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.     

A new ‘hydrogen‐bond rule' applied to the structure of l‐seryl‐l‐alanine and pairs of dipeptide retroanalogues

A new `rule' for the association of hydrogen‐bond donors and acceptors in crystal structures is presented. It implies that ranks are assigned to each donor and each acceptor (1 is best, 2 is next best etc.), and that hydrogen bonds should be formed between donors and acceptors in rank order. l ‐Ser‐l ‐Ala, C₆H₁₂N₂O₄, is used together with its retroanalogue, l ‐Ala‐l ‐Ser, and three other pairs of dipeptide retroanalogues to illustrate this rule and the reasons why it may not always be followed.     

N‐(tert‐Butoxycarbonyl)‐O‐allyl‐l‐seryl‐α‐aminoisobutyryl‐l‐valine methyl ester: a protected tripeptide with an allylated serine residue

The title compound [systematic name (6S,12S)‐methyl 6‐(allyloxymethyl)‐12‐isopropyl‐2,2,9,9‐tetramethyl‐4,7,10‐trioxo‐3‐oxa‐5,8,11‐triazatridecan‐13‐oate], C₂₁H₃₇N₃O₇, containing the little studied O‐allyl‐l ‐serine residue [Ser(All)], crystallizes in the monoclinic space group C2 with one molecule in the asymmetric unit. The compound is an analogue of the Ser140‐Val142 segment of the water channel aquaporin‐4 (AQP4). It forms a distorted type‐II β‐turn with a P_II–3_10L–P_II backbone conformation (P_II is polyproline II). The overall backbone conformation is markedly different from that of the CO(Pro139)–Val142 stretch of rat AQP4, but is quite similar to the corresponding segment of human AQP4, despite significant differences at the level of the individual residues. The side chain of the Ser(All) residue adopts a gauche conformation relative to the backbone CO—C^α and C^α—N bonds. The H atoms of the two CH₂ groups in the Ser(All) side chain are almost eclipsed. The crystal packing of the title compound is divided into one‐molecule‐thick layers, each layer having a hydrophilic core and distinct hydrophobic interfaces on either side.     

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.     

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.     

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.     

Pearls on a string: a Z′ = 7 structure for glycyl‐l‐valine

The title peptide, C₇H₁₄N₂O₃, crystallizes with seven independent mol­ecules in the asymmetric unit. All have essentially the same overall conformation, but some flexibility is exhibited by the glycine residue. It appears that the high Z′ value, observed only three times before for an organic compound, permits formation of shorter hydrogen bonds in one of the two head‐to‐tail chains involving the N‐terminal amino groups and the C‐terminal carboxyl­ate groups than found in a hypothetical model structure of glycyl‐l ‐valine with Z′ = 1, and that it furthermore alleviates strain associated with an eclipsed orientation of the amino group.     

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.     

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.     

Water polymers in l‐alanyl‐l‐methionine hemihydrate

The side chains of l ‐alanyl‐l ‐me­thionine hemihydrate, C₈H₁₆N₂O₃S·0.5H₂O, form hydro­phobic columns within a three‐dimensional hydrogen‐bond network that includes extended polymers of cocrystallized water mol­ecules and C^α—H⋯S interactions.     

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.     

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.     

Proton‐transfer and non‐transfer in compounds of quinoline and quinaldic acid with l‐tartaric acid

The structures of two compounds of l ‐tartaric acid with quinoline, viz. the proton‐transfer compound quinolinium hydrogen (2R,3R)‐tartrate monohydrate, C₉H₈N⁺·C₄H₅O₆⁻·H₂O, (I), and the anhydrous non‐proton‐transfer adduct with quinaldic acid, bis­(quinolinium‐2‐carboxyl­ate) (2R,3R)‐tar­taric acid, 2C₁₀H₇NO₂·C₄H₆O₆, (II), have been determined at 130 K. Compound (I) has a three‐dimensional honeycomb substructure formed from head‐to‐tail hydrogen‐bonded hydrogen tartrate anions and water mol­ecules. The stacks of π‐bonded quinolinium cations are accommodated within the channels and are hydrogen bonded to it peripherally. Compound (II) has a two‐dimensional network structure based on pseudo‐centrosymmetric head‐to‐tail hydrogen‐bonded cyclic dimers comprising zwitterionic quinaldic acid species which are inter­linked by tartaric acid mol­ecules.     

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‐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.     

A non‐natural dinucleotide containing an isomeric l‐related deoxy­nucleoside: dinucleotide inhibitors of anti‐HIV integrase activity

The first X‐ray crystal structure of a non‐natural dinucleotide, 5′‐O‐phosphoryl‐1′‐deoxy‐2′‐isoadenylyl‐(3′ → 5′)‐cytidine 6.5‐hydrate (pIsodApC), C₁₉H₂₆N₈O₁₃P₂·6.5H₂O, belonging to a family of dinucleotides that contain an isomeric nucleoside component, is described. A complex system of hydrogen bonds between water mol­ecules and various sites on the dinucleotide was found. All H atoms were located from electron‐density difference maps, which allowed identification of protonation sites. Compounds of this family have been found to bind at the active site of HIV integrase and to be inhibitors of this key viral enzyme. These dinucleotides are completely resistant to cleavage by exonucleases; an abnormal dihedral angle twist in an inter­nucleotide phosphate bond revealed in the X‐ray crystal structure may be contributing to this unusual stability towards nucleases.     

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.     

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].