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Five new HRSMC Fellowships awarded October 2019

dr. André Severo Pereira Gomes
dr. André Severo Pereira Gomes

Relativistic coupled cluster theory in real-time

Guest:  Dr. André Severo Pereira Gomes, CNRS Researcher, University of Lille.
Hosted by Prof. dr. L. Visscher

2 Visits : total of 1.5 months

Spectroscopic measurement are central to our understanding of the electronic structure of molecules and materials. The increasing complexity of experiments, and the ever smaller timescales that can be accessed nowadays, require robust theoretical frameworks. These are used to create models to explain the physical and chemical processes at work, or for predicting the outcome of experiments when these are very challenging or can hardly be done at all, as it can be the case for radioactive elements. During the visits of Dr. Severo Pereira Gomes, we plan to further develop the relativistic coupled cluster (RCC) approach to allow for directly solving the time-dependent many-body Dirac equation (rt-RCC) instead of employing the more commonly used perturbative approaches based on response theory. These developments, done on the novel, massively parallel RCC implementation in the DIRAC code being developed in the group of Prof. dr. Visscher, will provide us with the tools to reliably explore processes taking place at very small timescales (attoseconds) or that involve the interactions between electrons and strong perturbing fields, for species containing elements across the whole periodic table.

Prof. dr. Vitaly Gitis

Zeolites by design: Towards a fundamental understanding of zeolite formation

Guest: Prof. dr. Vitaly Gitis, Associate Professor Ben Gurion University of the Negev (BGU), Israel
Hosted by Gadi Rothenberg, David Dubbeldam, Evert Jan Meijer (UvA)

Visit: Total of 3 months

Zeolites are extremely important materials, with a global annual market topping $30Bn. But even though these crystalline materials are critical for the chemical industry, we still don't understand how they form, or even why some form and others not. Only 290 zeolite topologies were synthesized to date, out of millions of possible structures. The syntheses still rely mainly on trial and error, closer to art than to science. A fundamental understanding of the molecular processes that govern zeolite formation would enrich the fields of catalysis and materials science. The goal of this project is to develop a better understanding of the zeolite formation process. We will combine computational and experimental studies to gain insight into the molecular processes involved in the oligomerization and nucleation of zeolite cages.


dr. Eva Pluhařová
dr. Eva Pluhařová

Catalysts for efficient capture and reduction of CO2

Guest: Dr. Eva Pluhařová (J. Heyrovský Institute of Physical Chemistry, Czech Republic);
Hosted by
Prof. Evert Jan Meijer (University of Amsterdam) and Prof. Jana Roithová (Radboud University)

3 Visits, Total of 7 weeks 

The capture of CO2 and its subsequent transformation to valuable chemicals is one of the key topics these days. So far, only methods which require compression of CO2 exist and no efficient catalysts operating at ambient conditions are available. In this project we will investigate catalysts based on metal porphyrin cages that mediate electrochemical reduction of CO2. The process of CO2 capture will be theoretically explored by molecular dynamics simulations and the reduction of CO2 will be described by ab initio calculations. Obtained results will allow us to suggest structural modifications of the porphyrin cage in order to obtain a more efficient catalyst. Next, we will experimentally characterize the capturing properties of the tuned catalysts. The combined fundamental insights from experiment and modelling studies will provide guidelines for designing novel porphyrin cages with an optimal shape, size, and catalytic activity of the capturing cavity.

dr. Otto T. Berg
dr. Otto T. Berg

Assigning IR modes for CO(2) and reaction products on Cu particles and surfaces

Guest: dr. Otto T. Berg, lecturerCSU Fresno, Fresno, CA, USA
Hosted by: Ludo Juurlink (UL). Joost Bakker (RU/FELIX). Jörg Meyer (UL)

Visit: 1,5 month

An ongoing Mat4Sus research project (680.M4SF.028) of three research groups at the Universities of Leiden and Nijmegen aims to understand the chemical reactions of CO2 on Cu-based model catalysts. These systems range from unsupported nano-sized Cu particles to macroscopic Cu single crystals. The concepts required to bridge and connect results from experiments and theoretical results will be developed with the help of dr. Otto Berg. As an expert in IR spectroscopy, Dr. Berg will be based in Leiden to aid in developing experiments and the interpretation of results on Cu single crystals, and travel to Nijmegen regularly for experiments on Cu nano-sized particles and discussions on compatibility of results in the group of Bakker. He will be uniquely positioned to compare results and to help bridge the gap between the techniques and model systems in use. His contribution will sensitize and educate the various participants to these differences in the Mat4Sus collaboration.

dr. William C. Swope
dr. William C. Swope

Including anisotropic electronic polarization into a polarizable force field derived from first principles

Guest:  dr. William C. Swope, Senior Research Staff member
IBM Almaden Research Center (San Jose, CA, USA)
Host: Daan Geerke (VU)

Visit: 2 weeks 

Force field parametrization involves a complex set of linked optimization problems, with the goal of describing complex molecular interactions by using simple classical potential energy functions that model Coulomb interactions, dispersion and exchange repulsion. These nonbonded interaction functions comprise a set of atomic parameters and together with the bonded terms they constitute the molecular mechanics force field. Traditionally, many of these parameters have been fitted in a calibration approach in which experimentally measures for thermodynamic and other relevant properties of small-molecule compounds are used for fitting and validation. As these approaches are laborious and time consuming and represent an underdetermined optimization problem, we study methods to fit and derive an increasing number of parameters directly from electronic structure calculations, in order to greatly reduce possible parameter space for the remaining free parameters.

We do this by using a higher-order dispersion model and treating electronic polarization explicitly in our model, while retaining the relative simplicity and relatively low computational costs of our (polarizable) force field. At the same time, we have until now managed to prevent the introduction of special nonbonded parameters for specific pair-wise atom-atom interactions, which are typically included in currently available force fields (including other polarizable models) and which make the corresponding parameter sets inherently less transferable between different moieties and/or chemical environments of interest. 

As proof of principle of our approach to derive force-field parameters as much as possible directly from electronic structure calculations and to thus increase parameter transferability in a general way, we recently succeeded in calibrating a single molecular model that properly describes the thermodynamic properties of 49 simple neutral compounds (representing apolar as well as polar protein building blocks). For this purpose, most of the nonbonded parameters (132 out of 138) and all bonded parameters were directly obtained from quantum chemical calculations, and refinement based on experimental data was only needed for the remaining six free parameters (i.e. the atomic radii). An important step to make this possible has been the development, in collaboration with Dr. William Swope, of a combined quantum mechanical/molecular mechanical (QM/MM) approach to enable calculation of atomic polarizabilities for direct use in our condensed-phase simulations. 

In our data set of (49) small molecules mentioned above, we have until now on purpose excluded compounds with functional groups that add a strong anisotropic components to the molecular polarizability. The reason for excluding such compounds is that in our current model, atomic polarizabilities are described in a purely isotropic way. As a next step towards a generalizable (transferable) polarizable model derived from first principles, we want to examine if anisotropic atomic polarizabilities are necessary to correctly describe molecular interactions with and between aromatic, (sulfon)amide and nitro groups or other building blocks of biological, toxicological and/or pharmaceutical interest. In order to tackle the challenges in defining an appropriate (but still sufficiently efficient) way to incorporate anisotropy into our polarizable force field, we want to invite Dr. Swope for two weeks to our laboratory. This will make it possible to intensively work together and correctly and effectively define treatment of anisotropy in our QM/MM based fitting scheme and our simulation software. By integrating these solutions into our methods and models we will enable a systematic comparison of using isotropic or anisotropic polariizabilities, in terms of our force-field description of relevant thermodynamic properties of (bio)molecular systems. If necessary and upon integration this will allow direct use of QM/MM calculations to derive anisotropic polarizabilities for use in our first-principle force field.