DFT and ab initio potential energy scan and hydrogen bond analysis of N-substituted hydrazino acetamides: Characterization of the “hydrazinoturn” hydrogen bonding pattern

We studied a series of model primary amides in gas phase at the DFT (B3LYP) and HF at 6-31+G/6-31+G** levels of theory in order to shed light on their conformation, structure, and intramolecular hydrogen bonding network. A potential energy scan was performed by rotating around the appropriate bond for each molecule studied in this paper. In this manner, it was possible to show that the amidic group of these model compounds acts as H-bond donor and interacts with two different H-bond acceptors which stabilizes a C₈ pseudocycle, the so called “hydrazinoturn”. This study was addressed theoretically in order to understand the conformation adopted by hydrazino acetamides as model compounds for aza-β³-peptides. We thus investigated the conformational analysis of hydrazinoturns computationally and showed that these systems represent a very stabilizing folding driving force, provided that the neighboring molecular functional groups do not imply other competing hydrogen bonding patterns.     

Semi-Rigid Nitroxide Spin Label for Long-Range EPR Distance Measurements of Lipid Bilayer Embedded β-Peptides

β-Peptides are an interesting new class of transmembrane model peptides based on their conformationally stable and well-defined secondary structures. Herein, we present the synthesis of the paramagnetic β-amino acid β³-hTOPP (4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-d -β³-homophenylglycine) that enables investigations of β-peptides by EPR spectroscopy. This amino acid adds to the, to date, sparse number of β-peptide spin labels. Its performance was evaluated by investigating the helical turn of a 3₁₄-helical transmembrane model β-peptide. Nanometer distances between two incorporated β³-hTOPP labels in different environments were measured by using pulsed electron/electron double resonance (PELDOR/DEER) spectroscopy. Due to the semi-rigid conformational design, the label delivers reliable distances and sharp (one-peak) distance distributions even in the lipid bilayer. The results indicate that the investigated β-peptide folds into a 3.25₁₄ helix and maintains this conformation in the lipid bilayer.     

Synthesis and conformation of fluorinated β-peptidic compounds

Experimental and theoretical data indicate that, for α-fluoroamides, the F-C-C(O)-N(H) moiety adopts an antiperiplanar conformation. In addition, a gauche conformation is favoured between the vicinal C-F and C-N(CO) bonds in N-β-fluoroethylamides. This study details the synthesis of a series of fluorinated β-peptides (1-8) designed to use these stereoelectronic effects to control the conformation of β-peptide bonds. X-ray crystal structures of these compounds revealed the expected conformations: with fluorine β to a nitrogen adopting a gauche conformation, and fluorine α to a C=O group adopting an antiperiplanar conformation. Thus, the strategic placement of fluorine can control the conformation of a β-peptide bond, with the possibility of directing the secondary structures of β-peptides.     

β-Peptides: Synthesis by Arndt-Eistert homologation with concomitant peptide coupling. Structure determination by NMR and CD spectroscopy and by X-ray crystallography. Helical secondary structure of a β-hexapeptide in solution and its stability towards pepsin

The β-hexapeptide (H-β-HVal-β-HAla-β-HLeu)₂-OH ( 2 ) was prepared from the component L -β-amino acids by conventional peptide synthesis, including fragment coupling. A cyclo-β-tri- and a cyclo-β-hexapeptide were also prepared. The β-amino acids were obtained from α-amino acids by Arndt-Eistert homologation. All reactions leading to the β-peptides occur smoothly and in high yields. The β-peptides were characterized by their CD and NMR spectra (COSY, ROESY, TOCSY, and NOE-restricted modelling), and by an X-ray crystal-structure analysis. β-Sheet-type structures (in the solid state) and a compact, left-handed or (M) 3₁ helix of 5-Å pitch (in solution) were discovered. Comparison with the analogous secondary structures of α-peptides shows fundamental differences, the most surprising one at this point being the greater stability of β-peptide helices. There are structural relationships of β-peptides with oligomers of β-hydroxyalkanoic acids, and dissimilarities between the two classes of compounds are a demonstration of the power of H-bonding. The β-hexapeptide 2 is stable to cleavage by pepsin at pH 2 in H₂O for at least 60 h at 37°, while the corresponding α-peptide H-(Val-Ala-Leu)₂-OH is cleaved instantaneously under these conditions. The implication of the described results are discussed.     

Conformation of N(alpha)-substituted hydrazino acetamides in CDCl3, the precious help of the analysis of Deltadelta between amidic hydrogens, and correlation to the conformation of aza-beta3-peptides

[structures: see text] We studied the conformation of a series of primary amides in a solution of chloroform. Classical NMR tools such as dilution experiments, influence of DMSO, and 2D-NOESY, together with X-ray diffraction, were combined with an analysis of the difference of the chemical shift Deltadelta between the geminal amidic protons. This study was addressed in order to understand the conformation adopted by hydrazino acetamides 1a and 1b as model compounds for aza-beta3-peptides. In this manner, it was possible to show that the amidic group of these compounds acts as a H-bond donor and interacts with two different H-bond acceptors. We concluded that the hydrazinoturn, a specific bifurcated H-bond system observed in the solid state, is also the preferred conformation of hydrazino acetamides 1a and 1b in solution. Our results show that the short-range interaction with the N(alpha)-nitrogen lone pair not only stabilizes the C8 pseudocycle but could also contribute to the folding process of aza-beta3-peptides. In light of this, it could explain why aza-beta3-peptides develop a different H-bond network in comparison to their isosteric beta3-peptides analogues. Our work is in keeping with the recent interest of hydrazino peptides as an extension of the beta-peptide concept.     

Water-Insensitive Synthesis of Poly-β-Peptides with Defined Architecture

Biocompatible and proteolysis-resistant poly-β-peptides have broad applications and are dominantly synthesized via the harsh and water-sensitive ring-opening polymerization of β-lactams in a glovebox or using a Schlenk line, catalyzed by the strong base LiN(SiMe₃)₂. We have developed a controllable and water-insensitive ring-opening polymerization of β-amino acid N-thiocarboxyanhydrides (β-NTAs) that can be operated in open vessels to prepare poly-β-peptides in high yields, with diverse functional groups, variable chain length, narrow dispersity and defined architecture. These merits imply wide applications of β-NTA polymerization and resulting poly-β-peptides, which is validated by the finding of a HDP-mimicking poly-β-peptide with potent antimicrobial activities. The living β-NTA polymerization enables the controllable synthesis of random, block copolymers and easy tuning of both terminal groups of polypeptides, which facilitated the unravelling of the antibacterial mechanism using the fluorophore-labelled poly-β-peptide.     

Preparation of new monomers aza-β-aminoacids for solid-phase syntheses of aza-β-peptides

The preparation of new N^β-Fmoc-protected aza-β³-amino acids (aza-β³-aa) with proteinogenic side chains as well as their N^β-Fmoc, N^β-Cbz or N^β-Boc aza-β³-amino esters (from Pro, Asn, Asp, Glu, Gln) by successive nucleophilic substitutions will be described.     

Cyclic Heptapeptides Axinastatin 2, 3, and 4: Conformational analysis and evaluation of the biological potential

The conformational analysis of naturally occurring cytostatic cyclic heptapeptides axinastatin 2, 3, and 4 was carried out by two-dimensional NMR spectroscopy in combination with distance-geometry (DG) and molecular-dynamics (MD) calculations in explicit solvents. The synthesized secondary metabolites were examined in (D₆)DMSO. Axinastatin 2 was also investigated in CD₃OH. In all structures, Pro² is in the i + 1 position of a βI turn and Pro⁶ occupies the i + 2 position of a βVIa turn about the cis amide bond between residue 5 and Pro^6. In all peptides, a bifurcated H-bond occurs between residue 4 CO and the amide protons of residue 1 and 7. For axinastatin 2 and 3, an Asn I_g turn was found about Asn¹ and Pro^2. We compared these structures with conformations of cyclic heptapeptides obtained by X-ray and NMR studies. A β-bulge motif with two β turns and one bifurcated H-bond is found as the dominating backbone conformation of cyclic all-L-heptapeptides. Axinastatin 2, 3, and 4 can be characterized by six trans and one cis amide bond resulting in a β/βVI(a)-turn motif, a conformation found for many cyclic heptapeptides. Detailed biological tests of the synthetic compounds in different human cancer cell lines indicates these axinastatins to be inactive or of low activity.     

‘Mixed’ β-peptides: A unique helical secondary structure in solution. Preliminary communication

β-Hexapeptides 1–5 and a β-dodecapeptide 6 with sequences containing two different types of β-amino acids (aliphatic proteinageous side chains in the 2- or in the 3-position) have been prepared. CD (Fig. 1) and NMR measurements indicate that, with one exception, the secondary structures formed by these new β-peptides differ from those of isomers studied previously. Detailed NMR analysis of the β-hexapeptide 5 (with alternating β²,β³-building blocks) and molecular-dynamics simulations have produced a minimum energy conformation (Fig. 2,b)which might be described as a novel irregular helix containing ten- and twelve-membered H-bonded rings. This demonstrates the great structural variability of β-peptides, since three different helical secondary structures have been discovered to date.     

Investigation of folding patterns in homo-oligomers of (R)-β2,2-amino acids with carbohydrate side chain

The study describes the synthesis of new β^2,2-peptides made from geminally disubstituted β^2,2-amino acid and their folding propensities. The (R)-C-linked carbo-β^2,2-amino acid [(R)-β^2,2-Caa] was prepared from d-glucose and converted into the homo-oligomeric di-, tetra-, and hexapeptides. The conformational studies were carried out using NMR (in CDCl₃), CD, IR, and MD calculations. These β^2,2-peptides were interestingly stabilized by five-membered (mr) inter-residue H-bonds NH(i)?O(i-1) (furanoside) and a 6-mr intra-residue H-bond between amide proton (NH(i)) and the oxygen of –OMe(i) at the C3 carbon of the carbohydrate side chain. These results amply demonstrate that the ‘epimerization’ at the spiro carbon center has an effect on the conformational behavior of these peptides. Finding of these, H-bonding patterns, which are not so common to stabilize the folds in this class of β^2,2-Caa derived peptides would further facilitate augmentation in the domain of foldamer.     

Sheet-like assemblies of charged amphiphilic α/β-peptides at the air-water interface

There is growing interest in the design of molecules that undergo predictable self-assembly. Bioinspired oligomers with well-defined conformational propensities are attractive from this perspective, since they can be constructed from diverse building blocks, and self-assembly can be directed by the identities and sequence of the subunits. Here we describe the structure of monolayers formed at the air-water interface by amphiphilic α/β-peptides with 1:1 alternation of α- and β-amino acid residues along the backbone. Two of the α/β-peptides, one a dianion and the other a dication, were used to determine differences between self-assemblies of the net negatively and positively charged oligomers. Two additional α/β-peptides, both zwitterionic, were designed to favor assembly in a 1:1 molar ratio mixture with parallel orientation of neighboring strands. Monolayers formed by these α/β-peptides at the air-water interface were characterized by surface pressure-area isotherms, grazing incidence X-ray diffraction (GIXD), atomic force microscopy and ATR-FTIR. GIXD data indicate that the α/β-peptide assemblies exhibited diffraction features similar to those of β-sheet-forming α-peptides. The diffraction data allowed the construction of a detailed model of an antiparallel α/β-peptide sheet with a unique pleated structure. One of the α/β-peptide assemblies displayed high stability, unparalleled among previously studied assemblies of α-peptides. ATR-FTIR data suggest that the 1:1 mixture of zwitterionic α/β-peptides assembled in a parallel arrangement resembling that of a typical parallel β-sheet secondary structure formed by α-peptides. This study establishes guidelines for design of amphiphilic α/β-peptides that assemble in a predictable manner at an air-water interface, with control of interstrand orientation through manipulation of Coulombic interactions along the backbone.     

Probing the Helical Secondary Structure of Short-Chain β-Peptides

Structural prerequisites for the stability of the 3₁ helix of β-peptides can be defined from inspection of models (Figs. 1 and 2): lateral non-H-substituents in 2- and 3-position on the 3-amino-acid residues of the helix are allowed, axial ones are forbidden. To be able to test this prediction, we synthesized a series of heptapeptide derivatives Boc-(β-HVal-β-HAla-β-HLeu-Xaa-β-HVal-β-HAla-β-HLeu)-OMe 13–22 (Xaa = α- or β-amino-acid residue) and a β-depsipeptide 25 with a central (S)-3-hydroxybutanoic-acid residue (Xaa = –OCH(Me)CH₂C(O)–) (Schemes 1 3). Detailed NMR analysis (DQF-COSY, HSQC, HMBC, ROESY, and TOCSY experiments) in methanol solution of the β-hexapeptide H(-β-HVal-β-HAla-β-HLeu)₂-OH ( 1 ) and of the β-heptapeptide H-β-HVal-β-HAla-β-HLeu-(S,S)-β-HAla(αMe)-β-HVal-β-HAla- β-HLeu-OH ( 22 ), with a central (2S,3S)-3-amino-2-methylbutanoic-acid residue, confirm the helical structure of such β-peptides (previously discovered in pyridine solution) (Fig.3 and Tables 1–5). The CD spectra of helical β-peptides, the residues of which were prepared by (retentive) Arndt-Eistert homologation of the (S)- or L -α-amino acids, show a trough at 215 nm. Thus, this characteristic pattern of the CD spectra was taken as an indicator for the presence of a helix in methanol solutions of compounds 13–22 and 25 (including partially and fully deprotected forms) (Figs.4–6). The results fully confirm predicted structural effects: incorporation of a single ‘wrong’ residue ((R)-β-HAla, β-HAib, (R,S)-β-HAla(α Me), or N-Me-β-HAla) in the central position of the β-heptapeptide derivatives A (see 17, 18, 20 , or 21 , resp.) causes the CD minimum to disappear. Also, the β-heptadepsipetide 25 (missing H-bond) and the β-heptapeptide analogs with a single α-amino-acid moiety in the middle ( 13 and 14 ) are not helical, according to this analysis. An interesting case is the heptapeptide 15 with the central achiral, unsubstituted 3-aminopropanoic-acid moiety: helical conformation appears to depend upon the presence or absence of terminal protection and upon the solvent (MeOH vs. MeOH/H₂O).     

Umsetzung von 1,5-Dimethyl-2,3,3,4-tetrachlor-1,5,2,4-diazadiphosphorinan-6-on mit Anilinderivaten,Heptamethyldisilazan und tert.-Butylamin: Oxidative Addition von Tetrachlor-o-benzochinon an einige P(III)-haltige Produkte

The reaction of the title compound 1 with the p-R-aniline derivatives (R═H, F, OCH₃, NO₂, and NH₂) led to the formation of the aza-2σ³,4σ³-diphosphetidines 2a– 2e, whereas 2-trimethylsiloxyaniline furnished the azadiphosphetidine 2f. The reaction of the sterically crowded 2,6-dimethylaniline with 1 furnished the disubstituted derivative 3. The tricyclic compound 5 was formed during the reaction of 1,2-phenylenediamine with 1. Heptamethyldisilazane formed the aza-2σ ³ ,4σ ³ -diphosphetidine 6 on reaction with 1. The bulkier tert.-butylamine formed with 1 a mixture of the aza-2,4-diphosphetidine 7a and the disubstituted derivative 7b, which could not be separated. The reaction of 2b and 6 with tetrachloro-o-benzoquinone resulted in the formation of the bis-spirophosphoranes 8 and 9b, respectively. The formation of the monospirophosphorane 9a was observed in the ³¹P NMR spectrum. The characterization of compounds is based in particular on NMR investigations (¹H, ¹³C, ³¹P). 2a was characterized by a single-crystal X-ray structure analysis. The dimethylurea fragment is planar; the four-membered ring is folded about the P···P vector by 38.7°.     

Tapes of water hexamer clusters in the interlayer space of a 2D MOF: Structural, spectroscopic and computational insight of the confined water

The synthesis, crystal structure and characterization of [Er₂(C₄H₄O₄)₃(H₂O)₄]·6H₂O, with particular emphasis on the structural details and the vibrational behavior of the highly organized sub-net of water are reported. X-ray structural analysis reveals that the hybrid framework, which can be classified as belonging to the I⁰O² type, acts as a host of an infinite tape of six-membered water rings with distorted chair conformation. The water network extends between the hybrid layers helping the close packing and the stabilization of the structure through H-bond interactions, with further development of the supramolecular tridimensional structure. The self-assembly of the hydration water molecules is conditioned by the hybrid host, forcing them to adopt a less stable conformation when compared with hexagonal ice. The vibrational spectra of partially and completely dehydrated samples as well as of partially isotopic diluted ones have been obtained and analyzed. In order to guide the assignment of the vibrational spectra a theoretical calculation was performed at the B3LYP/6-31G^∗∗ level for a model consisting of three water clusters.     

Weak intramolecular interactions as controlling factors in the diastereoselective formation of 3-phosphinoxido- and 3-phosphono-1,2,3,6-tetrahydrophosphinine 1-oxides

A series of 3-phosphinoxido-and 3-phosphono-1,2,3,6-tetrahydrophosphinine oxides was synthesized by the diastereoselective addition of diphenylphosphine oxide and dialkyl phosphites to the α,β-double-bond of 1,2-dihydrophosphinine oxides. Further refunctionalizations led to a 3-P(O)(OH)₂ derivative and to a disulfide. The conformation of the products was evaluated using the B3LYP/6-31+G^∗//B3LYP/3-21G^∗ method, validated by calculation for a simple tetrahydrophosphinine oxide with a known stereostructure. The preferred conformers of the 3-P(X)Z₂-tetrahydrophosphinine derivatives were among the twist-boat forms containing the exocyclic P-function in the axial position due to three kinds of favorable intramolecular interactions. Only the 3-P(O)(OH)₂ derivative was found to adopt a half-chair conformation as a consequence of intramolecular H-bonding.     

H and C NMR spectroscopy of 9-acridinones

The ¹H and ¹³C NMR spectra of 9-acridinone and its five derivatives dissolved in CDCl₃, CD₃CN and DMSO-d₆ were measured in order to reveal the influence of the constitution of the compounds and features of the solvents on chemical shifts and ¹H-¹H coupling constants. Experimental data were compared with theoretically predicted chemical shifts, on the GIAO/DFT level of theory, for DFT (B3LYP)/6-31G^∗∗ optimized geometries of molecules—also for four other 9-acridinones. This comparison helped to ascribe resonance signals in the spectra to relevant atoms and enabled revelation of relations between chemical shifts and physicochemical features of the compounds. It was found that experimentally or theoretically determined ¹H and ¹³C chemical shifts of selected atoms correlate with theoretically predicted values of dipole moments of the molecules, as well as bond lengths, atomic partial charges and energies of HOMO.     

Supramolecular Self-Assembly of β3-Peptides Mediated by Janus-Type Recognition Units

To gain mechanistic insights, natural systems with biochemical relevance are inspiring for the creation of new biomimetics with unique properties and functions. Despite progress in rational design and protein engineering, folding and intramolecular organization of individual components into supramolecular structures remains challenging and requires controlled methods. Foldamers, such as β-peptides, are structurally well defined with rigid conformations and suitable for the specific arrangement of recognition units. Herein, we show the molecular arrangement and aggregation of β³-peptides into a hexameric helix bundle. For this purpose, β-amino acid side chains were modified with cyanuric acid and triamino-s-triazine as complementary recognition units. The pre-organization of the β³-peptides leads these Janus molecule pairs into a hexameric arrangement and a defined rosette nanotube by stacking. The helical conformation of the subunits was indicated by circular dichroism spectroscopy, while the supramolecular arrangement was detected by dynamic light scattering and confirmed by high-resolution electrospray ionization mass spectrometry (ESI-HRMS).     

Highly diastereoselective preparation of anti-α,β-dialkyl β-amino acids containing natural α-amino acid side chains

An efficient synthesis of anti-2-alkyl β³-amino acids was developed starting from the fully protected β³-amino acids. The strategy allows the introduction of the side chain of natural α-amino acids such as Ala, Phe and Ser at the C-2 position, with high diastereoselectivity. The preparation of 2-methyliden-β³-amino acids is also reported. This methodology does not need the use of expensive chiral reagents and/or chiral auxiliaries, and leads to compounds with orthogonal protecting groups.     

Synthesis of Fmoc-protected aza-β-amino acids via reductive amination of glyoxylic acid

The reductive amination of glyoxylic acid, with a protected Fmoc hydrazine, has been developed as a simple and efficient method for the preparation of Fmoc-aza-β³-amino acid residues (aza-β³-aa). Anchoring on resin of these residues will be described as well as the synthesis of hybrid peptide.     

Positional screening and NMR structure determination of side-chain-to-side-chain cyclized β3-peptides

Many β-peptides fold in a 14-helical secondary structure in organic solvents, but similar 14-helix formation in water requires additional stabilizing elements. Especially the 14-helix stabilization of short β-peptides in aqueous solution is critical, due to the limited freedom for incorporating stabilizing elements. Here we show how a single lactam bridge, connecting two β-amino acid side-chains, can lead to high 14-helix character in short β(3)-peptides in water. A comparative study, using CD and NMR spectroscopy and structure calculations, revealed the strong 14-helix inducing power of a side-chain-to-side-chain cyclization and its optimal position on the β(3)-peptide scaffold with respect to pH and ionic strength effects. The lactam bridge is ideally incorporated in the N-terminal region of the β(3)-peptide, where it limits the conformational flexibility of the peptide backbone. The lactam bridge induces a 14-helical conformation in methanol and water to a similar extent. Based on the presented first high resolution NMR 3D structure of a lactam bridged β(3)-peptide, the fold shows a large degree of high order, both in the backbone and in the side-chains, leading to a highly compact and stable folded structure.