Geometry Optimization with GAUSSIAN 03W

Click For Summary
Creating input files for computational chemistry using Gaussian requires a three-dimensional structure, which can be challenging for polymeric systems. For the coordination polymer [Cd(μ-pydc)(2-mim)]n, it's recommended to model one or two monomer units rather than attempting to simulate the entire polymer. The discussion highlights the importance of understanding the distinction between DFT and HF calculations, with a suggestion to clarify whether hybrid-DFT methods are being utilized. To optimize geometry and calculate IR spectra, users should consider building a model that includes capping hydrogens to prevent unrealistic distortions during optimization. Implementing geometric constraints may help maintain realistic interatomic distances but can complicate frequency calculations due to frozen vibrational modes. Additionally, molecular mechanics methods could provide insights into frequencies and geometries for the entire polymer, though their accuracy for heavy elements like cadmium may be limited.
leader07
Messages
2
Reaction score
0
Hello,
I am new in computational chemistry. I was calculating by "DFT and HF theory" (using GAUSSIAN 03W) molecular parameters of "2D coordination polymer, [Cd(μ-pydc)(2-mim)]n (pydc = pyridine-2,3-dicarboxylate, 2-mim = 2-methylimidazole)" . I have Crystallographic data are belong to this structure. My problem is to create the input file. I don't know How to create input file for polymeric structure in 2D.
Thanks in advance for your help.
 
Chemistry news on Phys.org
Gaussian needs a three dimensional structure. But you can't calculate a polymer. You need a specific model with a specific number of atoms. For your purposes, probably one or two monomer units. What kind of parameters are you trying to calculate, specifically?

And by "DFT and HF theory" do you mean DFT calculations and Hartree-Fock calculations, respectively, or do you mean hybrid-DFT methods (which utilize HF to calculate exchange)?
 
First of all thanks for your comments. My aim is to calculate IR spectra and geometry optimization by DFT and HF calculation respectively. I did not know how to create models.Because, as a Crystallographic structure is continued in three dimensions. What you write, I realize I have to choose only one or two asymmetric unit.



alxm said:
Gaussian needs a three dimensional structure. But you can't calculate a polymer. You need a specific model with a specific number of atoms. For your purposes, probably one or two monomer units. What kind of parameters are you trying to calculate, specifically?

And by "DFT and HF theory" do you mean DFT calculations and Hartree-Fock calculations, respectively, or do you mean hybrid-DFT methods (which utilize HF to calculate exchange)?
 
Right. Well for the sake of accuracy, I should probably mention that there does exist programs (mostly for solid state DFT) that implement periodic boundary conditions, but that's usually for quite well-ordered, tightly-bound crystals. So I'm not sure it'd be either usable or necessary here.

Depending on the resolution though, a QM model is not always more accurate than a x-tal structure. Anyhow, I'd suggest building a model of one or two monomers ('capping' the ends with hydrogens or whatever), and see what happens if you optimize the geometry. If the geometry gets unrealistically distorted due to the model being small, you could perhaps try adding some geometric constraints ('freezing' certain interatomic distances/angles) to model the constraining effect of the chain.. E.g. if you'd model a polymer as CH3-(monomer unit)n-CH3 you might try constraining the methyl-methyl distance, thus keeping the thing from "balling up" in an unrealistic fashion, but still giving the thing some mobility to flex about.

Be aware though, that any such constraints will screw up your frequency calculation though, for any vibrational mode coupled to the atoms which are frozen. So you'll end up with number of bad frequencies.

You could also get frequencies and geometries for an entire polymer using some Molecular Mechanics type method. I have no idea how good they are though (and for a system with a Cd atom, parameters may not be available). (In fact, Cd is almost too heavy an element to treat properly with nonrelativistic QM methods. You'll need a basis set with an ECP!)
 

Thread 'Gold hydride - what is the significance?'

I came.across a headline and read some of the article, so I was curious. Scientists discover that gold is a 'reactive metal' by accidentally creating a new material in the lab https://www.earth.com/news/discovery-that-gold-is-reactive-metal-by-creating-gold-hydride-in-lab-experiment/ From SLAC - A SLAC team unexpectedly formed gold hydride in an experiment that could pave the way for studying materials under extreme conditions like those found inside certain planets and stars undergoing...
View full post »