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UserWiki:Meisam: Difference between revisions
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== FAQ == | == FAQ == | ||
*What do I do here? | *What do I do here? | ||
*:I calculate the stable geometry of the molecules with [https://en.wikipedia.org/wiki/Austin_Model_1 Austin Model 1] | *: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. | ||
*How accurate are these results? | *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 is hard to say. But AM1 results are fairly good and B3LYP results are mostly accurate for geometry of organic molecules. | ||
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*:No! All my calculations are done on isolated molecules (basically molecules in low pressure gas phase). The geometries depend on the environment and do change in presence of solvents. But based on the property you are interested in, they are generally a good approximation or a first guess. | *:No! All my calculations are done on isolated molecules (basically molecules in low pressure gas phase). The geometries depend on the environment and do change in presence of solvents. But based on the property you are interested in, they are generally a good approximation or a first guess. | ||
*Are these geometries the most stable molecular configuration? | *Are these geometries the most stable molecular configuration? | ||
*:There's no guarantee | *:There's no guarantee that these geometries are fully relaxed or are the most stable one. 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'm just searching for local energy minima on potential energy surface. If a molecule have several [https://en.wikipedia.org/wiki/Stereoisomerism stereoisomers], my calculations only finds one of them which is similar to my initial guess. | ||
*:I start my B3LYP calculations from the geometry obtained by AM1 method | *:I start my B3LYP calculations from the geometry obtained by AM1 method. | ||
*:Also, I do not check for existence of any imaginary vibrational frequencies. | |||
*Can people use these geometries for their own research? | *Can people use these geometries for their own research? | ||
*:Absolutely! Please read the terms of use for [https://creativecommons.org/licenses/by-sa/4.0/ CC-BY-SA-4.0 license]. | *:Absolutely! Please read the terms of use for [https://creativecommons.org/licenses/by-sa/4.0/ CC-BY-SA-4.0 license]. | ||
*: | *:Just keep in mind that B3LYP implementation of Gaussian (VWN functional part) may be different from the one you are going to use in other computational packages. | ||
*What is the Z-matrix? | *What is the Z-matrix? | ||
*:A method for representing molecular geometries. You can use that for you research or to make a better image of molecules (if you want to!) More info [https://en.wikipedia.org/wiki/Z-matrix_(chemistry) here]! | *:A method for representing molecular geometries. You can use that for you research or to make a better image of molecules (if you want to!) More info [https://en.wikipedia.org/wiki/Z-matrix_(chemistry) here]! | ||