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Structure-activity relationships of thiostrepton derivatives: implications for rational drug design
(2014)
Wo Laborexperimente zu aufwendig, zu teuer, zu langsam oder zu gefährlich oder Stoffeigenschaften gar nicht erst experimentell zugänglich sind, können Computersimulationen von Atomen und Molekülen diese ersetzen oder ergänzen. Sie ermöglichen dadurch Reduktion von Kosten, Entwicklungszeit und Materialeinsatz. Die für diese Simulationen benötigten Molekülmodelle beinhalten zahlreiche Parameter, die der Simulant einstellen oder auswählen muss. Eine passende Parametrierung ist nur bei entsprechenden Kenntnissen über die Auswirkungen der Parameter auf die zu berechnenden Größen und Eigenschaften möglich. Eine Gruppe von Standardparametern in molekularen Simulationen sind die Partialladungen der einzelnen Atome innerhalb eines Moleküls. Die räumliche Ladungsverteilung innerhalb des Moleküls wird durch Punktladungen auf den Atomzentren angenähert. Für diese Annäherung existieren diverse Ansätze für verschiedene Molekülklassen und Anwendungen. In diesem Teilprojekt des Promotionsvorhabens wurde systematisch der Einfluss der Wahl des Partialladungssatzes auf potentielle Energien und ausgewählte makroskopische Eigenschaften aus Molekulardynamik-Simulationen evaluiert. Es konnte gezeigt werden, dass insbesondere bei stark polaren Molekülen die Auswahl des geeigneten Partialladungssatzes entscheidenden Einfluss auf die Simulationsergebnisse hat und daher nicht naiv, sondern nur ganz gezielt getroffen werden darf.
Energy Profiles of the Ring Puckering of Cyclopentane, Methylcyclopentane and Ethylcyclopentane
(2019)
Computational chemistry began with the birth of computers in the mid 1900s, and its growth has been directly coupled to the technological advances made in computer science and high-performance computing. A popular goal within the field, be it Newtonian or quantum based methods, is the accurate modelling of physical forces and energetics through mathematics and algorithm design. Through reliable modelling of the underlying forces, molecular simulations frequently provide atomistic insights into macroscopic experimental observations.
Liquid–liquid equilibria of dipropylene glycol dimethyl ether and water by molecular dynamics
(2011)
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.
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.
Modeling of magic water clusters (H2O)20 and (H2O)21H+ with the PM3 quantum-mechanical method
(1993)