Writing Reaction Mechanisms in Organic Chemistry, Third Edition

510 Pages·2014·23.13 MB·English

by  Kenneth A. Savin

WRITING
REACTION
MECHANISMS
IN ORGANIC
CHEMISTRY
THIRD EDITION
KENNETH A. SAVIN
EliLillyandCompany
ButlerUniversity
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Acknowledgments for the
Third Edition
Forthe third edition ofthis text, the focus I am indebted to the authors of the first
on the how of writing organic reaction two editions of this book, Philippa Solomon
mechanisms remains the foremost objective. and Audrey Miller, for the original con-
The book has been expanded with a new ceptualarchitectureandcontent.Ihavetried
chapter focused on oxidation and reduction to hold to the original philosophy and
mechanisms as well as new material organizational design of the material from
throughoutthetext.Althoughoxidationand thepreviousversions.Ifeelitispresentedin
reduction reactions were considered for pre- the best way possible for a text used as a
viousversionsofthetext,itwasdecidedthat “teaching book”.
this important and yet often under repre- IamgratefulforthehelpIreceivedfromthe
sented topic should be included to better reviewers who took the time to read and
equipthereader.Thisnewchapterissetupto improve the text. Their suggestions go far
allowstudentstoseehowourunderstanding beyond the grammatical corrections, but are
of mechanisms has developed and apply expressive of a group of individuals who are
whattheyhavelearnedintheearlierchapters committed to learning and have a bias for
ofthebooktoagreaternumberofsituations doing chemistry, not just talking about it. In
and more sophisticated systems. We have particularIwouldliketothankAlisonCamp-
added new problems throughout the text to bell for her contributions to the discussions
update and provide illustrative examples to aroundmetals,DougKjellwhoreviewedand
the text that will aid in identifying key sit- suggested problems, LuAnne McNulty for
uationsandpatterns.Theoxidationschapter lookingatthetextfromboththeperspectiveof
also allows us to touch on other mechanistic astudentaswellasfromthestandpointofthe
topics including organometallics, stereo- professor, and Andrea Frederick and Nick
chemistry, radiolabeling, and a more philo- Magnus for their key discussion around the
sophical view of the mechanistic models we orderinwhichthematerialispresented,how
areapplying.Thisnewchapter,aswellasthe oxidation number should be described, and
changestothepreviouschapters,hasallbeen how to draw connections to topics that the
done with consideration to the ultimate studentshavealreadybeenexposedto.
lengthofthebookandthegoalofkeepingit I would, of course, also like to thank my
portableandreasonableinlength. family. Mywife Lisa and myboys Zachand
Additional references for the examples, Cory, for their support and prodding
problems, and key topics have been expan- throughallthe long evenings and weekends
ded with an eye toward the practical spent in developing the manuscript and for
application of the concepts to yet to be being tolerant of the time together we have
encountered challenges. missed as a result of this effort.
vii
C H A P T E R
1
d
Introduction Molecular
Structure and Reactivity
Reaction mechanisms offer us insights into how molecules react, enable us to manipu-
late the course of known reactions, aid us in predicting the course of known reactions us-
ing new substrates, and help us to develop new reactions and reagents. In order to
understand and write reaction mechanisms, it is essential to have a detailed knowledge
ofthestructuresofthemoleculesinvolvedandtobeabletonotatethesestructuresunam-
biguously. In this chapter, we present a review of the fundamental principles relating to
molecular structure and of the ways to convey structural information. A crucial aspect
ofstructurefromthemechanisticviewpointisthedistributionofelectrons,sothischapter
outlines how to analyze and depict electron distributions. Mastering the material in this
chapter will provide you with the tools you need to propose reasonable mechanisms
and to convey these mechanisms clearly to others.
1. HOW TO WRITE LEWIS STRUCTURES
AND CALCULATE FORMAL CHARGES
The ability to construct Lewis structures is fundamental to writing or understanding
organic reaction mechanisms. It is particularly important because lone pairs of electrons
frequently arecrucial to the mechanism but often areomitted from structuresappearing in
the chemical literature.
There are two methods commonly used to show Lewis structures. One shows all elec-
trons as dots. The other shows all bonds (two shared electrons) as lines and all unshared
electrons as dots.
WritingReactionMechanismsinOrganicChemistry
http://dx.doi.org/10.1016/B978-0-12-411475-3.00001-4 1 Copyright(cid:1)2014ElsevierInc.Allrightsreserved.
2 1. INTRODUCTIONdMOLECULARSTRUCTUREANDREACTIVITY
A. Determining the Number of Bonds
HINT 1.1
TofacilitatethedrawingofLewisstructures,estimatethenumberofbonds.
For a stable structurewith aneven numberof electrons, the numberof bonds is given by the
equation:
ðElectronDemand(cid:2)ElectronSupplyÞ=2 ¼ NumberofBonds
The electrondemand is two forhydrogen and eight for all other atoms usually considered in
organicchemistry.(Thetendencyofmostatomstoacquireeightvalenceelectronsisknownasthe
octetrule.)ForelementsingroupIIIA(e.g.,B,Al,Ga),theelectrondemandissix.Otherexceptions
arenoted,astheyarise,inexamplesandproblems.
For neutral molecules, the contribution of each atom to the electron supply is the number
of valence electrons of the neutral atom. (This is the same as the group number of the
element when the periodic table is divided into eight groups.) For ions, the electron supply is
decreased by one for each positive charge of a cation and is increased by one for each
negative charge of an anion.
Usetheestimatednumberofbondstodrawthenumberoftwo-electronbondsinyourstructure.
Thismayinvolvedrawinganumberofdoubleandtriplebonds(seethefollowingsection).
B. Determining the Number of Rings and/or p Bonds (Degree of Unsaturation)
Thetotalnumberofringsand/orpbondscanbecalculatedfromthemolecularformula,
bearinginmindthatinanacyclicsaturatedhydrocarbonthenumberofhydrogensis2nþ2,
wherenisthenumberofcarbonatoms.Eachtimearingorpbondisformed,therewillbe
two fewerhydrogens needed to complete thestructure.
HINT 1.2
Onthebasisofthemolecularformula,thedegreeofunsaturationforahydrocarboniscalculated
as(2mþ2(cid:2)n)/2,wheremisthenumberofcarbonsandnisthenumberofhydrogens.Thenumber
calculated is the number of rings and/or p bonds. For molecules containing heteroatoms, the
degreeofunsaturationcanbecalculatedasfollows:
Nitrogen:Foreachnitrogenatom,subtract1fromn.
Halogens:Foreachhalogenatom,add1ton.
Oxygen:Usetheformulaforhydrocarbons.
Thismethodcannotbeusedformoleculesinwhichthereareatomslikesulfurandphosphorus
whosevalenceshellcanexpandbeyondeight.
3
1. HOWTOWRITELEWISSTRUCTURESANDCALCULATEFORMALCHARGES
EXAMPLE 1.1. CALCULATE THE NUMBER OF RINGS AND/OR p
BONDS CORRESPONDING TO EACH OF THE FOLLOWING
MOLECULAR FORMULAS
a. C H Cl Br
2 2 2 2
There are a total of four halogen atoms. Using the formula (2mþ2(cid:2)n)/2, we calculate the
degreeofunsaturationtobe(2(2)þ2(cid:2)(2þ4))/2¼0.
b. C H N
2 3
Thereisonenitrogenatom,sothedegreeofunsaturationis(2(2)þ2(cid:2)(3(cid:2)1))¼2.
C. Drawing the Lewis Structure
Start by drawing the skeleton of the molecule, using the correct number of rings or p
bonds, and then attach hydrogen atoms to satisfy the remaining valences. Fororganic mol-
ecules, the carbon skeleton frequently isgiven in anabbreviated form.
Oncetheatomsandbondshavebeenplaced,addlonepairsofelectronstogiveeachatom
a total of eight valence electrons. When this process is complete, there should be two elec-
trons for hydrogen; six for B, Al, or Ga; and eight for all other atoms. The total number of
valence electrons for each element in the final representation of a molecule is obtained by
counting each electron around the element as one electron, even if the electron is shared
with another atom. (This should not be confused with counting electrons for charges or
formalcharges;seeSection1.D.)Thenumberofvalenceelectronsaroundeachatomequals
the electron demand. Thus, when the number of valence electrons around each element
equals the electrondemand,the numberof bonds willbeas calculated in Hint 1.1.
Atomsofhigheratomicnumbercanexpandthevalenceshelltomorethaneightelectrons.
These atoms include sulfur, phosphorus, and the halogens (exceptfluorine).
HINT 1.3
WhendrawingLewisstructures,makeuseofthefollowingcommonstructuralfeatures.
1. Hydrogenisalwaysontheperipherybecauseitformsonlyonecovalentbond.
2. Carbon,nitrogen,andoxygenexhibitcharacteristicbondingpatterns.Intheexamplesthat
follow,theRgroupsmaybehydrogen,alkyl,orarylgroups,oranycombinationofthese.These
substituentsdonotchangethebondingpatterndepicted.
(a) Carboninneutralmoleculesusuallyhasfourbonds.Thefourbondsmayallbesbonds,or
theymaybevariouscombinationsofsandpbonds(i.e.,doubleandtriplebonds).
4 1. INTRODUCTIONdMOLECULARSTRUCTUREANDREACTIVITY
Thereareexceptionstotherulethatcarbonhasfourbonds.TheseincludeCO,isonitriles
(RNC),andcarbenes(neutralcarbonspecieswithsixvalenceelectrons;seeChapter4).
(b) Carbonwithasinglepositiveornegativechargehasthreebonds.
(c) Neutralnitrogen,withtheexceptionofnitrenes(seeChapter4),hasthreebondsandalone
pair.
(d) Positivelychargednitrogenhasfourbondsandapositivecharge;exceptionsarenitrenium
ions(seeChapter4).
(e) Negativelychargednitrogenhastwobondsandtwolonepairsofelectrons.
(f) Neutraloxygenhastwobondsandtwolonepairsofelectrons.
(g) Oxygeneoxygenbondsareuncommon;theyarepresentonlyinperoxides,hydroperoxides,
anddiacylperoxides(seeChapter5).Theformula,RCO R,impliesthefollowingstructure:
2
5
1. HOWTOWRITELEWISSTRUCTURESANDCALCULATEFORMALCHARGES
(h) Positiveoxygenusuallyhasthreebondsandalonepairofelectrons;exceptionsarethevery
unstableoxeniumions,whichcontainasinglebondtooxygenandtwolonepairsof
electrons.
3. Sometimesaphosphorusorsulfuratominamoleculeisdepictedwith10electrons.Because
phosphorusandsulfurhavedorbitals,theoutershellcanbeexpandedtoaccommodatemorethan
eightelectrons.Iftheshell,andthereforethedemand,isexpandedto10electrons,onemorebond
willbecalculatedbytheequationusedtocalculatethenumberofbonds.SeeExample1.5.
Intheliterature,aformulaofteniswrittentoindicatethebondingskeletonforthemolecule.This
severelylimits,oftentojustone,thenumberofpossiblestructuresthatcanbewritten.
EXAMPLE 1.2. THE LEWIS STRUCTURE FOR ACETALDEHYDE,
CH CHO
3
ElectronSupply ElectronDemand
2C 8 16
4H 4 8
1O 6 8
18 32
Theestimatednumberofbondsis(32(cid:2)18)/2¼7.
The degree of unsaturation is determined by looking at the corresponding saturated hydro-
carbonC H .BecausethemolecularformulaforacetaldehydeisC H Oandtherearenonitrogen,
2 6 2 6
phosphorus, or halogen atoms, the degree of unsaturation is (6(cid:2)4)/2¼1. There is either one
doublebondoronering.
ThenotationCH CHOindicatesthatthemoleculeisastraight-chaincompoundwithamethyl
3
group,sowecanwrite
Wecompletethestructurebyaddingtheremaininghydrogenatomandtheremainingvalence
electronstogive
6 1. INTRODUCTIONdMOLECULARSTRUCTUREANDREACTIVITY
NotethatifwehadbeengivenonlythemolecularformulaC H O,asecondstructurecouldbe
2 6
drawn
A third possible structure differs from the first only in the position of the double bond and a
hydrogenatom.
Thisenolstructureisunstablerelativetoacetaldehydeandisnotisolable,althoughinsolution
smallquantitiesexistinequilibriumwithacetaldehyde.
D. Formal Charge
Eveninneutralmolecules,someoftheatomsmayhavecharges.Becausethetotalcharge
ofthemoleculeiszero,thesechargesarecalledformalchargestodistinguishthemfromionic
charges.
Formalchargesareimportantfortworeasons.First,determiningformalchargeshelpsus
pinpoint reactive sites within the molecule and can help us in choosing plausible mecha-
nisms.Also,formalchargesarehelpfulindeterminingtherelativeimportanceofresonance
forms (seeSection 5).
HINT 1.4
Tocalculateformalcharges,usethecompletedLewisstructureandthefollowingformula:
FormalCharge ¼ NumberofValenceShellElectrons(cid:2)ðNumberofUnsharedElectrons
þHalftheNumberofSharedElectronsÞ
The formal charge is zero if the number of unshared electrons, plus the number of shared
electronsdividedbytwo,isequaltothenumberofvalenceshellelectronsintheneutralatom(as
ascertainedfromthegroupnumberintheperiodictable).Asthenumberofbondsformedbythe
atomincreases,sodoestheformalcharge.Thus,theformalchargeofnitrogenin(CH ) Niszero,
33
buttheformalchargeonnitrogenin(CH ) Nþisþ1.
34
Note: An atom always “owns” all unshared electrons. This is true both when counting the
number of electrons for determining formal charge and in determining the number of valence
electrons. However, in determining formal charge, an atom “owns” half of the bonding electrons,
whereas in determining the number of valence electrons, the atom “owns” all the bonding
electrons.
7
1. HOWTOWRITELEWISSTRUCTURESANDCALCULATEFORMALCHARGES
EXAMPLE 1.3. CALCULATION OF FORMAL CHARGE FOR THE
STRUCTURES SHOWN
(a)
Theformalchargesarecalculatedasfollows:
Hydrogen
1$(no.ofvalenceelectrons)(cid:2)2/2$(2bondingelectronsdividedby2)¼0
Carbon
4$(no.ofvalenceelectrons)(cid:2)8/2$(8bondingelectronsdividedby2)¼0
Nitrogen
5(cid:2)8/2$(8bondingelectrons)¼þ1
Therearetwodifferentoxygenatoms:
Oxygen(doublebonded)
6(cid:2)4$(unsharedelectrons)(cid:2)4/2$(4bondingelectrons)¼0
Oxygen(singlebonded)
6(cid:2)6$(unsharedelectrons)(cid:2)2/2$(2bondingelectrons)¼(cid:2)1.
(b)
Thecalculationsforcarbonandhydrogenarethesameasthoseforpart(a).
Formalchargeforeachoxygen:
6(cid:2)6(cid:2)(2/2)¼(cid:2)1
Formalchargeforsulfur:
6(cid:2)0(cid:2)(8/2)¼þ2
EXAMPLE 1.4. WRITE POSSIBLE LEWIS STRUCTURES FOR C H N
2 3
ElectronSupply ElectronDemand
3H 3 6
2C 8 16
1N 5 8
16 30
Theestimatednumberofbondsis(30e16)/2¼7.