UserWiki:Meisam: Difference between revisions

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*Why the molecular bonds look different than the [https://en.wikipedia.org/wiki/Skeletal_formula skeletal formula] representation?

*: Skeletal formula predictions for bonds are not accurate. The visualization software that I'm using, is guessing the bond type based on the bond length. (which may be a better estimation!) The correct way is to perform a [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO] analysis to accurately determine the bond types. (Unfortunately, I don't have enough free time to do that)

*~~It this geometry~~ the most stable molecular configuration?

*Are these geometries valid for molecules in water/SBF/blood/urine, etc?

*: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?

*: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. 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]!

*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 computational packages.

*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]!

*Which software do I use?

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

@@ Line 8: / Line 8: @@
 *Why the molecular bonds look different than the [https://en.wikipedia.org/wiki/Skeletal_formula skeletal formula] representation?
 *: Skeletal formula predictions for bonds are not accurate. The visualization software that I'm using, is guessing the bond type based on the bond length. (which may be a better estimation!) The correct way is to perform a [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO] analysis to accurately determine the bond types. (Unfortunately, I don't have enough free time to do that)
-*It this geometry the most stable molecular configuration?
+*Are these geometries valid for molecules in water/SBF/blood/urine, etc?
+*: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?
 *: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. 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]!
-*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 computational packages.
+*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]!
 *Which software do I use?
 *:I use Gaussian 09 for calculations and GaussView 5 for visualization.