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

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470 Charged Particle and Photon Interactions with Matter

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473

Low-Energy Electron-

Stimulated

Reactions in

Nanoscale

Water Films

andWater–DNA

Interfaces

Gregory A. Grieves

Georgia Institute of Technology

Atlanta,

Georgia

Jason L. McLain

Georgia Institute of Technology

Atlanta,

Georgia

Thomas M. Orlando

Georgia Institute of Technology

Atlanta,

Georgia

Contents

18.1 Introduction .......................................................................................................................... 474

18.2 Low-Energy

Electrons and Energy-Loss Channels.............................................................. 475

18.3

Overview

of Experimental Designs, Samples, and Strategies ............................................. 476

18.3.1

Sample

Preparation................................................................................................... 477

18.3.1.1

Water

Ice Preparation ................................................................................ 478

18.3.1.2

DNA Sample Preparation ..........................................................................479

18.3.2 Neutral

Detection Using Time-of-Flight Techniques............................................... 479

18.3.3

Postirradiation

Temperature-Programmed Desorption............................................480

18.3.4

Postirradiation

Gel Electrophoresis..........................................................................480

18.4

Useful Multiple Scattering Formalism ............................................................................. 481

18.5

Low-Energy Electron Interactions with Water Interfaces.................................................... 481

18.5.1 Electronic

Structure of Water Thin Films................................................................482

18.6

Stimulated

Dissociation and Desorption of Water Thin Films and Interfaces ....................484

18.6.1

LEE-Stimulated

Desorption of Anions ....................................................................484

18.6.2

LEE-Stimulated

Desorption of Cations....................................................................486

18.6.2.1

Mechanisms for LEE-Stimulated Cation Desorption................................487

18.6.3 LEE-Stimulated

Desorption of Neutral Fragments and Products............................489

18.6.4

Effect

of Porosity on LEE-Stimulated Production and Release of O

and H

......... 491

18.7 Low-Energy-Electron-Induced

Damage of DNA................................................................. 491

18.7.1

Elastic

Scattering Calculation...................................................................................492

18.7.2

Comparison

of Theory and Experimental Measurements of SSBs and DSBs.........494

18.7.3

DNA

Damage ...........................................................................................................495

18.7.4

The Role of Water and Diffraction in DNA Damage............................................... 495

474 Charged Particle and Photon Interactions with Matter

18.1 introduCtion

When high-energy ions, electrons, x-rays, and gamma rays strike material surfaces, physical and

chemical transformations are often induced. Although linear energy and momentum transfer plays

a signicant role in producing track structures and displacement-driven damage, we concentrate

on low-energy secondary electrons that are very important in stimulating nonthermal chemical

changes in materials. For heterogeneous surfaces, mixed interfaces, and soft targets (i.e., molecular

solids), conventional track structures may not describe the primary inelastic events and radiation-

driven chemistry occurring under highly nonequilibrium conditions. Ingeneral, it is important to

realize that radiation chemistry is essentially governed by the physics associated with the initial

ionization

channels and the subsequent inelastic scattering of low-energy electrons (LEEs).

Low-energy

(1–100eV) electron–molecule and electron–atom collisions are very important as

these (1) initiate and drive many of the processes leading to radiation damage of biological media

(Zamenhof etal., 1958; Ahnstrom, 1974; Van der Schans etal., 1989; Sognier etal., 1991; Ahmed,

1993; Beach etal., 1994; Banath etal., 1999; Chen and Chao, 2004), (2) are largely responsible for

the nonthermal chemical synthesis/destruction in naturally occurring plasmas, and (3) are key to the

formation of planetary atmospheres within and beyond our solar system (Johnson and Quickenden,

1997; Madey etal., 2002; Johnson etal., 2005, 2006). Electron collisions are also of obvious tech-

nological and environmental concern, since they are involved in modifying materials and surfaces

present in radioactive containment facilities, plasma processing of substrates and interfaces used in

the electronics device industry, and in electron-beam-based lithography. Despite the general impor-

tance of electron scattering, a complete understanding and accurate theoretical description only

exists for electron–atom collisions. Good approximations exist to describe electron scattering with

diatomic targets, and progress is being made in understanding and describing electron interactions

with polyatomic collision partners. The latter is complicated due to additional degrees of freedom

(vibration and rotation) and the subsequent dissociation events that occur as a result of the energy

exchanged during the collision. The reactive scattering of atomic and molecular fragments and the

production of electronically excited states lead to important chemical transformations.

The reactions of LEEs in dense matter often differ greatly from those in a low-pressure gas. In

the latter case, the electrons are normally free and the collision mean free path, l, is much longer

than the de Broglie wavelength, while in the former case, l is smaller than the de Broglie wavelength

and as the medium density increases, the electrons become constrained to move within bands of

a nite width. These differences introduce changes in the symmetries of electron–molecule scat-

tering resonances (Azria etal., 1987), polarization effects that can enhance resonance lifetimes

(Sanche, 1995a,b; Nagesha and Sanche, 1998; Lu and Sanche, 2004), suppression of autoioniz-

ing states (Kimmel etal., 1997), removal of high n Rydberg states (Rowntree etal., 1993), and

new channels that involve reactive scattering of the ion and neutral (radical) products (Sieger etal.,

1998). Methods that utilize state-of-the-art laser detection of the quantum-state distributions of neu-

tral fragments and measurements of threshold/energy-resolved desorption/damage events are new

techniques that can help unravel the overall interactions involved in the inelastic scattering of LEEs

at interfaces and in the condensed phase (Kimmel and Orlando, 1995, 1996; Alexandrov etal.,

2001). These new approaches are discussed and illustrated in this chapter with regard to the LEE

beam–induced damage of nanoscale lms of water adsorbed on metal or metal-oxide surfaces and

LEE interactions at hydrated biological interfaces such as DNA. The chapter also involves a discus-

sion of a theoretical formalism to describe multiple elastic scattering of LEEs within condensed-phase

targets or at interfaces. The theoretical approach is a modication of the scattering theory used to

describe photoelectron diffraction (Chen etal., 1998) and X-ray absorption ne structure (XAFS)

18.8 Summary .............................................................................................................................. 496

Acknowledgments..........................................................................................................................497

References......................................................................................................................................497

Low-Energy Electron-Stimulated Reactions in Nanoscale Water Films 475

(Rehr andAlbers, 1990). It is most applicable to structurally ordered targets and should be generally

useful

for describing electron interactions with many biomolecules.

18.2 low-energy eleCtrons and energy-loss Channels

The emission of LEEs produced during high-energy electron radiation of surfaces and interfaces

is very well known. The secondary-electron yields have been measured from many solid-phase

targets, including surfaces containing multilayers of ice. The LEE yields depend primarily upon

stopping power, ionization probability, and the material’s work function. The LEEs produced in

condensed water and released from nanoscale water interfaces or surfaces are shown approximately

in Figure 18.1 as N(E). As these electrons move through the media, they undergo elastic and

inelastic energy-loss scattering with cross sections that depend upon the electron kinetic energy.

This is shown in Figure 18.1 as σ(E) (circles) measured by Sanche and coworkers (Michaud etal.,

2003). Superimposed for comparison is the electronic scattering cross section of gas-phase water

(triangles)

(Ness and Robson, 1988).

shown in Figure 18.1, the electron energy distribution is weighted by LEEs, and, thus, the

convolution of N(E)

σ (E) yields a damage probability function that is weighted by the LEE distri-

bution and the excited states and resonances that occur at excitation energies <20eV. The inelastic

0 10 20

Electron energy (eV)

DEA Ionization

Ice damage

cross section σ(E)

Gas-phase

cross section

N(E)

σ(E) (arb. units)N(E)

σ(E)

Secondary-electron tail N(E)

30 40 50

Figure 18.1 Upper frame: Schematic representation of the secondary-electron yields, N(E), and the cross

section for excitation/energy loss as a function of incident electron energy, (E). Also shown is the total cross

section, σ(E), for elastic and inelastic scattering of LEEs with amorphous water ice target (Michaud etal.,

2003) and for gas-phase water (Ness and Robson, 1988). Lower frame: The convolution of N(E

)

(E) yields

a damage probability function that is weighted by the LEE distribution and the excited states and resonances

that occur at excitation energies <20eV.

476 Charged Particle and Photon Interactions with Matter

channels primarily involve excitations of the outer and inner valence levels and the formation of

complicated, congurationally mixed, excited electronic states. When these complicated excita-

tions localize at a surface or interface, dissociation and desorption can occur. As described in more

detail in Section 18.5, the excited states can be parent states to core-excited Feshbach resonances.

These resonances can decay to form neutral and anionic molecular fragments. In general, the dam-

age probability function illustrates the general importance of LEEs and the need to unravel the

details of all the energy-loss channels within this energy range.

A general schematic of some of the interactions that occur during electron scattering in this energy

range is presented in Figure 18.2a. As an incident electron collides with a molecule (AB), pathways

include (1) elastic scattering, (2) inelastic scattering, (3) dissociation intoneutrals, (4)dissociation into

a neutral and an excited-state neutral, (5) ionization of the parent molecule, (6) dissociation into a

neutral and cation, (7) dissociation into an excited-state neutral and cation, (8) dipolar dissociation,

and (9) electron attachment forming a transient negative ion (TNI). A summary of several important

decay pathways of TNIs is shown in Figure 18.2b. These include (1) detachment without transfer of

energy; (2) detachment leaving the neutral molecule in a rotationally and vibrationally excited state;

(3) detachment leaving the neutral molecule in an electronically, rotationally, and vibrationally excited

state that can predissociate; (4) dissociation producing a neutral and an anion; (5) dissociation produc-

ing an excited-state neutral and an anion; (6) energy transfer that stabilizes the TNI; and (7) ionization

through electron emission (Sanche, 1995a,b; Chutjian etal., 1996; Christophorou and Olthoff, 2002).

When a TNI decays to form a stable negative-ion fragment, the process is normally referred to as

dissociative electron attachment (DEA). DEA channels have been examined extensively for many

molecules in the gas phase (Christophorou and Olthoff, 2004) and, more recently, at interfaces (thin

lms) and in condensed molecular solids (Sanche, 2002).

18.3 overview oF experimental designs, samples, and strategies

The experimental systems used to study the chemical transformations brought about by the

inelastic scattering of LEEs with thin lms of molecular solids such as water require ultrahigh

vacuum (UHV) systems, such as the ones shown in Figures 18.3 and 18.4. These are custom-

designed UHV systems with a typical base pressure of 1 × 10

−10

Torr. The chamber in Figure 18.3

is equipped with a compressed He or liquid-nitrogen-cooled rotatable sample holder, a pulsed

LEE gun, a quadrupole mass spectrometer (QMS), and a time-of-ight (ToF) mass spectrometer.

Coverages ranging from submonolayer to several hundred monolayers are usually studied. The

surfaces are usually prepared under UHV conditions and are bombarded with LEEs. Though

continuous-beam measurements are common, pulsed beams coupled to ToF methods tend to be

more sensitive and reduce the probability of charge buildup on or within the lm. When using

(a)

AB*

–

+AB

–

A*+B

+2e

–

A+B

+2e

–

A+B*+ e

–

A+B + e

–

+2e

–

AB*+e

–

AB+e

–

(b)

AB*

–

AB+e

–

A+B

–

A*+B

–

or A

–

+B*

AB*

–

+2e

–

–ΔE

AB*

(r,v)

–

AB*

(n,r,v)

–

A+B + e

–

Figure 18.2 The decay channels that can result from LEE interactions with an arbitrary molecule AB.

(a) Shows direct decay channels, while (b) illustrates those that proceed viaTNI. (From Lane, C.D. and

Orlando, T.M., Applied Surface Science, Elsevier, 2007. With permission.)

Low-Energy Electron-Stimulated Reactions in Nanoscale Water Films 477

continuous-beam methods, the desorbing cations or anions are typically detected with a QMS.

The pulsed methods also allow the use of the ToF, and depending upon the signal intensity, data

can be taken under applied eld-free conditions so that the kinetic energy distributions of the

desorbing ions can be directly measured. Using a well-controlled electron beam, the yields

of the ions can also be measured as a function of the incident electron energy. This allows the

determination of threshold energies and is very helpful with regard to assessing the states most

important in the LEE-induced dissociation and desorption events.

18.3.1 SaMple preparation

Nanoscale lms of pure water or solutions containing biological molecules such as DNA are typi-

cally deposited on very clean and ordered single crystals of metals, metal oxides, or graphite sample

substrates. These substrates are usually sputtered and annealed, and then cleaned by ash heating to

above 1000K prior to lm deposition. In order to study the phase dependence of the damage prob-

ability of ice, a substrate that allows the nucleation and growth of crystalline ice (CI) should be used

(Lofgren etal., 2003; Ahlstrom etal., 2004). In this case, we use a Pt(111) crystal. In general, single

crystals are not necessary since many layers of amorphous ice are often studied. Amorphous ice is

chosen since the geometric structure factors and electronic properties are reminiscent of liquid water.

Tunable

pulsed

e-gun

FTIR

Doser

E-beam or laser desorption

cryohead

Rotatable

sample

surface

REMPI

VUV

TOF QMS

ToF

Field-free flight tube

Signal

Extraction pulse

Desorption pulse

Focused

REMPI laser

O Atom

(

Ion

REMPI

Sample surface

Laser pulse

Figure 18.3 Upper frame: Typical UHV system developed to understand the role of LEE interactions with

nanoscale water lms. Lower frame: Illustration of the ToF mass spectrometer setup used for resonance enhanced

multi photon ionization (REMPI) and vacuum ultra violet single photon ionization (VUV SPI) detection.

478 Charged Particle and Photon Interactions with Matter

18.3.1.1 water ice preparation

Water ice samples are deposited in the UHV chamber using background and directional dosing.

The water samples are normally puried by several freeze-pump-thaw cycles prior to dosing. Water

condensation at temperatures below 100K forms microporous amorphous ice (Mayer and Pletzer,

1986). We refer to this as porous amorphous solid water (PASW), which is characterized by a very

high surface area (∼640m

/g) and low density. Sintering the microporous ice between 100 and

120 K or deposition at these temperatures forms normal amorphous ice or simply amorphous solid

water (ASW). Films grown above 140K form cubic, Ic(001), which we refer to as simply crystalline

ice (CI). Amorphous ice annealed at 150K undergoes a phase transition to polycrystalline cubic ice

(Smith etal., 1996) and sublimates rapidly in vacuum above 165K. The samples discussed in this

chapter are PASW, ASW, and CI grown on either Pt(111), Cu(111), ZrO

, or graphite surfaces. Water

coverage is usually calibrated relative to the temperature-programmed desorption (TPD) of water

on Pt(111). A minimum of 40ML was found to be sufcient to decouple the surface of the ice from

the substrate, and all samples were >50ML to ensure the measurements were not affected by the

underlying

substrate.

The

porosity of the ice can also be controlled using directional dosing techniques (Stevenson

etal., 1999). Ices produced in this way are highly porous and can adsorb large amounts of materi-

als due to the large effective surface area. As described below, the pore surfaces can also provide

“buried” interfaces, surfaces, and free-space volumes for reactions within the condensed lms.

Since amorphous ice has an intrinsically higher defect density resulting from increased disorder, the

ionization efciency is expected to be higher and the resultant chemical transformations may have

higher

yields. This is described in more detail in Section 18.6.2.1.

Loading dock

Manipulator

Temperature

control

XYZ manipulator

E-gun

controller

QMS

Amplifier

Data

acquisition

Pulse

generator

Nd:YAG

laser

VUV THG cell

(xenon)

Turbo

pump

Mechanical

pump

Linear

stage

Loading chamber

Gate valve

E-gun

355 nm118 nm

LiF lens

Figure 18.4 Custom UHV system developed to understand the role of LEEs in the damage of biological

targets such as DNA. The system is unique since it contains an antechamber region for the deposition of bio-

molecules and a VUV photon source for neutral product detection using SPI. The system can also use laser

detection schemes such as REMPI. (From Chen, Y.F. et al., Int. J. Mass. Spectrom., 277, 314, 2008. With

permission.)

Low-Energy Electron-Stimulated Reactions in Nanoscale Water Films 479

18.3.1.2 dna sample preparation

The DNA lms were deposited in a differentially pumped antechamber that was initially backlled

with gas-phase nitrogen (Figure 18.4). These lms were deposited on a 5 × 5mm tantalum substrate

using a nebulizer spray or a calibrated syringe. The Ta substrate was cleaned using acetone and

methanol, and sonicated in nanopure water for 10 min prior to lm deposition. Aliquots of only a

few microliters of solution were deposited per sample. The solutions contained P14 double-stranded

circular DNA derived from pBluescript SK II (-). These P14 strands contained 6360 base pairs with

a molecular weight of ∼4.2 × 10

Da. Because some biomolecules chemically decompose upon

adsorption onto metal surfaces (Sanche, 2005), relatively thick lms were typically studied. The

thick DNA layers (>100 nm) also prevent effects of back-scattered electrons from the metal sub-

strate. Since the penetration depth/mean free path of 5–100eV electrons is in the range of 15–35 nm

in liquid water or amorphous ice (Meesungnoen etal., 2002), the thick lms ensured that the mea-

sured signals were produced from electron interaction with the DNA molecules within the con-

densed overlayer. The DNA sample was either held in a desiccator for 10 min and then moved into

the loading chamber to be vacuum-dried or deposited directly onto the sample held in a nitrogen

background. The solid DNA lms were then transferred into the analysis chamber for LEE irradia-

tion

experiments.

The

puried P14 plasmids were present as fully solvated species in a dilute (200mg of DNA/mL)

aqueous buffer solution. DNA lms with good alignment and unitary orientation can be formed

by the simple deposition and drying techniques described above, provided the concentration

allows initial formation of a nematic-like crystalline phase (Morii etal., 2004). The deposited

and vacuum-dried samples were characterized by a scanning electron microscope and were found

to be polycrystalline with some aggregation. Under the sample deposition conditions described

above, it is impossible to remove all of the water from DNA at room temperature. Thus, the

DNA samples studied contain trapped water mainly in the form of primary and secondary waters

of hydration.

18.3.2 neutral detection uSing tiMe-of-flight techniQueS

In order to detect the neutral fragments from ice or other complicated targets, we routinely uti-

lize a very sensitive laser detection technique known as resonance-enhanced multiphoton ioniza-

tion (REMPI)/time-of-ight (ToF) mass spectrometry (Kimmel and Orlando, 1995; Kimmel etal.,

1995; Orlando etal., 1999) or single-photon ionization (SPI) (Chen etal., 2008). For REMPI, the

laser wavelengths that we use vary from 198 to 250nm and are generated by frequency doubling

or tripling the outputs of Nd:YAG-pumped dye lasers or Nd:YAG-pumped master oscillator power

oscillator (MOPO) solid-state lasers. For SPI, we typically triple the 355nm (or other wavelengths)

in Xe (or other rare gas mixtures) using nonlinear third harmonic generation. The approach using

355nm beams produces coherent 118 nm light. The ToF we use is shown in more detail in Figure

18.3b. Since we use a pulsed electron beam, varying the delay time between the electron-beam pulse

and the focused laser beam allows us to map out a quantum-resolved velocity distribution of the

desorbing neutrals. Typically, all desorbing ions are removed by an initial pulsed extraction eld fol-

lowed by an ionization of the neutrals under constant eld conditions. The detection sensitivities of

this arrangement when using REMPI are ∼10

atoms/quantum state/cm

. The detection sensitivities

using SPI are similar, but, unlike REMPI, the detection is not state specic. Also, our SPI scheme

can only detect molecules having ionization potentials (IPs) below 10.5eV. Since all the atomic

and molecular products of electron-induced

dissociation have

IPs above 10.5eV, in

this

chapter,

illustrate the utility of neutral detection using REMPI through a discussion on the neutral H(

S) and

), and O(

D) and H

∑

( )

yields from ice. The two-photon-resonant, one-photon ionization

(2 + 1) REMPI schemes utilized to detect D(

S), O(

2,1,0

), and O(

) atomic fragments were the

S ← 1s

S at 205.1nm, 3p

2,1,0

← 2p

2,1,0

at 225.7–226.2nm, and 3p

←

at 203.8nm,