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1. Sticky ends in a self-assembling ABA triblock copolymer: the role of ureas in stimuli-responsive hydrogels

   https://doi.org/10.1039/C8ME00063H  

   Shafranek, Ryan T. ; Leger, Joel D. ; Zhang, Song ; Khalil, Munira ; Gu, Xiaodan ; Nelson, Alshakim ( February 2019 , Molecular Systems Design & Engineering)

   Directing polymer self-assembly through noncovalent interactions is a powerful way to control the structure and function of nanoengineered materials. Dynamic hydrogen bonds are particularly useful for materials with structures that change over time or in response to specific stimuli. In the present work, we use the supramolecular association of urea moieties to manipulate the morphology, thermal response, and mechanical properties of soft polymeric hydrogels. Urea-terminated poly(isopropyl glycidyl ether)- b -poly(ethylene oxide)- b -poly(isopropyl glycidyl ether) ABA triblock copolymers were synthesized using controlled, anionic ring-opening polymerization and subsequent chain-end functionalization. Triblock copolymers with hydroxy end-groups were incapable of hydrogelation, while polymers terminated with meta -bis-urea motifs formed robust gels at room temperature. Rheometric analysis of the bulk gels, variable-temperature infrared spectroscopy (VT-IR), differential scanning calorimetry (DSC), and small-angle X-ray scattering (SAXS) confirmed the formation of structured hydrogels via association of the meta -bis-urea end-groups. Monourea end-groups did not result in the same regular structure as the meta -bis-urea. In future, the reported hydrogels could be useful for elastomeric, shape-morphing 3D-printed constructs, or as biomimetic scaffolds with precisely tailored porosity and mechanical properties.
2. Florida mangrove saltmarsh reference surface soils

   https://doi.org/10.6073/pasta/0e08cbe07c84488cb7b9dd16669946d0  

   Lewis, David Bruce ( January 2021 )

   Abstract

   Site description. This data package consists of data obtained from sampling surface soil (the 0-7.6 cm depth profile) in black mangrove (Avicennia germinans) dominated forest and black needlerush (Juncus roemerianus) saltmarsh along the Gulf of Mexico coastline in peninsular west-central Florida, USA. This location has a subtropical climate with mean daily temperatures ranging from 15.4 °C in January to 27.8 °C in August, and annual precipitation of 1336 mm. Precipitation falls as rain primarily between June and September. Tides are semi-diurnal, with 0.57 m median amplitudes during the year preceding sampling (U.S. NOAA National Ocean Service, Clearwater Beach, Florida, station 8726724). Sea-level rise is 4.0 ± 0.6 mm per year (1973-2020 trend, mean ± 95 % confidence interval, NOAA NOS Clearwater Beach station). The A. germinans mangrove zone is either adjacent to water or fringed on the seaward side by a narrow band of red mangrove (Rhizophora mangle). A near-monoculture of J. roemerianus is often adjacent to and immediately landward of the A. germinans zone. The transition from the mangrove to the J. roemerianus zone is variable in our study area. An abrupt edge between closed-canopy mangrove and J. roemerianus monoculture may extend for up to several hundred meters in some locations, while other stretches of ecotone present a gradual transition where smaller, widely spaced trees are interspersed into the herbaceous marsh. Juncus roemerianus then extends landward to a high marsh patchwork of succulent halophytes (including Salicornia bigellovi, Sesuvium sp., and Batis maritima), scattered dwarf mangrove, and salt pans, followed in turn by upland vegetation that includes Pinus sp. and Serenoa repens. Field design and sample collection. We established three study sites spaced at approximately 5 km intervals along the western coastline of the central Florida peninsula. The sites consisted of the Salt Springs (28.3298°, -82.7274°), Energy Marine Center (28.2903°, -82.7278°), and Green Key (28.2530°, -82.7496°) sites on the Gulf of Mexico coastline in Pasco County, Florida, USA. At each site, we established three plot pairs, each consisting of one saltmarsh plot and one mangrove plot. Plots were 50 m^2 in size. Plots pairs within a site were separated by 230-1070 m, and the mangrove and saltmarsh plots composing a pair were 70-170 m apart. All plot pairs consisted of directly adjacent patches of mangrove forest and J. roemerianus saltmarsh, with the mangrove forests exhibiting a closed canopy and a tree architecture (height 4-6 m, crown width 1.5-3 m). Mangrove plots were located at approximately the midpoint between the seaward edge (water-mangrove interface) and landward edge (mangrove-marsh interface) of the mangrove zone. Saltmarsh plots were located 20-25 m away from any mangrove trees and into the J. roemerianus zone (i.e., landward from the mangrove-marsh interface). Plot pairs were coarsely similar in geomorphic setting, as all were located on the Gulf of Mexico coastline, rather than within major sheltering formations like Tampa Bay, and all plot pairs fit the tide-dominated domain of the Woodroffe classification (Woodroffe, 2002, "Coasts: Form, Process and Evolution", Cambridge University Press), given their conspicuous semi-diurnal tides. There was nevertheless some geomorphic variation, as some plot pairs were directly open to the Gulf of Mexico while others sat behind keys and spits or along small tidal creeks. Our use of a plot-pair approach is intended to control for this geomorphic variation. Plot center elevations (cm above mean sea level, NAVD 88) were estimated by overlaying the plot locations determined with a global positioning system (Garmin GPS 60, Olathe, KS, USA) on a LiDAR-derived bare-earth digital elevation model (Dewberry, Inc., 2019). The digital elevation model had a vertical accuracy of ± 10 cm (95 % CI) and a horizontal accuracy of ± 116 cm (95 % CI). Soil samples were collected via coring at low tide in June 2011. From each plot, we collected a composite soil sample consisting of three discrete 5.1 cm diameter soil cores taken at equidistant points to 7.6 cm depth. Cores were taken by tapping a sleeve into the soil until its top was flush with the soil surface, sliding a hand under the core, and lifting it up. Cores were then capped and transferred on ice to our laboratory at the University of South Florida (Tampa, Florida, USA), where they were combined in plastic zipper bags, and homogenized by hand into plot-level composite samples on the day they were collected. A damp soil subsample was immediately taken from each composite sample to initiate 1 y incubations for determination of active C and N (see below). The remainder of each composite sample was then placed in a drying oven (60 °C) for 1 week with frequent mixing of the soil to prevent aggregation and liberate water. Organic wetland soils are sometimes dried at 70 °C, however high drying temperatures can volatilize non-water liquids and oxidize and decompose organic matter, so 50 °C is also a common drying temperature for organic soils (Gardner 1986, "Methods of Soil Analysis: Part 1", Soil Science Society of America); we accordingly chose 60 °C as a compromise between sufficient water removal and avoidance of non-water mass loss. Bulk density was determined as soil dry mass per core volume (adding back the dry mass equivalent of the damp subsample removed prior to drying). Dried subsamples were obtained for determination of soil organic matter (SOM), mineral texture composition, and extractable and total carbon (C) and nitrogen (N) within the following week. Sample analyses. A dried subsample was apportioned from each composite sample to determine SOM as mass loss on ignition at 550 °C for 4 h. After organic matter was removed from soil via ignition, mineral particle size composition was determined using a combination of wet sieving and density separation in 49 mM (3 %) sodium hexametaphosphate ((NaPO_3)_6) following procedures in Kettler et al. (2001, Soil Science Society of America Journal 65, 849-852). The percentage of dry soil mass composed of silt and clay particles (hereafter, fines) was calculated as the mass lost from dispersed mineral soil after sieving (0.053 mm mesh sieve). Fines could have been slightly underestimated if any clay particles were burned off during the preceding ignition of soil. An additional subsample was taken from each composite sample to determine extractable N and organic C concentrations via 0.5 M potassium sulfate (K_2SO_4) extractions. We combined soil and extractant (ratio of 1 g dry soil:5 mL extractant) in plastic bottles, reciprocally shook the slurry for 1 h at 120 rpm, and then gravity filtered it through Fisher G6 (1.6 μm pore size) glass fiber filters, followed by colorimetric detection of nitrite (NO_2^-) + nitrate (NO_3^-) and ammonium (NH_4^+) in the filtrate (Hood Nowotny et al., 2010,Soil Science Society of America Journal 74, 1018-1027) using a microplate spectrophotometer (Biotek Epoch, Winooski, VT, USA). Filtrate was also analyzed for dissolved organic C (referred to hereafter as extractable organic C) and total dissolved N via combustion and oxidation followed by detection of the evolved CO_2 and N oxide gases on a Formacs HT TOC/TN analyzer (Skalar, Breda, The Netherlands). Extractable organic N was then computed as total dissolved N in filtrate minus extractable mineral N (itself the sum of extractable NH_4-N and NO_2-N + NO_3-N). We determined soil total C and N from dried, milled subsamples subjected to elemental analysis (ECS 4010, Costech, Inc., Valencia, CA, USA) at the University of South Florida Stable Isotope Laboratory. Median concentration of inorganic C in unvegetated surface soil at our sites is 0.5 % of soil mass (Anderson, 2019, Univ. of South Florida M.S. thesis via methods in Wang et al., 2011, Environmental Monitoring and Assessment 174, 241-257). Inorganic C concentrations are likely even lower in our samples from under vegetation, where organic matter would dilute the contribution of inorganic C to soil mass. Nevertheless, the presence of a small inorganic C pool in our soils may be counted in the total C values we report. Extractable organic C is necessarily of organic C origin given the method (sparging with HCl) used in detection. Active C and N represent the fractions of organic C and N that are mineralizable by soil microorganisms under aerobic conditions in long-term soil incubations. To quantify active C and N, 60 g of field-moist soil were apportioned from each composite sample, placed in a filtration apparatus, and incubated in the dark at 25 °C and field capacity moisture for 365 d (as in Lewis et al., 2014, Ecosphere 5, art59). Moisture levels were maintained by frequently weighing incubated soil and wetting them up to target mass. Daily CO_2 flux was quantified on 29 occasions at 0.5-3 week intervals during the incubation period (with shorter intervals earlier in the incubation), and these per day flux rates were integrated over the 365 d period to compute an estimate of active C. Observations of per day flux were made by sealing samples overnight in airtight chambers fitted with septa and quantifying headspace CO_2 accumulation by injecting headspace samples (obtained through the septa via needle and syringe) into an infrared gas analyzer (PP Systems EGM 4, Amesbury, MA, USA). To estimate active N, each incubated sample was leached with a C and N free, 35 psu solution containing micronutrients (Nadelhoffer, 1990, Soil Science Society of America Journal 54, 411-415) on 19 occasions at increasing 1-6 week intervals during the 365 d incubation, and then extracted in 0.5 M K_2SO_4 at the end of the incubation in order to remove any residual mineral N. Active N was then quantified as the total mass of mineral N leached and extracted. Mineral N in leached and extracted solutions was detected as NH_4-N and NO_2-N + NO_3-N via colorimetry as above. This incubation technique precludes new C and N inputs and persistently leaches mineral N, forcing microorganisms to meet demand by mineralizing existing pools, and thereby directly assays the potential activity of soil organic C and N pools present at the time of soil sampling. Because this analysis commences with disrupting soil physical structure, it is biased toward higher estimates of active fractions. Calculations. Non-mobile C and N fractions were computed as total C and N concentrations minus the extractable and active fractions of each element. This data package reports surface-soil constituents (moisture, fines, SOM, and C and N pools and fractions) in both gravimetric units (mass constituent / mass soil) and areal units (mass constituent / soil surface area integrated through 7.6 cm soil depth, the depth of sampling). Areal concentrations were computed as X × D × 7.6, where X is the gravimetric concentration of a soil constituent, D is soil bulk density (g dry soil / cm^3), and 7.6 is the sampling depth in cm.
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3. Sustainable glucose-based block copolymers exhibit elastomeric and adhesive behavior

   https://doi.org/10.1039/c6py00700g  

   Nasiri, Mohammadreza ; Reineke, Theresa M. ( January 2016 , Polymer Chemistry)

   Herein, we present the direct modification of glucose, an abundant and inexpensive sugar molecule, to produce new sustainable and functional polymers. Glucose-6-acrylate-1,2,3,4-tetraacetate (GATA) has been synthesized and shown to provide a useful glassy component for developing an innovative family of elastomeric and adhesive materials. A series of diblock and triblock copolymers of GATA and n -butyl acrylate (n-BA) were created via Reversible Addition–Fragmentation Chain Transfer (RAFT) polymerization. Initially, poly(GATA)- b -poly(n-BA) copolymers were prepared using 4-cyano-4-[(ethylsulfanylthiocarbonyl)sulfanyl] pentanoic acid (CEP) as a chain transfer agent (CTA). These diblock copolymers demonstrated decomposition temperatures of 275 °C or greater and two glass transition temperatures ( T g ) around −45 °C and 100 °C corresponding to the PnBA and PGATA domains, respectively, as measured by differential scanning calorimetry (DSC). Triblock copolymers of GATA and n-BA, with moderate dispersities ( Đ = 1.15–1.29), were successfully synthesized when S , S -dibenzyl trithiocarbonate (DTC) was employed as the CTA. Poly(GATA)- b -poly(nBA)- b -poly(GATA) copolymers with 14–58 wt% GATA were prepared and demonstrated excellent thermomechanical properties ( T d ≥ 279 °C). Two well-separated glass transitions near the values for homopolymers of n-BA and GATA (∼−45 °C and ∼100 °C, respectively) were measured by DSC.more »The triblock with 14% GATA exhibited peel adhesion of 2.31 N cm −1 (when mixed with 30 wt% tackifier) that is superior to many commercial pressure sensitive adhesives (PSAs). Use of 3,5-bis(2-dodecylthiocarbonothioylthio-1oxopropoxy)benzoic acid (BTCBA) as the CTA provided a more efficient route to copolymerize GATA and n-BA. Using BTCBA, poly(GATA)- b -poly(nBA)- b -poly(GATA) triblock copolymers containing 12–25 wt% GATA, with very narrow molar mass distributions ( Đ ≤ 1.08), were prepared. The latter series of triblock copolymers showed excellent thermal stability with T d ≥ 275 °C. Only the T g for the PnBA block was observed by DSC (∼−45 °C), however, phase-separation was confirmed by small-angle X-ray scattering (SAXS) for all of these triblock copolymers. The mechanical behavior of the polymers was investigated by tensile experiments and the triblock with 25% GATA content demonstrated moderate elastomeric properties, 573 kPa stress at break and 171% elongation. This study introduces a new family of glucose-based ABA-type copolymers and demonstrates functionality of a glucose-based feedstock for developing green polymeric materials.« less
4. Surface plastic flow in polishing of rough surfaces

   https://doi.org/10.1038/s41598-019-46997-w  

   Iquebal, Ashif S. ; Sagapuram, Dinakar ; Bukkapatnam, Satish T. S. ( July 2019 , Scientific Reports)

   We present experimental evidence for a new mechanism for how smooth surfaces emerge during repetitive sliding contacts, as in polishing. Electron microscopy observations of Ti-6Al-4V surface with a spherical asperity structure—realized via additive manufacturing—during successive polishing stages suggest that asperity-abrasive contacts exhibit viscous behavior, where the asperity material flows in the form of thin (1–10 μm) fluid-like layers. Subsequent bridging of these layers among neighboring asperities results in progressive surface smoothening. Using analytical asperity-abrasive contact temperature modeling and microstructural characterization, we show that the sliding contacts encounter flash temperatures of the order of 700–900 K which is in the range of the dynamic recrystallization temperature of the material considered, thus supporting the experimental observations. Besides providing a new perspective on the long-held mechanism of polishing, our observations provide a novel approach based on graph theory to quantitatively characterize the evolution of surface morphology. Results suggest that the graph representation offers a more efficient measure to characterize the surface morphology emerging at various stages of polishing. The research findings and observations are of broad relevance to the understanding of plastic flow behavior of sliding contacts ubiquitous in materials processing, tribology, and natural geological processes as well as present unique opportunities to tailormore »the microstructures by controlling the thermomechanics of the asperity-abrasive contacts.

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5. Convergent allostery in ribonucleotide reductase

   https://doi.org/10.1038/s41467-019-10568-4  

   Thomas, William C. ; Brooks, III, F. Phil ; Burnim, Audrey A. ; Bacik, John-Paul ; Stubbe, JoAnne ; Kaelber, Jason T. ; Chen, James Z. ; Ando, Nozomi ( June 2019 , Nature Communications)

   Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organismBacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.