reverse path and are then advected away from the source region.

Aluminum speeds up the hydrothermal alteration of olivine

The reactivity of ultramafic rocks under hydrothermal conditions controls chemical fluxes at the interface between the internal and external reservoirs of silicate planets. On Earth, hydration of ultramafic rocks is ubiquitous and operates from deep subduction zones to shallow lithospheric environments where it considerably affects the physical and chemical properties of rocks and can interact with the biosphere. This process also has key emerging societal implications, such as the production of hydrogen as a source of carbon-free energy. To date, the chemical model systems used to reproduce olivine hydrothermal alteration lead to the formation of serpentine with sluggish reaction rates. Here, we use in situ diamond-anvil cell experiments and show that the presence of aluminum in hydrothermal fluids increases the rate of olivine serpentinization by one to two orders of magnitude. Aluminum increases the solubility of olivine and enhances the precipitation of aluminous serpentine. After two days, olivine crystals were fully transformed to aluminous serpentine under conditions typical for natural hydrothermal environments, i.e., 200 and 300 °C, 200 MPa. This result motivates a re-evaluation of the natural rates of olivine serpentinization and of olivine hydrolysis in general in a wide range of settings. This discovery also opens the potential of the serpentinization reaction for industrial scale production of hydrogen at economically feasible timescales and temperature.

Analysis of a chemical model system leading to chiral symmetry breaking: Implications for the evolution of homochirality

Explaining the evolution of a predominantly homochiral environment on the early Earth remains an outstanding challenge in chemistry. We explore here the mathematical features of a simple chemical model system that simulates chiral symmetry breaking and amplification towards homochirality. The model simulates the reaction of a prochiral molecule to yield enantiomers via interaction with an achiral surface. Kinetically, the reactions and rate constants are chosen so as to treat the two enantiomeric forms symmetrically. The system, however, incorporates a mechanism whereby a random event might trigger chiral symmetry breaking and the formation of a dominant enantiomer; the non-linear dynamics of the chemical system are such that small perturbations may be amplified to near homochirality. Mathematical analysis of the behavior of the chemical system is verified by both deterministic and stochastic numerical simulations. Kinetic description of the model system will facilitate exploration of experimental validation. Our model system also supports the notion that one dominant enantiomeric structure might be a template for other critical molecules.

Chemopreventive and antioxidant activity of 6-substituted imidazo[2,1-b]thiazoles

The synthesis of new imidazo[2,1-b]thiazoles bearing phenolic groups is reported. These compounds and some previously described analogs were evaluated as antioxidant agents with three chemical model systems, and cancer chemopreventive potential was examined by inhibition of NO production, TNF-α activated NFκB activity, and aromatase activity, as well as induction of QR1 and RXRE binding. Two of the test compounds, 9 and 12, displayed promising activity by inhibiting iNOS, NFκB and aromatase in dose–dependent manner, with IC50 values in low micromolar range. The same compounds activated QR1 in a bifunctional manner. When incubated with human liver microsomes, the active compounds were further hydroxylated on the parent ring system, suggesting the next logical step in the development of these promising leads will entail synthetic production of metabolites followed by additional assessment of biological activity.

Statistical estimations of the number of future ozone exceedances due to climate change in Europe

AbstractA statistical model to examine the potential impact of increasing future temperatures due to climate change on ozone exceedances (days with daily maximum 8 h average ≥ 60 ppb) is developed for Europe. We employ gridded observed daily maximum temperatures and hourly ozone observations from nonurban stations across Europe, together with daily maximum temperatures for 2021–2050 and 2071–2100 from three regional climate models, based on the Intergovernmental Panel on Climate Change Special Reports on Emissions Scenarios A1B scenario. A rotated principal components analysis is applied to the ozone stations yielding five principal components, which divide the study domain in five subregions. The historical ozone‐temperature relationship is examined and then used to provide estimates of future ozone exceedance days under current emissions and under the assumption that this relationship will retain its main characteristics. Results suggest that increases in the upper temperature percentiles lead to statistically significant increases (95% statistical significance level) of the ozone exceedances for both future periods. The greatest average increases depending on the particular regional climate model range from 5 to 12 extra ozone days/yr for 2021–2050 and from 16 to 25 for 2071–2100, in southeast Europe. The lowest average increases range from 0 to 2 extra ozone days/yr for 2021–2050 and from 2 to 4 for 2071–2100 and are seen in northwest Europe. The simulations with the dynamical Goddard Institute of Space Studies/GEOS‐CHEM climate chemistry modeling system shows decreases instead of increases in eastern Europe, higher increases in northwest Europe, whereas for the other subregions similar results to the statistical model are obtained.

Statistically testing the validity of analytical and computational approximations to the chemical master equation

The master equation is used extensively to model chemical reaction systems with stochastic dynamics. However, and despite its phenomenological simplicity, it is not in general possible to compute the solution of this equation. Drawing exact samples from the master equation is possible, but can be computationally demanding, especially when estimating high-order statistical summaries or joint probability distributions. As a consequence, one often relies on analytical approximations to the solution of the master equation or on computational techniques that draw approximative samples from this equation. Unfortunately, it is not in general possible to check whether a particular approximation scheme is valid. The main objective of this paper is to develop an effective methodology to address this problem based on statistical hypothesis testing. By drawing a moderate number of samples from the master equation, the proposed techniques use the well-known Kolmogorov-Smirnov statistic to reject the validity of a given approximation method or accept it with a certain level of confidence. Our approach is general enough to deal with any master equation and can be used to test the validity of any analytical approximation method or any approximative sampling technique of interest. A number of examples, based on the Schlögl model of chemistry and the SIR model of epidemiology, clearly illustrate the effectiveness and potential of the proposed statistical framework.

The Supramolecular Chemistry of β-Sheets

Interactions among β-sheets occur widely in protein quaternary structure, protein-protein interaction, and protein aggregation and are central in Alzheimer's and other amyloid-related diseases. This Perspective looks at the structural biology of these important yet under-appreciated interactions from a supramolecular chemist's point of view. Common themes in the supramolecular interactions of β-sheets are identified and richly illustrated though examples from proteins, amyloids, and chemical model systems. β-Sheets interact through edge-to-edge hydrogen bonding to form extended layers and through face-to-face hydrophobic or van der Waals interactions to form layered sandwich-like structures. Side chains from adjacent layers can fit together through simple hydrophobic contacts or can participate in complementary interdigitation or knob-hole interactions. The layers can be aligned, offset, or rotated. The right-handed twist of β-sheets provides additional opportunities for stabilization of edge-to-edge contacts and rotated layered structures.

Investigation on semi-direct and indirect climate effects of fossil fuel black carbon aerosol over China

A Regional Climate Chemistry Modeling System that employed empirical parameterizations of aerosol-cloud microphysics was applied to investigate the spatial distribution, radiative forcing (RF), and climate effects of black carbon (BC) over China. Results showed high levels of BC in Southwest, Central, and East China, with maximum surface concentrations, column burden, and optical depth (AOD) up to 14 μg m−3, 8 mg m−2, and 0.11, respectively. Black carbon was found to result in a positive RF at the top of the atmosphere (TOA) due to its direct effect while a negative RF due to its indirect effect. The regional-averaged direct and indirect RF of BC in China was about +0.81 and −0.95 W m−2, respectively, leading to a net RF of −0.15 W m−2 at the TOA. The BC indirect RF was larger than its direct RF in South China. Due to BC absorption of solar radiation, cloudiness was decreased by 1.33 %, further resulting in an increase of solar radiation and subsequently a surface warming over most parts of China, which was opposite to BC’s indirect effect. Further, the net effect of BC might cause a decrease of precipitation of −7.39 % over China. Investigations also suggested large uncertainties and non-linearity in BC’s indirect effect on regional climate. Results suggested that: (a) changes in cloud cover might be more affected by BC’s direct effect, while changes in surface air temperature and precipitation might be influenced by BC’s indirect effect; and (b) BC second indirect effect might have more influence on cloud cover and water content compared to first indirect effect. This study highlighted a substantial role of BC on regional climate changes.

Formation of genotoxic 2-amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP) and its kinetics in a model system

The influence of important precursors (amino acids and sugars) and heating conditions on the formation of 2-amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP), an abundant heterocyclic amine compound, and its formation kinetics were evaluated in a chemical model system. Phenylalanine containing α-amino propenoic acid (NH2CH2CHCOOH) may be involved in PhIP formation whereas glycine is not. Adding different amounts of 4 sugars (glucose, galactose, fructose, and ribose) resulted in significant differences (p<0.05) in PhIP formation in the model system. All sugars used may have been a limiting factor for PhIP formation. The formation of PhIP increased with increasing time and heating temperature and was correlated with browning reaction intensity. The rate constant of PhIP formation also increased with increasing temperature. Based on the values of activation energy, enthalpy, and activation entropy, PhIP formation was assumed to be a temperature-sensitive, endothermic, and bimolecular reaction. The results offer meaningful information for controlling the risk of PhIP formation in cooked foods.

Dissipativity analysis for networks of process systems

The paper presents stability and stabilizability analysis for plant-wide chemical processes. The process is modeled as a network of process systems with multiple recycle streams and energy integration. One of the key problems that we address in the paper is how to determine dissipativity properties of the process network from the dissipativity properties of the individual process systems and the topology of the network. The results in the paper extend the dissipativity analysis based on thermodynamics for individual processes to dissipativity-based conditions (storage functions and supply rates) suitable for process network analysis. The new storage and supply functions are based on balance equations represented in terms of temperatures and compositions rather than internal energy and chemical potentials. This makes the theory easier to apply to typical chemical process model systems. A simple example is provided to illustrate the application of the theory.

Modeling Tyrosinase and Catecholase Activity Using Newm-Xylyl-Based Ligands with Bidentate Alkylamine Terminal Coordination

Chemical model systems possessing the reactivity aspects of both tyrosinase and catechol oxidase are presented. Using two m-xylyl-based ligands providing bidentate alkylamine terminal coordination, 1,3-bis[(N,N-dimethylaminoethyl)aminomethyl]benzene (L(H,H)) and 1,3-bis[(N,N,N'-trimethylaminoethyl)aminomethyl]benzene (L(Me,Me)), four new dicopper(I) complexes, [Cu(I)(2)(L(H,H))(MeCN)(4)][ClO(4)](2) (1), [Cu(I)(2)(L(H,H))(PPh(3))(2)(MeCN)(2)][ClO(4)](2) (2), [Cu(I)(2)(L(Me,Me))(MeCN)(2)][ClO(4)](2) (3), and [Cu(I)(2)(L(Me,Me))(PPh(3))(2)][ClO(4)](2) (4), have been synthesized and characterized. Complex 2 has been structurally characterized. Reaction of the dicopper(I) complex 3(2+) with dioxygen at 183 K generates putative bis(μ-oxo)dicopper(III) intermediate (absorption spectroscopy). Oxygenation of 1 and 3 brings about m-xylyl-ring hydroxylation (monooxygenase-like activity), with a noticeable color change from pale-yellow to dark green. The presence of phenoxo- and hydroxo-bridges in the end products [Cu(II)(2)(L(H,H)-O)(OH)(MeCN)(2)][ClO(4)](2) (5) and [Cu(II)(2)(L(Me,Me)-O)(OH)(OClO(3))][ClO(4)]·MeCN(6) has been authenticated by structural characterization. Oxygenation of 3 afforded not only the green complex 6 isolation but also a blue complex [Cu(II)(2)(L(Me,Me))(OH)(2)][ClO(4)](2) (7). Variable temperature magnetic susceptibility measurements on 5 and 6 establish that the Cu(II) centers are strongly antiferromagnetically coupled [singlet-triplet energy gap (J) = -528 cm(-1) (5) and -505 cm(-1) (6)]. The abilities of phenoxo- and hydroxo-bridged dicopper(II) complexes 5 and 6, the previously reported complex [Cu(II)(2)(L(1)-O)(OH)(OClO(3))(2)]·1.5H(2)O (8) (L(1)-OH = 1,3-bis[(2-dimethylaminoethyl)iminomethyl]phenol), and [Cu(II)(2)(L(2)-O)(OH)(OClO(3))()][ClO(4)]() (9) (L(2)-OH = 1,3-[(2-dimethylaminoethyl)iminomethyl][(N,N,N'-trimethyl)aminoethyl]-4-methylphenol) have been examined to catalyze the oxidation of catechol to quinone (catecholase activity of tyrosinase and catechol oxidase-like activity) by employing the model substrate 3,5-di-tert-butylcatechol. Saturation kinetic studies have been performed on these systems to arrive at the following reactivity order [k(cat)/K(M) (catalytic efficiency) × 10(-3) (M(-1) h(-1))]: 470 (6) > 367 (5) > 128 (9) > 90 (8).

Surface active properties of isobornylphenols in systems with different degrees of complexity

Interrelations between the structure of the semi-synthetic phenolic antioxidants -- isobornylphenols and their surface active properties were studied in the chemical (the lecithin aggregation in hexane) and biological (the incubation with the blood erythrocytes) model systems. It has been shown that all studied compounds are able to affect the lecithin aggregation in hexane: the share of the main fraction of the L micelles decreases with increasing the share of particles of greater size. The effect substantially depends on hindered OH group and the presence of the intramolecular hydrogen bond in molecule. The cytotoxic properties of isobornylphenols (the concentration is 100 M) are predominantly due to the molecule structure. The interrelation between the aggregate size of the main fraction of L in the presence of the studied compounds and the discocyte share during mice blood erythrocyte incubation in their presence for 4 h is revealed. Thus, this provides the possibility to assume that the ability of the different biological active substances to affect the lecithin aggregation in non-polar solvent could be used as a model system for the initial assessment of their surface active properties.

The role of transboundary air pollution over Galicia and North Portugal area

In summer, high levels of ozone (O3) are frequently measured at both Galicia and Northern Portugal air quality monitoring stations, even exceeding the limit values imposed by legislation. This work aims to investigate the origin of these high O3 concentrations by the application of a chemical transport modelling system over the northwestern area of the Iberian Peninsula. The WRF-CHIMERE modelling system was applied with high resolution to simulate the selected air pollution episodes that occurred simultaneously in Galicia and North Portugal and in order to study both the contribution of local emission sources and the influence of transboundary pollution. Emission inputs have been prepared based on the development of the Portuguese and Galician emission inventories. The obtained results for O3 have been evaluated and validated against observations. Modelling results show possible contribution of the transboundary transport over the border of two neighbour regions/countries, indicating that the O3 episode starts over the urban and industrialised area of North coast of Portugal, reaching the maximum peaks over this region; at the same time, O3 levels increased over Galicia region, where lower concentrations, but still high, were observed. These results pointed out that air quality management should not be driven by political boundaries and highlight the importance of joining efforts between neighbouring countries.

GEM-AQ/EC, an on-line global multi-scale chemical weather modelling system: model development and evaluation of global aerosol climatology

Abstract. A global air quality modeling system GEM-AQ/EC was developed by implementing tropospheric chemistry and aerosol processes on-line into the Global Environmental Multiscale weather prediction model – GEM. Due to the multi-scale features of the GEM, the integrated model, GEM-AQ/EC, is able to investigate chemical weather at scales from global to urban domains. The current chemical mechanism is comprised of 50 gas-phase species, 116 chemical and 19 photolysis reactions, and is complemented by a sectional aerosol module CAM (The Canadian Aerosol Module) with 5 aerosols types: sulphate, black carbon, organic carbon, sea-salt and soil dust. Monthly emission inventories of black carbon and organic carbon from boreal and temperate vegetation fires were assembled using the most reliable areas burned datasets by countries, from statistical databases and derived from remote sensing products of 1995–2004. The model was run for ten years from from 1995–2004 with re-analyzed meteorology on a global uniform 1° × 1° horizontal resolution domain and 28 hybrid levels extending up to 10 hPa. The simulating results were compared with various observations including surface network around the globe and satellite data. Regional features of global aerosols are reasonably captured including emission, surface concentrations and aerosol optical depth. For various types of aerosols, satisfactory correlations were achieved between modeled and observed with some degree of systematic bias possibly due to large uncertainties in the emissions used in this study. A global distribution of natural aerosol contributions to the total aerosols is obtained and compared with observations.

Chemical Radioprotection and Radiosensitization of Mammalian Cells Growingin Vitro

The radiosensitizing and radioprotective effects of various compounds have been characterized in Chinese hamster fibroblasts growing in vitro and in a model chemical system utilizing DNA as target. The contribution to the lethal action of ionizing radiation in mammalian cells from the indirect effect of OH has been measured. The data are consistent with the “oxygen fixation hypothesis,” whereby target free radicals react either with radical-reducing species, resulting in “chemical repair,” or with radical-oxidizing species, resulting in “fixation” of radical damage to a potentially lethal form. Radical repair–fixation competition has been demonstrated in the in vitro chemical system with a sensitizer other than O2.Dimethyl sulfoxide is shown to radioprotect in both the cellular and chemical systems by scavenging OH. Cysteamine, on the other hand, is shown to protect primarily by adding to the pool of radical-reducing species, resulting in enhanced repair of free-radical damage in the targets. Electron-affinic compounds are shown to radiosensitize, predominantly, by adding to the pool of radical-oxidizing species, resulting in enhanced fixation of free-radical damage in the targets. Diamide is shown to radiosensitize mammalian cells by a mechanism which is additive to that of the electron-affinic compounds. N-Ethylmaleimide shows radiosensitizing characteristics, in mammalian cells, which, in some respects, are qualitatively similar to those of Diamide. These compounds may radiosensitize cells by chemically and/or biochemically altering the pool of radical-reducing species in the vicinity of the cellular targets, resulting in enhanced fixation of radical damage in the targets by endogenous radical-oxidizing species. The oxygen enhancement ratio for hamster cells is shown to depend upon the intracellular target environment, and can be made to vary between near 1 and 3.3.

Post-Trapping Derivatization of Radical-Derived EPR-Silent Adducts: Application to Free Radical Detection by HPLC/UV in Chemical, Biochemical, and Biological Systems and Comparison with EPR Spectroscopy

Free radicals are conventionally detected by electron paramagnetic resonance (EPR) spectroscopy after being trapped as spin adducts. Albeit this technique has demonstrated utmost efficacy in studying free radicals, its application to biological settings is intrinsically hampered by the inevitable bioreduction of radical-derived paramagnetic adducts. Herein, we describe a reliable technique to detect and quantify free radical metabolites, wherein reduced alkyl- and phenyl-5,5-dimethyl-1-pyrroline N-oxide (DMPO) adducts are converted into ultrastable N-naphthoate esters. To mimic the ubiquitous in vivo microenvironment, bioreductants, exogenous thiols, and sodium borohydride were studied. Nitroxyl reduction was confirmed using EPR and triphenyltetrazolium chloride. The formation of the N-naphthoyloxy derivatives was established by liquid chromatography/mass spectrometry (LC/MS). The derivatives were chromatographed using a binary eluent. HPLC and internal standards were synthesized using Grignard addition. The labeled DMPO adduct is (1) fluorescent, (2) stable as opposed to nitroxyl radical adducts, (3) biologically relevant, and (4) excellently chromatographed. Applications encompassed chemical, biochemical, and biological model systems generating C-centered radicals. Different levels of phenyl radicals produced in situ from whole blood were successfully determined. The method is readily applicable to the detection of hydroxyl radical. Analogously, DMPO, the spin trap, could be detected with extreme sensitivity suitable for in vivo applications. The developed method proved to be a viable alternative to EPR, where for the first time the reductive loss of paramagnetic signals of DMPO-trapped free radicals is transformed into fluorescence emission. We believe the proposed methodology could represent a valuable tool to probe free radical metabolites in vivo using DMPO, the least toxic spin trap.