Chemistry

1303 Submissions

[14] viXra:1303.0200 [pdf] submitted on 2013-03-26 11:45:33

Comment on "Policies for Chemical Hazard and Risk Priority Setting: Can Persistence, Bioaccumulation, Toxicity, and Quantity Information be Combined?"

Authors: Sierra Rayne
Comments: 2 Pages.

In their article, Arnot and Mackay [Environ. Sci. Technol., 2008, 42, 4648-4654] use 200 chemicals from the Canadian Domestic Substances List (DSL) to illustrate a model that integrates persistence, bioaccumulation, toxicity, and quantity information for a specific substance to assess chemical exposure, hazard, and risk. The authors claim that the DSL chemicals used in their study are not expected to appreciably ionize at environmental pH. In contrast, a number of the compounds in this study have ionizable functional groups with environmentally relevant pKa values, meaning the corresponding partitioning properties are highly pH dependent, thereby rendering the modeling approach applied by these authors subject to a fatal conceptual and practical flaw. In addition, several compounds in the authors' dataset are expected to hydrolyze rapidly in aquatic systems, resulting in negligible environmental persistence.
Category: Chemistry

[13] viXra:1303.0199 [pdf] submitted on 2013-03-26 12:51:25

Chatelier's Principle (Foundations of Science Part I)

Authors: Andrew Nassif
Comments: 3 Pages. This report is part of a series I am doing on science which will later be published into a book. This is part 1.

Henry Louis Le Chatelier was one of the most influential chemists of all time. This paper will guide you to his greatest discovery in the world of physics and chemistry.
Category: Chemistry

[12] viXra:1303.0175 [pdf] submitted on 2013-03-23 21:55:23

Comment on "QSPR Model for Bioconcentration Factors of Nonpolar Organic Compounds Using Molecular Electronegativity Distance Vector Descriptors"

Authors: Sierra Rayne
Comments: 1 Page.

In their article, Qin et al. [Mol Divers (2010) 14:67-80] construct a quantitative structure-property relationship model to predict the bioconcentration factors of purportedly nonpolar organic compounds. A number of the compounds examined by these authors are not nonpolar as claimed, but instead have associated pKa values that would render the molecules significantly, and - in some cases - effectively entirely, ionized under conditions relevant for bioconcentration in freshwater and/or marine aquatic systems.
Category: Chemistry

[11] viXra:1303.0162 [pdf] submitted on 2013-03-21 22:19:09

Comment on "Serum Albumin Binding of Structurally Diverse Neutral Organic Compounds: Data and Models"

Authors: Sierra Rayne
Comments: 1 Page.

In their article, Endo and Goss [Chem. Res. Toxicol. 2011, 24, 2293-2301] claim to measure the bovine serum albumin water partition coefficients for 83 structurally diverse neutral organic chemicals and correlate the resulting values against corresponding octanol-water partition coefficients and polyparameter linear free energy relationship models based on descriptors for the neutral forms of each compound. However, several compounds in the authors' dataset would be significantly ionized under the experimental conditions being modeled against, and such ionization must be accounted for in any serum albumin binding modeling efforts.
Category: Chemistry

[10] viXra:1303.0150 [pdf] submitted on 2013-03-20 14:07:39

Comment on "Correlation of Aqueous pKa Values of Carbon Acids with Theoretical Descriptors: A DFT Study"

Authors: Sierra Rayne
Comments: 3 Pages.

In their article, Charif et al. [J. Mol. Struct. THEOCHEM 818 (2007) 1] used the B3LYP/6-311++G(d,p) density functional level of theory to estimate gas phase standard state (298.15 K, 1 atm) free energies of acid dissociation (ΔacidG°(g)) for 21 carbon acids. These authors then examined correlations between their B3LYP/6-311++G(d,p) ΔacidG°(g) values and corresponding experimental aqueous pKa measurements. Large errors are evident between experimental values and the B3LYP/6-311++G(d,p) calculated ΔacidG°(g) for propanedioic acid, diethyl ester, dimedone, isopropylidene malonate, barbituric acid, and toluene from this study. The findings call into question the generality of the correlation between ΔacidG°(g) and aqueous experimental pKa values for carbon acids proposed by Charif et al., and also highlight the need for additional studies to investigate what other carbon acid moieties may be outliers. In the present case, either the experimental aqueous pKa of toluene in the literature is incorrect, or the quantitative structure-property relationship proposed in Charif et al. is subject to large outliers that greatly diminish its broad applicability.
Category: Chemistry

[9] viXra:1303.0148 [pdf] submitted on 2013-03-20 10:08:12

Comment on “Thermodynamic Stability of Neutral and Anionic Pfos: a Gas-Phase, N-Octanol, and Water Theoretical Study”

Authors: Sierra Rayne
Comments: 2 Pages.

In their article, Montero-Campillo et al. [J. Phys. Chem. A, 114 (2010) 10148-10155] use the B3LYP density functional with the 6-311+G(d,p) basis set to calculate the relative thermodynamic stabilities of the 89 linear and branched perfluorooctane sulfonic acid (PFOS) isomers in their molecular acid and dissociated anionic forms for the gas phase and aqueous and n-octanol solvent phases. A substantial body of work over the past decade has clearly demonstrated the inability of the B3LYP functional (and the majority of other widely employed density functionals) to accurately represent the relative thermodynamic stabilities of linear and branched alkanes (including perhydro, poly- and perhalogenated, and other functionalized derivatives). It has been specifically demonstrated using a range of theoretical methods (semiempirical, Hartree-Fock [HF], various density functionals, and second order Moller-Plesset perturbation theory) that the B3LYP branching error for perhydroalkane isomerizations also applies to perfluoroalkanes, and particularly to classes of compounds such as the 89 PFOS isomers, as well as the perfluoroalkanoic acids and perfluoralkyl sulfonyl/acyl fluorides in their acid and (where applicable) anionic forms. Consequently, the relative thermodynamic stabilities of the molecular acid and anionic PFOS isomers at the B3LYP/6-311+G(d,p) level of theory put forward by Montero-Campillo et al. are in substantial error, and the authors and readers are referred elsewhere to more accurate calculations.
Category: Chemistry

[8] viXra:1303.0142 [pdf] submitted on 2013-03-19 11:08:41

Comment on "Oxidation of Antibiotics During Water Treatment with Potassium Permanganate: Reaction Pathways and Deactivation [Hu et al., Environ. Sci. Technol., 2011, 45, 3635-3642]"

Authors: Sierra Rayne
Comments: Pages.

In their work, Hu et al. [Environ. Sci. Technol., 2011, 45, 3635-3642] investigate the oxidation of three antibiotics (ciprofloxacin, lincomycin, and trimethoprim) by potassium permanganate in buffered solutions at pH 7. The authors propose detailed mechanistic pathways for the oxidation of these substrates, but apparently do not consider the acid/base behavior of the compounds under consideration, resulting in erroneous mechanistic interpretations throughout the manuscript.
Category: Chemistry

[7] viXra:1303.0141 [pdf] submitted on 2013-03-19 11:46:07

Comment on "Determination of Diffusion Coefficient of Organic Compounds in Water Using a Simple Molecular-Based Method [Gharagheizi, Ind. Eng. Chem. Res. 2012, 51, 2797-2803]"

Authors: Sierra Rayne
Comments: 1 Page.

In his article, Gharagheizi [Ind. Eng. Chem. Res. 2012, 51, 2797-2803] claims to develop a novel three-parameter equation for the calculation/prediction of the diffusion coefficient of nonelectrolyte organic compounds in water at infinite dilution. In contrast, many of the compounds investigated in this work are electrolytes in pure water at infinite dilution. Consequently, the molecular modeling efforts on the non-ionized molecular speciation of each compound were - in many cases - conducted on species that would not be dominantly present under the experimental conditions the modeling efforts are being developed against.
Category: Chemistry

[6] viXra:1303.0103 [pdf] submitted on 2013-03-14 09:47:34

Comment on "Visualising the Equilibrium Distribution and Mobility of Organic Contaminants in Soil Using the Chemical Partitioning Space [Wong and Wania, J. Environ. Monit., 2011, 13, 1569-1578]"

Authors: Sierra Rayne
Comments: 1 Page.

In their article, Wong and Wania [J. Environ. Monit., 2011, 13, 1569-1578] claim to estimate the partitioning properties (air-water partition coefficients and soil organic carbon-water partition coefficients) of twenty neutral organic chemicals using poly-parameter linear free energy relationships. Five of the 20 compounds in this study have ionizable functional groups with environmentally relevant pKa values, meaning the corresponding partitioning properties are highly pH dependent, thereby rendering the modeling approach applied by these authors subject to a fatal conceptual and practical flaw.
Category: Chemistry

[5] viXra:1303.0093 [pdf] submitted on 2013-03-12 22:54:13

Comment on "The Sorptive Capacity of Animal Protein [DeBruyn and Gobas. 2007. Environ Toxicol Chem 26:1803-1808]"

Authors: Sierra Rayne
Comments: 1 Page.

In their article, DeBruyn and Gobas [2007. Environ Toxicol Chem 26:1803-1808] claim to "present a compilation and meta-analysis of published data to estimate the relative sorptive capacities of animal proteins and lipids for neutral organic chemicals." However, the dataset of these authors contains compounds that would be effectively entirely ionized at physiological pH values, rendering the assumption of neutrality and any subsequent analyses based thereupon incorrect.
Category: Chemistry

[4] viXra:1303.0073 [pdf] submitted on 2013-03-09 20:47:12

Comment on "Modelling Physico-Chemical Properties of (Benzo)triazoles, and Screening for Environmental Partitioning [bhhatarai and Gramatica, Water Res. 45, 2011, 1463-1471]"

Authors: Sierra Rayne
Comments: 1 Page.

In their article, Bhhatarai and Gramatica [Water Res. 45, 2011, 1463-1471] employ a quantitative structure-property relationship approach to model the physico-chemical properties of compounds they refer to as benzotriazoles, and to subsequently screen these compounds for environmental partitioning behavior. A substantial number of these compounds are not benzotriazoles and do not have similar properties as benzotriazoles. Consequently, it appears that the approach, assumptions, and results in this work must be viewed as potentially fundamentally flawed.
Category: Chemistry

[3] viXra:1303.0071 [pdf] submitted on 2013-03-09 22:03:28

Comment on "Are Mechanistic and Statistical QSAR Approaches Really Different? MLR Studies on 158 Cycloalkyl-Pyranones [Bhhatarai et al., Mol. Inf. 2010, 29, 511-522]"

Authors: Sierra Rayne
Comments: 1 Page.

In their study, Bhhatarai et al. [Mol. Inf. 2010, 29, 511-522] develop quantitative structure-activity relationships (QSARs) for the inhibition of HIV protease by 158 so-called 4-OH cycloalkyl-pyranones. A number of compounds termed 4-OH cycloalkyl-pyranones in this work do not appear to be cycloalkyl-pyranones.
Category: Chemistry

[2] viXra:1303.0070 [pdf] submitted on 2013-03-09 14:53:05

Comment on "Acid-Catalyzed Conversion of Xylose, Xylan and Straw into Furfural by Microwave-Assisted Reaction [Yemis and Mazza, 2011, Bioresour. Technol. 102, 7371-7378]"

Authors: Sierra Rayne
Comments: 1 Page.

In their article, Yemis and Mazza [Yemis and Mazza, 2011, Bioresour. Technol. 102, 7371-7378] study the effects of different Bronsted acids, temperatures, times, substrate concentrations, and pH on the acid-catalyzed conversion of xylose, xylan and straw into furfural by microwave-assisted reaction. The authors appear to incorrectly classify phosphoric acid as a mineral acid, and claim to achieve pH values in solutions of acetic and formic acid below the apparent theoretical limits.
Category: Chemistry

[1] viXra:1303.0044 [pdf] submitted on 2013-03-07 09:55:14

Automated Identification and Classification of Stereochemistry: Chirality and Double Bond Stereoisomerism

Authors: Ana L. Teixeira, João P. Leal, Andre O Falcao
Comments: 26 Pages.

Stereoisomers have the same molecular formula and the same atom connectivity and their existence can be related to the presence of different three-dimensional arrangements. Stereoisomerism is of great importance in many different fields since the molecular properties and biological effects of the stereoisomers are often significantly different. Most drugs for example, are often composed of a single stereoisomer of a compound, and while one of them may have therapeutic effects on the body, another may be toxic. A challenging task is the automatic detection of stereoisomers using line input specifications such as SMILES or InChI since it requires information about group theory (to distinguish stereoisomers using mathematical information about its symmetry), topology and geometry of the molecule. There are several software packages that include modules to handle stereochemistry, especially the ones to name a chemical structure and/or view, edit and generate chemical structure diagrams. However, there is a lack of software capable of automatically analyzing a molecule represented as a graph and generate a classification of the type of isomerism present in a given atom or bond. Considering the importance of stereoisomerism when comparing chemical structures, this report describes a computer program for analyzing and processing steric information contained in a chemical structure represented as a molecular graph and providing as output a binary classification of the isomer type based on the recommended conventions. Due to the complexity of the underlying issue, specification of stereochemical information is currently limited to explicit stereochemistry and to the two most common types of stereochemistry caused by asymmetry around carbon atoms: chiral atom and double bond. A Webtool to automatically identify and classify stereochemistry is available at http://nams.lasige.di.fc.ul.pt/tools.php
Category: Chemistry