1. University of Trieste
PHD school in Nanotechnology
Development and applications of DFT
methodologies for the description of
spectroscopic observables in
condensed systems
Dr. Michele Romeo
michele.romeo@phd.units.it
www.nanotech.units.it
Supervisor - Prof. Giovanna Fronzoni
Theoretical Chemistry Group, DSCF – Chemical and Pharmaceutical
Sciences Department, Trieste

2. Motivation
We have tuned a computational strategy at DFT level to simulate the
angle-resolved NEXAFS spectra for molecules adsorbed on surfaces

3. Motivation
We have tuned a computational strategy at DFT level to simulate the
angle-resolved NEXAFS spectra for molecules adsorbed on surfaces
Study on interactions of molecules with surfaces is important for
technological applications such as molecular electronic devices, chemical
sensors, and nonlinear optics (main framework)

4. Motivation
We have tuned a computational strategy at DFT level to simulate the
angle-resolved NEXAFS spectra for molecules adsorbed on surfaces
Study on interactions of molecules with surfaces is important for
technological applications such as molecular electronic devices, chemical
sensors, and nonlinear optics (main framework)
When combined with a good theoretical stress in the modelling, angle-
resolved NEXAFS is a powerful tool to investigate the orientation of the
adsorbed molecule with respect to the surface

5. The fine structure corresponds to transitions of core
electrons towards unoccupied valence states
Electric dipole selection rules require p final states for K edge
1s
characterization of electronic structure
NEXAFS spectroscopy refers to the absorptionabsorption finefine
structurestructure around the absorption edgearound the absorption edge of a specific atomic
species in the sample
Introductory Overview

6. NEXAFS spectrum corresponds to transitions of core electrons towards
unoccupied states
NEXAFS (Near Edge X-ray Absorption Fine Structure)
Great asset of NEXAFS : polarization dependencepolarization dependence
when the molecule is oriented, the peak intensity
depends on the angle between the E vector of the
synchrotron beam and the transition moment vector
 largest if E vector points along
the direction of the MO
 vanishes if E is perpendicular
to the direction of the MO
Angle resolved NEXAFS : ideal technique for
probing the orientation of molecules adsorbed
on a surface
NEXAFS spectroscopy

7. NEXAFS spectrum corresponds to transitions of core electrons towards
unoccupied states
NEXAFS (Near Edge X-ray Absorption Fine Structure)
Great asset of NEXAFS : polarization dependencepolarization dependence
when the molecule is oriented, the peak intensity
depends on the angle between the E vector of the
synchrotron beam and the transition moment vector
 largest if E vector points along
the direction of the MO
 vanishes if E is perpendicular
to the direction of the MO
Angle resolved NEXAFS : ideal technique for
probing the orientation of molecules adsorbed
on a surface
NEXAFS spectroscopy

8. NEXAFS spectrum corresponds to transitions of core electrons towards
unoccupied states
NEXAFS (Near Edge X-ray Absorption Fine Structure)
Great asset of NEXAFS : polarization dependencepolarization dependence
when the molecule is oriented, the peak intensity
depends on the angle between the E vector of the
synchrotron beam and the transition moment vector
 largest if E vector points along
the direction of the MO
 vanishes if E is perpendicular
to the direction of the MO
Angle resolved NEXAFS : ideal technique for
probing the orientation of molecules adsorbed
on a surface
NEXAFS spectroscopy
In this view, NEXAFS Spectroscopy
allows to:
> characterize the adsorbing process
> estimate the entity of interaction at the adsorption
interface and with neighbouring molecules
> study the structural features of the adsorbed
molecule

9. PERIODIC
CALCULATIONS
CLUSTER MODEL
FOR SOLID SYSTEM
NEXAFS SIMULATION
Total and polarizedTotal and polarized spectra
• periodic slab methodology to simulate the surface
• surface recontruction
• optimization of the adsorbate systems
(G.Balducci - Quantum ESPRESSO calculations)
• molecular Orbital (MO) scheme (interpretation)
• explicit treatment of core orbitals
• Core excitation energies and oscillator strengths
• DFT–TS approximation (K-edge transitions)
(M.Romeo – finite level ADF calculations and post-
processing analysis)
from the periodic structure a suitable
finite cluster is manually cutted out
Very efficient and accurate to simulate NEXAFS due to
the localized nature of core excitation processes
Computational strategy

10. DFT – TP
K-edge spectra calculations
excitation energies
oscillator strengths for fixed in
space molecule
2
2 TP
i
TP
fiiffi nf  rε 
 : light polarization vector
TP
i
TP
f
TP
fi  
oscillator strengths for randomly
oriented molecules
2
3
2 TP
i
TP
f
iif
fi
n
f 

r
when the molecule is
oriented, the peak
intensity depends on
the angle between the
E vector of the
synchrotron beam and
the transition moment
vector
DFT-TP calculations
are provided from
subtracted half an
electron of the core
orbital and computing
the electronic structure
by DFT approach
(ADF computations)
Polarized Spectra
Polarized spectra environment was implemented
in the suite of codes during the 1st year of work

11. Approach guideline
Computational strategy
DFT periodic computation of a minimum-energy
adsorbate (Quantum ESPRESSO environment)
Cutting of a model-cluster from periodic geometry
Satisfaction of unsaturated bonds by using pseudo-
hydrogens (when needed)
It roughly needs of...
Check where the cut has to be refined (sometime...)
DFT – TP computations of energies and oscillator
strengths to simulate NEXAFS spectroscopy
(ADF environment)
1
2
3
4
5

12. System outline
Computational strategy
(ethene) - C2
H4
@ Si (100)
(pyridine) - C5
H5
N @ Si (100)
(molecular oxygen) - O2
@ Ag (110)
(1,4-diaminobenzene) - C6
H8
N2
@ Au (111)
Si (100) surfaceSi (100) surface
Metal surfaces – Ag , AuMetal surfaces – Ag , Au

13. System outline
Computational strategy
(ethene) - C2
H4
@ Si (100)
(pyridine) - C5
H5
N @ Si (100)
(molecular oxygen) - O2
@ Ag (110)
(1,4-diaminobenzene) - C6
H8
N2
@ Au (111)
Si (100) surfaceSi (100) surface
Metal surfaces – Ag , AuMetal surfaces – Ag , Au

14. Investigated systems
C2H4 on Si(100) – a study-case
Bridge geometry
On-top geometry
M.Romeo et al. - J. Phys. Chem.
C, 2012, 116 (35),
pp 18910–18919
*CC
*CSi
*CH2
*CC
*CH2*CSi
The main experimental
trend is well reproduced
On-top geometry is the
prevalent one

15. System outline
Computational strategy
(ethene) - C2
H4
@ Si (100)
(pyridine) - C5
H5
N @ Si (100)
Si (100) surfaceSi (100) surface

16. C5H5N on Si(100) : increasing complexity
Both N1s and C1s NEXAFS spectra were performed
Adsorbtion results in a large series of adducts - up to 14 geometries
Investigated systems
M.Romeo et al. - J. Phys. Chem. C – 2014, 118, 1049-1061
Dative geometry (Mode XII)
Di-sigma “cross-trench” geometry Di-sigma “on-dimer” geometry
Tetra-sigma bridge geometry (Mode VII)
(Mode IV)

17. Exp (200 K)
*(C=N)
*(C=N)
*(Si-N)
*(N-C)
These 4 configurations
recover completely the
main experimental features
All the calculated bands
have been assigned and
compared with the
experiments: good match
C5H5N on Si(100): N1s spectra calculations

18. XII
VII
On-dimer
IV
Cross-trench IV
* (C=C)
C ortho,
meta
* (C=C)
C para
*(C-H)
* (C=C)
* (C=C)
*(C-H)
*(Si-C)
* (C=C)
* (C=C)
Exp (300 K)
C5H5N on Si(100): C1s spectra calculations
*(N-C)
*(C=N)
*(C=N)

19. XII
VII
On-dimer
IV
Cross-trench IV
* (C=C)
C ortho,
meta
* (C=C)
C para
*(C-H)
* (C=C)
* (C=C)
*(C-H)
*(Si-C)
* (C=C)
* (C=C)
Exp (300 K)
C5H5N on Si(100): C1s spectra calculations
*(N-C)
*(C=N)
*(C=N)
Mode IX
N=C5
Mode IX gives rise only to a single *
peak associated to the transitions from
the ortho-carbon core electron (C5)
Mode IX gives rise only to a single *
peak associated to the transitions from
the ortho-carbon core electron (C5)
The mode IX can explain the presence
of the experimental lower energy peak
in the y polarization as well as the
higher intensity of the * (C-C)
transitions just above threshold.
The mode IX can explain the presence
of the experimental lower energy peak
in the y polarization as well as the
higher intensity of the * (C-C)
transitions just above threshold.
A further tetra-sigma geometryA further tetra-sigma geometry

20. XII
VII
On-dimer
IV
Cross-trench IV
* (C=C)
C ortho,
meta
* (C=C)
C para
*(C-H)
* (C=C)
* (C=C)
*(C-H)
*(Si-C)
* (C=C)
* (C=C)
Exp (300 K)
C5H5N on Si(100): C1s spectra calculations
*(N-C)
*(C=N)
*(C=N)
Mode IX
N=C5
Mode IX gives rise only to a single *
peak associated to the transitions from
the ortho-carbon core electron (C5)
Mode IX gives rise only to a single *
peak associated to the transitions from
the ortho-carbon core electron (C5)
The mode IX can explain the presence
of the experimental lower energy peak
in the y polarization as well as the
higher intensity of the * (C-C)
transitions just above threshold.
The mode IX can explain the presence
of the experimental lower energy peak
in the y polarization as well as the
higher intensity of the * (C-C)
transitions just above threshold.
The first band at N1s level
is not present at low
temperature (200 K)
It is well reproduced from
mode IX at RT (300 K)
The first band at N1s level
is not present at low
temperature (200 K)
It is well reproduced from
mode IX at RT (300 K)
A further tetra-sigma geometryA further tetra-sigma geometry

21. System outline
Computational strategy
(ethene) - C2
H4
@ Si (100)
(pyridine) - C5
H5
N @ Si (100)
(molecular oxygen) - O2
@ Ag (110)
Si (100) surfaceSi (100) surface
Metal surfaces – Ag , AuMetal surfaces – Ag , Au

22. Investigated systems – O2
on Ag(110)
Silver surface has
important implications in
the oxygen dissociation,
in the oxidation of
surface and in catalytic
processes
O2 on Ag(110) : simple system
- only one adsorption geometry -
Experimental O1s NEXAFS polarized
spectra not completely assigned
Molecules adsorbed on transition metal surfaces – the Ag(110) case
O.Baseggio,M.Romeo,
G.Fronzoni, M.Stener,
Surf. Sci., v. 616 (2013),p.178-185

23. System outline
Computational strategy
(ethene) - C2
H4
@ Si (100)
(pyridine) - C5
H5
N @ Si (100)
(molecular oxygen) - O2
@ Ag (110)
(1,4-diaminobenzene) - C6
H8
N2
@ Au (111)
Si (100) surfaceSi (100) surface
Metal surfaces – Ag , AuMetal surfaces – Ag , Au

24. Investigated systems - PDB on Au(111)
PDB on Au(111) N1s NEXAFS
experiments
Adsorption geometries of PDB
on Au(111) are not clear
Experimentalists use NEXAFS
to discriminate among different
PDB adsorption responses
depending on coverage level
Theoretical calculations aim to
provide models suitable for
reproducing the main
experimental NEXAFS features

25. Computational Spectra
Free PDB and in thick crystalline film - N1s NEXAFS
H-bond
The crystalline form of PDB
results in the “lone pair”
energy shift due to the H-bond

26. Coupled C6H8N2@Au(111) models
Mono
Facing
Investigated systems

27. Computational Spectra
Coupled C6H8N2@Au(111) - N1s NEXAFS
N1
N2
N1L N1R
N2L N2R
H-bond
H-bond seems to play an
important role in stabilizing tilted
configurations
Good experimental match

28. Computational Spectra
Coupled C6H8N2@Au(111) - N1s NEXAFS
N1
N2
N1L N1R
N2L N2R
H-bond
H-bond seems to play an
important role in stabilizing tilted
configurations
Good experimental match
Total charge density for relaxed
"tilted-facing" configuration
3D plot of the N2R-A667 unoccupied
MO of the tiltedfacing cluster from the
DFT-TP relaxed calculation on N2R site

29. Computational Spectra
Coupled C6H8N2@Au(111) - N1s NEXAFS
N1
N2
N1L N1R
N2L N2R
H-bond
H-bond seems to play an
important role in stabilizing tilted
configurations
Good experimental match
 low photon energy range :
Au−N interaction (N1L and N1R)
that involve the lone pair electrons
of the amino group in contact with
the substrate.
 resonance at 401 eV :
fingerprint of the intermolecular
coupling (N2L and N2R) in the
tilted phase corresponding to
the σ*(NH) transition

30. Flat C6H8N2@Au(111) models
Hollow
On-top
Investigated systems

31. 396 398 400 402 404 406
arbitraryunits
Computational Spectra
Flat C6H8N2@Au(111) - N1s NEXAFS
on-top
hollow
Ryd
All the spectral features were assigned
On-top- and hollow-flat geometries do not
differ substantially
This results from a small shift in the position
on Au(111)
Experimental matching is not satisfying
N
N
Arbitraryunits

32. Conclusions
In the end, we have:

33. - tuned a satisfactory reproduction of the experimental spectra
from a mixed periodic/cluster approach (DFT – TS level)
In the end, we have:
Conclusions

34. - tuned a satisfactory reproduction of the experimental spectra
from a mixed periodic/cluster approach (DFT – TS level)
- highlighted the importance of the angle resolved spectra to get
informations on adsorption geometry and to assign the spectral
features
In the end, we have:
Conclusions

35. - tuned a satisfactory reproduction of the experimental spectra
from a mixed periodic/cluster approach (DFT – TS level)
- highlighted the importance of the angle resolved spectra to get
informations on adsorption geometry and to assign the spectral
features
- validated the methodology by analyzing the simple systems
C2H4 on Si(100) and O2 on Ag (110)
In the end, we have:
Conclusions

36. - tuned a satisfactory reproduction of the experimental spectra
from a mixed periodic/cluster approach (DFT – TS level)
- highlighted the importance of the angle resolved spectra to get
informations on adsorption geometry and to assign the spectral
features
- validated the methodology by analyzing the simple systems
C2H4 on Si(100) and O2 on Ag (110)
- applied the methodology to more complex systems:
In the end, we have:
Conclusions

37. - tuned a satisfactory reproduction of the experimental spectra
from a mixed periodic/cluster approach (DFT – TS level)
- highlighted the importance of the angle resolved spectra to get
informations on adsorption geometry and to assign the spectral
features
- validated the methodology by analyzing the simple systems
C2H4 on Si(100) and O2 on Ag (110)
- applied the methodology to more complex systems:
C5H5N on Si(100) surface
In the end, we have:
Conclusions

38. - tuned a satisfactory reproduction of the experimental spectra
from a mixed periodic/cluster approach (DFT – TS level)
- highlighted the importance of the angle resolved spectra to get
informations on adsorption geometry and to assign the spectral
features
- validated the methodology by analyzing the simple systems
C2H4 on Si(100) and O2 on Ag (110)
- applied the methodology to more complex systems:
C5H5N on Si(100) surface
1,4-Diaminobenzene on Au(111) surface
Balducci G.,Romeo M.,Stener M.,Fronzoni G.,Cvetko D.,Cossaro A.,Dell’Angela M., Kladnik G.,
Venkataraman L.,Morgante A. - J. Phys. Chem. C - December, 2014 - web version
In the end, we have:
Conclusions

39. Capital publications
G. Fronzoni, G. Balducci, R. De Francesco, M. Romeo, and M. Stener - Density Functional Theory Simulation of NEXAFS
Spectra of Molecules Adsorbed on Surfaces: C2H4 on Si(100) Case Study - J. Phys. Chem. C 2012, 116, 18910−18919
M. Romeo, G. Balducci, M. Stener, and G. Fronzoni - N1s and C1s Near-Edge X‑ray Absorption Fine Structure Spectra of
Model Systems for Pyridine on Si(100): A DFT Simulation - J. Phys. Chem. C 2014, 118, 1049−1061
Oscar Baseggio, Michele Romeo, Giovanna Fronzoni, Mauro Stener - The near-edge X-ray-absorption fine-structure of O2
chemisorbed on Ag(110) surface studied by density functional theory - Surface Science 616 (2013), 178–185
Gabriele Balducci, Michele Romeo, Mauro Stener, Giovanna Fronzoni, Dean Cvetko, Albano Cossaro, Martina Dell’Angela,
Gregor Kladnik, Latha Venkataraman, Alberto Morgante - Computational Study of Amino Mediated Molecular Interaction
Evidenced in N 1s NEXAFS: 1,4-Diaminobenzene on Au (111) - J. Phys. Chem. C - December, 2014 - web version

40. Software environment
Cluster design:
- ClusterSAT® *, a self-developed utility to cut and make solid state clusters
properly saturated; it works jointly to VMD®, a visual molecular dynamics tool
web: www.micheleromeo.com
Quantum computations:
- QUANTUM Espresso® for periodic computations, ADF® for DFT computations of
electronic structures and Time Dependent-DFT computations of NEXAFS spectra
web: http://http://www.quantum-espresso.org , http://www.scm.com
Data rendering:
- TRANSM, to compute NEXAFS excitation energies starting from computed
ADF transition moments from single point ADF elaborations
- ADF External® *, a self-developed ADF utility to compute
angle-resolved spectra starting from TDDFT-ADF or TRANSM outputs
web: www.micheleromeo.com
* - M.Romeo - ADF External Utility®, a Fortran implementation to compute angle-resolved
spectra from ADF®, 2011 - source: www.micheleromeo.com
Computational tools

41. Group members
Prof. G. Fronzoni
Prof. M. Stener
Dott. G. Balducci
Dott. O. Baseggio
Dott. R. De Francesco
Dott. M. Romeo
Thank you for your listening
Acknowledgements