UserWiki:Meisam: Difference between revisions

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==About me==

Theoretical molecular chemist/physicist. Interested in finding stable geometries of molecules (mostly research chemicals).

Theoretical molecular chemist/physicist. Interested in finding stable geometries of molecules (mostly research chemicals) as a base for further research by other scientists.

=== ~~Methods~~ I ~~am using~~ here~~: ===~~

== FAQ ==

* [https://en.wikipedia.org/wiki/Austin_Model_1 Austin Model 1]

*What do I do here?

* [https://en.wikipedia.org/wiki/Hybrid_functional#B3LYP B3LYP]

*:I calculate the stable geometry of the molecules with [https://en.wikipedia.org/wiki/Austin_Model_1 Austin Model 1], (AM1) and [https://en.wikipedia.org/wiki/Hybrid_functional#B3LYP B3LYP] [https://en.wikipedia.org/wiki/Density_functional_theory density functional approximation] method and upload my results here.

* [https://en.wikipedia.org/wiki/~~Minnesota_functionals#Minnesota_06 M06~~-2X]

*How accurate are these results?

*:It is hard to say. But AM1 results are fairly good and B3LYP results are mostly accurate for geometry of organic molecules.

*It this geometry the most stable molecular configuration?

*:There's no guarantee for that. I'm just searching for local energy minima on potential energy surface. These molecules have a high degree of freedom and I have not enough time to check for all stable geometries and find the most stable one.

*:I start my B3LYP calculations from the geometry obtained by AM1 method and usually do not check for imaginary vibrational frequencies.

*What is the Z-matrix?

*:A method for representing molecular geometries. More info [https://en.wikipedia.org/wiki/Z-matrix_(chemistry) here]!

*Are these results valid for molecules in solution/blood/urine, etc?

*:No! All my calculations are done on isolated molecules (basically gas phase molecules). The geometries depend on the environment and change in presence of solvents. But based on the property you are interested in, they are generally a good approximation or first guess.

*Can I use these geometries for my own research?

*:Absolutely! Please read the terms of use for [https://creativecommons.org/licenses/by-sa/4.0/ CC-BY-SA-4.0 license].

*:Also keep in mind that B3LYP implementation of Gaussian (VWN functional part) may be different from the one you are going to use in other packages.

*Which software do I use?

*:Gaussian 09 for calculations and GaussView 5 for visualization.

*What are my convergence criteria?

*:Unless stated otherwise:

*:Maximum Force: 0.000450

*:RMS Force: 0.000300

*:Maximum Displacement: 0.001800

*:RMS Displacement: 0.001200

==My works==

[[File:4AcoMET-UAM1.png|thumb|[[4-AcO-MET]]]]

@@ Line 1: / Line 1: @@
 ==About me==
-Theoretical molecular chemist/physicist. Interested in finding stable geometries of molecules (mostly research chemicals).
+Theoretical molecular chemist/physicist. Interested in finding stable geometries of molecules (mostly research chemicals) as a base for further research by other scientists.
-=== Methods I am using here: ===
+== FAQ ==
-* [https://en.wikipedia.org/wiki/Austin_Model_1 Austin Model 1]
+*What do I do here?
-* [https://en.wikipedia.org/wiki/Hybrid_functional#B3LYP B3LYP]
+*:I calculate the stable geometry of the molecules with [https://en.wikipedia.org/wiki/Austin_Model_1 Austin Model 1], (AM1) and [https://en.wikipedia.org/wiki/Hybrid_functional#B3LYP B3LYP] [https://en.wikipedia.org/wiki/Density_functional_theory density functional approximation] method and upload my results here.
-* [https://en.wikipedia.org/wiki/Minnesota_functionals#Minnesota_06 M06-2X]
+*How accurate are these results?
+*:It is hard to say. But AM1 results are fairly good and B3LYP results are mostly accurate for geometry of organic molecules.
+*It this geometry the most stable molecular configuration?
+*:There's no guarantee for that. I'm just searching for local energy minima on potential energy surface. These molecules have a high degree of freedom and I have not enough time to check for all stable geometries and find the most stable one.
+*:I start my B3LYP calculations from the geometry obtained by AM1 method and usually do not check for imaginary vibrational frequencies.
+*What is the Z-matrix?
+*:A method for representing molecular geometries. More info [https://en.wikipedia.org/wiki/Z-matrix_(chemistry) here]!
+*Are these results valid for molecules in solution/blood/urine, etc?
+*:No! All my calculations are done on isolated molecules (basically gas phase molecules). The geometries depend on the environment and change in presence of solvents. But based on the property you are interested in, they are generally a good approximation or first guess.
+*Can I use these geometries for my own research?
+*:Absolutely! Please read the terms of use for [https://creativecommons.org/licenses/by-sa/4.0/ CC-BY-SA-4.0 license].
+*:Also keep in mind that B3LYP implementation of Gaussian (VWN functional part) may be different from the one you are going to use in other packages.
+*Which software do I use?
+*:Gaussian 09 for calculations and GaussView 5 for visualization.
+*What are my convergence criteria?
+*:Unless stated otherwise:
+*:Maximum Force: 0.000450
+*:RMS Force: 0.000300
+*:Maximum Displacement: 0.001800
+*:RMS Displacement: 0.001200
 ==My works==
 [[File:4AcoMET-UAM1.png|thumb|[[4-AcO-MET]]]]