Probing mixed valence in a new tppz-bridged diruthenium(III,II) complex {(mu-tppz)[Ru(bik)Cl]2}3+ (tppz=2,3,5,6-tetrakis(2-pyridyl)pyrazine, bik=2,2'-bis(1-methylimidazolyl)ketone): EPR silence, intervalence absorption, and nu(CO) line broadening

The complex dication of the diruthenium(II) compound {(mu-tppz)[Ru(bik)Cl]2}(ClO4)2 can be oxidized and reduced in two one-electron steps each. In CH3CN/0.1 M Bu4NPF6, the odd-electron intermediates{(mu-tppz)[Ru(bik)Cl]2}n+, n=1 and 3, have comproportionation constants of 7x10(8) and 1x10(5), respectively. Both exhibit near-infrared absorptions, in the case of n=3 the 1640 nm band (epsilon=1200 M-1 cm-1, Deltanu1/2=1560 cm-1) is attributed to an intervalence charge-transfer transition. While the mixed-valent intermediate (n=3) is EPR silent even at 4 K, the n=1 form shows g(parallel) 2.005 and g( perpendicular) 1.994 at that temperature, signifying a diruthenium(II) complex of the tppz*- radical anion. The variation of energy and intensity of nuCO and of the ring vibration band around 1590 cm-1 has been monitored not only for {(mu-tppz)[Ru(bik)Cl]2}n+, n=0-4, but also for the mononuclear {(tppz)Ru(bik)Cl}n+, n=0-2. In the dinuclear complex the carbonyl stretching bands of the spectator ligand bik are shifted by about 15 cm-1 on each one-electron-transfer step, increasing with the positive charge. The mixed-valent {(mu-tppz)[Ru(bik)Cl]2}3+ shows a perceptibly broader nuCO band, suggesting incomplete valence averaging (partial localization).     

Theoretical study of the structures and vibrational spectra of the hydrogen-bonded systems of 4-cyanophenol with N-bases

The structural and vibrational features of the hydrogen bonded complexes of 1,5,7-triazabicyclo [4.4.0] dec-5-ene (TBD) with one and two 4-CNPhOH molecules have been studied extensively by ab initio SCF/6-31G(d,p) and BLYP calculations with various basis sets: 6-31G(d,p), 6-31+G(d,p) and 6-31++G(d,p). Full geometry optimization was made for the complexes studied. The nature of the hydrogen bonding and the influence of the hydrogen bonding on the structural and vibrational characteristics of the monomers have been investigated. The corrected values of the dissociation energy for the hydrogen-bonded complexes have been calculated in order to estimate their stability. The calculated values of the dissociation energy per phenol molecule indicate that the complex: TBD: 4-CNPhOH (1:1) is more stable than the complex: TBD: 4-CNPhOH (1:2). The changes in the structural and vibrational characteristics upon hydrogen bonding depend on the strength of the hydrogen bonds. In agreement with the experiment, the calculations show that the complexation between TBD and 4-CNPhOH leads to considerably changes in the vibrational characteristics of the stretching O-H vibration. The vibrational frequency of the O-H stretching vibration is shifted to lower wave numbers upon hydrogen bonding. The predicted frequency shifts Deltanu(O-H) for the complexes--TBD: 4-CNPhOH (1:1) and TBD: 4-CNPhOH (1:2) are in the range from -190 cm(-1) to -586 cm(-1). In the same time the IR intensity of the O-H stretching vibration increases dramatically in the hydrogen-bonded complexes.     

Quadruplex formation by a guanine-rich PNA oligomer

A guanine-rich PNA dodecamer having the sequence H-G4T4G4-Lys-NH2 (G-PNA) hybridizes with a DNA dodecamer of homologous sequence to form a four-stranded quadruplex (Datta, B.; Schmitt, C.; Armitage, B. A. J. Am. Chem. Soc. 2003, 125, 4111-4118). This report describes quadruplex formation by the PNA alone. UV melting curves and fluorescence resonance energy transfer experiments reveal formation of a multistranded structure stabilized by guanine tetrads. The ion dependency of these structures is analogous to that reported for DNA quadruplexes. Electrospray ionization mass spectrometry indicates that both dimeric and tetrameric quadruplexes are formed by G4-PNA, with the dimeric form being preferred. These results have implications for the use of G-rich PNA for homologous hybridization to G-rich targets in chromosomal DNA and suggest additional applications in assembling quadruplex structures within lipid bilayer environments.     

Artificial G-wire switch with 2,2'-bipyridine units responsive to divalent metal ions

Development of a guanine nanowire (G-wire) that is controllable and can be switched by external signals is important for the creation of molecular electronic technologies. Here, we constructed a G-wire in which the thymines of the main chain of d(G4T4G4) were replaced with 2,2'-bipyridine units, which have two aromatic rings that rotate arbitrarily upon coordination with metal ions. Circular dichroism of the DNA oligonucleotides with or without the 2,2'-bipyridine unit showed that divalent metal ions induce the bipyridine-containing oligonucleotide to switch from an antiparallel to a parallel G-quadruplex. Native polyacrylamide gel electrophoresis showed that the parallel-stranded G-quadruplex DNA had a high-order structure. Circular dichroism and native gel electrophoresis analyses suggested that adding Na2EDTA causes a reverse structural transition from a parallel-stranded high-order structure to an antiparallel G-quadruplex. Moreover, atomic force microscopy showed a long nanowire ( approximately 200 nm) in the presence of Ni2+ but no significant image in the absence of Ni2+ or in the presence of both Ni2+ and Na2EDTA. These observations revealed that the parallel-stranded high-order structure is a G-wire containing numerous DNA oligonucleotide strands bound together via divalent metal ion-2,2'-bipyridine complexes. Finally, we found that alternating addition of Ni2+ and Na2EDTA can cycle the G-wire between the high-order and disorganized structures, with an average cycling efficiency of 0.95 (i.e., 5% loss per cycle). These results demonstrate that a DNA oligonucleotide incorporating the 2,2'-bipyridine unit acts as a G-wire switch that can be controlled by chemical input signals, namely, divalent metal ions.     

Small change in a G-rich sequence,a dramatic change in topology: new dimeric G-quadruplex folding motif with unique loop orientations

NMR study has shown that DNA oligonucleotide d(G(3)T(4)G(4)) adopts an asymmetric bimolecular G-quadruplex structure in solution. The structure of d(G(3)T(4)G(4))(2) is composed of three G-quartets, overhanging G11 residue and G3, which is part of the loop. Unique structural feature of d(G(3)T(4)G(4))(2) fold is the orientation of the two loops. Thymidine residues T4-T7 form a diagonal loop, whereas T15-T18 form an edge type loop. The G-quadruplex core of d(G(3)T(4)G(4))(2) consists of two stacked G-quartets with syn-anti-anti-anti alternation of dG residues and one G-quartet with syn-syn-anti-anti alternation. Another unusual structural feature of d(G(3)T(4)G(4))(2) is a leap between G19 and G20 over the middle G-quartet and chain reversal between G19 and G20 residues. The presence of one antiparallel and three parallel strands reveals the hitherto unknown G-quadruplex folding motif consisting of antiparallel/parallel strands and diagonal as well as edge type loops. Further examination of the influence of different monovalent cations on the folding of d(G(3)T(4)G(4)) showed that it forms a bimolecular G-quadruplex in the presence of K+, Na+, and NH4+ ions with the same general fold.     

Infrared spectra and ab initio calculations for the F- -(CH4)n (n = 1-8) anion clusters

Infrared spectra of mass-selected F- -(CH4)n (n = 1-8) clusters are recorded in the CH stretching region (2500-3100 cm-1). Spectra for the n = 1-3 clusters are interpreted with the aid of ab initio calculations at the MP2/6-311++G(2df 2p) level, which suggest that the CH4 ligands bind to F- by equivalent, linear hydrogen bonds. Anharmonic frequencies for CH4 and F--CH4 are determined using the vibrational self-consistent field method with second-order perturbation theory correction. The n = 1 complex is predicted to have a C3v structure with a single CH group hydrogen bonded to F-. Its spectrum exhibits a parallel band associated with a stretching vibration of the hydrogen-bonded CH group that is red-shifted by 380 cm-1 from the nu1 band of free CH4 and a perpendicular band associated with the asymmetric stretching motion of the nonbonded CH groups, slightly red-shifted from the nu3 band of free CH4. As n increases, additional vibrational bands appear as a result of Fermi resonances between the hydrogen-bonded CH stretching vibrational mode and the 2nu4 overtone and nu2+nu4 combination levels of the methane solvent molecules. For clusters with n < or = 8, it appears that the CH4 molecules are accommodated in the first solvation shell, each being attached to the F- anion by equivalent hydrogen bonds.     

A conformationally constrained nucleotide analogue controls the folding topology of a DNA g-quadruplex

Guanine-rich DNA and RNA sequences can fold into unique structures known as G-quadruplexes. The structures of G-quadruplexes can be divided into several classes, depending on the parallel or antiparallel nature of the strands and the number of G-rich tracts present in an oligonucleotide. Oligonucleotides with single tracts of guanines form intermolecular parallel tetrameric G-quadruplexes. Oligonucleotides with two tracts of guanosines separated by two or more bases can form both intermolecular antiparallel fold-back dimeric and parallel tetrameric G-quadruplexes, and those with four tracts of guanosines can form both intramolecular parallel and antiparallel structures. Intramolecular G-qaudruplexes can fold into several folding topologies including antiparallel crossover basket, antiparallel chair, and parallel propeller. The ability to control the folding of G-quadruplexes would allow the physical, biochemical, and biological properties of these various folding topologies to be studied. Previously, the known methods to control the folding topology of G-quadruplexes included changing the buffer by varying the mono- and divalent cations that are present, and by changing the DNA sequence. Because the glycosidic bonds in the G-quartets of G-quadruplexes with parallel strands are in the anti conformation, we reasoned that incorporation of nucleoside analogues that prefer the anti conformation of the glycosidic bond into G-rich sequences would increase the preference for parallel G-quadruplex formation. As predicted, by positioning the conformationally constrained nucleotide analogue 2'-O-4'-C-methylene-linked ribonucleotide into specific positions of a DNA G-quadruplex we were able to shift the thermodynamically favored structure of a G-quadruplex from an antiparallel to a parallel structure.     

Direct NMR detection of alkali metal ions bound to G-quadruplex DNA

We describe a general multinuclear (1H, 23Na, 87Rb) NMR approach for direct detection of alkali metal ions bound to G-quadruplex DNA. This study is motivated by our recent discovery that alkali metal ions (Na+, K+, Rb+) tightly bound to G-quadruplex DNA are actually "NMR visible" in solution (Wong, A.; Ida, R.; Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363). Here solution and solid-state NMR methods are developed for studying ion binding to the classic G-quadruplex structures formed by three DNA oligomers: d(TG4T), d(G4T3G4), and d(G4T4G4). The present study yields the following major findings. (1) Alkali metal ions tightly bound to G-quadruplex DNA can be directly observed by NMR in solution. (2) Competitive ion binding to the G-quadruplex channel site can be directly monitored by simultaneous NMR detection of the two competing ions. (3) Na+ ions are found to locate in the diagonal T4 loop region of the G-quadruplex formed by two strands of d(G4T4G4). This is the first time that direct NMR evidence has been found for alkali metal ion binding to the diagonal T4 loop in solution. We propose that the loop Na+ ion is located above the terminal G-quartet, coordinating to four guanine O6 atoms from the terminal G-quartet and one O2 atom from a loop thymine base and one water molecule. This Na+ ion coordination is supported by quantum chemical calculations on 23Na chemical shifts. Variable-temperature 23Na NMR results have revealed that the channel and loop Na+ ions in d(G4T4G4) exhibit very different ion mobilities. The loop Na+ ions have a residence lifetime of 220 micros at 15 degrees C, whereas the residence lifetime of Na+ ions residing inside the G-quadruplex channel is 2 orders of magnitude longer. (4) We have found direct 23Na NMR evidence that mixed K+ and Na+ ions occupy the d(G4T4G4) G-quadruplex channel when both Na+ and K+ ions are present in solution. (5) The high spectral resolution observed in this study is unprecedented in solution 23Na NMR studies of biological macromolecules. Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA.     

IR photodissociation spectroscopy and theory of Au+(CO)n complexes: nonclassical carbonyls in the gas phase

Au+(CO)n complexes are produced in the gas phase via pulsed laser vaporization, expanded in a supersonic jet, and detected with a reflectron time-of-flight mass spectrometer. Complexes up to n = 12 are observed, with mass channels corresponding to the n = 2 and n = 4 showing enhanced intensity. To investigate coordination and structure, individual complexes are mass-selected and probed with infrared photodissociation spectroscopy. Spectra in the carbonyl stretching region are measured for the n = 3-7 species, but no photodissociation is observed for n = 1, 2 due to the strong metal cation-ligand binding. The carbonyl stretch in these systems is blue-shifted 50-100 cm-1 with respect to the free CO vibration (2143 cm-1), providing evidence that these species are so-called "nonclassical" metal carbonyls. Theory at the MP2 and CCSD(T) levels provides structures for these complexes and predicted spectra to compare to the experiment. Excellent agreement is obtained between experiment and theory, establishing that the n = 3 complex is trigonal planar and the n = 4 complex is tetrahedral.     

氨基聚酯树脂固化过程的FTIR跟踪

用FTIR内标法跟踪氨基聚酯树脂的固化过程,选取815cm~(-1)的三嗪环面外振动峰作内标峰,913cm~(-1)处的甲氧基变形振动峰和3500cm~(-1)左右的羟基伸缩振动峰为特征吸收峰。结果表明,随着固化的进行,涂膜的羟基、甲氧基和羧基递减,醚键和羰基递增,说明固化过程是以交联反应为主,伴有自缩合反应和酯化反应的复杂过程。     

Formation of an interlocked quadruplex dimer by d(GGGT)

A tetranucleotide sequence d(GGGT) has been shown to self-assemble into an interlocking quadruplex dimer. UV-melting studies indicated the existence of two species that each showed distinct quadruplex melting transitions, a low-T(m) species, Q(l), and a high-T(m) species, Q(h). Conditions were controlled to favor the formation of either Q(l) or Q(h). Q(l) and Q(h) each showed circular dichroism spectra characteristic of parallel quadruplexes. Negative ion nano-electrospray ionization mass spectrometry confirmed that Q(l) was a tetrameric complex, d(GGGT)(4), and Q(h) was an octameric complex, d(GGGT)(8). High-resolution (1)H NMR spectroscopy evidenced that d(GGGT)(4) was a C(4)-symmetric parallel tetramolecular quadruplex. The (1)H NMR spectrum of d(GGGT)(8) was consistent with a structure formed by the dimerization of a parallel, "slipped" tetramolecular quadruplex that has its diagonal strands staggered by one base. This "slippage" results in two guanine bases at the 5' end of the quadruplex being presented diagonally that are not involved in tetrads. Two such "slipped" quadruplexes dimerize via these free G-bases at the 5' ends by forming an extra G-tetrad. Each "slipped" quadruplex contributes two guanine bases to this extra G-tetrad. The formation of a novel GTGT tetrad is also observed at both the 3' ends of the interlocked quadruplex dimer.     

H2SiCl2分子Si-H振动"基座"SiCl2的有效质量

用傅立叶变换光谱仪和激光腔内吸收光谱仪记录了H2SiCl2分子2000～9000和12000～12900 cm-1的红外吸收光谱.依据局域模理论的非谐性耦合非谐振子(ACAO)模型,分析并拟合了Si-H的对称伸缩振动和反对称伸缩振动,得到描述Si-H伸缩振动的Morse离解能De 、 Morse振子参数α和键振子势能耦合系数frr′.分析中忽略了SiCl2"基座"对Si-H伸缩振动的影响,拟合结果与实验值符合的很好,拟合方差小于 1 cm-1,表明这一近似是可取的.分析拟合结果表明, Si-H振动时"基座"SiCl2的有效质量为75.     

四-(对-十二酰氧基)苯基卟啉过渡金属配合物的合成及其液晶行为研究

合成了5,10,15,20-四-(对-十二酰氧基)苯基卟啉(简称TLPPH₂)及其Mn(Ⅲ),Fe(Ⅲ),Co(Ⅱ),Ni(Ⅱ),Cu(Ⅱ)和Zn(Ⅱ)配合物,通过元素分析、紫外可见光谱、红外光声光谱、核磁共振氢谱和摩尔电导等分析方法表征了它们的组成和结构.用DSC和偏光显微镜研究了配体及其锌配合物的液晶行为.结果表明,锌配合物的液晶相变温度始于-50.67℃,相区宽度达143℃.     

Conformational conversion of DNA G-quadruplex induced by a cationic porphyrin

The interactions between cationic meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) and the G-quadruplex (G4) of human telomeric single-strand oligonucleotide d(TTAGGG)₂ (S12) have been investigated by means of circular dichroism (CD), UV–visible absorption and fluorescence spectroscopies. It is found that TMPyP4 can preferentially induce the conformational conversion of the G4 structure from the parallel type to the parallel/antiparallel mixture in the presence of K⁺, and that it can directly induce the formation of antiparallel G4 structure from the single-strand oligonucleotide S12 in the absence of K⁺. Furthermore, the comparable experiments of TMPyP4 with two single-strand oligonucleotides S6 d(TTAGGG) and S24 d(TAGGG(TTAGGG)₃T) in the absence of K⁺ show that TMPyP4 can also induce the formation of antiparallel G4 from S24 but not from S6, indicating that the end-loops of the G4 structure are the key factors for the formation of G4 induced by TMPyP4.     

Comparative study of the hydrogen-bonded complexes of phenol and o-cyanophenol with CO Ab initio and DFT approachs

The structures, stability and vibrational spectra of the hydrogen-bonded complexes of carbon monoxide (CO) with phenol and o-cyanophenol (syn and anti) have been studied using ab initio and DFT calculations. Full geometry optimization has been performed for the studied complexes by DFT (BLYP/6-311++G(d,p)) calculations. The calculations show that the hydrogen-bond formation of carbon monoxide (CO) with phenol and o-cyanophenol (syn and anti) leads to the following stable structures: C6H5OH...CO (1A); C6H5OH...OC (1B); (syn) o-CNC6H4OH...CO (2A-syn); (syn) o-CNC6H4OH...OC (2B-syn); (anti) o-CNC6H4 OH...CO (2A-anti) and (anti) o-CNC6H4OH...OC (2B-anti). Having in mind the corrected values of the dissociation energy, the studied hydrogen-bonded complexes can be ordered according their stability as follows: 2A-anti>2A-syn>1A>2B-anti>1B>2B-syn. The predicted red-shifts for the nuOH vibration with the B3LYP/6-311++G(d,p) calculations for the structures 1A (-46 cm-1), 2A-syn (-60 cm-1) and 2A-anti (-73 cm-1) are in very good agreement with the experimentally observed. The magnitudes of the wavenumber shifts are indicative of relatively weak OH...C hydrogen-bonded interactions. The calculations predict an increase of the IR intensity of the nuOH vibration in the complexes 1A, 2A-anti and 2A-syn up to five times.     

Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads

Nucleic acid tetraplexes and lipophilic self-assembling G-quadruplexes contain stacked base tetrads with intercalated metal ions as basic building blocks. Thus far, quantum-chemical studies have been used to explore the geometric and energetic properties of base tetrads with and without metal ions. Recently, for the first time, work on a sandwiched G-tetrad complex has been studied. We report here results of a systematic B3LYP density functional study on sandwiched G-, C-, U-, and T-tetrads with Na+ and K+ at different symmetries that substantially extend the recent work. The results include detailed information on total energies as well as on metal ion tetrad and base-base interaction energies. The geometrical parameters of the sandwiched metal ion complexes are compared to both experimental structures and to calculated geometries of complexes of single tetrads with metal ions. A microsolvation model explains the ion selectivity preference of K+ over Na+ in a qualitative sense.     

含氮杂冠醚双亲聚合物纳米球的制备及性能

设计、合成了含氮杂冠醚和腺嘌呤的双亲聚合物,聚[N,N-二乙氧基-1,10-二氮杂-18冠-6-5-甲基-腺嘌呤-异酞酸酯](PCASE).SEM观测到在水溶液中该聚合物与5-氟尿嘧啶(5-flu)小分子识别后自发聚集成直径约140～210nm的纳米球,用动态光散射测得水溶液中PCASE/5-flu纳米球的粒径主要集中在120～230nm范围内,FTIR研究了PCASE/5-flu纳米球内聚合物PCASE中腺嘌呤与底物5-氟尿嘧啶的分子识别,结果表明,识别后5-氟尿嘧啶环上C(2)=O伸缩振动峰从1724cm-1位移至1718cm-1,且聚合物中腺嘌呤NH2峰3324cm-1消失,出现了一个新的NH2峰3432cm-1,说明5-氟尿嘧啶环上C(2)=O与聚合物PCASE中腺嘌呤上NH2间形成了氢键.变温红外谱显示,识别后的羰基峰1718cm-1随温度的升高逐渐向高波数回移,并最终稳定在5-氟尿嘧啶环上C(2)=O识别前的1724cm-1处,且识别后产生的新NH2峰3432cm-1随温度的升高逐渐减弱至消失,表明所形成的氢键断裂.     

不同电解质体系水的拉曼谱的研究

通过一系列电解质体系水的拉曼光谱测量，得到了阴、阳离子种类和浓度引起的水伸缩振动和弯曲振动谱带丰富的变化信息，ＣｌＯ４＾－能有效地破坏水分子间的氢键，随着ＣｌＯ４浓度的增加，水分子间的氢键并非逐步被打断，而是氢键被破坏的水分子越来越多，从而使水分子有序度增大，这种氢键破坏方式符合水的混合模型（ＭｉｘｔｕｒｅＭｏｄｅｌ）ＳＯ＾２－４浓度的增对水的Ｒａｍａｎ光谱影响较小，是由于ＳＯ＾２－４与水分了间的     

Direct measurement of excited-state intervalence transfer in [(tpy)Ru(III)(tppz(*-))Ru(II)(tpy)](4+) by time-resolved near-infrared spectroscopy

Extension of time-resolved infrared (TRIR) measurements into the near-infrared region has allowed the first direct measurement of a mixed-valence band in the metal-to-ligand charge transfer (MLCT) excited state of a symmetrical ligand-bridged complex. Visible laser flash excitation of [(tpy)Ru(tppz)Ru(tpy)]4+ (tppz is 2,3,5,6-tetrakis(2-pyridyl)pyrazine; tpy is 2,2':6',6' '-terpyridine) produces the mixed-valence, MLCT excited state [(tpy)RuIII(tppz*-)RuII(tpy)]4+* with the excited electron localized on the bridging tppz ligand. A mixed-valence band appears at numax = 6300 cm-1 with a bandwidth-at-half- maximum, Deltanu1/2 = 1070 cm-1. In the analogous ground-state complex, [(tpy)Ru(tppz)Ru(tpy)]5+, a mixed-valence band appears at numax = 6550 cm-1 with Deltanu1/2 = 970 cm-1 which allows a comparison to be made of electronic coupling across tppz0 and tppz*- as bridging ligands.     

Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

Four individual quadruplexes, which are self-assembled in ammonium acetate solution from telomeric sequences of closely related DNA strands--d(G(4)T(4)G(4)), d(G(3)T(4)G(4)), d(G(3)T(4)G(3)), and d(G(4)T(4)G(3))--have been detected in the gas phase using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The bimolecular quadruplexes associate with the same number of NH(4)(+) in the gas phase as NMR shows that they do in solution. The quadruplex structures formed in solution are maintained in the gas phase. Furthermore, the mass spectra show that the bimolecular quadruplexes generated by the strands d(G(3)T(4)G(3)) and d(G(4)T(4)G(3)) are unstable, being converted into trimolecular and tetramolecular structures with increasing concentrations of NH(4)(+) in the solution. Circular dichroism (CD) spectra reveal structural changes during the process of strand stoichiometric transitions, in which the relative orientation of strands in the quadruplexes changes from an antiparallel to a parallel arrangement. Such changes were observed for the strand d(G(4)T(4)G(3)), but not for the strand d(G(3)T(4)G(3)). The present work provides a significant insight into the formation of various DNA quadruplexes, especially the higher-order species.