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Disclaimer: These are preliminary results and may contain errorsIn a previous post I showed that minimising RDKit-generated conformers generated with MMFF led to slightly worse PM3/COSMO pKa predictions. One reason might be that the MMFF minimisation is done...
A few days ago I presented some preliminary pKa results.  Almost all the molecules in the set have more than one ionisable group. Here's how I compute the apparent pKa valuesThe microscopic pKa values are computed by\begin{equation}\label{eqn:pka}\mathrm{pK_a}=\mathrm{pK_a^{ref}}...
In this post I outlined the (possible) need for conformational analysis using a continuum model. Anders reminded me that Tinker can do this so I looked in to it. This blogpost and this GitHub repo were particularly helpful.  Here's what I found.Generating...

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When we submitted our last paper for publication, we also posted the manuscript on the pre-print server arXiv.  This has several advantages:(1) It makes the work freely accessible to everyone while the paper is being reviewed(2) It makes the work freely...
What is Computational Chemistry Highlights?CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years.  CCH is not affiliated with any publisher: it is a free resource...
Mathematician Timothy Gowers' recent public boycott of Elsevier has been joined by thousands of other people and I am one of them.My boycott, mainly because of their support for the Research Work Act (RWA), was not a very courageous move.  I have published...

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The February issue of Computational Chemistry Highlights is out.CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any...
The July issue of Computational Chemistry Highlights is out.CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher:...
The February issue of Computational Chemistry Highlights is out.CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any...