Chemistry

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Recent Submissions

Any replacements are listed further down

[49] viXra:1403.0946 [pdf] submitted on 2014-03-27 09:42:54

Do Triatomic Molecules Echo Atomic Periodicity?

Authors: Ray Hefferlin, Josh Barrow
Comments: 20 Pages.

The objective of this work is to test whether vibration frequencies ν1 of free, ground-state, main-group triatomic molecules manifest a periodicity similar to those of atomic spectroscopic constants. This test and an earlier test on energies of atomization underscore the role of the periodic law as a foundation of chemistry. Using data from four data bases and from computation, we have collected and have mapped ν1 data in mathematical spaces of fixed-period molecules. These spaces are 9x9x9-atom cubes with rare-gas molecules on each face. The ν1 collected from various sources might be of use in optical or near-optical searches for cold triatomics in interstellar space.
Category: Chemistry

[48] viXra:1403.0022 [pdf] submitted on 2014-03-05 03:38:21

Chemiosmosis and Microscopic Reversibility: Irreconcilable. Thermodynamic Limitations of Coupled Equilibria and the Role of Atp

Authors: Sosale Chandrasekhar
Comments: 25 Pages.

It is argued that the chemiosmotic theory, in positing the egress and ingress of protons across a membrane via different routes, violates the principle of microscopic reversibility (PMR). The theory was proposed as a mechanism for coupling the exergonic oxidation of NADH to the endergonic synthesis of ATP, believed to be a ready-to-use form of biochemical energy. The key proton-pump mechanism, however, should also operate in reverse by the PMR, hence is unlikely to be valid. Generally, the transfer of free energy via coupled equilibria is problematical, as neither of the coupled processes would go to completion. (However, it may be feasible in the case of entropy-driven reactions, as happens in the reactions of the Krebs cycle that lead to the formation of NADH.) Furthermore, reported thermodynamic data do not support the idea of ATP as a ‘high energy’ molecule, but rather indicate that ATP hydrolysis is driven by release of phosphate. In fact, many of the reactions believed to be thermodynamically driven by ATP hydrolysis are likely exergonic per se. ATP possibly provides part of the activation energy for the reaction in many cases. An alternative (non-equilibrium) mechanism for ATP synthesis is proposed based on the increase in pH that would accompany the oxidation of NADH. This would generate ADP3- and HPO42- which could form ATP4- in a thermodynamically favoured process within hydrophobic pockets.
Category: Chemistry

[47] viXra:1402.0121 [pdf] submitted on 2014-02-18 08:22:58

A Comparative Study of Oil Palm and Japanese Beech on Their Fractionation and Characterization as Treated by Supercritical Water

Authors: M. Varman, S. Saka
Comments: 24 Pages. M. Varman and S. Saka. "A Comparative Study of Oil Palm and Japanese Beech on Their Fractionation and Characterization as Treated by Supercritical Water" Waste and Biomass Valorization 2(3) (2011): 309-315.

Supercritical water treatment (380°C/100 MPa/ 8 s) was applied to extractive-free oil palm trunk and sapwood portion of Japanese beech and their fractionated products were comparatively characterized, for water-soluble portion and water-insoluble portion composed of methanol-soluble portion and methanol-insoluble residue. As a result, the water-soluble portion was determined to be composed of carbohydrate-derived products such as organic acids, sugar decomposed products and lignin- derived products, etc. for both species. The oil palm, however, shows higher yield of organic acids (12.9%) and lignin-derived products (12.2%) compared to Japanese beech, in which organic acids were 4.7% in yield and lignin-derived products 9.8%. The methanol-soluble portion was, on the other hand, mainly composed of lignin-derived products, and in oil palm, these lignin-derived products consisted of both syringyl and guaiacyl-type similar to Japanese beech. The methanol-insoluble residue, was also mainly composed of lignin to be 99.2% in its content in the oil palm, compared to Japanese beech 93.7%. Moreover, the phenolic hydroxyl content deter- mined by aminolysis method was higher in oil palm (36.5 PhOH/100C9) compared to Japanese beech (16.9 PhOH/100C9). Furthermore, an alkaline nitrobenzene oxidation analysis indicated that, the methanol-insoluble residue of the oil palm was less in oxidation products whereas in Japanese beech nitrobenzene oxidation products completely diminished. These lines of evidence suggest that methanol-insoluble residue is composed of lignin with more condensed-type of linkages with high phenolic hydroxyl groups. In addition, the water-soluble portion could be utilized for organic acid production, whereas the methanol-soluble portion and its insoluble residue for phenolic chemical production, with oil palm showing higher potential compared to Japanese beech.
Category: Chemistry

[46] viXra:1402.0112 [pdf] submitted on 2014-02-17 11:40:45

One-Step Salt-Assisted Deposition of Carbon Material onto the Polymer Substrate

Authors: Nikolay Dementev
Comments: 6 Pages.

It was found that a water-based ink in the presence of table salt forms deposits on the surface of polymer substrate. Without the salt, no distinct deposits were formed.
Category: Chemistry

[45] viXra:1401.0216 [pdf] submitted on 2014-01-29 09:21:36

Fractionation and Characterization of Oil Palm (Elaeis Guineensis) as Treated by Supercritical Water

Authors: M.Varman, H. Miyafuji, S. Saka
Comments: 21 Pages. M.Varman, H. Miyafuji, and S. Saka. "Fractionation and characterization of oil palm (Elaeis guineensis) as treated by supercritical water" Journal of Wood Science 56(6) (2010): 484-494.

    In order to investigate a potential for the efficient utilization of oil palm (Elaeis guineensis), supercritical water treatment (380ºC/100MPa/8s) has been applied to fractionate into water-soluble portion and water-insoluble portion composing of methanol-soluble portion and methanol-insoluble residue for various parts of oil palm such as trunk, frond, mesocarp fibers, shell, empty fruit bunch (EFB) and kernel cake. These fractionated products were then characterized analytically, in which the water-soluble and methanol-soluble portions were determined to be mainly composed of carbohydrate-derived products and lignin-derived products, respectively. Besides, the methanol-insoluble residue was mainly composed of lignin more than 84wt%, and the phenolic hydroxyl contents determined by aminolysis method was higher than the untreated oil palm sample. In addition, an alkaline nitrobenzene oxidation analysis indicated that, the methanol-insoluble residue was less in oxidation products. These lines of findings implicate that the water-soluble portion could be utilized for organic acid production, whereas the methanol-soluble portion and its insoluble residue for phenolic chemical production.
Category: Chemistry

[44] viXra:1401.0002 [pdf] submitted on 2014-01-01 05:28:21

The Enigma of Bragg's Law

Authors: Sosale Chandrasekhar
Comments: 10 Pages.

It is argued that the fundamental theory of X-ray diffraction is based on a flawed model of wave interference. This is because the macroscopic distances between the crystalline sample on the one hand, and the X-ray source and the detector on the other, cannot be defined to the accuracy of a fractional wave-length. Thus, the inherent ‘graininess’ of the detector surface does not support the idea of constructive or destructive interference of electromagnetic radiation. This critique then applies equally to the presumed extensions of ‘Bragg’s Law’, particularly the so-called phase problem. The phase problem is thus a theoretical construct that is, practically, an artefact of the Bragg derivation. The Bragg approach, however, has been ingeniously adapted to make contact with the structural theory of chemistry by various guises and protocols. These are, inter alia, based on ideas about crystal morphology and internal structure that preceded the Bragg approach. An alternative theory of X-ray scattering, however, needs also to be compatible with the structural theory to be practically meaningful. A model of scattering is proposed herein, that is based on absorption and emission by groups of atoms that are defined by a conventional lattice plane. The Bragg equation is thus re-interpreted as relating the energy of the emitted radiation and the angle of ‘reflection’. It is argued that the Bragg approach is essentially empirical, and that its apparent consistency with the structural theory is based on a synergistic evolution of theoretical ideas and experimental observation. In this, therefore, it is not unlike other spectroscopic techniques in common use for structure determination.
Category: Chemistry

[43] viXra:1311.0163 [pdf] submitted on 2013-11-23 19:43:28

Comment on "Towards Rational Molecular Design: Derivation of Property Guidelines for Reduced Acute Aquatic Toxicity [Voutchkova et al., Green Chem., 2011, 13, 2373]"

Authors: Sierra Rayne
Comments: 2 Pages.

In their article, Voutchkova et al. (Green Chem., 2011, 13, 2373) claim to use a dataset of 865 neutral organic compounds. Because a substantial proportion of the compounds that the authors do provide molecular identifiers for in their supporting information are not neutral organic compounds as the authors claim, one must reasonably conclude that the true set of ionizable compounds among the total dataset of 865 molecules is likely larger than presented herein. Properties such as the molecular weight, partitioning coefficients between various matrices (where at least one of the matrices is water), aqueous solubility, solvent accessible surface area, polar surface area, molecular volume, number of H-bonds, HOMO/LUMO energies, etc., are all pH dependent (i.e., speciation dependent) for ionizable compounds. Since Voutchkova et al. appear to have conducted all their molecular modeling efforts on the neutral forms of all compounds, the authors appear to have obtained molecular descriptors for speciations of the compounds that are not relevant for the toxicological properties being modeled against.
Category: Chemistry

[42] viXra:1311.0162 [pdf] submitted on 2013-11-23 19:46:38

Comment on "Towards Rational Molecular Design for Reduced Chronic Aquatic Toxicity [Voutchkova et al., Green Chem., 2012, 14, 1001]"

Authors: Sierra Rayne
Comments: 2 Pages.

In their article, Voutchkova et al. (Green Chem., 2012, 14, 1001) claim to use a dataset of 865 neutral organic compounds. Because a substantial proportion of the compounds that the authors do provide molecular identifiers for in their supporting information are not neutral organic compounds as the authors claim, one must reasonably conclude that the true set of ionizable compounds among the total dataset of 865 molecules is likely larger than presented herein. Properties such as the molecular weight, partitioning coefficients between various matrices (where at least one of the matrices is water), aqueous solubility, solvent accessible surface area, polar surface area, molecular volume, number of H-bonds, HOMO/LUMO energies, etc., are all pH dependent (i.e., speciation dependent) for ionizable compounds. Since Voutchkova et al. appear to have conducted all their molecular modeling efforts on the neutral forms of all compounds, the authors appear to have obtained molecular descriptors for speciations of the compounds that are not relevant for the toxicological properties being modeled against.
Category: Chemistry

[41] viXra:1309.0076 [pdf] submitted on 2013-09-11 06:38:38

Mpemba Effect

Authors: Ilias J.Tyrovolas
Comments: 2 Pages. possible explanation for Mpemba effect copyrighted in 2012

Water molecules are dipoles positioned and oriented joined by hydrogen bonds. When water is heated this structure collapses (increasing entropy).If after the water is recooled to a lower temperature the structure is not reconstructed immediately but needed some time. This time is not always available inside a freezer because the cooling process is fast. The entropy reduction curves function of temperature S=f(T) appear retardation (lagging) relative to entropy growth curves. So, the water after was heated and recooled at the starting temperature, has more entropy than before it was heated. This means that molecules have now the same kinetic energy, but thermal motion before heating was more oriented by the structure mentioned above. So, after recooling random collisions are more possible leading to faster temperature’s reduction. The rate of temperature decrease is proportional to temperature.
Category: Chemistry

[40] viXra:1308.0154 [pdf] submitted on 2013-08-31 12:46:35

Comment on "Representation and Prediction of Molecular Diffusivity of Nonelectrolyte Organic Compounds in Water at Infinite Dilution Using the Artificial Neural Network-Group Contribution Method [Gharagheizi et al., J. Chem. Eng. Data 2011, 56, 1741-1750]

Authors: Sierra Rayne
Comments: 1 Page.

In their article, Gharagheizi et al. [J. Chem. Eng. Data 2011, 56, 1741-1750] claim to develop a model to predict the molecular diffusivity of "nonelectrolyte organic compounds" in water using an artificial neural network-group contribution method. Many of these compounds have ionizable functionalities with pKa values that result in either substantial or effectively complete ionization in water (making them electrolytes, in contrast to the claims of Gharagheizi et al.). Consequently, the model developed and applied by Gharagheizi et al. does not computationally model the actual speciation(s) of each compound expected to be present under the experimental conditions for which the underlying data has been obtained and erroneously classifies many organic compounds as non-electrolytes.
Category: Chemistry

[39] viXra:1308.0153 [pdf] submitted on 2013-08-31 13:00:18

Comment on "Comparison of New and Existing Threshold Methods for Evaluating Sulfur Compounds in Different Base Wines"

Authors: Sierra Rayne
Comments: 1 Page.

In their article (Cliff et al., J. Sens. Stud., 2011, 26, 184-196), the authors plot the log mean aroma threshold concentrations for three sulfur aroma compound analytes on the y-axis against the qualitative descriptors of the wine (i.e., "model," "neutral," and "fruity") on the x-axis, and proceed to fit three log-linear regression models through the sets of data. The statistical validity of this exercise seems problematic (particularly with only three datapoints, and four significant figures in the resulting quoted regression constants), and the reason behind this choice of data analysis is unclear. Some type of statistical test (e.g., ANOVA) designed to investigate relative trend differences between categorical variables would perhaps be more appropriate, especially when such nebulous categorical descriptors as "neutral" and "fruity" are being employed along the x-axis and ordered in an arbitrary manner.
Category: Chemistry

[38] viXra:1305.0139 [pdf] submitted on 2013-05-23 07:04:36

Comment on "Using COSMOtherm to Predict Physicochemical Properties of Poly- and Perfluorinated Alkyl Substances (PFASs)"

Authors: Sierra Rayne
Comments: 1 Page.

In their study, Wang et al. [Environ. Chem. 2011, 8, 389] use the COSMOtherm software program in an attempt to shed some insights into the physicochemical properties of various poly- and perfluorinated compounds. During the conformation dependent pKa investigations on n-perfluorooctanoic acid (PFOA), the authors appear to make a critical error in their analyses. Wang et al. appear to have allowed a transition from an acid form geometry to a very different anionic form geometry, which is not a correct way of calculating free energy changes during acid dissociation. This error explains why these authors obtained widely ranging conformation dependent pKa values (0.9 to 2.9) for PFOA dissociation. As has been previously shown [Rayne and Forest, J. Mol. Struc. THEOCHEM 2010, 949, 60], there are negligible conformation dependent effects on the pKa value of PFOA.
Category: Chemistry

[37] viXra:1304.0123 [pdf] submitted on 2013-04-22 22:24:14

Comment on "QSAR Modeling is not 'Push a Button and Find a Correlation': A Case Study of Toxicity of (Benzo-)triazoles on Algae"

Authors: Sierra Rayne
Comments: 2 Pages.

In their manuscript, Gramatica et al. [Mol. Inf. 2012, 31, 817-835] claim to conduct quantitative structure-activity relationship (QSAR) modeling on a suite of triazoles, benzotriazoles, and additional azo-aromatic compounds. However, a number of the compounds examined by these authors do not appear to be triazoles, benzotriazoles, or other azo-aromatic compounds. In some cases, the authors also appear to publish incorrect molecular structures which may affect the structural descriptors employed for QSAR development.
Category: Chemistry

[36] viXra:1304.0015 [pdf] submitted on 2013-04-03 21:56:39

Comment on "Sorption of Organic Chemicals to Soil Organic Matter: Influence of Soil Variability and pH Dependence"

Authors: Sierra Rayne
Comments: Pages.

In their article, Bronner and Goss [Environ. Sci. Technol., 2011, 45, 1307-1312] investigate the pH dependence of organic chemical sorption to soil organic matter. The authors report a log Koc value for benzoyl chloride in aqueous solution, despite this compound having a known hydrolysis half-life of only 16 seconds in water. This timeframe is far too short to allow the measurement of any equilibrium based partitioning coefficients. Consequently, one suspects that the log Koc value reported for benzoyl chloride is likely that of its hydrolysis product: benzoic acid. The authors also may have chosen two experimental conditions (pH 4.5 and 7.2) between which the ionization state of the carboxylic acids in the organic matter may have changed very little, and could instead have remained in effectively the same net ionization state between the two experimental pH endpoints. Thus, there does not appear to be sufficient evidence in this work to support the general claim therein that "protonation/deprotonation of carboxylic groups in humic matter has no significant influence on sorption ... even for polar organic molecules."
Category: Chemistry

[35] viXra:1304.0014 [pdf] submitted on 2013-04-03 22:15:51

Comment on "QSPR Study on the Bioconcentration Factors of Nonionic Organic Compounds in Fish by Characteristic Root Index and Semiempirical Molecular Descriptors"

Authors: Sierra Rayne
Comments: Pages.

In their article, Sacan et al. [J. Chem. Inf. Comput. Sci. 2004, 44, 985-992] construct a quantitative structure-property relationship model to predict the bioconcentration factors of purportedly nonionic organic compounds. A number of the compounds examined by these authors are not nonionic 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

[34] viXra:1304.0007 [pdf] submitted on 2013-04-01 16:57:34

Comment on "Dependence of Persistence and Long-Range Transport Potential on Gas-Particle Partitioning in Multimedia Models"

Authors: Sierra Rayne
Comments: 1 Page.

In their article, Gotz et al. [Environ. Sci. Technol., 2008, 42, 3690-3696] use three different multimedia contaminant fate models to analyze the impact of implementing a two-particle-size polyparameter linear free energy relationship approach on metrics of persistence and long-range transport, and on calculated concentrations of semivolatile organic chemicals in the Arctic. One of the twelve compounds investigated is 2,4-D (2,4-dichlorophenoxyacetic acid), which is effectively entirely dissociated in aqueous systems. The authors do not appear to have considered the ionization of 2,4-D during their multimedia modeling exercises, particularly the effects of ionization on octanol-water and air-water partitioning behavior. Consequently, all modeling results presented for 2,4-D appear to be in significant error and should not be employed for risk assessment purposes.
Category: Chemistry

[33] 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

[32] 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

[31] 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

[30] 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

[29] 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

[28] 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: 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

[27] 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

[26] 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

[25] 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

[24] 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

[23] 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

[22] 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

[21] 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

[20] 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

[19] viXra:1302.0069 [pdf] submitted on 2013-02-11 22:15:01

Density Functional Theory Investigation of RSNNSR Systems

Authors: Vadim V Nazarenko
Comments: 99 Pages.

DENSITY FUNCTIONAL THEORY (DFT) INVESTIGATION OF RSNNSR SYSTEMS The structural variations and stabilities of RSNNSR systems were studied using the hybrid density functional theory (B3LYP) at various basis set levels. Computational methodology was based on the locally dense basis set approach (LDBS) that assigns various levels of the basis sets accordingly to the previously calibrated results that could be correlated to the experimental data. The present study investigated the effect of the substituents (R) on the structure and the stabilities of RSNNSR systems. There were totally ten systems studied where R: H, CH3, CF3, tert-Butyl, C6H6, p-NO2C6H6 , p-CH3OC6H6. The calculations revealed that the stability of the S-N bond is enhanced if there is a combination of the electron-releasing effect and the electron-withdrawing one that creates a push-pull effect (captodative effect) in the system. An increase of a positive charge on one of the sulfur atoms and a negative charge on the adjacent nitrogen atom increases delocalization of one the S’s lone pairs that creates a conjugation with the neighboring N atom and the β carbons through 2pπ-3pπ interactions. The push-pull effect also influenced structural characteristics of the systems. One of the most notable ones is the variation of the NSCC dihedral angle in some of our systems from 89° to 21°
Category: Chemistry

[18] viXra:1302.0021 [pdf] submitted on 2013-02-04 11:10:19

ThermInfo: Collecting, Retrieving, and Estimating Reliable Thermochemical Data

Authors: Ana L. Teixeira, Rui C. Santos, João P. Leal, José A. Martinho Simões, Andre O. Falcao
Comments: 26 Pages.

Standard enthalpies of formation are used for assessing the efficiency and safety of chemical processes in the chemical industry. However, the number of compounds for which the enthalpies of formation are available is many orders of magnitude smaller than the number of known compounds. Thermochemical data prediction methods are therefore clearly needed. Several commercial and free chemical databases are currently available, the NIST WebBook being the most used free source. To overcome this problem a cheminformatics system was designed and built with two main objectives in mind: collecting and retrieving critically evaluated thermochemical values, and estimating new data. In its present version, by using cheminformatics techniques, ThermInfo allows the retrieval of the value of a thermochemical property, such as a gas-phase standard enthalpy of formation, by inputting, for example, the molecular structure or the name of a compound. The same inputs can also be used to estimate data (presently restricted to non-polycyclic hydrocarbons) by using the Extended Laidler Bond Additivity (ELBA) method. The information system is publicly available at http://www.therminfo.com or http://therminfo.lasige.di.fc.ul.pt. ThermInfo’s strength lies in the data quality, availability (free access), search capabilities, and, in particular, prediction ability, based on a user-friendly interface that accepts inputs in several formats.
Category: Chemistry

[17] viXra:1301.0179 [pdf] submitted on 2013-01-29 12:08:33

The Math & Science Behind & Beyond Chemistry

Authors: Andrew Nassif
Comments: 3 Pages.

Chemistry requires lots of conceptual thinking as well as analytical actions. Chemistry is a science of measurement. Like physics, it also requires much mathematical sequences in it. Chemistry is the bridge of science, because it is a sub-subject of every major field of science including physics and geology. Boyle describes chemistry as the subject of major bodies. Chang describes chemistry as the study of matter and the changes it undergoes. Chang's definition, is the most commonly used today. Chemistry was thought to be created by the greeks (atomism), however, it was created hundreds of years before as a way ancient Egyptians used herbs to create a remedy, or used the science of proper mechanics to build the pyramids using a special chemical combination as the glue that held bricks together. Cleopatra herself was an alchemist.
Category: Chemistry

[16] viXra:1301.0177 [pdf] submitted on 2013-01-28 14:28:07

Accuracy of Computational Solvation Free Energies for Neutral and Ionic Compounds: Dependence on Level of Theory and Solvent Model

Authors: Sierra Rayne, Kaya Forest
Comments: 22 Pages.

Gas to aqueous phase standard state (1 atm to 1 mol/L; 298.15 K) free energies of solvation (ΔGosolv) were calculated for a range of neutral and ionic inorganic and organic compounds using various levels and combinations of Hartree-Fock and density functional theory (DFT) and composite methods (CBS-Q//B3, G4MP2, and G4) with the IEFPCM-UFF, CPCM, and SMD solvation models in Gaussian 09 (G09). For a subset of highly polar and generally polyfunctional neutral organic compounds previously identified as problematic for prior solvation models, we find significantly reduced ΔGosolv errors using the revised solvent models in G09. The use of composite methods for these compounds also substantially reduces their apparent ΔGosolv errors. In contrast, no general level of theory effects between the B3LYP/6-31+G** and G4 methods were observed on a suite of simpler neutral, anionic, and cationic molecules commonly used to benchmark solvation models. Further investigations on mono- and polyhalogenated short chain alkanes and alkenes and other possibly difficult functional groups also revealed significant ΔGosolv error reductions by increasing the level of theory from DFT to G4. Future solvent model benchmarking efforts should include high level composite method calculations to allow better discrimination of potential error sources between the levels of theory and the solvation models.
Category: Chemistry

[15] viXra:1301.0149 [pdf] submitted on 2013-01-24 13:15:06

A Theorist's Guide to Macro-Molecular Chemistry

Authors: Andrew Nassif
Comments: 5 Pages.

Chemistry is a branch of physical science that has to do with the study of the composition of matter and the study of everything composed of matter as well as based on the basis of atomism, fluid dynamics, and particle physics, as well as the action of measurements applied as a stoichiometry and a method in using chemistry. Chemistry in basically the central science, though it may be a branch of physical science, it is very distinct from physics. The world chemistry itself comes from the word alchemy which is derived from لكيمياء which is then derived from the greek word χημεία, this means he study of material, which is then translated to being the study of everything composed of matter. Ancient Egyptians themselves used synthetic chemistry as a study of herbs as well as using this branch of chemistry to help them plant crops in the fertile crust. Democritus's theory of atomism became the foundation of chemistry and elementary physics itself. Eventually Atomism brought forth ideas of models of the atoms around us and many generations later, the Quantum Mechanical Model was born. This is how the fundamental of chemistry came to be.
Category: Chemistry

[14] viXra:1301.0069 [pdf] submitted on 2013-01-12 12:39:20

The Partitioning of Disparlure Between Hydrophobic Organic Solvents and Water

Authors: Sierra Rayne, Kaya Forest
Comments: 2 Pages.

The partitioning behavior of disparlure ((7R,8S)-7,8-epoxy-2-methyloctadecane) - a sex pheromone of the gypsy moth, Lymantria dispar - between aqueous solutions and the organic solvents chloroform and n-heptane has been re-evaluated. Prior estimates from the literature of the aqueous-organic solvent partitioning coefficients (log P) for disparlure in these two solvent systems appear to have been underestimated by about 5-6 orders of magnitude. In the current work, we provide corrected log P(chloroform/water) and log P(heptane/water) values for disparlure of 9.87 and 9.15, respectively.
Category: Chemistry

[13] viXra:1301.0039 [pdf] submitted on 2013-01-07 12:08:49

Emission of EMR Lab Analysis

Authors: Andrew Nassif
Comments: 4 Pages.

Element must be heated to produce emitted light, this is due to its chemical reaction caused by absorbed energy, which is required in order to emit light. This is why elements acquire being heated in order to emit light. Sometimes absorbed energy can cause electromagnetic radiation, also these spectrums are different waves of lights due to the different energy levels of a chemical reaction.
Category: Chemistry

[12] viXra:1212.0152 [pdf] submitted on 2012-12-26 20:21:48

There Are Only 92 Stable Elements in Nature

Authors: Chun-Xuan Jiang
Comments: 5 Pages.

using mathematical method we prove that there are only 92 stable elements in nature and obtain the correct valence electron configurations of the elements.In Mendeleev periodic table the elements(1-18,29-36 and 46)have correct valence electron configurations and the elements(19-28,37-45 and 47-92)have wrong valence electron configurations.
Category: Chemistry

[11] viXra:1212.0097 [pdf] submitted on 2012-12-16 14:44:57

Reassessing Atmospheric Deposition Rates of Polycyclic Aromatic Compounds to the Athabasca River (Alberta, Canada) Watershed from Oil Sands Related Activities

Authors: Sierra Rayne
Comments: 5 Pages.

In an earlier study (Kelly et al., PNAS, 2009, 106, 22346-22351), spatial patterns for the concentrations of particulate matter, particulate polycyclic aromatic compounds (PAC), and dissolved PAC in the snowpack around the Syncrude and Suncor upgrader facilities near the oil sands development at Fort McMurray, Alberta, Canada were determined. A reassessment of the datasets employed in this work yields significantly different deposition rates (by up to an order of magnitude) than reported, as well as reveals substantial sensitivity in deposition rate estimates depending on a range of equally valid regression types chosen. A high degree of uncertainty remains with regard to the quantities of particulate matter and PAC being deposited in the Athabasca River watershed from oil sands related activities.
Category: Chemistry

[10] viXra:1212.0031 [pdf] submitted on 2012-12-04 14:23:18

Synthesis of Fullerene-Terminated Molecular Wires

Authors: Filippo Busolo
Comments: 9 Pages.

Three new C60–end-capped molecular wires for molecular electronics were prepared, characterized and studied by cyclic voltammetry.
Category: Chemistry

[9] viXra:1210.0102 [pdf] submitted on 2012-10-19 02:55:41

Macromolecular Aggregation, Supramolecular Stability and Polymer Strength: Has the Van Der Waals Force been Underestimated?

Authors: Sosale Chandrasekhar
Comments: 18 Pages.

Macromolecular aggregation and mechanical strength characterize polymer behavior, but apparently remain enigmatic: small molecules prefer to be solvated but macromolecules prefer to aggregate. This is a consequence of the enormous loss of solvent entropy attending macromolecular solvation. The additivity of weak (e.g., van der Waals) forces in a macromolecule cannot explain aggregation, as the accompanying entropy loss would also be additive. However, even this would be overshadowed by the loss of solvent entropy in the case of its solvation. A thermodynamic basis for the aggregation, however, needs a reassessment of the van der Waals equation of state, a reinterpretation of the coefficient ‘a’ suggesting that the van der Waals force may be stronger (~15 kcal mol--1) than believed. Its manifestation is normally thwarted by the dominance of entropic effects in the weak interactions. The phenomenal mechanical properties of polymers are explicable by the above reassessment of current ideas.
Category: Chemistry

[8] viXra:1209.0055 [pdf] submitted on 2012-09-18 12:02:35

A New Source of Petroleum, Diesel and Kerosene

Authors: Mohit Kumar
Comments: 2 Pages.

Petrol, diesel and kerosene are important hydrocarbons which are widely used in different form in our life. The manufacture of hydrocarbons, such as petroleum, form paraffin is familiar commercial process. However, this process is very costly, involves elaborate method and is time consumable. Consequently, this process does not seem to be economically viable.
Category: Chemistry

[7] viXra:1208.0026 [pdf] submitted on 2012-10-01 12:44:19

Internuclear Separations Using Least Squares and Neural Networks for 46 New S and P Electron Diatomics

Authors: Ray Hefferlin
Comments: 9 Pages. May appear in Int. J. Mol. Model, Vol 4, #1

Combined least-squares and neural-network forecasts for internuclear separations of main-group diatomic molecules, most with from 9 to 12 atomic valence electrons, are presented. We require that the standard-deviation bounds of the forecasts overlap each other; this requirement is met by 65 molecules, of which 46 seem not to have been studied previously. The composite errors average 0.1036Å on either side of the composite predictions. There is agreement with 33 of 41 independent test data (80.5%), and those not in agreement fall outside the composite error limits by an average of 1.83%.
Category: Chemistry

[6] viXra:1204.0075 [pdf] submitted on 2012-04-18 06:01:16

Reformulation of Activated Complex Theory

Authors: Sosale Chandrasekhar
Comments: 15 Pages.

The key assumption of activated complex theory (ACT), that the AC is in thermodynamic equilibrium with the reactants, needs to be reconsidered. This is because the formation of the AC is slower than its collapse to product. However, this can be remedied by assuming that the AC is formed in a rapid pre-equilibrium as a thermally activated species, which collapses to products in a slow step involving the diffusion of another AC molecule (or solvent in the case of a unimolecular reaction). This implies a violation of the principle of microscopic reversibility (PMR), as also the relation between standard free energy change and equilibrium constant (ΔGo = -RTlnK). However, it may be argued that not only do these not apply to processes performed irreversibly, but also that irreversibility requires the breakdown of the PMR. Accordingly, catalysts may alter equilibrium constants, and enzymes may regulate biochemical processes in hitherto unsuspected ways.
Category: Chemistry

[5] viXra:1011.0060 [pdf] submitted on 24 Nov 2010

New Lewis Structures Through the Application of the Hypertorus Electron Model

Authors: Omar Yépez
Comments: 12 pages

The hypertorus electron model is applied to the chemical bond. As a consequence, the bond topology can be determined. A linear correlation is found between the normalized bond area and the bond energy. The normalization number is a whole number. This number is interpreted as the Lewis's electron pair. A new electron distribution in the molecule follows. This discovery prompts to review the chemical bond, as it is understood in chemistry and physics.
Category: Chemistry

[4] viXra:1008.0016 [pdf] submitted on 7 Aug 2010

On the Limit for the Periodic Table of the Elements

Authors: Chun-Xuan Jiang
Comments: 7 Pages.

It has been proved that the 5g = 18 is unstable, the heaviest element that occurs naturally is uranium with an atomic number of 92 and the island of stability does not exist using the modified Pauli principle. This is the Book proof.
Category: Chemistry

[3] viXra:1003.0099 [pdf] submitted on 6 Mar 2010

Methods in Industrial Biotechnology for Chemical Engineers

Authors: W. B. Vasantha Kandasamy, Florentin Smarandache
Comments: 126 pages

Industrial Biotechnology is an interdisciplinary topic to which tools of modern biotechnology are applied for finding proper proportion of raw mix of chemicals, determination of set points, finding the flow rates etc., This study is significant as it results in better economy, quality product and control of pollution. The authors in this book have given only methods of industrial biotechnology mainly to help researchers, students and chemical engineers. Since biotechnology concerns practical and diverse applications including production of new drugs, clearing up pollution etc. we have in this book given methods to control pollution in chemical industries as it has become a great health threat in India. In some cases, the damage due to environmental pollution outweighs the benefits of the product.
Category: Chemistry

[2] viXra:1003.0090 [pdf] submitted on 8 Mar 2010

Observation of Anomalous Potential Electric Energy in Distilled Water Under Solar Heating

Authors: Florentin Smarandache, V. Christianto
Comments: 9 pages

In this paper, we describe a very simple experiment with distilled water which could exhibit anomalous potential electrical energy with very minimum preparation energy. While this observed excess energy here is less impressive than [1][2] and the material used is also far less exotic than common LENR-CANR experiments, from the viewpoint of minimum preparation requirement - and therefore less barrier for rapid implementation--, it seems that further experiments could be recommended in order to verify and also to explore various implications of this new proposition.
Category: Chemistry

[1] viXra:0808.0005 [pdf] submitted on 17 Aug 2008

The Arata Demonstration: A Review Summary

Authors: Talbot Chubb
Comments: 4 pages

On May 22, a special announcement/presentation was held at Osaka University by Prof. Yoshiaki Arata in the presence of colleagues, guests, and press. The announcement of new results took place in Arata Hall, a campus building named for Prof. Arata, and a demonstration took place in the Arata-Zhang laboratory room in a nearby research building. A research paper describing recent results was made available in Japanese and English versions.
Category: Chemistry

Recent Replacements

[3] viXra:1403.0946 [pdf] replaced on 2014-04-04 09:31:12

Do Triatomic Molecules Echo Atomic Periodicity?

Authors: Ray Hefferlin, Joshua Barrow
Comments: 20 Pages. 20. Lecture at APMAS Congress in Turkey, April 25, will include much of the material in this article. The article has not been submitted to any journal and may not be

An early test for periodicity among triatomic molecular energies of atomization underscores the role of the periodic law as a foundation of chemistry. The objective of this work is to prepare for a similar test using vibration frequencies ν1 of free, ground-state, main-group triatomic molecules. Using data from four data bases and from computation, we have collected and ν1 data for molecules formed from second period atoms. The collected ν1 might be of use in optical or near-optical searches for cold triatomics in interstellar space.
Category: Chemistry

[2] viXra:1212.0152 [pdf] replaced on 2012-12-29 03:57:17

There Are Only 92 Stable Elements in Nature

Authors: Chun-Xuan Jiang
Comments: 8 Pages.

Using the stable number theory we prove there are only 92 stable elements in nature and obtain the correct valence electron configurations of the elementsd. In Mendeleev periodic table the elements(1-18,29-36 and 46) have correct valence electron configurations and the elements(19-28,37-45 and 46-92) have wrong valence electron configurations.The elements have no periods.Appendix is wrong Mendeleev periodic table of electron configurations of the elements
Category: Chemistry

[1] viXra:1212.0152 [pdf] replaced on 2012-12-27 18:20:29

There Are Only 92 Stable Elements in Nature

Authors: Chun-Xuan Jiang
Comments: 5 Pages.

using stable number theory[3] we prove there are only 92 stable elements n nature and obtain the correct valence electron configurations of the elements.In Mendeleev periodic table the elements(1-18,29-36 and 46)have correct valence electron configurations and the elements(19-28,37-45 and 47-92) have wrong valence electron configurations. The elements have no periods.
Category: Chemistry