Noteworthy Chemistry

April 21, 2014

How does ATE1 arginylate proteins at midchain residues? Arginylation is an emerging posttranslational protein modification method. It is mediated by the arginyltransferase ATE1 that transfers arginine (Arg) from the Arg-tRNA (transfer RNA) onto proteins, mainly aspartine (Asp) and glutamine (Glu).

This modification is essential in key physiological events and has an important biological role, but little is known about the way ATE1 links Arg to proteins. It was thought that ATE1 attaches Arg via a peptide bond to the N-terminal α-amino group of a polypeptide chain, which would require proteolysis or Met-aminopeptidase activity to expose the target residue within the protein chain. This suggests that intact proteins cannot be arginylated in vivo.

Recent work identified a regulatory peptide that was arginylated on an internal Glu side chain through an amide bond with the Arg amino group. Modifications on the acidic side chains of internal Asp and Glu residues require different chemistry than N-terminal Arg linkages, and it was unclear whether this side-chain linkage occurs in vivo and whether ATE1 can mediate the linkage.

A. Kashina and colleagues at the University of Pennsylvania (Philadelphia), the Scripps Research Institute (La Jolla, CA), Fox Chase Cancer Center (Philadelphia), Tufts University School of Medicine (Boston), and Brandeis University (Waltham, MA) report that this internal side-chain modification occurs in vivo in multiple proteins through an unconventional chemical linkage that uses the carboxyl groups at the target site and does not need to be preprocessed. The side-chain reaction is functionally regulated and directly mediated by ATE1. Presumably, arginylation by this method allows regulation of intact proteins.

The authors used mass spectrometry to identify midchain Arg additions to Asp and Glu residues. Additional experiments showed that ATE1 mediates this tRNA-dependent side-chain arginylation of internal residues. Their results suggest that ATE1 facilitates arginylation through two types of chemical linkages, using the conventional N-terminal peptide bond or using the carboxyl group of the target residue that is likely linked to the Arg α-amino group. The Arg α-amino posttranslational linkage allows ATE1 to attach Arg to the side chains of acidic amino acid residues in intact proteins and peptides. This implies that arginylation can modify proteins transiently or stably and can facilitate biological regulation.

Proposed mechanism for N-terminal or side-chain arginylation

The authors suggest a mechanism in which N-terminal and side chain arginylation arise from a common intermediate (see figure). In this setting, the Asp β-carboxylate attacks the Arg-tRNA ester to form an anhydride intermediate in which both carboxylate groups are activated. If the Asp is at the N terminus of a peptide, the intermediate reacts with the free amino group. If the Asp is internal, the intermediate reacts with the Arg amino group. These divergent routes create N-terminal or side-chain arginylation, respectively. (Chem. Biol. 2014, 21, 331–337; Abigail Druck Shudofsky)

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Well-defined microporous carbons outperform activated carbons. D. Wu and co-workers at Sun Yat-sen University (Guangzhou, China) and K. Matyjaszewski at Carnegie Mellon University (Pittsburgh) generated microporous carbons by templating polyhedral oligomeric silsesquioxanes (POSS). In the authors’ interfacial engineering technique, Friedel–Crafts–cross-linked octaphenyl POSS (xPh-POSS) forms a molecular-scale, 3-D, inorganic–organic spherical template for carbonization. The inorganic/organic ratio is 28/72 w/w; the average sphere diam is 360 nm.

Pyrolysis at 900 ºC gives a carbonization yield of 57%. The spherical nanostructure (average diam 330 nm) is retained with no silica clustering. Etching the silica domains with aq HF produces 1.3-nm nanopores within the microporous carbon framework. The Brunauer–Emmett–Teller (BET) surface area of the microporous carbon is as high as ≈1900 m2/g.

The authors tuned the pore morphology by controlling the carbonization conditions. For example, increasing in the pyrolysis temperature or decreasing the carbonization increases the BET surface area.

The large surface areas of these inorganic–organic templated microporous carbons provide CO2 sequestration levels and selectivity over nitrogen that are superior to commercially available activated carbons. The authors emphasize the carbon structures’ size-selective liquid adsorption properties and their electrochemical capacitance. (J. Am. Chem. Soc. 2014, 136, 4805–4808; LaShanda Korley)

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Obtain optically pure (R)-tetrahydrothiophene-3-ol by using bioreduction and cold crystallization. (R)-Tetrahydrothiophene-3-ol (2) is a key intermediate in the production of penem-based antibiotics. (Penems are β-lactams fused to an unsaturated five-membered heterocyclic ring.) Several methods can be used to prepare 2 with moderate optical purity; but because it is liquid at room temperature, ordinary recrystallization cannot be used to improve its purity. In addition, it has no functional groups that allow its enantiomers to be separated as diastereomeric salts.

K. Konuki and co-workers at MicroBiopharm (Shizuoka, Japan) developed a route to compound 2 by biologically reducing ketone 1. They chose microorganisms in the PenicilliumAspergillus, or Streptomyces genera for the enzymatic reduction and obtained the alcohol in 70–92% ee. They then used three repetitions of low-temperature (–15 ºC) crystallization from acetone–hexane to improve the purity to as high as 98.7% ee at the gram scale.

The authors scaled up the reaction to 3.6 kg of 1. To avoid melting the crystals of 2 during the filtration steps after crystallization, they used a jacketed pressure filtration vessel with an agitator. They obtained 363 g of (R)-alcohol 2 in 97% ee. (Org. Process Res. Dev. 2014, 18, 310–314; José C. Barros)

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Predict chemical shifts to assign small-molecule structures. NMR spectroscopy continues to evolve; it is the most powerful and reliable method to characterize organic compounds. Among the parameters that can be measured in NMR experiments, chemical shifts can identify the local chemical and magnetic environments of nuclei; they are indispensable for assigning the structures of newly synthesized molecules.

In a stereochemically complex environment, however, it is challenging and sometimes impossible to assign structures solely on the basis of chemical shift information. Because chemical shifts are easy to predict by using computational methods, P. H Willoughby, M. J Jansma, and T. R. Hoye* at the University of Minnesota (Minneapolis) developed a protocol that uses chemical-shift prediction to assist the structure assignment of small organic molecules.

The authors’ protocol requires basic commercial calculation packages such as Gaussian and MacroMode. The method is straightforward for chemists who have little background in computational chemistry. A typical procedure includes the following steps:

  1. Perform a molecular mechanics search to generate a library of conformers.
  2. Use density functional theory (DFT) to optimize the geometry and calculate the frequency of each conformer.
  3. Use DFT to calculate NMR shielding tensor values.
  4. Boltzmann-weight the shielding tensors in all conformers and convert the tensors to chemical shifts.
  5. Compare the calculated values with experimental data.

Based on this protocol, the authors verified the structures of the cis- and trans-3-methylcyclohexanol. The time required for these calculations is ideal for small organic molecules: from ≈2 h of effort over 2 days to ≈3–6 h over 2 weeks, depending on the complexity of the target compound. (Nat. Protoc. 2014, 9, 643–660; Xin Su)

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Synthesize labile chiral α-aryl-α-aryloxyacetates via this palladium-catalyzed enantioselective O–H bond insertion reaction. Palladium complexes catalyze many reactions that are used in organic synthesis. Palladium-catalyzed asymmetric carbene transfer reactions, however, are rare and pose a challenge for organic chemists.

Asymmetric carbene transfer reactions that can be run under mild conditions would be ideal for making α-aryl-α-aryloxyacetates. This moiety is widely found in bioactive molecules. The difficulty in synthesizing it is attributable to the high acidity of its α-hydrogen, which easily leads to epimerization reactions under basic conditions or at high temperatures.

S.-F. Zhu, Q.-L. Zhou and co-workers at Nankai University (Tianjin, China) developed a palladium-catalyzed asymmetric phenolic O–H bond insertion reaction that proceeds under mild conditions. It provides an easy synthetic route to chiral α-aryl-α-aryloxyacetates (3) in good yields (up to 87%) and excellent enantioselectivity (96–99% ee).

In the authors’ method, α-diazo-α-phenylacetates (1) react with phenols (2) under neutral conditions. The authors tested several palladium ligands with general structure 4; the one with R = Ph gave the best results. In the figure, NaBArF (sodium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate) is an additive that stabilizes the catalyst and increases the yield. Molecular sieves are added to absorb byproduct water.

Synthesis of α-aryl-α-aryloxyacetates with palladium and a chiral ligand

The reaction tolerates a broad range of substrates and meets the conditions that are necessary to avoid byproduct formation. It is easily performed at the gram scale and should be useful for synthetic chemists. (Angew. Chem., Int. Ed. 2014, 53, 2978–2981; Ben Zhong Tang)

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Don’t take anything for granted in a classical resolution. A. W. Kruger, D. S. Welch, and co-workers at AbbVie (North Chicago, IL) used two routes to prepare a chiral chromanamine intermediate in the synthesis of a transient receptor potential vanilloid-1 antagonist. In the first route, a Corey–Itsuno ketone reduction generates a chiral alcohol that is converted to the corresponding azide with (PhO)P(O)N3. The azide is then reduced to a free base amine that is 65–75% pure with ≈95% ee.

Because the azide intermediate is unstable and unsafe to handle, the authors developed an alternative route. The starting ketone is reductively aminated with Ellman’s chiral t-BuSONH2. The sulfinyl group is then cleaved with methanolic HCl. This sequence gives the HCl salt of the target amine in 96% purity and 92% ee.

The chemical and chiral purity of the amine produced in the first route can be upgraded to >99% by forming its D-tartaric acid salt. Unexpectedly, the enantiopurity is not improved when the same operation is applied to the product from the second route. A comparison of the tartrate salts showed that the salt of the route 1 amine exists as an MeCN solvate whereas the route 2 salt is not solvated.

Even when it is seeded with nonsolvated salt crystals, the route 1 salt still crystallizes as the MeCN solvate. The chiral purity of the route 2 amine can be upgraded to 99.6% ee by using the L-pyroglutamic acid salt. (Org. Process Res. Dev. 2014, 18, 303–309; Will Watson)

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Mine residues are oxygen carriers for biomass fuel processing. Biomass fuels are often pretreated by using a mild form of pyrolysis to release water and volatiles in a process called torrefaction. The result is a dry, energy-dense product that is not subject to rotting. Integrated torrefaction uses the volatiles released from the biomass itself as the fuel source, but these volatiles must be processed first to prevent combustion and uneven heating.

A. Sarvaramini and F. Larachi* at Laval University (Quebec City) report a method for processing gas emitted during torrefaction that uses magnesium iron silicate residues from a nickel mining operation. The mineral residue provides an abundant, inexpensive source of solid oxygen carriers (iron oxides) for chemical looping combustion (CLC). The magnesium forms carbonates that act as a carbon sink.

The authors found that almost all of the carbon released during CLC is converted to CO2. A subsequent carbonation reaction captures as much as 20% of this CO2. The figure shows a schematic drawing of the combined procedures.

Bioreduction of ketone 1 to alcohol 2
Schematic of the experimental torrefaction−chemical looping−carbonation assembly

Birch wood chips are torrefied under an oxygen-free nitrogen atmosphere. The released volatiles flow into a CLC reactor vessel that contains mine residue particles—17.3 wt% Fe, 13.8 wt% Mg, and 16.5 wt% Si—in the 100−250 μm size range. Before use, the residue was air-calcined to increase the extra-framework oxidized iron content. This reactor burns the volatiles in the flue gas to produce CO2 and water. The authors reused the residue particles for as many as five consecutive oxidation−reduction cycles without a significant loss of activity.

The effluent from the CLC passes into a third vessel that contains magnesium-rich material leached from spent calcined mineral residues. This material has ≈50% of its pore volume filled with water, into which the CO2 from the flue gas dissolves. The solution reacts with the magnesium to form solid carbonates. The gas that leaves this reactor passes through a cold trap to collect water and condensable volatiles, and the remaining CO2, CO, hydrogen, and methane are recirculated to the torrefaction vessel to serve as fuel for the pyrolysis process.

The authors note that other mine residues they tested produced more carbonates, probably because they had a higher content of free magnesium oxides. The reaction rate increases with temperature, but increasing the temperature to >50 ºC causes the water to evaporate, which impedes the carbonation reaction. (Energy Fuels 2014, 28, 1983–1991; Nancy McGuire

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