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Organic chemistry

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https://www.readbyqxmd.com/read/28644993/long-term-toxicity-of-surface-charged-polystyrene-nanoplastics-to-marine-planktonic-species-dunaliella-tertiolecta-and-artemia-franciscana
#1
E Bergami, S Pugnalini, M L Vannuccini, L Manfra, C Faleri, F Savorelli, K A Dawson, I Corsi
Plastic pollution has been globally recognized as a critical issue for marine ecosystems and nanoplastics constitute one of the last unexplored areas to understand the magnitude of this threat. However, current difficulties in sampling and identifying nano-sized debris make hard to assess their occurrence in marine environment. Polystyrene nanoparticles (PS NPs) are largely used as nanoplastics in ecotoxicological studies and although acute exposures have been already investigated, long-term toxicity on marine organisms is unknown...
June 15, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28644476/enantioselective-intermolecular-benzylic-c-h-amination-catalysed-by-an-engineered-iron-haem-enzyme
#2
Christopher K Prier, Ruijie K Zhang, Andrew R Buller, Sabine Brinkmann-Chen, Frances H Arnold
C-H bonds are ubiquitous structural units of organic molecules. Although these bonds are generally considered to be chemically inert, the recent emergence of methods for C-H functionalization promises to transform the way synthetic chemistry is performed. The intermolecular amination of C-H bonds represents a particularly desirable and challenging transformation for which no efficient, highly selective, and renewable catalysts exist. Here we report the directed evolution of an iron-containing enzymatic catalyst-based on a cytochrome P450 monooxygenase-for the highly enantioselective intermolecular amination of benzylic C-H bonds...
July 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28643351/quality-specifications-of-routine-clinical-chemistry-methods-based-on-sigma-metrics-in-performance-evaluation
#3
Jun Xia, Su-Feng Chen, Fei Xu, Yong-Lie Zhou
INTRODUCTION: Sigma metrics were applied to evaluate the performance of 20 routine chemistry assays, and individual quality control criteria were established based on the sigma values of different assays. METHODS: Precisions were expressed as the average coefficient variations (CVs) of long-term two-level chemistry controls. The biases of the 20 assays were obtained from the results of trueness programs organized by National Center for Clinical Laboratories (NCCL, China) in 2016...
June 23, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28640998/oximes-and-hydrazones-in-bioconjugation-mechanism-and-catalysis
#4
Dominik K Kölmel, Eric T Kool
The formation of oximes and hydrazones is employed in numerous scientific fields as a simple and versatile conjugation strategy. This imine-forming reaction is applied in fields as diverse as polymer chemistry, biomaterials and hydrogels, dynamic combinatorial chemistry, organic synthesis, and chemical biology. Here we outline chemical developments in this field, with special focus on the past ∼10 years of developments. Recent strategies for installing reactive carbonyl groups and α-nucleophiles into biomolecules are described...
June 22, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28640616/the-twist-of-a-silicon-silicon-double-bond-selective-anti-addition-of-hydrogen-to-an-iminodisilene
#5
Daniel Wendel, Tibor Szilvási, Christian Jandl, Shigeyoshi Inoue, Bernhard Rieger
Hydrogenation of alkenes with C=C bonds is a ubiquitous reaction in organic chemistry. However, this transformation remains unknown for heavier counterparts, disilenes with Si=Si bonds. Here we report the isolation of (Z)-diiminodisilyldisilene 2 featuring a highly trans-bent and twisted structure and the longest silicon-silicon double bond reported to date. In silico studies suggested that the Si=Si bond in 2 is described as very weak double donor-acceptor bond. We utilized the remarkable electronic and structural features of this product to achieve the first demonstration of hydrogen activation by a multiply bonded silicon compound under ambient conditions...
June 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28640577/laser-ablation-molecular-isotopic-spectrometry-for-molecules-formation-chemistry-in-fs-laser-ablated-plasmas
#6
Huaming Hou, Xianglei Mao, Vassilia Zorba, Richard E Russo
Recently, laser ablated molecular isotopic spectrometry (LAMIS) has expanded its capability to explore molecules formation mechanism in laser induced plasma in addition to isotope analysis. LAMIS is powerful tool for tracking the origination of atoms that involved in formation of investigated molecules by labeling atoms with its isotopic substitution. The evolutionary formation pathways of organic molecules, especially of C2 dimers and CN radicals, were frequently reported. However, very little is known about the formation pathways for metallic radicals and heterodimers in laser ablated plasma...
June 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28638140/imaging-dynamic-fingerprints-of-competing-e2-and-sn2-reactions
#7
Eduardo Carrascosa, Jennifer Meyer, Jiaxu Zhang, Martin Stei, Tim Michaelsen, William L Hase, Li Yang, Roland Wester
The competition between bimolecular nucleophilic substitution and base-induced elimination is of fundamental importance for the synthesis of pure samples in organic chemistry. Many factors that influence this competition have been identified over the years, but the underlying atomistic dynamics have remained difficult to observe. We present product velocity distributions for a series of reactive collisions of the type X(-) + RY with X and Y denoting the halogen atoms fluorine, chlorine and iodine. By increasing the size of the residue R from methyl to tert-butyl in several steps, we find that the dynamics drastically change from backward to dominant forward scattering of the leaving ion relative to the reactant RY velocity...
June 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28636761/molecular-tools-for-facilitative-carbohydrate-transporters
#8
Marina Tanasova, Joseph R Fedie
Facilitative carbohydrate transporters - Gluts - have received a wide attention over decades due to their essential role in the nutrient uptake and links with various metabolic disorders, including diabetes, obesity, and cancer. Endeavors into understanding mechanisms of Glut-mediated nutrient uptake have resulted in the multidisciplinary research field, branching protein chemistry, chemical biology, organic synthesis, crystallography, and biomolecular modeling. Gluts became attractive targets for cancer research and medicinal chemistry, leading to the development of new approaches to cancer diagnostics and providing avenues for cancer-targeting therapeutics...
June 21, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28636596/selective-sp-3-c-h-alkylation-via-polarity-match-based-cross-coupling
#9
Chip Le, Yufan Liang, Ryan W Evans, Ximing Li, David W C MacMillan
The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp(3))-C(sp(2)) coupling, there is a growing demand for C-H alkylation reactions, wherein sp(3) C-H bonds are replaced with sp(3) C-alkyl groups...
June 21, 2017: Nature
https://www.readbyqxmd.com/read/28636383/gene-expression-profiling-in-human-lung-cells-exposed-to-isoprene-derived-secondary-organic-aerosol
#10
Ying-Hsuan Lin, Maiko Arashiro, Phillip W Clapp, Tianqu Cui, Kenneth G Sexton, William Vizuete, Avram Gold, Ilona Jaspers, Rebecca C Fry, Jason Douglas Surratt
Secondary organic aerosol (SOA) derived from the photochemical oxidation of isoprene contributes a substantial mass fraction to atmospheric fine particulate matter (PM2.5). The formation of isoprene SOA is influenced largely by anthropogenic emissions through multiphase chemistry of its multi-generational oxidation products. Considering the abundance of isoprene SOA in the troposphere, understanding mechanisms of adverse health effects through inhalation exposure is critical to mitigating its potential impact on public health...
June 21, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28636366/oxygenation-via-c-h-c-c-bond-activation-with-molecular-oxygen
#11
Yu-Feng Liang, Ning Jiao
The selective oxidation of organic molecules is a fundamentally important component of modern synthetic chemistry. In the past decades, direct oxidative C-H and C-C bond functionalization has proved to be one of the most efficient and straightforward methods to synthesize complex products from simple and readily available starting materials. Among these oxidative processes, the use of molecular oxygen as a green and sustainable oxidant has attracted considerable attention because of its highly atom-economical, abundant, and environmentally friendly characteristics...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28636358/transferable-atom-centered-potentials-for-the-correction-of-basis-set-incompleteness-errors-in-density-functional-theory
#12
Alberto Otero-de-la-Roza, Gino A DiLabio
Recent progress in the accurate calculation of non-covalent interactions has enabled density-functional theory (DFT) to model systems relevant in biological and supramolecular chemistry. The application of DFT methods using atom-centered Gaussian basis sets to large systems is limited by the number of basis functions required to accurately model thermochemistry and, in particular, weak intermolecular interactions. Basis-set incompleteness error (BSIE) arising from the use of incomplete basis sets leads to erroneous intermolecular energies, bond dissociation energies, and structures...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636351/heats-of-formation-of-medium-size-organic-compounds-from-contemporary-electronic-structure-methods
#13
Yury Minenkov, Heng Wang, Zhandong Wang, S Mani Sarathy, Luigi Cavallo
Computational electronic structure calculations are routinely undertaken to predict thermodynamic properties of the various species. However, the application of highly accurate wave function theory methods, such as the "gold standard" coupled cluster approach including single, double and partly triple excitations in perturbative fashion, CCSD(T), to large molecules is limited due to high computational cost. In this work, the promising domain based local pair natural orbital coupled cluster approach, DLPNO-CCSD(T), has been tested to reproduce 113 accurate formation enthalpies of medium-size molecules (few dozens heavy atoms) important for bio- and combustion chemistry via the reaction based Feller-Peterson-Dixon approach...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636313/iodine-iii-reagents-in-radical-chemistry
#14
Xi Wang, Armido Studer
The chemistry of hypervalent iodine(III) compounds has gained great interest over the past 30 years. Hypervalent iodine(III) compounds show valuable ionic reactivity due to their high electrophilicity but also express radical reactivity as single electron oxidants for carbon and heteroatom radical generation. Looking at ionic chemistry, these iodine(III) reagents can act as electrophiles to efficiently construct C-CF3, X-CF3 (X = heteroatom), C-Rf (Rf = perfluoroalkyl), X-Rf, C-N3, C-CN, S-CN, and C-X bonds...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28636310/sensing-mechanisms-in-the-redox-regulated-2fe-2s-cluster-containing-bacterial-transcriptional-factor-soxr
#15
Kazuo Kobayashi
Bacteria possess molecular biosensors that enable responses to a variety of stressful conditions, including oxidative stress, toxic compounds, and interactions with other organisms, through elaborately coordinated regulation of gene expression. In Escherichia coli and related bacteria, the transcription factor SoxR functions as a sensor of oxidative stress and nitric oxide (NO). SoxR protein contains a [2Fe-2S] cluster essential for its transcription-enhancing activity, which is regulated by redox changes in the [2Fe-2S] cluster...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28636272/development-of-biotic-ligand-model-based-freshwater-aquatic-life-criteria-for-lead-following-us-environmental-protection-agency-guidelines
#16
David K DeForest, Robert C Santore, Adam C Ryan, Brian G Church, M Jasim Chowdhury, Kevin V Brix
The US Environmental Protection Agency's (USEPA's) current ambient water quality criteria (AWQC) for lead (Pb) in freshwater were developed in 1984. The criteria are adjusted for hardness, but more recent studies have demonstrated that other parameters, especially dissolved organic carbon (DOC) and pH, have a much stronger influence on Pb bioavailability. These recent studies have been used to support development of a biotic ligand model (BLM) for Pb in freshwater, such that acute and chronic Pb toxicity can be predicted over a wide range of water chemistry conditions...
June 21, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28634602/recent-advances-in-the-computational-chemistry-of-soft-porous-crystals
#17
Guillaume Fraux, François-Xavier Coudert
Here we highlight recent progress in the field of computational chemistry of nanoporous materials, focusing on methods and studies that address the extraordinary dynamic nature of these systems: the high flexibility of their frameworks, the large-scale structural changes upon external physical or chemical stimulation, and the presence of defects and disorder. The wide variety of behavior demonstrated in soft porous crystals, including the topical class of metal-organic frameworks, opens new challenges for computational chemistry methods at all scales...
June 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28632984/aging-induced-changes-in-biochar-s-functionality-and-adsorption-behavior-for-phosphate-and-ammonium
#18
Shamim Mia, Feike A Dijkstra, Balwant Singh
Biochar, a form of pyrogenic carbon, can contribute to agricultural and environmental sustainability by increasing soil reactivity. In soils, biochar could change its role over time through alterations in its surface chemistry. However, a mechanistic understanding of the aging process and its role in ionic nutrient adsorption and supply remain unclear. Here, we aged a wood biochar (550 °C) by chemical oxidation with 5-15% H2O2 and investigated the changes in surface chemistry and the adsorption behavior of ammonium and phosphate...
June 20, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28632338/difluoromethylation-reactions-of-organic-compounds
#19
Damian E Yerien, Sebastian Barata-Vallejo, Al Postigo
The relevance of the -CF2H moiety has attracted considerable attention from organic synthetic and medicinal chemistry communities, because this group can act as a more lipophilic isostere of the carbinol, thiol, hydroxamic acid or amide groups. Being weakly acidic, the CF2H moiety can establish hydrogen bonding interactions to improve the binding selectivity of biologically active compounds. Therefore, the hydroxyl, amino, and thio substituents of lead structures are routinely replaced by a CF2H motif in drug discovery, with great benefits in the pharmacological activity of drugs and drug candidates and agrochemicals...
June 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28631486/melding-caged-compounds-with-supramolecular-containers-photogeneration-and-miscreant-behavior-of-the-coumarylmethyl-carbocation
#20
Nareshbabu Kamatham, José P Da Silva, Richard S Givens, V Ramamurthy
By merging well-established concepts of supramolecular chemistry, protecting group strategy, and photochemistry, we have solubilized in water hydrophobic organic molecules consisting of a photoactive protecting group and masked carboxylic acids, released the desired acid, and confined a reactive carbocation intermediate within a capsule. Confinement of the photogenerated carbocation brought out the latent radical-like behavior. This observation is consistent with the recent theoretical prediction of the 7-(diethylamino)coumarinyl-4-methyl carbocation having a triplet diradical ground-state electronic contribution...
June 20, 2017: Organic Letters
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