Water is a Lewis acid and a Lewis base at the same time. Both its electrostatic properties and its frontier orbitals are important for understanding the chemical reactions of water. Water is important in biology because water acts as a solvent and it participates in important enzymatic reactions (e.g. enzymatic hydrolysis).
|Atom||X (ångström)||Y (ångström)||Z (ångström)|
Water molecules in liquid water and in ice interact withone another by forming hydrogen bonds. Hexogonal ice is the form of natural ice and snow.
Enzymes control most biochemical reactions in living organisms, they do this by means of catalysis and inhibition. The enzymes (and proteïns in general) usually contain one or more polypeptides. Polypeptides are polymers and amino acids are the monomers comprising the polypeptides. As a consequence the chemical properties of these amino acids are very important to understand the properties of enzymes.
A lot of research has been done on enzymes. You can crystalize purified enzymes and then obtain their 3-dimensional molecular structure with x-ray and neutron diffraction experiments. Scientist often deposit the result of their research on the protein databank. You can view and download these structures directly from their website.
Calculations on amino acids :
We calculated equilibruim structures for the aminoacids shown in the table below. These calculation serve as examples of what results can be obtained with electronic structure calculations. These are the equilibrium structures for the neutral aminoacids in vacuum. The results from these calculations cannot be exptrapolated to a biological context.
We used a 6-31G+(d,p) basis set. The charges and the equilibrium geometry were calculated with density functional methods. The HOMO and the LUMO were calculated with HF MP2 methods. We did not use DFT to calculate the HOMO and the LUMO because Hartree Fock orbitals have a phsysical meaning.The Kohn Sham orbitals should be used the calculate the electron density and the properties that can be derived from these ( e.g. molecular structure and molecular electrostatic potential ) .
Then we calculated the charges on the atoms so that they fit to the molecular electrostatic potential. These charges are reactivity indexes that can be used to predict reaction mechanisms of charge controlled reactions. They will provide information about the initial step of a reaction mechnism.When two or more molecule approach later in the reaction, these charges can change due the intermolecular interaction. Note that the charges on atoms "inside" the molecule have little value because other molecule cannot get ot them.
We also calculated the mulliken analysis of the HOMO and the LUMO of these amino acids.
|Alanine (Ala)||Arginine (Arg)||Arginine protonated (Arg)||Aspartate (Asp)|
|Aspartate anion (Asp)||Asparagine (Asn)||Cysteine (Cys)||Glutamate (Glu)|
|Glutamine (Gln)||Histidine (His)||Histidine protonated (His)||Glycine (Gly)|
|IsoLeucine (Ile)||Leucine (Leu)||Lysine (Lys)||Lysine protonated (Lys)|
|Methionine (Met)||Phenylalanine (Phe)||Proline (Pro)||Serine (Ser)|
|Threonine (Thr)||Thyrosine (Tyr)||Thryptophan (Trp)||Valine (Val)|
Biological organisms use carbohydrates for energy storage and as structural components. Carbohydrates can be linked to serine, asparagine or threonine through glycosidic bonds. Monosaccharides are aldehydes or ketones. Dihydroxyacetone and d-glyceraldehyde are the smallest monosaccharides they have three carbon centers.
We calculated the Lewis acid base reactivity indices for both molecules. These reactivity indices predict that the C-O ketone bond and the C-O aldehyde bond are a Lewis acids and that the ketone and aldehyde oxygen are a Lewis bases. We did a Mulliken population analysis for the atomic orbitals for the HOMO and the LUMO. This analysis gives detailed information about the electronic rearrangement in the molecule at the initial stage of the reaction.
Dihydroxyacetone and d-glyceraldehyde equilibrium structures and reactivity indices
|dihydroxyacetone||XYZ file||Results summary|
|d-glyceraldehyde||XYZ file||Results summary|
Other monosaccharides like d-ribose and d-glucose have five and six carbon atoms. The carbon atoms of these molecules are asymmetric as a consequence there are many monosaccharides that differ only in the 3 dimensional arrangement of their atoms
α-d-glucopyranose and d-glucose equilibrium structures and reactivity indices
|d-glucose||XYZ file||Results summary|
|α-d-glucopyranose||XYZ file||Results summary|
Sucrose equilibrium structure with charges ( XYZ file )
DNA and RNA, the molecules that carry genetic information are called nucleic acids. Four nucleotides GMP, AMP, CMP, TMP are be linked through phosphoester bonds. This results in long unbranched polymers that interact with other polynucleotids through hydrogen bonding. The phosphodiester bridges acts as a Lewis base and allow for interaction with proteins.
Molecular genetics is the field of biology and genetics that studies the structure and function of genes at a molecular level. Most important biological and chemical molecular properties of nucleic acids are Lewis acid base reactions.
We calculated the equilibrium structures and the charges for these nucleotides. We used a 6-31G+(d,p) basis set. The charges and the equilibrium geometry were calculated with density functional methods.
Results for nucleic acids equilibrium structures :
|GMP||XYZ file||Results summary|
|AMP||XYZ file||Results summary|
|CMP||XYZ file||Results summary|
|TMP||XYZ file||Results summary|