Tag Archives: 3D

Covid19 – videos

COVID19 Under the microscope

Show COVID19 under the microscope and also animated to see its parts, how attacks our cells, and how we can destroy it

3D Visualization of COVID 19 surface for researchers

Proteins Data used (color red indicate links):

Spike (S): 6CRV

Envelope (E): 5X29

Membrane (M): 316G

How the Coronavirus Hijacks Our Cells

Similar virus to COVID19, how attacks, replicates, symptoms. Temperature effect. Herd immunity, vaccine.

How the coronavirus looks like up close

Transmission and Scanning Electron Microscope (TEM and SEM) to see Coronavirus


We are going to use the Periodic Table to talk about a very important element, which is Carbon, one of the stars of modern chemistry because is present in almost every compound  around us. Carbon itself is the principal protagonist of the part of Chemistry called Organic Chemistry.


Carbon is located in Group 4A of the Periodic Table of the Elements, that means this Element will be forming compounds sharing until 4 electrons.

Carbon and Organic Chemistry are present in different kind of materials for example in paints, rubbers, oils (and all petrochemical derivates), plastics (polymers of carbon), and even in Steel forming alloys with  metals.

In live organisms Carbon is part of the skin, hair, blood (as amino acids and proteins), fats (or lipids), carbohydrates such us glucose, DNA, RNA, vitamins, and carbon dioxide, that is why is important for Pharmaceutical  and Food industries.

Carbon is also present in graphites (as in pencils) and diamonds.

Organic Chemistry is based in an element called Carbon.

How Carbon is present in all different compounds?

There are two principal characteristic of this Element, that make him different and special from other Elements:

1st) When form compounds, they share electrons, that means that they don’t take or give electrons (they do not create ionic bonding). They form covalent bondings

2nd) They are able to share until 4 electrons. Most Elements win or take less than 3 electrons.

Now, we’ll try to see How Carbon creates compounds

We know that Carbon has 4 electrons in its valence shell, these electrons are in orbitals, one electron in one orbital.

The orbitals are around Carbon, not forming 90º or 180º  among them, but 109.5º in all cases.

To complete each orbital we need 1 electron, that can be provided for an Hydrogen for example. If that is the case, one Carbon will need 4 Hydrogens, and the final molecule is Methane, CH4.

A better representation of, methane, is this. One Carbon surrounded by 4 Hydrogens at the same distance and same angle among them.

When Carbon wants to create a bigger molecule, it replaces one Hydrogen for another Carbon and complete the other bondings with other atoms, as Hydrogens or another Carbon.

For example, when in a molecule we have 3 Carbons, then we will need 8 Hydrogens, and in that case the molecule is called Propane.


It is the process by which a solute (solid, liquid or gaseous) in contact with a solvent is dispersed forming a mixture in which the components are not distinguishable. The best example of a solution is a salt dissolved in water, the most common salt is the one we use every day at the table by the time we eat, this salt has a crystal form, is composed of ions sodium positively charged, and ions chloride with negative charge.

When a salt crystal is in contact with big amount of water, ions Chloride, negative charged, will be attracted by the positive side of water which are the hydrogen atoms, they take the ions from the crystal lattice, and the original solid pass to same state of the solvent.
The final mix is homogeneous and have the same properties in the whole mix.

In Chemistry is important to know the amount of solute in a solution, this value is known as Concentration of the solution. The concentration of a solution is calculated using

Concentration\text{ of Solution = }\tfrac{Amount\text{ }of\text{ Solute}}{Amount\text{ of Solute + Amount of Solvent}}

Molarity\text{ = }\tfrac{Moles\text{ }of\text{ Solute}}{Volume\text{ of Solution}}

Next chapter will show different ways to express concentration of solutions.


Water is one of the most important molecules in human life, not only because makes up more than two thirds of human body weight, but also because all the cell and organ functions depend on water for their functioning. Something similar occurs in animals and plants. This means that without water most kind of life on earth would disappear in a few days.

Water is composed of one Oxygen atom and two Hydrogen atoms. Oxygen has six electrons in its valence shell, and needs two electrons to acquire great stability, those two electrons are taken from two Hydrogen atoms.

The molecule of H2O is a three dimensional structure, Oxygen is the centre of the molecule, around him there are two pairs of electrons, and two Hydrogen atoms with angles around 107º among them.


Oxygen and Hydrogen have electronegativity values of  3.5 and 2.1 respectively, when they are bonded the shared electrons are attracted to the Oxygen side, leaving the Hydrogen atoms with a slightly positive charge, and producing a final polar molecule.

When a water molecule is surrounded by another water molecule, they will interact each other through those slight charges. This interaction is called “Hydrogen Bonding”, which is a weak electrostatic attraction between slight positive and negative charges of different molecules.


In a Non polar Covalent Bond, atoms share their electrons equally. That happens when, they have the same electronegativity or the same electron affinity. The best examples for this  kind of bonds are molecules created through the union of atoms of the same element, as in H2, N2, O2, Cl2  

When non-polar molecules interact among them, there are negligible forces of attraction, and they remain as individual molecules, that means these substances are gases.

In our environment we have these substances in the Air, which has approximately the following composition, 78% of N2, 21% of O2, 0.9% Ar (noble gas)




Covalent bonds involve the sharing of electrons by two atoms, in contrast to the transfer of electrons in Ionic Bonds.

Covalent Bond is another way to create a noble gas configuration for each atom. For example, Hydrogen has 1 electron, and needs another to have the same electronic configuration as gas noble Helium. Chloride, has 7 electrons, and with one more acquire the distribution of Argon.
However, when H-Cl bond is formed, there is still an unequal sharing of the electrons, because the electrons spend more time around the more nonmetallic atom, and more electronegative, in this case the Chloride, giving us a Polar Covalent Bond.
In a Polar Covalent Bond there is an atom being slightly more positive (H) than the other (Cl), i.e., the bond will produce a dipole moment, which can be evident when many H-Cl molecules interact among them, because the positive extreme of one molecule will be attracted by the negative part of the other. producing, in most of the cases, liquid substances. The most popular compound with Polar Covalent Bond is Water, where the Oxygen is the slightly negative extreme of the molecule.