In Situ X-ray Structural Analysis of In Situ X-ray Structural - - PowerPoint PPT Presentation

In Situ X-ray Structural Analysis of In Situ X-ray Structural Analysis of Nanoscale Molecular Self-Assemblies on Nanoscale Molecular Self-Assemblies on Functionalized Surfaces Functionalized Surfaces

Michael Bedzyk, Joe Libera and Hua Jin Nanoscale Science & Engineering Center Northwestern University Evanston, IL USA

Funding: NSF & NIH

X-rays: APS, NSLS, ESRF, NU X-ray Lab

Outline:

• 1. Review experimental approach for X-ray analysis of

layer-by-layer molecular assembly on functionalized surfaces:

• 2. Examples:

a.) RNA adsorbed to amine terminated Self-Assembled Monolayer b.) Porphyrin-based nanoporous molecular films c.) Functionalized SAM attached to H-passivated Si(111) d.) In situ analysis of RNA adsorbed to charged surface

Experimental Approach

Thin Film Characterization X-ray Tools:

• X-ray Reflectivity (XRR)  e- density profile, thickness &

interface roughness

• X-ray Fluorescence (XRF)  Composition, Heavy atom coverages
• X-ray Standing Waves (XSW): Heavy atom density profile

Also study same samples with AFM and XPS

X-ray Vision

Pros: Weak interaction with matter High penetrating power

• -> In situ analysis
• --> buried structures

Non destructive Atomic-scale resolution Cons: Weak interaction with matter Need very intense X-ray source

• -> Synchrotron X-ray Source

Advanced Photon Source

Some X-ray Basics:

Wave Property -> Structural Info λ = 0.1 to 10 Å wavelength E-M radiation X-rays scatter coherently from electrons Particle Property -> Compositional Info Eγ= 1 to 100 keV energy Photo effect: Inner shell (K, L) ionization XRF energy spectrum: Decay of excited ion to ground state by characteristic XRF emission

Some X-ray Basics: (continued) Optics: Index of refraction: n < 1 for x-ray frequencies Snell’s Law: n1 cosθ1 = n2 cosθ2 --> Total External Reflection (TER) of X-rays θ2 = 0 --> TER --> θ1 = θC (critical angle) θC = (2δ)1/2, where n=1-δ, δ ~ Ne

• Eg. Si at λ = 1.54 Å, δ = 7.4 x 10-6,

θC = 3.9 mrad = 0.22° TER -> Evanescent Wave Effect

θ1 θ1

θ2

1 s l a b m

• d

e l

10

• 12

10

• 10

10

• 8

10

• 6

10

• 4

10

• 2

10 0.1 0.2 0.3 0.4 0.5 0.6 0.7

Reflectivity Reflectivity

q q (Å (Å

• 1
• 1

) SAM-2 SAM-2 SAM-1 SAM-1 H-Si H-Si

XRR data and fit

X-Ray Reflectivity Analysis Example: SAM / Si(111) q = 4π sinθ /λ , reciprocal space coord. Fresnel Theory: R~ 1 for q < qC = 0.031 Å-1 Si mirror TER

RF = (2q/qC)-4 for q>>qC . Fourier transform of a step function.

1 s l a b m

• d

e l

10

• 12

10

• 10

10

• 8

10

• 6

10

• 4

10

• 2

10 0.1 0.2 0.3 0.4 0.5 0.6 0.7

Reflectivity Reflectivity

q q (Å (Å

• 1
• 1

) SAM-2 SAM-2 SAM-1 SAM-1 H-Si H-Si

XRR data and fit

X-Ray Reflectivity Analysis Example: SAM / Si(111)

• At 1st dip, the 2 scattered plane-waves from the top and bottom

interfaces have a λ/2 path-length difference (or π phase difference).

• Modulation period -> film thickness Range: 1 to 100 nm
• Modulation Amplitude -> relative electron density of film
• Modulation damping -> roughness of interface(s) Range: < 2 nm

X-Ray Reflectivity Analysis Fundamentals

R(q) = R

F(q) | Φ(q) |

2

Φ(q) = 1 ρ∞ dρ dz ∫ e

iqzdz

R(q) RF(q) = (1− b) +be

−iqt 2e −q

2σ 2

ρ = e- density, b = ρF/ρSi, σ = σs = σI = (rms) roughness, t = film thickness 1 slab model Kinematical approach: Dynamical approach: Parratt’s recursive formulation

q = 4π sinθ /λ θ θ

X-ray Standing Wave Fundamentals SW Period:

D = 1 Q = λ 2sinθ

SW Intensity:

I = ET 2 = I0 +IR + 2 I0IR cos(v−2πQz)

SW Vector:

Q = KR − K0

Superposition of 2 Plane-Waves

ET = E0 e2πi(K0 • r −νt) + ER e2πi(KR • r −νt)

X-ray Standing Wave Generated by Reflection

XSW Period:

D= λ 2sinθ

Fringe Visibility: V =

Imax− Imin Imax+ Imin

XSW Generated by Strong Reflection: R=1 → V = 1

• 1. Dynamical Bragg Diffraction: D = d-spacing

a) Single crystal d = 1 to 10 Å surface structure b) Multilayer (LSM) d = 20 to 200 Å ultrathin organic film

• 2. Total External Reflection: D = 70 Å to 1 µm diffuse double-layer

Angle

Phase v

θ π

R

1 θ

d Crystal k kH XSW

XSW Generated by Dynamical Bragg Diffraction from Single Xtal

I = I0[1 + R + 2 R cos(v−2πH •r )] H •r =Δd d

XSW π phase shift → d/2 inward shift Low-angle side → Nodes on diffraction planes Hi-angle side → Antinodes on diffraction planes

Y(θ) = I(θ,r )ρ(r ) ∫ dr

Y(θ) = 1+R(θ)+ 2fH R(θ)cos v(θ)-2πPH

( )

[ ]

XSW Fluorescence Yield

fH : Coherent Fraction: Amplitude: 0 --> 1 PH : Coherent Position: Phase : 0 --> 1 Hth Fourier Comp. of the fluorescence-selected atom distribution ρ(r).

XSW analysis of strain in a buried heteroepitaxial film Can measure strain down to the level of 1 atomic layer. HRXRD needs > 10 layers

Si cap Si(001) substrate 1 ML Ge

ε ⊥ = −2c12 c

11

ε||

[001] [110] [110]

• Si(001)

Substrate Si(001) Cap Ge layer Ge Kα Si Kα

X-Ray Experimental Setup X-Ray Experimental Setup

5ID-C, DND-CAT Advanced Photon Source, Argonne National Lab

Sample Undulator

e-

LN -cooled Si(111) double crystal monochromator

2

Ion chambers Slits X-ray detector Horizontal focussing mirrors Synchrotron ring DuPont-Northwestern-Dow Collaborative Access Team

Solid-state fluorescence detector Fluorescence slits

Total External Reflection Total External Reflection X-ray Standing Waves X-ray Standing Waves

R ν z = 0 z = 2DC Normalized Incident Angle - θ / θC

ER E0 = ER E0 eiv = θ − θ 2 − 2δ − 2iβ

( )

1/ 2

θ + θ 2 − 2δ − 2iβ

( )

1/ 2

E − Field Intensity : I θ,z

( ) =1+ R + 2 R cos ν − 2πQz ( )

Q = 2sinθ λ Critical Period : DC = λ 2θC = π 2 r

eNe

= 80Å for Au 200Å for Si     

Fresnel Theory : n = 1 - δ - iβ n = 1

LB Multilayer Film / Au Mirror Wang, Bedzyk, Penner, Caffrey Nature (1991).

Zn Kα R x4

Zn Fluorescence Yield Angle θ (mrad)

Raw TER-XSW Data

ZnA 2ωTA Au 160 Å ZnA 8ωTA Au 500 Å ZnA 14ωTA Au 900 Å

Y(θ)= ∫ ρ(z) I(θ,z) dz

Multilayer X-ray Mirror -> Nanometer Variable Period XSW

• Si / Mo Layered -Synthetic Microstructure made by DC magnetron sputtering
• Large d-spacing (d = 22 nm) provides XSW periods of D = 5 - 20 nm
• Top Si surface w/ native oxide SiOx supports primer layer for self-assembly

Dxsw = 13.0 nm 8.9 6.4 5.1

12.4 keV @NSLS/x15a Nov. 2002

20.0 Si substrate Si/Mo multilayer x-ray mirror

+ NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 Hg Hg Hg Hg Hg Hg Hg _ _ _ _ _ _ _ _ _ _ _

Simple Test Case Evaluation of Variable Period XSW

Hg modeled as a 0.5 nm thick slab at the substrate surface

Si substrate Si/Mo multilayer x-ray mirror

+ NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 + NH3 Hg Hg Hg Hg Hg Hg Hg _ _ _ _ _ _ _ _ _ _ _

Hg-polyU 12.4 keV @NSLS/x15a Nov. 2002

12.4 keV @NSLS/x15a Nov. 2002

Hg modeled as slab on top of NH3

+ layer 0.5 1 1.5 2

• 2
• 1

1 2 3 4 0.02 0.04 0.06 0.08 0.1 0.12

Reflectivity Hg Lα Fluorescence Yield (CPS)

Q (1/Å)

t = 0.5 nm t = 10 nm

RNA is laying flat down on surface, not coiled

Mercurated Poly U

The RNA molecule → mercurated Poly-uridylic Acid Potassium salt

• Molecular weight: 1,400,000 - 1,700,000
• link number: 2382 - 2905

C9N2O8H9KPHgCl HgCl (Hg replaced H) (Hg replaced H) Unit weight: 579.28 Concentration: 47 µg/mL

• ne Hg atom per units
• H
• H

N N H H H H O CH2 O OH P O O O- K+ Cl Hg Cl Hg Cl Hg

X-ray Nanoscale Profiling of Layer-by-Layer Assembled Metal/Organo-Phosphonate Films

Libera, Gurney, Nguyen, Hupp, Liu, Conley, Bedzyk Langmuir (2004)

• Nanoporous molecular thin films based
• n Porphyrin single- and multi-layer

molecular membranes. Developed for biological sensor application.

• Self-assembly using the metal-

phosphonate scheme. Zr

• X-ray characterization of Films
• 1. (a) thickness and density - XRR
• 2. (b) z atom-profile of metal atom

layers - XSW

• 3. (c) areal packing density by

coverage measurements - XRF

P O O O Hf O O O Zr P P O O O

R 1 2 3 4 R = alkane chain = porphyrin = porphyrin square

(a) Zr (c) Hf Reflectivity Normalized Fluorescence Yield

q (Å-1)

(d) (b) Y

ρHf ρZr ρY

2 1 2

z0=0.8 nm σ=0.4 nm

CZr = 0.8 CY = 0.6

19 18 1

CHf = 1.0

z0=18.5 nm σ=0.8 nm

CHf = 0.0

1

XSW Analysis of 8 Layer Porphyrin Film

Zr Hf

0 nm 2.5 nm

Por.

Hf

Por.

Hf

Por.

Hf

Por.

Hf

Por.

Hf

Por.

Hf

Por.

Y

20.0 nm

Por.

Si/Mo multilayer substrate SiO2 surface

Si Mo

X-ray E-field Intensity Surface for sample A8

XSW Fluorescense Yield :Y(θ) = I θ,z

( )

t

∫ ρ z

( ) dz

ρ z

( ) = distributionof fluorescent species

i n c i d e n t a n g l e

• m

r a d distance above substrate - nm E-field Intensity resonant cavity E-field enhancement EFI > 4

Zr Hf A8 Hf Hf Hf Hf Hf Hf Zr Y A1 C2 Zr Zr Hf C4 Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr Zr C8 D8 Hf Si/Mo LSM plain Si substrate Y Hf Hf

N N N N P O O O Hf O O O Zr P P O O O N NH N HN P O O O Hf O O O Zr P P O O O

2.1 nm

= Porphyrin = Porphyrin Square porphyrin = primer

Nanoporous Molecular Film - Model Structure

Re CO OC OC Cl Re OC OC CO Cl Re CO CO Cl CO Re CO Cl CO CO N N N N N N N N N N N N PO3Et2 Et2O3P N N Zn 24 A

Porphyrin Square Macromolecule

Summary of 8 Layer Porphyrin Molecular Assembly

• Areal coverage of 1-1.6/nm2 close to theoretical maximum packing of 1.7 based
• n 5 OH nm-2 on SiO2 and 3 OH's reacted by each 3-APTMS molecule.
• Layer thickness of 19.0 nm close to theoretical maximum of 20.0 nm.
• Layer electron density of ~ 0.7 x Si >> 0.3 theoretical. Attributed to residual

DMSO from the porphyrin deposition step and Y not accounted for in the model

• Y does not selectively occupy the terminal phosphonate position as planned and

was found to be uniformly distributed throughout the film possibly bound to unsaturated phosphonate sites or complexed by DMSO

• Nominal position of Hf provides an excellent fit.

X-ray Studies of Self-Assembled Organic Monolayers Grown on Hydrogen-Terminated Si(111)

H:Si(111) after immersion in Br-ethyl undecylenate with UV CH2CH(CH2)8COOCH2CH2Br Thickness ~1.2 Å longer than UDAME UDAME Monolayer on H:Si(111) UDAME: CH2CH(CH2)8COOCH3 Thickness ~ 13-18 Å

Si(111)

O

O

Br

O

O

Br

Used in Liquid Phase Nano-Lithography Jin, Kinser, Bertin, Kramer, Libera, Hersam, Nguyen, Bedzyk, Langmuir (2004)

UDAME- & Br-UDAME-Si(111) XRR thin film characterization

Sample ρF (e-/Å3) t (Å) σS (Å) σI (Å) α (o) Coverage Θ (ML) H-Si(111)

• 4.0(2)
• SAM-1

0.35(2) 12.2(2) 2.3(2) 3.2(2) 38(4) 0.50(4) SAM-2 0.37(2) 13.2(2) 3.0(2) 3.6(2) 23(3) 0.53(4) Results from the XRR fits

1 s l a b m

• d

e l

10

• 12

10

• 10

10

• 8

10

• 6

10

• 4

10

• 2

10 0.1 0.2 0.3 0.4 0.5 0.6 0.7

Reflectivity Reflectivity

q q (Å (Å

• 1
• 1

) SAM-2 SAM-2 SAM-1 SAM-1 H-Si H-Si

XRR data and fit

SAM-1

UDAME

Br

Where is Br?

Br Br Br Br

? ? ?

SAM-2

Where is Br in SAM-2?

0.2 0.4 0.6 0.8 1

1.5 2 2.5 3 3.5

• 20
• 10

10 20 30 40 50

R

Br Br Fluorescence Fluorescence Yield Yield (CPS) (CPS)

θ-θ

B (µrad)

f

111 = 0.82(2)

P

111 = 0.83(2)

R Y

B r

Single Crystal Si(111) XSW of SAM-2

• Identical to monoatomic Br

adsorbed on Si(111)

• 0.5 ML Br covalently bonded to

surface Si atoms at T1 site at h = 2.17 Å, i.e., Br detached from UDAME

XRF  Total ΘBr = 0.6 ML

Counts (Arbitrary Units) 76 74 72 70 68 66 64 Binding Energy (eV)

XPS of Br3d in SAM-2

Si-Br C-Br

Si-Br bond Br detachment to Si surface

Br-Si bonding confirmed by XPS

Conclusion The 1/2 ML of Br-UDAME (SAM-2) can be partitioned as:

Br Br Br Br Br

≤ 0.1 ML ≥ 0.25 ML ≤ 0.15 ML

Br at the interface -> more stable and provides marker layer

Future Work

• Use UV activated UDAME as a primer layer for subsequent chemical

steps for DNA covalent attachment.

• These studies compliment the Scanned Probe DNA attachment scheme

Conclusions: X-ray analysis of layer-by-layer self-assembly compliments SPM, e-M

• in situ
• Buried structures
• Non destructive
• Atomic resolution
• XRF -> atomic composition
• XRR -> e- density profile
• XSW -> atomic density profiles with multi-length-scale: 0.1 to 100 nm
• It helps to have a synchrotron x-ray source

Acknowledgements: Funding: NSF & NIH Northwestern University NSEC Research Group: Joe Libera, Hua Jin, Kai Zhang Collaborators: NU: MSE: Reagan Kinser, Don Kramer, Mark Hersam , Hao Cheng, Monica Olvera, Chem: Rich Gurney, Paul Bertin, SonBinh Nguyen, Joe Hupp ANL: Chian Liu, Paul Fenter X-rays: APS, NSLS, ESRF, NU X-ray Lab