Aromatic δ-peptides: design, synthesis and structural studies of helical, quinoline-derived oligoamide foldamers

Oligoamides of 8-amino-4-isobutoxy-2-quinolinecarboxylic acid were designed and synthesized, and their helical structures were characterized in the solid state by single crystal X-ray diffraction, and in solution by ¹H NMR. The monomer methyl 4-isobutoxy-8-nitro-2-quinolinecarboxylate is easily prepared in three steps from 2-nitroaninile and dimethyl acetylene dicarboxylate. Successive hydrogenations of nitro groups, saponifications of esters and couplings of amines and acids via the acid chlorides gave a dimer, tetramer, hexamer, octamer, and decamer in a convergent fashion. The oligomers were shown to adopt a bent conformation stabilized by intramolecular hydrogen bonds between amide hydrogens and adjacent quinoline nitrogens. In the solid, the dimer adopts a planar crescent shape and the octamer a helical conformation. All NMR data are consistent with similar conformations in solution. The helices are apparently remarkably stable. Some of them remain helical even at 120°C in deuterated DMSO. The structural studies confirm the predictions made by computer and demonstrate the high potency of the design principles.     

Bend ribbon-forming tetrahydrofuran amino acids

Short oligomeric chains of C-glycosyl beta-D-arabinofuranose configured tetrahydrofuran amino acids (where the C-2 and C-5 substituents of the tetrahydrofuran ring are cis to each other) exhibit a well-defined repeating turn secondary structure stabilised by (i, i - 2) inter-residue hydrogen bonds. This is in contrast to the epimeric alpha-D-arabinofuranose oligomer (where the C-2 and C-5 substituents of the tetrahydrofuran ring are trans to each other) in which there is no indication of any secondary structure in solution.     

Tetrahydrofuran Calpha-tetrasubstituted amino acids: two consecutive beta-turns in a crystalline linear tripeptide

The synthesis of tetrahydrofuran Calpha-tetrasubstituted amino acids (TAAs) and their effect on the conformation in small peptides are reported. The synthesis starts from the protein amino acid methionine, which is protected at the C and N terminus and converted into the corresponding sulfonium salt by alkylation. Simple base treatment in the presence of an aryl aldehyde leads to the formation of tetrahydrofuran tetrasubstituted Calpha-amino acids in a highly diastereoselective (trans/cis ratio up to 97:3) reaction with moderate to good yields (35-78%) depending on the aldehyde used. Palladium-catalyzed coupling reactions allow a subsequent further functionalization of the TAA. The R,S,S-TAA-Ala dipeptide amide adopts a beta-turn type I conformation, whereas its S,R,S isomer does not. The R,S,S-Gly-TAA-Ala tripeptide amide shows in the solid state and in solution a conformation of two consecutive beta-turn type III structures, stabilized by i+3-->i intramolecular hydrogen bonds.     

N,N′-二[3-氯-5S-(l-孟氧基)-2(5H)-4-呋喃酮基]-1,4-丁二胺的合成及晶体结构(英文)

合成了N,N′-二[3-氯-5S-(l-孟氧基)-2(5H)-4-呋喃酮基]-1,4-丁二胺,并通过IR,1H NMR,MS和X射线单晶衍射对其进行了表征.X射线单晶衍射结果表明:标题化合物的不对称结构单元中包含一个平面的呋喃酮环和一个椅式的环己烷环,四个手性中心.标题化合物通过N—H…O分子间氢键作用实现空间堆积.     

Conformation of the piperidine ring: Part IV. Investigations of 4-tert-butyl-4-hydroxy-2,2,6,6-tetramethylpiperidine derivatives*

Methods of synthesis of 4-tert-butyl-4-hydroxy-2,2,6,6-tetramethylpiperidine(1), 4-tert-butyl-4-hydroxy-1,2,2,6,6-pentamethylpiperidine (2) and 4-tert-butyl-4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl(3) are described. Interaction of the axial hydroxyl group with axial methyl groups in a chair form of these compounds causes a downfield shift of the methyl proton NMR signal of about 0.2 ppm. IR spectra of 1 and 2 indicate a considerable contribution in solution of non-chair forms stabilized by intramolecular hydrogen bonds. In 3 only intermolecular hydrogen bonds were found. The crystal and molecular structure of 2 have been determined by direct methods and refined to R = 0.0468. The molecules exist in the solid state in a chair conformation only. Van der Waals interactions of bulky substituents hinder a close approach of neighbouring molecules necessary for the formation of intermolecular hydrogen bonds.     

Synthesis of newN-acylantipyrylureas and the crystal structure ofN-benzoyl-N′-[4-(2,3-dimethyl-1-phenylpyrazol-5-one)]urea

New derivatives of acylheterylureas were synthesized by reactions of acylisocyanates with 4-amino-2,3-dimethyl-l-phenylpyrazol-5-one. The structures of the compounds obtained have been established by IR and¹H NMR spectroscopy.N-Benzoyl-N′-[4-(1-phenyl-2,3-dimethylpyrazol-5-one)]urea has been studied by X-ray structural analysis. It was found that the molecule adopts ananti-syn conformation stabilized by an intermolecular hydrogen bond. In the crystal, molecules are linked in centrosymmetric dimers via intermolecular hydrogen bonds.     

Origin of chiral selectivity in gas-phase serine tetramers

Serine "magic-number" clusters have attracted substantial experimental and theoretical interest since their discovery. Serine undergoes marked chiral enrichment upon sublimation, which has been associated with the homochiral selectivity of the octamer. This process has been implicated in one possible mechanism leading to the origin of biological homochirality. While the octamer is the best known of the serine clusters, here we focus on the tetramer, the smallest serine cluster known to exhibit homochiral preference. This choice is based on its greater simplicity and tractability with accessible computational resources. Basin-hopping molecular dynamics simulations coupled to density functional theory calculations yield a "structural landscape" for low-lying configurations on the potential energy surface. The full range of enantiomeric compositions and charge states is investigated. Global energy minimum serine tetramers consist of a cage structure bonded by zwitterionic terminal groups. The participation of the serine hydroxyl side chains in hydrogen bonds with adjacent monomers drives the homochiral selectivity of serine tetramers. The configuration of the hydrogen bonding network is strongly dependent on enantiomeric composition and charge state. Smaller cations are incorporated into the center of the tetramer cage and effectively disable all side chain hydrogen bonding, while larger cations appear not to incorporate into the tetramer cage and are stabilized outside only in the homochiral case. The current theoretical data requires the introduction of a kinetic barrier to complete the model, limiting rearrangement from the basic cage configuration in some cases, which is discussed and probed directly by doubly-nudged elastic band transition state searches. These calculations elucidate a large barrier for reorganization of the cage, completing the theoretical understanding of the tetramers.     

N，N’-二[3-氯-5S-（l-孟氧基）-2（5H）-4-呋喃酮基]-1，4-丁二胺的合成及晶体结构

合成了N,N’-二[3-氯-5S-（l-孟氧基）-2（5H）-4-呋喃酮基]-1,4-丁二胺,并通过IR,^1H NMR,MS和X射线单晶衍射对其进行了表征．X射线单晶衍射结果表明：标题化合物的不对称结构单元中包含一个平面的呋喃酮环和一个椅式的环己烷环,四个手性中心．标题化合物通过N—H…O分子间氢键作用实现空间堆积．     

Dimeric molecular capsules under redox control

A new tetraferrocenylurea calix[4]arene was prepared in order to investigate its dimerization properties. 1H NMR spectroscopic data clearly established that this calixarene forms stable dimeric molecular capsules in chloroform solution. The dimeric capsules are stabilized by the formation of multiple hydrogen bonds between the urea functional groups on the calixarene upper rims. In the dimer, eight ferrocene groups are held in proximity to the "seam" of hydrogen bonds. Upon oxidation of the ferrocene residues, electrochemical, PGSE NMR, and IR spectroscopic data revealed that the hydrogen bonds are broken, leading to the dissociation of the dimeric molecular capsule.     

Molecular modeling study for a novel structured oligomer subunit selection: the example of 2-aminomethyl-phenyl-acetic acid

Oligomers derived from dipeptide mimics were selected by computational study for their suitability to fold in ordered structures. After selection of a monomeric unit, short oligomers were synthesized and analyzed by NMR and IR. Oligomers built from 2-aminomethyl-phenyl-acetic acid were shown to adopt a helical structure stabilized by 10-membered ring hydrogen bonds.     

Sterically and guest-controlled self-assembly of calix[4]arene derivatives

In solvents such as chloroform or benzene, tetraurea calix[4]arenes 1 form dimeric capsules in which one solvent molecule is usually included as guest. To explore the structural requirements for the formation of such hydrogen-bonded dimers we replaced one p-tolylurea residue by a simple acetamide function. The resulting calix[4]arene 2 a, substituted at its wide rim with one acetamide and three p-tolylurea functions, assumes a C(1)-symmetrical conformation in apolar solvents as shown by (1)H NMR, which is not compatible with the usual capsule. In the crystalline state, four molecules of 2 a, adopting a pinched cone conformation, assemble into a quasi S(4)-symmetrical tetramer stabilized by a cyclic array of 24 NH.O==C hydrogen bonds and four NH.pi interactions. Four acetamide groups are hydrogen-bonded to each other and pack tightly in the center of the assembly. All polar residues are buried inside the tetramer, the surface of which is lipophilic. Extensive NMR studies revealed similar structures in apolar solvents such as [D]chloroform or [D(6)]benzene for calixacetamides 2 a-c. The formation of these tetramers in solution is critically dependent on the size of the amide fragment, so that propionamide 2 d, butyramide 2 e, and p-tolylamide 2 f form only ill-defined aggregates. This is caused by steric crowding inside the tetrameric assembly. The tetramers persist during molecular dynamics simulations, and the optimized average structure of the MD run is similar to that found in the crystalline state. Theoretical studies revealed that cooperation of hydrogen bonds with multiple NH.pi, C--H.pi, and pi.pi attractions make the tetramer more stable than the capsular dimer with the solvent as guest. In the presence of tetraethylammonium salts, however, compounds 2 a-e form dimeric capsular assemblies, each incorporating a single ammonium cation. Only one of two possible regioisomeric dimers is formed, in which both acetamide groups are surrounded by two urea residues. These examples give striking evidence of how self-assembly in solution can be strongly dependent on subtle structural factors and of how the formation of dimeric capsules can be induced by the presence of an appropriate guest.     

A novel intramolecular hydrogen bonding between a side-chain pyridine ring and an amide hydrogen of the peptide backbone in tripeptides containing the new amino acid, alpha,alpha-di(2-pyridyl)glycine

Four tripeptides (Z-AA1-2Dpy-AA3-OMe; AA1, AA3 = Gly, Aib) containing a novel amino acid, alpha, alpha-di(2-pyridyl)glycine (2Dpy), were synthesized by the modified Ugi reaction. NMR analysis clearly indicated that the 2Dpy-containing tripeptides except the peptide in which AA1, AA3 = Aib, adopt a unique conformation with two intramolecular hydrogen bonds between 2Dpy-NH and a pyridine nitrogen and between AA3-NH and another pyridine nitrogen. This conformation has so far not been reported. On the other hand, the peptide Z-Aib-2Dpy-Aib-OMe probably adopts a beta-turn structure which is stabilized by two intramolecular hydrogen bonds between 2Dpy-NH and a pyridine nitrogen and between AA3-NH and the C=O of the Z group.     

The conformation of biliverdin in dimethyl sulfoxide: implications for the coordination with copper

Biliverdin (BV) structure was analyzed by using NMR techniques and unrestricted density function theory simulations to explain the incapacity of BV to build coordination complex(es) with Cu²⁺ in dimethyl sulfoxide, which was confirmed by UV-Vis, EPR and NMR spectroscopy. NMR showed that N atoms are protonated in all four pyrrole rings. The structure is stabilized by two hydrogen bonds between NH moieties and carbonyl oxygens from opposite terminal pyrrole rings, and by the bending of propionyl chain with carboxyl group out of the plain toward central position of BV. The simulations of deprotonated BV, which builds copper complexes in water and chloroform as described previously, showed a different conformation and organization of hydrogen bonds. Taking into account that deprotonation represents a critical step in coordinate bonds formation, the protonation of an additional N atom may represent a key difference between the interactions of BV with copper in different solvents.

     

Synthese photochimique et etude structurale d'alcoxy-spirocetals et de trioxa-bis-spirocetals

The spiroketal systems can be obtained easily by a Norrish type II reaction applied to tetrahydropyranic ketoacetals having a carbonyl group in δ position of the acetalic hydrogen. The structures of spirans and bispirans established by IR, NMR (¹H and ¹³C show an axial conformation for the C-O bond of the tetrahydrofuran ring. With the bispirans this anomeric effect requires for some isomers a twist boat conformation of the tetrahydropyran ring.     

Hydrogen Bonds, Tautomers, and Conformation in 2-Hydroxyphenyl 2-hydroxy-2-(β-naphthyl)vinyl Ketone

Single crystal X-ray diffraction and IR spectroscopy have been used to study the conformation of 2-hydroxyphenyl 2-hydroxy-2-(-naphthyl)vinyl ketone in solid state. It was found that one of the two possible enol tautomeric forms is stabilized in the crystal. The 1-hydroxy-3-oxo-1,3-propenylene moiety, O=C—CH=C—OH, shows a strong intramolecular H bond with a definite character of reasonance-assisted hydrogen bond in spite of being in competition with ring intermolecular hydrogen bonds. The comparison of the present results with solution NMR data indicates that the molecular geometry in solid state and in solution are similar.     

Ring-closing metathesis of olefinic peptides: design, synthesis, and structural characterization of macrocyclic helical peptides

Heptapeptides containing residues with terminal olefin-derivatized side chains (3 and 4) have been treated with ruthenium alkylidene 1 and undergone facile ring-closing olefin metathesis (RCM) to give 21- and 23-membered macrocyclic peptides (5 and 6). The primary structures of peptides 3 and 4 were based upon a previously studied heptapeptide (2), which was shown to adopt a predominantly 3(10)-helical conformation in CDCl(3) solution and an alpha-helical conformation in the solid state. Circular dichroism, IR, and solution-phase (1)H NMR studies strongly suggested that acyclic precursors 3 and 4 and the fully saturated macrocyclic products 7 and 8 also adopted helical conformations in apolar organic solvents. Single-crystal X-ray diffraction of cyclic peptide 8 showed it to exist as a right-handed 3(10)-helix up to the fifth residue. Solution-phase NMR structures of both acyclic peptide 4 and cyclic peptide 8 in CD(2)Cl(2) indicated that the acyclic diene assumes a loosely 3(10)-helical conformation, which is considerably rigidified upon macrocyclization. The relative ease of introducing carbon-carbon bonds into peptide secondary structures by RCM and the predicted metabolic stability of these bonds renders olefin metathesis an exceptional methodology for the synthesis of rigidified peptide architectures.     

Amino acid cluster formation studied by electrospray ionization mass spectrometry

The association properties of natural and non-natural amino acids were studied in detail using electrospray ionization mass spectrometry. The results show a highly diverse cluster formation behavior of amino acids. There are differences regarding the degree of clustering (average cluster size), the presence or absence of one or several 'magic' clusters of special stability and the influence of chirality on cluster stability. Cluster formation does not show a good correlation with simple physico-chemical properties (such as solubility), indicating that it is a specific process and not only a simple aggregation during evaporation/ionization. A systematic study of cluster formation of serine derivatives reveals that all functional groups play a prominent role in the binding of the magic octamer. The results support the idea of the zwitterionic character of the octamer. Electrospray ionization of the side-chain acetylated serine shows the formation of a very stable tetramer with a strong preference for homochirality. The results suggest that Ser8 is made up of two tetramer subunits, held together by hydrogen bonds of the side-chain.     

Preparation ofN-chloroacetyl-N′-arylsulfonylureas and the crystal structure ofN-chloroacetyl-N′-(4-methylphenylsulfonyl)urea

Novel arylsulfonylureas were prepared by the reaction of chloroacetyl isocyanate with arylsulfamides. The structures of the compounds synthesized were determined by IR and¹H NMR spectra. An X-ray structural analysis ofN-chloroacetyl-N-(4-methylphenylsulfonyl)urea was carried out. It was found that the molecule has theanti-syn conformation stabilized by an intramolecular H-bond. In the crystal, the molecules are combined into centrosymmetrical dimers by intermolecular hydrogen bonds. The compounds considered exhibit moderate fungicide activity.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1786–1788, October, 1994.     

Multiple conformational states in crystals and in solution in alphagamma hybrid peptides. Fragility of the C12 helix in short sequences

The conformational properties of foldamers generated from alphagamma hybrid peptide sequences have been probed in the model sequence Boc-Aib-Gpn-Aib-Gpn-NHMe. The choice of alpha-aminoisobutyryl (Aib) and gabapentin (Gpn) residues greatly restricts sterically accessible conformational space. This model sequence was anticipated to be a short segment of the alphagamma C12 helix, stabilized by three successive 4-->1 hydrogen bonds, corresponding to a backbone-expanded analogue of the alpha polypeptide 3(10)-helix. Unexpectedly, three distinct crystalline polymorphs were characterized in the solid state by X-ray diffraction. In one form, two successive C12 hydrogen bonds were obtained at the N-terminus, while a novel C17 hydrogen-bonded gamma alpha gamma turn was observed at the C-terminus. In the other two polymorphs, isolated C9 and C7 hydrogen-bonded turns were observed at Gpn (2) and Gpn (4). Isolated C12 and C9 turns were also crystallographically established in the peptides Boc-Aib-Gpn-Aib-OMe and Boc-Gpn-Aib-NHMe, respectively. Selective line broadening of NH resonances and the observation of medium range NH(i) <--> NH(i+2) NOEs established the presence of conformational heterogeneity for the tetrapeptide in CDCl3 solution. The NMR results are consistent with the limited population of the continuous C12 helix conformation. Lengthening of the (alphagamma) n sequences in the nonapeptides Boc-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Xxx (Xxx = Aib, Leu) resulted in the observation of all of the sequential NOEs characteristic of an alphagamma C12 helix. These results establish that conformational fragility is manifested in short hybrid alphagamma sequences despite the choice of conformationally constrained residues, while stable helices are formed on chain extension.     

Helical molecular duplex strands: multiple hydrogen-bond-mediated assembly of self-complementary oligomeric hydrazide derivatives

Careful examination of the X-ray structure of a ditopic hydrazide derivative 7 led to the concept that with malonyl groups as interhydrazide linkers hydrogen-bonding-mediated molecular duplex strands might be obtained. Complexation studies between 7, 8, and 9 confirmed this hypothesis. Two quadruple hydrogen-bonded heterodimers formed, in which spectator repulsive secondary electrostatic interaction was found to play an important role in determining the stability of the complexes. Extensive studies on 1-4 indicated that the hydrogen-bonding mode could persist in longer oligomeric hydrazide derivatives with chain extension from monomer to tetramer. Molecular duplex strands via two to fourteen interstrand hydrogen bonds were obtained. In addition to affecting the stability of the duplex strands, spectator repulsive secondary electrostatic interaction also played an important role in determining dynamic behavior of the duplex strands as exemplified by variable temperature (1)H NMR experiments. IR studies confirmed stronger hydrogen bonding in the longer oligomers. The assemblies of 1-4 on HOPG were also studied by STM technology. Molecular mechanical calculations further revealed double-helical structures for the longer oligomers. The results provide new opportunities for development of polymeric helical duplexes with well-defined structures.