Finnish CoE of Computational Molecular Science Laskennallisen molekyylitutkimuksen huippuyksikkö Spetsenheten för datorstödd molekylforskning Kanslerin.

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