Polyatomic Species: Hybrid & Molecular Orbitals

Polyatomic species like methane, CH4, can be described in terms of molecular orbital theory, however,
the diagrams can be very difficult to visualise. However, structures built up from hybrid atomic orbitals
are much easier comprehend.

Introduction: Methane, CH4

Using the carbon and hydrogen atomic orbitals, methane, CH4, is constructed by
overlapping the carbon's one 2s and three 2p AOs with the four hydrogen 1s AOs.

Methane's MOs have a topology similar to the AOs of carbon, but the structure can be very difficult to
visualise, so the methane MO construction diagrams A, B and C (below) are shown with the AOs and
MOs superimposed upon line structures of the methane. But, remember that the lines are "not there", it
is the bonding MOs that hold the molecule together.

It is possible to devise an infinite number of MO methane constructs depending upon how the five
nuclei (which are tetrahedral with respect to each other, with the carbon at the centre) are positioned in
space with respect to the x, y and z Cartesian axes defined px, py and pz orbitals. On other words, the
four hydrogen atoms can be regarded as sitting on a hypothetical spherical shell which is able to freely
rotate with respect to the p orbitals.

We shall examine three methane LCAO MO constructions: A, B and C below.

MO Methane: Construction A

In construction A, the three MOs derived from the carbon's three p orbitals are
degenerate, as are the four hydrogen AOs, but it is not entirely obvious how
any of the hydrogen AOs are overlapping with the carbon AOs.

The hydrogens appear to be avoiding overlap with the p orbitals.

Note, however, that these LCAO diagrams are schematic, drawn to emphasise
LCAO construction rather than attempting to represent the orbital overlap
integral.

MO Methane: Construction B
Atoms and the Chemical Bond
An ATOM consists of a nucleus, which itself consists of positively charged particles, the
protons , and of electrically neutral particles, the neutrons. Most of the mass of the atom
is concentrated in the nucleus. In the vicinity of the nucleus -- the nucleus being very
small with respect to the volume of the whole atom -- are situated the electrons . These
are negatively charged, very small entities. Their number is the same as the number of
protons of the given atom and because of this an atom is generally electrically neutral.
These electrons are situated at several energy levels in the electric field generated by the
nucleus. These energy levels are called shells. An atom is thus a configuration of nucleus
and electrons and this configuration is such that the whole system (the atom) is in a state
of lowest total energy. As such it is then as stable as possible. The atom accordingly is as
it were a stable end-product of a ' congregation ' of the relevant constituents. Which
configuration is necessary, in order for an atom to be as stable as possible (i.e. with the
lowest possible energy), is prescribed by the Schrödinger Wave Equation of Quantum
Mechanics, and this for every species of atom.
When, starting with the Hydrogen atom (this is the simplest kind of atom), which consists
of a proton (nucleus) and an electron, we want to ascend towards larger (and
consequently other) species of atom, we must add protons (and neutrons) to the nucleus,
and at the same time a corresponding number of electrons (with the number of protons
and electrons being the same, the atoms remain electrically neutral). With respect to the
electrons this is not possible just like that. The atom displays 'shells' (around the atomic
nucleus) which can be filled successively with electrons (giving rise, together with the
addition of protons and neutrons in the nucleus, to other new species of atom). The
Schrödinger Wave Equation dictates that this filling up of shells must take place in a
determined way, in order to guarantee a maximal stability of the (new) atomic species.
This goes as follows :
The first shell (the lowest energy level) can accomodate two electrons only. When besides
these still more electrons are added, then these latter must be recieved by a second shell
(a second -- higher -- energy level). This second shell can accomodate maximally eight
electrons. Yet further addition of electrons demands a third shell which also can
accomodate electrons till a certain maximum.
Every species of atom represents a Chemical Element.
We shall confine ourselves mainly to (an exposition of) the lighter Elements (i.e. to atoms
with, say, only two shells). These are the atoms Hydrogen (H), Helium (He), Lithium
(Li), Beryllium (Be), Borium (B), Carbon (C), Nitrogen (N), Oxygen (O), Fluorine (F)
and Neon (Ne).

In fact we only consider Hydrogen
consideration the Elements Helium
states, also important. The other
merely meant as illustration with
of the outer electron shell.
and Carbon, but with respect to that
and Neon are, concerning stable
Elements from the following list are
respect to the increasing saturation

The electron configurations of the above mentioned atomic species are as follows (if your
browser does not support images then click here ) :
The first shell is saturated (i.e. totally filled) when it contains two electrons.
The second shell is saturated when it contains eight electrons. When there are more
shells, then all shells up to the last (= outer) one (but this one not included) are saturated.
This outer shell sometimes (i.e. in the case of some elements) is saturated, sometimes not.
For an atom the most stable state means that the outer shell is saturated. This is, for
example, the case with Helium (He) and Neon (Ne). That is why these gases are totally
inert, they do not 'want' to change anymore ("To change " here means that the
outer shell takes in or gives up one or more electrons. But because in
such a process -- taking place in reality -- the number of protons in
the nucleus remains the same, the species of atom also remains the
same.). In order to obtain more stability, atoms, having an outer shell which is not
saturated, try to give up electrons from the outer shell to another (species of) atom, or
take in electrons from another (species of) atom, or try to obtain one or more pairs of
electrons in common with other atoms. And all these cases result in obtaining a saturated
outer shell.
Giving up or gaining of electrons gives rise to ions, these are therefore electrically
charged because a difference has been generated between the amount of positive charge
in the atomic nucleus and the amount of negative charge of the area surrounding the
atomic nucleus. The common possession of pairs of electrons with other atoms gives rise
to molecules.
These ions and molecules are entities which are more stable than the relevant atoms. A
transition from atoms to molecules (which, it is true, in most cases needs a small energy
boost), to which we, first of all, confine ourselves, can, provided that some external
conditions are satisfied, proceed spontaneously. Because of the lower energy state of the
generated molecule energy is given off into the environment. When the situation is
energetically the other way round, energy must be supplied, and certain conditions must
be such that the reaction does not reverse spontaneously.
This is possible.
From all this it is clear that the chemical properties of an (species of) atom are
determined almost entirely by the condition of the 'outer' shell, i.e. by the configuration of
the electrons in the highest energy level.

Until now we considered the distribution of the electrons among the shells. It remains to
consider in what way the electrons are distributed within each shell. Only then we will
obtain an adequate picture of the state of affairs of the area around the atomic nucleus.
But this picture can be really adequate only when we abandon the image of an electron as
a particle which performs revolutions around the nucleus.
Every material particle, big or small, shows, according to Quantum Mechanics, a Wave-
Particle Duality. This means that such a 'particle' (i.e. the same individual particle)
sometimes behaves like a (continuous) wave, somtimes as a (discrete) particle. But this
phenomenon becomes significant only in the case of very small entities. The electron is
effectively the biggest particle for which the wave-particle duality must be taken into
consideration. And this determines the behavior of atoms, especially the way they can
form bonds with each other resulting in molecules. The wave-like properties of complete
atoms or molecules can be ignored for almost all practical purposes.
An electron in an atom can be most appropriately imagined as a diffuse cloud spreading
itself out over almost the whole atom. Such a cloud, corresponding with a single electron,
is at some locations denser than at other locations. When we still think, for a moment,
about an electron as a particle, then we could say that the chance to find the particle
(electron) is greatest in the denser regions of the cloud. But after this it is best to again
forget this particle-image and interpreting the diffuse cloud as the 'real' electron. This
diffuse cloud -- (sometimes only) representing one electron -- is in fact something like a '
standing wave ' around the atomic nucleus. Electrons of an atom are standing waves,
trapped in the electrical potential field of the atomic nucleus. Because the image of an
electron as a cloud is still a little vague we must specify it a little more.
The electrons are, as has been said, divided over shells. These shells should not be taken
too litterally, but should be understood as energy levels . More accurately expressed :
shells, but not shells alone, determine the energy levels. The division of electrons within
an energy level implies a location of electrons in the form of the clouds mentioned. These
clouds are called atomic orbitals . An atomic orbital is a cloud with a determined form
and orientation, and can maximally accomodate two electrons. When such an orbital
contains two electrons then those two electrons are not in the same state, but each of them
in a different state. This state is called the spin of the electron. Electron-spin does not at
all show any similarity with the rotation (spinning) of a top, but is an abstract state of the
electron. Two spin-states are possible, up and down. When there are two electrons in an
orbital then one of them has a spin up and the other a spin down. An orbital with two such
electrons represents the most stable state. Just like the atom strives for a totally saturated
outer shell, because this is a very stable state, the atom also strives for having two such
paired electrons in every orbital (in the relevant shell) permitted by the Schrödinger Wave
Equation. These two electrons are waves which 'mix' themselves up in such a way that a
state of lowest energy results.
If we confine our discussion to the lighter elements (i.e. the lighter atomic species) then
we find two main types of orbitals. In the lowest energy levels we find spherical orbitals
(with the atomic nucleus in the center), and a little higher up on the energy ladder we find
dumbbell-shaped orbitals (with the atomic nucleus in the ' waist '). The spherical orbitals
are called s-orbitals, and the dumbbell-shaped orbitals are called p-orbitals.

We just said that the dumbbell-shaped orbitals appear at a next higher

energy level. This is true for all chemical elements except Hydrogen.
Here the energy of the electron levels depends only on the ' shell
number ' (meaning in which shell the hydrogen electron is situated),
wich implies that in Hydrogen the s-orbital of the second shell (= the
2s-orbital) lies in the same energy level as the p-orbital of the
second shell (= the 2p-orbital). In all other elements the s- and p-
orbitals lie in different energy levels. The first shell has (in all
the elements) only a s-orbital (= the 1s-orbital). When energy is
supplied to the atom, their electrons, also the one electron of the
Hydrogen atom, can 'jump' from one energy level to another.
(BALL, Ph., 1994, Designing the Molecular World, p. 24, fig. 1.7)

Because the p-orbitals can differ in orientation, three types of p-orbitals are possible,
namely px-orbitals, which are oriented along the X-axis of the 3-dimensional carthesian
coordinate system, the py-orbitals, which are oriented along the Y-axis, and the pz-
orbitals, which are oriented along the Z-axis (consequently posited vertically with respect
to the other two).

Figure 1. Shapes of s and p orbitals.

(After MOORE, J. & BARTON, Th., 1978, Organic Chemistry : An Overview )

By means of a number in front of the " s " of " s-orbital ", and in front of the "p" of " p-
orbital ", we can denote the shell (energy level) to which the relevant orbital belongs.
With a number as superscript we can denote the number of electrons in the relevant
orbital.
The innermost shell always contains an s-orbital only, and in all cases of the existence of
more shells containing electrons, this s-orbital consists of two electrons (this is the
maximum number of electrons, not only for the orbital, but also for the first shell). Thus
we can denote this s-orbital as : 1s2. Now the Schrödinger Wave Equation demands (i.e.
predicts) the following state of affairs at the next (higher) energy level (the next shell) :
First of all there is again an s-orbital, which can be written as 2s2, but along with this one
we find three other standing-wave patterns, with almost the same energy as the electrons
in the just mentioned s-orbital, the px, py and pz orbitals, which, as has been said, are
dumbbell-shaped, posited perpendicular to each other. Thus the second shell contains four
orbitals : 2s2, 2px2, 2py2 and 2pz2. And when each orbital of this shell has (received) the
maximum number of two electrons -- as indicated in the notation just given -- then the
saturated second shell contains eight electrons.
This state of affairs becomes still more complicated at higher energy levels (thus -- in this
context -- in cases of heavier atoms (atomic species)). But the quantum mechanical Wave
Equation exactly predicts how many electrons fit in each shell. Also the form and
orientation of the orbitals is predicted by the mathematics of the Quantum Theory.
Having this knowledge it is now possible to precisely set out what the covalent chemical
bond exactly is, and this means in what way the first Totalities (molecules) are formed
from atoms.

The Hydrogen molecule

We'll start our exposition with the formation of the smallest (above the atomic level)
Totality, the Hydrogen molecule . The Hydrogen molecule (H2) is a chemical compound
of an hydrogen atom with another hydrogen atom, and in this case the bonding-type is a
covalent (chemical) bond :

H+H becomes H--H (= H2)

A covalent bond between two atoms is formed by an overlap of two atomic orbitals (one
from each atom) giving rise to a molecular orbital. The two atomic orbitals each contain
one electron which is a less stable state. The resulting molecular orbital now contains two
electrons (these become, as a pair, a common possession of the two atoms), and this is a
stable state. Each hydrogen atom has an 1s-orbital, containing one electron. At the
formation of the hydrogen molecule from two atoms of hydrogen these orbitals overlap
and now form one molecular orbital with two electrons. Such a bonding molecular orbital
now comprises both hydrogen atoms, it has a cylindrical symmetry, and is called a
sigma-bond.
But things are a little more complicated than this : A rigorous quantum mechanical
description of the bonding in the H2 molecule demands that the total number of orbitals
must be conserved. We started with two atomic orbitals, so we must end up with two
molecular orbitals. One such orbital we have just described, it is called the bonding
orbital in which the electron pair resides. The other molecular orbital is empty, it does not
contain any electron. The energy of this empty orbital, i.e. the energy of an electron, if it
were situated in -- or boosted up to -- this orbital, is higher, than the energy in the atomic
orbitals. Putting electrons into this orbital will weaken the bond, since the total energy is
then greater than that when electrons occupy just the molecular bonding orbital. The
orbital is therefore called an antibonding orbital (BALL, 1994, op. cit.).
Because H2 is a more stable configuration than two (freely existing) hydrogen atoms,
energy is released to the environment during the formation of H2 from two hydrogen
atoms. This is called the bonding energy. The same amount of energy is required to break
the bond (here the covalent bond between two hydrogen atoms) up again, in order to get
back again the two hydrogen atoms from a hydrogen molecule.
So we now have described the formation of the smallest molecular Totality, namely a
Hydrogen molecule.
Each hydrogen atom in itself is -- considered after the fact -- a result of the gathering of a
proton and an electron. This whole is in the most stable state when the electron finds
itself in a spherical orbital, a 1s-orbital. This state of affairs is dictated by the Schrödinger
Wave Equation. But atoms show a strong propensity to saturate their outer electron shell,
and for a hydrogen atom this means that its (only) shell will strive to obtain two electrons
(In the case of representatives of the other atomic species, all (except
Helium) having more than one shell, the second shell is saturated not
until it contains eight electrons ). The hydrogen atom can achieve this by, for
example, entering into a covalent bond with another hydrogen atom. The resulting
hydrogen molecule is, according to the mathematics of Quantum Mechanics, more stable
than the two freely existing atoms. A H2 molecule is accordingly the stable end-state of
the interaction process of the two hydrogen atoms. Expressed alternatively, the dynamical
system, consisting of two system elements, resulted (under appropriate external
conditions) in the generation of a real intrinsical, but still microscopical, stable Totality, a
new being. The dynamical law which has operated in this case is immanent in the two
hydrogen atoms, and can be understood from the quantum math. This quantum math
describes the energy states of atoms and molecules. And every system strives -- when not
interfered with -- for a lowest energy state, because that guarantees the highest stability.

The Methane molecule

Methane is an ' organic ' molecule, it is moreover the simplest organic molecule.
This terminology dates back to the time in which one was convinced that
such molecules (such compounds) could be fabricated only by organisms.
This turned out not to be true. "Organic compounds" nowadays means :
Carbon compounds, with the exception of some very simple ones, as
Carbon dioxide (CO2), and the like.
Methane (CH4) is a compound of one carbon atom (C) with four hydrogen atoms (H).
Also in this case I am not concerned with the actual production of Methane (for example
in an industrial process), but in what way Methane -- after the fact -- is composed from its
constituents.
The electron configuration of Carbon (C) is : 1s2, 2s2, 2px, 2py, i.e. an inner, first shell
with an s-orbital, containing two electrons (1s2), and a second (and last) shell containing
an s-orbital, containing two electrons (2s2), and three (dumbbell-shaped) p-orbitals (2px,
2py and 2pz, perpendicular to each other. 2px and 2py contain one electron each, 2pz is
empty. Bonding with four hydrogen atoms -- each with one 1s-orbital, containing one
electron -- could be viewed as an overlap of the four orbitals of the outer electronshell of
Carbon with the four times one = four orbitals of the four hydrogen atoms. In this way we
should obtain four covalent bonds, three of which are perpendicular to each other, namely
there where we have overlap with the 2px, 2py and 2pz orbitals, and a fourth covalent
bond which does not have a specific orientation, because here we have an overlap of two
spherical orbitals (1s of the hydrogen and 2s of the carbon).
But it is improbable that Methane is structured that way, because the four bonds would
not have a symmetrical position with respect to each other. Bonds consist of electrons,
and because like electrical charges repel each other, these bonds try to be as far away as
possible from each other. The four bonds (in Methane) will diverge maximally from each
other, and this means that the complete spatial structure of Methane should be a regular
tetrahedron with a carbon atom in the center and the four hydrogen atoms at the vertices
of the tetrahedron. Observations show that this is indeed the case (concerning the
Methane molecule). OK, but what must happen to the orbitals in order to realize this?
An electron from the 2s-orbital of the carbon atom is transferred to the empty 2pz orbital,
which results in now having four orbitals each containing one electron : 2s, 2px, 2py and
2pz. These four orbitals are mixed up in such a way that four new, totally equivalent
orbitals appear, each still having one electron. Such an orbital is called an sp3 hybrid
orbital , and we now have four of them. And so we have obtained sp3 hybridized carbon.
An overlap of each sp3 orbital with a 1s-orbital of a hydrogen atom is now possible,
resulting in four totally equivalent covalent bonds, which are, just as in the case of the
hydrogen molecule, sigma-bonds. Because they are equivalent, these bonds can now form
the axes (reaching out from the center to the vertices) of a regular tetrahedron. Each
molecular orbital (in the case of Methane) contains two electrons, which is a stable
configuration (i.e. more stable than the orbitals possessing only one electron before the
bond was generated), and these two electrons are symmetrically distributed around the
axis between the two bonded atoms, and because of this it is called a sigma bond.

Figure 2. Orbital construction of Methane

(After MOORE & BARTON, 1978)

Also in this case (of Methane) the configuration is more stable than the case of four free
hydrogen atoms and a carbon atom before the bonding took place. So also here we can
speak of a dynamical system, consisting of five system elements, namely four hydrogen
atoms and a carbon atom. This system generates a stable Totality -- a Methane molecule
-- when certain external conditions are satisfied. Expressed in another way : When these
external conditions prevail, then the dynamical law for (the generation of) Methane (i.e.
the generation of a Methane molecule) will ' start to operate ', and, consequently, the
Totality, the Methane molecule, will appear. This dynamical law can be understood on the
basis of the quantum math, which predicts the energy states.

Carbon--Carbon Bonds. The Ethane molecule

Carbon plays an important role in the formation of molecules that make Life possible,
because the orbitals of two carbon atoms can overlap resulting in strong carbon--carbon
bonds. In this way a chain of carbon atoms of unlimited length can be generated, making
possible the formation of very complex molecules. Being "complex molecules" means
that such molecules can perform FUNCTIONS, very special functions, as is the case with
enzymes. This capacity to form long stable chains is unique for carbon. Other chemical
elements, for instance Silicon, can form only short chains, because the bonding-energy is
low (so only relatively little energy is needed to break up these bonds again). Thus carbon
is the very element making possible the formation of very large complex biomolecules,
and consequently the very element for the formation of Life. The bio-liquid in which the
life processes take place is Water. Because of the very special electrical properties of
water, it is, in spite of the fact of the smallness of its molecules, at normal temperatures a
liquid. In living things this liquid serves as a medium of transport.
The special electrical properties of water just mentioned consists of
the following : The propensity to the formation of hydrogen bonds
between the molecules. Because of this the molecules are less free and
water remains a liquid at normal conditions.

With the help of the theory of orbitals we can show the structure of the carbon--carbon
bonds (of course (the explanation of) this bond is also based on the quantum math).
When we have a sp3 hybridized carbon atom, thus with four sp3 orbitals, then three of
them can overlap with, say, hydrogen (Here we expound the formation of the Ethane
molecule). In this way we obtain a so-called Methyl radical, CH3. This still contains a
left-over sp3 orbital. We now can couple two such methyl radicals together by letting
these left-over sp3 orbitals overlap each other, resulting accordingly in a sigma-bond
between the two carbon atoms (The bonds with the hydrogen atoms also are sigma-
bonds).
What we obtain is an Ethane molecule, H3CCH3 (= C2H6).

Figure 3. Orbital construction of Ethane

(After MOORE & BARTON, 1978)
Also in this case a more stable (with respect to the free hydrogen atoms and free carbon
atoms) Totality is generated, an Ethane molecule, in which all atoms possess a totally
saturated outer electronshell, because of having electron pairs in common. Moreover each
orbital contains two electrons and so it is stable too.
The dynamical system, with system elements H, H, H, H, H, H, C and C, generated the
Totality H3CCH3, or, denoted in a more elaborated fashion :

H
HCH
HCH
H

It generated an Ethane molecule.

This is accordingly a pattern, generated from the system elements
(initially randomly located and not bonded) mentioned. This pattern is
(in the present case of an Ethane molecule) 3-dimensional, meaning that
it is not the case that everything of the structure lies in one and the
same plane as the diagram might suggest. Also here the bonds of the
carbon atoms show a tetrahedral orientation.
Also the formation of this Totality is dictated by the quantum formalism which predicts
the energy states.

The Ethylene molecule

In order to understand the formation of an Ethylene molecule, and consequently the
formation of a double bond, we must dig a little deeper in the phenomenon of the
hybridization of atomic orbitals.
In the sp3 hybridization, considered above, all three p-orbitals, 2px, 2py and 2pz were
used. These were mixed up with the 2s-orbital, resulting in four equivalent orbitals,
which, after overlapping with the hydrogen orbitals, form the four equivalent bonds (in
the case of Methane).
But it is also possible that hybridization (of, say, carbon) involves only two p-orbitals,
resulting accordingly in three sp2 hybrid orbitals. Because of the mutual repellence these
orbitals order themselves in a plane and include angles of 120 degrees between each
other. It is also possible that only one p-orbital is involved in the hybridization, resulting
in two sp hybrid orbitals. Because of their mutual repellence they will orientate
themselves in each others direction, i.e. they will be in line with each other, making an
angle of 180 degrees with each other. The remaining p-orbitals, not involved in the
hybridization, orient themselves perpendicular to the plane of the sp2 hybrid orbitals and
perpendicular to the axis of the sp hybrid orbitals.

Carbon atoms can also form double bonds with each other. Such a covalent double bond
has a particular structure, which we shall explain with the (help of the) formation of an
Ethylene molecule.
When we have sp2 hybridized carbon (which as such is generated in the case of certain
bondings), then we have three sp2 hybrid orbitals. And a p-orbital was still left over,
oriented perpendicular to the plane of the three sp2orbitals. When we now couple two
hydrogen atoms to two (out of the three) sp2 orbitals of the carbon atom (consequently
everytime an overlap of an 1s-orbital -- containing one electron -- of hydrogen, with an
sp2 orbital -- containing one electron), then we obtain a H2C unit in which there are still
two orbitals left, having both only one electron, namely an sp2 orbital and the left-over p-
orbital.
We can now couple two such units together by letting their sp2 orbitals (which have not
participated in the bonding with hydrogen) overlap (resulting also in this case in a
maximally filled -- with two electrons -- molecular orbital). Consequently the carbon
atoms will then be bonded to each other with a sigma-bond. But both H2C units also still
have the mentioned left-over p-orbital, i.e. two p-orbitals perpendicular to the other
orbitals. These can overlap sideways with each other resulting in a stable molecular
orbital. But because this molecular orbital is perpendicular to the remaining orbitals, the
bonding is still, it is true, a covalent one -- because it is based on a common possession of
one (or more) electronpairs -- but is of a different type (within the covalent bonds) than
the sigma-bond. Such a bond is called
a pi-bond.
While the bonding-orbital in the case of a sigma-bond lies in the axis (conceptually)
connecting the two bonded atoms, it lies in the case of a pi-bond above and below (but
not in) that axis. The resulting molecule is an Ethylene molecule, H2C==CH2. It reveals
the following pattern :

H H
C
C
H H

It is a flat molecule with the sigma-bond between the two C-atoms lying in that plane
(The same is the case with the sigma-bonds with the four hydrogen atoms) and the pi-
bond between these two C-atoms lying above and below that plane.
The double bond between the carbon atoms thus consists of a sigma-bond and a pi-bond.
Figure 4. Construction of the double bond
(After MOORE & BARTON, 1978)

Also in this case a stable Totality has been formed from the system elements
H, H, H, H, C and C.

In a comparable manner also the generation of a triple bond between two carbon atoms is
possible. When they saturate themselves subsequently with hydrogen then we have
Acetylene, HCCH, where the C-atoms are bonded with each other by means of three
bonds.

Isomerism
It often occurs that a same number and type of atoms, i.e. one and the same collection of
atoms, can, in each case, form different (possible) compounds, each consisting of all the
atoms of that collection, thus (can form) different configurations of those constituent
atoms, for example in the case of the hydrocarbon Buthane.
Buthane consists of four C-atoms (= carbon atoms) and ten H-atoms (= hydrogen atoms),
C4H10. A possible structure of this set of atoms is a straight C-chain, another one is a
branched C-chain :

H H H H
H C C C C H
H H H H

and
 H
H H C H H
H C C C H
H H H

Thus a same collection of four C-atoms and ten H-atoms can give two different patterns
of those same atoms. These are two different -- concerning content -- Totalities, but
having the same empirical formula C4H10. They are called isomers .
Because such molecules have different forms (patterns) they also have different physical
properties, for instance different boiling-points, melting-points and solubilities.
Accordingly the straight chain isomer of C4H10 has a boiling-point of 0 degrees Celcius
and a melting-point of minus 138 degrees Celcius, while the branched isomer of C4H10
has a boiling-point of minus 12 degrees Celcius and a melting-point of minus 159 degrees
Celcius.
Here we see how properties (in this case per se properties) eventually must originate from
concrete structural aspects of the Totality (the uniform thing) in question.
The boiling point, melting point and solubility are, it is true, 'bulk-
properties', and so it does not make sense to speak about the boiling
point etc. of a Buthane-molecule. But such bulk-properties are rooted
in the properties of the individual molecules, for instance their form,
their electrical properties, their weight.

When the chain lenght increases, the number of isomers grows very rapidly.
When the carbon is bonded not only with hydrogen but also with other chemical
elements, for instance with oxygen (O) then there are even more possibilities for
isomerism. Let's look to two compounds with the formula C2H6O, where one of them
contains two C--O bonds and the other a C--O bond and a O--H bond. These isomers
possess very different chemical properties, one of them is an unreactive ether and the
other is a very reactive alcohol:

H H
H C O C H
H H

Dimethylether

H
H C H
H C H
O
H
 Ethylalcohol

The ether is almost totally insoluble in water, while the alcohol is infinitely soluble in
water.

The fact that the extremities of a carbon chain can bond with each other, resulting in a
cyclic structure, offers new possibilities for isomerism.
The formula C5H10 can represent a 5-carbon chain, straight or branched, with a double
bond, or a ring structure with single bonds only.

A very interesting recently discovered (and synthesized) family of molecules are the
Fullerenes. These are molecules consisting solely of carbon atoms. Until this discovery
only two types of carbon 'molecules' were known : Diamond and Graphite. Both are
crystalline structures consisting of an indefinite number of carbon atoms, arranged in
periodic arrays. So these are crystals -- and so not molecules in the strict sense.
But the recently discovered carbon structures are real molecules, because in them a
definite number of individual carbon atoms is involved. Such a molecule consists of
carbon atoms arranged, not in a periodic way, but forming a closed cage of relatively few
atoms.
The first discovered (in the 1980's) Fullerene is a molecular cage consisting of 60 carbon
atoms. The cage is a closed hollow ball of 60 carbon atoms arranged in the form of a
soccer ball. This ball is in fact a polyhedron consisting of twelve pentagons and twenty
hexagons, just like the patches of a soccer ball. The carbon atoms reside at the vertices
(one atom at each vertex). Because in such a structure each atom is connected to three
others, one of those three bonds must be a double bond, making four bonds for each
carbon atom (so no bonds are unsatisfied dangling bonds). The inspiration that the new
molecule should have this cage-like structure consisting of polygons, came from the
structure of the geodesic dome at the Montreal Expo of 1967, designed by the American
architect Richard Buckminster Fuller. So the new molecule was christined
buckminsterfullerene.
Structure of Buckminsterfullerene
Top : The structure of the sixty-carbon-atom cluster, called buckminsterfullerene.
Left : The pattern of single and double bonds which allows all of the atoms to form four
bonds.
Right : The pattern of hexagons and pentagons in this highly symmetrical shape is the
same as that in a soccer ball.
Each carbon atom in the cage is equivalent.
(After BALL, 1994)

Because of mathematical reasons such closed molecular cages can only be formed when,
in addition to a number of hexagons, there are precisely twelve pentagons present in the
structure ( NOTE 4 ). A second restriction is that the pentagons should not be located
adjacent to each other -- this would give rise to an unstable bonding pattern, which would
rapidly rearrange. All pentagons must be isolated from one another. This clearly is a
chemical restriction. For C60 (buckminsterfullerene) there are 1812 possible ways of
arranging the pentagonal and hexagonal rings, but only one in which no pentagons are
adjacent. So C60 has no isomers.
But also larger fullerenes have become known, and these do have isomers. But their
number is limited because of the restriction mentioned. So C76 has just two, it seems, and
C78 perhaps eight or so. The giant fullerenes C120, C240 and C540 are expected to have some
particularly symmetrical isomers, but these molecules haven't yet been isolated in
sufficient quantities to put this to the test.

So it is clear from the first examples that isomers, having, accordingly, a same empirical
formula (= a same number and type of atoms), can strongly differ from each other. Such a
group of isomers represents a collection of possible combinations (configurations) of a
same mumber and type of atoms.
Seen after the fact it is clear that the same dynamical systems (in which " the same "
means : consisting of a same number and type of system elements) can result in the
generation of different (with respect to content) Totalities. This implies that those
dynamical systems turn out to be not the same, with respect to content, only their pool of
elements was the same. It follows that the Dynamical Law for such a Totality (generated
thing) is not equivalent to the complete collection of system elements, because in that
case only one dynamical law would be possible. In the case of isomerism many
Dynamical Laws are possible, relating to a same pool of system elements. And in the case
of the generation of the several Fullerene species we see that a large enough collection of
specifically the same elements can give rise to several possible species of Totality. Now it
is also clear that the nature of such a dynamical law (and, in general, every dynamical
law) is abstract.

Let's give a brief exposition about the seat of a dynamical law, and how the above
mentioned phenomena are thought to be possible.
(See for more details the Essay on Dynamical Systems ) The Dynamical Law of a
dynamical system must reside in some way in the system elements, more precisely in
some of the properties of the system elements.
The actually existing properties relating to each freely existing system element (i.e. as
such distinguished from the Essence of such a system element) either are actual and
constant structural configurations, or an interaction (result) with external factors. These
last mentioned actually existing properties of a system element are as such dependent on
the outside world. In this context the " outside world " not only comprises the remaining
system elements but also the other entities not belonging to the dynamical system as such
(not being system elements). Abiding in all these actually existing properties (including
the constant properties) of all those system elements is the Dynamical Law relating to the
generation of a certain Totality (a uniform thing), predetermined by this law. Altered
external conditions result in a change of some of these properties (i.e. resulting in an
exchange of some properties) implying that a part of the actually existing properties is
now different, and this new garnish of actually existing properties of system elements
now harbours a new (i.e. different with respect to content) Dynamical Law, resulting in
the generation of a different, with respect to content, Totality.
Of course the effects of environmental changes on (the alternation of)
actually existing (i.e. actually being present) properties of system
elements are partially rooted in the nature of those system elements
themselves (i.e. in certain constant structures in each of those system
elements).

Molecules are Totalities, each consisting of a definite and fixed number and proportion of
individual atoms [ in contrast to crystals, where the proportion is, it is
true, also constant (except in the case of mixed crystals, that
constitute a special problem, discussed earlier), but where the number
of individual atoms participating in the crystal structure is not fixed
: a single crystal consists of the periodic stacking of microscopic
units in three directions, resulting in the fact that its size is not
fixed ]. A molecule consists of a definite number of parts giving rise to a definite shape
and size. Such a structure we call tectological (in contrast to that of single crystals).
This tectological structure we also encounter in certain twinned crystals, that can be
considered as consisting of several single crystals grown together in a regular and
repeatable way, according to one or another twin law. And almost all organisms, and their
parts, show this structure too, which allows them to have certain definite imaginary body
axes, that, together with the quality of their poles (namely being homopolar or
heteropolar) allow for their stereometric basic form to be determined. On the basis of
this we can classify such organisms as Axonia, while the few organisms that do not
admit of such a stereometric basic form to be determined, can be called Anaxonia (The
Axonia can be further classified into Homaxonia, Polyaxonia, Monaxonia, Stauraxonia
and Spiraxonia, depending on the differentiation and nature of their axes and poles).

On the second (part of this) website, accessible by clicking on the last entry of the contents frame
Continuation of this Series, we have laid down the complete theories about the tectological
structure (TECTOLOGY) and stereometric basic form (PROMORPHOLOGY) in organisms.

Many molecules, especially the smaller ones, are Axonia, they all have a definite
stereometric basic form. A nice example is the Methane molecule, CH4, that has the shape
of a regular tetrahedron. And of course such a form is one of the effects of the relevant
Dynamical Law.

In all the above we have demonstrated how the very small Totalities generally look like,
and in what way their structure is dictated by energy-states.
Because the carboncompounds can attain any degree of complexity, they can constitute
the machinery of Life and Consciousness.

Crystals
In addition to molecules chemical bonds also occur in Crystals.
In many crystals these are ionic bonds. For example the constituents of a crystal of
common salt (NaCl) are held together by such ionic bonds. These bonds originate by
reason of the fact that atoms (as we now know from the foregoing) strive for a fully
saturated outer shell. Sodium (Na) possesses one electron in the outer electronshell.
Saturation of this shell would demand seven more atoms. But it is easier just to give up
that one electron, resulting in the last shell but one becoming the last (= outer) shell, and
this one was already saturated (otherwise the atom would never have started to fill a next
shell). Because of the giving up of this electron the sodium atom becomes positively
charged, it now is a sodium ion. Chlorine has seven electrons in the outer shell. It
saturates this shell by taking up the electron that was given up by the sodium atom.
Because of that the chlorine atom becomes negatively charged, it has become a chlorine
ion. The positively charged sodium ions attract (with an electrostatical force) the
negatively charged chlorine ions, resulting, when they form a supersaturated solution in
water, in a crystal lattice, in which each sodium ion tries to collect as many chlorine ions
as possible, and vice versa.
In several kinds of other crystals (crystal species) the constituents are held together by
covalent bonds. Also other bonding types (for instance the hydrogen bond) can play a
role in the formation of crystals.

So in this Essay we have learned that the Chemical Bond is crucial for the possibility of
the formation of whatever Totality above the atomic level.
In Organisms this means the formation of complex biomolecules, which together can
form a macroscopical pattern. The latter will involve concentrations of such, and other,
molecules, especially concentration differences and aggregations steered by intrinsic
dynamical laws. In addition to the resulting, generally dynamical, structures (which we
can already encounter in non-living dissipative structures), organisms also display a
never-ceasing and coherent chemism. Important for all this is the capacity of an organism
to extract energy from the environment, by which it can maintain its far-from-equilibrium
state (in thermodynamic respect), and thus can continue to function.
In the case of crystals matters are different. They are almost completely statical Totalities
without a metabolism. They are, just like the molecules, equilibrium structures.

Atomic orbitals
So far, we've seen that we can explain some experimentally observed properties
using simple models like Lewis Dot structure and VSEPR. These models still do
not explain many chemical properties. In this section, we will develop a new
model that explains further some of the chemical reactivities we observe and also
ties in our knowledge of atomic orbitals and expands it further.

So far, we've been saying that molecular bonding involves atomic orbitals in
some way. We will now explore atomic orbitals and develop an understanding of
their involvement in molecular orbitals (e.g. bonds).

Lets look at the VSEPR models identify the places where they are lacking in
explanations. We'll then look at the model of localized molecular orbitals and see
how this new model is better.

To make a molecular orbital (bond), we must use an atomic orbital from each
atom involved in the bond. What do these atomic orbitals look like?

In the molecule BeCl2 , we saw that there are two electron domains
on opposite sides of the beryllium atom involved in the bonds to the two
chlorines. How do these domains arise? Our atom of beryllium has atomic
orbitals for its valence shell (n = 2) of type s and p. If we try to make bonds using
two of these orbitals, we find that we cannot come up with two orbitals that are
identical and have lobes on opposite sides of the Be.

Image of probability domains of electrons in orbitals 2s and 2p.

The color indicates the phase of the wave-function (the wave-like
properties of the electron). In-phase functions add positively
(constructive interference) and out of phase functions add
negatively (destructive interference).

If we use one of these orbitals for one bond and the other for the other bond, we
will obviously not have two identical bonds. We obviously need another model for
the atomic orbitals in order to explain their participation in bonding. One thing
many students forget when thinking of this process is that the orbitals them
selves are not really entities and are not really the thing that matters. What
matters is the overall energy of the system and its symmetry. An atom in free
space is symmetrical (as much as its electrons will permit. The atomic orbitals s,
p, d, f,... are merely the basis functions that we use to add up to the overall space
occupied by the electrons. Note that any sub shell always adds up to be
spherically symmetrical. We can easily choose a different set of basis functions
(orbitals) to describe the space occupied by the electrons. Whatever basis set we
use must exactly define the same space as our spdf model. We are free to
divide up the space any way we want in order to more easily understand and
calculate what we need.
What we need to do is use different (linear)
combinations of the spdf domains to create new As an analogy, let's consider
domains (orbitals). a point in 2 dimensional
cartesian space.
We divide up the space (sphere) in such a way that
each domain (orbital) of the sphere is involved in only
one bond. This makes it much easier for any
calculations we might have to do.

Let's first consider what happens in the BeCl2 case:

First, we overlap the 2s and 2p in two different ways.

(remember, we're just creating new functions, not
moving electrons)

If the point is represent in the

normal set of cartesian
coordinates (basis set), we
Here, we see that the two different ways of adding up need an x value and a y
the orbitals result in the phases interacting indifferent value. On the other hand we
ways. In the 2s+2p case, the left-hand side will be can represent the same point
smaller since the phases of the original s and p are using the alternate (rotated
opposite and vice versa for the 2s-2p case. set) coordinate system
(alternate basis set) In the
The two new orbitals we get will look like the rotated system, notice that
following picture. one of the coordinates is zero
(It still exists though.) and we
can more easily ignore it in
any calculations involving the
point. We do the same with
the space occupied by the
atom's electrons. Redefine
the basis set we use so that
we can simplify the
mathematics.

Two sp hybridized orbitals made from

an s and a p orbital. The two hybrid orbitals have
Now, we can see that the two different orbitals (coloured blue and green) still
have properties that look like the p orbitals (two lobes, of different phase) and
some properties like an s orbital (large bulbous, surrounding the nucleus (a bit).
Most importantly, the two will sum up to make the same shaped space as has
using the spdf model so these two orbitals will exactly describe the same space
as the original s and p orbitals did. Now, we can look at using these to make
molecular bonds.

In the case of BF3, we have three fluorenes bonded to the central boron with
what are experimentally observed to be identical bonds. Again, we cannot find a
way of using the spdf model to easily describe the orbitals used for this so we will
re-slice the sphere to make use of the space in a new way. First, we need only
use three orbitals to create three bond so lets use s,p,p and leave one p orbital
untouched on the atom.

An s and two p orbitals add up their shapes to give a fat disk (note the color
 coding is used here to indicate different orbitals, not different phases). The
three orbitals are 120º apart.

In the diagram here, we show the electron densities only resulting from each of
three orbitals, s, p, p. colored differently If we add up the three sets of densities
we get a picture of the space we need to divide up. It is a thick disk, sort of like a
ball what is somewhat squashed in one direction. We now divide this up into
three equal domains.

Three sp2 hybridized orbitals are made from an s

and two p orbitals. Each hybrid has some p
character and some s character.

and see that these three also add up to regenerate the original fat disk the the
spp did.
 Here, we see the three orbital spaces added
back together. Color coding helps remind us of
the original sp2 hybridized orbitals.

The next set of hybrid orbitals is not so easy to show using these electron-cloud
diagrams since the resulting set of hybrids will be evenly distributed in three
dimensions rather than in just two. Hence, I will resort to stick diagrams to
represent these orbitals.

In the molecule CH4 there are four equal electron domains on the carbon each
involved in one bond with a hydrogen. How do we explain these using localized
atomic orbitals.

First of all, recall that each sub shell will sum up to be a sphere. That means that
if we add all the p orbitals with the s orbital for the n=2 level (or any n level), we
still get a sphere. We divide the sphere into four equal parts and come up with
domains that are 109.5º apart.

Here are the four sp3 hybrid orbitals after dividing up the
space created by the s and the three p orbitals. The four
new orbitals are all equal and have axes that are 109.5º
apart.

More complicated hybridization can be found for atoms in the n > 3 shell. In these
shells, there are d orbitals that can participate in the hybridizing. Thus, if an atom
forms 5 bonds with 5 other atoms, it will need 5 atomic orbitals to do this. We
take s, p, p, p, d of our n = 3 available orbitals and combine them. The resulting
set of sp3d hybrids will have a trigonal bipyramidal arrangement exactly as
describe in the VSEPR section. Finally, if there are six bond to six atoms, the
hybridization will be sp3d2 (6 atomic orbitals needed) and the geometric
arrangement of the electron domains will be octahedral (see VSEPR section).

Molecular orbitals (Bonds and antibonds)

Valence Bond approach: (Localized Bonding)

In the Valence-bond approach, we assume that the molecules are made up by

simply overlapping the atomic orbitals (hybridized if necessary) from the
individual atoms. In this approach, the electrons from one atomic orbital AO don't
interact with those of other AOs. We get great three-dimensional pictures of what
the molecules and bonds may look like but the information we can get from this
approach is still not perfect. We'll see MO theory later that can be used in
parallel to obtain other information that this approach does a poor job at
calculating.

We've seen various ways of visualizing atomic orbitals. It is important to

remember that these orbitals are only models of what happens on an atom in the
gaseous state (unattached to anything). How we deal with bonding these atoms
together to form molecules is a whole different story again.

To form a bond between two atoms, we must combine atomic orbitals from the
two atoms in such a way that the energy level of the combination (molecular
orbital, MO) is lower than the original atomic orbital (AO). This is most easily
visualized using the s orbitals of two hydrogen atoms as they approach each
other. Consider, for a moment the following diagrams.
 Two H atoms
approach each
other. Their
Atomic Orbitals
begin to overlap.

Overall space is
shaped like a
rugby ball. We
now divide this
space into two
new (Molecular)
orbitals.

The best way to do this is such that the energy of the

resulting molecule is lowest. In the case of hydrogen, there
are two electrons to place in the new orbitals. If we define
them such that one has a much lower energy than the other
then we will see the stable molecule form when both
electrons are situated in the low-energy orbital while the
high-energy orbital is empty.

The division that best accomplishes this is one where the

orbitals are added in phase (with normalization) and out of
phase as is shown below.
 in-phase out-of-phase

Molecular orbitals created by taking linear combinations of

atomic orbitals (LCAO). On the left is the in-phase
combination (addition) of the two atomic s orbitals (σ
orbital; Bonding orbital) and on the right is the out-of-phase
combination (subtraction) of the same two orbitals (σ*
orbital; anti-bonding). These two add up to give the same
space as the two original atomic orbitals but now each is a
single 'localized' orbital spanning the whole molecule.
We see here the combination of two atomic s orbitals on
Hydrogen atoms to form an H2 molecule. Just like in the
atomic case, we always end up with the same number of
orbitals that we started with.

If we look at the energy of these two orbitals we come up with a correlation

diagram like this
The Molecule H2 has an electron configuration (σ 1s)2. It has an overall bond
order of 1.

The two electrons from the hydrogen have a low-energy orbital and a high-
energy orbital available to them. Provided they can loose energy (collision with
the walls or a third atom or emission of light photon) the electrons will settle into
the lower energy level and hence a net release of energy is observed. This
released energy is called the bond energy.

The molecular electronic configuration can be named using molecular orbitals

just as we saw in individual atoms. In this case, the only occupied orbital in the
hydrogen atom is the s-orbital that was created from the 1s orbitals of the
individual atoms. This molecular orbital (MO) is thus called a σ1s orbital. Thus,
since both electrons are in this MO, we have a very simple molecular electron
configuration (σ1s)2.

If we try the same thing using Helium. we can quickly see from the correlation
diagram below why the helium does not form a He2 diatomic molecule.

The He2 molecule will not remain

stable since it's overall bond order The two types of bond theory we're
is zero. The MO electronic discussing in this section, VB and MO
theories give virtually identical results for
configuration is (σ 1s)2(σ *1s)2, i.e., one
the H2 or He2 cases. Both predict the
bond and one antibond. shapes and energies to be the same.
The difference comes into play when
There are four electrons in the there are more than only one orbital on
molecular orbitals which means that each atom as in n>2. We'll look at MO
while two electrons can go to a lower theory later. For now, let's continue with
the VB discussion.
energy level, the other two must go to the higher one. The total energy is
unchanged. Hence, the two atoms don't form a bond at all since there is no net
release of energy.

We will revisit this further. First, let's look at a different type of bond. The σ bond
we just looked at is a bond that has it's major lobe on the axis joining the nuclei of
the two atoms. This is in contrast to a π bond where the overlap is above and
below (or on opposing sides) of the axis.

Here, we see that the overlap occurs off axis. It may be noticeable that the
overlap is not as great as it could be if the lobes were overlapping end-to-end (σ
bond)
We now see that the definition of σ and π bonds does not depend on the type of
orbitals used in their creation. They refer to the location of the overlap region
with respect to the bond axis.

There are two different models that Chemists use when describing bonding in
molecules. The one they choose depends on their purpose. For some
purposes, VB theory is easiest; hybridized orbitals coming together to form σ
and the left-over atomic orbitals (p and d) form π bonds. This is most easily
seen in organic molecules. The simplest of these is, of course, CH4 in which
we've already seen the carbon atom to be sp3 hybridized and the carbon sp3
orbitals form σ bonds with the hydrogen s orbital.

What about a molecule with double bonds? Let's look at the simplest of these;

C2H4.
If we draw these orbitals, using solid lines to represent the shape of the orbitals
rather than the electron-cloud images, we get something like the following.

First, we hybridize an s and two p orbitals on each carbon to form trigonal planer
sp2 orbitals which we use in making σ bonds.

The σ bonds on the

ethene molecule.

Now we look at the p orbital from each carbon that we didn't yet touch and use it
to form a π bond.

The π bonds on
the ethene molecule

The complete picture looks like the following

The σ and π bonds

on the ethene molecule

This scheme does a good job of helping us understand the properties of this
molecule. We can see that the molecule is rigid and planar. It cannot rotate
about the central C=C double bond because of the way the p orbitals overlap.
We also see that the bond angle should be ca. the trigonal planar angle of 120º.
the HCH angle is actually slightly smaller while the CCH angle is larger.

Triple bonds are even harder to draw. Consider the molecule ethyne C2H2. The
carbons on this molecule are sp hybridized, leaving two p orbitals on each to
form two π bonds. The final picture looks something like the following diagram.
The σ and π and π bonds on the ethene molecule.

Again, we see this model does a reasonably good job of modeling the shape of
the real molecule. Ethyne is linear and has a C≡C triple bond.

In both the cases previously, the bonds used are localized orbitals.

Molecular Orbital approach: (Distributed orbitals)

Another model chemists studying inorganic compounds use is a more complete

molecular-orbital approach. The previous model, for example is not useful at all
in describing diatomic molecules like B2, C2, N2 and O2. For this, we need a more
complete Molecular Orbital approach where all atomic orbitals can interact
simultaneously to form molecular orbitals. In this approach, we don't bother with
the hybridization. All Atomic orbitals in the valence shell are involved in
producing a molecular orbital scheme that mimics the experimentally observed
properties. The four molecules mentioned above all use their n=2 valence shell
to do the bonding. Let's look at the correlation diagram that result when the 2s
and 2p orbitals from two such atoms interact. It is important to note that the MO
energy levels (σ2p) and (π2p) may not remain in this sequence for all atomic pairs.
For example, the (π2p) levels are higher then the (σ2p) for O2 and F2. For our
purposes, however, it will be sufficient to always use this one correlation diagram
for any n=2 diatomic molecule, recognising that it is not necessarily an exact
representation of the energy levels for certain molecules.
First, we'll consider the Boron molecule. It has three electrons from each atom
for a total of 6 electrons that we must place in the molecular orbitals. So the final
scheme will look like the diagram below.
In this diagram, we can easily see that the MO electronic configuration is (σ
2s) (σ 2s) (π 2p) for an overall bond order of 1 ( (1 bond + 2 half bonds – 1
2 ∗ 2 2

antibond)) but where the (π 2p) orbitals contain unpaired electrons (Hund's
Rule) because they are degenerate (Identical energies).

This model predicts that the boron diatomic molecule is paramagnetic (two
unpaired electrons). This is exactly what is observed experimentally. Note also
that the bond order is essentially 1. The σ bond and σ* anti-bond cancel out,
leaving the two π bonds each half occupied. How does this correlate with the
Lewis dot structure?

. .
.B:B.

The molecule of C2 is different. Experimentally, it is diamagnetic (no unpaired

electrons) and has a bond order of 2.
In this diagram, we can easily see that the MO electronic configuration is (σ
2s) (σ 2s) (π 2p) for an overall bond order of 2 (3 bonds – 1 antibond).
2 ∗ 2 4

We see that there are no σ bonds in carbon dimer. It is held together with π
bonds only. This contradicts the other model where hybridization always predicts
the first bond in a multiple bond is a σ bond.

Nitrogen molecules are triple bonded as we can see in the following diagram.
In this diagram, we can easily see that the MO electronic configuration is (σ2s)2(σ∗
2s) (π2p) (σ2p) for an overall bond order of 3 (4 bonds – 1 antibond).
2 4 2

We see that there is a (σ2p) bond and two (π2p) bonds holding the molecule
together in this model. The (σ2s) and (σ*2s) cancel each other out and don't
contribute to the bonding.

Finally, Oxygen is paramagnetic with a bond-order of two. Lewis dot and VB

theory doesn't properly predict the paramagnetic properties. A good Lewis dot
diagram of O2 shows a double bond with two lone pairs on each oxygen.
In this diagram, we can easily see that the MO electronic configuration is (σ
2s) (σ 2s) (π 2p) (σ 2p) (π 2p) for an overall bond order of 2 (4 bonds – 2
2 ∗ 2 4 2 ∗ 2

antibonds). Again, the upper two electrons are unpaired in the π ∗ 2p

degenerate orbitals. This molecule is paramagnetic because of Hund's Rule.

Hund's rule says we must put the last two electrons to into the π∗ orbitals one at a
time. This gives us two unpaired electrons (Paramagnetic) and lowers the overall
bond order to 2.

We can use these same diagrams for diatomic molecules or ions for any
combination of n=2 elements. for elements of n=3 or n=4, there is no guarantee
that the sequence of the MOs will remain the same. It will always remain as
pictured above for n=2 valence levels.

Let's Try the NO molecule:

In this diagram, we can easily see that the MO electronic configuration is (σ
2s) (σ 2s) (π 2p) (σ 2p) (π 2p) for an overall bond order of 2 ½ (4 bonds – 1½
2 ∗ 2 4 2 ∗ 1

antibonds). Here, the upper electron is unpaired in one of the two π ∗ 2p

orbitals. They are no longer degenerate since one is empty. This molecule is
paramagnetic, containing an odd number of electrons.
 CHEMISTRY OF ETHYNE

INTRODUCTION
Molecular formula = C2H2
Empirical formula = CH
Molecular mass = 26
Empirical mass = 13
Common name = Acetylene
Homologous series = Alkynes
ORBITAL STRUCTURE
OF ETHYNE
COMPOSITION OF ETHYNE MOLECULE:
Ethyne molecule consists of two C-atoms and two H-atoms (C2H2).
NATURE OF HYBRIDIZATION:
In ethyne molecule, each carbon atom is Sp-hybridized. Due to Sp-hybridization
each carbon atom generates two Sp-hybrid orbitals. In this way there exists four
Sp-orbital in ethyne. These Sp-orbital are arranged in linear geometry and 180o
apart. Remaining py and pz unhybrid orbitals of each carbon atom lie perpendicular
to the plane of Sp-orbitals.
SIGMA BOND FORMATION:
One Sp-hybrid orbital of each carbon atom overlaps to produce one sigma bond
between two
C-atoms.The remaining one Sp-orbital of each C-atom overlaps with one H-atom
to produce sigma bond.
Pi-BOND FORMATION:
Py and Pz orbital of two carbon atoms are un-hybrid and make parallel overlapping
to produce pi-bond.
BOND LENGTH:
The C--H bond is 1.09A and C-C is 1.2A.o.
BOND ANGLE:
HCC bond angle is 180o.
Orbital Hybridization
We've learned how constructive and destructive interference of atomic orbitals explains
the formation of bonding and anti-bonding orbitals. We also leaned about two types of
bonding: σ and π bonding. So you might expect that for polyatomic molecules, all you
need to do is put the atoms of the molecule near each other in the right geometry and then
see what σ or π bonds form between all the atomic orbitals.

Well, it is almost that simple. The only problem is that for most molecular geometries the
atomic orbitals on an atom do not point in the right direction for a σ or π bond to form.
Let's look at BF3 as an example. From VSEPR we know the geometry around the Boron
atom should be trigonal planar.

But for a Boron atom all the valence elelctrons are in the 2s, 2px, 2py, 2pz orbitals. Recall
their shapes:

The problem you'll find is that there's no way you can put three Fluorine atoms around
the s and p orbitals of Boron in a trigonal planar configuration and form 3 equivalent σ or
3 equivalent π bonds. Yet, we know the B-F bonds are all equivalent because they all
have the same bond dissociation energy.
Actually, what happens is that as you bring the three Fluorine atoms near Boron, the
atomic orbitals on Boron change (or hybridize) so that they can form σ bonds in a
trigonal planar shape.

In this example, one s, and two p orbitals, i.e., px, and py, hybridize to form 3 new orbitals
that point along the correct direction to form σ bonds with all 3 Fluorines. This is called
sp2 hybridization;

Let's look at another example, BeF2. From the VSEPR model we know its structure is
In Be, the s and px orbitals hybridize to give two similar sp hybrid orbitals.

Remember that the atomic orbitals are standing waves associated with the electrons
bound to a nucleus. When you bring atoms together the boundary conditions for these
standing waves change and so the standing waves which were the atomic orbitals change.
That is all hybridization is. It's analogous to holding down and releasing a violin string
while you're playing. There's one standing wave (one frequency) while you're holding
down the string, and another standing wave (another frequency) when you release the
string.

Let's conside another example, CH4.

To get these bonds you hybridize one s and three p orbitals. These are called sp3 hybrid
orbitals.

Sometimes it is not necessary for all the valence electron orbitals to hybridize. For
example, ethylene has the following structure:

The bonds between C and H are all σ bonds between sp2 hybridized C atoms and the s-
orbitals of Hydrogen. The double bond between the two C atoms consists of a σ bond
(where the electron pair is located between the atoms) and a π bond (where the electron
pair occupies the space above and below the σ-bond).
You should remember that we learned about molecules where the central atom gets more
than an octet of electrons.

We learned earlier that the extra bonding electron pairs are possible if we include the d-
orbitals of phosphorous. This is done by forming hybrid orbitals from s, p, and now d
orbitals. For trigonal bipyramidal the central atom is bonded through dsp3 hybrid
orbitals.

In the case of molecules with an octahedral arrangement of electron pairs, another d-

orbital is used and the hybridization of the central atom is d2sp3

In summary
Total # of L.P. and B.P
Arrangement Hybridization
about atom
2 linear sp
3 trigonal planar sp2
4 tetrahedral sp3
5 trigonal d sp3
 Total # of L.P. and B.P
Arrangement Hybridization
about atom
bipyramidal
6 octahedral d2sp3

What is the hybridization of Xe in XeF4?

Starting with the # of valence electrons = 8 + 4 ( 7 ) = 36 e- (i.e., 18 pairs), and using the
VSEPR model we predict an octahedral arrangement of electron pairs about Xe:

Therefore we say that Xe has a d2sp3 hybridization.

 9.4 Hybrid Orbitals

For polyatomic molecules we would like to be able to explain:

• The number of bonds formed

• Their geometries

sp Hybrid Orbitals

Consider the Lewis structure of gaseous molecules of BeF2:

• The VSEPR model predicts this structure will be linear

• What would valence bond theory predict about the structure?

The fluorine atom electron configuration:

• 1s22s22p5
 • There is an unpaired electron in a 2p orbital
• This unpaired 2p electron can be paired with an unpaired electron in the
Be atom to form a covalent bond

The Be atom electron configuration:

• 1s22s2

• In the ground state, there are no unpaired electrons (the Be atom is

incapable of forming a covalent bond with a fluorine atom
• However, the Be atom could obtain an unpaired electron by promoting
an electron from the 2s orbital to the 2p orbital:

This would actually result in two

unpaired electrons, one in a 2s orbital and another in a 2p orbital

• The Be atom can now form two covalent bonds with fluorine atoms
• We would not expect these bonds to be identical (one is with a 2s
electron orbital, the other is with a 2p electron orbital)

However, the structure of BeF2 is linear and the bond lengths are identical

• We can combine wavefunctions for the 2s and 2p electrons to produce a

"hybrid" orbital for both electrons
• This hybrid orbital is an "sp" hybrid orbital
 • The orbital diagram for this hybridization would be represented as:

Note:

• The Be 2sp orbitals are identical and oriented 180° from one another (i.e.
bond lengths will be identical and the molecule linear)
• The promotion of a Be 2s electron to a 2p orbital to allow sp hybrid
orbital formation requires energy.
•
o The elongated sp hybrid orbitals have one large lobe which can
overlap (bond) with another atom more effectively
o This produces a stronger bond (higher bond energy) which offsets
the energy required to promote the 2s electron

sp2 and sp3 Hybrid Orbitals

Whenever orbitals are mixed (hybridized):

• The number of hybrid orbitals produced is equal to the sum of the

orbitals being hybridized
• Each hybrid orbital is identical except that they are oriented in different
directions

BF3

Boron electron configuration:

• The three sp2 hybrid orbitals have a trigonal planar arrangement to

minimize electron repulsion

• An s orbital can also mix with all 3 p orbitals in the same subshell
 CH4

• Thus, using valence bond theory, we would describe the bonds in

methane as follows: each of the carbon sp3 hybrid orbitals can overlap
with the 1s orbitals of a hydrogen atom to form a bonding pair of
electrons

H2O
 Oxygen

Hybridization Involving d Orbitals

Atoms in the third period and higher can utilize d orbitals to form hybrid
orbitals
 PF5

Similarly hybridizing one s, three p and two d orbitals yields six identical
hybrid sp3d2 orbitals. These would be oriented in an octahedral geometry.

• Hybrid orbitals allows us to use valence bond theory to describe

covalent bonds (sharing of electrons in overlapping orbitals of two
atoms)
• When we know the molecular geometry, we can use the concept of
hybridization to describe the electronic orbitals used by the central atom
in bonding

Steps in predicting the hybrid orbitals used by an atom in bonding:

1. Draw the Lewis structure

2. Determine the electron pair geometry using the VSEPR model

3. Specify the hybrid orbitals needed to accommodate the electron pairs in the
geometric arrangement

NH3
 1. Lewis structure

2. VSEPR indicates tetrahedral geometry with one non-bonding pair of

electrons (structure itself will be trigonal pyramidal)

3. Tetrahedral arrangement indicates four equivalent electron orbitals

9.5 Multiple Bonds

 The "internuclear axis" is the imaginary axis which passes through the two

nuclei in a bond:

The covalent bonds we have been considering so far exhibit bonding orbitals
which are symmetrical about the internuclear axis Bonds in which the electron
density is symmetrical about the internuclear axis are termed "sigma" or
"σ " bonds

In multiple bonds, the bonding orbitals arise from a different type arrangement:

• Multiple bonds involve the overlap between two p orbitals

• These p orbitals are oriented perpendicular to the internuclear (bond)
axis

This type of overlap of two p orbitals is called a

"pi" or "" bond

In π bonds:

• The overlapping regions of the bonding orbitals lie above and below the
internuclear axis (there is no probability of finding the electron in that
region)
• The size of the overlap is smaller than a σ bond, and thus the bond
strength is typically less than that of a σ bond
Generally speaking:

• A single bond is composed of a σ bond

• A double bond is composed of one σ bond and one π bond
• A triple bond is composed of one σ bond and two π bonds

C2H4 (ethylene; see structure above)

• The arrangement of bonds suggests that the geometry of the bonds

around each carbon is trigonal planar
• Trigonal planar suggests sp2 hybrid orbitals are being used (these would
be σ bonds)

What about the electron configuration?

Carbon: 1s2 2s2 2p2

• Thus, we have an extra unpaired electron in a p orbital available for

bonding
• This extra p electron orbital is oriented perpendicular to the plane of the
three sp2 orbitals (to minimize repulsion):
 • The unpaired electrons in the p orbitals can overlap one another above
and below the internuclear axis to form a covalent bond

• This interaction above and below the internuclear axis represents the
single π bond between the two p orbitals

Experimentally, we know that the 6 atoms of ethylene lie in the same plane. If
there was a single σ bond between the two carbons, there would be nothing
stopping the atoms from rotating around the C-C bond. But, the atoms are held
rigid in a planar orientation. This orientation allows the overlap of the two p
orbitals, with formation of a π bond. In addition to this rigidity, the C-C bond
length is shorter than that expected for a single bond. Thus, extra electrons
(from the π bond) must be situated between the two C-C nuclei.

C2H2 (acetylene)

• The linear bond arrangement suggests that the carbon atoms are utilizing
sp hybrid orbitals for bonding
 • This leaves two unpaired electrons in p orbitals
• To minimize electron replusion, these p orbitals are at right angles to
each other, and to the internuclear axis:

• These p orbitals can overlap two form two π bonds in addition to the
single σ bond (forming a triple bond)

Delocalized Bonding

localized electrons are electrons which are associated completely with the
atoms forming the bond in question

In some molecules, particularly with resonance structures, we cannot associate

bonding electrons with specific atoms
 C6H6 (Benzene)

Benzene has two resonance forms

• The six carbon - carbon bonds are of equal length, intermediate between
a single bond and double bond
• The molecule is planar
• The bond angle around each carbon is approximately 120°

The apparent hybridization orbital consistent with the geometry would be sp2
(trigonal planar arrangement)

• This would leave a single p orbital associated with each carbon

(perpendicular to the plane of the ring)
With six p electrons we could form three discrete π bonds

• However, this would result in three double bonds in the ring, and three
single bonds
• This would cause the bond lengths to be different around the ring (which
they are not)
• This would also result in one resonance structure being the only possible
structure

The best model is one in which the π electrons are "smeared" around the ring,
and not localized to a particular atom

• Because we cannot say that the electrons in the π bonds are localized to a
particular atom they are described as being delocalized among the six
carbon atoms

Benzene is typically drawn in two different ways:

• The circle indicates the delocalization of the p bonds

back to RJC Chem Web

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The Molymod molecular orbital system uses standard shiny colored atom parts to
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The pink and purple pear-shaped lobes and concave pi links represent the +ve and -ve
signs of the wave functions Ψ of the lobes of atomic and molecular orbitals. The gray
pieces represent hybridized sigma bonds. The light brown spheres are used to indicate
lone electron pair orbitals. Where the electrons are involved in hydrogen bonding, a light
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Atomic Orbitals

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Electron Repulsion Theory

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Z54,457-4