Length-Dependent Transition from Extended to Folded Shapes in Short Oligomers of an Azetidine-Based α-Amino Acid: The Critical Role of NH···N H-Bonds.

Hydrogen bonds (H-bonds) are ubiquitous in peptides and proteins and are central to the stabilization of their structures. Inter-residue H-bonds between non-adjacent backbone amide NH and C=O motifs lead to the well-known secondary structures of helices, turns and sheets, but it is recognized that other H-bonding modes may be significant, including the weak intra-residue H-bond (called a C5 H-bond) that implicates the NH and C=O motifs of the same amino acid residue. Peptide model compounds that adopt stable C5 H-bonds are not readily available and the so-called 2.05-helix, formed by successive C5 H-bonds, is an elusive secondary structure. Using a combination of theoretical chemistry and spectroscopic studies in both the gas phase and solution phase, we have demonstrated that derivatives of 3-amino-1-methylazetidine-3-carboxylic acid, Aatc(Me) can form sidechain-backbone N-H···N C6γ H-bonds that accompany-and thereby stabilize-C5 H-bonds. In the capped trimer of Aatc(Me), extended C5/C6γ motifs are sufficiently robust to challenge classical 310-helix formation in solution and the fully-extended 2.05-helix conformer has been characterized in the gas phase. Concurrent H-bonding support for successive C5 motifs is a new axiom for stabilizing the extended backbone secondary structure in short peptides.

Characterization of Asx Turn Types and Their Connate Relationship with ß-Turns.

Models of asparagine-containing dipeptides specifically designed to favor intrinsic folding into an Asx turn were characterized both theoretically, by using quantum chemistry, and experimentally, by using laser spectroscopy in the gas phase. Both approaches provided evidence for the spontaneous folding of both the Asn-Ala and Asn-Gly dipeptide models into the most stable Asx turn, a conformation stabilized by a C10 H-bond that was very similar to a type II' ß-turn. In parallel, analysis of Asx turns implicating asparagine in crystallized protein structures in the Protein Data Bank revealed a sequence-dependent behavior. In Asn-Ala sequences, the Asx turn was found in conjunction with a type I ß-turn for which the first of the four defining residues was Asn. The observation that the Asx turn in these structures is mostly of type II' (i. e., its most stable innate structure) suggests that this motif might foster the formation and/or enhance the stability of the backbone ß-turn. In contrast, the Asx turns observed in Asn-Gly sequences extensively adopted a type II Asx-turn structure, thus suggesting that their formation should be ascribed to other factors, such as hydration. The fact that the Asx turn in a Asn-Gly sequence is also often found in combination with a hydrated ß-bulge supports the premise that a Asn-Gly sequence might efficiently promote the formation of the ß-bulge secondary structure.

Characterization of Asx Turn Types and Their Connate Relationship with ß-Turns.

Invited for the cover of this issue are David J. Aitken, Michel Mons, and co-workers at Université Paris-Saclay. The image depicts the investigation strategies used to document the intrinsic structures of an important secondary structure in proteins, the so-called Asx turn. Read the full text of the article at 10.1002/chem.202104328.

A case study of the MAC (masked acyl cyanide) oxyhomologation of N,N-dibenzyl-L-phenylalaninal with anti diastereoselectivity: preparation of (2S,3S)-allophenylnorstatin esters.

The three-component reaction between a protected α-amino aldehyde, an alcohol and an α-silyloxymalononitrile provides an expedient access to protected α-hydroxy-ß-amino acid derivatives. The prototypical process, performed on N-Cbz-phenylalaninal, is known to proceed with syn diastereoselectivity. The present study demonstrates that the diastereoselectivity of the reaction can be inverted, using the rationale of a Felkin-Anh interaction model. Reactions performed on N,N-dibenzyl-L-phenylalaninal proceed with a high anti diastereoselectivity, providing a panel of synthetically useful ester derivatives of (2S,3S)-allophenylnorstatin. The procedure is exploited to accomplish one of the most efficient syntheses of the title compound to date, in 3 steps (66% yield) from N,N-dibenzyl-L-phenylalaninal.

Pyrrolidinyl peptide nucleic acids bearing hydroxy-modified cyclobutane building blocks: Synthesis and binding properties.

The conformationally constrained pyrrolidinyl PNA with a dipeptide consisting of an alternating nucleobase-modified D-proline and a cyclic ß-amino acid "spacer" exhibited improved nucleic acid binding properties compared to the original PNA. The pyrrolidinyl PNA with the four-membered ring spacer (1S,2S)-2-aminocyclobutanecarboxylic acid (acbcPNA) are among the best performed members of the pyrrolidinyl PNA family. However, these PNA suffer some limitations such as aqueous solubility and non-specific interactions due to their extreme hydrophobicity. In the present work, a hydroxy group is introduced onto the cyclobutane ring spacer of the acbcPNA with the aim of decreasing its hydrophobicity. To this end, a Fmoc/tBu ether-protected 4-hydroxy-2-aminocyclobutanecarboxylic acid building block was synthesized and resolved by chiral HPLC. Each enantiomer was used to synthesize the hydroxy-modified acbcPNA employing Fmoc solid-phase peptide synthesis. DNA/RNA binding studies indicated that the introduction of the hydroxy group to the acbcPNA decreases the binding affinity toward complementary DNA and RNA while maintaining the sequence and directional specificity of unmodified acbcPNA. The hydrophobicity of the hydroxy-modified acbcPNA decreased with the number of hydroxy groups added as indicated by the decrease in the logP values. Only two modifications were sufficient to decrease the logP by an order of magnitude without excessively lowering the binding affinity nor the specificity. This work thus demonstrated that the specific structural modifications for this type of PNA model can be performed in a modular fashion, which paves the way toward the future realization of improving hydrophilicity and nucleic acid binding affinity as well as specificity.

Ion Pair Supramolecular Structure Identified by ATR-FTIR Spectroscopy and Simulations in Explicit Solvent*.

The present work uses ATR-FTIR spectroscopy assisted by simulations in explicit solvent and frequency calculations to investigate the supramolecular structure of carboxylate alkali-metal ion pairs in aqueous solutions. ATR-FTIR spectra in the 0.25-4.0 M concentration range displayed cation-specific behaviors, which enabled the measurement of the appearance concentration thresholds of contact ion pairs between 1.9 and 2.6 M depending on the cation. Conformational explorations performed using a non-local optimization method associated to a polarizable force-field (AMOEBA), followed by high quantum chemistry level (RI-B97-D3/dhf-TZVPP) optimizations, mode-dependent scaled harmonic frequency calculations and electron density analyses, were used to identify the main supramolecular structures contributing to the experimental spectra. A thorough analysis enables us to reveal the mechanisms responsible for the spectroscopic sensitivity of the carboxylate group and the respective role played by the cation and the water molecules, highlighting the necessity of combining advanced experimental and theoretical techniques to provide a fair and accurate description of ion pairing.

A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine.

S-containing amino acids can lead to two types of local NH···S interactions which bridge backbone NH sites to the side chain to form either intra- or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-L-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas-phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C- and N-capped model compound for one Cys(Me) residue adopts a preferred C5-C6γ conformation which combines an intra-residue N-H···O=C backbone interaction (C5) and an inter-residue N-H···S interaction implicating the side-chain sulfur atom (C6γ). In contrast, the dominant conformation of the C- and N-capped model compound featuring two consecutive Cys(Me) residues is a regular type I ß-turn. This structure is incompatible with concomitant C6γ interactions, which are no longer in evidence. Instead, C5γ interactions occur, that are fully consistent with the turn geometry and additionally stabilize the structure. Comparison with the thietane amino acid Attc, which exhibits a rigid cyclic side chain, pinpoints the significance of side chain flexibility for the specific conformational behavior of Cys(Me).

A Brønsted acid catalyzed tandem reaction for the diastereoselective synthesis of cyclobuta-fused tetrahydroquinoline carboxylic esters.

A novel Brønsted acid catalyzed tandem reaction provides highly functionalized cyclobuta-fused tetrahydroquinoline carboxylic esters from anilines and 2-alkylenecyclobutanones in good to high yield. During the reaction a dynamic diastereoselective cyclization is achieved, resulting in the formation of three contiguous stereocenters with high stereoselectivity.

Local versus Global Control of Helical Folding in ß-Peptide Segments Using Hydrazino Turns.

Rational control of the self-organization of ß-peptides sequences to adopt regular secondary structures is an important challenge in peptidomimetic foldamer science. By replacing the N- and C-terminal residues of homooligomers of trans-2-aminocyclobutanecarboxylic acid (tACBC)n with N-aminoazetidine-2-carboxylic acid, an 8-helical topology is shown to dominate for sequences up to n = 7. This constitutes an atomic-level tool to override locally the preferred global 12-helix secondary structure of the corresponding tACBC homooligomers of the same length.

Stereocontrolled Preparation of Diversely Trifunctionalized Cyclobutanes.

The expedient and stereoselective syntheses of small libraries of trifunctionalized cyclobutane scaffolds bearing an acid, an amine, and a third functional group are described. Starting from a single precursor, the readily available protected derivative of all-cis-2-amino-3-hydroxycyclobutane-1-carboxylic acid, cis-trans stereoisomers are obtained following an SN2-type reaction, while all-trans stereoisomers are obtained using the same strategy preceded by a C1 epimerization reaction.

Synthesis of ß-sulfinyl cyclobutane carboxylic amides via a formal α to ß sulphoxide migration process.

An original tandem reaction consisting of a thermal elimination-addition process was developed. Highly substituted ß-sulfinyl cyclobutane carboxylic acid derivatives were obtained from isomeric α-sulfinyl derivatives in a single operation in good to high yields and with high trans diastereoselectivity.

Identification of ion pairs in solution by IR spectroscopy: crucial contributions of gas phase data and simulations.

In a context where structure elucidation of ion pairs in solution remains a contemporary challenge, this work explores an original approach where accurate gas phase spectroscopic data are used to refine high level quantum chemistry calculations of ion pairs in solution, resulting in an unprecedented level of accuracy in vibrational frequency prediction. First, gas phase studies focus on a series of isolated contact ion pairs (M+, Ph-CH2-COO-, with M = Li, Na, K, Rb, Cs) for which conformer-selective IR spectra in the CO2- stretch region are recorded. These experiments reveal the interactions at play in isolated contact ion pairs, and provide vibrational frequencies enabling us to assess the accuracy of the theoretical approach used, i.e., mode-dependent scaled harmonic frequency calculations at the RI-B97-D3/dhf-TZVPP level. This level of calculation is then employed on large water clusters embedding either a free acetate ion or its contact or solvent-shared pairs with a sodium cation in order to simulate the individual vibrational spectra of these species in solution. This study shows that the stretching modes of carboxylate are sensitive to both solvent-shared and contact ion pair formation. FTIR spectra of solutions of increasing concentrations indeed reveal several spectral changes consistent with the presence of specific types of solvent-shared and contact ion pairs. By providing relevant guidelines for the interpretation of solution phase IR spectra, this work illustrates the potential of the approach for the elucidation of supramolecular structures in electrolyte solutions.

Vibrational circular dichroism as a probe of solid-state organisation of derivatives of cyclic ß-amino acids: Cis- and trans-2-aminocyclobutane-1-carboxylic acid.

Peptide models built from cis- and trans-2-aminocyclobutane-1-carboxylic acids (ACBCs) are studied in the solid phase by combining Fourier-transform infrared spectroscopy (FTIR) absorption spectroscopy, vibrational circular dichroism (VCD), and quantum chemical calculations using density functional theory (DFT). The studied systems are N-tert-butyloxycarbonyl (Boc) derivatives of 2-aminocyclobutanecarboxylic acid (ACBC) benzylamides, namely Boc-(cis-ACBC)-NH-Bn and Boc-(trans-ACBC)-NH-Bn. These two diastereomers show very different VCD signatures and intensities, which of the trans-ACBC derivative being one order of magnitude larger in the region of the ν (CO) stretch. The spectral signature of the cis-ACBC derivative is satisfactorily reproduced by that of the monomer extracted from the solid-state geometry of related ACBC derivatives, which shows that no long-range effects are implicated for this system. In terms of hydrogen bonds, the geometry of this monomer is intermediate between the C6 and C8 structures (exhibiting a 6- or 8-membered cyclic NH⋯O hydrogen bond) previously evidenced in the gas phase. The benzyl group must be in an extended geometry to reproduce satisfactorily the shape of the VCD spectrum in the ν (CO) range, which qualifies VCD as a potential probe of dispersion interaction. In contrast, reproducing the IR and VCD spectrum of the trans-ACBC derivative requires clusters larger than four units, exhibiting strong intermolecular H-bonding patterns. A qualitative agreement is obtained for a tetramer, although the intensity enhancement is not reproduced. These results underline the sensitivity of VCD to the long-range organisation in the crystal.

Strategic C to N Replacement in ß-Peptides: Atomic Level Control of Helical Folding.

Single residue control of the helical topology of ß-peptides is a contemporary challenge in foldamer science. We present the conformational preferences of oligomers of trans-2-aminocyclobutanecarboxylic acid ( tACBC), in which a central residue has been replaced by a single N-aminoazetidine-2-carboxylic acid (AAzC) moiety. The latter has such a strong demand for local 8-helical conformers that the usual 12-helix secondary structure of a tACBC octamer is switched to a fully 8-helical conformation as a result of the single residue substitution.

A Photochemical Route to 3- and 4-Hydroxy Derivatives of 2-Aminocyclobutane-1-carboxylic Acid with an all-cis Geometry.

Short gram-scale syntheses of both enantiomers of 2-amino-3-hydroxycyclobutane-1-carboxylic acid and of 2-amino-4-hydroxycyclobutanecarboxylic acid with an all-cis geometry are described. The sequences feature highly endo-selective [2 + 2]-photocycloaddition reactions followed by fully regioselective ring opening/Hofmann rearrangement/nitrogen protection, in a consecutive or one-pot protocol, followed by efficient resolution using a chiral oxazolidinone.

Preparation of Cyclobutene Acetals and Tricyclic Oxetanes through Photochemical Tandem and Cascade Reactions.

We describe a photochemical reaction using two starting materials, a cyclopent-2-enone and an alkene, which are transformed in a controlled manner via the initial [2+2]-photocycloaddition adducts into cyclobutene aldehydes (conveniently trapped as stable acetals) or unprecedented angular tricyclic 4:4:4 oxetane-containing skeletons. These compounds are formed through tandem or triple cascade photochemical reaction processes, respectively. Small libraries of each compound class were prepared, thus suggesting that this photochemistry approach opens new opportunities for synthesis design and for widening molecular diversity.

ß-Cyclodextrin-Mediated Enantioselective Photochemical Electrocyclization of 1,3-Dihydro-2H-azepin-2-one.

The photochemical electrocyclization reaction of the title compound in the presence of ß-cyclodextrin was examined in different conditions. No enantioselectivity was observed in solution, but solid-state reactions of a 1:1 complex as a suspension or a thin film, followed by reduction, provided (1R,5R)-2-azabicyclo[3.2.0]heptan-3-one in isolated yields up to 79% and with ee values up to 45%.

Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure.

A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

Studies on cyclization reactions of 3-amino-2,4-dihydroxybutanoic acid derivatives.

A number of cyclic derivatives of 3-amino-2,4-dihydroxybutanoic acid are known in the literature but they are often prepared from other cyclic precursors. This study showed that the title compound too may serve as a convenient substrate for cyclization reactions. Using orthogonally-protected linear derivatives, regioselective cyclizations were performed, leading to original and highly-functionalized γ-lactones, oxazolidinones, oxazolines and aziridines. In these reactions a key role was played by the C3 nitrogen group function, while the C2 alcohol function showed no propensity for participation in cyclization reactions.

Acid-catalyzed reaction of 2-hydroxycyclobutanone with benzylic alcohols.

The acid-promoted syntheses of 2-(benzyloxy)cyclobutanones and bis(benzyloxy)dioxatricyclo decanes were achieved starting from 2-hydroxycyclobutanone and variously functionalized benzyl alcohols. The reaction sequences afforded the desired products in good to high yields and in a solvent-dependent chemoselective fashion.