Organic Chemistry Notes

Chapter 1 The Basics: BONDING AND MOLECULAR STRUCTURE

1.1 Life and The Chemistry of Carbon Compounds—We are stardust
Organic chemistry: the chemistry of compounds that contain the element carbon
Why should an entire field of chemistry be based on the chemistry of compounds
that contain this one element, carbon?
Carbon compounds are central to the structure of living organisms and
therefore to the existence of life on Earth. We exist because of carbon
compounds.
What is it about carbon that makes it the element that nature has chosen for living
organisms?
There are two important reasons: carbon atoms can form strong bonds
to other carbon atoms to form rings and chains of carbon atoms, and carbon
atoms can also form strong bonds to elements such as hydrogen, nitrogen,
oxygen, and sulfur. Because of these bond-forming properties, carbon can be
the basis for the huge diversity of compounds necessary for the emergence
of living organisms.
1.1A What Is the Origin of the Element Carbon?
 Light elements (hydrogen and helium) were formed during the Big Bang.
 Lithium, beryllium, and boron formed shortly after, as the universe cooled.
 Heavier elements formed millions of years later inside stars through nuclear
fusion.
 Stars generate energy primarily through the fusion of hydrogen nuclei into
helium nuclei.
 This nuclear fusion is the reason stars shine.
 As stars run out of hydrogen, they collapse and can explode as supernovae.
 Supernovae scatter heavy elements throughout space.
 Some of these heavy elements, influenced by gravity, became part of planets
like Earth.
1.1B How Did Living Organisms Arise?
 An adequate answer to the question about the emergence of life cannot be
given currently due to many unknowns.
 Organic compounds, including complex ones, are found in outer space and
meteorites have brought these compounds to Earth.
 A 1969 meteorite in Murchison, Australia, contained over 90 amino acids, 19
of which are found in living organisms on Earth.
 This suggests that events in outer space may have contributed to the
emergence of life on Earth.
  In 1924, biochemist Alexander Oparin suggested that life on Earth developed
from carbon-based molecules in a "primordial soup" of methane, hydrogen,
water, and ammonia on prebiotic Earth.
 In 1952, Stanley Miller and Harold Urey at the University of Chicago tested
this idea by passing an electric spark through a mixture of these compounds,
simulating the early atmosphere.
 Their 1953 publication reported the formation of five amino acids, but later
examination in 2008 revealed 22 amino acids were actually formed.
 Similar experiments have shown that other biomolecule precursors, such as
ribose and adenine (components of RNA), can also be synthesized this way.
 Some RNA molecules can store genetic information and act as catalysts, like
enzymes.
 While much remains to be discovered about how these compounds became
living organisms, it is certain that the carbon atoms in our bodies were
formed in stars, making us, in a sense, stardust.
1.1 C Development of the Science of Organic Chemistry
Science of organic chemistry began with the 19 th century theory called vitalism
According to vitalism, organic compounds were only those that came from living
organisms, and only living things could synthesize organic compounds through
intervention of a vital force.
Inorganic compounds were considered those compounds that came from nonliving
sources.
In 1828, Friedrich Wöhler discovered that evaporating an aqueous solution of the
inorganic compound ammonium cyanate could be made into urea (a constituent of
urine).
With this discovery, the synthesis of an organic compound, began the evolution of
organic chemistry as a scientific discipline.

THE CHEMISTRY OF NATURAL PRODUCTS

 "Organic" is still used to mean "coming

from living organisms" (e.g., organic
vitamins, organic fertilizers).
 "Organic food" means food grown
without synthetic fertilizers and
pesticides.
  "Organic vitamin" means a vitamin isolated from a natural source, not
synthesized by a chemist.
 There are valid arguments against using food with certain pesticides.
 Organic farming may have environmental benefits.
 "Natural" vitamins may contain beneficial substances not found in synthetic
vitamins.
 Pure "natural" and pure "synthetic" vitamin C are identical and equally
healthy.
 The study of compounds from living organisms is known as natural products
chemistry.

Atomic Structure
 Compounds are made up of elements combined in different proportions.
 Elements are made up of atoms.
 Atom is consisting of a dense, positively charges nucleus containing protons
and neutrons and a surrounding cloud of electrons.
 Proton bears one positive charge
 Electron bears one negative charge
 Neutron bears no charge
 Protons and neutrons have nearly equal masses and are about 1800 times
heavy as electrons.
 Most of the mass of an atom comes from the nucleus, the atomic mass
contributed by the electron is negligible.
 Most of the volume of an atom comes from the electrons, electrons occupy
about 10, 000 times volume larger than that of nucleus.
 Element is distinguished by its atomic number (Z)
 Atomic number=number of protons=number of electrons
 Elements commonly found in organic molecules:
o Carbon
o Hydrogen
o Nitrogen
o Oxygen
o Phosphorus
o Sulfur
o Fluorine
o Chlorine
o Bromine
o Iodine

1.2A Isotopes
ISOTOPES: atoms of the same element that have the same number of protons but
have different masses due to different numbers of neutrons.
(Give example: Carbon-12, Carbon-13, Carbon-14)
(Neutron calculation for isotopes:
 mass number−atomic number=neutrons
(Abundance Formula)
Isotope 1= x
Isotope 2=1-x

mass of Isotope 1 ( x )+ mass of isotope 2 ( 1−x )=atomic mass of normal element

1.2B Valance Electrons

-electrons that surround the nucleus exist in shells of increasing energy and at
increasing distances from the nucleus
-Valance shell: the outermost shell containing the electrons used by an atom in
making chemical bonds with other atoms to form compounds.
Number of electrons of an atom in its Valance Shell:
The number of electrons in the valance shell is equal to the group number of the
atom.
Examples:
Carbon, group IVA, 4 valance electrons
Oxygen, group VIA, 6 valance electrons
All halogens, group VIIA, 7 valance electrons
1.3 Chemical Bonds: The Octet Rule
Lewis & Kӧssel, from University of California,Berkeley and University of Munich, respectively
advanced the explanations of the nature of chemical bonds in 1916. They proposed two major types of
chemical bonds:
Ionic (or electrovalent) bonds are formed by the transfer of one or more electrons
from one atom to another to create ions.
Covalent bonds result when atoms share electrons.
Central Idea in their work:
atoms without the electronic configuration of a noble gas generally react to produce
such a configuration because these configurations are known to be highly stable.
For all the noble gases except helium, this means achieving an octet of electrons in
the valence shell.
 The valence shell is the outermost shell of electrons in an atom.
 The tendency for an atom to achieve a configuration where its valence shell
contains eight electrons is called the octet rule.
1.3A Ionic Bonds
Atoms may gain or lose electrons and form charged particles called ions.
 An ionic bond is an attractive force between oppositely charged ions. One
source of such ions is a reaction between atoms of widely differing
electronegativities.
 Electronegativity is a measure of the ability of an atom to attract electrons.
 Electronegativity increases as we go across a horizontal row of the periodic
table from left to right and it increases as we go up a vertical column

 Ions form because atoms can achieve the electronic configuration of a noble
gas by gaining or losing electrons.
 Ionic compounds, often called salts, form only when atoms of very different
electronegativities transfer electrons to become ions.
1.3B Covalent Bonds and Lewis Structures
When two or more atoms of the same or similar electronegativities react, a
complete transfer of electrons does not occur. In these instances, the atoms achieve
noble gas configurations by sharing electrons.
 Covalent bonds form by sharing electrons between atoms of similar
electronegativities to achieve the configuration of a noble gas.
 Molecules are composed of atoms joined exclusively or predominantly by
covalent bonds.
Molecules may be represented by electron-dot formulas or, more conveniently, by
formulas where each pair of electrons shared by two atoms is represented by a line.
 A dash structural formula has lines that show bonding electron pairs and
includes elemental symbols for the atoms in a molecule.
1.4 How to write Lewis Structures
1. Lewis structures show the connections between atoms in a molecule or ion using
only the valence electrons of the atoms involved.
2. For main group elements, the number of valence electrons a neutral atom brings
to a Lewis structure is the same as its group number in the periodic table.
3. If the structure we are drawing is a negative ion (an anion), we add one electron
for each negative charge to the original count of valence electrons. If the structure
is a positive ion (a cation), we subtract one electron for each positive charge.
4. In drawing Lewis structures, we try to give each atom the electron configuration
of a noble gas.
5. If necessary, we use multiple bonds to satisfy the octet rule (i.e., give atoms the
noble gas configuration).
6. Before we can write some Lewis structures, we must know how the atoms are
connected to each other.
1.4A Exceptions to the Octet Rule
Atoms share electrons, not just to obtain the configuration of an inert gas, but
because sharing electrons produces increased electron density between the positive
nuclei. The resulting attractive forces of nuclei for electrons is the “glue” that holds
the atoms together
Elements of the second period of the periodic table can have a maximum of
four bonds (i.e., have eight electrons around them) because these elements
have only one 2s and three 2p orbitals available for bonding.
Each orbital can contain two electrons, and a total of eight electrons fills these
orbitals. The octet rule, therefore, only applies to these elements, and even here, as
we shall see in compounds of beryllium and boron, fewer than eight electrons are
possible.
Elements of the third period and beyond have d orbitals that can be used for
bonding.
These elements can accommodate more than eight electrons in their valence shells
and therefore can form more than four covalent bonds. Examples are compounds
such as PCl5 and SF6. Bonds written as (dashed wedges) project behind the plane of
the paper. Bonds written as (solid wedges) project in front of the paper.

Some highly reactive molecules or ions have atoms with fewer than eight electrons
in their outer shell. An example is boron trifluoride (BF3). In a BF3 molecule the
central boron atom has only six electrons around it:

1.5 Formal Charges & How to Calculate Them

 First, examine each atom and, using the periodic table, determine how many
valence electrons it would have if it were an isolated atom. This is equal to
the group number of the atom in the periodic table.
 Assign to each atom half of the electrons it is sharing with another atom and
all of its unshared (lone) electron pairs.
 Do the following calculation for the atom:

1
Formal charge=number of valence electrons− number of shared electrons
2
 −number of unshared electrons
Or

( 12 ) S−U
F=Z−

where F is the formal charge, Z is the group number of the element, S

equals the number of shared electrons, and U is the number of
unshared electrons.
 Important note: the arithmetic sum of all the formal charges in a molecule or
ion will equal the overall charge on the molecule or ion.
 Example:

1.5A Summary of Formal Charges

1.6 Isomers: Different Compounds that have the same molecular formula
Isomers are compounds that have the same molecular formula but different
structures.
Constitutional isomers are different compounds that have the same molecular
formula but differ in the sequence in which their atoms are bonded—that is, their
connectivity.
Constitutional isomers usually have different physical properties (e.g., melting
point, boiling point, and density) and different chemical properties (reactivity).
Example:

1.7 How to Write And Interpret Structural Formulas

1.7A More About Dash Structural Formulas

Dash structural formulas have lines that show bonding electron pairs and include
elemental symbols for all the atoms in a molecule.
In problems you will often be asked to write structural formulas for all the isomers
that have a given molecular formula. Do not make the error of writing several
equivalent formulas, like those that we have just shown, mistaking them for
different constitutional isomers.
1.7B Condensed Structural Formulas
Condensed structural formulas are somewhat faster to write than dash formulas
and, when we become familiar with them, they will impart all the information that is
contained in the dash structure. In condensed formulas all the hydrogen atoms that
are attached to a particular carbon are usually written immediately after the
carbon. In fully condensed formulas, all the atoms that are attached to the carbon
are usually written immediately after that carbon, listing hydrogens first. For
example,

1.7C Bond-Line Formulas

The most common type of structural formula used by organic chemists, and the
fastest to draw, is the bond-line formula. (Some chemists call these skeletal
formulas.) The formula in Fig. 1.3e is a bond-line formula for propyl alcohol. The
sooner you master the use of bond-line formulas, the more quickly you will be able
to draw molecules when you take notes and work problems. And, lacking all the
symbols that are explicitly shown in dash and condensed structural formulas, bond-
line formulas allow you to more quickly interpret molecular connectivity and
compare one molecular formula with another.
How to Draw Bond-Line Formulas
We apply the following rules when we draw bond-line formulas:
Each line represents a bond.
Each bend in a line or terminus of a line represents a carbon atom, unless another
group is shown explicitly.
No Cs are written for carbon atoms, except optionally for CH 3 groups at the end of a
chain or branch.
No Hs are shown for hydrogen atoms, unless they are needed to give a three-
dimensional perspective, in which case we use dashed or solid wedges (as
explained in the next section).
The number of hydrogen atoms bonded to each carbon is inferred by assuming that
as many hydrogen atoms are present as needed to fill the valence shell of the
carbon, unless a charge is indicated.
When an atom other than carbon or hydrogen is present, the symbol for that ele
ment is written at the appropriate location (i.e., in place of a bend or at the terminus
of the line leading to the atom).
Hydrogen atoms bonded to atoms other than carbon (e.g., oxygen or nitrogen) are
written explicitly.
Examples: