Guys, long time no see again. You must be wondering where I was gone lately..??
Actually I am a little bit excess with my activity as a wife, a mother and as a student. I stop to write this blog for a long time and it is not as easy as I thought to be able to do anything that you wish. But it doesn’t means all that activity make you become un-capable to do anything!!
So let me start to tell you my story..
I am still doing my study in Shizuoka University as a master student under Prof. Enoch. Y Park as my supervisor. He accepting me as his student among other 25 students that doing their research under his laboratory. I am very grateful for what Allah ta`ala already bless to me. You know why, because not everyone has the same opportunity as I am. You can click this link for the detail information about Prof. Enoch Y Park and his laboratories here (http://www.green.shizuoka.ac.jp/ and http://www.agr.shizuoka.ac.jp/c/biotech/park/en/index.html).
Now I am doing my 2nd semester until the end of this month. I take several subject which are Advanced organic chemistry of natural product, Advanced lecture on environmental bioethics and seminar in applied biological chemistry III. The last 2 subject were finish, but the first one “Advanced organic chemistry of natural product” isn’t finish yet. I still need to study about 2 kind of topic, which are Intermolecular Interactions and Conformations of molecular shape. These are the basis of “drug design”, to create novel chemicals to probe the living systems and to develop medicines and agrochemicals, such as herbicides, pesticides and fungicides.
It is difficult to understand and I am very regret that I didn`t study well about Organic chemistry when I was conduct my Bachelor degree..hehe..:) That`s why I should write about this, so I can remember better for what I have been studied.
I would like to tell about the first topic “Intermolecular Interactions”. There are 4 interactions that we will discuss about:
Van der waals interactions
This is an attractive force between charges, in the case of cations and anions of metals. For organic molecules, instead of point charges, the dipole-dipole interactions are dominant. In metal chelating agents, we can see the charge-dipole interactions. The energy of electrostatic interactions are -1 to -10 kcal/mol.
For proteins in aqueous solutions, hydrophobic pockets inside the protein has a lower dielectric constant than an outer solvent. The solvent with a high dielectric constant disrupts electrostatic interactions between molecules, so electrostatic interactions between proteins and ligands are more effective in a hydrophobic pocket than in an outer surfaces.
Here the practical example of electrostatic interactions. This is PYR1 protein, one of the plant hormone Abscisic acid (ABA) receptors. ABA is a plant hormone that acts as a stress messenger of plant. When plants are exposed to especially, dry, cold, and osmotic stresses, adaptive responses to these stresses are mediated by ABA. We have just developed an inhibitor of ABA receptors, AS6. This is a complex of PYR1 bound AS6. The most important interaction is this, a carboxylate of AS6 and an ammonium group of lysin reside of PYR1. Zoom up this:
You can see a salt bridge between a carboxylate anion with a negative charge and an ammonium cation with a positive charge. These specific interactions are responsible for the specific recognition between proteins and ligands.
The second interaction is hydrogen bonds. This is the typical hydrogen bonds, as you know well, between XH and Y, where X and Y are atoms with a large electronegativity, O, N, S, F, Cl, Br, and I. We call this type of typical hydrogen bonds as “conventional hydrogen bonds”. The energy is -1 to -5 kcal/mol.
When an unoccupied orbital and an occupied orbital interacts, a new, more stable orbital is generated. This stabilizes the molecular complex. The best orbital interaction requires a large overlapping area of two orbitals. Thus, the angle is very important. When the angle XHY is 180 degree, the two orbitals is able to interact on the stragiht to overlap effectively.
A practical example of conventional hydrogen bonds. In this case also, I take up ABA receptors. This complex is a PYR1-ABA-HAB1 complex. HAB1 is a protein phosphatase which inactivates ABA signalling. The ABA receptor, PYR1 and ABA complex acts as an inhibitor of this phosphatase, thereby, ABA signaling is activated. Zoom up this area.
There are 2 kind of Hydrogen bonds:
- Hydrogen bond via a water molecules and
- HOMO-LUMO interactions.
- XH- pai hydrogen bonds( where X: C, O, N, S)
- HOMO-LUMO interactions
Van der Waals interactions.
The van der waals interactions are formed by two forces: one is attractive forces derived from dispersion forces, the other is repulsive forces derived from Pauli exclusion principle. The energy is about -0.5 kcal/mol, which is smaller than conventional electrostatic interactions and hydrogen bonds.
Dispersion forces, or called as London forces, are electrostatic interactions between induced dipoles. Generally, only polar molecules have dipoles, and non-polar molecules have no dipoles. Nevertheless, when you see a non-polar molecule with a much small time scale, an instantaneous dipole caused by instantaneous deviation of electrons can be observed. An instantaneous dipole occured in one molecule induces a new dipole for the neighboring molecule. This positive charge attracts electrons of an adjacent molecule, so this molecule has a dipole. This is an “induced dipole.
On the other hand, the repulsive term. You must know very well Pauli excusion principle. This is a very important principle for determining electron configulation of atoms. Generally, this principle is described by the explanation that electrons occupying an identical orbital=space must have the opposite spin.(one orbital 2 opposite direction)
The last term of intermolecular interactions is “hydrophobic interactions”. This work only in aqueous solution. This is very important. This interactions never work in vaccuum or in non-polar solvents. In the separating funnel, water and hexane are mixed and shaked, but then hexane is not mixed with water. The two solvents are separated. Why?
A hydrophobic molecule is surrounded by water molecules. These water molecules are called as hydrated water. The hydrated water molecules are unable to move freely. The move restriction results in low entropy of the system. I will discuss about entropy later.
If hydrophobic molecules assemble, a few hydrated water molecules are released into bulk water. The released waters are not restricted, so the entropy increases. That is, hydrophobic interactions are derived by an increase in entropy, which is derived by the release of the hydrated water molecules.
I think this is the end of my write about my lesson. Oh god my head become so hot and some smoke came out from it..hihi..:P
Next time I hope the author or the lecturer whoever they are they should present this subject attractively and easier to understand!!! Its time to say good bye my friends..Thank you for reading..and take a good rest…:)
PS. I already got my record for this subject and I have no regret for making this note since its really proper with the score..:)