One-pot synthesis of hybrid macrocyclic pentamers with variable functionalizations around the periphery

Rather than four- or six-residue macrocylces, one-pot macrocyclization allows for the highly selective formation of five-residue macrocycles rigidified by intramolecular hydrogen bonds. Variable functionalizations around the pentameric periphery were achieved by reacting monomers with higher oligomers bearing different exterior side chains. The formation of these hybrid pentamers suggests a chain-growth mechanism for the one-pot macrocyclization where the successive addition of monomers onto higher oligomers is faster than those between two monomers or two higher oligomers.     

Cyclam‐Cored Dendrimers Appended with Four Dendrons of Two Different Types: Intradendrimer Energy Transfer

We have synthesized two cyclam‐cored dendrimers appended with dendrons of two different types by proper protection/deprotection of the cyclam unit. The resulting dendrimers contain six naphthyl and two dansyl units ( N6 D2 ) or two dansyl and six naphthyl units ( N2 D6 ) at the periphery. Their photophysical properties have been compared to those of a dendrimer containing 8 dansyl units ( D8 ) and a previously investigated dendrimer containing 8 naphthyl units ( N8 ). The absorption spectra are those expected on the basis of the number of chromophores, demonstrating that no ground state interaction takes place. The emission spectra of N2 D6 and N6 D2 show naphthalene localized and naphthalene excimer emission similar to those observed in the case of N8 , together with a much stronger dansyl emission with maximum at 525 nm. Addition of CF₃SO₃H to dendrimer solutions in CH₃CN/CH₂Cl₂ 1:1 (v/v) leads to protonation of the aliphatic amine units of the cyclam core at first and then of the aromatic amine of each dansyl chromophores. Cyclam can be diprotonated and this affects dansyl absorption and, most significantly, emission bands by a charge perturbation effect. Each dansyl unit is independently protonated in both dendrimers. The most interesting photophysical feature of these heterofunctionalized cyclam‐cored dendrimers is the occurrence of an intradendrimer photoinduced energy transfer from naphthyl to dansyl chromophores of two different dendrons (interdendron mechanism). The efficiency of this process is 50 % for N6 D2 and it can be increased up to 75 % upon protonation of the cyclam core and formation of N6 D2 (2H⁺). This arises from the fact that protonation of the amine units of the cyclam prevents formation of exciplexes upon naphthyl excitation, thus shutting down one of the deactivation processes of the fluorescent naphthyl excited state.     

Synthesis and energy-transfer properties of poly(amidoamine) dendrons modified with naphthyl and dansyl groups

Poly(amidoamine) dendrons of 1-3 generations with naphthyl groups at the periphery and a dansyl group at the focal point were synthesized and carefully characterized. Intramolecular energy-transfer properties of these flexible aliphatic-scaffold light-harvesting dendrons were investigated by UV-vis absorption and fluorescence spectroscopy. Efficient energy transfer from the naphthyl groups to the dansyl group occurred for both the first and the second generation dendrons (the energy-transfer efficiency was 94.3% and 76.9%, respectively), whereas the third generation dendron exhibited a low energy-transfer efficiency of 17.8%. The average donor-acceptor distances between the naphthyl and dansyl groups were calculated for different generation dendrons. Different degrees of the backfolding of dendritic branches were used to interpret the different donor-acceptor distances.     

Homopolymeric pyrrolidine-amide oligonucleotide mimics: Fmoc-synthesis and DNA/RNA binding properties

By chemically modifying or replacing the backbone of oligonucleotides it is possible to modulate the DNA and RNA recognition properties and fine-tune the physiochemical properties of oligomers. This is important because it challenges our understanding of natural nucleic acid structural and recognition properties and can lead to nucleic acid mimics with a wide range of applications in nucleic acid targeting, analysis or diagnostics. In this paper we describe the solid phase synthesis of pyrrolidine-amide oligonucleotide mimics (POMs) using Fmoc-peptide chemistry. This required the synthesis of adeninyl, cytosinyl, thyminyl and guaninyl pyrrolidine monomers, with Fmoc- and standard acyl-protecting groups on the exocyclic amino groups and nucleobases respectively. These monomers were used to synthesise several thyminyl and adeninyl POM pentamers, with modest coupling efficiency. The pentamers were purified by RP-HPLC, characterised by mass spectrometry and their DNA and RNA binding properties were investigated using UV thermal denaturation/renaturation experiments. This revealed that all the pentamers exhibit strong affinity for complementary nucleic acids. The further evaluation of longer mixed-sequence POMs is described in a second accompanying paper (R. J. Worthington et al., Org. Biomol. Chem., 2006, DOI: 10.1039/b613386j).     

Synthesis of bi-fluorescence-labeled lactoside: A substrate for continual assay of ceramide glycanase

A bi-fluorescence labeled derivative suitable for analysis of ceramide glycanase activity was constructed from 4-pentenyl lactoside. Selective modification of the galactosyl residue was attained by formation of 4′,6′-naphthylmethylidene derivative, which was followed by regioselective reductive ring opening. The aglycon was extended by Michael addition of 2-aminoethanetiol, and dansylated at the terminal amino group. Excitation of the naphthyl group results in emission from the dansyl group, while the emission from the naphthyl group is quenched by the dansyl group. Upon digestion with ceramide glycanase, the energy transfer is severed and a decrease in the dansyl emission concommitant with an increase in the naphthyl emission was observed. This substrate was successfully used to analyze ceramide glycanase activity.     

One‐Pot Multimolecular Macrocyclization for the Expedient Synthesis of Macrocyclic Aromatic Pentamers by a Chain Growth Mechanism

POCl₃‐mediated one‐pot macrocyclization allows the highly selective formation of five‐residue macrocycles that are rigidified by internally placed intramolecular hydrogen bonds. Mechanistic investigation by using tailored competition experiments and kinetic simulation provides a comprehensive model, supporting a chain‐growth mechanism underlying the one‐pot formation of aromatic pentamers, whereby the successive addition of a bifunctional monomer unit onto either another monomer or the growing oligomeric backbone is faster than other types of bimolecular condensations involving oligomers longer than monomers. DFT calculations at the B3LYP/6‐31G* level reveal the five‐residue pentamer to be the most stable with respect to alternative four‐, six‐, and seven‐residue macrocycles. These novel mechanistic insights may become useful in analyzing other macrocyclization, oligomerization, and ploymerization reactions.     

Maximizing the stereochemical diversity of spiro-ladder oligomers

[reaction: see text] We introduce all stereoisomers of a bis-amino acid building block derived from trans-4-hydroxy-L-proline. This small library of monomers allows arbitrary stereochemical configuration at any chiral center within our spiro-ladder oligomers. Three tetramer oligomers containing several combinations of the monomers 1-4 were synthesized; we explored the effect of monomer sequence on scaffold conformation by NMR.     

Density Functional Theory Study of Water Diffusion and Clustering on Pd（111）

1 INTRODUCTION The interaction of water molecules with metal sur- faces plays a vital role in a number of important pro- cesses, such as corrosion, heterogeneous catalysis, electrochemical processes in aqueous solutions, hydrogen production, etc.[1] The structure and pro- perties of water adsorbed on well-defined metal sur- faces have been the subject of numerous experi- mental and theoretical investigations. There have been a number of experimental studies of water on metal surfaces throu…     

Flexibility and lengths of bis-peptide nanostructures by electron spin resonance

We demonstrate the use of electron spin resonance (ESR) to determine long-range distances and flexibility in water-soluble bis-peptide molecular rods. Bis-peptide oligomers with 4-8 monomer units were synthesized. ESR determined that the end-to-end length of the peptides is linearly proportional to the number of monomers. The linear shape is, therefore, easily interpreted from the data. In addition, the flexibility of the rods was quantified directly from the ESR-determined distance distribution functions. Quantitative information on chain length and flexibility is important to develop the use of these oligomers as rodlike structural elements for applications such as bivalent display of ligands and as elements of future nanoscale devices.     

One‐stage synthesis of narrowly dispersed polymeric core‐shell microspheres

A method of one‐stage soap‐free emulsion polymerization to synthesize narrowly dispersed core‐shell microspheres is proposed. Following this method, core‐shell microspheres of poly(styrene‐co‐4‐vinylpyridine), poly(styrene‐co‐methyl acrylic acid), and poly[styrene‐co‐2‐(acetoacetoxy)ethyl methacrylate‐co‐methyl acrylic acid] are synthesized by one‐stage soap‐free emulsion polymerization of a mixture of one or two hydrophobic monomers and a suitable hydrophilic monomer in water. The effect of the molar ratio of the hydrophobic monomer to the hydrophilic one on the size, the core thickness, and the shell thickness of the core‐shell microspheres is discussed. The molar ratio of the hydrophobic and hydrophilic monomers and the hydrophilicity of the resultant oligomers of the hydrophilic monomer are optimized to synthesize narrowly dispersed core‐shell microspheres. A possible mechanism of one‐stage soap‐free emulsion polymerization to synthesize core‐shell microspheres is suggested and coagglutination of the oligomers of the hydrophilic monomers on the hydrophobic core is considered to be the key to form core‐shell microspheres. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1192–1202, 2008     

Cryoscopy on sulfuric acid solutions of a heterocyclic polymer (BBB) and related compounds

Cryoscopic measurements have been carried out on solutions in sulfuric acid of a heterocyclic polymer, its monomers, and certain of its oligomers. The polymer, BBB, is prepared by the polycondensation of 1,4,5,8-naphthalenetetracarboxylic acid (NTC) with 3,3′-diaminobenzidine (DAB). The results show that the polymer, its oligomers and one of its monomers, DAB, are all extensively protonated in sulfuric acid, whereas its other monomer is not. The degree of protonation appears to be greater for the polymer than for its low molecular weight oligomers.     

Oligodeoxyfluorosides: Strong Sequence Dependence of Fluorescence Emission

We describe the properties of a series of oligomeric polyfluorophores assembled on the DNA backbone. The 11 oligomers (oligodeoxyfluorosides, ODFs), 4-7 monomers in length, were composed of only two fluorescent monomers and a spacer in varied sequences, and were designed to test how fluorescent nucleobases can interact electronically to yield complexity in fluorescence emission. The monomer fluorophores were deoxyribosides of pyrene and perylene, which emit light in violet and blue wavelengths, respectively. The experiments show that simple variation in sequence and spacing can dramatically change fluorescence, yielding emission maxima ranging from 380 to 557 nm and visible colors from violet to orange-red. Fluorescence lifetime data, excitation spectra, and absorption data point to a number of multi-fluorophore electronic interactions, including pyrene-pyrene and perylene-perylene excimers, pyrene-perylene exciplexes, as well as monomer dye emissions, contributing to the final spectral outcomes. Thus, two simple fluorophores can be readily combined to give emissions over much of the visible spectrum, all requiring only a single excitation. The results demonstrate that fluorescent nucleobases in oligomeric form can act cooperatively as electronic units, and that fluorophore sequence in such oligomers is as important as fluorophore composition in determining fluorescence properties.     

Affinity Polymers Tailored for the Protein A Binding Site of Immunoglobulin G Proteins

Rational design in combination with a screening process was used to develop affinity polymers for a specific binding site on the surface of immunoglobulin G (IgG) proteins. The concept starts with the identification of critical amino acid residues on the protein interface and their topological arrangement. Appropriate binding monomers were subsequently synthesized. Together with a sugar monomer (2–5 equiv) for water solubility and a dansyl monomer (0.5 equiv) as a fluorescent label, they were subjected in aqueous solution to linear radical copolymerization in various compositions (e.g., azobisisobutyronitrile (AIBN), homogeneous water/DMF mixtures). After ultrafiltration and lyophilization, colorless dry water‐soluble powders were obtained. NMR spectroscopic and gel permeation chromatography (GPC) characterization indicated molecular weights between 30 and 500 kD and confirmed retention of monomer composition as well as the absence of monomers. In a competitive enzyme‐linked immunosorbent assay (ELISA) screen of the polymer libraries (20–50 members), few copolymers qualified as strong and selective binders for the protein A binding site on the Fc fragment of the antibody. Their monomer composition precisely reflected the critical amino acids found at the interface. The simple combination of a charged and a nonpolar binding monomer sufficed for selective submicromolar IgG recognition by the synthetic polymer. Affinities were confirmed by fluorescence titrations; they increased with decreasing salt load but remained largely unaltered at lowered pH. Other proteins, including those of similar size and isoelectric point (pI), were bound 10–1000 times less tightly. This example indicates that interaction domains in other proteins may also be targeted by synthetic polymers if their comonomer composition reflects the nature and arrangement of amino acid residues on the protein surface.     

Model problems in depolymerization kinetics of chain oligomers: 1. Successive detachment of monomer units from the chain end

For the successive detachment of monomer units from the end of a macroradical (one of the two main depolymerization mechanisms, of which the other is random chain scission), the time dependence of the monomers concentration, the average chain length, and width of the chain-length distribution of oligomers with allowance for the reverse reactions of monomer attachment to the radicals has been revealed without the use of the quasi-steady state approximation. The conditions under which the chain scission and the monomer evaporation occur at thermal equilibrium have been found.     

Automated Solid-Phase Oligo(disulfide) Synthesis

A method for automated solid-phase synthesis of oligo(disulfide)s was developed. It is based on a synthetic cycle comprising removal of a protecting group from a resin-bound thiol followed by treatment with monomers containing a thiosulfonate as an activated precursor. For ease of purification and characterization, the disulfide oligomers were synthesized as extensions of oligonucleotides on an automated oligonucleotide synthesizer. Six different dithiol monomer building blocks were synthesized. Sequence-defined oligomers of up to seven disulfide units were synthesized and purified. The sequence of the oligomer was confirmed by tandem MS/MS analysis. One of the monomers contains a coumarin cargo that can be released by a thiol-mediated release mechanism. When the monomer was incorporated into an oligo(disulfide) and subjected to reducing conditions, the cargo was released under near-physiological conditions, which underlines the potential use of these molecules in drug delivery systems.     

Solid-phase Synthesis of PNA Monomer by Ugi Four-component Condensation Reaction

Peptide nucleic acids (PNA) oligomers were synthesized in most cases by peptide a peptide synthesis from N-protected monomers. In this work a new method of obtaining PNA monomer by Ugi four-component condensation reaction was tested by solid-phase synthesis. The Fmoc protected PNA monomer was build up with thymin-l-yl acetic acid, 3-methylbutyl aldehyde, Fmoc protected aminoethyl isocyanide and Gly-Wang resin.     

Conformational control in the cyclization of hydrogen-bonded supramolecular polymers

Bifunctional 2-ureido-4[1H]-pyrimidinone (UPy) derivatives can form small cyclic oligomers as well as long supramolecular polymers in chloroform solutions using the quadruple hydrogen-bonding motif. Ring-chain equilibria of a set of supramolecular monomers containing methyl-substituted alkyl linkers between the hydrogen-bonding UPy moieties were investigated by (1)H NMR spectroscopy and viscometry. The data were characterized in terms of critical concentration (CC, denoting the onset of polymerization) and equilibrium cyclic dimer concentration (EDC, representing preorganization of the monomer toward selective formation of cyclic dimer). Methyl substituents in the monomer were found to promote conformations favorable for cyclic dimerization, leading to an increase in both the EDC and the CC with respect to unsubstituted monomer. Furthermore, we observed an odd-even effect in the CC and EDC with increasing length of the linker between the hydrogen-bonding units. The combined results allow tuning of the critical concentration over a broad range and offer detailed information on the correlation between monomer structure, conformation, and polymerizability which may provide new insights for the study and design of other ring-chain equilibria or helix-random coil transitions.     

Radiation-induced reactions in poly(1,2,2,2-tetrachloroethyl methacrylate)/monomer mixtures

The work has been aimed at characterizing final products of radiation-induced reactions in polymer/monomer mixtures particularly by analytical and preparative HPLC. Poly(1,2,2,2-tetrachloroethyl methacrylate) (PTCEMA) was used as polymer while p-cumylphenythacrylate (CUPMA) was mainly added as monomer. The substances were irradiated with γ-doses up to 160 kGy. The electron beam doses at an acceleration voltage of 30 kV corresponded to this value.With the HPLC method a CUPMA-grafted PTCEMA and CUPMA oligomers were detected. UV and ¹H-NMR spectra of these separated substances obtained by preparative HPLC confirmed the formation of a graft polymer. IR and Cl-elementary analyses revealed a Cl-substitution in CUPMA oligomers. Evidently, the conversion of unsaturated monomers is decisively determined by the radiation-chemical behaviour of the polymer.     

Substitution effects on the molecular structures and the longitudinal molecular polarizabilities of all‐trans polyacetylene oligomers of increasing size

AM1 calculations have been performed on all‐trans polyacetylene (PA) oligomers with an increasing number of unit cells to study the effect of donor or acceptor groups capped at opposite ends of PA chains, substituents included in the monomers, substituents' number and position in the monomers, on the molecular structures, and the static longitudinal polarizabilities (α_L) and second‐order hyperpolarizabilities (γ_L). Substitution of CH₃, Cl, or F group at opposite ends of an oligomer results in an increase of α_L and γ_L, but the substitution effects on Δα_L(N) and Δγ_L(N) are very small. The asymptotic limit values are unaffected by the substitution. F substituent included in the monomer of an oligomer enhances the Δα_L(N) and Δγ_L(N) values, especially at large N, but including monomers with CH₃ or Cl substituents substantially reduces the Δα_L(N) and Δγ_L(N) values. We alter the number of F substituents included in the monomers of oligomers and find that including two F substituents in the monomer leads to the larger enhancement of Δγ_L(N). The effect of F substituents' position in the monomers of oligomers on Δα_L and Δγ_L is obvious. The results may be helpful for the design of new materials for applications in nonlinear optics, particularly in the area of poled polymer films. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Chimeric (aeg-pyrrolidine)PNAs: synthesis and stereo-discriminative duplex binding with DNA/RNA

The design and facile conversion of naturally occurring 4-hydroxyproline to all four diastereomers of thymine pyrrolidine PNA monomer, (2R,4S)-adenine, -guanine and -cytosine monomers and their incorporation into duplex forming PNA oligomers is reported. The interesting results of the hybridization studies with complementary DNA/RNA sequences in either parallel or antiparallel orientation reveal the stereochemistry-dependent DNA vs. RNA discriminations and parallel/antiparallel orientation selectivity.