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PubMedDate not supplied

Aza-amino acid scanning of secondary structure suited for solid-phase peptide synthesis with fmoc chemistry and aza-amino acids with heteroatomic side chains.

Aza-peptides, peptide analogues in which the alpha-carbon of one or more of the amino acid residues is replaced with a nitrogen atom, exhibit a propensity for adopting beta-turn conformations. A general Fmoc-protection protocol for the stepwise solid-phase synthesis of aza-peptides has now been developed based on the activation of N'-alkyl fluoren-9-ylmethyl carbazates with phosgene for coupling the aza-amino acid residues. This method has proven effective for introducing aza-amino acid residues with aliphatic (Ala, Leu, Val, and Gly) and aromatic (Phe, Tyr, and Trp) side chains. Acid promoted loss of aromatic side chains was noted with aza-Trp and aza-Tyr residues during peptide cleavage and suppressed by temperature control in the case of the latter. In addition, aza-peptides with heteroatomic side chain residues (Lys, Orn, Arg, and Asp) were conveniently synthesized using this protocol. Partial aza-amino acid scans were performed on three biologically active peptides: the potent tetrapeptide melanocortin receptor agonist, Ac-His-d-Phe-Arg-Trp-NH2; the growth hormone secretagogue hexapeptide, GHRP-6, His-d-Trp-Ala-Trp-d-Phe-Lys-NH2; and the human calcitonin gene-related peptide (hCGRP) antagonist, FVPTDVGPFAF-NH2. This practical procedure for aza-amino acid scanning using Fmoc-based solid-phase synthesis should find general utility for probing the existence and importance of beta-turn conformations in bioactive peptides.

Amino Acid Sequence↗
PubMed2002

Hydrocarbon oxidation by Bis-mu-oxo manganese dimers: electron transfer, hydride transfer, and hydrogen atom transfer mechanisms.

Described here are oxidations of alkylaromatic compounds by dimanganese mu-oxo and mu-hydroxo dimers [(phen)(2)Mn(IV)(mu-O)(2)Mn(IV)(phen)(2)](4+) ([Mn(2)(O)(2)](4+)), [(phen)(2)Mn(IV)(mu-O)(2)Mn(III)(phen)(2)](3+) ([Mn(2)(O)(2)](3+)), and [(phen)(2)Mn(III)(mu-O)(mu-OH)Mn(III)(phen)(2)](3+) ([Mn(2)(O)(OH)](3+)). Dihydroanthracene, xanthene, and fluorene are oxidized by [Mn(2)(O)(2)](3+) to give anthracene, bixanthenyl, and bifluorenyl, respectively. The manganese product is the bis(hydroxide) dimer, [(phen)(2)Mn(III)(mu-OH)(2)Mn(II)(phen)(2)](3+) ([Mn(2)(OH)(2)](3+)). Global analysis of the UV/vis spectral kinetic data shows a consecutive reaction with buildup and decay of [Mn(2)(O)(OH)](3+) as an intermediate. The kinetics and products indicate a mechanism of hydrogen atom transfers from the substrates to oxo groups of [Mn(2)(O)(2)](3+) and [Mn(2)(O)(OH)](3+). [Mn(2)(O)(2)](4+) is a much stronger oxidant, converting toluene to tolyl-phenylmethanes and naphthalene to binaphthyl. Kinetic and mechanistic data indicate a mechanism of initial preequilibrium electron transfer for p-methoxytoluene and naphthalenes because, for instance, the reactions are inhibited by addition of [Mn(2)(O)(2)](3+). The oxidation of toluene by [Mn(2)(O)(2)](4+), however, is not inhibited by [Mn(2)(O)(2)](3+). Oxidation of a mixture of C(6)H(5)CH(3) and C(6)H(5)CD(3) shows a kinetic isotope effect of 4.3 +/- 0.8, consistent with C-H bond cleavage in the rate-determining step. The data indicate a mechanism of initial hydride transfer from toluene to [Mn(2)(O)(2)](4+). Thus, oxidations by manganese oxo dimers occur by three different mechanisms: hydrogen atom transfer, electron transfer, and hydride transfer. The thermodynamics of e(-), H(*), and H(-) transfers have been determined from redox potential and pK(a) measurements. For a particular oxidant and a particular substrate, the choice of mechanism is influenced both by the thermochemistry and by the intrinsic barriers. Rate constants for hydrogen atom abstraction by [Mn(2)(O)(2)](3+) and [Mn(2)(O)(OH)](3+) are consistent with their 79 and 75 kcal mol(-)(1) affinities for H(*). In the oxidation of p-methoxytoluene by [Mn(2)(O)(2)](4+), hydride transfer is thermochemically 24 kcal mol(-)(1) more facile than electron transfer; yet the latter mechanism is preferred. Thus, electron transfer has a substantially smaller intrinsic barrier than does hydride transfer in this system.

Anthracenes↗
PubMed2003

Oxidation of C-H bonds by [(bpy)2(py)RuIVO]2+ occurs by hydrogen atom abstraction.

Anaerobic oxidations of 9,10-dihydroanthracene (DHA), xanthene, and fluorene by [(bpy)(2)(py)Ru(IV)O](2+) in acetonitrile solution give mixtures of products including oxygenated and non-oxygenated compounds. The products include those formed by organic radical dimerization, such as 9,9'-bixanthene, as well as by oxygen-atom transfer (e.g., xanthone). The kinetics of these reactions have been measured. The kinetic isotope effect for oxidation of DHA vs DHA-d(4) gives k(H)/k(D) > or = 35 +/- 1. The data indicate a mechanism of initial hydrogen-atom abstraction forming radicals that dimerize, disproportionate and are trapped by the oxidant. This mechanism also appears to apply to the oxidations of toluene, ethylbenzene, cumene, indene, and cyclohexene. The rate constants for H-atom abstraction from these substrates correlate well with the strength of the C-H bond that is cleaved. Rate constants for abstraction from DHA and toluene also correlate with those for oxygen radicals and other oxidants. The rate constant for H-atom transfer from toluene to [(bpy)(2)(py)Ru(IV)O](2+) appears to be close to that predicted by the Marcus cross relation, using a tentative rate constant for hydrogen atom self-exchange between [(bpy)(2)(py)Ru(III)OH](2+) and [(bpy)(2)(py)Ru(IV)O](2+).

Anthracenes↗
PubMed2004

A highly discriminating quencher-free molecular beacon for probing DNA.

We inserted a fluorene-labeled deoxyuridine derivative, synthesized using Sonogashira coupling, efficiently into the loop region of a DNA hairpin using phosphoramidite chemistry. This molecular beacon, which features no additional fluorescence quencher, discriminates between perfect and one-base-mismatched base pairing by changes in its fluorescence intensity. The discrimination factor is 14.7 for the recognition of a single (A/C) base mismatch.

Base Pair Mismatch↗
PubMed2006

Optimization of the molecular orbital energies of conjugated polymers for optical amplification of fluorescent sensors.

Cationic water-soluble poly(fluorene-co-phenylene)s with electron withdrawing or donating substituents on the conjugated backbone were designed and synthesized. Fluorescence resonance energy transfer (FRET) experiments between these conjugated polymers and dye-labeled single-stranded DNA (ssDNA-C*) reveal the importance of matching donor and acceptor orbital energy levels to improve the sensitization of C* emission. Quenching of polymer fluorescence with ssDNA-C* and differences in C* emission suggest involvement of photoinduced charge transfer (PCT) as an energy wasting mechanism. The HOMO and LUMO energy levels of the conjugated polymers and C serve as a preliminary basis to understand the competition between FRET and PCT. Dilution of C in polymer/ssDNA-C complexes by addition of ssDNA yields insight into C*...C self-quenching. Under optimized conditions, where there is no probe self-quenching and minimum PCT, efficient signal amplification is demonstrated despite poor spectral overlap between polymer and C.

Biosensing Techniques↗
PubMed2006

Nature and energies of electrons and holes in a conjugated polymer, polyfluorene.

Electrons and holes were injected selectively into poly-2,7-(9,9-dihexylfluorene) (pF) dissolved in a tetrahydrofuran (THF) and a 1,2-dichloroethane (DCE) solution, respectively, using pulse radiolysis. Transient absorption spectra of monoions of both signs revealed two bands attributable to formation of polarons, one in the visible region (pF+* at 580 nm, pF-* at 600 nm) and another in the near-IR region. Additional confirmation for the identification of pF+* and pF-* comes from bimolecular charge-transfer reactions, such as bithiophene-* + pF --> pF-* or pF+* + TTA --> +TTA+* (TTA = tri-p-tolylamine), in which known radical ions transfer charge to pF or from pF. Difference absorption spectra of pF chemically reduced by sodium in THF provided a ratio of absorbance of anions formed to bleaching of the neutral band at 380 nm. In conjunction with pulse-radiolysis results, the data show that each polaron occupies 4.5 +/- 0.5 fluorene units, most probably contiguous units. Extensive reduction of pF by sodium also revealed resistance to formation of bipolarons: excess electrons reside as separate polarons when two or more electrons were injected. Redox equilibria with pyrene and terthiophene by pulse radiolysis established reversible one-electron redox potentials of E0(pF+/0) = +0.66 V and E0(pF0/-) = -2.65 V vs Fc+/0. Together with the excited-state energy, these results predict a singlet exciton binding energy of 0.2 eV for pF in the presence of 0.1 M tetrabutylammonium tetrafluoroborate. This binding energy would increase substantially without an electrolyte.

Biology↗
PubMed1993

Synthesis and pharmacological evaluation of hexahydrofluorenamines as noncompetitive antagonists at the N-methyl-D-aspartate receptor.

The noncompetitive (PCP) site of the N-methyl-D-aspartate (NMDA) receptor complex has been implicated in a number of pathologies, including the etiology of ischemic stroke. Recent testing has shown that cis-1,2,3,4,9,9a-hexahydro-N-methyl-4aH-fluoren-4a-amine (1), a rigid analog of PCP, is a potent antagonist at this site (IC50 = 30 nM for displacement of [3H]TCP). On the basis of this finding, a number of derivatives encompassing variations in stereochemistry, amine substitution and position, aromatic and aliphatic ring substitution, and heteroatom ring substitution have been prepared to explore the structure-activity relationships around this ring system. All compounds were evaluated for their PCP receptor affinity; potent compounds were also tested in vitro (cultured neurons) and in vivo (prevention of NMDA-induced lethality in mice). The present hexahydrofluorenamines demonstrated a wide range of potencies, with optimal affinity concentrated in analogs containing a heteroatom (sulfur) in the B ring (IC50 of 11 nM versus [3H]TCP for 16b), methyl substitution on the amine, and R stereochemistry at the 4a position. No significant improvement in affinity was seen with aromatic ring substitution. Aliphatic ring substitution, large amine substituents, and alterations in the position of amine substitution on the ring system resulted in a loss of potency. To explore the effect of simultaneous hydrogen bonding with a putative receptor atom from two directions, the 2-hydroxymethyl derivatives were prepared. This substitution resulted in a loss in receptor binding affinity. Molecular modeling, X-ray, and NMR studies have been used to determine an optimal conformation of the hexahydrofluoreneamines at the receptor site.

Animals↗
PubMed2001

Structure-based generation of a new class of potent Cdk4 inhibitors: new de novo design strategy and library design.

As a first step in structure-based design of highly selective and potent Cdk4 inhibitors, we performed structure-based generation of a novel series of Cdk4 inhibitors. A Cdk4 homology model was constructed according to X-ray analysis of an activated form of Cdk2. Using this model, we applied a new de novo design strategy which combined the de novo design program LEGEND with our in-house structure selection supporting system SEEDS to generate new scaffold candidates. In this way, four classes of scaffold candidates including diarylurea were identified. By constructing diarylurea informer libraries based on the structural requirements of Cdk inhibitors in the ATP binding pocket of the Cdk4 model, we were able to identify a potent Cdk4 inhibitor N-(9-oxo-9H-fluoren-4-yl)-N'-pyridin-2-ylurea 15 (IC(50) = 0.10 microM), together with preliminary SAR. We performed a docking study between 15 and the Cdk4 model and selected a reasonable binding mode which is consistent with the SAR. Further modification based on the proposed binding mode provided a more potent compound, N-[(9bR)-5-oxo-2,3,5,9b-tetrahydro-1H-pyrrolo[2,1-a]isoindol-9-yl]-N'-pyridin-2-ylurea 26a (IC(50) = 0.042 microM), X-ray analysis of which was accomplished by the soaking method. The predicted binding mode of 15 in Cdk4 was validated by X-ray analysis of the Cdk2-26a complex.

CDC2-CDC28 Kinases↗
PubMed2005

Synthesis of new benzoxazinone derivatives as neuropeptide Y5 antagonists for the treatment of obesity.

Screening of our internal chemical collection against the neuropeptide Y5 (NPY Y5) receptor allowed the identification of a benzoxazine derivative 5f as a hit that showed moderate affinity (IC(50) = 300 nM). With the aim of improving the in vitro potency, a series of 2-benzoxazinone derivatives have been synthesized and tested for NPY Y5 activity. Most of the compounds were found to be potent and selective NPY Y5 antagonists having nanomolar binding affinities for the NPY Y5 receptor and showing functional antagonism in the forskolin-induced cyclic AMP test. Prelimminary studies in order to understand the structure-activity relationship were undertaken. Selected compounds were further evaluated for in vivo efficacy, affording the lead compound 2-[4-(8-methyl-2-oxo-4H-benzo[d][1,3]oxazin-1-yl)piperidin-1-yl]-N-(9-oxo-9H-fluoren-3-yl)acetamide 5p, which displayed in vivo activity reducing food intake in rodents.

Animals↗
PubMed2006

Solubilization of polyelectrolytic hairy-rod polyfluorene in aqueous solutions of nonionic surfactant.

We report on the solubilization, phase behavior, and self-organized colloidal structure of a ternary water-polyfluorene-surfactant (amphiphile) system comprised of polyelectrolytic poly{1,4-phenylene[9,9-bis(4-phenoxybutylsulfonate)]fluorene-2,7-diyl} (PBS-PFP) in nonionic pentaethylene glycol monododecyl ether (C12E5) at 20 degrees C. We show in particular how a high amount (milligrams per milliliter) of polyfluorene can be solubilized by aqueous C12E5 via aggregate formation. The PBS-PFP and C12E5 concentrations of 0.31 x 10(-4)-5 x 10(-4) M and 2.5 x 10(-4)-75 x 10(-4) M, respectively, were used. Under the studied conditions, the photoluminescence (PL), surface tension, static contact angle, and (pi-A) isotherm measurements imply that D2O-PBS-PFP(C12E5)x realizes three phase regimes with an increasing molar ratio of surfactant over monomer unit (x). First, for x < or = 0.5, the mixture is cloudy. In this regime polymer is only partially dissolved. Second, for 1 < or = x < or = 2, the solution is homogeneous. In this regime polymer is dissolved down to the colloidal level. Small-angle neutron scattering (SANS) patterns indicate rigid elongated (polymer-surfactant) aggregates with a diameter of 30 A and mean length of approximately 900 A. The ratio between contour length and persistence length is less than 3. Third, for x > or = 4, the solution is homogeneous and there is cooperative binding between polymer and surfactant. Surface tension, contact angle, and surface pressure remain essentially constant with increasing x. A PL spectrum characteristic of single separated polyfluorene molecules is observed. SANS curves show an interference maximum at q approximately 0.015 A(-1), indicating an ordered phase. This ordering is suggested to be due to the electrostatic repulsion between polymer molecules adsorbed on or incorporated into the C12E5 aggregates (micelles). On dilution the distance between micelles increases via 3-dimensional packing. In this regime the polymer is potentially dissolved down to the molecular level. We show further that the aggregates (x = 2) form a floating layer at the air-water interface and can be transferred onto hydrophilic substrates.

Fluorenes↗
PubMed2005

Self-assembly and multistage redox chemistry of strong electron acceptors on metal surfaces: polynitrofluorenes on gold and platinum.

Nitrofluoren-9-one and nitrofluoren-9-dicyanomethylene electron acceptors 7, 8, and 11 functionalized with a terminal thioctic acid unit have been synthesized from 2,4,5,7-tetranitrofluorenone. The self-assembled monolayers (SAMs) of these compounds on gold, formed via gold-sulfur interaction, have been fully characterized by electrochemical, FTIR, ellipsometry, and contact angle measurements. Cyclic voltammetry of SAMs reveals two reversible single-electron reduction waves for fluorenone derivatives 7a,b and 11, and three single-electron reductions for the dicyanomethylene-fluorene 8b, providing the first observation of a radical trianion species in SAMs. The tendency of the thioctic anchor to form multilayers via disulfide links is noted.

Electrochemistry↗
PubMed2006

Photoinduced charge transfer and efficient solar energy conversion in a blend of a red polyfluorene copolymer with CdSe nanoparticles.

We present measurements of charge transfer and the photovoltaic effect in a blend of the alternating polyfluorene copolymer poly(2,7-(9,9-dioctyl-fluorene)-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)) with branched CdSe nanoparticles. Quasi-steady-state photoinduced absorption measurements identified a long-lived charged species that formed after photoexcitation at room temperature. Photovoltaic devices based on this blend system showed a spectral response extending to 650 nm and gave a solar power conversion efficiency of 2.4% under Air Mass 1.5 Global (AM1.5G) conditions.

Cadmium Compounds↗
PubMed2002

The rearrangement of fluorenylideneallene oxide. A DFT study.

[reaction: see text] Density functional calculations indicate that the rearrangement of fluorenyl allene oxide to the spiro fluorenyl cyclopropanone proceeds through the reactive intermediate fluorenyl oxyallyl. The calculated energetics of this conversion are in agreement with that observed experimentally. The spiro fluorenyl cyclopropanone was calculated to have a low activation energy for its conversion to fluorene and carbon monoxide.

Alkadienes↗
PubMed2003

Synthesis and relationships between the structures and properties of monodisperse star-shaped oligofluorenes.

[structure: see text] A convenient approach to a series of star-shaped pi-conjugated organic materials with oligofluorenes (OF) as the branches and a benzene ring as the core has been developed. The optical properties of these materials are liable to be tuned by introduction of more fluorene rings. The investigation of the structure-property relationship of these materials has indicated differences between star-shaped oligofluorenes and linear oligofluorenes, as well as polyfluorenes.

Cross-Linking Reagents↗
PubMedDate not supplied

Arylamine-nucleoside adduct formation: evidence for arylnitrene involvement in the reactions of an N-acetoxyarylamine.

N-Acetoxyarylamines are reactive metabolites that are produced from N-arylhydroxamic acids by N-arylhydroxamic acid N,O-acyltransferase and by the acetyl coenzyme A-dependent O-acetylation of N-arylhydroxylamines. Solvolytic decomposition of 7-acetyl-2-(N-acetoxyamino)fluorene (3) afforded 7-acetyl-2-aminofluorene (4) and 7,7'-diacetyl-2,2'-azofluorene (5). Solvolysis of 3 in the presence of 2'-deoxyguanosine resulted in formation of N-(deoxyguanosin-8-yl)-7-acetyl-2-aminofluorene (2), along with smaller yields of 4 and 5 than were obtained in the absence of 2'-deoxyguanosine. The inclusion of nitrene trapping agents, such as piperylene, triethyl phosphite, 1-chloro-4-nitrosobenzene, and oxygen, in the reaction medium with 3 and 2'-deoxyguanosine caused a reduction in the yields of 2, 4, and 5. Additionally, products that would be expected to be formed through reaction with an arylnitrene intermediate were obtained when triethyl phosphite, 1-chloro-4-nitrosobenzene, and oxygen were included in the incubations with 3 and 2'-deoxyguanosine. The results support the proposal that a nitrene intermediate is involved in the formation of 2, 4, and 5 from 3.

Amines↗
PubMed1999

Efficiency of defined strains and of soil consortia in the biodegradation of polycyclic aromatic hydrocarbon (PAH) mixtures.

The microbiological characteristics of the bacterial degradation of mixtures of five polycyclic aromatic hydrocarbons (PAH), phenanthrene, fluorene, anthracene, fluoranthene and pyrene, were investigated. Three pure bacterial strains using one or several of these PAH as carbon sources were selected. The interactions between PAH during the degradation of PAH pairs by each of these strains were studied and their effects on the kinetics and the balance of degradation were characterised. Competition between PAH and degradation by cometabolism were frequently observed. Mixed cultures of two or three strains, although possessing the global capacity to mineralise the set of five PAH, achieved limited degradation of the mixture. In contrast, a consortium from a PAH-contaminated soil readily mineralised the five-PAH mixture. The results suggested that soil consortia possessed a wider variety of strains capable to compensate for the competitive inhibition between PAH as well as specialised strains that mineralised potentially inhibitory PAH metabolites produced by cometabolism.

Anthracenes↗
PubMed2003

Arylamine N-acetyltransferases: covalent modification and inactivation of hamster NAT1 by bromoacetamido derivatives of aniline and 2-aminofluorene.

Kinetic analysis of the inactiviation of hamster NAT1 by 2-(bromoacetylamino)fluorene (Br-AAF) and bromoacetanilide revealed that Br-AAF is an active site directed affinity label whereas bromoacetanilide acts as a bimolecular alkylating agent. ESI MS analysis of NAT1 treated with Br-AAF showed that a single molecule of 2-acetylaminofluorene had been incorporated. Proteolysis with pepsin followed by sequencing of adducted peptides by ESI MS/MS identified the modified residue as the catalytically essential Cys-68. ESI Q-TOF MS analysis of NAT1 that had been treated with bromoacetanilide resulted in identification of a monoadducted protein as the primary product and a diadducted protein as a minor product. Pepsin digestion of bromoacetanilide-inactivated NAT1 and sequencing by ESI MS/MS identified Cys-68 as the primary site of adduct formation. Additional proteolysis of the bromoacetanilide-treated NAT1 led to the identification of a second modified peptide which was adducted at Cys-44. The data reveal substantial differences in the interactions of small hydrophobic alkylating reagents with hamster NAT1.

2-Acetylaminofluorene↗