Creation of molecules

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Creation of Molecules

The electrical field of the nucleus reaches beyond the electron orbitals of the atom. This field can act as an attractive force on the electrons of nearby atoms and as a repulsive force on their nuclei. This mutual attraction-repulsion is the basis of attraction of atoms to one another in a specific spatial manner. And once in contact, the atoms bind to create molecules with specific geometrical shapes. The figures below show the attraction and binding of two hydrogen atoms to form a molecule (distance in angstroms, source: Dr. Richard Bader, McMaster University).

The shape of the atom is determined by the electron orbitals. As previously discussed, the orbitals occupy valid states within the shells of an atom. All orbitals, except the orbitals of the first shell, are not symmetric. The figures below show a few orbitals of the carbon atom (source: http://dauger.com/orbitals/).

So an atom exerts an asymmetric electrical field into space, i.e. the field has positive and negative regions in space. As atoms interact in space, the mutual positive and negative fields exert an attractive force on their electrons and nuclei respectively, thereby drawing them to one another, and once in contact they can bind. Quantum theory predicts, and experiments verify, that binding electrons from various atoms can occupy valid orbitals of each others atoms, thereby filling their outer electron shells. This gives rise to specific shapes for the forming molecules. The figure below demonstrates the shape of a planar water molecule (O = oxygen, H= hydrogen , p = oxygen orbital, s = hydrogen orbital) and a tetrahedral methane molecule.

The strength of the bonds and the shape of the molecules determine the nature of their behavior. Molecules in turn form their own composite orbitals. That would determine how they react with other molecules. The figure below shows the electrical field profile of water molecule (positive and negative are displayed as blue and red, respectively, source: http://departments.oxy.edu/chemistry/wreef/Intro_Modeling.html). By the virtue of this electrical field, a weak hydrogen bond is established between the positive side of the oxygen atom in one molecule and the negative side of a hydrogen atom in another molecule. This allows for the existence of liquid water between 0C and 100C. The gif animation shows water molecules, by the virtue of their weak binding, sliding over one another as the result of the force of motion applied to the liquid (source: http://www.chem.purdue.edu/gchelp/liquids/index.html). If heat is applied to liquid water it would eventually boil (100 C). At that energy level, the vibration energies of the water molecules are larger than the hydrogen bond energy of the molecules, so the molecules fly apart, i.e. they form a gaseous state. On the other hand if the temperature of water drops below 0 C, the natural vibration of the molecules are too small compared to their hydrogen bond energy, so they no longer slide over each other and form solid ice crystals (source: http://snobear.colorado.edu/Markw/SnowHydro/mol.html).

These molecules, in turn, interact with other molecules, first through electrical attraction, and once in contact through chemical reaction.

The nature of the bindings of molecules effects their properties. Some bindings involve mutual sharing of electrons (covalent bond as in the case of methane, shown above). Some are ionic (or valent), that is one atom takes over an electron of the other atom, as in the case of sodium chloride, or salt, where sodium looses the one electron of its outer shell to chloride. In such a case the sodium and chlorine atom become ionized (Na+, Cl-) in water. And in the absence of water they bind to form a crystal structure (right, source for crystal structures: http://whisky.ill.fr/dif/3D-crystals/salt.html, Cl- = yellow, Na+ = green):

Water attracts Cl- and Na+ more than they attract each other. So, in the presence of water, the Cl- and Na+ ions detach from one another and electro-statically bind to the water molecules. That is what we see when salt dissolves in water.

Some crystals form extremely strong bonds. Diamond, i.e. carbon crystal formed under extreme pressure and temperatures, is considered to be the hardest substance in nature. It's structure is shown to the right:

Where as graphite, another carbon crystal, has a layered structure. The sheets of layers bind strongly, while the layers themselves bind weakly (as shown to the right). Pencil makes tracks on paper when the sheets detach from one another and attach to the paper.

We find similar crystal structures among many solid molecular compounds we see. In metals, e.g. copper shown to the right, the outer electrons form what is called an electron sea. These electrons can move when electricity is applied to them, i.e. metals are conductors of electricity (as opposed to insulators, where applied electricity doesn't move the electrons). You will find similar electron sea structures in other metals such as iron, aluminum, gold, silver, or any other solid metallic conductor of electricity.

Of all of the solid molecular structures about, silicates are the most abundant. They not only form the very solid earth beneath our feet but when liquefied under volcanic conditions they have an amazing property of binding with pretty much anything. This property allows them to incorporate a whole slue of metals and non metals alike. The importance of that, in terms of morphological flows, is multi-fold. Under various circumstances these materials are released in a variety of forms in volcanic-aquifer regions close to the surface of the earth. As we will see in the next chapter, these materials act as catalysts facilitating reactions that turn base and intermediary organic compounds into proto-biotic compounds needed for creating proto-cells. Many of the material such as calcium, potassium, iron, etc. are incorporated in proto-cell organic structures and are therefore indispensable to the functionalities of the said structures. Furthermore, these material become food for the most primitive of cell structures that formed (and still exist) in volcano-aquifer regions as well as deep caves, as we will see later on. In the next series of slides below you will see a number of silicate structures bound with iron, magnesium, calcium, beryllium, aluminum, sodium, potassium, etc: (source: http://ccp14.minerals.csiro.au/ccp/web-mirrors/xtaldraw/crystal/silicate.htm)

Quartz (SiO2)

Biotite (K(Mg,Fe)3(AlSi3O10)(OH)2)

Beryl (Be3Al2(Si6O18))

Ilvaite (CaFe3Si2O8(OH))

Tremolite (Ca2Mg5Si8O22(OH)2)

In the next chapter we will concentrate on a special class of molecules: organic molecules. There we will build morphological pathways that turn base organic molecules into intermediary organic molecules and into proto-biotic molecules needed for building proto-cells, i.e. the reactions that give rise to the origin of life as we know it.

Chapter Key:

Morphological Flows, entities going through functional constructs

thereby creating more complex entities with more complex functionalities:

atoms == molecular orbital constructors (valent, covalent bonds - Electro-Magnetism) ==> molecules  == molecular orbital constructors (valent, covalent bonds - Electro-Magnetism) ==> more complex molecules

Courses

http://ocw.mit.edu/OcwWeb/Chemistry/5-111Fall-2005/VideoLectures/index.htm - Video Lecture Series: - Chemistry - 5.111 Principles of Chemical Science - from MIT OCW (OpenCourseWare) in Chemistry

Online Course From McMaster U. in Canada (Dr. Richard Bader, Dept. of Chemistry )

http://www.chemistry.mcmaster.ca/esam/ - Electronic structures of atoms and molecules-

http://www.chemistry.mcmaster.ca/aim/aim_0.html - Theory of Atoms in Molecules

3QA-Review

links

wikipedia:Molecule Molecules at wikipedia

http://whisky.ill.fr/dif/3D-crystals/index.html - Atomic structure of materials

http://www.ch.cam.ac.uk/magnus/molecules/ - Cool 3D interactive visualization tool

http://www.nyu.edu/pages/mathmol/library/ - Library of 3-D Molecular Structures

http://www.worldofmolecules.com/ - World of Molecules, including neat interactive Jmol applets for k-12

http://www.nyhallsci.org/marvelousmolecules/index.html - Molecules for kids- from NY Hall of Science

Next: The Proto-Biotic Cascade

Previous: Creation of Orbitals

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