Control of chirality-organized structures of ferrocene-dipeptide bioconjugates

A variety of ferrocene-dipeptide bioconjugates have been designed to induce chirality-organized structures in both solid and solution states. The ferrocene serves as a reliable organometallic scaffold for the construction of protein secondary structures via intramolecular hydrogen bonding, here the attached dipeptide strands are regulated within the appropriate dimensions. The configuration and sequence of the amino acids play an important role in the construction of the chirality-organized bio-inspired systems under controlled hydrogen bonding.     

Self-assembly of dipeptidyl ureas: a new class of hydrogen-bonded molecular duplexes

The dipeptidyl urea 1 composed of two dipeptide chains bearing the C-terminal pyridyl moiety (-L-Ala-L-Pro-NHPy) was prepared. Two molecules of 1 are revealed to be held together by six intermolecular hydrogen bonds to form a hydrogen-bonded duplex by the single-crystal X-ray structure determination. Proton magnetic resonance nuclear Overhauser effect (NOE) study indicates the hydrogen-bonded duplex even in solution. Furthermore, a shuttle-like molecular dynamics based on recombination of the hydrogen bonds was observed. The dipeptidyl urea composed of two dipeptide chains bearing the C-terminal pyrenyl moiety (-L-Ala-L-Pro-NHCH(2)Pyr) exhibited both monomer and eximer emissions in the fluorescence spectra, supporting the formation of a duplex. A combination of the C-terminal amide NH function in each side and the designed sequence of hydrogen-bonding sites are considered to be a crucial factor for the duplex formation.     

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.     

Chirality organization of ferrocenes bearing dipeptide chains of heterochiral sequence

[structures: see text] The symmetrical introduction of two dipeptide chains of heterochiral sequence (-L-Ala-D-Pro-NHPy) into the ferrocene scaffold as a central reverse-turn unit was demonstrated to induce both antiparallel beta-sheet-like and type II beta-turn-like structures simultaneously, affording the chirality-organized structure. The ferrocene bearing only one dipeptide chain (-L-Ala-D-Pro-NHPy) exhibited a left-handed helically ordered molecular assembly through a network of intermolecular hydrogen bonds instead of intramolecular hydrogen bonds.     

Design and controlled emission properties of bioorganometallic compounds composed of uracils and organoplatinum(II) moieties

The bioorganometallic platinum(II) compounds PtU6 and PtU5 were designed by the conjugation of the corresponding uracil derivative and the organoplatinum(II) compound [4-octyloxy-(C^N^N)PtCl]. The single crystal X-ray structure determination of PtU6 revealed the formation of the dimeric structure through intermolecular hydrogen bonds between the uracil moieties of two independent molecules, wherein each hydrogen-bonded dimer was connected through Pt(II)-Pt(II) and π-π interactions. The tuning of the emission properties of the organoplatinum(II) compounds was achieved by changing the direction of hydrogen bonding sites and the molecular scaffold having two 2,6-dihexamidopyridine moieties as a complementary hydrogen bonding site for the uracil moiety, which depends on the regulation of the aggregated structures, to induce the Pt(II)-Pt(II) and π-π interactions.     

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.     

Induction of gamma-turn-like structure in ferrocene bearing dipeptide chains via conformational control

[structure: see text] A combination of the ferrocene scaffold as a central reverse-turn unit with the dipeptide chains (-L-Pro-L-Ala-NHPy) was demonstrated to induce both inverse gamma-turn-like and antiparallel beta-sheet-like structures. Only the antiparallel beta-sheet-like structure was formed in the ferrocene bearing the heterochiral dipeptide chains (-L-Pro-D-Ala-NHPy), in which highly organized self-assembly was achieved through a network of intermolecular hydrogen bonds.     

碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

正确理解核酸碱基和蛋白质多肽间的作用机制有助于人们利用这些生物分子有效地进行分子设计,进而制备具有特殊纳米结构和功能的生物分子材料.本文优化得到了碱基腺嘌呤与N-甲基乙酰胺、甘氨酸二肽、丙氨酸二肽形成的20个氢键复合物的结构并计算了结合能,探讨了腺嘌呤与多肽酰胺间氢键作用的最佳位点.研究发现:腺嘌呤可以使用两个不同位点(A1位点和A2位点)与N-甲基乙酰胺形成N―H…N型或者N―H…O=C型氢键复合物,腺嘌呤使用A1位点与N-甲基乙酰胺形成的N―H…N型氢键复合物更稳定;二肽分子可以使用主链上两个不同位点(丙氨酸的Ala7位点和Ala5位点或者甘氨酸的Gly7位点和Gly5位点)与腺嘌呤形成含有N―H…N和N―H…O=C两条氢键的复合物,二肽分子使用Ala7或Gly7位点与腺嘌呤形成的氢键复合物更稳定;腺嘌呤与多肽间的氢键作用强于其与N-甲基乙酰胺的作用.基于分子中的原子理论与自然键轨道计算结果分析了氢键作用的本质.     

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.     

Gold nanoparticle assemblies through hydrogen-bonded supramolecular mediators

The synthesis of spherical gold nanoparticle assemblies with multicomponent double rosette molecular boxes as mediators is presented. These nine-component hydrogen-bonded supramolecular structures held together by 36 hydrogen bonds induce gold nanoparticle assembly. The morphologies of the nanoparticle assemblies can be tuned easily by changing the quantity of the building block chemisorbed on the nanoparticle surface.     

Design and Synthesis of a Highly Stable Six-hydrogen-bonded Self-assembly Yellowish Green Electroluminescent Molecular Duplex

Since the first fabrication of thin-layer organic electroluminescent(OEL)device in1987by C.W.Tang et al1.,OEL materials had been of ever increasing interest2,3.While up to now,full-color display has been commercialized with small molecules having different structures.In general,host-dopant systems are often employed in RGB OLEDs.This procedure,however,would lead to relatively poor performance for OEL devices,because of the easy aggregation and crystallization of the dopants,which would…     

Hydrogen bonds between hydrogen halides and unsaturated hydrocarbons

Ab initio molecular orbital theory is used to study geometrics and energies of hydrogen-bonded complexes between hydrogen fluoride, hydrogen chloride (as proton donors) and acetylene, ethylene (as proton acceptors). Symmetrical T-shaped structures are found to be equilibrium structures for all four complexes. The strengths of the hydrogen bonds are found to be less than for conventional hydrogen bonds involving lone pairs of electrons.     

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.     

The serine-proline turn: a novel hydrogen-bonded template for designing peptidomimetics

Serine-Proline (SP) dipeptide motifs have been shown to form unique hydrogen-bonding patterns in protein crystal structures. Peptides were designed to mimic these patterns by forming the 6 + 10 and the 9 + 10 hydrogen-bonded rings. Factors that contribute to the formation of SP turns include controlling backbone flexibility and amino acid chirality along with creating a hydrophobic environment around the intramolecular hydrogen bonds.     

Resorcarenes in the boat conformation as building blocks for hydrogen-bonded assemblies including two ammonium cations

Crystal structures are reported for various co-crystals of rccc-resorcarenes with triethylammonium chloride. Usually, two molecules of a C2v-symmetric tetraester 2 in the boat conformation are linked through four hydrogen-bonded chloride anions to give dimeric assemblies. Two of the chloride anions may be replaced by four hydrogen-bonded ethanol molecules in an otherwise similar structure. These assemblies, which consist of six or eight components, posses voluminous, negatively charged chambers in which two triethylammionium cations, 3+, are included as guests by strong electrostatic and hydrogen-bonding interactions. The host-guest N-H...Cl hydrogen bonds were clearly detected at 173 K. These are the first examples of hydrogen-bonded, solid-state capsules trapping two ions of the same charge in close proximity. In the 1:2 complex with 3+ Cl-, the molecule of the parent resorcarene 1 also adopts a boat conformation whose cavity is considerably extended by four hydrogen-bonded chloride anions. The pocket formed in this way again includes two 3+ ions as a result of electrostatic and hydrogen bonding host-guest interactions. All these structures show that the boat conformers of resorcarenes can be used as a novel motif for the construction of hydrogen-bonded assemblies capable of molecular inclusion and encapsulation.     

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

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

Duplex and hairpin dimer structures for perylene diimide-oligonucleotide conjugates

Perylene diimide-oligonucleotide conjugates can form either duplex or hairpin dimer structures, depending upon the choice of oligonucleotide base sequence; we have used a combination of optical spectroscopy and molecular modeling to investigate the structures of the duplex and hairpin dimer.     

Heteromolecular grids of free-base and zinc-tetra(4-pyridyl)porphyrins with benzenetetracarboxylic acid

This study describes the formation of hetero-molecular networks involving the 1,2,4,5-benzenetetracarboxylic acid (BTCA) and either the free-base or zinc-metallated tetra(4-pyridyl)porphyrin (TPyP or Zn–TPyP, respectively), taking advantage of the complementary tetradentate H-atom donor and H-atom acceptor capacity of the component species. The reaction of BTCA with TPyP yields flat square-grid-type hydrogen bonded arrays, wherein every BTCA moiety interacts with four different porphyrin units and each one of the latter links laterally to four different tetraacid molecules. Replacement of TPyP by Zn–TPyP adds axial coordination capacity to the porphyrin unit and changes the intermolecular interaction pattern. In this case, the supramolecular self-assembly involves trans-axial coordination of BTCA to Zn–TPyP, into a 2:1 complex of the two species, as well as extended hydrogen bonding in four lateral directions between the (BTCA)₂(Zn–TPyP) units thus formed. The hydrogen-bond networking takes place between the four N(pyridyl)-sites of the porphyrin scaffold and the axial tetracid ligands of four neighboring complexes. In the two crystals, the open hydrogen bonded molecular networks stack in an offset manner, incorporating molecules of the 1,1,2,2-tetrachloroethane solvent within channel zones that penetrate through the layered structure. Application of the TPyP scaffold in the formation of hydrogen-bonded (rather than coordination-driven) assemblies has not been explored prior to our work on this subject.     

Cyclic Octamer of Hydroxyl-functionalized Cations with Net Charge Q=+8e Kinetically Stabilized by a ‘Molecular Island’ of Cooperative Hydrogen Bonds

Cyclic octamers are well-known structural motifs in chemistry, biology and physics. These include covalently bound cyclic octameric sulphur, cylic octa-alkanes, cyclo-octameric peptides as well as hydrogen-bonded ring clusters of alcohols. In this work, we show that even calculated cyclic octamers of hydroxy-functionalized pyridinium cations with a net charge Q=+8e are kinetically stable. Eight positively charged cations are kept together by hydrogen bonding despite the strong Coulomb repulsive forces. Sufficiently long hydroxy-octyl chains prevent “Coulomb explosion” by increasing the distance between the positive charges at the pyridinium rings, reducing the Coulomb repulsion and thus strengthen hydrogen bonds between the OH groups. The eightfold positively charged cyclic octamer shows spectroscopic properties similar to those obtained for hydrogen-bonded neutral cyclic octamers of methanol. Thus, the area of the hydrogen bonded OH ring represents a ‘molecular island’ within an overall cationic environment. Although not observable, the spectroscopic properties and the correlated NBO parameters of the calculated cationic octamer support the detection of smaller cationic clusters in ionic liquids, which we observed despite the competition with ion pairs wherein attractive Coulomb forces enhance hydrogen bonding between cation and anion.     

Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study

The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.