The Lewis acid-base principle allows us to understand most reactions between biological structures that scale between 10 and 0.1 nanometer.
The presence and the properties of hydrogen bonds are often directly linked to the macroscopic properties of biological substances (e.g. hydrocarbons, proteins, nucleic acids). Hydrogen bonds often result in properties that have economical value.
The UIPAC(1) recommended definition of hydrogen bond is : The hydrogen bond is an attractive interaction between a hydrogen atom from a molecule or a molecular fragment X–H in which X is more electronegative than H, and an atom or a group of atoms in the same or a different molecule, in which there is evidence of bond formation.
The molecular electrostatic potential ( M.E.P.) is the coulombic interaction energy between a positive charge represented by an empty 1s orbital and 'rigid' molecule. The molecule is rigid because its properties do not change because of the 1s orbital.
The M.E.P. predicts the structure of the hydrogen bond very well. We calculated the M.E.P. for Hydrogen Fluoride, Formic Acid, Boric Acid and Water with GAMESS and MacMolPlt. These calculations show the usefulness of the M.E.P. A geometry optimization using GAMESS allows us to calculate the structure of the h-bonded complex. We can use the mulliken population analysis to evaluate the charge transfer upon h-bonding.
The M.E.P. of the adenine part of adenosine
Hydrogen fluoride has a boiling point of 19.74°C, it is extremely usefull as solvent. The molecule is monomeric above 80°C, at a lower temperature the monomer HF is in equilibrium with the hexamer HF6.
We calculated the equilibrium structure of the monomer, the dimer and the hexamer with electronic structure methods.
| HF monomer | HF dimer (HF2) | HF hexamer (HF6) |
|---|---|---|
| CML file | CML file | CML file |
| gamess input file | gamess input file | gamess input file |
Use Avogadro to read the CML files. Avogadro allows you to analyse molecular the geometry. The .inp files are the gamess input files we used this allows you to reproduce the calculations we have done.
We calculated the molecular electrostatic potential (M.E.P.) for HF monomer using Gamess(1) and MacMolPlt(2). The results are shown in the contourplot below. Positive contourlines are blue, red lines are negative contourlines.
The Lewis acid will attack the Lewis base where the M.E.P. is the most negative. This will be true for chemical reactions that are predominantly charge controlled. The formation of a hydrogen bond can thus be seen as a Lewis acid-base reaction.
Compare this result with the pictures below. These pictures show the structures of the HF dimer and the HF hexamer. The color show the extend of charge transfer that happened upon hydrogen bonding. An atom with the color red looses electron upon hydrogen binding, atoms colored bleu gain electrons upon binding. If you hoover the mouse over an atom the tooltip shows the calculated values.
In vapor at temperatures above 80°C HF is a monomer at temperatures below 80°C the monomer is in equilibrium with a hexamer (3). We calculated the equilibrium structure of the hexamer. The charge transfer was calculated by comparing the atomic Mulliken charges of the hexamer and the dimer with the atomic Mulliken charges on the HF monomer.
We calculate Mulliken charges with Hartree-Fock and MP2 methods because the molecular orbitals obtained from these methods have an (approximate) physical meaning. The Kohn-Sham orbitals obtained from density functional methods have no clear physial meaning.
The HF hydrogen bonded distance is 1.478 Angstrom for the hexamer and there is considerable charge transfer upon H-binding. The length of the HF hydrogen bond of the dimer is 1.8 Angstrom and the charge transfer is weak compared to the hexamer.
Hydrogen Fluoride dimer : charge transfer
The colors range from blue to red, the blue atoms gained electrons, the red atoms lost electrons.
Hydrogen Fluoride hexamer : charge transfer
The colors range from blue to red, the blue atoms gained electrons, the red atoms lost electrons.
Boric Acid Boric acid is manufactured on a large scale by the acidification of aqueous solutionq Borax.
We calculated the equilibrium structure of the monomer and the dimer and with electronic structure methods. In solid form boric acid has a sheetlike structure ( like graphite ), it is a weak Lewis acid.
| B(OH)3 monomer | B(OH)3 dimer |
|---|---|
| CML file | CML file |
| gamess input file | gamess input file |
Use Avogadro to read the CML files. Avogadro allows you to analyse molecular the geometry. The .inp files are the gamess input files we used this allows you to reproduce the calculations we have done.
We calculated the molecular electrostatic potential (M.E.P.) for B(OH)3 monomer using Gamess(1) and MacMolPlt(2). The results are shown in the contourplot below. Positive contourlines are blue, red lines are negative contourlines.
The Lewis acid will attack the Lewis base where the M.E.P. is the most negative. This will be true for chemical reactions that are predominantly charge controlled. The formation of a hydrogen bond can thus be seen as a Lewis acid-base reaction.
We calculated the Fukui function for B(OH)3 as a Lewis acid and the fukui function of B(OH)3 as a Lewis base. These functions predict that the electron donor will attack near the boron atom, the electron acceptor near the oxygen atom.
B(OH)3 : Lewis Acid
The colors range from bleu to red, the more blue the more likely the atom will accept an electron pair. White atoms are neutral.
B(OH)3 : Lewis Base
The colors range from bleu to red, the more blue the more likely the atom will donate an electron pair. White atoms are neutral.
Charge transfer in the hydrogen bonded boric acid dimer.
The colors range from blue to red, the blue atoms gained electrons, the red atom lost electrons.
Formic Acid Formic acid is well known as ant venom.
We calculated the equilibrium structure of the monomer, the dimer and the hexamer with electronic structure methods.
| Formic acid monomer | Formic acid dimer |
|---|---|
| CML file | CML file |
| gamess input file | gamess input file |
Use Avogadro to read the CML files. Avogadro allows you to analyse molecular the geometry. The .inp files are the gamess input files we used this allows you to reproduce the calculations we have done.
We calculated the molecular electrostatic potential (M.E.P.) for formic acid monomer using Gamess(1) and MacMolPlt(2). The results are shown in the contourplot below. Positive contourlines are blue, red lines are negative contourlines.
The Lewis acid will attack the Lewis base where the M.E.P. is the most negative. This will be true for chemical reactions that are predominantly charge controlled. The formation of a hydrogen bond can thus be seen as a Lewis acid-base reaction.
We calculated the Fukui function for formic acid as a Lewis acid and the fukui function of formic acid as a Lewis base. These functions predict that the electron donor will attack near the carbon atom, the electron acceptor near the oxygen atom.
Formic Acid : Lewis Acid
The colors range from bleu to red, the more blue the more likely the atom will accept an electron pair. White atoms are neutral.
Formic Acid : Lewis Base
The colors range from bleu to red, the more blue the more likely the atom will donate an electron pair. White atoms are neutral.
Charge transfer in the hydrogen bonded formic acid dimer.
The formic acid molecules are arranged in the form of inifinite hydrogen bonded chains in the crystal. The molecular electrostatic potential predicts the structure of the hydrogen bond.
The colors range from blue to red, the blue atoms gained electrons, the red atom lost electrons.
