Archive for the ‘Catalysis’ Category
Where to publish non-physics preprints? or where to find a chemistry preprint server without the arxiv.org like endorsement system?
A good friend, and former follow graduate student, and I recently finished a scientific manuscript we have been working for some years now. Since we are both out of academia, and busy with other things, putting an article into peer review is not our top priority at the moment. Nevertheless, we would still like the world (or at least a few people) know about our work, and also secure our intellectual property, by not letting others publish the exact same ideas. We came up with the idea of publishing it on a pre-print server, and then time should tell if we would submit to a peer-reviewed journal. The best known (physics) pre-print server is the arxiv.org hosted by Cornell University Library. Although our work probably could be classified into some subtopic physics category, strictly speaking, chemistry would be more appropriate, chemical kinetics and catalysis to be more accurate. Furthermore, the endorsement system used by arxiv.org is also frustrating, to put it mildly. Once you’re out of research it seems very difficult to get endorsement. I consider my scientific network to be quite broad and large, however I do not know a single soul who can endorse me. Thus, arxiv.org seemed out of the question. Then, where to find a chemistry pre-print server with a less strict endorsement system? It turns out that Nature has started their own pre-print service known as Nature precedings, and they are embracing chemistry. Thank you. So now our manuscript is public available. As a note to those wanting to publish physics preprints without endorsement (and chemistry as well), the so-called vixra.org (arxiv reversed) is an option. However, I have not been able to really judge the quality of the content being published. Well to be honest the same goes to Nature precedings, but since Nature Scientific Publishing is behind, it sounds better in my ears.
Years ago I made some on-line material available on my (old) website in order to supplement some of my publications. In the meantime I have closed down the old website, and guess what, now the material has been requested (cough!). What to do now? Use the the internet archive/waybackmachine.
“Browse through over 150 billion web pages archived from 1996 to a few months ago. To start surfing the Wayback, type in the web address of a site or page where you would like to start, and press enter. Then select from the archived dates available. The resulting pages point to other archived pages at as close a date as possible. Keyword searching is not currently supported.”
This page contains supplementary material to some of my publications
|Table of contents [showhide]|
Linux gazette 114
In order to try out Example 3 in the article Python for scientific use. Part I: Data visualization in Linux Gazette 114 (2005) (http://linuxgazette.net/114/andreasen.html) a number of data files are needed.
tar xvfz 3ddata.tar.gz
in the directory from which the python script is run.
Linux gazette 115
In order to try out Example 3 in the article Python for scientific use. Part II: Data analysis in Linux Gazette 115 (2005) (http://linuxgazette.net/115/andreasen.html) a number of data files are needed.
tar xvfz 3dtdata.tar.gz
in the directory from which the python script is run.
The kinetic models published in Simplified kinetic models of methanol oxidation on silver are all implemented in a number of octave (http://www.octave.org) scripts. You can see all individual files in the table below. All files can be obtained either by downloading octavefiles.tar.gz (http://andr.dk/octavefiles/octavefiles.tar.gz) or by
wget -i FILELIST.txt
|MeOH_test.m (http://andr.dk/octavefiles/MeOH_test.m)||Main file|
|Keqsel.m (http://andr.dk/octavefiles/Keqsel.m)||Reaction step equilibrium constants calculated using statistical thermodynamics|
|K_HandS.m (http://andr.dk/octavefiles/K_HandS.m)||Reaction step equilibrium constants calculated using enthalpies and entropies|
|fullrateorig.m (http://andr.dk/octavefiles/fullrateorig.m)||The original rate law from quasi equilibrium approximation and stat. therm. with a plug-flow reactor model included|
|fullrate.m (http://andr.dk/octavefiles/fullrate.m)||The original rate law from quasi equilibrium approximation and classical thermodynamics with a plug-flow reactor model included|
|marirate.m (http://andr.dk/octavefiles/marirate.m)||The MARI approximation|
|israte.m (http://andr.dk/octavefiles/israte.m)||The IS approximation|
|powerlawrate.m (http://andr.dk/octavefiles/powerlawrate.m)||The clean surface approximation|
|qtransA.m (http://andr.dk/octavefiles/qtransA.m)||Calculation of the translational partition function|
|qvibA.m (http://andr.dk/octavefiles/qvibA.m)||Calculation of the vibrational partition function for a single vibration (cm-1)|
|qvibAJ.m (http://andr.dk/octavefiles/qvibAJ.m)||Calculation of the vibrational partition function for a single vibration (J/mol)|
|qrotA2D.m (http://andr.dk/octavefiles/qrotA2D.m)||Calculation of the 2-D rotational partition function (cm-1)|
|qrotA2DJ.m (http://andr.dk/octavefiles/qrotA2DJ.m)||Calculation of the 2-D rotational partition function for a single vibration (J/mol)|
|qrotA3D.m (http://andr.dk/octavefiles/qrotA3D.m)||Calculation of the 3-D rotational partition function (cm-1)|
|qvibtotA.m (http://andr.dk/octavefiles/qvibtotA.m)||Calculation of the total vibrational partition function for a molecule (cm-1)|
|HvibA.m (http://andr.dk/octavefiles/HvibA.m)||Calculation of the vibrational enthalpy of a single vibration (cm-1)|
|HvibAJ.m (http://andr.dk/octavefiles/HvibAJ.m)||Calculation of the vibrational enthalpy of a single vibration (J/mol)|
|HvibtotA.m (http://andr.dk/octavefiles/HvibtotA.m)||Calculation of the total vibrational enthalpy for a molecule (cm-1)|
Nørskov et al. recently wrote a perspective in Science Magazine entitled “Rate Control and Reaction Engineering” with a short description “A concept for evaluating. the relative importance of steps in complex reactions may guide the development of better catalysts”. The article also addresses our recently published paper “Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates” in JACS. Thanks guys!
JACS cover: Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates
The paper “Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates” co-authored with Carsten Stegelmann and Charles T. Campbell has finally been published in Journal of the American Chemical Society. The full citation info is:
Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates,
Carsten Stegelmann, Anders Andreasen, Charles T. Campbell Journal of the American Chemical Society 2009 131 (23), 8077-8082 DOI: 10.1021/ja9000097
As an additional honor our graphich has been selected for the cover page.
Recently I co-authored a paper with Carsten Stegelmann and Charlie Campbell. I have the pleasure to announce that the paper has just been published as an ASAP article in the Journal of the American Chemical Society (doi:10.1021/ja9000097). In Nature Magazine a Research Highlight by Gavin Armstrong is addressing the publication.
Here’s the abstract:
For many decades, the concept of a “rate-determining step” has been of central importance in understanding chemical kinetics in multistep reaction mechanisms and using that understanding to advantage. Yet a rigorous method for identifying the rate-determining step in a reaction mechanism was only recently introduced, via the “degree of rate control” of elementary steps. By extending that idea, we argue that even more useful than identifying the rate-determining step is identifying the rate-controlling transition states and the rate-controlling intermediates. These identify a few distinct chemical species whose relative energies we could adjust to achieve a faster or slower net reaction rate. Their relative energies could be adjusted by a variety of practical approaches, such as adding or modifying a catalyst, modifying the solvent, or simply modifying a reactant’s molecular structure to affect electronic or steric control on the relative energies of the key species. Since these key species are the ones whose relative energies most strongly influence the net reaction rate, they also identify the species whose energetics must be most accurately measured or calculated to achieve an accurate kinetic model for any reaction mechanism. Thus, it is very important to identify these rate-controlling transition states and rate-controlling intermediates for both applied and basic research. Here, we present a method for doing that.