The achiral tetrapeptide Z‐Aib‐Aib‐Aib‐Gly‐OtBu

The title achiral peptide N‐benzyloxycarbonyl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐α‐aminoisobutyrylglycine tert‐butyl ester or Z‐Aib‐Aib‐Aib‐Gly‐OtBu (Aib is α‐aminoisobutyric acid, Z is benzyloxycarbonyl, Gly is glycine and OtBu indicates the tert‐butyl ester), C₂₆H₄₀N₄O₇, is partly hydrated (0.075H₂O) and has two different conformations which together constitute the asymmetric unit. Both molecules form incipient 3₁₀‐helices. They differ in the relative orientation of the N‐terminal protection group and at the C‐terminus. There are two 4→1 intramolecular hydrogen bonds.     

The peptide Z‐Aib‐Aib‐Aib‐L‐Ala‐OtBu

The title peptide, N‐benzyloxycarbonyl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐L‐alanine tert‐butyl ester or Z‐Aib‐Aib‐Aib‐L‐Ala‐OtBu (Aib is α‐aminoisobutyric acid, Z is benzyloxycarbonyl and OtBu indicates the tert‐butyl ester), C₂₇H₄₂N₄O₇, is a left‐handed helix with a right‐handed conformation in the fourth residue, which is the only chiral residue. There are two 4→1 intramolecular hydrogen bonds in the structure. In the lattice, molecules are hydrogen bonded to form columns along the c axis.     

Synthesis of Aib‐Pro Oligopeptides by Repeated Azirine Coupling with the Aib‐Pro Synthon

A new synthesis of (Aib‐Pro)_n oligopeptides (n=2, 3, and 4) via azirine coupling by using the dipeptide synthon methyl N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)‐L ‐prolinate ( 1b ; Fig. 1) is presented. The most important feature of the employed protocol is that no activation of the acid component is necessary, i.e., no additional reagents are required, and the coupling reaction is performed under mild conditions at room temperature. As an attempt to provide an answer to the question of the preferred conformation of the prepared molecules, we carried out experiments by using NMR techniques and X‐ray crystallography. For example, in the case of the hexapeptide 11 , it was possible to compare the conformations in the crystalline state and in solution. After the selective hydrolysis of the methyl ester p‐BrBz‐(Aib‐Pro)₄‐OMe ( 13 ) under basic conditions, the corresponding octapeptide acid was obtained, which was then converted into the octapeptide amide p‐BrBz‐(Aib‐Pro)₄‐NHC₆H₁₃ ( 15 ) by using standard coupling conditions and activating reagents (HOBt/TBTU/DIEA) of the peptide synthesis. The conformation of this compound, as well as those of the tetrapeptides 14 and 18 , was also established by X‐ray crystallography and in solution by NMR techniques. In the crystalline state, a β‐bend ribbon structure is the preferred conformation, and similar conformations are formed in solution.     

The first N‐terminal unprotected (Gly‐Aib)n peptide: H‐Gly‐Aib‐Gly‐Aib‐OtBu

Glycine (Gly) is incorporated in roughly half of all known peptaibiotic (nonribosomally biosynthesized antibiotic peptides of fungal origin) sequences and is the residue with the greatest conformational flexibility. The conformational space of Aib (α‐aminoisobutyric acid) is severely restricted by the second methyl group attached to the C_α atom. Most of the crystal structures containing Aib are N‐terminal protected. Deprotection of the N‐ or C‐terminus of peptides may alter the hydrogen‐bonding scheme and/or the structure and may facilitate crystallization. The structure reported here for glycyl‐α‐aminoisobutyrylglycyl‐α‐aminoisobutyric acid tert‐butyl ester, C₁₆H₃₀N₄O₅, describes the first N‐terminal‐unprotected (Gly‐Aib)_n peptide. The achiral peptide could form an intramolecular hydrogen bond between the C=O group of Gly1 and the N—H group of Aib4. This hydrogen bond is found in all tetrapeptides and N‐terminal‐protected tripeptides containing Aib, apart from one exception. In the present work, this hydrogen bond is not observed (N...O = 5.88 Å). Instead, every molecule is hydrogen bonded to six other symmetry‐related molecules with a total of eight hydrogen bonds per molecule. The backbone conformation starts in the right‐handed helical region (and the left‐handed helical region for the inverted molecule) and reverses the screw sense in the last two residues.     

Synthesis of Poly‐Aib Oligopeptides and Aib‐Containing Peptides via the ‘Azirine/Oxazolone Method’, and Their Crystal Structures

The protected poly‐Aib oligopeptides Z‐(Aib)_n‐N(Me)Ph with n=2–6 were prepared according to the ‘azirine/oxazolone method’, i.e., by coupling amino or peptide acids with 2,2,N‐trimethyl‐N‐phenyl‐2H‐azirin‐3‐amine ( 1a ) as an Aib synthon (Scheme 2). Following the same concept, the segments Z‐(Aib)₃‐OH ( 9 ) and H‐L ‐Pro‐(Aib)₃‐N(Me)Ph ( 20 ) were synthesized, and their subsequent coupling with N,N′‐dicyclohexylcarbodiimide (DCC)/ZnCl₂ led to the protected heptapeptide Z‐(Aib)₃‐L ‐Pro‐(Aib)₃‐N(Me)Ph ( 21 ; Scheme 3). The crystal structures of the poly‐Aib oligopeptide amides were established by X‐ray crystallography confirming the 3₁₀‐helical conformation of Aib peptides.     

A New Germanium Complex Containing Chelating Pyridinecarboxylate Ligands: cis‐Dihydroxybis(pyridine‐2‐carboxylato‐κN1,κO2)germanium Hydrate (1 : 2) (cis‐[Ge(pyca)2(OH)2]⋅2 H2O)

A new germanium complex, cis‐[Ge(pyca)₂(OH)₂]?2 H₂O ( 1 ; pyca=pyridine‐2‐carboxylato), was synthesized by the reaction of [Ge(acac)₂Cl₂] (acac=acetylacetonato=pentane‐2,4‐dionato) with potassium pyridine‐2‐carboxylate (Kpyca) in H₂O/THF. According to the single‐crystal X‐ray diffraction analysis, each Ge‐atom of 1 is coordinated by two pyca ligands and two OH^? groups (Fig. 1). These molecules are bonded to each other via a system of H‐bonds resulting in a sheet‐like structure (Fig. 2). The complex is decomposed during heating with stepwise mass loss and formation of GeO₂ as final product (Fig. 3).     

A Novel 2H‐Azirin‐3‐amine as a Dipeptide (Aib‐Hyp) Synthon

The synthesis of methyl (2S,4R)‐4‐(benzyloxy)‐N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)prolinate ( 10 ), a novel 2H‐azirin‐3‐amine (`3‐amino‐2H‐azirine'), is described (Scheme 1). The reaction of methyl (2S,4R)‐N‐(2‐methylpropanoyl)‐4‐(benzyloxy)prolinate ( 7 ) with Lawesson reagent gave methyl (2S,4R)‐4‐(benzyloxy)‐N‐[2‐(methylthio)propanoyl]prolinate ( 8 ) and consecutive treatment with COCl₂, 1,4‐diazabicyclo[2.2.2]octane (DABCO), and NaN₃ led to 10 . The use of 10 as a building block of the dipeptide Aib‐Hyp (Aib=2‐aminoisobutyric acid, Hyp=(2S,4R)‐4‐hydroxyproline) is demonstrated by the syntheses of several model peptides (Scheme 2 and Table). The benzyl protecting group of the 4‐OH function in Hyp in the model peptides has been removed in good yields.     

N‐(tert‐Butoxycarbonyl)‐α‐aminoisobutyryl‐α‐aminoisobutyric acid methyl ester: two polymorphic forms in the space group P21/n

The title compound (systematic name: methyl 2‐{2‐[(tert‐butoxycarbonyl)amino]‐2‐methylpropanamido}‐2‐methylpropanoate), C₁₄H₂₆N₂O₅, (I), crystallizes in the monoclinic space group P2₁/n in two polymorphic forms, each with one molecule in the asymmetric unit. The molecular conformation is essentially the same in both polymorphs, with the α‐aminoisobutyric acid (Aib) residues adopting ϕ and ψ values characteristic of α‐helical and mixed 3₁₀‐ and α‐helical conformations. The helical handedness of the C‐terminal residue (Aib2) is opposite to that of the N‐terminal residue (Aib1). In contrast to (I), the closely related peptide Boc‐Aib‐Aib‐OBn (Boc is tert‐butoxycarbonyl and Bn is benzyl) adopts an α_L‐P_II backbone conformation (or the mirror image conformation). Compound (I) forms hydrogen‐bonded parallel β‐sheet‐like tapes, with the carbonyl groups of Aib1 and Aib2 acting as hydrogen‐bond acceptors. This seems to represent an unusual packing for a protected dipeptide containing at least one α,α‐disubstituted residue.     

Synthesis of Aib‐ and Phe(2Me)‐Containing Cyclopentapeptides

Some recently described pentapeptides containing the α,α‐disubstituted α‐amino acids Aib and Phe(2Me) have been cyclized in DMF solution using diphenyl phosphorazidate (DPPA), O‐(1H‐benzotriazol‐1‐yl)‐N,N,N′,N′‐tetamethyluronium tetrafluoroborate/1‐hydroxybenzotriazole (TBTU/HOBt), and diethyl phosphorocyanidate (DEPC), respectively, to give the corresponding cyclopentapeptides in fair‐to‐good yields. In the case of peptides with L ‐amino acids, and (R)‐ and (S)‐Phe(2Me), the yields differed significantly in favor of the L /(R) combination. The conformations in the crystals of cyclo(Gly‐Aib‐(R,S)‐Phe(2Me)‐Aib‐Gly) and cyclo(Gly‐(R)‐Phe(2Me)‐Pro‐Aib‐Gly) have been determined by X‐ray crystallography, leading to quite different results. In the latter case, the conformation in solution has been elucidated by NMR studies.     

2‐tert‐Butylamino‐4‐chloro‐6‐ethylamino‐1,3,5‐triazine: a structure with Z′ = 4 containing two different molecular conformations and two independent chains of hydrogen‐bonded R22(8) rings

The title compound (trivial name terbutylazine), C₉H₁₆ClN₅, (I), crystallizes with Z′ = 4 in the space group Pca2₁, and equal numbers of molecules adopt two different conformations for the ethylamine groups. The four independent molecules form two approximately enantiomorphic pairs. Eight independent N—H...N hydrogen bonds link the molecules into two independent chains of R₂²(8) rings, in which the arrangement of the alkylamine substituents in the independent molecules precludes any further crystallographic symmetry. The significance of this study lies in its finding of two distinct molecular conformations within the structure and two distinct ways in which the molecules are organized into hydrogen‐bonded chains, and in its comparison of the hydrogen‐bonded structure of (I) with those of analogous 1,3,5‐triazines and pyrimidines.     

2,4,6‐Trifluorobenzonitrile

The title compound, C₇H₂F₃N, contains three crystallographically independent molecules in the crystal structure; two of these molecules have symmetry m and the third has symmetry mm. Each independent molecule forms a planar or approximately planar layer with its own kind. There are three different types of interlayer contacts, two of which are similar to each other, while the third is distinctly different. The packing within the layers is similar to that found in 2,5‐ and 3,6‐difluorobenzonitrile, with weak C—H...N interactions holding the molecules in the layers. The remarkable feature of this structure is the presence of more than one type of interlayer interaction.     

The ‘Azirine/Oxazolone Approach’ to the Synthesis of Aib‐Pro Endothiopeptides

The reaction of methyl N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)‐L ‐prolinate ( 2a ) with thiobenzoic acid at room temperature gave the endothiopeptide Bz‐AibΨ[CS]‐Pro‐OMe ( 7 ) in high yield. In an analogous manner, (benzyloxy)carbonyl (Z)‐protected proline was transformed into the thioacid, which was reacted with 2a to give the endothiotripeptide Z‐Pro‐AibΨ[CS]‐Pro‐OMe ( 12 ). The corresponding thioacid of 7 was prepared in situ via saponification, formation of a mixed anhydride, and treatment with H₂S. A second reaction with 2a led to the endodithiotetrapeptide 9 , but extensive epimerization at Pro² was observed. Similarly, saponification of 12 and coupling with either 2a or H‐Phe‐OMe and 2‐(1H‐benzotriazol‐1‐yl)‐1,1,3,3‐tetramethyluronium tetrafluoroborate/1‐hydroxy‐1H‐benzotriazole (TBTU/HOBt) gave the corresponding endothiopeptides as mixtures of two epimers. The synthesis of the pure diastereoisomer BzΨ[CS]‐Aib‐Pro‐AibΨ[CS]‐N(Me)Ph ( 21 ) was achieved via isomerization of 7 to BzΨ[CS]‐Aib‐Pro‐OMe ( 16 ), transformation into the corresponding thioacid, and reaction with N,2,2‐trimethyl‐N‐phenyl‐2H‐azirin‐3‐amine ( 1a ). The structures of 12 and 21 were established by X‐ray crystallography.     

Scope and Limitation of the Acid‐Catalyzed Isomerization of Aib‐Containing Thiopeptides

The use of amino thio S‐acids in the `azirine/oxazolone method' and a novel isomerization led to Aib‐containing endothiopeptides. With the aim of generalizing this method, a variety of Aib‐containing dipeptide thioanilides have been prepared. By their treatment with ZnCl₂ in AcOH, followed by HCl‐saturated AcOH, the C=S group was shifted from the last to the penultimate amino acid in high yield and without epimerization. As this methodology is very useful for the specific introduction of a thioamide group, it was extended to Aib‐containing tripeptides. In addition, it could be shown that a mechanism via spirocyclic intermediates (cf. Scheme 4) is most likely for this isomerization. To establish the proposed neighboring‐group participation of the N‐acyl group, model dipeptide thioanilides containing no N‐terminal C=O group were synthesized. These derivatives did not undergo rearrangement.     

catena‐Poly[bis[1‐chloromethyl‐1,4‐diazoniabicyclo[2.2.2]octane] [cadmium(II)‐tri‐μ‐chlorido‐[chloridocadmium(II)]‐di‐μ‐chlorido‐[chloridocadmium(II)]‐tri‐μ‐chlorido] tetrahydrate]

The title compound, {(C₇H₁₅N₂Cl)₂[Cd₃Cl₁₀]·4H₂O}_n, consists of 1‐chloromethyl‐1,4‐diazoniabicyclo[2.2.2]octane dications, one‐dimensional inorganic chains of {[Cd₃Cl₁₀]⁴⁻} anions and uncoordinated water molecules. Each of the two independent Cd^II ions, one with site symmetry 2/m and the other with site symmetry m, is octahedrally coordinated by chloride ions (two with site symmetry m and one with site symmetry 2), giving rise to novel polymeric zigzag chains of corner‐sharing Cd‐centred octahedra parallel to the c axis. The organic cations, bisected by mirror planes that contain the two N atoms, three methylene C atoms and the Cl atom, are ordered. Hydrogen bonds (O—H...Cl and O—H...O) between the water molecules (both with O atoms in a mirror plane) and the chloride anions of neighbouring chloridocadmate chains form a three‐dimensional supramolecular network.     

A Novel Route to 1‐Substituted 3‐(Dialkylamino)‐9‐oxo‐9H‐indeno[2,1‐c]pyridine‐4‐carbonitriles

Heptalenecarbaldehydes 1 / 1′ as well as aromatic aldehydes react with 3‐(dicyanomethylidene)‐indan‐1‐one in boiling EtOH and in the presence of secondary amines to yield 3‐(dialkylamino)‐1,2‐dihydro‐9‐oxo‐9H‐indeno[2,1‐c]pyridine‐4‐carbonitriles (Schemes 2 and 4, and Fig. 1). The 1,2‐dihydro forms can be dehydrogenated easily with KMnO₄ in acetone at 0° (Scheme 3) or chloranil (=2,3,5,6‐tetrachlorocyclohexa‐2,5‐diene‐1,4‐dione) in a ‘one‐pot’ reaction in dioxane at ambient temperature (Table 1). The structures of the indeno[2,1‐c]pyridine‐4‐carbonitriles 5′ and 6a have been verified by X‐ray crystal‐structure analyses (Fig. 2 and 4). The inherent merocyanine system of the dihydro forms results in a broad absorption band in the range of 515–530 nm in their UV/VIS spectra (Table 2 and Fig. 3). The dehydrogenated compounds 5, 5′ , and 7a – 7f exhibit their longest‐wavelength absorption maximum at ca. 380 nm (Table 2). In contrast to 5 and 5′, 7a – 7f in solution exhibit a blue‐green fluorescence with emission bands at around 460 and 480 nm (Table 4 and Fig. 5).     

Di‐ and tripeptide segments of zervamicin II‐2: Z‐Thr(OBn)‐Aib‐N(Me)Ph and Z‐Val‐Aib‐Hyp(OBn)‐OMe

The title compounds, O‐benzyl‐N‐(benzyl­oxy­carbonyl)­threonyl‐2,N‐dimethyl­alanin­anilide, C₃₀H₃₅N₃O₅, and methyl (4R)‐4‐benzyl­oxy‐N‐(benzyl­oxy­carbonyl)­valyl‐2‐(methyl­alanyl)prolinate, C₃₀H₃₉N₃O₇, were obtained from the `azirine coupling' of the corresponding protected amino acids with 2,2,N‐trimethyl‐2H‐azirin‐3‐amine and methyl (4R)‐4‐(benzyl­oxy)‐N‐(2,2‐dimethyl‐2H‐azirin‐2‐yl)prolinate, respectively. The Aib unit in each mol­ecule has the greatest turn‐ or helix‐inducing effect on the mol­ecular conformation. Inter­molecular N—H⋯O inter­actions link the mol­ecules of the tripeptide into sheets and those of the dipeptide into extended chains.     

Crystallographic study of self‐organization in the solid state including quasi‐aromatic pseudo‐ring stacking interactions in 1‐benzoyl‐3‐(3,4‐dimethoxyphenyl)thiourea and 1‐benzoyl‐3‐(2‐hydroxypropyl)thiourea

1‐Benzoylthioureas contain both carbonyl and thiocarbonyl functional groups and are of interest for their biological activity, metal coordination ability and involvement in hydrogen‐bond formation. Two novel 1‐benzoylthiourea derivatives, namely 1‐benzoyl‐3‐(3,4‐dimethoxyphenyl)thiourea, C₁₆H₁₆N₂O₃S, (I), and 1‐benzoyl‐3‐(2‐hydroxypropyl)thiourea, C₁₁H₁₄N₂O₂S, (II), have been synthesized and characterized. Compound (I) crystallizes in the space group P , while (II) crystallizes in the space group P 2₁/c . In both structures, intramolecular N—H…O hydrogen bonding is present. The resulting six‐membered pseudo‐rings are quasi‐aromatic and, in each case, interact with phenyl rings via stacking‐type interactions. C—H…O, C—H…S and C—H…π interactions are also present. In (I), there is one molecule in the asymmetric unit. Pairs of molecules are connected via two intermolecular N—H…S hydrogen bonds, forming centrosymmetric dimers. In (II), there are two symmetry‐independent molecules that differ mainly in the relative orientations of the phenyl rings with respect to the thiourea cores. Additional strong hydrogen‐bond donor and acceptor –OH groups participate in the formation of intermolecular N—H…O and O—H…S hydrogen bonds that join molecules into chains extending in the [001] direction.     

Crystalline Structure of Mangiferin,a C‐Glycosyl‐Substituted 9H‐Xanthen‐9‐one Isolated from the Stem Bark of Mangifera indica

The crystalline structure of mangiferin (=2‐β‐D ‐glucopyranosyl‐1,3,6,7‐tetrahydroxy‐9H‐xanthen‐9‐one; 1 ), a biologically active xanthenone C‐glycoside, isolated from the stem bark of Mangifera indica (Anacardiaceae), was unambiguously determined by single‐crystal X‐ray diffraction (XRD). The crystal structure is summarized as follows: triclinic, P1, a=7.6575(5), b=11.2094(8), c=11.8749(8) Å, α=79.967(5), β=87.988(4), γ=72.164(4)°, V=955.3(1) ų, and Z=2. The structure also shows two molecules in the asymmetric unit cell and five crystallization H₂O molecules. The packing is stabilized by several intermolecular H‐bonds involving either the two symmetry‐independent mangiferin molecules 1a and 1b , or the H₂O ones.     

Crystal packing of two 5‐substituted 2‐methyl‐4‐nitro‐1H‐imidazoles

Infinite chains connected by N—H...N hydrogen bonding form the primary packing motif in two closely related 4‐nitroimidazole derivatives, viz. 5‐bromo‐2‐methyl‐4‐nitro‐1H‐imidazole, C₄H₄BrN₃O₂, (I), and 2‐methyl‐4‐nitro‐1H‐imidazole‐5‐carbonitrile, C₅H₄N₄O₂, (II). These chains are almost identical, even though in (II) there are two symmetry‐independent molecules in the asymmetric unit. The differences appear in the interactions between the chains; in (I), there are strong C—Br...O halogen bonds, which connect the chains into a two‐dimensional grid, while in (II), the cyano group does not participate in specific interactions and the chains are only loosely connected into a three‐dimensional structure.     

(Acetato‐κO)aqua(1H‐imidazole‐κN3)(picolinato‐κ2N,O)copper(II) 0.87‐hydrate: a Z′> 1 structure

The crystal structure of the title compound, [Cu(C₆H₄NO₂)(C₂H₃O₂)(C₃H₄N₂)(H₂O)]·0.87H₂O, has a square‐pyramidal‐coordinated Cu^II centre (the imidazole is trans to the picolinate N atom, the acetate is trans to the picolinate –CO₂ group and the aqua ligand is in a Jahn–Teller‐elongated apical position) and has two symmetry‐independent molecules in the unit cell (Z′ = 2), which are connected through complementary imidazole–picolinate N—H...O hydrogen bonding. The two partially occupied solvent water molecules are each disordered over two positions. The disordered solvent water molecules, together with pseudosymmetry elements, support the notion that a crystal structure with multiple identical chemical formula units in the structural asymmetric unit (Z′ > 1) can represent a crystal `on the way', that is, a kinetic intermediate form which has not yet reached its thermodynamic minimum. Neighbouring molecules form π–π stacks between their imidazole and picolinate N‐heterocycles, with centroid–centroid distances in the range 3.582 (2)–3.764 (2) Å.