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Here's som prototype code for performing a conformer search for a transition state.  The idea is that you have found a TS for small model of the system and now you want to attach floppy ligands, generate different conformers for these ligands, and MMFF...
Jimmy Kromann, Alexander Welford, Anders Christensen, and I have been testing the connectivity-based hierarchy (CBH) approach, developed by Raghavachari and co-workers, for semempirical methods. For most methods the improvement has been quite modest and here...
Many TS search algorithms interpolate between reactants and products and require that the atom order is identical. This is time consuming to enforce by hand and hard to automate, but this paper by the folks at Schrdinger describe a solution that seems to work...

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And it's called ... arXiv!arXiv accepts chemistry papers, even though there isn't a "chemistry" category (yet?).  If you don't believe me, here are some examples filed under chemical physics (phys.chem-ph):Synthesis and conformational analysis of new derivatives...
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...

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The November 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 October 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 September 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...