l‐Phenyl­alanyl‐l‐alanine dihydrate

A new type of molecular arrangement for dipeptides is observed in the crystal structure of l ‐phenyl­alanyl‐l ‐alanine dihydrate, C₁₂H₁₆N₂O₃·2H₂O. Two l ‐Phe and two l ‐Ala side chains aggregate into large hydro­phobic columns within a three‐dimensional hydrogen‐bond network.     

l‐Phenyl­alanyl‐l‐tryptophan 0.75‐hydrate

The title compound, C₂₀H₂₁N₃O₃·0.75H₂O, crystallizes as exceedingly thin fibers. The crystal packing arrangement is related to those of other hydro­phobic dipeptides with phenyl­alanine residues, but the structure has pseudo‐tetra­gonal symmetry in an ortho­rhom­bic space group with four peptide mol­ecules and three water mol­ecules in the asymmetric unit.     

l‐Phenyl­alanyl‐l‐isoleucine 0.88‐hydrate

The asymmetric unit in the crystal structure of the title compound, C₁₅H₂₂N₂O₃·0.88H₂O, contains two peptide mol­ecules with completely different conformations. The structure is divided into hydro­phobic and hydro­philic layers, with channels of water mol­ecules at the layer interface.     

l‐Isoleucyl‐l‐serine 0.33‐hydrate,l‐phenyl­alanyl‐l‐serine and l‐methionyl‐l‐serine 0.34‐hydrate

The structures of the title dipeptides, C₉H₁₈N₂O₄·0.33H₂O, C₁₂H₁₆N₂O₄ and C₈H₁₆N₂O₄S·0.34H₂O, complete a series of investigations focused on l ‐Xaa‐l ‐serine peptides, where Xaa is a hydro­phobic residue. All three structures are divided into hydro­philic and hydro­phobic layers. The hydro­philic layers are thin for l ‐phenyl­alanyl‐l ‐serine, rendered possible by an unusual peptide conformation, and thick for l ‐isoleucyl‐l ‐serine and l ‐methionyl‐l ‐serine, which include cocrystallized water mol­ecules on the twofold axes.     

Two modifications of l‐alanyl‐l‐tyrosyl‐l‐alanine with different solvent mol­ecules in the crystal lattice

The low‐temperature crystal and mol­ecular structure analyses of two modifications of l ‐alanyl‐l ‐tyrosyl‐l ‐alanine with water, C₁₅H₂₁N₃O₅·2.63H₂O [(I), at 9 K], and ethanol, C₁₅H₂₁N₃O₅·C₂H₅O [(II), at 20 K], solvent mol­ecules in the crystal lattice show that the overall conformations of both modifications of the title tripeptide are practically the same. Moreover, despite the presence of different solvent mol­ecules in the crystal lattice, the specific inter­molecular inter­actions characteristic for individual tripeptide mol­ecules of (I) and (II) are conserved. The crystal packing of the two modifications of Ala‐Tyr‐Ala differ from each other only in the solvent region. The tight arrangements of tripeptide mol­ecules seem to be responsible for similar displacement parameters for all non‐H atoms, despite the different distances from the mol­ecular centre of mass. Comparison of the displacement parameters between the room‐ and low‐temperature structures shows that an average U_eq value decrease of about 80% takes place at 9 K [for (I)] and 20 K [for (II)] with respect to room temperature.     

An NH3+⃛phenyl interaction in l‐­phenyl­alanyl‐l‐valine

One of the amino H atoms of l ‐phenyl­alanyl‐l ‐valine, C₁₄H₂₀N₂O₃, participates in a rare secondary interaction in being accepted by the aromatic ring of the phenyl­alanine side chain. The phenyl group is also a donor in a weak hydrogen bond to the peptide carbonyl group.     

N‐Amidino‐4‐hydroxy‐l‐proline monohydrate and N‐amidino‐l‐methionine monohydrate

The title amidino‐amino acids (a‐Hpro), C₆H₁₁N₃O₃·H₂O, (I), and a‐Met, C₆H₁₃N₃O₂S·H₂O, (II), respectively, exist in the form of zwitterions. The five‐membered pyrrolidine ring in (I) adopts an envelope conformation, with the Cγ atom out of the plane defined by the rest of the ring atoms, and with the hydroxyl and carboxyl­ate groups in a trans configuration relative to the ring plane. The two crystallographically independent zwitterions in (II) reveal quite different conformations of their side chains and a slightly different orientation of the guanidine moiety with respect to the carboxyl­ate group. The crystal structures of both (I) and (II) are stabilized by extensive networks of O—H·O, N—H·O and C—H·O hydrogen bonds, the network being three‐dimensional in (I) and two‐dimensional in (II).     

The monohydrates of the four polar dipeptides l‐seryl‐l‐asparagine,l‐seryl‐l‐tyrosine,l‐tryptophanyl‐l‐serine and l‐tyrosyl‐l‐tryptophan

The crystal structures of the four dipeptides l ‐seryl‐l ‐asparagine monohydrate, C₇H₁₃N₃O₅·H₂O, l ‐seryl‐l ‐tyrosine monohydrate, C₁₂H₁₆N₂O₅·H₂O, l ‐tryptophanyl‐l ‐serine monohydrate, C₁₄H₁₇N₃O₄·H₂O, and l ‐tyrosyl‐l ‐tryptophan monohydrate, C₂₀H₂₁N₃O₄·H₂O, are dominated by extensive hydrogen‐bonding networks that include cocrystallized solvent water molecules. Side‐chain conformations are discussed on the basis of previous observations in dipeptides. These four dipeptide structures greatly expand our knowledge on dipeptides incorporating polar residues such as serine, asparagine, threonine, tyrosine and tryptophan.     

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.     

l‐Seryl‐l‐phenyl­alanine

The peptide bond in the crystal structure of the title compound, C₈H₁₆N₂O₄, deviates substantially from planarity in the same manner as in other l ‐Ser‐l ‐Xaa dipeptides, where Xaa is a hydro­phobic residue.     

Rose Bengal‐Sensitized Photooxidation of the Dipeptides l‐Tryptophyl‐l‐Phenylalanine,l‐Tryptophyl‐l‐Tyrosine and l‐Tryptophyl‐l‐Tryptophan: Kinetics,Mechanism and Photoproducts¶

The Rose Bengal‐sensitized photooxidations of the dipeptides l ‐tryptophyl‐l ‐phenylalanine (Trp‐Phe), l ‐tryptophyl‐l ‐tyrosine (Trp‐Tyr) and l ‐tryptophyl‐l ‐tryptophan (Trp‐Trp) have been studied in pH 7 water solution using static photolysis and time‐resolved methods. Kinetic results indicate that the tryptophan (Trp) moiety interacts with singlet molecular oxygen (O₂(¹Δ_g)) both through chemical reaction and through physical quenching, and that the photooxidations can be compared with those of equimolecular mixtures of the corresponding free amino acids, with minimum, if any, influence of the peptide bond on the chemical reaction. This is not a common behavior in other di‐ and polypeptides of photooxidizable amino acids. The ratio between chemical (k_r) and overall (k_t) rate constants for the interaction O₂(¹Δ_g)‐dipeptide indicates that Trp‐Phe and Trp‐Trp are good candidates to suffer photodynamic action, with k_rlk_t values of 0.72 and 0.60, respectively (0.65 for free Trp). In the case of Trp‐Tyr, a lower k_rlk_t value (0.18) has been found, likely as a result of the high component of physical deactivation of O₂(¹Δ_g) by the tyrosine moiety. The analysis of the photooxidation products shows that the main target for O₂(¹Δ_g) attack is the Trp group and suggests a much lower accumulation of kynurenine‐type products, as compared with free Trp. This is possibly because of the occurrence of another accepted alternative pathway of oxidation that gives rise to 3a‐oxidized hydrogenated pyrrolo[2,3‐b]indoles.     

l‐Isoleucyl‐l‐phenyl­alanine dihydrate

The structure of the title compound, C₁₅H₂₂N₂O₃·2H₂O, was derived from data collected on a very thin twinned needle. The peptide mol­ecule is in a rare conformation normally associated with hydro­phobic dipeptides that form nanotubes. Nevertheless, the present structure is divided into hydro­phobic and hydro­philic layers.     

A non‐planar peptide bond in l‐seryl‐l‐valine

The C^α—C′—N—C^α (ω) torsion angle of the peptide bond in the crystal structure of the title compound, C₈H₁₆N₂O₄, is 157.37 (15)°. This is the second‐largest deviation from planarity observed for a small linear peptide.     

Methyl 4‐O‐β‐l‐fucopyranosyl α‐­d‐­glucopyranoside hemihydrate

The crystal structure of methyl 4‐O‐β‐l ‐fuco­pyran­osyl α‐d ‐gluco­pyran­oside hemihydrate C₁₃H₂₄O₁₀·0.5H₂O is organized in sheets with antiparallel strands, where hydro­phobic interaction accounts for partial stabilization. Infinite hydrogen‐bonding networks are observed within each layer as well as between layers; some of these hydrogen bonds are mediated by water mol­ecules. The conformation of the disaccharide is described by the glycosidic torsion angles: ?_H = ?6.1° and ψ_H = 34.3°. The global energy minimum conformation as calculated by molecular mechanics in vacuo has ?_H = ?58° and ψ_H = ?20°. Thus, quite substantial changes are observed between the in vacuo structure and the crystal structure with its infinite hydrogen‐bonding networks.     

Ethane‐1,1,2‐trisphosphonic acid hemihydrate

Ethane‐1,1,2‐trisphosphonic acid crystallizes as a hemihydrate, C₂H₉O₉P₃·0.5H₂O, in which the water O atom lies on an inversion centre in the space group P2₁/c. The acid component, which contains a short but noncentred O—H...O hydrogen bond, adopts a gauche conformation. The acid components are linked by an extensive series of O—H...O hydrogen bonds to form layers, which are linked into pairs by the water molecules.     

N‐(l‐2‐Aminobutyryl)‐l‐alanine and 2‐(l‐alanylamino)‐l‐butyric acid 0.33‐hydrate

The crystal structure of N‐(l ‐2‐amino­butyryl)‐l ‐alanine, C₇H₁₄N₂O₃, is closely related to the structure of l ‐alanyl‐l ‐alanine, both being tetragonal, while the retro‐analogue 2‐(l ‐alanyl­amino)‐l ‐butyric acid 0.33‐hydrate, C₇H₁₄N₂O₃·­0.33H₂O, forms a new type of molecular columnar structure with three peptide mol­ecules in the asymmetric unit.     

l‐Alanylglycyl‐l‐alanine monohydrate at 20 K

The X‐ray crystal structure of the title compound, C₈H₁₅N₃O₄·H₂O, at 20 K (space group P2₁) reveals that the mol­ecular conformation of the tripeptide is remarkably different from the water‐free form (space group P2₁2₁2₁) reported previously [Padiyar & Seshadri (1996), Acta Cryst. C 52 , 1693–1695].     

l‐Arginine‐Triggered Self‐Assembly of CeO2 Nanosheaths on Palladium Nanoparticles in Water

Pd@CeO₂ core–shell nanostructures with a tunable Pd core size, shape, and nanostructure as well as a tunable CeO₂ sheath thickness were obtained by a biomolecule‐assisted method. The synthetic process is simple and green, as it involves only the heating of a mixture of Ce(NO₃)₃, l ‐arginine, and preformed Pd seeds in water without additives. Importantly, the synthesis is free of thiol groups and halide ions, thus providing a possible solution to the problem of secondary pollution by Pd nanoparticles in the sheath‐coating process. The Pd/CeO₂ nanostructures can be composited well with γ‐Al₂O₃ to create a heterogeneous catalyst. In subsequent tests of catalytic NO reduction by CO, Pd@CeO₂/Al₂O₃ samples based on Pd cubes (6, 10, and 18 nm), Pd octahedra (6 nm), and Pd cuboctahedra (9 nm) as well as a simply loaded Pd cube (6 nm)–CeO₂/Al₂O₃ sample were used as catalysts to investigate the effects of the Pd core size and shape and the hybrid nanostructure on the catalytic performance.     

Hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry method for the simultaneous determination of l‐valine,l‐leucine,l‐isoleucine,l‐phenylalanine,and l‐tyrosine in human serum

l ‐Valine, l ‐leucine, l ‐isoleucine, l ‐phenylalanine, and l ‐tyrosine are important proposed biomarkers for the early detection and diagnosis of type 2 diabetes. A simple and selective hydrophilic interaction chromatography with tandem mass spectrometry method was developed for the simultaneous determination of these amino acids in human serum, using stable isotope‐labeled amino acids as internal standards. Chromatographic separation was carried out on a Syncronis HILIC column (150 mm × 2.1 mm, 5 μm) with the column temperature of 35°C and a mobile phase consisted of acetonitrile/120 mM ammonium acetate (89:11, v/v), and the run time was 11.0 min. The mass spectrometric analysis was performed using a QTRAP 5500 mass spectrometer coupled with an electrospray ionization source in positive ion mode. As these five amino acids are endogenous compounds in serum, we used the corresponding stable isotope‐labeled amino acids to evaluate the matrix effect and recovery in serum. The matrix effect was 98.7–107.3%, and the recovery was 92.7–102.3%. Calibration curves spiked unlabeled amino acids in water were linear over the range of 0.200–100 μg/mL. The accuracy, inter‐, and intraday precision were below 10.2%. Analytes were stable during the study. This assay method has been validated and applied to the early diagnosis research of type 2 diabetes.     

One‐Pot Bioconversion of l‐Arabinose to l‐Ribulose in an Enzymatic Cascade

This work reports the one‐pot enzymatic cascade that completely converts l ‐arabinose to l ‐ribulose using four reactions catalyzed by pyranose 2‐oxidase (P2O), xylose reductase, formate dehydrogenase, and catalase. As wild‐type P2O is specific for the oxidation of six‐carbon sugars, a pool of P2O variants was generated based on rational design to change the specificity of the enzyme towards the oxidation of l ‐arabinose at the C2‐position. The variant T169G was identified as the best candidate, and this had an approximately 40‐fold higher rate constant for the flavin reduction (sugar oxidation) step, as compared to the wild‐type enzyme. Computational calculations using quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) showed that this improvement is due to a decrease in the steric effects at the axial C4‐OH of l ‐arabinose, which allows a reduction in the distance between the C2‐H and flavin N5, facilitating hydride transfer and enabling flavin reduction.