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Organic Synthesis
Using Biocatalysis
Edited by
Animesh Goswami
Chemical Development, Bristol-Myers Squibb,
New Brunswick, NJ, USA
Jon D. Stewart
Department of Chemistry, University of Florida,
Gainesville, FL, USA
No part of this publication may be reproduced or transmitted in any form or by any means, electronic
or mechanical, including photocopying, recording, or any information storage and retrieval system,
without permission in writing from the publisher. Details on how to seek permission, further
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such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our
website: www.elsevier.com/permissions.
This book and the individual contributions contained in it are protected under copyright by the
Publisher (other than as may be noted herein).
Notices
Knowledge and best practice in this field are constantly changing. As new research and experience
broaden our understanding, changes in research methods, professional practices, or medical
treatment may become necessary.
Practitioners and researchers must always rely on their own experience and knowledge in evaluating
and using any information, methods, compounds, or experiments described herein. In using
such information or methods they should be mindful of their own safety and the safety of others,
including parties for whom they have a professional responsibility.
To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume
any liability for any injury and/or damage to persons or property as a matter of products liability,
negligence or otherwise, or from any use or operation of any methods, products, instructions, or
ideas contained in the material herein.
ISBN: 978-0-12-411518-7
Samantha K. Au
School of Chemical and Biomolecular Engineering, Georgia Institute of
Technology, Parker H. Petit Institute of Bioengineering and Bioscience, vii
Atlanta, GA, USA
Andreas S. Bommarius
School of Chemical and Biomolecular Engineering, Georgia Institute
of Technology, Parker H. Petit Institute of Bioengineering and Bioscience;
School of Chemistry and Biochemistry, Georgia Institute of Technology,
Atlanta, GA, USA
Chen Cao
Department of Bioengineering, Graduate School of Bioscience and
Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku,
Yokohama, Japan
Pere Clapés
Department Química Biológica y Modelización Molecular, Instituto de Química
Avanzada de Cataluña, IQAC-CSIC, Barcelona, Spain
Rodrigo O.M.A. de Souza
Biocatalysts and Organic Synthesis Lab, Organic Chemistry Department,
Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
Brent D. Feske
Chemistry and Physics Department, Armstrong State University, Savannah,
GA, USA
Michael J. Fink
Vienna University of Technology, Institute of Applied Synthetic Chemistry,
Vienna, Austria
Animesh Goswami
Chemical Development, Bristol-Myers Squibb, New Brunswick, NJ, USA
Gideon Grogan
Department of Chemistry, University of York, Heslington, York, UK
Harald Gröger
Faculty of Chemistry, Bielefeld University, Universitätsstr,
Bielefeld, Germany
viii List of Contributors
Jonathan Groover
Chemistry and Physics Department, Armstrong State University, Savannah,
GA, USA
Melissa L.E. Gutarra
Escola de Química, Federal University of Rio de Janeiro, Pólo Xerém, Estrada
de Xerém, Xerém, Duque de Caxias, Rio de Janeiro, Brazil
Romas Kazlauskas
Department of Biochemistry, Molecular Biology & Biophysics and The
Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
Tomoko Matsuda
Department of Bioengineering, Graduate School of Bioscience and
Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku,
Yokohama, Japan
Marko D. Mihovilovic
Vienna University of Technology, Institute of Applied Synthetic Chemistry,
Vienna, Austria
Leandro S.M. Miranda
Biocatalysts and Organic Synthesis Lab, Organic Chemistry Department,
Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
Thomas S. Moody
Department of Biocatalysis and Isotope Chemistry, Almac, Craigavon,
Northern Ireland, UK
Ramesh N. Patel
SLRP Associates, Consultation in Biotechnology, Bridgewater, NJ, USA
Laila Roper
Department of Chemistry, University of York, Heslington, York, UK
J. David Rozzell
Provivi, Santa Monica, CA, USA
Florian Rudroff
Vienna University of Technology, Institute of Applied Synthetic Chemistry,
Vienna, Austria
Jon D. Stewart
Department of Chemistry, University of Florida, Gainesville, FL, USA
CHAPTER 1
Introduction, Types of
Reactions, and Sources
of Biocatalysts
1
1 INTRODUCTION
1.1 Enzymes and Their Roles in Nature
Enzymes are nature’s catalysts, facilitating the creation, functioning, mainte-
nance, and ultimately the demise of all living cells. Enzymes are proteins com-
posed of 20 natural amino acids joined together by peptide bonds, in some
cases augmented with additional organic or inorganic species known as cofac-
tors.1 In addition to their primary molecular structures dictated by the amino
acid sequence, enzyme catalytic function also depends upon subsequent fold-
ing into specific three-dimensional shapes that contain a variety of secondary
and tertiary structural elements. These architectures determine not only enzyme
function but also how they interact with the external solvent medium in which
they are dissolved or suspended. This can have important ramifications when
enzymes are employed under partially or completely nonaqueous conditions.
Like all catalysts, enzymes increase reaction rates by lowering their activation
energies. The most important difference between enzymes and simple catalysts
such as a proton or hydroxide is that the former are much more restrictive in the
range of acceptable substrates. The three dimensional structure of the enzyme
allows binding of only those starting materials (usually referred to as substrates)
whose structures are congruent with the size, shape and polarity of the catalytic
portion of the enzyme (the “active site”). Formation of this noncovalent complex
prior to chemical conversion is the key to the high selectivity of enzyme-catalyzed reac-
tions since it places the substrate into a specific location where its functional groups are
oriented precisely with those on the enzyme.
1
Some RNA molecules also possess catalytic abilities; however, their substrate and range of chemical
conversions seems rather limited and for this reason, catalytic RNA molecules lie outside the scope
of this book.
Organic Synthesis Using Biocatalysis. http://dx.doi.org/10.1016/B978-0-12-411518-7.00001-9
Copyright © 2016 Elsevier Inc. All rights reserved.
2 Organic Synthesis Using Biocatalysis
2 DEFINITION OF BIOCATALYSIS
In nature, enzymes catalyze transformations of metabolites that occur within
and/or outside of living cells. Although some enzymes accept only a limited
variety of substrates, a large fraction is more tolerant and allows conversions
of nonnatural starting materials. The field of biocatalysis rests upon this partial
promiscuity. If enzymes were truly selective for only a single substrate, it would
be impossible to utilize them for synthesizing new molecules from nonnatural
substrates. The goal is to identify or engineer enzymes that are sufficiently gen-
eral to accept a variety of related substrates, but selective enough to yield single
products or stereoisomers. We use the term “biocatalysis” to describe the use of
enzymes (either native or modified) for synthetic transformations of nonnatural
starting materials. Enzymes used for in vitro synthetic transformations are called
biocatalysts, and the processes are called biocatalytic transformations.
links a simpler starting material such as glucose with a final intracellular target
product such as butanol or lysine. In some cases, the complete pathway already
exists within a single organism; in others, enzymes from different sources are
assembled into an artificial metabolic pathway in a suitable host cell. The key
difference between biocatalysis and metabolic engineering is that the molecu-
lar skeletons are provided in vitro in the former case and in vivo in the latter.
Although it is economically attractive to produce a target molecule by meta-
bolic engineering, this benefit must be balanced against the (usually) lengthy
optimization phase required for efficient production and the restriction that
intermediates and the final product should be nontoxic to the host cells.
FIGURE 1.1
Types of selectivity exhibited by enzymes. Biocatalytic processes can provide chemo-,
regio-, and stereoselective conversions. Representative examples can be observed in reactions
catalyzed by nitrile hydratases, lipases and dehydrogenases.
5.2 Coenzymes
Although some enzyme-catalyzed reactions utilize only functional groups found
in the protein, the limited number and variety of amino-acid side-chain moieties
severely limits the range of accessible reactions. For example, there are neither
common amino acids with electrophilic side chains nor amino-acid functional
groups suitable for redox catalysis.3 Nature has circumvented this problem by
evolving a suite of coenzymes (also known as cofactors) that specialize in par-
ticular types of chemical conversions. Table 1.1 lists some common cofactors
for biocatalytic processes. In some cases, for example, biotin and some flavins,
these cofactors are covalently coupled to the enzyme within the active site. Other
cofactors such as nicotinamides are bound reversibly by noncovalent forces dur-
ing the entire catalytic cycle. Finally, a few cofactors such as pyridoxal phosphate
form reversible covalent linkages with the resting form of the enzyme that are
cleaved during the catalytic cycle, and then re-formed at the end. When needed
by specific enzymes, provision for cofactor supply must also be made. Because
of their expense, cofactors are normally supplied in substoichiometric quanti-
ties (usually ≪ 0.1 mole %). This means that they must be regenerated prior to
the start of the next catalytic cycle, and strategies for cofactor regeneration have
been developed as an essential adjunct for biocatalytic reactions, particularly for
reductions and oxidations.
3
The only exception is disulfide bond formation between a pair of suitably positioned cysteine
side-chains.
Introduction, Types of Reactions, and Sources of Biocatalysts Chapter 1
Table 1.1 Cofactors Commonly Encountered in Biocatalytic Reactions Applied to Chemical Synthesis
Name Cofactor Structure Chemical Function Enzyme
Nicotin- Donates a hydride for polar Alcohol dehydrogenase/
amide adenine reductions of functional ketoreductase; alkene
dinucleotide, groups such as C ═ O and reductase/enoate reductase;
reduced form C ═ N; acts as an electron amino acid dehydrogenase;
(NADH)a source for monooxygenases monooxygenase;
dioxygenase
(Continued)
7
8
Organic Synthesis Using Biocatalysis
Table 1.1 Cofactors Commonly Encountered in Biocatalytic Reactions Applied to Chemical Synthesis (cont.)
Name Cofactor Structure Chemical Function Enzyme
Flavin adenine Forms a hydroperoxy Alkene reductase/enoate
dinucleotide (FAD) intermediate from O2 that is reductase; amino acid
used by monooxygenases; oxidase; Baeyer–Villiger
following 2 electron monooxygenase
reduction, donates a hydride
for reductions of electron-
deficient C ═ C bonds
FIGURE 1.2
Three possible kinetic mechanisms for a two-substrate/two-product reaction depicted in
Cleland notation. Substrates are designated as “A” and “B”, products as “C” and “D” while “E”
represents the enzyme and “E*” is a covalently modified enzyme that forms transiently as part
of the normal catalytic pathway in the ping-pong mechanism.
(B) until it previously bound the first (A). Enzymes that follow this scheme of-
ten show substrate inhibition when the concentration of B is very high (relative
to that of A) since this favors formation of a dead-end E · B complex that must
dissociate prior to re-joining the productive pathway. A random mechanism re-
moves this restriction and either substrate can be bound first. Product release
steps can be similarly described.4 From a kinetic standpoint, cofactors that do
not remain permanently bound to the enzyme are equivalent to substrates and/
or products. Cofactors that remain bound to the enzyme during turnover are
kinetically treated as part of the enzyme itself. In either an ordered or random
4
It should be noted that “substrate” and “product” are meaningful only when the direction of the
reaction is specified. Like all catalysts, enzymes accelerate both the forward and reverse reactions.
10 Organic Synthesis Using Biocatalysis
mechanism, the key species is the ternary complex of enzyme with both sub-
strates (E · A · B) since this must be formed in order for the reaction to occur.
Enzymes that form a covalent bond with a part of the substrate often follow a
ping-pong mechanism (Figure 1.2). By definition, these must be ordered mech-
anisms. Ping-pong mechanisms always share two essential features. First, they
involve a covalently modified form of the enzyme (or cofactor) as an obligate
intermediate.5 In addition, the first product must be released from the active site
before the second substrate binds. Together, these two properties of enzymes that
follow ping-pong mechanisms open the possibility that the covalent intermedi-
ate might be redirected into alternative products by restricting access to the nor-
mal second substrate. Employing lipases for synthetic (rather than hydrolytic)
acyl transfer reactions is a very common example of this strategy and others can
be found in the appropriate sections of later chapters.
Although the methods for determining steady-state kinetic parameters can be
complex and the details lie outside the scope of this book, a general understand-
ing of their meaning is useful for applications to biocatalysis. It should be borne
in mind that most substrates and products in biocatalytic reactions have limited
aqueous solubilities. This complicates kinetic studies since the actual concentra-
tion “seen” by the enzyme may not be the same as the concentration added to
the reaction mixture unless all of the material is fully dissolved. Therefore, one
must be cautious when applying kinetic constants measured under one set of
experimental conditions (often dilute aqueous solutions) to reactions run un-
der process conditions that may involve partially dissolved substrates, organic
cosolvents, etc.
6
This is not an uncommon situation in practice, particularly when enzymes catalyze reactions of
nonnatural substrates.
12 Organic Synthesis Using Biocatalysis
7
Finding products that are completely racemic nearly always indicates that the catalyst concentration
and or reaction time is too great. Even poorly stereoselective enzymes typically afford some optical
enrichment and only reaching true thermodynamic equilibrium completely erases this preference.
Introduction, Types of Reactions, and Sources of Biocatalysts Chapter 1 13
base. The reverse reaction (ester and amide synthesis) cannot be carried out un-
der aqueous conditions due to the large molar excess of water (whose concentra-
tion is 55 M in pure water). Enzymes can catalyze the reverse reaction – ester and
amide synthesis from acids and alcohols or amines – under nonaqueous con-
ditions, although the yields are limited by thermodynamic constraints unless
steps are taken to remove the water formed during the reaction. This limitation
can be circumvented by using enzymes to catalyze transesterification and trans-
amidation, using an ester or amide as the starting material and relying on Le
Chatêlier’s principle to shift the equilibrium to the desired product (Figure 1.3).
Acyl transferase enzymes have been widely used to synthesize chiral esters, am-
ides, alcohols, and amines. In many cases, these conversions involve kinetic
resolutions of alcohols, acids, esters, amines, and amides. Of course, since each
enantiomer makes up half of the racemic mixture, kinetic resolutions can pro-
vide a maximum 50% yield. This limitation can be overcome by racemizing
or inverting the configuration of the unreacted substrate during the enzymatic
reaction. Such a scheme is referred to as a dynamic kinetic resolution and theoreti-
cally allows complete substrate conversion to product along with 100% chemi-
cal yield of a single product enantiomer.
FIGURE 1.3
Hydrolysis and synthesis of carboxylic acid derivatives such as esters and amides.
FIGURE 1.4
Carbonyl reductions to alcohols.
8
The “alcohol dehydrogenase” nomenclature is more common in the biochemical literature where-
as “ketoreductase” is typically used in biocatalysis since this is the synthetically more useful direc-
tion for the reaction.
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