Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution

Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.     

In search of 1,3-disila/germa/stannabicyclo[1.1.1]pentanes with short bridgehead-bridgehead distances and low ring strain energies

The strain energies and through-space distances between the two bridgehead E atoms of a selection of 1,3-dimethyl-1,3-ditetrelbicyclo[1.1.1]pentanes (tetrel E = Si, Ge or Sn) were examined by quantum chemical calculations at MP2 and B3LYP levels. The aim is to identify which bridges lead to short through-space E,E distances, and simultaneously, to as low strain as possible. A short E,E distance should improve through-space interaction, and a low strain should promote the thermal stability and possibly also facilitate their synthesis. The bridges examined included CH₂, CMe₂, CtBu₂, C(CH₂)n (n = 2–4), O, NMe, S, PMe, SiMe₂, GeMe₂, and SnMe₂. The calculations indicate that the phospha bridge is a good compromise providing reasonably low strain as well as E,E through-space distances which are only longer than normal E–E single bonds by factors of 1.06–1.10. This paper is dedicated to Professor Mitsuo Kira in recognition of his stimulating Si chemistry and his 2005 Wacker Award.     

An iron carbonyl approach to the influenza neuraminidase inhibitor oseltamivir

A novel synthetic route towards oseltamivir, an influenza neuraminidase inhibitor, has been achieved employing a cationic iron carbonyl complex, providing an alternate pathway with the potential to access diverse analogues.     

Isolation of Escherichia coli inner membranes by metal affinity two-phase partitioning

As reduction of sample complexity is a central issue in membrane proteomic research, the need for new pre-fractionation methods is significant. Here we present a method for fast and efficient enrichment of Escherichia coli inner membranes expressing a His-tagged integral membrane L-fucose-proton symporter (FucP). An enriched inner membrane fraction was obtained from a crude membrane mixture using affinity two-phase partitioning in combination with nickel-nitrilotriacetic acid (Ni-NTA) immobilized on agarose beads. Due to interaction between the beads and FucP, inner membranes were selectively partitioned to the bottom phase of a polymer/polymer aqueous two-phase system consisting of poly(ethylene glycol) (PEG) and dextran. The partitioning of membranes was monitored by assaying the activity of an inner membrane marker protein and measuring the total protein content in both phases. The enrichment of inner membrane proteins in the dextran phase was also investigated by proteomic methodology, including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), trypsin digestion and liquid chromatography in combination with tandem mass spectrometry (LC-MS/MS). Using a high level of significance (99.95%) in the subsequent database search, 36 proteins assigned to the inner membrane were identified in the bottom phase, compared to 29 when using the standard sucrose gradient centrifugation method for inner membrane isolation. Furthermore, metal affinity two-phase partitioning was up to 10 times faster than sucrose gradient centrifugation. The separation conditions in these model experiments provide a basis for the selective isolation of E. coli membranes expressing His-tagged proteins and can therefore facilitate research on such membrane proteomes.     

Solvothermal synthesis of new metal organic framework structures in the zinc-terephthalic acid-dimethyl formamide system

Two new metal organic framework (MOF) structures have been obtained from the Zn-terephthalic acid (H₂BDC)-dimethyl formamide (DMF) system and examined by single-crystal X-ray diffraction: Zn(C₈H₄O₄)(C₃H₇NO), 1, monoclinic C2/m, a=11.1369(5), b=14.0217(7), , β=106.316(1)°, , , Z=4, R₁=0.060, wR₂=0.169, S=1.27; Zn(HCO₂)₃(C₂H₈N), 2, trigonal , a=8.1818(1), , , , Z=6, R₁=0.014, wR₂=0.039, S=1.11. Contrary to previously published structures in the same system, the crystals were obtained by solvothermal synthesis at 381 K. Structure 1 consists of 2-D layers stacked in an offset manner to accommodate DMF moieties coordinated to Zn²⁺ within voids in adjacent layers. Structure 2 consists of a 3-D network constructed from Zn²⁺ ions bridged by deprotonated formic acid moieties. Over time, the structure of 1 rearranges to Zn(C₈H₄O₄)(C₃H₇NO)(H₂O) [monoclinic P2₁/n, a=6.6456(2), b=15.2232(5), , β=104.110(2)°, , , Z=4, R₁=0.048, wR₂=0.100, S=1.07], which is identical to the known MOF-2 structure, obtained by crystallization at ambient conditions. The three structures were determined from crystals with similar crystal habits picked from a single solvothermal synthesis batch. The study demonstrates that MOF syntheses can give not only multiple crystal structures under different conditions, but also that numerous different structures, including some that are metastable, can be formed under identical conditions.     

Electronic spectroscopy of C2 in solid rare gas matrixes

Electronic spectroscopy of the C(2) molecule is investigated in Ar, Kr, and Xe matrixes in the 150-500 nm range. In the Ar matrix, the D ((1)Sigma(u)(+)) <-- ((1)Sigma(g)(+)) Mulliken band near 240 nm is the sole absorption in the UV range, whereas in the Kr matrix additional bands in the 188-209 nm range are assigned to the Kr(n)()(+)C(2)(-) <-- Kr(n)()C(2) charge-transfer absorptions. Because of the formation of a bound C(2)Xe species, the spectral observations in the Xe matrix differ dramatically from the lighter rare gases: the Mulliken band is absent and new bands appear near 300 and 423 nm. The latter is assigned to the forbidden B'((1)Sigma(g)(+)) <-- X ((1)Sigma(g)(+)) transition, but the origin of the former remains unclear. The spectral assignments are aided by electronic structure calculations at the MCSCF, CCSD(T), and BCCD(T) levels of theory and correlation consistent basis sets. A significant presence of multireference character of the C(2)Xe system was noted and a linear ground-state structure is predicted. The computational results contradict previous density functional studies on the same system.     

l‐Valyl‐l‐serine trihydrate

The valine side chains in the crystal structure of the title compound [systematic name: 2‐(2‐ammonio‐3‐methyl­butan­amido)‐3‐hydroxy­propano­ate tri­hydrate], C₈H₁₆N₂O₄·3H₂O, stack along an a axis of 4.77 Å to form hydro­phobic columns surrounded by remarkable water/hydroxyl shells. The peptide main chains are connected by hydrogen bonds in two‐dimensional layers. The peptide mol­ecules in each layer are related only by translation, and generate a very rare pattern. This is rendered possible through the formation of the shortest C^α—H·O(carboxyl­ate) inter­action ever recorded.     

Synthesis and characterisation of Gd2O3 nanocrystals functionalised by organic acids

Nanocrystals of Gd2O3 have been prepared by various methods, using, e.g., trioctylphosphine oxide (TOPO), diethylene glycol (DEG) or glycine. The crystalline particles were of sizes 5 to 15 nm. Different carboxylic acids, e.g., oleic acid or citric acid, were adsorbed onto the surface of the particles made with DEG. IR measurements show that the molecules coordinate to the Gd2O3 surface via the carboxylate group in a bidentate or bridging manner. The organic-acid/particle complexes were characterised by XRPD, TEM, FTIR, Raman, and XPS.     

Amino acid catalyzed neogenesis of carbohydrates: a plausible ancient transformation

Hexose sugars play a fundamental role in vital biochemical processes and their biosynthesis is achieved through enzyme-catalyzed pathways. Herein we disclose the ability of amino acids to catalyze the asymmetric neogenesis of carbohydrates by sequential cross-aldol reactions. The amino acids mediate the asymmetric de novo synthesis of natural L- and D-hexoses and their analogues with excellent stereoselectivity in organic solvents. In some cases, the four new stereocenters are assembled with almost absolute stereocontrol. The unique feature of these results is that, when an amino acid is employed as the catalyst, a single reaction sequence can convert a protected glycol aldehyde into a hexose in one step. For example, proline and its derivatives catalyze the asymmetric neogenesis of allose with >99 % ee in one chemical manipulation. Furthermore, all amino acids tested catalyzed the asymmetric formation of natural sugars under prebiotic conditions, with alanine being the smallest catalyst. The inherent simplicity of this catalytic process suggests that a catalytic prebiotic "gluconeogenesis" may occur, in which amino acids transfer their stereochemical information to sugars. In addition, the amino acid catalyzed stereoselective sequential cross-aldol reactions were performed as a two-step procedure with different aldehydes as acceptors and nucleophiles. The employment of two different amino acids as catalysts for the iterative direct aldol reactions enabled the asymmetric synthesis of deoxysugars with >99 % ee. In addition, the direct amino acid catalyzed C(2)+C(2)+C(2) methodology is a new entry for the short, highly enantioselective de novo synthesis of carbohydrate derivatives, isotope-labeled sugars, and polyketide natural products. The one-pot asymmetric de novo syntheses of deoxy and polyketide carbohydrates involved a novel dynamic kinetic asymmetric transformation (DYKAT) mediated by an amino acid.