Probing the role of the C-H...O hydrogen bond stabilized polypeptide chain reversal at the C-terminus of designed peptide helices. Structural characterization of three decapeptides

The structural characterization in crystals of three designed decapeptides containing a double d-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val-(D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all l analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed alpha-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with (D)Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-H.O hydrogen bond between residue 4 C(alpha)H and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C(alpha) atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt alpha(L) conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-H.O hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.     

Hybrid peptide hairpins containing alpha- and omega-amino acids: conformational analysis of decapeptides with unsubstituted beta-, gamma-, and delta-residues at positions 3 and 8

The effects of inserting unsubstituted omega-amino acids into the strand segments of model beta-hairpin peptides was investigated by using four synthetic decapeptides, Boc-Leu-Val-Xxx-Val-D-Pro-Gly-Leu-Xxx-Val-Val-OMe: peptide 1 (Xxx=Gly), peptide 2 (Xxx=betaGly=betahGly=homoglycine, beta-glycine), peptide 3 (Xxx=gammaAbu=gamma-aminobutyric acid), peptide 4 (Xxx=deltaAva=delta-aminovaleric acid). 1H NMR studies (500 MHz, methanol) reveal several critical cross-strand NOEs, providing evidence for beta-hairpin conformations in peptides 2-4. In peptide 3, the NMR results support the formation of the nucleating turn, however, evidence for cross-strand registry is not detected. Single-crystal X-ray diffraction studies of peptide 3 reveal a beta-hairpin conformation for both molecules in the crystallographic asymmetric unit, stabilized by four cross-strand hydrogen bonds, with the gammaAbu residues accommodated within the strands. The D-Pro-Gly segment in both molecules (A,B) adopts a type II' beta-turn conformation. The circular dichroism spectrum for peptide 3 is characterized by a negative CD band at 229 nm, whereas for peptides 2 and 4, the negative band is centered at 225 nm, suggesting a correlation between the orientation of the amide units in the strand segments and the observed CD pattern.     

Conformational heterogeneity of tripeptides containing Boc-Leu-Aib as corner residues in the solid state

A critical analysis of single crystal X-ray diffraction studies on a series of terminally protected tripeptides containing a centrally positioned Aib (α-aminoisobutyric acid) residue has been reported. For the tripeptide series containing Boc-Ala-Aib as corner residues, all the reported peptides formed distorted type II β-turn structures. Moreover, a series of Phe substituted analogues (tripeptides with Boc-Phe-Aib) have also shown different β-turn conformations. However, the Leu-modified analogues (tripeptides with Boc-Leu-Aib) disrupt the concept of β-turn formation and adopt various conformations in the solid state. X-ray crystallography sheds some light on the conformational heterogeneity at atomic resolution.     

A series of chiral coordination polymers containing helicals assembled from a new chiral (R)-2-(4'-(4'-carboxybenzyloxy)phenoxy)propanoic acid: syntheses, structures and photoluminescent properties

Ten new chiral coordination polymers, namely, [Ni(L)(H(2)O)(2)] (1), [Co(L)(H(2)O)(2)] (2), [Cd(L)(H(2)O)] (3), [Cd(L)(phen)] (4), [Mn(2)(L)(2) (phen)(2)]·H(2)O (5), [Cd(2)(L)(2)(biim-4)(2)] (6), [Zn(2)(L)(2)(biim-4)(2)] (7), [Cd(L)(pbib)] (8), [Cd(L)(bbtz)] (9) and [Cd(L)(biim-6)] (10), where phen = 1,10-phenathroline, biim-4 = 1,1'-(1,4-butanediyl)bis(imidazole), pbib = 1,4-bis(imidazole-1-ylmethyl)benzene, bbtz = 1,4-bis(1,2,4-triazol-1-ylmethyl)benzene, biim-6 = 1,1'-(1,6-hexanedidyl)bis(imidazole), and H(2)L = (R)-2-(4'-(4'-carboxybenzyloxy)phenoxy)propanoic acid, have been synthesized under hydrothermal conditions. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by infrared spectra (IR), powder X-ray diffraction (PXRD), elemental analyses and thermogravimetric (TG) analyses. Compounds 1 and 2 exhibit similar 1D left-handed helical chains, which are further extended into 3D supramolecular structures through O-H···O hydrogen-bonding interactions, respectively. Compound 3 shows a 2D double-layer architecture containing helical chains. Compound 4 features two types of 2D undulated sheets with helical chains, which are stacked in an ABAB fashion along the c direction. Compound 5 possesses a 1D double chain ribbon structure containing unusual meso-helical chains, which is linked by π-π interactions into a 2D supramolecular layer. These layers are further extended by hydrogen-bonding interactions to form a 3D supramolecular assembly. Compounds 6 and 7 are isostructural and exhibit 2D (4(4))-sql networks with helical chains. Neighboring sheets are further linked by C-H···O hydrogen-bonding interactions to generate 3D supramolecular architectures. Compounds 8-10 are isostructural and display 3D 3-fold interpenetrating diamond frameworks with helical chains. The effects of coordination modes of L anions, metal ions and N-donor ligands on the structures of the coordination polymers have been discussed. The luminescent properties of 3, 4 and 6-10 have also been investigated in detail.     

Local protein backbone folds determined by calculated NMR chemical shifts

NMR chemical shifts (CSs: δN(NH), δC(α), δC(β), δC', δH(NH), and δH(α)) were computed for the amino acid backbone conformers (α(L), β(L), γ(L), δ(L), ε(L), α(D), γ(D), δ(D), and ε(D) [Perczel et al., J Am Chem Soc 1991, 113, 6256]) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single β-strands, hairpins with type I and II β-turns, as well as double- and triple-stranded β-sheet models. The so-called "capping effect" was analyzed: residues at the termini of a homoconformer sequence unit usually have different CSs than the central residues of an adequately long homoconformer model. In heteroconformer sequences capping effect ruins the direct applicability of several chemical shift types (δH(NH), δC', and δN(NH)) for backbone structure determination of the parent residue. Experimental δH(α), δC(α), and δC(β) values retrieved from protein database are in good agreement with the relevant computed data in the case of the common backbone conformers (α(L), β(L), γ(L), and ε(L)), even though neighboring residue effects were not accounted for. Experimental and computed ΔδH(α)-ΔδC(α), ΔδH(α)-ΔδC(β), and ΔδC(α)-ΔδC(β) maps give qualitatively the same picture, that is, the positions of the backbone conformers relative to each other are very similar. This indicates that the H(α), C(α), and C(β) chemical shifts of alanine depend considerably on the backbone fold of the parent residue also in proteins. We provide tabulated CSs of the chiral amino acids that may predict the various structures of the residues.     

Characterization of Nα-Fmoc-protected dipeptide isomers by electrospray ionization tandem mass spectrometry (ESI-MS(n)): effect of protecting group on fragmentation of dipeptides

A series of positional isomeric pairs of Fmoc-protected dipeptides, Fmoc-Gly-Xxx-OY/Fmoc-Xxx-Gly-OY (Xxx=Ala, Val, Leu, Phe) and Fmoc-Ala-Xxx-OY/Fmoc-Xxx-Ala-OY (Xxx=Leu, Phe) (Fmoc=[(9-fluorenylmethyl)oxy]carbonyl) and Y=CH(3)/H), have been characterized and differentiated by both positive and negative ion electrospray ionization ion-trap tandem mass spectrometry (ESI-IT-MS(n)). In contrast to the behavior of reported unprotected dipeptide isomers which mainly produce y(1)(+) and/or a(1)(+) ions, the protonated Fmoc-Xxx-Gly-OY, Fmoc-Ala-Xxx-OY and Fmoc-Xxx-Ala-OY yield significant b(1)(+) ions. These ions are formed, presumably with stable protonated aziridinone structures. However, the peptides with Gly- at the N-terminus do not form b(1)(+) ions. The [M+H](+) ions of all the peptides undergo a McLafferty-type rearrangement followed by loss of CO(2) to form [M+H-Fmoc+H](+). The MS(3) collision-induced dissociation (CID) of these ions helps distinguish the pairs of isomeric dipeptides studied in this work. Further, negative ion MS(3) CID has also been found to be useful for differentiating these isomeric peptide acids. The MS(3) of [M-H-Fmoc+H](-) of isomeric peptide acids produce c(1)(-), z(1)(-) and y(1)(-) ions. Thus the present study of Fmoc-protected peptides provides additional information on mass spectral characterization of the dipeptides and distinguishes the positional isomers.     

Intestinal permeability of cyclic peptides: common key backbone motifs identified

Insufficient oral bioavailability is considered as a key limitation for the widespread development of peptides as therapeutics. While the oral bioavailability of small organic compounds is often estimated from simple rules, similar rules do not apply to peptides, and even the high oral bioavailability that is described for a small number of peptides is not well understood. Here we present two highly Caco-2 permeable template structures based on a library of 54 cyclo(-D-Ala-Ala(5)-) peptides with different N-methylation patterns. The first (all-trans) template structure possesses two β-turns of type II along Ala(6)-D-Ala(1) and Ala(3)-Ala(4) and is only found for one peptide with two N-methyl groups at D-Ala(1) and Ala(6) [(NMe(1,6)]. The second (single-cis) template possesses a characteristic cis peptide bond preceding Ala(5), which results in type VI β-turn geometry along Ala(4)-Ala(5). Although the second template structure is found in seven peptides carrying N-methyl groups on Ala(5), high Caco-2 permeability is only found for a subgroup of two of them [NMe(1,5) and NMe(1,2,4,5)], suggesting that N-methylation of D-Ala(1) is a prerequisite for high permeability of the second template structure. The structural similarity of the second template structure with the orally bioavailable somatostatin analog cyclo(-Pro-Phe-NMe-D-Trp-NMe-Lys-Thr-NMe-Phe-), and the striking resemblance with both β-turns of the orally bioavailable peptide cyclosporine A, suggests that the introduction of bioactive sequences on the highly Caco-2 permeable templates may result in potent orally bioavailable drug candidates.     

A new peptide motif in the formation of supramolecular double helices

The single crystal X-ray diffraction studies of a new tripeptide motif Boc-Tyr-Aib-Xaa-OMe (Xaa = Leu/Ile/Ala) reveal that the peptides adopt β-turn conformations which self-assemble to form a supramolecular double helical structure using various non-covalent interactions in the solid state and the peptides exhibit a type-III N(2) sorption isotherm.     

Hybrid peptides: expanding the beta turn in peptide hairpins by the insertion of beta-, gamma-, and delta-residues

The beta turn segment in designed peptide hairpins has been expanded by the insertion of beta-, gamma- and delta-amino acids at the i+2 position. The model octapeptides Boc-Leu-Phe-Val-DPro-Ac6c-Leu-Phe-Val-OMe (1), Boc-Leu-Phe-Val-DPro-beta3-Ac6c-Leu-Phe-Val-OMe (2), and Boc-Leu-Phe-Val-DPro-Gpn-Leu-Phe-Val-OMe (3) have been shown to adopt beta hairpin conformations in methanol by the observation of key diagnostic nuclear Overhauser effects. Boc-Leu-Val-Val-DPro-delta-Ava-Leu-Val-Val-OMe (4) adopts a beta hairpin conformation in crystals; this is stabilized by three cross-strand hydrogen bonds as demonstrated by X-ray diffraction. The canonical C10 turn in an alpha-alpha segment is expanded to C11, C12, and C13 turns in alpha-beta, alpha-gamma, and alpha-delta segments, respectively. The crystal structures of Piv-LPro-beta3-Ac6c-NHMe (5) and Boc-Ac6c-Gpn-Ac6c-OMe (6) reveal intramolecularly hydrogen-bonded C11 and C12 conformations, respectively. Computer modeling of octapeptide sequences that contain centrally positioned hybrid-turn segments, by using turn parameters derived from the structures of peptides 5 and 6, establishes the stereochemical acceptability of the beta hairpins in the cases of peptides 2 and 3. Accommodation of omega-amino acids into the turn segments is achieved by the adoption of gauche conformations around the backbone C--C bonds.     

β‐Turn Analogues in Model αβ‐Hybrid Peptides: Structural Characterization of Peptides Containing β2,2Ac6c and β3,3Ac6c Residues

The effect of gem‐dialkyl substituents on the backbone conformations of β‐amino acid residues in peptides has been investigated by using four model peptides: Boc‐Xxx‐β^2,2Ac₆c(1‐aminomethylcyclohexanecarboxylic acid)‐NHMe (Xxx=Leu ( 1 ), Phe ( 2 ); Boc=tert‐butyloxycarbonyl) and Boc‐Xxx‐β^3,3Ac₆c(1‐aminocyclohexaneacetic acid)‐NHMe (Xxx=Leu ( 3 ), Phe ( 4 )). Tetrasubstituted carbon atoms restrict the ranges of stereochemically allowed conformations about flanking single bonds. The crystal structure of Boc‐Leu‐β^2,2Ac₆c‐NHMe ( 1 ) established a C₁₁ hydrogen‐bonded turn in the αβ‐hybrid sequence. The observed torsion angles (α(?≈?60°, ψ≈?30°), β(?≈?90°, θ≈60°, ψ≈?90°)) corresponded to a C₁₁ helical turn, which was a backbone‐expanded analogue of the type III β turn in αα sequences. The crystal structure of the peptide Boc‐Phe‐β^3,3Ac₆c‐NHMe ( 4 ) established a C₁₁ hydrogen‐bonded turn with distinctly different backbone torsion angles (α(?≈?60°, ψ≈120°), β(?≈60°, θ≈60°, ψ≈?60°)), which corresponded to a backbone‐expanded analogue of the type II β turn observed in αα sequences. In peptide 4 , the two molecules in the asymmetric unit adopted backbone torsion angles of opposite signs. In one of the molecules, the Phe residue adopted an unfavorable backbone conformation, with the energetic penalty being offset by a favorable aromatic interaction between proximal molecules in the crystal. NMR spectroscopy studies provided evidence for the maintenance of folded structures in solution in these αβ‐hybrid sequences.     

Designed peptides with homochiral and heterochiral diproline templates as conformational constraints

Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a) isolated D-Pro-L-Pro segments which form type II' beta-turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II'-I (betaII'-I, consecutive beta-turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive beta-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa beta-turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5-->1 hydrogen bonded alpha-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx=L-Ala (19).     

Homochiral porous lanthanide phosphonates with 1D triple-strand helical chains: synthesis, photoluminescence, and adsorption properties

Four homochiral porous lanthanide phosphonates, [Ln(H2L)3].2H2O, (H3L = (S)-HO3PCH2-NHC4H7-CO2H, Ln = Tb (1), Dy (2), Eu (3), Gd (4)), have been synthesized under hydrothermal conditions. These compounds are isostructural, and they possess a 3D supramolecular framework built up from 1D triple-strand helical chains. Each of the helical chain consists of phosphonate groups bridging adjacent Ln(III) ions. The helical chains are stacked through hydrogen bonds to form 1D tubular channels along the c axis. Moreover, helical water chains are located in the 1D channels, and after removal of these water chains, the compounds exhibit selective adsorption capacities for N2, H2O, and CH3OH molecules. Compounds 1 and 3 show strong green and red fluorescent emissions, respectively, in the solid state at room temperature. Crystal data for 1: TbP3O17N3C18H37, tetragonal (No.76), space group P4(1), a = 12.4643(3) Angstrom, b = 12.4643(3) Angstrom, c = 18.7577(5) Angstrom, V = 2914.17(13) Angstrom(3), and Z = 4. For 2: DyP3O17N3C18H37, a = 12.4486(3) Angstrom, b = 12.4486(3) Angstrom, c = 18.7626(5) Angstrom, V = 2907.60(13) Angstrom(3), and Z = 4. For 3, EuP3O17N3C18H37, a = 12.4799(3) Angstrom, b = 12.4799(3) Angstrom, c = 18.8239(5) Angstrom, V = 2931.78(13) Angstrom(3), and Z = 4. For 4: GdP3O17N3C18H37, a = 12.4877(18) Angstrom, b = 12.4877(18) Angstrom, c = 18.824(4) Angstrom, V = 2935.5(8) Angstrom(3), and Z = 4.     

Supramolecular Structures with the 2‐Propyl‐4,5‐dicarboxy‐1H‐imidazole Ligand: Hydrothermal Synthesis,Structures, and Photoluminescence

Self‐assembly of the rigid organic ligand 2‐propyl‐4,5‐dicarboxy‐1H‐imidazole ( L ) with different metal ions (Zn²⁺, Ni²⁺, Cu²⁺, Cd²⁺) led to four new complexes, namely, [M( L )(phen)] [M = Zn ( 1 ); Ni ( 2 ); Cd ( 3 )] and [Cu( L )( 4 )] (phen = 1,10‐phenanthroline). Their structures were determined by single‐crystal X‐ray diffraction analyses, and they were further characterized by elemental analysis, IR spectroscopy, and thermogravimetric analysis. Whereas compounds 1 , 2 , and 3 are discrete units, hydrogen‐bonding interactions play a vital role in these complexes. Compounds 1 and 2 form one‐dimensional (1D) and two‐dimensional (2D) structures through hydrogen‐bondinginteractions with helical character. In 1 , the hydrogen bonds (O–H ··· O) alternately bridge the M^II cations of the discrete units to form a one‐dimensional (1D) infinite helical chain. Complex 2 forms a 2D helical layer through parallel hydrogen bonds (N/O–H ··· O/N) between two adjacent helical chains. In 3 , the hydrogen bonds (N–H ··· O) connect adjacent discrete units into a ten‐membered ring with extension into a one‐dimensional double‐chain supramolecular structure. Complex 4 is a two‐dimensional gridlike (4,4) topological layer which is extended to a 3D network by hydrogen bonding. The solid‐state fluorescence spectrum of complex 3 was determined.     

Gas-phase models of gamma turns: effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry

The conformations of laser-desorbed jet-cooled short peptide chains Ac-Phe-Xxx-NH2 (Xxx=Gly, Ala, Val, and Pro) have been investigated by IR/UV double resonance spectroscopy and density-functional-theory (DFT) quantum chemistry calculations. Singly gamma-folded backbone conformations (betaL-gamma) are systematically observed as the most stable conformers, showing that in these two-residue peptide chains, the local conformational preference of each residue is retained (betaL for Phe and gamma turn for Xxx). Besides, beta turns are also spontaneously formed but appear as minor conformers. The theoretical analysis suggests negligible inter-residue interactions of the main conformers, which enables us to consider these species as good models of gamma turns. In the case of valine, two similar types of gamma turns, differing by the strength of their hydrogen bond, have been found both experimentally and theoretically. This observation provides evidence for a strong flexibility of the peptide chain, whose minimum-energy structures are controlled by side-chain/backbone interactions. The qualitative conformational difference between the present species and the reversed sequence Ac-Xxx-Phe-NH2 is also discussed.     

A bridge between pillared-layer and helical structures: a series of three-dimensional pillared coordination polymers with multiform helical chains

Rational self-assembly of a long V-shaped 3,3',4,4'-benzophenonetetracarboxylate (bptc) ligand and metal salts in the presence of linear bidentate ligand yield a series of novel pillared helical-layer complexes, namely, [Cu2(bptc)(bpy)2] (1), [M3(Hbptc)2(bpy)3(H2O)4].2 H2O (M = Fe(2) and Ni(3)), [Co2(bptc)(bpy)(H2O)].0.5 bpy (4), [Cd2(bptc)(bpy)(H2O)2].H2O (5), [Mn2(bptc)(bpy)1.5(H2O)3] (6) and [M2(bptc)(bpy)0.5(H2O)5].0.5 bpy (M = Mn(7), Mg(8) and Co(9), bpy=4,4'-bipyridine). Their structures were determined by single-crystal X-ray diffraction analyses and further characterized by elemental analyses, IR spectra, and thermogravimetric (TG) analyses. The structure of 1 consists of two types of chiral layers, one left-handed and the other right-handed, which are connected by bpy pillars to generate a novel 3D open framework featuring four distinct helical chains. Compounds 2 and 3 are isostructural and feature 3D structures formed from the interconnection of arm-shaped helical layers with bpy pillars. Compound 4 is a pillared helical double-layer complex containing four different types of helices, among which the nine-fold interwoven helices constructed from triple-stranded helical motifs are unprecedented. Compound 5 exhibits a novel 3D covalent framework which features nanosized tubular channels. These channels are built from helical layers pillared by bptc ligands. The structure of 6 is constructed from {Mn(bptc)(H2O)}n2n- layers, which consist of left- and right-handed helical chains, pillared by [Mn2(bpy)3(H2O)4]4+ complexes into a 3D framework. To the best of our knowledge, compounds 1-6 are the first examples of pillared helical-layer coordination polymers. Compounds 7-9 are isostructural and exhibit interesting 2D helical double-layer structures, which are constructed from {M(bptc)(H2O)2}n2n- ribbons cross-linked by [M2(bpy)(H2O)6]4+ complexes. Furthermore, the 3D supramolecular structures of 7-9 are similar to the 3D structure of 6, and the 2D structure of 7 can be transformed into the 3D structure of 6 at higher reaction temperature. By inspection of the structures of 1-9, it is believed that the V-shaped bptc ligand and V-shaped phthalic group of the bptc ligand are important for the formation of the helical structures. The magnetic behavior of compounds 1, 2, 4, 6, and 9 was studied and indicated the existence of antiferromagnetic interactions. Moreover, compound 5 shows intense photoluminescence at room temperature.     

The energy landscape of unsolvated peptides: the role of context in the stability of alanine/glycine helices

Ion mobility measurements have been used to examine the conformations present for unsolvated Ac-(AG)(7)A+H(+) and (AG)(7)A+H(+) peptides (Ac = acetyl, A = alanine, and G = glycine) over a broad temperature range (100-410 K). The results are compared to those recently reported for Ac-A(4)G(7)A(4)+H(+) and A(4)G(7)A(4)+H(+), which have the same compositions but different sequences. Ac-(AG)(7)A+H(+) shows less conformational diversity than Ac-A(4)G(7)A(4)+H(+); it is much less helical than Ac-A(4)G(7)A(4)+H(+) at the upper end of the temperature range studied, and at low temperatures, one of the two Ac-A(4)G(7)A(4)+H(+) features assigned to helical conformations is missing for Ac-(AG)(7)A+H(+). Molecular dynamics simulations suggest that the different conformational preferences are not due to differences in the stabilities of the helical states, but differences in the nonhelical states: it appears that Ac-(AG)(7)A+H(+) is more flexible and able to adopt lower energy globular conformations (compact random looking three-dimensional structures) than Ac-A(4)G(7)A(4)+H(+). The helix to globule transition that occurs for Ac-(AG)(7)A+H(+) at around 250-350 K is not a direct (two-state) process, but a creeping transition that takes place through at least one and probably several intermediates.     

A new molecular scaffold for the formation of supramolecular peptide double helices: the crystallographic insight

[structure: see text]. A series of water-soluble synthetic dipeptides (1-3) with an N-terminally located beta-alanine residue, beta-alanyl-l-valine (1), beta-alanyl-l-isoleucine (2), and beta-alanyl-l-phenylalanine (3), form hydrogen-bonded supramolecular double helices with a pitch length of 1 nm, whereas the C-terminally positioned beta-alanine containing dipeptide (4), l-phenylalanyl-beta-alanine, does not form a supramolecular double helical structure. beta-Ala-Xaa (Xaa = Val/Ile/Phe) can be regarded as a new motif for the formation of supramolecular double helical structures in the solid state.     

Coordination chemistry of conformation-flexible 1,2,3,4,5,6-cyclohexanehexacarboxylate: trapping various conformations in metal-organic frameworks

To study the conformations of 1,2,3,4,5,6-cyclohexanehexacarboxylic acid (H(6)L), eleven new coordination polymers have been isolated from hydrothermal reactions of different metal salts with 1e,2a,3e,4a,5e,6a-cyclohexanehexacarboxylic acid (3e+3a, H(6)L(I)) and characterized. They are [Cd(12)(mu(6)-L(II))(mu(10)-L(II))(3)(mu-H(2)O)(6)(H(2)O)(6)]16.5 H(2)O (1), Na(12)[Cd(6)(mu(6)-L(II))(mu(6)-L(III))(3)]27 H(2)O (2), [Cd(3)(mu(13)-L(II))(mu-H(2)O)] (3), [Cd(3)(mu(6)-L(III))(2,2'-bpy)(3)(H(2)O)(3)]2 H(2)O (4), [Cd(4)(mu(4)-L(VI))(2)(4,4'-Hbpy)(4)(4,4'-bpy)(2)(H(2)O)(4)]9.5 H(2)O (5), [Cd(2)(mu(6)-L(II))(4,4'-Hbpy)(2)(H(2)O)(10)]5 H(2)O (6), [Cd(3)(mu(11)-L(VI))(H(2)O)(3)] (7), [M(3)(mu(9)-L(II))(H(2)O)(6)] (M=Mn (8), Fe (9), and Ni (10)), and [Ni(4)(OH)(2)(mu(10)-L(II))(4,4'-bpy)(H(2)O)(4)]6 H(2)O (11). Three new conformations of 1,2,3,4,5,6-cyclohexanehexacarboxylate, 6e (L(II)), 4e+2a (L(III)) and 5e+1a (L(VI)), have been derived from the conformational conversions of L(I) and trapped in these complexes by controlling the conditions of the hydrothermal systems. Complexes 1 and 2 have three-dimensional (3D) coordination frameworks with nanoscale cages and are obtained at relatively low temperatures. A quarter of the L(I) ligands undergo a conformational transformation into L(II) while the others are transformed into L(III) in the presence of NaOH in 2, while all of the L(I) are transformed into L(II) in the absence of NaOH in 1. Complex 3 has a 3D condensed coordination framework, which was obtained under similar reaction conditions as 1, but at a higher temperature. The addition of 2,2'-bipyridine (2,2'-bpy) or 4,4'-bipyridine (4,4'-bpy) to the hydrothermal system as an auxiliary ligand also induces the conformational transformation of H(6)L(I). A new L(VI) conformation has been trapped in complexes 4-7 under different conditions. Complex 4 has a 3D microporous supramolecular network constructed from a 2D L(III)-bridged coordination layer structure by pi-pi interactions between the chelating 2,2'-bpy ligands. Complexes 5-7 have different frameworks with L(II)/L(VI) conformations, which were prepared by using different amounts of 4,4'-bpy under similar synthetic conditions. Both 5 and 7 are 3D coordination frameworks involving the L(VI) ligands, while 6 has a 3D microporous supramolecular network constructed from a 2D L(II)-bridged coordination layer structure by interlayer N(4,4'-Hbpy)--HO(L(II)) hydrogen bonds. 3D coordination frameworks 8-11 have been obtained from the H(6)L(I) ligand and the paramagnetic metal ions Mn(II), Fe(II), and Ni(II), and their magnetic properties have been studied. Of particular interest to us is that two copper coordination polymers of the formulae [{Cu(II) (2)(mu(4)-L(II))(H(2)O)(4)}{Cu(I) (2)(4,4'-bpy)(2)}] (12 alpha) and [Cu(II)(Hbtc)(4,4'-bpy)(H(2)O)]3 H(2)O (H(3)btc=1,3,5-benzenetricarboxylic acid) (12 beta) resulted from the same one-pot hydrothermal reaction of Cu(NO(3))(2), H(6)L(I), 4,4'-bpy, and NaOH. The Hbtc(2-) ligand in 12 beta was formed by the in situ decarboxylation of H(6)L(I). The observed decarboxylation of the H(6)L(I) ligand to H(3)btc may serve as a helpful indicator in studying the conformational transformation mechanism between H(6)L(I) and L(II-VI). Trapping various conformations in metal-organic structures may be helpful for the stabilization and separation of various conformations of the H(6)L ligand.     

Vibrational spectroscopic detection of H-bonded β- and γ-turns in cyclic peptides and glycopeptides

The conformation of N-glycoproteins and N-glycopeptides has been the subject of many spectroscopic studies over the past decades. However, except for some preliminary data, no detailed study on the vibrational spectroscopy of glycosylated peptides has been published until recently.

This paper reports FTIR spectroscopic properties in DMSO and TFE of the N-glycosylated cyclic peptides cyclo[Gly-Pro-Xxx(GlcNAc)-Gly-δ-Ava] 3a and 3b in comparison with data on the non-glycosylated parent peptides cyclo(Gly-Pro-Xxx-Gly-δ-Ava) 2a and 2b [a, Xxx = Asn; b, Xxx = Gln; δ-Ava = NH-(CH₂)₄-CO] and N-acetyl 2-acetamido-2-deoxy-β- -gluco pyranosylamine (GlcNAc-NHAc, 4). The assignment of amide I band frequencies to conformation is based on ROESY experiments and determination of the temperature coefficients in DMSO-d₆ solution. (For the synthesis and NMR characterization of 2a and 3a see Ref. [19].)

Cyclic peptides are expected to adopt folded (β- and/or γ-turn) conformations which may be fixed by intramolecular H-bonding(s). A comparison of the temperature coefficients of the NH protons and amide I band frequencies and intensities suggests that in DMSO there is no significant difference in the backbone conformation and H-bond system of the N-glycosylated models and their parent cyclic peptides. The common feature of the backbone conformation of models 2 and 3 is the predominance of a 1 ← 4 (C₁₀) H-bonded type II β-turn encompassing Pro-Xxx or Pro-Xxx(GlcNAc), respectively. The ROESY connectivities in the Asn(GlcNAc) model (3a) have not been found to reflect intramolecular H-bondings between the peptide and the sugar.

The unique feature of the FTIR spectra in DMSO of the cyclic models is the lack or weakness of low-frequency (< 1640 cm⁻¹) amide I component bands. In TFE the amide I region of the FTIR spectra shows an increased number of components below 1650 cm⁻¹ reflecting a mixture of open and H-bonded β- and γ-turn conformers.

Because of its destabilizing effect upon γ-turns and other weakly H-bonded structures, DMSO decreases the number of backbone conformers. DMSO also destroys side-chain-backbone H-bondings of type C₇, C₆ or C₈. Possible ‘glyco’ C₇ H-bondings in GlcNAc-NHAc (4) or in glycopeptides 3a and 3b cannot resist the effect of DMSO either.

The FTIR data in TFE of models 2–4 suggest that the acceptor amide group of strong C₇ H-bondings in peptides and glycopeptides absorbs at 1630 ± 5 cm⁻¹ and that of bifurcated H-bondings between 1600–1620 cm⁻¹.     

1H,89Y HMQC and Further NMR Spectroscopic and X‐ray Diffraction Investigations on Yttrium‐Containing Complexes Exhibiting Various Nuclearities

2D ¹H,⁸⁹Y heteronuclear shift correlation through scalar coupling has been applied to the chemical‐shift determination of a set of yttrium complexes with various nuclearities. This method allowed the determination of ⁸⁹Y NMR data in a short period of time. Multinuclear NMR spectroscopy as function of temperature, PGSE NMR‐diffusion experiments, heteronuclear NOE measurements, and X‐ray crystallography were applied to determine the structures of [Y₅(OH)₅(L ‐Val)₄(Ph₂acac)₆] ( 1 ) (Ph₂acac=dibenzoylmethanide, L ‐Val=L ‐valine), [Y( 2 )(OTf)₃] ( 3 ), and [Y₂( 4 )(OTf)₅] ( 5 ) ( 2 : [(S)P{N(Me)N?C(H)Py}₃], 4 : [B{N(Me)N?C(H)Py}₄]^?) in solution and in the solid state. The structures found in the solid state are retained in solution, where averaged structures were observed. NMR diffusion measurements helped us to understand the nuclearity of compounds 3 and 5 in solution. ¹H,¹⁹F HOESY and ¹⁹F,¹⁹F EXSY data revealed that the anions are specifically located in particular regions of space, which nicely correlated with the geometries found in the X‐ray structures.