Gamess (US) frequently asked questions part 6: Obtaining proper SCF convergence (Anti-)ferromagnetic coupled Fe-S clusters

Obtaining SCF convergence of FeS clusters is a very demanding task.

The problem in FeS clusters is the arrangement of spins on the Fe atoms: if you have a cluster with 4 Fe atoms, each of them with 5 up-spins, and a total spin of zero, the arrangement of spins on the atoms could be

• Fe1 and Fe2  up-spin, Fe3 and Fe4 down-spin; or
• Fe1 and Fe4  up-spin, Fe2 and Fe3 down-spin; or
• Fe1 and Fe3  up-spin, Fe2 and Fe4 down-spin;

The problem is compounded if you have a mixture of Fe²⁺ and Fe³⁺, which may lead to 12 (or more) different spin arrangements, depending on the number of Fe²⁺ atoms. However, if you have a good guess SCF for one instance instance, you may simply substitute the coordinates of Fe2 with those of Fe4 to get a comparably good guess for the second instance, and so forth... This is the approach suggested by Greco, Fantucci, Ryde, de Gioia (2011) Int. J. Quantum Chem. 111, 3949-3960. Obtaining the guess for one of the instances is in itself quite difficult, and I usually follow the approach outlined by Szilagyi, R. K. and Winslow, M. A. (2006) J. Comput. Chem., 27: 1385–1397  .

It goes like this:

- obtain orbitals for bare Fe²⁺, Fe³⁺, S^2-, and isolated ligands, with proper spins on the Fe atoms (5/2 for Fe³⁺, 2 for Fe²⁺)

- Manually split the "alpha/up" and "beta/down" portions of the resulting  $VEC groups. For example, assuming you have a system with three Fe atoms (two Fe²⁺ and one Fe³⁺) with total spin S=5/2 and the $VEC groups for bare Fe²⁺ and bare Fe³⁺, you should cut the $VEC groups of Fe²⁺ and Fe³⁺ as:

$VEC  for the alpha (up) electrons of Fe²⁺   (let's call it "Fe2+_5_d_electrons")
$VEC  for the alpha (up) electrons of Fe³⁺   (let's call it "Fe3+_5_d_electrons")
$VEC  for the beta (down) electrons of Fe²⁺   (let's call it "Fe2+_1_d_electron")
$VEC  for the beta (down) electrons of Fe³⁺   (let's call it "Fe3+_0_d_electrons")

The total spin S=5/2 in this sample problem implies that  both Fe²⁺ atoms spins should annull each other, i.e., one Fe²⁺ is mostly "up" and the other is mostly "down". Building the new guess for the "up" electrons should therefore include:

"Fe2+_5_d_electrons" for one of the  Fe²⁺ ions,
"Fe2+_1_d_electrons" for the other  Fe²⁺,
"Fe3+_5_d_electrons" for the Fe³⁺

Building the new guess for the "down" electrons should  include:
"Fe2+_1_d_electrons" for the FIRST Fe²⁺ ions,
"Fe2+_5_d_electrons" for the other Fe²⁺,
"Fe3+_0_d_electrons" for the Fe³⁺

- combine the orbitals using the small utility called combo, which you may obtain from Alex Granovsky's Firefly website.

- Manually paste the "alpha" and "beta" guesses  into a single $vec group, which would be the proper guess.

- cross all your fingers and toes, and expect it to converge into the proper state. If it does not converge, change convergers (SOSCF=.T. DIIS=.F.), onset of SOSCF (SOGTOL=1e-3) , etc.

- after SCF optimization using this guess, manually scramble the ordering of Fe atoms in your input, to ascertain whether a lower energy solution can be obtained with a different spin distribution.



Good Luck!

Moving towards Open Access...

In physics and mathematics, publishing Preprints of papers in the arXiv is the most common form of distributing scientific papers. All the major journals in those areas have therefore been "forced" to accept papers previously available as preprints.
In Chemistry and Biology, however, most journals do not accept preprints and therefore authors are quite loath to make their work available as a preprint. The lack of this "free preprint" culture then enables journals to keep increasing their subscription prices way above inflation levels, which further gives publishers an extra incentive to keep rejecting sound work that might otherwise be available as costless preprints. This is a classic instance of Catch-22.
I believe that, as authors, we should do our utmost to fight this status quo. Our science should be evaluated on its merits, rather than on the accidental name of the journal where it has appeared. Therefore, I will henceforth submit all my Biochemistry work to PeerJ / PeerJPrePrints. PeerJ is an innovative and remarkably inexpensive Open Access Publisher with transparent peer-review and the option of publishing the paper's reviews alongside the manuscript.  The integrity of the reviewing process is therefore above reproach, ensuring that it will be both rigorous and fair.
PeerJ does not (yet?) accept submissions outside the field of Biology. My Chemistry work must continue to be submitted elsewhere. I am thinking of given the Beilstein Journal of Organic Chemistry a shot: completely free, open access, and rigorous. It does not have a stellar IF (around 2.8, I think), but who cares? Playing the IF game is ultimately detrimental to quick publication, as several journals insist on publishing only the "extra-sexy" work to prevent their IFs from falling, and often even refuse to send manuscripts for review simply because some editor feels they are not "hot" enough (ACS, I am talking to you....)

The power to change is, after all, in our hands. It may be a very small amount of power, and the odds of effecting any change may be vanishingly small, but if we do not use it, nothing will change for sure.