Syntheses, structures, and reactivity of new pentamethylcyclopentadienyl-rhodium(III) and -iridium(III) 4-acyl-5-pyrazolonate complexes

New [CpM(Q)Cl] complexes (M = Rh or Ir, Cp = pentamethylcyclopentadienyl, HQ = 1-phenyl-3-methyl-4R(C=O)-pyrazol-5-one in general, in detail HQ(Me), R = CH(3); HQ(Et), R = CH(2)CH(3); HQ(Piv), R = CH(2)-C(CH(3))(3); HQ(Bn), R = CH(2)-(C(6)H(5)); HQ(S), R = CH-(C(6)H(5))(2)) have been synthesized from the reaction of [CpMCl(2)](2) with the sodium salt, NaQ, of the appropriate HQ proligand. Crystal structure determinations for a representative selection of these [CpM(Q)Cl] compounds show a pseudo-octahedral metal environment with the Q ligand bonded in the O,O'-chelating form. In each case, two enantiomers (S(M)) and (R(M)) arise, differing only in the metal chirality. The reaction of [CpRh(Q(Bn))Cl] with MgCH(3)Br produces only halide exchange with the formation of [CpRh(Q(Bn))Br]. The [CpRh(Q)Cl] complexes react with PPh(3) in dichloromethane yielding the adducts CpRh(Q)Cl/PPh(3) (1:1) which exist in solution in two different isomeric forms. The interaction of [CpRh(Q(Me))Cl] with AgNO(3) in MeCN allows generation of [CpRh(Q(Me))(MeCN)]NO(3).3H(2)O, whereas the reaction of [CpRh(Q(Me))Cl] with AgClO(4) in the same solvent yields both [CpRh(Q(Me))(H(2)O)]ClO(4) and [CpRh(Cl)(H(2)O)(2)]ClO(4); the H(2)O molecules derive from the not-rigorously anhydrous solvents or silver salts.     

Synthesis and characterisation of luminescent fluorinated organoboron compounds

The reaction of 8-hydroxyquinoline (HQ) with B(C(6)F(5))(3) leads to the formation of the zwitterionic compound (C(6)F(5))(3)BQH (1), involving a proton migration from O to N. Compound 1 can be converted thermally to (C(6)F(5))(2)BQ (2), which can also be prepared from (C(6)F(5))(2)BCl and HQ. The reaction of HQ with (C(6)F(5))B(OC(6)F(5))(2) generates initially (C(6)F(5))(OC(6)F(5))BQ (3), which easily hydrolyses to give the diboron compound ((C(6)F(5))BQ)(2)O (4). Compounds 1, 2 and 4 have been fully characterised, including X-ray analysis. The spectroscopic properties of these compounds, including photoluminescence (PL) have been investigated and compared with the non-fluorinated luminescent boron compound (C(6)H(5))(2)BQ and also with AlQ(3). The changes in luminescent behaviour upon fluorination of these boron quinolinate compounds have been rationalised using computational studies.     

Oligomers with Intercalating Cytosine–Cytosine+ Base Pairs and Peptide Backbone: DNA i-Motif Analogues

Alanyl peptide nucleic acids organize in a similar manner to the DNA structure motif by stabilizing two cytosine–cytosine⁺ pairing double strands by intercalation (i-motif). These analogues demonstrate that a tetrameric arrangement of nucleobases is necessary for C–C⁺ pairing (see diagram), whereas formation of the i-motif does not depend on the ribosyl–phosphodiester backbone.     

Effects of PEO length and phenyl unit structure on ionic conductivities of the complexes of LiClO4 and alternating copolymers of PEO having various phenyl units in the backbone

A series of copolymers of predominantly poly(ethylene oxide) (PEO) with mono-phenyl (HQ), biphenyl (BP) units, or both of them (HQ/BP) in the backbone were synthesized. The solid polymer electrolytes (SPEs) were prepared from three different types of copolymers (HQ-PEG, BP-PEG, and HQ/BP-PEG) employing lithium perchlorate (LiClO₄) as a lithium salt at a fixed salt concentration of [EO]/[Li⁺]=8. Their ionic conductivities were investigated to exploit the structure–ionic conductivity relationships as a function of structural change in rigid phenyl units and chain length ratio between flexible PEO chain and rigid phenyl units. As more rigid phenyl units were incorporated in the backbone chain, the formation inter- and intra-molecular complex with LiClO₄ became weaker and lower ionic conductivities were observed. And it was also found that higher ionic conductivity is obtained with increasing PEO chain length because inter- and intra-molecular dissociation power of PEO increases.     

Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

Folded RNA molecules are shaped by an astonishing variety of highly conserved noncanonical molecular interactions and backbone topologies. The dinucleotide platform is a widespread recurrent RNA modular building submotif formed by the side-by-side pairing of bases from two consecutive nucleotides within a single strand, with highly specific sequence preferences. This unique arrangement of bases is cemented by an intricate network of noncanonical hydrogen bonds and facilitated by a distinctive backbone topology. The present study investigates the gas-phase intrinsic stabilities of the three most common RNA dinucleotide platforms - 5'-GpU-3', ApA, and UpC - via state-of-the-art quantum-chemical (QM) techniques. The mean stability of base-base interactions decreases with sequence in the order GpU > ApA > UpC. Bader's atoms-in-molecules analysis reveals that the N2(G)…O4(U) hydrogen bond of the GpU platform is stronger than the corresponding hydrogen bonds in the other two platforms. The mixed-pucker sugar-phosphate backbone conformation found in most GpU platforms, in which the 5'-ribose sugar (G) is in the C2'-endo form and the 3'-sugar (U) in the C3'-endo form, is intrinsically more stable than the standard A-RNA backbone arrangement, partially as a result of a favorable O2'…O2P intra-platform interaction. Our results thus validate the hypothesis of Lu et al. (Lu Xiang-Jun, et al. Nucleic Acids Res. 2010, 38, 4868-4876), that the superior stability of GpU platforms is partially mediated by the strong O2'…O2P hydrogen bond. In contrast, ApA and especially UpC platform-compatible backbone conformations are rather diverse and do not display any characteristic structural features. The average stabilities of ApA and UpC derived backbone conformers are also lower than those of GpU platforms. Thus, the observed structural and evolutionary patterns of the dinucleotide platforms can be accounted for, to a large extent, by their intrinsic properties as described by modern QM calculations. In contrast, we show that the dinucleotide platform is not properly described in the course of atomistic explicit-solvent simulations. Our work also gives methodological insights into QM calculations of experimental RNA backbone geometries. Such calculations are inherently complicated by rather large data and refinement uncertainties in the available RNA experimental structures, which often preclude reliable energy computations.     

Steric control of the excited-state intramolecular proton transfer in 3-hydroxyquinolones: steady-state and time-resolved fluorescence study

3-Hydroxyquinolones (3HQs), similarly to their 3-hydroxychromone analogs, undergo excited state intramolecular proton transfer (ESIPT) resulting in dual emission. In the ground state, 2-phenyl-3HQ derivatives are not flat due to a steric hindrance between the 2-phenyl group and the 3-OH group that participates in the ESIPT reaction. To study the effect of this steric hindrance on the ESIPT reaction, a number of 3HQ derivatives have been synthesized and characterized in different organic solvents by steady-state and time-resolved fluorescence techniques. According to our results, 2-phenyl-3HQ derivatives undergo much faster ESIPT (by nearly 1 order of magnitude) than their 2-methyl-3HQ analogs. Moreover, 1-methyl-2-phenyl-3HQ having a strongly twisted 2-phenyl group undergoes a two- to three-fold slower ESIPT compared to 2-phenyl-3HQ. These results suggest that the flatter conformation of 2-phenyl-3HQ, which allows a close proximity of the 2-phenyl and 3-OH groups, favors a fast ESIPT reaction. The absorption and fluorescence spectra of the 3HQ derivatives additionally confirm that the steric rather than the electronic effect of the 2-phenyl group is responsible for the faster ESIPT reaction. Based on the spectroscopic studies and quantum chemical calculations, we suggest that the 2-phenyl group decreases the rotational freedom of its proximal 3-OH group in the more planar conformation of 2-phenyl-3HQ. As a result, the conformations of 3HQ, where the 3-OH group orients to form an intramolecular H-bond with the 4-carbonyl group, are favored over those with a disrupted intramolecular H-bond. Therefore, the 2-phenyl group sterically favors the intramolecular H-bond and thus accelerates the ESIPT reaction. This conclusion provides a new understanding of the ESIPT process in 3-hydroxyquinolones and related systems and suggests new possibilities for the design of ESIPT based molecular sensors and switchers.     

Synthesis and antimicrobial activities of silver(I) sulfanylcarboxylates. Structural isomers with identically or unequally coordinated Ag centers in an Ag4S4 ring

We have investigated the reactions of silver nitrate and 3-(aryl)-2-sulfanylpropenoic acids [H(2)xspa, x: p = 3-phenyl-, f = 3-(2-furyl)-, t = 3-(2-thienyl)-, py = 3-(2-pyridyl)-] and 2-cyclopentylidene-2-sulfanylacetic acid (H(2)L) in 1 : 1 and 2 : 1 molar ratios. The 1 : 1 molar ratio gave compounds of type [Ag(HL)]; reaction of these compounds with diisopropylamine and NaOH gave [HQ][Ag(L)] (HQ = diisopropylammonium) and Na[Ag(L)] x H(2)O, respectively. These compounds, as well as those of type [Ag(2)(L)] obtained with the 1 : 2 molar ratio, were isolated and characterized by IR and NMR ((1)H and (13)C) spectroscopy. (109)Ag NMR spectroscopy and ESI-MS spectrometry were also used in some cases. The crystal structures of [HQ][Ag(pspa)] (11), in which the presence of structural isomers was detected, and [HQ][Ag(cpa)] (15) were determined by X-ray diffractometry. The antimicrobial activity of the complexes against E. coli, S. aureus, B. subtilis, P. aeruginosa/Resistant P. aeruginosa, and C. albicans was tested.     

Excited-state hydrogen-atom transfer along solvent wires: water molecules stop the transfer

Excited-state hydrogen-atom transfer (ESHAT) along a hydrogen-bonded solvent wire occurs for the supersonically cooled n = 3 ammonia-wire cluster attached to the scaffold molecule 7-hydroxyquinoline (7HQ) [Tanner, C.; et al. Science 2003, 302, 1736]. Here, we study the analogous three-membered solvent-wire clusters 7HQ.(NH3)n.(H2O)m, n + m = 3, using resonant two-photon ionization (R2PI) and UV-UV hole-burning spectroscopies. Substitution of H2O for NH3 has a dramatic effect on the excited-state H-atom transfer: The threshold for the ESHAT reaction is approximately 200 cm(-1) for 7HQ.(NH3)3, approximately 350 cm(-1) for both isomers of the 7HQ.(NH3)2.H2O cluster, and approximately 600 cm(-1) for 7HQ.NH3.(H2O)2 but increases to approximately 2000 cm(-1) for the pure 7HQ.(H2O)3 water-wire cluster. To understand the effect of the chemical composition of the solvent wire on the H-atom transfer, the reaction profiles of the low-lying electronic excited states of the n = 3 pure and mixed solvent-wire clusters are calculated with the configuration interaction singles (CIS) method. For those solvent wires with an NH3 molecule at the first position, injection of the H atom into the wire can occur by tunneling. However, further H-atom transfer is blocked by a high barrier at the first (and second) H2O molecule along the solvent wire. H-atom transfer along the entire length of the solvent wire, leading to formation of the 7-ketoquinoline (7KQ) tautomer, cannot occur for any of the H2O-containing clusters, in agreement with experimentally observed absence of 7KQ fluorescence.     

Coordination copolymerization of severely encumbered isoalkenes with ethylene: enhanced enchainment mediated by binuclear catalysts and cocatalysts

This contribution describes the implementation of the binuclear organotitanium "constrained geometry catalysts" (CGCs), (mu-CH(2)CH(2)-3,3'){(eta(5)-indenyl)[1-Me(2)Si((t)()BuN)](TiMe(2))}(2)[EBICGC(TiMe(2))(2); Ti(2)] and (mu-CH(2)-3,3'){(eta(5)-indenyl)[1-Me(2)Si((t)BuN)](TiMe(2))}(2)[MBICGC(TiMe(2))(2); C1-Ti(2)], in combination with the bifunctional bisborane activator 1,4-(C(6)F(5))(2)BC(6)F(4)B(C(6)F(5))(2) (BN(2)) in ethylene + olefin copolymerization processes. Specifically examined are the classically poorly responsive 1,1-disubstituted comonomers, methylenecyclopentane (C), methylenecyclohexane (D), 1,1,2-trisubstituted 2-methyl-2-butene (E), and isobutene (F). For the first three comonomers, this represents the first report of their incorporation into a polyethylene backbone via a coordination polymerization process. C and D are incorporated via a ring-unopened pathway, and E is incorporated via a novel pathway involving 2-methyl-1-butene enchainment in the copolymer backbone. In ethylene copolymerization, Ti(2) + BN(2) enchains approximately 2.5 times more C, approximately 2.5 times more D, and approximately 2.3 times more E than the mononuclear catalyst analogue [1-Me(2)Si(3-ethylindenyl)((t)BuN)]TiMe(2) (Ti(1)) + B(C(6)F(5))(3) (BN) under identical polymerization conditions. Polar solvents are found to weaken the catalyst-cocatalyst ion pairing, thus influencing the comonomer enchainment selectivity.     

On the structure and dynamics of duplex GNA

Glycol nucleic acid (GNA), with a nucleotide backbone comprising of just three carbons and the stereocenter derived from propylene glycol (1,2-propanediol), is a structural analog of nucleic acids with intriguing biophysical properties, such as formation of highly stable antiparallel duplexes with high Watson-Crick base pairing fidelity. Previous crystallographic studies of double stranded GNA (dsGNA) indicated two forms of backbone conformations, an elongated M-type (containing metallo-base pairs) and the condensed N-type (containing brominated base pairs). A herein presented new crystal structure of a GNA duplex at 1.8 ? resolution from self-complementary 3'-CTC(Br)UAGAG-2' GNA oligonucleotides reveals an N-type conformation with alternating gauche-anti torsions along its (O3'-C3'-C2'-O2') backbone. To elucidate the conformational state of dsGNA in solution, molecular dynamic simulations over a period of 20 ns were performed with the now available repertoire of structural information. Interestingly, dsGNA adopts conformational states in solution intermediate between experimentally observed backbone conformations: simulated dsGNA shows the all-gauche conformation characteristic of M-type GNA with the higher helical twist common to N-type GNA structures. The so far counterintuitive, smaller loss of entropy upon duplex formation as compared to DNA can be traced back to the conformational flexibility inherent to dsGNA but missing in dsDNA. Besides extensive interstrand base stacking and conformational preorganization of single strands, this flexibility contributes to the extraordinary thermal stability of GNA.     

L-alpha-lyxopyranosyl (4'-->3') oligonucleotides: a base-pairing system containing a shortened backbone

[formula: see text] The L-alpha-lyxopyranosyl (4'-->3') oligonucleotide system shows cooperative base-pairing in spite of containing only five instead of the usual six covalent bonds per repetitive backbone unit. In contrast, corresponding D-beta-ribofuranosyl (4'-->3') oligonucleotides do not show adenine-thymine pairing under comparable conditions. The difference in pairing behavior relates to the conformation of the two systems' vicinal 3',4'-phosphodiester substituents, which is diaxial in the lyxopyranosyl system and 3'-axial-4'-equatorial in the ribopyranosyl system.     

Modulating affinities of di-2-picolylamine (DPA)-substituted quinoline sensors for zinc ions by varying pendant ligands

We have developed a series of di-2-picolylamine (DPA)-substituted quinoline sensors, HQ1- 4, bearing a pendant ligand at the 8 position of quinoline. UV-vis spectra of HQ1- 4 showed similar variations to that of HQ5 but with different varying extents upon the titration of zinc ions. Fluorescence intensities of HQ1, HQ3, and HQ4 were enhanced 4-6 times upon the addition of 1 equiv of zinc ions under an aqueous buffer. Somewhat unexpectedly, HQ2 is nonfluorescent in the presence of metal ions, including zinc ions. The affinities of HQ sensors are distributed in a broad range from nanomolarity to femtomolarity by varying the pendant ligands near the coordination unit. More importantly, these new sensors exhibited very high selectivity for Zn(2+) over Na(+), K(+), Mg(2+), and Ca(2+) at the millimolar level and over other transition metal ions at the micromolar level, except for Cd(2+). These findings indicated that the incorporations of the pendant groups exerted no effect on the spectroscopic properties and selectivity of the parent fluorescent sensor, with the exception of HQ2. Finally, X-ray crystal structures of ZnHQ's revealed that the auxiliary pendant groups at the 8 position participated in zinc coordination and were able to tune the affinities of HQ sensors.     

根据计算结构因子重新指定镍(II)8-羟基喹啉的两个络合物

晶体学研究曾认为,分子式是Na[NiQ2(HQ)](CLO4)的结构并不含有钠而应为[H3O][NiQ2(HQ)](CLO4).相似地,稀土－Ni络合物[YQ(HQ)2][NiQ3](CLO4)也不含有钇而应为[H3O][Ni2Q3(HQ)3](CLO4).晶体结构描述的修正系根据文献报导的原子坐标计算结构因子所导出的结果.     

Crystal structure of a B-form DNA duplex containing (L)-alpha-threofuranosyl (3'-->2') nucleosides: a four-carbon sugar is easily accommodated into the backbone of DNA

(L)-alpha-Threofuranosyl-(3'-->2')-oligonucleotides (TNA) containing vicinally connected phosphodiester linkages undergo informational base pairing in an antiparallel strand orientation and are capable of cross-pairing with RNA and DNA. TNA is derived from a sugar containing only four carbon atoms and is one of the simplest potentially natural nucleic acid alternatives investigated thus far in the context of a chemical etiology of nucleic acid structure. Compared to DNA and RNA that contain six covalent bonds per repeating nucleotide unit, TNA contains only five. We have determined the atomic-resolution crystal structure of the B-form DNA duplex [d(CGCGAA)Td(TCGCG)](2) containing a single (L)-alpha-threofuranosyl thymine (T) per strand. In the modified duplex base stacking interactions are practically unchanged relative to the reference DNA structure. The orientations of the backbone at the TNA incorporation sites are slightly altered in order to accommodate fewer atoms and covalent bonds. The conformation of the threose is C4'-exo with the 2'- and 3'-substituents assuming quasi-diaxial orientation.     

Side chain homologation of alanyl peptide nucleic acids: pairing selectivity and stacking

Alanyl peptide nucleic acids (alanyl-PNAs) are oligomers based on a regular peptide backbone with alternating configuration of the amino acids. All side chains are modified by covalently linked nucleobases. Alanyl-PNAs form very rigid, well defined, and linear double strands based on hydrogen bonding of complementary strands, stacking, and solvation. Side chain homology was examined by comparing a methylene linker (alanyl-PNA) with an ethylene linker (homoalanyl-PNA), a trimethylene linker (norvalyl-PNA), and PNA sequences with mixed linker length between nucleobase and backbone. Side chain homology in combination with a linear double strand topology turned out to be valuable in order to selectively manipulate pairing selectivity (pairing mode) and base pair stacking.     

An unusual mode of DNA duplex association: Watson-Crick interaction of all-purine deoxyribonucleic acids

Nucleic acid duplexes associating through purine-purine base pairing have been constructed and characterized in a remarkable demonstration of nucleic acids with mixed sequence and a natural backbone in an alternative duplex structure. The antiparallel deoxyribose all-purine duplexes associate specifically through Watson-Crick pairing, violating the nucleobase size-complementarity pairing convention found in Nature. Sequence-specific recognition displayed by these structures makes the duplexes suitable, in principle, for information storage and replication fundamental to molecular evolution in all living organisms. All-purine duplexes can be formed through association of purines found in natural ribonucleosides. Key to the formation of these duplexes is the N(3)-H tautomer of isoguanine, preferred in the duplex, but not in aqueous solution. The duplexes have relevance to evolution of the modern genetic code and can be used for molecular recognition of natural nucleic acids.     

Fluorescence properties of 2-aryl-3-hydroxyquinolin-4(1H)-one-carboxamides

The fluorescence properties of 2-aryl-3-hydroxyquinolin-4(1H)-one-carboxamides (3HQCs) with carboxylic alkylamide groups at positions 6, 7 or 8 (3HQ6Cs, 3HQ7Cs, and 3HQ8Cs) have been studied to evaluate their potential as molecular probes.     

Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)(2) (3-), (CCGG)(2) (3-), (AATTAAT)(2) (3-), (CCGGCCG)(2) (3-), A(7).T(7) (3-), A(7).A(7) (3-), T(7).T(7) (3-), and A(7).C(7) (3-) were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 10(13) to 10(19) s(-1). Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a - base) and w ions. Four pieces of evidence are presented which indicate that Watson-Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A(7).T(7) (3-), to the single strands is significantly higher than that for the related noncomplementary A(7).A(7) (3-) and T(7).T(7) (3-) dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A(7).A(7) (3-) and A(7).C(7) (3-) but not for A(7).T(7) (3-) consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (-DeltaH(d)) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A(7).T(7) (3-) duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent.     

Chemo‐ and Regioselective Dihydroxylation of Benzene to Hydroquinone Enabled by Engineered Cytochrome P450 Monooxygenase

Hydroquinone (HQ) is produced commercially from benzene by multi‐step Hock‐type processes with equivalent amounts of acetone as side‐product. We describe an efficient biocatalytic alternative using the cytochrome P450‐BM3 monooxygenase. Since the wildtype enzyme does not accept benzene, a semi‐rational protein engineering strategy was developed. Highly active mutants were obtained which transform benzene in a one‐pot sequence first into phenol and then regioselectively into HQ without any overoxidation. A computational study shows that the chemoselective oxidation of phenol by the P450‐BM3 variant A82F/A328F leads to the regioselective formation of an epoxide intermediate at the C3=C4 double bond, which departs from the binding pocket and then undergoes fragmentation in aqueous medium with exclusive formation of HQ. As a practical application, an E. coli designer cell system was constructed, which enables the cascade transformation of benzene into the natural product arbutin, which has anti‐inflammatory and anti‐bacterial activities.