Seminars usually held on selected Fridays, from 10:15 to 11:00 in the Chemicum building (lecture room varies from time to time)
For the exact venue, see the programme below.
- A large number of research groups are active in the fields of computational physics and chemistry at the Kumpula campus of the University of Helsinki alone. The "Kumpula Computational Chemistry and Physics" seminar series attempts to increase the awareness of the people, tools and topics involved in this work, as well as to establish new and enhance existing collaborations. Over the years of its running, the series has become a regular means of communication at the Kumpula campus and beyond.
- Everyone (from students to senior researchers to professors) doing computational science in the greater Helsinki region is cordially welcome to propose a talk on any of the vacant dates. Besides the scientific topic, the talks should preferably also contain a brief presentation of the overall activity of the speaker's group. A brief abstract of the talk is also appreciated.
The first seminar this semester (spring term 2019) will be on Friday 01.02.
The presentations are in English.
Students can take the course (code 55317) for 3 ECTS credits by giving one talk, and participating in about 10 others. (Participation points can be collected over multiple semesters, and KCCP seminars can also be substituted by other relevant seminars on computational topics.)
Further info: contact Theo Kurtén (email@example.com) for any details, for volunteering to give a talk, and for joining the mailing list.
PROGRAMME FOR SPRING TERM 2019:
|Date & time||Place||Lecturer||Affiliation||Title||Abstract|
|26.02 14:15||Chemicum A120||James Avery||University of Copenhagen, Denmark||Wave Equations without Coordinates|
Can we solve electronic wave equations ab- sent a coordinate system? The question arises from the wish to treat polyhedral molecules such as fullerenes as two-dimensional closed surfaces. This would allow us to study electronic struc- ture on intrinsic surface manifolds, which can be derived directly from the bond structure. The wave equation restricted to the (non-Euclidean) surface could then be solved without reference to any three-dimensional geometry of the molecule, and hence without the need for quantum chem- ical geometry optimization. The resulting 2D system can potentially be solved several orders of magnitude faster than the full wave equation.
But because these curved surfaces do not admit any simple coordinate system, we must devise methods that can do without. In this talk, I will describe how surface geometries can be derived from fullerene bond graphs as combinatorial objects, and how electronic structure may be studied by solving wave equations directly on these intrinsic surface manifolds, without needing to find three- dimensional geometries. The goal is approximation methods that are rapid enough to systematically analyze entire isomer spaces consisting of millions of molecules, so as to identify structures with desired properties.
|01.03 10:15||Chemicum B143||Rasmus Otkjaer||University of Copenhagen, Denmark||Trends in Peroxy Radical Hydrogen Shift Rate Constants||Unimolecular hydrogen shift (H-shift) reactions in peroxy radicals have been shown to be important in the atmospheric oxidation of isoprene and α-pinene. The role of these reactions in the oxidation of organics in the atmosphere has received less attention due, in part, to the lack of kinetic data at relevant temperatures. We have used an experimentally verified theoretical approach based on Multi-Conformer Transition State Theory (MC-TST) to calculate rate constants for a systematic set of H-shifts. We have shown that H-shift reaction rate constants can reach 1 s^-1. Thus H-shift reactions are likely much more prevalent in the atmosphere than previously considered.|
|Chemicum A129||Patrik Španěl|
J. Heyrovsky Institute of Physical Chemistry
Prague, Czech Republic
|Selected Ion Flow Tube Mass Spectrometry, SIFT-MS, for real time analyses of trace concentrations of volatile compounds in air and breath||The need for rapid and accurate measurement of trace concentrations of compounds present in air and human breath has led to construction of specialised mass spectrometers based on the Selected Ion Flow Tube Mass Spectrometry. It is possible currently to analyse vapours of volatile organic compounds and other gases including ammonia, hydrogen sulphide or hydrogen cyanide present in concentrations as low as a part per billion by volume (ppbv). Reagent ions are formed in electrical discharges and ion-molecule reactions with analyte molecules in the sample take place during a defined reaction time providing mass spectra from which analyte concentrations can be calculated. The lecture will outline construction of the instrumentation, physical and chemical principles of the analytical methods and present interesting examples of their use including clinical breath analysis.|
Maarten de Zeeuw
|Wageningen University, the Netherlands (also Greenpeace Global Air Pollution Unit, Helsinki)||Quantifying NOx emissions with TROPOMI high-resolution satellite observations|
Air pollution is responsible 800,000 premature deaths in Europe every year, according to a recent study (Lelieveld et al., 2019). Satellite observations of NO2 have not only shown the global extend of the air pollution problem, but also provide important insight into pollution trends and emission source strengths. Now the new TROPOMI satellite sensor provides daily global measurements of air pollutants, including NO2, at a much higher resolution of 3.5 by 7 km2. I will present how these high-resolution observations can be used to quantify the NOx emission strength and temporal variability with a simple box model approach. Estimated NOx emissions from the city of Paris for eleven days showed a clear weekly cycle, with higher emissions during weekdays. NOx emission estimates for coal power plants in the United States showed good agreement with measured emissions by the EPA for source averages but strong deviations for daily estimates. These results show the potential of day-to-day monitoring of NOx emissions with TROPOMI measurements, while it appears that it remains a challenge to correctly describe wind speeds and account for chemical decay. This approach can be an important tool for evaluating the effectiveness of air pollution mitigation, such as policies that aim to curb emissions from traffic in cities or emission abatement technologies in power plants.
|Chemicum A129||Pekka Pyykkö||University of Helsinki, Dept. of Chemistry|
Simple Estimates for Eutectic Behavior
Simple estimates can be derived for the eutectic points (x B,eut ,Teut ) of binary A-B systems in terms of the freezing-point depression from both ends, or by using the Schröder-van Laar equation. Further virial-type expressions are possible (red and blue curves). The results for choline chloride – urea mixtures are shown below . The green straight lines are the present estimates. The experimental points are from Abbott et al. . As seen, such an elementary colligative treatment gives in that case a fair estimate for ΔT.
1. P. Pyykkö, ChemPhysChem 20 (2019) 123-127.
|Chemicum A129||Enrico Riccardi||NTNU Trondheim, Norway||Path Sampling: Theory, Software and Applications||T. B. A.|
|04.06 10:15||Chemicum A128||Stephan Schlemmer||University of Cologne, Germany||Molecular Collisions as a Tool for Spectroscopy||Action spectroscopy in ion traps has turned into a standard tool of molecular spectroscopy. Using the reaction products from bimolecular collisions has developed over the last 20 years into a rather versatile spectroscopy method. In the beginning laser induced reactions (LIR) were employed for recording rotationally resolved spectra of N2+, the ro-vibrational spectra of C2H2+ and such enigmatic molecules like CH5+. Later also the distortion of the ternary association of molecular ions with He atoms were used as a LIR variant. More recently double resonance schemes have been used to infer pure rotational spectra of ions for which first high-resolution ro-vibrational spectra are recorded. Very recently we also find ion molecule reactions which are slowed down as a consequence of a ro-vibrational excitation. These findings show that the molecular collision is an important part of this approach to spectroscopy and our experiments teach us also some of their details.|
|18.6 10:15||Chemicum A129||Iris Sokka||University of Helsinki, Dept. of Chemistry||Virtual structure modifications of cancer drugs MMAE and MMAF||"Monomethyl auristatin E (MMAE) and monomethyl auristatin F (MMAF) are mitosis inhibiting, microtubule binding agents, used in antibody-drug conjugates (ADCs) in the treatment of cancers. It was recently shown that the auristatins exists in an equal mixture of two conformers (cis and trans), of which only one (trans) is active. Employing high-level quantum chemical modelling and virtual docking studies, we show how simple one-atom substitutions can shift the equilibrium almost completely to the biologically active trans-form . This should additionally increase drug safety, as the dormant cis isomer loses its potential for attacking healthy tissue.|
 M.P. Johansson, H. Maaheimo, F.S. Ekholm, "New insight on the structural features of the cytotoxic auristatins MMAE and MMAF revealed by combined NMR spectroscopy and quantum chemical modelling", Sci. Rep. 7 (2017) 15920.
 I.K. Sokka, F.S. Ekholm, M.P. Johansson, "Increasing the Potential of the Auristatin Cancer-Drug Family by Shifting the Conformational Equilibrium" (submitted)."
PROGRAMME FOR FALL TERM 2018:
|Date & time||Place||Lecturer||Affiliation||Title||Abstract|
|14.08 13:15||Chemicum A128||Philip Bunker||National Research Council, Ottawa, Canada||The Planck constant, its units, quantity calculus, and the kilogram||-|
(note updated time)
|Chemicum A127||Michael Patzschke||Helmholtz-Zentrum Dresden-Rossendorf, Germany||Molecular Dynamics of Actinide Compounds for EXAFS, MS and more||Actinide research is a fascinating topic. The rich chemistry of actinides make them a fascinating research target. Their radiotoxicity necessitates good knowledge of their chemical properties in order to plan repositories for the storage of nuclear waste. The computational chemistry of actinides is also full of challenges. Actinide compounds are often open-shell systems which makes it necessary to perform high-level multi-reference calculations. Relativistic effects become important for the structure of actinide compounds and even more for their spectroscopical properties. When it comes to actinide interactions with biologically relevant molecules, many different binding sites can be found. This means, that “simple” structure optimisations are often not good enough and one needs to perform molecular dynamics calculations (MD) to see how these species behave. In this talk, we will present a few examples of calculations involving MD calculations on actinide compounds. In the second part, we will deal with the precipitation of MoO3 from aqeous solutions. Molybdenum is important as a matrix material for the nuclear fuel of Gen IV nuclear reactors. For these reactors, the fuel cycle will be optimised with recycling in mind. Therefore the dissolution of the nuclear fuel (and its Mo matrix) is important. We will discuss features of the mass spectrum of molybdenum-oxide clusters and ways to simulate such spectra using tight-binding DFT based MD calculations.|
|Chemicum A129||Christopher Johnson||Stony Brook University, U.S.A.||Disentangling the Intermolecular Interactions Governing Atmospheric New Particle Formation||Despite extensive study, significant questions remain regarding the role of intermolecular interactions in the formation and growth of clusters and particles in the atmosphere. We are using vibrational spectroscopy and temperature-controlled ion trap techniques on isolated clusters of amines and sulfuric acid that play a role in this process to characterize their structures, interactions, and reactivity. We have found that simple chemical principles can explain structure and hydration of clusters of this type, with the goal of generating “rules” for how molecules in these clusters drive the mechanism of their formation and growth.|
|Chemicum A129||Joseph Lane||University of Waikato, New Zealand|
Quantifying the strength of intramolecular interactions
Hydrogen bonding is important in a diverse range of applications in the fields of chemistry and biology including solvation, crystal packing, and protein folding. While several theoretical approaches exist to estimate the strength of intermolecular hydrogen bonds, the absence of a zeroth-order wavefunction for the donor and acceptor fragments of intramolecular hydrogen bonds makes this task non-trivial. In this work, we show that the integrated kinetic energy density can be used as a predictor of hydrogen bond strength. A series of complexes exhibiting intermolecular hydrogen bonds is used to predict the strength of some prototypical intramolecular hydrogen bonds.
|Chemicum A129||Daniel Reason||Cannasouth Plant Research, New Zealand||An Investigation into the Production of Cannabinoids for the Medical Industry Using Supercritical Fluid Extraction and Counter-Current Chromatography.||Medical cannabis products currently suffer from poor reliability and environmentally unfriendly production methods. This project is aimed at improving both of these issues using reproducible and environmentally friendly technologies that results in medical cannabis products compliant with good manufacturing practices (GMP). Included will be an investigation into the degradation of cannabinoids that will provide information on how degradation conditions may be utilised to target potentially significant cannabinoids that are present in low concentration in original plant material.|
|Chemicum A129||Henri Paulamäki||University of Helsinki||Bayesian optimization structure search|
Tailoring a material to have functional properties meeting the needs of an advanced device requires knowledge and control of the atomic level structure of the material. The atomic configuration is often the decisive factor in whether the device works as intended. While such tailored materials are needed in many technologically important applications, finding the most favorable configurations through atomistic quantum mechanical simulation methods has been computationally infeasible. There exist approximate simulation methods of lesser computational cost but so far their results are accurate enough for only certain types of materials at a time, and hence they cannot be used for studying e.g. organic/inorganic interfaces in heterogeneous devices - such as for example organic solar cells. I describe a 'building block'-based Bayesian Optimization Structure Search (BOSS) method to address such structural optimization problems by the means of machine learning.
|Chemicum A129||Susi Lehtola||University of Helsinki||Basis set limit Hartree-Fock and density functional theory calculations on atoms and diatomic molecules via finite elements||In order to understand the interactions of highly energetic particles in e.g. the radiation shielding material of fusion reactors, it is necessary to have a good grasp on the interatomic potential at large energies. The interatomic potential can be calculated to a good approximation from diatomic molecules. However, the modeling of the interaction of nuclei at close range is fundamentally different from that around the equilibrium, as the interactions do not arise from the outermost electrons only, but also the behavior of the innermost core electrons may undergo significant changes. Furthermore, the most commonly used computational electronic structure method, the linear combination of atomic orbitals (LCAO) approach, breaks down at small internuclear distances, signaling significant difficulties for modeling efforts.|
However, purely numerical calculations for diatomics have been possible since the 1970s. Unfortunately, the few programs that exist are difficult to use, have a limited set of features, and often do not converge. We describe the implementation of a modern finite element program, which is able to produce exact solutions for atoms and diatomic molecules at the Hartree-Fock or density functional level of theory. We show that in most cases, the program produces micro-eV accuracy total energies with minimal user intervention, demonstrating great promise for modeling materials in extreme environments.
|Chemicum A110||Chris Daub||University of Helsinki||Ab Initio Molecular Dynamics Simulations of the Liquid-Vapour Interface of Aqueous Lithium Bromide||Lithium bromide is an interesting salt, with relevance in industry due to its very high solubility in water and use as a dessicant. Both Li+ and Br- have somewhat unique properties in water, in particular their behaviours at the air-solution interface are of interest. These ions and other alkali halides in aqueous systems continue to be subject to intense study in physical and theoretical chemistry.|
In this talk I will give some historical perspective on aqueous alkali halides, leading up to discussing our recent work using ab initio DFT-based simulations to study the air-solution interface of aqueous LiBr. This is part of a longer term project we are working on to understand interactions between molecules and the aqueous solution surface. Time permitting, I will also talk about out preliminary results regarding the influence of LiBr on formic acid deprotonation.
|Chemicum B143||Emil Levo||University of Helsinki||Irradiation Response in Equiatomic Multicomponent Alloys|
High entropy alloys (HEAs) have been realised to be potential candidates as components for future nuclear reactors, partly due to their promising radiation tolerance. HEAs are built up of at least five elements at near-equimolar concentrations, with a subcategory called equiatomic multicomponent (EAMC) alloys that are built up of less than five elements. An overall presentation of HEAs is given in this work, with an emphasis on radiation damage in them. Three molecular dynamics studies regarding irradiated EAMC-alloys are presented. We found that complex alloys showed a higher tolerance to irradiation, in form of a lesser defect accumulation. A lesser dislocation mobility and different defect nanostructures were found to be contributing factors.
PROGRAMME FOR SPRING TERM 2018:
|Date & time||Place||Lecturer||Affiliation||Title||Abstract|
|Chemicum A129||Ville Kaila||Department of Chemistry, Technical University Munich||Molecular Mechanisms of Energy-Converting Proteins from Simulations Across Scales||Biological energy conversion is driven by remarkable proteins that capture and convert chemical and light energy into other energy forms. In this talk, I will show how multi-scale quantum and classical molecular simulations can be used to obtain a molecular-level understanding of the structure, energetics and dynamics of energy-capturing proteins, and to characterize their spectroscopic properties in different intermediate states. By combing large-scale classical molecular dynamics simulations with quantum chemical cluster models and hybrid quantum mechanics-classical mechanics (QM/MM) calculations, we have studied the function of respiratory and photosynthetic enzymes, as well the mechanisms of light-capture in many photobiological systems. We find that coupled electrostatic-, conformational-, and hydration changes provide essential functional elements in these systems.|
|Chemicum A128||multiple speakers|
mini-symposium Computational chemistry across scales
12:00-12:20 Heike Fliegl: Theoretical studies as a tool for understanding the aromaticcharacter of porphyrinoid compounds
12:20-12:40 Markus Rauhalahti: To be announced
12:40-13:00 Filip Ekholm: Antibody-drug conjugates – the future of anti-cancer therapeutics?
13:00-13:20 Maria Dimitrova: Halomethanes in strong magnetic fields
13:20-13:40 Lukas Wirz: To be announced
14:15-15:00 Leonardo Guidoni: Molecular Simulations in Photosynthesis
15:00-15:20 Ana Gamiz: Redox potentials in iron-sulphur proteins
15:20-15:40 Andrea Di Luca: Long-range Electrostatic Coupling in the Membrane Domain ofRespiratory Complex I
16:00-16:20 Michael Röpke: MultiQ: on-the-fly state change QM/MM simulations with multiple QMregions
16:20-16:40 Vivek Sharma: To be announced
16:40-17:00 Pauli Parkkinen: To be announced
|Chemicum A127||Lukas Wirz||University of Helsinki, Dept. of Chemistry|
Nomenclature and construction of fullerenes and other molecular cages (with an introduction to graph theory)
Fullerenes and other molecular cages are a vast and rapidly growing class of structures. One subclass of them, the fullerenes, which have only been discovered about thirty years ago grows as N^9 with the number of atoms, yet only a few examples have been synthesised and studied. While there is a large number of carbon cages, their bond structure and some properties are simple enough to be well represented by molecular graphs. We have devised an efficient (scaling linearly), unique, and complete nomenclature for all polyhedral molecules which is particularly compact for fullerenes. Furthermore, we present an embedding algorithm which together with a subsequently applied forcefield yields fullerene structures that are close to the respective DFT structures. These are the prerequisites for describing and studying molecular cages.
Programme for fall term 2017:
|Date & time||Place||Lecturer||Affiliation||Title||Abstract|
|Chemicum A129||Minna Palmroth||University of Helsinki, Dept. of Physics||Towards exascale: Near-Earth physics and computational challenges||Space is an emerging global megatrend. Increasing numbers of small satellites threaten the sustainable use of space, as without removal, space debris will eventually make certain critical orbits unusable. A central factor affecting small spacecraft health and leading to debris is the radiation environment, which is unpredictable due to an incomplete understanding of plasma dynamics. Ultimately, this stems from sparse measurements and insufficient models. Vlasiator is an HPC code having no precedent in space physics: it was deemed impossible due to the incredible challenge it presents to computational systems. Vlasiator targets to model the near-Earth space in six dimensions, three for the ordinary space and three for the velocity space. It is regularly run on some of the largest supercomputers in Europe. This presentation highlights the Vlasiator code, and its recent results, as well as explains why Vlasiator is central in the new Centre of Excellence in Research of Sustainable Space.|
|Chemicum A127||Markus Battarbee||University of Helsinki, Dept. of Physics||Supercomputational hybrid-Vlasov modelling of heliospheric shocks: Reformation, reflection and erosion||The inner heliosphere is populated by a variety of shocks, ranging from coronal ejections close to the Sun to interplanetary propagating shock fronts and magnetospheric bow shocks around planets. Accurate modelling of collisionless plasma shocks requires tools beyond those provided by magnetohydrodynamics (MHD). We discuss the possibilities and challenges of numerical modelling of heliospheric shocks, focusing on the Vlasiator hybrid-Vlasov code. We compare local and global results and examine set-up questions and data analysis procedures suitable for each case. Previous knowledge of plasma physics is not required.|
|Physicum D112||Christopher Daub||University of Helsinki, Dept. of Chemistry||Using Molecular Simulations to Study Electric Fields in Aqueous Systems||Electric fields, both as external forces and as responses to other perturbations, are connected with many interesting effects in water. In this talk I will present some of the work I have done over the last 10 years using molecular simulations to explore electric fields in a variety of aqueous systems, including bulk and confined water, water nanodroplets and molecular clusters, and ionic solutions in silica pores. These investigations have led to new insights into the mechanisms of solvent loss in electrosprays and suggestions for novel methods of electric energy conversion.|
|Chemicum A129||Josep Anglada|
Institute of Advanced Chemistry of Catalonia, Barcelona
Oxidation of atmospheric trace gases. A perspective from theoretical chemistry
Oxidation reactions are ubiquitous in the Earth’s atmosphere and are mainly driven by OH and NO3 radicals and by O3 as well. In this talk, some of the main features of several gas phase oxidation processes originated by reaction of different species with hydroxyl radical, but also by other radicals, will be analyzed from a perspective of its electronic features. Many of these oxidation reactions occur through the conventional hydrogen atoms abstraction mechanism, but in some cases, a different process takes place which involve a proton coupled electron transfer reaction.
|Chemicum A127||Kai Nordlund||University of Helsinki, Dept. of Physics||Molecular dynamics of antiprotons||The slowing down of energetic ions in materials is determined by the nuclear and electronic stopping powers. Both of these have been studied extensively for ordinary matter ions. For antiprotons, however, there are numerous studies of the electronic stopping power, but none of the nuclear one. Here, we use quantum chemical methods to calculate interparticle potentials between antiprotons and different atoms, and derive from these the nuclear stopping power of antiprotons in solids. The results show that the antiproton nuclear stopping powers are much stronger than those of protons, and can also be stronger than the electronic stopping power at the lowest energies. The interparticle potentials are also implemented in a molecular dynamics ion range calculation code, which allows to simulate antiproton transmission through degrader foil materials. Foil transmission simulations carried out at conditions relevant for antiproton transmission at CERN show that the choice of antiproton-atom interaction model has a large effect on the predicted yield of antiprotons slowed down to low (a few keV) energies.|
|-||note: seminar by Nanna Myllys moved to the spring semester|