while optimizing host-guest complex in GAUSSIAN at any level, we have the option of only mentioning overall charge on the system not on a particular atom. In such case, if I want to represent the oxidation state of an atom (metal centre), then how would i go for mentioning the oxidation state.
Dear Mohd,
In the input file you should write the correct charge (net charge of the molecule) and multiplicity. Once both are correct the optimization will go smoothly and be optimized (converge).
Herein two examples which help in understanding the above mentioned concept:
The first challenge in computing the energy is choosing the correct charge and multiplicity. Most organic molecules are singlets (i.e. all orbitals are doubly occupied) and have an easily identifiable charge. This is often not the case with molecules containing transition metals. Many transition metal atoms have unpaired d electrons and can have several different charges (oxidation states). Also, the charge of the ligands is not always obvious, though they almost always are singlets.
The zinc finger model is relatively easy: zinc is almost always Zn2+ and has 5 doubly occupied d orbitals, so that's a pretty safe bet. The zinc finger model contains two neutral groups (the imidazole rings) and two negatively charged groups (CH3-S-). So the charge of the entire system is zero and the multiplicity is 1.
The ferrocene model is a bit more complicated: iron is commonly found in both the +2 and +3 oxidation state. Before one starts the calculation it is important to find out which one is appropriate for ferrocene. Google says +2 (meaning 6 d electrons) and all doubly occupied orbitals (see the orbitals at the bottom of the page), so a singlet. Furthermore, it is also important to know that each ring has a -1 charge, so the total charge of the complex is 0 and the mutiplicity is 1.
http://molecularmodelingbasics.blogspot.com/2009/11/trouble-with-transition-metals-ii-scf.html
hoping this will be helpful,
Rafik
Hoping this will be helpful,
Rafik
thanks for the reply.
I still having the problem of convergence failure. I want to optimise the complex having cerium metal (in +3 oxidation state) with another host molecule. While making input for gaussian, I am mentioning +3 charge on the overall molecule placing the cerium metal in the centre.
you please suggest me that how to go for optimization at DFT/b3lyp/6-31g so that there would not be any convergence failure.
For one, you should definitely use the 6-31G* basis set, which is the smallest reasonable set to obtain paper-quality data.
Two: gaussian (and qm software) has problems with converging systems with a large positive or negative charge. Bear in mind, that such sitauation is unphysical, since in reality there are always counterions in solution. From my personal experience, having a +1/-1 is usually OK from the convergence point of view, but anything larger usually causes problems. Try adding reasonable counterions (as small as possible for the calculations time sake) and see how it converges.
Also, there is a set of commonly used gaussian commands that help in difficult cases, particularly helpful when optimizing systems consisting of two or more molecules: check scf=qc or scf=xqc, and opt=z-matrix or opt=cartesian and different combinations of them.
Dear Mohd,
I suggest that you use the following as the second row in your input file:
# B3LYP/6-311+G* Opt=(Z-matrix,MaxCycle=300,CalcFC) GFINPUT IOP(6/7=3)
It is a high basis set with diffuse function.
Good luck,
Rafik
Dear Mohd,
also, for solving the issue with the convergence you can do the following:
first, you can try and optimize your complex at the lower level of theory, for instance, B3LYP/Lanl2dz, and run frequency calculations for this level of theory. Then, you need to read the optimized geometry and wavefunction for your higher level calculation, for instance, like this:
#B3LYP/6-311+G* scf=xqc guess=read geom=check opt=(maxcycle=500,readfc,cartesian)
Or, you can try this trick too:
stop the non-converging calculation at some point, run frequency calculation, which would give you some imaginary frequencies. Then you take Cartesian coordinates of your complex from this frequency calculation as an input for the next-step geometry optimization, and you should make some changes to those coordinates, some small distortions. Your command line in this case, for the next-step geometry optimization, would look like this:
#B3LYP/6-311+G* scf=xqc guess=read opt=(maxcycle=500,readfc,cartesian)
And one more point: for Ce, actually, you cannot use the full-electron basis set like 6-311+G*, http://gaussian.com/g_tech/g_ur/m_basis_sets.htm , you should use pseudopotentials, like Lanl2dz, for instance. Then you would have to use the Gen keyword in your input, as described here:
http://gaussian.com/g_tech/g_ur/k_gen.htm
Best regards,
Aleksey.
thanks Rafik, Bartosz and Aleksey,
As mentioned by Aleksey, I will do the frequency calculations of unconverged molecule and correct the imaginary frequencies(bond). I feel that it should work.
Moreover, I am using SDD pseudopotentials for Cerium with 6-311G(d) for others.
https://www.researchgate.net/deref/http%3A%2F%2Fgaussian.com%2Fg_tech%2Fg_ur%2Fk_gen.htm
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