surface characterization studies of carbon materials: ss-dna

Birck Nanotechnology Center

Surface character ization studies of carbon mater ials:

ss-DNA, SWCNT, graphene, HOPGDmitry Zemlyanov

Surface Science Application ScientistBirck Nanotechnology Center,

Purdue [email protected]

http://www.purdue.edu/dp/Nanotechnology/facilities/XPS.php

January 28, 2010 1Surface characterization studies of carbon materials, Birck Nanotechnology Center Purdue University



Outline

• XPS: technical/theoretical details

• A few graphene layers grown on the SiC surfaces

• Covalent Cross-linking Between polythymidine DNA and Single-walled Carbon Nanotubes (SWCNT) and HOPG

• Modification of HOPG surface with cold AC plasma


Goal

To demonstrate advantages (and disadvantages) of X-ray Photoelectron Spectroscopy (XPS) in application to carbon materials



Co-AuthorsLaura Biedermann, Gyan Prakash and Ronald Reifenberger

Department of Physics, Purdue University, West Lafayette, Indiana 47907Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907

Sara Harrison, Michael Bolen and Michael CapanoElectrical Engineering, Purdue University, West Lafayette, Indiana 47907

Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907

Vladimir DrachevElectrical Engineering, Purdue University, West Lafayette, Indiana 47907


Bridget D. Dolash and Donald E. BergstromDepartment of Medicinal Chemistry and Molecular Pharmacology, Purdue University,

West Lafayette, Indiana 47907Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907


Outline






Goal

To demonstrate advantages (and disadvantages) of X-ray Photoelectron Spectroscopy (XPS) in application to carbon materials



Co-AuthorsLaura Biedermann, Gyan Prakash and Ronald Reifenberger

Department of Physics, Purdue University, West Lafayette, Indiana 47907Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907

Sara Harrison, Michael Bolen and Michael CapanoElectrical Engineering, Purdue University, West Lafayette, Indiana 47907


Vladimir DrachevElectrical Engineering, Purdue University, West Lafayette, Indiana 47907


Bridget D. Dolash and Donald E. BergstromDepartment of Medicinal Chemistry and Molecular Pharmacology, Purdue University,

West Lafayette, Indiana 47907Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907


Outline






• The Kratos patented magnetic immersion lens

• A charge neutralization system

• Spherical mirror and concentric hemispherical analyzers combined with the newly developed delay-line detector (DLD)

• Fast load lock with cryo/heating options

• A catalytic cell to facilitate substrate treatment and preparation

• Monochromatic Al and Ag anodes

• External ports for user-supplied facilities

Kratos Ultra DLD Imaging XPS (Birck 1077)

Contact to Dmitry Zemlyanov

[email protected] http://www.purdue.edu/dp/Nanotechnology/facilities/XPS.php



• Surface sensitive techniqueXPS can provide element composition of topmost ~100Å (10nm) layer with sensitivity ~0.1 at.%.

• Quantitative analysisXPS can measure the element concentration with accuracy ~0.5 at.%.

• Qualitative analysisChemical state, hybridization, chemical environment etc. can be analyzed with XPS.


XPS: technical/theoretical details


The process of using photons (light) to remove electrons from a bulkmaterial is called photoemission.


"Universal curve" of electron inelastic mean free path l (IMFP) versus KE (eV)IMFP is average distance between inelastic collisions (Å)




Energy

1s

Vacuum level

Fermi edge

Ek

EB

hνφ

Spectrometer work function

Spectrometer ground

EKspec

φsp

Analyzer

Connected if a sample is conducting

specB K spE h Eν φ= − −1s2s 2p

1s 2s 2p

ω


ELEMENT and QUANTITIES ANALYSISEvery chemical element has an unique electronic structure, thereby the electrons areemitted with specific kinetic energies. The emission lines for almost all elements arewell tabulated.1The intensity of a photoemission peak is proportional to the element concentrationand a Relative Sensitivity Factor (RSF) of a photoemission peak. RSFs are known.

1 See, for instance, NIST X-ray Photoelectron Spectroscopy Database (the National Institute of Standards and Technology, http://srdata.nist.gov/xps/)



∑= N

jj

ii

AreaNormalised

AreaNormalisedatomicC %)(

Re ( )i

ii kin

Area of Photoemission PeakNormalised Arealative Sensitivity Factor Transmission Fanction E IMFP

=× ×

kB

initialfinalB

EnEnEE

ε−≈

−−= )()1((Koopmans’ Theorem)

INITIAL STATE EFFECT(Chemical Shift)If the energy of the atom’s initialstate changed, for example byformation of chemical bond withother atoms, the EB of theelectrons in that atom willchange.

kBE ε∆=∆

Fermi level+δ

Original level

−δ

EΒ(+δ)

EE

EΒ(−δ)



The C 1s spectrum obtained from the powder RGD peptide

C*-CType 1

C*-NType 2

C*-OType 3

O=C*-N(amide)

Type 4

O=C*-OH(carboxyl)

Type 5

C*-N3Type 6

RGD silane 20 13 7 18 2 1

295 290 285 280

* *

C*-C

C -N & C-O

Amide

OH-C*=O

C*N3Experimental dataCurve-fitting result

Inte

nsity

, arb

. uni

ts

Binding Energy, eV

Peptide constraint

Residual Hydrocarbons

C*Fx



• Surface sensitive technique• Quantitative analysis• Qualitative analysis




C.S. Fadley “Basic Concepts of X-ray Photoelectron Spectroscopy”From “Electron Spectroscopy, Theory, Techniques, and Applications” C.R. Brundle and A.D. Baker, Eds., Pergamon Press, 1978, Volume 11, Chapter 1

Photoelectron Peak IntensitiesPhotoelectron peak intensity Nk produced bysubshell k can be calculated within a three-step-like model (absorption of radiation, atomionization, transport of photoelectron tosurface and to a detector) by integrating thedifferential intensities dNk originating in thevarious volume elements of the specimen.

, , , ,

( ), , sec

k

InstrumentX ray flux Acceptance solid angle of

dN detectionat x y z electron analyser at x y z

efficiency

Number of atoms molecules Differential crossat dx dy dz tion for k subshell

− = × × ×

− × ×

Probability for no lossescape from speciment withneglegible direction change

− ×


Z

X

t

dz

dx

e-

A , 0 Ω0

I , x-ray0

α

θ

∆θ


0 0 ( , , , ) exp( )cos

ssubst kin

e kin

d zdN I D E x y z dxdydzd Eσρ

θ −

= × × Ω × × × Ω Λ

For a uniform-density specimen, is the path length to escape from the specimen into vacuum.

cosz θ

1. Semi-infinite specimen, atomically clean surface, peak k with Ekin≡Es

0 0 0 0( ) ( ) ( ) ( )co sssubst s s e s

dN I E A E D Edσθ ρ θ= × Ω × × × × × ΛΩ


[ ] ( )[ ] [ ] [ ] [ ]co s

Photoemission peak IntensitySpectrometer parameters Element density RSF EAL

θθ

=× × ×

RSF – Relative Sensitivity FactorEAL – Electron Attenuation Length

Z

X

t

dz

dx

e-

A , 0 Ω0

I , x-ray0

α

θ

∆θ


Z

X

t

dz

dx

e-

A , 0 Ω0

I , x-ray0

α

θ

∆θ


2. Specimen of thickness t atomically clean surface, peak k with Ekin≡Es:

0 0 0 0( ) ( ) ( ) ( )co s

1 exp( )cos

ssubst s s e s

e s

dN I E A E D Ed

tE

σθ ρ θ

θ

= × Ω × × × × × ΛΩ

−× − Λ

( ) 1 exp( ) ( )cos

subst

subst e s

N tN E

θθ θ∞

−= − Λ

[ ] ( )

[ ] [ ] [ ] [ ]co s 1 ex p( )cose s

Photoemission Peak Intensity

tSpectrometer parameters Element density RSF EALE

θ

θθ

=

−× × × × − Λ

[ ]( ) 1 exp[ ]( ) ( )cose s

Intensity for Thin Film tIntensity for Infinite Film E

θθ θ

−= − Λ


.

3. Semi-infinite substrate with uniform overlayer of thickness t


1 exp( ) ( )cos( )( ) ( ) exp

( )cos

overll overloverl e le loverl

substssubstsubst e s overl

e s

td E EN ddN tEd E

σρ θθσθ ρ

θ

−− × × Λ Λ Ω= ×

−× × Λ Ω Λ

Z

X

t

dz

dx

e-

A , 0 Ω0

I , x-ray0

α

θ

∆θ

4. Semi-infinite substrate with a non-attenuating overlayer at fractional monolayer coverage

( )cos( )( )

substke s

overl l

lsubst s

d Es N dCoverage ds N dd

σ θθσθ

× ΛΩ≡ =

×Ω

• Thickness of thin film or adsorbed layer



• Coverage of adsorbed species

[ ]( ) 1 exp[ ]( ) ( )cose s

Intensity for Thin Film tIntensity for Infinite Film E

θθ θ

−= − Λ

1 exp( ) ( )cos( )( ) ( ) exp

( )cos



e s

td E EN ddN tEd E

σρ θθσθ ρ

θ

−− × × Λ Λ Ω= ×

−× × Λ Ω Λ

( )cos( )( )

substke s

overl l

lsubst s


σ θθσθ

× ΛΩ≡ =

×Ω


Few graphene layers (FGL) grown on the SiCsur faces


Laura B. Biedermann, Gyan Prakash, Ronald G. ReifenbergerSTM/AFM characterization

Michael L. Bolen, Michael A. CapanoFGL growing on SiC

Vladimir DrachevRaman characterization

• Chemical shift (identification of chemical state of element)• Thickness of thin film


1 exp( ) ( )cos( )( ) ( ) exp

( )cos



e s

td E EN ddN tEd E

σρ θθσθ ρ

θ

−− × × Λ Λ Ω= ×

−× × Λ Ω Λ

FGL grown on the SiC surfaces



A characterization of the graphitic overlayer that forms on 4H-SiC substrates heatedfor ten minutes to temperatures T>1350oC under vacuum conditions has been performed. X-ray photoelectron spectroscopy of the C-face reveals the presence of graphitic carbon with athickness that increases with growth temperature.

( )0001

Chemical Shift

Fermi level+δ

Original level

−δ

EΒ(+δ)

EE

EΒ(−δ)

Thickness of FGL



NG (θ)NSiC (θ)

=

ρGΛeG (EC1s) 1− exp

−tΛe

G (EC1s)cosθ

ρSiC ΛeSiC (EC1s)exp

−tΛe

G (EC1s)cosθ

lnNG (θ)NSiC (θ)

ρSiC

ρG

ΛeSiC (EC1s)

ΛeG (EC1s)

+1

=

tΛe

G (EC1s)1

cosθ

lnNG (θ)

NSiC (θ)ρSiC

ρG

ΛeSiC (EC1s)

ΛeG (EC1s)

+1

tΛe

G (EC1s)A linear least-squares fit to a plot of 1/cos(θ) versus yielded the ratio . Since Λe

G(EC1s) = 3.10 nm, the thickness of the graphene layer was estimated to be 2.4 ± 0.2 nm.



Growth Temperature Average Graphene

Thickness

Equivalent

Monolayers

1475oC 1.8 0.1 nm ~5

1500oC 2.4 0.2 nm ~7

1550oC 3.7 0.2 nm ~11

Summary of thickness data for FLG growth on 4H SiC ( )0001



From A. Ferrari, Solid State communications 143 (2007) 47-57

Evolution of 2D peak versus number of Graphene layers



0

10

20

30

2 600 2 650 2 700 2 750 2 800

Raman Shift, 1/cm

Inte

nsity

, cnt

0

50

100

150

200

250

2 600 2 650 2 700 2 750 2 800 Raman Shift, 1/cm

Inte

nsity

, cnt 1 layer

5 layers

Raman (488 nm) and optical images from different positions for graphene prepared on SiC by heating at 1475C. XPS average thickness was ~5ML

(0001)



0

20

40

60

2 600 2 650 2 700 2 750 2 800 1

Raman Shift, 1/cm

Inte

nsity

, cnt 2 layers

Raman (488 nm) for graphene prepared on SiC by heating at 1550C. XPS average thickness was ~11ML

(0001)



R

Hei

ght (

nm)

X(nm)

0

5

10

15

20

100 200 300 400

300 350 400 450-120

-100

-80

-60

-40

-20

0

20

X(nm)

Hei

ght(n

m)

measuredfitted

R=129 nm

(a) (b)

(c)

(d)

2a

s Rβ=

βR

Hei

ght (

nm)

X(nm)

0

5

10

15

20

100 200 300 400

Hei

ght (

nm)

X(nm)

0

5

10

15

20

100 200 300 400

300 350 400 450-120

-100

-80

-60

-40

-20

0

20

X(nm)

Hei

ght(n

m)

measuredfitted

R=129 nm

300 350 400 450-120

-100

-80

-60

-40

-20

0

20

X(nm)

Hei

ght(n

m)

measuredfitted

R=129 nm

(a) (b)

(c)

(d)

2a

s Rβ=

β

In (a), an AFM image of primary ridges on FLG grown at 1550o C on 4H-SiC. In (b), the cross-sectional line profile along the line in (a). In (c), aschematic cross-section of a ridge of width 2a. In (d), the results of a leastsquares fit of the ridge profile to a circle. The radius of curvature of the ridgeis found to be 129 nm.



0

10

20

30

2 600 2 650 2 700 2 750 2 800

Raman Shift, 1/cm

Inte

nsity

, cnt

0

50

100

150

200

250

2 600 2 650 2 700 2 750 2 800 Raman Shift, 1/cm

Inte

nsity

, cnt 1 layer

5 layers


(0001)



R

Hei

ght (

nm)

X(nm)

0

5

10

15

20

100 200 300 400

300 350 400 450-120

-100

-80

-60

-40

-20

0

20

X(nm)

Hei

ght(n

m)

measuredfitted

R=129 nm

(a) (b)

(c)

(d)

2a

s Rβ=

βR

Hei

ght (

nm)

X(nm)

0

5

10

15

20

100 200 300 400

Hei

ght (

nm)

X(nm)

0

5

10

15

20

100 200 300 400

300 350 400 450-120

-100

-80

-60

-40

-20

0

20

X(nm)

Hei

ght(n

m)

measuredfitted

R=129 nm

300 350 400 450-120

-100

-80

-60

-40

-20

0

20

X(nm)

Hei

ght(n

m)

measuredfitted

R=129 nm

(a) (b)

(c)

(d)

2a

s Rβ=

β

In (a), an AFM image of primary ridges on FLG grown at 1550o C on 4H-SiC. In (b), the cross-sectional line profile along the line in (a). In (c), aschematic cross-section of a ridge of width 2a. In (d), the results of a leastsquares fit of the ridge profile to a circle. The radius of curvature of the ridgeis found to be 129 nm.



Conclusions• Identification of FGL on SiC was done• Average thickness of FGL on SiC was measured by XPS

for different preparation temperatures • XPS data were compared with Raman data. The apparent

discrepancy can be explained by resonance nature of Raman effect.



0

10

20

30

2 600 2 650 2 700 2 750 2 800

Raman Shift, 1/cm

Inte

nsity

, cnt

0

50

100

150

200

250

2 600 2 650 2 700 2 750 2 800 Raman Shift, 1/cm

Inte

nsity

, cnt 1 layer

5 layers


(0001)


Covalent Cross-linking Between ss-DNA and SWCNT


Bridget D. Dolash, Donald E. BergstromBiochemical/biological part of the study

Roya R. Lahiji, Laura B. Biedermann, Ronald Reifenberger AFM/STM characterization




• Chemical shift (identification of chemical state of element)• Element quantification



Binding model of a (10,0) carbon nanotube wrapped by a poly(T) sequence.The right-handed helical structure shown here is one of several binding structures found,including left-handed helices and linearly adsorbed structures. In all cases, the bases (red)orient to stack with the surface of the nanotube, and extend away from the sugar-phosphatebackbone (yellow).The single stranded (ss) DNA wraps to provide a tube within which the carbon nanotubecan reside, hence converting it into a water-soluble object.

Ming Zheng et al., Nature Materials 2 (2003) 338



OH

Radical recombination

SWCNT-conjugated T30

Sonication mediated pyrolysis

N

N OO

H3C T30

T30 alkylation& H2O addition

OH

N

HN

O

OCH3

OO

PO

O

OO (T29 - n)

(Tn)

OH

N

HN

O

OCH3

OO

PO

O

OO (T29 - n)

(Tn)

OH

H2O addition

OH

n = 0-29

H2O addition

Radical mediated SWCNT fragmentation

HO OHO O

OH

N

NO O

CH3T30

OH OH

O4-alkylation O2-alkylation

CNT

Proposed mechanism for sonication mediated covalent cross-linking of T30:SWCNTs. Sonication of SWCNTs inaqueous buffer creates radical cations on the nanotube sidewalls. The radicals recombine leaving cations to react with oxygenmolecules in water and on thymidine bases that are strong nucleophiles. This also suggestive of a mechanism of radicalmediated SWCNT fragmentation that is seen with increased sonication times.



FINAL STATE EFFECTS: SATELLITESShake-up and shake-off satellites arisewhen the photoelectron imparts energy toanother electron of the atom (typicallyvalence band electrons).

– Shake-up satellite– Shake-off satellite

Since CNT has aromatic structure, a shake-up satellite is one of importantcharacteristics of CNT. The shake-upsatellites are typical photoemission processin aromatic systems, which is two electronphenomenon leading to π→π* transitioninvolving the highest filled and lowestunfilled valence levels. Aromatic systemsshow shake-up peaks with intensities of upto 5-10%. C1s spectra for (a) as-received SWCNT, (b) SWCNT

sonicated in aqueous solution for 120 min, SWCNTssonicated in aqueous solution in the presence of Trolox.



OH


SWCNT-conjugated T30

Sonication mediated pyrolysis

N

N OO

H3C T30

T30 alkylation& H2O addition

OH

N

HN

O

OCH3

OO

PO

O

OO (T29 - n)

(Tn)

OH

N

HN

O

OCH3

OO

PO

O

OO (T29 - n)

(Tn)

OH

H2O addition

OH

n = 0-29

H2O addition

Radical mediated SWCNT fragmentation

HO OHO O

OH

N

NO O

CH3T30

OH OH

O4-alkylation O2-alkylation

CNT

Proposed mechanism for sonication mediated covalent cross-linking of T30:SWCNTs. Sonication of SWCNTs inaqueous buffer creates radical cations on the nanotube sidewalls. The radicals recombine leaving cations to react with oxygenmolecules in water and on thymidine bases that are strong nucleophiles. This also suggestive of a mechanism of radicalmediated SWCNT fragmentation that is seen with increased sonication times.



O

HO O

OHTrolox

HO

O

O O

OH

Trolox radical

HO

hydrogen abstraction

H2O or H2

O

O

O

OH

OH

OH

H HOH



and H

H H

HO

H2O HO HSonication

HOH

Elimination - H2O

Proposed mechanism for interaction of Trolox with sonication-assisted dispersion of SWCNTs.Sonication creates hydrogen (H·) and hydroxyl (OH·) radicals from water. These radicals can be interceptedby hydrogen abstraction from Tolox leaving Trolox as a radical. The reaction of H· and OH· with the SWCNTsidewalls can then cause recombination with other radicals on the sidewall, other H· and OH· in solution, orwith the Trolox radical.



FINAL STATE EFFECTS: SATELLITESShake-up and shake-off satellites arisewhen the photoelectron imparts energy toanother electron of the atom (typicallyvalence band electrons).

– Shake-up satellite– Shake-off satellite

Since CNT has aromatic structure, a shake-up satellite is one of importantcharacteristics of CNT. The shake-upsatellites are typical photoemission processin aromatic systems, which is two electronphenomenon leading to π→π* transitioninvolving the highest filled and lowestunfilled valence levels. Aromatic systemsshow shake-up peaks with intensities of upto 5-10%. C1s spectra for (a) as-received SWCNT, (b) SWCNT

sonicated in aqueous solution for 120 min, SWCNTssonicated in aqueous solution in the presence of Trolox.



O

HO O

OHTrolox

HO

O

O O

OH

Trolox radical

HO

hydrogen abstraction

H2O or H2

O

O

O

OH

OH

OH

H HOH



and H

H H

HO

H2O HO HSonication

HOH

Elimination - H2O

Proposed mechanism for interaction of Trolox with sonication-assisted dispersion of SWCNTs.Sonication creates hydrogen (H·) and hydroxyl (OH·) radicals from water. These radicals can be interceptedby hydrogen abstraction from Tolox leaving Trolox as a radical. The reaction of H· and OH· with the SWCNTsidewalls can then cause recombination with other radicals on the sidewall, other H· and OH· in solution, orwith the Trolox radical.



Model System: HOPGIn order to simplify the ss-DNA-SWCNT system and to study details of DNA interactionwith graphitic materials, we have performed the investigation of ss-DNA interaction withhighly-orientated pyrolytic graphite (HOPG), which can be considered as a modelsubstitution of SWCNTs. Since a SWCNT is a single warped sheet of graphene, weexpect that chemical properties of SWCNT and HOPG surface should be similar.However, the C-C bond in SWCNT is bended therefore SWCNT might be more reactiveat certain conditions.



C 1s spectra obtained from HOPG freshly peeled, sonicated in H2O,sonicated in aqua solutions of TG15 and racket DNA. The photoemissionangle was 0°. The left panel represents differential spectra between thespectra of sonicated in H2O, sonicated in aqua solutions of TG15 and racketDNA and the C 1s spectrum of HOPG.



Carbon at% (C 1s)

Nitrogen at% (N 1s)

Oxygen at% (O 1s)

Phosphor us at% (P 2p)

Silicon at % (Si 2p)

Nitrogen to Phosphor us ratio (3.5)

Oxygen toPhosphor us ratio (7)

HOPG + TG15 90.9±0.1 1.7±0.2 7.2±0.3 0.2±0.0 7.5±0.6 1 32.4±1.21

HOPG + racket DNA 90.3 2.4 6.5 0.2 0.6 10.02 22.32

SWCNT+ TG15 72.3±0.9 6.0±0.6 17.6±0.1 1.7±0.2 1.2±0.2 3.5±0.11 8.2±0.41

1 In TG15 the ideal nitrogen to phosphorus and oxygen to phosphorus ratios are 3.5 and 7.2 In racket DNA the ideal nitrogen to phosphorus and oxygen to phosphorus ratios are 3.65 and 6.61



Conclusions• Identification of ss-DNA/SWCNT hybrids can be done by

XPS• The possibility of Covalent Cross-linking Between ss-

DNA and SWCNT was demonstrated• Interaction between ss-DNA and HOPG was discussed


New state of carbon mater ials made with plasma modification


Sara E. Harrison, Ronald G. ReifenbergerSTM characterization



Modification of HOPG surface with cold AC plasma

• Chemical shift (identification of chemical state of element)• Coverage of adsorbed species

( )cos( )( )

substke s

overl l

lsubst s


σ θθσθ

× ΛΩ≡ =

×Ω



Graphene hydrogenation and Graphane formation was reported.*

* D. C. Elias et.al., SCIENCE 323 (2009) 610



Chemical Shift

Fermi level+δ

Original level

−δ

EΒ(+δ)

EE

EΒ(−δ)

The C 1s spectra obtained from freshly peeledHOPG, HOPG treated in H2/O2/Ar/He plasmaand then heated in UHV at 250°C.

Carbonyl

HOPG

New state of carbon ???

New state of carbon - ~0.25 MLCarbonyl - ~1 ML



1/k: 2.74 ±0.12 Å



Chemical Shift

Fermi level+δ

Original level

−δ

EΒ(+δ)

EE

EΒ(−δ)

The C 1s spectra obtained from freshly peeledHOPG, HOPG treated in H2/O2/Ar/He plasmaand then heated in UHV at 250°C.

Carbonyl

HOPG

New state of carbon ???



Conclusion• New state of carbon materials made with plasma

modification was observed



Acknowledgements

• Laura Biedermann,• Gyan Prakash,• Ronald Reifenberger• Sara Harrison• Michael Bolen• Bridget Dolash,• Donald Bergstrom• Michael Capano• Vladimir Drachev• Birck Administration/Staff/Members

• Timothy Sands

The work was supported by Kirk Endowment Exploratory Research Recharge Grant

surface characterization studies of carbon materials: ss-dna

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