Geometry Optimization with GAUSSIAN 03W

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Discussion Overview

The discussion revolves around the challenges of creating input files for computational chemistry calculations using GAUSSIAN 03W, specifically for a 2D coordination polymer structure. Participants explore methods for geometry optimization and IR spectra calculations using DFT and HF theories.

Discussion Character

  • Exploratory
  • Technical explanation
  • Debate/contested

Main Points Raised

  • One participant expresses uncertainty about how to create an input file for a polymeric structure in 2D, seeking guidance.
  • Another participant suggests that GAUSSIAN requires a three-dimensional structure and recommends modeling one or two monomer units instead of the entire polymer.
  • There is a clarification regarding the terms "DFT and HF theory," with a question about whether the participant refers to standard DFT and Hartree-Fock calculations or hybrid-DFT methods.
  • A later reply mentions the existence of programs for solid state DFT that implement periodic boundary conditions, although their applicability to the current case is questioned.
  • Participants discuss the potential need for geometric constraints when modeling to prevent unrealistic distortions in the optimized geometry.
  • Concerns are raised about the impact of constraints on frequency calculations, particularly for vibrational modes associated with frozen atoms.
  • Another participant suggests that molecular mechanics methods could be used to obtain frequencies and geometries for the entire polymer, though the reliability of such methods is uncertain, especially for systems involving heavier elements like cadmium.

Areas of Agreement / Disagreement

Participants generally agree that modeling one or two monomer units is necessary for the calculations, but there is no consensus on the best approach to handle the polymeric structure or the implications of using constraints in the model.

Contextual Notes

Limitations include the dependence on the choice of model (monomer units vs. entire polymer) and the potential inaccuracies introduced by constraints in geometry optimization and frequency calculations.

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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.
 
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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!)