A stochastic model for chemical kinetics.
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Kinetics↗
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Chemical kinetic modeling study of the effects of oxygenated hydrocarbons on soot emissions from diesel engines.
A detailed chemical kinetic modeling approach is used to examine the phenomenon of suppression of sooting in diesel engines by the addition of oxygenated hydrocarbon species to the fuel. This suppression, which has been observed experimentally for a few years, is explained kinetically as a reduction in concentrations of soot precursors present in the hot products of a fuel-rich diesel ignition zone when oxygenates are included. The kinetic model is also used to show how different oxygenates, ester structures in particular, can have different soot-suppression efficiencies due to differences in the molecular structure of the oxygenated species.
Journal Article↗
Quantum chemical calculations of model systems for ascorbic acid adducts with Schiff bases of lysine side chains: possibility of internal charge transfer in proteins.
Ab initio self-consistent field calculations for neutral and cationic ascorbic acid and model compounds have been performed. Furthermore, the bicyclic addition products of alpha-hydroxytetronic acid with methylglyoxal and with the Schiff base formed between methylglyoxal and methylamine have been calculated, again in their neutral and cationic forms, respectively. The results indicate that the investigated cations can act as strong electron acceptors. With the help of space-filling molecular models it has been demonstrated that such conformations of the Schiff base formed between the primary amino group of lysine side chains in proteins and the ascorbic acid methylglyoxal acetal are possible in which the lactone carbonyl group comes near to the N atoms of the peptide groups, so that charge can be transferred between these subunits.
Ascorbic Acid↗
An extension of ASM2d including pH calculation.
This paper presents an extension of the Activated Sludge Model No. 2d (ASM2d) including a chemical model able to calculate the pH value in biological processes. The developed chemical model incorporates the complete set of chemical species affecting the pH value to ASM2d describing non-equilibrium biochemical processes. It considers the system formed by one aqueous phase, in which biochemical processes take place, and one gaseous phase, and is based on the assumptions of instantaneous chemical equilibrium under liquid phase and kinetically governed mass transport between the liquid and gas phase. The ASM2d enlargement comprises the addition of every component affecting the pH value and an ion-balance for the calculation of the pH value and the dissociation species. The significant pH variations observed in a sequencing batch reactor operated for enhanced biological phosphorus removal were used to verify the capability of the extended model for predicting the dynamics of pH jointly with concentrations of acetic acid and phosphate. A pH inhibition function for polyphosphate accumulating bacteria has also been included in the model to simulate the behaviour observed. Experimental data obtained in four different experiments (with different sludge retention time and influent phosphorus concentrations) were accurately reproduced.
Bioreactors↗
A theoretical study of 31P NMR chemical shielding models for concentrated phosphoric acid solution.
Calculations on the hydrates, dimer, and trimer of phosphoric acid were carried out in an effort to obtain a viable model of the phosphorus NMR chemical shielding in 85% phosphoric acid solution. The theoretical approaches used the gauge-including-atomic-orbital (GIAO) 6-311+G(nd,p) basis set at both scaled density functional theory (sB3LYP) and estimated infinite order Møller-Plesset (EMPI) approaches and with the aug-cc-pvtz basis in the sB3LYP approach. Shieldings and hydrogen bonding stabilization energies are similar in the three approaches and indicate that the faster sB3LYP/6-311+G(nd,p) approach can be used with larger systems. The changes in shielding compared to the isolated species are small and suggest that the undissociated acid dihydrate could serve as a model entity for modeling the phosphorus shielding in concentrated phosphoric acid solution.
Journal Article↗
A connection rule for alpha-carbon coarse-grained elastic network models using chemical bond information.
A sparser but more efficient connection rule (called a bond-cutoff method) for a simplified alpha-carbon coarse-grained elastic network model is presented. One of conventional connection rules for elastic network models is the distance-cutoff method, where virtual springs connect an alpha-carbon with all neighbor alpha-carbons within predefined distance-cutoff value. However, though the maximum interaction distance between alpha-carbons is reported as 7 angstroms, this cutoff value can make the elastic network unstable in many cases of protein structures. Thus, a larger cutoff value (>11 angstroms) is often used to establish a stable elastic network model in previous researches. To overcome this problem, a connection rule for backbone model is proposed, which satisfies the minimum condition to stabilize an elastic network. Based on the backbone connections, each type of chemical interactions is considered and added to the elastic network model: disulfide bonds, hydrogen bonds, and salt-bridges. In addition, the van der Waals forces between alpha-carbons are modeled by using the distance-cutoff method. With the proposed connection rule, one can make an elastic network model with less than 7 angstroms distance cutoff, which can reveal protein flexibility more sharply. Moreover, the normal modes from the new elastic network model can reflect conformational changes of a given protein better than ones by the distance-cutoff method. This method can save the computational cost when calculating normal modes of a given protein structure, because it can reduce the total number of connections. As a validation, six example proteins are tested. Computational times and the overlap values between the conformational change and infinitesimal motion calculated by normal mode analysis are presented. Those animations are also available at UMass Morph Server (http://biomechanics.ecs.umass.edu/umms.html).
Carbon↗
Electron transfer in natural and unnatural flavoporphyrins.
The development of chemical models for enzymes and their chemical and physical studies constitutes an important area of research from a scientific as well as an industrial point of view. Covalently linked flavin and porphyrin (flavoporphyrins) have attracted attention due to their applications as chemical models for flavoproteins and related enzymes. In this review, the literature has been surveyed to provide a comprehensive coverage of the synthetic methodology and characterization techniques of various types of synthetic flavoporphyrins.
Amides↗
The emergence of collective vibrations in cluster models: quantum chemical study of the methyl-terminated Si(111) surface.
In this paper we present structures and harmonic vibrational frequencies for the methylated silicon (111) surface from quantum chemical calculations using both cluster models and periodic boundary conditions. The results from both calculations are in very good agreement with experimentally determined frequencies. We demonstrate that relatively small cluster models already show the emergence of collective vibrational modes and provide a general method for the assignment of vibrational frequencies for extended surfaces from cluster models. Finally, we discuss a vibrational mode that results from the coupling between near-surface phonons and the silicon-carbon bending modes.
Journal Article↗
Time-dependent retardation model for chemical oxygen demand removal in a subsurface-flow constructed wetland for winery wastewater treatment.
The relative success of chemical oxygen demand (COD) removal models to describe measured rates of COD removal in a pilot-scale constructed wetland designed for treatment of high-strength winery wastewater are evaluated using retention times determined from tracer studies. Not surprisingly, two-parameter residual and retardation models better fit the measured removal data than single-parameter, first-order decay models for wastewater at average COD loadings up to nearly 5000 mg/L. The residual and retardation models yielded nearly equivalent fits to the measured data. However, the retardation model had more consistent parameters for COD removal data across different depth levels in the constructed wetland and at different loadings, and a slightly smaller sum of least-squared errors. The retardation model seems to be appropriate for constructed wetland design because it allows a steady decrease in COD with increased treatment time rather than a constant residual COD (C*) value. From the least-squares optimization procedure used to estimate model parameters (a volumetric rate constant, Kv, range of 3 to 12 d(-1)), nonrealistic, or physically meaningless, large C* values (C* range of 23 to 450 mg COD/L) that were dependent on COD loading were obtained, potentially underestimating the constructed wetland system's actual winery wastewater treatment potential. The optimal parameters for the retardation model applied to the pilot-scale constructed wetland ranged from 9 to 12 d(-1) for the initial degradation rate constant, Ko, and 2 to 5 d(-1) for the time-based retardation coefficient, b. These values should be verified for full-scale field systems based on field measurements currently underway.
Algorithms↗
Selenium prevents tumor development in a rat model for chemical carcinogenesis.
Previous studies in animals and humans have shown that selenium compounds can prevent cancer development. In this work we studied the tumor preventive effect of selenium supplementation, administrated as selenite, in the initiation, promotion and progression phases in a synchronized rat model for chemically induced hepatocarcinogenesis, the resistant hepatocyte model. Selenite in supra-nutritional but subtoxic doses (1 and 5 p.p.m.) was administrated to the animals through the drinking water. Such supplementation during the initiation phase did not have a tumor preventive effect. However, selenite treatment during the promotion phase decreased the volume fraction of pre-neoplastic liver nodules from 38% in control animals to 25 (1 p.p.m.) and 14% (5 p.p.m.) in the selenite-supplemented groups. In addition the cell proliferation within the nodules decreased from 42% in the control to 22 (1 p.p.m.) and 17% (5 p.p.m.). Immunohistochemical staining for the selenoenzyme thioredoxin reductase 1 revealed an increased expression of the enzyme in liver nodules compared with the surrounding tissue. The activity was reduced to 50% in liver homogenates from selenium-treated animals but the activity of the selenoenzyme glutathione peroxidase was essentially unaltered. Selenite treatment (5 p.p.m.) during the progression phase resulted in a significantly lower volume fraction of liver tumors (14 compared with 26%) along with a decrease in cell proliferation within the tumors (34 compared with 63%). Taken together our data indicate that the carcinogenetic process may be prevented by selenium supplementation both during the promotion and the progression phase.
Animals↗
Analysis of an algae-based CELSS. Part 1: model development.
A steady state chemical model and computer program have been developed for a life support system and applied to trade-off studies. The model is based on human demand for food and oxygen determined from crew metabolic needs. The model includes modules for water recycle, waste treatment, CO2 removal and treatment, and food production. The computer program calculates rates of use and material balance for food. O2, the recycle of human waste and trash, H2O, N2, and food production supply. A simple non-iterative solution for the model has been developed using the steady state rate equations for the chemical reactions. The model and program have been used in system sizing and subsystem trade-off studies of a partially closed life support system.
Ammonia↗
An alternative perspective: a critical evaluation of the Waddell threshold extrapolation model in chemical carcinogenesis.
In a recent Perspective article (Toxicologic Pathology 31: 260-262, 2003) Waddell asserts that he has developed a log linear extrapolation model that can demonstrate a threshold and resolve for once and for all the uncertainies associated with low dose cancer risk extrapolation. However, his method essentially forces, rather than demonstrates, a threshold, and has many serious flaws that result in significant under-estimation of low dose risk. It would be a serious mistake for the scientific community to adopt Waddell's log linear extrapolation model for chemical carcinogenesis risk assessment.
Animals↗
Modular chemical mechanism predicts spatiotemporal dynamics of initiation in the complex network of hemostasis.
This article demonstrates that a simple chemical model system, built by using a modular approach, may be used to predict the spatiotemporal dynamics of initiation of blood clotting in the complex network of hemostasis. Microfluidics was used to create in vitro environments that expose both the complex network and the model system to surfaces patterned with patches presenting clotting stimuli. Both systems displayed a threshold response, with clotting initiating only on isolated patches larger than a threshold size. The magnitude of the threshold patch size for both systems was described by the Damköhler number, measuring competition of reaction and diffusion. Reaction produces activators at the patch, and diffusion removes activators from the patch. The chemical model made additional predictions that were validated experimentally with human blood plasma. These experiments show that blood can be exposed to significant amounts of clot-inducing stimuli, such as tissue factor, without initiating clotting. Overall, these results demonstrate that such chemical model systems, implemented with microfluidics, may be used to predict spatiotemporal dynamics of complex biochemical networks.
Blood Coagulation↗
The analgesic effect profile of FR122047, a selective cyclooxygenase-1 inhibitor, in chemical nociceptive models.
The pharmacological profile of the analgesic agent, 1-[(4, 5-bis(4-methoxyphenyl)-2-thiazoyl)carbonyl]-4-methylpiperazine hydrochloride (FR122047), was investigated. In recombinant human cyclooxygenase enzyme assays, the inhibition of prostaglandin E(2) formation by FR122047 was 2300 times more selective for cyclooxygenase-1 than cyclooxygenase-2. Oral administration of FR122047 (3.2-100 mg/kg) dose dependently reduced the phase 2 response (10-60 min) of the formalin test in rats. This effect was 3 times less potent than that of indomethacin. FR122047 (1-32 mg/kg; p. o.) showed a dose-dependent analgesic effect against the acetic acid-induced writhing response in mice. Furthermore, FR122047 (0. 01-10 mg/kg, p.o.) inhibited the increase in 6-keto prostaglandin F(1alpha) level in acetic acid-injected mouse peritoneal cavity. However, a selective cyclooxygenase-2 inhibitor, NS-398, had no effect in these cyclooxygenase-1 sensitive pain models. These results suggest that FR122047, a selective cyclooxygenase-1 inhibitor, shows an analgesic effect in chemical nociceptive models and may be a useful analgesic agent.
Acetic Acid↗
Screening level risk assessment model for chemical fate and effects in the environment.
A screening level risk assessment model is developed and described to assess and prioritize chemicals by estimating environmental fate and transport, bioaccumulation, and exposure to humans and wildlife for a unit emission rate. The most sensitive risk endpoint is identified and a critical emission rate is then calculated as a result of that endpoint being reached. Finally, this estimated critical emission rate is compared with the estimated actual emission rate as a risk assessment factor. This "back-tracking" process avoids the use of highly uncertain emission rate data as model input. The application of the model is demonstrated in detail for three diverse chemicals and in less detail for a group of 70 chemicals drawn from the Canadian Domestic Substances List. The simple Level II and the more complex Level III fate calculations are used to "bin" substances into categories of similar probable risk. The essential role of the model is to synthesize information on chemical and environmental properties within a consistent mass balance framework to yield an overall estimate of screening level risk with respect to the defined endpoint. The approach may be useful to identify and prioritize those chemicals of commerce that are of greatest potential concern and require more comprehensive modeling and monitoring evaluations in actual regional environments and food webs.
Animals↗
Evaluation of the immunogenicity of polymerized hemoglobin solutions in a rabbit model.
Chemical modification of proteins carries the risk that neo-antigens are introduced. To investigate the potential immunogenicity of human glutaraldehyde-polymerized hemoglobin (polyHbX1), we analyzed the antibody responses of rabbits after hyperimmunization with complete Freund's adjuvant. In view of the species difference, we also tested rabbit hemoglobin that was modified in the same way as human polyHbX1. Thereafter, we studied the antibody response after weekly intravenous infusion of clinically relevant doses of polyHbX1 to evaluate whether an immune response is likely to occur when modified hemoglobin is used as blood substitute. The occurrence of an antibody response was tested by using an enzyme immunoassay (ELISA). To find out whether antibodies were directed against neo-epitopes on human polyHbX1 we used a competitive ELISA. The results showed that polymerized hemoglobin may weakly activate the immune system in special conditions, but is unlikely to do so when it is used as blood substitute.
Animals↗
Bis(bioreductive) alkylating agents: synthesis and biological activity in a nude mouse human carcinoma model.
Chemical investigations leading to the construction of bis(bioreductive) alkylating agents having both conformationally restricted and mobile spacer regions are described. Two targets having the conformationally mobile ethylene spacer group, namely, 2,2'-ethylenebis[6-(hydroxymethyl)-p-benzoquinone] diacetate (3b) and 2,2'-ethylenebis[6-(bromomethyl)-p-benzoquinone] (3c), were studied in vivo and in vitro using an established epithelial/Burkitt lymphoma hybrid cell line (D98/HR1) previously shown to induce carcinomas in nude mice. Inactivity of both test compounds in vitro, the relative resistance of these cells to test drugs in vitro, and the selective antitumor properties of the bis(bromomethyl) analogue in vivo lead to the proposal that this compound undergoes bioreduction to an alkylating species in the hypoxic core of the tumor, thereby exerting its action.
Animals↗
Thrombolytic and pharmacokinetic properties of a conjugate of recombinant single-chain urokinase-type plasminogen activator with a monoclonal antibody specific for cross-linked fibrin in a baboon venous thrombosis model.
Chemical conjugates between recombinant single-chain urokinase-type plasminogen activator (rscu-PA) and a murine monoclonal antibody directed against fragment D-dimer of cross-linked human fibrin (MA-15C5), rscu-PA/MA-15C5, and between rscu-PA and a control monoclonal antibody (MA-1C8), rscu-PA/MA-1C8, were produced by cross-linking with N-succinimidyl 3-(2-pyridyldithio) propionate (SPDP). In an in vitro system composed of a [125 I]fibrin-labeled baboon plasma clot immersed in autologous citrated plasma, dose- and time-dependent lysis was obtained with a ratio of the potencies of free and conjugated rscu-PA similar to that in human plasma: 50% lysis in 2 hours required 4.3 micrograms/ml rscu-PA, 1.0 microgram/ml urokinase-type plasminogen activator (u-PA) equivalent rscu-PA/MA-15C5, or 15 micrograms/ml u-PA equivalent rscu-PA/MA-1C8. The thrombolytic and pharmacokinetic properties of rscu-PA and of rscu-PA/MA-15C5 were compared in baboons with a 0.8-1.0 ml [125 I]fibrin-labeled autologous blood clot produced in a femoral vein. Continuous intravenous infusion of these compounds during a 2-hour period resulted in dose- and time-dependent lysis. The thrombolytic potency of rscu-PA/MA-15C5 was 3.0 +/- 0.5 times higher (50% lysis with 0.3 +/- 0.02 mg u-PA equivalent/kg body wt) than that of rscu-PA measured by ex vivo isotope recovery from the femoral vein segment (p less than 0.001) and was 2.7 +/- 0.5 times higher (50% lysis with 0.35 +/- 0.02 mg/kg rscu-PA/MA-15C5) by external radioisotope counting (p less than 0.001). A dose of 0.5 mg/kg of rscu-PA/MA-1C8 was much less active than rscu-PA. After the end of the infusion, u-PA-related antigen disappeared from plasma in a biphasic manner with an initial half-time of 2.7 +/- 0.5 for rscu-PA, 24 +/- 1.2 for rscu-PA/MA-15C5, and 21 +/- 0.5 minutes for rscu-PA/MA-1C8 with corresponding plasma clearances of 340 +/- 40, 20 +/- 3, and 24 +/- 2 ml/min, respectively. In conclusion, the increased thrombolytic potency of rscu-PA/MA-15C5 is the result of a reduction of the thrombolytic potency due to coupling of rscu-PA to the antibody molecule, which is counter-balanced by an enhancement of the thrombolytic potency due to fibrin targeting by the specific idiotype.
Animals↗