Apr 15

IboView v20150424 released

IboView icon

linux and Windows 64 versions of IboView v20150424 were just released at www.iboview.org. Improvements include:

  • Support for importing wave functions from Orca and Molcas; Fixes for import from Turbomole (thanks to Arne Wagner, Kjell Jorner, and Thomas Driant for reporting problems and providing example files)
  • Various user-interface improvements (e.g., the program now remembers how large windows were, which improves handling on high-resolution displays)
  • Fixed some data alignment issues which could cause crashes if compiled with g++ 4.9.x
  • Properties of elements and atoms (e.g., colors, size, covalent radius) can now be changed via scripts.

If you have comments or suggestions for IboView: Do not hesitate to contact me!

— cgk

Mar 15

Curly arrow paper online \o/

The curly arrow in reaction mechanisms is one of the most iconic figureheads of chemistry. It allows us to derive, describe, and rationalize bond re-arrangements during a reaction. And, retroactively, the controversies over priority and the feuds between Robinson and Ingold (I’d like to call them the father and the mentor of the arrows, respectively) make a good showcase for how science is not always played nice—but even that cannot stop a good concept from taking over.

Nevertheless, one thing which has never been clear is how the curly arrows relate to physical reality and first-principles quantum mechanics. Unlike everyday objects, electrons in molecules always behave as quantum mechanically, and one electron is fundamentally indistinguishable from the other. That means that, according to our physical understanding, it does not even make sense to ask whether or how a lone electron pair attacks a molecule at a certain position—the question is already ill-posed at identifying the electron pair which is attacking. Electrons cannot be distinguished, after all. Added to that, the bond transformations written down in curly arrow pictures show little resemblance to anything which can be read off of canonical orbitals obtained from Hartree-Fock or Kohn-Sham DFT.


However, in the just-online paper Electron flow in reaction mechanisms—revealed from first principles, Johannes Klein and I were able to show that the curly arrow mechanisms CAN be identified in first-principles quantum chemistry—and all one has to do is to follow the change of intrinsic bond orbitals (an exact, localized description of a realistic ab-initio wave function) along reaction paths. The key here is that (a) we follow the orbitals along reaction paths (i.e., we do not only look at the starting and end structures, but also everything in-between) and (b) we follow bond orbitals, not electrons. Orbitals are not indistinguishable.

While this approach may seem obvious in retrospect, the connection between localized orbitals and curly arrows seemed to be completely absent from the literature. The matter is complicated by the fact that, apart from the IBOs, not many orbital localization techniques can follow the bond transformations; in particular, the immensely powerful Natural Bond Orbitals of Weinhold, which have been (and still are) the primary tool for interpreting electronic structure since two decades, cannot do this directly.

We hope that this direct link between first principles quantum chemistry and empirical reaction mechanisms will prove useful in understanding reactivity in real world labs. I certainly see a lot of potential in the technique. And, as a sceptic myself who is more familiar with viewing molecules as sets of a few GB of unknowns which need to be solved for, I was quite surprised with how suddenly everything fell into place.

If you want to try it yourself for your own reactions: You can, with IboView, which was also just released.

— cgk

Feb 15

IboView released — first public version

Do you do research in/with theoretical chemistry? Have you been thinking “Well, quantum chemistry is a great science, but you know what is missing? *Really* shiny orbitals.”? Then you can be helped! Behold the first public release of IboView (http://www.iboview.org).reme8-dianion

Of course, the program’s main point is not making pretty orbital plots (although it is really good at this). Its main point is to make the recently introduced IAO/IBO methodology accessible to a broader community, especially with regards to its extension for tracing reaction mechanisms, described in the upcoming article G Knizia & JEMN Klein — “Electron flow in reaction mechanisms — revealed from first principles”. These techniques allow for a simple and straight-forward interpretation of first-principles electronic structure in terms of classical bonding concepts, like covalent bonds and curly arrows (more on that once the article comes online). And this works despite IAOs/IBOs being constructed in an almost completely non-empirical fashion.

If you like, try it out. IboView is released in a source version for linux, and a source/binary version for Windows 64bit. IboView can also do simple electronic structure calculations by itself for a quick visualization of what the bonding in molecule looks like. More complex wave functions can be imported from Molpro or Turbomole, with support for other software to come.

— cgk

Feb 15

Hello, Everyone! New Site Launched.

One of the boons of starting a new research group is that you get to set up a group homepage. With colors and pictures \o/. Only… how do you do it? Traditional raw HTML and CSS? Or blog style? I decided to give WordPress a try, not the least because it is already set up by the nice people at ITS at Penn State. Yes, I am a blogger now! We will see how it goes. Until this page is populated, I would also like to point to http://www.theochem.uni-stuttgart.de/~knizia/, which still contains information not moved yet—including the source code to various software I developed over the years. Over time things will hopefully become available here, once I find more time and… figure out how to upload files.

Isn’t it great how technology simplifies everything? 8)

– cgk

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