Monthly Archives: February 2015

London Dispersion interactions

The attractives forces that exists between molecules are known as intermolecular forces.

Intermolecular forces includes:

  1. Ionic Interactions
  2. Dipole-Dipole interactions
  3. Dispersion of London

london

The London dispersion force is the weakest intermolecular force and are referred to as Van der Waals Force.

Unequal position of electrons in molecule causes a rapid polarization and confer-polarization of the electron cloud forming short lived dipole. These dipole interact with the electron clouds of neighboring atom or molecule forming more dipoles.

They don’t exist on a long distance : about 1/r^6.

More the electrons cloud is high more it’s the polarizability of the molecule is easy and stronger is the London dispersion.

The dispersive interactions are always attractive.

This video explains very well London Dispersion:

and, an amazing natural application of the non-covalent interactions London dispersion is the Gecko. This animal is notorious for its climbing, prowess, regardless of the surface.

gecko

gecko1

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How to make grow a crystal-example of solvent diffusion

Practically all chemists knows the necessity of recrystallization as a method of purification of solid products . Less known, this method is useful for make growing crystals. The goal in growing crystals for X- Ray diffraction experiment is to grow sigle crystals. The optimum size for a crystal is about 0.2 to 0.4 mm in at least two directions of space. The factors during crystal growth which affect the size of the crystal are:

  1. The solubility of the compound in the solvent chosen for recrystallization
  2. Mechanical agitation to the system

Solvent: Choose a solvent in which your compound is moderately soluble. If the solute is too soluble, this will result in small crystal size. And supersaturated solutions tends to give crystals which are too small in size too.

Mechanics: Mechanical disturbance of the crystal growing results in smaller crystals. The crystals have to grow with a minimum of disturbance. So, don’t check how your crystals are growing every days!!! Set up the crystals growing attempt in a quiet, out of the way place for a week.

Experimental method for solvent diffusion

This method is good for mg amounts of materials which are sensitive to ambient laboratory conditions (air, moisture,..).

A compound C1 was dissolved in a solvent S1(this mixture is called M1) and placed in the diffusion tube. A mixture of the solvents which dissolved compound 1 and then the second compound was placed on the top of the first mixture M1.

The second compound C2 was dissolved in a solvent (this mixture is called M2) and placed in the top of pure solvents.

The diffusion tube is closed, then placed stand in a frizzer for several days.

The slow diffusion of M1 and M2 through pure solvent will cause crystals to form.

cristal

beauty of chemistry

Chemistry could be seen also as an art.

On these three videos you will see different things, the first one shows you reaction permitting to change the oxydation state of metals, consequently colors of it.

After, you will see in the second video, how it’s easy to make some beautiful crystals.

To finish, this last video, is about the violent reaction of some alcalin ( potassium and sodium here)

Reactions with metals, gives wonderful colors, movements of fluids

 Crystal

Sodium & potassium reactions in water!!

Both, Potassium and sodium are alcalin, you can see on this video potassium is still more reactive than sodium, be careful!

Circular dichroism and peptide

Circular dichroism (CD) is a very useful tool in peptide drug discovery.

Light absorption spectroscopy helps to determine secondary structure of polypeptide.

CD is the difference in the absorption of left-handed circularly polarized light (L-CPL) and right-handed circularly polarized light (R-CPL) and occurs when a molecule is chiral.

Example of CD spectra

CD

The measures are taken on a range of wavelengths.

The most important applications is for study a large biological molecule.

As told before, it permits to study secondary structure or also conformation of macromolecules. Because the secondary structure is very sensitive to its environment, temperature, pH, CD is crucial.

Dichroism circular can be used to see how the secondary structure changes with the environmental conditions, interaction with other molecules.

So, obtention of thermodynamic, kinetic and structural informations can be deducted.

Frustrated Lewis Pairs (FLPs)

Do you know what is a frustrated lewis pairs?

All chemists know lewis pairs: the combinaison of a lewis acid and a lewis base forming a dative (or covalent) bond.

Frustated Lewis Pairs can’t form a covalent bond. In fact, the adduct is synthesized using bulky lewis acid (for instance: B(PhF5)3 and a lewis base P(MePh)3,..

Unknown

The bond because of this steric interaction can’t be strong . It’s very low about the scale of supramolecular bond (electrostatic).

this adducts react with small molecules then according to Van der Waals interaction can pre orient the FLP for essential reaction :

For instance with: CO2, H2, …

PB

The manipulation of these FLP is very sensitive.

1) These compounds have to be manipulated under Argon or an other inert gas

2) All about staff (mass, ..) have to be into a glovebox

b

3) The glassware is name “Schlenck tube” permitting thanks to the ramps Argon/Vacuum to be into an inert and dry atmosphere.

gb                                                                   ra

4) Solvents have to be distilled under an argon atmosphere.

Crucial links for chemists (students as well as teachers)

Infrared spectroscopy

http://chemwiki.ucdavis.edu/Organic_Chemistry/Spectroscopy/Infrared_Spectroscopy

http://orgchem.colorado.edu/Spectroscopy/specttutor/irchart.pdf

Molecules

http://www.compoundchem.com/2014/11/13/vsepr/

http://www.chemguide.co.uk/atoms/bonding/shapes.html

http://winter.group.shef.ac.uk/vsepr/

Chemical reactions

http://www.compoundchem.com/2014/05/07/chemical-reactions-posters-part-i/

http://www.compoundchem.com/2014/05/11/chemical-reactions-posters-part-ii/

Elements of periodic table

Group 1: http://www.compoundchem.com/wp-content/uploads/2013/12/Group-1-Infographic.pdf

Group 2: http://www.compoundchem.com/wp-content/uploads/2013/12/Group-2-Infographic.png

Group 3: http://www.compoundchem.com/wp-content/uploads/2013/12/grp-3-infographic.png

Group 4: http://www.compoundchem.com/wp-content/uploads/2013/12/group-4-infographic.png

Group 5 : http://www.compoundchem.com/2014/01/02/element-infographics-group-5/

Group 6 :http://www.compoundchem.com/2014/01/04/element-infographics-group-6/

Group 7 :http://www.compoundchem.com/2014/01/06/element-infographics-group-7/

Group 8 :http://www.compoundchem.com/2014/01/08/element-infographics-group-8/

Transition metal: http://www.compoundchem.com/2014/01/10/element-infographics-transition-metals/

Lanthanides: http://www.compoundchem.com/2014/01/13/element-infographics-the-lanthanides/

Actinides: http://www.compoundchem.com/2014/01/18/element-infographics-the-actinides/

Tansactinides: http://www.compoundchem.com/2014/01/20/element-infographics-the-transactinides/

Antimicrobial peptides (part seven)

Mecanism about the action of antimicrobial peptides

Until today, the exact mechanism in despite of many recherches is still unknown.

We know the interactions between peptides and lipids which lead to membrane permeation.

Mechanism of action 

Carpet model-lysine interacts with anionic phospholipids head groups.

The hydrophobic region interacts with the lipid bilayer disrupting bacterial membrane.

Hydrophobicity of the core residues determines ability of peptide to insert onto the membrane.

Antimicrobial peptides

Antimicrobial peptides (part six)

1.Structure of antimicrobial peptides

Most of them are cationic and amphipathic. They contain lots of lysine and arginine residues. The simplest are alpha-helical or beta-sheets.

Both of them are the structural motifs

2. Some review

Alpha helix, beta sheets, and hairpins are examples of secondary structures of proteins.

a) Alpha helix

Antimicrobial peptides-1

Alpha helix  are stabilized by intra-chain hydrogen bonds.

Also, we can see some proteins-keratin and collagen-almost entirely alpha helical in structure.

Globular proteins contain alpha helical and beta sheets regions in addition of region without one of the both.

An alpha helix is formed by making a rope coil in a left handed direction.

Into proteins, the rope is represented by the N-C-C-N-C-C-N-…backbone of the polypeptide chain.

We find also beta sheets.

b) Beta sheets

There are two categories of beta sheets.

One is called parallel :

Antimicrobial peptides-2

We can see the chains are stackable.

The second is called anti-parallel:

Antimicrobial peptides-3

Here, on contrary, the two chains are anti parallel.

These anti parallel beta-sheets are more stable than the parallel.

Like the alpha helix, beta-sheets are held by H-bonds.

Also, in secondary structures we find hairpins

c) Hairpins

hairpins are over loop which permit a flexibility and directionality of the chains:

Antimicrobial peptides-4