Studies in Surface Science and Catalysis 164
Advisory Editors: B. Delmon and J. T. Yates
Series Editor: G. Centi
Vol. 164
BIOCATALYSIS IN OIL REFINING
M. M. Ramírez-Corredores
Strategic Options-Refining Technology, B.P. International Ltd., Sudbury on
Thames, UK.
Abhijeet P. Borole
Oak Ridge National Laboratory, Oak Ridge, Knoxville, USA.
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PREFACE
Biotechnology is a powerful enabling technology to achieve clean industrial products and
processes while promoting industrial sustainability. Biotechnology has been penetrating
industrial operations in many sectors, because of its ability to reduce the number of
manufacturing steps, thereby reducing material and energy consumption, and reduction
in pollution and waste generation, for the same level of industrial production. Numerous
applications of biotechnology can be found in Pharmaceuticals, Fine Chemicals, Life
Science Research, Agriculture, Food & Beverage, and Cosmetics industries but not in
the Oil industry. The potential of biotechnology in the oil refining industry is the subject
of this book. Significant research has been done in one major area, biodesulfurization,
although commercialization has not taken place. This book describes the efforts in
biodesulfurization and other areas of oil refining.
The need for this book was realized due to the large gap in the knowledge of a
typical researcher in a petroleum or petrochemical industry in investigating or developing
a biotechnology-based solution to a refinery problem. Secondly, there was a need to
compile all the findings in the petroleum biorefining and bioupgrading area to facilitate
future research in this area. Thus, this book is geared towards helping researchers and
technologists catch up on previous and current research in this field.
Chapter 1 describes the current scenario and the need for biotechnological solutions.
In the first Chapter, we have also provided definitions of some general biology terms to
bring the petroleum industry researcher up to speed and referred to the particular appli­
cation where the terms may be useful. Chapter 2 gives an overview of the conventional
hydroprocessing schemes currently in use in refining operations. This Chapter is included
for the biotechnology researcher who has little knowledge of the refinery operations.
Chapter 3 provides the details of the biocatalyst and bioprocess developments to date.
This includes the widely studied biodesulfurization (BDS) as well as the less studied bio­
denitrogenation (BDN), biodemetallization (BDM), and bioconversion or bioupgrading
(BCK). Chapter 4 is included to provide the reader with an information resource to help
with research and development activities. This Chapter lists companies actively involved
in the biotechnology arena, both for R&D and for commercial operations, which can
be used to find molecular biology and enzyme supplies, or to find companies offering
services in the biotechnology area. Chapter 5 describes the technological results, in the
form of awarded patents and analyzes their chronology and implications for refining
operations.
Developing a bioprocess for removing heteroatoms from petroleum or for upgrad­
ing heavy crudes involves two main components. The first is biocatalyst development
and second is bioprocess development. Both of these topics are discussed in this book,
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Preface
although there has been much more work done in biocatalyst development compared
to the processing aspects. The complexity of finding a suitable biocatalyst for say,
biodesulfurization or any other refining operation, is enormous. This is because of two
reasons. First reason is related to the complexity of the material to be converted and
second, is related to the multi-phase bioprocess involving, an oil, aqueous, gas (usually
air), and a solid (biocatalyst) phase. The effort needed to find the solution is no doubt
a multi-disciplinary one, involving petroleum chemistry, analytical chemistry, microbi­
ology, molecular biology, enzymology, and chemical engineering. The first problem is
that petroleum or any refined stream contains numerous species of molecules on which
the biocatalyst needs to act on. Thus, the substrate specificity needed is very broad.
Unfortunately, biocatalysts, by design are supposed to be very specific. This is what
enables the biocatalysts to overcome reaction energy barriers at low temperatures and
pressures, unlike chemical catalysts. To develop suitably broad and highly active bio­
catalysts, newly developed genetic engineering and molecular biology techniques have
to be employed. These techniques are discussed in the book as well, with reference to
their application. Companies involved in providing services in these areas are listed in
Chapter 4 and cover expertise in gene identification, sequencing, strain development
and bioprocess engineering needs. In addition, several Universities and research orga­
nizations are also discussed with reference to screening of microorganisms, enzyme
characterization, and pathway identification.
In addition to the bioprocessing of petroleum, the book also contains a small section
on bioremoval of hydrogen sulfide from gaseous streams. This applies to removal of
hydrogen sulfide from effluents from hydrotreatment operations. It forms an essential
part of the biotechnology portfolio for the petroleum refining industry. Chapter 3 as well
as Chapter 5 includes discussion on bioprocesses capable of removing hydrogen sulfide.
The Chapter 5 provides an integrated list of companies and research organizations
involved in petroleum biorefining research. The background of each company and its
efforts leading to its patent portfolio in this area are discussed. We have tried to include
all known companies that have participated to date in this area; however, the list is not
strictly exhaustive.
Finally, hoping that this book provides every reader with the information he/she is
looking for. If you do not, you may contact us the address provided and we will make
every effort to respond. You may reach us to provide your feedback or tell us about the
deficiencies in this book. We wish you an informative and pleasant reading.
Abhijeet P. Borole and Maria Magdalena Ramírez-Corredores
September 2006.
CONTENTS
Foreword
vii
Preface
ix
Chapter 1 Introduction
1
1. Refining Scenarios
2. Biocatalysis
1
3
Chapter 2 Conventional refining processes
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1. Introduction
2. Hydrotreating Processes
2.1. Chemistry
2.1.1. Reactions
2.1.2. Catalysts
2.2. Process
3. Gasoline Hydrotreating
3.1. Chemistry
3.2. Process
4. Diesel Hydrotreating
4.1. Chemistry
4.2. Process
5. Vacuum Gas Oil Hydroprocessing
5.1. Vacuum Gas Oil Hydrotreating
5.2. Vacuum Gas Oil Hydrocracking
6. Residue Hydroprocessing
6.1. Residue Hydrotreating
6.2. Residue Hydrocracking
References
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Chapter 3 Emerging biocatalytic processes
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1. Preamble
2. BDS
2.1. General
2.2. Biocatalytic Technologies (Microorganisms and Derivations)
2.2.1. Initial biodesulfurization efforts
2.2.2. Anaerobic Pathways
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Contents
2.2.3.
2.2.4.
2.2.5.
2.2.6.
2.3.
2.4.
2.5.
Aerobic sulfur-specific pathways
Aerobic Destructive and Ring Opening Pathways
Genetics of desulfurizing organisms
Purification and characterization of desulfurization
enzymes
2.2.7. Specificity of desulfurization enzymes
2.2.8. Enzymatic desulfurization
2.2.9. Biocatalyst production, recycle, and regeneration
2.2.10. Engineered strains for desulfurization
2.2.11. Strategies for further microbial catalyst
improvement
Process Aspects
2.3.1. Overall process designs and patented technologies
2.3.2. Process parameters and operating conditions
2.3.3. Bioreactor design and development
2.3.4. Separation of oil-water-biocatalyst mixtures
2.3.5. Other process options
2.3.6. Diesel biodesulfurization
2.3.7. Biodesulfurization of gasoline
Desulfurization of Gaseous Streams
Summary
2.5.1. Pioneering biocatalytic work
2.5.2. Biocatalyst concept and BDS-active
Microorganisms
2.5.3. Biocatalytic enzymes
2.5.4. Activity improvement
2.5.5. Specificity improvement
2.5.6. Biocatalyst production and regenerability
2.5.7. Bioreactor and process schemes
2.5.8. Product separation
3. BDN
3.1. General
3.2. Metabolic Pathways
3.2.1. Acridine
3.2.2. Carbazole and derivatives
3.2.3. Quinoline and derivatives
3.2.4. Isoquinoline
3.2.5. Indole
3.2.6. Pyridine and derivatives
3.3. Enzymes
3.3.1. Quinoline and related compounds
3.3.2. Carbazole
3.3.3. Indole
3.3.4. General
3.4. Microorganisms
3.5. Process Aspects
3.6. Summary of BDN Advances
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Contents
4. BDM
4.1. General
4.2. Technical findings
4.2.1. Enzymatic work
4.2.2. Microbial work
5. Bio-Upgrading
5.1. General
5.1.1. Heavy oil characteristics
5.1.2. Pathways for upgrading heavy crudes
5.2. Viscosity and MW reduction
5.2.1. Structural splitting
5.2.2. Oxygen introduction
5.2.3. Aromatic ring saturation
5.3. Processes
5.3.1. Viscosity reduction processes
5.3.2. Chemical conversion processes
References
Chapter 4 Biotechnology and supporting companies
1. General
2. Biology-Based Organizations
2.1. Introduction
2.2. Molecular Biology Companies
2.2.1. 454 Corporation
2.2.2. Advance ChemTech
2.2.3. Agowa
2.2.4. AlphaGene
2.2.5. Alpha Innotech
2.2.6. Amplicon Express
2.2.7. Ana-Gen
2.2.8. Anaspec, Inc.
2.2.9. Applera
2.2.10. Aurora Biomolecules
2.2.11. Biacore
2.2.12. Biopro International, Inc.
2.2.13. Bioserve Biotechnologies, Ltd.
2.2.14. BioVentures
2.2.15. BioWorld Products
2.2.16. Caliper Life Sciences
2.2.17. ChemGenes Corporation
2.2.18. Commonwealth Biotechnologies, Inc.
2.2.19. DGT Digital Gene Technologies
2.2.20. European Molecular Biology Laboratory’s
2.2.21. GATC Biotech
2.2.22. Miltenyi Biotec
2.2.23. Proteinlabs, Inc.
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2.2.24. Structural Genomics Consortium
2.2.25. Structural Genomics Centers
2.2.26. Zyomyx, Inc.
2.3. Genetic Engineering Companies
2.3.1. Aptagen Gene
2.3.2. Biotage
2.3.3. Cambio
2.3.4. Entelechon
2.3.5. Geneart
2.3.6. Invitrogen
2.3.7. Joint Center for Structural Genomics
2.3.8. Operon Technologies, Inc.
2.3.9. Orchid Cellmark
2.3.10. Oxford Gene Technologies
2.4. (Microbiology) Depositary Agencies
2.4.1. American Type Culture Collection (ATCC)
2.4.2. German Collection of Microorganisms and Cell Culture
2.4.3. Ferm
3. Biocatalyst (Enzyme/Protein) Companies
3.1. Altus Biologics, Inc.
3.2. Applied Enzyme Technology Ltd.
3.3. Bachem
3.4. Biocatalysts Ltd.
3.5. BioCatalytics, Inc.
3.6. Biopract
3.7. BioResearch Products, Inc.
3.8. Diversa Corporation
3.9. Enzyme Services and Consultancy
3.10. Iogen Corporation
3.11. Maps (India) Ltd.
3.12. Novozymes A/S
3.13. N-Zyme BioTec GmbH
3.14. Worthington Biochemical Corporation
4. Biotechnology-Based Companies
4.1. Acacia Research Corp.
4.2. Affymetrix
4.3. Apocom Genomics
4.4. Aurora Biosciences Corporation
4.5. Avecia Biotechnology
4.6. AVIVA Biosciences Corporation
4.7. Ben Venue Laboratories
4.8. Beyond Genomics, Inc.
4.9. Bio-Concept Laboratories Inc.
4.10. BioZone Laboratories
4.11. Biologics Process Development, Inc.
4.12. Bio Science Contract Production
4.13. BioMetics
Contents
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Contents
4.14. Cedra Corporation
4.15. Cell & Molecular Technologies, Inc. (CMT)
4.16. ChemOvation Ltd.
4.17. Ciphergen Biosystems
4.18. Cogenics
4.19. deCODE Genetics
4.20. Delaware Biotechnology Institute
4.21. DiscoveRX Corporation
4.22. Dyadic International, Inc.
4.23. Enchira Biotechnology
4.24. Genencor International, Inc.
4.25. Goodwin Biotechnology, Inc.
4.26. GPC Biotech’s
4.27. HyClone
4.28. Illumina, Inc.
4.29. Integrated Genomics
4.30. Large Scale Biology Corporation
4.31. Maxygen, Inc.
4.32. MediChem International
4.33. Millipore
4.34. Molecular Machines & Industries GmbH
4.35. Nanogen, Inc.
4.36. Novagen, Inc.
4.37. Organix, Inc.
4.38. PerkinElmer Life Sciences (Formerly: NEN Life Science Products)
4.39. Prior Separation Technology
4.40. Proteus
4.41. Sangamo BioSciences, Inc.
4.42. The Center for Biotechnology
4.43. Xencor
References
Chapter 5 R&D technological results
Overview
1. Agip Petroli (Italy); Enichem Anic Spa (Italy), and Eni Tecnologie
Spa (Italy)
2. Archaeus Technology Group Ltd. (Great Britain)
3. Arctech Inc/Atlantic Research Corporation (United States)
4. ASS Universities Inc/Brookhaven Science (United States)
5. Atlantic Richfield Co (United States)
6. Atlas, Ronald/Southern Pacific Petroleum (United States)
7. Babcock & Wilcox Co (United States)
8. BHP Minerals International Inc. (United States)
9. Biostar BV (Netherlands)
10. BWN Live Oil (Australia)
11. Clean Diesel Technologies, Inc. (United States & International)
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Contents
12. Combustion Engineering (United States)
13. Environmental Bioscience Corporation/Energy Biosystems Corp./Enchira
Biotechnology Corp. (United States)
13.1. Environmental Bioscience Corp (EBC1)
13.2. Energy Biosystems Corporation (EBC2)
13.3. Enchira Biotechnology Corporation (EBC3)
14. Exxon Research and Engineering (ER&E) Co (United States)
15. Gas Research Institute (United States)
16. Houston Industries Inc. (United States)
17. Imperatrix (United States)
18. Institute Francais Du Petrol (France)
19. Instituto Mexicano De Petroleo/Universidad Nacional Autonoma
De Mexico (Mexico)
20. Institute of Gas Technology (United States)
21. Institute of Process Engineering (China)
22. Intevep S. A. (Venezuela)
23. Japanese Cooperating Organizations (Japan)
23.1. Agency of Industrial Science & Technology/National Institute
of Advanced Industrial Science & Technology
23.2. Japan Cooperation Center, Petroleum (JCCP)
23.3. Petroleum Energy Center (PEC)
24. Kansai Electric Power (Japan)
25. Korea Advanced Institute of Science and Technology (Korea)
26. Kurashov, Viktor Mikhajlovich (Russia)
27. Kyushu Kankyo Kanri Kyokai (Japan)
28. Lambda Group Inc. (United States)
29. Marine Biotechnology Institute Co Ltd (Japan)
30. Microbes Inc. (United States)
31. Ni Aoot; Vatel Skij Inst Neftepromyslov (Russia)
32. Nippon Oil Co Ltd (Japan)
33. Oldfield, Christopher, Court of Napier University
34. Paques Biological Systems BV (Netherlands)
35. Petroleo Brasileiro SA (Brazil)
36. Petrozyme Technologies Inc (Canada)
37. Petroleum Industry Development Center (Sekiyu Sangyo Kasseika
Center); Mitsubishi Oil Co Ltd (Japan)
38. Plummer, Mark A (United States)
39. Shell Oil Co (Netherlands)
40. Standard Oil Co (United States)
41. Technology Licensing Organization
42. Tonen Corp (Japan)
43. Unitika Ltd (Japan)
44. Universidad De Alcalá, Universidad Complutense De Madrid, and
Consejo Superior De Investigaciones Científicas (Spain)
45. University of Osaka (Japan)
46. University of Shandong (China)
47. University of Waseda (Japan)
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Contents
48. UOP LLC (United States)/Paques Biological Systems BV
(Netherlands)
49. Valentine, James M (United States)
General Discussion
References
Chapter 6 Research needs and future directions
1. Research Needs
1.1. Biodesulfurization
1.1.1. Over-expression of DszB
1.1.2. Substrate specificity of Dsz enzymes
1.1.3. Thermostability
1.1.4. Benzothiophene desulfurization
1.1.5. Desulfurization of highly substituted alkyl and aryl DBTs
1.1.6. Process Development
1.2. Biodenitrogenation
1.3. Biodemetallization
1.4. Bioupgrading
2. Future Directions
2.1. Future scenario
2.2. Technology needs
References
Subject Index
xvii
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