Svend J. Knak Jensen

ESR Spectra from Paramagnetic Centers in Irradiated KClO4. III. Centers Appearing between 10 and 200°K

ESR spectra of KClO4 crystals irradiated with x rays at 10 and at 26°K contain three “families” of intense signals. The signals are assumed to derive from primary defects constituted by electrons and holes trapped on ClO4− ions. The families of signals are assigned to the species ClO4=, ClO4, and (ClO4)2−, each trapped in a number of distinct sites. ClO4= and ClO4 appear to be stabilized by intraionic configuration change, whereas interionic configuration change may stabilize (ClO4)2−. Thermal processes starting at 30°K result in formation of the secondary defects O3− from ClO4= and ClO2 from ClO4 and in destruction of (ClO4)2−.

Hydration Dynamics of Aqueous Nitrate

Aqueous nitrate, NO3(-)(aq), was studied by 2D-IR, UV-IR, and UV-UV time-resolved spectroscopies in combination with molecular dynamics (MD) simulations with the purpose of determining the hydration dynamics around the anion. In water, the D3h symmetry of NO3(-) is broken, and the degeneracy of the asymmetric-stretch modes is lifted. This provides a very sensitive probe of the ion-water interactions. The 2D-IR measurements reveal excitation exchange between the two nondegenerate asymmetric-stretch vibrations on a 300-fs time scale concomitant with fast anisotropy decay of the diagonal-peak signals. The MD simulations show that this is caused by jumps of the transition dipole orientations related to fluctuations of the hydrogen bonds connecting the nitrate ion to the nearest water molecules. Reorientation of the ion, which is associated with the hydrogen-bond breaking, was monitored by time-resolved UV-IR and UV-UV spectroscopy, revealing a 2-ps time constant. These time scales are very similar to those reported for isotope-labeled water, suggesting that NO3(-)(aq) has a labile hydration shell.

Comparison of the mineralogical effects of an experimental forest fire on a goethite/ferrihydrite soil with a topsoil that contains hematite, maghemite and goethite

Abstract A long-standing unresolved puzzle related to the Danish temperate humid climate is the presence of extended areas with large Fe contents, where goethite and ferrihydrite are present in the topsoil along with hematite and maghemite. Hematite and, particularly, maghemite would normally be interpreted as the result of high temperature as found after forest fires. However, a body of evidence argues against these sites having been exposed to fire. In an attempt to get closer to an explanation of this Fe mineralogy, an experimental forest fire was produced. The results showed a clear mineralogical zonation down to 10 cm depth. This was not observed at the natural sites, which contained a mixture of goethite/ferrihydrite, hematite and maghemite down to 20 cm depth. The experimental forest fire left charcoal and ashes at the topsoil, produced high pH and decreased organic matter content, all of which is in contrast to the natural sites. The conclusion from this work is that the mineralogy of these sites is not consistent with exposure to forest fire, but may instead result from long-term transformation in a reducing environment, possibly involving microbiology.

Femtosecond Photolysis of Aqueous Formamide

In this work, we investigate the primary photodynamics of aqueous formamide. The formamide was photolyzed using 200 nm femtosecond pulses, and formation of products and their relaxation was followed with approximately 300 fs time resolution using probe pulses covering the range from 193 to 700 nm. Following excitation, the majority of formamide molecules (approximately 80%) converts the electronic excitation energy to vibrational excitation, which effectively is dissipated to the solvent through vibrational relaxation in just a few picoseconds. The vibrational relaxation is observed as a distinct modulation of the electronic absorption spectrum of formamide. The relaxation process is modeled by a simple one-dimensional wavepacket calculation. A smaller fraction of the excited formamide molecules dissociates to the CHO and NH2 radical pairs, of which 50% escape recombination. In addition to the electronic excitation of formamide, we also observe a small contribution from one-photon ionization of formamide and two-photon ionization and dissociation of the water solvent.

Primary Formation Dynamics of Peroxynitrite Following Photolysis of Nitrate

The photolysis of nitrate, NO3-, in D2O solution has been investigated by femtosecond infrared spectroscopy. In accordance with previous investigations, we observe that the peroxynitrite ion, ONOO-, is the dominant photochemical product following the excitation of nitrate at 200 nm. Moreover, we are able to identify the cis/trans isomers of peroxynitrite and the dynamics of their formation in solution. We observe that the trans- ONOO- isomer is formed directly and solely from the excited NO3- ion within the first two picoseconds after excitation. Subsequently, about half of the trans-ONOO- isomerizes to cis-ONOO- in 25 ps; thereafter, the ratio between the two isomers remains constant for the 300 ps duration of the experiment. The observed vibrational frequencies of the terminal O=N bonds are at 1515 and 1580 cm(-1) for trans- and cis-peroxynitrite, respectively. The detailed analysis of the infrared bands of cis- and trans-peroxynitrite is facilitated by electronic structure calculations on the conformers in a cluster of 11 D2O molecules and by steady-state infrared spectroscopy of ONOO- in D2O. In addition to the formation of ONOO-, the experiments also reveal a slow approximately 50 ps formation of NO2 following the photolysis of nitrate.

Reproductive death of cancer cells induced by femtosecond laser pulses

We investigate the efficacy of inducing reproductive death of cancer cells by ultraviolet, visible and near infrared femtosecond laser pulses. The reproductive cell death may result from (numerous) single photon absorption events or from multi-photon absorption processes. The high intensity of femtosecond laser pulses facilitate multi-photon processes, which potentially may arrest the reproduction of cells at wavelengths that otherwise are harmless.

Atropisomerism of the Asn α radicals revealed by ramachandran surface topology

C radicals are typically trigonal planar and thus achiral, regardless of whether they originate from a chiral or an achiral C-atom (e.g., C-H + (•)OH → C• + H2O). Oxidative stress could initiate radical formation in proteins when, for example, the H-atom is abstracted from the Cα-carbon of an amino acid residue. Electronic structure calculations show that such a radical remains achiral when formed from the achiral Gly, or the chiral but small Ala residues. However, when longer side-chain containing proteogenic amino acid residues are studied (e.g., Asn), they provide radicals of axis chirality, which in turn leads to atropisomerism observed for the first time for peptides. The two enantiomeric extended backbone structures, •βL and •βD, interconvert via a pair of enantiotopic reaction paths, monitored on a 4D Ramachandran surface, with two distinct transition states of very different Gibbs-free energies: 37.4 and 67.7 kJ/mol, respectively. This discovery requires the reassessment of our understanding on radical formation and their conformational and stereochemical behavior. Furthermore, the atropisomerism of proteogenic amino acid residues should affect our understanding on radicals in biological systems and, thus, reframes the role of the D-residues as markers of molecular aging.

The effect of oxidative stress on the bursopentin peptide structure: A theoretical study

Bursopentin (BP(5), H-Cys(1)-Lys(2)-Arg(3)-Val(4)-Tyr(5)-OH), found in the bursa Fabricius of the chicken, is a pentapeptide that protects the organism from oxidative stress by reducing the intracellular generation of reactive oxygen species. Hydrogen abstraction, a common oxidative reaction occurring in proteins, often results in the formation of d amino acid residues. To study the effect of this phenomenon on the structure of bursopentin, each of its residues were converted from the l configuration to the d configuration, and the structures of these peptide epimers were compared to that of the wild-type bursopentin. The conformations, secondary structures, compactness and hydrogen bonding of bursopentin were compared to its epimers using molecular dynamics simulations and first principles quantum chemical computations. It was discovered that the repulsion between the side chains of Lys(2) and Arg(3) influenced the conformation of the peptide regardless of the configuration of these residues. Epimerisation of the Val(4) and Tyr(5) caused a reduction in the compactness of bursopentin. In all cases, the occurrence of a turn structure was relatively high, especially when Arg(3) was in the d configuration. Thermodynamic analysis of the epimerisation process showed that the formation of d amino acid residues is favourable.

Characterization of ultraviolet femtosecond pulse propagation in aluminum-coated capillary fibers

We demonstrate that hollow core fibers with aluminum-coated bores of ϕ=0.7mm and ϕ=1.0mm are well suited for guiding high-power ultraviolet femtosecond pulses. We consider 1-m-long fibers in two geometries: straight and bent with a 30-cm radius of curvature. The straight fibers transmit approximately 60% of the power at 200nm and 85% at 266nm, while the corresponding numbers for the bent fibers are 25% and 35%. The duration of the femtosecond pulses increases by 10% and 50% per meter at 200 and 266nm, respectively. The broadening increases to a factor of two when the fiber is bent. The maximum transmitted pulse energy at 266nm is 100μJ corresponding to 0.5GW or an intensity of 1011W∕cm2. However, this value is limited only by the 266nm pulse generation and is expected to go even higher. The applicability of the powerful femtosecond pulses from the fiber is demonstrated by an experiment in which water is ionized by two-photon absorption. This experiment indicates the potential of using aluminized hollow co...

Silicates Eroded under Simulated Martian Conditions Effectively Kill Bacteria—A Challenge for Life on Mars

The habitability of Mars is determined by the physical and chemical environment. The effect of low water availability, temperature, low atmospheric pressure and strong UV radiation has been extensively studied in relation to the survival of microorganisms. In addition to these stress factors, it was recently found that silicates exposed to simulated saltation in a Mars-like atmosphere can lead to a production of reactive oxygen species. Here, we have investigated the stress effect induced by quartz and basalt abraded in Mars-like atmospheres by examining the survivability of the three microbial model organisms Pseudomonas putida, Bacillus subtilis, and Deinococcus radiodurans upon exposure to the abraded silicates. We found that abraded basalt that had not been in contact with oxygen after abrasion killed more than 99% of the vegetative cells while endospores were largely unaffected. Exposure of the basalt samples to oxygen after abrasion led to a significant reduction in the stress effect. Abraded quartz was generally less toxic than abraded basalt. We suggest that the stress effect of abraded silicates may be caused by a production of reactive oxygen species and enhanced by transition metal ions in the basalt leading to hydroxyl radicals through Fenton-like reactions. The low survivability of the usually highly resistant D. radiodurans indicates that the effect of abraded silicates, as is ubiquitous on the Martian surface, would limit the habitability of Mars as well as the risk of forward contamination. Furthermore, the reactivity of abraded silicates could have implications for future manned missions, although the lower effect of abraded silicates exposed to oxygen suggests that the effects would be reduced in human habitats.