Organic Molecules: Depiction of Structure The Basics

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Organic Molecules Depiction of Structure - The
Basics
Organic compounds are three dimensional entities
that, for convenience, need to be represented in
two dimensions when depicted on paper. There are
certain conventions that are employed to ensure
that these 2D abbreviations are as realistic as
possible. These conventions can be quite
complicated when applied to complex molecules but
there are all underpinned by certain basic rules.
The purpose of this tutorial is to highlight and
illustrate these basic rules of representing
organic molecules on paper. First some
preliminaries
Atoms are represented by their atomic symbol
which may be identified from the periodic
table. Covalent bonds are represented by a
straight line between two atoms. Each line
represents two electrons being shared between the
atoms at either end of the bond. Molecules are
drawn out such that the longest carbon chain is
depicted in a linear form going from left to
right on the page. The number of covalent bonds
that can be formed at a given atom is governed by
their valency. Thus, carbon has a valency of 4
and can from 4 covalent bonds nitrogen has a
valency of 3 oxygen has a valency of 2 hydrogen
has a valency of 1.
The structure of butan-2-ol, illustrated above
shows the depiction of atoms, of covalent bonds,
and demonstrates the correct valency at each
atom. Before going onto the depiction of
structures it is worthwhile revising the shapes
of the various sorts of carbon atoms found in
organic molecules -
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Some comments on the 3D shape of organic compounds
Alkanes are compounds containing carbon atoms
that have four single bonds attaching them to
four other atoms. Carbon atoms in this state are
called sp3 hybridised (hybridisation is a term
that will be discussed in some depth in the early
part of your degree). The shape of a sp3
hybridised carbon atom and the atoms surrounding
it is tetrahedral. That is, the central carbon
atom is at the centre of an imaginary tetrahedron
and each of the attached atoms are at its
corners. The angle between any two of the bonds
is very close to 109. The simplest alkane,
methane, is shown on the right.
Alkenes are compounds containing at least two
carbon atoms which are joined together by a
double bond. That is, each carbon atom involved
in the double bond is attached to one double bond
(to another carbon atom) and two single bonds
The carbon atoms involved in the double bond are
sp2 hydridised. The two carbon atoms of the
double bond and the four atoms attached to the
double bond are all in same plane and are
separated by a bond angle of 120. The simplest
alkene, ethene, is shown on the right.
Alkynes are compounds containing at least two
carbon atoms which are joined together by a
triple bond. That is, each carbon atom involved
in the double bond is attached to one triple bond
(to another carbon atom) and one single bond.
The carbon atoms involved in the triple bond are
sp hydridised. The two carbon atoms of the
triple bond and the atoms attached to each end of
the triple bond are all in same plane and the
atoms are all aligned along the axis of the
triple bond. The simplest alkyne, acetylene,
is shown on the right.
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Depiction of Alkanes on Paper
The sp3 hybridised carbon atoms that feature in
alkanes are the hardest to accurately represent
in two dimensions. The picture of butan-2-ol on
the left illustrates this. Only those with a
particular ability at visualising 3D objects from
2D representations will be able to see that the
substituents around each carbon atom are arranged
as at the points of a tetrahedron. Even this
attempt at accurate representation becomes too
cumbersome when representing complex structures.
As a consequence there are some conventions for
simplifying structures on paper.
The C representing the carbon atom is not written
out unless necessary or more convenient to do so.
If two bonds join together and there is no atom
symbol at their junction it is assumed that the
junction represents a C atom. NO OTHER ATOM MAY
BE REPRESENTED IN THIS WAY.
Carbon to hydrogen bonds, and the hydrogen atoms
themselves, are not depicted on structures. It
is assumed that any carbon atom with less than 4
covalent bonds has its valency satisfied by bonds
to hydrogen atoms. For instance carbon-1, which
only has one bond attached to it, must be
covalently bonded to three hydrogen atoms to
ensure that the valency of 4 is satisfied.
Carbon-2 has three bonds depicted and therefore
must have only one hydrogen atom attached to it.
HYDROGEN ATOMS MUST BE DRAWN OUT IN FULL WHEN
ATTACHED TO ANY ATOM OTHER THAN CARBON. These two
simplifications allow for structures to be drawn
and read quickly without losing any structural
information.
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Depiction of Alkenes and Alkynes on Paper
Alkenes (sp2 hybridisation) and alkynes (sp
hybridisation) are much easier to depict on paper
given that their planar characteristics (in 3D)
are clearly being accurately depicted when in two
dimensions. For illustrative purposes the
structure of buten-3-ol is depicted in the long
hand style used at the beginning of this tutorial
and then converted into the accepted style
according to the rules mentioned for alkanes
(that is sp3 hybridised carbon atoms). Note that
the bond angles around the double bond should be
approximately 120.
Similarly, butyn-3-ol is given the same
treatment. Note how the bond angles around the
triple bond are kept to 180.
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Put your knowledge to the test. Each of the
structures below contains two mistakes. Can you
pick them out?
The basic rules for depiction of organic
compounds are extremely simple. Always remember
that your structure, although abbreviated, should
remain true to any 3D shape characteristics which
it is possible to represent in 2D. Always take
time in making sure your structures are correct -
it makes understanding of a organic chemistry a
great deal easier.