Conformational preferences and self-template macrocyclization of squaramide-based foldable modules

Secondary squaramides have considerable potential as hydrogen bond donors and acceptors. In CHCl(3) both, anti- and syn-squaramide rotamers are observed by NMR. The energetic barrier for anti/syn mutual interconversion determined by complete band shape analysis is approximately 63 kJ mol(-1). As in proline derivatives, a low rotational barrier is crucial for the design of foldable modules. In this paper, folding based on the low rotational barrier of squaramides is driven by donor atoms (N or O) located in the gamma position of an alkyl chain of a secondary squaramide. We demonstrate that the resulting minimal module exists as a folded conformer through the formation of a nine-membered ring stabilized by intramolecular hydrogen bonding. Molecular mechanics calculations and NMR studies support the existence of these folded conformers. The intramolecularly hydrogen bonded conformers are clearly visible even in CHCl(3)-EtOH mixtures. Folding occurs even in pure ethanol. As an indirect test, we studied the effectiveness of macrocyclization reactions in pure ethanol that require an effective templating effect to take place. The high yields obtained support the dominant role of a folded conformer even in this solvent.     

A 1,4-diphenyl-1,2,3-triazole-based β-turn mimic constructed by click chemistry

A series of 1,4-diphenyl-1,2,3-triazole-incorporated amide derivatives have been designed and prepared. X-ray crystallographic and (1D and 2D) (1)H NMR studies reveal that these compounds fold into stable U-shaped conformations driven by three-center intramolecular C-H···O hydrogen-bonding formed between the triazole C-5 H atom and the two ether O atoms. Such folded structures make this 1,4-diphenyl-1,2,3-triazole skeleton a good candidate to be used as β-turn mimic. To prove this, the formation of a β-hairpin structure induced by this β-turn motif has been further demonstrated.     

含氟β-二酮类化合物在质子溶剂中光稳定机理的研究

本工作利用吸收光谱及核磁共振氢谱的方法对两种含-CF₃基的β-二酮类化合物在质子溶剂中引起分子内氢键的破坏,缩醛化的发生及其动力学等进行了研究。工作探讨了光照使缩醛化产物回复至原有的分子内氢键结构以及回复后体系在暗场下继续进行缩醛化的过程,虽然光照使缩醛化产物破坏的原因尚待进一步研究,但这类含有-CF₃基的β-二酮类化合物在光照条件下能回复到含有分子内氢键的体系,这一特性可使这类化合物用作一种能在质子溶剂中应用的光稳定剂。其光稳定能力在本工作中已被证实。     

Phe-Ala-based diazaspirocyclic lactam as nucleator of type II' β-turn

The synthesis of a novel Phe-Ala dipeptide mimic, built up on a diazaspirocyclic lactam core, is presented. This new scaffold was evaluated for conformational mimicry of reverse turn by combining molecular modeling, IR, NMR, and X-ray diffraction experiments. All these tools agree on the presence of a strong intramolecular hydrogen bond, thus demonstrating the ability of this spiro compound to act as a type II' β-turn inducer.     

Synthesis and conformational studies of 3,4-di-O-acylated furanoid sugar amino acid-containing analogs of the receptor binding inhibitor of vasoactive intestinal peptide

Structural analysis of the di-O-caprylated Gaa-containing analog of the receptor binding inhibitors of vasoactive intestinal peptide by various NMR techniques and constrained molecular dynamics (MD) simulation studies established a well-defined β-turn structure in DMSO-d₆ with an intramolecular hydrogen bond between TyrNH → MetCO.     

Preparation, solid-state characterization, and computational study of a crown ether attached to a squaramide

[structure: see text] Crystals of a disecondary squaramide covalently linked to a crown ether presents a great variety of inter- and intramolecular nonbonded interactions including C-H/pi contacts, C-H...O and N-H...O hydrogen bonds, and pi-pi stacking between squaramide rings. Latter interaction, the stacking between squaramide rings, can be considered as an experimental evidence for the proposed aromaticity of squaramide when it is forming hydrogen bonds, either as acceptor or donor.     

1′-Acetylferrocene amino acid esters and amides. A simple model for parallel β-helical peptides

In this study we present a synthesis and conformational analysis of 1′-acetylferrocene amino acid derivatives of type Ac–Fn–CO–AA–Y (Fn=ferrocene-1,1-diyl; AA=Gly, Ala or Val; Y=OMe or NHMe) as a simple model for parallel β-helical peptides. Derivatives with only one amino acid adopt a reduced number of total conformations and allow a more exact analysis of intramolecular hydrogen bonds (IHB) close to the ferrocene unit. Conformational analysis of these bioconjugates was performed by a combination of spectroscopic techniques (IR, NMR and CD) and corroborated by solution-phase DFT calculations. The investigation of ester conjugates 1–3 indicates the coexistence of non-bonded (an open forms) and hydrogen bonded NH_a group forming a 7-membered ring (γ-turn). The amide derivatives 4–6 with an additional NH_b hydrogen bond donor are mostly constituted of conformers with a 10-membered ring (β-turn) as a single IHB pattern or the β-turn accompanied by a 7-membered ring (γ-turn) containing NH_a group. The exchange of the amino acid side-chain does not significantly affect the conformational properties and IHB pattern of the studied conjugates 1–6.     

Stabilization of β-turn conformations in Pro-X sequences by disulphide bridging. Synthesis and solution conformations of five cyclic cystine peptides

Five cyclic peptide disulphides of the type

have been synthesized, where X = Gly (1), L-Ala (2), D-Ala (3), Aib (4) and L-Leu (5). ¹H NMR studies at 270 MHz in CDCl₃ and (CD₃)₂SO provide evidence of a Pro-X β-turn conformation, stabilized by a transannular 4→1 hydrogen bond involving the Cys(4) NH, in all the peptides. In addition peptides 2, 4 and 5 also possess a second intramolecular hydrogen bond involving the -NHMe group. The spectroscopic data are consistent with a consecutive type III β-turn conformation for peptides 2, 4 and 5, a type I(III) β-turn structure for 1 and a type II turn for 3.     

Brønsted Base Catalyzed One‐Pot Synthesis of Stereodefined Six‐Member Carbocycles Featuring Transient Trienolates and a Key Intramolecular 1,6‐Addition

A catalyst‐driven one‐pot reaction sequence is developed for the enantio‐ and diastereoselective synthesis of tetrasubstituted cyclohexenes from simple unsaturated ketones or thioesters. The method involves a tertiary amine/squaramide‐catalyzed α‐selective addition of transiently generated trienolates to nitroolefins, subsequent base‐catalyzed double bond isomerization, and an intramolecular (vinylogous) 1,6‐addition reaction, a rare key carbocyclization step that proceeded with essentially perfect stereocontrol.     

Carbonyl groups as molecular valves to regulate chloride binding to squaramides

Environment-sensitive binding of anions to synthetic receptors is important for the functional mimicry of ion channels. We describe new squaramide-based chloride ion receptors whose anion binding cavity can be opened and closed by using carbonyl groups as valves. In nonpolar solvents, the carbonyls preclude chloride binding via intramolecular hydrogen bonding with the squaramide NHs. In polar solvents, disruption of the intramolecular hydrogen bonds reorients the carbonyl groups and opens the anion-binding cavity.     

m-Aminobenzoic acid inserted β-turn in acyclic tripeptides: a peptidomimetic design

X-ray diffraction studies show that peptides Boc-Leu-Aib-m-ABA-OMe (I) (Aib, α-aminoisobutyric acid; m-ABA, meta-aminobenzoic acid) and Boc-Phe-Aib-m-ABA-OMe (II) adopt a type-II β-turn conformation, solely stabilized by co-operative steric interactions amongst the amino acid residues. This type of β-turn without any intramolecular hydrogen bonding is generally referred to as an open turn. Although there are some examples of constrained cyclic peptides in which o-substituted benzenes have been inserted to mimic the turn region of the neurotrophin, a nerve growth factor, peptides I and II present novel two examples where m-aminobenzoic acid has been incorporated in the β-turn of acyclic tripeptides. The result also demonstrates the first crystallographic evidence of a β-turn structure containing an inserted m-aminobenzoic acid, which can be considered as a rigid γ-aminobutyric acid with an all-trans extended configuration.     

Carbohydrate intramolecular hydrogen bonding cooperativity and its effect on water structure

Molecular dynamics (MD) simulations combined with water-water H-bond angle analysis and calculation of solvent accessible surface area and approximate free energy of solvation were used to determine the influence of hydroxyl orientation on solute hydration and surrounding water structure for a group of chemically identical solutes-the aldohexopyranose sugars. Intramolecular hydrogen bond cooperativity was closely associated with changes in water structure surrounding the aldohexopyranose stereoisomers. The OH-4 group played a pivotal role in hydration as it was able to participate in a number of hydrogen bond networks utilizing the OH-6 group. Networks that terminated within the molecule (OH-4 --> OH-6 --> O-5) had relatively more nonpolar-like hydration than those that ended in a free hydroxyl group (OH-6 --> OH-4 --> OH-3). The OH-2 group modulated the strength of OH-4 networks through syndiaxial OH-2/4 intramolecular hydrogen bonding, which stabilized and induced directionality in the network. Other syndiaxial interactions, such as the one between OH-1 and OH-3, only indirectly affected water structure. Water structure surrounding hydrogen bond networks is discussed in terms of water-water hydrogen bond populations. The impact of syndiaxial versus vicinal hydrogen bonds is also reviewed. The results suggest that biological events such as protein-carbohydrate recognition and cryoprotection by carbohydrates may be driven by intramolecular hydrogen bond cooperativity.     

Synthesis of tetrahydroisoquinoline-based pseudopeptides and their characterization as suitable reverse turn mimetics

New peptidomimetics containing the Tic moiety were synthesized in enantiomerically pure form and their conformational features were studied by NMR, IR, and molecular modeling techniques. The presence of a reverse turn conformation was observed in all the structures, suggesting the key role of the scaffold as reverse turn inducer. In particular, all the analyses led to the conclusion that a β-turn conformation is mostly stabilized in tetrapeptide mimetic 4b and in hexapeptide mimetics 5a,b. In the case of 5a,b, the C1 stereochemistry plays a central role in determining stable conformations, supporting the formation of a β-hairpin arrangement with a 14-membered intramolecular hydrogen bond ring only in 5b.     

Isolated monohydrates of a model peptide chain: effect of a first water molecule on the secondary structure of a capped phenylalanine

The formation of monohydrates of capped phenylalanine model peptides, CH(3)-CO-Phe-NH(2) and CH(3)-CO-Phe-NH-CH(3), in a supersonic expansion has been investigated using laser spectroscopy and quantum chemistry methods. Conformational distributions of the monohydrates have been revealed by IR/UV double-resonance spectroscopy and their structures assigned by comparison with DFT-D calculations. A careful analysis of the final hydrate distribution together with a detailed theoretical investigation of the potential energy surface of the monohydrates demonstrates that solvation occurs from the conformational distribution of the isolated peptide monomers. The distribution of the monohydrates appears to be strongly dependent on both the initial monomer conformation (extended or folded backbone) and the solvation site initially occupied by the water molecule. The solvation processes taking place during the cooling can be categorized as follows: (a) solvation without significant structural changes of the peptide, (b) solvation inducing significant distortions of the backbone but retaining the secondary structure, and (c) solvation triggering backbone isomerizations, leading to a modification of the peptide secondary structure. It is observed that solvation by a single water molecule can fold a β-strand into a γ-turn structure (type c) or induce a significant opening of a γ-turn characterized by an elongated C(7) hydrogen bond (type b). These structural changes can be considered as a first step toward the polyproline II condensed-phase structure, illustrating the role played by the very first water molecule in the solvation process.     

Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding

Thioamides are sterically almost identical to their oxoamide counterparts, but they are weaker hydrogen bond acceptors. Therefore, thioamide amino acids are excellent candidates for perturbing the energetics of backbone-backbone H-bonds in proteins and hence should be useful in elucidating protein folding mechanisms in a site-specific manner. Herein, we validate this approach by applying it to probe the dynamic role of interstrand H-bond formation in the folding kinetics of a well-studied β-hairpin, tryptophan zipper. Our results show that reducing the strength of the peptide's backbone-backbone H-bonds, except the one directly next to the β-turn, does not change the folding rate, suggesting that most native interstrand H-bonds in β-hairpins are formed only after the folding transition state.     

NMR study of the influence of β-substituents on the intramolecular hydrogen bond in β-dicarbonyl compounds

The hydroxyl proton chemical shifts of β-dicarbonyl compounds involving various β-substituents have been studied. An additive influence of β-substituents on the δ_OH shift values has been found. The results obtained suggested the existence of only one potential proton energy minimum in the intramolecular hydrogen bond of the enol forms of the β-diketones. It has been shown that the enol forms of β-keto esters do not follow the additivity of the δ_OH values for the same substituents, which may be due to a change in the proton distribution potential function in the intramolecular hydrogen bond.     

The crystalline behavior of poly(L-lactide) induced by nucleating agents with amide structure: The effect of benzamide molecule symmetry

Amide nucleating agents have been reported to be effective in promoting poly(_L-lactide) (PLLA) crystallization, while few research efforts have focused on the structure–activity relationship of the nucleating agents which is one basic issue to develop new agents. In this work, three amide nucleating agents with different symmetry were designed and synthesized to investigate the effect of the symmetry of benzamide nucleating agents on PLLA crystallization. It is found that the C3 symmetric amide structure of N, N′, N″-tricyclohexyl-1,3,5-benzenetriamine (BTCA) agent can form a highly oriented structure by a triple hydrogen bond of π–π bond and benzene ring and can act as efficient nucleation sites. In addition, the strong intramolecular hydrogen bond with PLLA would further promote the crystallization of PLLA. In general, it is the self-assembled ability and intramolecular hydrogen bonding with PLLA affects the rate and degree of PLLA crystallinity, and we find the C3 symmetric amide structure exhibits the best performance.     

Time-resolved infrared spectroscopy of thiopeptide isomerization and hydrogen-bond breaking

The photoisomerization of the protected tetrathioxopeptide Boc-Ala-Gly(=S)-Ala-Aib-OMe was followed using time-resolved infrared spectroscopy in the amide I region in combination with isotope labeling. In acetonitrile at room temperature, approximately half of the molecules are found in a loop conformation, restrained by an intramolecular hydrogen bond, while the other half adopts more extended conformations. UV-excitation of the thioxopeptide unit immediately weakens the intramolecular hydrogen bond. After the molecules have relaxed to the electronic ground state with a 130 ps time-constant, a delayed re-formation of the intramolecular hydrogen bond is observed for molecules returning to the initial trans conformation of the thioamide bond, while the loop structure is permanently broken when the molecules isomerize to the cis conformation.     

Synthesis of 3,4-di-O-acylated glucose-derived furanoid sugar amino acids (Gaa): conformational analysis of a Leu-enkephalin analog containing di-O-myristoylated Gaa

3,4-Di-O-acylated derivatives 1-3 of a glucose-derived furanoid sugar amino acid (Gaa) were synthesized as novel peptide building blocks to study their effects on peptide conformation. Structural analysis of the di-O-myristoylated Gaa 3-containing Leu-enkephalin analog 4 by various NMR techniques and constrained molecular dynamics (MD) simulation studies established a well-defined β-turn structure in DMSO-d₆ with an intramolecular hydrogen bond between PheNH → TyrCO.     

A C-N insertion of β-lactam to benzyne: unusual formation of acridone

Intermolecular insertion of benzyne into the C-N bond of a β-lactam is described. This σ-insertion is followed by ring expansion that produces dihydroquinolinone, which rapidly reacts with an additional benzyne unit to afford an acridone through intramolecular C-C bond formation to the carbonyl group and rapid elimination of ethylene.