Naphthalene diimide-amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA.

Two novel unnatural amino acids, prepared by linking a dicationic purple-coloured and fluorescent naphthalene diimide (NDI) at core position to amino acid side chains of variable length, strongly interacted with ds-DNA/RNA by threading intercalation. Different from a reference NDI dye with identical visible range absorbance (520-540 nm) and Stokes shifts in emission (+60 nm, quantum yield > 0.2), only these amino acid-NDI conjugates showed selective fluorimetric response for GC-DNA in respect to AT(U)-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450-550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA.

Calix[4]arene-based bis[2]catenanes: synthesis and chiral resolution.

The exclusive formation of hydrogen-bonded dimers between tetraaryl and tetratosylurea calix[4]arenes has been used to prepare a series of ten "bisloop" tetraurea calix[4]arenes 3, in which adjacent phenylurea groups are covalently linked through alpha,omega-dioxyalkane chains. This dimerization with tetratosylurea 2 as template preorganizes the alkenyl residues of tetra(m-alkenyloxyphenyl) ureas 1 and enables their selective connection in high yield (up to 95 %) by olefin metathesis followed by hydrogenation. The "bisloop" calixarenes 3 also exclusively form heterodimers with 1. Thus, in a separated metathesis/hydrogenation sequence, a series of 14 cyclic bis[2]catenanes 4, in which two calix[4]arenes are connected through their wide rims by two pairs of interlocked rings (total size 29 to 41 atoms), were prepared in yields of up to 97 %. Optical resolution of these chiral bis[2]catenanes was studied by HPLC on chiral stationary phases. The single-crystal X-ray structure of one example (4(P,10)) confirmed the interlocking rings and revealed that the hydrogen-bonded dimeric capsule of the calix[4]arene can be "completely" opened.

Topologically novel multiple rotaxanes and catenanes based on tetraurea calix[4]arenes.

Calix[4]arenes bearing at their wide rim four urea residues easily form hydrogen bonded dimeric capsules. This has been used to preorganise alkenyl functions attached to these urea groups for their controlled connection via metathesis reaction. Multimacrocyclic tetraurea derivatives are thus obtained in excellent yields via heterodimers which are formed exclusively with tetratosylurea derivatives. Heterodimerisation of such bis- and tetraloop tetraureas leads analogously to multicatenanes, or to rotaxanes by stoppering. Huge macrocycles are detached from tetraloop derivatives by cleavage of the urea function.

Orientational preferences of aromatic guests in dimeric capsules of tetraurea calix[4]arenes--MD and NMR studies.

Molecular dynamics (MD) simulations have been performed for complexes of a dimeric capsule of a tetraurea calixarene with a series of twelve aromatic guests. A distinct orientational preference and a restriction of the internal mobility was found which depend on the size and electronic properties of the guests. The results are in agreement with the CIS values obtained from (1)H NMR spectroscopic measurements and with complexation selectivities obtained by competition experiments.

Wide rim urethanes derived from calix[4]arenes: synthesis and self-assembly.

[reaction: see text] Calix[4]arenes 4, substituted at the wide rim by four N-tolyl-urethane groups, were synthesized, as well as derivatives 10a,b bearing two or three tolyl-urea groups beside of one or two urethane group(s). In contrast to tetra-tolyl urea 11, the urethane derivatives do not form hydrogen-bonded, dimeric capsules in CDCl3 or benzene-d6, but the dimerization can be induced for the triurea 10b by tetraethylammonium cations as guests. The quantitative formation of heterodimers is observed for all urethanes 4 and 10a,bin benzene-d6 in mixtures with a "tetra-loop" tetraurea 14, while "bisloop" tetraureas 13 require di- or triurea derivatives 10a,b for a clean heterodimerization.

Energy transfer in calixarene-based cofacial-positioned perylene bisimide arrays.

The synthesis of multichromophoric perylene bisimide-calix[4]arene arrays with up to five perylene units (containing orange, violet, and green perylene bisimide chromophores) and of monochromophoric model compounds was achieved by subsequent imidization of mono-Boc functionalized calix[4]arene linkers with three different types of perylene bisimide dye units. The optical properties of all compounds were studied with UV/vis absorption and steady state and time-resolved fluorescence spectroscopy. Upon excitation of the inner orange dye at 490 nm of array 3, strong fluorescence emission of the outer green perylene bisimide (PBI) chromophore at 744 nm is observed. The fluorescence excitation spectra of compounds 3 and 4 (lambdadet = 850 nm) show all absorption bands of the parent chromophores (e.g., all perylene units contribute to the emission from S1 state of the green PBI). Thus, the fluorescence emission and excitation spectra as well as time-resolved data of fluorescence lifetimes in the absence (tauD = 5.1 ns) and in the presence of an acceptor (tauDA = 0.8 ns) suggest efficient energy transfer processes between the perylene bisimide dye units. For the bichromophoric array 4, the energy transfer rate is calculated to a value of 1.05 x 109 s-1. These results demonstrate highly efficient energy transfer in cofacially assembled dye arrays.

Guest exchange in dimeric capsules of a tetraurea calix[4]arene in the solid state.

A solid powder of hydrogen bonded dimers of a tetraurea calix[4]arene is able to exchange the encapsulated guest in contact with the vapor of a second guest. The molecules of a guest-free powder obtained from a polar solvent cannot rearrange in the solid phase to form new guest-filled capsules under these conditions.

Fourfold [2]rotaxanes based on calix[4]arenes.

Tetraurea calix[4]arenes with four loops form exclusively heterodimers with open-chain urea calix[4]arenes when they are dissolved in aprotic solvents. These assemblies can be considered as pseudorotaxanes. If open-chain tetraureas ending with maleic imide functions are used, their Diels-Alder reaction with 1,4,5,8-tetrapentoxyanthracene leads to tetra[2]rotaxanes which cannot be split into the single calixarene parts by hydrogen bond breaking solvents.

Synthesis of huge macrocycles using two calix[4]arenes as templates.

Macrocycles with up to 100 atoms have been synthesised using two calix[4]arenes as templates: first, (3,5-dialkenyloxy)phenyl groups are attached to the wide rim of a calix[4]arene via urea links, then the alkenyl groups are connected via a metathesis reaction using a tetratosylurea calix[4]arene for their correct prearrangement and finally the urea functions are cleaved to detach the newly formed macrocycles.

Preferred dimerization of tetra-tolyl- and tetra-tosylurea derivatives of flexible and rigidified calix[4]arenes.

The dimerization of tetratolyl- and tetratosyl-urea derivatives 1 and 2, derived from a tetrapentoxy calix[4]arene in the cone conformation and of the corresponding tetra-urea derivatives 3 and 4, in which the cone conformation is rigidified by the two crown-3 tethers, have been studied. All six possible equimolar mixtures were examined by 1H NMR using CDCl3 and CD2Cl2 as solvents. While no heterodimers are found for the combinations 1/3 and 2/4 in either solvent, all remaining combinations lead to the (exclusive) formation of heterodimers in CD2Cl2. In CDCl3 heterodimers are only observed for the combinations of 3 with 2 or 4. These results are discussed in terms of entropic and enthalpic contributions and compared with MD-simulations in a box of chloroform solvent molecules.

Enhanced thermodynamic and kinetic stability of calix[4]arene dimers locked in the cone conformation.

Wide rim tetraurea derivatives (2a,b) have been prepared from a calix[4]arene rigidified in the cone conformation by two diethyleneglycol ether bridges between adjacent oxygens. In comparison to the analogous tetraurea derivatives (3a,b) of a tetrapentoxy calix[4]arene, 2a,b show an increased thermodynamic stability in mixtures of CDCl(3) and DMSO-d(6). Their kinetic stability as expressed by the rate of guest exchange (benzene or cyclohexane against the solvent benzene-d(6)) is also strongly increased by factors of 30-38. Noticeable differences for the inclusion of selected guests are found.

Rational synthesis of multicyclic bis[2]catenanes.

Bis-loop tetraurea calix[4]arene 6 has been prepared by acylation of the wide-rim calix[4]arene tetraamine 1 with the activated bis(urethane) 8 under dilution conditions. Similarly the bis(Boc-protected) tetraamine 2 is converted into the mono-loop derivative 3 which after deprotection and acylation gives the bisalkenyl derivative 5. In apolar solvents this tetraurea calix[4]arene 5 forms regioselectively a single hydrogen-bonded homodimer, from which the bis[2]catenane 10a is formed in 49% by a metathesis reaction followed by hydrogenation. Bis-loop derivative 6 forms no homodimers for steric reasons, but a stoichiometric mixture with the open-chain tetraalkenyl derivative 7a contains exclusively the heterodimer. Metathesis and subsequent hydrogenation now yields 65 % of the pure bis[2]catenane 10a which could not be isolated from the complex reaction mixture obtained from the homodimer 7a.7a. The chirality of 10a (D(2) symmetry) has been verified by optical resolution using HPLC on a chiral stationary phase.

Multiple catenanes derived from calix[4]arenes.

A multicatenane is described in which two belts consisting of four annelated rings attached to the wide rims of two calix[4]arenes are interwoven in such a way that each ring of one belt penetrates two adjacent rings of the other belt and vice versa. The key step of the synthesis of this [8]catenane is the exclusive formation of preorganized heterodimers between a multimacrocyclic tetraurea calix[4]arene and an "open-chain" tetraurea calix[4]arene containing eight omega-alkenyl groups. When a tetraurea calix[4]arene containing four alkenyl groups is used, a bis-[3]catenane is formed analogously.

Sterically and guest-controlled self-assembly of calix[4]arene derivatives.

In solvents such as chloroform or benzene, tetraurea calix[4]arenes 1 form dimeric capsules in which one solvent molecule is usually included as guest. To explore the structural requirements for the formation of such hydrogen-bonded dimers we replaced one p-tolylurea residue by a simple acetamide function. The resulting calix[4]arene 2 a, substituted at its wide rim with one acetamide and three p-tolylurea functions, assumes a C(1)-symmetrical conformation in apolar solvents as shown by (1)H NMR, which is not compatible with the usual capsule. In the crystalline state, four molecules of 2 a, adopting a pinched cone conformation, assemble into a quasi S(4)-symmetrical tetramer stabilized by a cyclic array of 24 NH.O==C hydrogen bonds and four NH.pi interactions. Four acetamide groups are hydrogen-bonded to each other and pack tightly in the center of the assembly. All polar residues are buried inside the tetramer, the surface of which is lipophilic. Extensive NMR studies revealed similar structures in apolar solvents such as [D]chloroform or [D(6)]benzene for calixacetamides 2 a-c. The formation of these tetramers in solution is critically dependent on the size of the amide fragment, so that propionamide 2 d, butyramide 2 e, and p-tolylamide 2 f form only ill-defined aggregates. This is caused by steric crowding inside the tetrameric assembly. The tetramers persist during molecular dynamics simulations, and the optimized average structure of the MD run is similar to that found in the crystalline state. Theoretical studies revealed that cooperation of hydrogen bonds with multiple NH.pi, C--H.pi, and pi.pi attractions make the tetramer more stable than the capsular dimer with the solvent as guest. In the presence of tetraethylammonium salts, however, compounds 2 a-e form dimeric capsular assemblies, each incorporating a single ammonium cation. Only one of two possible regioisomeric dimers is formed, in which both acetamide groups are surrounded by two urea residues. These examples give striking evidence of how self-assembly in solution can be strongly dependent on subtle structural factors and of how the formation of dimeric capsules can be induced by the presence of an appropriate guest.

Compensation of steric demand by cation-pi interactions, cobaltocenium cations as guests in tetraurea calix[4]arene dimers.

The affinities of ferrocene (2) and the cobaltocenium cation (3+), which have roughly the same size and differ in their charge, towards the inner cavity of the dimeric capsule formed by tetraurea calix[4]arene (1) were studied in C2D4Cl2 solutions. While 3+, which occupies more than 75% of the internal volume of the dimer, is readily encapsulated this is not the case for 2. This is probably due to cation-pi interactions, which operate only between 3+ and the aromatic rings of the calix[4]arene dimer. We found that the affinity of the cobaltocenium cation is higher than that of the tropylium cation (4+) and is only 2-3 times less than that of the tetraethylammoniun cation (5+). From the variable temperature 1H NMR spectra of this capsule, the free energy of activation at 298 K (deltaGdouble dagger(298K)) for the reorientation of the hydrogen bonded belt between the two parts of the dimer could be determined by total line shape analysis for the aromatic protons of the calixarene. The value of 14.3 +/- 0.2 kcal mol(-1) for the dimeric capsules of 3+ PF6- is very similar to the free activation energy found for dimeric capsules of 1 with 4+ PF6- and 5+ PF6- in C2D4Cl2. It becomes significantly lower, if PF6- is replaced by BF4-. We also found that ten times more DMSO is needed to disrupt the capsule 1 x 3+ x 1 than the corresponding 1 x 1 dimer containing benzene as guest. This demonstrates again the importance of the cation-pi interactions for the stability of such hydrogen-bonded dimeric capsules.

New molecular topologies by fourfold metathesis reactions within a hydrogen-bonded calix[4]arene dimer.

A calix[4]arene tetrapentyl ether in the cone conformation substituted at its wide rim by four m-(omega-octenyloxy)phenyl urea groups forms hydrogen-bonded dimeric capsules in dichloromethane/benzene (95:5). Metathesis reaction with Grubbs' catalyst under high-dilution conditions (1.1 x 10(-4) M) followed by hydrogenation leads to a covalent connection of all the urea groups within a dimer. Three topologically different products may be expected in such a reaction: a bis[2]catenane, a doubly bridged monocatenane and a tetrabridged capsule. All three possible reaction products could be isolated in an overall yield up to 60 % for the separated and purified compounds. Their identification was based on the NMR patterns which reflect the characteristic symmetry properties of the isomeric products especially in the region of the hydrogen-bonded NH protons and were further confirmed by MALDI-TOF mass spectra. Further structural support for the bis[2]catenane comes from a single-crystal X-ray structure, although severe disorder prevents the localization of all atoms in the aliphatic chains connecting the two calix[4]arenes. Kinetic studies for the guest release/exchange (cyclohexane against the solvent [D(6)]benzene) do not show remarkable differences between the starting dimer and the additionally linked dimers, while the mobility of an included tetraethylammonium cation is obviously more restricted.

Self-assembled dimers with supramolecular chirality.

The possibilities to form dimeric capsules with supramolecular chirality from tetraurea calix[4]arenes composed of two different phenolic urea units are discussed in general and demonstrated experimentally for various selected examples.

Calix[4]arene-functionalized naphthalene and perylene imide dyes.

[reaction: see text] Calix[4]arenes bearing one, two, or four 1,8-naphthyl imide groups at the wide rim and bis-calix[4]arenes connected via perylene-bisimide dye spacers have been synthesized. The low-temperature NMR spectrum of the tetranaphthylimide suggests, in agreement with a crystal structure, a C2-symmetrical pinched cone conformation stabilized via face-to-face pi-pi interactions between opposite naphthylimide groups. UV-vis and fluorescence studies have been carried out for the perylene bis-calix[4]arene dyes.