Verification and Biophysical Characterization of a New Three‐Color Förster Resonance‐Energy‐Transfer (FRET) System in DNA

We report on a new three‐color FRET system consisting of three fluorescent dyes, i.e., of a carbostyril (=quinolin‐2(1H)‐one)‐derived donor D, a (bathophenanthroline)ruthenium complex as a relay chromophore A₁, and a Cy dye as A₂ (FRET=Förster resonance‐energy‐transfer) (cf. Fig. 1). With their widely matching spectroscopic properties (cf. Fig. 2), the combination of these dyes yielded excellent FRET efficiencies. Furthermore, fluorescence lifetime measurements revealed that the long fluorescence lifetime of the Ru complex was transferred to the Cy dye offering the possibility to measure the whole system in a time‐resolved mode. The FRET system was established on double‐stranded DNA (cf. Fig. 3) but it should also be generally applicable to other biomolecules.     

Comparative Studies of Different Quinolinone Derivatives as Donors in Fluorescence‐Resonance‐Energy Transfer (FRET) – Systems in Combination with a (Bathophenanthroline)ruthenium(II) Complex as Acceptor

We describe the preparation as well as a detailed photophysical study of Fmoc‐amino acid building blocks carrying different carbostyril (=quinolin‐2(1H)‐one) heterocycles as donors in a FRET (fluorescence‐resonance‐energy transfer) system in combination with a [Ru^II(bathophenanthroline)] complex (bathophenanthroline=4,7‐diphenyl‐1,10‐phenanthroline). The efforts resulted in a clear preference for building block 16 due to its ease of synthesis (Scheme 2), its chemical robustness, and the FRET efficiency when incorporated into peptides.     

Molybdenum‐ and Tungsten‐Based Coordination Polymers as Catalysts for an Efficient and Rapid Synthesis of Hexahydro‐5‐oxoquinoline‐3‐carboxylates and 1,4‐Dihydropyridine‐3,5‐dicarboxylates

Hexahydro‐5‐oxoquinoline‐3‐carboxylates and 1,4‐dihydropyridine‐3,5‐dicarboxylates were synthesized efficiently and rapidly (2 min) in the presence of molybdenum‐ and tungsten‐based coordination polymers [M(Bu₃Sn)₂O₄)]_n (M=Mo or W) as catalysts (Schemes 1 and 2; Tables 2 and 3). The products were formed at room temperature in excellent yields (90–98%). The catalysts worked under heterogeneous conditions and were recyclable. The earlier reports for the application of these polymers to conduct organic synthesis are limited. The present method explores a new and useful application of these catalysts.     

Efficient Synthesis of a Styryl Analogue of (2S,3R,4E)‐N2‐Octadecanoyl‐4‐tetradecasphingenine via Cross‐Metathesis Reaction

The first total synthesis of sphingolipid (2S,3R,4E)‐N²‐octadecanoyl‐4‐tetradecasphingenine ( 1a ), a natural sphingolipid isolated from Bombycis Corpus 101A, and of its styryl analogue 1b was achieved in good overall yield (Schemes 1 and 2). The key step involved the installation with (E) stereoselectivity of a long lipophilic chain or phenyl group on allyl alcohol derivative 3 via a cross‐metathesis reaction (→ 5a or 5b ). The N‐Boc protected 3 was easily accessible from (S)‐Garner aldehyde.     

Report on an Unusual Cascade Reaction between Azulenes and 2,3‐Dichloro‐5,6‐dicyano‐1,4‐benzoquinone (=4,5‐Dichloro‐3,6‐dioxocyclohexa‐1,4‐diene‐1,2‐dicarbonitrile; DDQ)

The oxidation of 1‐(3,8‐dimethylazulen‐1‐yl)alkan‐1‐ones 1 with 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone (=4,5‐dichloro‐3,6‐dioxocyclohexa‐1,4‐diene‐1,2‐dicarbonitrile; DDQ) in acetone/H₂O mixtures at room temperature does not only lead to the corresponding azulene‐1‐carboxaldehydes 2 but also, in small amounts, to three further products (Tables 1 and 2). The structures of the additional products 3 – 5 were solved spectroscopically, and that of 3a also by an X‐ray crystal‐structure analysis (Fig. 1). It is demonstrated that the bis(azulenylmethyl)‐substituted DDQ derivatives 5 yield on methanolysis or hydrolysis precursors, which in a cascade of reactions rearrange under loss of HCl into the pentacyclic compounds 3 (Schemes 4 and 7). The found 1,1′‐[carbonylbis(8‐methylazulene‐3,1‐diyl)]bis[ethanones] 4 are the result of further oxidation of the azulene‐1‐carboxaldehydes 2 to the corresponding azulene‐1‐carboxylic acids (Schemes 9 and 10).     

A One‐Pot Synthesis of 1,3‐Dihydro‐1,3,3‐tris(perfluoroalkyl)isobenzofuran‐1‐olates and Their Complete NMR Spectroscopic Analysis on the Basis of 1D and 2D Experiments

A convenient synthesis of the 1,3‐dihydro‐1,3,3‐tris(perfluoroalkyl)isobenzofuran‐1‐ols 3a , b was elaborated starting from commercially available phthaloyl dichloride and trimethyl(perfluoroalkyl)silanes (Me₃SiR_f) 1a , b (R_f=CF₃, C₂F₅) in the presence of a fluoride source (Schemes 1 and 3). In a reaction analogous to alkyl Grignard reagents, double chloride substitution by two perfluoroalkyl groups and subsequent addition of one perfluoroalkyl group with concomitant ring closure led to this new class of compounds (Scheme 2). The syntheses of the alcohols and some alcoholates, as well as of the corresponding trimethylsilyl ethers are described. A combination of special 1D and 2D NMR experiments allowed the assignment of all atoms of the new compounds. The solid‐state structure of 1,3‐dihydro‐1,3,3‐tris(trifluoromethyl)isobenzofuran‐1‐ol ( 3a ) was elucidated by X‐ray diffraction methods.     

A New Robust and Highly Sensitive FRET Donor–Acceptor Pair: Synthesis,Characterization, and Application in a Thrombin Assay

The synthesis of a new, robust fluorescence‐resonance‐energy‐transfer (FRET) system is described. Its donor chromophore is derived from an N‐allyl‐substituted quinolinone attached to 4‐bromophenylalanine via Heck cross‐coupling. The resulting Fmoc‐protected derivative 11 was used as building block in solid‐phase peptide synthesis (SPPS). As FRET acceptor, a sulfonylated ruthenium(II)–bathophenanthroline complex with a peripheral COOH function was prepared for covalent attachment to target molecules. The UV/VIS absorption and emission spectra of peptides bearing only the donor (D) or acceptor (A) dye showed a good overlap of the emission band of the donor with the absorption band of the acceptor. The fluorescence spectra of a peptide bearing both dyes revealed an additional emission after excitation of the donor, which is due to indirect excitation of the acceptor via FRET. The long fluorescence lifetime of the Ru^II complex (0.53 μs) makes it well‐suited for time‐resolved measurements. As a first application of this new FRET system, the peptide 18 , with the recognition sequence for the protease thrombin, flanked by the two dyes, was synthesized and successfully cleaved by the enzyme. The change in the ratio of the fluorescence intensities could be determined.     

1,3‐Diethynylallenes: Carbon‐Rich Modules for Three‐Dimensional Acetylenic Scaffolding

Regioselective Pd⁰‐catalyzed cross‐coupling of substrates, which bear bispropargylic leaving groups with silyl‐protected alkynes, has provided access to a variety of 1,3‐diethynylallenes, a new family of modules for three‐dimensional acetylenic scaffolding. In enantiomerically pure form, these C‐rich building blocks could provide access – by oxidative oligomerization – to a fascinating new class of helical oligomers and polymers with all‐carbon backbones (Fig. 2). In the first of two routes, a bispropargylic epoxide underwent ring opening during S_n 2′‐type cross‐coupling, and the resulting alkoxide was silyl‐protected, providing 1,3‐diethynylallenes (±)‐ 8 , (±)‐ 12 (Scheme 3), and (±)‐ 15 (Scheme 5). A more general approach involved bispropargylic carbonates or esters as substrates (Scheme 6–8), and this route was applied to the preparation of a series of 1,3‐diethynylallenes to investigate how their overall stability against undesirable [2+2] cycloaddition is affected by the nature of the substituents at the allene moiety. The investigation showed that the 1,3‐diethynylallene chromophore is stable against [2+2] cycloaddition only when protected by steric bulk and when additional π‐electron delocalization is avoided. The regioselectivity of the cross‐coupling to the bispropargylic substrates is entirely controlled by steric factors: attack occurs at the alkyne moiety bearing the smaller substituent (Schemes 9 and 10). Oxidative Hay coupling of the terminally mono‐deprotected 1,3‐diethynylallene (±)‐ 49 afforded the first dimer 50 , probably as a mixture of two diastereoisomers (Scheme 12). Attempts to prepare a silyl‐protected tetraethynylallene by the new methodology failed (Scheme 13). Control experiments (Schemes 14–16) showed that the Pd⁰‐catalyzed cross‐coupling to butadiyne moieties in the synthesis of this still‐elusive chromophore requires forcing conditions under which rapid [2+2] cycloaddition of the initial product cannot be avoided.     

Formal Synthesis of (−)‐Cephalotaxine

A formal synthesis of (?)‐cephalotaxine ( 1 ) by means of a highly stereoselective radical carboazidation process is reported. The synthesis begins with the protected (S)‐cyclopent‐2‐en‐1‐ol derivative 10 and uses the concept of self‐reproduction of a stereogenic center (Schemes 5 and 6). For this purpose, the double bond adjacent to the initial chiral center in 10 is converted into an acetonide after stereoselective dihydroxylation. The initial alcohol function is used to build an exocyclic methylene group suitable for the carboazidation process 8 → 7 (Scheme 7). Finally the protected diol moiety is converted back to an alkene ( 14 → 15 → 6 ) and used for the formation of ring B via a Heck reaction ( 6 →(?)‐ 16 ; Scheme 8).     

Palladium‐Catalyzed Amination of 3,5‐Dihalopyridines – a Convenient Route to New Polyazamacrocycles

Pd‐Catalyzed amination of 3,5‐dibromo‐ and 3,5‐dichloropyridine ( 1a and 1b , resp.) with linear polyamines 2 leads to the formation of a new family of pyridine‐containing macrocycles 3 with an ‘exo’‐oriented pyridine N‐atom (Schemes 1 and 2). The dependence of the macrocycle yield on the nature of the halogen atom, the length of the polyamine chain and C/N atom ratio, and the composition of the catalytic system is studied. The synthesis of mono‐ and bis(5‐halopyridin‐3‐yl)‐substituted polyamines 4, 5, 8, 9 , and of 3,5‐bis(polyamino)‐substituted pyridines 6 is described (Schemes 3 and 4), and the use of these compounds as intermediates on the way to the macrocycles 7, 16 , and 18 with larger cavity (‘cyclodimers’ and ‘cyclotrimers’) is demonstrated (Schemes 5–10).     

‘Click Synthesis’ of Some Novel O‐Substituted Oximes Containing 1,2,3‐Triazole‐1,4‐diyl Residues as New Analogs of β‐Adrenoceptor Antagonists

The ‘click synthesis’ of some novel O‐substituted oximes, 7a – 7t , which contain 1,2,3‐triazolediyl residues, as new analogs of β‐adrenoceptor antagonists is described (Schemes 1–4). The synthesis of these compounds was achieved in four to five steps. The formation of oximes of 9H‐fluoren‐9‐one and benzophenone, i.e., 9a and 9b , respectively, followed by their reaction with propargyl bromide, afforded O‐propargyl oximes 10a and 10b , respectively, which by a subsequent CuI‐catalyzed Huisgen cycloaddition with prepared β‐azido alcohols 11a – 11j (Schemes 2 and 3), led to the target compounds 7a – 7t in good yields.     

Synthesis of Optically Active 1‐(1‐Phenylethyl)‐1H‐imidazoles Derived from 1‐Phenylethylamine

The three‐component reaction of (R)‐ or (S)‐1‐phenylethylamine ( 6 ), formaldehyde, and an α‐(hydroxyimino) ketone 5 , i.e., 3‐(hydroxyimino)butan‐2‐one ( 5a ) or 2‐(hydroxyimino)‐1,2‐diphenylethanone ( 5b ), yields the corresponding enantiomerically pure 1‐(1‐phenylethyl)‐1H‐imidazole 3‐oxide 7 in high yield (Schemes 2 and 3). The reactions are carried out either in MeOH or in AcOH. Smooth transformations of the N‐oxides into optically active 1‐(1‐phenylethyl)‐1H‐imidazoles 10 and 2,3‐dihydro‐1‐(1‐phenylethyl)‐1H‐imidazole‐2‐thiones 11 are achieved by treatment of 7 with Raney‐Ni and 2,2,4,4‐tetramethyl‐3‐thioxocyclobutanone ( 12 ), respectively (Scheme 4).     

Low‐Temperature Olefin Syntheses in View of Parent Fulvenes and Fulvalenes

Parent fulvenes and fulvalenes are thermally unstable cross‐conjugated olefins for which low‐temperature syntheses are indispensable. In this review 5 syntheses (in the temperature range between ?100 and ?10°) are discussed: 1. Reaction of sodium cyclopentadienide with 1‐acetoxy‐1‐chloroalkanes or 1‐acetoxy‐1‐bromoalkanes ( 26 ) gives acetoxy‐alkyl‐cyclopentadienes ( 27 ) which are easily converted to pentafulvenes ( 2 ) by low‐temperature HOAc‐elimination with NEt₃. This synthesis has been applied to parent pentafulvene ( 2a ), heptafulvene ( 3a ), nonafulvene ( 4a ) and sesquifulvalene ( 19a ) (Schemes 8–11). 2. Based on a nearly quantitative oxidative coupling of cyclononatetraenide ( 8 ) to give dihydrononafulvalene ( 38 ) (Scheme 10), a general synthetic plan for fulvalenes has been outlined (Scheme 11) and applied to the synthesis of pentafulvalene ( 12 ), nonapentafulvalene ( 16 ) and nonafulvalene ( 14 ). Several applications of oxidative couplings of Hückel anions are discussed (Schemes 20 and 21). 3. Trifunctional cyclopropanes 67 (in most cases 1,1‐dibromo‐2‐X‐cyclopropanes) are attractive precursors of parent triafulvene ( 1a ) and calicene ( 17 ) (Scheme 18). Contrary to classical procedures they are transformed into nucleophiles ( 67 → 68 ) by halogen‐lithium exchange, methylation ( 68 → 69 ) and HBr‐elimination to give 1‐methylidene‐2‐X‐cyclopropanes of type 71 . By subsequent HX‐elimination triafulvene ( 1a ) has been synthesized and trapped as a [4+2]‐cycloadduct 73 (Scheme 20). Furthermore, calicene precursors 77 are available by using cyclopentenone as an electrophilic cyclopentadiene equivalent. 4. Similarly, 1‐lithio‐1‐bromo‐2‐X‐cyclopropanes 68 are directly transformed into triafulvalene precursors 81 (Scheme 26) by a novel CuCl₂‐catalyzed oxidative coupling. 5. In view of the synthesis of parent triafulvene ( 1a ), triafulvalene ( 11 ) and calicene ( 17 ), retro‐Diels? Alder reactions of stable precursors – prepared by low‐temperature reactions (described in chapters 3 and 4 ) – have been explored.     

Stereoselective Synthesis of (−)‐(1R,1′R,5′R,7′R)‐1‐Hydroxy‐exo‐brevicomin and (+)‐exo‐Brevicomin from 3,4,6‐Tri‐O‐acetyl‐D‐glucal

Stereoselective syntheses of (?)‐(1R,1′R,5′R,7′R)‐1‐hydroxy‐exo‐brevicomin ( 1 ) and (+)‐exo‐brevicomin ( 2 ) were accomplished from 3,4,6‐tri‐O‐acetyl‐D ‐glucal ( 5 ; Schemes 2 and 3). Chemoselective reduction, Grignard reaction, Barton? McCombie deoxygenation, and ketalization were used as key steps.     

Cationic Pentaheteroaryls as Selective G‐Quadruplex Ligands by Solvent‐Free Microwave‐Assisted Synthesis

We report herein a solvent‐free and microwaved‐assisted synthesis of several water soluble acyclic pentaheteroaryls containing 1,2,4‐oxadiazole moieties ( 1 – 7 ). Their binding interactions with DNA quadruplex structures were thoroughly investigated by FRET melting, fluorescent intercalator displacement assay (G4‐FID) and CD spectroscopy. Among the G‐quadruplexes considered, attention was focused on telomeric repeats together with the proto‐oncogenic c‐kit sequences and the c‐myc oncogene promoter. Compound 1 , and to a lesser extent 2 and 5 , preferentially stabilise an antiparallel structure of the telomeric DNA motif, and exhibit an opposite binding behaviour to structurally related polyoxazole ( TOxaPy ), and do not bind duplex DNA. The efficiency and selectivity of the binding process was remarkably controlled by the structure of the solubilising moieties.     

Synthesis of 4‐Aryl‐4,6‐dihydropyrimido[4,5‐d]pyridazine‐2,5(1H,3H)‐diones from Biginelli Compounds

Biginelli compounds 1 were first brominated at Me? C(6) with 2,4,4,6‐tetrabromocyclohex‐2,5‐dien‐1‐one to give Br₂CH? C(6) derivatives 2 . The hydrolysis of the 6‐(dibromomethyl) group of 2c to give the 6‐formyl derivative 3c in the presence of an expensive Ag salt followed by reaction with N₂H₄?H₂O yielded tetrahydropyrimido[4,5‐d]pyridazine‐2,5(1H,3H)‐dione ( 4c ; Scheme 1). However, treatment of the 6‐(dibromomethyl) derivatives 2 directly with N₂H₄?H₂O led to the fused heterocycles 4 in better overall yield (Schemes 1 and 2; Table).     

Novel Fluoride‐Labile Nucleobase‐Protecting Groups for the Synthesis of 3′(2′)‐O‐Aminoacylated RNA Sequences

With the aim to develop a general approach to a total synthesis of aminoacylated t‐RNAs and analogues, we describe the synthesis of stabilized, aminoacylated RNA fragments, which, upon ligation, could lead to aminoacylated t‐RNA structures. Novel RNA phosphoramidites with fluoride‐labile 2′‐O‐[(triisopropylsilyl)oxy]methyl (=tom) sugar‐protecting and N‐{{2‐[(triisopropylsilyl)oxy]benzyl}oxy}carbonyl (=tboc) base‐protecting groups were prepared (Schemes 4 and 5), as well as a solid support containing an immobilized N⁶‐tboc‐protected adenosine with an orthogonal (photolabile) 2′‐O‐[(S)‐1‐(2‐nitrophenyl)ethoxy]methyl (=(S)‐npeom) group (Scheme 6). From these building blocks, a hexameric oligoribonucleotide was prepared by automated synthesis under standard conditions (Scheme 7). After the detachment from the solid support, the resulting fully protected sequence 34 was aminoacylated with L ‐phenylalanine derivatives carrying photolabile N‐protecting groups (→ 42 and 43 ; Scheme 9). Upon removal of the fluoride‐labile sugar‐ and nucleobase‐protecting groups, the still stabilized, partially with the photolabile group protected precursors 44 and 45 , respectively, of an aminoacylated RNA sequence were obtained (Scheme 9 and Fig. 3). Photolysis of 45 under mild conditions resulted in the efficient formation of the 3′(2′)‐O‐aminoacylated RNA sequence 46 (Fig. 4). Additionally, we carried out model investigations concerning the stability of ester bonds of aminoacylated ribonucleotide derivatives under acidic conditions (Table) and established conditions for the purification and handling of 3′(2′)‐O‐aminoacylated RNA sequences and their stabilized precursors.     

Synthesis of Photolabile 5′‐O‐Phosphoramidites for the Photolithographic Production of Microarrays of Inversely Oriented Oligonucleotides

The photolabile 3′‐O‐{[2‐(2‐nitrophenyl)propoxy]carbonyl}‐protected 5′‐phosphoramidites ( 16 – 18 ) were synthesized (see Scheme) for an alternative mode of light‐directed production of oligonucleotide arrays. Because of the characteristics of these monomeric building blocks, photolithographic in situ DNA synthesis occurred in 5′→3′ direction, in agreement with the orientation of enzymatic synthesis. Synthesis yields were as good as those of conventional reactions. The resulting oligonucleotides are attached to the surface via their 5′‐termini, while the 3′‐hydroxy groups are available as substrates for enzymatic reactions such as primer extension upon hybridization of a DNA template (see Fig. 2). The production of such oligonucleotide chips adds new procedural avenues to the growing number of applications of DNA microarrays.     

From Dark to Light to Fluorescence Resonance Energy Transfer (FRET): Polarity‐Sensitive Aggregation‐Induced Emission (AIE)‐Active Tetraphenylethene‐Fused BODIPY Dyes with a Very Large Pseudo‐Stokes Shift

The work presented herein is devoted to the fabrication of large Stokes shift dyes in both organic and aqueous media by combining dark resonance energy transfer (DRET) and fluorescence resonance energy transfer (FRET) in one donor–acceptor system. In this respect, a series of donor–acceptor architectures of 4,4‐difluoro‐4‐bora‐3a,4a‐diaza‐s‐indacene (BODIPY) dyes substituted by one, two, or three tetraphenylethene (TPE) luminogens were designed and synthesised. The photophysical properties of these three chromophore systems were studied to provide insight into the nature of donor–acceptor interactions in both THF and aqueous media. Because the generation of emissive TPE donor(s) is strongly polarity dependent, due to its aggregation‐induced emission (AIE) feature, one might expect the formation of appreciable fluorescence emission intensity with a very large pseudo‐Stokes shift in aqueous media when considering FRET process. Interestingly, similar results were also recorded in THF for the chromophore systems, although the TPE fragment(s) of the dyes are non‐emissive. The explanation for this photophysical behaviour lies in the DRET. This is the first report on combining two energy‐transfer processes, namely, FRET and DRET, in one polarity‐sensitive donor–acceptor pair system. The accuracy of the dark‐emissive donor property of the TPE luminogen is also presented for the first time as a new feature for AIE phenomena.     

Oligonucleotides Containing Novel 4′‐C‐ or 3′‐C‐(Aminoalkyl)‐Branched Thymidines

The synthesis of four novel 3′‐C‐branched and 4′‐C‐branched nucleosides and their transformation into the corresponding 3′‐O‐phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′‐C‐branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′‐O‐methyl and 2′‐deoxy‐2′‐fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′‐C‐(aminomethyl)‐2′‐O‐methyl monomer X and 4′‐C‐(aminomethyl)‐2′‐deoxy‐2′‐fluoro monomer Y (Schemes 2 and 3). In general, increased binding affinity towards complementary single‐stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Table 1). The presence of monomer X or monomer Y in a 2′‐O‐methyl‐RNA oligonucleotide had a negative effect on the binding affinity of the 2′‐O‐methyl‐RNA oligonucleotide towards DNA and RNA. Starting from the 3′‐C‐allyl derivative 28 , 3′‐C‐(3‐aminopropyl)‐protected nucleosides and 3′‐O‐phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′‐C‐(3‐aminopropyl)thymidine monomer Z or the corresponding 3′‐C‐(3‐aminopropyl)‐2′‐O,5‐dimethyluridine monomer W (Schemes 4 and 5). Incorporation of the 2′‐deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′‐O‐methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Table 2).