Chromophore/DNA interactions: femto- to nanosecond spectroscopy, NMR structure, and electron transfer theory

The mechanism of photoinduced hole injection into DNA has been studied using an integrated approach that combines NMR structural analysis, time-resolved spectroscopy, and quantum-chemical calculations. A covalently linked acridinium derivative, the protonated 9-amino-6-chloro-2-methoxyacridine (X+), is replacing a thymine and separated from either guanine (G) or the easier to oxidize 7-deazaguanine (Z) by one adenine.thymine (A.T) base pair. The key features of this donor/acceptor system are the following: (i) In more than 95% of the duplexes, X+ is located in a central, coplanar position between the neighboring A.T base pairs with its long axis in parallel showing minimal twist and tilt angles (<15 degrees). The complementary adenine base is turned out into the extrahelical space. In a minority of less than 5%, X+ is found to be still attached to the duplex. X+ is most probably associated with one of the phosphates, since it is neither intercalated between more remote base pairs nor bound to sugars or grooves. This minority characterized by an excited state lifetime >10 ns gives rise to a small background signal in time-resolved measurements and contributes predominantly to steady-state fluorescence spectra. (ii) Although the intercalation mode of X+ is well defined, the NMR structure reveals that there are two conformations of X+ with respect to the arrangement of its methoxy substituent. In one conformation, the methoxy group is in the plane of the chromophore, while, in the other extraplanar conformation, the methoxy group forms an angle of 70 degrees with the acridinium ring. The fluorescence decay of 5'-ZAX and 5'-GAX tracts can be fitted to a biexponential function with similar amplitudes, reflecting the oxidation dynamics of G and Z, with the slower rate being determined by larger thermal activation energy. The attribution of biexponential electron transfer (ET) dynamics to the bimodal orientation of the methoxy group at the acridinium is supported by quantum-chemical calculations. These predict a larger free energy change for hole transfer in the nonplanar conformation as compared to the planar one, whereas the difference in the electronic couplings is negligible. (iii) Kinetic studies of the directionality of the 1(X+)* induced hole injection reveal similarly fast decay components in both directions of the duplex, that is, in 5'-ZAX and 5'-XAZ, with the amplitude of the fast component being significantly reduced in 5'-XAZ. The NMR structure shows that local structural deviations from B-DNA are much more pronounced in the 3'-5' direction than in the 5'-3' direction. According to quantum-chemical calculations, the directionality of charge injection is not a universal feature of the DNA duplex but depends critically on the rotation angle of the aromatic plane of the acridinium within the pi stack. The arrangement of X+ in 5'-ZAX and 5'-XAZ corresponds to a conformation with weak directionality of the electronic couplings. The increased disorder in the 3'-5'direction favors slow hole transfer components at the expense of the fast ones. (iv) A comparison of the hole transfer in 5'-GAX and 5'-ZAG shows that classical Marcus theory can explain the ratio of the charge shift rates of more than 2 orders of magnitude on the basis of a free energy difference between G and Z of 0.3 eV. Both NMR structures and quantum-chemical calculations justify the appreciable neglect of differences of electronic couplings as well as in the reorganization energy in 5'-GAX and 5'-ZAG. Despite the attractive concept for the behavior of floppy DNA oligonucleotides, in this acridinium/DNA system, there is no evidence for conformational gating, that is, for fluctuations in the electronic couplings that permit the ET to occur.     

Two‐Dimensional Infrared Spectroscopy Reveals the Structure of an Evans Auxiliary Derivative and Its SnCl4 Lewis Acid Complex

Determining the structure of reactive intermediates is the key to understanding reaction mechanisms. To access these structures, a method combining structural sensitivity and high time resolution is required. Here ultrafast polarization‐dependent two‐dimensional infrared (P2D‐IR) spectroscopy is shown to be an excellent complement to commonly used methods such as one‐dimensional IR and multidimensional NMR spectroscopy for investigating intermediates. P2D‐IR spectroscopy allows structure determination by measuring the angles between vibrational transition dipole moments. The high time resolution makes P2D‐IR spectroscopy an attractive method for structure determination in the presence of fast exchange and for short‐lived intermediates. The ubiquity of vibrations in molecules ensures broad applicability of the method, particularly in cases in which NMR spectroscopy is challenging due to a low density of active nuclei. Here we illustrate the strengths of P2D‐IR by determining the conformation of a Diels–Alder dienophile that carries the Evans auxiliary and its conformational change induced by the complexation with the Lewis acid SnCl₄, which is a catalyst for stereoselective Diels–Alder reactions. We show that P2D‐IR in combination with DFT computations can discriminate between the various conformers of the free dienophile N‐crotonyloxazolidinone that have been debated before, proving antiperiplanar orientation of the carbonyl groups and s‐cis conformation of the crotonyl moiety. P2D‐IR unequivocally identifies the coordination and conformation in the catalyst–substrate complex with SnCl₄, even in the presence of exchange that is fast on the NMR time scale. It resolves a chelate with the carbonyl orientation flipped to synperiplanar and s‐cis crotonyl configuration as the main species. This work sets the stage for future studies of other catalyst–substrate complexes and intermediates using a combination of P2D‐IR spectroscopy and DFT computations.     

Mass transport characteristics of alkyl amines in a water/n-decane system

Rhenium (Re) nanoparticles have been synthesized by pulsed-laser decomposition of ammonium perrhenate (NH(4)ReO(4)) or dirhenium decacarbonyl (Re(2)(CO)(10)) in the presence of 3-mercaptopropionic acid (MPA) as capping agent, in both aqueous and organic media. Preliminary studies showed that the MPA-capped Re nanoparticles are capable of catalyzing the isomerization of 10-undecen-1-ol to internal alkenols via long chain migration of the C=C double bond at ca. 200°C. A one-pot synthesis of graphite-coated Re nanoparticles has also been achieved by pulsed-laser decomposition of Re(2)(CO)(10), due to photo-induced catalytic graphitization of the phenyl groups of PPh(3) on the surface of rhenium nanoparticles.     

A new synthesis for thermolabile low-valent palladium complexes by electron transfer reactions from nickel(0) to palladium(II) compounds

The nickel(0) complex [Ni(bpy)(cod)] (bpy: 2,2′-bipyridine, cod: cycloocta-1,5-diene) was used as a mild reducing reagent for the synthesis of the extremely reactive low-valent palladium complexes [Pd₂X₂(cod)₂] (1: X = Cl, 2: X = Br), Pd(cod)₂ (3) and Pd(norbornene)₃ (4). The X-ray analysis of 1 showed that the two [Pd(cod)(Cl)] moieties are only connected by a short Pd(I)-Pd(I) bond (bond length: 2.5379(4) Å) with the chloride ions as monodentate ligands. The X-ray structure of 3 which is also known to be an extremely reactive compound could be determined by X-ray diffraction. As expected, the Pd(0) centre is surrounded by the two cod ligands to form a PdC₄ tetrahedron with typical Pd-C bond lengths. The crystal structure of 3 shows it to be very similar to the closely related complexes M(cod)₂ (M: Ni, Pt). The X-ray structure of 4 displays that the Pd(0) centre is in a trigonal planar environment of the three olefin groups. According to ¹H NMR measurements the complexes have the same structure in solution as found in the solid state.     

Functionalized nanodiamonds: triamantane and [121]tetramantane

The selective functionalizations of the fundamental hydrogen-terminated nanodiamonds triamantane 1, as well as the most symmetrical representative of the tetramantanes (C(2h)-[121]tetramantane 2) were elaborated. Electrophilic reagents (Br2, HNO3) predominantly attack the medial C-H positions of the cages; bromination of 2 gave the medial 2-bromo derivative almost exclusively. Highly selective apical substitution in 1 and 2 is possible either under single-electron-transfer oxidations via hydrocarbon radical cations or through photoacetylation with diacetyl. The mono- and the bis-acetyl derivatives of 1 and 2 were converted through Bayer-Villiger oxidation and subsequent hydrolysis to the respective apical mono- and dihydroxy derivatives. This exceptional synthetic specificity facilitates the transformation of 2, and perhaps larger nanodiamond molecules, into functionalized building blocks needed for a wide range of applications such as nanotechnology.     

Electron emission from photo-excited testosterone in water–ethanol solution

Testosterone (TES; 4-androstene-17β-ol-3-on) is found for the first time to eject electrons from its singlet excited state in water–ethanol solvent mixture. This ability was very recently also observed for 17β-estradiol (17βE2) and progesterone (PRG)/1/. With increasing TES-concentration, the yield of solvated electrons (${\text{e}}_{\text{s}}^{-}$) is decreasing, because of “associate” formation. At higher absorbed UV-doses (λ = 254 nm) the ${\text{e}}_{\text{s}}^{-}$ yield is passing a sharp maximum by formation of TES–ethanol adducts, which are able likewise to emit electrons when excited. At prolonged irradiation the resulting photolytic products of TES–ethanol adducts are also able to emit electrons.The capability of the hormones: 17βE2, PRG and TES to eject electrons and the resulting metabolites, some of which can induce cancer, is discussed.     

The plumbing of interactive graphics

What is a pipeline, and why do we need one for interactive graphics? This conceptual paper attempts to answer these questions, building on previous work. A pipeline controls the transformation from data to graphical objects on our screens, and we argue that the pipeline must be present, in some form, in all graphics software. The pipeline is made explicit in descendants of DataViewer.     

Evaluation of different calibration strategies for the analysis of pure copper and zinc samples using femtosecond laser ablation ICP-MS

Solution-doped metal powder pellets as well as aspirated liquids were used as calibration samples to analyze pure copper and zinc certified reference materials (CRMs) by femtosecond laser ablation ICP-MS. It was demonstrated that calibration by copper pellets resulted in relative deviations up to 20%, whereas fs-LA-ICP-MS among copper-based CRMs led to inaccuracies in the same range unless nominal mass fractions were chosen to be <3 mg/kg. Calibration by zinc pellets generally provided better accuracy. Depending on the analyte considered, deviations below 10% were obtained even for mass fractions close to the limit of quantification. Our data, therefore, indicate solution-doped metal powder pellets to be suitable as calibration samples for fs-LA-ICP-MS of metals. Furthermore, the utilization of liquid standards for calibration was found to result in stronger deviations of up to 50% for both copper and zinc samples which, in addition, turned out to be dependent on the plasma conditions.