http://precedings.nature.com/users/b5da04a6b4295591b5947537cc300488/ Documents posted by Sierra Rayne Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3928/version/1 A systematic and comprehensive semiempirical, Hartree-Fock (HF) ab initio, and B3LYP density functional theory (DFT) study was conducted on the relative thermodynamic properties of various linear and branched perfluorinated and perhydrogenated alkyl compounds. The semiempirical AM1, PM3, and PM6 methods all consistently and accurately predict that branched alkyl compounds will generally be more thermodynamically stable than their linear counterparts. In contrast, HF and B3LYP calculations with the 6-31G(d,p), 6-31++G(d,p), and 6-311++G(d,p) basis sets predict that linear isomers will be more stable than branched analogs. These different linear versus branched perfluoroalkyl/perhydroalkyl thermodynamic property trends between semiempirical and ab initio/DFT methods were evident in both gas and aqueous phase calculations. Comparison of experimentally determined thermodynamic properties for several classes of linear and branched alkanes and alcohols with values calculated at the PM6 and B3LYP/6-311++G(d,p) levels of theory supported the well known findings that such DFT and HF approaches incorrectly predict branched alkyl compounds will be less thermodynamically stable than linear isomers. Calculations at the MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) and M05-2X/6-311++G(d,p) levels of theory on a representative subset of the linear and branched perfluorinated compounds supported the thermodynamic conclusions from the PM6 method. Strong agreement between PM6 estimated thermodynamic properties and available experimental data supports use of this computational method for accurately calculating the well established higher thermodynamic stability of branched alkyl compounds. Branched perfluoroalkyl compounds are thus expected to be more thermodynamically stable than their linear analogs. http://precedings.nature.com/documents/3928/version/1 Mon, 02 Nov 2009 15:24:31 UTC Comparative semiempirical, ab initio, and DFT study on the thermodynamic properties of linear and branched PFSA/Fs, PFCA/Fs, and perhydroalkyl sulfonic acids, alkanes, and alcohols hdl:10101/npre.2009.3928.1 2009-11-03 Sierra Rayne Nature Precedings 2009-11-02T15:24:31Z Manuscript Chemistry Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3882.1 The KOWWIN and ALOGPS octanol-water partition coefficient (Kow) estimation software programs were compared for their capacity to accurately predict log Kow values of 1596 organic compounds on the publicly available Domestic Substances List (DSL) from Environment Canada for which experimental data is available. KOWWIN contained a significantly lower number and magnitude of prediction errors compared to ALOGPS, particularly at experimental log Kow values ow data on the Canadian DSL. Predictive differences of up to 40 log Kow units were found between KOWWIN and ALOGPS, and in some cases, the discrepancies were sufficiently large that strongly opposing hydrophobicity classifications were obtained. http://dx.doi.org/10.1038/npre.2009.3882.1 Wed, 21 Oct 2009 15:02:21 UTC Performance of the ALOGPS 2.1 program for octanol-water partition coefficient prediction with organic chemicals on the Canadian Domestic Substances List doi:10.1038/npre.2009.3882.1 2009-10-21 Sierra Rayne Nature Precedings 2009-10-21T15:02:21Z Manuscript Chemistry Pharmacology Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3837/version/1 A molecular mechanics force field method (MMFF94) systematic rotor conformational search was conducted on the well known environmental contaminant n-perfluorooctanoic acid (n-PFOA). The MMFF94 conformational search yielded 2915 separate low- through high-energy conformers of n-PFOA. Ranking of these structures gave the 94 lowest MMFF94 energy conformations that were subjected to subsequent density functional theory (DFT) computational investigations at the B3LYP/6-311++G(d,p) level of theory. Application of a thermodynamic cycle approach, coupled with aqueous and gas phase DFT calculations on the molecular and anionic forms for each of the 94 lowest energy n-PFOA conformers, gave estimated acidity constants (pKa values) for a final converged set of twelve n-PFOA conformers, including the global minimum helical perfluoroalkyl chain geometry and eleven non-helical higher energy conformations. Collectively, the twelve lowest energy conformers appear to encompass 85% of the total conformational space for n-PFOA, indicating no higher energy conformations likely remain that could appreciably influence the observed composite aqueous pKa of this compound. The estimated pKa values of all eleven non-helical n-PFOA conformers were within 0.2 pKa units of the helical conformer pKa. The findings support previous predictions and recent experimental evidence for an aqueous phase n-PFOA monomeric pKa of about zero. http://precedings.nature.com/documents/3837/version/1 Thu, 08 Oct 2009 11:39:32 UTC Theoretical studies on the pKa values of perfluoroalkyl carboxylic acids: Non-helical conformation acidity constants for n-perfluorooctanoic acid (n-PFOA) hdl:10101/npre.2009.3837.1 2009-10-08 Sierra Rayne Nature Precedings 2009-10-08T11:39:32Z Manuscript Chemistry Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3829/version/1 Semiempirical, ab initio, and density functional theory (DFT) studies were conducted on a homologous series of straight chain perfluoroalkyl carboxylic acids (PFCAs) ranging in chain length from C1 (trifluoroacetic acid; TFA) to C9 (perfluorodecanoic acid). Regardless of perfluoroalkyl chain length and computational method and level employed, no significant change in the electrostatic or steric characteristics of the carboxylate head group was found between C2 and C9. Application of a thermodynamic cycle to calculations at the B3LYP/6-311++G(3df,2p) level provided an accurate prediction of the experimental monomeric pKa for TFA. At this – and similar – levels of theory, monomeric pKa values of longer straight chain PFCAs are expected to display no significant increase with increasing chain length, having a relatively constant pKa value of about 0 that is in excellent agreement with earlier predictions and with recent experimental evidence. Contrary to previous claims, perfluoroalkyl chain helicity does not appear to result in increased monomeric PFCA pKa values at chain lengths >5 perfluorocarbons. http://precedings.nature.com/documents/3829/version/1 Tue, 06 Oct 2009 10:26:45 UTC Theoretical studies on the pKa values of perfluoroalkyl carboxylic acids: Chain helicity hdl:10101/npre.2009.3829.1 2009-10-06 Sierra Rayne Nature Precedings 2009-10-06T10:26:45Z Manuscript Chemistry Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3728/version/1 Temperature dependent rate constants were estimated for the acid- and base-catalyzed and neutral hydrolysis reactions of perfluorinated telomer acrylates (FTAcrs) and phosphate esters (FTPEs), and the SN1 and SN2 hydrolysis reactions of fluorotelomer iodides (FTIs). Under some environmental conditions, hydrolysis of monomeric FTAcrs could be rapid (half-lives of several years in marine systems and as low as several days in some landfills) and represent a dominant portion of their overall degradation. Abiotic hydrolysis of monomeric FTAcrs may be a significant contributor to current environmental loadings of fluorotelomer alcohols (FTOHs) and perfluoroalkyl carboxylic acids (PFCAs). Polymeric FTAcrs are expected to be hydrolyzed more slowly, with estimated half-lives in soil and natural waters ranging between several centuries to several millenia absent additional surface area limitations on reactivity. Poor agreement was found between the limited experimental data on FTPE hydrolysis and computational estimates, requiring more detailed experimental data before any further modeling can occur on these compounds or their perfluoroalkyl sulfonamidoethanol phosphate ester (PFSamPE) analogs. FTIs are expected to have hydrolytic half-lives of about 130 days in most natural waters, suggesting they may be contributing to substantial FTOH and PFCA inputs in aquatic systems. Perfluoroalkyl sulfonamides (PFSams) appear unlikely to undergo abiotic hydrolysis at the S-N, C-S, or N-C linkages under environmentally relevant conditions, although potentially facile S-N hydrolysis via intramolecular catalysis by ethanol and acetic acid amide substituents warrants further investigation. http://precedings.nature.com/documents/3728/version/1 Tue, 08 Sep 2009 21:20:37 UTC Modeling the hydrolysis of perfluorinated compounds containing carboxylic and phosphoric acid ester functions, alkyl iodides, and sulfonamide groups hdl:10101/npre.2009.3728.1 2009-09-08 Sierra Rayne Nature Precedings 2009-09-08T21:20:37Z Manuscript Chemistry Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3011.2 Organic carbon normalized soil and sediment-water partitioning coefficients (Koc) were estimated for all C1 through C8 perfluoroalkyl carboxylic (PFCA) and sulfonic (PFSA) acid congeners. The limited experimental Koc dataset for the straight chain C7 through C10 PFCAs and C8 and C10 PFSAs was correlated to SPARC and ALOGPS computationally estimated octanol-water partitioning / distribution constants and used to predict Koc values for both branched and linear C1 through C8 isomers. Branched and linear congeners in this homologue range are generally expected to have Koc values >1, leading to their accumulation in organic matter on sediments and soils, retardation during ground and pore water flow, and the preferential association with dissolved organic matter in aquatic systems. Both increasing perfluoroalkyl chain length and linearity increase Koc values with substantial intra- and inter-homologue variation and interhomologue mixing. Variability in Koc values among the PFCA and PFSA congeners will likely lead to an enrichment of more linear and longer chain isomers in organic matter fractions, resulting in aqueous phases fractionated towards shorter chain branched congeners. The expected magnitude of fractionation will require inclusion in source apportionment models and risk assessments. A comparison of representative established quantitative structure property relationships for estimating Koc values from octanol-water partitioning constants suggests that these equilibrium partitioning frameworks may be applicable towards modeling PFCA and PFSA environmental fate processes. http://dx.doi.org/10.1038/npre.2009.3011.2 Mon, 08 Jun 2009 08:44:24 UTC Congener specific organic carbon normalized soil and sediment-water partitioning coefficients for the C1 through C8 perfluoroalkyl carboxylic and sulfonic acids doi:10.1038/npre.2009.3011.2 2009-06-08 Sierra Rayne Nature Precedings 2009-06-08T08:44:24Z Manuscript Chemistry Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3282.2 New experimental data is available in the literature regarding the octanol-water distribution behavior of representative straight chain perfluoroalkyl carboxylate (PFCA) and sulfonate (PFSA) congeners. The current study provides the first investigation into the predictive ability of various software programs for estimating the corresponding octanol-water partitioning (log P) and distribution (log D) constants of PFCAs and PFSAs. Wide predictive variation was found within and between the various methods. Several programs were able to accurately estimate the log P/D fragmental contributions of a -CF2- group for PFCAs, as well as the associated Gibbs free energies for partitioning into octanol from water due to the hydrophobic character of the perfluoroalkyl chain (ΔhydrophobicGow). Only the SPARC log D method accurately predicted the electrostatic contributions of the carboxylate head group (ΔelectrostaticGow) towards octanol-water partitioning for PFCAs. Similar log D values and organic carbon normalized sediment-water partitioning coefficients (Koc) for PFCAs and PFSAs having equivalent perfluoroalkyl chain lengths suggests potentially equivalent ΔelectrostaticGow and ΔhydrophobicGow contributions towards lipophilic partitioning for these two contaminant classes at near neutral pH values, regardless of head group identity. In contrast, there are potentially different ΔelectrostaticGow and ΔhydrophobicGow contributions towards proteinophilic partitioning under biologically relevant conditions. http://dx.doi.org/10.1038/npre.2009.3282.2 Mon, 01 Jun 2009 10:51:14 UTC A comparative assessment of octanol-water partitioning and distribution constant estimation methods for perfluoroalkyl carboxylates and sulfonates doi:10.1038/npre.2009.3282.2 2009-06-01 Sierra Rayne Nature Precedings 2009-06-01T10:51:14Z Manuscript Chemistry Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3256/version/1 SPARC, KOWWIN, and ALOGPS octanol-water partitioning (log Kow) and distribution (log D) constants were calculated for all C1 through C8 and the straight chain C9 through C15 perfluoroalkyl sulfonic acids (PFSAs) and carboxylic acids (PFCAs). Application of five established models for estimating bioconcentration factors (BCFs) were applied to the PFSA and PFCA log Kow and log D data and compared to available field and laboratory BCF data. Wide variability was observed between the methods for estimating log Kow and log D values, ranging up to several log units for particular congeners, and which was further compounded by additional variability introduced by the different BCF equations applied. With the exception of n-perfluorooctanecarboxylic acid (n-PFOA), whose experimental BCF was poorly modeled by all approaches, the experimental BCF values of the other PFSA and PFCA congeners were reasonably approximated by the ALOGPS log P values in combination with any of the five log Kow based BCF equations. The SPARC and KOWWIN log Kow and log D values provided generally less accurate BCF estimates regardless of the BCF equation applied. However, the SPARC Kow values did provide BCF estimates for PFSA congeners with errors http://precedings.nature.com/documents/3256/version/1 Mon, 18 May 2009 14:05:29 UTC An assessment of organic solvent based equilibrium partitioning methods for predicting the bioconcentration behavior of perfluorinated sulfonic acids, carboxylic acids, and sulfonamides hdl:10101/npre.2009.3256.1 2009-05-18 Sierra Rayne Nature Precedings 2009-05-18T14:05:29Z Manuscript Chemistry Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3162/version/1 A statistical analysis was conducted on long-term climate records in the Okanagan Valley wine grape growing region of British Columbia, Canada. No observable trends for average annual temperatures were found in the region. Analyses of monthly mean and extreme temperatures show wide spatial and temporal heterogeneity, indicating that future studies using downscaling of global climate models for this region will require resolutions on the order of several kilometers. Mean winter temperatures are increasing throughout the valley, and extreme minimum temperatures are also increasing during the winter at the central and northern sites which have historically presented the most risk of winter damage to grapevines. Only the most southern and northern sub-regions are expected to see significant changes in their heat unit accumulations during the growing season. Over the coming century, the southern end of the valley will likely move from Winkler heat unit region 1 to 2. All regions of the Okanagan will continue to have latitude-temperature indices among the lowest of the world’s fine table wine producing regions over the coming century. Growing season and dormant season average temperatures are expected to change by only a modest amount by 2100. Current climate maturity groupings for ripening grape varieties will likely stay constant at cool (central and southern areas) and intermediate (south-central) for all sites except Osoyoos (south). The climate trendings at Osoyoos suggest it will transition from an intermediate to a warm grouping by about 2050. The early to mid-season ripening capacity of the region may improve due to climate changes, but there is a risk of the asymmetric late season increases in minimum daily temperatures lowering the daily temperature range at some sites, possibly leading to difficulties in maintaining a balanced between sugar and sensory profiles as wine grapes approach maturity. The projected warming at the southern end of the valley should favor improved and increased Merlot production, will require Chardonnay production to shift northwards, and will allow growing of warmer climate wine grape varieties currently inaccessible because of low winter temperatures and a lack of growing season heat units. Increasing winter temperatures throughout the region are expected to result in increased risk of pests such as Pierce’s disease. http://precedings.nature.com/documents/3162/version/1 Fri, 24 Apr 2009 19:20:12 UTC Projected Climate Change Impacts on Grape Growing in the Okanagan Valley, British Columbia, Canada hdl:10101/npre.2009.3162.1 2009-04-24 Sierra Rayne Nature Precedings 2009-04-24T19:20:12Z Manuscript Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2981/version/1 The pKa estimation ability of the semiempirical PM6 method was evaluated across a broad range of oxyacids and compared to results obtained using the SPARC software program. Compound classes under consideration included acetic acids, alicyclic and aromatic heterocyclic acids, benzoic acids, boronic acids, hydroxamic acids, oximes, peroxides, peroxyacids, phenols, α-saturated acids, α-saturated alcohols, sulfinic acids, α-unsaturated acids, and α-unsaturated alcohols. PM6 accurately predicts the acidity of acetic and benzoic acids and their derivatives, but is less reliable for alicyclic and aromatic heterocyclic acids and phenols. α-Saturated acids are reliably modeled by PM6 except for polyacid derivatives with α-alcohol moieties. α-Saturated alcohols only appear to yield reliable PM6 results where an α-hydroxy or α-alkoxy moiety is absent. Carboxylic acids with simple α-alkene unsaturation are well approximated by PM6 except where alkyne α-unsaturation or α-carboxylation are also present. The PM6 and SPARC methods exhibit approximately equal pKa prediction performance for the acetic, alicyclic, and benzoic acids. SPARC outperforms PM6 on the peroxides, peroxyacids, phenols, and α-saturated acids and α-saturated alcohols. pKa values for boron, nitrogen, and sulfur oxyacids do not appear to be reliably estimated by either the PM6 or SPARC methods. The findings will help guide the potential appropriateness of results from the PM6 pKa estimation method for waste treatment and environmental fate investigations. http://precedings.nature.com/documents/2981/version/1 Thu, 26 Mar 2009 10:03:59 UTC Examining the PM6 semiempirical method for pKa prediction across a wide range of oxyacids hdl:10101/npre.2009.2981.1 2009-03-26 Sierra Rayne Nature Precedings 2009-03-26T10:03:59Z Manuscript Chemistry Pharmacology Earth & Environment http://creativecommons.org/licenses/by/3.0/