Coding CompChem software by blocks

https://arxiv.org/abs/2005.05756

Coding is hard. Coding for CompChem is hard, cumbersome and repetitive (in the end, how many ways to code the HF equations can there be?). The CECAM electronic structure library proposes a digital repository of codes for bits and pieces used in CompChem so as for them to be easily assembled as required and adapted to evolving hardware. It will give a chance to have custom software specially to those with low computational resources and low coding skills. Sounds really cool!

 

The CECAM Electronic Structure Library and the modular software development paradigm
Micael J. T. Oliveira, Nick Papior, Yann Pouillon, Volker Blum, Emilio Artacho, Damien Caliste, Fabiano Corsetti, Stefano de Gironcoli, Alin M. Elena, Alberto Garcia, Victor M. Garcia-Suarez, Luigi Genovese, William P. Huhn, Georg Huhs, Sebastian Kokott, Emine Kucukbenli, Ask H. Larsen, Alfio Lazzaro, Irina V. Lebedeva, Yingzhou Li, David Lopez-Duran, Pablo Lopez-Tarifa, Martin Luders, Miguel A. L. Marques, Jan Minar, Stephan Mohr, Arash A. Mostofi, Alan O’Cais, Mike C. Payne, Thomas Ruh, Daniel G. A. Smith, Jose M. Soler, David A. Strubbe, Nicolas Tancogne-Dejean, Dominic Tildesley, Marc Torrent, Victor Wen-zhe Yu

London Dispersion native in DFT

#TodayILearned that there are functions called ‘dispersals’. These are 1e functions which work as basis for the construction of exchange-correlation holes density functionals for the correct inclusion of London dispersion in the calculation of interaction energies.

Maybe this will become a standard method for constructing DFs for calculating interaction energies in one go to chemical accuracy.

London dispersion forces without density distortion: a path to first principles inclusion in density functional theory
Derk P. Kooi, Paola Gori-Giorgi

arXiv:2005.05900

NMR calculations for calixarenes (not a good one)

Calixarenes, mon amour. This paper looks terrible right of the abstract, claiming high level GIAO NMR calculations for calixarene host -guest systems but there is no reference to the work of Tantillo et al whose scaling factors should be by now mandatory in such calculations (not to mention the ominous use of B3LYP). There is however an interesting idea that the h bonded groups become disturbed at a distance by the guests but also they’re not that far away to not ascribe those shifts to steric effects.

Monatshefte für Chemie – Chemical Monthly volume 151, pages743–749(2020)

POAP pipeline for Autodock+Openbabel

https://doi.org/10.1016/j.compbiolchem.2018.02.012

Computational Biology and Chemistry
POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening

For all those #COVIDOCKING people out there. This POAP bash program handles virtual screening by coupling Open Babel and Autodock (4 and Vina apparently). This should come in handy for drugs repurposing so common nowadays, thus creating a pipeline which handles 3d structures, conformers, erroneous datasets and more.

Vibrational Energy Transfer in solution

Xiang et al., Science 368, 665–667 (2020)

This cool paper describes an optical experiment in which a W(CO)6 / W(13CO)6 solution exhibits intermolecular VET which is rare because excited vibrational states decay via Förster or Dexter mechanisms; VET is more of an intramolecular phenomenon but the weak intermolecular interactions through a medium make solute-solute VET a non-competing event with intramolecular vibration rearrangement.

Note to self. check references 3 and 4 for VET in biological processes // 5 and 6 regarding Förster Dexter mechanisms.