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Organofluorine Chemistry
Organofluorine Chemistry
Synthesis and Applications
V. Prakash Reddy
Department of Chemistry, Missouri University of Science
and Technology, Rolla, MO, United States
Elsevier
Radarweg 29, PO Box 211, 1000 AE Amsterdam, Netherlands
The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom
50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States
Copyright © 2020 Elsevier Inc. All rights reserved.
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 information about the
Publisher’s permissions policies and our arrangements with organizations 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.
vii
viii Contents
5. Pharmaceutical applications of
organofluorine compounds 133
5.1 Introduction 134
5.2 Antibacterial pharmaceuticals 141
Contents ix
Index 329
Preface
This book is focused on modern synthetic methods for the incorporation of fluorine and
fluoroalkyl moieties into organic compounds, and on the pharmaceutical and materials
applications of organofluorine compounds. It is hoped that this book would serve as a text
book for the specialized graduate-level courses in organofluorine chemistry as well as a refer-
ence book for industrial and academic scientists involved in the drug design, materials
chemistry, and organofluorine chemistry. Rapid advances in the efficient synthetic methods
of organofluorine compounds contribute to their ever-increasing application in diverse areas,
including the design of materials, pharmaceuticals, agrochemicals, and a wide range of con-
sumer goods. Notably, fluoropolymers, which include poly(tetrafluoroethylene), poly(vinyli-
dene fluoride), poly(vinyl fluoride), and Nafion, a perfluorinated ion-exchange membrane,
are integral parts of chemical industry.
Chapters 1 4 are focused on the synthetic methods for the fluorinations, fluoroalkyla-
tions, fluoroalkoxylations, and fluoroalkylthiolations. The synthetic methods are broadly clas-
sified to include nucleophilic, electrophilic, free-radical, and organotransition
metal catalyzed/mediated reactions. Emphasis is placed on those reactions that are of
broad significance in the synthesis of fluorinated pharmaceuticals, positron emission tomog-
raphy (PET) imaging agents, and materials.
Chapter 1, Nucleophilic reactions in the synthesis of organofluorine compounds, outlines
a variety of commercially available nucleophilic fluorination reagents, including DAST,
DeoxoFluor, XtalFluor, PhenoFluor, and FluoLead. Nucleophilic trifluoromethylations,
difluoromethylations, trifluoromethoxylations, and trifluoromethylthiolations have been
widely used in the design of pharmaceuticals and materials. Deoxyfluorination of alcohols,
phenols, and carboxylic acids can be achieved with a variety of commercially available
reagents, including PhenoFluor, PyFluor, XtalFluor, DAST, and related reagents.
Nucleophilic fluorinating reagents of broader scope are being continually developed as task-
specific reagents in the synthesis of pharmaceutically interesting compounds. There is
emerging interest in the enantioselective nucleophilic fluorinations and trifluoromethyla-
tions. Enantioselective trifluoromethylation, in some cases, can be achieved with up to 93%
enantioselectivity using cinchonidine-based chital catalysts.
Chapter 2, Electrophilic reactions in the synthesis of organofluorine compounds, outlines
various electrophilic reagents, such as Selectfluor and NFSI, and electrophilic fluoroalkylations,
fluoroalkylthiolations, and fluoroalkoxylations, focusing on electrophilic trifluoromethylation,
trifluoromethylthiolations, and difluoromethylthiolation reactions. Electrophilic trifluoromethy-
lation of a wide variety of alkynes, aromatics, amines, and alcohols has found applications in
the synthesis of pharmaceuticals. Electrophilic difluoromethylation of alcohols provides access
to the corresponding difluoromethoxy compounds, and these reactions can be used in the
xi
xii Preface
nucleotide analog inhibitor of the HCV NS5B RNA-polymerase3 inhibitor, for the treatment
of hepatitis C), antibacterial agents (e.g., fluoroquinolones and tetracyclines), cancer (e.g.,
afatinib, dacomitinib, and lorlatinib), cardiovascular diseases (e.g., ezetimibe and atorvasta-
tin), and as inti-inflammatory agents (e.g., celecoxib, a selective COX-2 inhibitor, to treat
rheumatoid arthritis). Fluorine-containing compounds have emerging interest as pharma-
ceutical candidates to treat AD. Although several clinical trials using organofluorine drug
candidates (and other drug candidates), as BACE-1 inhibitors, γ-secretase inhibitors, and
γ-secretase modulators have not been successful to date, a fluorinated selective BACE-1
inhibitor, CNP540, is currently undergoing clinical trials for its efficacy in preventing AD in
individuals susceptible to the development of AD.
Chapter 6, Synthesis and applications of 18F-labeled compounds, outlines the recent
progress in the synthesis and applications of the 18F-PET tracers in the diagnosis of various
diseases, including the AD and cancers. Synthetic methods using the late-stage radiofluorina-
tions have significantly contributed to the advancement of this area. 18F-labeled PET tracers,
in combination with magnetic resonance imaging (MRI), PET/MRI, are emerging as alterna-
tive to the widely used PET/computed tomography (PET/CT), a technique that requires
patients to be exposed to hazardous X-ray radiation, in the diagnosis and monitoring of the
disease progression in various cancers, Alzheimer’s disease, and cardiovascular diseases.
Furthermore, in some cases, the PET/MRI provides superior imaging of the sites of lesions
over that of the PET/CT scans. PET/MRI can be used in probing the blood brain barrier of
pharmaceuticals, a key feature for a drug to be active in the neurological disorders. 18F-PET/
MRI imaging of the lung cancers, including adenocarcinoma, squamous cell carcinoma, and
small-cell lung carcinoma, is indispensable in monitoring the effectiveness of the various
chemotherapeutic agents. Until recently, 2-[18F]-fluoro-2-deoxy-D-glucose is the only FDA-
approved 18F-PET imaging agent, for the clinical diagnosis of AD, cancers, and other glucose
metabolism linked lesions. Emerging, efficient synthetic methods for the late-stage radio-
fluorination are now being adapted for the synthesis of various disease-specific 18F-PET
agents. For example, FDA-approved 18F-PET imaging agents, florbetapir (Amyvid), florbeta-
ben (Neuraceq), and flutemetamol (Vizamyl), show high specificity for binding to the Aβ pla-
ques and are now widely used in the clinical diagnosis of the AD patients. On the other
hand, flortaucipir (AV-1451) shows substantial selectivity in its binding to the neurofibrillary
tangles and is useful to distinguish AD from other neurodegenerative diseases, such as
behavioral variant frontotemporal dementia, Parkinson’s disease with or without cognitive
impairment, and vascular dementia. The latter PET imaging agent is also useful in the diag-
nosis of the chronic traumatic encephalopathy, also called traumatic brain injury, as demon-
strated in the PET scans of the football players with concussion symptoms. Fluciclovine is an
18
F-PET tracer that is used the diagnosis of prostate cancer.
Chapter 7, Materials applications of organofluorine compounds, outlines synthesis and
applications of a wide range of organofluorine-based materials. Numerous materials, bioma-
terials, smart materials, liquid crystal displays, solar cells, fuel cells, and numerous consumer
goods are fluorine-containing compounds. For example, fluorinated ionomers, such as
Nafion-H and fluorinated versions of poly(ether sulfone) and poly(imide) materials, are
xiv Preface
1.1 Introduction
Nearly one-third of the pharmaceuticals are fluorinated compounds. Often a single fluorine
at the strategic site modulates the pharmacokinetic properties of the pharmaceuticals.
18
F-labeled compounds are used as the state-of-the-art positron emission tomography (PET)
tracers in the diagnosis of cancers, cardiovascular diseases, and neurodegenerative diseases.
Furthermore, fluorinated compounds are increasingly used in the design of novel materials
for a broad range of applications, including photovoltaic solar cells and energy storage
devices. Polyfluorinated compounds (fluorous compounds) are used in the 19F nuclear mag-
netic resonance (19F-NMR) imaging (also called as 19F-magnetic resonance imaging,
19
F-MRI), and as recyclable fluorous catalysts, fluorous solvents, and fluorous stationary
phases, in organic synthesis. Early synthetic methods for nucleophilic fluorinations relied on
hydrogen fluoride (HF) and its amine complexes [e.g., Olah’s reagent, pyridinium poly
(HF; PPHF), and sulfur tetrafluoride (SF4)]. There are currently many safer and more effec-
tive fluorinating reagents that have wide functional group tolerance and that would afford
high regio- and stereoselectivity. These selective fluorinating agents are invaluable in the
synthesis of complex fluorine-containing organic compounds. Nucleophilic fluoroalkylations,
especially gem-difluoromethylation and trifluoromethylation, are widely used in the design
of functional materials and pharmaceuticals because of the unique and favorable physico-
chemical and pharmacokinetic properties of these fluoroalkyl compounds.
gem-Difluoromethylene (CF2) moiety is isopolar and, to some extent, isosteric with
respect to oxygen, and thus the gem-difluoromethyl (CHF2) and difluoromethylene
(CF2) moieties serve as bioisosteres of alcohols and ethers, respectively, in the drug
design applications. It is also a lipophilic bioisostere of SH and CH3 when attached to the
aryl or alkyl moieties. The CF2H is a hydrogen-bond donor as well as acceptor, and the
lipophilicity of the compounds is dramatically enhanced when this moiety is introduced
adjacent to the ether, sulfoxide, and sulfone moieties.1,2 The trifluoromethyl moiety is
bioisosteric with respect to the tert-butyl and isopropyl groups and is used, for example, in
the design of γ-secretase inhibitors.3 Many of the nucleophilic reagents for fluorination and
fluoroalkylation are now commercially available. This chapter aims to give a comprehensive
coverage of the nucleophilic fluorinations and fluoroalkylations that have broad scope in the
design of pharmaceuticals, agrochemicals, and materials.
F iPr iPr
OH PhenoFluor/toluene
N N
CsF (3 equiv) F F
iPr iPr
110 ºC
89%
PhenoFluor
Selected examples:
F N F
O N
Me
N N
N F N
F
58% 34% 78% 93%
FIGURE 1–2 PhenoFluor-mediated deoxyfluorination of phenols.
Selective fluorinating reagents, especially those that can be used in the stereoselective deoxy-
fluorination of alcohols, are of great importance for the synthesis of pharmaceutical com-
pounds. Among several such reagents recently developed, PhenoFluor and PyFluor are of
broad scope in the deoxyfluorination of alcohols, although DAST is still widely used for deox-
yfluorination reactions.18 XtalFluor reagents (XtalFluor-E and XtalFluor-M) show improved
selectivity in deoxyfluorination reactions, compared to DAST, as the elimination byproducts
are minimized. Similar to that of DAST and Deoxo-Fluor-mediated deoxyfluorination reac-
tions, the XtalFluor reagentmediated deoxyfluorination of alcohols proceed through a SN2
mechanism, with predominant inversion of configuration.14
PhenoFluor was originally discovered by Ritter and coworkers for the deoxyfluorination
of phenols.19,20 Phenols as well as heteroaryl phenolic compounds were deoxyfluorinated to
their corresponding fluorinated compounds using this reagent. To overcome the moisture
instability of this reagent, toluene solutions of this reagent can be used for the deoxyfluorina-
tions (Fig. 12).
PhenoFluor can also be used for the deoxyfluorination of primary and secondary alco-
hols, using slightly different conditions as for the phenols.21 Addition of Hunig’s base, in
these reactions, shortens the reaction time, and potassium fluoride (KF) minimizes the elimi-
nation products from the aliphatic alcohols. Deoxyfluorinations of secondary alcohols using
PhenoFluor proceed in high yields with inversion of configuration.21 Although these deoxy-
fluorinations proceed at 0 C to room temperature, elimination products are formed as
minor byproducts. However, at 80 C in toluene, the elimination reaction is suppressed, and
the reaction proceeds in high yields to give the corresponding deoxyfluorination products.
A variety of pharmaceutically interesting compounds, such as morphine, galantamine, testos-
terone, and epi-androsterone, could be stereoselectively transformed into their correspond-
ing fluorinated products with the inversion of configuration in high yields and with high
stereoselectivity (Fig. 13). PhenoFluor provides access to the late-stage fluorination of phar-
maceuticals and is suitable for the preparation of 18F-labeled compounds for the PET.
16 Organofluorine Chemistry
CF3
N Br
N Br
CF3 CF3
OBu
OH N
N
CF3
F3C CF3
18 19
O
F 3C OH 1. Chiral resolution
Cl 18 or 19 ; 10 mol% Cl 2. Fe/AcOH
Me3 SiCF3 (2.0 equiv)
NO2
NO2
Me4 NF, DCM
20 –60 °C 21
88%; 50% ee for catalyst 18
93% ee for catalyst 19
NO2
O
F 3C OH
Cl Cl O F3C NO2
23 Cl
O +
NH 2
HO
N O
22 H
Efavirenz, 88%
(anti-HIV drug)
FIGURE 1–15 Enantioselective trifluoromethylation for the synthesis of Efavirenz.
We have reserved to the end of the ants the consideration of the two
groups Dorylides and Amblyoponides, recent investigations having
rendered it somewhat doubtful whether they can be maintained as
distinct from Ponerides. The chief character of the Dorylides is that
the males are much less ant-like in form than they are in the other
groups, and that the distinction between the females and workers
are enormous. The little that is known as to the males and females of
this group suggests the view that these sexes may offer sufficient
reason for keeping the Dorylides as a group distinct from the other
ants; but it must be admitted that it is very difficult to find satisfactory
characters to distinguish the workers of the Dorylides in some cases
from the Ponerides, in others (Eciton) from the Myrmicides.[72]
The Dorylides are of great interest, for they exhibit the remarkable
phenomenon of a nomadic social life, accompanied by imperfect
sight in the wanderers. The sub-family includes two apparently
distinct groups: (1) the Ecitonini, peculiar to the New World, and
having a close relationship with the Myrmicides; and (2) the Dorylini
existing chiefly in the eastern hemisphere, and related closely by its
workers to the Ponerides and Amblyoponides. (i.) The Ecitonini
consist of the species of the genus Eciton, the wandering ants of
America, and of Labidus, which there is now good reason for
believing to consist of the males of Eciton. The female is still
uncertain. The Eciton are nomad ants having no fixed abode, but
wandering from place to place in search of prey, and forming
temporary resting-places. The species are rather numerous, and the
habits of several have been described by Bates, who, however, was
not acquainted with some of the most peculiar features in their
biology, these having been since revealed by Belt and W. Müller.
These ants are predaceous in their habits, and some of the species
travel in vast hordes; they occasionally enter houses and clear them
of much of the vermin with which they may be infested. They have
no facetted eyes, some of the forms being quite blind, while others
have a pair of peculiar lenses in the position normally occupied by
the compound eyes. Usually there are two castes of the workers,
and in some species these are very different from one another, the
mandibles being in the larger form very elongate, cylindrical and unfit
for industrial purposes, while the individuals of the smaller caste
have the outer jaws shorter, with their edges apposed and
coadapted: in other species individuals with mandibles differentiated
from the normal form do not exist. The nomad habits of these ants
were described by Bates, but the detection of their temporary
resting-places was reserved for Belt, who found that, after their
plundering raids, they retired to a place of concealment, and there
clustered together in a compact mass like a swarm of bees. Belt
says: "They make their temporary habitations in hollow trees and
sometimes underneath large fallen trunks that offer suitable hollows.
A nest that I came across in the latter situation was open at one side.
The ants were clustered together in a dense mass, like a great
swarm of bees, hanging from the roof, but reaching to the ground
below. Their innumerable long legs looked like brown threads
binding together the mass, which must have been at least a cubic
yard in bulk, and contained hundreds of thousands of individuals,
although many columns were outside, some bringing in the pupae of
ants, others the legs and dissected bodies of various Insects. I was
surprised to see in this living nest tubular passages leading down to
the centre of the mass, kept open, just as if it had been formed of
inorganic materials. Down these holes the ants who were bringing in
booty passed with their prey. I thrust a long stick down to the centre
of the cluster and brought out clinging to it many ants holding larvae
and pupae."
ii. The group Dorylini includes the genus Dorylus, which was founded
many years ago for Insects very like Labidus. As in the case of the
American Insect named, males only were known; two or three allied
genera, consisting exclusively of individuals of the sex mentioned,
were subsequently described. In the regions inhabited by these
males numerous species of blind ants are known, but only in the
worker form, and were, or still are, referred to genera called
Typhlopone and Anomma. Nothing that could be considered to be a
female pertaining to any of these Insects was discovered until
Gerstaecker described under the generic name Dicthadia an
extraordinary apterous female ant found in Java, and it was
suspected that it might be the long-expected female of the male
Dorylus and of the worker Typhlopone or Anomma. This remained
for many years without confirmation, but in 1880 Trimen announced
the discovery in South Africa of an enormous apterous female ant,
allied to Dicthadia; it had been disinterred from a nest of small red
ants believed (wrongly) to be Anomma. As Dorylus had been
previously found in connection with allied worker ants it has since
then been clear that notwithstanding the enormous differences
existing between these three forms they may all pertain to one (or to
closely allied) species. From this summary the student should
understand that he will find in myrmecological literature many
references to two or three genera that really belong to one species.
The females of the Dorylides are amongst the rarest of Insects, and
are also amongst the greatest of natural curiosities. Although worker
ants and female ants are merely forms of one sex—the female—yet
in this sub-family of ants they have become so totally different from
one another in size, form, structure, and habits that it is difficult to
persuade oneself they can possibly issue from similar eggs. In the
Insect world there are but few cases in which males differ from
females so greatly as the workers of Dorylides do from the females,
the phenomena finding their only parallel in the soldiers and females
of Termites; the mode in which this difference is introduced into the
life of the individuals of one sex is unknown. The largest of all the
Dorylides are the African Insects of the genus Rhogmus. Only the
male is known.
Much attention has been given to the relations between ants and
their guests by Wasmann.[74] He arranges them in four categories; 1,
"Symphily" for the true guests, which are fed and tended by the ants,
the guests often affording some substance the ants delight in; 2,
"Metochy," the class of tolerated guests, being so far as is known not
disagreeable to the hosts; 3, "Synecthry," including those Insects,
etc., to which the ants are hostile, but which nevertheless maintain
themselves in the midst of their foes; 4, Parasites, dwelling in the
bodies of the adult, or of the young ants. Many of these ants'-nest
Insects present a more or less perfect resemblance to the ants in
one or more points, such as sculpture, colour, size, or form. To these
resemblances Wasmann attaches great importance. We should, too,
notice that some of the inquilines[75] have become acquainted with
the movements and habits of the ants, and stroke them (as the ants
do one another) to induce them to disgorge food in the manner we
have alluded to. According to Janet, ants of the genus Lasius are
infested by Acari of the genus Antennophorus. The ants carry the
mites, which assume positions so as not to cause greater
inconvenience than is inevitable. Moreover, the ants give food to the
mites when requested, and behave in a most obliging way to them,
though there is not any reason for supposing that in this case the
ants derive any benefit from the Symphily.
The relations between ants and plants have been of late years much
discussed. We have already briefly alluded to the subject when
speaking of the Pseudomyrmini. We will here only remark that ants
frequent plants not only for the purpose of securing the sweet stuff
excreted by the Aphidae that live on them, but also for the sake of
getting the sweet products the plants themselves afford. Mr. Aitken,
speaking of ants in India, says: "I have come to the conclusion that
one of the most important sources of food-supply which ants have is
the sacchariferous glands to be found at the bases of so many
leaves." It is supposed that the ants are on the whole beneficial to
the plants that thus afford them supply; and this fact is considered by
many to afford an adequate explanation of the existence of these
interesting relations.
CHAPTER V
COLEOPTERA—OR BEETLES
Order V. Coleoptera.
The first and second series, with much of the third, form the
Pentamera, the fifth and sixth the Tetramera [or
Pseudotetramera[78]]. The term Isomera was applied by Leconte and
Horn to a combination of series 1, 2, 3, and 5.
Series 1. Lamellicornia.