UserWiki:Meisam: Difference between revisions

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

*: Skeletal formula predictions for bonds/shapes are not accurate. My calculations find the geometry which have the least energy (therefore is the most stable one). These geometries may or may not be the same shape as their skeletal formula as most the complex molecules are not planar.

*:The proper method for finding the bond order is by [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO]<ref>Natural Bond Orbital</ref> analysis. I'm using the bond order from my B3LYP calculations for all my molecules. Note that NBO is not possible in [https://en.wikipedia.org/wiki/NDDO NDDO]<ref>Neglect of Diatomic Differential Overlap</ref> methods such as AM1.

*:The proper method for finding the bond order is by [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO]<ref>Natural Bond Orbital</ref> analysis. I'm using the bond order from my B3LYP calculations for all my molecules. Other than highly symmetric structures, the [https://en.wikipedia.org/wiki/Resonance_(chemistry) mesomerism] (resonance) is not stable in molecules.<ref>For example, if you replace only one of the benzene ring hydrogens with a different group, most probably you will loose the stability of delocalized electronic structure.</ref> Note that NBO is not possible in [https://en.wikipedia.org/wiki/NDDO NDDO]<ref>Neglect of Diatomic Differential Overlap</ref> methods such as AM1.

*Are these geometries valid for molecules in water/SBF<ref>Simulated Body Fluid</ref>/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.

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 *Why the molecular bonds/shapes look different than the [https://en.wikipedia.org/wiki/Skeletal_formula skeletal formula] representation?
 *: Skeletal formula predictions for bonds/shapes are not accurate. My calculations find the geometry which have the least energy (therefore is the most stable one). These geometries may or may not be the same shape as their skeletal formula as most the complex molecules are not planar.
-*:The proper method for finding the bond order is by [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO]<ref>Natural Bond Orbital</ref> analysis. I'm using the bond order from my B3LYP calculations for all my molecules. Note that NBO is not possible in [https://en.wikipedia.org/wiki/NDDO NDDO]<ref>Neglect of Diatomic Differential Overlap</ref> methods such as AM1.
+*:The proper method for finding the bond order is by [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO]<ref>Natural Bond Orbital</ref> analysis. I'm using the bond order from my B3LYP calculations for all my molecules. Other than highly symmetric structures, the [https://en.wikipedia.org/wiki/Resonance_(chemistry) mesomerism] (resonance) is not stable in molecules.<ref>For example, if you replace only one of the benzene ring hydrogens with a different group, most probably you will loose the stability of delocalized electronic structure.</ref> Note that NBO is not possible in [https://en.wikipedia.org/wiki/NDDO NDDO]<ref>Neglect of Diatomic Differential Overlap</ref> methods such as AM1.
 *Are these geometries valid for molecules in water/SBF<ref>Simulated Body Fluid</ref>/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.