Molecular dynamics of a peptide chain, studied by intramolecular excimer formation

Picolinamide-assisted ortho-C-H functionalization of pyrenylglycine derivatives using aryl iodides

Chemical transformations involving the pyrenylglycine motif (an unnatural amino acid) and practical methods toward it are seldom known. This work aimed at developing a method for synthesizing novel pyrenylglycine (pyrene-based glycine) unnatural amino acid derivatives. To realize this, initially, a new pyrenylglycine substrate possessing the picolinamide moiety was assembled via the Ugi multicomponent reaction. The picolinamide moiety linked to amine substrates is a well-known bidentate directing group for accomplishing the site-selective γ-C-H functionalization of amines. Subsequently, it was aimed at using a Pd(II)-catalyzed bidentate directing group-aided γ-C-H arylation strategy for generating a wide range of unprecedented examples of C(2)-H arylated pyrenylglycines. Accordingly, pyrenylglycine possessing the picolinamide moiety was subjected to Pd(II)-catalyzed C(2)-H arylation in the non-K-region to afford a library of C(2)-arylated pyrenylglycines (π-extended pyrenes). Additionally, pyrenylglycine-based small peptides were assembled using C(2)-arylated pyrenylglycines. The X-ray structure of a representative compound was obtained, which corroborated the structure of pyrenylglycine and the regioselectivity of C(2)-H arylation of the pyrene in the non-K-region.

Pyrene based materials as fluorescent probes in chemical and biological fields

Molecules that experience a change in their fluorescence emission due to the effect of fluorescence enhancement upon binding events, like chemical reactions or a change in their immediate environment, are regarded as fluorescent probes.

Fluorescence Quenching of Dipyrenylalkanes by an Electron/Charge Acceptor

Compounds possessing two fluorophoric moieties may exhibit dual fluorescence, one characterizing the monomeric fluorophore unit and the other characterizing the intramolecular aggregate. Fluorescence quenching of two dipyrenylalkanes, 1,3-bis(1-pyrenyl)propane [1Py(3)1Py] and 1,10-bis(1-pyrenyl)decane [1Py(10)1Py] having different alkyl chains separating the two termini pyrenyl groups that are capable of forming an intramolecular excimer, by an electron/charge-accepting quencher, nitromethane, is investigated in four different solvents-nonpolar (cyclohexane (CH)), polar-aprotic (acetonitrile (ACN)), polar-protic (ethanol (EtOH)), and chlorinated (dichloromethane (DCM))-under ambient conditions. For a given probe in a solvent, fluorescence from the monomer and the intramolecular excimer are quenched with similar efficiencies; the efficiency of quenching is higher for the probe with the longer alkyl chain separating the two fluorophores. Quenching efficiency is significantly higher in chlorinated solvent DCM. The bimolecular quenching rate constants for intramolecular excimer, however, are either comparable or lower for the longer alkyl chain compound. It is suggested that, while the donor electronic excited-state energetics is more favorable for the long alkyl chain compound, the approach of the quencher to the intramolecular excimer appears to be hindered by the presence of a longer alkyl chain.

Bis-pyrene probes of foldamer conformation in solution and in phospholipid bilayers

Exploring the detailed structural features of synthetic molecules in the membrane phase requires sensitive probes of conformation. Here we describe the design, synthesis and characterization of bis(pyrene) probes that report conformational changes in membrane-active dynamic foldamers. The probes were designed to distinguish between left-handed (M) and right-handed (P) screw-sense conformers of 3₁₀-helical α-aminoisobutyric acid (Aib) peptide foldamers, both in solution and in bilayer membranes. Several different bis(pyrene) probes were synthesized and ligated to the C-terminus of Aib tetramers that had different chiral residues at the N-terminus, residues that favored either an M or a P screw-sense in the 3₁₀-helix. The readily synthesized and conveniently incorporated N-acetyl-1,2-bis(pyren-1'-yl)ethylenediamine probe proved to have the best properties. In solution, changes in foldamer screw-sense induced substantial changes in the ratio of excimer/monomer fluorescence emission (E/M) for this reporter of conformation, with X-ray crystallography revealing that opposite screw-senses produce very different interpyrene distances in the reporter. In bilayers, this convenient and sensitive fluorescent reporter allowed, for the first time, an investigation of how the chirality of natural phospholipids affects foldamer conformation.

Excimer Formation Dynamics of Dipyrenyldecane in Structurally Different Ionic Liquids

Ionic liquids, being composed of ions alone, may offer alternative pathways for molecular aggregation. These pathways could be controlled by the chemical structure of the cation and the anion of the ionic liquids. Intramolecular excimer formation dynamics of a bifluorophoric probe, 1,3-bis(1-pyrenyl)decane [1Py(10)1Py], where the fluorophoric pyrene moieties are separated by a long decyl chain, is investigated in seven different ionic liquids in 10-90 °C temperature range. The long alkyl separator allows for ample interaction with the solubilizing milieu prior to the formation of the excimer. The ionic liquids are composed of two sets, one having four ionic liquids of 1-butyl-3-methylimidazolium cation ([bmim⁺]) with different anions and the other having four ionic liquids of bis(trifluoromethylsulfonyl)imide anion ([Tf₂N^-]) with different cations. The excimer-to-monomer emission intensity ratio (I_E/I_M) is found to increase with increasing temperature in sigmoidal fashion. Chemical structure of the ionic liquid controls the excimer formation efficiency, as I_E/I_M values within ionic liquids with the same viscosities are found to be significantly different. The excited-state intensity decay kinetics of 1Py(10)1Py in ionic liquids do not adhere to a simplistic Birk's scheme, where only one excimer conformer forms after excitation. The apparent rate constants of excimer formation (k_a) in highly viscous ionic liquids are an order of magnitude lower than those reported in organic solvents. In general, the higher the viscosity of the ionic liquid, the more sensitive is the k_a to the temperature with higher activation energy, E_a. The trend in E_a is found to be similar to that for activation energy of the viscous flow (E_a,η). Stokes-Einstein relationship is not followed in [bmim⁺] ionic liquids; however, with the exception of [choline][Tf₂N], it is found to be followed in [Tf₂N^-] ionic liquids suggesting the cyclization dynamics of 1Py(10)1Py to be diffusion-controlled and to depend on the viscosity of the ionic liquid irrespective of the identity of the cation. The dependence of ionic liquid structure on cyclization dynamics to form intramolecular excimer is amply highlighted.

Viscosity dependence of intramolecular excimer formation with 1,5-bis(1-pyrenylcarboxy)pentane in alkane solvents as a function of temperature

Intramolecular excimer formation with 1,5-bis(1-pyrenylcarboxy)pentane, (1PC(5)1PC) is studied as a function of temperature in a series of alkane solvents and in toluene, covering a wide range of solvent viscosities η, from 0.2 to 125 cP. The rate constant k(a) of the monomer → excimer reaction is determined from the effectively single exponential monomer fluorescence decays. For the viscosity dependence of k(a) in n-alkanes, the Stokes-Einstein relation k(a) ∼ η(-1.0) does not hold. Instead, k(a) is proportional to η(-α), with α increasing upon cooling, from 0.56 at 85 °C to 0.86 at -30 °C. The activation energy E(a) of excimer formation with 1PC(5)1PC, always larger than the activation energy E(T/η) of solvent viscous flow, decreases when the solvent viscosity becomes smaller, from 20.7 kJ/mol in n-hexadecane to 11.8 kJ/mol in n-butane, approaching a value of 11-12 kJ/mol for the low viscosity solvents. As the excimer formation process depends on the restricted diffusion of the 1PC end groups as well as on the C-O and C-C rotations in the -O(CH(2))(5)O- chain, the limiting barrier of 11-12 kJ/mol is attributed to the activation energy E(c) of the multiple bond rotations. This fractional viscosity dependence (α < 1.0) is caused by the multidimensional character of the barrier crossing in the excimer formation process. This multidimensional character should also be taken into account in investigations of polymers and biological media employing excimer formation.

Diastereodifferentiation of Novel Naphthalene Dyads by Fluorescence Quenching and Excimer Formation

Four new bichromophoric naphthalene dyads in form of diastereomeric pairs are synthesized and photophysically characterized. For a closely related group of compounds (NAP-NAP, MNAP-NAP, MNAP-MNAP), systematic variation of the urea linker led to the observation of intramolecular fluorescence quenching for tertiary urea, but not for secondary urea. Chiral information contained in the dyads has an impact on the efficiency of this process. Furthermore, for the case of (R,R)-MNAP-MNAP, excimer formation in the pre-organized dyad was noted, while being absent in the corresponding (R,S) diastereomer. These differences in photophysical behavior are ascribed to the geometry of the linker and to the chiral information contained in the diastereomeric compounds. Other dyads, such as NPX-NPX, included naproxen as the chromophore. For these compounds strong excimer emission is obtained, however, only very small diastereodifferentiation is observed for the two investigated stereoisomers.

Contribution of a pyrene fluorescence probe to the aggregation propensity of polypeptides

[structure: see text] Two synthetic polypeptides, TT1p and TT1b, have been used in comparative aggregation equilibrium studies. The findings reveal that a single alkylpyrene moiety in TT1p contributes about 30% of the polypeptide dimerization energy in aqueous media. This result not only is informative with regard to the aggregation properties of these particular photoactive polypeptides but also provides a quantitative understanding of the limitations on the use of pyrene chromophores as emission probes.

Side reaction of pyrenylalanine-peptides containing NG-tosylarginine during detosylation with hydrogen fluoride

Formation of by-products of pyrenylalanine-peptides was observed during the cleavage of a tosyl group in pyrenylalanine-peptides containing an Arg(Tos) residue with HF. NMR and fluorescence experiments showed that by-products were compounds in which a pyrenyl group was modified with a tosyl group(s). The side reaction was little suppressed by the addition of usual scavengers such as anisole, 1,2-ethanedithiol, thioanisole and p-cresol. Under the conditions used for the cleavage of N alpha-Boc group, i.e., trifluoroacetic acid or 4 M HCl in dioxane, the pyrenylalanine residue was stable. No side reaction was, furthermore, observed in the reductive cleavage with sodium in liquid ammonia. These results suggest that the side reaction may be due to an electrophilic attack of tosyl cations to the electron-rich pyrenyl group in the pyrenylalanine residue under the HF-mediated acidic conditions.

The spectroscopic analysis for binding of amphipathic and antimicrobial model peptides containing pyrenylalanine and tryptophan to lipid bilayer

The binding of basic amphipathic fluorescent peptides to lipid bilayers was studied in relation to their antimicrobial activity. Four fluorescent peptides containing pyrenylalanine or tryptophan in an amphipathic basic peptide (4(4] consisting of four repeated units of tetrapeptide, -L-Leu-L-Ala-L-Arg-L-Leu-, were found to have antimicrobial activities against Gram-positive bacteria and to take conformations with fairly high alpha-helical content both in aqueous solutions and liposomes. The fluorescence spectroscopic data suggested that the pyrenylalanine-peptide existed as a monomer in methanol or liposomes but as an oligomer in aqueous solutions to form an excimer between pyrenylalanyl residues. Upon binding with liposomes, the fluorescence spectra of the tryptophan-containing peptide shifted to a shorter wavelength, indicating the change in the state of tryptophan from hydrophilic environment to hydrophobic one. The analytical data for the quenching of tryptophan fluorescence by I- anion suggest that the tryptophan residue in the peptide is not deeply buried in the hydrophobic core of the bilayers. Based on these findings, it is suggested that the peptides may interact with liposomes in such a manner that they lie parallel to the surface of the lipid bilayers with their hydrophobic regions shallowly in the amphipathic moiety of the bilayers.

Synthesis, receptor binding activity and fluorescence property of fluorescent enkephalin analogs containing L-1-pyrenylalanine

The novel fluorescent amino acid, L-1-pyrenylalanine (L-Pya), was prepared by the asymmetric hydrogenation of cyclic dehydrodipeptide. Fluorescent enkephalins containing one or two Pya residues at position 1,4 or 5 of [D-Ala2, Leu5]enkephalin were synthesized by the solution method. Mono-Pya-enkephalins showed strong fluorescence intensities and potent binding affinities with specificity and selectivity for opiate receptors. However, di-Pya-enkephalins showed markedly decreased receptor binding affinities. These results indicate that the incorporation of two Pya residues into enkephalin makes the peptide unable to interact with the opiate receptors, although introduction of one Pya residue is effective to elicit a specific receptor interaction. Di-Pya-enkephalins showed intramolecular excimer spectra, indicating that the peptides are able to take possible folded conformations.