Hydrogen bonds of RNA are stronger than those of DNA, but NMR monitors only presence of methyl substituent in uracil/thymine

Recently, Vakonakis and LiWang (J. Am. Chem. Soc. 2004, 126, 5688) reported experimental evidence for stronger hydrogen bonds in RNA A:U than in DNA A:T base pairs, which was based on differences in NMR shielding for adenine C2. We have analyzed the proposed correlation between NMR shielding and hydrogen-bond strength using density functional theory. Although we agree with the conclusion that A:U is more strongly bound, we find no correlation between the hydrogen-bond strength and the NMR shielding of C2. Our study shows that NMR merely probes the presence/absence of the methyl group in thymine/uracil, without any relation to the strength of the hydrogen bonds involved. In other words, one cannot infer the Watson-Crick hydrogen-bond strength from the NMR shielding constant of adenine C2.     

An expeditious,solvent-free synthesis of some 5-aryl-2-(2-hydroxyphenyl)-1,3,4-oxadiazoles

An efficient, rapid, microwave-accelerated one-step synthesis of some 5-aryl-2-(2-hydroxy-phenyl)-1,3,4-oxadiazoles by reaction of salicylic hydrazide with carboxylic acids in the presence of thionyl chloride under neat conditions is described. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1264–1267, August, 2007.     

Relativistic calculations on the ground and excited states of AgH and AuH in cylindrical harmonic confinement

The relativistic ground and low-lying excited state potential energy curves of AgH and AuH in the presence of a cylindrical harmonic confining potential were calculated using the multi-state multi-reference perturbation theory with the spin-free no-pair Hamiltonian obtained via the third-order Douglas–Kroll transformation, incorporated with the full two-electron Breit–Pauli spin–orbit operator. The spectroscopic parameters were obtained for both the scalar- and quasi-relativistic potentials. The spin–orbit coupling constants were calculated for several strengths of the confining potential, and the effects of the applied potential on the coupling constants were analyzed using configuration interaction. This paper is dedicated to Serafín Fraga—colleague, mentor, and friend.     

Drag on two nonuniformly structured flocs moving along the axis of a cylindrical tube

The boundary effect on the drag on two identical, nonuniformly structured flocs moving along the axis of a cylindrical tube filled with a Newtonian fluid is investigated at a small to medium larger Reynolds number. A two-layer model is adopted to simulate various possible structures of a floc, and the flow field inside is described by Darcy–Brinkman model. The results of numerical simulation reveal that a convective flow is present in the rear region of a floc when Reynolds number is on the order of 40. The presence of the tube wall and/or the porous structure of a floc has the effect of reducing that convective flow. For a fixed level of the volume-average permeability of a floc, the influence of the tube wall on the drag depends upon floc structure; the influence on a nonuniformly structured floc is more significant than that on a uniformly structured floc. The more nonuniform the floc structure, the more appreciable the deviation of the drag coefficient–Reynolds number curve from a Stokes’-law-like relation becomes. The smaller the volume-average permeability of a floc and/or the smaller the separation distance between the two flocs, the greater is the deviation, but the presence of the tube wall has the effect of reducing that deviation.     

Electrochemical monitoring of indigo preparation using Maya’s ancient procedures

The preparation of indigo from Indigofera suffruticosa following the procedures attributed to ancient Mayas was electrochemically monitored using the voltammetry-of-microparticles approach. The mechanism formation of indigotin and indirubin from its precursors, indican and isatan, is discussed. Comparison of voltammetric profiles for differently prepared and commercial indigos and genuine Maya Blue samples suggests that the preparation procedure of indigo changed during the Late Classical Maya period. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Elemental analysis of Korean women’s blood serums using instrumental neutron activation analysis

Instrumental neutron activation analysis was used to assess the concentration of the inorganic trace elements in Korean women’s blood serums. It was found that a high concentration of Na and Cl incurs an analytical interference, but the 12 elements such as Br, Ca, Cl, Co, Cr, Cs, Fe, K, Na, Rb, Se and Zn could be determined under the condition of an interference minimization. Serum samples collected from 63 women were analyzed and the concentration level and range of the elements were evaluated. NIST SRMs were analyzed simultaneously for quality control. The average values of the Na and Cl determined in the serum samples were 3,365 and 3,533 mg/l, Ca was 96.4 mg/l and K was 191 mg/l. Besides, Br, Se and Zn have a concentration level of 6.46, 0.13 and 0.98 mg/l, respectively. It was found that there is no significant difference between the present values and the reported values.     

Characterisation of poly(neutral red) modified carbon film electrodes; application as a redox mediator for biosensors

The polymer redox mediator, poly(neutral red) (PNR), has been synthesised and characterised electrochemically to investigate the best electropolymerisation and mediation conditions for application in enzyme biosensors and to clarify the mechanism of action. Neutral red was electropolymerised by potential cycling on carbon film electrode substrates by allowing the monomer to be oxidised during the full 20 cycles of polymerisation or reducing the positive limit of the potential window after the first 2 cycles to impede monomer oxidation with a view to obtaining longer polymer chains and a lesser degree of branching. Comparison was made with glassy carbon substrates. The PNR films on carbon film electrodes were characterised using cyclic voltammetry and electrochemical impedance spectroscopy, as well as in glucose biosensors prepared with PNR. Glucose oxidase enzyme was immobilised by encapsulation in silica sol-gel and compared with that obtained by cross-linking with glutaraldehyde. The biosensors were evaluated by chronoamperometry in 0.1 M phosphate buffer saline solution, pH 7.0, and showed evidence of electron transfer between the enzyme cofactor flavin adenine dinucleotide and PNR dissolved in the enzyme layer competing with PNR-mediated electrochemical degradation of H₂O₂ formed during the enzymatic process. This paper is dedicated to Professor Dr. Algirdas Vaskelis on the occasion of his 70th birthday.     

Reaktionen von 2- und 3-phenylsubstituierten Alkylakyliden-iminium-Ionen in der Gasphase. 5. Mitteilung über stossinduzierte Fragmentierungen von felddesorbierten Kationen

Reactions of 2- and 3-Phenyl Substituted Alkylalkylidene Iminium Ions in the Gas Phase The collision-induced fragmentations of 2- and 3-phenyl substituted alkylalkylidene iminium ions are reported. Besides the homolytic cleavage of the azaallyl bond a nucleophilic attack of the unsubstituted phenyl group at the iminium function is observed in the gas phase, yielding carbonium ions such as cyclopropanspirobenzenium ( 3 ), indanylium ( 10 ) and indenylium ions ( 11 ).     

Determination of internuclear distances in uniformly labeled molecules by rotational-resonance solid-state NMR

Rotational-resonance magic-angle spinning NMR experiments are frequently used to measure dipolar couplings and to determine internuclear distances. So far most measurements were performed on samples containing isolated spin pairs. Thus, extensive structure elucidation, for example in biomolecules, requires the preparation of a whole set of doubly labeled samples. Here, we describe the analysis of the rotational-resonance polarization-exchange curves obtained from a single, uniformly labeled sample. It is shown experimentally that, at a magnetic field of 14.09 T, the rotational-resonance conditions in uniformly (13)C-labeled threonine are sufficiently narrow to permit the measurement of five distances between the four carbon spins with an accuracy of better than 10%. The polarization-exchange curves are analyzed using a modified two-spin model consisting of the two active spins. The modified model includes an additional offset in the final polarization, which comes from the coupling to the additional, passive, spins. The validity of this approach is experimentally verified for uniformly (13)C-labeled threonine. The broader applicability of such a model is demonstrated by numerical simulations which quantify the errors as a function of the most relevant parameters in the spin system.