Pseudopotentials in Spartan'10

Posted on February 27, 2012 by alan

The Setup: Calculations dialog in Spartan’10 does not contain a checkbox for pseudopotentials, but they are there (just hidden).

I tried the following experiments with M(CO)4 and B3LYP. Each produced a slightly different result.

  • Setup: M = Ni, 6-31G* (menu). Result: All-electron calculation with 6-31G* basis for Ni, C, O (149 fns, 29 on Ni, 15 on C, 15 on O)
  • Setup: M = Ni, 6-31G* (menu) + BASIS = LACVP* (typed in Options box). Result: 10 fewer electrons (Ni core has been replaced) & 5 fewer functions (24 on Ni)
  • Setup: M = Pd, 6-31G* (menu). Result: Output file states “Basis set = 6-31G* & LANL2DZ > Kr”. Same number of basis functions as Ni(CO)4 with BASIS = LACVP*. (Number of electrons is somewhat uncertain and I’ve contacted Wavefunction about this.)

The first and third experiments are at least partially consistent with information in the Spartan’10 manual (see p. 288, 372, and 521). Pseudopotentials (LACVP) are automatically selected for elements larger than Kr, i.e., for anything beyond the first row of transition elements.

Wavefunction informs me (Feb 25, 2012):

The “new default” for “6-31G*” in Spartan 10, is 6-31G* for atoms
<= Kr, and LANL2DZ > Kr.
In Spartan 8 “6-31G*” meant 6-31G* for atoms <= Ar and LANL2DZ
> Ar.  (Referred to as LACVP*)
For completeness LANL2DZ implies 6-31G for atoms <= Ne and
pseudopotential for atoms above Ar.

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Bond, Valence Bond

Posted on August 8, 2011 by alan

I’m on sabbatical from Aug 2011 (“today”) until Aug 2012. So what does a prof do while he’s on sabbatical? I’ve done a lot of things in the past, but this sabbatical is going to be devoted to teaching chemistry + molecular modeling. Project ideas are still taking shape, but here’s a list that I’m currently fooling around with.

  • Organic chemistry (Chem 201) – develop a syllabus that is independent of all current textbooks and incorporates molecular models (particularly electrostatic potential maps)
  • Organic chemistry (Chem 201) – develop learning units that tell students my learning objectives and how to ‘get there’ (I’ve used these before in connection with a modified Keller Plan)
  • Organic chemistry (Chem 201) – develop POGIL learning activities (and incorporate molecular models, particularly electrostatic potential maps)
  • Write a book, maybe two books
    • An introduction to molecular modeling. Something that gets you started quickly and persuades you that making a plausibly useful model is never hard, always easy. Readers who want to dig deeper into computational algorithms and cutting edge computational strategies for research will need to look elsewhere (and there are plenty of good books out there for this kind of thing).
    • Stories about chemistry told through the ‘eye’ of an electrostatic potential map. Mainly organic chemistry, but perhaps some organometallics and inorganic thrown in too?
  • Explore the wonderful wacky world of iPads
    • Design apps
  • Learn more about valence bond models and how they can be exploited in chemical education. Drs. Sason Shaik and Philippe Hiberty have done chemists a huge favor by dusting off these models and applying them to all kinds of problems. Unfortunately, there is still a gap between the language they use and the language that your typical bench chemist or chemistry teacher can understand. Perhaps I can close the gap?
  • Investigate Fe-O chemistry using computational models. I’m not the first computational chemist to look into iron-catalyzed oxidation chemistry, but most of the studies I have seen have left out something that I think is really interesting: the relationship between (iron) catalyst structure and the energetics of the oxidation chemistry. Structure-reactivity relationships need to be understood if one wants to design really effective ‘green oxidants’. Look out Fe-TAML cuz here I come!
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Lab family feud

Posted on December 20, 2010 by alan

Science magazine (Nov 26, 2010) recently published a letter from Prof. Chamovitz of Tel Aviv University. He described how “the social fabric” in his lab during a recent year-long sabbatical “had deteriorated to a point where squabbling, backstabbing, and even screaming were common.” Help was eventually obtained from an unlikely source: a trained family therapist.

The therapist talked to everyone in the lab and then gave her diagnosis, “we were a dysfunctional family, complete with rebellious adolescents (senior students), impressionable children (junior students),and impotent parents (technicians and the principal investigator).” The good news? Some forced group therapy sessions for the lab workers produced results. “The students and technicians relearned how to live and work together, the new students in the lab weren’t exposed to continued tension, and I [Chamovitz] regained control of the lab.”

Who says science isn’t a human activity?

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Summer reading

Posted on March 31, 2010 by alan

It may feel a little early to start thinking about that summer research project, especially since the thesis students are still hanging around the lab, but summer will be here before you know it so let me orient you towards our Fe-TAML work now.

We have a loose collaboration with Prof. Terry Collins and the Institute of Green Science at Carnegie-Mellon University. They make all the big discoveries and we hope to find something that they have overlooked or haven’t had time to check out. It’s an extremely fair arrangement.

One of the really nice things about this arrangement is the exceptional quality of their web site. If you really dive into it, you can find all sorts of things about Fe-TAML and about green chemistry more generally. Please bookmark the Institute’s URL (if you lose track of this enry, I have added a link to the Institute under Links: Off Campus Resources) and explore it when you get a chance. It takes time to read so use it or lose it.

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Chemistry Dictionary

Posted on January 15, 2010 by alan

Finally, a dictionary of technical terms so that I won’t get all those red squigglies in MS Word every time I type ‘orbital’ or ‘toluene’. And its free!

I first read about this in the digital briefs section of C&E News (Feb 2, 2009), but the info wandered around my desk for nearly a year before I tried it out. The home for the chemistry dictionary is actually ChemistryBlog and version 2 was posted all the way back in Dec, 2008. How did I manage all this time without it?

Important: read the install.txt file when you download this and follow the instructions exactly (they are simple and they work exactly as advertised – nothing extra, nothing missing).

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Waste Not, Want Not – A Special Report

Posted on July 16, 2009 by alan

Americans have a lifestyle that is the envy of the world, or so Americans like to think. A prominent feature of our lifestyle is that we throw away a lot of stuff. OK, some of us recycle, but before we pat ourselves on the back for our full-to-the-brim recycling bins, recall that recycling, while ranking above “throw it out”, ranks below “reduce” and “reuse”. Recycling is not the solution to our trash problem.

Worse, we have almost no awareness as consumers of the waste that goes into manufacturing of consumer products. When you go to the store, do you carry along some notion of the (invisible) mound of trash that lies behind the manufacture of your Levis, your lab notebook, your iPhone, your hummus and pita bread?

If you’d like to know more about trash problems, read some of the short articles in Mother Jones’ magazine’s special report, Waste Not, Want Not (May 2009).

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Some Reading Recommendations

Posted on July 14, 2009 by alan

Following up on today’s lunch discussion, it just so happens that I have a small trove of articles to recommend. These come from the May/June 2009 issue of Sierra magazine (publishes by the Sierra Club) and all are available online. I’ll also throw my copy of the magazine in the office so that you can read real paper if you prefer. Naturally, I’m available to discuss these topics.

  • King Coal in Court (p. 39), The Enemy of the Human Race (p. 41), The Dirtiest Fuel (p. 42) – why do enviros freak out when they hear about coal-powered plants for making electricity? Here are some answers.
  • Message in a Bottle (p. 44) – Plastic is a petroleum product so we know where it comes from, but do we know where it goes? If you think about it, all persistent substances, plastic or otherwise, should follow the same route: they migrate until they can’t migrate anymore. But what does that mean for the organisms at the termini of these migrations?
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Fe-TAML vs Fe-porphyrin (HRP)

Posted on June 23, 2009 by alan

Yesterday’s discussion of Fe-TAML vs. Fe-porphyrin gave me an opportunity to spout off on some subjects that I know very little about. In an effort to provide some more reliable information, I’m going to post some info on Fe-porphyrin complexes. Here’s the first installment.

(Note: most of the following links are to Wikipedia pages. I make no promises about the accuracy or usefulness of the info provided. It was simply the most convenient way for me to make links. The image of HRP was obtained by “searching” Google images and taking the first likely-looking picture.)

The following image shows a crystal structure of horseradish peroxidase, HRP, as determined by x-ray diffraction. The image was taken from the web page of Dr. Shyamalava Mazumdar and you can find more information about this enzyme, and others, on that page.

Hrp_structure

 

 

Some features of interest (fyi – click on image to enlarge it):

  • There are actually two images here. The image in the upper left shows Fe (red sphere) surrounded by the porphyrin ligand (violet), and some axial ligands (blue). I can’t explain all of the groups that appear in this image, but if you can identify the Fe-porphyrin unit here, you can use these colors and shapes to locate this unit in the peroxidase enzyme.
  • The larger image, lower right, shows the protein (ribbon format), the Fe-porphyrin cofactor embedded in it, and some other atoms as well.
  • The “curly pasta” (red) sections of the protein are referred to as “alpha helices“. This structure permits a large number of intrahelix hydrogen bonds and is a common feature in proteins.
  • The gray sections of the protein are sometimes called “random coils” because they don’t follow any structural pattern.

Note: feel free to add comments. For example, links to better information about these topics, or links to other Fe-porphyrin protein images, would be welcome. Questions are also welcome, but you can always ask those in person when I finally get to work.

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