Therein, the lactone formation from pyrazines is analyzed, with some resulting orientations not quite in accordance with the common orientation patterns yield by electrondonor and electronwithrdawing groups. In order to assess the electronic structure of the intermediates and its influence on the resulting orientations, I performed a Fukui analysis based on the Natural Population formalism.

In this paper we address the calculations of the cavity of a small family of calixarenes and explore the electrostatic interactions present when some s block cations are inserted within. Two main factors affect the stability of the complexes: Fitting. The ratio between the cation radius and the mean size of the cavity; The second factor is the ionic-π interactions with the aromatic rings that make the cavity.

As usual the paper is available in pdf format at your request from this author.

Reference:

Barroso-Flores, Joaquín; Silaghi-Dumitrescu, Ioan; Petrar, P. M.; Kunsagi-Mate, Sandor* Ab initio calculations of electronic interactions in inclusion complexes of calix- and
thiacalix[n]arenes and block s cations J. Incl. Phenomena April 2012
DOI:10.1007/10847-012-0144-6

So first, as in any other part of the world, it all begins with a proposal being submitted for evaluation. In this particular case there is a specific application for “Young Researchers”, that is people who are newcomers to any scientific institution in the country, who are in need for a large amount of resources in order to get their own labs going. The notion of an “associate researcher” is not well understood, I think. After the submission is complete and the paperwork validated, the proposal is sent to a few other researchers in the field who either accept or decline to review the project and then are asked concise questions about the originality and relevance of the project; its feasibility; the proponent’s profile about how well suited he or she is to deliver what is being promised, and finally they are asked to evaluate how well justified is the requested budget. The reviewers then turn their comments, and rankings, to CONACyT in which a committee gathers all the data and ranks all the projects. Those projects with the higher ranking get their funding with, maybe, minor adjustments in order to stretch the reach of funding to as many projects as possible. Some other criteria are used, for example researchers at institutions with small budgets have increased chances of being funded than those on a large institution. It is a matter of balance: giving the money to those who need it but that at the same time will sure do more (and better) with it.

So far it all sounds pretty good and fair to me! except there is a problem: Reviewers don’t always do their job properly and sometimes you get to read comments such as

the proponent has no experience in graduating students

well, thats why I clicked the “Young Researcher” button. Some other pearls of wisdom include

the proponent didn’t take into consideration the latest publications in the field he is trying to study

and then he/she enlists references with publication dates posterior to the date of the proposal’s submission! Sometimes our proposals may not be thoroughly well read (or, lets admit, written) and reviewers give you a bad review for omitting things that you indeed covered. But once you get a bad review (from an anonymous peer) there is no turning around, you only find out what they wrote once you have been declined the grant.

My little suggestion: Let the review process be questioned, just once per reviewer and without the possibility of modifying the proposal. That is, once a reviewer emits his or her comments then I could get to read them and address their concerns in a single letter. If I can prove them something so evident as a conflicting set of dates between missing references and the proposal submission’s, then they would have to change their ranking, but without giving me the chance to modify the project anymore as to fit their comments. The process would take longer, maybe, but it already takes more than half a year! a few more months could be worthy if a more fair ranking is obtained.

Science needs funding; not all the scientific proposals deserve funding, true.

I have found through the statistics page in this blog that CCIQS is a somewhat popular search term but unfortunately there is still no website available due to some technical dificulties. Therefore I here upload the link to our proto-website (only Spanish for the time being, sorry)

I hope this helps people find some info about what we do and how to get in touch with us. Opportunities for scholarships are available both for graduate and undergraduate students. If you are interested in working with us, please get in touch with the researcher of your choice and ask for any available positions; we look forward to having more students to interact with!

As a scientist I believe the free share of information (which is not the same as to say of property) should prevail throughout the vastness of this global tool we have available. I’ve worked for private companies and I do believe in their right to keeping private the information they have invested in. But with SOPA there is an issue with freedom of speech and nobody wants to have their accounts monitored by a government, any government. Please read “1984″ by George Orwell to have a better understanding of how false security and safety is not worthy of a captive society under surveillance.

You have all gained something by the free share of knowledge in this blog, as I’ve had from other online resources such as the CCL. If SOPA is passed, then I, we, may not be able to provide help with the use of commercial software such as Gaussian, for instance, and the progress of science would be directly hurt.

I do not endorse piracy. Private companies are entitled to profit as a return of their investments. But laws such as SOPA would only hurt those trying to make the most out of the largest communication media ever created in the history of mankind, while doing little to protect investors and developers. Many are the examples of developments arising from public effort: Wikipedia; Linux; OpenGL; The GNUproject. Open share of ideas have brought this and many other resources which ultimately result in the development of science and technology. Please read this article (in Spanish) by Dr. Alejandro Pisanty, a former teacher of mine at the Chemistry School. He was the head of the Academic Computing Services at UNAM, and one of the founders of the Computational Chemistry List (CCL); He most definitely knows a thing or two about information technologies.

It should be clear that the openness of the Internet has clear advantages as seen a year ago when the people from Tunisia got organized online and got rid of a dictatorship. Control of communication is a common treat of fascist and authoritative regimes. Information set them free.

Please rate/like/comment this post if you are also against SOPA and for the freedom

of speech over the Internet.

http://sopastrike.com/strike/

Also, the manual in pdf format is included; in it you can find the proper citation which must be included in any publication that makes use of Molekel. Just in case you can’t find it, here it is:

MOLEKEL 4.3, P. Flükiger, H.P. Lüthi, S. Portmann, J. Weber, Swiss Center for Scientific
Computing, Manno (Switzerland), 2000-2002.
Stefan Portmann & Hans Peter Lüthi. MOLEKEL: An Interactive Molecular Graphics Tool.
CHIMIA (2000) 54 766-770.

Now some considerations:

1. This is an old program. It was generated back in the WindowsXP days, so it wouldn’t be a surprise if it doesn’t work in more recent platforms or under any other 32 bit OS.
2. The manual is included. Please read it. This blog is not Molekel’s help desk; I may help but I can’t solve everything, I just don’t have the time for it.
3. I didn’t participate/collaborate/helped or got involved in any way in the development of this program, i.e., don’t shoot the messenger. The Molekel homepage is: http://molekel.cscs.ch/wiki/pmwiki.php
4. I strongly recommend to make use of the NEW version. A bit more obscure but also great once you figure it out, plus there is available support for it from the actual developers.
5. I also strongly recommend to look over the internet for other visualization softwares. I don’t recall having reviewed any in this blog. Perhaps some other time.
6. Since this is not my development I will remove it from the server upon the request of the rightful owners A.S.A.P! My guess is they wont mind all that much since its an old version and it was given away for free from their server anyway.
7. I can’t think of anything else to put on this list right now but I reserve the right to come back to it and add something more. I just don’t want any trouble.

So, here it is! Right click on the link and download it; Use it to generate nice plots of your orbitals, densities, electrostatic potentials, etc. Consider this a Happy New Year’s gift!

Molekel4.3.win32 (zip)

Rate and comment this and all the other posts you find interesting in this blog. Please!

UPDATE: Thanks to Yuekui Wang for the following information.

This copy doen’t work on some WinXP machine with ATI monitor card. The original copy is still available on the cscs web site. Download link is as follows:
ftp://ftp.cscs.ch/out/molekel/molekel_4.3
It works fine on many macjines, I am sure.

But there is another striking difference between our worlds, one that during this holiday season led our friends (actually my girlfriend’s circle of which I’m now a part) to manufacture and give me this t-shirt as a holiday present:

"Live long and prosper" (BTW I also got a fancy bottle of wine, thanks Poncho!)

Yes. I’m a chemist, I have a PhD and work at a university doing research; that is enough to qualify for The Big Bang Theory cast, right? and if all resemblance is transitive then I for sure spend my Wednesday evenings at a local comic book store, right? Well, wrong! (ha! I loved that one!) But to be completely honest accurate, I do enjoy science fiction a lot. I like the classics such as Asimov and Bradbury as well as Lem and Vonegut. When it comes to cinema I consider myself a huge fan; I prefer Star Wars over Star Trek (if pressed) but particularly enjoyed the latest Star Trek installment more than any of the ones in the new SW trilogy, except maybe for “Revenge of the Sith“. When it comes to fantasy I prefer movies than literature; I’ve never read LOTR and I don’t think I will, but I’m about to re-read The Hobbit during the holidays (I need my leisure reading during the next two weeks).

Back to my pragmatic girlfriend. She doesn’t like sci-fi or fantasy; “fakey” she calls them. For her, achieving suspension of disbelief is nearly impossible and that has made me reflect on where this cliché of us liking sci-fi and fantasy so much comes from.

Science fiction is very appealing to us because allows us to set our imaginations wild and dream about what we could achieve in the future with our own work in terms of technology development (Does Gina dream about building a corporate empire? I’ll ask her tonight). Some of these achievements would involve the verification of wacky scientific theories (think about warp speed in Star Trek and how it implies that speeds faster than light are achievable via the Alcubierre metric in this instance) or the advent of a new set of them. Despite the popular belief, those in the science business have to be very creative people; we cannot simply spend the rest of our careers doing what others have already achieved (although there is an increasing number of people trying) so we all try to stay on the cutting edge even if that only generates a million different cutting edges, some of which become sharper than others. We have to be imaginative, believers of the unbelievable, for only this way we can come up with the technology that eventually makes current sci-fi look fakey. The real world of stock exchange, bills, mergers, negotiations and taxes is very elusive to most of us if not just down boring. The really remarkable thing between us is that both our worlds are able to coexist, and even more so, we support each other in our careers through success and failure, despite the fact we often don’t understand what is going on.

I will continue being the geek within her -now our- circle of friends; I will embrace it and own it. Gina on the other hand will continue being the business woman among my circle of friends from grad school; she will have to keep on nodding when we talk about academia and sci-fi; when we complain about the scarcity of liquid Nitrogen in our labs or we get excited about a new computing cluster with an increasing number of Xeon processors. It’s just a lot of real fun to merge these two real worlds.

Happy holidays, blogosphere! Live long and prosper.

PS To wrap things up this year, I’d like to thank to everyone who has liked, shared, commented, followed and subscribed. I want to wish you all a very happy new year! See you all in the future

There are nowadays some serious games which are nothing more than an internet-based platform in which tons of data are loaded and accessed by many users who analyze them while being scored on their achievements in many different ways according to the rules of each game. Remember that famous NASA screensaver (SETI@home) which used the idle time on your computer to crunch data from the SETI (Search for Extraterrestrial Intelligence) project; that is a more passive example of exo-collaboration simply called distributed computing, since the user has to do nothing but allowing the entrance of data into their computers for further processing.

Fold.it is a videogame (that actually began as a distributed computing screensaver called Rosetta@home) that allows you to play around with a protein and fold it in many different ways while you score points according to the conformer’s plausibility. Obtaining the native tertiary (and even the secondary) structure of a protein from no other information than the primary structure is extremely difficult given the enormous amount of available degrees of freedom. Molecular dynamics alone is unable to predict the native tertiary structure of the protein; the number p of possible disulfide bonds present in a protein is p = n!/[(n/2)!2^n/2]  where n is the number of cysteine residues available, plus computers know nothing about proteins or enzymatic catalysis so a hand from us fellow humans and our chemical insight is widely needed. Therefore our previous knowledge of chemistry, biochemistry and the nature of related proteins can help us help those programs in finding the best possible answer to ‘how does this protein look like in 3D space?’ but since this human-helped process is slow and cumbersome you need thousands of people working on it a great deal of time; almost as if every person playing with the same structure was a single core in your computer. Fold.it thus, is a sort of protein self docking, if you will, in which players are ranked according to their skills and rewarded according to how well your structure complies with three simple rules: 1) lack of voids (packing) 2) keeping the orange hydrophobic chains unexposed to the aqueous exterior and 3) avoiding clashes. Scoring functions for these three concepts are calculated and then yield a score for the player which is then ranked to other players folding the same protein (or to other players in their overall performance).

Image via Fold.it wiki

Fold.it has already collected some major success stories such as the one published on Nature Structural & Molecular Biology by David Baker (founder of Fold.it) et al. on September 2011 (doi:10.1038/nsmb.2119) in which players helped in solving the crystal structure of a protease from a retrovirus which causes AIDS in monkeys. The determination of this structure had already taken 15 years of work with only partial success; but the data was available in Fold.it for only three weeks when the appropriate match to the diffraction experiments was found! This case alone has stirred too much attention and for a beautifully written piece about it, you can check this article at the Discover Magazine by Ed Yong.

Other such examples of crowdsourcing in scince, more specifically in astronomy, are Galaxy Zoo and Moon Zoo in which thousands of images from the Hubble telescope and numerous moon probes are made available for users to sort and classify. The aim of Moon Zoo is to study the amount, shape and occurrence of craters, which basically never erode unlike those on Earth. This analysis will let us know more about the origin of our natural satellite and ultimately about the origins of our solar system.

To the participants in this specific kind of scientific crowdsourcing the term Citizen Science is applied and even publications such as the Scientific American magazine host a section where you can call out for volunteers in your projects. Some sort of classified ads for the lonely scientists in their labs in search for “idle” hands that can make a significant contribution to science. Some Citizen Science projects are intended for kids and teenagers as a way to get more people interested in scientific disciplines by engaging them directly in activities with a measurable progress of their own contributions. It is worth mentioning that projects like Fold.it, Moon Zoo and Galaxy Zoo are developed in a way that can be used by people with no expertise in the field in order to recruit as many people as possible just to perform a very specific task, proving thus that the human brain is a powerful and beautiful machine whose insight isn’t equaled by any artificial system, yet.

Well, it is now time to go back to work before I’m deemed a permanent exo-collaborator by my bosses. Just a final thought: What were our mothers saying about us playing too much with our video games?

2011, International Year of Chemistry

As usual please share your thoughts in the comments section, rate this post and let me know that you are out there reading this.

New basis sets and ECPs are published continuously in specialized journals all the time. The same happens with functionals for DFT calculations. The format in which they are published is free and usually only a list of coefficients and exponents are shown and one has to figure out how to introduce it in ones calculation. The EMSL Basis Set Exchange site helps you get it right! It has a clickable periodic table and a list of many (not all) different basis sets at the left side. Below the periodic table there is a menu from which one can select which program we want our basis set for; finally we click on “get basis set” and a pop-up window shows the result in the selected format along with the corresponding references for citation. A multiple query can be performed by selecting more than one element on the table, which generates a list that almost sure can be used as input without further manipulations. Dr. David Feller is to be thanked for leading the creation of this repository. More on the history and mission of the EMSL can be found on their About page. Because of my experience, the rest of the post addresses the inclusion of external basis sets in Gaussian, other programs such as NwChem will be addressed in a different post soon.

The correct format for inclusion of an external basis set is exemplified below with the inclusion of the 3-21G basis set for Carbon as obtained from the EMSL Basis Set Exchange site (blank lines are marked explicitly just to emphasize their location:

spin multiplicity
Molecular coordinates
- blank line -
C     0
S   3   1.00
    172.2560000              0.0617669
     25.9109000              0.3587940
      5.5333500              0.7007130
SP   2   1.00
      3.6649800             -0.3958970              0.2364600
      0.7705450              1.2158400              0.8606190
SP   1   1.00
      0.1958570              1.0000000              1.0000000
****
- blank line -

The use of four stars ‘****’ is mandatory to indicate the end of the basis set specification for any given atom. If a basis set is to be declared for a second atom, it should be included after the **** line without any blank line in between.

WARNING! Sometimes we can find more than one basis set in a single file this is due to different representations, spherical or cartesian basis sets. Gaussian by default uses cartesian (5D,7F) functions. Pure gaussian use 6 functions for d-type orbitals and 10 for f-type orbitals (6D, 10F). Calculations must be consistent throughout, hence all basis functions should be either cartesian or pure.

Inclusion of a pseudopotential allows for more computational resources to be used for calculation of the electronic structure of the valence shell by replacing the inner electrons for a set of functions which simulate the presence of these and their effect (such as shielding) on the valence electrons. There are full core pseudopotentialas, which replace the entire core (kernel). There are also medium core pseudopotentials which only replace the previous kernel to the full one, allowing for the outermost core electrons to be explicitly calculated. The correct inclusion of a pseudopotential is shown below exemplified by the LANL2DZ ECP by Hay and Wadt for the Chlorine atom.

spin multiplicity
Molecular coordinates
- blank line -
basis set for atom1
****
basis set for atom2 (if there is any)
****
- blank line -
CL     0
CL-ECP     2     10
d   potential
  5
1     94.8130000            -10.0000000
2    165.6440000             66.2729170
2     30.8317000            -28.9685950
2     10.5841000            -12.8663370
2      3.7704000             -1.7102170
s-d potential
  5
0    128.8391000              3.0000000
1    120.3786000             12.8528510
2     63.5622000            275.6723980
2     18.0695000            115.6777120
2      3.8142000             35.0606090
p-d potential
  6
0    216.5263000              5.0000000
1     46.5723000              7.4794860
2    147.4685000            613.0320000
2     48.9869000            280.8006850
2     13.2096000            107.8788240
2      3.1831000             15.3439560

If a second ECP is to be introduced, it should be placed right after the first one without any blank line! If a blank line is detected then the program will assume it’s done reading all ECPs and Basis Sets.

Finally, here is an example of a combination of both keywords. If a second ECP was needed then we’d place it at the end of the first one without a blank line. The molecule is any given chlorinated hydrocarbon (H, C and Cl atoms exclusively)

#P B3LYP/gen pseudo=read ADDITIONAL-KEYWORDS
- blank line -
0 1
Molecular Coordinates
- blank line -
H     0
S   3   1.00
     19.2384000              0.0328280
      2.8987000              0.2312040
      0.6535000              0.8172260
S   1   1.00
      0.1776000              1.0000000
****
C     0
S   7   1.00
   4233.0000000              0.0012200
    634.9000000              0.0093420
    146.1000000              0.0454520
     42.5000000              0.1546570
     14.1900000              0.3588660
      5.1480000              0.4386320
      1.9670000              0.1459180
S   2   1.00
      5.1480000             -0.1683670
      0.4962000              1.0600910
S   1   1.00
      0.1533000              1.0000000
P   4   1.00
     18.1600000              0.0185390
      3.9860000              0.1154360
      1.1430000              0.3861880
      0.3594000              0.6401140
P   1   1.00
      0.1146000              1.0000000
****
Cl     0
S   2   1.00
      2.2310000             -0.4900589
      0.4720000              1.2542684
S   1   1.00
      0.1631000              1.0000000
P   2   1.00
      6.2960000             -0.0635641
      0.6333000              1.0141355
P   1   1.00
      0.1819000              1.0000000
****
- blank line -
CL     0
CL-ECP     2     10
d   potential
  5
1     94.8130000            -10.0000000
2    165.6440000             66.2729170
2     30.8317000            -28.9685950
2     10.5841000            -12.8663370
2      3.7704000             -1.7102170
s-d potential
  5
0    128.8391000              3.0000000
1    120.3786000             12.8528510
2     63.5622000            275.6723980
2     18.0695000            115.6777120
2      3.8142000             35.0606090
p-d potential
  6
0    216.5263000              5.0000000
1     46.5723000              7.4794860
2    147.4685000            613.0320000
2     48.9869000            280.8006850
2     13.2096000            107.8788240
2      3.1831000             15.3439560
- blank line -

If you like this post or found it useful please leave a comment, share it or just give it a like. It is as much fun to find out people is reading as it is finding the answer to ones questions in someone else’s blog

Peace out!

The SCFVAC keyword used to calculate the Gibbs Solvation Energy change is no longer available. It is now replaced by DoVacuum which should be included in the SCRF options as SCRF=(DoVacuum,etc.). However, the absolute solvation energy now requires a gas-phase optimization along with a frequency calculation followed by the same calculations with the SCRF=SMD option in the desired solvent and with the appropriate variables.

Gaussian 03 used to calculate and report non-electrostatic contributions to the solvation energy, however they were not included in the total energy nor during optimization procedures. These non-electrosatic interactions are no longer calculated in the default. In order to include these terms during the SCF procedure, and to have them reported separately, the SCRF=SMD option should be used.

My previous post on PCM mentioned the usage of the options OFac=0.8 & RMin=0.5 as part of the additional input. These ‘magic numbers’ (I hate the term) were used to modify the way by which the overlapping spheres were treated in order to create the surface which in turn defined the cavity. G09 uses a new algorithm to make the overlaps generate a smoother surface. I recommend to use the default values before including ‘magic parameters’.

All the default values which G03 used can be retrieved with the G03Defaults keyword, but it is strongly suggested to use it only for comparison with calculations previously done with the older version.

As with some other so-called ‘white papers’ this post will be further improved as more information arises during my own calculations. Thanks for reading! Please comment/like/share this post, as well as others in the blog, if you found useful the information within.