Biodesulfurization in

Petroleum Refining

Scrivener Publishing

100 Cummings Center, Suite 541J

Beverly, MA 01915-6106

Publishers at Scrivener

Martin Scrivener (martin@scrivenerpublishing.com)

Phillip Carmical (pcarmical@scrivenerpublishing.com)

Biodesulfurization in

Petroleum Refining

Nour Shafik El-Gendy Hussein Nabil Nassar

This edition first published 2018 by John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA

and Scrivener Publishing LLC, 100 Cummings Center, Suite 541J, Beverly, MA 01915, USA

© 2018 Scrivener Publishing LLC

For more information about Scrivener publications please visit www.scrivenerpublishing.com.

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or

transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or other-

wise, except as permitted by law. Advice on how to obtain permission to reuse material from this title

is available at http://www.wiley.com/go/permissions.

Wiley Global Headquarters

111 River Street, Hoboken, NJ 07030, USA

For details of our global editorial offices, customer services, and more information about Wiley prod-

ucts visit us at www.wiley.com.

Limit of Liability/Disclaimer of Warranty

While the publisher and authors have used their best efforts in preparing this work, they make no rep-

resentations or warranties with respect to the accuracy or completeness of the contents of this work and

specifically disclaim all warranties, including without limitation any implied warranties of merchant-

ability or fitness for a particular purpose. No warranty may be created or extended by sales representa-

tives, written sales materials, or promotional statements for this work. The fact that an organization,

website, or product is referred to in this work as a citation and/or potential source of further informa-

tion does not mean that the publisher and authors endorse the information or services the organiza-

tion, website, or product may provide or recommendations it may make. This work is sold with the

understanding that the publisher is not engaged in rendering professional services. The advice and

strategies contained herein may not be suitable for your situation. You should consult with a specialist

where appropriate. Neither the publisher nor authors shall be liable for any loss of profit or any other

commercial damages, including but not limited to special, incidental, consequential, or other damages.

Further, readers should be aware that websites listed in this work may have changed or disappeared

between when this work was written and when it is read.

Library of Congress Cataloging-in-Publication Data

ISBN 978-1-119-22358-0

Cover image: Oil Refinery at Dusk, Oleg Yermolov | Dreamstime.com

Cover design by Kris Hackerott

Set in size of 11pt and Minion Pro by Exeter Premedia Services Private Ltd., Chennai, India

Printed in the USA

10 9 8 7 6 5 4 3 2 1

v

Contents

Preface xiii

1 Background 1List of Abbreviations and Nomenclature 11.1 Petroleum 21.2 Petroleum Composition 7

1.2.1 Petroleum Hydrocarbons 81.2.2 Petroleum Non-Hydrocarbons 12

1.2.2.1 Problems Generated by Asphaltenes 141.3 Sulfur Compounds 151.4 Sulfur in Petroleum Major Refinery Products 20

1.4.1 Gasoline 201.4.2 Kerosene 231.4.3 Jet Fuel 231.4.4 Diesel Fuel 231.4.5 Heating/Fuel Oils 241.4.6 Bunker Oil 24

1.5 Sulfur Problem 251.6 Legislative Regulations of Sulfur Levels in Fuels 29References 32

2 Desulfurization Technologies 39List of Abbreviations and Nomenclature 392.1 Introduction 432.2 Hydrodesulfurization 472.3 Oxidative Desulfurization 712.4 Selective Adsorption 1082.5 Biocatalytic Desulfurization 127

2.5.1 Anaerobic Process 1272.5.2 Aerobic Process 128

References 130

vi Contents

3 Biodesulfurization of Natural Gas 159List of Abbreviations and Nomenclature 1593.1 Introduction 1613.2 Natural Gas Processing 1693.3 Desulfurization Processes 183

3.3.1 Scavengers 1833.3.2 Adsorption 1873.3.3 Liquid Redox Processes 1933.3.4 Claus Plants 195

3.3.4.1 Classic Claus Plant 1963.3.4.2 Split-Flow Claus Plant 1983.3.4.3 Oxygen Enrichment Claus Plant 1993.3.4.4 Claus Plant Tail Gas 199

3.3.5 Absorption/Desorption Process 2013.3.6 Biodesulfurization 203

3.3.6.1 Photoautotrophic Bacteria 2063.3.6.2 Heterotrophic Bacteria 2113.3.6.3 Chemotrophic Bacteria 212

3.3.7 Other Approaches Concerning the Biodesulfurization of Natural Gas 231

References 242

4 Microbial Denitrogenation of Petroleum and its Fractions 263List of Abbreviations and Nomenclature 2634.1 Introduction 2654.2 Denitrogenation of Petroleum and its Fractions 269

4.2.1 Hydrodenitrogenation 2694.2.2 Adsorptive Denitrogenation 2724.2.3 Extractive and Catalytic Oxidative Denitrogenation 278

4.3 Microbial Attack of Nitrogen Polyaromatic Heterocyclic Compounds (NPAHs) 279

4.4 Enhancing Biodegradation of NPAHs by Magnetic Nanoparticles 295

4.5 Challenges and Opportunities for BDN in Petroleum Industries 300

References 307

5 Bioadsorptive Desulfurization of Liquid Fuels 327List of Abbreviations and Nomenclature 3275.1 Introduction 3295.2 ADS by Agroindustrial-Wastes Activated Carbon 3325.3 ADS on Modified Activated Carbon 3425.4 ADS on Carbon Aerogels 352

Contents vii

5.5 ADS on Activated Carbon Fibers 3535.6 ADS on Natural Clay and Zeolites 3555.7 ADS on New Adsorbents Prepared from

Different Biowastes 360References 365

6 Microbial Attack of Organosulfur Compounds 375List of Abbreviations and Nomenclature 3756.1 Introduction 3776.2 Biodegradation of Sulfur Compounds in the Environment 3806.3 Microbial Attack on Non–Heterocyclic Sulfur–Containing

Hydrocarbons 3836.3.1 Alkyl and Aryl Sulfides 3836.3.2 Non – Aromatic Cyclic Sulfur – Containing

Hydrocarbons 3866.4 Microbial Attack of Heterocyclic Sulfur – Hydrocarbons 388

6.4.1 Thiophenes 3896.4.2 Benzothiophenes and Alkyl-Substituted

Benzothiophenes 3906.4.3 Naphthothiophenes 4026.4.4 Dibenzothiophene and Alkyl-Substituted

Dibenzothiophenes 4066.4.4.1 Aerobic Biodesulfurization of DBT 4066.4.4.2 Aerobic Biodesulfurization of Alkylated DBT 4196.4.4.3 Anaerobic Biodesulfurization of DBT 421

6.5 Recent Elucidated DBT-BDS Pathways 422References 439

7 Enzymology and Genetics of Biodesulfurization Process 459List of Abbreviations and Nomenclature 4597.1 Introduction 4617.2 Genetics of PASHs BDS Pathway 462

7.2.1 Anaerobic BDS Pathway 4627.2.2 Aerobic BDS Pathway 463

7.2.2.1 Kodama Pathway 4637.2.2.2 Complete Degradation Pathway 4647.2.2.3 4S-Pathway 466

7.3 The Desulfurization dsz Genes 4687.4 Enzymes Involved in Specific Desulfurization

of Thiophenic Compounds 4727.4.1 The Dsz Enzymes 472

7.4.1.1 DszC Enzyme (DBT-Monooxygenase) 4747.4.1.2 DszA Enzyme (DBTO

2-Monooxygenase) 476

viii Contents

7.4.1.3 DszB Enzyme (HBPS- Desulfinase) 4777.4.1.4 DszD Enzyme (Flavin-Oxidoreductase

Enzyme) 4787.5 Repression of dsz Genes 4807.6 Recombinant Biocatalysts for BDS 484References 506

8 Factors Affecting the Biodesulfurization Process 521List of Abbreviations and Nomenclature 521 8.1 Introduction 524 8.2 Effect of Incubation Period 525 8.3 Effect of Temperature and pH 527 8.4 Effect of Dissolved Oxygen Concentration 530 8.5 Effect of Agitation Speed 532 8.6 Effect of Initial Biomass Concentration 536 8.7 Effect of Biocatalyst Age 538 8.8 Effect of Mass Transfer 541 8.9 Effect of Surfactant 5418.10 Effect of Initial Sulfur Concentration 5448.11 Effect of Type of S-Compounds 5468.12 Effect of Organic Solvent and Oil to Water Phase Ratio 5538.13 Effect of Medium Composition 5608.14 Effect of Growing and Resting Cells 5798.15 Inhibitory Effect of Byproducts 5808.16 Statistical Optimization 590References 616

9 Kinetics of Batch Biodesulfurization Process 639List of Abbreviations and Nomenclature 6399.1 Introduction 6429.2 General Background 643

9.2.1 Phases of Microbial Growth 6439.2.1.1 The Lag Phase 6449.2.1.2 The Log Phase 6449.2.1.3 The Stationary Phase 6459.2.1.4 The Decline Phase 645

9.2.2 Modeling of Population Growth as a Function of Incubation Time 645

9.3 Microbial Growth Kinetics 6459.3.1 Exponential Growth Model 6459.3.2 Logistic Growth Model 648

9.4 Some of the Classical Kinetic Models Applied in BDS-Studies 650

Contents ix

9.5 Factors Affecting the Rate of Microbial Growth 6519.5.1 Effect of Temperature 6519.5.2 Effect of pH 6549.5.3 Effect of Oxygen 654

9.6 Enzyme Kinetics 6549.6.1 Basic Enzyme Reactions 6569.6.2 Factors Affecting the Enzyme Activity 657

9.6.2.1 Enzyme Concentration 6579.6.2.2 Substrate Concentration 6589.6.2.3 Effect of Inhibitors on Enzyme Activity 6599.6.2.4 Effect of Temperature 6609.6.2.5 Effect of pH 661

9.7 Michaelis-Menten Equation 6629.7.1 Direct Integration Procedure 6649.7.2 Lineweaver-Burk Plot Method 6669.7.3 Eadie-Hofstee 666

9.8 Kinetics of a Multi-Substrates System 667 9.9 Traditional 4S-Pathway 668

9.9.1 Formulation of a Kinetic Model for DBT Desulfurization According to 4S-Pathway 669

9.10 Different Kinetic Studies on the Parameters Affecting the BDS Process 673

9.11 Evaluation of the Tested Biocatalysts 7349.11.1 Kinetics of the Overall Biodesulfurization Reaction 7359.11.2 Maximum Percentage of Desulfurization (XBDS

MAX %) 7359.11.3 Time for Maximum Biodesulfurization tBDSmax (min) 7359.11.4 Initial DBT Removal Rate RDBT

O (μmol/L/min) 7369.11.5 Maximum Productivity PBDS

MAX (%/min) 7369.11.6 Specific Conversion Rate (SE %L/g/min) 736

References 737

10 Enhancement of BDS Efficiency 753List of Abbreviations and Nomenclature 75310.1 Introduction 75610.2 Isolation of Selective Biodesulfurizing Microorganisms

with Broad Versatility on Different S-Compounds 75710.2.1 Anaerobic Biodesulfurizing Microorganisms 75810.2.2 Bacteria Capable of Aerobic Selective DBT-BDS 75910.2.3 Microorganisms with Selective BDS of

Benzothiophene and Dibenzothiophene 76910.2.4 Microorganisms with Methoxylation Pathway 770

x Contents

10.2.5 Microorganisms with High Tolerance for Oil/Water Phase Ratio 771

10.2.6 Thermotolerant Microorganisms with Selective BDS Capability 772

10.2.7 BDS Using Yeast and Fungi 77610.3 Genetics and its Role in Improvement of BDS Process 77810.4 Overcoming the Repression Effects of Byproducts 78910.5 Enzymatic Oxidation of Organosulfur Compounds 79310.6 Enhancement of Biodesulfurization via Immobilization 795

10.6.1 Types of Immobilization 80010.6.1.1 Adsorption 80010.6.1.2 Covalent Binding 80910.6.1.3 Encapsulation 80910.6.1.4 Entrapment 810

10.7 Application of Nano-Technology in BDS Process 82610.8 Role of Analytical Techniques in BDS 849

10.8.1 Gas Chromatography 85010.8.1.1 Determination of Sulfur Compounds

by GC 85010.8.1.2 Assessment of Biodegradation 851

10.8.2 Presumptive Screening for Desulfurization and Identification of BDS Pathway 85210.8.2.1 Gibb’s Assay 85310.8.2.2 Phenol Assay 853

10.8.3 More Advanced Screening for Desulfurization and Identification of BDS Pathway 85410.8.3.1 High Performance Liquid

Chromatography 85410.8.3.2 X-ray Sulfur Meter and other

Techniques for Determining Total Sulfur Content 855

References 857

11 Biodesulfurization of Real Oil Feed 895List of Abbreviations and Nomenclature 89511.1 Introduction 89711.2 Biodesulfurization of Crude Oil 90311.3 Biodesulfurization of Different Oil Distillates 90911.4 BDS of Crude Oil and its Distillates by Thermophilic

Microorganisms 92111.5 Application of Yeast and Fungi in BDS of Real Oil Feed 92311.6 Biocatalytic Oxidation 924

Contents xi

11.7 Anaerobic BDS of Real Oil Feed 92611.8 Deep Desulfurization of Fuel Streams by Integrating

Microbial with Non-Microbial Methods 92811.8.1 BDS as a Complement to HDS 92811.8.2 BDS as a Complementary to ADS 93911.8.3 Coupling Non-Hydrodesulfurization with BDS 94511.8.4 Three Step BDS-ODS-RADS 945

11.9 BDS of other Petroleum Products 946References 952

12 Challenges and Opportunities 973List of Abbreviations and Nomenclature 973 12.1 Introduction 975 12.2 New Strains with Broad Versatility 983 12.3 New Strains with Higher Hydrocarbon Tolerance 990 12.4 Overcoming the Feedback Inhibition of the

End-Products 994 12.5 Biodesulfurization under Thermophilic Conditions 995 12.6 Anaerobic Biodesulfurization 997 12.7 Biocatalytic Oxidation 1000 12.8 Perspectives for Enhancing the Rate of BDS 1001

12.8.1 Application of Genetics in BDS 100212.8.2 Implementation of Resting Cells 100912.8.3 Microbial Consortium and BDS 101112.8.4 Surfactants and BDS 101412.8.5 Application of Nanotechnology in the BDS

Process 1017 12.9 Production of Valuable Products 102812.10 Storage of Fuel and Sulfur 103112.11 Process Engineering Research 103312.12 BDS Process of Real Oil Feed 105312.13 BDS as a Complementary Technology 106112.14 Future Perspectives 106312.15 Techno-Economic Studies 106612.16 Economic Feasibility 106812.17 Fields of Developments 107712.18 BDS Now and Then 108012.19 Conclusion 1083References 1084

Glossary 1119

Index 1155

xiii

Preface

Biotechnology is now accepted as an attractive means of improving the efficiency of many industrial processes and resolving serious environmen-tal problems. One of the reasons for this is the extraordinary metabolic capability that exists within the bacterial world. Microbial enzymes are capable of biotransforming a wide range of compounds and the increas-ing worldwide attention paid to this concept can be attributed to several factors, including the presence of a wide variety of catabolic enzymes and the ability of many microbial enzymes to transform a broad range of unnatural compounds (xenobiotics), as well as natural compounds. Biotransformation processes have several advantages compared to chemi-cal processes, such as: (i) Microbial enzyme reactions often being more selective; (ii) Biotransformation processes often being more energy-effi-cient; (iii) Microbial enzymes being active under mild conditions; and (iv) Microbial enzymes being environmentally friendly biocatalysts. Although many biotransformation processes have been described, only a few of these have been used as part of the industrial process. Many opportunities remain in this area.

Biotechnology has been successfully applied at the industrial level in the medical, fine chemical, agricultural, and food sectors. Petroleum biotech-nology is based on biotransformation processes. Petroleum microbiology research is advancing on many fronts, spurred on most recently by new knowledge of cellular structure and function gained through molecular and protein engineering techniques, combined with more conventional microbial methods. Several applications of biotechnology in the oil and energy industry are becoming foreseen. Current applied research on petro-leum microbiology encompasses oil spill remediation, fermenter- and wet-land-based hydrocarbon treatment, bio-filtration of volatile hydrocarbons, enhanced oil recovery, oil and fuel biorefining, fine-chemical production, and microbial community based site assessment. The production of bio-fuels in large volumes is now a reality, although there are some concerns

xiv Preface

about the use of land, water, and crops to produce fuels. These come from the biofuels produced by agroindustrial wastes, lignocellulosic wastes, waste oils, and micro- and macro-algae. In the oil industry, biotechnology has found its place in bioremediation and microbial enhanced oil recov-ery (MEOR). There are other opportunities in the processing (biorefin-ing) and upgrading (bio-upgrading) of problematic oil fractions and heavy crude oils. In the context of increasing energy demand, conventional oil depletion, climate change, and increased environmental regulations on atmospheric emissions, biorefining is a possible alternative to some of the current oil-refining processes. The major potential applications of biore-fining are biodesulfurization, biodenitrogenation, biodemetallization, and biotransformation of heavy crude oils into lighter crude oils, i.e., upgrad-ing heavy oils (degradation of asphaltenes and removal of metals). The most advanced area is biodesulfurization, for which pilot plants exist and the results obtained for biodesulfurization may be generally applicable to other areas of biorefining.

This book reviews the worldwide status of current regulations regard-ing fuel properties that have environmental impacts, such as sulfur and nitrogen content, cetane number, and aromatic content, summarizes the cumulative, and highlights the recent scientific and technological advances in different desulfurization techniques, including: physical (for example, adsorptive desulfurization ADS), chemical (for example, hydrodesulfurization HDS, oxidative desulfurization ODS), and bio-logical (for example, bio-adsorptive desulfurization BADS, aerobic and anaerobic biodesulfurization BDS, and biocatalytic oxidation as alterna-tive to BODS) techniques. It will also cover denitrogenation processes (physical, chemical and biological ones). Since basic nitrogen com-pounds inactivate HDS catalysts and non-basic compounds can be con-verted to basic ones during the refining/catalytic cracking process, they are also potential inhibitors of the HDS process. So, denitrogenation is advantageous both from an environmental point of view (reduction of NOx emissions) and from an operational point of view (to avoid catalyst deactivation, corrosion of refinery equipment, and chemical instability of refined petroleum).

The advantages and limitations of each technique are discussed. The application of molecular biology and the possibility of integration of bio-nano-technology in oil production plants, future oil refineries and bioprocessing of oil, for the production of ultra-low sulfur fuels are also summarized in this book. Challenges and future perspectives of BDS in the petroleum industry and their applications for detoxification of chemi-cal warfare agents, or the production of other valuable products, such as:

Preface xv

surfactants, antibiotics, polythioesters, and various specialty chemicals are also covered in this book.

Dr. Nour Sh. El-GendyProfessor of Petroleum and

Environmental Biotechnology

Dr. Hussein N. NassarResearcher of Petroleum and

Environmental Biotechnology

October 2017

1

1Background

List of Abbreviations and Nomenclature

4,6-DMDBT 4,6-Dimethydibenzothiophene

4-MDBT 4-Methyldibenzothiophene

API American Petroleum Institute

BT Benzothiophene

BTEX Benzene, Toluene, Ethylbenzene and Xylene

Cu Cupper

DBT Dibenzothiophene

EEB European Environmental Burean

FCC Fluid Catalytic Cracking

FSU Former Soviet Union

HCR Hydrocracking

HDS Hydrodesulfurization

ICCT International Council on Clean Transportation

IEA International Energy Agency

LPG Liquid Petroleum Gas

Ni Nickel

NOx

Nitrogen Oxides

2 Biodesulfurization in Petroleum Refining

NSO Nitrogen, Sulfur and Oxygen

OPEC Organization of the Petroleum Exporting Countries

PAHs Polyaromatic Hydrocarbons

PASH Polycyclic Aromatic Sulfur Heterocycles

Ph Phytane

PM Particulate Matters

ppm Parts Per Million

Pr Pristane

SOx

Sulfur Oxides

Th Thiophene

TLV Threshold Limit Value

UE Union European

ULS Ultra-Low Sulfur

USA United States of America

US-EPA United States Environmental Protection Agency

V Vanadium

WTI West Texas Intermediate

1.1 Petroleum

Nowadays, although the percentage of energy obtained from fossil fuels has decreased, over 83% of the world’s energy is still from fossil fuels, approximately half of which comes from crude oil (OPEC, 2013). Crude oil or petroleum (Black Gold) was formed under the surface of the earth millions of years ago. It is the most important renewable energy source. The largest growth in demand is from developing countries, but the larg-est consumers of oil are industrial nations. The OPEC has forecasted the demand for crude oil for a long-term period from 2010 to 2035, with an increasing capacity of 20 Mb/d, reaching 107.3 Mb/d by 2035 (Duissenov, 2013). It is estimated that the world consumes about 95 million barrels/per day (i.e. 5.54 trillion barrels/day) in many applications: industry, heating, transportation, generating electricity, and production of chemical reagents that can be used in making synthetics, polymers, plastics, pharmaceuticals, solvents, dyes, synthetic detergents and fabrics, fertilizers, pesticides, lubri-cants, waxes, tires, tars and asphalts, and many other products (Varjani, 2017). In a typical barrel, approximately 84% of the hydrocarbons present in petroleum are converted into energy-rich fuels (i.e. petroleum-based fuels); including gasoline, diesel, jet, heating, and other fuel oils, and lique-fied petroleum gas. Constituents of crude oil are resulted from aerobic and anaerobic enzymatic degradation of organic matter under suitable condi-tions of temperature and pressure. Crude oils vary widely in appearance

Background 3

and viscosity from field to field. They range in color, odor, and in the properties they contain according to their origin and geographical place. Although all crude oils are essentially hydrocarbons that occur in the sedi-mentary rock in the forms of natural gas, liquid, semisolid (i.e. bitumen) or solid (i.e. wax or asphaltene), they differ in properties and in molecular structure (Berger and Anderson, 1981). It has been reported that the larg-est estimated crude oil reserves are in Canada, Iran, and Kazakhstan and approximately 56% of the world’s oil reserves are in the Middle East. Thus, according to the regional basis, the Middle East accounts for nearly 48% of the world’s reserves. Central and South America are the second with approximately 20%, with Brazil and Venezuela leading, and North America is the third with approximately 13%. Table 1.1 summarizes the world wide petroleum reserves as reported by Duissenov in 2013. However, there is a depletion of the high quality low sulfur content light crude oil coming with the increment of the production and use of high sulfur content heavy crude oil (Montiel et al., 2009; Srivastava, 2012; Alves et al., 2015). In the near future, with a harsh worldwide increase in energy demand, the petro-leum industry will have to face the fact that sour crude oil and natural gas with high sulfur content is the only energy source of choice. For example, the sulfur content of crude oil input to refineries in USA was 0.88% in 1985, while it reached to 1.44% by 2013 (EIA, 2013).

The word of petroleum is derived from the Latin words “petra” and “elaion” (petraoleum) which mean rock and oil, respectively (Varjani, 2017). It is formed when large quantities of dead organisms, usually zooplankton and algae, are buried underneath sedimentary rock and subjected to both intense heat and pressure. It is a sticky, thick, flammable, yellow to black vis-cous mixture of gas, liquid, and solid hydrocarbons (Vieira et al., 2007). It is also believed to be formed from the decomposition of animal and plants, where heat and geological pressure transform this organic matter into oil and gas during the geologic periods. Crude oil can exist either deep down in the earth’s surface (onshore) or deep below the ocean beds (offshore).

Crude oils are roughly classified into three groups according to the nature of the hydrocarbons they contain: Paraffin–Base Crude Oils, Asphaltic–Base Crude Oils, and Mixed–Base Crude Oils (Varjani, 2014).

Crude oils are liquid, but may contain gaseous or solid compounds or both in solution. Crude oil varies considerably in its physical properties; the majority of crude oils are dark in color, but there are exceptions. There are also differences in odor. Many oils, such as those of Iran, Iraq, and Arabia have a strong odor of hydrogen sulfide and other sulfur compounds. There are, however, several kinds of crude oil which contain little sulfur and have unpleasant odor. This variation in properties is due to the differences in

4 Biodesulfurization in Petroleum Refining

composition and these differences greatly affect the methods of refining and the products obtained from it (El-Gendy and Speight, 2016).

A petroleum reservoir is an underground reservoir that contains hydro-carbons which can be recovered through a producing well as a reservoir fluid. In the reservoir, these fluids are usually found in contact with water

Table 1.1 The Estimated Proven Reserve Holders as of January 2013 (Duissenov,

2013).

Country

Proven reserves

(billions of barrels) Share of total

Venezuela 297.6 18.2%

Saudi Arabia 265.4 16.2%

Canada 173.1 10.6%

Iran 154.6 9.4%

Iraq 141.4 8.6%

Kuwait 101.5 6.2%

UAE 97.8 6.0%

Russia 80.0 5.0%

Libya 48.0 2.9%

Nigeria 37.2 2.3%

Kazakhstan 30.0 1.8%

China 25.6 1.6%

Qatar 25.4 1.6%

United States 20.7 1.3%

Brazil 13.2 0.8%

Algeria 12.2 0.7%

Angola 10.5 0.6%

Mexico 10.3 0.6%

Ecuador 8.2 0.5%

Azerbaijan 7.0 0.4%

Oman 5.5 0.3%

India 5.48 0.3%

Norway 5.37 0.3%

World total 1,637.9 100

Total OPEC 1,204.7 73.6

Background 5

in a porous media such as sandstone and sometimes limestone. Under natural conditions, the fluids are lighter than water; they always stay above the water level and migrate upward through the porous rocks until they are blocked by nonporous rock such as shale or dense limestone. Where petroleum deposits came to be trapped can be caused by geologic features such as folding, faulting, and erosion of the Earth’s crust. In most oil fields, oil and natural gas occur together, gas being the top layer on top of crude oil under which water is found.

The oil industry classifies “crude” by the location of its origin and by its relative weight or viscosity (“light”, “intermediate”, or “heavy”). Light oils can contain up to 97% hydrocarbons, while heavier oils and bitumens might contain only 50% hydrocarbons and larger quantities of other ele-ments. The sulfur content and the American Petroleum Institute (API) gravity are the two properties that determine the quality and value of the crude oil. The API is a trade association for businesses in the oil and natural gas industries. API gravity is a measure of the density of petro-leum liquid compared to water. The petroleum can be classified as light (API > 31.1), medium (API  22.3–31.1), heavy (API < 22.3), and extra heavy (API < 10.0). But, in general, if the API gravity is greater than 10, it is considered “light,” and floats on top of water. While if the API gravity is less than 10, it can be considered “heavy,” and sinks in water (El-Gendy and Speight, 2016).

In most of the international standards, the sulfur content is expressed in ppmw S or mgS/ kg (Al-Degs et al., 2016). The relative content of sulfur in natural oil deposits also results in referring to oil as “sweet”, which means it contains relatively little sulfur (<0.5% S), or as “sour”, which means it contains substantial amounts of sulfur (>0.5% S) (El-Gendy and Speight, 2016). Sweet oil is usually much more valuable than sour because it does not require as much refining and is less harmful to the environment. Light oils are preferred because they have a higher yield of hydrocarbons. Heavier oils have greater concentrations of metals and sulfur and require more refining. Petroleum geochemists are using aromatic sulfur compounds as a maturity parameter. The immature oils are characterized by a relatively high abundance of thermally unstable non-thiophenic sulfur compounds, while mature oils are marked by a relatively high concentration of the more stable benzo- and dibenzo-thiophenes (Wang and Fingas, 1995). Table 1.2 summarizes the classification of crude oil according to the sulfur content and API gravity (Duissenov, 2013). The major locations for sweet crude are the Appalachian Basin in Eastern North America, Western Texas, the Bakken Formation of North Dakota and Saskatchewan, the North Sea of Europe, North Africa, Australia, and the Far East including Indonesia.

6 Biodesulfurization in Petroleum Refining

While those for sour ones are North America (Alberta, Canada, the United States’ portion of the Gulf of Mexico, and Mexico), South America (Venezuela, Colombia, and Ecuador), and the Middle East (Saudi Arabia, Iraq, Kuwait, Iran, Syria, and Egypt) (Duissenov, 2013).

Oil is drilled all over the world. However, there are three primary sources of crude oil that set reference points for ranking and pricing other oil supplies:

Brent Crude is a mixture that comes from 15 different oil fields between Scotland and Norway in the North Sea. These fields supply oil to most of Europe.

West Texas Intermediate (WTI) is a lighter oil that is produced mostly in the U.S. state of Texas. It is “sweet” and “light” and considered very high quality. WTI supplies much of North America with oil.

Dubai crude, also known as Fateh or Dubai-Oman crude, is a light, sour oil that is produced in Dubai, part of the United Arab Emirates. The nearby country of Oman has recently begun producing oil. Dubai and Oman crudes are used as a reference point for pricing Persian Gulf oils that are mostly exported to Asia.

The OPEC Reference Basket is another important oil source. OPEC is the Organization of Petroleum Exporting Countries. The OPEC Reference Basket is the average price of petroleum from OPEC’s twelve member countries: Algeria, Angola, Ecuador, Iran, Iraq, Kuwait, Libya, Nigeria, Qatar, Saudi Arabia, the United Arab Emirates, and Venezuela.

Table 1.2 Crude oil classifications according to S-content and API-gravity

(Duissenov, 2013).

Crude oil class API-gravity Sulfur content (wt.%)

Ultra-light >50 <0.1

Light and sweet 35–50 <0.5

Light and medium sour 35–50 0.5–1

Light and sour 35–50 >1

Medium and sweet 26–35 <0.5

Medium and medium sour 26–35 0.5–1

Medium and sour 26–35 >1

Heavy and sweet 10–26 <0.5

Heavy and medium sour 10–26 0.5–1

Heavy and sour 10–26 >1

Background 7

1.2 Petroleum Composition

The chemical composition of crude oils from different producing regions, and even from within a particular formation, can vary tremendously. That depends on the location of the oil field, its age, and the depth of the oil well (Varjani, 2017). Crude oil is a complex mixture of several hundred chemical compounds, mainly hydrocarbons (mostly alkanes) of various lengths. The approximate length range is C

5H

12 to C

18H

38. Any shorter hydrocarbons are

considered natural gas or natural gas liquids, while long-chain hydrocar-bons are more viscous, and the longest chains are paraffin wax. Generally, petroleum consists of four main fractions; saturates, aromatics, resins and asphaltenes (SARA) (Varjani, 2014). The composition percentage within the petroleum is dependent on its type. However, they are typically pres-ent in petroleum at the following percentages: paraffins (15% to 60%), nap-thenes (30% to 60%), aromatics (3% to 30%), with asphaltics making up the remainder. But, in light oils, asphaltenes and resins constitute 1 to 5%. While in heavy oils, they may constitute up to 20% (Radwan, 2008). Light and less dense petroleum is more profitable as a fuel source due to its higher percentage of hydrocarbons. Since heavy and denser petroleum with high sulfur content is expensive to refine, it increases the price of gasoline (petro), diesel oil, and other important petroleum distillates. Heavy oil is character-ized with high proportions of carbon and NSO and lower hydrogen and overall low quality. The world’s reserves of light petroleum (light crude oil) are severely depleted and refineries are forced to refine and process more and more heavy crude oil and bitumen (El-Gendy and Speight, 2016).

Riazi (2005) has reported that crude oil composition can be summa-rized as follows:

PONA (paraffins, olefins, naphthenes, and aromatics)PINA (paraffins, iso-paraffins, naphthenes, and aromatics)PNA (paraffins, naphthenes, and aromatics)PIONA (paraffins, iso-paraffins, olefins, naphthenes and aromatics)SARA (saturates, aromatics, resins, and asphaltenes)Based on elemental analysis (C, H, S, N, and O)

Most of the petroleum fractions are free of olefins, thus the petroleum composition can be expressed in terms of its PINA composition only. For light oils, the paraffin and iso-paraffin contents can be combined and the petroleum composition can be expressed as PNA. But, for heavy oils which are characterized by high concentrations of aromatics, resins, and

8 Biodesulfurization in Petroleum Refining

asphaltenes, the petroleum composition is expressed as SARA. Elemental analysis is very important, as it gives an indication of the hydrogen and sulfur contents as well as the C/H ratio, which is diagnostic for the quality of petroleum and its products.

Hydrocarbons are the most abundant compounds in crude oils account-ing for 50–98% of the total composition (Clarck and Brown, 1977). While carbon (80–87%) and hydrogen (10–15%) are the main elements in petro-leum, sulfur (0.05–6%), nitrogen (0.1–2%), and oxygen (0.05–1.5%) are important minor constituents present as elemental sulfur or as heterocy-clic constituents and functional groups (Chandra et al., 2013). Compounds containing N, S, and/or O as constituents are often collectively referred to as NSO compounds. Crude oils contain widely varying concentrations of trace metals such as V, Ni, Fe, Al, Na, Ca, Cu, and U (Ni plus V, <1000 ppm w/w and Fe plus Cu, <200 ppm w/w) (El-Gendy and Speight, 2016).

There are known contaminates in petroleum, which are sulfur, vanadium, iron, and zinc. Sour crude oil needs a more expensive and longer refin-ing process, thus higher price fuel distillates and petroleum products. The foul-smelling gas, or sewer gas, mainly comes from hydrogen sulfide, which results from the decay of organic matter. All vanadium compounds are con-sidered toxic. The V is an oxidant; it is one of the main components of diesel fuel. It causes high temperature corrosion and contributes to the corrosion of oil transport pipelines, ships, and tanker trucks. Such corrosion would cause the petroleum to be contaminated with iron which can lead to sludge build-up in pumps, refinery exchangers, and other fuel delivery systems. Moreover, V can react with other contaminates, such as sodium and sulfur, producing vandates salts which increase the corrosion of steel. If the V con-centration is >2 ppm in fuels, it would lead to severe corrosion in turbine blades and deteriorate the refractories in furnaces. Moreover, heavy metals like Ni, V, and Cu severely affect the catalytic activities of refining processes and decrease the production of valuable products. Zinc is another type of contaminant which never occurs as a natural component of oil. It generally comes from the recycling of lubricating oils and interferes with the removal of salts from petroleum. This increases the salt levels which would, conse-quently, increase the corrosion of refinery systems, engine parts, etc.

1.2.1 Petroleum Hydrocarbons

Petroleum is a complex mixture of different identifiable hydrocarbons. Hydrocarbons are organic compounds that contain only carbon and hydrogen (C

xH

y). Petroleum hydrocarbons consist of aliphatic (paraffins,

olefins, and naphthenes) and aromatic compounds containing at least one benzene ring.

Background 9

The alkanes, or aliphatic hydrocarbons, are a part of saturate fractions which represent the main constituent in crude oil. They consists of fully saturated normal alkanes (n-alkanes, also called paraffins) and branched alkanes of the general formula (C

nH

2n+2), with n ranging from 1 to usu-

ally around 40, although compounds with 60 carbons have been reported. Above C

13, the most important group of branched compounds is the iso-

prenoid hydrocarbons consisting of isoprene building blocks. Pristane (Pr, isomer of C

19) and phytane (Ph, isomer of C

20) are usually the most

abundant isoprenoids and, while the C10

–C20

isoprenoids are often major petroleum constituents, extended series of isoprenoids (C

20–C

40) have been

reported (Albaiges and Albrecht, 1979). The ratio of Pr to Ph is usually used to give information about the redox conditions at the time of sedi-mentation of the biogenic material. Moreover, this ratio can help on iden-tification of the origin of oil in a given area (Peters et al., 2005).

Pristane

2,6,10,14-Tetramethylpentadecane

Phytane

2,6,10,14-Tetramethylhexadecane

For fuel purposes only, the alkanes from the following groups will be used: pentane and octane will be refined into gasoline, hexadecane and nonane will be refined into kerosene or diesel or used as a component in the production of jet fuel, and hexadecane will be refined into fuel oil or heating oil. Alkanes with less than five carbon atoms form natural petro-leum gas and will either be burned away or harvested and sold under pres-sure as liquid petroleum gas (LPG). Hydrocarbons longer than 10 carbon atoms in length are generally broken down through the process known as “cracking” to yield molecules with lengths of 10 atoms or less. Alkanes with a carbon number >17 are considered paraffinic waxes and are the main cause for the increase in cloud and pour points (Maldonado et al., 2006). In waxy crudes, alkanes can reach up to 60%, while in low-paraffinic oils the content is recorded at about 1.2% (Duissenov, 2013).

The olefins are the unsaturated non-cyclic hydrocarbons that have at least one double bond between the carbon-carbon atoms. The monoolefins have the general formula of C

nH

2n. When there are two double bonds, it is called

diolefin or diene. Those hydrocarbons that have one or more double bonds between carbon atoms are called alkenes. Those with one or more triple bonds between carbon atoms are called alkynes. There are two types of isom-erization in olefins: the structural isomers, which is related to the location of the double bond, and the geometric isomerism, which is related to the way the atoms are oriented in the space. The configurations are differentiated by

10 Biodesulfurization in Petroleum Refining

the prefixes; cis- and trans-. Olefins and compounds with triple bonds (e.g. cis- and trans-2-butene, butadiene CH

2=CH–CH=CH

2, acetylene CH–CH,

etc.) are not commonly found in petroleum because of their tendency to become saturated with hydrogen, but they are formed during the cracking reactions in the refining process. Olefins are valuable products in refineries as they are the precursors of polymers such as polyethylene.

C C

CH3 CH3

H

C C

CH3

H CH3

H

H

cis-and trans-2-butene

Many of the cycloalkanes or saturated ring structures, also called cyclopar-affins or naphthenes, have the general formula C

nH

2n. These hydrocarbons

display almost identical properties to paraffins, but have a much higher point of combustion. The content of naphthenes in crude oil can reach to 60%. However, in naphthenic crude oils it can reach to 80% (Duissenov, 2013). Saturated multi-rings attached to each other are called polycycloparaffins or polynaphthenes and are mainly found in heavy oils. Naphthenes that con-sist of important minor constituents like that of the isoprenoids which have specific animal or plant precursors (e.g., steranes, diterpanes, triterpanes, hopanes) serve as important molecular markers in oil spill and geochemi-cal studies, as they are resistant to weathering. Moreover, they are used as internal preserved standard compounds in investigation of oil weathering (Albaiges and Albrecht, 1979; Daling et al., 2002; El-Gendy et al., 2014).

C27 Steranes

C30 Hopanes

Oleanane

Aromatic hydrocarbons, usually less abundant than the saturated hydro-carbons, contain one or more aromatic (benzene) rings connected as fused rings (e.g., naphthalene) or lined rings (e.g., biphenyl). Some of the com-mon aromatics that can be found in petroleum are benzene and its deriva-tives and methyl-, ethyl-, propyl-, or higher alkyl groups (i.e. alkylbenzens, with general formula of C

nH

2n–6, where n ≥ 6). Monoaromatics consist

of BTEX (the collective name for the benzene, toluene, ethylbenzene

Background 11

and xylene) and mainly contribute to the octane number in gasoline. Polyaromatic hydrocarbons (PAHs) are compounds that consist of two or more aromatic rings. The United States Environmental Protection Agency (US-EPA) has selected 16 PAHs (Figure 1.1) as representative models for the toxic, mutagenic, and carcinogenic PAHs (Arun et al., 2011). The PAHs up to three aromatic rings are considered low in molecular weight or light PAHs, while PAHs made up of four aromatic rings or higher are considered high in molecular weight or heavy PAHs (Wilkes et al., 2016). The content of aromatics normally ranges from 15 to 20%. Usually, heavy crude oils contain more aromatics than the light ones. While in aromatic-base crude oil, aromatics content can reach to approximately 35% (Duissenov, 2013). Petroleum contains many homologous series of aromatic hydrocarbons consisting of unsubstituted or parent aromatic structures (e.g., phenan-threne) and like structures with alkyl side chains that replace hydrogen atoms. Alkyl substitution is most prevalent in 1-, 2-, and 3-ringed aromat-ics, although the higher polynuclear aromatic compounds (>3 rings) do contain alkylated (1–3 carbons) side groups. The polycyclic aromatics with

Figure 1.1 Molecular Structure of the 16-PAHs Selected by the US-EPA as Priority

Pollutants.

Naphthalene Acenaphthylene Acenaphthene Fluorene

PhenanthreneAnthracene Fluoranthene Pyrene

Benzo[a]anthraceneChrysene Benzo[b]fluoranthene

Benzo[k]fluorantheneBenzo[a]pyrene

Dibenzo(a,h)anthracene

Benzo(ghi)perylene Indeno(1,2,3-cd)pyrene

12 Biodesulfurization in Petroleum Refining

more than 3 rings consist mainly of pyrene, chrysene, benzanthracene, benzopyrene, benzofluorene, benzofluoranthene and perylene structures. The naphthenoaromatic compounds consist of mixed structures of aro-matic and saturated cyclic rings. This series increases in importance in the higher boiling fractions along with the saturated naphthenic series. The naphthenoaromatics appear related to resins, kerogen, and sterols.

Petroleum generation usually involves the formation of some naphthe-noaromatic structures. The resins and asphaltenes fractions differ in the proportion of aromatic carbon (Speight, 2004).

1.2.2 Petroleum Non-Hydrocarbons

Petroleum non-hydrocarbons occur in crude oils and petroleum products in small quantity, but some of them have considerable influence on product quality. They can be grouped into six classes: sulfur compounds, nitrogen compounds, oxygen compounds, porphyrins, asphalthenes, and trace metals. Nitrogen is present in all crude oils in compounds as pyridines, quinolines, benzoquinolines, acridines, pyrroles, indoles, carbazoles, and benzocarba-zoles (Clarck and Brown, 1977; Hunt, 1979; Tissot and Welte, 1984).

The porphyrins are nitrogen-containing compounds derived from chlorophyll and consist of four linked pyrroles rings. Porphyrins occur as organometallic complexes of vanadium (V) and nickel (Ni); V and Ni are the most abundant metallic constituents of crude oil, sometimes reaching thousands of part per million. They are present in porphyrins complexes and other organic compounds (Yen, 1975). Oxygen compounds in crude oils (0 to 2%) are found primarily in distillation fractions above 400oC and consist of phenols, carboxylic acids, ketones, esters, lactones, and ethers. Generally, organometallic compounds are precipitated with asphaltene and resin. Sulfur compounds comprise the most important group of nonhydro-carbon constituents. In many cases, they have harmful effects and must be removed or converted to less harmful compounds during refining process.

The heteroatom contaminants must be removed before the distil-late fraction is further upgraded because they poison the hydrocracking (HCR), catalytic reforming, and fluid catalytic cracking (FCC) catalysts used in subsequent downstream refining processes (Burns et al., 2008).

The resins and asphaltenes contain non-hydrocarbon polar compounds, with very complex carbon structure, but the resins have lower molecu-lar weight and are soluble in n-alkanes. The resins are amorphous solids that are completely dissolved in petroleum (Speight, 2004). However, asphaltenes are colloidally dispersed in saturates and aromatic fractions (Speight, 2007). The resins act as peptizing agents, acting as surface-active