Parallel Homochiral and Anti‐Parallel Heterochiral Hydrogen‐Bonding Interfaces in Multi‐Helical Abiotic Foldamers

A hydrogen‐bonding interface between helical aromatic oligoamide foldamers has been designed to promote the folding of a helix‐turn‐helix motif with a head‐to‐tail arrangement of two helices of opposite handedness. This design complements an earlier helix‐turn‐helix motif with a head‐to‐head arrangement of two helices of identical handedness interface. The two motifs were shown to have comparable stability and were combined in a unimolecular tetra‐helix fold constituting the largest abiotic tertiary structure to date.     

Halogen Bonding Directed Supramolecular Quadruple and Double Helices from Hydrogen‐Bonded Arylamide Foldamers

Halogen bonding has been used to glue together hydrogen‐bonded short arylamide foldamers to achieve new supramolecular double and quadruple helices in the solid state. Three compounds, which bear a pyridine at one end and either a CF₂I or fluorinated iodobenzene group at the other end, engage in head‐to‐tail N???I halogen bonds to form one‐component supramolecular P and M helices, which stack to afford supramolecular double‐stranded helices. One of the double helices can dimerize to form a G‐quadruplex‐like supramolecular quadruple helix. Another symmetric compound, which bears a pyridine at each end, binds to ICF₂CF₂I through N???I halogen bonds to form two‐component supramolecular P and M helices, with one turn consisting of four (2+2) molecules. Half of the pyridine‐bearing molecules in two P helices and two M helices stack alternatingly to form another supramolecular quadruple helix. Another half of the pyridine‐bearing molecules in such quadruple helices stack alternatingly with counterparts from neighboring quadruple helices, leading to unique quadruple helical arrays in two‐dimensional space.     

N‐Alkylacylamides in Thin Films Display Infrared Spectra of 310‐, α‐, and π‐Helices with Visible Static and Dynamic Growth Phases

A peptide model is a physical system containing a CONH group, the simplest being HCONHCH₃, N‐methylformamide (NMF). We have discovered that NMF and N‐methylacetamide (NMA), which form hydrogen‐bonded oligomers in thin films on a planar AgX fiber, display infrared (IR) spectra with peaks like those of polypeptide helices. Structures can be assigned by their amide I maxima near 1672 (3₁₀), 1655 (3₁₀), 1653 (α), 1655 (π), and 1635 cm^?1 (π), which are the first IR data for the π‐helix. Sharp peaks are an outcome of immobilization of polar species on the polar surface of silver halides. We report the first use of expanded thin‐film IR spectroscopy, in which plots of every spectrum over the amide I–II range show pauses or slow stages in the increase or decrease of absorption. These are identified as static phases followed by dynamic phases, with the incremental gain or loss of a helix turn. A general theory can be stated for such processes. Density functional calculations show that the NMA α‐helix pentamer (crystal structure geometry) is transformed into a π‐helix‐like form. For the first time, an entire sequence (3₁₀‐helix, α‐helix, π‐helix, quasiplanar species) of spectra has been recorded for NMA.     

Double‐helix pattern in a model compound of non‐linear optical polymers

Mol­ecules of the title compound, 3,3′‐[4‐(4‐nitro­phenyl­diazenyl)phenyl­imino]dipropionic acid, C₁₈H₁₈N₄O₆, a model compound of second‐order non‐linear optically active polymers, form helicoidal rows via hydrogen bonding between carboxy groups. Pairs of helices are wrapped around the common axis in a double‐helix arrangement unprecedented in dicarboxylic acids. The lateral packing of the helices shows an inter­digitated anti­parallel arrangement of the chromophore units.     

N‐Methyl‐trimethylacetamide in Thin Films Displays Infrared Spectra of π‐Helices,with Visible Static and Dynamic Growth Phases,and then a β‐Sheet

The simplest (minimal) peptide model is HCONHCH₃. An increase in the π‐helix content with increased substitution in the acyl portion suggested the examination of N‐methyl‐trimethylacetamide) (NMT). NMT displays spectra, in which there is evolution of a set of helices defined by their amide I maxima near 1686 (3₁₀), 1655 (first π), and, most importantly, at 1637 cm^?1 (π). Expanded thin‐film infrared spectroscopy (XTFIS) shows pauses or slow stages, which are identified as static phases followed by dynamic phases with the incremental gain or loss of a helix turn. In addition, absorbance at 1637 cm^?1 suddenly increases at 82.1 s (30 % over 0.3 s), indicating a phase change and crystallization of the π‐helix, along with a coincidental decrease in the absorbance for the first π‐helix. A sharp peak occurs at the maximum of the phase change at 82.5 s, representing a pure NMT π‐helix. The spectra then undergo a decreasing general absorption loss over 150 s, with the π‐helix evolving further to an antiparallel β‐sheet fragment. The spectral quality arises from the immobilization of polar molecules on polar surfaces. The crystal structure is that of an antiparallel β‐sheet.     

Synthesis of β‐Peptides with β‐Helices from New C‐Linked Carbo‐β‐Amino Acids: Study on the Impact of Carbohydrate Side Chains

The design and synthesis of β‐peptides from new C‐linked carbo‐β‐amino acids (β‐Caa) presented here, provides an opportunity to understand the impact of carbohydrate side chains on the formation and stability of helical structures. The β‐amino acids, Boc‐(S)‐β‐Caa_(g)‐OMe 1 and Boc‐(R)‐β‐Caa_(g)‐OMe 2 , having a D ‐galactopyranoside side chain were prepared from D ‐galactose. Similarly, the homo C‐linked carbo‐β‐amino acids (β‐hCaa); Boc‐(S)‐β‐hCaa_(x)‐OMe 3 and Boc‐(R)‐β‐hCaa_(x)‐OMe 4 , were prepared from D ‐glucose. The peptides derived from the above monomers were investigated by NMR, CD, and MD studies. The β‐peptides, especially the shorter ones obtained from the epimeric (at the amine stereocenter C_β) 1 and 2 by the concept of alternating chirality, showed a much smaller propensity to form 10/12‐helices. This substantial destabilization of the helix could be attributed to the bulkier D ‐galactopyranoside side chain. Our efforts to prepare peptides with alternating 3 and 4 were unsuccessful. However, the β‐peptides derived from alternating geometrically heterochiral (at C_β) 4 and Boc‐(R)‐β‐Caa_(x)‐OMe 5 (D ‐xylose side chain) display robust right‐handed 10/12‐helices, while the mixed peptides with alternating 4 and Boc‐β‐hGly‐OMe 6 (β‐homoglycine), resulted in left‐handed β‐helices. These observations show a distinct influence of the side chains on helix formation as well as their stability.     

Metal‐Helix Frameworks from Short Hybrid Peptide Foldamers

The potential of structured peptides has not been explored much in the design of metal‐organic frameworks (MOFs). This is partly due to the difficulties in obtaining stable secondary structures from the short α‐peptide sequences. Here we report the design, crystal conformations, coordination site dependent different silver coordinated frameworks of short α,γ‐hybrid peptide 12‐helices consisting of terminal pyridyl moieties and the utility of metal‐helix frameworks in the adsorption of CO₂. Upon silver ion coordination the 12‐helix terminated by the 3‐pyridyl derivatives adopted a 2:2 macrocyclic structure, while the 12‐helix terminated by the 4‐pyridyl derivatives displayed remarkable porous metal‐helix frameworks. Both head‐to‐tail intermolecular H‐bonds of the 12‐helix and metal ion coordination have played an important role in stabilizing the ordered metal‐helix frameworks. The studies described here open the door to design a new class of metal‐organic‐frameworks from peptide foldamers.     

Helicene‐Grafted Silica Nanoparticles Capture Hetero‐Double‐Helix Intermediates during Self‐Assembly Gelation

A mixture of a pseudoenantiomeric ethynylhelicene (M)‐tetramer and a (P)‐pentamer forms a hetero‐double‐helix in a solution, which self‐assembles and gelates solvents. When gelation was conducted in the presence of chiral silica (P)‐nanoparticles grafted with (P)‐helicene, the resulting hetero‐double‐helix intermediate was adsorbed on the (P)‐nanoparticles, and was removed from the solution by aggregation and precipitation. The resulting precipitates contained only the hetero‐double‐helix, not random coil or clusters of the hetero‐double‐helix. (P)‐Nanoparticles did not extract the hetero‐double‐helix from the self‐assembly gels. The hetero‐double‐helix was then isolated by liberating it from the precipitates in 2‐bromopropionic acid, and was crystallized from the solution. The crystalline hetero‐double‐helices were isolated for several other combinations of pseudoenantiomeric ethynylhelicene oligomers.     

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.     

Inorganic Double‐Helix Nanotoroid of Simple LithiumPhosphorus Species

A theoretical study of Li₉₀P₉₀, which possesses a circular double‐helix structure that resembles the Watson–Crick DNA structure, is reported. This is a new bonding motif in inorganic chemistry. The calculations show that the molecule might become synthesized and that it could be a model for other inorganic species which possess a double‐helix structure.     

Crystalline poly(4‐methyl‐1‐pentene): Structure and solubility of gas molecules

Monte Carlo (MC) simulations have been used to study the crystal structure of isotactic poly(4‐methyl‐1‐pentene). Four different tetragonal packing models, each one containing two right‐handed and two left‐handed 7/2 helices, have been considered in an investigation of the up‐and‐down chain statistical disorder proposed on the basis of X‐ray data. Simulations have been performed with the isotropic united‐atom parameterization of the AMBER force field. The influence on the more stable packing models of the force‐field parameterization has been investigated with respect to the anisotropic united‐atom and all‐atom models. Results reveal that packing consisting of two upward and two downward helices arranged at random is more stable than packing with three or four helices with the same sense. Furthermore, the fiber period length for the 7/2 helix is predicted to be 0.56 Å larger than that experimentally determined. The microstructures generated from MC simulations have been employed to study the solubility of gas molecules (He, H₂, Ar, O₂, CH₄, and CO₂) with Widom's test‐particle insertion method. Special attention has been paid to the solubility of CH₄ and CO₂ because experimental data are available for these penetrants, the latter being described by both spherical and explicit models. The results are in good agreement with experimental measures only when a suitable model is used for the penetrant. The solubility of gas molecules in crystalline poly(4‐methyl‐1‐pentene) has been correlated with that measured for the crystal phases of other helical polymers. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2037–2049, 2002     

Three‐Residue Turn in β‐Peptides Nucleated by a 12/10 Helix

A new three‐residue turn in β peptides nucleated by a 12/10‐mixed helix is presented. In this design, β peptides were derived from the 1:1 alternation of C‐linked carbo‐β‐amino acid ester [BocNH‐(R)‐β‐Caa_(r)‐OMe] (Boc=tert‐butyloxycarbonyl), which consisted of a D ‐ribo furanoside side chain, and β‐hGly residues. The hexapeptide with (R)‐β‐Caa_(r) at the N terminus showed the ‘turn’ stabilized by a 14‐membered NH(4) ??? CO(6) hydrogen bond at the C terminus nucleated by a robust 12/10‐mixed helix, thus providing a ‘helix‐turn’ (HT) motif. The turn and the helix were additionally stabilized by intraresidue electrostatic interaction between the furan oxygen in the carbohydrate side chain and NH in the backbone. However, the hexapeptide with a β‐hGly residue at the N terminus demonstrated the presence of a 10/12 helix through its entire length, which again showed the intraresidue interaction between NH and furan oxygen. The intraresidue NH ??? O? Me electrostatic interactions observed in the monomer, however, were absent in the peptides.     

Isotactic polypropylene reversible crystallization investigated by modulated temperature and quasi‐isothermal FTIR

Modulated temperature techniques allow to separate the reversing and non‐reversing contributions of material transitions. To investigate reversible crystallization and melting of isotactic polypropylene (iPP) at microstructural level, in this research, modulated temperature Fourier transform infrared (MTFTIR) and quasi‐isothermal FTIR (QIFTIR) analyses are used. By following the intensity variation of iPP regularity bands, associated with 3₁ helix structures of different lengths (n repeating units), MTFTIR evidences that, independently from helix length, a reversing coil–helix transition takes place few degrees below the non‐reversing crystallization onset. By comparing spectroscopic and differential scanning calorimetry experiments performed in quasi‐isothermal conditions, the reversing transition was found to be associated with the reversible melting‐crystallization phenomenon. Moreover, QIFTIR evidences that helices of different lengths contribute differently to the reversible transition: the helices composed of n = 10 and n = 12 are active into all the explored temperature range (30–130 °C) whereas the shortest (n = 6) and the longest (n > 15) helices contribute to reversibility at T > 100 °C. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 922–931     

Heavy‐Atom Labeled Transmembrane β‐Peptides: Synthesis,CD‐Spectroscopy,and X‐ray Diffraction Studies in Model Lipid Multilayer

Transmembrane β‐peptides are promising candidates for the design of well‐controlled membrane anchors in lipid membranes. Here, we present the synthesis of transmembrane β‐peptides with and without tryptophan anchors, as well as a novel iodine‐labeled d ‐β³‐amino acid. By using one or more of the heavy‐atom labeled amino acids as markers, the orientation of the helical peptide was inferred based on the electron‐density profile determined by X‐ray reflectivity. The β‐peptides were synthesized through manual Fmoc‐based solid‐phase peptide synthesis (SPPS) and reconstituted in unilamellar vesicles forming a right‐handed 3₁₄‐helix secondary structure, as shown by circular dichroism spectroscopy. We then integrated the β‐peptide into solid‐supported membrane stacks and carried out X‐ray reflectivity and grazing incidence small‐angle X‐ray scattering to determine the β‐peptide orientation and its effect on the membrane bilayers. These β‐peptides adopt a well‐ordered transmembrane motif in the solid‐supported model membrane, maintaining the basic structure of the original bilayer with some distinct alterations. Notably, the helical tilt angle, which accommodates the positive hydrophobic mismatch, induces a tilt of the acyl chains. The tilted chains, in turn, lead to a membrane thinning effect.     

Theoretical Study of β‐Peptide Models: Intrinsic Preferences of Helical Structures

β‐Peptides form various secondary structures, such as 14‐helix, 12‐helix, 10/12‐helix, 10‐helix, 2₈‐ribbon, C6‐ribbon, and pleated‐sheet. Thus, it is useful to understand the intrinsic backbone conformational preferences of these basic structures. By using a simple repeating‐unit method, we have calculated the preferences of C6‐ribbon, β‐strand, 10/12‐helix, 14‐helix, 12‐helix, 10‐helix, and 2₈‐ribbon of a series of poly‐β‐alanine models, Ac‐(β‐Ala)_n‐NH₂, with n=1–9. Interactions among single amino acids result in cooperative residue energies. This is not found for the formations of β‐strands, 2₈‐ribbons, and C6‐ribbons, which possess constant residue energies. In contrast, the 12‐helix, 10‐helix, and 14‐helix are characterized by increasing residue energies as the peptide elongates. Therefore, there is a considerable positive cooperative impetus in the gas phase for their formation. The residue energy of the 10/12‐helix increases significantly for n=2 and 3, and then displays a zigzag pattern. Meanwhile, there is a good correlation between calculated residue energies and residue dipole moments, indicating the importance of long‐range electrostatic interactions to the cooperative residue energy. Efforts have been made to separate the electrostatic and torsional interactions between residues. Thereby, the 12‐, 10‐, and 10/12‐helices all benefit from electrostatic interactions, while the 14‐helix has the most intrinsic preference in terms of torsional interaction. The effect of MeOH on the secondary structures has also been evaluated by SCIPCM solvent model calculations.     

Hybridization of Long Pyridine‐Dicarboxamide Oligomers into Multi‐Turn Double Helices: Slow Strand Association and Dissociation,Solvent Dependence,and Solid State Structures

Oligoamides of 2,6‐diaminopyridine and 2,6‐pyridinedicarboxylic acid comprised of 5, 7, 9, 11, or 13 units and bearing 4‐isobutoxychains on all pyridine rings and tert‐butyl‐carbamate terminal groups have been synthesized stepwise, along with an 11 mer having benzyl‐carbamate terminal groups. The crystal structure of all five Boc‐terminated compounds has been obtained and shows a highly regular and conserved double helical hybridization motif of up to 3 complete turns for the 13 mer. Four pyridine units span one helical turn and define a helix pitch of ca 7 Å. Solution studies in CDCl₃ demonstrated that the Boc‐terminated oligomers strongly hybridize in this solvent, and that K_dim values increase with oligomer length. The K_dim values are 31000 and 7×10⁵ L mol^?1 for the 7 mer and the 9 mer, respectively, and are too high to be measured by NMR for the 11 mer and the 13 mer. Hybridization and dissociation kinetics at 2 mM proceed at decreasing rates upon increasing oligomer length. The rate was faster than minutes for the 7 mer, of the order of hours for the 9 mer, and days for the 11 mer and 13 mer. The same trend was observed in [D₅]pyridine but with considerably lower K_dim values and faster kinetics. The benzylcarbamate 11 mer was also found to hybridize into a double helix but with reduced K_dim values and faster kinetics compared to its Boc‐terminated analogue. Combined with previous studies, the results presented here frame a global understanding of the hybridization of these pyridinecarboxamide oligomers and provide useful guidelines for the design of other artificial double helices.     

Helical Structures of Bicyclic α‐Amino Acid Homochiral Oligomers with the Stereogenic Centers at the Side‐Chain Fused‐Ring Junctions

Chiral bicyclic α‐amino acid (R,R)‐Ab_5,6=c with stereogenic centers at the γ‐position of fused‐ring junctions, and its enantiomer (S,S)‐Ab_5,6=c, were synthesized. The CD spectra of (R,R)‐Ab_5,6=c oligomers indicated that the (R,R)‐Ab_5,6=c hexapeptide formed a mixture of right‐handed (P)‐ and left‐handed (M)‐3₁₀‐helices, while, in the (R,R)‐Ab_5,6=c nonapeptide, a right‐handed (P)‐3₁₀‐helix slightly dominated over the (M)‐helix. X‐Ray crystallographic analyses of (S,S)‐tripeptide and (R,R)‐hexapeptide revealed that both the tripeptide and hexapeptide formed a mixture of (P)‐ and (M)‐3₁₀‐helices, respectively. These results indicated that the side‐chain environments around the stereogenic centers are particularly important to control the helical‐screw handedness of foldamers.     

catena‐Poly[[aqua­(2,2′‐bipyridine‐κ2N,N′)cadmium(II)]‐μ‐4‐carboxyl­atophenoxy­acetato‐κ3O:O4,O4′]

In the title compound, [Cd(C₉H₆O₅)(C₁₀H₈N₂)(H₂O)]_n, the Cd^II atom is coordinated in a distorted octa­hedral fashion by two carboxyl­ate groups (one in a monodentate and one in a bidentate fashion) from two 4‐carboxyl­ato­phenoxy­acetate anions, two N atoms from a 2,2′‐bipyridine ligand and one aqua ligand. The structure is a helix with a long pitch of 16.441 (5) Å. A three‐dimensional supra­molecular network is further constructed through π–π stacking and hydrogen‐bonding inter­actions between the helices.     

One‐Handed Helical Screw Direction of Homopeptide Foldamer Exclusively Induced by Cyclic α‐Amino Acid Side‐Chain Chiral Centers

Chiral cyclic α,α‐disubstituted amino acids, (3S,4S)‐ and (3R,4R)‐1‐amino‐3,4‐(dialkoxy)cyclopentanecarboxylic acids ((S,S)‐ and (R,R)‐Ac₅c^dOR; R: methyl, methoxymethyl), were synthesized from dimethyl L ‐(+)‐ or D ‐(?)‐tartrate, and their homochiral homoligomers were prepared by solution‐phase methods. The preferred secondary structure of the (S,S)‐Ac₅c^dOMe hexapeptide was a left‐handed (M) 3₁₀ helix, whereas those of the (S,S)‐Ac₅c^dOMe octa‐ and decapeptides were left‐handed (M) α helices, both in solution and in the crystal state. The octa‐ and decapeptides can be well dissolved in pure water and are more α helical in water than in 2,2,2‐trifluoroethanol solution. The left‐handed (M) helices of the (S,S)‐Ac₅c^dOMe homochiral homopeptides were exclusively controlled by the side‐chain chiral centers, because the cyclic amino acid (S,S)‐Ac₅c^dOMe does not have an α‐carbon chiral center but has side‐chain γ‐carbon chiral centers.     

Cysteine‐Containing Polyisocyanides as Versatile Nanoplatforms for Chromophoric and Bioscaffolding

The straightforward syntheses of polyisocyanides containing the alanine–cysteine motif in their side chains have been achieved. Detailed characterization of the polymers revealed a well‐defined and highly stable helical conformation of the polyimine backbone responsible for the formation of rodlike structures of over one hundred nanometers. The 4₁ helix is further stabilized by β‐sheet‐like interactions between the peptide arms. As a result, the cysteine sulfur atoms are regularly aligned along the polymer axis, which provides a unique platform for the scaffolding of various entities by using versatile click‐chemistry postmodification approaches. For instance, pyrene derivatives were introduced through thio‐specific reactions involving either maleimide, iodoacetamide, or thioester groups, leading to arrays of stacked chromophores with excimer‐like emission. A water‐soluble cysteine‐rich polyisocyanide was successfully biotinylated and coupled to streptavidin.