Dose-Rate Effects in Breaking DNA Strands by Short Pulses of Extreme Ultraviolet Radiation.

In this study, we examined dose-rate effects on strand break formation in plasmid DNA induced by pulsed extreme ultraviolet (XUV) radiation. Dose delivered to the target molecule was controlled by attenuating the incident photon flux using aluminum filters as well as by changing the DNA/buffer-salt ratio in the irradiated sample. Irradiated samples were examined using agarose gel electrophoresis. Yields of single- and double-strand breaks (SSBs and DSBs) were determined as a function of the incident photon fluence. In addition, electrophoresis also revealed DNA cross-linking. Damaged DNA was inspected by means of atomic force microscopy (AFM). Both SSB and DSB yields decreased with dose rate increase. Quantum yields of SSBs at the highest photon fluence were comparable to yields of DSBs found after synchrotron irradiation. The average SSB/DSB ratio decreased only slightly at elevated dose rates. In conclusion, complex and/or clustered damages other than cross-links do not appear to be induced under the radiation conditions applied in this study.

Breaking DNA strands by extreme-ultraviolet laser pulses in vacuum.

Ionizing radiation induces a variety of DNA damages including single-strand breaks (SSBs), double-strand breaks (DSBs), abasic sites, modified sugars, and bases. Most theoretical and experimental studies have been focused on DNA strand scissions, in particular production of DNA double-strand breaks. DSBs have been proven to be a key damage at a molecular level responsible for the formation of chromosomal aberrations, leading often to cell death. We have studied the nature of DNA damage induced directly by the pulsed 46.9-nm (26.5 eV) radiation provided by an extreme ultraviolet (XUV) capillary-discharge Ne-like Ar laser (CDL). Doses up to 45 kGy were delivered with a repetition rate of 3 Hz. We studied the dependence of the yield of SSBs and DSBs of a simple model of DNA molecule (pBR322) on the CDL pulse fluence. Agarose gel electrophoresis method was used for determination of both SSB and DSB yields. The action cross sections of the single- and double-strand breaks of pBR322 plasmid DNA in solid state were determined. We observed an increase in the efficiency of strand-break induction in the supercoiled DNA as a function of laser pulse fluence. Results are compared to those acquired at synchrotron radiation facilities and other sources of extreme-ultraviolet and soft x-ray radiation.

Experimental and theoretical study of neutral AlmCn and AlmCnHx clusters.

Neutral Al(m)C(n) and Al(m)C(n)H(x) clusters are investigated both experimentally and theoretically for the first time. Single photon ionization through 193, 118, and 46.9 nm lasers is used to detect neutral cluster distributions through time of flight mass spectrometry (TOFMS). Al(m)C(n) clusters are generated through laser ablation of a mixture of Al and C powders pressed into a disk. An oscillation of the vertical ionization energies (VIEs) of Al(m)C(n) clusters is observed in the experiments. The VIEs of Al(m)C(n) clusters change as a function of the numbers of Al and C atoms in the clusters. Al(m)C(n)H(x) clusters are generated through an Al ablation plasma-hydrocarbon reaction, an Al-C ablation plasma reacting with H(2) gas, or through cold Al(m)C(n) clusters reacting with H(2) gas in a fast flow reactor. The VIEs of Al(m)C(n)H(x) clusters are observed to vary as a function of the number of H atoms in the clusters. Density functional theory and ab initio calculations are carried out to explore the structures, ionization energies, and electronic structures of the Al(m)C(n) and Al(m)C(n)H(x) clusters. C=C bonds are favored for the lowest energy structures for Al(m)C(n) clusters. H atoms can be bonded to either Al or C atoms in forming Al(m)C(n)H(x) clusters, with little difference in energy. Electron density plots of the highest occupied molecular orbitals (HOMOs) for closed shell species and the singly occupied molecular orbitals (SOMOs) for open shell species of Al(m)C(n) and Al(m)C(n)H(x) clusters are presented and described to help understand the physical and chemical properties of the observed species. VIEs do not simply depend on open or closed shell valence electron configurations, but also depend on the electronic structure details of the clusters. The calculational results provide a good and consistent explanation for the experimental observations, and are in general agreement with them. All calculated clusters are found to have a number of low lying isomeric structures.

Oxidation reactions on neutral cobalt oxide clusters: experimental and theoretical studies.

Reactions of neutral cobalt oxide clusters (Co(m)O(n), m = 3-9, n = 3-13) with CO, NO, C(2)H(2), and C(2)H(4) in a fast flow reactor are investigated by time of flight mass spectrometry employing 118 nm (10.5 eV) single photon ionization. Strong cluster size dependent behavior is observed for all the oxidation reactions; the Co(3)O(4) cluster has the highest reactivity for reactions with CO and NO. Cluster reactivity is also highly correlated with either one or more following factors: cluster size, Co(iii) concentration, the number of the cobalt atoms with high oxidation states, and the presence of an oxygen molecular moiety (an O-O bond) in the Co(m)O(n) clusters. The experimental cluster observations are in good agreement with condensed phase Co(3)O(4) behavior. Density functional theory calculations at the BPW91/TZVP level are carried out to explore the geometric and electronic structures of the Co(3)O(4) cluster, reaction intermediates, transition states, as well as reaction mechanisms. CO, NO, C(2)H(2), and C(2)H(4) are predicted to be adsorbed on the Co(ii) site, and react with one of the parallel bridge oxygen atoms between two Co(iii) atoms in the Co(3)O(4) cluster. Oxidation reactions with CO, NO, and C(2)H(2) on the Co(3)O(4) cluster are estimated as thermodynamically favorable and overall barrierless processes at room temperature. The oxidation reaction with C(2)H(4) is predicted to have a very small overall barrier (<0.23 eV). The oxygen bridge between two Co(iii) sites in the Co(3)O(4) cluster is responsible for the oxidation reactions with CO, NO, C(2)H(2), and C(2)H(4). Based on the gas phase experimental and theoretical cluster studies, a catalytic cycle for these oxidation reactions on a condensed phase cobalt oxide catalyst is proposed.

Reactions of neutral vanadium oxide clusters with methanol.

Reactions of neutral vanadium oxide clusters with methanol and ethanol in a fast-flow reactor are investigated by time-of-flight mass spectrometry. Single-photon ionization through soft X-ray (46.9 nm, 26.5 eV) and vacuum ultraviolet (VUV, 118 nm, 10.5 eV) lasers is employed to detect both neutral cluster distributions and reaction products. In order to distinguish isomeric products generated in the reactions V(m)O(n) + CH(3)OH, partially deuterated methanol (CD(3)OH) is also used as a reactant in the experiments. Association products are observed for most vanadium oxide clusters in reaction with methanol. Products VOD, V(2)O(3)D, V(3)O(6)D, and V(4)O(9)D are observed for oxygen-deficient vanadium oxide clusters reacting with methanol, while oxygen-rich and the most stable clusters can extract more than one hydrogen atom (H/D) from CD(3)OH to form products VO(2)DH(0,1), V(2)O(4)DH(0,1), V(2)O(5)DH(0,1), V(3)O(7)DH(0,1), and V(4)O(10)DH(0,1). Species VO(2)(CH(3))(2), VO(3)(CH(3))(2), V(2)O(5)(CH(3))(2), V(3)O(7)(CH(3))(2), and V(3)O(8)(CH(3))(2) are identified as some of the main products generated from a dehydration reaction for V(m)O(n) + CH(3)OH. A minor reaction channel that generates VOCH(2)O (VOCD(2)O) and VO(2)CH(2)O (VO(2)CD(2)O) can also be identified. An obviously different behavior appears in the reaction V(m)O(n) + C(2)H(5)OH. The main observed products for this reaction are association products of the form V(m)O(n)C(2)H(5)OH. In order to explore the mechanism of V(m)O(n) + CH(3)OH reactions, DFT calculations are performed to study the reaction pathways of VO(2) + CH(3)OH and VO + CH(3)OH reaction systems. The calculation results are in good agreement with the experimental observations.

Investigation of the reactions of small neutral iron oxide clusters with methanol.

Reactions of neutral iron oxide clusters (Fe(m)O(n), m=1-2, n=0-5) with methanol (CH(3)OH) in a fast flow reactor are investigated by time of flight mass spectrometry. Detection of the neutral iron oxide cluster distribution and reaction intermediates and products is accomplished through single photon ionization by a 118 nm (10.5 eV) VUV laser. Partially deuterated methanol (CD(3)OH) is employed to distinguish reaction products and reaction mechanisms. Three major reactions are identified experimentally: CH(3)OH association with FeO; methanol dehydrogenation on FeO(1,2) and Fe(2)O(2-5); and (CH(2)O)Fe formation. Density functional theory calculations are carried out to identify reaction products, and to explore the geometric and electronic structures of the iron oxide clusters, reaction intermediates, and transition states, and to evaluate reaction pathways. Neutral formaldehyde is calculated to be formed on FeO(1,2) and Fe(2)O(2-5) clusters. Hydrogen transfer from methanol to iron oxide clusters occurs first from the O-H moiety of methanol, and is followed by a hydrogen transfer from the C-H moiety of methanol. Computational results are in good agreement with experimental observations and reveal reaction mechanisms for neutral iron oxide clusters taking methanol to formaldehyde through various reaction intermediates. Based on the experimental results and the calculated reaction mechanisms and pathways, complete catalytic cycles are suggested for the heterogeneous reaction of CH(3)OH to CH(2)O facilitated by an iron oxide catalyst.

C=C bond cleavage on neutral VO3(V2O5)n clusters.

The reactions of neutral vanadium oxide clusters with alkenes (ethylene, propylene, 1-butene, and 1,3-butadiene) are investigated by experiments and density function theory (DFT) calculations. Single photon ionization through extreme ultraviolet radiation (EUV, 46.9 nm, 26.5 eV) is used to detect neutral cluster distributions and reaction products. In the experiments, we observe products (V(2)O(5))(n)VO(2)CH(2), (V(2)O(5))(n)VO(2)C(2)H(4), (V(2)O(5))(n)VO(2)C(3)H(4), and (V(2)O(5))(n)VO(2)C(3)H(6), for neural V(m)O(n) clusters in reactions with C(2)H(4), C(3)H(6), C(4)H(6), and C(4)H(8), respectively. The observation of these products indicates that the C=C bonds of alkenes can be broken on neutral oxygen rich vanadium oxide clusters with the general structure VO(3)(V(2)O(5))(n=0,1,2...). DFT calculations demonstrate that the reaction VO(3) + C(3)H(6) --> VO(2)C(2)H(4) + H(2)CO is thermodynamically favorable and overall barrierless at room temperature. They also provide a mechanistic explanation for the general reaction in which the C=C double bond of alkenes is broken on VO(3)(V(2)O(5))(n=0,1,2...) clusters. A catalytic cycle for alkene oxidation on vanadium oxide is suggested based on our experimental and theoretical investigations. The reactions of V(m)O(n) with C(6)H(6) and C(2)F(4) are also investigated by experiments. The products VO(2)(V(2)O(5))(n)C(6)H(4) are observed for dehydration reactions between V(m)O(n) clusters and C(6)H(6). No product is detected for V(m)O(n) clusters reacting with C(2)F(4). The mechanisms of the reactions between VO(3) and C(2)F(4)/C(6)H(6) are also investigated by calculations at the B3LYP/TZVP level.

Reactions of sulfur dioxide with neutral vanadium oxide clusters in the gas phase. II. Experimental study employing single-photon ionization.

Single-photon ionization through vacuum ultraviolet (VUV, 10.5 eV) and soft X-ray (extreme ultraviolet, EUV, 26.5 eV) laser radiation is successfully employed for the study of the reactions of neutral vanadium oxide clusters (V(m)O(n)) with sulfur dioxide (SO2) in the gas phase. V(m)O(n) clusters are generated by reaction of a laser-generated vanadium plasma with O2 in a supersonic expansion. The clusters are cooled in the expansion and are reacted with SO2 in a fast-flow reactor. Detection of neutral clusters and products is through ionization employing VUV and EUV laser radiation and time-of-flight mass spectrometry. Many association reaction intermediates [V(m)O(n)SO2 and V2O4(SO2)2] are observed. Isolated SO is also observed, as a product as predicted by theoretical studies presented in part I (J. Phys. Chem. A 2007, 111, 13339). A weak feature at the SO3 mass channel (80 amu) is suggested to be present in the product mass spectra. Further reactions of the intermediates with O2 are positively identified for VO2SO2, V3O7SO2, and V5O10SO2. Reaction mechanisms are interpreted on the basis of the observations and preliminary theoretical calculations. Molecular level reaction mechanisms for oxidation of SO2 to SO3 facilitated by condensed-phase vanadium oxides as catalysts are suggested.

Partial oxidation of propylene catalyzed by VO3 clusters: a density functional theory study.

Density functional theory (DFT) calculations are carried out to investigate partial oxidation of propylene over neutral VO 3 clusters. C=C bond cleavage products CH 3CHO + VO 2CH 2 and HCHO + VO 2CHCH 3 can be formed overall barrierlessly from the reaction of propylene with VO 3 at room temperature. Formation of hydrogen transfer products H 2O + VO 2C 3H 4, CH 2=CHCHO + VO 2H 2, CH 3CH 2CHO + VO 2, and (CH 3) 2CO + VO 2 is subject to tiny (0.01 eV) or small (0.06 eV, 0.19 eV) overall free energy barriers, although their formation is thermodynamically more favorable than the formation of C=C bond cleavage products. These DFT results are in agreement with recent experimental observations. VO 3 regeneration processes at room temperature are also investigated through reaction of O 2 with the CC bond cleavage products VO 2CH 2 and VO 2CHCH 3. The following barrierless reaction channels are identified: VO 2CH 2 + O 2 --> VO 3 + CH 2O; VO 2CH 2 + O 2 --> VO 3C + H 2O, VO 3C + O 2 --> VO 3 + CO 2; VO 2CHCH 3 + O 2 --> VO 3 + CH 3CHO; and VO 2CHCH 3 + O 2 --> VO 3C + CH 3OH, VO 3C + O 2 --> VO 3 + CO 2. The kinetically most favorable reaction products are CH 3CHO, H 2O, and CO 2 in the gas phase model catalytic cycles. The results parallel similar behavior in the selective oxidation of propylene over condensed phase V 2O 5/SiO 2 catalysts.

Experimental and theoretical study of the reactions between neutral vanadium oxide clusters and ethane, ethylene, and acetylene.

Reactions of neutral vanadium oxide clusters with small hydrocarbons, namely C2H6, C2H4, and C2H2, are investigated by experiment and density functional theory (DFT) calculations. Single photon ionization through extreme ultraviolet (EUV, 46.9 nm, 26.5 eV) and vacuum ultraviolet (VUV, 118 nm, 10.5 eV) lasers is used to detect neutral cluster distributions and reaction products. The most stable vanadium oxide clusters VO2, V2O5, V3O7, V4O10, etc. tend to associate with C2H4 generating products V(m)O(n)C2H4. Oxygen-rich clusters VO3(V2O5)(n=0,1,2...), (e.g., VO3, V3O8, and V5O13) react with C2H4 molecules to cause a cleavage of the C=C bond of C2H4 to produce (V2O5)(n)VO2CH2 clusters. For the reactions of vanadium oxide clusters (V(m)O(n)) with C2H2 molecules, V(m)O(n)C2H2 are assigned as the major products of the association reactions. Additionally, a dehydration reaction for VO3 + C2H2 to produce VO2C2 is also identified. C2H6 molecules are quite stable toward reaction with neutral vanadium oxide clusters. Density functional theory calculations are employed to investigate association reactions for V2O5 + C2H(x). The observed relative reactivity of C2 hydrocarbons toward neutral vanadium oxide clusters is well interpreted by using the DFT calculated binding energies. DFT calculations of the pathways for VO3+C2H4 and VO3+C2H2 reaction systems indicate that the reactions VO3+C2H4 --> VO2CH2 + H2CO and VO3+C2H2 --> VO2C2 + H2O are thermodynamically favorable and overall barrierless at room temperature, in good agreement with the experimental observations.