[Chemical structural model of acetylcholine release through electrical impulse].
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Acetylcholine↗
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Activated enzyme catalysis as a possible realization of the stable linear chemical oscillator model.
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Catalysis↗
The chemical dynamics of mutagenesis and carcinogenesis. I. A chemical-kinetic model of dose-response relationships.
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Alkylation↗
Chemical kinetic modeling of de novo synthesis of PCDD/F in municipal waste incinerators.
A kinetic model is developed for de novo synthesis of PCDD/F from carbon in incinerator fly ash. The main mechanistic steps considered in the model are carbon gasification, PCDD/F formation, desorption and degradation. Rate equations are derived which can relate PCDD/F formation with process variables including carbon concentration of fly ash, partial pressure of oxygen, reaction temperature and time. The kinetic model has been verified using laboratory de novo synthesis data reported in the literature. When the model is applied to industrial incinerator conditions, PCDD/F formation levels of 0.1-0.5 microg/N m3 in the gas phase and 0.1-1.2 microg/g in the solid phase are calculated, and both are in good agreement with incinerator measurements.
Benzofurans↗
Chemical kinetic modelling of PCDD formation from chlorophenol catalysed by incinerator fly ash.
A kinetic model is developed for PCDD formation from chlorophenol catalysed by incinerator fly ash. The key step in the model is a Langmuir-Hinshelwood type elementary step for the coupling of two adsorbed chlorophenol species to PCDD. Kinetic expression is derived which can relate PCDD formation rates with process variables including temperature, precursor concentration, fly ash loading and number of active sites in fly ash. Calculated PCDD formation rates based on this kinetic model are in good agreement with laboratory measurements reported in the literature. When the model is applied to industrial incinerator conditions, at maximum a PCDD yield of 10(-3) microg/N m3 is calculated.
Air Pollution↗
Comparison of rac- and meso-2,3-dimercaptosuccinic acids for chelation of mercury and cadmium using chemical speciation models.
The formation constants of various mercury and cadmium chelates of the stereoisomers of 2,3-dimercaptosuccinic acid (DMSA) have been determined from potentiometric titrations in the presence of the competing ligand EDTA. The mercury chelates formed at pH 7.4 are the monomeric HgL of the DMSA diastereoisomers and HHgL2 of rac-DMSA. Mercury is completely complexes at pH greater than 3.0 in solutions containing more than 1 equiv of either rac- or meso-DMSA. At high concentrations (10 microM and above) mercury tends to bind to a greater extent to rac- than to meso-DMSA. At pH 7.4, the predominant cadmium meso-DMSA chelate species in solution is CdL, and HCdL is present at a much smaller concentration. With rac-DMSA, however, the predominant cadmium chelate species is HCdL at a low concentration of the ligand, and at a high concentration of the ligand the species CdL2 predominates. Cadmium is completely chelated at pH 7.4 in solutions containing more than 1 equiv of either rac- or meso-DMSA. At pH around 5.5, which corresponds to the pH of the kidney, however, a significant amount of free cadmium is present in solutions containing 1 equiv or less of either DMSA stereoisomer. From the results of an analysis of speciation models, probable kidney damage, that may result from free cadmium ion release in the kidney during chelation therapy, is inferred when meso-DMSA is used for mobilizing cadmium. In contrast, the release of free cadmium ion is negligible in the pH range in the kidney when rac-DMSA is used. On the basis of the speciation models, rac-DMSA is found to be far superior to meso-DMSA in the treatment of acute cadmium poisoning.
Cadmium↗
An information-theory model of cellular survival, mutation and transformation and the relevance of this model to chemical carcinogenesis.
A model of cellular survival, mutation and transformation is presented in accordance with information theory. A cellular system is considered to be stable with respect to its environment when the vital information the cell expresses at least equals the information requirements of the environment. Environmental agents, such as mutagens, perturb the cell's expression of information such that an imbalance occurs between the cell's information requirement and the cell's ability to express vital information. This imbalance, which is interpreted as the intrinsic entropy of the cell, serves as a measure of biological cell death. If the cell compensates for the altered ability to express information by adapting to a less restricted set of information requirements, then one may view the cell as having undergone a "transformation" to a less restricted phenotype. This paper will elucidate the mathematical inter-relationships of cellular survival, mutation and transformation and will relate these mathematical concepts to chemical carcinogenesis.
Animals↗
The Iowa therapeutic community model of chemical dependency treatment.
A model of inpatient chemical dependency treatment used in several facilities in Iowa is described. Through combining 12 Step, Therapeutic Community and Reality Therapy concepts, the issues of denial, control, and self centeredness are addressed in developmental phases. Individualizing the program through multidisciplinary input is explained in terms of identifying hindrances in perceiving reality and assisting the patients reduce resistance in a downhill process of increasing wholeness and growth.
Adult↗
Chemical leasing: cooperative business models for sustainable chemicals management. Summary of research projects commissioned by the Austrian Federal Ministry of Agriculture, Forestry, Environment and Water Management.
BACKGROUND, AIM AND SCOPE: Chemicals play a vital role in the day-to-day life of industrialised societies. Their use is not restricted to the chemical enterprises per se, but is a crucial part of production processes in a lot of industrial sectors. Traditional instruments of environmental policy (such as bans, restrictions) can only deal with the most hazardous substances. The Johannesburg Implementation Plan of 2002 calls for more sustainable patterns of production and consumption, and sets the year of 2020 as a goal to use chemicals in a way that human health and the environment are not endangered. Political instruments should not only gather more knowledge about the properties of chemicals, but should also stimulate the environmentally sound use of chemicals. Existing business models should therefore be reviewed in relation to this strategic approach to encourage marketing options with respect to the environmental focus. MAIN FEATURES: Business models were examined for their effects on the consumption of chemicals and amount of waste emissions in relation to their economic potential. Different possibilities for cooperation of supplier, user and disposal companies were elaborated and examined with a view to the specific situation in Austria. RESULTS AND DISCUSSION: A range of cooperative models--summarised under the term 'chemical leasing'--was identified, which can contribute to a more efficient use of resources. 12 main possible application areas (cleaning, lubrication, paint stripping and others) have been identified in Austria. If chemical leasing models were applied in these areas, the amounts of chemicals currently used could be reduced by one third (53,000 tonnes per year). Cost reductions of up to 15% can be expected. CONCLUSION: The application of chemical leasing models can contribute considerably to achieving more sustainable and resource-efficient patterns of production. The Austrian Ministry for Environment has therefore decided to subsidise the further practical implementation of these new service-oriented business models. Pilot projects in 4 enterprises, which are supervised by consulting companies, are currently being carried out. RECOMMENDATION AND OUTLOOK: The experiences of the pilot projects will serve as valuable building blocks for the wider use of chemical leasing models. Furthermore, the UNIDO Cleaner Production Centres have expressed their clear interest and will examine the possibility to use chemical leasing as a part of their Cleaner Production Programmes.
Austria↗
ORCHESTRA: an object-oriented framework for implementing chemical equilibrium models.
This work presents a new object-oriented structure for chemical equilibrium calculations that is used in the modeling framework ORCHESTRA (Objects Representing CHEmical Speciation and TRAnsport). In contrast to standard chemical equilibrium algorithms, such as MINEQL, MINTEQ2A, PHREEQC, and ECOSAT, model equations are not hard-coded in the source code, but instead all equations are defined in text format and read by the ORCHESTRA calculation kernel at run time. This makes model definitions easily accessible and extendible by users. Furthermore, it results in a very compact and efficient calculation kernel that is easy to use as a submodel within mass transport or kinetic models. Finally, the object-oriented structure of the chemical model definitions makes it possible to implement a new object-oriented framework for implementing chemical models. This framework consists of three basic object types, entities, reactions, and phases, that form the building blocks from which other chemical models are composed. The hierarchical approach ensures consistent and compact model definitions and is illustrated here by discussing the implementation of a number of commonly used chemical models such as aqueous complexation, activity correction, precipitation, surface complexation ion exchange, and several more sophisticated adsorption models including electrostatic interactions, NICA, and CD-MUSIC. The ORCHESTRA framework is electronically available from www.macaulay.ac.uk/ORCHESTRA.
Adsorption↗
Morphological and carbogen-based functional MRI of a chemically induced liver tumor model in mice.
A multifocal mouse liver tumor model chemically induced with 5,9-dimethyl-7H-dibenzo[c,g]carbazole was investigated by respiratory-triggered morphological and functional MRI (fMRI) at 4.7 Tesla. The model is characterized by the presence of two tumor types: hypovascular cholangioma and vascularized hepatocellular carcinoma (HCC). Growth curves measured by 3D-MRI showed limited growth of cholangiomas and rapid growth of HCCs after a latency of about 25 weeks. Functional imaging based on T(2) (*)-weighted fast gradient-echo MRI and carbogen breathing was optimized for liver imaging in mice. A response to carbogen was observed in HCCs but not in cholangiomas. Transversal analysis (50 HCCs) of signal change upon carbogen revealed four different types of response patterns: 1) signal increase upon carbogen administration (74%); 2) small or insignificant signal change (10%), 3) transient signal decrease and delayed increase (8%), and 4) signal decrease (8%). Longitudinal follow-up of a subgroup (N = 17) showed that an initially observed type 1 response, attesting to the presence of a functional vasculature, remained stable for at least 3 weeks in 14 HCCs. A switch from a type 1 response to another response type may be useful for demonstrating, in a noninvasive manner, a disturbance of tumor vasculature induced by anti-vascular or anti-angiogenic therapy.
Animals↗
A quantum chemical study of the mechanism of action of Vitamin K epoxide reductase (VKOR) II. Transition states.
A reaction path including transition states is generated for the Silverman mechanism [R.B. Silverman, Chemical model studies for the mechanism of Vitamin K epoxide reductase, J. Am. Chem. Soc. 103 (1981) 5939-5941] of action for Vitamin K epoxide reductase (VKOR) using quantum mechanical methods (B3LYP/6-311G**). VKOR, an essential enzyme in mammalian systems, acts to convert Vitamin K epoxide, formed by Vitamin K carboxylase, to its (initial) quinone form for cellular reuse. This study elaborates on a prior work that focused on the thermodynamics of VKOR [D.W. Deerfield II, C.H. Davis, T. Wymore, D.W. Stafford, L.G. Pedersen, Int. J. Quant. Chem. 106 (2006) 2944-2952]. The geometries of proposed model intermediates and transition states in the mechanism are energy optimized. We find that once a key disulfide bond is broken, the reaction proceeds largely downhill. An important step in the conversion of the epoxide back to the quinone form involves initial protonation of the epoxide oxygen. We find that the source of this proton is likely a free mercapto group rather than a water molecule. The results are consistent with the current view that the widely used drug Warfarin likely acts by blocking binding of Vitamin K at the VKOR active site and thereby effectively blocking the initiating step. These results will be useful for designing more complete QM/MM studies of the enzymatic pathway once three-dimensional structural data is determined and available for VKOR.
Epoxy Compounds↗
Methodological approach towards the definition of new storage conditions for inert wastes.
In 1997, the French Ministry of Environment launched studies aiming to define a specific regulation concerning inert waste disposal in order to limit potential impact of such facilities on the environment by fixing minimum requirements. A model (chemical model/hydrodynamic model) was developed to determine dumping conditions. This model was then applied on two defined scenarios (landfill surface, effective rainfalls...) in order to study the sulphate concentrations in aquifer system immediately downstream from the storage facility. Results allow us to determine in which conditions the sulphates concentrations are compatibles with the potentially drinkable character of the groundwater. They more specifically concern the nature of the waste disposed of, the efficient rainfalls and the landfill area.
Environmental Monitoring↗
Tetrahedral intermediates in thiamin diphosphate-dependent decarboxylations exist as a 1',4'-imino tautomeric form of the coenzyme, unlike the michaelis complex or the free coenzyme.
Two circular dichroism signals observed on thiamin diphosphate (ThDP)-dependent enzymes, a positive band in the 300-305 nm range and a negative one in the 320-330 nm range, were investigated on yeast pyruvate decarboxylase (YPDC) and on the E1 subunit of the Escherichia coli pyruvate dehydrogenase complex (PDHc-E1). Addition of the tetrahedral ThDP-acetaldehyde adduct, 2-alpha-hydroxyethylThDP, to PDHc-E1 generates the positive band at 300 nm, consistent with the formation of the 1',4'-iminopyrimidine tautomer, as also demonstrated for phosphonolactylthiamin diphosphate, a stable analogue of the tetrahedral ThDP-pyruvate adduct 2-alpha-lactylThDP (Jordan, F. et al. (2003) J. Am. Chem. Soc. 125, 12732-12738). Therefore, we suggest that all tetrahedral ThDP-bound covalent complexes will also prefer this tautomer, and that the 4'-aminopyrimidine of ThDP participates in multiple steps of acid-base catalysis on ThDP enzymes. Studies with YPDC and PDHc-E1, and their active center variants, in conjunction with chemical models, enabled assignment of the negative band at 330 nm to a charge-transfer transition between the 4'-aminopyrimidine tautomer (presumed electron donor) and the thiazolium ring (presumed electron acceptor) of ThDP, with no significant contributions from any amino acid side chain of the proteins. However, in both YPDC and PDHc-E1, the presence of substrate or substrate surrogate was required to enable detection, suggesting that the band at 320-330 nm be used as a reporter for the Michaelis complex, involving the amino tautomer, on both enzymes. As the positive band near 300 nm reports on the 1',4'-imino tautomer of ThDP, methods are now available for kinetic monitoring of both tautomeric forms.
Binding Sites↗
A mechanism from quantum chemical studies for methane formation in methanogenesis.
The mechanism for methane formation in methyl-coenzyme M reductase (MCR) has been investigated using the B3LYP hybrid density functional method and chemical models consisting of 107 atoms. The experimental X-ray crystal structure of the enzyme in the inactive MCR(ox1)(-)(silent) state was used to set up the initial model structure. The calculations suggest a mechanism not previously proposed, in which the most remarkable feature is the formation of an essentially free methyl radical at the transition state. The reaction cycle suggested starts from a Michaelis complex with CoB and methyl-CoM coenzymes bound and with a squareplanar coordination of the Ni(I) center in the tetrapyrrole F(430) prosthetic group. In the rate-limiting step the methyl radical is released from methyl-CoM, induced by the attack of Ni(I) on the methyl-CoM thioether sulfur. In this step, the metal center is oxidized from Ni(I) to Ni(II). The resulting methyl radical is rapidly quenched by hydrogen-atom transfer from the CoB thiol group, yielding the methane molecule and the CoB radical. The estimated activation energy is around 20 kcal/mol, which includes a significant contribution from entropy due to the formation of the free methyl. The mechanism implies an inversion of configuration at the reactive carbon. The size of the inversion barrier is used to explain the fact that CF(3)-S-CoM is an inactive substrate. Heterodisulfide CoB-S-S-CoM formation is proposed in the final step in which nickel is reduced back to Ni(I). The suggested mechanism agrees well with experimental observations.
Binding Sites↗
Insights into the reaction mechanism of soluble epoxide hydrolase from theoretical active site mutants.
Density functional theory calculations of active site mutants are used to gain insights into the reaction mechanism of the soluble epoxide hydrolases (sEHs). The quantum chemical model is based on the X-ray crystal structure of the human soluble epoxide hydrolase. The role of two conserved active site tyrosines is explored through in silico single and double mutations to phenylalanine. Full potential energy curves for hydrolysis of (1S,2S)-beta-methylstyrene oxide are presented. The results indicate that the two active site tyrosines act in concert to lower the activation barrier for the alkylation step. For the wild-type and three different tyrosine mutant models, the regioselectivity of epoxide opening is compared for the substrates (1S,2S)-beta-methylstyrene oxide and (S)-styrene oxide. An additional part of our study focuses on the importance of the catalytic histidine for the alkylation half-reaction. Different models are presented to explore the protonation state of the catalytic histidine in the alkylation step and to evaluate the possibility of an interaction between the nucleophilic aspartate and the catalytic histidine.
Alkylation↗
The absorption spectra of anisole-h8, anisole-d3 and anisole-d8. The assignment of fundamental vibrations in the S0 and the S1 states.
The REMPI spectra of anisole-h8, anisole-d3 and anisole-d8 have been measured. The assignment of the fundamental vibrations of anisole in the S(1) state is supported by quantum chemical model calculations, the isotopic shifts, the comparison with the frequencies of corresponding vibrations in other monosubstituted benzenes, especially phenol, and the overtones, combinations and progressions observed in the spectrum of anisole-h8. The frequencies of the 42 fundamental vibrations of anisole in the S(1) state are evaluated and compared with the frequencies of the corresponding vibrations in the electronic ground state. Some assignments given earlier in the literature have been revised.
Absorption↗
The rate of the reaction between C2H and C2H2 at interstellar temperatures.
The reaction between the radical C2H and the stable hydrocarbon C2H2 is one of the simplest neutral-neutral hydrocarbon reactions in chemical models of dense interstellar clouds and carbon-rich circumstellar shells. Although known to be rapid at temperatures > or = 300 K, the reaction has yet to be studied at lower temperatures. We present here ab initio calculations of the potential surface for this reaction and dynamical calculations to determine its rate at low temperature. Despite a small potential barrier in the exit channel, the calculated rate is large, showing that this reaction and, most probably, more complex analogs contribute to the formation of complex organic molecules in low-temperature sources.
Acetylene↗