Face-to-face and edge-to-face pi-pi interactions in a synthetic DNA hairpin with a stilbenediether linker

Synthetic conjugates possessing bis(2-hydroxyethyl)stilbene-4,4'-diether linkers (Sd2) form the most stable DNA hairpins reported to date. Factors that affect stability are length and flexibility of the linkers and pi-stacking of the stilbene moiety on the adjacent base pair. The crystal structure of the hairpin d(GT(4)G)-Sd2-d(CA(4)C) was determined at 1.5 A resolution. The conformations of the two molecules in the asymmetric unit differ both in the linker and the stem portions. One of them shows a planar stilbene that is stacked on the adjacent G:C base pair. The other displays considerable rotation between the phenyl rings and an unprecedented edge-to-face orientation of stilbene and base pair. The observation of considerable variations in the conformation of the Sd moiety in the crystal structure allows us to exclude restriction of motion as the reason for the absence of Sd photoisomerization in the hairpins. Conformational differences in the stem portion of the two hairpin molecules go along with different Mg(2+) binding modes. Most remarkable among them is the sequence-specific coordination of a metal ion in the narrow A-tract minor groove. The crystal structure provides unequivocal evidence that a fully hydrated Mg(2+) ion can penetrate the narrow A-tract minor groove, causing the groove to further contract. Overall, the structural data provide a better understanding of the origins of hairpin stability and their photochemical behavior in solution.     

Intramolecular hydrogen bonding of novel o-hydroxythioacetophenones and related compounds evaluated by deuterium isotope effects on 13C chemical shifts

A new class of compounds, the 2-hydroxythioacetophenones, and related compounds have recently been synthesized. The hydrogen-bond system has been characterized by NMR chemical shifts and deuterium isotope effects on these as well as by DFT calculations. Use of solid-state (13)C NMR has enabled measurements of the intrinsic deuterium isotope effects of the most abundant tautomer of beta-thioxoketones. The compounds show very interesting long-range deuterium isotope effects on the thiocarbonyl carbon. The intramolecular hydrogen bonds of o-hydroxythioacetophenones are found to be slightly stronger than those of the corresponding acetophenones. The reactivity and stability of the compounds can be related to hydrogen bonding and to the presence of electron donating substituents.     

Hydrogen-bonding interactions in acetic acid monohydrates and dihydrates by density-functional theory calculations

Equilibrium structures and the respective binding energies of acetic acid monohydrates and dihydrates have been determined by density-functional theory calculations with different basis sets, including 6-31+G(3d,p), 6-311++G(d,p), and 6-311++G(3df,3pd). Given that the C=O and OH groups in acetic acid provide the predominant hydrogen-bonding interactions with water, six stable conformer structures have been found each for the monohydrate and syn-dihydrate. Of the three syn- and three anti-conformers of acetic acid with water, the most stable monohydrate structure is found to be that of the syn-conformer bonding with water in a cyclic double H-bonded geometry. Similarly, the syn-conformer bonding with two water molecules in a cyclic double H-bonded geometry has also been determined to be the most stable among the six plausible structures for the syn-dihydrate. Frequency analysis of the stable conformers has been performed and the vibrational spectra of the most stable monohydrate and dihydrate structures are compared with the experimental gas-phase and matrix data. Furthermore, the calculated binding energies between an acetic acid and a water molecule for both monohydrate and dihydrate are larger than that between two water molecules, which supports our recent experimental observation of coevaporation of acetic acid with water upon annealing acetic acid on ice.     

Carbon-13 NMR spectra of all the isomeric methyl hydroxy- and acetoxyoctadecanoates. Determination of chemical shifts by deuterium isotope effects

Carbon-13 NMR spectra of the 17 isomeric methyl hydroxyoctadecanoates and the corresponding acetate derivatives have been measured and chemical shifts assigned to most carbons. Sixteen specifically deuterated hydroxy esters, and their acetates, were employed to make unambiguous assignments from the deuterium isotope effects on the spectra. When substituents are separated from the ends of the chain by 2–3 methylene groups their effects are largely additive. Long range effects of the hydroxyl group were γ, +0.01; δ, ?0.09; ε, ?0.11; ζ, ?0.06; η, ?0.05; and θ, ?0.04 ppm, and of the acetate group were γ, ?0.20; δ, ?0.20; ε, ?0.16; ζ, ?0.11; η, ?0.08 and θ, ?0.07 ppm, showing that they extend across seven methylene groups.     

Benzene dilution shifts and steric interactions in N,N-dialkylamides

The NMR spectra of ten disubstituted amides have been recorded at 0°C in carbon tetrachloride and in benzene solutions. The benzene dilution shifts (ASIS) and proton spin decoupling were used to make the chemical shift assignments. A time-averaged solvent cluster model for the association between the amide and benzene is consistent with the observed ASIS values. The assignments for the N-methine and N-methyl resonance peaks in RCON[CH(CH₃)₂]₂, where R is methyl, ethyl or propyl are inverted from the assignments for N,N-diisopropylformamide (R ? H).     

Determination of the configuration in six-membered saturated heterocycles (N,P, S,Se) and their oxidation products using experimental and calculated NMR chemical shifts

The six-membered saturated heterocycles—4-tert-butyl-1-methylpiperidine, 4-tert-butyl-1-methylphosphine, 4-tert-butyl-tetrahydro-2H-thiopyran, and 4-tert-butyl-tetrahydro-2H-selenopyran—were prepared as suitable model compounds with well-defined geometry for an NMR study of their oxidation products. The corresponding epimeric N-oxides, phosphinoxides, sulfoxides, and selenoxides were obtained by standard chemical preparation and also by in situ oxidation with meta-chloroperbenzoic acid directly in the NMR tube. The experimental ¹H and ¹³C chemical shifts were compared with corresponding calculated data obtained by GIAO approach with DFT, MP2, and HF methods and various basis sets. The correlation of experimental versus calculated data showed the possibility to determine the stereochemistry of the epimeric oxidation products using fast DFT B3LYP/6-31G* method for both geometry optimization and NMR chemical shifts calculation.     

Hydride reduction of NAD+ analogues by isopropyl alcohol: kinetics, deuterium isotope effects and mechanism

Observed pseudo-first-order rate constants (k(obs)) of the hydride-transfer reactions from isopropyl alcohol (i-PrOH) to two NAD(+) analogues, 9-phenylxanthylium ion (PhXn(+)) and 10-methylacridinium ion (MA(+)), were determined at temperatures ranging from 49 to 82 degrees C in i-PrOH containing various amounts of AN or water. Formations of the alcohol-cation ether adducts (ROPr-i) were observed as side equilibria. The equilibrium constants for the conversion of PhXn(+) to PhXnOPr-i in i-PrOH/AN (v/v = 1) were determined, and the equilibrium isotope effect (EIE = K(i-PrOH)/K(i-PrOD)) at 62 degrees C was calculated to be 2.67. The k(H) of the hydride-transfer step for both reactions were calculated on the basis of the k(obs) and K. The corresponding deuterium kinetic isotope effects (e.g., KIE(OD)(H) = k(H)(i-PrOH)/k(H)(i-PrOD) and KIE(beta-D6)(H) = k(obs)(i-PrOH)/k(obs)((CD3)2CHOH)), as well as the activation parameters, were derived. For the reaction of PhXn(+) (62 degrees C) and MA(+) (67 degrees C), primary KIE(alpha-D)(H) (4.4 and 2.1, respectively) as well as secondary KIE(OD)(H) (1.07 and 1.18) and KIE(beta-D6)(H) (1.1 and 1.5) were observed. The observed EIE and KIE(OD)(H) were explained in terms of the fractionation factors for deuterium between OH and OH(+)(OH(delta+)) sites. The observed inverse kinetic solvent isotope effect for the reaction of PhXn(+) (k(obs)(i-PrOH)/k(obs)(i-PrOD) = 0.39) is consistent with the intermolecular hydride-transfer mechanism. The dramatic reduction of the reaction rate for MA(+), when the water or i-PrOH cosolvent was replaced by AN, suggests that the hydride-transfer T.S. is stabilized by H-bonding between O of the solvent OH and the substrate alcohol OH(delta+). This result suggests an H-bonding stabilization effect on the T.S. of the alcohol dehydrogenase reactions.     

Hydrogen-bonding interactions in crown-(thio)urea complexes with anions,chemical warfare agents and simulants

ABSTRACT

Benzocrown ethers incorporating phenyl and nitrophenyl urea and thiourea moieties were synthesised. Both the nitrophenyl urea and thiourea derivative gave a fluoride-specific colorimetric response but only the urea derivative bound the organophosphonate nerve agent simulants dimethyl methylphosphonate (DMMP) and diisopropyl methylphosphonate (DIMP). This suggested an application as sensors for the nerve agents sarin, soman and cyclosarin which release fluoride upon hydrolysis. Although no fluoride-induced response was observed in the UV-visible spectrum, binding to soman was determined by ¹H NMR. DFT computational simulations suggested that the two crowns adopt different conformations in which both can bind fluoride but only the urea derivative can bind DMMP, DIMP and soman. The results show that, for this system, simulant- and soman-binding behaviours are in good agreement.     

Simultaneous quantification of methylated purines in DNA by isotope dilution LC-MS/MS coupled with automated solid-phase extraction

Since methylation at the N-7 and O⁶ positions of guanine and the N-3 position of adenine in DNA are the predominant reaction sites, N ⁷-methylguanine (N ⁷-MeG), O ⁶-methylguanine (O ⁶-MeG), and N ³-methyladenine (N ³-MeA) have been suggested as good biomarkers for assessing exposure to methylating agents. Here, we report the development of a sensitive and selective assay based on liquid chromatography–tandem mass spectrometry (LC-MS/MS) to simultaneously measure N ⁷-MeG, O ⁶-MeG, and N ³-MeA in DNA hydrolysates. With the use of isotope internal standards (¹⁵N₅-N ⁷-MeG, d ₃-O ⁶-MeG, and d ₃-N ³-MeA) and online solid-phase extraction, DNA hydrolysates can be directly analyzed within 12 min without prior sample purification. The limits of detection were 0.02, 0.002, and 0.01 ng/mL on-column (6.1, 0.6, and 3.4 fmol) for N ⁷-MeG, O ⁶-MeG, and N ³-MeA, respectively. Inter- and intraday imprecision (CV) were 3.6–9.6% and 2.7–13.6%, respectively. Mean recoveries were 96–109%. This method was then applied to quantitate the amounts of methylated purines in calf thymus DNA treated with methyl methanesulfonate (MMS). The levels of N ⁷-MeG, O ⁶-MeG, and N ³-MeA in calf thymus DNA increase with MMS concentration and incubation time. The ratio of relative yields of N ⁷-MeG, O ⁶-MeG, and N ³-MeA in MMS-treated DNA was found to be 1.00:0.0032:0.119, respectively. This LC-MS/MS assay provides the sensitivity and high throughput required to evaluate the extent of methylated lesions in DNA induced by methylating agents.     

Determination of carbon isotope ratios in amino acids,proteins, and oligosaccharides by inductively coupled plasma-mass spectrometry

Carbon isotope ratios ((12)C/(13)C) are measured for aqueous solutions of tryptophan, myoglobin, and beta-cyclodextrin using C(+) ions from an inductively coupled plasma (ICP) and a prototype twin quadrupole mass spectrometer (MS). (13)C/(12)C ratios can be determined with a relative standard deviation (RSD) of approximately 1%. This precision is close to the limiting value predicted by counting statistics (1.16%). Spectral interference on (13)C(+), presumably from (12)C(1)H(+), comes from the incomplete dissociation of myoglobin and/or beta-cyclodextrin, but not tryptophan. Decreasing the aerosol gas flow rate slightly from that which yields maximum signal eliminates this (12)C(1)H(+) interference. The count rate of the minor isotope ((13)C(+)) can be artificially enhanced by increasing the voltage of the (13)C(+) detector, and/or by shifting the ion beam splitter offset from the central axis. Instrumental modifications to the MS that improve the sensitivity are also described.     

Long-range deuterium isotope effects on fluorine-19 chemical shifts of 4-substituted bicyclo[2.2.2]octyl- and bicyclo[2.2.1]heptyl-1-fluorides : Deuterium as a substituent

²H/¹H isotope effects on the ¹⁹F chemical shifts of 4-substituted bicyclo[2.2.2]oct-1-yl and bicyclo[2.2.1]hept-1-yl fluoride are significantly shielding and deshielding, respectively. This result is consistent with deuterium being viewed as an $\text{electronegative}$ substituent relative to hydrogen when attached to an sp³ hybridised carbon.     

Structural analysis of aristolochic acids and aristolactams by correlations between calculated and experimental <Superscript>13</Superscript>C NMR chemical shifts

Aristolactam AII (1) and aristolochic acid I (2) were employed as examples in choosing the most suitable theoretical methodology for computing carbon chemical shifts (^Calc δ _C) and for the structural elucidations of aristolactams and aristolochic acids. Geometries of 1 and 2 optimized using HF, BLYP, B3LYP, and PBE methods and 6-311++G** basis set were subjected to δ_C calculations and the calculated chemical shifts obtained were correlated with their ¹³C NMR data. Different possibilities were considered (in the gaseous phase, model PCM (DMSO), and for dimeric systems 1-1 and 2-2), and an explicit solvent (DMSO) model employing BLYP/6-31G* calculations was determined to be the most efficient (R ² = 0.99631 and 0.97713, for 1 and 2, respectively).     

Density functional calculation of the 2D potential surface and deuterium isotope effect on 13C chemical shifts in picolinic acid N-oxide. Comparison with experiment

2D free energy surfaces V = V(rOH, rO...O) for the intramolecular H-bond in the title compound were calculated by the DFT method and used in the calculation of primary and secondary chemical shifts of the compound dissolved in chloroform and acetonitrile. Solvent effects were accounted for by the SCRF/PCM method. The corresponding two-dimensional chemical shift surfaces with included solvent reaction field were obtained using the Continuous Set of Gauge Transformations approach at the B3LYP/6-311+G(2d,2p) level of theory. The chemical shifts were estimated as quantum averages along the two internal coordinates in the hydrogen bond and along several vibrational levels according to the Boltzmann distribution at room temperature. Fairly good agreement between the experimental and calculated isotope effects was obtained. 1D and 2D NMR spectra of solutions of picolinic acid N-oxide and its deuterated analogue were recorded and assigned.     

茶叶和蔬菜中铅的同位素稀释电感耦合等离子体质谱的测定

采用同位素稀释电感耦合等离子体质谱(ID-ICP-MS)法测定了铅的含量,通过对茶叶标准物质(GBW-07605)中铅的测定,考察了方法的准确度和精密度,比较了同位素稀释法与普通外标定量法的测定结果。在5mLHNO3～0.5mLHF～1mLH2O2的消解体系中,ID-ICP-MS法测量茶叶中铅的回收率可达97.7%,相对标准偏差(RSD)小于1.2%。实验对市售的12种茶叶和10种蔬菜中Pb进行测定,铅含量符合相应国家标准的样品分别占总样品数的83%和90%。该法适合于植物样品中微量铅的测定。     

Deuterated ammonium formate as deuterium source in a mild catalytic deuterium transfer reaction of pyridines, pyrazines and isoquinolines

The application of deuterated ammonium formate as deuterium source in transfer deuteration reactions of aromatic heterocycles (4-6) for the synthesis of highly deuterated, substituted piperidines (1), piperazines (2) and tetrahydroisoquinolines (3) has been developed.     

Direct measurements of the interaction between pyrene and graphite in aqueous media by single molecule force spectroscopy: understanding the pi-pi interactions

Pyrene derivatives can absorb onto the surface of carbon nanotubes and graphite particles through pi-pi interactions to functionalize these inorganic building blocks with organic surface moieties. Using single molecule force spectroscopy, we have demonstrated the first direct measurement of the interaction between pyrene and a graphite surface. In particular, we have connected a pyrene molecule onto an AFM tip via a flexible poly(ethylene glycol) (PEG) chain to ensure the formation of a molecular bridge. The pi-pi interaction between pyrene and graphite is thus indicated to be approximately 55 pN with no hysteresis between the desorption and adhesion forces.     

Precise isotope ratio measurements for uranium, thorium and plutonium by quadrupole-based inductively coupled plasma mass spectrometry

Precise long-term measurements of uranium and thorium isotope ratios was carried out in 1 μg/L solutions using a quadrupole inductively coupled plasma mass spectrometer (ICP-QMS). The isotopic ratios of uranium (²³⁵U/ ²³⁸U = 1, 0.02 and 0.00725) were determined using a cross-flow nebulizer (CFN, at solution uptake rate of 1 mL/min) and a low-flow microconcentric nebulizer (MCN, at solution uptake rate of 0.2 mL/min) over 20 h. For 1 μg/L uranium solution (²³⁵U/²³⁸U = 1) relative external standard deviations (RESDs) of 0.05% and 0.044% using CFN and MCN, respectively, can be achieved. Additional short term isotope ratio measurements using a direct injection high-efficiency nebulizer (DIHEN) of 1 μg/L uranium solution (²³⁵U/²³⁸U = 1) at a solution uptake rate of 0.1 mL/min yielded an RSD of 0.06–0.08%. The sensitivity of solution introduction by DIHEN for uranium, thorium and plutonium (145 MHz/ppm, 150 MHz/ppm and 177 MHz/ppm, respectively) increased significantly compared to CFN and MCN and the solution uptake rate can be reduced to 1 μL/ min in DIHEN-ICP-MS. Isotope ratio measurements at an ultralow concentration level (e.g. determination of ²⁴⁰Pu/ ²³⁹Pu isotope ratio in a 10 ng/L Pu waste solution) were carried out for the characterization of radioactive waste and environmental samples.     

Precise isotope ratio measurements for uranium, thorium and plutonium by quadrupole-based inductively coupled plasma mass spectrometry

Precise long-term measurements of uranium and thorium isotope ratios was carried out in 1 μg/L solutions using a quadrupole inductively coupled plasma mass spectrometer (ICP-QMS). The isotopic ratios of uranium (²³⁵U/ ²³⁸U = 1, 0.02 and 0.00725) were determined using a cross-flow nebulizer (CFN, at solution uptake rate of 1 mL/min) and a low-flow microconcentric nebulizer (MCN, at solution uptake rate of 0.2 mL/min) over 20 h. For 1 μg/L uranium solution (²³⁵U/²³⁸U = 1) relative external standard deviations (RESDs) of 0.05% and 0.044% using CFN and MCN, respectively, can be achieved. Additional short term isotope ratio measurements using a direct injection high-efficiency nebulizer (DIHEN) of 1 μg/L uranium solution (²³⁵U/²³⁸U = 1) at a solution uptake rate of 0.1 mL/min yielded an RSD of 0.06–0.08%. The sensitivity of solution introduction by DIHEN for uranium, thorium and plutonium (145 MHz/ppm, 150 MHz/ppm and 177 MHz/ppm, respectively) increased significantly compared to CFN and MCN and the solution uptake rate can be reduced to 1 μL/ min in DIHEN-ICP-MS. Isotope ratio measurements at an ultralow concentration level (e.g. determination of ²⁴⁰Pu/ ²³⁹Pu isotope ratio in a 10 ng/L Pu waste solution) were carried out for the characterization of radioactive waste and environmental samples. Received: 1 December 1998 / Revised: 25 January 1999 / Accepted: 31 January 1999