Understanding the factors controlling the photo-oxidation of natural DNA by enantiomerically pure intercalating ruthenium polypyridyl complexes through TA/TRIR studies with polydeoxynucleotides and mixed sequence oligodeoxynucleotides

Ruthenium polypyridyl complexes which can sensitise the photo-oxidation of nucleic acids and other biological molecules show potential for photo-therapeutic applications. In this article a combination of transient visible absorption (TrA) and time-resolved infra-red (TRIR) spectroscopy are used to compare the photo-oxidation of guanine by the enantiomers of [Ru(TAP)₂(dppz)]²⁺ in both polymeric {poly(dG-dC), poly(dA-dT) and natural DNA} and small mixed-sequence duplex-forming oligodeoxynucleotides. The products of electron transfer are readily monitored by the appearance of a characteristic TRIR band centred at ca. 1700 cm⁻¹ for the guanine radical cation and a band centered at ca. 515 nm in the TrA for the reduced ruthenium complex. It is found that efficient electron transfer requires that the complex be intercalated at a G-C base-pair containing site. Significantly, changes in the nucleobase vibrations of the TRIR spectra induced by the bound excited state before electron transfer takes place are used to identify preferred intercalation sites in mixed-sequence oligodeoxynucleotides and natural DNA. Interestingly, with natural DNA, while it is found that quenching is inefficient in the picosecond range, a slower electron transfer process occurs, which is not found with the mixed-sequence duplex-forming oligodeoxynucleotides studied.

Efficient electron transfer requires the complex to be intercalated at a G-C base-pair. Identification of preferred intercalation sites is achieved by TRIR monitoring of the nucleobase vibrations before electron transfer.     

International Measurement Evaluation Programme: IMEP-9, trace elements in water

The International Measurement Evaluation Programme (IMEP) is an interlaboratory comparison scheme, founded, owned and coordinated by the Institute for Reference Materials and Measurements (IRMM) since 1988. IMEP-9 is the third round of trace elements in water evaluation following IMEP-3 and IMEP-6. Reference values for 15 elements stating total concentrations and combined uncertainties (according to GUM) were established. The reference values were established mainly by isotope dilution mass spectrometry (IDMS) as a primary method of measurement, and values traceable to the SI were obtained. The four elements that could not be certified by IDMS were assigned values by means of other measurement techniques. Results from 201 laboratories from 35 countries and four continents were evaluated against the reference values and the comparability between the laboratories is presented graphically.     

Dynamics and energetics of the self-assembly of a hydrophobically modified polyelectrolyte: Naphthalene-labeled poly(acrylic acid)

Steady-state and time-resolved fluorescence studies were performed on aqueous solutions of poly(acrylic acid) hydrophobically modified with two very different levels of naphthalene (Np). It is demonstrated that unique information on association phenomena involving hydrophobe-modifed polymers can be obtained from an extended fluorescence study by using data for a less-modified polymer as a reference. For the more highly modified polymer, the presence of excited-state (as well as ground-state) dimers in addition to monomer emission due to locally excited naphthalene gives evidence for hydrophobic association between naphthalene groups. This association becomes, as expected, much less important at higher pH due to the electrostatic repulsion between different chain segments. However, it is noted that even at high pH there is a significant self-association. The coexistence of static and dynamic quenching phenomena of the Np monomer label was also revealed in the time-resolved fluorescence data. The data are compatible with the existence of two types of monomers and one excimer and suggest that the essential contribution to the monomer emission comes from isolated chromophores, whereas excimer formation arises from both a dynamic route (excited Np chromophores able to produce a dynamic excimer) and a static route (excitation of ground-state Np dimers). At room temperature, the dissociative reaction, excimer-to-monomer, can be neglected, and thus the rate constant for excimer formation and decay could be obtained with and without considering the influence of preformed dimers. Temperature has shown to induce different behavior in the polymer photophysics. In the case of the less-labeled polymer, the decays were found to be single-exponential with the fluorescence lifetime decreasing with increasing temperature. From the temperature dependence of the steady-state fluorescence data, the activation energy for excimer formation and the binding energy of the excimer were evaluated at different pH values, through the Stevens-Ban-type plots of the excimer-to-monomer intensity ratio. With the time-resolved data, measured in the temperature range of 5-60 degrees C, it was possible to extract the intrinsic activation energies for excimer formation. The thermodynamic driving force for the intrapolymeric association was found to be dependent on a balance between hydrophobic and electrostatic interactions, which are dependent on the pH, temperature, and hydrophobic content of the polymer.     

Encapsulated guest molecules in the dimer of octahydroxypyridine[4]arene

Recently a new type of calix[4]arenes has been synthesized via condensation of 2,6-dihydroxypyridine and a number of aldehydes. This type of pyridine[4]arenes forms capsules consisting of two single pyridine[4]arenes. These capsules can incorporate different guest molecules, like carboxylic acids and amides in this case. We proved that the guest acids really are incorporated inside the cavity of the capsules by electrospray mass spectrometry, NMR spectroscopy, and theoretical calculations.     

Two phenanthroline hydro­chlorides

The crystal and molecular structures of two phenanthroline hydro­chlorides have been determined at 173 K. 1,10‐Phenanthrolin‐1‐ium chloride, C₁₂H₉N₂⁺·Cl^?, crystallizes in two stacks of exactly planar mol­ecules. Both stacks are approximately parallel to the (02) plane and the planes composing the different stacks enclose an angle of 13.29 (3)°. Tris(1,10‐phenanthrolin‐1‐ium) dichloride (hydrogen chloride) chloride chloro­form solvate, 3C₁₂H₉N₂⁺·2Cl^?·HCl·Cl^?·CHCl₃, displays an interesting network of Cl^? mediated hydrogen bonds between the two different phenanthrolinium moieties and between a phenanthrolinium and the chloro­form solvate. In addition, a hydrogen bond between the HCl and the third Cl^? ion is formed. The C—N—C angle at the protonated N atoms is, in all phenanthrolinium units of both structures, significantly larger than the C—N—C angle at the non‐protonated N atom.     

A closed-shell coupled-cluster treatment of the Breit-Pauli first-order relativistic energy correction

First-order relativistic corrections to the energy of closed-shell molecular systems are calculated, using all terms in the two-component Breit-Pauli Hamiltonian. In particular, we present the first implementation of the two-electron Breit orbit-orbit integrals, thus completing the first-order relativistic corrections within the two-component Pauli approximation. Calculations of these corrections are presented for a series of small and light molecules, at the Hartree-Fock and coupled-cluster levels of theory. Comparisons with four-component Dirac-Coulomb-Breit calculations demonstrate that the full Breit-Pauli energy corrections represent an accurate approximation to a fully relativistic treatment of such systems. The Breit interaction is dominated by the spin-spin interaction, the orbit-orbit interaction contributing only about 10% to the total two-electron relativistic correction in molecules consisting of light atoms. However, the relative importance of the orbit-orbit interaction increases with increasing nuclear charge, contributing more than 20% in H(2)S.     

On describing the steady absorption of brownian particles by a restricted random walk

This paper is concerned with idealizing brownian motion as a random walk, using the diffusion equation, and finding the boundary condition at an absorbing surface - all with an eye towards chemical kinetics. Three models of random walk (due to Smoluchowski, Fermi, and Lorentz) are considered, and it is concluded that the lorentzian model is the most appropriate.     

The complete 51V MAS NMR spectrum of surface vanadia nanoparticles on anatase (TiO2): vanadia surface structure of a DeNOx catalyst

The first observations of the complete manifold of spinning sidebands (ssbs) including both the central and satellite transitions in (51)V MAS NMR spectra of surface vanadia nanoparticles on titania in DeNO(x) catalysts are presented. (51)V quadrupole coupling and chemical shift anisotropy parameters for the dominating vanadia structure are determined from (51)V MAS NMR spectra recorded at 9.4 and 14.1 T. Based on correlations previously established between (51)V NMR parameters and crystal structure data for inorganic vanadates, the NMR data are consistent with vanadium in a distorted octahedral oxygen coordination environment for the so-called strongly bonded vanadia species on the surface. The investigation includes two vanadia-titania model catalysts and six industrial-type DeNO(x) catalysts.     

Chemical studies on antioxidant mechanisms and free radical scavenging properties of lignans

The antioxidant activity, in terms of radical scavenging capacity, of altogether 15 different lignans was measured by monitoring the scavenging of the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH). The effect of differences in skeletal arrangement or the degree of oxidation of the lignans was investigated in a structure-activity relationship study. A large variety in the radical scavenging capacities of the different lignans was observed and related to some structural features. Lignans with catechol (3,4-dihydroxyphenyl) moieties exhibited the highest radical scavenging capacity, while the corresponding guaiacyl (3-methoxy-4-hydroxyphenyl) lignans showed a slightly weaker scavenging capacity. In addition, the butanediol structure was found to enhance the activity, whereas a higher degree of oxidation at the benzylic positions decreased the activity. Additionally, the readily available lignans (-)-secoisolariciresinol, a mixture of hydroxymatairesinol epimers and (-)-matairesinol were studied in more detail, including kinetic measurements and identification of oxidation products in the reactions with DPPH and ABAP (2,2-azobis(2-methylpropionamidine) dihydrochloride. The identification of reaction products, by GC-MS, HPLC-MS and NMR spectroscopy, showed that dimerisation of the two aromatic moieties was the major radical termination reaction. Also, the formation of adducts was a predominant reaction in the experiments with ABAP. The kinetic data obtained from the reactions between the lignans and DPPH indicated a complex reaction mechanism.     

Molecular recognition: comparative study of a tunable host-guest system by using a fluorescent model system and collision-induced dissociation mass spectrometry on dendrimers

Host-guest interactions between the periphery of adamantylurea-functionalized dendrimers (host) and ureido acetic acid derivatives (guest) were shown to be specific, strong and spatially well-defined. The binding becomes stronger when using phosphonic or sulfonic acid derivatives. In the present work we have quantified the binding constants for the host-guest interactions between two different host motifs and six different guest molecules. The host molecules, which resemble the periphery of a poly(propylene imine) dendrimer, have been fitted with an anthracene-based fluorescent probe. The two host motifs differ in terms of the length of the spacer between a tertiary amine and two ureido functionalities. The guest molecules all contain an acidic moiety (either a carboxylic acid, a phosphonic acid, or a sulfonic acid) and three of them also contain an ureido moiety capable of forming multiple hydrogen bonds to the hosts. The binding constants for all 12 host-guest complexes have been determined by using fluorescence titrations by monitoring the increase in fluorescence of the host upon protonation by the addition of the guest. The binding constants could be tuned by changing the design of the acidic part of the guest. The formation of hydrogen bonds gives, in all cases, higher association constants, demonstrating that the host is more than a proton sensor. The host with the longer spacer (propyl) shows higher association constants than the host with the shorter spacer (ethyl). The gain in association constants are higher when the urea function is added to the guests for the host with the longer spacer, indicating a better fit. Collision-induced dissociation mass spectrometry (CID-MS) is used to study the stability of the six motifs using the corresponding third generation dendrimer. A similar trend is found when the six different guests are compared.