Molecular orbital analysis of chemical carcinogens

Simple molecular orbital calculations are employed in searching electronic parameters which may characterize the chemical carcinogens. Using frontier orbitals, the carcinogen-DNA bond formation is described as an electron transfer from the highest occupied molecular orbital (HOMO) of DNA to the lowest unoccupied molecular orbital (LUMO) of the carcinogen. Analysis of the DNA bases units shows that the electron donation occurs preferentially at the guanine site. The calculated low LUMO energy of several carcinogens indicate correctly the electrophilic character of these compounds. The difference between the carcinogen and the ultimate carcinogen is analyzed. Epoxides, free radicals, alkylating agents, and other metabolite forms are studied. A reasonable correlation is found between the LUMO energy and the carcinogenic function. © 1997 John Wiley & Sons, Inc.     

Global dynamic optimization for parameter estimation in chemical kinetics

We present the first method guaranteed to find the best possible least-squares (chi2) fit of experimental data by a nonlinear kinetic model. Several important advantages of knowing with certainty the best possible fit rather than a locally optimum fit are discussed and demonstrated using data from the recent literature. This is particularly important when the model and the data appear to be inconsistent. With the new method, one can rigorously demonstrate that a nonlinear kinetic model with several adjustable rate parameters is inconsistent with measured experimental data. The numerical method presented is a valuable tool in evaluating the validity of a complex kinetics model.     

A bootstrap estimation scheme for chemical compositional data with nondetects

The bootstrap method is commonly used to estimate the distribution of estimators and their associated uncertainty when explicit analytic expressions are not available or are difficult to obtain. It has been widely applied in environmental and geochemical studies, where the data generated often represent parts of whole, typically chemical concentrations. This kind of constrained data is generically called compositional data, and they require specialised statistical methods to properly account for their particular covariance structure. On the other hand, it is not unusual in practice that those data contain labels denoting nondetects, that is, concentrations falling below detection limits. Nondetects impede the implementation of the bootstrap and represent an additional source of uncertainty that must be taken into account. In this work, a bootstrap scheme is devised that handles nondetects by adding an imputation step within the resampling process and conveniently propagates their associated uncertainly. In doing so, it considers the constrained relationships between chemical concentrations originated from their compositional nature. Bootstrap estimates using a range of imputation methods, including new stochastic proposals, are compared across scenarios of increasing difficulty. They are formulated to meet compositional principles following the log‐ratio approach, and an adjustment is introduced in the multivariate case to deal with nonclosed samples. Results suggest that nondetect bootstrap based on model‐based imputation is generally preferable. A robust approach based on isometric log‐ratio transformations appears to be particularly suited in this context. Computer routines in the R statistical programming language are provided. Copyright © 2014 John Wiley & Sons, Ltd.     

Scanning electron microscopy of differentiated liver cells transformed in vitro by chemical carcinogens

A scanning electron microscopy study was carried out on differentiated liver cells transformed in vitro by three chemical carcinogens into cells that give rise to carcinomas. The results indicate that the transformed cells grow as a rule in tightly adherent monolayers but differ in topography. There is a tendency toward heterogeneity in cell shape compared to the normal and on the whole toward a larger number of surface microvilli in the malignant cell population. However, both in sparse and confluent cultures the topographic differences are often not striking enough to unequivocally distinguish single neoplastic cells from the normal.     

Metabolic activation of chemical carcinogens and binding of metabolites with nucleic acid bases

A free radical was produced enzymatically by incubating benzo(a)pyrene with liver microsomes. This radical, identified as the 6-oxybenzo(a) pyrene radical, was sufficiently reactive to bind covalently with nucleic acid bases. Similar reactive free radicals were produced enzymatically from anthanthrene and 10-aza-benzo(a)pyrene, which are carcinogenic in spite of lacking so-called “bay regions.” Hepatocarcinogens such as 3′-methyl-4-dimethylaminoazobenzene and related compounds, naphthylamines, and 2-acetylaminofluorene yield free radicals after being incubated with liver microsomes. Thus, various kinds of chemical carcinogens are found to be converted to free radicals, suggesting causal significance for the formation of free radicals in chemical carcinogenesis.     

Treatment of uncorrected measurement bias in uncertainty estimation for chemical measurements

Consistent treatment of measurement bias, including the question of whether or not to correct for bias, is essential for the comparability of measurement results. The case for correcting for bias is discussed, and it is shown that instances in which bias is known or suspected, but in which a specific correction cannot be justified, are comparatively common. The ISO Guide to the Expression of Uncertainty in Measurement does not provide well for this situation. It is concluded that there is a need for guidance on handling cases of uncorrected bias. Several different published approaches to the treatment of uncorrected bias and its uncertainty are critically reviewed with regard to coverage probability and simplicity of execution. On the basis of current studies, and taking into account testing laboratory needs for a simple and consistent approach with a symmetric uncertainty interval, we conclude that for most cases with large degrees of freedom, linear addition of a bias term adjusted for exact coverage ("U(e)") as described by Synek is to be preferred. This approach does, however, become more complex if degrees of freedom are low. For modest bias and low degrees of freedom, summation of bias, bias uncertainty and observed value uncertainty in quadrature ("RSSu") provides a similar interval and is simpler to adapt to reduced degrees of freedom, at the cost of a more restricted range of application if accurate coverage is desired.     

A computer program for the automatic estimation of H NMR chemical shifts

A computer program has been developed for predicting ¹H NMR chemical shifts. It automatically finds the various substructures of a given molecule for which additivity rules are available. Several strategies have been used to widen the range of applicability. with 200 test compounds, over 90% of the assigned chemical shifts of protons bonded to a carbon atom could be predicted. The mean deviation between observed and predicted values was 0.08 ppm with a standard deviation of 0.19ppm.     

A wet chemical method for the estimation of carbon in uranium carbides

A wet chemical method for the estimation of carbon in uranium carbides has been developed, based on oxidation with a saturated solution of sodium dichromate in 9M sulphuric acid, absorption of the evolved carbon dioxide in a known excess of barium hydroxide solution, and titration of the excess of barium hydroxide with standard potassium hydrogen phthalate solution. The carbon content obtained is in good agreement with that obtained by combustion and titration.     

Electrochemical methods for monitoring of environmental carcinogens

The use of modern electroanalytical techniques, namely differential pulse polarography, differential pulse voltammetry on hanging mercury drop electrode or carbon paste electrode, adsorptive stripping voltammetry and high performance liquid chromatography with electrochemical detection for the determination of trace amounts of carcinogenic N-nitroso compounds, azo compounds, heterocyclic compounds, nitrated polycyclic aromatic hydrocarbons and aromatic and heterocyclic amines is discussed. Scope and limitations of these methods are described and some practical applications based on their combination with liquid-liquid or solid phase extraction are given.     

Quantum chemical estimation of the macrocyclization of 1,4-dithiine

Ab initio quantum chemical methods are employed to study the spatial and electronic structure of a 1,4-dithiine molecule. Calculations are performed with electron correlation treatment by MP2 and B3LYP methods in 6-311++G(d,p) and 6-311G basis sets. It is found that the macrocyclization of 1,4-dithiine is energetically favorable. The addition of each subsequent dithiine ring decreases the relative energy of the system by ??0.5÷2.3 kcal/mol. The cycle consisting of 7 dithiine rings is the most comfortable from the standpoint of the internal strain of the macrocycle. With an increase in the number of rings up to 10, the macrocycle starts to break into 4-, 5-, 6-, or 7-membered fragments. The formation of a nanotube based on a 7-membered macrocycle is energetically favorable. The inner diameter of this nanotube is 6.9     

Quick estimation of the Dpb for predicting the strength of chemical bond in situ

An approximate method has been established to calculate the depth of the potential acting on an electron in a molecule at the saddle point along a chemical bond, denoted by Dpb. It is a new indicator which can be used for predicting the strength of a chemical bond. In this work, as a practical application for demonstrating thismethod, we calculated the Dpb of deoxyribonucleosides and ribonucleosides along all C-H and N-H chemical bonds using the method. The results are in fair agreement with those results of previously reported experimental and theoretical observations.     

On the estimation of an unexpected large chemical shift anisotropy

An unexpected large chemical shift tensor is found for the proton-bearing carbon atoms (C₂ and C₄) in the 1,1,3,5,5,-pentacyano-penta-1,4-diene-3-ide anion. The measurement of the chemical shift tensor (Δσ = σ_z.snfc;-σ_⊥) is thereby performed via a normal mode analysis of the ¹³C relaxation behaviour. It turns out that the chemical shift anisotropy is roughly 370 ppm. Quantum-mechanical calculations including such designed to deliver information on the chemical shift anisotropy (IGLO-method [W. Kutzelnigg, Israel J. Chem. 19, 193 (1980); M. Schindler and W. Kutzelnigg, J. Chem. Phys. 76, 1919 (1982)]) are performed to corroborate our results.     

Rapid estimation of chemical kinetics by implicit calibration. II

This study continues the development of a method, implicit calibration, for estimating kinetic parameters from on-line measurements of batch reactions. The basic idea of implicit calibration is to combine non-linear parameter estimation with the calibration of measured spectra with concentrations calculated by an assumed kinetic model. A new example is studied, an esterification reaction with a rather complicated kinetic mechanism, where activities, instead of concentrations, and NIR spectra are used as measurements. The emphasis in the study is on estimating the uncertainty of the kinetic parameters. Two approaches, linearization and bootstrap, are applied. In the case studied, the two approaches give closely similar estimates of the uncertainty. As well, a new way is introduced to control the rigidity of the implicit calibration, based on minimizing the lack of fit of the model. It is also shown that ‘mixed implicit calibration’, i.e. implicit calibration combined with a few off-line calibrated concentrations, greatly enhances the identifiability of the kinetic model. Copyright © 2003 John Wiley & Sons, Ltd.     

Crystal chemical estimation of polymorphic transformation pressures of covalent compounds

A procedure for the calculation of molar volumes of solids in their polymorphic transformations with increased coordination number is described. Assuming that these transformations occur under high pressures we have calculated the pressures responsible for volume changes using the Murnaghan equation. The same values were estimated based on the principle of equalized intermolecular distances in polymorphic transformations, in satisfactory agreement with the first method. To realize the second procedure, we have obtained volume values of van der Waals radii for the elements of Subgroups 5 to 7b of the Periodic Table.Center of Dynamic High Pressures. Translated fromZhurnal Strukturnoi Khimii, Vol. 34, No. 4, pp. 112–116, July–August, 1993.Translated by T. Yudanova