Prof. Dr. Wolfgang Heiden
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Energy Profiles of the Ring Puckering of Cyclopentane, Methylcyclopentane and Ethylcyclopentane
(2019)
The Covid-19 pandemic has challenged educators across the world to move their teaching and mentoring from in-person to remote. During nonpandemic semesters at their institutes (e.g. universities), educators can directly provide students the software environment needed to support their learning - either in specialized computer laboratories (e.g. computational chemistry labs) or shared computer spaces. These labs are often supported by staff that maintains the operating systems (OS) and software. But how does one provide a specialized software environment for remote teaching? One solution is to provide students a customized operating system (e.g., Linux) that includes open-source software for supporting your teaching goals. However, such a solution should not require students to install the OS alongside their existing one (i.e. dual/multi-booting) or be used as a complete replacement. Such approaches are risky because of a) the students' possible lack of software expertise, b) the possible disruption of an existing software workflow that is needed in other classes or by other family members, and c) the importance of maintaining a working computer when isolated (e.g. societal restrictions). To illustrate possible solutions, we discuss our approach that used a customized Linux OS and a Docker container in a course that teaches computational chemistry and Python3.
Quantum mechanical theories are used to search and optimized the conformations of proposed small molecule candidates for treatment of SARS-CoV-2. These candidate compounds are taken from what is reported in the news and in other pre-peer-reviewed literature (e.g. ChemRxiv, bioRxiv). The goal herein is to provided predicted structures and relative conformational stabilities for selected drug and ligand candidates, in the hopes that other research groups can make use of them for developing a treatment.
In an effort to assist researchers in choosing basis sets for quantum mechanical modeling of molecules (i.e. balancing calculation cost versus desired accuracy), we present a systematic study on the accuracy of computed conformational relative energies and their geometries in comparison to MP2/CBS and MP2/AV5Z data, respectively. In order to do so, we introduce a new nomenclature to unambiguously indicate how a CBS extrapolation was computed. Nineteen minima and transition states of buta-1,3-diene, propan-2-ol and the water dimer were optimized using forty-five different basis sets. Specifically, this includes one Pople (i.e. 6-31G(d)), eight Dunning (i.e. VXZ and AVXZ, X=2-5), twenty-five Jensen (i.e. pc-n, pcseg-n, aug-pcseg-n, pcSseg-n and aug-pcSseg-n, n=0-4) and nine Karlsruhe (e.g. def2-SV(P), def2-QZVPPD) basis sets. The molecules were chosen to represent both common and electronically diverse molecular systems. In comparison to MP2/CBS relative energies computed using the largest Jensen basis sets (i.e. n=2,3,4), the use of smaller sizes (n=0,1,2 and n=1,2,3) provides results that are within 0.11--0.24 and 0.09-0.16 kcal/mol. To practically guide researchers in their basis set choice, an equation is introduced that ranks basis sets based on a user-defined balance between their accuracy and calculation cost. Furthermore, we explain why the aug-pcseg-2, def2-TZVPPD and def2-TZVP basis sets are very suitable choices to balance speed and accuracy.
The elucidation of conformations and relative potential energies (rPEs) of small molecules has a long history across a diverse range of fields. Periodically, it is helpful to revisit what conformations have been investigated and to provide a consistent theoretical framework for which clear comparisons can be made. In this paper, we compute the minima, first- and second-order saddle points, and torsion-coupled surfaces for methanol, ethanol, propan-2-ol, and propanol using consistent high-level MP2 and CCSD(T) methods. While for certain molecules more rigorous methods were employed, the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pV5Z theory level was used throughout to provide relative energies of all minima and first-order saddle points. The rPE surfaces were uniformly computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ level. To the best of our knowledge, this represents the most extensive study for alcohols of this kind, revealing some new aspects. Especially for propanol, we report several new conformations that were previously not investigated. Moreover, two metrics are included in our analysis that quantify how the selected surfaces are similar to one another and hence improve our understanding of the relationship between these alcohols.
The work being described in this paper is the result of a cooperation project between the Institute of Visual Computing at the Bonn-Rhein-Sieg University of Applied Sciences, Germany and the Laboratory of Biomedical Engineering at the Federal University of Uberlândia, Brazil. The aim of the project is the development of a virtual environment based training simulator which enables for better and faster learning the control of upper limb prostheses. The focus of the paper is the description of the technical setup since learning tutorials still need to be developed as well as a comprehensive evaluation still needs to be carried out.
The Virtual Memory Palace
(2006)
The intention of the Virtual Memory Palace is to help people memorize information by addressing their visual memory. The concept is based on the “Memory Palace” as an ancient Greek memorization technique, where symbols are placed in a certain way within an imaginative building in order to remember the original information whenever the mind goes through the vision of this building again. The goal of this work was to create such a Memory Palace in a virtual environment, so it requires less creative effort of the contemporary learner than was necessary in ancient Greece. The Virtual Memory Palace offers the possibility to freely explore a virtual 3d architectural model and to place icons at various locations within this model. Specific behaviors were assigned to these locations to make them more memorable. To test the benefit of this concept, an experiment with 15 subjects was conducted. The results show a higher remembrance rate of items learned in the Virtual Memory Palace compared to a wordlist. The observations made during the test showed that most of the subjects enjoyed the memorization environment and were astonished how well the Virtual Memory Palace worked for them.
Augmented Perception - AuPer
(2004)