Supramolecular structures containing ‘isolated’ pentaborate anions and non-metal cations: Crystal structures of [Me3NCH2CH2OH][B5O6(OH)4] and [4-MepyH, 4-Mepy][B5O6(OH)4]

The solid-state structures of two non-metal pentaborates [Me₃NCH₂CH₂OH][B₅O₆(OH)₄] (1) and [4-MepyH, 4-Mepy][B₅O₆(OH)₄] (2) have been determined by single-crystal X-ray diffraction methods. Structures 1 and 2 both contain supramolecular pentaborate frameworks held together by extensive H-bond interactions. The framework of 1 exists essentially as planes of pentaborate anions linked via three pairwise ‘planar’ β → α interactions, with a fourth β → β interaction crosslinking the planes. The framework of 2 is very similar except that one of the three pairwise linkages within the plane is replaced by pairwise ‘step-like’ bifurcated H-bonds to both α sites of a neighboring anion. The cations in 1 and the cations and neutral 4-Mepy ligands in 2 are present in the framework cavities and channels, with additional H-bond interactions existing between cations and anions.     

Copper(I) complexes of a thioether-functionalized short-bite aminobis(phosphonite), [PhN{P(–OC10H6(μ-S)C10H6O–)}2]

Copper(I) complexes of short-bite aminobis(phosphonite), PhN{P(–OC₁₀H₆(μ-S)C₁₀H₆O–)}₂ (1) have been synthesized. Reactions of 1 with an excess of CuX (X = Cl, Br, and I) afforded the ligand-bridged binuclear complexes, [PhN(PR-κP)₂{Cu(μ-X)(MeCN)}₂] (2, X = Cl; 3, X = Br; 4, X = I; R = –OC₁₀H₆(μ-S)C₁₀H₆O–), whereas treatment with 0.5 equiv. of [Cu(MeCN)₄]PF₆ produces the mononuclear bischelated cationic complex, [{PhN(PR-κP)₂}₂Cu](PF₆) (5). Single crystal X-ray structures of complexes 3 and 4 are reported. Complex 3 shows strong π–π stacking interactions between the naphthyl moieties, whereas complex 4 shows ligand-supported Cu?Cu metallophilic interactions.     

Two significantly different conformations in crystal: formation of a molecular dimer governed by cation-π interactions

Two significantly different conformations were observed in crystal of 1, which form an unsymmetrical molecular dimer governed by cation-π interactions between a pyridinium cation and a phenyl ring, whereas compound 2 forms a head-to-tail type of dimer.     

New N-heterocyclic carbene mercury(II) and silver(I) complexes

The complexes [1-(9-anthracenylmethyl)-3-octylimy]₂Hg[HgCl₄] (2a) (imy = imidazol-2-ylidene) and [1-(9-anthracenylmethyl)-3-butylbimy]₂AgPF₆ (2b) (bimy = benzimidazol-2-ylidene) have been prepared and characterized. Crystal packing of complex 2a revealed that 1D polymeric chains are formed by [1-(9-anthracenylmethyl)-3-octylimy]Hg and [HgCl₄]²⁻ through weak Hg…Cl bonds. The packing diagram of 2b showed that 1D supramolecular chains are formed by both benzimidazole ring head to tail π–π stacking interactions and anthracene ring face-to-face π–π stacking interactions.     

Quinoxaline-walled π-stacking molecules: synthesis,conformation, and luminescence properties

A series of semi-rigid N-phenylsuccinimides I (11Xy), N-arylmethylsuccinimides II (18Xy), and N,N′-(1,4-arylenebis(methylene))disuccinimides III (19XyX) walled by quinoxaline (QX), dimethylquinoxaline (diMQX), or benzoquinoxaline (BQX) ring were synthesized. Intramolecular π–π interactions in solution were detected by NMR and fluorescence spectroscopy, in terms of reciprocal anisotropic shielding and exciplex formation, respectively. The X-ray crystallographic analysis revealed the preferential conformations in solid state, which were compatible with the results of conformational studies by NMR and fluorescence spectroscopy. The results collectively indicated that 18Xy and 19XyX are driven by intramolecular π–π interactions in the mode of π-stacking (face-to-face) or T-shaped (edge-to-face) configuration to preferentially adopt the folded- and the double folded-conformation, respectively, where the spaced aromatic rings are oriented syn to each other in close proximity.     

New N-heterocyclic carbene silver(I) and mercury(II) 2-D supramolecular layers by the π-π stacking interactions

The precursor 1-(9-anthracenylmethyl)-3-alkylbenzimidazolium chlorides (1a, alkyl = C₄H₉, 1b, alkyl = C₆H₁₃) and their three new NHC silver(I) and mercury(II) complexes {[1-(9-anthracylmethyl)-3-alkylbimy]MCl}₂ (2a, alkyl = C₄H₉, M = Ag; 2b, alkyl = C₆H₁₃, M = Ag; 3a, alkyl = C₄H₉, M = Hg; bimy = benzimidazol-2-ylidene) have been prepared and characterized. The crystal structures of 2a, 2b and 3a showed that 2-D supramolecular layers are formed by both benzimidazole ring head to tail π-π stacking interactions and anthracene ring face-to-face π-π stacking interactions.     

Self-assembly of a new series of quadruply hydrogen bonded heterotrimers driven by the donor-acceptor interaction

This paper describes the self-assembly of a new series of heterotrimers in chloroform-d by utilizing the cooperative interaction of hydrogen bonding and donor-acceptor interaction. Compounds 1 and 11, in which an 2-ureido-4[1H]-pyrimidinone unit is connected to 34-crown-10 or 36-crown-10, were used as donor monomer, and 2 and 19, in which an 2-ureido-4[1H]-pyrimidinone unit is connected to NDI, were used as acceptor monomer, while linear compound 4, which contains two diamido-1,8-naphthyridines, was used as template. A large tri-p-(t-butyl)phenylmethoxyl group was introduced to 19 in order to compare its assembling behavior with that of 2. Mixing 4 with dimer 1·2 caused 1·2 to fully decompose and to afford 55% of ‘in-in’-oriented heterotrimer 1·4·2. Adding 4 to the solution of 2·11 or 11·19 in chloroform-d also led to full dissociation of the dimers. However, in these systems the ‘in-in’-arranged heterotrimer 2·4·11 or 11·4·19 could be produced exclusively.     

Diversity of coordination architecture of silver(Ι) complexes with different 2-aminopyrimidyl derivatives: Effect of counter anions and ligands

Five new silver(Ι) complexes of the formula [Ag(L₁)(CF₃SO₃)(H₂O)]_n (1), [Ag₄(L₁)₄(CF₃CO₂)₄]_n (2), [Ag₂(L₁)₄(ClO₄)₂] (3), [Ag(L₂)(ClO₄)]_n (4), and [Ag(L₃)(ClO₄)]_n (5) have been synthesized by reactions of varied silver(Ι) salts with the corresponding 2-aminopyrimidyl ligands (namely, 2-amino-4,6-dimethylpyrimidine (L₁), 2-amino-4-methoxy-6-methylprimidine (L₂), and 2-amino-4,6-dimethoxyprimidine (L₃)). The influences of counter anions and ligands on the structure of the complexes are discussed. Two complexes, 1 with one-dimensional (1D) zigzag chain and 2 with 1D ladder network are obtained by using the same ligand L₁ but different silver(Ι) salts. On the other hand, using the same silver(Ι) perchlorate but different ligands under the same synthetic conditions, complexes 3–5 are isolated, respectively. In the case of 3, two metal atoms and four L₁ ligands form dimeric [Ag₂(L₁)₄] unit further connected by intermolecular hydrogen bonds and π–π interactions to form an infinite 2D layer structure. Complex 4 displays a two-dimensional (2D) grid network. Complex 5 has a 1D zigzag chain but different from that of 1. An extended 3D framework arises from N–H···O intermolecular hydrogen bonds and Ag···O weak interaction. The results reveal that the nature of the counter anions and organic ligands all has great impact on the structure of the complexes. In addition, the hydrogen-bonding interactions and π–π stacking also play important roles in the formation of supramolecular architectures, for instance, to link low-dimensional entities to high-dimensional frameworks. The luminescence properties of the synthesized silver complexes were investigated in the solid state at room temperature.     

A Wacker-Cook synthesis of isoflavones: formononetine

A total synthesis of the isoflavone formononetine 1 by an oxidative Pd-mediated cyclization of α-methylenedeoxybenzoins 4a-c is described. Substrates 4a-c were rapidly assembled using ‘protected cyanohydrin’ chemistry.     

‘Two-point’-bound supramolecular complexes from semi-rigidified dipyridine receptors and zinc porphyrins

Two linear compounds 1 and 2 have been designed and synthesized as new receptors for zinc porphyrins. Both compounds consist of two folded aromatic amide moieties, which are connected with an acetylene linker in 1 or directly in 2. The rigid conformations of their folded moieties are stabilized by intramolecular tri-centered hydrogen bonding, while the whole molecule adopts a ‘S’- or ‘C’-styled conformation depending on the relative orientation of the two rigid moieties. Two pyridine units are introduced at the ends of 1 and 2 for the complexation of zinc porphyrin guests. Although the ¹H NMR investigation indicated that both compounds can bind two zinc porphyrin guests at high concentrations (≥5 mM) in chloroform, the UV-vis studies revealed that, at low concentration of 1 and 2 (4 μM), both compounds complex one zinc porphyrin guest to form structurally unique ‘two-point’-bound 1:1 complexes. The association constants of the 1:1 complexes have been determined with the UV-vis titration experiments.     

Role of edge-to-face interaction between aromatic rings in clathrate formation of 1-benzoyl-2-hydroxyindoline derivatives with benzene. X-ray crystal and PM6 analyses of the interaction

(4-Nitrophenyl- and 4-chlorophenyl)(2-hydroxy-3,3-dimethylindolin-1-yl)methanone (4a,b) serve as clathrate hosts for benzene guests. X-ray crystal analyses of the inclusion compounds of 4a and 4b with benzene indicate that the ‘edge-to-face interaction’ plays an important role in the formation of the inclusion complexes with benzene as well as in the host-host interactions. PM6 molecular orbital calculations were found to reproduce the characteristic structural features of both intra- and intermolecular edge-to-face interactions.     

Synthesis and ‘double click’ density functionalization of 8-aza-7-deazaguanine DNA bearing branched side chains with terminal triple bonds

The 7-[di(prop-2-ynl)amino]prop-1-ynyl derivative of 8-aza-7-deaza-2′-deoxyguanosine (1) was synthesized from 7-iodo-8-aza-7-deaza-2′-deoxyguanosine (7) by Sonogashira cross-coupling and converted into the phosphoramidite building block 10. Oligonucleotides bearing branched side chains with terminal triple bonds were prepared by solid-phase synthesis containing single or multiple residues of 1 as 2′-deoxyguanosine surrogates. T_m measurements demonstrate that compound 1 has a positive effect on duplex stability, which is comparable to the stabilizing effect of the octa-1,7-diynylated non-branched nucleoside 2. Nucleoside 1 and corresponding oligonucleotides were functionalized by the Cu(I)-mediated 1,3-dipolar cycloaddition ‘double click’ reaction with diverse ligands (AZT 3, benzyl azide 4, 11-azidoundecanol 5 and m-dPEG™₄-azide 6). The conjugation reactions were carried out in solution and on solid support. Nucleoside 1 allowed ‘double’ functionalization of a single residue with two reporter groups. The ‘double click’ reaction proceeded smoothly even when two residues of nucleoside 1 were arranged in proximal positions. Hybridization with complementary strands led to a stable oligonucleotide duplex. Molecular modeling indicates that inspite of the crowded steric situation with four AZT ligands within closest proximal positions, all ligands are well accommodated in the major groove not disturbing the DNA helix.     

Structural revision and absolute configuration of lateritin

‘Lateritin’ (1), a morpholine-2,5-dione (depsipeptide), was reinvestigated for its structure and absolute configuration. On the basis of thorough 1D and 2D NMR and mass spectrometrical analyses, the structure of 1 was revised to be identical with beauvericin (8) and confirmed that beauvericin (8) is the trimeric lactone of ‘lateritin’ (1). The absolute configuration was determined by acidic hydrolysis, followed by application of Marfey’s method, menthyl ester derivatization, and GC–MS analysis. In addition, the specific optical rotation values of the hydrolysis products were compared with those of available standards.     

Water-soluble aminocalix[4]arene receptors with hydrophobic and hydrophilic mouths

We report the new water-soluble aminocalix[4]arene hosts 1 and 2 with deep hydrophobic cavity facilitating hydrophobic mouth and hydrophilic mouth, respectively. The ¹H NMR titrations revealed that host 1 shows high selectivity for neutral guests 9 and 10, with log K of 4.2 and 4.6, respectively. The host 2 shows log K of 4.9 for binding with guest 15. Moreover, the binding ability of the host 2 for guest 14 is stronger by a factor of 1000 than that of the host 1.     

FRET-derived ratiometric fluorescence sensor for Cu

New N-(pyrenylmethyl)naphtho-azacrown-5 (1) was synthesized as an ‘On-Off’ fluorescent chemosensor for Cu²⁺. Excited at 240 nm corresponding to the absorption of naphthalene unit (energy donor) of 1, emission at 380 nm from pyrene unit (energy acceptor) is observed, indicating that intramolecular fluorescence resonance energy transfer (FRET-On) occurs in 1. When Cu²⁺ is added to a solution of 1, however, the fluorescence of pyrene is strongly quenched (FRET-Off) whereas that of naphthalene group is revived. Such FRET ‘On-Off’ behavior of 1 is observed only in the case of Cu²⁺ binding, but not for other metal cations. The high selectivity of 1 toward Cu²⁺ can be potentially applied to a new kind of FRET-based chemosensor. The FRET On-Off behavior is supported by computational studies. The calculated molecular orbitals of HOMO and LUMOs suggest the excited-state interactions leading to FRET from naphthalene to pyrene in 1, but no electron density changes in 1·Cu²⁺ complex.     

Towards the synthesis of osteoclast inhibitor SB-242784

Osteoclast inhibitor SB-242784 (1) was prepared from pivotal indol intermediate 4. A ‘Stille’ cross coupling of organotin 2c with bromo acrylate 11 afforded diene 12 which was also obtained via a reduction-isomerization process of enyne 16. Bromoamide 3 was prepared from the corresponding acid 7 which was readily obtained from bromopyruvic acid.     

Tubular structures bearing channels in organic crystals composed of adamantane-based macrocycles

Five macrocyclic molecules (1–5) were efficiently synthesized from the dimerization and trimerization of di-substituted adamantane derivatives, which were composed of three different aromatic units and two different linker groups. Three single-crystals were obtained from these macrocyclic molecules, including a set of pseudopolymorphs (3a and 3b) of macrocycle 3 and another macrocycle 5 (5a). Single crystal X-ray analysis revealed that the three monocyclic compounds were rectangular or square in shape with solvent molecules in the cavity. Macrocycle 3 in 3a formed stacks to produce tubular structures with channels that assembled into three-dimensional networks through CH/π interactions.     

Three different fluorescent responses to transition metal ions using receptors based on 1,2-bis- and 1,2,4,5-tetrakis-(8-hydroxyquinolinoxymethyl)benzene

The dipod 1,2-bis(8-hydroxyquinolinoxymethyl)benzene (3) and tetrapod 1,2,4,5-tetrakis(8-hydroxyquinolinoxymethyl)benzene (5) have been synthesized through nucleophilic substitution of respective 1,2-bis(bromomethyl)benzene (2) and 1,2,4,5-tetra(bromomethyl)benzene (4) with 8-hydroxyquinoline (1). For comparison, 1,3,5-tris(8-hydroxyquinolinoxymethyl)benzene derivatives (7a and 7b) have been obtained. The complexation behavior of these podands towards Ag⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, and Cd²⁺ metal ions has been investigated in acetonitrile by fluorescence spectroscopy. The sterically crowded 1,2,4,5-tetrapod 5 displays unique fluorescence ‘ON-OFF-ON’ switching through fluorescence quenching (λ_max 395 nm, switch OFF) with <1.0 equiv of Ag⁺ and fluorescence enhancement (λ_max 495 nm, switch ON) with >3 equiv Ag⁺ and can be used for estimation of two different concentrations of Ag⁺ at two different wavelengths. The addition of Cu²⁺, Ni²⁺, and Co²⁺ metal ions to tetrapod 5 causes fluorescence quenching, i.e., ‘ON-OFF’ phenomena at λ_max 395 nm for <10 μM (1 equiv) of these ions but addition of Zn²⁺ and Cd²⁺ to tetrapod 5 results in fluorescence enhancement with a gradual shift of λ_em from 395 to 432 and 418 nm, respectively. Similarly, dipod 3 behaves as an ‘ON-OFF-ON’ switch with Ag⁺, an ‘ON-OFF’ switch with Cu²⁺, and an ‘OFF-ON’ switch with Zn²⁺. The placement of quinolinoxymethyl groups at the 1,3,5-positions of benzene ring in tripod 7a-b leads to simultaneous fluorescence quenching at λ_max 380 nm and enhancement at λ_max 490 nm with both Ag⁺ and Cu²⁺. This behavior is in parallel with 8-methoxyquinoline 8. The rationalization of these results in terms of metal ion coordination and protonation of podands shows that 1,2 placement of quinoline units in tetrapod 5 and dipod 3 causes three different fluorescent responses, i.e., ‘ON-OFF-ON’, ‘ON-OFF’, and ‘OFF-ON’ due to metal ion coordination of different transition metal ions and 1, 3, and 5 placement of three quinolines in tripod 7, the protonation of quinolines is preferred over metal ion coordination. In general, the greater number of quinoline units coordinated per metal ion in 5 compared with the other podands points to organization of the four quinoline moieties around metal ions in the case of 5.     

A new chiral diol derived from tetralone for the complexation of Lewis acids

A new approach to the rational design of Lewis acids based on face-face π-π interactions is described. The synthesis of two novel diols (−)(1R,3R)-2,2-dimethyl-1,2,3,4-tetrahydronaphthalene-1,3-diol (−)-1 and (−)(1S,3R)-trans-2,2-dimethyl-1,2,3,4-tetrahydronaphthalene-1-3-diol (−)-9 is reported in six and five steps respectively starting from α-tetralone. Complexation of (−)(1R,3R)-2,2-dimethyl-1,2,3,4-tetrahydronaphthalene-1,3-diol (−)-1 to phenylboronic acid shows the interplanar distance between the boron atom and the aromatic ring to be 3.05 Å, which is ideal for the proposed interactions.