Thermodynamics for the Formation of Double‐Stranded DNA–Single‐Walled Carbon Nanotube Hybrids

For the first time, the thermodynamics are described for the formation of double‐stranded DNA (ds‐DNA)–single‐walled carbon nanotube (SWNT) hybrids. This treatment is applied to the exchange reaction of sodium cholate (SC) molecules on SWNTs and the ds‐DNAs d(A)₂₀–d(T)₂₀ and nuclear factor (NF)‐κB decoy. UV/Vis/near‐IR spectroscopy with temperature variations was used for analyzing the exchange reaction on the SWNTs with four different chiralities: (n,m)=(8,3), (6,5), (7,5), and (8,6). Single‐stranded DNAs (ss‐DNAs), including d(A)₂₀ and d(T)₂₀, are also used for comparison. The d(A)₂₀–d(T)₂₀ shows a drastic change in its thermodynamic parameters around the melting temperature (T_m) of the DNA oligomer. No such T_m dependency was measured, owing to high T_m in the NF‐κB decoy DNA and no T_m in the ss‐DNA.     

Quercetin 2,4‐Dioxygenase Activates Dioxygen in a Side‐On O2–Ni Complex

Quercetin 2,4‐dioxygenase (quercetinase) from Streptomyces uses nickel as the active‐site cofactor to catalyze oxidative cleavage of the flavonol quercetin. How this unusual active‐site metal supports catalysis and O₂ activation is under debate. We present crystal structures of Ni‐quercetinase in three different states, thus providing direct insight into how quercetin and O₂ are activated at the Ni²⁺ ion. The Ni²⁺ ion is coordinated by three histidine residues and a glutamate residue (E⁷⁶) in all three states. Upon binding, quercetin replaces one water ligand at Ni and is stabilized by a short hydrogen bond through E⁷⁶, the carboxylate group of which rotates by 90°. This conformational change weakens the interaction between Ni and the remaining water ligand, thereby preparing a coordination site at Ni to bind O₂. O₂ binds side‐on to the Ni²⁺ ion and is perpendicular to the C2?C3 and C3?C4 bonds of quercetin, which are cleaved in the following reaction steps.     

X‐Ray Near‐Edge Absorption Study of Temperature‐Induced Low‐Spin‐to‐High‐Spin Change in Metallo‐Supramolecular Assemblies

X‐ray absorption near the iron K edge (XANES) was used to investigate the characteristics of temperature‐induced low‐spin‐to‐high‐spin change (SC) in metallo‐supramolecular polyelectrolyte amphiphile complexes (PAC) containing FeN₆ octahedra attached to two or six amphiphilic molecules. Compared to the typical spin‐crossover material Fe(phen)₂(NCS)₂ XANES spectra of PAC show fingerprint features restricted to the near‐edge region which mainly measures multiple scattering (MS) events. The changes of the XANES profiles during SC are thus attributed to the structure changes due to different MS path lengths. Our results can be interpreted by a uniaxial deformation of FeN₆ octahedra in PAC. This is in agreement with the prediction that SC is originated by a structural phase transition in the amphiphilic matrix of PAC, but in contrast to Fe(phen)₂(NCS)₂, showing the typical spin crossover being associated with shortening of all the metal–ligand distances.     

Hydrothermal synthesis and extended structure of poly[aqua(μ5‐ethylenediaminetetraacetato)dizinc(II)]

In the extended structure of the title compound, [Zn₂(C₁₀H₁₂N₂O₈)(H₂O)], prepared under hydrothermal conditions, there are two distinct Zn^II sites. The first, with octahedral geometry, bonds to two N and three O atoms from one ethylenediaminetetraacetate tetraanion (EDTA) and one water molecule. The second, with tetrahedral geometry, coordinates to O atoms from four different EDTA ligands. The EDTA ligand almost encapsulates the octahedral Zn^II ion and binds to four symmetry‐related tetrahedral Zn^II ions, hence generating the extended structure. One noncoordinated O‐atom site on the EDTA ligand connects to the water molecule by hydrogen bonding. Structural comparisons are made with other compounds containing zinc, EDTA and water.     

DNA Binding and Cleavage Activity of cis‐Cobalt Aromatic Oxime Complexes and Its Pyridine/imidazole Adducts

cis‐Cobalt complexes with salicycaldoxime(SAO), (Z)‐1‐(2‐hydroxyphenyl)ethanonoxime (HEO), (Z)‐1‐(2,5‐dihydroxyphenyl)ethanonoxime (DEO), (Z)‐1‐(2,5‐dihydroxyphenyl)(phenyl)methanonoxime (DPO) and their adducts with pyridine (Py) and imidazole (Im) were synthesized and characterized by elemental analysis, magnetic susceptibility, UV‐Vis and IR spectra. The electrochemical studies were carried by cyclic voltammeter, the peak potential separation and formal potential of complexes were independent of sweep rate or scan rate (ν) indicating a quasi reversible one‐electron redox process. Absorption studies and thermal denature studies revealed that each of these octahedral complexes is an avid binder of calf thymus DNA. The apparent binding constants for mixed ligand complexes are in order of ～10³‐10³ M^?1. Based on the data obtained in the DNA binding studies a partial intercalative mode of binding is suggested for these complexes. The nucleolytic cleavage activity of parent complexes and their pyridine adduct were carried out on double stranded pBR322 circular plasmid DNA by using a gel electrophoresis experiment in the presence and absence of oxidant (H₂O₂). All the metal complexes show enhanced cleavage activity in presence of oxidant. The hydrolytic cleavage of DNA of Co(DEO)₂ and Co(DPO)₂ is evidenced from the control experiments showing discernable cleavage inhibition in the presence of the hydroxyl radical inhibitor DMSO and EDTA.     

Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low‐Energy Electron Attachment

To elucidate the role of guanosine in DNA strand breaks caused by low‐energy electrons (LEEs), theoretical investigations of the LEE attachment‐induced C? O σ‐bonds and N‐glycosidic bond breaking of 2′‐deoxyguanosine‐3′,5′‐diphosphate (3′,5′‐dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3′,5′‐diphosphate in the gas phase excludes either C? O bond cleavage or N‐glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3′,5′‐dGDP and the VDE of 3′,5′‐dGDP^?. Furthermore, the solvent–solute interactions greatly reduce the activation barriers of the C? O bond cleavage to 1.06–3.56 kcal mol^?1. These low‐energy barriers ensure that either C_5′? O_5′ or C_3′? O_3′ bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N‐glycosidic bond rupture implies that this reaction pathway is inferior to C? O bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE‐induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE‐induced DNA damage resembles that of the solvent.     

Theoretical study of the photochemical reaction mechanism of bicyclo[4.1.0]hept‐2‐ene upon direct photolysis

Ab initio multiconfigurational CASSCF/MP2 method with the 6‐31G* basis set has been employed in studying the photochemistry of bicyclo[4.1.0]hept‐2‐ene upon direct photolysis. Our calculations involve the ground state (S₀) and excited states (S₁, T₁, and T₂). The ground‐state reaction pathways corresponding to the formation of the six products derived from bicyclo[4.1.0]hept‐2‐ene via two important diradical intermediates (D1 and D2) were mapped. It was found that there are various crossing points (conical intersections and singlet–triplet crossings) in the regions near D1 and D2. These crossing points imply that direct photolysis can lead to two possible radiationless relaxation routes: (1) S₁ → S₀, (2) S₁ → T₂ → T₁ → S₀. Computation indicates that the second route is not a competitive path with the first route during direct photolysis. The first route is initiated by barrierless cyclopropane bond cleavage to form two singlet excited diradical intermediates, followed by efficient decay to the ground‐state surface via three S₁/S₀ conical intersections in the regions near the diradical intermediates. All six ground‐state products can be formed via the three conical intersections almost without barrier after the decays. The barriers separating the diradical minima on S₁ from the S₁/S₀ conical intersections were found to be very small with respect to the vertical excitation energy, which can explain why the product distribution is independent of excitation wavelength. Triplet surfaces are not involved in the first route, which agrees with the fact that the product contribution was unchanged by the addition of naphthalene. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Iridium‐Catalyzed Reductive Carbon–Carbon Bond Cleavage Reaction on a Curved Pyridylcorannulene Skeleton

The cleavage of C? C bonds in π‐conjugated systems is an important method for controlling their shape and coplanarity. An efficient way for the cleavage of an aromatic C? C bond in a typical buckybowl corannulene skeleton is reported. The reaction of 2‐pyridylcorannulene with a catalytic amount of IrCl₃?n H₂O in ethylene glycol at 250 °C resulted in a structural transformation from the curved corannulene skeleton to a strain‐free flat benzo[ghi]fluoranthene skeleton through a site‐selective C? C cleavage reaction. This cleavage reaction was found to be driven by both the coordination of the 2‐pyridyl substituent to iridium and the relief of strain in the curved corannulene skeleton. This finding should facilitate the design of carbon nanomaterials based on C? C bond cleavage reactions.     

Ring‐opening polymerization of 1,4‐dioxan‐2‐one initiated by lanthanum isopropoxide in bulk

Lanthanum isopropoxide (La(OiPr)₃) has been synthesized and employed for ring‐opening polymerization of 1,4‐dioxan‐2‐one in bulk as a single‐component initiator. The influences of reaction conditions such as initiator concentration, reaction time, and reaction temperature on the polymerization were investigated. The kinetics indicated that the polymerization is first‐order with respect to the monomer concentration. The Mechanistic investigations according to ¹H NMR spectrum analysis demonstrated that the polymerization of PDO proceeded through a coordination‐insertion mechanism with a rupture of the acyl‐oxygen bond of the monomer rather than the alkyl‐oxygen bond cleavage. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5214–5222, 2008     

Manipulation of Single‐Stranded DNA by Using an Artificial Site‐Selective DNA Cutter Composed of Cerium(IV)/EDTA and Phosphonate–Oligonucleotide Conjugates

An artificial site‐selective DNA cutter to hydrolyze single‐stranded DNA at a desired site was prepared from Ce^IV/ethylenediamintetraacetic acid (EDTA) and two ethylenediamine‐N,N,N′,N′‐tetrakis(methylenephosphonic acid)–oligonucleotide conjugates. By using this cutter, the sense strand of a blue fluorescent protein (BFP) gene was selectively cut at a predetermined site in the chromophore‐coding region. The upstream fragment obtained by the site‐selective scission was ligated with the downstream fragment of the closely related green fluorescent protein (GFP) gene so that the 5′‐ and 3′‐end portions of the chromophore came from the BFP fragment and the GFP fragment, respectively. The recombinant gene was successfully expressed in E. coli and the chimeric chromophore emitted green fluorescence as expected.     

Novel 13,14‐dimethyl‐5,8‐dioxa‐2,11,13,14‐tetraaza‐1,12‐diphosphabicyclo [10.1.1] tetradecane 1,12‐dioxide ligand and its Ni(II), Co(II), and Cu(II) complexes: Synthesis,characterization, antimicrobial,DNA cleavage,and computational studies

A novel diazadiphosphetidine ligand derived from the reaction of 2,4‐dichloro‐1,3‐dimethyl‐1,3,2,4‐diazadiphosphetidine‐2,4‐dioxide and 2,2′‐(ethane‐1,2‐diylbis[oxy])bis(ethan‐1‐amine) and its Ni(II), Cu(II), and Co(II) complexes have been synthesized, characterized by spectroscopic, elemental analyses, magnetic susceptibility, and conductivity methods, and screened for antimicrobial, DNA binding, and cleavage properties. Spectroscopic analysis and elemental analyses indicate the formula [M(H₂L)Cl₂] for the Cu(II), Co(II), Ni(II), and Zn(II) complexes and octahedral geometry for all the complexes. The non‐electrolytic nature of the complexes in dimethyl sulfoxide (DMSO) was confirmed by their molar conductance values, which are in the range 12.32–6.73 Ω^?1 cm² mol^?1. Computational studies have been carried out at the density functional theory (DFT)‐B3LYP/6‐31G(d) level of theory on the structural and spectroscopic properties of diazadiphosphetidine H₂L and its binuclear Cu(II), Co(II), Ni(II), and Zn(II) complexes. Six tautomers and geometrical isomers of the diazadiphosphetidine ligand were confirmed using semiempirical AM1 and DFT method from DMOL³ calculations. The copper complex had the best antibacterial activity against Staphylococcus aureus (ATCC 29213). DNA cleavage activities of the compounds, evaluated on pBR322 DNA by agarose gel electrophoresis in the presence and absence of an oxidant (H₂O₂) and a free‐radical scavenger (DMSO), indicated no activity for the ligand and moderate activity for the complexes, with the copper complex cleaving pBR322 DNA more efficiently in the presence of H₂O₂.     

The Radiative Lifetime in Near‐IR‐Luminescent Ytterbium Cryptates: The Key to Extremely High Quantum Yields

A powerful strategy for the improvement of near‐IR lanthanoid luminescence has been successfully employed for the first time, which involves the rational and deliberate shortening of the radiative luminescence lifetimes τ_rad in molecular ytterbium complexes. In this context, the bidentate chelating unit 2,2′‐bipyridine‐N,N′‐dioxide has been identified as being responsible for decreasing τ_rad substantially in macrobicyclic Yb cryptates. This strategy, when combined with conventional approaches, yields unprecedented absolute near‐IR quantum yields of up to 12 %. This extraordinary efficiency represents the highest value measured for any molecular lanthanoid near‐IR emitter. The proof‐of‐concept for the implementation of the new strategy opens up entirely new prospects for the field of lanthanoid luminescence.     

Crystal structure of a NIR‐Emitting DNA‐Stabilized Ag16 Nanocluster

DNA has been used as a scaffold to stabilize small, atomically monodisperse silver nanoclusters, which have attracted attention due to their intriguing photophysical properties. Herein, we describe the X‐ray crystal structure of a DNA‐encapsulated, near‐infrared emitting Ag₁₆ nanocluster (DNA–Ag₁₆NC). The asymmetric unit of the crystal contains two DNA–Ag₁₆NCs and the crystal packing between the DNA–Ag₁₆NCs is promoted by several interactions, such as two silver‐mediated base pairs between 3′‐terminal adenines, two phosphate–Ca²⁺–phosphate interactions, and π‐stacking between two neighboring thymines. Each Ag₁₆NC is confined by two DNA decamers that take on a horse‐shoe‐like conformation and is almost fully shielded from the solvent environment. This structural insight will aid in the determination of the structure/photophysical property relationship for this class of emitters and opens up new research opportunities in fluorescence imaging and sensing using noble‐metal clusters.     

Mechanistic Insights into the Radical S‐adenosyl‐l‐methionine Enzyme NosL From a Substrate Analogue and the Shunt Products

The radical S‐adenosyl‐l ‐methionine (SAM) enzyme NosL catalyzes the transformation of l ‐tryptophan into 3‐methyl‐2‐indolic acid (MIA), which is a key intermediate in the biosynthesis of a clinically interesting antibiotic nosiheptide. NosL catalysis was investigated by using the substrate analogue 2‐methyl‐3‐(indol‐3‐yl)propanoic acid (MIPA), which can be converted into MIA by NosL. Biochemical assays with different MIPA isotopomers in D₂O and H₂O unambiguously indicated that the 5′‐deoxyadenosyl (dAdo)‐radical‐mediated hydrogen abstraction is from the amino group of l ‐tryptophan and not a protein residue. Surprisingly, the dAdo‐radical‐mediated hydrogen abstraction occurs at two different sites of MIPA, thereby partitioning the substrate into different reaction pathways. Together with identification of an α,β‐unsaturated ketone shunt product, our study provides valuable mechanistic insight into NosL catalysis and highlights the remarkable catalytic flexibility of radical SAM enzymes.     

A Mini‐Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class

Nucleolytic ribozymes catalyze site‐specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild‐type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine‐6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pK_a value of 5.1 was determined for a ¹³C2‐labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pK_a of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine‐6 in the catalytic mechanism besides the previously identified invariant guanine‐48 and a Mg²⁺ ion, both of which are directly coordinated to the non‐bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn²⁺ or Cd²⁺ accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 Å X‐ray structure of a 2′‐OCH₃‐U5 modified twister ribozyme.     

Calix[4]arene‐Phosphine Dimers: Precursors of Flexible Metallo‐Capsules and Self‐Compacting Molecules

The first diphosphines based on a double calixarene, namely 1,4 (or 1,3)‐bis‐(5‐diphenylphosphino‐25,26,27,28‐tetrapropoxycalix[4]aren‐17‐yl)benzene ( L² , L³ ) were each prepared in four steps starting from 5,17‐dibromo‐25,26,27,28‐tetrapropoxycalix[4]arene. Upon reaction of L² with [Au(tht)(thf)]BF₄, (tht=C₄H₈S) a rigid metallo‐capsule was quantitatively formed, which adopts an oblique form owing to the distinct nature of the spacers linking the two calixarene half‐spheres. In the solid state, the 1,4‐substituted phenylene linker is turned towards the gold ion, suggesting the existence of weak bonding interactions between two aromatic CH protons of this ring and the metal centre (Au???H=2.67 Å). In contrast to this gold complex, the related silver complex shows dynamic behaviour in solution, the exchange between two enantiomeric oblique forms being facilitated by the greater stereochemical flexibility of Ag^I vs. Au^I. A heteronuclear ¹⁰⁹Ag{¹H} HMQC experiment established strong correlations between the CH protons of the phenylene linker and the ¹⁰⁹Ag ion. Dynamic behaviour similar to that observed for the silver complex was further observed in trans‐[PtCl₂? L² ], a chelate complex that could be obtained quantitatively from L² and [PtCl₂(PhCN)₂]. The intended formation of a chelate complex leading to a capsule with an endo‐oriented metal centre was achieved by reacting L³ with [Pd(allyl)(thf)₂]BF₄. The complex thus formed constitutes the first organometallic transition metal complex embedded in a cavity with large portals. Binding of [RuCl₂(p‐cymene)] to L² and L³ resulted in self‐compacting bimetallic complexes in which each calixarene basket entraps a Ru(p‐cymene) unit, thereby forming molecules occupying a minimal volume.     

Synthesis,structure and DNA cleavage of mononuclear Fe(III) complexes with 1,2,4‐triazole‐base ligand

Two new mononuclear iron(III) complexes, [Fe(HL)₂](ClO₄) · (H₂O)_1.75· CH₃CN (1) and [Fe(HL)Cl₂] · DMF (2) [H₂L = 3‐(2‐phenol)‐5‐(pyridin‐2‐yl)‐1,2,4‐triazole] have been synthesized and characterized by X‐ray single‐crystal structure analysis. The single crystal X‐ray crystallographic studies reveal that the central iron atom has a distorted octahedral environment for 1 and a distorted square pyramidal geometry for 2. The DNA cleavage activity of the iron(III) complexes was measured, indicating that the six‐coordinated iron(III) (complex 1) was cleavage inactive and only five‐coordinated complex 2 effectively promoted the cleavage of plasmid DNA in the presence and/or absence of activating agents (peroxide oxygen) at physiological pH and temperature. The mechanism of plasmid DNA cleavage was also studied by adding standard radical scavengers. Copyright © 2010 John Wiley & Sons, Ltd.     

X‐ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases

[NiFe] hydrogenases are complex model enzymes for the reversible cleavage of dihydrogen (H₂). However, structural determinants of efficient H₂ binding to their [NiFe] active site are not properly understood. Here, we present crystallographic and vibrational‐spectroscopic insights into the unexplored structure of the H₂‐binding [NiFe] intermediate. Using an F₄₂₀‐reducing [NiFe]‐hydrogenase from Methanosarcina barkeri as a model enzyme, we show that the protein backbone provides a strained chelating scaffold that tunes the [NiFe] active site for efficient H₂ binding and conversion. The protein matrix also directs H₂ diffusion to the [NiFe] site via two gas channels and allows the distribution of electrons between functional protomers through a subunit‐bridging FeS cluster. Our findings emphasize the relevance of an atypical Ni coordination, thereby providing a blueprint for the design of bio‐inspired H₂‐conversion catalysts.     

基于镱和铒的α-噻吩甲酰丙酮-哌啶配合物与DNA之间相互作用的DNA探针和切割研究

两种[Ln(TTA)4].HP (Ln =Yb, Er)配合物被合成并表征。通过紫外可见光谱、荧光光谱、粘度和分子模拟研究了他们与DNA的键合特征。研究结果表明：它们能插入双链的DNA。更重要的是它们的荧光强度能被DNA增强,因此,一种灵敏的荧光检测DNA的方法被发展。两种配合物与质粒DNA的切割反应在凝胶电泳上展开。有意义的是,我们发现在pH=7.2 和 37℃下,两种化合物都能切割超螺旋质粒DNA。另外,我们选择BDNPP作为模型化合物进一步研究了它们对质粒DNA的切割机理,从一级动力学方程,我们间接证明可能是水解切割机理。