Supramolecular helix and β-sheet through self-assembly of two isomeric tetrapeptides in crystals and formation of filaments and ribbons in the solid state

Single crystal X-ray diffraction studies show that the β-turn structure of tetrapeptide I, Boc-Gly-Phe-Aib-Leu-OMe (Aib: α-amino isobutyric acid) self-assembles to a supramolecular helix through intermolecular hydrogen bonding along the crystallographic a axis. By contrast the β-turn structure of an isomeric tetrapeptide II, Boc-Gly-Leu-Aib-Phe-OMe self-assembles to a supramolecular β-sheet-like structure via a two-dimensional (a, b axis) intermolecular hydrogen bonding network and π-π interactions. FT-IR studies of the peptides revealed that both of them form intermolecularly hydrogen bonded supramolecular structures in the solid state. Field emission scanning electron micrographs (FE-SEM) of the dried fibrous materials of the peptides show different morphologies, non-twisted filaments in case of peptide I and non-twisted filaments and ribbon-like structures in case of peptide II.     

Supramolecular double helix from capped γ-peptide

The single crystal X-ray diffraction study of capped γ-peptide reveal that the peptide adopts helical conformation which self-assemble to form a supramolecular parallel double helical structure using intermolecular hydrogen bonding as well as π-π stacking interactions in the solid state.     

Chirality organization of ferrocenes bearing podand dipeptide chains: synthesis and structural characterization

A variety of ferrocenes bearing podand dipeptide chains have been synthesized to form an ordered structure in both solid and solution states and have been investigated by 1H NMR, FT-IR, CD, and X-ray crystallographic analyses. Conformational enantiomerization through chirality organization was achieved by the intramolecular hydrogen bondings between the podand dipeptide chains. The single-crystal X-ray structure determination of the ferrocene 2 bearing the podand dipeptide chains (-D-Ala-D-Pro-OEt) revealed two C2-symmetric intramolecular hydrogen bondings between CO (Ala) and NH (another Ala) of each podand dipeptide chain to induce the chirality-organized structure. The molecular structures of the ferrocene 1 composed of the podand L-dipeptide chains (-L-Ala-L-Pro-OEt) and 2 are in a good mirror image relationship, indicating that they are conformational enantiomers. An opposite helically ordered molecular arrangement was formed in the crystal packing of 2 as compared with 1. The ferrocene 2 exhibited induced circular dichroism (CD), which appeared at the absorbance of the ferrocene moiety. The mirror image of the CD signals between 1 and 2 was observed, suggesting that the chirality-organized structure via intramolecular hydrogen bondings is present even in solution. The ferrocene 4 bearing the podand dipeptide chains (-Gly-L-Leu-OEt) also showed an ordered structure in the crystal based on two intramolecular hydrogen bondings between CO (Gly) and NH (another Gly) of each podand dipeptide chain, together with intermolecular hydrogen bondings between CO adjacent to the ferrocene unit and NH (neighboring Leu) to create the highly organized self-assembly. A different self-assembly was observed in the crystal of the ferrocene 5 composed of the podand dipeptide chains (-Gly-L-Phe-OEt), wherein each molecule is bonded to two neighboring molecules through two pairs of symmetrical intermolecular hydrogen bonds to form a 14-membered intermolecularly hydrogen-bonded ring. These ordered structures based on the intramolecular hydrogen bondings in the solution state are also confirmed by 1H NMR and FT-IR.     

Intermolecular hydrogen bonding of steroid compounds: PFG NMR diffusion study, cold-spray ionization (CSI)-MS and X-ray analysis

An extensive analysis of hydrogen bonding of steroid compounds in diluted solution is preformed by pulsed field gradient (PFG) NMR and cold-spray ionization (CSI)-MS, in the solid state by X-ray crystallographic analysis. The formation of hydrogen bond interaction are quantified and discussed. Although X-ray analysis in the crystalline state and CSI-MS measurement in solution suggested that the observed diffusion coefficient D(obs) of the steroid compounds may vary in accordance with the number of hydrogen bonds, the actual observed D(obs) value determined from the diffusion studies diminished constantly without correlation on the decreasing numbers of hydrogen bonds. Comparison of two different calibration profiles of calculated molecular volume (V(cal)) vs. D(obs), which are obtained from compounds possessing no hydrogen bonding and the steroid compounds, formation of a chain structure (cluster) based on intermolecular hydrogen bonding of the steroid compounds is unambiguously confirmed.     

Molecular Structure of Amyloid Fibrils Formed by Residues 127 to 147 of the Human Prion Protein

Amyloid fibrils are filamentous and insoluble forms of peptides or proteins. Proline has long been considered to be incompatible with the cross‐β structural motif of amyloid fibrils. On the basis of solid‐state NMR spectroscopy data, we present a structural model of an in‐register parallel β sheet for the amyloid fibrils formed from a human prion protein fragment, huPrP_127–47. We have developed a simple solid‐state NMR spectroscopy technique to identify solvent‐protected backbone amide protons in a H/D exchange experiment without disaggregating the amyloid fibrils, from which we find that proline residue P₁₃₇ does not disrupt the β‐sheet structure from G₁₂₇ to G₁₄₂. We suggest that the resultant kink at P₁₃₇ generates a twist between adjacent peptide strands to maintain hydrogen bonding in the β‐sheet regions flanking the P₁₃₇ residue. Although proline can be well integrated into the cross‐β structure of amyloid fibrils, the kink formed at the position of the proline residue will considerably weaken the hydrogen bonding between the neighboring strands, especially when the mutation site is near the central region of a β sheet.     

有机和生物晶体固态核磁共振参数的准确预测

理论计算有助于复杂的有机和生物系统光谱的鉴定.对于核磁共振光谱,固体结晶中的化学位移和四极耦合常数(QCC)受到邻近的分子和晶格的氢键和范德华作用较大的影响,从而显示出与气态单体分子不同的NMR参数.因此,在固体晶体NMR参数的理论计算中有必要将氢键和范德华作用这两个因素考虑进来.基于周期性方法,本文采用L-Ala-Gly二肽和硝基苯晶体作为模型体系来考察该方法计算NMR参数的精度.研究结果显示周期结构模型能够将分子间的氢键和范德华作用考虑进来,得到的化学位移和QCC值明显优于传统的单分子模型和超分子模型得到的结果,采用该方法计算的结果能够重现NMR实验结果.     

Synthesis and structural analysis of the anilides of glucuronic acid and orientation of the groups on the carbohydrate scaffolding

[structures: see text] The synthesis of anilides derived from glucuronic acid is described. Secondary anilides had a Z configuration in the solid state and showed intramolecular and intermolecular hydrogen bonding. However, on the basis of NMR and IR studies, there was generally no evidence for the same hydrogen bonding in solution. Tertiary anilides showed a strong preference for the E configuration on the basis of NOE studies and molecular mechanics calculations. The alkylation of the secondary anilides induces a configurational switch that alters the orientation of the aromatic group with respect to the pyranose, which has relevance for presentation or orientation of pharmacophoric groups on carbohydrate scaffolds.     

Revisiting the electronic excited-state hydrogen bonding dynamics of coumarin chromophore in alcohols: Undoubtedly strengthened not cleaved

In the present work, the electronic excited-state hydrogen bonding dynamics of coumarin chromophore in alcohols is revisited. The time-dependent density functional theory (TDDFT) method has been performed to investigate the intermolecular hydrogen bonding between Coumarin 151 (C151) and methanol (MeOH) solvent in the electronic excited state. Three types of intermolecular hydrogen bonds can be formed in the hydrogen-bonded C151–(MeOH)₃ complex. We have demonstrated again that intermolecular hydrogen bonds between C151 and methanol molecules can be significantly strengthened upon photoexcitation to the electronically excited state of C151 chromophore. Our results are consistent with the intermolecular hydrogen bond strengthening in the electronically excited state of Coumarin 102 in alcoholic solvents, which has been demonstrated for the first time by Zhao et al. At the same time, the electronic excited-state hydrogen bond cleavage mechanism of photoexcited coumarin chromophores in alcohols proposed in some other studies about the hydrogen bonding dynamics is undoubtedly excluded. Hence, we believe that the two contrary dynamic mechanisms for intermolecular hydrogen bonding in electronically excited states of coumarin chromophores in alcohols are clarified here.     

Complexation-induced conformational regulation of ferrocene-dipeptide conjugates to nucleate γ-turn-like structure

The complexation of the ferrocene-dipeptide conjugate bearing one dipeptide chain of heterochiral sequence (-l-Ala-d-Pro-NHPy) with PdCl₂(MeCN)₂ was demonstrated to afford the 2:1 trans palladium complex, which is present in the pseudo-helical conformation and γ-turn-like structure in the crystal structure through complexation and intramolecular hydrogen bonding. Furthermore, the left-handed pseudo-helical molecular arrangement was formed through a network of intermolecular hydrogen bonds.     

Low Molecular Weight Gelators for Organic Fluids: Gelation Using a Family of Cyclo(dipeptide)s

Simple cyclo(dipeptide)s consisting of diverse amino acids are able to cause physical gelation in a wide variety of organic fluids, including edible oils, glyceryl esters, alcohols, and aromatic molecules. Minimum gel concentrations, FTIR spectroscopy, NMR spectroscopy, and electron micrograph are used to characterize gel phenomenon. The intermolecular hydrogen bonding between N-H and C=O in cyclo(dipeptide)s plays an important role in gelation. FTIR and X-ray diffraction data suggest that the aggregate responsible for gel is an assembly of hydrogen-bonded molecular ladders, which are initially formed from numerous molecules through intermolecular hydrogen bonding. The ladder-like aggregates are intertwined and interlocked, and finally immobilize organic fluids. The gelation ability is discussed in connection with the three-component solubility parameters of solvents. Copyright 2000 Academic Press.     

Dipeptide-induced chirality organization

This review describes an outline of dipeptide-induced chirality organization by using molecular scaffolds. A variety of ferrocene-dipeptide conjugates as bioorganometallics are designed to induce chirality-organized structures of peptides. The ferrocene serves as a reliable organometallic scaffold with a central reverse-turn unit for the construction of protein secondary structures via intramolecular hydrogen bondings, wherein the attached dipeptide strands are constrained within the appropriate dimensions. Another interesting feature of ferrocene-dipeptide conjugates is their strong tendency to self-assemble through contribution of available hydrogen bonding sites for helical architectures in solid states. Symmetrical introduction of two dipeptide chains into a urea molecular scaffold is performed to induce the formation of the chiral hydrogen-bonded duplex, wherein each hydrogen-bonded duplex is connected by continuous intermolecular hydrogen bonds to form a double helix-like arrangement.     

Explosives Sensing by Using Electron‐Rich Supramolecular Polymers: Role of Intermolecular Hydrogen Bonding in Significant Enhancement of Sensitivity

We demonstrate here that supramolecular interactions enhance the sensitivity towards detection of electron‐deficient nitro‐aromatic compounds (NACs) over discrete analogues. NACs are the most commonly used explosive ingredients and are common constituents of many unexploded landmines used during World War II. In this study, we have synthesised a series of pyrene‐based polycarboxylic acids along with their corresponding discrete esters. Due to the electron richness and the fluorescent behaviour of the pyrene moiety, all the compounds act as sensors for electron‐deficient NACs through a fluorescence quenching mechanism. A Stern–Volmer quenching constant determination revealed that the carboxylic acids are more sensitive than the corresponding esters towards NACs in solution. The high sensitivity of the acids was attributed to supramolecular polymer formation through hydrogen bonding in the case of the acids, and the enhancement mechanism is based on an exciton energy migration upon excitation along the hydrogen‐bond backbone. The presence of intermolecular hydrogen bonding in the acids in solution was established by solvent‐dependent fluorescence studies and dynamic light scattering (DLS) experiments. In addition, the importance of intermolecular hydrogen bonds in solid‐state sensing was further explored by scanning tunnelling microscopy (STM) experiments at the liquid–solid interface, in which structures of self‐assembled monolayer of the acids and the corresponding esters were compared. The sensitivity tests revealed that these supramolecular sensors can even detect picric acid and trinitrotoluene in solution at levels as low as parts per trillion (ppt), which is much below the recommended permissible level of these constituents in drinking water.     

Synthesis and structure of ruthenium(IV) complexes featuring N-heterocyclic ligands with an N-H group as the hydrogen-bond donor: hydrogen interactions in solution and in the solid state

The synthesis and characterization of novel ruthenium(IV) complexes [Ru(η(3):η(3)-C(10)H(16))Cl(2)L] [L = 3-methylpyrazole (2b), 3,5-dimethylpyrazole (2c), 3-methyl-5-phenylpyrazole (2d), 2-(1H-pyrazol-5-yl)phenol (2e), 6-azauracile (3), and 1H-indazol-3-ol (4)] are reported. Complex 2e is converted to the chelated complex [Ru(η(3):η(3)-C(10)H(16))Cl(κ(2)-N,O-2-(1H-pyrazol-3-yl)phenoxy)] (5) by treatment with an excess of NaOH. All of the ligands feature N-H, O-H, or C═O as the potential hydrogen-bonding group. The structures of complexes 2a-2c, 2e, 3, and 5 in the solid state have been determined by X-ray diffraction. Complexes 2a-2c and 3, which contain the pyrazole N-H group, exhibit intra- and intermolecular hydrogen bonds with chloride ligands [N-H···Cl distances (?): intramolecular, 2.30-2.78; intermolecular, 2.59-2.77]. Complexes 2e and 3 bearing respectively O-H and C═O groups also feature N-H···O interactions [intramolecular (2e), 2.27 ?; intermolecular (3), 2.00 ?]. Chelated complex 5, lacking the O-H group, only shows an intramolecular N-H···Cl hydrogen bonding of 2.42 ?. The structure of complex 3, which turns out to be a dimer in the solid state through a double intermolecular N-H···O hydrogen bonding, has also been investigated in solution (CD(2)Cl(2)) by NMR diffusion studies. Diffusion-ordered spectroscopy experiments reveal an equilibrium between monomer and dimer species in solution whose extension depends on the temperature, concentration, and coordinating properties of the solvent. Preliminary catalytic studies show that complex 3 is highly active in the redox isomerization of the allylic alcohols in an aqueous medium under very mild reaction conditions (35 °C) and in the absence of a base.     

Vibrational and theoretical study of the 2',6'-dimethoxyflavone cis-formic acid inclusion compound

The FT-infrared and Raman microscopy spectra of the 2',6'-dimethoxyflavone and its 1:1 complex with formic acid in solid state have been recorded and analysed. Some vibrational components appear as specific to the cis-rotamer of formic acid in the crystalline sample, especially the CH group stretching vibration feature. The broad and intense infrared absorption observed in the range 3400-1900 cm(-1) and assigned to the hydrogen bonded OH group stretching vibration exhibits the characteristic ABC structure of strong hydrogen bonded complexes. This ABC pattern corroborates previous X-ray crystallographic data showing that cis-formic acid is strongly hydrogen bonded to the flavonic compound. The inclusion complex is quite unstable and the infrared spectrum clearly shows that formic acid disappears after a period of a few months. In order to get some information on the stability criterions of the intermolecular hydrogen bonded complex, semiempirical AM1 calculations have been investigated. The comparison of the calculated heats of complexation (deltacH) for chelates involving the cis- and trans-conformers of formic acid suggests that the reaction of hydrogen bonding complexation with the cis-rotamer is surely favoured.     

Designing Foldamer–Foldamer Interactions in Solution: The Roles of Helix Length and Terminus Functionality in Promoting the Self‐Association of Aminoisobutyric Acid Oligomers

The biological activity of antibiotic peptaibols has been linked to their ability to aggregate, but the structure–activity relationship for aggregation is not well understood. Herein, we report a systematic study of a class of synthetic helical oligomer (foldamer) composed of aminoisobutyric acid (Aib) residues, which mimic the folding behavior of peptaibols. NMR spectroscopic analysis was used to quantify the dimerization constants in solution, which showed hydrogen‐bond donors at the N terminus promoted aggregation more effectively than similar modifications at the C terminus. Elongation of the peptide chain also favored aggregation. The geometry of aggregation in solution was investigated by means of titrations with [D₆]DMSO and 2D NOE NMR spectroscopy, which allowed the NH protons most involved in intermolecular hydrogen bonds in solution to be identified. X‐ray crystallography studies of two oligomers allowed a comparison of the inter‐ and intramolecular hydrogen‐bonding interactions in the solid state and in solution and gave further insight into the geometry of foldamer–foldamer interactions. These solution‐based and solid‐state studies indicated that the preferred geometry for aggregation is through head‐to‐tail interactions between the N and C termini of adjacent Aib oligomers.     

Terahertz time-domain spectra of aromatic carboxylic acids incorporated in nano-sized pores of mesoporous silicate.

Terahertz time-domain spectroscopy (THz-TDS) is used to study the intra- and intermolecular vibrational modes of aromatic carboxylic acids, for example, o-phthalic acid, benzoic acid, and salicylic acid, which form either intra- or intermolecular hydrogen bond(s) in different ways. Incorporating the target molecules in nano-sized spaces in mesoporous silicate (SBA-16) is found to be effective for the separate detection of intramolecular hydrogen bonding modes and intermolecular modes. The results are supported by an analysis of the differences in the peak shifts, which depend on temperature, caused by the different nature of the THz absorption. Raman spectra revealed that incorporating the molecules in the nano-sized pores of SBA-16 slightly changes the molecular structures. In the future, THz-TDS using nanoporous materials will be used to analyze the intra- and intermolecular vibrational modes of molecules with larger hydrogen bonding networks such as proteins or DNA.     

Induced smectic G phase through intermolecular hydrogen bonding

A new series of mesomorphic complexes formed through intermolecular hydrogen bonding between p-n-alkoxybenzoic acids (where alkoxy denotes chains from propoxy- to decyloxy- and dodecyloxy-) and non-mesogenic p-hydroxybutyl benzoate, have been synthesized and characterized by thermal microscopy, differential scanning calorimetry, infrared spectroscopy (IR) and 1H NMR studies. A detailed IR spectral investigation in the solid state and in solution suggests that the acid and phenol groups are complementary to each other, each acting as both proton donor and proton acceptor. The results of comparative thermal analyses of both free p-n-alkoxybenzoic acids and H-bonded complexes exhibited an induced crystal smectic G phase in the complexes throughout the series, its thermal range increasing with alkoxy carbon number.     

Synthesis and Crystal Structure of a New Cadmium（Ⅱ） Supramolecular Network Containing Chelating Imidazole-4-carboxylate Ligand

A new complex, [Cd（Himc）2（H2O）2] 1, obtained from imidazole-4-carboxylatic acid （H2imc） and Cd（ClO4）2·6H2O, has been synthesized. The crystal structure was determined by X-ray diffraction. The title compound crystallizes in the orthorhombic system, space group Pccn, with a = 7.4886（11）, b = 11.9667（18）, c = 13.550（2） A, V= 1214.3（3） A3, Z = 4, Mr= 370.60, Dc = 2.027 mg/m3, F（000） = 728,μ （MoKa） = 1.829 mm^-1, the final R = 0.0243 and wR = 0.0591 for 1150 unique reflections with I 〉 2σ（I）. The cadmium（II） center in the title complex is coordinated with two oxygen and two nitrogen atoms from two bidentate chelated imidazole-4-carboxlate ligands together with two water molecules, giving a distorted octahedral coordination geometry. A one-dimensional hydrogen bonding chain is formed via intermolecular O-H...O hydrogen bonds, and such adjacent chains are further stacked through intermolecular π-π and hydrogen bonding interactions to form a 3D supramolecular framework. Complex 1 exhibits a fluorescent emission band at 290 nm （λex = 236 nm） in the solid state.     

Parallel sheet structure in cyclopropane gamma-peptides stabilized by C-H...O hydrogen bonds

A three-residue trans-cyclopropane gamma-peptide adopts an infinite parallel sheet structure in the solid state stabilized by intermolecular C-H...O hydrogen bonds, as demonstrated by single crystal X-ray diffraction.     

Induced crystal G phase through intermolecular hydrogen bonding II. Influence of alkyl chain length of n-alkyl p-hydroxybenzoates on thermal and phase behaviour

A new series of intermolecular hydrogen-bonded complexes have been synthesized using p-n-alkoxybenzoic acid (alkyl chain length varies from propyl- to decyl- and dodecyl-) and methyl p-hydroxybenzoate moieties. The thermal and phase behaviour of these complexes were studied by thermal microscopy and differential scanning calorimetry. Further, the stabilization of intermolecular hydrogen bonding in solution was studied by IR spectroscopy. A detailed IR spectral investigation in the solid and dissolved states suggests that the acid and phenol groups act as proton donor and proton acceptor, respectively. The thermal studies also reveal the inducement of a crystal G phase in the complexes.