INTRODUCTION TO ORGANIC

GEOCHEMISTRY
Nisa Nurul Ilmi, M.Sc
FAKULTAS TEKNIK GEOLOGI
UNIVERSITAS PADJADJARAN

2016 N. ILMI FTG UNPAD

 Organic Chemistry
The chemistry of carbon that
does not belong to inorganic
carbon
Inorganic carbon: the oxides of
carbon, the bicarbonate and
carbonates of metal ions, the
cyanides

2015 N. ILMI FTG UNPAD

The Chemistry of Carbon

2015 N. ILMI FTG UNPAD

 Organic Geochemistry

The study of planetary carbon cycle

In general, organic geochemistry covers the fate of carbon

(in all possible chemical form) in the Earth system
(Killops & Killops, 2005)

2015 N. ILMI FTG UNPAD

The role of carbon in the origin of life
Why is carbon important?
carbon could form a large range of compounds with
mainly sulfur, oxygen, nitrogen to form all natural
compounds
The compounds have a lot of different properties,
that allows them to be the basic in creation and
maintenance of life
The strength of the carbon compounds is so strong
and low at the same time for different purposes

2015 N. ILMI FTG UNPAD

Sediment and sedimentary rocks
sediment and sedimentary rocks have a strong role
in organic geochemistry

Organic compound can be absorbed into

sedimentary rocks and preserved for millions of
years

2015 N. ILMI FTG UNPAD

 Sediment
(from killops&killops, 2005)

Sediment is the solid material, inorganic or organic,

that settles out of suspension from a fluid phase
(normally water, ice or air) in which it has been
transported.
Over time, under the right conditions, it can undergo
lithification (i.e. conversion into a solid body of rock).
Various processes can be involved in lithification:
compaction, cementation, crystallization and
desiccation.

2015 N. ILMI FTG UNPAD

The Carbon Cycle

Source: ohs-Bio.www1.50megs.com/
ch47/Bio_Chap_47_Textbook.htm
2015 N. ILMI FTG UNPAD
 Chemical composition of living
organism
Living organism = the source of organic matter in
sediment
From the lowest to the highest in the living hierarchy.
From prokaryotes to eukaryotes.

Living organism division after Killops & Killops (2005) From Britannica.com
2015 N. ILMI FTG UNPAD
Primary Producers of Organic Carbon
The most important producers quantitatively are:
Bacteria
Higher plants
Phytoplankton
Zooplankton

2015 N. ILMI FTG UNPAD

Major contributors to sedimentary organic matter
(after Clayton, 1995)

2015 N. ILMI FTG UNPAD

Biochemical constituent of organic
matter

2015 N. ILMI FTG UNPAD

Fundamentals Organic Chemistry
SATURATED COMPOUND

Bonding in organic compound: covalent bond

Saturated = alkanes
Can be both cyclic or acyclic2015 N. ILMI FTG UNPAD
Fundamentals Organic Chemistry
UNSATURATED COMPOUND

Unsaturated = alkenes
Unsaturated compounds have double bonds; stronger than
single bonds
Can undergo addition reaction to form saturated compound
2015 N. ILMI FTG UNPAD
Hydrocarbon

2015 N. ILMI FTG UNPAD

Aliphatic vs Aromatic Compounds

From: Britannica.com
2015 N. ILMI FTG UNPAD
Geochemically important functional groups
(killops & killops, 2005)
Functional groups: atoms or heteroatoms
(mainly O, S, N) that incorporated into
basic hydrocarbon structure
A functional group confers characteristic
chemical properties on a compound
compounds are often considered
collectively under the name of the
functional group they contain, e.g.
carboxylic acids for the compounds bearing
a carboxyl group.
2015 N. ILMI FTG UNPAD
 orThe
a combination
most commonof these. Many natural in
heteroatoms products
naturalin-products
lectively under
amidesthe name of the
can be functional group
considered they
to comprise amino and
volve cyclic structures, with rings of six carbon atoms contain, e.g. carboxylic acids for the compounds
carbonyl groups, and carboxylic acids to comprise
being particularly common. The simplest organic bearing a carboxyl group. The main types of function-
carbonyl and hydroxyl groups, although the behav-
Geochemically important functional groups
compounds
Table 2.1contain only hydrogen
Geochemically atoms functional
important bonded to groups
al groups encountered in natural products are listed
the basic carbon skeleton and are called hydrocar- in Table 2.1. iour of each group is modified by the neighbouring
formula*
bons. Atoms of other group/compound
elements (heteroatoms)namecan group.
More than Theof double
one type functionalbond
groupof mayanbealkene
pre- can also be

(killops & killops, 2005)

be incorporated in the basic hydrocarbon structure, sent in a molecule, thought of asas a functional
in amino group.
acids, which contain
R in
often OHthe form of hydroxyl:
peripheral alcohol (R =
functional alkyl group)
groups. both carboxylic acid and amino
Heteroatoms can be groups. Similarly, into cyclic sys-
incorporated
The most common heteroatoms phenol (R = products
in natural phenyl group)
amides can be considered to comprise
tems, and some of the geochemically amino and important are
carbonyl groups, and carboxylic
shown in Table 2.2. acids to comprise
C O carbonyl: aldehyde (R = H) carbonyl and hydroxyl groups, although the behav-
Table 2.1 Geochemically important functional groups
ketone (R = alkyl or phenyl)
iour of each group is modified by the neighbouring
R
formula* group/compound name group. The Table
double 2.2 Geochemically
bond of an alkeneimportant
can also be cyclic units
thought of as a functional group.
R OH C O carboxyl:
hydroxyl: alcoholcarboxylic acid (R = H) Heteroatoms
(R = alkyl group) formula unit into
can be incorporated name cyclic sys-
phenolester
(R = (R = alkyl
phenyl group) tems, and some of the geochemically important are
group)
OR O 2.2. O
shown in Table
C O carbonyl: aldehyde (R = H)
O etherketone (R = alkyl or phenyl) 1 O 1 quinones (1,2 and 1,4)
2
R Table 2.2 Geochemically important cyclic
(i.e. units
2 carbonyl groups within
NH2 amine 4
C O carboxyl: carboxylic acid (R = H) formula unit name a cyclic system)
C O amideester (R = alkyl group)
OR O
O O
cyclopentadiene (Z = CH2)
O NH2 ether O quinones (1,2furan
and 1,4)
1
2
1 (Z = O)
(i.e. 2 carbonyl groups within
NHSH
2 amine
thiol (or mercaptan) pyrrole (Z = NH)
Z4 a cyclic system)
thiophene (Z = S)
C SO amide
sulphide O
cyclopentadiene (Z = CH2)
furan (Z = O)benzene (phenyl group) (Z = CH)
NH2
C C alkene
SH thiol (or mercaptan) pyridine (Z = N)
pyrrole (Z = NH)
Z Z
*SR is used tosulphide
represent aliphatic chains (alkyl thiophene (Z = S)
groups) or aromatic rings. The latter can also be benzene (phenyl group) (Z = CH)
alkene and are sometimes represented
C C aryl groups,
called pyran
O pyridine (Z = N)
by Ar. Z
* R is used to represent aliphatic chains (alkyl
groups) or aromatic rings. The latter can also be
called aryl groups, and are sometimes represented pyran
O
by Ar.

which is the hydrogen bond. It is 1020 times weaker

2015 is directly
N. ILMI FTG UNPADcovalently bonded.The hydrogen is attracted
than a normal single covalent bond, and involves an to another slightly negatively charged heteroatom in a
 Carbon cycle on Earth and its
Contribution to Petroleum Formation

2015 N. ILMI FTG UNPAD

 Why Geochemistry?
The role of geochemistry in exploration:

To apply an understanding of chemistry and

physics fluids in sedimentary basins to the
prediction and risking of trapped petroleum
composition

After Clayton (1995)

2015 N. ILMI FTG UNPAD
Compounds in Petroleum

2015 N. ILMI FTG UNPAD

 Chemical composition of petroleum
(Clayton, 1995)
Gas:
Fairly simple mixture of compound. It generally
consists of methane, ethane, butane and pentane
along with some inorganic gases
Oil:
More complex mixture of compound, dominated by
hydrocarbon but with varying amounts of compounds
containing sulfur, nitrogen, oxygen and metals such as
vanadium. Oil component can be divided into 4 main
compound groups: saturated, aromatic, NSO,
asphaltene

2015 N. ILMI FTG UNPAD

 Saturated
2015 N. ILMI FTG UNPAD compounds
 Aromatic
Compounds

2015 N. ILMI FTG UNPAD

The NSO compounds

2015 N. ILMI FTG UNPAD

2015 N. ILMI FTG UNPAD
2015 N. ILMI FTG UNPAD
2015 N. ILMI FTG UNPAD
 Asphaltene
from
http://tigger.uic.edu/
~mansoori/
Asphaltene.Molecule_html

2015 N. ILMI FTG UNPAD