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.     

Photo‐Tethers for the (Multi‐)Cyclic,Conformational Caging of Long Oligonucleotides

Intramolecular circularization of DNA oligonucleotides was accomplished by incorporation of alkyne‐modified photolabile nucleosides into DNA sequences, followed by a Cu^I‐catalyzed alkyne–azide cycloaddition with bis‐azido linker molecules. We determined a range of ring sizes, in which the caged circular oligonucleotides exhibit superior duplex destabilizing properties. Specific binding of a full‐length 90 nt C10 aptamer recognizing human Burkitt's lymphoma cells was then temporarily inhibited by locking the aptamer in a bicircularized structure. Irradiation restored the native aptamer conformation resulting in efficient cell binding and uptake. The photo‐tether strategy presented here provides a robust and versatile tool for the light‐activation of longer functional oligonucleotides, noteworthy without prior knowledge on the structure and the importance of specific nucleotides within a DNA aptamer.     

Photo‐Tethers for the (Multi‐)Cyclic,Conformational Caging of Long Oligonucleotides

Intramolecular circularization of DNA oligonucleotides was accomplished by incorporation of alkyne‐modified photolabile nucleosides into DNA sequences, followed by a Cu^I‐catalyzed alkyne–azide cycloaddition with bis‐azido linker molecules. We determined a range of ring sizes, in which the caged circular oligonucleotides exhibit superior duplex destabilizing properties. Specific binding of a full‐length 90 nt C10 aptamer recognizing human Burkitt's lymphoma cells was then temporarily inhibited by locking the aptamer in a bicircularized structure. Irradiation restored the native aptamer conformation resulting in efficient cell binding and uptake. The photo‐tether strategy presented here provides a robust and versatile tool for the light‐activation of longer functional oligonucleotides, noteworthy without prior knowledge on the structure and the importance of specific nucleotides within a DNA aptamer.     

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.     

Synthesis and Self‐Organization of Zinc β‐(Dialkoxyphosphoryl)porphyrins in the Solid State and in Solution

The first synthesis and self‐organization of zinc β‐phosphorylporphyrins in the solid state and in solution are reported. β‐Dialkoxyphosphoryl‐5,10,15,20‐tetraphenylporphyrins and their Zn^II complexes have been synthesized in good yields by using Pd‐ and Cu‐mediated carbon–phosphorous bond‐forming reactions. The Cu‐mediated reaction allowed to prepare the mono‐β‐(dialkoxyphosphoryl)porphyrins 1 Zn – 3 Zn starting from the β‐bromo‐substituted zinc porphyrinate ZnTPPBr (TPP=tetraphenylporphyrin) and dialkyl phosphites HP(O)(OR)₂ (R=Et, iPr, nBu). The derivatives 1 Zn – 3 Zn were obtained in good yields by using one to three equivalents of CuI. When the reaction was carried out in the presence of catalytic amounts of palladium complexes in toluene, the desired zinc derivative 1 Zn was obtained in up to 72 % yield. The use of a Pd‐catalyzed C? P bond‐forming reaction was further extended to the synthesis of β‐poly(dialkoxyphosphoryl)porphyrins. An unprecedented one‐pot sequence involving consecutive reduction and phosphorylation of H₂TPPBr₄ led to the formation of a mixture of the 2,12‐ and 2,13‐bis(dialkoxy)phosphorylporphyrins 5 H₂ and 6 H₂ in 81 % total yield. According to the X‐ray diffraction studies, 1 Zn and 3 Zn are partially overlapped cofacial dimers formed through the coordination of two Zn centers by two phosphoryl groups belonging to the adjacent molecules. The equilibrium between the monomeric and the dimeric species exists in solutions of 1 Zn and 3 Zn in weakly polar solvents according to spectroscopic data (UV/Vis absorption and NMR spectroscopy). The ratio of each form is dependent on the concentration, temperature, and traces of water or methanol. These features demonstrated that zinc β‐phosphorylporphyrins can be regarded as new model compounds for the weakly coupled chlorophyll pair in the photosynthesis process.     

Conformational Studies by Dynamic NMR. 71.(1) Stereodynamics of Triisopropyl(aryl)silanes in Solution and in the Solid State

A study has been carried out of the conformations of triisopropyl(aryl)silanes (i-Pr)(3)SiAr, (Ar = phenyl, 1-naphthyl, and 2-naphthyl) both as to the orientation of the three isopropyl groups and the conformation about the silicon-aromatic bonds. The report comprises dynamic NMR studies of conformational interconversions in solution and in the solid state as well as molecular mechanics calculations. The barriers for the stereomutation processes measured in the crystalline state were found significantly higher than those in solution.     

Conformational Flexibility of Tetralactam Macrocycles and Their Intermolecular Hydrogen‐Bonding Patterns in the Solid State

Flexible rigidity : Tetralactam macrocycles of the Hunter type bear a rigid scaffold (see space‐filling representation), but can still widely adapt to the properties of a guest molecule inside their cavities. X‐ray crystal structures of a series of differently substituted macrocycles reveal a remarkably broad variety of intermolecular hydrogen‐bonding patterns organizing the macrocycles in the crystals in intriguingly different ways.

     

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.     

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.     

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.     

Conformational Transformations of (C12H25NH3+)(Pyridinesulfonate) in the Solid State

The phase‐transition behaviors, crystal structures, and dielectric properties of four kinds of simple 1:1 organic salts of (C₁₂H₂₅NH₃⁺)(benzenesulfonate) and (C₁₂H₂₅NH₃⁺)(pyridine sulfonates) were examined from the viewpoint of intermolecular hydrogen‐bonding interactions and dynamic conformational transformation in molecular assemblies. Crystals of (C₁₂H₂₅NH₃⁺)(benzenesulfonate) and (C₁₂H₂₅NH₃⁺)(3‐pyridinesulfonate) were isostructural and solid–solid and solid–liquid‐crystal smectic A (SmA) phase transitions were observed. These two crystals formed rodlike cation–anion assemblies. However, the two salts, (C₁₂H₂₅NH₃⁺)(2‐pyridinesulfonate) and (C₁₂H₂₅NH₃⁺)(4‐pyridinesulfonate), formed largely bent L ‐shaped cation–anion conformations. Interesting conformational transformations from rodlike to L ‐shaped assemblies were observed in (C₁₂H₂₅NH₃⁺)(2‐pyridinesulfonate) and (C₁₂H₂₅NH₃⁺)(3‐pyridinesulfonate).     

Dicarboxylic Acid Separation by Dynamic and Size‐Matched Recognition in Solution and in the Solid State

Bis(trimethylammonium) alkane diiodides dynamically encapsulate dicarboxylic acids through intermolecular hydrogen bonds between the I^? anions of the hosts and the carboxylic OH groups of the guests. A selective recognition is realized when the size of the I^????HOOC(CH₂/CF₂)_nCOOH???I^? superanion matches the dication alkyl chain length. Dynamic recognition is also demonstrated in solution, where the presence of the size‐matching organic salt boosts the acid solubility profile, thus allowing efficient mixture separation.     

Solid‐State Conformational Flexibility at Work: Zipping and Unzipping within a Cyclic Peptoid Single Crystal

A peptidomimetic compound undergoes a reversible single‐crystal‐to‐single‐crystal transformation upon guest release/uptake with the transformation involving a drastic conformational change. The extensive and reversible alteration in the solid state is connected to the formation of an unprecedented “CH–π zipper” which can reversibly open and close (through the formation of CH–π interactions), thus allowing for guest sensing.     

Halogen‐Bonded Supramolecular Capsules in the Solid State,in Solution,and in the Gas Phase

Supramolecular capsules were assembled by neutral halogen bonding (XB) and studied in the solid state, in solution, and in the gas phase. The geometry of the highly organized capsules is shown by an X‐ray crystal structure which features the assembly of two XB hemispheres, geometrically rigidified by H‐bonding to eight MeOH molecules and encapsulation of two benzene guests. To enhance capsular association strength, tuning the XB donor is more efficient than tuning the XB acceptor, due to desolvation penalties in protic solvents, as shown for a tetraquinuclidine XB acceptor hemisphere. With a tetra(iodoethynyl) XB donor and a tetralutidine XB acceptor, the association in deuterated benzene/acetone/methanol 70:30:1 at 283 K reaches K _a=(2.11±0.39)×10⁵ m ⁻¹ (ΔG =−6.9±0.1 kcal mol⁻¹). The stability of the XB capsules in the gas phase was confirmed by electrospray ionization mass spectrometry (ESI‐MS). A new guest binding site was uncovered within the elongated iodoethynyl capsule.     

Conformational structure of the tetrapeptide Boc–Aib–Leu–Leu–Aib–OMe–the central fragment of the nonapeptide antibiotic leucinostatin A

The conformational structure of the tetrapeptide Boc–Aib–Leu–Leu–Aib–OMe has been investigated by the PCILO method. The computational results show the formation of two closed β-turns, both of which are of type III, and the peptide backbone folds into a right-handed 3₁₀-helical conformation stabilized by two intramolecular 4 → 1 hydrogen bonds. The helix thus formed generates a pore of ～3 Å along helix axis with hydrophobic amino acid side chains located on the outside of the helix, and this tendency of leucine side chains may enable leucinostatin A to fit into the membrane bilayer. The pore thus formed is cation-selective, and through this pore, the cation can pass only in a single file.     

Lanthanide(III) Complexes of 4,10‐Bis(phosphonomethyl)‐1,4,7,10‐tetraazacyclododecane‐1,7‐diacetic acid (trans‐H6do2a2p) in Solution and in the Solid State: Structural Studies Along the Series

Complexes of 4,10‐bis(phosphonomethyl)‐1,4,7,10‐tetraazacyclododecane‐1,7‐diacetic acid (trans‐H₆do2a2p, H₆ L ) with transition metal and lanthanide(III) ions were investigated. The stability constant values of the divalent and trivalent metal‐ion complexes are between the corresponding values of H₄dota and H₈dotp complexes, as a consequence of the ligand basicity. The solid‐state structures of the ligand and of nine lanthanide(III) complexes were determined by X‐ray diffraction. All the complexes are present as twisted‐square‐antiprismatic isomers and their structures can be divided into two series. The first one involves nona‐coordinated complexes of the large lanthanide(III) ions (Ce, Nd, Sm) with a coordinated water molecule. In the series of Sm, Eu, Tb, Dy, Er, Yb, the complexes are octa‐coordinated only by the ligand donor atoms and their coordination cages are more irregular. The formation kinetics and the acid‐assisted dissociation of several Ln^III–H₆ L complexes were investigated at different temperatures and compared with analogous data for complexes of other dota‐like ligands. The [Ce( L )(H₂O)]^3? complex is the most kinetically inert among complexes of the investigated lanthanide(III) ions (Ce, Eu, Gd, Yb). Among mixed phosphonate–acetate dota analogues, kinetic inertness of the cerium(III) complexes is increased with a higher number of phosphonate arms in the ligand, whereas the opposite is true for europium(III) complexes. According to the ¹H NMR spectroscopic pseudo‐contact shifts for the Ce–Eu and Tb–Yb series, the solution structures of the complexes reflect the structures of the [Ce(H L )(H₂O)]^2? and [Yb(H L )]^2? anions, respectively, found in the solid state. However, these solution NMR spectroscopic studies showed that there is no unambiguous relation between ³¹P/¹H lanthanide‐induced shift (LIS) values and coordination of water in the complexes; the values rather express a relative position of the central ions between the N₄ and O₄ planes.     

ortho‐Phenylene‐Bridged Cyclic Oligopyrroles: Conformational Flexibilities and Optical Properties

ortho‐Phenylene‐bridged cyclic trimeric oligopyrrole C3 and hexameric oligopyrrole C6 were synthesized by Suzuki–Miyaura coupling reactions. The twisted structures of C3 and C6 were unambiguously revealed by X‐ray diffraction analysis. The optical properties of these cyclic oligopyrroles were compared with linear oligopyrrole L3 and cyclic tetramer C4 . The cyclic oligopyrroles exhibited large Stokes shifts and blue fluorescence with high quantum yields in solution and in the solid state. In addition, selective N‐methylation and N‐tolylation of C3 were used to tune the optical and electrochemical properties by changing the molecular twists and conformational flexibilities. Throughout these studies, the structure–property relationship of these cyclic strained oligopyrroles has been illustrated as an interesting molecular motif for novel cyclic π‐conjugated systems.