Cu2+对腺嘧啶-胸腺嘧啶碱基对阴离子质子转移的影响

采用B3LYP/DZP++方法研究了腺嘌呤-胸腺嘧啶(A-T)碱基对阴离子(AT)-的单质子转移机理以及金属离子Cu2+对(AT)-碱基对质子转移的影响.(AT)-碱基对的单质子转移路径是由胸腺嘧啶N25位上的质子H26沿分子间的氢键N25-H26…N10转移到腺嘌呤的N10位.金属Cu2+可通过络合作用分别吸附在(AT)-碱基对O24、O28、N4、N13上,从而影响(AT)-碱基对中质子转移过程.Cu2+络合作用在胸腺嘧啶(T)的O24、O28上时,发生了从胸腺嘧啶到腺嘌呤方向上的单质子转移反应;而作用在腺嘌呤(A)的N4、N13上时,得到了双质子转移的稳定产物.     

Logic gates for multiplexed analysis of Hg2+ and Ag+

The design of devices with multiple functions, simple handling procedures and sufficient sensitivity has drawn great interests in the field of analysis. Metal-nucleotide based pairs, such as T-Hg(2+)-T and C-Ag(+)-C complexes accompanied by SYBR Green I (SG), are used to selectively bind duplex-strand DNA by observing a bright fluorescence signal in this work, thus yielding a simple method for the rapid detection of Hg(2+) and Ag(+) without a complex labeling process. Based on this principle, 'OR' and 'AND' logic gates for the multiplexed analysis of Hg(2+) and Ag(+) were developed, and their practical application for the detection of Hg(2+) and Ag(+) in drinking water was reported.     

A squaraine-based colorimetric and "turn on" fluorescent sensor for selective detection of Hg2+ in an aqueous medium

A novel squaraine-based chemosensor SQ-1 has been synthesized, and its sensing behavior toward various metal ions was investigated by UV-vis and fluorescence spectroscopies. In AcOH-H(2)O (40:60, v/v) solution, Hg(2+) ions coordinate with SQ-1 causing a deaggregation which induces a visual color and absorption spectral changes as well as strong fluorescence. In contrast, the addition of other metals (e.g., Pb(2+), Cd(2+), Cu(2+), Zn(2+), Al(3+), Ni(2+), Co(2+), Fe(3+), Ca(2+), K(+), Mg(2+), Na(+), and Ag(+)) does not induce these changes at all. Thus SQ-1 is a specific Hg(2+) sensing agent due to the inducing deaggregation of the dye molecule by Hg(2+).     

Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: a correlated ab initio quantum chemical study

Interactions of adenine, cytosine, guanine, and thymine with Na(+), Mg(2+), and Zn(2+) cations were studied using an approximate resolution of identity correlated second-order MP2 (RI-MP2) method with the TZVPP ([5s3p2d1f/3s2p1d]) basis set. All existing tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine were considered. Cations bind mostly in a bidentate manner, and stabilization energies of these complexes are larger than those in the case when cations bind in a unidentate manner. The cation...Y (Y equal to N or O) distances for divalent metals are shorter than those for Na(+) and for Zn(2+) are mostly shorter than the Mg(2+)...Y distance. The intermolecular distances between the cation and the base for complexes containing adenine and cytosine are systematically shorter than those for complexes containing guanine and thymine. Only for cytosine the canonical keto/amino tautomer structure with ions represents the global minimum. For guanine, the metalated canonical form is again the most stable, but its stabilization energy is within less than 5% of the stabilization energies of the two other rare tautomers, which indicates that the canonical form and these two rare tautomers could coexist. The canonical structures of adenine and thymine in the presence of ions are considerably less stable (by more than 10%) than the complexes of the rare tautomers. It can be concluded that the interaction of Na(+), Mg(2+), and Zn(2+) cations with cytosine in the gas phase will not induce the change of the canonical form to the rare tautomeric form. In the case of isolated guanine, the equilibrium of the canonical form with rare tautomers can be found. For isolated adenine and thymine the presence of rare tautomers is highly probable.     

取代基对腺嘌呤与胸腺嘧啶氢键复合物体系结合能的影响简

优化得到了17个取代胸腺嘧啶与腺嘌呤形成的氢键复合物的结构,并计算了这些复合物的结合能,探讨了胸腺嘧啶上不同取代基对结合能的影响. 结果表明,CF3取代的胸腺嘧啶与腺嘌呤间的结合能大于胸腺嘧啶与腺嘌呤间的结合能,这可能是屈氟尿苷具有阻止病毒及肿瘤扩散功能的原因所在. SO3H,CN和NO2取代的胸腺嘧啶与腺嘌呤间具有更大的结合能,表明这3个基团取代的胸腺嘧啶也可能具有潜在的抗肿瘤作用. 分子中原子理论与自然键轨道分析表明,在所有体系中,氢键N—H…N最强,N—H…O=C次之,C—H…O=C最弱,轨道作用在氢键作用中占有重要地位.     

取代基对腺嘌呤与胸腺嘧啶氢键复合物体系结合能的影响

优化得到了17个取代胸腺嘧啶与腺嘌呤形成的氢键复合物的结构, 并计算了这些复合物的结合能, 探讨了胸腺嘧啶上不同取代基对结合能的影响. 结果表明, CF₃取代的胸腺嘧啶与腺嘌呤间的结合能大于胸腺嘧啶与腺嘌呤间的结合能, 这可能是屈氟尿苷具有阻止病毒及肿瘤扩散功能的原因所在. SO₃H, CN和NO₂取代的胸腺嘧啶与腺嘌呤间具有更大的结合能, 表明这3个基团取代的胸腺嘧啶也可能具有潜在的抗肿瘤作用. 分子中原子理论与自然键轨道分析表明, 在所有体系中, 氢键N—H…N最强, N—H…O=C次之, C—H…O=C最弱, 轨道作用在氢键作用中占有重要地位.     

A coumarin-based fluorescent probe for Hg2+ and Ag+ with an N'-acetylthioureido group as a fluorescence switch

For detection of Hg(2+) and Ag(+), we have developed a coumarin-based probe with an N'-acetylthioureido group as a novel fluorescence switch, in which the hydrogen bond formation between the N-hydrogen and the acetyl O atom markedly increases the susceptibility of the probe toward desulfurization by Hg(2+) and Ag(+).     

A "turn-on" fluorescent Hg2+ chemosensor based on Ferrier carbocyclization

A "turn-on" fluorescent chemosensor with excellent selectivity and satisfactory sensitivity on Hg(2+) detection in 100% water media has been established employing a carbohydrate based Ferrier carbocyclization reaction. The probe has also presented satisfactory results for the imaging of Hg(2+) ions in cells and organisms.     

Cu2+ colorimetric sensing and fluorescence enhancement and Hg2+ fluorescence diminution in "scorpionate"-like tetrathienyl-substituted boron-dipyrrins

Four novel tetrathienyl-substituted boron-dipyrrin-type (BODIPY-type) complexes, 3-(R')-4,4-di(R')-8-R-4-bora-3a,4a-diaza-s-indacene (4a, R = 2-T, R' = 2-T; 4b, R = 3-T, R' = 2-T; 5a, R = 2-T, R' = 3-T; 5b, R = 3-T, R' = 3-T; T = thienyl) have been prepared and fully characterized to explore patterns of stoichiometric Mn+ recognition in solution. Treatment of the respective parent BF2 dipyrrin with 2- or 3-thienyllithium gave the unexpected asymmetric tetrathienyl-substituted products in 8.5-35% yield. Compounds 4a and 4b bear a neutral "scorpionate"-like [SSS] tridentate binding pocket. Extensive NMR and UV-vis spectroscopic studies were performed on 4a-5b; 5a, 4b, and 5b were structurally characterized. The PhiF values for 4a-5b all decrease compared to the BF2-containing parent molecules (0.00058, 0.012, 0.00090, and 0.0051, respectively), with lambda(abs,max) values (epsilon, M(-1) cm(-1)) of 563 (44,000), 553 (29,000), 539 (33,000), and 531 (44,000) nm, respectively, and Stokes' shifts of 25-36 nm. Upon treatment with metal ion (Ca2+, Cs+, Mn2+, Co2+, Cu2+, Ag+, Zn2+, Cd2+, Hg2+, Pb2+) perchlorate salts, the solution of 4b undergoes rapid pink-to-clear switch-off behavior upon Cu2+ addition (10 microM scale) with smaller effects seen for 4a. Further, there were 2- to 19-fold Cu2+ fluorescence enhancements for these ligands. Cu2+- and Hg2+-L (L = 4a-5b) binding was modeled, and response patterns for Mn+-L 1:1 molar solutions upon Cu2+ addition were measured. Upon treatment with Hg2+, all ligand solutions show a significant fluorescence decrease accompanied by minor absorption increases. The UV-vis spectroscopic detection limit for Cu2+ and Hg2+ is approximately 270 ppb and approximately 1.7 ppm, respectively; the naked eye detection limit for Cu2+ with 4b (1.0 x 10(-5) M) is approximately 23 microM. DFT calculations gave HOMO-LUMO gaps of 478 (4a), 462 (4b), 448 (5a), and 442 nm (5b). Molecular orbital diagrams for 4a-5b revealed that the HOMO and LUMO electron density is distributed onto the 3-position-thienyl group and to a lesser degree the B(thienyl)2 moiety.     

An organoselenium-based highly sensitive and selective fluorescent "turn-on" probe for the Hg2+ ion

An organoselenium-based NSe(3) type of tripodal system 2 as a Hg(2+)-selective fluorescence "turn-on" probe is described. The "turn-on" fluorescence behavior of this selenotripod 2 is significant because it depends on Hg-Se bond formation and acts as a reporting unit for this system. The system exhibits immediate response (15 s) with a subnanomolar detection limit (0.1 nM) for the Hg(2+) ion. It efficiently detects both aqueous and nonaqueous Hg(2+) at 2 nM concentration.     

NIR-SERS studies of DNA and DNA bases attached on polyvinyl alcohol (PVA) protected silver grass-like nanostructures

In this work, polyvinyl alcohol (PVA) protected silver grass-like nanostructure (PVA–Ag–GNS) with near infrared surface-enhanced Raman scattering (NIR-SERS) activity was prepared and employed to detect DNA and DNA bases. The PVA–Ag–GNS demonstrated high NIR-SERS activity and good optical reproducibility in the detection of adsorbates such as the case of crystal violet, DNA and DNA bases. By using of the tested molecule of thymine, the PVA–Ag–GNS shows a high enhancement factor (EF) of ∼10⁸. For NIR-SERS detection of DNA molecules, Raman signals from the DNA bases of guanine (630 cm⁻¹) and adenine (720 cm⁻¹) are greatly enhanced. For DNA molecules NIR-SERS detection, Raman signals from the DNA bases of guanine (630 cm⁻¹), adenine (720 cm⁻¹) and cytosine (1010 cm⁻¹) are greatly enhanced. The experimental results show that the NIR-SERS spectrum of DNA is dominated by guanine mode, which is followed by adenine and cytosine modes, respectively. Meanwhile, the NIR-SERS signal intensities of the DNA bases increase in the order of thymine (T) < cytosine (C) < adenine (A) < guanine (G). One can conclude that the adsorption strength of the DNA bases in DNA molecule with the silver surface is in the order T < C < A < G, which is different from that of the four DNA bases in individual molecule adsorbed on silver surface (T < A < G < C). On the other hand, the geometry optimization and calculated wavenumber of the complexes of adenine–Ag, guanine–Ag, cytosine–Ag and thymine–Ag for the ground states are performed with DFT, B3LYP functional and the LanL2DZ basis set. The calculated wavenumbers match well with the experimental results. According to our experiment and calculations, DNA base molecules adsorbed on silver surface via the intra-annular nitrogen atom which is adsorbed on the silver nanoparticle and formed metal–molecule complexes by the available lone pair.     

Functional monomers and polymers. XCIV. Photochemical reactions on the synthetic polymers containing thymine bases in the presence of adenine derivatives

Photodimerization reactions of polyacrylate and polymethacrylate derivatives and the dimer model compound containing thymine bases were studied in the presence of adenine derivatives in dimethyl sulfoxide; N,N-dimethylformamide; and dimethyl sulfoxide–ethylene glycol solutions. The photodimerization of thymine bases both in the polymers and in the dimer model compound was found to be quenched by the addition of adenine derivatives. Base-base interaction in the ground state was also studied by ultraviolet (UV) spectroscopy in the three solvents. The quenching of the photodimerizationof thymine bases in the presence of adenine derivatives was discussed in terms of the specific interaction between adenine and thymine bases both in ground and excited states.     

"Turn-on" fluorescent sensor for Hg2+ via displacement approach

A new Cu2+ compound Cu- NB, (where H2 NB is bis(2-hydroxyl-naphthalene-carboxaldehyde) benzil dihydrazone) was synthesized as a highly selective fluorescence chemosensor for the detection of Hg2+ in aqueous media through a displacement "turn-on" signaling strategy. Whereas the coordination of Cu2+ resulted in a considerable quenching of the typical luminescence of the naphthol rings in Cu-NB, the addition of Hg2+ ion led to a dramatic increase in the emission intensity of Cu-NB at about 530 nm (excitation at 430 nm). The competitive fluorescent experiments showed that alkali, alkaline earth metal ions, the group 12 metals Zn2+, Cd2+, the first-row transition-metal ions such as Mn2+, Fe2+, Co2+, and Ni2+, as well as Pb2+ could not inhibit the Hg2+-binding fluorescent enhancement. It is postulated that the existence of Cu2+ in the luminescent probe Cu-NB could turn away the interferences of other metal cations from Hg2+ detection. The optical responses of the free ligand upon addition of Cu2+ ion, and of the Hg-H2NB compound upon the addition of Cu2+ were also investigated for comparisons.     

Dual-mode unsymmetrical squaraine-based sensor for selective detection of Hg2+ in aqueous media

A novel chemosensor based on unsymmetrical squaraine dye (USQ-1) for the selective detection of Hg(2+) in aqueous media is described. USQ-1 in combination with metal ions shows dual chromogenic and "turn-on" fluorogenic response selectivity toward Hg(2+) as compared to Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ba(2+), Al(3+), Cu(2+), Cd(2+), Mn(2+), Fe(3+), Ag(+), Pb(2+), Zn(2+), Ni(2+) and Co(2+) due to the Hg(2+)-induced deaggregation of the dye molecule. A recognition mechanism based on the binding mode is proposed based on the absorption and fluorescence changes, (1)H NMR titration experiments, ESI-MS study, and theoretical calculations.     

Gold nanoparticles generated through "green route" bind Hg2+ with a concomitant blue shift in plasmon absorption peak

We discuss here a quick, simple, economic and ecofriendly method through a completely green route for the selective detection of Hg(2+) in aqueous samples. Here we exploited the ability of chitosan to generate gold nanoparticles and subsequently to act as a stabilizer for the formed nanoparticles. When chitosan stabilized gold nanoparticles (CH-Au NPs) are interacted with Hg(2+) a blue shift for its localized surface plasmon resonance absorbance (LSPR) band is observed. The blue shift is reasoned to be due to the formation of a thin layer of mercury over gold. A concentration as low as 0.01 ppm to a maximum of 100 ppm Hg(2+) can be detected based on this blue shift of the CH-Au NPs. While all other reported methods demand complex reaction steps and costly chemicals, the method we reported here is a simple, rapid and selective approach for the detection of Hg(2+). Our results also show that the CH-Au NPs have excellent selectivity to Hg(2+) over common cations namely, Pb(2+), Cd(2+), Mn(2+), Fe(2+), Ag(1+), Ce(4+), Ni(2+), and Cu(2+).     

Contiguous metal-mediated base pairs comprising two Ag(I) ions

The incorporation of transition‐metal ions into nucleic acids by using metal‐mediated base pairs has proved to be a promising strategy for the site‐specific functionalization of these biomolecules. We report herein the formation of Ag⁺‐mediated Hoogsteen‐type base pairs comprising 1,3‐dideaza‐2′‐deoxyadenosine and thymidine. By defunctionalizing the Watson–Crick edge of adenine, the formation of regular base pairs is prohibited. The additional substitution of the N3 nitrogen atom of adenine by a methine moiety increases the basicity of the exocyclic amino group. Hence, 1,3‐dideazaadenine and thymine are able to incorporate two Ag⁺ ions into their Hoogsteen‐type base pair (as compared with one Ag⁺ ion in base pairs with 1‐deazaadenine and thymine). We show by using a combination of experimental techniques (UV and circular dichroism (CD) spectroscopies, dynamic light scattering, and mass spectrometry) that this type of base pair is compatible with different sequence contexts and can be used contiguously in DNA double helices. The most stable duplexes were observed when using a sequence containing alternating purine and pyrimidine nucleosides. Dispersion‐corrected density functional theory calculations have been performed to provide insight into the structure, formation and stabilization of the twofold metalated base pair. They revealed that the metal ions within a base pair are separated by an Ag???Ag distance of about 2.88 Å. The Ag–Ag interaction contributes some 16 kcal mol^?1 to the overall stability of the doubly metal‐mediated base pair, with the dominant contribution to the Ag–Ag bonding resulting from a donor–acceptor interaction between silver 4d‐type and 4s orbitals. These Hoogsteen‐type base pairs enable a higher functionalization of nucleic acids with metal ions than previously reported metal‐mediated base pairs, thereby increasing the potential of DNA‐based nanotechnology.     

Alkaline-earth metal mercury intermetallics A11-xHg54+x (A = Ca, Sr)

Re-examination of the mercury-rich regions of the Ca-Hg and Sr-Hg phase diagrams has shown that the phases previously identified as "AHg 3.6" should be reformulated as A(11-x) Hg(54+x) (A = Ca, Sr). The crystal structures for representative members of these A 11- x Hg 54+ x phases were determined from single-crystal X-ray diffraction data (Pearson symbol hP65, space group P6; a = 13.389(1) A, c = 9.615(1) A for Ca(10.92(2))Hg(54.08) (x = 0.08(2)); a = 13.602(2) A, c = 9.818(1) A for Sr(10.48(4))Hg(54.52) ( x = 0.52(4))) and confirmed by powder Rietveld refinements ( R B = 0.020 for Ca(10.7(2))Hg(54.3) and 0.014 for Sr(10.7(3))Hg(54.3)). Diverse coordination polyhedra surround the A (CN14-16, multiply capped pentagonal or hexagonal prisms as well as Friauf polyhedra) and Hg atoms (CN11-13, pentacapped trigonal prisms and icosahedra). Partial disorder of Hg into one of the A sites accounts for the nonstoichiometry in the A(11-x)Hg(54+ x) phases. If this disordered A site is completely occupied by Hg atoms, the composition is constrained to a maximum of x = 2 in A(11-x)Hg(54+ x), corresponding to a small homogeneity range of "A(0.14-0.17)Hg(0.86-0.83)"; the true homogeneity range is likely narrower. The structure can be regarded as being built up from a stacking of triangular nets with hexagonal voids that are filled with single atoms or various clusters. In particular, the presence of triangular Hg 3 clusters in ordered orientations distinguishes this structure from that of the related Gd 14Ag 51-type structure, in which triangular Ag 3 clusters are in disordered orientations. Band structure calculations reveal a small degree of electron transfer from the A to Hg atoms, supporting the presence of a partially anionic mercuride substructure.     

Novel fluorescent chemosensor for Ag^ ＋ based on coumarin fluorophore

A novel chemosensor 1 （CS1） bearing one coumarin and two carbodithioate groups was synthesized and its fluorescent sensing behavior toward metal ions was investigated. Ag^＋ addition to a CH3COCH3/H2O （3：7, v：v） solution of CS1 gave a significantly quenched fluorescence. Other ions including Pb^2＋, Zn^2＋, Cu^2＋, Ca^2＋, Cd^2＋, Co^2＋, Mg^2＋, Mn^2＋, Hg^2＋, Ag^＋, Ni^2＋ induced no or much smaller spectral changes. This constitutes an ON-OFF Ag^＋-selective fluorescent chemosensor.     

含氮杂冠醚和核酸碱基双亲聚合物的合成及性能

设计合成了含氮杂冠醚和胸腺嘧啶的双亲聚合物聚[N,N-二乙氧基-1,10-二氮杂-18冠-6-5-甲基-胸腺嘧啶-异酞酸酯](PCTSE). 用SEM观测到其在水溶液中自发聚集成直径为150~220 nm的纳米球; 用动态光散射测得PCTSE纳米球水溶液的粒径分布主要集中在130~240 nm, 用FTIR研究了PCTSE/腺嘌呤中胸腺嘧啶与底物腺嘌呤的分子识别作用, 结果表明, 聚合物中胸腺嘧啶环上C₄=O伸缩振动峰从1670 cm^-1位移至1664 cm^-1, 表明胸腺嘧啶与腺嘌呤间形成了氢键. 变温红外光谱表明, 该峰又随温度的升高逐渐向高波数位移, 最后位移到识别前的1670 cm^-1处, 表明所形成的氢键断裂.     

The synthesis of double-headed nucleosides by the CuAAC reaction and their effect in secondary nucleic acid structures

Four double-headed nucleosides were prepared by the CuAAC reaction. Hereby, a triazole-containing linker connects an additional thymine or adenine to the 2'-position of 2'-deoxyuridine, a thymine to the 5'-position of thymidine and a thymine to the 6'-position of an LNA-thymidine monomer. Whereas no conclusive recognition effects of the additional thymines were found when introduced in LNA or at the 5'-position, both thymine and adenine in the 2'-position were found to stabilise three-way junctions in both dsDNA and DNA?:?RNA contexts and to give cross-strand interactions in a DNA-duplex, when specifically introduced in a so-called (+1)-zipper motif.