Hatano Y., Katsumura Y., Mozumder A. (Eds.) Charged Particle and Photon Interactions with Matter - Recent Advances, Applications, and Interfaces

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490 Charged Particle and Photon Interactions with Matter

The atomic oxygen and OH radicals can react further to produce stable products and, eventu-

ally, molecular oxygen (Sieger etal., 1998; Orlando and Sieger, 2003; Johnson etal., 2005). As

shown in Figure 18.11, the thresholds for producing O

and H

are also close to 7 eV, indicating

that reactive scattering of atomic oxygen is possible (Kimmel etal., 1994). Oxygen molecules are

not produced immediately upon electron bombardment; an “incubation dose” is required before

the yield becomes appreciable. A similar incubation dose has been observed in ion (Reimann

etal., 1990; Johnson etal., 2005) and vacuum ultraviolet (VUV) photon-stimulated “sputtering”

of ice (Westley et al., 1995), and implies a two-step, precursor-mediated mechanism. A dose-,

energy-, and temperature-dependent study on the electron-beam-induced production and release

of O

from ice lead to the formulation of a simple mechanism that initially involves reactive scat-

tering of atomic oxygen or OH radicals to produce a stable precursor (on the timescale of at least

an hour at 120K), such as H

O-O, HO

, or H

. Careful molecular-beam dosing studies using

isotope (H

O versus H

O)-labeled water and kinetic modeling indicate that most of the oxygen

is produced at the vacuum–surface interface and may likely involve H

. We note that H

O-O,

, and H

are all known to be produced in irradiated ice, but the yields are highly dependent

on the dose and substrate temperature. At low temperature (<120 K), an H

O-O species can be

trapped, and a kinetic model involving direct excitation of this precursor to form O

has also been

proposed. We note that the trapped O atom can be formed from intrinsic ice defects and it can by

easily converted to H

. Thus, the peroxide route may dominate at temperatures above 120 K and

at high electron doses.

1.0

0.8

0.6

0.4

0.2

0.0

0 5 10 15 20 25 30

0 5 10

Electron energy (eV)

Relative intensity (arb. units) Relative intensity (arb. units)

15 20 25 30

Figure 18.11 Electron stimulated desorption (ESD) thresholds for neutral desorbed atoms and molecules.

Molecular hydrogen and oxygen share the same threshold as the ground and electronically excited atomic

fragments,

suggesting that hot-atom reactive scattering is the source term for their production.

Low-Energy Electron-Stimulated Reactions in Nanoscale Water Films 491

We have also measured the quantum-state distributions of the molecular hydrogen produced

and desorbed from ice using sensitive REMPI techniques (Kimmel et al., 1995; Orlando et al.,

1999). The formation of extremely vibrationally and rotationally excited molecular hydrogen dur-

ing 100eV electron bombardment was attributed primarily to the formation and decay of surface

excitons with triplet character. In the lower-energy region, vibrationally excited hydrogen was also

observed with a distinct propensity for even vibrational quantum numbers. This propensity, along

with the energy dependence of the yields, was interpreted in terms of the decay of core-excited

Feshbach resonances, particularly the

state, which is thought to asymptotically produce O

−

+ H

∑

( )

. This state can also undergo autodetachment, leaving a highly excited electronic state that

can

undergo molecular elimination.

Unfortunately,

little is known regarding the nature of the excited states that can lead to the direct

formation of molecular hydrogen. The production of atomic oxygen and molecular hydrogen fol-

lowing UV/VUV photoexcitation of gas-phase water has received limited attention. Initial work

(Slanger and Black, 1982) demonstrated that approximately 10% of the dissociation cross section

using 121.6nm excitation leads to O + H

. This was an indirect measurement obtained by analyzing

the OH A-X emission. The formation of O(

D) is likely correlated with a conical intersection

on the B-state surface. A very recent quantum mechanical calculation that includes nonadiabatic

effects has reported cross sections for the formation of O(

D) and rovibrational distributions of

the H

following excitation of water vapor with 121.6nm photons (van Harrevelt and van Hemert,

2008). We assume that similar decay pathways are available for water molecules at surfaces and

buried interfaces, and that the decay of these “exciton-like” states leads to the formation of O(

and vibrationally and rotationally excited H

. This important channel is currently under further

investigation.

18.6.4 effect of poroSity on lee-StiMulated production and releaSe of o

and h

Molecular ices, particularly polar ices and those capable of hydrogen bonding, facilitate chemistry

in a number of ways, both physical and electronic. The diffusion of sparsely distributed molecules

trapped within ice matrices is unlikely to occur at low temperatures. This would suggest that

the morphology of ice, in particular, its porosity, is of critical importance to ice chemistry. The

physical morphology of porous ice also affects the energetic processes governing the excitation

and transport of energy through the matrix. We have demonstrated the production and release of

molecular hydrogen and oxygen from electron-beam-irradiated low-temperature ice. The formation

and release of molecular hydrogen was found to be strongly correlated with the presence of pores.

The yields of H

and O

increase with the degree of disorder in the ice, which implies that their

production occurs primarily at interfaces and grain boundaries. After irradiation, the release of H

occurs via diffusion through micropores and when macropores collapse (∼80K). O

is retained until

ice undergoes an amorphous-to-crystalline phase transition (∼160K), a point where grain boundaries

sinter

and clathrate hydrates decompose.

18.7 low-energy-eleCtron-induCed damage oF dna

Biologically important molecules such as DNA, RNA, amino acids, and nucleobases are con-

stantly bombarded with ionizing radiation from a variety of sources both anthropogenic and non-

anthropogenic. A complete description of the effects of ionizing radiation on DNA in living cells is

fundamental to radiobiology, public health, and clinical applications such as radiation protection,

chemotherapy, and radiosensitizer development. It is well known that high-energy ionization radia-

tion can cause sugar–phosphate cleavage (strand breaks) in DNA, which might be critical DNA

lesions responsible for toxic, mutagenic, and cell malfunction, or death. Depending on the site of

chemical bond dissociation on double-helix backbones, the DNA damage could be either in the

form

of an SSB or a DSB.

492 Charged Particle and Photon Interactions with Matter

Radiation-induced DNA damage is usually divided into two groups: (1) “direct” damage, resulting

from direct ionization of DNA and/or the closely bound water molecule, and (2) “indirect” damage,

resulting from radicals generated by energy deposition in water molecules or other biological mol-

ecules surrounding the DNA (Purkayastha and Bernhard, 2004). It is estimated that the direct/

indirect DNA damage ratio is about 1:2 in all cellular damage (Michael and O’Neill, 2000). Most

of the energy deposited in living cells by ionizing radiation produces secondary species, such as

ballistic electrons (1–20 eV), neutrals, or ionic radicals (Sonntag, 1987). Electrons are the most

abundant secondary species with an estimated yield of about 10

electrons per MeV, and most

have initial kinetic energies below 20 eV (Cobut etal., 1998). Pioneering work by Sanche and

coworkers has demonstrated that LEEs could localize on various DNA components (base, deoxy-

ribose, phosphate, or waters of hydration) to form TNIs. The decay of the local transient anions

into dissociating pathways, such as DEA or autoionization, directly leads to the DNA strand

breakage (Boudaiffa etal., 2000).

It has been reported that strand breaks in supercoiled DNA were induced by free ballistic elec-

trons (3–20eV) (Boudaiffa etal., 2000). The electron energy dependence of SSB and DSB pre-

sented strong resonance features in the energy range of 5–15eV, with a maximum around 8–10eV.

These results provided a fundamental challenge to the traditional view that genotoxic damage by

secondary electrons can only occur at energies above the onset of ionization, or upon solvation

when they become slowly reacting chemical species. Recently, the DEA of related molecules (water,

bases, deoxyribose analog, and phosphate) in the condensed phase has been intensively investigated

by measuring electron-energy-dependent desorption yields of negative ions (H

−

, OH

−

, or R

−

) (Sieger

etal., 1998; Antic etal., 1999; Boudaiffa etal., 2000; Abdoul-Carime etal., 2001; Zheng etal.,

2005). The yields of desorbing anions below 15 eV supported the hypothesis that electron resonance

can

contribute to DNA damage (Huels etal., 2003; Pan etal., 2003).

One

factor that could contribute signicantly to the investigation of DNA damage is the effects

of water on the formation and reaction of radiation-induced species. It has been reported that water

molecules in DNA hydration shells have unique properties (Tao etal., 1989; Swarts etal., 1992).

They are less mobile than free water, more mobile than ice water molecules, and impermeable to

cations. The unique properties of waters of hydration in DNA could play a major role in the interac-

tion between slow electrons and DNA. In other words, DNA damage resulting from LEE irradiation

could be greatly affected by intrinsic water molecules close to DNA. In the studies of LEE-induced

DNA damage, plasmid DNA molecules were usually transferred into a UHV chamber for electron

bombardment and mass spectrometric analysis. Under these conditions, most of the free water mol-

ecules around DNA have been removed by evaporation. However, water molecules tightly bound to

or trapped in supercoiled plasmid DNA likely remained. Limited studies have been performed to

assess the role of water content and water-plasmid DNA interactions under UHV condition. This is

critical

to understand the mechanisms of LEE-induced strand breaks.

This

problem has now been approached from both a theoretical and an experimental perspective.

We have carried out elastic scattering calculations to describe potential diffraction effects involving

intrinsic waters within the major and minor grooves. We have also carried out experiments on LEE-

induced DNA SSBs and DSBs (Orlando etal., 2008). These approaches are explicitly described and

compared

in the remaining part of the chapter.

18.7.1 elaStic Scattering calculation

The elastic scattering calculation uses the multiple scattering formalism described previously and

does not require extensive computational resources. The A-tract DNA 5′-D(CGCGAATTCGCG)-3′

and B-DNA 5′-D(CCGGCGCCGG)-3′ targets and collision geometries used in our calculations are

shown in Figure 18.12. Note that C, G, A, and T represent cytosine, guanine, adenine, and thymine,

respectively. Because the inelastic mean free path is short for LEEs (we use 10.6Å for biological

molecules), the dimensions of these 10 or 12 base-pair DNA strands are large enough to sample

Low-Energy Electron-Stimulated Reactions in Nanoscale Water Films 493

all atomic scattering centers and guarantee convergence. We introduce a spherically symmetric

mufn-tin potential to represent each scatterer of the condensed DNA target. We also use an inner

potential of ∼6eV, a value derived from electron holography measurements on biological targets

(Stoyanova etal., 1968) and the maximum value of the optical potential used in previous R-matrix

calculations

on a model DNA target (Caron and Sanche, 2003, 2004, 2005).

order to compare our calculations with experimental results, the DNA strand is directed so

that its symmetry axis is normal to the electron k-vector. Phosphate-, sugar-, or water-absorber

sites are chosen, and charge densities at each atom that constitute functional groups are summed

together to give the total localized charge density around the respective groups. For water, we sum

the charge on the oxygen. We examined theoretically only molecules in the primary shell, speci-

cally those in the major and minor grooves and those coupled to the bases and sugar–phosphate

groups. For example, 8 waters within the minor groove and 14 waters within the major groove

were used in the calculation for the B-DNA 5′-D(CCGGCGCCGG)-3′ target. For the A-tract DNA

5′-D(CGCGAATTCGCG)-3′ target, 14 waters within the minor groove and 24 waters within the

major

groove were used.

The

directly irradiated component is obtained by xing the phase and decaying the amplitude

at the absorber. First-order scattered amplitudes are then calculated and phase summed with the non-

scattered amplitude. Complex phase shifts for each atomic scatterer are calculated with the

modied FEFF 8.2 code developed by Ankudinov etal. (1996). The elastically scattered electron

intensities (not shown) are calculated to be highest when examining the sugar groups, and the over-

all scattered intensity is greatest for electrons with incident energy less than 15eV. There is only a

very weak structure superimposed upon the sugar components between 22 and 30 eV. The scattered

electron intensity is similar for the phosphates; however, there is a very weak structure observable

between 8–12 and 22–30eV for the B-DNA 5′-D(CCGGCGCCGG)-3′ target and 12–20eV for the

A-tract DNA 5′-D(CGCGAATTCGCG)-3′ target. Although the overall scattered intensity is less

for structural waters, the constructive buildup of electron intensity due to elastic scattering is most

discernable for the water components. We therefore determined the contributions of the minor and

major groove waters separately, and these are shown in Figure 18.13. There is essentially no struc-

ture observed for what has been assigned as the minor groove waters, whereas a considerable structure

the charge density buildup is associated with the assigned major groove waters (solid line).

The

theoretical results can be summarized as follows: (1) There is considerable LEE intensity

present on the phosphates, sugars, and structural waters, especially for incident electron energies

below 15eV. (2) The resonance structure is primarily associated with the structural water within

B-DNA—5΄-D(CCGGCGCCGG)-3

΄ A-tract-DNA—5΄-D(CGCGAATTCGCG)-3΄

–

Major groove

Minor groove

Major groove

Figure 18.12 Geometric congurations for the DNA targets used in the scattering calculations. (From

Orlando,

T.M. et al., J. Chem. Phys., 128, 195102/1, 2008. With permission.)

494 Charged Particle and Photon Interactions with Matter

the major grooves. (3) The amplitude buildup occurs between 5–10, 12–18, and 22–28eV for the

B-DNA 5′-D (CCG GCGCCGG)-3′ target and between 7–11, 12–18, and 18–25eV for the A-tract

DNA

5′-D(CGCGAATT CGCG)-3′ target.

18.7.2 coMpariSon of theory and experiMental MeaSureMentS of SSbS and dSbS

Although the DNA sequences examined theoretically are only surrogates for more complex DNA

targets, it is useful to compare the results to recent experiments on LEE-induced SSBs and DSBs.

These experiments were carried out using the apparatus already described above. A comparison

of the calculated electron density buildup on the major groove waters with our measured SSB and

DSB probabilities as a function of incident electron energy is shown in Figure 18.13. Although the

samples studied are much more complicated than the targets used in the calculation, the comparison

serves to qualitatively illustrate the potential importance of diffraction and structural water in the

overall electron-induced break probability. The calculated charge density buildups on the major

groove waters of hydration for both DNA targets are shown on the topmost part of Figure 18.13. The

measured SSB (open diamonds) and DSB (open triangles) yields as a function of incident electron

energy are shown in the center part of Figure 18.13. Each point was taken on a separate DNA lm

~2 eV

Major groove

-D(CCGGCGCCGG)-3

Major groove

-D(CGCGAATTCGCG)-3

3.5

3.0

2.5

1.2

0.8

5 10 15

Incident electron energy(eV)

Intensity

(arb. units)

Intensity

(arb. units)

SSB yields

(arb. units)

DSB yields

(arb. units)

–

yields

(arb. units)

20 25 30

Figure 18.13 Upper plots show the resultant scattering intensities for major groove absorber sites for the

two DNA oligomers studied. SSB (diamonds) and DSB (triangles) yields (Chen etal., 2008). For comparison,

the

−

DEA spectrum is also shown (Simpson etal., 1997).

Low-Energy Electron-Stimulated Reactions in Nanoscale Water Films 495

and each point is the average of three or four separate measurements. Although the density of points

is low, there is a general correspondence of the SSB and DSB probabilities with the calculated

interference structure in the scattered electron intensity associated with the structural waters found

in the major groove. These results are also generally consistent with the rst experiments by Sanche

and colleagues on DNA plasmid thin lms (Boudaiffa etal., 2000) and more recent experiments

demonstrating maxima in the SSB and DSB yields at ∼9.5eV in linear and supercoiled DNA (Huels

etal.,

2003; Pan etal., 2003).

18.7.3 dna daMage

Figure 18.13 shows a resonant structure in the SSB and DSB probabilities, which is higher in energy

than the single-particle shape resonances discussed above. SSBs and DSBs in this energy range can

be associated with core-excited Feshbach resonances and dissociative excitation of phosphates, sug-

ars, and bases. As already discussed, the core-excited Feshbach resonances can decay via DEA. In

fact, recent studies on the DEA of DNA bases in the gas phase have revealed the formation of many

fragment anions, especially at energies between 5 and 15eV (Huels etal., 1998; Deni etal., 2004;

Ptasińska et al., 2005a,b). Similar experiments on condensed lms of cytosine and thymine also

revealed DEA resonances; however, the overall fragmentation appeared to be less due to interac-

tions with the surroundings (Huels etal., 1995). There is recent work on the DEA of gas-phase thy-

midine (thymine bound to 2-deoxyribose) that addresses coupling of the base resonances with the

attached sugar (Ptasińska etal., 2006), and work on condensed short GCAT oligomers (Zheng etal.,

2006) that examines base coupling as well as energy transfer to the sugar and phosphate groups.

There are not many studies on the DEA of ribose sugars comprising DNA (Ptasińska etal., 2004),

nor has there been much work on isolated phosphates or phosphoric acid (Konig etal., 2006; Pan

and Sanche, 2006). In the case of phosphoric acid and aligned self-assembled monolayers of DNA

lms (Pan and Sanche, 2005), the resonance between 4 and 12eV leading to O

−

and OH

−

desorption

was attributed to a core-excited resonance localized on the phosphate group. This was investigated

further in an attempt to experimentally address the role of water in DNA damage (Ptasińska and

Sanche, 2007). The data suggested that the water coupling was with the phosphate groups or bases

and

that compound states may be important in DNA damage.

18.7.4 the role of water and diffraction in dna daMage

Since water is likely involved in electron-induced damage of DNA, we recall the primary electronic

excitations that lead to the DEA of water. The positions of the DEA states in nanoscale water lms

are shown in Figure 18.13, while the H

−

) yield is shown in the lower part. The vertical lines

indicate potential correspondences with features in the SSB and DSB yields. Specically, the SSB

and DSB features between 5–10 and 10–17eV may potentially correlate with the

and

reso-

nances, respectively (Kimmel and Orlando, 1996). As noted in Figure 18.13, the damage features

near 10–17eV are ∼2eV higher in energy and broader than the condensed water

resonance.

They are also higher in energy than the resonance known to produce O

−

directly via DEA of the

phosphate group (Ptasińska and Sanche, 2006), but seem to be in reasonable agreement with the

position of the compound resonance reported from hydrated GCAT (Ptasińska and Sanche, 2007).

The observed energy shifts may be a consequence of stronger coupling relative to hydrogen bond-

ing in water and modied Franck–Condon factors associated with compound states involving water

and DNA constituents, such as sugar–phosphate groups and bases/counter ions. The reproducible

shifts to higher energy (relative to DEA resonances of water and phosphate) are not due to charging.

Calculations indicate the presence of resonances in phosphoric acid at 7.7 and 12.5eV (Ptasińska

and Sanche, 2006), and experiments indicate prominent DEA resonances peaking at 5 and 10eV

for most bases (Ptasińska and Sanche, 2006). Since these states are nearly degenerate with the DEA

resonances of water, they can easily mix, and, depending upon the lifetimes, the coupled states

496 Charged Particle and Photon Interactions with Matter

could lead to enhanced DEA or increased autodetachment (i.e., electron emission). Therefore, SSBs

can be partially attributed to the formation of H

−

, O

−

, OH

−

, H, O, or OH via the decay of the com-

pound (H

O:DNA) DEA resonances and dissociative excited states. The presence of these reactive

anions and radicals in the vicinity of the phosphate–sugar or within the major groove leads to facile

bond

breakage and is a well-known damage mechanism for RNA (Soukup and Breaker, 1999).

Calculations

indicate that facile C–O σ bond cleavage between the sugar and phosphate groups

can occur as a result of excitation of the low-lying phosphate σ

or π

orbitals. This excitation could

initially involve the π* level of the base, but could be transferred through the sugar to the phosphate.

If LEEs (i.e., those emitted during decay of resonances at and above 5eV) undergo inelastic scatter-

ing within their mean free paths, they can excite a phosphate in the near vicinity or on the opposite

strand. Since both the initial excitation and the secondary scattering can lead to strand breaks, this

could be an efcient path for DSBs. This process is consistent with a DSB threshold energy of ∼5eV

and indicates that DSBs may actually require major groove waters and a compound resonance that

simultaneously forms very reactive fragments and an LEE. Overall, our results indicate that the

diffraction amplitude associated with the major groove waters can enhance both the SSB and DSB

probabilities by providing a spatially varying charge density at the energy necessary for excitation

water–DNA compound resonances.

18.8 summary

In this chapter, we have discussed and summarized the role of LEEs in the nonthermal dissociation

and desorption of nanoscale water lms and water–DNA interfaces. Initially, we discussed the con-

volution integral of N(E)

σ(E) and the nature of the accessible electronic states in condensed-phase

water between 5 and 25eV. The importance of the temperature dependence of the a

-type bands in

ice was pointed out and the effect on hole lifetimes was shown. The role of core-excited Feshbach

resonances in water (i.e.,

, and

) and their decay via DEA have been shown to lead to the

formation and release of reactive negative ions (H

−

, D

−

) and neutral fragments. Complex multihole

states can result in the formation and release of protons at excitation energies above 22–25eV.

Inelastic channels that primarily involve excitations of the outer and inner valence levels, and the

formation of complicated, congurationally mixed excited electronic states were discussed. When

these complicated excitations localize at a surface or interface, dissociation and desorption can

occur. The excited states can be parent states for core-excited Feshbach resonances. These reso-

nances can decay to form neutral and anionic molecular fragments. In general, the damage prob-

ability function illustrates the general importance of LEEs and the need to unravel the details of all

the

energy-loss channels within this energy range.

Many

of the recent experimental techniques used to examine the energy-loss features, which

involved the production and release of anions, cations, and neutrals, were discussed. UHV systems

are typically used to study the chemical transformations initiated by the inelastic scattering of LEEs

with thin lms of molecular solids. Samples are usually prepared under UHV conditions and are

bombarded with LEEs. Typically, these systems are custom-designed and equipped with a cryo-

cooled rotatable sample holder to utilize multiple analysis techniques. The detection of charged

species is often accomplished with either a quadrupole or a ToF mass spectrometer. Ion yields can

be measured as a function of the incident electron energy, allowing threshold energies to be deter-

mined, and are very helpful with regard to assessing the states most important in the LEE-induced

dissociation and desorption events. The detection of neutral fragments from ice or other complex

targets can be accomplished by utilizing very sensitive laser detection techniques, for example, laser

REMPI/ToF spectrometry and SPI.

The chemistry initiated by the LEE inelastic energy-loss channels was examined by postirra-

diation TPD, and postirradiation gel electrophoresis has been shown to be a useful technique for

determining quantitatively SSB and DSB probabilities, thus allowing measurements of the SSB and

DSB probabilities as a function of electron-beam energy and dose. In addition, multiple scattering

Low-Energy Electron-Stimulated Reactions in Nanoscale Water Films 497

formalisms can be used to investigate diffraction effects in LEE-induced damage of water and

water–DNA interfaces. Specically, these calculations use the separable representation of a free-

space electron propagator and a curved-wave multiple scattering formalism. They reveal construc-

tive interference features arising from diffraction when examining the structural waters within the

major groove that are localized within an 8–10Å sphere around each base and the sugar–phosphate

backbone units. Since the diffraction intensity is localized, compound (H

O:DNA) states involving

core-excited Feshbach-type resonances may contribute to the LEE-induced SSB and DSB prob-

abilities. These results have illustrated the potential importance of diffraction and structural water

in the overall electron-induced break probability, and suggested that the water coupling was with

the phosphate groups or bases. SSB mechanisms have been shown to be partially attributed to the

formation of H

−

, O

−

, OH

−

, H, O, or OH via decay of the compound (H

O:DNA) resonance. The

presence of these reactive anions and radicals in the vicinity of the phosphate–sugar or within

the major groove facilitates bond breakage. Electron autodetachment has been shown as an impor-

tant decay channel that can lead to secondary scattering and excitation of lower-lying σ

or π

orbitals of the phosphate. Radiation damage involves the phased sum of multiple scattering events;

however, internal diffraction may enhance the DNA damage probability, especially for electron

energies below 15eV.

aCknowledgments

Much of the work discussed in this chapter was supported by the U.S. Department of Energy, Ofce

of Science, Contract DE-FG02-02ER15337. We thank Matt Sieger and T. C. Chiang for supplying

the

photoemission data presented in Figure 18.6.

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