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  • 1
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    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanographic Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2019.
    Description: Marine microbes are key drivers of biogeochemical transformations within the world’s oceans. Although seawater appears uniform at scales that humans often interact with and sample, the world that marine microbes inhabit can be highly heterogeneous, with numerous biological and physical processes giving rise to resource hotspots where nutrient concentrations exceed background levels by orders of magnitude. While the impact of this microscale heterogeneity has been investigated in the laboratory with microbial isolates and theoretical models, microbial ecologists have lacked adequate tools to interrogate microscale processes directly in the natural environment. Within this thesis I introduce three new technologies that enable interrogation of microbial processes at the microscale in natural marine communities. The IFCB-Sorter acquires images and sorts individual phytoplankton cells, directly from seawater, allowing studies exploring connections between the diversity of forms present in the plankton and genetic variability at the single-cell level. The In Situ Chemotaxis Assay (ISCA) is a field-going microfluidic device designed to probe the distribution and role of motility behavior among microbes in aquatic environments. By creating microscale hotspots that simulate naturally occurring ones, the ISCA makes it possible to examine the role of microbial chemotaxis in resource acquisition, phytoplankton-bacteria interactions, and host-symbiont systems. Finally, the Millifluidic In Situ Enrichment (MISE) is an instrument that enables the study of rapid shifts in gene expression that permit microbial communities to exploit chemical hotspots in the ocean. The MISE subjects natural microbial communities to a chemical amendment and preserves their RNA in a minute-scale time series. Leveraging an array of milliliter-volume wells, the MISE allows comparison of community gene expression in response to a chemical stimulus to that of a control, enabling elucidation of the strategies employed by marine microbes to survive and thrive in fluctuating environments. Together, this suite of instruments enables culture-independent examination of microbial life at the microscale and will empower microbial ecologists to develop a more holistic understanding of how interactions at the scale of individual microbes impact processes in marine ecosystems at a global scale.
    Description: I’d like to thank the Gordon and Betty Moore Foundation, the National Science Foundation, and NSERC for funding portions of my research.
    Description: I’d like to thank the Gordon and Betty Moore Foundation, the National Science Foundation, and NSERC for funding portions of my research.
    Keywords: Microorganisms ; Bacteria ; Marine ecology ; Scientific apparatus and instruments ; Plankton ; Plankton--Growth ; Phytoplankton ; Chemical oceanography ; Antarctic Ocean
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 2
    Publication Date: 2021-05-19
    Description: Quantitative and qualitative composition of the bacterioflora of biosediments produced by mussels and oysters were studied in the southern Kerch Strait, area of potential experimental and commercial culture of molluscs. Sampling was made from May to October 1993. A total of 45 various groups of microorganisms were determined and 50 pure bacterial cultures were isolated. On the basis of research into morphological, tinctorial, cultural and physiological and biochemical properties of the isolated strains, they were identified to species or genus level. Of 22 isolated strains of the enteric bacilli group, Escherichia coli accounted for 9.1%, Enterobacter agglomerans, 50%, Citrobacter freundii, 27.3%, C. diversus, 9.1%, C. amalonaticus 4.5%. Among enterococci, mainly Enterococcus faecium were determined, E. faecalis accounting for from 8 to 25% of the enterococci group. Bacteria of the genera Aeromonas, Pseudomonas, Bacillus, Vibrio, and a proteolytic biovariety of enterococcus were most active hydrolase producers. Among aerobic bacteria, Bacillus cereus were identified; anaerobic bacteria were represented mainly by Clostridium perfringens.
    Description: Выявлен обильный рост гетеротрофной (сапрофитной) микрофлоры. Сапрофитные бактерии используют органическое вещество биоотложений в своём конструктивном и энергетическом обмене их количество напрямую связано с наличием легкоусвояемых соединений углерода и азота, поэтому они могут рассматриваться как достаточно информативные биологические индикаторы процессов самоочищения среды. По отдельности определяли количество психрофильных бактерий с температурным оптимумом роста 20-22°С и мезофильных — растущих при температуре инкубации 37°С. Психрофилы в основном состоят из представителей морской флоры, циркулирующих в водной среде и организме гидробионтов. Среди мезофилов доминируют терригенные бактерии, поступающие в прибрежную зону моря с различными источниками антропогенного загрязнения и адаптированные к новым условиям существования. Сезонная динамика этих двух групп сапрофитов в биоотложениях моллюсков района размещения мидий- ных установок представлена на графиках. Общепринятые показатели санитарно-гигиенического и эпидемического состояния объектов внешней среды — бактерии группы кишечных палочек (БГКП) и энтерококки были обнаружены в среднем количестве 240 НВЧ/г. Численность энтерококков в биоотложениях была почти постоянной (за исключением единичного случая), БГКП — более вариабельна. БГКП были представлены в основном цитратассимилируюшими видами. Из 22 выделенных штаммов БГКП Escherichia соli составили 9,1%, Enterobacter agglomerans — 50,0%, Citrobacter freundii — 27,3%, С. diversus — 9,1%, С, amalonaticus — 4,5%. Среди энтерококков определены в основном Enterococcus faecium, а количество Е. faecalis составляло в общей группе энтерококков от 8 до 25%. Таким образом, показатели фекального загрязнения были обнаружены в биоотложениях в невысоких количествах.
    Description: Published
    Keywords: Taxonomy ; Bacterioflora ; Microorganisms ; Biological sedimentation ; Enterobacter agglomerans ; Citrobacter freundii ; Escherichia соli ; Bacillus cereus ; Biotechnologies ; Таксономия ; Микроорганизмы ; Биоотложения ; Анаэробные бактерии ; Энтерококки ; Биотехника
    Repository Name: AquaDocs
    Type: Journal Contribution , Non Refereed
    Format: pp.120-123
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  • 3
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    Universidade Estadual de Maringá. Departamento de Biologia. Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais
    Publication Date: 2022-09-07
    Description: Vertebrates and invertebrates are known as important biological vectors in the dispersal of terrestrial neotropical communities (e.g. plants, animals). However, its role in the formation and maintenance of the microbial community in aquatic ecosystems is, in general, greatly underestimated. The objective was to evaluate the relative role of different biological vectors (amphibians and odonates) in the dispersion and consequent structuring of ciliate protozoan communities. An experiment was carried out in the open air, simulated in polyethylene pots, for 33 days, 4 treatments were designated a control with only the action of the wind, without addition of propagules one with addition of propagules from odonatas washes, one with addition of propagules from amphibian washes and one with addition of propagules from washes of both vectors. There were 54 species of ciliates, distributed in 9 orders, being the most representative Hymenostomatida and Peritrichia. The results showed that animal vectors represent an important pathway for the dispersion of ciliates. The species richness and abundance of ciliates showed a significant increase in their values, markedly after the 12th day of experiment. For the species composition, differences were evidenced between the treatments, within each time, as well as between the different treatments throughout the experiment. The dynamics of the dispersion of ciliary protists was enhanced when mediated by biological vectors, especially amphibians. Emphasizing that the nature of the propagule (forms of resistance or active) seems to play a relevant role in the dispersion and colonization capacity, determining the structure and dynamics of the ciliate protist communities.
    Description: Vertebrados e invertebrados são conhecidos como vetores biológicos importantes na dispersão de comunidades neotropicais terrestres (e.g. plantas, animais). Entretanto, seu papel para formação e manutenção da comunidade microbiana em ecossistemas aquáticos é, em geral,subestimado. O objetivo foi avaliar o papel relativo de diferentes vetores biológicos (anfíbios e odonatas) na dispersão e consequente estruturação das comunidades de protozoários ciliados. Foi realizado um experimento ao ar livre, simulados em potes de politileneo, durante 33 dias, foram designados 4 tratamentos um controle com apenas ação do vento, sem adição de propágulos um com adição de propágulos a partir de lavagens de odonatas, um com adição de propágulos a partir de lavagens de anfíbios e um com adição de propágulos a partir de lavagens de ambos os vetores. Foram registradas 54 espécies de ciliados, distribuídos em 9 ordens, sendo as mais representativas Hymenostomatida e Peritrichia. Vetores animais representam uma via importante para a dispersão de ciliados. A riqueza de espécies e abundância de ciliados evidenciaram um aumento significativo em seus valores, marcadamente após o 12º dia de experimento. Para a composição de espécies, diferenças foram evidenciadas entre os tratamentos, dentro de cada tempo e entre os distintos tratamentos ao longo do experimento. A dinâmica da dispersão de protistas ciliados foi potencializada quando mediada por vetores biológicos, especialmente anfíbios. Enfatizando que a natureza do propágulo (formas de resistências ou ativas) parece ter papel relevante na capacidade de dispersão e colonização, determinando a estrutura e dinâmica das comunidades de protistas ciliados.
    Description: Masters
    Keywords: Protistas Ciliophora ; Ciliados planctônicos (Ciliophora) ; Ciliados de água doce ; Colonização ; Sucessão ; Dispersão ; Colonization ; Succession ; Potential dispersal ; Effective dispersal ; Microorganisms ; Passive dispersal ; Ecologia, Comunidades de ; ASFA_2015::P::Protists ; ASFA_2015::F::Freshwater ecology ; ASFA_2015::F::Freshwater organisms ; ASFA_2015::C::Communities (ecological) ; ASFA_2015::P::Plankton ; ASFA_2015::D::Dispersion ; ASFA_2015::C::Colonization
    Repository Name: AquaDocs
    Type: Thesis/Dissertation
    Format: 36pp.
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  • 4
    Publication Date: 2021-05-19
    Description: Bacterial and fungal microflora of Litopenaeus vannamei cultured in Choibdeh, Abadan was studied. For this purpose, PLs before and after stocking and those shrimps persisting on food tray from June to August, 2006 were taken randomly. Live samples transferred to microbiology laboratory of South Aquaculture Research Center, Ahwaz. Special culture media (e.g. Tryptic Soy Agar + 1.5-2% Nacl and Sabouraud Dextrose Agar + 1.5-2% Nacl) were used for bacterial and fungal culture. We isolated 10 bacterial species of which Vibrio alginolyticus (36.92%) had high abundance among bacterial species. We also isolated and identified three fungal species including Aspergillus niger (66.66%) A. fumigates (16.66%) and Fusarium sp. (16.66%). A. niger was predominant among fungal species. All bacterial and fungal species that were identified were opportunistic.
    Description: Published
    Keywords: Shrimp culture ; Litopenaeus vannamei ; Microorganisms ; Freshwater
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.161-168
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  • 5
    Publication Date: 2021-05-19
    Description: 0Genetic polymorphism by means of biochemical genetic markers using polyacrylamide gel electrophoresis system in four barbus fish species has been investigated. Species scientific name were Barbus sharpeyi ; Gunther, 1847 , Barbus grypus ; Heckel, 1843, Barbus xanthopterus ; Heckel, 1843 and Barbus esocinus ; Heckel, 1843.Sampling site and location were mainly in the rivers located in Khoozestan province such as Karoon and Karkheh rivers and the Dez dam. Different organs such as blood, muscle, kidney, eye and heart were sampled and analysed for the presence of tf, es, sod and pgm alleles. High polymorphism and presence of different alleles scored, but populations were not in the H-W equilibrium. Considring results, using current and avaiable genetic markers such as microsattelits is recommended for future works.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Chemistry ; Genetics ; Genetics Markers ; Distinguish ; Barbus ; Species ; Barbus sharpeyi ; Barbus xanthopterus ; Barbus esocinus
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 62pp.
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  • 6
    Publication Date: 2021-05-19
    Description: Fish sauce is a popular fermented product used in south Asian countries which is made from different species of small fishes. In this research it was attempted to produce fish sauce from kilka fishes of the Caspian Sea. The kilka sauce was made from three different preparations of kilka, such as whole kilka, cooked whole kilka and dressed kilka. Each of these preparations was fermented in four different ways, such as traditional, enzymatic, microbial and mixture of enzyme and microorganisms. The results of this study showed that times of fermentation for traditional, enzymatic, microbial and mixture of enzyme and microbe method were 6, 1,3 and 1 months, respectively. The least and the most rate of fermentation were recognized for dressed kilka and cooked whole kilka, respectively. Microbial, biochemical and organoleptic properties of kilka fish sauce were investigated. The total bacterial count was 2.1 to 6.15 log cfu/ml, total volatile nitrogen (TVN) in samples was 250 mg/100g and protein content of kilka sauce was between 10-13 percent. The score of the taste panel for flavour, odour and colour was between 3 to 5, which means this product can be acceptable to the consumer.
    Description: Published
    Keywords: Kilka Fish Sauce ; Fermentation ; Proteolitic ; Enzyme ; Microbial ; Species ; Microorganisms
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.79-94
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  • 7
    Publication Date: 2021-05-19
    Description: Cheshmehkileh River and adjacent mountainous streams, play a strategic role as a historical axis for anthropogenic civilization, human welfare also habitat and migration pathway of commercial – biologic valuable fishes e.g. Caspian trout, Caspian kuttum, members of Cyprinidae family in south Caspian Sea drainage. Treats such as overfishing of Caspian trout and Red spotted trout stocks in mountainous headwaters, barriers construction and manipulations those are out of river carrying capacity developed by human activities, affected normal function of river as well. Sand mining big factories establishment next to the river, legal and illegal trade of river sediments, direct entry of Tonekabon landfill leakage into the river, development of Rainbow trout farms since 3 decades and huge effluents into the river containing dead fish and types of solids, escapement of cultured Rainbow trouts into the river, … are major minimum factors which needs basic information for integrating inclusively drainage management system. Cheshmehkileh River contains Headwaters of Dohezar (Daryasar & Nusha), Sehezar and Valamroud rivers during 13 monthly sampling phases between September 2009 and October 2010 based on macrozoobenthoses investigations by EPT, EPT/C EPA protocols, measurements of nominated physic-chemical and microbiologic parameters. Probability of Rainbow trouts escapement and invasion, existence, nutrition in Cheshmehkileh environment indeed investigated. Data analysis explained significant differences (P〈0.05) between groups of measured parameters in different sampling stations. Dendogram of clustered analysis based on consolidation of major biologic/ physic-chemical and microbiologic parameters, separated stations No. 1, 3, 2, 4 in one group and remained classified in different groups. Station 8 and 9 similarly separated which expressed general similarities according to Sehezar river environment which were differs in comparison with other stations. Station 11 separated according to its natural quality of water and environment. Similarities between station 10 to Sehezar river stations 8 and 9 expressed general influence of Sehezar River more than Dohezar River in Cheshmehkileh condition especially in station No. 10. High scores of EPT and EPT/C indices in upstream stations 1, 3 and 8 also low score of indices in stations 7, 13 and 6 expressed levels of environment quality between these groups of stations. Maximum average biomass of macroinvertebrates belongs to Trichoptera order in Cheshmehkileh River. Significant decrease of biomass in stations 11, 12 and 13 in comparison with other stations stated environment degradation in mentioned stations relevant to excessive sand mining as well. Pollution resistant groups of invertebrates significantly increased in downstreams against upstream stations. Also disappearing of Plecoptera order in station No. 7, 9, 10 and 13 stated low quality of environment in comparison with upstream stations. Confirmation of effects quality and quantity for point and non-point sources of imported pollutants require specific management considerations in order to present exploitations, pollutants control and emergencies for river monitoring in forthcoming years.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: River ; Pollution ; Aquaculture ; EPTC ; Assessment ; Macroinvertebrates ; Chemistry ; Microbiology
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 138pp.
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  • 8
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    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2018
    Description: This thesis examines abiotic processes controlling the transformation and distribution of carbon compounds in seafloor hydrothermal systems hosted in ultramafic rock. These processes have a direct impact on carbon budgets in the oceanic lithosphere and on the sustenance of microorganisms inhabiting hydrothermal vent ecosystems. Where mantle peridotite interacts with carbon-bearing aqueous fluids in the subseafloor, dissolved inorganic carbon can precipitate as carbonate minerals or undergo reduction by H2(aq) to form reduced carbon species. In Chapters 2 and 3, I conduct laboratory experiments to assess the relative extents of carbonate formation and CO2 reduction during alteration of peridotite by CO2(aq)-rich fluids. Results from these experiments reveal that formation of carbonate minerals is favorable on laboratory timescales, even at high H2(aq) concentrations generated by serpentinization reactions. Although CO2(aq) attains rapid metastable equilibrium with formate, formation of thermodynamically stable CH4(aq) is kinetically limited on timescales relevant for active fluid circulation in the subseafloor. It has been proposed that CH4 and potentially longer-chain hydrocarbons may be sourced, instead, from fluid inclusions hosted in plutonic and mantle rocks. Chapter 4 analyzes CH4-rich fluid inclusions in olivine-rich basement rocks from the Von Damm hydrothermal field and the Zambales ophiolite to better understand the origin of abiotic hydrocarbons in ultramaficinfluenced hydrothermal systems. Comparisons of hydrocarbon abundances and stable isotopic compositions in fluid inclusions and associated vent fluids suggest that fluid inclusions may provide a significant contribution of abiotic hydrocarbons to both submarine and continental serpentinization systems.
    Description: This thesis research was funded by the National Science foundation through grants OCE- 1427274 and OCE-1634032. Louise Von Damm generously contributed financial support for research conducted in Chapter 4.
    Keywords: Carbon ; Ocean bottom ; Lithosphere ; Hydrothermal vents ; Microorganisms
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 9
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    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2018
    Description: Many chemical constituents are removed from the ocean by attachment to settling particles, a process referred to as “scavenging.” Radioisotopes of thorium, a highly particle-reactive element, have been used extensively to study scavenging in the ocean. However, this process is complicated by the highly variable chemical composition and concentration of particles in oceanic waters. This thesis focuses on understanding the cycling of thorium as affected by particle concentration and particle composition in the North Atlantic. This objective is addressed using (i) the distributions 228,230,234Th, their radioactive parents, particle composition, and bulk particle concentration, as measured or estimated along the GEOTRACES North Atlantic Transect (GA03) and (ii) a model for the reversible exchange of thorium with particles. Model parameters are either estimated by inversion (chapter 2-4), or prescribed in order to simulate 230Th in a circulation model (chapter 5). The major findings of this thesis follow. In chapters 2 and 3, I find that the rate parameters of the reversible exchange model show systematic variations along GA03. In particular, 𝑘1, the apparent first-order rate "constant" of Th adsorption onto particles, generally presents maxima in the mesopelagic zone and minima below. A positive correlation between 𝑘1 and bulk particle concentration is found, consistent with the notion that the specific rate at which a metal in solution attaches to particles increases with the number of surface sites available for adsorption. In chapter 4, I show that Mn (oxyhydr)oxides and biogenic particles most strongly influence 𝑘1 west of the Mauritanian upwelling, but that biogenic particles dominate 𝑘1 in this region. In chapter 5, I find that dissolved 230Th data are best represented by a model that assumes enhanced values of 𝑘1 near the seafloor. Collectively, my findings suggest that spatial variations in Th radioisotope activities observed in the North Atlantic reflect at least partly variations in the rate at which Th is removed from the water column.
    Description: This work was supported by the US National Science Foundation. Two US NSF grants have supported the research in this thesis (OCE-1232578 and OCE-155644).
    Keywords: Thorium ; Chemistry
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 10
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in International Journal of Environmental Research and Public Health 15 (2018): 723, doi:10.3390/ijerph15040723.
    Description: There has been a massive increase in recent years of the use of lead (Pb) isotopes in attempts to better understand sources and pathways of Pb in the environment and in man or experimental animals. Unfortunately, there have been many cases where the quality of the isotopic data, especially that obtained by quadrupole inductively coupled plasma mass spectrometry (Q-ICP-MS), are questionable, resulting in questionable identification of potential sources, which, in turn, impacts study interpretation and conclusions. We present several cases where the isotopic data have compromised interpretation because of the use of only the major isotopes 208Pb/206Pb and 207Pb/206Pb, or their graphing in other combinations. We also present some examples comparing high precision data from thermal ionization (TIMS) or multi-collector plasma mass spectrometry (MC-ICP-MS) to illustrate the deficiency in the Q-ICP-MS data. In addition, we present cases where Pb isotopic ratios measured on Q-ICP-MS are virtually impossible for terrestrial samples. We also evaluate the Pb isotopic data for rat studies, which had concluded that Pb isotopic fractionation occurs between different organs and suggest that this notion of biological fractionation of Pb as an explanation for isotopic differences is not valid. Overall, the brief review of these case studies shows that Q-ICP-MS as commonly practiced is not a suitable technique for precise and accurate Pb isotopic analysis in the environment and health fields
    Keywords: Lead isotopes ; ICP-MS ; TIMS ; MC-ICP-MS ; Environment ; Humans ; Rats ; Fractionation
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 11
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    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2018
    Description: Life is ubiquitous in the environment and an important mediator of Earth’s carbon cycle, but quantifying the contribution of microbial biomass and its metabolic fluxes is difficult, especially in spatially and temporally-remote environments. Microbes leave behind an often scarce, unidentifiable, or nonspecific record on geologic timescales. This thesis develops and employs novel geochemical and genetic approaches to illuminate diagnostic signals of microbial metabolisms. Field studies, laboratory cultures, and computational models explain how methanogens produce unique nonequilibrium methane clumped isotopologue (13CH3D ) signals that do not correspond to growth temperature. Instead, Δ13CH3D values may be driven by enzymatic reactions common to all methanogens, the C-H bond inherited from substrate precursors including acetate and methanol, isotope exchange, or environmental processes such as methane oxidation. The phylogenetic relationship between substrate-specific methyl-corrinoid proteins provides insight into the evolutionary history of methylotrophic methanogenesis. The distribution of corrinoid proteins in methanogens and related bacteria suggests that these substrate-specific proteins evolved via a complex history of horizontal gene transfer (HGT), gene duplication, and loss. Furthermore, this work identifies a previously unrecognized HGT involving chitinases (ChiC/D) distributed between fungi and bacteria (∼650 Ma). This HGT is used to tether fossil-calibrated ages from within fungi to bacterial lineages. Molecular clock analyses show that multiple clades of bacteria likely acquired chitinase homologs via HGT during the late Neoproterozoic into the early Paleozoic. These results also show that, following these HGT events, recipient terrestrial bacterial clades diversified ∼400-500 Ma, consistent with established timescales of arthropod and plant terrestrialization. Divergence time estimates for bacterial lineages are broadly consistent with the dispersal of chitinase genes throughout the microbial world in direct response to the evolution and expansion of detrital-chitin producing groups including arthropods. These chitinases may aid in dating microbial lineages over geologic time and provide insight into an ecological shift from marine to terrestrial systems in the Proterozoic and Phanerozoic eons. Taken together, this thesis may be used to improve assessments of microbial activity in remote environments, and to enhance our understanding of the evolution of Earth’s carbon cycle.
    Description: Supported by the National Science Foundation (NSF), the NSF Graduate Research Fellowship Program, the MIT Energy Initiative and its partnership with Shell, the Neil and Anna Rasmussen Foundation Fund, and the Grayce B. Kerr Fellowship. This research and its dissemination was supported by funds from the Deep Carbon Observatory, NASA Astrobiology Institute, WHOI Academic Programs Office, and the MIT Graduate Student Council.
    Keywords: Microorganisms ; Microbial metabolism ; Carbon cycle ; Phylogeny
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 12
    Publication Date: 2021-05-19
    Description: The cell walls of certain red algae such as Gracilaria is the sole source of a polysaccharide of major economic importance, agar. Agar is the best known for its use in preparing media for culturing microorganisms. Mariculture of the Gracilaria was conducted in 4 locations of the Qeshm Island during the spring and summer oi 1999. Three culture methods (net, rope, and basket) were tested. The results tested by ANOVA and indicated that the increase in matter up to 45 days after planting was significant (P0.05) Also the mean yield ropes and nets which were subjected to weekly cleaning was significantly higher than from the uncleaned ropes or nets. The yield net method of cultivation was significantly higher than rope. Experimental results showed that the light intensity, average of temperature, wind and wave action, water and sediment nutrition and some grazers such as turtle had a significant Influence on growth of Gracilaria.
    Description: Published
    Keywords: Cultivation ; Gracilaria ; Gracilaria corticata ; Algae ; Polysaccharide ; Culturing ; Microorganisms ; Mariculture ; ANOVA ; Temperature ; Sediment ; Nutrition ; Growth
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.21-36
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  • 13
    Publication Date: 2021-05-19
    Description: With the advent of the science of fisheries and aquaculture in the country, and the importance of reproduction and breeding of various species of aquatic animals (freshwater and salty water), attention has been paid to pathogenic factors in the process of aquaculture, one of these factors is pathogenic microorganisms and Nonpathogenic (bacterial, fungal, and viral) that can increase the environmental risk for aquatic organisms and, in some cases, human beings, and, with accurate knowledge of the disease, steps can be taken to prevent and treat withdrawal, as well as research and More studying on various pathogens in either natural or experimental conditions. Although many studies have been carried out over the years about aquatic microorganisms and aquatic environments, there is no complete information on genetic studies of microorganisms in the country, and if such research is feasible and not required, if Gathering information about these creatures and identifying their genetic reserves can provide the basis for research in various fields. What microorganisms are identified and maintained under standard conditions is a question that has remained unresolved so far and this study has tried to introduce a complete list of microorganisms, including bacteriafunges and viruses that have been isolated so far from aquatic and aqueous humor. And the aquatic microorganisms that have been identified in the microorganism bank are also included, and all the documentation shows that there is a huge potential for the identification and maintenance of these microorganisms. In this study, isolated and identified bacteria from northern waters, internal waters, and south of Iran were 73.39 40 genera and species, respectively. Viruses identified in northern waters, inland waters, and south of Iran were 4 species in aquatic and northern waters of Iran, 6 species in Iranian aquatic and inland waters and 7 species in aquatic and southern waters of Iran. Identification fungi have been reported in the waters of northern, inland and southern waters, respectively, 20,25 of the 12 genera and species. In the bank of the National Center for Genetic and Biotechnological Resources of Iran, there are some species that overlap with bacteria isolated from Iran's water resources. There are 20 species of bacteria, and this is not seen for fungi and viruses.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Database ; Aquatic ; Microorganisms ; Aquaculture
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 48pp.
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  • 14
    Publication Date: 2021-05-19
    Description: Influx of metallic pollutants such as iron and nickel into marine environment has been increased drastically in current era. Due to its harmful effects on living organisms, the aim of current thesis was isolation and identification of microorganisms which could reduce iron and nickel. In order to isolate bacterial strains resistant to iron and nickel, deposit samples were collected from five stations in Imam Khomeini Port cultured on BHI agar medium containing 1000 ppm of iron and 50 ppm of nickel and incubated for 24 hours in 30 oC. Endurance threshold of strains isolated to different concentrations of iron (1000- 15000 ppm) and nickel (100- 25000 ppm) in BHI broth medium were evaluated, the most resistant strains were selected and MIC and MBC were determined. Growth curve of selected strains in the presence and absence of iron and nickel were assessed by turbidity method. Along with above mentioned process, removal amount of metal by living cells and dead biomasses of selected strains were assessed by atomic absorption analysis and then 16S rRNA method was used to identify and approve the selected strains. Results of the current study were demonstrated that among of 16 and 12 resistant strains to nickel and iron, two selected strains (number16 and 7) as the most resistant strains had MIC and MBC (29800 and 29700) and (26300 and 26500), respectively. It should be mentioned that iron’s MIC was not assessable. Results of atomic absorption analysis was demonstrated that the highest amount of nickel reduction in a medium with concentration of 194 ppm and 71 ppm were 16.7% and 63% after 72 hours by selected strain number 16 respectively and in a medium containing 158 ppm iron, after 50 hours 8.4% by selected strain 7, while dead biomass of strain 16 reduced nickel to the amount of 40.6% and it reduced 21% and 4% of iron in solutions with 46 ppm and 792 ppm of iron. Results of molecular analysis demonstrated that strain 16 was Bacillus subtilis. In addition, Bacillus subtilis which has been isolated in this study with ability of nickel and iron removal is an appropriate candidate to be used in aquatic environments.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Rehabilitation ; Recovery ; Nickel ; Iron ; Environmental ; Microorganisms
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 60pp.
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  • 15
    Publication Date: 2021-05-19
    Description: Carp fishes culture is one of the most important subsector fisheries industry in Khouzestan province. Every year in summer high mortality occurred in carp fishes farms specially in silver carp of north Khouzestan province. Inspection of silver carp for identification microorganisms agents (Bacteria, Fungi, Parasite and virus: SVC,KHV), determine total plate count, examination physic chemical factors of farms water, histopathology, identification planktons, the main objectives of this study, which was held in 2012. 180 silver carp from 5 farms (10 ponds) with high mortality in years ago were collected in north Khouzestan province and then differents parts of fish body including: intestine, gills, body surface, eyes and liver were examined. Physico chemical parameters and plankton sampled monthly. Physico chemical parameters of water were measured all over culture period for 960 times as follows: Do(4.45-8.5 ppm), BOD5(1.1-9.25 ppm), temp(19-33•c), pH(6.82-8.6), total hardness(348-10053), turbidity(5-56 FTU), Amonia(0.001- 0.06 ppm) and co2( 0.88-13.2). From a total 180 fish examined, 136 (75%) showed unknown algae infestation and 126 (70%) showed parasitic (Dactylogyrus, Gyrodactylus and metacercaria Diplostomum). The results of biotic parameters in farms showed that cyanophycae (Cylindropermopsis, Merismopedia and Nitzeshia) were the most group of phytoplanktons. Histopathological studies have shown necrosis in tobules kidney, degeneration hepatocyte and hyperplasia in gill cells and also results demonstrated the mean of total plate count (0-376 CFU/ml103). 60 samples with sighn severe hemorrhagic on surface body were collected for virology studies by PCR procedure (IQ2000 kit) and have shown which 3 sample suspected to KHV but SVC was not identified.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Silver Carp ; Water physic chemical factor ; Microorganisms ; Histopathology ; Fresh water ; Mortality ; Fisheries ; Bacteria ; Fungi ; Parasite ; Virus ; Planktons ; Dactylogyrus ; Gyrodactylus ; Cyanophycae ; Cylindropermopsis ; Nitzeshia ; PCR
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 110pp.
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  • 16
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-16
    Keywords: Chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 17
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-16
    Description: The comment and response concerning the report of oxidation of methane to methanol by water (Reports, 5 May 2017, p. 523) do not fully capture the implications of thermodynamic limitations. A nonisothermal process in which each cycle requires a large temperature swing and permits only substoichiometric methane conversion surely could not be carried out on any practical scale.
    Keywords: Chemistry
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  • 18
    Publication Date: 2018-02-16
    Description: Labinger argues that stepwise reaction of methane with water to produce methanol and hydrogen will never be commercially feasible because of its substoichiometric basis with respect to the active site and the requirement of a large temperature swing. This comment is not touching any new ground, beyond describing the thermodynamic feasibility, thermal cycling, and the role of water as discussed previously. Most important, it does not have a solid numerical basis.
    Keywords: Chemistry
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  • 19
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-07-27
    Keywords: Chemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 20
    Publication Date: 2018-07-27
    Description: Vinyl carbocations have been the subject of extensive experimental and theoretical studies over the past five decades. Despite this long history in chemistry, the utility of vinyl cations in chemical synthesis has been limited, with most reactivity studies focusing on solvolysis reactions or intramolecular processes. Here we report synthetic and mechanistic studies of vinyl cations generated through silylium–weakly coordinating anion catalysis. We find that these reactive intermediates undergo mild intermolecular carbon-carbon bond–forming reactions, including carbon-hydrogen (C–H) insertion into unactivated sp 3 C–H bonds and reductive Friedel-Crafts reactions with arenes. Moreover, we conducted computational studies of these alkane C–H functionalization reactions and discovered that they proceed through nonclassical, ambimodal transition structures. This reaction manifold provides a framework for the catalytic functionalization of hydrocarbons using simple ketone derivatives.
    Keywords: Chemistry
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  • 21
    Publication Date: 2018-06-22
    Description: It is commonly assumed that recognition and discrimination of chirality, both in nature and in artificial systems, depend solely on spatial effects. However, recent studies have suggested that charge redistribution in chiral molecules manifests an enantiospecific preference in electron spin orientation. We therefore reasoned that the induced spin polarization may affect enantiorecognition through exchange interactions. Here we show experimentally that the interaction of chiral molecules with a perpendicularly magnetized substrate is enantiospecific. Thus, one enantiomer adsorbs preferentially when the magnetic dipole is pointing up, whereas the other adsorbs faster for the opposite alignment of the magnetization. The interaction is not controlled by the magnetic field per se, but rather by the electron spin orientations, and opens prospects for a distinct approach to enantiomeric separations.
    Keywords: Chemistry
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  • 22
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-29
    Keywords: Chemistry
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 23
    Publication Date: 2018-12-14
    Description: Theory has established the importance of geometric phase (GP) effects in the adiabatic dynamics of molecular systems with a conical intersection connecting the ground- and excited-state potential energy surfaces, but direct observation of their manifestation in chemical reactions remains a major challenge. Here, we report a high-resolution crossed molecular beams study of the H + HD -〉 H 2 + D reaction at a collision energy slightly above the conical intersection. Velocity map ion imaging revealed fast angular oscillations in product quantum state–resolved differential cross sections in the forward scattering direction for H 2 products at specific rovibrational levels. The experimental results agree with adiabatic quantum dynamical calculations only when the GP effect is included.
    Keywords: Chemistry
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  • 24
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-17
    Keywords: Chemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 25
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-17
    Keywords: Chemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 26
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-17
    Description: The chemistry of the carbonyl group is essential to modern organic synthesis. The preparation of substituted, enantioenriched 1,3- or 1,5-dicarbonyls is well developed, as their disconnection naturally follows from the intrinsic polarity of the carbonyl group. By contrast, a general enantioselective access to quaternary stereocenters in acyclic 1,4-dicarbonyl systems remains an unresolved problem, despite the tremendous importance of 2,3-substituted 1,4-dicarbonyl motifs in natural products and drug scaffolds. Here we present a broad enantioselective and stereodivergent strategy to access acyclic, polysubstituted 1,4-dicarbonyls via acid-catalyzed [3,3]-sulfonium rearrangement starting from vinyl sulfoxides and ynamides. The stereochemistry at sulfur governs the absolute sense of chiral induction, whereas the double bond geometry dictates the relative configuration of the final products.
    Keywords: Chemistry
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  • 27
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-17
    Keywords: Chemistry
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  • 28
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-17
    Description: With the recent soaring production of natural gas, the use of methane and other light hydrocarbon feedstocks as starting materials in synthetic transformations is becoming increasingly economically attractive, although it remains chemically challenging. We report the development of photocatalytic C–H amination, alkylation, and arylation of methane, ethane, and higher alkanes under visible light irradiation at ambient temperature. High catalytic efficiency (turnover numbers up to 2900 for methane and 9700 for ethane) and selectivity were achieved using abundant, inexpensive cerium salts as photocatalysts. Ligand-to-metal charge transfer excitation generated alkoxy radicals from simple alcohols that in turn acted as hydrogen atom transfer catalysts. The mixed-phase gas/liquid reaction was adapted to continuous flow, enabling the efficient use of gaseous feedstocks in scalable photocatalytic transformations.
    Keywords: Chemistry
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  • 29
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-24
    Keywords: Chemistry
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  • 30
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-24
    Keywords: Chemistry
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  • 31
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-31
    Keywords: Chemistry
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  • 32
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-31
    Description: Intrigued by the potential of nanoscale machines, scientists have long attempted to control molecular motion. We monitored the individual 0.7-nanometer steps of a single molecular hopper as it moved in an electric field along a track in a nanopore controlled by a chemical ratchet. The hopper demonstrated characteristics desired in a moving molecule: defined start and end points, processivity, no chemical fuel requirement, directional motion, and external control. The hopper was readily functionalized to carry cargos. For example, a DNA molecule could be ratcheted along the track in either direction, a prerequisite for nanopore sequencing.
    Keywords: Chemistry
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  • 33
    Publication Date: 2018-09-21
    Description: Phosphorothioate nucleotides have emerged as powerful pharmacological substitutes of their native phosphodiester analogs with important translational applications in antisense oligonucleotide (ASO) therapeutics and cyclic dinucleotide (CDN) synthesis. Stereocontrolled installation of this chiral motif has long been hampered by the systemic use of phosphorus(III) [P(III)]–based reagent systems as the sole practical means of oligonucleotide assembly. A fundamentally different approach is described herein: the invention of a P(V)-based reagent platform for programmable, traceless, diastereoselective phosphorus-sulfur incorporation. The power of this reagent system is demonstrated through the robust and stereocontrolled synthesis of various nucleotidic architectures, including ASOs and CDNs, via an efficient, inexpensive, and operationally simple protocol.
    Keywords: Chemistry
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  • 34
    Publication Date: 2018-09-21
    Description: Here we report an anomalous porous molecular crystal built of C–H···N-bonded double-layered roof-floor components and wall components of a segregatively interdigitated architecture. This complicated porous structure consists of only one type of fully aromatic multijoint molecule carrying three identical dipyridylphenyl wedges. Despite its high symmetry, this molecule accomplishes difficult tasks by using two of its three wedges for roof-floor formation and using its other wedge for wall formation. Although a C–H···N bond is extremely labile, the porous crystal maintains its porosity until thermal breakdown of the C–H···N bonds at 202°C occurs, affording a nonporous polymorph. Though this nonporous crystal survives even at 325°C, it can retrieve the parent porosity under acetonitrile vapor. These findings show how one can translate simplicity into ultrahigh complexity.
    Keywords: Chemistry
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  • 35
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Keywords: Chemistry
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  • 36
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Keywords: Chemistry
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  • 37
    Publication Date: 2018-09-28
    Description: Some of the simplest and most powerful carbon-carbon bond forming strategies take advantage of readily accessible ubiquitous motifs: carbonyls and olefins. Here we report a fundamentally distinct mode of reactivity between carbonyls and olefins that differs from established acid-catalyzed carbonyl-ene, Prins, and carbonyl-olefin metathesis reaction paths. A range of epsilon, zeta-unsaturated ketones undergo Brønsted acid–catalyzed intramolecular cyclization to provide tetrahydrofluorene products via the formation of two new carbon-carbon bonds. Theoretical calculations and accompanying mechanistic studies suggest that this carbocyclization reaction proceeds through the intermediacy of a transient oxetane formed by oxygen atom transfer. The complex polycyclic frameworks in this product class appear as common substructures in organic materials, bioactive natural products, and recently developed pharmaceuticals.
    Keywords: Chemistry
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  • 38
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Description: Alkene aminoarylation with a single, bifunctional reagent is a concise synthetic strategy. We report a catalytic protocol for the addition of arylsulfonylacetamides across electron-rich alkenes with complete anti-Markovnikov regioselectivity and excellent diastereoselectivity to provide 2,2-diarylethylamines. In this process, single-electron alkene oxidation enables carbon-nitrogen bond formation to provide a key benzylic radical poised for a Smiles-Truce 1,5-aryl shift. This reaction is redox-neutral, exhibits broad functional group compatibility, and occurs at room temperature with loss of sulfur dioxide. As this process is driven by visible light, uses readily available starting materials, and demonstrates convergent synthesis, it is well suited for use in a variety of synthetic endeavors.
    Keywords: Chemistry
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  • 39
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-05
    Keywords: Chemistry
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  • 40
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-05
    Keywords: Chemistry
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  • 41
    Publication Date: 2018-10-05
    Description: Photocatalysis based on optically active, "plasmonic" metal nanoparticles has emerged as a promising approach to facilitate light-driven chemical conversions under far milder conditions than thermal catalysis. However, an understanding of the relation between thermal and electronic excitations has been lacking. We report the substantial light-induced reduction of the thermal activation barrier for ammonia decomposition on a plasmonic photocatalyst. We introduce the concept of a light-dependent activation barrier to account for the effect of light illumination on electronic and thermal excitations in a single unified picture. This framework provides insight into the specific role of hot carriers in plasmon-mediated photochemistry, which is critically important for designing energy-efficient plasmonic photocatalysts.
    Keywords: Chemistry
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  • 42
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-12
    Keywords: Chemistry
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  • 43
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-12
    Keywords: Chemistry
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  • 44
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-12
    Description: Single-electron reduction of a carbonyl to a ketyl enables access to a polarity-reversed platform of reactivity for this cornerstone functional group. However, the synthetic utility of the ketyl radical is hindered by the strong reductants necessary for its generation, which also limit its reactivity to net reductive mechanisms. We report a strategy for net redox-neutral generation and reaction of ketyl radicals. The in situ conversion of aldehydes to α-acetoxy iodides lowers their reduction potential by more than 1 volt, allowing for milder access to the corresponding ketyl radicals and an oxidative termination event. Upon subjecting these iodides to a dimanganese decacarbonyl precatalyst and visible light irradiation, an atom transfer radical addition (ATRA) mechanism affords a broad scope of vinyl iodide products with high Z -selectivity.
    Keywords: Chemistry
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  • 45
    Publication Date: 2018-10-12
    Description: Reactions that form a product with the same reactive functionality as that of one of the starting compounds frequently end in oligomerization. As a salient example, selective aldol coupling of the smallest, though arguably most useful, enolizable aldehyde, acetaldehyde, with just one partner substrate has proven to be extremely challenging. Here, we report a highly enantioselective Mukaiyama aldol reaction with the simple triethylsilyl (TES) and tert -butyldimethylsilyl (TBS) enolates of acetaldehyde and various aliphatic and aromatic acceptor aldehydes. The reaction is catalyzed by recently developed, strongly acidic imidodiphosphorimidates (IDPi), which, like enzymes, display a confined active site but, like small-molecule catalysts, have a broad substrate scope. The process is scalable, fast, efficient (0.5 to 1.5 mole % catalyst loading), and greatly simplifies access to highly valuable silylated acetaldehyde aldols.
    Keywords: Chemistry
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  • 46
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-21
    Keywords: Chemistry
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  • 47
    Publication Date: 2018-12-21
    Description: Single-molecule magnets (SMMs) containing only one metal center may represent the lower size limit for molecule-based magnetic information storage materials. Their current drawback is that all SMMs require liquid-helium cooling to show magnetic memory effects. We now report a chemical strategy to access the dysprosium metallocene cation [(Cp i Pr5 )Dy(Cp*)] + (Cp i Pr5 , penta-iso-propylcyclopentadienyl; Cp *, pentamethylcyclopentadienyl), which displays magnetic hysteresis above liquid-nitrogen temperatures. An effective energy barrier to reversal of the magnetization of U eff = 1541 wave number is also measured. The magnetic blocking temperature of T B = 80 kelvin for this cation overcomes an essential barrier toward the development of nanomagnet devices that function at practical temperatures.
    Keywords: Chemistry
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  • 48
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-19
    Keywords: Chemistry
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  • 49
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-19
    Description: The development of highly reactive and stereoselective catalytic systems is required not only to improve existing synthetic methods but also to invent distinct chemical reactions. Herein, a homogenized combination of nickel-based Lewis acid–surfactant-combined catalysts and single-walled carbon nanotubes is shown to exhibit substantial activity in water. In addition to the enhanced reactivity, stereoselective performance and long-term stability were demonstrated in asymmetric conjugate addition reactions of aldoximes to furnish chiral nitrones in high yields with excellent selectivities. The practical and straightforward application of the designed catalysts in water provides an expedient, environmentally benign, and highly efficient pathway to access optically active compounds.
    Keywords: Chemistry
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  • 50
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-02
    Keywords: Chemistry
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  • 51
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-14
    Keywords: Chemistry
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  • 52
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-26
    Keywords: Chemistry
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  • 53
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-02
    Description: Exploration of intermediates that enable chemoselective cycloaddition reactions and expeditious construction of fused- or bridged-ring systems is a continuous challenge for organic synthesis. As an intermediate of interest, the oxyallyl cation has been harnessed to synthesize architectures containing seven-membered rings via (4+3) cycloaddition. However, its potential to access five-membered skeletons is underdeveloped, largely due to the thermally forbidden (3+2) pathway. Here, the combination of a tailored precursor and a Pd(0) catalyst generates a Pd-oxyallyl intermediate that cyclizes with conjugated dienes to produce a diverse array of tetrahydrofuran skeletons. The cycloaddition overrides conventional (4+3) selectivity by proceeding through a stepwise pathway involving a Pd-allyl transfer and ring closure sequence. Subsequent treatment of the (3+2) adducts with a palladium catalyst converts the heterocycles to the carbocyclic cyclopentanones.
    Keywords: Chemistry
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  • 54
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-16
    Keywords: Chemistry
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  • 55
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Keywords: Chemistry
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  • 56
    Publication Date: 2018-08-10
    Description: Understanding the practical limitations of chemical reactions is critically important for efficiently planning the synthesis of compounds in pharmaceutical, agrochemical, and specialty chemical research and development. However, literature reports of the scope of new reactions are often cursory and biased toward successful results, severely limiting the ability to predict reaction outcomes for untested substrates. We herein illustrate strategies for carrying out large-scale surveys of chemical reactivity by using a material-sparing nanomole-scale automated synthesis platform with greatly expanded synthetic scope combined with ultrahigh-throughput matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS).
    Keywords: Chemistry
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  • 57
    Publication Date: 2018-08-24
    Description: Researchers around the world have observed the formation of molecularly ordered structures of unknown origin on the surface of titanium dioxide (TiO 2 ) photocatalysts exposed to air and solution. Using a combination of atomic-scale microscopy and spectroscopy, we show that TiO 2 selectively adsorbs atmospheric carboxylic acids that are typically present in parts-per-billion concentrations while effectively repelling other adsorbates, such as alcohols, that are present in much higher concentrations. The high affinity of the surface for carboxylic acids is attributed to their bidentate binding. These self-assembled monolayers have the unusual property of being both hydrophobic and highly water-soluble, which may contribute to the self-cleaning properties of TiO 2 . This finding is relevant to TiO 2 photocatalysis, because the self-assembled carboxylate monolayers block the undercoordinated surface cation sites typically implicated in photocatalysis.
    Keywords: Chemistry
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  • 58
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-31
    Keywords: Chemistry
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  • 59
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-31
    Keywords: Chemistry
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  • 60
    Publication Date: 2018-08-31
    Description: The alkaline earth metals calcium (Ca), strontium (Sr), and barium (Ba) typically engage in chemical bonding as classical main-group elements through their n s and n p valence orbitals, where n is the principal quantum number. Here we report the isolation and spectroscopic characterization of eight-coordinate carbonyl complexes M(CO) 8 (where M = Ca, Sr, or Ba) in a low-temperature neon matrix. Analysis of the electronic structure of these cubic O h -symmetric complexes reveals that the metal–carbon monoxide (CO) bonds arise mainly from [M(d )] -〉 (CO) 8 backdonation, which explains the strong observed red shift of the C-O stretching frequencies. The corresponding radical cation complexes were also prepared in gas phase and characterized by mass-selected infrared photodissociation spectroscopy, confirming adherence to the 18-electron rule more conventionally associated with transition metal chemistry.
    Keywords: Chemistry
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  • 61
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-07
    Keywords: Chemistry
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  • 62
    Publication Date: 2018-09-07
    Description: Mystery surrounds the transition from gas-phase hydrocarbon precursors to terrestrial soot and interstellar dust, which are carbonaceous particles formed under similar conditions. Although polycyclic aromatic hydrocarbons (PAHs) are known precursors to high-temperature carbonaceous-particle formation, the molecular pathways that initiate particle formation are unknown. We present experimental and theoretical evidence for rapid molecular clustering–reaction pathways involving radicals with extended conjugation. These radicals react with other hydrocarbon species to form covalently bound complexes that promote further growth and clustering by regenerating resonance-stabilized radicals through low-barrier hydrogen-abstraction and hydrogen-ejection reactions. Such radical–chain reaction pathways may lead to covalently bound clusters of PAHs and other hydrocarbons that would otherwise be too small to condense at high temperatures, thus providing the key mechanistic steps for rapid particle formation and surface growth by hydrocarbon chemisorption.
    Keywords: Chemistry
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  • 63
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-14
    Keywords: Chemistry
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  • 64
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-27
    Keywords: Chemistry
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  • 65
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-27
    Keywords: Chemistry
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  • 66
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-27
    Description: Basic heteroarenes are a ubiquitous feature of pharmaceuticals and bioactive molecules, and Minisci-type additions of radical nucleophiles are a leading method for their elaboration. Despite many Minisci-type protocols that result in the formation of stereocenters, exerting control over the absolute stereochemistry at these centers remains an unmet challenge. We report a process for addition of prochiral radicals, generated from amino acid derivatives, to pyridines and quinolines. Our method offers excellent control of both enantioselectivity and regioselectivity. An enantiopure chiral Brønsted acid catalyst serves both to activate the substrate and induce asymmetry, while an iridium photocatalyst mediates the required electron transfer processes. We anticipate that this method will expedite access to enantioenriched small-molecule building blocks bearing versatile basic heterocycles.
    Keywords: Chemistry
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  • 67
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-05-25
    Keywords: Chemistry
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  • 68
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-05-25
    Keywords: Chemistry
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  • 69
    Publication Date: 2018-10-26
    Description: Primary amines are essential constituents of biologically active molecules and versatile intermediates in the synthesis of drugs and agrochemicals. However, their preparation from easily accessible alkenes remains challenging. Here, we report a general strategy to access primary amines from alkenes through an operationally simple iron-catalyzed aminochlorination reaction. A stable hydroxylamine derivative and benign sodium chloride act as the respective nitrogen and chlorine sources. The reaction proceeds at room temperature under air; tolerates a large scope of aliphatic and conjugated alkenes, including densely functionalized substrates; and provides excellent anti-Markovnikov regioselectivity with respect to the amino group. The reactivity of the 2-chloroalkylamine products, an understudied class of amphoteric molecules, enables facile access to linear or branched aliphatic amines, aziridines, aminonitriles, azido amines, and homoallylic amines.
    Keywords: Chemistry
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  • 70
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Chemistry
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  • 71
    Publication Date: 2018-11-09
    Description: Despite the enormous potential for the use of stereospecific cross-coupling reactions to rationally manipulate the three-dimensional structure of organic molecules, the factors that control the transfer of stereochemistry in these reactions remain poorly understood. Here we report a mechanistic and synthetic investigation into the use of enantioenriched alkylboron nucleophiles in stereospecific Pd-catalyzed Suzuki cross-coupling reactions. By developing a suite of molecular descriptors of phosphine ligands, we could apply predictive statistical models to select or design distinct ligands that respectively promoted stereoinvertive and stereoretentive cross-coupling reactions. Stereodefined branched structures were thereby accessed through the predictable manipulation of absolute stereochemistry, and a general model for the mechanism of alkylboron transmetallation was proposed.
    Keywords: Chemistry
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  • 72
    Publication Date: 2018-11-16
    Description: Heterobiaryls composed of pyridine and diazine rings are key components of pharmaceuticals and are often central to pharmacological function. We present an alternative approach to metal-catalyzed cross-coupling to make heterobiaryls using contractive phosphorus C–C couplings, also termed phosphorus ligand coupling reactions. The process starts by regioselective phosphorus substitution of the C–H bonds para to nitrogen in two successive heterocycles; ligand coupling is then triggered via acidic alcohol solutions to form the heterobiaryl bond. Mechanistic studies imply that ligand coupling is an asynchronous process involving migration of one heterocycle to the ipso position of the other around a central pentacoordinate P(V) atom. The strategy can be applied to complex drug-like molecules containing multiple reactive sites and polar functional groups, and also enables convergent coupling of drug fragments and late-stage heteroarylation of pharmaceuticals.
    Keywords: Chemistry
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  • 73
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-07-06
    Keywords: Chemistry
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  • 74
    Publication Date: 2018-07-06
    Description: Conical intersections play a critical role in excited-state dynamics of polyatomic molecules because they govern the reaction pathways of many nonadiabatic processes. However, ultrafast probes have lacked sufficient spatial resolution to image wave-packet trajectories through these intersections directly. Here, we present the simultaneous experimental characterization of one-photon and two-photon excitation channels in isolated CF 3 I molecules using ultrafast gas-phase electron diffraction. In the two-photon channel, we have mapped out the real-space trajectories of a coherent nuclear wave packet, which bifurcates onto two potential energy surfaces when passing through a conical intersection. In the one-photon channel, we have resolved excitation of both the umbrella and the breathing vibrational modes in the CF 3 fragment in multiple nuclear dimensions. These findings benchmark and validate ab initio nonadiabatic dynamics calculations.
    Keywords: Chemistry
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  • 75
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-07-13
    Keywords: Chemistry
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  • 76
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-22
    Keywords: Chemistry
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  • 77
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-13
    Keywords: Chemistry
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  • 78
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-05-04
    Keywords: Chemistry
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  • 79
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-05-11
    Keywords: Chemistry
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  • 80
    Publication Date: 2018-05-11
    Description: Common anionic nucleophiles such as those derived from inorganic salts have not been used for enantioselective catalysis because of their insolubility. Here, we report that merging hydrogen bonding and phase-transfer catalysis provides an effective mode of activation for nucleophiles that are insoluble in organic solvents. This catalytic manifold relies on hydrogen bonding complexation to render nucleophiles soluble and reactive, while simultaneously inducing asymmetry in the ensuing transformation. We demonstrate the concept using a chiral bis-urea catalyst to form a tridentate hydrogen bonding complex with fluoride from its cesium salt, thereby enabling highly efficient enantioselective ring opening of episulfonium ion. This fluorination method is synthetically valuable considering the scarcity of alternative protocols and points the way to wider application of the catalytic approach with diverse anionic nucleophiles.
    Keywords: Chemistry
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  • 81
    Publication Date: 2018-05-18
    Description: Carbon dioxide (CO 2 ) electroreduction could provide a useful source of ethylene, but low conversion efficiency, low production rates, and low catalyst stability limit current systems. Here we report that a copper electrocatalyst at an abrupt reaction interface in an alkaline electrolyte reduces CO 2 to ethylene with 70% faradaic efficiency at a potential of –0.55 volts versus a reversible hydrogen electrode (RHE). Hydroxide ions on or near the copper surface lower the CO 2 reduction and carbon monoxide (CO)–CO coupling activation energy barriers; as a result, onset of ethylene evolution at –0.165 volts versus an RHE in 10 molar potassium hydroxide occurs almost simultaneously with CO production. Operational stability was enhanced via the introduction of a polymer-based gas diffusion layer that sandwiches the reaction interface between separate hydrophobic and conductive supports, providing constant ethylene selectivity for an initial 150 operating hours.
    Keywords: Chemistry
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  • 82
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-05-25
    Keywords: Chemistry
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  • 83
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-23
    Description: White phosphorus, generated in the legacy thermal process for phosphate rock upgrading, has long been the key industrial intermediate for the synthesis of phosphorus-containing chemicals, including herbicides, flame-retardants, catalyst ligands, battery electrolytes, pharmaceuticals, and detergents. In contrast, phosphate fertilizers are made on a much larger scale from phosphoric acid, obtained by treating phosphate rock with sulfuric acid. Dehydration of phosphoric acid using sodium chloride gives trimetaphosphate, and here we report that trichlorosilane, primarily used for the production of high-purity silicon, reduces trimetaphosphate to the previously unknown bis(trichlorosilyl)phosphide anion. This anion offers an entry point to value-added organophosphorus chemicals such as primary and secondary alkyl phosphines, and thus to organophosphinates, and can also be used to prepare phosphine gas and the hexafluorophosphate anion, all previously available only downstream from white phosphorus.
    Keywords: Chemistry
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  • 84
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-06
    Keywords: Chemistry
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  • 85
    Publication Date: 2018-04-06
    Description: Cross-coupling chemistry is widely applied to carbon-carbon bond formation in the synthesis of medicines, agrochemicals, and other functional materials. Recently, single-electron–induced variants of this reaction class have proven particularly useful in the formation of C(sp 2 )–C(sp 3 ) linkages, although certain compound classes have remained a challenge. Here, we report the use of sulfones to activate the alkyl coupling partner in nickel-catalyzed radical cross-coupling with aryl zinc reagents. This method’s tolerance of fluoroalkyl substituents proved particularly advantageous for the streamlined preparation of pharmaceutically oriented fluorinated scaffolds that previously required multiple steps, toxic reagents, and nonmodular retrosynthetic blueprints. Five specific sulfone reagents facilitate the rapid assembly of a vast set of compounds, many of which contain challenging fluorination patterns.
    Keywords: Chemistry
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  • 86
    Publication Date: 2018-05-04
    Description: Plasmon-induced chemical reactions of molecules adsorbed on metal nanostructures are attracting increased attention for photocatalytic reactions. However, the mechanism remains controversial because of the difficulty of direct observation of the chemical reactions in the plasmonic field, which is strongly localized near the metal surface. We used a scanning tunneling microscope (STM) to achieve real-space and real-time observation of a plasmon-induced chemical reaction at the single-molecule level. A single dimethyl disulfide molecule on silver and copper surfaces was dissociated by the optically excited plasmon at the STM junction. The STM study combined with theoretical calculations shows that this plasmon-induced chemical reaction occurred by a direct intramolecular excitation mechanism.
    Keywords: Chemistry
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  • 87
    Publication Date: 2018-05-25
    Description: Identifying catalyst activation modes that exploit one-electron chemistry and overcome associated deactivation pathways will be transformative for developing first-row transition metal catalysts with performance equal or, ideally, superior to precious metals. Here we describe a zinc-activation method compatible with high-throughput reaction discovery that identified scores of cobalt-phosphine combinations for the asymmetric hydrogenation of functionalized alkenes. An optimized catalyst prepared from ( R , R )-Ph-BPE {Ph-BPE, 1,2-bis[(2 R ,5 R )-2,5-diphenylphospholano]ethane} and cobalt chloride [CoCl 2 ·6H 2 O] exhibited high activity and enantioselectivity in protic media and enabled the asymmetric synthesis of the epilepsy medication levetiracetam at 200-gram scale with 0.08 mole % catalyst loading. Stoichiometric studies established that the cobalt (II) catalyst precursor ( R , R )-Ph-BPECoCl 2 underwent ligand displacement by methanol, and zinc promoted facile one-electron reduction to cobalt (I), which more stably bound the phosphine.
    Keywords: Chemistry
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  • 88
    Publication Date: 2018-06-01
    Description: Transition metal–catalyzed arene functionalization has been widely used for molecular synthesis over the past century. In this arena, copper catalysis has long been considered a privileged platform due to the propensity of high-valent copper to undergo reductive elimination with a wide variety of coupling fragments. However, the sluggish nature of oxidative addition has limited copper’s capacity to broadly facilitate haloarene coupling protocols. Here, we demonstrate that this copper oxidative addition problem can be overcome with an aryl radical–capture mechanism, wherein the aryl radical is generated through a silyl radical halogen abstraction. This strategy was applied to a general trifluoromethylation of aryl bromides through dual copper-photoredox catalysis. Mechanistic studies support the formation of an open-shell aryl species.
    Keywords: Chemistry
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  • 89
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-05-18
    Keywords: Chemistry
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  • 90
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-01
    Keywords: Chemistry
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  • 91
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-23
    Keywords: Chemistry
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  • 92
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-23
    Keywords: Chemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 93
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-30
    Keywords: Chemistry
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 94
    Publication Date: 2018-03-30
    Description: The activation of olefins for asymmetric chemical synthesis traditionally relies on transition metal catalysts. In contrast, biological enzymes with Brønsted acidic sites of appropriate strength can protonate olefins and thereby generate carbocations that ultimately react to form natural products. Although chemists have recently designed chiral Brønsted acid catalysts to activate imines and carbonyl compounds, mimicking these enzymes to protonate simple olefins that then engage in asymmetric catalytic reactions has remained a substantial synthetic challenge. Here, we show that a class of confined and strong chiral Brønsted acids enables the catalytic asymmetric intramolecular hydroalkoxylation of unbiased olefins. The methodology gives rapid access to biologically active 1,1-disubstituted tetrahydrofurans, including (–)-Boivinianin A.
    Keywords: Chemistry
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  • 95
    Publication Date: 2018-04-13
    Description: Machine learning methods are becoming integral to scientific inquiry in numerous disciplines. We demonstrated that machine learning can be used to predict the performance of a synthetic reaction in multidimensional chemical space using data obtained via high-throughput experimentation. We created scripts to compute and extract atomic, molecular, and vibrational descriptors for the components of a palladium-catalyzed Buchwald-Hartwig cross-coupling of aryl halides with 4-methylaniline in the presence of various potentially inhibitory additives. Using these descriptors as inputs and reaction yield as output, we showed that a random forest algorithm provides significantly improved predictive performance over linear regression analysis. The random forest model was also successfully applied to sparse training sets and out-of-sample prediction, suggesting its value in facilitating adoption of synthetic methodology.
    Keywords: Chemistry
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  • 96
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-22
    Keywords: Chemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
    Publication Date: 2018-06-29
    Description: Chiral amines are widely used as catalysts in asymmetric synthesis to activate carbonyl groups for α-functionalization. Carbonyl catalysis reverses that strategy by using a carbonyl group to activate a primary amine. Inspired by biological carbonyl catalysis, which is exemplified by reactions of pyridoxal-dependent enzymes, we developed an N-quaternized pyridoxal catalyst for the asymmetric Mannich reaction of glycinate with aryl N -diphenylphosphinyl imines. The catalyst exhibits high activity and stereoselectivity, likely enabled by enzyme-like cooperative bifunctional activation of the substrates. Our work demonstrates the catalytic utility of the pyridoxal moiety in asymmetric catalysis.
    Keywords: Chemistry
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  • 98
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-07-13
    Keywords: Chemistry
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-07-13
    Description: Deconstructive functionalizations involving scission of carbon-carbon double bonds are well established. In contrast, unstrained C(sp 3 )–C(sp 3 ) bond cleavage and functionalization have less precedent. Here we report the use of deconstructive fluorination to access mono- and difluorinated amine derivatives by C(sp 3 )–C(sp 3 ) bond cleavage in saturated nitrogen heterocycles such as piperidines and pyrrolidines. Silver-mediated ring-opening fluorination using Selectfluor highlights a strategy for cyclic amine functionalization and late-stage skeletal diversification, establishing cyclic amines as synthons for amino alkyl radicals and providing synthetic routes to valuable building blocks.
    Keywords: Chemistry
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  • 100
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-07-20
    Keywords: Chemistry
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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