The self‐assembled of cyclic D,L‐α‐peptide systems: Insights into the structure and energetics

Cyclic D,L ‐α‐peptides are able to self‐assemble to nanotubes, although the inherent reason of the stability of this kind of nanotube as well as the intrinsic driving force of self‐assembly of the cyclic D ,L ‐α‐peptides still remain elusive. In this work, using several computational approaches, we investigated the structural and energy characteristics of a series of cyclo[(‐L ‐Phe‐D ‐Ala‐)₄] and cyclo[(‐L ‐Ala‐D ‐Ala‐)₄] oligomers. The results reveal that the thermodynamic stability, cooperativity, and self‐assembly patterns of cyclic D ,L ‐α‐peptide nanotubes are mainly determined by the interactions between cross‐strand side chains instead of those between backbones. For cyclo[(‐L ‐Phe‐D ‐Ala‐)₄] oligomers, the steric interaction between cross‐strand side chains, especially the electrostatic repulsion between the phenyls in Phe residues, brings anticooperative effect into parallel stacking mode, which is responsible for the preference of self‐assembling nanotube in antiparallel vs. parallel stacking orientation. Based on our results, a novel self‐assembling mechanism is put forward—it is the L ‐L antiparallel dimer of cyclo[(‐L ‐Phe‐D ‐Ala‐)₄], instead of the commonly presumed monomer, that acts as the basic building block in self assembly. It explains why these cyclic peptides uniquely self‐assemble to form antiparallel nanotubes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

侧链间氢键的协同效应对环状多肽自组装的影响

运用密度泛函(DFT)B3LYP方法和半经验分子轨道方法AM1对四种环状多肽[-(L-Asn-Ala)4-], [-(L-Asp-Ala)4-], [-(L-Gln-Ala)4-] 和[-(L-Glu-Ala)4-]的单体、平行和反平行二聚体到十聚体进行了理论研究. 结果表明, 四种环状多肽无论以平行还是以反平行的方式聚集, 聚集体中相邻两个环状多肽的侧链之间都能形成氢键. 侧链间氢键的相互作用使得这些环状多肽在组装过程中的结构和能量变化均表现出一定的协同效应, 这种协同效应加强了多肽纳米管的稳定性, 同时对聚集模式的选取起到了决定性作用.     

Self‐Assembled Cyclic Structures from Copper(II) Peptoids

Metal–ligand coordination is a key interaction in the self‐assembly of both biopolymers and synthetic oligomers. Although the binding of metal ions to synthetic proteins and peptides is known to yield high‐order structures, the self‐assembly of peptidomimetic molecules upon metal binding is still challenging. Herein we explore the self‐assembly of three peptoid trimers bearing a bipyridine ligand at their C‐terminus, a benzyl group at their N‐terminus, and a polar group (N‐ethyl‐R) in the middle position (R=OH, OCH₃, or NH₂) upon Cu²⁺ coordination. X‐ray diffraction analysis revealed unique, highly symmetric, dinuclear cyclic structure or aqua‐bridged dinuclear double‐stranded peptoid helicates, formed by the self‐assembly of two peptoid molecules with two Cu²⁺ ions. Only the macrocycle with the highest number of intermolecular hydrogen bonds is stable in solution, while the other two disassemble to their corresponding monometallic complexes.     

Quinoline‐2(1H)‐thione,a structure with Z′ = 8

The title compound, C₉H₇NS, crystallizes as the thione tautomer with Z′ = 8 (four independent dimers with local inversion symmetry via two N—H⋯S=C hydrogen‐bond systems). The dimers are arranged in chains parallel to [10], each chain being crystallographically independent. These chains are associated into layers via stacking of ring systems. The Z′ value can be rationalized in terms of a factor 2 for dimer formation without crystallographic symmetry and an additional factor 4 for differing stacking environments.     

Mechanochemical Encapsulation of Fullerenes in Peptidic Containers Prepared by Dynamic Chiral Self‐Sorting and Self‐Assembly

Molecular capsules composed of amino acid or peptide derivatives connected to resorcin[4]arene scaffolds through acylhydrazone linkers have been synthesized using dynamic covalent chemistry (DCC) and hydrogen‐bond‐based self‐assembly. The dynamic character of the linkers and the preference of the peptides towards self‐assembly into β‐barrel‐type motifs lead to the spontaneous amplification of formation of homochiral capsules from mixtures of different substrates. The capsules have cavities of around 800 ų and exhibit good kinetic stability. Although they retain their dynamic character, which allows processes such as chiral self‐sorting and chiral self‐assembly to operate with high fidelity, guest complexation is hindered in solution. However, the quantitative complexation of even very large guests, such as fullerene C₆₀ or C₇₀, is possible through the utilization of reversible covalent bonds or the application of mechanochemical methods. The NMR spectra show the influence of the chiral environment on the symmetry of the fullerene molecules, which results in the differentiation of diastereotopic carbon atoms for C₇₀, and the X‐ray structures provide unique information on the modes of peptide–fullerene interactions.     

Organization and Energy Transfer of Fused Aromatic Hydrocarbon Guests within Anion‐Confining Nanochannel MOFs

The self‐assembly of Zn^II ions with 1,3,5‐tris(isonicotinoyloxyethyl)cyanurate produces new topological (4²?12⁴)₃(4³)₄ 2D metal–organic frameworks (MOFs) with anion‐confining cages. The eclipsed assembly of each 2D MOF by π–π stacking of cyanurate moieties (3.352(5) Å) forms 3D MOFs consisting of nanochannels (10.5 Å). Two of the three anions are confined in each peanut‐type cage, resulting in hydrophobicity of the nanochannels. The hydrophobic nanochannel effectively adsorbs a wide range of fused aromatic hydrocarbons (FAHs) as monomers or dimers, rendering it potentially highly useful as an energy‐transfer material.     

Cyclic [2]Catenane Dimers,Trimers, and Tetramers

Dimeric, trimeric, and tetrameric cyclic [2]catenanes have been prepared directly through one‐pot sodium‐ion‐templated dynamic imine formation from a diamine and a tetraaldehyde. NaBH₄ mediated reduction of the labile imino bonds of these cyclic [2]catenane oligomers, followed by methylation of the resulting secondary amino groups enabled the isolation and characterization of oligomeric cyclic [2]catenanes as stable, covalently linked compounds.     

C—H…Cl Hydrogen Bond and π-π Interaction Based Two 3D Supramolecular Architectures of Cu(II) and Co(II) Complexes with Chiral 1,2-Bis(benzimidazol-2-yl) ethane Ligand Containing 2D Grids

合成了两个新的配合物CuLCl₂•2EtOH(1) 和CoLCl₂ (2) [L是( S , S )－1,2－二N－甲基苯并咪唑－1,2－二甲氧基－乙烷],并通过单晶X衍射确定它们的结构。配合物1中,L作为三齿[N, N, O]配体,而配合物2 中,L作为二齿[N, N]配体。这两个配合物共同的结构特点都是通过分子内氢键形成2维的格子结构,然后通过分子间的C－H···Cl型氢键和π–π堆积作用形成3维结构。     

Hydrogen‐Bond and Metal–Ligand Coordination Bond Hybrid Supramolecular Capsules: Identification of Hemicapsular Intermediate and Dual Control of Guest Exchange Dynamics

Hybrid supramolecular capsules self‐assemble by simultaneously forming hydrogen and metal–ligand coordination bonds on mixing a C₂‐symmetrical cavitand (calix[4]resorcinarene‐based cavitands with ureide and terminal 4‐pyridyl units) with platinum or palladium complexes ([Pt(OTf)₂] or [Pd(OTf)₂] with chelating bisphosphines) in 1:1 ratio. Hemicapsular assemblies formed in the presence of excess amounts of cavitand relative to the platinum or palladium complexes are identified as intermediates in the above self‐assembly process by 2D‐NOESY spectroscopy. External‐anion‐assisted encapsulation of a neutral guest, 4,4′‐diiodobiphenyl, inside the hybrid supramolecular capsules accompanied conformational changes in the hydrogen‐bonding moieties. The in/out exchange ratio of the encapsulated guest depends on the bite angle of the bisphosphine ligand. Addition of DMSO accelerates guest exchange by weakening the hydrogen bonds in the encapsulation complex. Therefore, variations in the structure of the metal complex and amount of polar solvent exert dual control on the dynamics of the guest exchange.     

A Bowl‐Shaped Circular Trinuclear Helicate Generated from a TiO4N2 Motif by a Multicomponent Self‐Assembly Approach

The synthesis of a bowl‐shaped trinuclear circular titanium‐based helicate is reported. The strategy allowing access to this neutral architecture is based on a multicomponent self‐assembly approach in which the ligands involved in the process are a bis‐biphenol strand and 2,2′‐ bipyrimidine. By reacting the bis‐biphenol ligand and 2,2′‐bipyrimidine with an equimolar amount [Ti(OiPr)₄], a bowl‐shaped architecture is obtained through the formation of 18 new coordination bonds. This aggregate built from three octahedral TiO₄N₂ nodes displays an unusually high stability in solution compared to related species. In addition, by modifying the stoichiometry of the initial components, two assemblies incorporating two titanium centers bridged by a 2,2′‐bipyrimidine ligand are obtained. The crystal structures of these species are reported.     

A New Supramolecular Assembly Formed by Melamine and Sulfuric Acid

Polymeric melaminium sulfate [(LH₂)₂(SO₄)₂]_n has been synthesized by reaction of melamine L with sulfuric acid in aqueous solution. The compound was characterized by elemental analysis, ¹H NMR, ESI MS and a single crystal X‐ray diffraction analysis. The architecture of the assembly formed is based on hydrogen bonded dimers of diprotonated melaminium cations (LH₂)²⁺ which are linked by a hydrogen bonded network with sulfate ions forming 2D sheets. A 3D polymeric structure results from the presence of mutual hydrogen bonds between sulfate ions and melaminium cations in different sheets. Significant π‐π stacking is also present between the aromatic cations in this supramolecular arrangement.     

Assembly of Supramolecular Networks with the Inclusion of Water Chains,Cyclic Hepta and Octa Water Clusters

Three new supramolecular compounds were synthesized and characterized with the formula of [Zn₄(picO)₄(phen)₄]·11.25H₂O ( 1 ), [Zn₄(picO)₄(2,2′‐bpy)₄(H₂O)₄]·12H₂O ( 2 ), and [Zn₃(picO)₃(bpe)₅(H₂O)₃]_n·8.5nH₂O ( 3 ) (H₂picO = 6‐hydroxypicolinic acid; phen = 1,10‐phenanthroline; 2,2′‐bpy = 2,2′‐bipyridine; bpe = 1,2‐bis(4‐pyridyl)ethane). For complexes 1 and 2 , picO ligands adopt tridentate, tetradentate and bidentate coordination modes to link zinc(II) ions into dimers, which are extended into 3D supramolecular structures through hydrogen bonds. Water chains with cyclic page‐like octamer and boat‐like heptamer water clusters are included, respectively. Complex 3 is of a 2D brick‐wall structure. Triple interpenetration occurs, and there are still cyclic chair‐like octamer water clusters in the channels. The fluorescent properties of complexes 1‐3 have also been investigated.     

Self‐Assembly and Gelation of Poly(aryl ether) Dendrons Containing Hydrazide Units: Factors Controlling the Formation of Helical Structures

Self‐assembly of AB₂ and AB₃ type low molecular weight poly(aryl ether) dendrons that contain hydrazide units were used to investigate mechanistic aspects of helical structure formation during self‐assembly. The results suggest that there are three important aspects that control helical structure formation in such systems with acyl hydrazide/hydrazone linkage: i) J‐type aggregation, ii) the hydrogen‐bond donor/acceptor ability of the solvent, and iii) the dielectric constant of the solvent. The monomer units self‐assemble to form dimer structures through hydrogen‐bonding and further assembly of the hydrogen‐bonded dimers leads to macroscopic chirality in the present case. Dimer formation was confirmed by NMR spectroscopy and by mass spectrometry. The self‐assembly in the system was driven by hydrogen‐bonding and π–π stacking interactions. The morphology of the aggregates formed was examined by scanning electron microscopy, and the analysis suggests that aprotic solvent systems facilitate helical fibre formation, whereas introduction of protic solvents results in the formation of flat ribbons. This detailed mechanistic study suggests that the self‐assembly follows a nucleation–elongation model to form helical structures, rather than the isodesmic model.     

Formation of o‐Phenylenediamine Oligomers and their Self‐Assembly into One‐Dimensional Structures in Aqueous Medium

Summary: Uniform one‐dimensional (1D) structures of o‐phenylenediamine (oPD) oligomers are obtained by direct mix of AgNO₃ and oPD aqueous solutions at room temperature. The formation of the 1D structures involves two stages: (1) oxidation of oPD by AgNO₃, yielding individual oPD oligomers; and (2) self‐assembly of the oligomers, forming the 1D structures. Upon decreasing medium pH, the 1D structures can break‐apart to form individual oligomers, or vice versa. It is also found that both the concentration and molar ratio of reactants can influence the morphology of the structures thus formed.

Schematic illustration of the formation mechanism of 1D structures from oPD and AgNO₃, and energy‐dispersed spectrum of the precipitate.     

π–π Stacking‐Interlinked Molecular Squares with Hepta‐Coordinated Cadmium(II) Corners, [Cd(DMAP)3(NO2)2]·0.5H2O

The single crystal X‐ray analysis data of the new hepta‐coordinate cadmium(II) complex of N,N‐dimethyl‐N‐(4‐pyridyl)amine (DMPA), [Cd(DMPA)₃(NO₂)₂]·0.5H₂O, shows that the coordination environment around the Cd^II is pentagonal bipyramidal. Furthermore, self‐assembly of this complex as molecular squares that interlink via π–π stacking interactions is observed. This network contains voids that are filled by water molecules.     

From Nongelating to Gelating: Synthesis and Structural Self‐Assembling Property Relationships of a Homologous Series of Oligo(amide–triazole)s

A homologous series of oligo(amide–triazole)s (OAT) [ OAT‐CO₂H‐2 n and OAT‐COPrg‐(2 n +1) ] with an increasing number of primary amide (CONH) and triazole hydrogen‐bonding functionalities was prepared by an iterative synthetic procedure. It was found that their self‐assembly and thermoreversible gelation strength had a strong correlation to the number of hydrogen‐bonding moieties in the oligomers. There also existed a threshold value of the number of CONH units, above which all the oligomers became organogelators. Hence, oligomers with ≤4 CONH units are devoid of intermolecular hydrogen bonding and also non‐organogelating, whereas those that contain >4 CONH units show intermolecular association and organogelating properties. For the organogelators, the T_gel value increases monotonically with increasing number of CONH units. On the basis of FTIR measurements, both the CONH and triazole C? H groups were involved in the hydrogen‐bonding process. A mixed xerogel that consisted of a 1:1 weight ratio of two oligomers of different lengths ( OAT‐CO₂H‐6 and OAT‐CO₂H‐12 ) was found to show microphase segregation according to differential scanning calorimetry, thus indicating that oligomers that bear a different number of hydrogen‐bonding units exhibited self‐sorting to maximize the extent of intermolecular hydrogen bonding in the xerogel state.     

Studies on the cross‐interaction between hIAPP and Aβ25–35 and the aggregation process in binary mixture by electrospray ionization‐ion mobility‐mass spectrometry

A wealth of epidemiological evidence indicates a strong link between type 2 diabetes (T2D) and Alzheimer's disease (AD). The fiber deposition with cross‐β‐sheet structure formed by self‐aggregation and misfolding of amyloidogenic peptides is a common hallmark of both diseases. For the patients with T2D, the fibrils are mainly found in the islets of Langerhans that results from the accumulation of human islet amyloid polypeptide (hIAPP). The major component of aggregates located in the brain of AD patients is amyloid‐β (Aβ). Many biophysical and physiological properties are shared by hIAPP and Aβ, and both peptides show similar cytotoxic mechanisms. Therefore, it is meaningful to investigate the possible cross‐interactions of hIAPP and Aβ in both diseases. In this article, the segment 25–35 of Aβ was selected because Aβ_25–35 was a core region in the process of amyloid formation and showed similar aggregation tendency and toxicity with full‐length Aβ. The electrospray ionization‐ion mobility‐mass spectrometry analysis and thioflavin T fluorescence kinetic analysis combined with transmission electron microscopy were used to explore the effects of the coexistence of Aβ_25–35 and hIAPP on the self‐aggregation of both peptides and whether there was co‐assembly in fibrillation. The results indicated that the aggregation of hIAPP and Aβ_25–35 had two nucleation stages in the binary mixtures. hIAPP and Aβ_25–35 had a high binding affinity and a series of hetero‐oligomers formed in the mixtures of hIAPP and Aβ_25–35 in the early stage. The cross‐reaction between hIAPP monomers and Aβ_25–35 monomers as well as a little of oligomers during primary nucleation stage could accelerate the aggregation of Aβ_25–35. However, owing to the obvious difference in aggregation ability between hIAPP and Aβ_25–35, this cross‐interaction had no significant impact on the self‐assembly of hIAPP. Our study may offer a better understanding for exploring the molecular mechanism of the association between AD and T2D observed in clinical and epidemiological studies and developing therapeutic strategies against amyloid diseases.     

基于二-吡嗪-(2, 3-f: 2′3′-h)-喹喔啉和吡啶-2，5-二羧酸混合配体的两个新奇金属有机超分子骨架的水热合成、晶体结构与光致发光

以二-吡嗪-(2, 3-f: 2′3′-h)-喹喔啉(Dpq)和吡啶-2,5-二羧酸(2,5-H2pda)两种混合配体与不同金属硝酸盐为原料,通过水热反应得到了两个新奇的金属有机骨架[Zn2(Dpq)2(2,5-pda)2(H2O)2]·2H2O(1)和[Cd2(Dpq)2(2,5-pda)2]·2H2O(2),并经元素分析、TG、IR、X-射线单晶衍射分析进行了表征。结构分析表明,2,5-pda采取不同的配位方式桥连金属离子分别形成了二聚物1和2D菱形网络2。在化合物1中,相邻的二聚物通过氢键和π-π堆积作用形成扭曲的a-Po超分子结构。在化合物2中,相邻的配位聚合物层通过氢键拓展成扭曲的a-Po超分子骨架,而π-π堆积起到巩固骨架的作用。化合物1和2的结构差异表明了金属离子和配体在配位聚合物自组装过程中对结构的影响。此外固态标题化合物在室温下表现出蓝色的发光性质。     

Understanding the Supramolecular Self‐Assembly of the Fullerene Derivative PCBM on Gold Surfaces

We report a DFT study on the self‐assembly of the fullerene derivative PCBM on the Au(111) surface. Recent STM experiments (Angew. Chem. 2007 , 119, 8020–8023^[1]) show a coverage‐dependent transition of the adsorption and self‐assembly of PCBM on this surface. To understand the origin of this observation, we compute the geometries and relative energies of ten PCBM dimers and four tetramers. The calculations show that the self‐assembly of PCBM at high coverage is mainly controlled by hydrogen bonding between the PCBM tails. Due to the large size of the fullerene cage, the hydrogen bonds are formed far away from the surface; hence they are very similar to those found in the gas phase. This picture successfully explains the observed site‐insensitive adsorption at high coverage and the 2D arrangement of PCBM on the surface.     

Tailoring the Structure of Two‐Dimensional Self‐Assembled Nanoarchitectures Based on NiII–Salen Building Blocks

The synthesis of a series of Ni^II–salen‐based complexes with the general formula of [Ni(H₂L)] (H₄L=R²‐N,N′‐bis[R¹‐5‐(4′‐benzoic acid)salicylidene]; H₄L1: R²=2,3‐diamino‐2,3‐dimethylbutane and R¹=H; H₄L2: R²=1,2‐diaminoethane and R¹=tert‐butyl and H₄L3: R²=1,2‐diaminobenzene and R¹=tert‐butyl) is presented. Their electronic structure and self‐assembly was studied. The organic ligands of the salen complexes are functionalized with peripheral carboxylic groups for driving molecular self‐assembly through hydrogen bonding. In addition, other substituents, that is, tert‐butyl and diamine bridges (2,3‐diamino‐2,3‐dimethylbutane, 1,2‐diaminobenzene or 1,2‐diaminoethane), were used to tune the two‐dimensional (2D) packing of these building blocks. Density functional theory (DFT) calculations reveal that the spatial distribution of the LUMOs is affected by these substituents, in contrast with the HOMOs, which remain unchanged. Scanning tunneling microscopy (STM) shows that the three complexes self‐assemble into three different 2D nanoarchitectures at the solid–liquid interface on graphite. Two structures are porous and one is close‐packed. These structures are stabilized by hydrogen bonds in one dimension, while the 2D interaction is governed by van der Waals forces and is tuned by the nature of the substituents, as confirmed by theoretical calculations. As expected, the total dipolar moment is minimized