Noteworthy Chemistry

March 24, 2014

Desalinate water with graphyne membranes. Although water is an abundant natural resource, the scarcity of fresh water is an increasingly serious problem. This shortage could be alleviated by additional resources for processing and distributing water. The current method of desalination relies on reverse osmosis (RO) membranes that are expensive and inefficient.

 In the search for new materials for affordable, efficient desalination, J. Kou, F. Wu, J. Fan, and colleagues at Zhejiang Normal University (Jinhua, China) and Cornell University (Ithaca, NY) used computational methods to identify graphynes as desalination membrane materials.

Whereas the structure of graphene is a planar network composed exclusively of sp2-hybridized carbon atoms, graphyne consists of sp- and sp2-hybridized carbon allotropes. Graphyne’s pore size can be tuned by the number of bridging acetylenic groups between benzene rings. The authors used molecular dynamics simulations to study the water permeability and salt-rejection capability of graphyne-3, -4, and -5 under a hydrostatic pressure of 132 MPa.

Generalized graphyne structure

The authors found that graphyne-3 and graphyne-4 provide excellent water permeability, 2–3 orders of magnitude greater than diffusive RO membranes. Both graphyne membranes exhibit high salt-rejection rates, especially graphyne-3 with 100% rejection. Water molecules penetrate graphyne pores under hydrostatic pressure, but the passage of hydrated sodium and chloride ions is energetically unfavorable.

The authors unravel the molecular mechanism for water permeability through and salt rejection by graphyne. They offer insights for designing graphyne-based, high-performance desalination materials. (Nanoscale 2014, 6, 1865–1870; Xin Su)

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Slowly freeze-dry chitin nanofibers to form porous structures. J. Wu and J. C. Meredith* at Georgia Tech (Atlanta) investigated the processing of chitin—an abundant renewable resource—beyond traditional deacetylation strategies. They used high-shear homogenization of purified chitin to obtain chitin nanofibers (CNFs) ≈20 nm diam in water. When dried, the fibers formed dense, transparent films.

The authors freeze-dried aqueous dispersions of CNFs at several temperatures to create porous structures when ice crystals nucleated and grew. These processes generate two opposing forces on the suspended fibers: a repulsive van der Waals force and an attractive force caused by viscous drag.

Depending on the freeze-drying temperature and the substrate, the authors obtained various architectures and degrees of porosity. Unlike porous sheets of chitin formed on an aluminum mold by rapid freeze-drying at –80 and –196 ºC, the authors obtained a 3-D fibrillar network architecture with 98.5% porosity and ≈3.2 μm pore size at a slower growth rate at –20 ºC.

The authors ascribe these differences to growth rate–mediated organization and CNF interactions. Switching to a stainless steel substrate gives a more porous (99.6%) network with much smaller pores (330 nm), a ≈10-fold size reduction. (ACS Macro Lett. 2014, 3, 185–190; LaShanda Korley)

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Silica and germania bond angles have diverse energy minima. Zeolite researchers often search databases of hypothetical structures for potentially useful configurations to synthesize. Energy optimization calculations help them select hypothetical structures that are most likely to be stable and practical to make. Zeolite models that use rigid TO4 tetrahedra (in which T is a generic tetrahedrally coordinated atom) connected at the oxygen vertices by force-free spherical joints are consistent with experimental data.

Ab initio calculations that compare the energy dependence of Si−O−Si and Ge−O−Ge bond angles suggest that the most stable structures for silicas are not necessarily the same as those for germanias. Several cluster models for germania structures have been studied, but M. M. J. Treacy and coauthors at Arizona State University (Tempe) and KAIST (Daejeon, Korea) believe that their study is the first to use a crystalline lattice model for the energy dependence of Ge−O−Ge angles. They calculated the energy dependence for the quartz and cristobalite structures and then extended their model to several known zeolite structures. The figure shows the transformation of the T−O−T angles in a calculated cristobalite structure from 180º to 113º.

Cristobalite structure with three different T–O–T angles

Silica and germania exhibit markedly different results for calculated energies over the range of T−O−T angles studied (120º–180º), but all of the energy curves for silica structures were similar, as were the curves for germania structures. The energy for silica structures decreases sharply as the T−O−T angle increases from 120º to 140º and then remains relatively constant up to 180º.

Germania structures exhibit an energy minimum at ≈128º−130º, and the energy rises steadily as the T−O−T angle increases to 180º. The energy penalty calculated when the full lattice model is used is even greater than that reported in previous cluster-model studies. For the economically important zeolite faujasite framework, the minimum range of T−O−T angles (141º−144º) is well within the stable range for silica, but probably prohibitive for germania.

The authors note that, of the 5824 low-energy frameworks described in the Atlas of Prospective Zeolite Structures, 48 have all of their T−O−T angles in the most favorable range for germania (117º−145º), but 994 lie in the optimal range for silica (135º−180º). Mixing germanium and silicon in the framework could extend the range of stable bond angles and increase the number of stable structures available for synthesis. (Chem. Mater. 2014, 26, 1523–1527; Nancy McGuire)

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Brew a cup of tea to trap methane. Methane is a cost-effective, relatively environment-friendly fuel, but the expense of storing and transporting it limits its use. Compression and liquefaction are the standard practices for methane storage and transportation. Several porous materials have been developed to store methane, but they are not yet practical.

Methane clathrates, in which methane is trapped in the polyhedral cavities of hydrogen-bonded water lattices, may be an attractive vehicle for storing and shipping methane. Methane hydrates can store ≈180 volumes of methane at STP per volume of clathrate.

The formation of methane clathrates in bulk water, however, is kinetically slow. To circumvent this problem, W. Wang, L. Sun, and coauthors at South China University of Technology (Guangzhou), Huazhong University of Science and Technology (Wuhan, China), and the University of Connecticut (Storrs) developed a strategy for rapidly forming methane clathrates that uses tea infusions.

The authors examined methane uptake kinetics at 0 ºC by forming methane clathrates in pure water and in aqueous infusions of various teas. They found that a green tea infusion took up 155 volumes of methane per volume of tea (90% saturation) in 20 min. Saturation (172 v/v) was reached in 1000 min. (The US Department of Energy vehicular methane storage target is 180 v/v.) Similar results were obtained for oolong tea, but black tea and water took up very little methane over this time scale.

The authors attribute the accelerated methane clathrate formation to tea polyphenols and saponins, most of which are oxidized during black tea production. Extracts of less expensive natural materials such as leaves from Bauhinia purpurea (orchid tree) and Mallotus apelta (an African spurge) are also efficient for accelerating the formation of methane clathrates (167 v/v and 170 v/v, respectively). This study may lead to alternative commercially practical methane storage and transportation methods. (Chem. Commun. 2014, 50, 1244–1246; Xin Su)

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Capture the true dynamics of miRNA expression in intact cells. MicroRNAs (miRNAs) play key roles in determining and regulating the fate of cells. Their significance is well known in cancer evolution and therapeutic response. Endogenous miRNAs can be used as biomarkers for diagnosis and prognosis and as intervention targets.

It is important to develop miRNA detection methods for preclinical and clinical applications. Current methods are costly and insufficiently sensitive; and they cannot be applied to intact live cells, which eliminates the possibility of monitoring expression during cell cycle progression.

Z. Medarova and colleagues at Massachusetts General Hospital/Harvard Medical School (Boston) and Boston Children’s Hospital developed a powerful signal amplification strategy that can report miRNA expression in intact cells. They created sensor oligonucleotides (oligos) composed of RNA bases that are complementary to particular target miRNAs and are labeled with a fluorescent dye at one end and a quencher at the opposite end.

When the sensor oligos enter a cell, they interact with their sequence-specific endogenous miRNA targets by base-pairing. This binding induces recruitment of the endogenous RNA-induced silencing complex to be assembled around the miRNA-sensor duplex and cleavage of the sensor oligo at a specific position in the conserved region where the miRNA engages the RNA substrate. Cleaving the oligo separates the quencher and dye and triggers fluorescence. The miRNA is released from the complex and is available to catalyze other cleavage reactions.

The authors demonstrated the feasibility of their process by focusing on one miRNA (miR-10b) implicated in breast cancer metastasis, but their method can be used to detect and profile a wide range of miRNA expression. They found that the sensor does not affect cell viability or spur an increase in apoptosis.

Using their technique, the authors quantified miRNA expression with flow cytometry and epifluorescence. They obtained values that fell within one standard deviation of the measurement obtained by using the real-time quantitative reverse transcription polymerase chain reaction. The method is fast and accurate; and it can analyze miRNA targets in an inexpensive, high-throughput format. Its ability to operate in intact cells should lead to a better understanding of cellular miRNA. (Chem. Biol. 2014, 21, 199–204; Abigail Druck Shudofsky)

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An overlooked superacid reveals the structure of the benzenium ion. Commonly called Wheland intermediates, arenium ions are nonaromatic protonated cyclohexadienyl cations that are believed to be the intermediates in electrophilic aromatic substitution reactions. Many arenium ions have been extensively characterized by IR, NMR, and X-ray diffraction spectroscopy, especially in superacidic media.

But the solid-state structure of the benzenium cation ([C6H7]+), the simplest arenium ion, has not been elucidated until now, mainly because of its instability. I. Krossing and colleagues at the University of Freiburg (Germany) obtained an ordered crystal structure of benzenium by using the superacid HBr–AlBr3.

Although NMR evidence of benzene protonation in HBr–AlBr3 exists, no benzenium salt has been isolated. The authors condensed in situ–generated HBr gas into AlBr3–benzene mixtures of various ratios at –78 ºC. They obtained benzene-solvated [C6H7]+[Al2Br7]·C6H6 (1) as colorless crystals at 0 ºC when they mixed HBr, AlBr3, and benzene in a 1:1:1 mol ratio.

Formation of the benzene-solvated benzenium cation

The crystal structure of 1 is a planar [C6H7]+ ion with elongated C–C bonds at the protonated carbon atom. These bonds are considerably shorter than ordinary C(sp2)–C(sp3) and C(sp3)–C(sp3) single bonds, indicating that they retain most of their aromatic character. The other C–C bond lengths are consistent with those in the pentadienyl cation. All of the bond angles deviated slightly from the characteristic 120º of benzene.

The authors developed a Born–Fajans–Haber cycle for this reaction from lattice-energy and quantum-chemical calculations. They identified the main driving force as the gain of lattice energy in the solid state. The benzene-solvated [C6H7]+ ion is stabilized by extra C–H–π and π–π interactions. (Angew. Chem., Int. Ed. 2014, 53, 1689–1692; Xin Su)

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Adjust the reaction and workup to minimize mutagenic impurity levels in a final product. The final step in the synthesis of filibuvir, a potential hepatitis C vaccine, is a reductive coupling between a β-keto lactone and a triazolopyrimidine aldehyde. N. D. Ide, J. A. Ragan, and co-workers at Pfizer (Groton, CT; Kent, UK; and Ringaskiddy, Ireland) found that the best reaction conditions are achieved by slowly adding a solution of the keto lactone to a mixture of 1.2 equiv of the aldehyde and 1.2 equiv of a Hantzsch ester in MeOH–THF–HOAc.

The reaction is worked up by adding n-propyl acetate and 10% aq citric acid, which transfers the ester and its pyridine byproduct into the organic layer. The pH of the aqueous layer is adjusted to 5.5–6.5, and the neutral product is extracted with n-propyl acetate to leave unreacted aldehyde in the aqueous layer.

The aldehyde is mutagenic. Initially, the limits for it were set at 7 ppm in the active pharmaceutical ingredient for phase II clinical trials and 4 ppm for phase III trials. To reduce the level of unreacted aldehyde, the authors added a temperature cycle to the workup procedure, but a better solution is to reduce the amount of aldehyde used in the reaction to 1.0 equiv, with 1.07 equiv of Hantzsch ester. This change minimally reduces the yield and gives product with aldehyde levels less than the limit of quantitation on the lab scale (0.4 ppm) and 1–2.2 ppm on the pilot plant scale.

The aldehyde is also an oxidative degradation product of filibuvir, but that is another story. (Org. Process Res. Dev. 2014, 18, 45–56; Will Watson)

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