On Thursday 24 March 2011, SCM and the Walker Molecular Dynamics Lab at the San Diego Supercomputer Center (SDSC) held a one-day ADF workshop for both beginners and expert users wishing to learn about the new ADF2010.02 release. The workshop was free of charge to participants. Dr. Matt Kundrat from SCM and Dr. Andreas Götz of SDSC organized the event at SDSC and acted as tutors. ADF developer Dr. Lou Noodleman was also present, as were several staff members of the SDSC, who were kind enough to give us all a tour of their machine room depicted below.
In the previous month Dr. Stan van Gisbergen and Dr. Matt Kundrat of SCM toured the south of England, giving talks at several locations. Our public visits there included The University of Cambridge, The University of Oxford, and University College London.
We are currently finalizing plans for a "virtual workshop" to be held remotely at sites in Australia sometime in early May... If you are currently using any of our software, or are interested in learning more about it and would be interested in hosting a future talk or workshop, please let us know, and we will gladly keep you in mind for future visits or web presentations.
This spring SCM attended three meetings on both sides of the Atlantic. First, SCM was represented by Dr. Olivier Visser and Dr. Stan van Gisbergen at a local Dutch meeting in Veldhoven organized by the Dutch Chemical Sciences Study groups. Next, Dr. Matt Kundrat of SCM and BAND developer Chris Verzijl represented us at the 2011 March Meeting of the American Physical Society in Dallas, Texas. The following week SCM had a booth at the Spring 2011 American Chemical Society National Meeting & Exposition in Anaheim, California. Here Dr. Kundrat was again accompanied by ADF developer Dr. Andreas Götz from the SDSC.
In July SCM plans to attend the 2011 World Congress of the World Association of Theoretical and Computational Chemists (WATOC). This event will be held at the University of Santiago in Santiago de Compostela, Spain from July 17-22, 2011. At the end of this summer we will also exhibit at the 14th International Density Functional Theory Conference to be held in Athens, Greece, from August 29 to September 2 of this year. If you will find yourself at either (or both) of these conferences, feel free to stop by and talk with us about ADF, BAND, COSMO-RS, ReaxFF and the recent developments in all of our programs.
DGrid is a program developed by Dr. Miroslav Kohout. The source files, modules for several visualization programs and manuals can be downloaded free of charge.
DGrid calculates various functions (derived from the wave function data obtained from TAPE21), for instance electron density, one-electron potential, Electron Localizability Indicator (ELI), Electron Localization Function (ELF), conditional pair density, etc. on an equidistant grid.
The fields can be searched for critical points and molecular graphs constructed. Basins can be determined and evaluated almost for all the computed functions. Visualization is possible with external programs.
In the November 2010 issue of ACS Nano, Jos Seldenthuis and coworkers at the Delft University of Technology published a design for an all-electric single-molecule motor which has drawn worldwide interest. The rotating moiety of the molecule exhibits a large dipole moment, which enables it to be driven by an external electric field. The molecule is conjugated when planar. During rotation the conjugation breaks, which enables the detection of the rotation through the modulation of the low-bias conductance. Advantages of this design over light- or thermally driven motors include full control over the speed of rotation through the frequency of the oscillating external field.
All relevant properties of the proposed molecular motors (dipole moment, rotational barrier potential and zero-bias off-resonance conductance as a function of the rotation angle) have been calculated with ADF. The fragment-based approach of ADF and the provided Python tools were particularly helpful in constructing the Green's function and made the implementation of the post-DFT transport calculations almost trivial.
At the moment the proposed motor exists only on paper. However, certain aspects of the design have already been verified experimentally, and the ADF calculations show that it should be possible to drive and measure the motor in current electromigrated break-junction setups. The group of Herre van der Zant is already talking to chemists who have expressed an interest in synthesizing the molecules and hopes to start measuring them sometime next year.
Left: Design of an all-electric single-molecule motor.
Right: Rotational barrier potential and zero-bias off-resonance
conductance as a function of the rotation angle.
In Early 2011, researchers Rajeev Ahuja, Andreas Blomqvist and Peter Larsson at Uppsala University along with Pekka Pyykkö and Patryk Zaleski-Ejgierd at the University of Helsinki published the results of an extensive computational study on the science behind the common lead-acid battery. Their work, published in Physical Review Letters, has since received attention in Chemical and Engineering News , Nature and other leading scientific journals. In addition to drawing the fascination of the scientific literature, various other news media throughout the world, including The Economist have also picked up on the story.
The standard lead - lead oxide battery has been around for over a century. It works because its galvanic cells produce just over 2 volts apiece, and stacking these cells together in series produces a battery powerful enough to drive the motors used to start automobiles. Tin, another group 14 element, has a similar chemistry to lead, but diminished relativistic effects (when compared to lead) result in a much smaller voltage for the theoretical tin-based battery. Some of the energetic differences between lead, tin and a hypothetical lead system devoid of relativity are illustrated below.
Left: Relativistic shifts in the Ef of various Pb and Sn systems. Right: Total and partial Density of states for Pb in PbO2.
These calculations were performed with SCM's BAND program for modeling periodic systems. The ZORA method was used to efficiently take into account the relativistic effects. ZORA has long been available in SCM's ADF program for molecular DFT, but its inclusion in the BAND program for periodic systems make it particularly well-suited for modeling the electrochemistry of extended systems comprised of heavy elements, in this case lead - lead oxide electrodes.
Very recent atomic force microscopy (AFM) measurements using carbon monoxide terminated tips have shown spectacular atomic resolution imaging on organic molecules. The image formation mechanism and the role of molecular relaxation in force spectroscopy experiments were studied in more detail in a recent article appearing in Physical Review Letters by Zhixiang Sun and co-workers at the Utrecht University.
The experiment involved the measurement of intermolecular forces between two CO molecules: one adsorbed on the Cu(111) single crystal substrate and the other on the AFM tip. The experimental results were compared with ADF calculations with TZ2P Slater basis sets and using a dispersion-corrected xc energy functional, PBE-D, to account for the van der Waals interactions that dominate at large CO-CO distances.
CO-terminated tips for quantitative AFM: dispersion-corrected DFT calculations compared to experiment.
The calculations were performed on two levels. Simple model calculation involving only the interaction between two isolated CO molecules was sufficient to reproduce the experimental results in a semi-quantitative fashion. However, at short tip-sample distances the repulsive interaction was strongly overestimated. Using Cu4 and Cu10 clusters as models of the tip and substrate, respectively, calculations including geometry relaxation of the CO molecules (see Figure) were carried out.
The adsorbed CO molecules reorient when the Pauli repulsion becomes too strong at short tip-substrate distances, which results in reduced repulsive interaction between the AFM tip and the sample. This brings the calculated interaction energy significantly closer to the experimental value.
The atomic reconfiguration at close tip-sample distances limits the achievable resolution both in imaging and force spectroscopy. These effects are expected to be general and occur in all non-contact AFM experiments employing molecule-terminated tips.
SCM announces a job opening - with start date between June 1, 2011 and January 1, 2012 - for a Ph.D. student or (junior) method developer DFT software. The position is planned for 1 + 3 = 4 years. Permanent employment at SCM in Amsterdam may be an option afterwards. Salary conditions and benefits will be similar to what is usual at Dutch universities with certain extra benefits. Very suitable and motivated postdoc candidates may also be considered under negotiable terms concerning employment duration and salary.
Detailed information on SCM and ADF can be found at SCM's website: http://www.scm.com. Those interested in this position are encouraged to contact Dr. Stan van Gisbergen, SCM's Chief Executive Officer (vangisbergen at scm dot com, tel: +31-20-5987626) for further information. Job applications can be sent by E-mail to the same address until June 15, 2011, but preferably sooner. Applications should contain a CV, a letter explaining the motivation for applying and, if applicable, a list of publications. References may be requested at a later stage.
We always welcome suggestions for new ADF functionality that you would like to see included in a future release. Any questions or comments regarding this Newsletter, or other questions related to ADF, are also welcome and can be sent to info@scm.com. Feel free to contact us also in case you have some information that may be of interest to other ADF users, and that may be suitable material for a future Newsletter or news item on the SCM website.
These news items and more can be found in the news section of our website.
