Finnish CoE of Computational Molecular Science
Laskennallisen molekyylitutkimuksen huippuyksikkö
Spetsenheten för datorstödd molekylforskning
Kanslerin vierailu
4.3.2008
Faculty of Science.
Government labs:
- Meteorology
- Marine Research
Including students,
about 9000 people.
Entire UoH: 38000
students.
8 national CoE:s, including ’Finnish
Centre of Excellence of
Computational Molecular Science’
(2006-2011). (CMS)
CMS groups: Pyykkö-Sundholm,
Halonen, Räsänen, Vaara, Nordlund.
About 60 people. Nordic ’umbrella’ of CoE:s.
The Kumpula Campus, University of Helsinki, Finland
Some key people employed on CMS monies
Group Pyykkö: Coordinator Dage Sundholm.
Graduate students Patryk Zaleski-Ejgierd and Cong Wang Group Halonen: Post-docs Delia Fernandez, Qinghua Ren.
Graduate students Tommi Lantta, Matti Rissanen, Teemu Salmi,
Markku Vainio. Group Nordlund: Senior scientists Mikko Hakala, Arkady
Krasheninnikov, Flyura Djurabekova. Graduate students
Carolina Björkas, Antti Tolvanen, Katharina Vörtler, Tommi Järvi Group Räsänen: Senior scientist Leonid Khriachtchev. Post-
docs Sebastian Hasenstab-Riedel (Lynen/Humboldt fellow), Antti
Lignell. Graduate students Karoliina Honkala, Kseniya
Marushkevich. Group Vaara: Post-doc Michal Straka, graduate students Matti
Hanni, Teemu O. Pennanen, Teemu S. Pennanen.
Running time 2006-2011.
Chairman 2006-08 Pekka Pyykkö, chairman 2009-11 Lauri Halonen.
Vice-chairman Kai Nordlund. Coordinator Dage Sundholm.
Budget 2007: Academy of Finland 392 060 euro.
University of Helsinki 167 000.
Output 2006: 60 papers, 9 FM, 3 FT.
2007: 77 papers, 8 FM, 4 FT.
Some numerical data
Some long-term activities of P. Pyykkö
Relativistic effects since 1970, first on hyperfine effects, then
on chemical bonding. Later QED: The earlier work was ’101%
right’. The chemical differences between Rows 5/6 (Ag/Au)
predominantly relativistic. Chem. Rev. 1988.
’Metallophilic attraction’ since 1991. Strong dispersion effect,
’strongest vdW in the World’. Au(I)...Au(I). CR 1997.
Prediction of new molecules, 1977- now.
Simple understanding of chemical bonding.
Predicted in 2008 [1]. Stabilized by relativity, 72-electron aromaticity
(s+p+d+f+g+h). Chiral, icosahedral, group I. Energetically more stable than Au20, for instance.
Not yet prepared.
[1] A. J. Karttunen, M. Linnolahti, T.A. Pakkanen, P. Pyykkö,
Chem. Comm. 465 (2008)
Au72
D. Sundholm: New explanation for how retinal works
R. Send, D. Sundholm, J. Phys. Chem. A, 111, 8766 (2007).
IR
The Räsänen group: The first trans-cis formic acid dimer in solid argon
K. Marushkevich et al., J. Am. Chem. Soc., 128, 12060 (2006); material courtesy of L. Khriachtchev
trans-trans
IRtunneling
trans-cis
0 10 20 30 400.0
0.5
1.0
Monomer
Dimer 1
Ar / 8 K
Con
cent
ratio
nTime (min)
cis-FA in dimer #1 decays more slowly than cis-FA monomer!
0 30 60 90 120 150 180
0
1000
2000
3000
4000
5000
Ene
rgy
(cm
-1)
Torsional angle (deg.)
Monomer Dimer #1
Theory
Different barrier heights (2676
cm1 for monomer and 3432 cm1
for dimer) explain the higher
stability of the dimer.
0.03 0.06 0.09 0.12-8
-6
-4
Monomer
Dimer 1
ln(tu
nnelin
g r
ate
/ s-1
)
1/T (1/K)
Ar matrix
The stability of the trans-cis dimer
does not change with
temperature, in contrast to the cis
monomer. Why?
K. Marushkevich et al., J. Am. Chem. Soc., 128, 12060 (2006); material courtesy of L. Khriachtchev
The Räsänen group: The first trans-cis formic acid dimer
Experiments with free-standing Si/SiO2
superlattice annealed at 1100 oC
HTA1: High-temperature laser annealing increases Raman intensity by 100, shifts the band up to 525 cm-1
LTA: Low-temperature laser annealing
shifts the band down to 516 cm-1
HTA2: The band can be shifted back to
525 cm-1 by high-temperature laser
annealing, and so on.
The Räsänen group: Laser-controlled stress of Si nanocrystals in silica
480 500 520 540
c-Si
Ram
an in
tens
ity
Raman shift (cm-1)
Khriachtchev et al. APL 88, 013102 (2006)
HTA2
LTA
HTA1
as-prepared x50
3 GPa
Laser-controlled stress of Si nanocrystals in silica
First, Si-nc is unstressed (low Raman shift)
HTA melts Si-nc and the silica surrounding relaxes (no
stress at high temperature)
Temperature decreases, Si particle crystallizes and the
volume increases (by 10%)
Si particle with volume VS inserted into a sphere with
volume VM in a SiO2 matrix
K - modulus of compression, G - shear modulus
No stress
No stress
Stress
/ 3 / 4S M
S M
V VP
V K V G
3 GPa
Halonen group: Water dimer problem
Energy balance and greenhouse
effects in Earth’s atmosphere:
Has the contribution of the water dimer
been neglected?
Why has the water dimer not been
observed in the atmosphere?
Our results indicate that the energy is
absorbed in such a wide wavelength
range that the observation of water
dimer becomes difficult.
Simple model
Realistic
model
Computed energy absorption in a wavelength region where
unsuccessful experimental attempts have been made
Diagnosis
Cavity ringdown spectroscopy
Breath transferred to cell
PatientDiseases
Helicobacter pylori
Laser Breath Analysis
NPT-Monte Carlo; 1610 particles interacting with the Gay-Berne potential
GB-Xe potential and Xe NMR response parametrised through B3LYP calculations of prototype atomistic mesogens
J. Lintuvuori, M. Straka and J. Vaara, Phys. Rev. E 75, 031707 (2007)
Vaara group: Xe dissolved in Model Liquid Crystal
Vaara group: 129Xe chemical shift inside cavity, Xe@C60
Systematic inclusion of different physical effects: relativity (BPPT), electron correlation (DFT), T-dependent dynamics with rigid (diatomic 3D) and flexible cage (BOMD) and solvent (PCM)
Correlation description (DFT functional) of NR shift most important Relativity is about +10% => necessary to include! Dynamical effect mainly due to thermal motion of the cage: ~ +10% (BOMD) Still +26 ppm is missing:
partly due to missing explicit, static or dynamic, solvent effects Most likely reason, however, is the imperfect DFT functional
M. Straka, P. Lantto, and J. Vaara, J. Phys. Chem. A, in press.
-50
0
50
100
150
200
250
300
NR FC-I SD-I p/mv p/Dar p-KE/OZ
BPPT Total
d (X
e)/p
pm
BLYPB3LYPBHandHLYP
Xe@C60
0
50
100
150
200
250
300
BLYP B3LYP BHandHLYP EXP
d (X
e)/
pp
m
BOMD
BPPT
NR
Vaara group: Effect of local environment on NMR parameters in liquid water
T. S. Pennanen, P. Lantto, A. J. Sillanpää, J. Vaara, J. Phys. Chem. A, 111, 182 (2007).
A detailed account of how local environment affects NMR parameters in liquid water the effect of broken/extra hydrogen bonds
B3LYP NMR parameter calculations for central molecules in clusters from liquid water NVE ensemble CPMD simulation
NMR parameters: shielding and NQCC for H/D and oxygen nuclei
NMR parameter averages for molecules in different local environments (different number of hydrogen bonds)
Expanded theory for nuclear magnetic resonance in open-shell systems
(T.O. Pennanen & J. Vaara, accepted for publication in Phys. Rev. Lett.)
Implementation of theory using molecular properties available in current quantum chemical programs.
Calculations for metal-containing systems, e.g. boranes with possible nanomachine applications.
(joint with D. Hnyk from Czech Academy of
Sciences)
Theory of paramagnetic NMR
Nordlund group (Physics): fusion reactor materials
Nuclear fusion could provide
nearly limitless energy to
humanity – known fuel reserves
exist for millions of years The biggest remaining hurdle
to develop a reliably energy-
producing fusion power plant
is the choice of materials for
the reactor Key problem: atoms and molecules which escape the 100
million degrees hot fusion plasma erode the reactor walls But how this happens is not well understood!
We are studying this as partners in the EU fusion organization
ITER fusion reactor, under construction
Nordlund group (Physics): fusion reactor materials
The worst erosion feature is that
any carbon-based material erodes This was known for ~30 years But the reason was not known
We have shown it is a
previously unknown
type of physico-chemical
reaction occuring when
the hot fusion H atoms
interact with any C-based
material Understanding now guides
ITER materials selection
CHx and C2Hy
erosion
C-based reactor wall
Incoming H atom
Outgoing CH3 molecule[Nordlund et al, Pure and Applied Chemistry (2006)]
Nordlund group (Physics): nanoscience
Controlled manipulation of materials at the nanoscale
holds great promise for the development of entirely new
kinds of functionality in materials Our atomistic simulations can treat entire nanoobjects
fully on an atomic level!Atomistic model of the Si nanocrystalmade in the Räsänen group showedimportance of interface defects
[Djurabekova and Nordlund, Physical Review B 2008]
Simulations of carbon nanotube-based materials has shown that their properties can be improved on with ion irradiation!
[Krasheninnikov and Banhart, Nature Materials (2007)]
Nordlund group (Physics): structures of ice and water