Hello, these are graphics generated with Gaussian for an already optimized molecule. Could you indicate from Figure 1, where an electrophilic attack and a nucleophilic attack are most likely? Why?
There are some articles that in their results show contour figures such as those shown in Figure 2 which they call "The contour surface of electrostatic potential" but, in some cases, the authors show few discussions about this type of figures. Could you tell me what information can be obtained from Figure 2? Does Figure 1 have any relationship with Figure 2 and 3? Indicate any article or website that shows how to interpret this type of Gaussian results. Thank you.
Dear Hans Floro Zenteno Gora,
I appreciate your question, the three figures have three different objectives. One can even correlate each one of them with a single objective of subject. Below, I will explain how to read each figure:
Figure.1=> Molecular Electrostatic Potential (MEP) surface, this is to locate the positive and negative charged electrostatic potential in the molecule. In each MEP surface, as few of them already mentioned, has a color scale that indicates the negative and positive value. In the figure.1 you have red as negative extreme and blue as positive extreme. The red color with negative indicate the minimum electrostatic potential (that means it is bound loosely or excess electrons) and act as electrophilic attack. The blue indicate the maximum of electrostatic potential, and it acts opposite. (https://doi.org/10.1002/wcms.19). Note: This MEP surface have been drawn for a selected iso-surface value.
Figure.2=> Starting from the above note, if we plot all MEP surfaces with all iso-surface values, we see only the top surface. In order to see all the MEP surfaces one can simply plot each surface as a contour around the molecule. Now look at the figure.2, the each contour curves around the molecule is MEP surface, the outer contour is with lower iso-surface value and inner contour is with higher iso-surface value. The explanation is as similar as Figure.1 for selected contour.
Figure.3=> It is entirely different from what has been plotted in the Figure.1 and Figure.2. However, it is just to correlate the same results that are drawn from the Figure.1 or Figure.2. This surface is to indicate the available unoccupied surface around the molecule where the excitation are going to reside around the molecule.
If you plot any kind of figure that listed above the conclusions will be the same, so fix your object and select the figures that are appealing for the subject and explain them. You can read my paper: Article Theoretical studies on aminoborane oligomers
I'd rather go the other way - what is the chemical/physical question you'd like to answer? Then let's see if potential maps can be of interest.
As for nucleo- or electrophilicity, you'd better look at frontier orbitals and Fukui functions
Mr. Gora,
There is better to give the values on the map - it is more informative.
The various charged regions are represented by different colours. The blue colour represents the positive region and it is prone to nucleophilic attack and the red colour represents the negative region and so electrophilic attack in Figure 1.
Dear Gora,
I would also stick to the comment of Gilles Berger. The key question here is: which properties of your system you want to investigate? In one of our publications (DOI: 10.1002/chem.201600249), we also used the ESP surfaces in conjunction with quadrupole moments and molecular polarizabilities in order to investigate the anion-pi interaction between the aromatic ring. No doubt, you can extract qualitative informations from these ESP maps such as electron depletion etc. but it is always helpful to support these statements by providing observables such as physical quantities.
Hope this helps!
Dear Hans Floro Zenteno Gora,
I appreciate your question, the three figures have three different objectives. One can even correlate each one of them with a single objective of subject. Below, I will explain how to read each figure:
Figure.1=> Molecular Electrostatic Potential (MEP) surface, this is to locate the positive and negative charged electrostatic potential in the molecule. In each MEP surface, as few of them already mentioned, has a color scale that indicates the negative and positive value. In the figure.1 you have red as negative extreme and blue as positive extreme. The red color with negative indicate the minimum electrostatic potential (that means it is bound loosely or excess electrons) and act as electrophilic attack. The blue indicate the maximum of electrostatic potential, and it acts opposite. (https://doi.org/10.1002/wcms.19). Note: This MEP surface have been drawn for a selected iso-surface value.
Figure.2=> Starting from the above note, if we plot all MEP surfaces with all iso-surface values, we see only the top surface. In order to see all the MEP surfaces one can simply plot each surface as a contour around the molecule. Now look at the figure.2, the each contour curves around the molecule is MEP surface, the outer contour is with lower iso-surface value and inner contour is with higher iso-surface value. The explanation is as similar as Figure.1 for selected contour.
Figure.3=> It is entirely different from what has been plotted in the Figure.1 and Figure.2. However, it is just to correlate the same results that are drawn from the Figure.1 or Figure.2. This surface is to indicate the available unoccupied surface around the molecule where the excitation are going to reside around the molecule.
If you plot any kind of figure that listed above the conclusions will be the same, so fix your object and select the figures that are appealing for the subject and explain them. You can read my paper: Article Theoretical studies on aminoborane oligomers
Dear Gora,
If what you really want is to characterize the sites for electrophilic and nucleophilic atacks then, as Berger said, the Fukui and dual descriptors are the most suitable descriptors for this task. Also it has been reported that ESP is not very suitable for analysing these properties.
Try the Fukui functions for assigning the neucleophilic/electrophilic descriptors.
The one on the top is the electrostatic 3D map, it is generated by Gaussian by placing a 1e test charge on the molecule charge distribution. It should has Work/charge units ( J/C probably if we observe the magnitude), since de test charge is positive, the reddish regions reprents electron concentred areas while the blue-ish is just the opposite.
I think those figures looks great on posters or even on a paper, but the formal charges, Mulliken charges for instance, give the same information in a more condesed format.
Is it possible to determine if a molecule is positively or negatively charged (e.g. Nicotinamide) from this analysis?
I have observed that Nicotinamide and Isonicotinamide collected and grow on different electrodes under an electric field (Isonicotinamide on anode, and Nicotinamide on cathode), and I would like to verify that they are charged.
Alvaro David Loaiza Regarding the units calculated in Gaussian: The electrostatic potential itself has units of energy/charge (congruent with voltage), however because the values are calculated by assuming a test charge interacting with the potential field, I think the units are actually charge*potential, which is just energy. Is this not the case?
But, perhaps this is pedantic...since Gaussian uses atomic units, the elementary charge of the test particle should be +1, so the magnitude and sign of the numbers reported will be the same regardless of whether actual potential or potential energy of the test particle is reported...so **I think** the values in the cube file might be Hartree or Hartree/(elementary charge). Is this your understanding?
What is the unit of electrostatic potential (ESP) in the Gaussian09 output file, Hartree?
How to convert it to kJ/mole?
1 Hartree = 2625.5 kJ/mole ?
Fukui function and electrophilicity are great. I have used them to probe halogen bond strength. However, together with electrostatic potential, they may fail to predict bond strength quantitatively.
Prasanta Bandyopadhyay They will almost always fail to predict bond strengths since they, by definition, only account for the electrostatic contribution and not the orbital overlap part. I use Vs,max (maximum surface electrostatic potentials) calculated with MultiWFN to ascribe a number that can be CORRELATED to bond strengths or other physicochemical properties but you need a good set of known molecules to do that.
A qualitative trend might be observed if the XB donor and acceptor atom remains same and the functional groups are changed. Any idea Joaquin Barroso-Flores which model can accurately predict the bond strength?
Prasanta Bandyopadhyay a quick way would be to use the energy differences AB-A-B, but you might need the BSSE taken into account. Another way would be to use the NBODel method if you have NBO5 or above available but you can also use NBO3.1 available in Gaussian.
Check it in my blog:
https://joaquinbarroso.com/2011/06/21/nbodel/
- Badges
- Science topic