Fairwell to Meeri Lambinen who goes to study to the Helsinki University for one semester.
From Tartu to Tallinn:
From Tallinn to Halsinki:
Finally, in Helsinki:
STSM to Trieste: Simulation of surface charge effect on the sliding friction of a nanoconfined ionic liquid
The interest towards using ionic liquids as lubricants has been increasing since ca. 2012 [1]. It was demonstrated that the interfacial structures in ionic liquids control the nanoscale friction. Experimental (see refs in [1]) and several computational studies [2–5] revealed that lubricity varies with the number and lateral structure of confined ion layers, which in turn are dependent on the applied potential. This opens a possibility of electrochemical control of friction, in other words a “Tantalizing prospect of tunning friction on small dimensions without changing surfaces with a self-replenishing layer, and could be easily integrated into niche situations, … because ionic liquids are cheaper than existing nonconducting molecular lubricants” (see refs in [1]). At the same time it was shown that the restructuring of the potential dependent interfacial structure happens in ionic liquids on a regular manner [6,7]. Therefore, there is a direct relation between various interfacial properties through the potential dependent interfacial structure [8]. For instance, it has not been marked in the literature that the potential dependent friction force [9–11] is proportional to the potential dependent capacitance [12–14]. The understanding of this structure-based relationship can help in controlling of the nanoscale friction in ionic liquids by a potential-tuned ionic lubricant layer.
During this STSM visit, we have initiated a comprehensive study: formulated a hypothesis, prepared a research plan, and obtained preliminary results. The later reveal a proportionality between potential dependent capacitance and friction force. Such structure-based relationship can be of use in controlling of the nanoscale friction in ionic liquids by an applied potential. Further work should verify the generic mechanism of the electrotunable lubricity and capacity. In the future study we plan to perform a detailed atomistic simulation to enable comparison between specific computational and experimental data.
This research was supported by a short term scientific mission funded by COST action MP1303.
References:
[1] R. Hayes, G.G. Warr, R. Atkin, Structure and Nanostructure in Ionic Liquids, Chem. Rev. 115 (2015) 6357–6426.
[2] R. Capozza, A. Vanossi, A. Benassi, E. Tosatti, Squeezout phenomena and boundary layer formation of a model ionic liquid under confinement and charging, J. Chem. Phys. 142 (2015) 64707.
[3] R. Capozza, A. Benassi, A. Vanossi, E. Tosatti, Electrical charging effects on the sliding friction of a model nano-confined ionic liquid, The Journal of Chemical Physics. 143 (2015) 144703.
[4] O.Y. Fajardo, F. Bresme, A.A. Kornyshev, M. Urbakh, Electrotunable Lubricity with Ionic Liquid Nanoscale Films, Sci. Rep. 5 (2015) 7698.
[5] O.Y. Fajardo, F. Bresme, A.A. Kornyshev, M. Urbakh, Electrotunable Friction with Ionic Liquid Lubricants: How Important Is the Molecular Structure of the Ions?, The Journal of Physical Chemistry Letters. 6 (2015) 3998–4004.
[6] V. Ivaništšev, K. Kirchner, T. Kirchner, M.V. Fedorov, Restructuring of the electrical double layer in ionic liquids upon charging, J. Phys.: Condens. Matter. 27 (2015) 102101.
[7] V. Ivaništšev, S. O’Connor, M.V. Fedorov, Poly(a)morphic portrait of the electrical double layer in ionic liquids, Electrochem. Commun. 48 (2014) 61–64.
[8] M.V. Fedorov, A.A. Kornyshev, Ionic liquids at electrified interfaces, Chem. Rev. 114 (2014) 2978–3036.
[9] J. Sweeney, F. Hausen, R. Hayes, G.B. Webber, F. Endres, M.W. Rutland, R. Bennewitz, R. Atkin, Control of Nanoscale Friction on Gold in an Ionic Liquid by a Potential-Dependent Ionic Lubricant Layer, Phys. Rev. Lett. 109 (2012) 155502.
[10] H. Li, R.J. Wood, M.W. Rutland, R. Atkin, An ionic liquid lubricant enables superlubricity to be “switched on” in situ using an electrical potential, Chem. Commun. 50 (2014) 4368–4370.
[11] H. Li, M.W. Rutland, R. Atkin, Ionic Liquid Lubrication: Influence of Ion Structure, Surface Potential and Sliding Velocity, Phys. Chem. Chem. Phys. 15 (2013) 14616–14623.
[12] M. Drüschler, N. Borisenko, J. Wallauer, C. Winter, B. Huber, F. Endres, B. Roling, New insights into the interface between a single-crystalline metal electrode and an extremely pure ionic liquid: slow interfacial processes and the influence of temperature on interfacial dynamics, Phys. Chem. Chem. Phys. 14 (2012) 5090–5099.
[13] R. Atkin, N. Borisenko, M. Drüschler, S.Z. El Abedin, F. Endres, R. Hayes, B. Huber, B. Roling, An in situ STM/AFM and impedance spectroscopy study of the extremely pure 1-butyl-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate/Au(111) interface: potential dependent solvation layers and the herringbone reconstruction, Phys. Chem. Chem. Phys. 13 (2011) 6849.
[14] R. Costa, C.M. Pereira, A.F. Silva, Charge Storage on Ionic Liquid Electric Double Layer: The Role of the Electrode Material, Electrochim. Acta. 167 (2015) 421–428.
Taming the equations in Libreoffice
Working on large documents with many equations in a word processor is a torture. In my case, booklets of chemistry problems require a lot of work. For certain reason I prefer to use LibreOffice. When is needed to reformat all equations in a document the following macro is very useful:
Sub FormulaFontSizeChanger
o = ThisComponent.getEmbeddedObjects()
fontSize = 12
fontFamily = “Arial”
For i = 0 to o.count-1
if (not IsNull(o(i))) and (not IsNull(o(i).Model)) then
o(i).Model.TopMargin = 0
o(i).Model.BottomMargin = 0
o(i).Model.LeftMargin = 0
o(i).Model.RightMargin = 0
o(i).Model.BaseFontHeight = fontSize
o(i).Model.FontNameVariables = fontFamily
o(i).Model.FontVariablesIsItalic = 1
o(i).Model.FontNameFunctions = fontFamily
o(i).Model.FontNameNumbers = fontFamily
o(i).Model.FontNameText = fontFamily
o(i).Component.BaseFontHeight = fontSize
o(i).ExtendedControlOverEmbeddedObject.update()
endif
Next i
End Sub
P.S. The script might be useful also when writing a thesis with a lot of chemistry inside and many Zotero references. LaTeX might not be so comfortable, and in Word one is still limited with few math fonts.
STSM to Vienna: MD simulations of ionic liquid mixtures with polarizable force fi elds
Generic force fields are widely used in molecular level computations. However, in real physical systems, the magnitude and localization of the charges are variable due to the interatomic polarization and the molecular dynamics. There are two ways to take these into account: (i) to reduce the atomic charges to non-integer values or (ii) to include polarizableforces.
In this STSM the latter method was used adding Drude oscillators to the system to add the polarizability to the particles. The polarizable force fields (FFs) developed by the group of Prof. Schroder where used to simulate the mixtures of ionic liquids with classical molecular dynamics. Namely mixture of [EMIm][BF4] and [EMIm]I was used. For comparison, the same system with non-polarizable FFs and the system of pure [EMIm][BF4] using polarizable FFs were simulated.
The main problem with classical MD simulations of ions is that the viscosity is overestimated which comes from the fact of imprecise non-bonding interactions. The polarizable FFs estimate it better and taken from the simulations the diffusion constant for the same system with polarizable FFs was much higher than for non-polarizable (1.03 A2/ns and 0.48 A2/ns respectively for cations). The system of pure [EMIm][BF4] showed that iodine affects the movement of ions as the diffusion constant differs by 10% (1.15 A2/ns for cations in pure system). All in all, the polarizable FFs improves the system and adding the small amount of iodine does not change the diffusion nor the structure that much.
Comp. perspective on the supercaps
In the recent years, a significant progress has been achieved in the modeling of realistic porous carbon electrodes [J. C. Palmer and K. E. Gubbins, Micropor. Mesopor. Mat., 154, 24–37 (2012).], simulations under constant potential conditions [D. T. Limmer et al., Phys. Rev. Lett., 111, 106102 (2013).], description of the electrode material electronic structure [E. Paek, A. J. Pak, and G. S. Hwang, J. Electrochem. Soc., 160, A1–A10 (2013).], and ion packing relation to the capacitance [S. Kondrat, C. R. Pérez, V. Presser, Y. Gogotsi, and A. A. Kornyshev, Energy Environ. Sci., 5, 6474–6479 (2012).]. Let us turn the readers’ attention to two aspects of the theoretical predicted relation between the ion size and the pore size, suggesting higher capacitance values for certain pore sizes. First, the molecular dynamics and density functional theory simulations do confirm the theory in case of slit-pore models with rigorously defined width [D. Jiang and J. Wu, J. Phys. Chem. Lett., 4, 1260–1267 (2013).] & [G. Feng, S. Li, V. Presser, and P. T. Cummings, J. Phys. Chem. Lett., 4, 3367–3376 (2013).]. Therefore, the theory suggests that some electrode materials with a certain pore distribution the capacitance is higher due to specific ion packing. Yet, as has been elegantly pointed by Cummings and co-workers [G. Feng, S. Li, V. Presser, and P. T. Cummings, J. Phys. Chem. Lett., 4, 3367–3376 (2013).], due to a wide distribution of pore sizes in the real electrode material this effect might not at all affect the experimentally measured capacitance. Second, as noted above, the capacitance is greatly determined by the electronic structure of the electrode material. The state-of-the-art molecular dynamics studies do not yet include the electronic structure into account [M. V. Fedorov and A. A. Kornyshev, Chem. Rev., 114, 2978–3036 (2014).]. The situation is about to change in the future, for example with the help of ab initio molecular dynamics [M. Salanne, Phys. Chem. Chem. Phys., 17, 14270–14279 (2015).].
Note, the following text appeared in the artile: E. Tee, I. Tallo, T. Thomberg, A. Jänes, E. Lust, J. Electrochem. Soc. 163 (2016) A1317–A1325. See at http://jes.ecsdl.org/content/163/7/A1317.abstract (DOI: 10.1149/2.0931607jes)
Travel tips
Summer is a great time for research visits, schools as well as vacations. Here is my check list for a safe trip from 2016.
- Passport, ID card and driving license (and a secure place for these documents)
- A bottle of water (stay hydrated)
- Snacks or meal replacement bars for sustenance during the trip
- Cough drops
- Wet wipes and napkins
- Something to read or listen (headphones)
- A notebook or something to write on
- A scarf or something to protect your neck from cold
- A cap or something to close your face while sleeping
- Sunglasses
- Compression socks
- Lightweight and water-resistant pair of shoes
- Some coins and some cash
- A universal adapter
Here is what I would like to add to the list in 2023 (thanks to chatGPT for ideas):
- A portable charger or power bank to keep your devices charged
- Hand sanitizer or disinfecting wipes to keep your hands and surfaces clean
- An extra set of clothes or a change of underwear in case of unexpected delays or lost luggage
- Maps or a guidebook for your destination to help you navigate and plan your trip
- A medical mask!
size limits of email boxes
Email is an essential part of the work. Sometimes the box gets full, thus preventing the work. With gmail there is a trick how to find and delete large emails that occupy most of the space. To search for attachments greater than 5 Mb search “size:5000000”.
Installing Gromacs and Lammps
FFTW:
./configure –enable-float –enable-shared –enable-sse2
make -j N
make install
===
Gromacs:
$ tar xvfz gromacs-x.y.z.tar.gz
$ ls
gromacs-x.y.z
$ mkdir build
$ cd build
$ cmake ../gromacs-x.y.z -DCMAKE_INSTALL_PREFIX=/home/yourUser/opt/gromacs.x.y.z -DGMX_CPU_ACCELERATION=SSE2 -DGMX_SIMD=SSE2
$ make -j N
$ make install
===
LAMMPS:
$ git clone git://git.lammps.org/lammps-ro.git LAMMPS
$ make yes-molecule
$ make mpi
===
To the .bashrc add:
#Gromacs
source /home/yourUser/opt/gromacs.x.y.z/bin/GMXRC
#or source /your/installation/prefix/here/bin/GMXRC
#LAMMPS
export LD_LIBRARY_PATH=~/LAMMPS/src:$LD_LIBRARY_PATH
export PATH=~/LAMMPS/src:$PATH
gsissh at ubuntu
To access one of the PRACE supercomputers, I was required to use gsissh. The corresponding gsi-openssh-clients package is not in the standard Ubuntu repositories. I have downloaded it from http://toolkit.globus.org/ftppub/gt5/5.2/stable/packages/deb/ubuntu/12.04/pool/contrib/g/gsi-openssh/.Besides that also globus-proxy-utils is needed. This one was easy to install via apt-get install globus-proxy-utils. Finally, everything got working when the bundle of X509 trusted certificates was downloaded from http://software.ligo.org/gridtools/debian/pool/main/o/osg-ca-certs/. Note, for some reason .globus folder did not appear in my home directory. To use gsissh, I had to create it and then move my user certificate to it with proper correct permissions -rw-------.
P.S. Do not forget to create a proxy certificate (grid-proxy-init) before login to your supercomputer.
6th Baltic Electrochemistry Conference
The 6th Baltic Electrochemistry Conference held in Helsinki, Finland during a period of 14-17 June and collects researchers dedicated to the science and technology of electrochemistry around the Baltic. This conference provides a forum for individuals from research organizations and companies to learn about the latest developments in this rapidly evolving field, to discuss with renowned experts and to build their networks in an informal and friendly atmosphere. The conference covers all forms of electrochemistry, including, but not limited to experimental and theoretical aspects of charge transfer at electrochemical interfaces, electrochemical materials science, and electrocatalysis. In addition, emergent technologies like electrodeposition of nanomaterials and functionalized electrodes, and electrochemical nanostructuring feature along with related poster presentation sessions.
I am taking part in these conference with the poster presentation “DFT-based modeling of associates of ionic liquid ions” where discuss the ability of prediction properties of novel type electrolytes by applying the results of the DFT calculations of simpler ionic associates. For this reason, the effect of the self-interaction and dispersion corrections on the results of DFT calculations for 48 ionic associates has been investigated [1]. The magnitude of the corrections strongly depends on the anion choice and especially in the case of halide anions. It is very important to pay particular attention to that fact because ionic liquid mixture with the addition of halides has attracted attention as a possible electrolyte for supercapacitors [2].
