Examining the PM6 semiempirical method for pKa prediction across a wide range of oxyacids

The pK~a~ 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 pK~a~ estimation method for waste treatment and environmental fate investigations

Extending the semi-empirical PM6 method for carbon oxyacid pKa prediction to sulfonic acids: Application towards congener-specific estimates for the environmentally and toxicologically relevant C1 through C8 perfluoroalkyl derivatives

A positive bias in the semi-empirical PM6 method for estimating pKa values of sulfonic acids was corrected by a correlation developed between non-adjusted PM6 pKa values and the corresponding experimentally obtained/estimated acidity constants for a range of representative alkyl, aryl, and halogen substituted sulfonic acids. Application of this correction to PM6 values allows for extension of this computational method to a new acid functional group

Congener-Specific Numbering Systems for the Environmentally Relevant C4 through C8 Perfluorinated Homologue Groups of Alkyl Sulfonates, Carboxylates, Telomer Alcohols and Acids, and Their Derivatives

We introduce a congener-specific numbering system for the C4 through C8 perfluorinated homologue groups of alkyl sulfonates, carboxylates, telomer alcohols and acids, and their derivatives. Increasing length of the carbon chain beyond C3 leads to a corresponding rapid increase in the number of potential isomers (C4 =4, C5 =8, C6 =17, C7 =39, and C8 =89 congeners). There is a need for clear and unambiguous chemical shorthand to ensure accuracy and consistency in the future perfluorinated alkyl substance (PFA) literature, and to correct previous misconceptions that may have restricted research efforts into developing full-congener PFA analysis. If adopted by the research community, introduction of a numbering system at this relatively early stage of investigations into the congener-specific analysis, environmental behavior, and toxicology of PFAs would not require an arduous and difficult reassignment of historical structures and naming conventions presented in the prior art. Many PFA congeners are chiral, necessitating a consideration of their enantiospecific environmental behavior and toxicology

Projected Climate Change Impacts on Grape Growing in the Okanagan Valley, British Columbia, Canada

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

Predicting the Congener-Specific Environmental Behaviour of Perfluorinated Acid Contaminants Using Semi-Empirical Computational Methods

Perfluorinated acids (PFAs) are contaminants detected worldwide in a range of abiotic and biotic environmental matrices. The two major classes of PFAs include the perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs), both of which are considered persistent and potentially bioaccumulative. Current research and regulatory efforts are focussed on the straight-chain members of each PFA class and homologue group, primarily because these congeners are the major components of technical mixtures and are also available as pure standards. However, the numerous potential branched congeners in each PFA class represent a poorly understood family of environmental contaminants whose environmental and toxicological properties may be more important than the more prevalent straight-chain members. To help broaden the current understanding of PFA environmental fate and toxicology, semi-empirical computational methods were used predict fundamental physico-chemical properties of all potential C4 to C8 PCFA and PFSA congeners. Established quantitative structure-activity models for other multi-class emerging and legacy contaminants were applied to estimate key parameters related to the toxicology, environmental partitioning, and abiotic and biotic degradation mechanisms for each PFA class. The findings provide guidance for developing new analytical methods for separating and identifying PFAs in environmental and technical mixtures, prioritizing efforts on synthesizing authentic standards, and focussing toxicological studies on the congeners most likely to be of concern

Parental environments and interactions with conspecifics alter salinity tolerance of offspring in the annual medicago truncatula

Summary: Based on expectations of the stress-gradient hypothesis for conspecific interactions, stress-sensitive genotypes may be able to persist in stressful environments when positive interactions between individuals occur under stressful environments. Additionally, we test how parental environmental effects alter responses to stress and outcomes of conspecific interactions in stress. While the stress-gradient hypothesis focuses on plant growth, earlier flowering may provide stress avoidance in short-lived organisms. We studied responses to soil salinity and conspecific neighbour using genotypes of Medicago truncatula (Fabaceae) originating from saline or non-saline environments, utilizing seeds from parental plants grown in saline or non-saline environments. During the early stages of reproduction, we quantified leaf number, as a measure of vegetative growth, and number of flowers, as a measure of early reproduction potential. Based on leaf counts, non-saline genotypes were better competitors than saline-origin genotypes and benefited from neighbouring plants in saline environments. This positive interaction was detected only when seeds were matured on parental plants grown in non-saline environments. Saline-origin genotypes displayed greater salinity tolerance in early flowering than non-saline genotypes. Plants with neighbours had greater early flowering, regardless of origin, consistent with facilitative interactions in stressful environments. Transgenerational plastic responses influenced neighbouring plant interactions on plant growth, and results suggest that facilitative interactions may be transient only persisting for one generation. However, earlier flowering of non-saline genotypes when grown with a neighbouring plant is consistent with facilitative interactions resulting in reproductive benefits in saline environments, if earlier flowering is favoured in saline environments. Synthesis. Adaptation to stressful environments allows tolerant genotypes to persist in these environments. Less appreciated is that stress-sensitive genotypes lacking such adaptations may persist in stressful environments via positive interactions with other individuals. Thus, positive interactions between individuals may explain the persistence of stress-sensitive genotypes within a population adapted to stressful environments. © 2013 British Ecological Society

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species