Investigation of the Interactions of β‐Peptides with DNA Duplexes by Circular Dichroism Spectroscopy

The interaction of β‐peptides with the DNA duplexes of dA₂₀dT₂₀ and a GCN4‐binding CRE sequence was examined. To gauge the factors that govern these interactions, two β‐pentadecapeptides, 1 and 2 , a β‐dodecapeptide, 3 , three β‐decapeptides, 4 – 6 , three β‐heptapeptides, 7 – 9 , and β‐octaarginine 10 were designed and synthesized. The β‐peptides were conceived to adopt a β‐peptide 3₁₄ helix, in which the side chains at position i and i + 3 are aligned vertically along one side of the helix. The side chains of Lys, Asn, and Arg were positioned such that potential H‐bonding sites were created for a helical conformation to interact with the base pairs of DNA. CD Analysis showed that β‐peptides 1, 2 , and 10 interacted with dA₂₀dT₂₀. In addition, β‐peptides 1 and 2 showed significant interaction with a DNA‐duplex 20mer containing the ATF/CREB recognition sequence for the regulatory protein GCN4. It is impossible, at this stage of the investigation, to make a safe proposal about the actual nature of the interaction of the structures(s) of the complexes, the formation of which is suggested by the CD spectra reported herein.     

catena‐Poly[4,4′‐bipyridinium [[cis‐di­chloro­manganese(II)]‐di‐μ‐chloro]], a novel manganese(II) coordination polymer with 4,4′‐bipyridinium

The title novel manganese(II) coordination polymer, {(C₁₀H₁₀N₂)[MnCl₄]}_n, consists of a one‐dimensional infinite zigzag chain composed of polymeric [MnCl₄]²⁻ units in which each Mn²⁺ ion is located on a twofold rotation axis and is coordinated to two terminal Cl atoms and four bridging chloro ligands. Adjacent Mn²⁺ ions are linked by double Cl bridges arranged about a centre of inversion, thus forming anionic chains of distorted edge‐sharing octa­hedra. Rows of approximately parallel 4,4′‐bipyridinium cations run side‐by‐side with the MnCl₄ chains. A two‐dimensional layer structure is constructed via hydrogen bonds and by additional π–π stacking inter­actions.     

NMR‐Solution Structures in Methanol of an α‐Heptapeptide,of a β3/β2‐Nonapeptide,and of an all‐β3‐Icosapeptide Carrying the 20 Proteinogenic Side Chains

The NMR‐solution structure of an α‐heptapeptide with a central Aib residue was investigated in order to verify that, in contrast to β‐peptides, short α‐peptides do not form a helical structures in MeOH. Although the central Aib residue was found to induce a bend in the experimentally determined structure, no secondary structure typical for longer α‐peptides or proteins was found. A β²/β³‐nonapeptide with polar, positively charged side chains was subjected to NMR analysis in MeOH and H₂O. Whereas, in MeOH, it folds into a 10/12‐helix very similar to the structure determined for a corresponding β²/β³‐nonapeptide with only aliphatic side chains, no dominant conformation could be determined in H₂O. Finally, the NMR analysis of a β³‐icosapeptide containing the side chains of all 20 proteinogenic amino acids in MeOH is described. It revealed that this 20mer folds into a 3₁₄‐helix over its whole length forming six full turns, the longest 3₁₄‐helix found so far. Together, our findings confirm that, in contrast to α‐peptides, β‐peptides not only form helices with just six residues, but also form helices that are longer than helical sections usually observed in proteins or natural peptides. The higher helix‐forming propensity of long β‐peptides is attributed to the conformation‐stabilizing effect of the staggered ethane sections in β‐peptides which outweighs the detrimental effect of the increasing macrodipole.     

catena‐Poly[[[cis‐aqua­bis(4‐carboxy­cyclo­hexane‐1‐carboxyl­ato‐κ2O,O′)cadmium(II)]‐μ‐4,4′‐bipyridine‐κ2N:N] monohydrate]

The title complex, {[Cd(C₈H₁₁O₄)₂(C₁₀H₈N₂)(H₂O)]·H₂O}_n, consists of linear chains formed through 4,4′‐bipyridine ligands linking seven‐coordinated Cd^II ions. Each Cd^II ion is in a distorted penta­gonal–bipyramidal environment, coordinated by one water ligand, two 4‐carboxy­cyclo­hexane‐1‐carboxyl­ate ligands and one bridging 4,4′‐bipyridine ligand to generate linear chains. The water mol­ecules and the Cd atom on one side, and the 4,4′‐bipyridine unit on the other, are bisected by two sets of twofold axes. The carboxylate group of the 4‐carboxy­cyclo­hexane‐1‐carboxyl ligand chelates a Cd^II ion, while the (protonated) carboxyl group forms hydrogen bonds with adjacent chains, resulting in a layered structure. This is the first reported occurrence of a dicarboxycyclo­hexane ligand exhibiting a non‐bridging coordination mode.     

A phase transition from monoclinic C2 with Z′ = 1 to triclinic P1 with Z′ = 4 for the quasiracemate l‐2‐aminobutyric acid–d‐methionine (1/1)

Racemates of hydrophobic amino acids with linear side chains are known to undergo a unique series of solid‐state phase transitions that involve sliding of molecular bilayers upon heating or cooling. Recently, this behaviour was shown to extend also to quasiracemates of two different amino acids with opposite handedness [Görbitz & Karen (2015). J. Phys. Chem. B, 119 , 4975–4984]. Previous investigations are here extended to an l ‐2‐aminobutyric acid–d ‐methionine (1/1) co‐crystal, C₄H₉NO₂·C₅H₁₁NO₂S. The significant difference in size between the –CH₂CH₃ and –CH₂CH₂SCH₃ side chains leads to extensive disorder at room temperature, which is essentially resolved after a phase transition at 229 K to an unprecedented triclinic form where all four d ‐methionine molecules in the asymmetric unit have different side‐chain conformations and all three side‐chain rotamers are used for the four partner l ‐2‐aminobutyric acid molecules.     

Unexpected proline coordination in the copper chain polymer [Cu(μ‐Cl)2(μ‐DL‐proline‐κ2O:O′)]1∞

In catena‐poly[copper(II)‐di‐μ‐chlorido‐μ‐proline‐κ²O:O′], [CuCl₂(C₅H₉NO₂)]_n, two symmetry‐independent metal cations adopt distorted octahedral coordination, typical for d⁹ Jahn–Teller systems. Each chloride bridge is involved in both a short and a very long interaction with a Cu^II centre. The centrosymmetric crystal structure contains homochiral chains of opposite handedness which extend along the shortest lattice parameter (i.e. a). The O:O′‐bridging coordination mode of proline, although a common motif for such complexes in general, is remarkable for Cu^II; the vast majority of amino acid derivatives of this cation are characterized by N,O‐chelation.     

Amyloid formation from an α-helix peptide bundle is seeded by 3(10)-helix aggregates

Transformation of proteins and peptides to fibrillar aggregates rich in β sheets underlies many diseases, but mechanistic details of these structural transitions are poorly understood. To simulate aggregation, four equivalents of a water‐soluble, α‐helical (65 %) amphipathic peptide (AEQLLQEAEQLLQEL) were assembled in parallel on an oxazole‐containing macrocyclic scaffold. The resulting 4α‐helix bundle is monomeric and even more α helical (85 %), but it is also unstable at pH 4 and undergoes concentration‐dependent conversion to β‐sheet aggregates and amyloid fibrils. Fibrils twist and grow with time, remaining flexible like rope (>1 μm long, 5–50 nm wide) with multiple strings (2 nm), before ageing to matted fibers. At pH 7 the fibrils revert back to soluble monomeric 4α‐helix bundles. During α→β folding we were able to detect soluble 3₁₀ helices in solution by using 2D‐NMR, CD and FTIR spectroscopy. This intermediate satisfies the need for peptide elongation, from the compressed α helix to the fully extended β strand/sheet, and is driven here by 3₁₀‐helix aggregation triggered in this case by template‐promoted helical bundling and by hydrogen‐bonding glutamic acid side chains. A mechanism involving α?α₄?(3₁₀)₄?(3₁₀)_n?(β)_n?m(β)_n equilibria is plausible for this peptide and also for peptides lacking hydrogen‐bonding side chains, with unfavourable equilibria slowing the α→β conversion.     

Exploiting Aromatic Interactions for β‐Peptide Foldamer Helix Stabilization: A Significant Design Element

Tetrameric H10/12 helix stabilization was achieved by the application of aromatic side‐chains in β‐peptide oligomers by intramolecular backbone–side chain CH–π interactions. Because of the enlarged hydrophobic surface of the oligomers, a further aim was the investigation of the self‐assembly in a polar medium for the β‐peptide H10/12 helices. NMR, ECD, and molecular modeling results indicated that the oligomers formed by cis‐[1S,2S]‐ or cis‐[1R,2R]‐1‐amino‐1,2,3,4‐tetrahydronaphthalene‐2‐carboxylic acid (ATENAC) and cis‐[1R,2S]‐ or cis‐[1S,2R]‐2‐aminocyclohex‐3‐enecarboxylic acid (ACHEC) residues promote stable H10/12 helix formation with an alternating backbone configuration even at the tetrameric chain length. These results support the view that aromatic side‐chains can be applied for helical structure stabilization. Importantly, this is the first observation of a stable H10/12 helix with tetrameric chain‐length. The hydrophobically driven self‐assembly was achieved for the helix‐forming oligomers, seen as vesicles in transmission electron microscopy images. The self‐association phenomenon, which supports the helical secondary structure of these oligomers, depends on the hydrophobic surface area, because a higher number of aromatic side‐chains yielded larger vesicles. These results serve as an essential element for the design of helices relating to the H10/12 helix. Moreover, they open up a novel area for bioactive foldamer construction, while the hydrophobic area gained through the aromatic side‐chains may yield important receptor–ligand interaction surfaces, which can provide amplified binding strength.     

catena‐Poly[[[4‐bromo‐2‐(2‐pyridyl­methyl­imino­meth­yl)­phenol­ato]­zinc(II)]‐μ‐chloro]

The title complex, [Zn(C₁₃H₁₀BrN₂O)Cl]_n, is a chloride‐bridged polynuclear zinc(II) compound. Each Zn^II ion is five‐coordinated in a square‐pyramidal configuration, with one O and two N atoms of one Schiff base and one bridging Cl atom defining the basal plane, and another bridging Cl atom occupying the apical position. The novelty of the compound lies in the bridging by chlorine of two square‐pyramidal Zn atoms, so that the bridging atom is apical for one Zn ion and basal for the other. This structural arrangement has not been observed before. The linked moieties form polymeric zigzag chains running along the a axis.     

Synthesis of β‐Hexa‐ and β‐Heptapeptides Containing Novel β2,3‐Amino Acids with Two Serine or Two Cysteine Side Chains – CD‐ and NMR‐Spectroscopic Evidence for 314‐Helical Secondary Structures in Water

Two representatives of a new type of β‐amino acids, carrying two functionalized side chains, one in the 2‐ and one in the 3‐position, have been prepared stereoselectively: a β‐Ser derivative with an additional CH₂OH group in the 2‐position (for β‐peptides with better water solubility; Scheme 2) and a β‐HCys derivative with an additional CH₂SBn group in the 2‐position (for disulfide formation and metal complexation with the derived β‐peptides; Scheme 3). Also, a simple method for the preparation of α‐methylidene‐β‐amino acids is presented (see Boc‐2‐methylidene‐β‐HLeu‐OH, 8 in Scheme 3). The two amino acids with two serine or two cysteine side chains are incorporated into a β‐hexa‐ and two β‐heptapeptides ( 18 and 23/24 , resp.), which carry up to four CH₂OH groups. Disulfide formation with the β‐peptides carrying two CH₂SH groups generates very stable 1,2‐dithiane rings in the centre of the β‐heptapeptides, and a cyclohexane analog was also prepared (cf. 27 in Scheme 6). The CD spectra in H₂O clearly indicate the presence of 3₁₄‐helical structures of those β‐peptides ( 18 , 23 , 24 , 27b ) having the `right' configurations at all stereogenic centers (Fig. 2). NMR Measurements (Tables 1 and 2, and Fig. 4) in aqueous solution of one of the new β‐peptides ( 24 ) are interpreted on the assumption that the predominant secondary structure is the 3₁₄‐helix, a conformation that has been found to be typical for β‐peptides in MeOH or pyridine solution, according to our previous NMR investigations.     

Alkaline Earth Metal Ion Induced Coil–Helix–Coil Transition of Lysine–Coumarin–Azacrown Hybrid Foldamers with OFF–OFF–ON Fluorescence Switching

A new metal‐ion‐responsive and fluorescent foldamer, OPLM₈ , composed of eight lysine–coumarin–azacrown units, has been designed and synthesized. The flexible OPLM₈ can be forced into a well‐defined helix structure only upon the addition of alkaline earth metal ions. The structural change is based on the crown ether moieties being positioned in the requisite arrangement along the peptide chain, that is, at i, i+4 spacing, such that the alkaline earth metal ions can mediate the formation of four sandwich complexes between them. Moreover, varying the chelator‐to‐metal‐ion ratio from 2:1 to 1:1 resulted in disassembly of the sandwich complexes leading to collapse of the helical structure to a random coil. These metal‐ion‐induced structural transitions could not only be monitored by the CD amplitude change but also easily probed by unique “OFF–OFF–ON” fluorescence intensity changes from 0.7‐fold to 14‐fold as the structure changed from the folded helix to a random coil. To further verify that the helix formation was indeed induced by metal‐ion complexation, two kinds of control octamers with only four metal‐ion chelators on the side chains were studied. One, which was capable of forming two sandwich complexes between the i and i+4 residues, displayed a negative Cotton couplet with the magnitude of its A value close to half that of OPLM₈ , and the second had four metal‐ion chelators positioned in the same turn, and hence was incapable of forming intramolecular metal complexes and showed different induced CD signals. Collectively, the photospectroscopic data and the results of the control studies suggest that alkaline earth metal ions can efficiently promote the flexible octamer OPLM₈ into a well‐organized helix by the formation of sandwich complexes between substituents at an i, i+4 spacing.     

catena‐Poly[[{4‐bromo‐2‐[2‐(dimethyl­amino)ethyl­imino­methyl]­phenol­ato}­copper(II)]‐μ‐azido]

The title complex, [Cu(C₁₁H₁₄BrN₂O)(N₃)]_n, is an inter­esting azide‐bridged polynuclear copper(II) compound. The Cu^II atom is five‐coordinated in a square‐pyramidal configuration, with one O and two N atoms of one Schiff base and one terminal N atom of a bridging azide ligand defining the basal plane, and another terminal N atom of another bridging azide ligand occupying the axial position. The {4‐bromo‐2‐[2‐(dimethyl­amino)ethyl­imino­meth­yl]phenolato}copper(II) moieties are linked by the bridging azide ligands, forming polymeric chains running along the b axis. Adjacent chains are further linked by weak Br⋯Br inter­actions into a sheet.     

β‐Peptidic Secondary Structures Fortified and Enforced by Zn2+ Complexation – On the Way to β‐Peptidic Zinc Fingers?

The correlation between β²‐, β³‐, and β^2,3‐amino acid‐residue configuration and stability of helix and hairpin‐turn secondary structures of peptides consisting of homologated proteinogenic amino acids is analyzed (Figs. 1–3). To test the power of Zn²⁺ ions in fortifying and/or enforcing secondary structures of β‐peptides, a β‐decapeptide, 1 , four β‐octapeptides, 2 – 5 , and a β‐hexadecapeptide, 10 , have been devised and synthesized. The design was such that the peptides would a) fold to a 14‐helix ( 1 and 3 ) or a hairpin turn ( 2 and 4 ), or form neither of these two secondary structures (i.e., 5 ), and b) carry the side chains of cysteine and histidine in positions, which will allow Zn²⁺ ions to use their extraordinary affinity for RS^? and the imidazole N‐atoms for stabilizing or destabilizing the intrinsic secondary structures of the peptides. The β‐hexadecapeptide 10 was designed to a) fold to a turn, to which a 14‐helical structure is attached through a β‐dipeptide spacer, and b) contain two cysteine and two histidine side chains for Zn complexation, in order to possibly mimic a Zn‐finger motif. While CD spectra (Figs. 6–8 and 17) and ESI mass spectra (Figs. 9 and 18) are compatible with the expected effects of Zn²⁺ ions in all cases, it was shown by detailed NMR analyses of three of the peptides, i.e., 2, 3, 5 , in the absence and presence of ZnCl₂, that i) β‐peptide 2 forms a hairpin turn in H₂O, even without Zn complexation to the terminal β³hHis and β³hCys side chains (Fig. 11), ii) β‐peptide 3 , which is present as a 14‐helix in MeOH, is forced to a hairpin‐turn structure by Zn complexation in H₂O (Fig. 12), and iii) β‐peptide 5 is poorly ordered in CD₃OH (Fig. 13) and in H₂O (Fig. 14), with far‐remote β³hCys and β³hHis residues, and has a distorted turn structure in the presence of Zn²⁺ ions in H₂O, with proximate terminal Cys and His side chains (Fig. 15).     

catena‐Poly[[{4‐bromo‐2‐[2‐(di­methyl­amino)­ethyl­imino­meth­yl]­phenolato}­copper(II)]‐μ‐thio­cyanato]

The title complex, [Cu(C₁₁H₁₄BrN₂O)(NCS)]_n, is an inter­esting thio­cyanate‐bridged polynuclear copper(II) compound, which crystallizes with two independent mol­ecules in the asymmetric unit. Each Cu^II atom is five‐coordinate in a square‐pyramidal configuration, with one O and two N atoms of one Schiff base ligand and one terminal N atom of a bridging thio­cyanate ligand defining the basal plane, and one terminal S atom of another bridging thio­cyanate ligand occupying the apical position. The {4‐bromo‐2‐[2‐(dimethyl­amino)ethyl­imino­meth­yl]phenolato}copper(II) units are linked by the bridging thio­cyanate ligands, forming polymeric chains running along the a axis. There are weak inter­molecular C—H⋯O and C—H⋯S hydrogen bonds between the chains in the crystal structure.     

A potential molecular ferroelectric material: poly[[bis(1‐aza‐4‐azoniabicyclo[2.2.2]octane)di‐μ3‐chlorido‐tetra‐μ2‐chlorido‐dichloridotricadmium(II)] dihydrate]

The title compound, {[Cd₃(C₆H₁₃N₂)₂Cl₈]·2H₂O}_n, consists of pendant protonated cationic diamine ligands bonded to an anionic one‐dimensional coordination polymer chloridocadmate scaffold. Each coordination chain features two kinds of Cd^II centre, each with distorted octahedral coordination geometry. One Cd^II cation lies on a centre of inversion and is coordinated by six bridging chloride ligands, while the other is coordinated by four bridging chloride ligands, one terminal chloride ligand and a 1‐aza‐4‐azoniabicyclo[2.2.2]octane aza N atom. This gives a reversible corner‐sharing half‐cubic linear polymer that lies along the crystallographic a direction. The chains interact through hydrogen bonding with solvent water, with each water molecule accepting one N—H...O interaction from a cation and donating to two O—H...Cl interactions with anionic chains, thus linking three separate chains and completing the packing structure.     

Three‐Way‐Switchable (Right/Left/OFF) Selective Reflection of Circularly Polarized Light on Solid Thin Films of Helical Polymer Blends

Two poly(quinoxaline‐2,3‐diyl) copolymers bearing miscibility‐enhancing 8‐chlorooctyloxy and (S)‐2‐methylbutoxy or n‐butoxy side chains were synthesized. After annealing in CHCl₃ vapor, a polymer‐blend film of these copolymers exhibited selective reflection of right‐handed circularly polarized light (CPL) in the visible region. The handedness of the CPL reflected was completely inverted upon annealing of the film in THF vapor. Annealing in n‐hexane vapor resulted in the phase separation of the polymer blend, which turned the selective reflection off. This three‐way‐switchable reflection, that is, reflection of right‐handed or left‐handed CPL, together with an OFF state, could be observed visually through right‐ and left‐handed CPL filters.     

catena‐Poly[[bis[5‐(4‐pyridyl‐κN)‐2‐(2‐pyridylmethylsulfanyl)‐1,3,4‐oxadiazole]cadmium(II)]‐di‐μ‐thiocyanato‐κ2N:S;κ2S:N]

The title compound, [Cd(NCS)₂(C₁₃H₁₀N₄OS)₂]_n, contains SCN⁻ anions acting as end‐to‐end bridging ligands which utilize both S and N atoms to link cadmium(II) centers into one‐dimensional double chains. The multidentate 5‐(4‐pyridyl)‐2‐(2‐pyridylmethylsulfanyl)‐1,3,4‐oxadiazole ligands behave as monodentate terminal ligands, binding metal centers only through the N atoms of the 4‐pyridyl groups. Two types of eight‐membered rings are formed by two SCN⁻ anions bridging Cd^II centers, viz. planar and chair conformation, which are alternately disposed along the same chain. Finally, chains define a two‐dimensional array through two different interchain π–π stacking interactions.     

catena‐Poly[[disilver(I)(Ag—Ag)‐bis[μ‐1,1′‐(butane‐1,4‐diyl)diimidazole‐κ2N3:N3′]] bis(perchlorate)]: a double helix stabilized by ligand‐unsupported argentophilic interactions

The title compound, {[Ag₂(C₁₀H₁₄N₄)₂](ClO₄)₂}_n, is a one‐dimensional coordination polymer formed by Ag^I atoms linearly bridged by 1,1′‐(butane‐1,4‐diyl)diimidazole molecules. The chains have a helical arrangement and pairs of chains are held together by the rarely reported ligand‐unsupported Ag—Ag interaction [2.966 (1) Å], which results in a double‐helix structure. The double helix contains twisted 24‐membered metallomacrocycles, which are composed of four Ag atoms and two ligands. The Ag atoms lie on twofold axes.     

π‐Stacking and hydrogen bonding in catena‐poly[[(4,4′‐bipyridine‐κN)­di­oxo­uranium(VI)]‐di‐μ‐hydroxo]

The title compound, [UO₂(OH)₂(C₁₀H₈N₂)]_n, was obtained under hydro­thermal conditions. The U atom is seven‐coordinated and its environment is penta­gonal bipyramidal, with the oxo atoms in axial positions, and one N atom and four hydroxide groups in the equatorial plane. The hydroxide ions are bridging, which results in the formation of infinite chains with the bipyridine mol­ecules alternately located on either side. Neighbouring chains inter­penetrate so that each bipyridine ligand is involved both in hydrogen bonds with two hydroxide ions and in π‐stacking with its two neighbours from the next chain.     

Do Valine Side Chains Have an Influence on the Folding Behavior of β‐Substituted β‐Peptides?

The influence of valine side chains on the folding/unfolding equilibrium and, in particular, on the 3₁₄‐helical propensity of β³‐peptides were investigated by means of molecular‐dynamics (MD) simulation. To that end, the valine side chains in two different β³‐peptides were substituted by leucine side chains. The resulting four peptides, of which three have never been synthesized, were simulated for 150 to 200 ns at 298 and 340 K, starting from a fully extended conformation. The simulation trajectories obtained were compared with respect to structural preferences and folding behavior. All four peptides showed a similar folding behavior and were found to predominantly adopt 3₁₄‐helical conformations, irrespective of the presence of valine side chains. No other well‐defined conformation was observed at significant population in any of the simulations. Our results imply that β³‐peptides show a structural preference for 3₁₄‐helices independent of the branching nature of the side chains, in contrast to what has been previously proposed on the basis of circular‐dichroism (CD) measurements.