Online Mud Logging Handbook Chapter 2 Summary

The On-line Mud Logging Handbook Alun Whittaker
The On-line
Mud Logging
Handbook
by Alun Whittaker
See Acrobat Document Properties

(in the Acrobat Reader > File menu)
for publication and revision dates
Petroleum Generation
Aegis Group
244 Ohio Street
Vallejo, CA 94590-5051
USA
mudlogman@yahoo.com
This is Page 1 of Chapter 2: Petroleum Generation Find Another Page Find Another Chapter
Petroleum Geology in general, and mud logging in particular, have as much to do with chemistry and physics as geology. Unfortunately, but
far too many universities allow their Geology undergraduates to drop all of their hard science and mathematical classes and, in their place,
to study taxonomic or soft science disciplines like zoology and geography.
So, before we explain how oil and gas are analyzed – using chemical detectors – we must learn something about what oil and gas are
chemically, and how they got to be that way. This chapter includes:
✔ Basic rules of chemistry, and chemical bonding
✔ Chemistry of oil, gas, water, gas and a few other things encountered in subsurface exploration
✔ How the dinosaurs all died out, and were turned into gasoline – not!
✔ Petroleum hydrocarbons: how they are formed, and how they mature.
Table of Contents
Combining Chemistry with Geology..............................................................................................................................................................6
A Short Lesson in Chemistry Basics.............................................................................................................................................................6
Electronic Structure.......................................................................................................................................................................................6
Chemical Bonding.......................................................................................................................................................................................12
Covalence..............................................................................................................................................................................................16
Physical State.............................................................................................................................................................................................18
Polar Covalent Compounds....................................................................................................................................................................19
Miscibility and Solubility .........................................................................................................................................................................24
Dissociation and Equilibrium Reactions .................................................................................................................................................28
Organic Chemistry......................................................................................................................................................................................34
Molecular Structure ...............................................................................................................................................................................35
Functional Groups .................................................................................................................................................................................39
Genesis of Petroleum....................................................................................................................................................................................41
The Carbon Cycle.......................................................................................................................................................................................42
Biochemical Building Blocks.......................................................................................................................................................................43
Lipids......................................................................................................................................................................................................44
Proteins..................................................................................................................................................................................................44
Carbohydrates........................................................................................................................................................................................44
Lignins and Tannins................................................................................................................................................................................44
The Biosphere.............................................................................................................................................................................................46
Environments of Deposition........................................................................................................................................................................47
Sedimentary Basins....................................................................................................................................................................................48
Petroleum Maturation....................................................................................................................................................................................50
Mineralogy..................................................................................................................................................................................................51
Geo-chemical Maturation............................................................................................................................................................................52
The Oil Window...........................................................................................................................................................................................55
Summing Up..................................................................................................................................................................................................58
And Next.........................................................................................................................................................................................................59
Didn't find what you needed here? Sorry.
Why not go back to the Chapter Summaries, and fine a better place to start, or use the Index to search for the subject you need.
List of Figures & Tables

Figure 1: Table of the atomic numbers, mass numbers, and relative abundance of carbon isotopes.................................................................8
Figure 2: Table of atomic numbers, atomic weights, and electron affinities for some of the common elements of interest in petroleum
exploration and engineering. ..........................................................................................................................................................................10
Figure 2 (continued): Table of atomic numbers, atomic weights, and electron affinities for some of the common elements of interest in
petroleum exploration and engineering. ..........................................................................................................................................................11
Figure 3: A simplified Periodic Table of the elements. The physical and chemical properties of an element can be deduced from its position in
the table. .........................................................................................................................................................................................................12
Figure 4: Ionic bonds are formed by the transfer of bond electrons to form oppositely charge cations and anions. .......................................13
Figure 5: Covalent bonds involve the sharing of electrons. .............................................................................................................................17
Figure 6: These different graphical representations of the methane molecule illustrate how its three dimensional configuration is governed by
the requirement for electronic neutrality and the minimum energy state..........................................................................................................18
Figure 7: Polarization of the water molecule contributes to the atypical properties of this unique compound. ................................................21
Figure 8: The electronic structures of water and hydrogen sulfide. The electronic similarities are strongly reflected in the physical properties
of the compounds. .........................................................................................................................................................................................23
Figure 9: The electronic structures of carbon dioxide and molecular oxygen. The electronic differences between these molecules and those
of water and hydrogen sulfide are strongly reflected in the compounds’ different physical properties. ............................................................24
Figure 10: Weak hydrogen bonding of polymerized water molecules in the pure liquid. In reality, the structure is three dimensional, and not
just sheet-like as shown here. .......................................................................................................................................................................26
Figure 11: Hydration of positive cations and negative anions in ionic solution. ...............................................................................................27
Figure 12: Auto-ionization, the partial dissociation of water into hydronium and hydroxyl ions........................................................................28
Figure 13: Dissolution and dissociation of hydrogen sulfide in water...............................................................................................................30
Figure 14: Dissolution and dissociation of carbon dioxide in water..................................................................................................................31
Figure 15: Common molecular structural units found in organic compounds include carbon chains and rings. ..............................................36
Figure 16: Common molecular structural units found in organic compounds include alicyclic chains, aromatic rings, and non-hydrocarbon
functional groups. ...........................................................................................................................................................................................37
Figure 17: Common molecular structural units and functional groups found in organic compounds, include chains and rings with
heterogeneous functional groups attached......................................................................................................................................................39
Figure 18: Crude petroleum is a mixture of simple examples from all of the major classes of organic compounds. .......................................41
Figure 19: Generation and re-generation of carbon-bearing compounds in sedimentary environments. ........................................................43
Figure 20: Living organisms are built from a limited range of organic compounds. The chemical composition and proportions of these
compounds effect the type and yield of petroleum produced from an organic source. ....................................................................................46
Figure 21: Marine organisms provide the richest and the most plentiful source material sources of petroleum hydrocarbons. Plants and
higher animals are much less significant sources. ..........................................................................................................................................47
Figure 22: Clay compaction, porosity reduction, and density increase all proceed with increasing depth of burial. ........................................50
Figure 23: Sheet silicate clay minerals consist of extensive silicon- oxygen sheets separated by
weakly hydrogen bonded water molecules and positive metal cations. ..........................................................................................................52
Figure 24: The yield of oil and gas from kerogen types I, II, III and IV is governed by the chemical composition and origin of the source
material. ..........................................................................................................................................................................................................54
Figure 25: The stages and products of petroleum maturation for kerogen, humic and sapropelic organic materials. .....................................55
Figure 26: The depth and vertical thickness of the oil window depends upon both the present and historic (or fossil) geothermal gradients. 57
Figure 27: Petroleum maturation is driven by both temperature and time. The total yield of hydrocarbons Increases with the age of burial
even without an increase in temperature. .......................................................................................................................................................58
Combining Chemistry with Geology
Forty-some years ago, when I was still an undergraduate at university in the UK, the Dean of Science advised me (actually, he advised
some underling to advise me) that a course of study combining such unrelated subjects as Geology and Chemistry was not the basis for a
successful career. If that course included specialization in organic chemistry, he opined, it was a guaranteed preparation for the
unemployment line. Of course, this was four years before the important North Sea gas and oil fields were discovered, and I’m sure that the
old gentleman had never heard of mud logging. On the other hand, he may have heard of it, and considered unemployment to be
preferable.
Since that time, geochemistry has become more appreciated. In particular, the organic geochemistry of petroleum and its precursors has
become recognized as an important tool in petroleum exploration. To me, mud logging is simply organic geochemistry carried out under
adverse conditions. The mud logger must understand the chemistry of hydrocarbons, drilling fluids and formation water, and order to
understand these, we must study a little basic chemistry.
A Short Lesson in Chemistry Basics

The atoms of all elements, we know, consist of a nucleus surrounded by orbiting electrons. The nucleus consists of similar numbers of
positively charged protons and uncharged neutrons, each of which have an integer mass of 1. The electrons each have a negative charge
equal and opposite to that of each of the protons, and a much smaller fractional mass. In the pure, elemental state there are equal numbers
of protons and electrons so that the total atom is electrically neutral.
Electronic Structure
The number of protons in the nucleus is called the atomic number of the element. It is unique to that element, and always an integer. Most
elements occur in variants called isotopes. Each isotope of an element has the same number of electrons but a different number of
neutrons, and all of the isotopes occur in a well known relative abundance in nature.
The sum of the numbers of protons and neutrons in the nucleus of an element is called the mass number and it is also an integer unique to
each isotope. The weighted average of the mass numbers of all isotopes, and their relative abundance is called the atomic weight. It is, of
course, rarely an integer, so that:
✔ Every different element has a unique, integer atomic number,

✔ Every different isotope of an element has the same integer mass number,
✔ If an element has only one isotopic form, then it’s atomic weight is an integer equal to it’s mass number,
✔ Most common elements occur in several isotopic forms, and so they have a non-integer atomic weight.
For example consider the element carbon (Figure1):
Atomic Mass Relative Abundance

Isotope
Number Number (ppm)
C-11 6 11 << 0.0000001
C-12 6 12 988850
C-13 6 13 1150
C-14 6 14 0.0000001
Figure1: Table of the atomic numbers, mass numbers, and relative abundance of carbon isotopes.
So that:
..................... Equation 1
Without getting into unnecessarily complex explanations, you can consider the nucleus as a tightly bound central mass about which the
electrons are small particles moving in fixed paths called orbitals. To achieve a state of stability, or minimum energy, the electrons must be
able to arrange themselves into discrete, separate orbitals each containing an even number of electrons. We shall see later that, although a
neutral atom has an fixed number of protons and neutrons, electrons can be removed or added to produce positively or negatively charged
ions of that element.
The greatest stability of all is achieved with two electrons in the innermost orbital, and eight electrons in each of the outer orbitals. Obviously,
therefore, the most stable elements have atomic numbers equal to a multiple of eight, plus two. For example, the highly stable and un-
reactive, inert or noble gases are configured like this:
✔ Helium: Atomic Number =2

✔ Neon: Atomic Number = 10, or = (2) + (8)
✔ Argon: Atomic Number = 18, or = (2) + (8) + (8)
Elements that have comparable, but slightly higher or slightly lower masses are less stable, more reactive, than the noble gases.
Atomic Atomic Electro-

Element Symbol
Weight Number Negativity
Aluminum Al 26.980 13 1.5
Barium Ba 137.340 56 0.9
Calcium Ca 40.080 20 1.0
Carbon C 12.011 12 2.5
Chlorine Cl 35.453 17 3.0
Chromium Cr 51.996 24 1.6
Copper Cu 63.540 29 1.8
Helium He 4.003 2
Hydrogen H 1.008 1 2.1
Iron Fe 55.847 26 1.7
Magnesium Mg 24.312 12 1.2
Manganese Mn 54.938 25 1.6
Figure 2: Table of atomic numbers, atomic weights, and electron affinities for some of the common elements of interest
in petroleum exploration and engineering.
Atomic Atomic Electro-

Element Symbol
Weight Number Negativity
Nickel Ni 58.710 28 1.8
Nitrogen N 14.007 7 3.0
Oxygen O 15.999 8 3.5
Phosphorus P 30.974 15 2.1
Potassium K 39.102 19 0.8
Silicon Si 28.086 14 2.2
Sodium Na 22.990 11 0.9
Sulfur S 32.064 16 2.5
Figure 2 (continued): Table of atomic numbers, atomic weights, and electron affinities for some of the common
elements of interest in petroleum exploration and engineering.
Now, consider hydrogen and the alkali metals. Their atoms contain one more electron than the nearest sized noble gas:
✔ Hydrogen: Atomic Number =1
✔ Lithium: Atomic Number =3 = (2) + 1
✔ Sodium: Atomic Number = 11 = (2) + (8) + 1
✔ Potassium: Atomic Number = 19 = (2) + (8) + (8) + 1
Figure 3: A simplified Periodic Table of the elements. The physical and chemical properties of an element can be
deduced from its position in the table.
The atoms of the halogen non-metals, on the opposite side of the periodic table (see Figure 3), contain one less electron than the nearest
sized noble gas:
✔ Fluorine: Atomic Number = 9 = (2) + 7
✔ Chlorine: Atomic Number = 17 = (2) + (8) + 7
The situation gets a little more complicated for the heavier elements (see the Bibliography for sources of more information), but this
explanation can suffice for our purposes.
Chemical Bonding
Elements that do not have the most stable electronic structure tend to reach this favorable, low energy state by gaining, losing or sharing
electrons with other elements and forming chemical bonds.
For example:
✔ Sodium which has one electron too many for a stable configuration donates an electron and in the process become a positively
charged sodium cation (see Figure 12).
✔ Sulfur, which has two few electrons for perfect stability can accept two donated electrons in order to become a doubly negative
charged sulfur anion.
Figure 4: Ionic bonds are formed by the transfer of bond electrons to form oppositely charge cations and anions.
Easily remembered because, between two electric poles (of a battery, for example), the positively
charged catio ns are attracted to the cath o d e (the negative electrode), and the negatively charged
anio ns are attracted to the ano d e (the positive electrode). On second thoughts, maybe it isn’t
that easy.
Moving an electron, against the attractive and repulsive forces of the atomic nuclei and electron clouds, requires energy to be expended.
This energy is provided from the atoms themselves as they become more stable, less energetic ions.
Further ionization -- transfer of a second, third or even fourth electron -- may occur but requires even more energy as the neutral atom
becomes a more highly charged ion, with greater electron-attracting force. With increasing electrostatic charge on the ion, moving a second
electron requires more energy than the first and so on. Ionization may only occur as long as the energy released by forming a stable
configuration is greater than that required to move the necessary electron.
The possibility of an electron transfer taking place depends upon three factors:
✔ How many electrons need to be transferred,
✔ How much energy is required to transfer each of them, and
✔ How much energy is released by the elements reaching their stable state. The transfer can only take place if the energy released by
stabilization is greater than that required to bring about the transfer, so that all atoms involved experience a net loss of energy.
The correct terms for these concepts are valence and electro-negativity. The valence number, or valency, of an element is the number of
electrons the element must gain or lose in order to achieve stability. For example,
..................... Equations 2 & 3
In which:
✔ Sodium, which needs to lose one electron is monovalent, and
✔ Sulfur which needs to gain two electrons is divalent: Or, in combination:
..................... Equation 4
The resultant compound of this interaction is sodium sulfide, which always forms with a composition reflecting the valencies of sodium (1)
and sulfur (2). The rules that govern the algebraic combination of atoms to form compounds in exact multiples of their valences are called
stoichiometry. These rules dictate that, for example, any sample of sodium sulfide will always contain exactly twice as many sodium ions
as sulfide ions.
Even after formation, the sodium and sulfur ions remain independent entities. They are not physically linked to each other in any way. In the
solid phase, however, an appropriate number of sodium and sulfur ions are electrostatically attracted to each other to form a neutral,
ordered lattice structure, a crystal. In other phases, melts or solutions, the charged ions are free to moved apart and no structure exists.
Compounds formed in this way are called ionic compounds.
The electro-negativity of an element is a numerical expression of its affinity for electrons. Values for some common elements are included
in Figure 2. In the following discussion, however, I would like to use an older and more expressive nomenclature for expressing the concept
of electron affinity and the tendency to form either positively or negatively charged ions:
✔ Electrophilic elements have a moderate to strong affinity for electrons and readily accept them in order to form negative anions.
They have an electro-negativity higher than 2.4.
For example: Sulfur which accepts two electron, in the above reaction (Equation 3), is said to be electrophilic. It’s electro-negativity
is 2.5 (that is greater than 2.4).
✔ Electrophobic elements have a much lower affinity for electrons and can more easily lose them to become positive cations. They
have an electro-negativity lower than 1.6.
For example: Sodium which donates an electron, in the above reaction (Equation 2), is said to be electrophobic. It’s electro-
negativity is 0.9 (that is less than 1.6).
In common language, we call sodium a metal and sulfur a non-metal. Some metals are more electrophilic than others, some non-metals
are more electrophobic than others. Other elements, those with an electro-negativity between 1.6 and 2.4, act as the swing voters
behaving sometimes as metals and at other times as non-metals, depending upon their bonding partner.
Since there are almost a hundred relatively common elements, keeping track of their bonding habits could be a problem. Fortunately,
Dmitry Mendeleev, a Russian chemist, developed the periodic law to predict the bonding behavior (and other characteristics) of elements
based upon their electronic structure. Using the periodic law, we can construct a periodic table of the common elements as shown in Figure
3.
The periodic law predicts that, in Mendeleev's Periodic Table:

✔ The most electrophobic metals are on the left side of the table, and
✔ The most electrophilic non-metals are to the right.
✔ Within each vertical column, the higher elements properties are more extreme than the lower.
✔ Within each horizontal row, the outermost elements are monovalent and valence increases moving toward the center.
Thus, starting at the top left, and following the table, we find:
✔ Lithium (Li) which is monovalent and the most electrophobic element (and so the most reactive metal),
Move down, two position to…

✔ Potassium (K) which also monovalent but slightly less
electrophobic,
Move right, one position to…

✔ Calcium (Ca) which is divalent and even less electrophobic,
Move right, thirteen positions to…

✔ Arsenic (As) which is trivalent and very weakly electrophobic,
Move right, two positions to…

✔ Bromine (Br) which is monovalent and fairly strongly
electrophilic, and
Finally, move up, two positions to…

✔ Fluorine (F) which is monovalent and the most strongly electrophilic element (and so the most reactive non-metal)
Using these rules and our knowledge of the properties of just a few elements it is possible, following the map provided by the periodic table,
to deduce something about the nature of all the other elements,
Remember that we’ve only covered the basics here and be prepared for a few surprises! For example, knowing that Gold (Au) is a dense,
malleable, un-reactive, high melting point metal, you might deduce that Silver (Ag) above it and Platinum (Pt) -- to the right of Gold -- would
have similar properties and you would be correct. You may not deduce that Mercury (Hg) to the right is also dense, metallic, shiny, a good
electrical conductor… and a liquid!
Why? That's too much to handle her — try a Google search!
Covalence
Even if an element does not have strong electrophilic tendencies it may still be promoted to form an ionic compound by an extremely
electrophobic partner. Thus lithium, the strongest electrophobe, can stimulate almost any non-metal to accept an electron. Similarly, fluorine
can coax an electron from even the most reluctant metallic donor.
But there are many cases, where neither partner in the reaction is strongly electrophilic nor electrophobic. When there is insufficient impetus
to form compounds by the complete transfer of electrons, the stable eight-fold electronic configuration is achieved by sharing of electrons to
form a covalent bond.
Figure 5: Covalent bonds involve the sharing of electrons.

A covalent bond still depends upon the combining elements having either surplus or deficit electrons (see Figure 5) following the rules of
stoichiometry. But in this case neither atoms relinquishes or gains full control of the bonding electrons. Instead the bonding results from
sharing of electrons, with neither party either losing or completely gaining electrons.
In the covalent bond, a hybrid orbital is formed between the bonding atoms such that each atom obtains an outer orbital with a share of eight
electrons. The linked atoms form a single unit of the compound called a molecule.
Figure 6 illustrates several conventional representations of the methane molecule.
Figure 6: These different graphical representations of the methane molecule illustrate how its three dimensional
configuration is governed by the requirement for electronic neutrality and the minimum energy state.
✔ The hydrogen atom has only a single electron in its single orbital which has a maximum capacity of two (the stable situation of
Helium).
✔ The carbon atom has two electrons in its inner orbital and four in the outer, which has a capacity for eight to achieve stability (like
Neon).
In the methane molecule, the outer orbital of the carbon atom is hybridized with the orbitals of four hydrogen atoms. Carbon is said to be
tetravalent, in that it achieves highest stability when forming four covalent bonds, donating a share of one electron to each.
Each hydrogen atoms donates a share of its own single electron to the carbon atom so that the carbon outer orbital gains a stable eight
electron configuration. In turn, each hydrogen atom gains a share of one electron from the carbon atom giving it a stable two electron
configuration. Hydrogen is said to be monovalent.
Notice that the whole molecule remains electrically neutral as do the component atoms. The total nuclear charge remains equal to the total
number of electrons: 10. Each of the elements gives up a half share of a number of electrons, gains a half share of an equal number and so
remains uncharged. Although I have drawn the molecule of methane to have overlapping orbitals within the plane of the page, the atoms
are, in fact, distributed symmetrically in space. Below the orbital diagram, is a more common stick figure representation of methane in which
it can be seen that the four hydrogen atoms surround the carbon atom in three dimensions at the points of a regular tetrahedron.
Obviously, a covalent bond, and the low energy stability of the bonding atoms, exists only if the atoms remain adjacent with the hybrid orbital
in place between them, Unlike an ionic compound, the covalent compound exists as distinct molecules in all physical states.
Also, unlike the ionic compound, each atom and the entire covalent molecule remain electrically uncharged. There is no electrostatic force
either attracting or repelling the molecules from each other. This too will have an effect on the properties of the compound. Covalent
compounds are commonly gases, like methane, or liquids, like hexane. When they are sufficiently cooled to solidify, covalent compounds
form amorphous solids without rigidity or crystalline structure. Most of the organic compounds involved in living organisms and, after
decomposition, in petroleum are covalent in nature.
Physical State
Even in the solid state, an ionic compound does not contain any discrete ionic molecules. Instead ions of opposite charge are packed into a
regular, repetitive crystal lattice. The distribution and spacing of this lattice is controlled by the relative size, charge and number of ions
required to preserve electrical neutrality. The crystal lattice formed by ions is continued throughout the mineral and even controls the
crystalline structure at the macroscopic scale. For example, the cubic symmetry of the halite crystal is a direct consequence of the cubic
arrangement of sodium and chloride ions in the crystal lattice.
Because of the strong electrostatic attraction between the ions in the crystal lattice, ionic compounds tend to form relatively hard, high
melting point solids. For example most rock forming minerals are ionic in nature. They are rarely liquid at normal geological temperatures
and pressures. When melted, of course, they cease to be true compounds and become randomly mixed melts of component ions. A random
sample of the melt will be found to be electrically neutral and to contain the stoichiometrically required number of component ions, but there
will be no observable molecular structure or bonding.
Covalent compounds are quite the opposite. The compound, in any physical state, consists of a large number of discrete molecules each
containing the stoichiometrically defined number of atoms of each element. Since the molecules are uncharged, there is no electrostatic
force between them (although there is a much weaker non-ionic, attractive force between covalent molecules, the Van der Waals force).
Covalent compounds tend to form softer, amorphous, unstructured solids with low melting points. Some true covalent compounds can and
do exist as liquids and gases at normal geological temperatures, for example hydrocarbon tars, oils and gases.
There is a practical rule in chemistry which states that: like dissolves like. This well describes the behavior of mixtures of ionic and
covalent compounds. Molecules of a covalent compounds are bound together only by the weak Van der Waals force. This force is attractive
and acts equally between all covalent molecules. Molecules of different compounds will therefore mix readily with each other in any
proportions achieving physical properties reflecting the composition of the mixture. Thus when we study a petroleum reservoir we are
always studying of mixtures of waxes, oils and gases all intimately mixed.
Ionic compounds do not strictly exist as liquids and not at all in the sedimentary environment which we are studying. However, we do see
solid solutions (see Deer, Howie, & Zussman in the Bibliography): solid crystal minerals which contain mixtures of ions of different species
forming composite compounds. Depending upon the relative size of the ions, the crystal lattice may be perfectly regular, or euhedral, or
distorted by the inclusion of larger ions. An example of this, is the calcite-dolomite- magnesite solid solution series. While calcite and
magnesite are pure crystalline compounds of stoichiometric composition, dolomite crystals have a range of chemical compositions between
the two end members and a crystal lattice consisting of alternating layers of a calcite and magnesite structure. The illite-mixed layer clay-
smectite series of clay minerals is another example of ionic solid solution.
Charged ionic and neutral covalent compounds cannot be mixed together. Consider adding a finely divided ionic solid to a covalent liquid,
for example, pouring salt into gasoline. The sodium and chloride ions are bound too closely together by electrostatic attraction to allow the
covalent molecules to enter the crystal lattice or to separate the ions.
Like dissolves like means that ionic solids and covalent liquids do not mix. This is true with one unique and very special exception!
Polar Covalent Compounds

Figure 7 shows the covalent bonding of oxygen and hydrogen in the water molecule. Notice that the oxygen atom's outer orbital contains six
electrons. Thus divalent oxygen combines with two atoms of monovalent hydrogen to obtain a stable eight-electron configuration.
In many ways, this covalent molecule, is similar to the methane molecule in Figure 6. However, there some small electronic differences that
result in some very significant differences in the physical properties of the water and methane. First, notice that not all of the oxygen’s outer
orbital electrons are involved in covalent bonding. Four of the oxygen electrons are not directly involved in the bonding process. These are
referred to as the two lone pairs. Strong mutual repulsion between the lone pairs and the bond electrons shared between the oxygen and
hydrogen atoms causes both lone pair electrons to be pushed to far sides of the molecule.
Figure 7: Polarization of the water molecule contributes to the atypical properties of this unique compound.
Instead of being arranged opposite each other on each side of the oxygen atom, the hydrogen atoms are forced toward each other by the
repulsive force of the un-bonded oxygen lone pairs of electrons. Of course, just as they are repulsed by the lone pairs, the bond electrons
attempt to repel each other. Similarly, the two positively charged hydrogen nuclei will try to repel each other. A balance is reached but, as the
figure shows, it is strongly to the advantage of the lone pairs with a smaller angle separating the hydrogen atoms and their bond electrons.
However, this is not the end of water’s unusual behavior.
The electrical neutrality of the methane molecule (Figure 6) is maintained because carbon and hydrogen have a similar degree of
electrophobia, so that both accept an equal share of the bond electrons. Also, the hydrogen atoms arrange themselves symmetrically in a
tetrahedral pattern around the carbon atom. As a result the electron distribution is uniform around the molecule and all attractive and
repulsive electrostatic forces within it’s molecule are evenly balanced.
As Figure 7 shows, the water molecule is not symmetrical, in either shape or electron distribution. The water molecule contains the oxygen
nucleus and its lone pairs to one side, and the two hydrogen nuclei bunched together on the other side. Oxygen is, in addition, strongly
electrophilic (almost as much so as fluorine) and therefore takes a more than equal share of the bond electrons. The uneven distribution of
electrons means that the two sides, or poles, of the molecule are electrically charged relative to each other:
✔ The oxygen side of the molecule, with two lone pairs of electrons repulsed by the four bond electrons, takes on a slightly negative
charge, and
✔ The opposite side of the molecule has the two hydrogen nuclei which have a less than equal share of the bond electrons. This side
therefore takes on a slightly positive charge.
Although the molecule as a whole retains total electrical neutrality there is a distribution or polarization of charge. The water molecule is said
to be a dipole and water is said to be a polar covalent compound. This phenomenon and its effect on the physical properties of water has
been described as having a controlling influence over …all biochemistry, much of geochemistry and a great deal of general
chemistry… (Heslop & Robinson) .
With its strong affinity for electrons, oxygen very commonly forms ionic compounds but when it does form covalent compounds, with weakly
electrophobic elements, such as carbon, hydrogen, and sulfur, the resulting covalent compounds are commonly polar in nature. Even the
oxygen molecule, in which two oxygen atoms are combined, itself shows this electron affinity and the action of the lone pairs to produce a
strongly anomalous molecule. Polar covalent compounds, as we shall see, have physical properties that reflect their transitional chemistry.
Two other polar covalent compounds that are of special interest to us in mud logging are carbon dioxide and hydrogen sulfide (Whittaker).
The structure and electronic nature of these two compounds are shown in Figure 8 and Figure 9.
Referring to the Periodic Table (Figure 3), you will see that sulfur (S) occurs amongst the non-metals, below and to the left of oxygen and
fluorine. This suggests that sulfur is elementally closely related to oxygen but has a weaker affinity for electrons. In confirmation of this, we
see in Figure 8 that, although the hydrogen sulfide molecule is polarized and asymmetric (like the water molecule), the charge distribution is
less extreme and the molecule is much less strongly polarized. Carbon dioxide forms a linear molecule in which the central carbon atom
forms two double covalent bonds in which four electrons are shard, two each with the oxygen atoms to each side. Double, triple and even
quadruple covalent bonds can readily occur so long as appropriate numbers of electrons are available to be shared by both partners.
However, as Figure 9 demonstrates, multiple bonds require energy investment in holding such a high electron density within the bond
region. They may also, by restricting bond angles, constrain the molecule from taking on a symmetrical shape.
Figure 8: The electronic structures of water and hydrogen sulfide. The electronic similarities are strongly reflected in the
physical properties of the compounds.
In nature, we therefore find that simplification and degradation processes, such as the maturation of petroleum from organic material, tend to
proceed by the breakage of double and triple bonds and their replacement with simpler single bonded structures.
Carbon dioxide is also a polar molecule although not a dipole. Again, due to the difference in electron affinity, the oxygen atoms take a
somewhat oversize share of the bond electrons repelling the electron lone pairs to the extreme ends of the molecule. This leaves the carbon
dioxide molecule with negative exposed ends and a positive, somewhat protected center. This negative-ended polarity causes the
molecules of carbon dioxide to be mutually repulsive since, in most orientations, two adjacent molecules of carbon dioxide will present each
other with negatively charged areas, either directly or in an oblique manner. The oxygen molecule (see Figure 9) has a similar positive
middle and negative-ended structure.
Figure 9: The electronic structures of carbon dioxide and molecular oxygen. The electronic differences between these
molecules and those of water and hydrogen sulfide are strongly reflected in the compounds’ different physical
properties.
Carbon dioxide and oxygen form covalent molecules that are small, electronically compact and, because of the symmetrical separation of
their oxygen lone pairs, their molecules are mutually repulsive. This is reflected in their common occurrences as light gases. The mutual
repulsion of the molecules reinforces the covalent nature of the compounds to form non- crystalline fluids.
Hydrogen sulfide and water molecules are asymmetric with positive and negative sides. Oppositely charged ends of molecules are therefore
mutually attractive. This mutual attraction acts against the covalent nature of the molecules; holding together in closer proximity, attempting
to form a coherent solid structure like an ionic crystal. Thus, hydrogen sulfide is found to be a much denser gas than either carbon dioxide or
oxygen. In the case of the water molecule, it is so polar and so attractive to its own molecules that it is a liquid at normal temperatures.
Under the rules of stoichiometry and the periodic law, a small, light, covalent molecule like water would be predicted to be a gas, like
methane or carbon dioxide. When cooled and condensed to a liquid form, it would be expected to be readily miscible or mutually soluble
with other covalent compounds such as oils. In fact, water is a high boiling point liquid which, on cooling, freezes readily to form a rigid,
crystalline solid: ice. It is poorly miscible with other covalent liquids and dissolves covalent solids sparingly. Quite the opposite, water is the
most worthwhile and useful solvent for ionic compounds. This is entirely due to the asymmetric polarization of the water molecule.
Miscibility and Solubility

As we have discussed, oppositely charge negative anions and positive cations have a strong electrostatic attraction for each other. Covalent
molecules have no charge but do exert a weak attraction between each other, known as the Van der Waals force. Ionic and covalent
compounds have little tendency to mix since the ions have such a strong attraction for each other, and little attraction for the covalent
molecules.
Water molecules which are both covalent and polar behave in manner
reflecting both these natures:
✔ The water molecule has weak Van der Waals attraction for other covalent molecules.
✔ The positive and negative fractionally charged “ends” of the water molecule have an electrostatic attraction for each other and for
appropriately charged ions.
Although electrostatic attraction of water molecules is less than that of a full integer charged positive or negative ion, it is stronger than the
Van der Waals force. So water is more likely to mix with ionic compounds than covalent ones. As we shall see, the same is true for other
polar covalent compounds.
The polarization of the water molecule allows a mutual attraction between the water molecules resulting in a type of weak bonding between
the molecules. Water molecules become oriented by the mutual attractive of charged ends producing a structure in the fluid of a water
macro-molecule or weak polymerization (see Figure 10).
Figure 10: Weak hydrogen bonding of polymerized water molecules in the pure liquid. In reality, the structure is three
dimensional, and not just sheet-like as shown here.
The presence of this weak bonding, known as hydrogen bonding explains a number of unusual characteristics of waters. For example, the
unusually high melting and boiling point and density of water results from the compactness of the polymerized water giving it the behavior of
a higher molecular weight compound.
So far, we have only discussed the behavior of ionic compounds in the solid crystalline state and as melts when they lose their identity with
the random mixing of ions. A third and most important occurrence of ionic compounds is dissolved in water as ionic, aqueous solutions.
Hydrogen bonds are a weaker equivalent of the electrostatic forces between oppositely charged ions. Because of this water molecules also
become hydrogen-bonded to the ions of other ionic compounds and water acts as a solvent for them.
When most solid ionic compounds are mixed with water, the ordered crystalline structure is lost and the ions move freely about separated
from each other’s attraction by the weaker attractions of the water dipoles. The water molecules orient themselves around the ions
according to the charge on the ion as shown in Figure 11, with the negative oxygen ends of the water molecule oriented toward positive
cations, and the positive hydrogen ends oriented toward the negative anions.
This process of stabilization of the dissolved ions is called hydration. Although the hydrated ions have the same charge as before, the
opposing charges are separated and shielded from each other by the water dipoles, and the electrostatic attraction between ions is
substantially reduced. Water is therefore said to have a high dielectric constant. The hydrated ions are sufficiently insulated from each
other to allow their free and random movement in solution in water.
Figure 11: Hydration of positive cations and negative anions in ionic solution.
In the extreme case of this behavior, some of the water molecules may auto- ionize (Figure 12), In this process, water molecules dissociate
and re-associate, to form hydroxyl and hydronium ions:
✔ A water molecule dissociates by losing one of it’s hydrogen atoms, but retains the extra bond electron. What is left behind is a
hydroxyl (OH) group which, because of its extra electron, is a negatively charged anion.
✔ The dissociated (electron-stripped, and hence positively charged) hydrogen atom cannot survive alone for long (except in very hot
flame). When surrounded by other water molecules, it becomes rapidly hydrated. Having a full positive charge it forms a much tighter
bond (than a hydrogen bond) with a water molecule to form a positively charged hydronium (H3O) cation.
This dissociation accounts for, among other anomalies, the fact that water, although covalent (and supposedly containing no charged ions)
is a good conductor of electricity.
Figure 12: Auto-ionization, the partial dissociation of water into hydronium and hydroxyl ions
Water molecules are not only attracted to themselves and to charged ions. They are also attracted to other polar molecules. The dielectric
property of water also serves to promote the dissociation of other polar covalent compounds to become truly ionic, and to form integer
charged single or complex ions. Carbon dioxide and hydrogen sulfide are polar covalent compounds and their molecules are readily
hydrated and dissociated in this way when they are dissolved in water.
Water molecules are not only attracted to themselves and to charged ions. They are also attracted to other polar molecules. The dielectric
property of water also serves to promote the dissociation of other polar covalent compounds to become truly ionic, and to form integer
charged single or complex ions. Carbon dioxide and hydrogen sulfide are polar covalent compounds and their molecules are readily
hydrated and dissociated in this way when they are dissolved in water.
Because the hydrogen sulfide molecule is similar in size and shape to the water molecule it can easily substitute in the polymerized water
chain. The linear carbon dioxide molecule is a less easy fit for the water molecules to cluster around and so it is less soluble in water than
hydrogen sulfide.
The solubility and dissociation of hydrogen sulfide and carbon dioxide can cause problems in mud logging by making it difficult to detect
these significant and hazardous gases dissolved in drilling fluid. On the other hand, we should be thankful that hydration results in the
unusually high solubility of carbon dioxide and oxygen in sea water. Without that, few organisms would have evolved to act as sources of
petroleum or, eventually, as mud loggers!
Dissociation and Equilibrium Reactions

In aqueous solution, the dielectric properties of water are so great that electron donation is possible even between elements that would form
only covalent bonds in other circumstances. When dissolved in water, polar covalent compounds may be converted into ionic compounds,
become dissociated into cations and anions, and behave much like ionic compounds.
The most common example of this is the auto-ionization of water itself, which is often illustrated in this simple but misleading manner.
..................... Equation 5
Hydrogen has an atomic number of one and an atomic weight only fractionally higher. The huge majority of hydrogen atoms (Figure 1)
consist on a single electron orbiting a single proton. Removing this electron leaves us with a free proton — a subatomic particle liberated by
a simple chemical process! You don’t need to have studied nuclear physics to realize that there is something wrong here, you simply don’t
split atoms that easily.
In reality, auto-ionization of water is a hydration process involving many water molecules:
..................... Equation 6
The hypothetical free proton, in fact, becomes attached to a second water molecule which, being short one electron, becomes a hydronium
ion with a full single charge. The water molecule that has lost the proton retains its electron to become a negatively charged hydroxyl anion.
Even in this form the ions would not survive long without the sheltering action of many other surrounding water molecules.
Figure 12 illustrates the electronic configurations of the new bonds with each orbital maintaining its share of a stable number of electrons:
either two or eight.
The hydronium cation and hydroxyl anion behave much as any other ion pair in solution in water. They have a strong electrostatic attraction
for each other and must be stabilized by clouds of other polar water molecules. However, the auto-ionization reaction is a reversible one.
Water molecules may be disassociated and re-associated between states to form new, uncharged, though, once again, polar molecules:
..................... Equation 7
Figure 13: Dissolution and dissociation of hydrogen sulfide in water
In any sample of pure water, at any given temperature we can predict exactly how much of the water will be ionized. At any moment,
individual molecules and ions will be reacting with each in a forward and reverse manner to maintain this equilibrium concentration. Forward
and reverse reactions are continuous with reactants and products continuously inter-converting. Both forward and reverse reactions are
affected by temperature, pressure and the relative concentration of reactants, products and other chemical species which do not take part in
the reaction but which may promote or inhibit it. When any of these factors change, the forward or reverse reaction will predominate until a
new equilibrium is reached, with a different relative composition of reactants and products.
When polar covalent compounds dissolve in water, they too undergo dissociation and ionization. The most important of these to us are,
carbon dioxide and hydrogen sulfide. This is because of their significance in petroleum reservoirs and also because of the way that their
ionization equilibrium is intimately linked to that of water (see Figure 13 and Figure 14). Ionization of hydrogen sulfide proceeds by a
number of equilibrium steps:
Figure 14: Dissolution and dissociation of carbon dioxide in water.
Ionization of hydrogen sulfide proceeds by a number of equilibrium steps.
..................... Equation 8
..................... Equation 9
..................... Equation 10
Each of these steps is a reversible, equilibrium reaction which is governed by temperature, relative concentration of the reactants. A fixed
equilibrium constant (K) governs each stage of
dissociation such that: In chemical arithmetic, the square bracket [ ] indicates concentration of the
enclosed species, so that in this case [HS] signifies the molar concentration of
bisulfide ion.
..................... Equation 11
..................... Equation 12
..................... Equation 13
However, the reactions are not independent of each other. In this case, two of the hydration stages result in the removal of water molecules
and the production of hydronium ions. This process also occurs in the ionization of water. When hydrogen sulfide dissolves in water all of the
reactions must be in equilibrium together. If the hydration reactions produce more hydronium ions then the auto-ionization of water will be
reversed to remove some of them, and consequently an equal number of hydroxyl ions. As a result, an acidic solution, an aqueous
solution containing a greater concentration of hydronium than hydroxyl ions, is formed.
Solution and ionization of carbon dioxide proceeds in a similar manner but with an extra feature: the formation of a new, true intermediate
ionic compound, carbonic acid:
..................... Equation 14
..................... Equation 15
..................... Equation 16
Once again, all of the equilibrium constants must be satisfied. Again, two of the stages produce hydronium ions and therefore will inhibit the
auto- ionization of water. Thus a solution of both gases in water will contain a more than sufficient number of hydronium ions but a deficit of
hydroxyl ions. This means, of course that they will be acidic solutions.
We will return to aqueous chemistry many times throughout this book. I hope that this, of necessity, limited review will assist you later when
we discuss such diverse aspects as detection of polar gases, drilling mud chemistry and carbonate sample processing.
Organic Chemistry
Maybe you were a little surprised at how much space I gave to inorganic and aqueous chemistry which has little to do with hydrocarbon oils
and gases. If so then you are going to be really amazed at how little space I am going to dedicate to organic geochemistry which, of course,
does.
The truth is that I’m going to give very little attention to organic geochemistry simply because some it is so simple that you can grasp it
immediately, and the rest is so complicated that you would need a master’s degree in chemistry to even make a dent in it. Fortunately, most
of the organic chemistry we need to use in mud logging and petroleum geology lies among the easy stuff.
Organic chemistry is commonly considered to be the chemistry of life and, as such, suggests the immensely complex chemistry of self-
replicating giant molecules. While this may be true at one end of the scale, it offers little help in our understanding of the simple products of
the decomposition of living — or to put it another way, dead — organisms.
Organic chemistry is the chemistry of carbon and hydrogen in simple predictable combinations with small amounts of a very small number of
other elements, most notably: oxygen, nitrogen and sulfur. Figure 6 illustrate almost everything that needs to be said about this chemistry. It
illustrates a molecule of methane which is probably the simplest compound which can still be called organic.
Carbon is tetravalent and has neither electrophilic nor electrophobic tendencies. It is most stable when forming four single covalent bonds
with four atoms of a monovalent element with a similar affinity for electrons, such as hydrogen In this state it will orient itself at the center of
a symmetrical tetrahedron with each of the bonds directed toward one of the points of the tetrahedron.
Figure 9 and Figure 14 illustrate that carbon, like hydrogen, can be stimulated to act in a metallic manner when combined with the extreme
electrophile, oxygen. However, also like hydrogen, it does not go to the extent of ionizing but, instead, it forms a polar covalent compound
which, in aqueous solution, may dissociate in part to form complex ions.
The final fact you need to know is that, more so than any other element, carbon atoms will happily form bonds with other carbon atoms in
order to produce very long chains, complicated branched or ring structures. Only by the development of molecules of such size and
complexity could the self replicating molecules, which are the essence of life, have evolved. Only silicon, carbon’s neighbor in the periodic
table (Figure 9), shows any tendency to form strong stable bonds with its own atoms. The rock forming silicate minerals are complex in form
and chemistry but they remain orders of magnitude simpler than biological, organic molecules.
On the other hand, remember that any organic molecule, from methane to DNA, is made up predominately of a skeletal structure of
tetravalent carbon atoms linked together by covalent bonds in a tetrahedral structure (Figure 6). Attached at various points to this structure,
also by covalent bonds, are atoms of hydrogen, oxygen, nitrogen, sulfur and possible traces of a small number of other elements. Though
the entire molecule is staggering in scale, the building blocks are simple and easy to understand.
Molecular Structure
Because a molecule of an organic compound may consist of a large number of atoms of a small number of elements it is sometimes
possible for the same combination of elements to be assembled in two or more different structural combinations. Each combination is an
entirely different compound with possibly very different chemical and physical properties. When naming an organic compound or writing its
molecular formula it is necessary to give some information regarding its geometrical structure as well as its chemical composition.
Figure 15: Common molecular structural units found in organic compounds include carbon chains and rings.
The simplest carbon compounds consist of a straight chain or spine of carbon atoms to which other atoms or functional groups may be
attached. Notice in Figure 15 how the tetrahedral geometry is reflected even in the longer chains. Also notice the three dimensional nature
of the structure. The chain is not a flat zig-zag, alternate atoms in the chain are closer to you, in the plane of the page and behind that plane.
In the most complex organic compounds variants may exist that are identical in every way except that the three dimensional structure of one
is the mirror image of the other, meaning that one is zig-ing forward, while the other is zag-ing back.
Figure 16: Common molecular structural units found in organic compounds include alicyclic chains, aromatic rings, and
non-hydrocarbon functional groups.
Long chain compounds may be complicated by the addition of short carbon chains as branches to their structure. Subtle changes will result
in a compounds properties depending on where on the chain the branch is attached: near the end, in the middle, and so on.
Although single carbon-carbon covalent bonds are the most stable, double and even triple bonds may be present in the chain. Again, the
properties of a compound may be different depending of where within its chain a multiple bond occurs. Multiple bonds tend to be weaker
and more easily broken than single bonds. The position of the bond in a chain affects the nature of the products of reaction and
decomposition of the compound. All chain-based carbon compounds, either straight or branched are called aliphatic organic compounds.
Carbon chains may also be linked end-to-end to form rings of almost any number although the most common are five and six membered
rings as these allow the bonds to adopt the stable tetrahedral angle with least stress. They may be linked to form multi-ring structures or
have straight and branched chains attached to them. All of this group are called alicyclic organic compounds. Rings may be made of all
carbon atoms, or may contain a single atom of another element. Rings containing both carbon and other elements are more specifically
called heterocyclic compounds.
A special group of six-membered carbon ring-bearing compounds are named aromatic compounds. The carbon atoms in the ring appear to
be linked by alternating single and double carbon-carbon covalent bonds. If this were in fact the case, this aromatic or benzene ring (named
for benzene, the simplest aromatic compound) would be less stable than a single bonded six-membered ring. Double carbon-carbon bonds
cannot form at the tetrahedral angle and are therefore less stable than single bonds. Surprisingly, the aromatic ring is many times stronger
than its single bonded equivalent. Further investigation indicates that the ring consists of six, single, carbon-carbon bonds utilizing a total of
twelve electrons. Six more electrons are available to form bonds outside the ring and the remaining six bond electrons (of the twenty four
available to six carbon atoms) are shared by all members of the ring equally, to give a special level of stability to the aromatic compounds.
The macro-molecules contained in living tissues are built up of structural units from each of these classes: aromatics, alicyclics,
heterocyclics and aliphatics. When the organism dies and is decomposed, the macro-molecules will break down into progressively smaller
fragments also falling into one of these categories.
To the geo-chemist, the chemical fragments can be as significant as bones and shell fragments to the paleontologist — a way to recognize,
reconstruct or even date the original living organism. To the mud logger or petroleum engineer, the nature of the fragments will influence the
type, density and mobility of the hydrocarbons derived from the petroleum maturation process.
Figure 17: Common molecular structural units and functional groups found in organic compounds, include chains and
rings with heterogeneous functional groups attached.
Functional Groups
The carbon structural skeleton has a simple, un-interesting chemistry. Minor reactions involve the breakage of the skeleton into smaller
fragments. The only major reactions are with oxygen to generate carbon dioxide, water and the oxides of sulfur and nitrogen. This may be
achieved rapidly and dramatically in combustion. It is also achieved more slowly, though less completely by micro- organisms and dissolved
oxygen in sediment pore waters. The really complex organic chemistry results from reactions of and between the functional groups attached
to the carbon chains, rings and branches of the carbon skeleton. These may be single atoms or complex groups consisting mainly of
carbon, hydrogen, oxygen, nitrogen, sulfur with traces of a few other elements.
The most common functional groups are, of course, just other carbon chains or just a hydrogen atom. We find that, just as complete
combustion of organic material in an oxygen atmosphere produces carbon dioxide, decomposition in an anoxic (oxygen-free) atmosphere
produces simpler, shorter chain length hydrocarbons, containing only carbon and hydrogen.
The simple hydrocarbons are classified according to the type of carbon skeleton (see Figure 18):
✔ Alkanes (Methane, ethane, propane and so on) consist of straight or branched aliphatic carbon chains, containing only single
covalent carbon-carbon bonds and with hydrogen atoms as the only other functional groups.
✔ Alkenes are analogous to alkanes but with the straight chain containing one or more carbon-carbon double bonds, and consequently
less hydrogen atoms (each carbon-carbon double bond means two less hydrogen atoms).
✔ Cyclo-Alkanes and Alkenes are single and double bonded alicyclic compounds that have hydrogen atoms as the only other atoms.
✔ Alkynes are analogous to alkanes but with the straight chain containing one or more carbon-carbon triple bonds and consequently
less hydrogen atoms (each carbon-carbon triple bond means four less hydrogen atoms).
✔ Phenolics contain one or more aromatic benzene rings with attached hydrogen atoms.
Many other, naturally occurring, organic compounds are hydrocarbons in which one, two or more hydrogen have been replaced with more
interesting functional groups. They are named accordingly. For example, ethyl alcohol is a ethane molecule from which one hydrogen atom
has been replaced with an alcohol (OH — stoichiometrically the same as the hydroxyl ion, but covalently bonded and so not charged)
functional group.
I could provide you with lists of the possible functional groups which can be assembled from CHONS (carbon, hydrogen, oxygen, nitrogen,
and sulfur) group of elements but it would not be of any real value to you. At various places in the book we will introduce organic compounds
that occur in petroleum or are used in the search for it. At that time, I will take the time to explain the structure and chemistry of the relevant
compounds.
Figure 18: Crude petroleum is a mixture of simple examples from all of the major classes of organic compounds.
Genesis of Petroleum
As a child, I remember being regaled with stories of oil accumulating in subterranean caverns, leaking from a veritable elephants graveyard
of slaughtered dinosaurs. The only thing that spoils my fond memory of this quaint fantasy is my regular observation of the number of
otherwise rational adults who still believe it
be a true picture of a petroleum reservoir. Some of the blame for the oil from dinosaurs theory lies with Sinclair Oil (later a part of
As an undergraduate, I remember being ARCO, and even later BP ). This was the company that used a Brontosaurus (for recent
taught a less amusing, though no less graduates, that’s an old name for the Aptasaurus) image on its company logo and lead to the
fantastic vision of the nature of petroleum blight of life-size dinosaur models that still perch beside filling stations across the USA.
source beds. Marine organisms had
replaced dinosaurs. At the same time, there Blame must also be shared Ch evro n , who used decomposing dinosaurs cartoons in its 1970’s
remained the concept of a source bed as a advertising and worse. A few years ago I visited their corporate headquarters in San
zone of limited thickness and geographically Francisco, and in the lobby they were hosting an “energy education fair”, and guess what!
extent with an extreme abundance of organic Amongst the multi-media displays was an animation of lumbering dinosaurs falling into
debris and decomposition products. In my swamps, being buried in sediment and rendered over time into skeletons and dinosaur-
minds eye, I continued to see a source bed shaped sub-surface bubbles of oil and gas. “It's just for kids”, they told me!
as dark brown, warm and moist, with
occasional mealy lumps and dripping with
rich sticky residues.
To me, a petroleum source had much in common with Aunt Bessie’s home made fruit cake. Experience in the field and laboratory has taught
me better. Yet again, my amusement at my early ignorance is tempered by a knowledge that it is widely shared by many people who know
about, talk about but never actually look at source rocks!
Let us spend a little time discussing source rocks: how they originate, how they mature, how and when they give up their yield of
hydrocarbons. We will find that in prescribing a successful petroleum source bed we select for quantity rather than quality. A great thickness
of sediment containing only a moderate distribution of microscopic organic debris can add up to a major volume source of hydrocarbons. In
addition, its thickness will provide the depth, temperature and time of burial necessary for the source to mature and yield those
hydrocarbons.
I hope that in the following you will gain an unromantic but realistic view of source beds: no dinosaurs, and no fruit cakes.
The Carbon Cycle

First, let us develop some perspective by viewing the processes of petroleum generation in a complete geological context. The chemical
composition of the earth is conveniently divided into four discrete regimes each with its own representative composition and processes. In
order of physical creation, these may be listed as:
✔ Lithosphere: consisting of all rocks and sediments: hard and soft, from crust to core,
✔ Hydrosphere: oceans, lakes, river and other major or minor bodies of water,
✔ Atmosphere: from surface to the stratosphere, and
✔ Biosphere: including all terrestrial and marine flora and fauna. Some would separate from this the so-called Technosphere,
including man and his technology.
Figure 19: Generation and re-generation of carbon-bearing compounds in sedimentary environments.
While of academic interest in encapsulating the origin, history of the planet these divisions cannot be used to represent the environments
and processes of recycling of carbonaceous material in our steady state environment. The terms used in Figure 19 are less academically
precise in definition but convey more meaning in describing the stages.
This figure shows that our zone of interest is centered very definitely on the atmosphere and only peripherally impinges on the other
regimes. The atmosphere acts as a sink for free oxygen and carbon, in the form of carbon dioxide, which is removed and eventually
returned by cyclical processes. From the atmosphere, carbon and oxygen are withdrawn by the living organisms of the biosphere. As you
might expect, number overpowers size here, and the total mass of micro-biological flora and fauna far exceed the
macroscopic alternatives both in total bulk and appetite for these gases. Within these organisms, the carbon and oxygen are utilized in
organic molecules that may be the precursors of eventual oil fields. The gases are also incorporated into the hard skeletal parts of
organisms, as calcium carbonates and phosphates. While organic in origin, these minerals are not, themselves, organic and can never yield
petroleum.
Most of the soft organic material is rapidly returned, on the death of the organism, to the atmosphere by the action of physical and biological
decomposition. The most important process for the preservation of organic remains is the deposition of micro-organic material along with
inorganic sediments in lacustrine or marine environments (no dinosaurs). Of the material buried in this manner, the majority is oxidized,
chemically or biologically, converted back into carbon dioxide and water and returned to the hydrosphere and atmosphere. In order to
survive burial, the organic debris must be deposited with a much larger inorganic sediment load producing rapid burial and build-up of
sediment overburden (no fruit cakes). In reality, a scant two percent of the total organic debris is this rapidly removed from the presence of
dissolved oxygen and oxygen-using organisms.
Sedimentary and structural rock forming processes now take over. These too, may result in destruction or loss of the organic material. Of
the total sedimentary rocks of the earth, it has been estimated that only 18 percent of the carbon is present in an organic form (see Tissot &
Welte). The remaining 82 percent represents carbonates of primary (organic) or secondary (chemical) origin.
Finally, from these geological processes, petroleum is generated, matures and, in some cases, migrates to a porous, permeable reservoir.
Statistically, from a ton of organic matter deposited in marine sediments, only 3 ounces or about
0.001 percent survives the entire process to accumulate as producible oil and gas. Eventually, all of the organic material is returned by
geological, biological or technological processes back into the atmosphere as free carbon dioxide.
Biochemical Building Blocks

Just as most organic compounds are produced from a small number of elements and molecular structures, so most living organisms are
made of a relatively small number of organic compounds. These may be categorized into four groups: lipids, proteins, carbohydrates and
lignins. The chemistry of each group is not only significant to the living state of the organism but will also control the nature of the
decomposition products of the organism including the amount and type of petroleum hydrocarbons they may yield (see Figure 20).
Petroleum hydrocarbons consist almost entirely of carbon and hydrogen in an approximate two-to-one ratio. The closer the composition of
an organic compound to this, the more suitable is to be a source of petroleum.
Lipids
Lipids are present in almost all organisms, comprising the fats of animals, and the oils and waxes in plants. They are generally aliphatic
compounds, rich in carbon and hydrogen.
Vegetable lipids generally contain numerous double carbon-carbon bonds. These are referred to as unsaturated and are typical lighter and
more mobile oils.
Animal lipids contain predominately single bonds and are more heavy and solid. Consisting predominately of carbon and hydrogen, lipids,
and especially saturated animal lipids are the richest source of petroleum hydrocarbons.
Proteins
Proteins are polymeric compounds containing a carbon skeleton of aromatic and aliphatic structures with numerous functional groups
containing hydrogen, nitrogen and sulfur with other trace elements. Proteins are present in most organisms but predominate, with lipids, in
the soft tissues of animals of all sizes. They are a good source of petroleum hydrocarbons and the primary origin of the sulfur and nitrogen
bearing compounds that are commonly associated with petroleum.
Carbohydrates
Carbohydrates are also polymeric compounds. They include the sugars and starches that provide the major substance of plants.
Carbohydrates contain carbon and hydrogen but are also very rich in oxygen, and this composition is not favorable as a source of
petroleum. During maturation, carbohydrates lose oxygen and gain extra hydrogen. Oxygen is lost in the form of carbon dioxide, removing
further carbon and reducing the potential yield of hydrocarbons.
Lignins and Tannins

Lignins and tannins occur most commonly in higher plants in which they are used to construct the strong three-dimensional skeletal
structure of plant stems, trunks and limbs. They are large polymeric molecules made up primarily of aromatic alcohols and are therefore
rich in carbon and hydrogen in the form of stable aromatic benzene rings. Lignins are in fact, the most important source of the aromatic
component of petroleum. Being built up from alcohols, lignins also have a relatively high oxygen content which reduces their yield as a
petroleum source material.
Figure 20: Living organisms are built from a limited range of organic compounds. The chemical composition and proportions of
these compounds effect the type and yield of petroleum produced from an organic source.
The Biosphere
Figure 21 shows the general distribution of organisms as sources of petroleum hydrocarbons. Marine micro-organisms: phytoplankton,
zooplankton and bacteria far outweigh any other source both in terms of richness and yield. Rich in lipid and proteins, they provide the best,
highest yielding source of petroleum. They also compose over 95 percent of the mass of living tissue in the oceans and therefore comprise
the majority of organic material deposited and buried in an anoxic environment to be preserved and converted into petroleum hydrocarbons.
Higher animals are only slightly less rich in proteins and lipids. However, they constitute such a small proportion of the total mass of living
tissue, especially in the ocean that they have no significance in the production of hydrocarbons.
Figure 21: Marine organisms provide the richest and the most plentiful source material sources of petroleum
hydrocarbons. Plants and higher animals are much less significant sources.
Higher plants are rich in carbohydrates and lignins and are therefore low-yield sources of hydrocarbons. The processes that lead to the
removal of the high oxygen content is so destructive of the organic mass that, after maturation, only a low yield of smaller organic molecules
(mostly hydrocarbon gases) remains. However in a few rare cases, plants adapted for dry climates can produce heavy waxy oil. These
plants have thick, lipid rich coatings covering their leaves to prevent evaporation. With sufficient abundance and preservation, these plants
have proven to be unique oil sources.
Finally, since higher plants commonly live and die in an oxygen rich environment they are rarely preserved in sufficient quantity to be a
useful petroleum source. On the other hand, don’t forget that in a suitable shallow, sub-aqueous environment, higher plant debris can be
preserved in massive quantities to be decomposed and preserved as peat, lignite and coal. Under further suitable condition of temperature
and depth of burial, these materials may also act as low
yield sources of petroleum producing so-called non- For example, the rich natural gas fields of the southern British and Dutch North
associated natural gas. Sea, and Sacramento Delta in California. These fields produce almost pure methane,
Sea,
with only small amounts of the heavier hydrocarbon gases commonly asso ciated
with oil reservoirs.
Environments of Deposition
From what we have discussed above, you should now be able to define the ideal depositional environment for the survival of a rich
petroleum source. These are:
✔ A major source of organic debris consisting primarily of marine micro- organisms.
✔ A low-energy, low-oxygen environment allowing rapid deposition of the organic debris with minimum transportation and oxidation.
✔ An optimum source of fine-grained inorganic sediment supplying just enough material to ensure burial and preservation of the
organic debris while maintaining the maximum concentration of organic material in the source bed.
The classic example of such an environment is the euxinic basin, a stagnant marine environment. the best modern example of this is the
Black Sea, for which Mare Euxine is the latin name.
In the euxinic environment, rich surface fauna sink on death to the anoxic bottom waters where biological activity is limited to anaerobic
(oxygen-free) sulfate-reducing bacteria. Even with a large inorganic sediment influx to the land-locked sea, the bottom sediments have an
extremely high organic content of ten percent or more (see Hunt, 1979) . Unfortunately, with the exception of a few isolated fjords and the
Black Sea itself, there are very few basins of this perfect source type at the present time or even in the geological record. We must look for
less perfect but more common basin types.
Obviously, the terrestrial environment fails to meet any of the criteria. Even in a sub-aqueous terrestrial environment, the source material is
unsuitable and the environment too oxygenated for good hydrocarbon survival.
The oceans offer an extremely wide range of depositional environments.
Of these some are not suited for petroleum source beds:
✔ Shallow water commonly has excellent sources of organic debris and inorganic sediments. Unfortunately, they are also commonly
turbulent and oxygenated. Organic debris may be destroyed before sedimentation, during later re-working or from the circulation of
oxygenated pore waters through coarse sediments.
✔ Deep ocean basins are equally unsuitable. Shallower waters provide many sources of organic debris whereas at great water depth
there is a quiet, anoxic environment. On the other hand, sedimentation rates are extremely low in deep ocean basins: too low to
ensure survival of the organic debris even in the anoxic environment.
Bodies of water at or near continental margins can provide the best sedimentary environments for petroleum source beds, for example
lagoons, estuaries and marginally, near-shore basins. Being adjacent, and usually downstream, to the shallower, highly oxygenated
environments, these basins are provided with a source of organic sediments. Distance from shore and greater water depth have an
influence in reducing the proportion of higher plant and terrestrial organic material, and this improves the overall quality of the source
material. Basins at continent margins may also have access to the up-welling of warmer, faunally-rich ocean currents.
The moderate depth and quiescence of these environments provides relatively low oxygenation of the water-sediment interface. Low energy
in the environment also ensures that only the finest grades of inorganic sediment reach this environment. Clays and silt-sized sediment
particles serve two purposes in organic preservation:
✔ The fine particle size and proportionately high active surface area of these particles very efficiently sweep from the water dissolved
and finely dispersed, light organic material at a rate much faster than would occur with simple settling.
✔ The clays and silts also produce closely packed, impermeable sediments that are less likely to be re-worked, or to allow the free
circulation of oxygenated pore waters.
The clays, claystones and shales deposited in these quiescent, near-shore environments normally contain between 0.5 and 1.5 percent by
weight of organic material. This is two to three times higher than is usually found in sandstones from shallower, higher energy environments,
or deeper water carbonates.
Sedimentary Basins
Given the existence of a suitable basin with adequate sources of organic debris and inorganic sediments, what else is required to provide a
productive petroleum source bed?
Obviously, the first requirement is time and uniformity:

✔ The basin and its adjuncts must remain in their original condition long enough for a considerable thickness of organic source bed to
have been deposited.
✔ Down-warp of the basin must be uniform (to maintain basin depth) and continuous to allow normal compaction and diagenesis to
complete the process of burial and sealing of the organic material. Hydrated wet clays at the sediment-water interface may contain
as much as 60 to 90 percent water by volume. Soon after sedimentation this will fall to 40 or 50 percent. Progressive de-watering and
compaction of the clays gradually reduces the water content to 15 percent or less at depth (see Figure 22).
Figure 22: Clay compaction, porosity reduction, and density increase all proceed with increasing depth of burial.
There must be a balance between the rate of sediment deposition, basin subsidence, de-watering, compaction and the resultant loss of
permeability. Flow of expelled pore water is generally upward allowing the deeper sediments to compact and preventing the influx of
oxygenated pore water from the higher basin margins. If compaction rate exceeds the ability of the sediments to expel water then the
sediments become geo-pressured: water becomes trapped and, since water cannot be compressed, it must assume a pressure in excess
of normal hydrostatic pressure (see Geopressure Logging in Chapter 12).
Geo-pressuring may be a temporary phenomenon: the fluids flow out slowly and pressures deplete, eventually returning the basin to a
normal state. In other cases, the geo-pressured zone may become sealed and preserved preventing the completion of the normal
diagenesis of both the sediments and the organic material.
Petroleum Maturation
The most significant minerals present in the clay source bed will be detrital silica and the sheet silicates:
✔ Illite
✔ Smectite (vermiculite and the montmorillonites)
✔ Kaolinite, and
✔ Chlorite
The clay minerals (see Whittaker & Dyson, 1980) are usually the products of sub-aerial weathering of igneous rocks. The actual
composition of clay minerals is strongly dictated by the sediment source and the environments of weathering, transportation and deposition:
✔ Acidic rocks poor in calcium, magnesium and sodium most likely produce kaolinite,
✔ Alkaline rocks will yield smectites,
✔ Vermiculite may also be derived from the decomposition of micas or may occur with chlorite as a detrital or re-cycled mineral in
sediments.
✔ Rocks that are rich in potassium and aluminum may yield illite which may also be detrital to some extent.
Mineralogy
The actual clay mineral lattice sheet is strong and stable - silicon, like carbon, forms stable bonds with its own atoms. However, between the
silicate sheets are water molecules and positively charged metal cations, weakly bound by electrostatic attraction and hydrogen bonding
(see Figure 23). Just as in other forms of bonding, some positive cations in the clay interlayer space may be strongly bound whereas others
are relatively mobile depending upon their valence and electro-negativity. These so-called exchange positive cations, weakly held at clays
lattice will readily move in and out of the lattice space, exchanging with other ions in pore waters in response to relative differences in
composition.
The polar water molecules are held in place on the lattice and to the positive cations by hydrogen bonding in a similar manner to hydration in
solution. Although not permanently bound within the mineral structure, this water should not be considered to be in a truly liquid form. Within
the clay lattice, its polymeric, hydrogen-bonded structure is even more compact and rigid than in liquid water. Instead it has an ice-like
immobility, and an even greater effective density. Under extreme pressure some of this water may be displaced from the inter-lattice space
as the mineral is compacted. However, a small proportion of the water — that which is directly bonded to the lattice — cannot be excluded
by pressure alone. It requires a diagenetic, chemical process.
Figure 23: Sheet silicate clay minerals consist of extensive silicon- oxygen sheets separated by
weakly hydrogen bonded water molecules and positive metal cations.
Soon after burial and the initial physical de-watering, exclusion of inter-layer water begins to reduce the water content of the clay to about 10
percent. Although a physical process this inter-layer de-watering requires pressures far in excess of those required to drive out normal pore
water (see Weaver, 1958).
True diagenesis involves the partial conversion of smectite clay minerals to illite, and does not begin until greater burial has been achieved.
Relatively unaffected by pressure, diagenesis is slowly initiated when formation temperature reaches 80° C (176° F). The rate of reaction
accelerates between 100 and 110°C (212° and 230° F) and continues to 200°C (392° F). Diagenesis involves potassium ions entering the
smectite clay mineral lattice, from the pore space, and becoming strongly attached at lattice ion exchange sites. When this occurs the lattice
spacing of the mineral contracts and the previously hydrogen bonded bound water is displaced into the pore space. In the pore space, the
compact structure of the hydrogen bonded water is lost and it must return to a truly fluid state with a consequent increase in volume.
This increase in water volume causes pore pressure to increase and promotes a new phase of de-watering in order to bring the clay porosity
to a minimum of five percent or less. As we shall see in the next chapter this final de-watering is significant to petroleum migration.
Geo-chemical Maturation
The organic matter which is buried in the subsiding sediment will consist of organic macro-molecules which have already begun to
decompose and react with their environment. Under the action of dissolved oxygen and micro- organisms within the pore water some
decomposition to carbon dioxide and water can occur:
..................... Equation 17
In the absence of oxygen, sulfur bacteria can reduce the organic material in an analogous manner to produce methane and hydrogen
sulfide. The organic debris from marine micro-organic sources are called sapropel. This material is rich in carbon and hydrogen but also in
sulfur and nitrogen. Even at low temperatures, below 50°C (122° F), sapropels begin to break down and, in the process, liberate light
hydrocarbons, carbon dioxide and hydrogen sulfide.
Humic organic material, derived from terrestrial sources and higher plants, is equally unstable yielding some light hydrocarbons along with
carbon dioxide. Under suitable circumstances, this thermo-biogenic natural gas may accumulate in sufficient quantities to be economically
viable, but, in general, it is retained in the sediment and is of little value.
Some minor reactions of other kinds may also occur between the organic debris, pore water solutions and the minerals. Carboxylic or fatty
acid groups within the bio-polymers can become ionized in aqueous solution and the ion exchange sites on the clay mineral lattice can act
as catalysts for complex reactions (see Weaver, 1960).
Larger molecules may undergo numerous processes generally referred to as reforming. In reforming, the structure of the large molecules
are simplified, non-hydrocarbon functional groups are lost or modified. Some large polymeric molecules may be broken down into smaller
monomer units whereas others may remain large though simplified in structure. Yet others may be broken into bio-monomer units only to be
re-combined into new large geo-polymer compounds. This new mass of material which is no longer organic but not yet truly petroleum is
called kerogen.
Figure 24: The yield of oil and gas from kerogen types I, II, III and IV is governed by the chemical composition and
origin of the source material.
Figure 25: The stages and products of petroleum maturation for kerogen, humic and sapropelic organic materials.
Kerogen is amorphous and indeterminate in composition but is generally divided into four types:
✔ Type I Kerogen or Alginite is sapropelic material derived from fresh water algae and marine micro-organisms.
✔ Type II Kerogen or Exinite is a mixture of sapropelic material with some humic material of a vegetable source.
✔ Type III Kerogen or Vitrinite is humic material primarily of carbohydrate origin with small amounts of woody material containing
lignins and tannins.
✔ Type IV Kerogen or Inertinite is the least productive form of kerogen derived from woody and recycled materials like coals and peat.
Figure 24 shows the range of chemical composition of each of these types of kerogen. This representation, called a Van Krevelen
Diagram, was originally used to display the rank or quality of coal measures. It is equally useful in representing petroleum source rock
quality. Notice the similarities between this figure and Figure 21 confirming the statement that the organic compounds most chemically
similar to petroleum provide the most productive source material.
Above 50°C (122° F), the process of maturation becomes more severe. diagenesis and its accompanying biochemical processes comes to
an end and, between 50°C (122° F) and 200°C (392° F), the process of catagenesis occurs.
During catagenesis the real process of oil and gas production begins. Large geo-polymers are repetitively cracked into smaller and simpler
hydrocarbon molecules. Complex and poly-atomic functional groups are stripped away and displaced in the form of carbon dioxide, water,
nitrogen and hydrogen sulfide. The bond sites made available are filled with hydrogen atoms liberated from the destruction of other macro-
molecules.
At this stage, the products of catagenesis are true mobile petroleum hydrocarbon oils and gases. Driven by the coincident late expulsion of
inter- layer water from the clays, the oil and gas begins its migration from the source bed.
The processes commenced in catagenesis continue with increasing temperature so long as source material remains. However, beyond
200°C (392° F) the processes become too extreme to produce useful petroleum products. In this phase known as metagenesis, increased
cracking produces smaller hydrocarbons. Oil production declines and the majority of the produced fluid consists of light hydrocarbon gases
leaving a solid residue of graphite or extremely hard coal-like material.
The Oil Window

The region of maximum oil generation is often referred to as the oil window and a range of 107°C (225° F) to 177°C (350° F) is commonly
assumed to define the oil window for all sedimentary source beds. This is a gross though fairly useful generalization. In the most sensitive
work, account must be taken of the chemical nature of the kerogen. In addition, the age of the kerogen and initial chemistry of the clay
sediment needs to be considered since time, temperature and catalysis are all drivers of the rate at which kerogen is converted into
hydrocarbons.
Figure 26: The depth and vertical thickness of the oil window depends upon both the present and historic (or fossil)
geothermal gradients.
Figure 27: Petroleum maturation is driven by both temperature and time. The total yield of hydrocarbons Increases with
the age of burial even without an increase in temperature.
The depth and vertical thickness of the oil window is controlled by the geothermal gradient (Figure 26). If the regional geothermal gradient is
known for a basin then it is possible to compute the depth interval representing the oil window. If the gradient is higher then the oil window
will be less thick. If no potential source beds fall within or below this zone, then no oil can have been generated in the section. On the other
hand, if no potential reservoirs fall within or higher than this zone then all accumulated hydrocarbons will have been destroyed in the
reservoir by the thermal action of metagenesis.
Unfortunately, in many basins the situation is not so simple. Remember that the oil window is governed not by the current temperature of the
formations but the maximum temperature that they have experienced during their geological history. If a basin has a complex structural
history and formations have been deeply buried, uplifted or otherwise displaced then it is necessary to determine the fossil geothermal
gradient for the section. This may be done by calibrating certain temperature indicative characteristics of minerals, kerogen or hydrocarbons
(see Tissot, Pelet, & Ungerer, 1987). Using this calibration, a variable Thermal Alteration Index (TAI) or Time-Temperature Index (TTI) can
be computed based upon the actual rock maturity which includes the effect of the rock’s age and its entire thermal history (see Figure 27).
Summing Up
Organic molecules, although very large are really very simple. They are built up from a carbon skeleton which will contain repetitions of a
few simple structures consisting of straight and branched chains and rings. In addition to carbon, organic materials are made up of
hydrogen, oxygen, nitrogen and sulfur with trace quantities of a few other elements.
Water, on the other hand, although small has a complex and fascinating chemistry. Because of the polar nature of the water molecule, it is
much denser and less volatile than its formula would suggest. It will dissolve ionic and other polar compounds well but has low solubilities
for non-polar covalent and organic compounds. In aqueous solution ionic and polar compounds become separated into ions which are
hydrated and stabilized by surrounding water molecules.
The quality of a petroleum reservoir is governed by the quality of the source bed. The quality of the source bed is equally controlled by:
✔ The nature of weathered host from which its sediments are derived.
✔ The environment of transportation of the sediment.
✔ The living environment and nature of the organic material.
✔ The environment of deposition of these materials.
✔ The geological history and temperature record through which the materials pass.
All of this, and we haven't even got to talking about migration of hydrocarbons into the reservoir!
Mud logging is much more than reservoir evaluation. On an exploration well, the evaluation of non-reservoirs can yield just as much useful
information (maybe more). Good mud logging, well interpreted, should be a universal geological evaluation tool. The information gained
from each foot of the well can assist in the understanding of the sedimentary and petroleum history and the discovery of commercial
hydrocarbons on this or a subsequent well. An exploration borehole can yield a lot of information relevant to finding oil without even
penetrating a single reservoir.
And Next
Chapter 2 has given us a good foundation in the chemistry of two of the most complex components of a sedimentary succession:
hydrocarbons and clay minerals. We have left off at the point where oil, gas and water are being cooked out of the source bed.
In Chapter 3 we’ll take a look at the physical properties that control how the expelled oil, gas and water travel through the rocks, and reach
a point where they can accumulate to form a producible reservoir.
We shall introduce the important concepts of porosity and permeability, and discuss how they are created and modified over time.
Again, if this all bores you, you're free to skip ahead to Chapter 5, and start reading about gas traps and hot-wire detectors. But then you
may not really understand what is being detected, or why!

Online Mud Logging Handbook Chapter 2 Summary

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Online Mud Logging Handbook Chapter 2 Summary

Uploaded by

Copyright:

Available Formats

The On-line Mud Logging Handbook Alun Whittaker

See Acrobat Document Properties

Didn't find what you needed here? Sorry.

List of Figures & Tables

A Short Lesson in Chemistry Basics

✔ Every different element has a unique, integer atomic number,

For example consider the element carbon (Figure1):

Atomic Mass Relative Abundance

C-11 6 11 << 0.0000001

✔ Helium: Atomic Number =2

Atomic Atomic Electro-

Aluminum Al 26.980 13 1.5

Barium Ba 137.340 56 0.9

Calcium Ca 40.080 20 1.0

Carbon C 12.011 12 2.5

Chlorine Cl 35.453 17 3.0

Chromium Cr 51.996 24 1.6

Copper Cu 63.540 29 1.8

Hydrogen H 1.008 1 2.1

Iron Fe 55.847 26 1.7

Magnesium Mg 24.312 12 1.2

Manganese Mn 54.938 25 1.6

Atomic Atomic Electro-

Nickel Ni 58.710 28 1.8

Nitrogen N 14.007 7 3.0

Oxygen O 15.999 8 3.5

Phosphorus P 30.974 15 2.1

Potassium K 39.102 19 0.8

Silicon Si 28.086 14 2.2

Sodium Na 22.990 11 0.9

Sulfur S 32.064 16 2.5

..................... Equations 2 & 3

The periodic law predicts that, in Mendeleev's Periodic Table:

Move down, two position to…

Move right, one position to…

Move right, thirteen positions to…

Move right, two positions to…

Finally, move up, two positions to…

Figure 5: Covalent bonds involve the sharing of electrons.

Polar Covalent Compounds

Miscibility and Solubility

petroleum or, eventually, as mud loggers!

Dissociation and Equilibrium Reactions

Figure 13: Dissolution and dissociation of hydrogen sulfide in water

Figure 14: Dissolution and dissociation of carbon dioxide in water.

Ionization of hydrogen sulfide proceeds by a number of equilibrium steps.

The Carbon Cycle

Figure 19: Generation and re-generation of carbon-bearing compounds in sedimentary environments.

Biochemical Building Blocks

Lignins and Tannins

Obviously, the first requirement is time and uniformity:

The Oil Window

You might also like