1 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
Supplemental Information for
“A Hierarchical Structure
for an Organic Chemistry Course”
Jef Struyf
A retired instructor of the Health and Technology Department,
Katholieke Hogeschool Leuven (KHLeuven),
Gasthuisberg, Herestraat 49, Be-3000 Leuven, Belgium
URL: http://www.khleuven.be, E-mail: [email protected]
1.0 Introduction
The Supplemental Information discusses the use of oxidation levels in organic reaction schemes. The schemes are
more or less deformed by adapting them to the pages of the Word file. To read the Supplemental Information
independently, it contains some repeating text, Scheme 1 and 3-D graph 1 of the main article. Note that NECA is the
acronym for Neon Electron Configuration Analogy, the hierarchical structure for an organic chemistry course
proposed in the main article. The Figures and Tables of the main article are included in a larger format at the end of
the Supplemental Information. The call-out numbers for the cited literature do not refer to the main article.
2.0 Oxidation Levels in Organic Reaction Schemes
2.1. Introduction
In a traditional organic chemistry course, the name of most course modules refers to the main functional group of
which reactions and mechanisms are discussed. The sequence of the course modules nearly follows the oxidation
levels (OLs) of the functional group (attached) carbon(s). It is a good educational practice to explicitly communicate
this knowledge to our audience in the form of a basic reaction scheme that presents an overview of the reaction
landscape in a well structured way and that can be extended to a Basic Organic Reaction Knowledge Space
(BORKS) and further on, to an overview of most reactions of the course. Three properties of the functional groups
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“A Hierarchical Structure for an Organic Chemistry Course”
are appropriate for this purpose: functional groups can be related to the periodic table [1], they can be classified by
OL [2, 3, 4], and they are involved in acid-base reactions. These three properties make the scheme three-dimensional.
Oxidation-reduction has been proposed for a logical characterization of organic structures as part of a three-
dimensional reaction overview by type [5]. OLs are already used in reaction schemes [6].
Most courses introduce functional groups in introductory course modules. The functional groups can already be
mastered in nomenclature and physical properties such as boiling points [7, 8] before the student meets them again in
reactions and mechanisms. Therefore, at the 2s NECA subshell, the students are not really surprised that functional
groups can be interconverted by means of reactions.
The BORKS is at best introduced in connection with the acid-base topic at the 2s NECA subshell. The BORKS
consists of two parts: A basic reaction scheme (Reaction scheme 1) and how acid-base reactions can be connected to
this scheme.
2.2. A Basic Organic Reaction Scheme
Reaction scheme 1 shows reactions for a selection of appropriate functional groups. The scheme is also appropriate
for the functional groups of biomolecules. Very few of them are halogenated, which eliminates main group VII
functional groups. Consequently, the basic functional groups are related to the main groups IV A, V A and VI A,
which correspond to functional groups with carbon-carbon, carbon-nitrogen and carbon-oxygen bonds. These three
bond types exist in single-, double- or triple bonds, except that carbon-oxygen cannot form triple bonds. However,
carboxylic acids have three bonds from carbon to oxygen atoms. If a bond type exists in more than one functional
group, then the most representative one is chosen. For example, alcohols are chosen instead of ethers. R1, R
2, R
3 and
R4 are used to enumerate the R groups or to denote hydrogen.
The location of a functional group depends on two variables. The position of the most specific (hetero) atom of a
functional group in the periodic table is the horizontal variable. The OL of a functional group (attached) carbon(s) is
the vertical variable. These two variables do not determine the location of a functional group on a linear scale.
Abscissa and ordinate lines are omitted. Both variables are introduced for educational reasons. In the progress of the
course and possibly also by consulting textbooks and/or internet information, students will gradually discover that
neither of them is necessary in common reaction schemes.
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“A Hierarchical Structure for an Organic Chemistry Course”
The OL for the following functional group (attached) carbon(s) is: alkanes (OL 0), alkyl halides, alkenes, alcohols
and amines (OL 1), alkynes, benzene, alkylbenzenes, aldehydes and ketones (OL 2), carboxylic acids and derivatives
(OL 3).
Reaction scheme 1 extends the periodic table classification of the functional groups [1] (1s NECA shell) to an
overview of organic reactions (2s NECA subshell). The reactions are not chosen by synthetic relevance, but because
they are appropriate to form an easy and logical scheme to which other structures, other reactions and their
mechanisms can be related. The functional groups at a given OL can be converted into each other without oxidizing
or reducing agents. Redox reactions convert functional groups between different OLs. The redox reaction arrows
accentuate the vertical dimension of the scheme. For the sake of simplicity, the scheme does not specify the
necessary reactant(s) needed for the oxidation or reduction of a specific functional group. Specific reagents would
only distract student's attention away from the purpose of the scheme. Therefore [O] and [H] are used to describe
oxidizing and reducing reactants respectively. Not all the redox reactions can be obtained in both directions.
Some reactions of Scheme 1 have side reactions such as the products of the carbocation rearrangements. Side
reactions confront students with the shortcomings of Scheme 1 and the further on related schemes. A more
comprehensive approach including reaction mechanisms will be necessary.
4 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
Petrochemical [O] [H]
[O]
RNH2 (eliminate H
2O)
H2O, H+
NH3, P
2O
5, heat
H2O, H+
R1
R2
R1
R2
R1
R2
Trimerisation
+ H2O, H+
- H2O, H+
OL 0OL 0
OL 2
OL 1
OL 3OL 3
OL 1
Group IV A carbon-carbon
functional groupsGroup V A carbon-nitrogen
functional groups
Group VI A carbon-oxygen
functional groups
Group IV A
carbon-carbon
functional groups
Group V A
carbon-nitrogen
functional groups
Group VI A
carbon-oxygen
functional groups
if R2 = H
1) X2
2) KOH (ethanol)
RH Alkanes
RNR1R2 Amines Alcohols ROHAlkenes R1R3C=CR2R4
R1R2C=NR
Imines
R1R2CO
Aldehydes
Ketones
R1COOH
Carboxylic acids
R1CN
Nitriles
R1C CR
2
Alkynes
Aromatic
HydrocarbonsH2O, H+
[H][H]
[H] [H]
[H]
[H]
[O]
if R3 and R
4 are H
Reaction scheme 1. The 2s NECA subshell basic organic reaction scheme, which is ordered by
periodic table connections and oxidation levels. Groups IVA, VA and VIA indicate the position of
the most specific (hetero) atom of a functional group in the periodic table. R1, R
2, R
3 and R
4 are used
to enumerate the R groups or to denote hydrogen. The numbers 1) and 2) next to a reagent indicate
consecutive reactions.
Reproduced with permission The Chemical Educator, http://chemeducator.org.
5 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
2.3 The Basic Organic Reaction Knowledge Space
The periodic table group numbers and OLs are the x-y coordinates of Reaction scheme 1. The third dimension of
BORKS is acid-base. Acid-base reactions convert the functional groups into ionic derivatives. The pKa value of a
functional group acid-base half-reaction determines the necessary acid or base strength for the corresponding
reaction. The cationic derivatives are positioned in the positive direction of the z-axis and the anionic derivatives in
the negative direction. Such a third dimension is not easily achieved and is therefore reduced to a mental exercise.
An alternative is developed in Graph 1, which shows a 3-D graph corresponding to Reaction scheme 1 including the
pKa values [9, 10] of the functional groups in the z-dimension. Alkyl and aryl derivatives of some functional groups
and the alkyloxoniums are included.
Reference 1 overviews also ionic derivatives of the functional groups and consequently reference 1 combines the x-
axis (the periodic table connections) and z-axis (ionic formulas) of Reaction scheme 1. For students, reference 1 is
the best introduction to the BORKS. The BORKS will cause no further problems to the students, if the acid-base
reactions are discussed in detail in a previous course module. Acid-base in the z-dimension of the scheme is related
to their applications. They are not intended to create a new functional group. They change the reactivity or solubility
of a compound. The BORKS orientates the student in the possible overwhelming field of reactions. The next two
sections show how this can be further developed. The mental process required from the students to relate other
reactions and mechanisms to this scheme results in a coherent knowledge space on reactions and mechanisms.
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“A Hierarchical Structure for an Organic Chemistry Course”
OL=0
OL=1
OL=2
OL=3-10
0
10
20
30
40
50 Alk
an
es,
50
Alk
enes,
44
Ary
l A
mm
oniu
ms,
4,5
Alk
yl A
mm
oniu
ms,
10,8
Phenols
, 10
Alc
oho
ls, 16
Alk
oxoniu
ms,
-2
Alk
ynes
; 25
Imin
es;
31
Ald
eh
ydes;
17
Keto
nes;
19
Nit
rile
s, 2
5A
ryl
Carb
oxyli
c A
cid
s, 4
,19
Alk
yl
Carb
oxy
lic A
cid
s , 4,7
5
pKa
Graph 1. A 3-D graph corresponding to Reaction scheme 1 including the pKa values of the
functional groups.
2.4. Instructional aids and Extension of the Basic Reaction Scheme 1.
The condensed functional group formulas in Reaction scheme 1 will cause some problems to beginning students
when they are faced to the functional group conversion reactions. It is not obvious to beginning students that for
example ROH becomes R1R2CO in an oxidation reaction. Compared to the alcohol, the aldehyde/ketone shows an
extra R-group and an extra carbon atom. Reaction scheme 2 helps students in that respect. There is a better structure
correspondence in the conversion reactions. In the correspondent reactions, alcohols, amines and aldehydes/ketones
show structure correspondent formulas. Each of these functional groups are presented by two formulas that are
pooled together at near the same position in Reaction scheme 2 as in Reaction scheme 1. Reaction scheme 1 has the
advantage of a rather easy overview. Reaction scheme 2 helps for the structural details in specific reactions. The
7 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
structural correspondent aldehyde/ketone product of the hydration of alkynes is located just below the Reaction
scheme 1 aldehydes/ketones location. Consequently, OL 2 is broadened by a second row.
At best, the study of the interconversions are started for each OL separately. Combining the conversions at OL 1
respectively OL 2 in Reaction scheme 1 and 2 result in Reaction schemes 3 and 4. Reaction schemes 2, 3 and 4 are
the instructional aids for Reaction schemes 1. Reaction scheme 3 already contains the particular structure related
formulas of amines and alcohols for the redox reactions. The students must become aware, that the formula variants
of the same functional group in the same and in subsequent reaction schemes are not exchangeable if the R1 (and
possibly also the R2,....) have identical structures. For example R
1CH2OH and R
1(CH2)2OH are not identical if R
1 in
both structures is H.
Thereafter, Reaction scheme 2 is used to show the redox conversions.
Reaction scheme 5 shows an extension of Reaction scheme 1 with alkyl halides, amides, carboxylates and esters but
without arenes. OL 2 and OL 3 each show two rows. The alkyl halides are also present as reactants on the reaction
arrows of two OL 3 functional groups. The horizontal location of some functional groups, such as amides and
carboxylates, does not correspond anymore to their periodic table connection. The periodic table strictly related
location of functional groups in reaction schemes is restricted to the basic organic reaction schemes and their
instructional aids (Reaction schemes 1, 2, 3 and 4). Reaction scheme 6 is the instructional aid to introduce Reaction
scheme 5.
2.5 An Overview of Most Reactions of the Course:
The Reaction scheme 1 Related Reaction Schemes
The 2s NECA subshell allows for a further overview of reactions by schemes based on OLs. The additional schemes
are already advisable at the 2s subshell because the 1s shell and acid-base also promotes a total approach on
functional groups, which means that the learning process integrates as many functional groups as possible in each 1s
and 2s topic (nomenclature, physical properties, isomers, stereochemistry, acid-base …). The additional schemes
(Reaction schemes 7, 8 and 9) show how their functional groups are related to the basic Reaction scheme 1. They
help the students to develop their knowledge space on reactions. In the additional schemes, the functional group
formulas that connect to Reaction scheme 1 are in bold.
The alkyl halide reactions are further related to the basic Reaction scheme 1 by Reaction scheme 7. Reaction
schemes 7, 8 and 9 show selected reactions according to OLs for respectively alkyl halides, benzene and carbonyls.
8 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
In Reaction scheme 7, the alkyl halides are concerned in OLs 0, 1 and 3. Reaction schemes 8 (benzene reactions) and
9 (carbonyl reactions) are concerned in OLs 2 and 3.
Reaction scheme 9 is an overview of selected carbonyl reactions. The carboxylic acids and their derivatives are at
OL 3, which is split in three rows. Note the central position of R1COZ in which Z can be NR
1R
2, OH, O
-, OR,
OCOR and X. If Z is OH, the central OL 3 formulas are carboxylic acids that are also OL 3compounds in the basic
Reaction scheme 1. If Z is OH, the two central located functional groups in bold font; the aldehydes/ketones and the
carboxylic acids at respectively OL 2 and 3 connect Reaction scheme 9 to the basic Reaction scheme 1. The students
can derive from Reaction scheme 9 that if Z in RCOZ is OH and with a (H+) catalyst, the active formula is oxonium.
Oxonium is also the active formula for aldehydes/ketones and (hemi)acetals/ketals if a H+ catalyst is present. In the
hydrolyze reactions at OL 3, Z is always OH or O- (with a base as a catalyst).
At this stage of the course, it is not strictly necessary that the students can derive reaction equations from the
presented schemes. Although, the first step to achieve this goal may or must be done. It is also not yet possible that
the student overview the whole presented reaction landscape. More important is that the students understand how
these schemes are constructed, interconnected and how they find their way in them.
The 2s NECA subshell terminates with a study of specific oxidation and reduction reactions including their
corresponding reactants.
9 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
R4
R3
R1
R2
Petrochemical [O][H]
R1
R2
1) X2 as [O]
2) KOH (ethanol)
OH
R1
R2
H
N
H
R
R1
H
R2
N
R
R1
R2
R1
OH
O
NR1
O
R1
R2
[O] [H]
if R2 = H
RNH2 (eliminate H
2O)
H2O, H+
NH3, P
2O
5, heat
H2O, H+
R1
R2
R1
R2
R1
R2
Trimerisation
+ H2O, H+
- H2O, H+
OL 0 OL 0
OL 2
OL 1
OL 3OL 3
OL 1
[H]
Group IV A carbon-carbon functional groups
Group V A carbon-nitrogen
functional groups
Group VI A carbon-oxygen
functional groups
Group IV A
carbon-carbon
functional groups
Group V A
carbon-nitrogen
functional groups
Group VI A
carbon-oxygen
functional groups
OH
R2
R1
R4
H
R3
H
R3
R1
R2
R4
H
+ H2O, H+
R2 is H
R1 R
2
O
OL 2
[O]
[H]
[H]
[O]
[H]
[H]
Arenes
Alkynes Imines Aldehydes, Ketones
Carboxylic acidsNitriles
Alkanes
AlcoholsAmines
Alkenes
if R3 and R
4 are H
R1CH2NH2
Reaction scheme 2. A Reaction scheme 1 variant that has a clearer correspondence in formula structure
between conversed functional groups.
Reproduced with permission The Chemical Educator, http://chemeducar.org.
10 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
OL 1
Group IV A carbon-carbon functional groups
Group V A carbon-nitrogen
functional groups
Group VI A carbon-oxygen
functional groups
Group IV A
carbon-carbon
functional groups
Group V A
carbon-nitrogen
functional groups
Group VI A
carbon-oxygen
functional groups
R2
R3
R1
R4
OH
R1
R2
H
N
H
R
R1
H
R2
+ H2O, H
+
- H2O, H+
OL 1 OH
R4
R1
R2
H
R3
AlcoholsAmines
Alkenes
+ H2O, H+
- H2O, H+
OL 1OL 1 RNR1R2 Alcohols ROHAlkenes R1R3C=CR2R4 Amines
From Reaction scheme 1
From Reaction scheme 2
R1CH2NH2
Reaction scheme 3. Instructional aid for oxidation level 1.
11 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
R1
OH
O
NR1
NH3, P2O5, heat
H2O, H+
OL 3OL 3
Group IV A carbon-carbon functional groups
Group V A carbon-nitrogen
functional groups
Group VI A carbon-oxygen
functional groups
Group IV A
carbon-carbon
functional groups
Group V A
carbon-nitrogen
functional groups
Group VI A
carbon-oxygen
functional groups
R1
R2 N
R
R1
R2
O
R1
R2
RNH2 (eliminate H2O)
H2O, H+
R1
R2
R1
R2
R1
R2
TrimerisationOL 2
+ H2O, H+
R1 R
2
O
OL 2Arenes
Alkynes Imines Aldehydes, Ketones
Carboxylic acidsNitriles
RNH2 (eliminate H2O)
H2O, H+
R1
R2
R1
R2
R1
R2
Trimerisation
OL 2R1R2C=NR
Imines
R1C CR
2
Alkynes
H2O, H+
R1R2CO
Aldehydes
Ketones
H2O, H+
OL 3OL 3 R1COOH
Carboxylic acids
R1CN
Nitriles
Arenes
From reaction scheme 1
From reaction scheme 2
From reaction scheme 1
From reaction scheme 2
NH3, P2O5, heat
Reaction scheme 4. Instructional aid for oxidation levels 2 and 3.
12 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
KOH (ethanol)
[O]
NH3, P
2O
5, heat
H2O, H+
OL 0 OL 0
OL 2
OL 1
OL 3OL 3
OL 1
RH
RX
R1CN
RNR1R2HX
OH , H2O
X2 light
R1COOR' + H2O
R'OH, H+
R1CONR2R3R1COO R2R3NH
2
R2R
3NH
heat
P2O5, heat
if R2R3 are H2
OL 3 OL 3
ROH
R1C CR
2
if R3 and R
4 are H
R1R
3C CR
2R
4
R1COOH
OL 2
Alkenes
Alkynes
AlcoholsAmines
Imines
Carboxylic acids
Esters
Nitriles
Amides
Aldehydes, Ketones
R1R3CXCXR2R4 OL 2
X2
Alkyl Halides
Alkanes
Petrochemical [O]
1) NH3, 2) OH-
HX
KOH (ethanol)
R1R2C=NR R1R2CO
if R2 is H
RNH2
H2O, H+
H2O, H+
R1COO
-OH- , H2O
RX
CN- R
1X
Cyanides
R1COOR + X-
Esters
Carboxylates
[H][H]
[O]
[H]
H2O, H+
+
Reaction scheme 5. An extension of Reaction scheme 1 with alkyl halides, carboxylates, esters and amides but
without arenes.
Reproduced with permission The Chemical Educator, http://chemeducator.org.
13 Supplemental Information for
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KOH (ethanol)
NH3, P
2O
5, heat
H2O, H+
OL 1
OL 3OL 3
OL 1 RX
R1CN
RNR1R2HX
OH , H2O
R1COOR' + H2O
R'OH, H+
R1CONR2R3R1COO R2R3NH
2
R2R
3NH
heat
P2O5, heat
if R2R3 are H2
OL 3 OL 3
ROH
R1C CR
2
if R3 and R4 are H
R1R
3C CR
2R
4
R1COOH
OL 2
Alkenes
Alkynes
AlcoholsAmines
Carboxylic acids
Esters
Nitriles
Amides
R1R3CXCXR2R4 OL 2
X2
Alkyl Halides
1) NH3, 2) OH-
HX
KOH (ethanol)
R1COO
-OH- , H2O
RX
CN- R
1X
Cyanides
R1COOR + X-
Esters
Carboxylates
H2O, H+
+
R2
R3
R1
R4
Cl
R2
R1
R4
H
R3
Dihaloalkanes
Reaction scheme 6. Instructional aid for Reaction scheme 5.
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R2
R3
R1
R4
OL 0
OL 1OL 1
X
R4
R1
R2
H
R3
RXHX
OH- or SH
- + H2O
RNHR1 1) R
1NH2 2) OH
-
HX
KOH in ethanol
RH
X2, light
OL 1 OL 1
Alkanes
Alkyl Halides
AlkenesAlkyl Halides
Alcohols or ThiolsAmines
[H]
OR'- or SR'
-
ROR' or RSR'
Ethers or Thioethers
RR
Na Wurtz reaction
RI
I-
ROH or RSH
OL 0
R1COO
- RXCN
-RXRCN + X
-
Nitriles
OL 3
Cyanides Carboxylates
R1COOR + X
-OL 3
Esters
R1
R
C-
R1
OL 1OL 1
Alkynes Alkyl Iodides
Reaction scheme 7. An overview of selected alkyl halide reactions according to oxidation levels.
15 Supplemental Information for
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H
H
R
H
H
H
H
H
X
H
H
H
H
H
H
H
H
H
H
H
COR
H
H
H
H
H
NO2
H
H
H
H
H
SO3H
H
H
H
OL 2OL 2
OL 3OL 3
RX (AlCl3) RCOCl (AlCl3)
X2 (FeX3)HNO3 (H2SO4)H2SO4 (SO3)
+ HX + HCl
+ HX+ H2O + H2O
Alkylation Acylation
HalogenationNitrationSulfonation
in benzene R1 and R
2 are H
Reaction scheme 8. An overview of selected substitution reactions on benzene according to oxidation
levels.
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OL 2N
R
R1
R2 O
R1
R2
RNH2
OH
R1
R2
N
H
R
OH
R1
R2
O R
O
R1
R2
O R
R
If Z is OHCarboxylic Acid Anhydrides
iminesHemiacetals, Hemiketals Acetals, Ketals
Aldehydes, Ketones
H2O, H+
ROH, H+
ROH, H+
H2O, H+
H2O, H+
+ H2O+ H2O
OL 3
OL 2
R1
Z
O
H2O, H+
OL 3
OH
R1
Z O R
R1
O
O
R
OH
R1
Z NR2R
3R
1
O
NR2R
3
R1
X
OR
O
O
R
O
H2O, H+ H
2O, H+
NHR2R
3
SOX2P2O5
+ HZ+ HZ
ROH
if Z is X or OOCR or OR
if Z is OH (+ H+) or X or OOCR
H2OH2O
R1
O-
O
R1
Z
OH+
N+H2R
2R
3
if Z is OH
H+NHR
2R
3
heat, - H2O
EstersAmides
Oxoniums
(Alkyl)Ammonium Carboxylates
Acyl Halides
OL 3
OL 3
Carboxylic Acids (if Z is OH)
+ H2OSO2 + HX +
RCN
Nitriles
heat, - H2O
P2O5
if NR2R
3 is NH2
OH- + H2O
R1COO
-Carboxylates + HZ
Reaction scheme 9. An overview of selected carbonyl reactions according to oxidation levels
Reproduced with permission The Chemical Educator, http://chemeducator.org.
17 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
3.0. Addendum: Oxidation Levels of Functional Group (Attached) Carbon(s)
For functional groups containing heteroatom(s), the OL is identical to the number of bonds from carbon to hetero
atoms3. The OL of the carbons in alkanes is 0.
More generally, the OL is the number of carbon-carbon pi-bonds to the intended carbon increased by the number of
bonds from that carbon to hetero atoms. For example, the carboxylic carbon in acetic acid has three carbon-oxygen
bonds, but no carbon-carbon pi-bonds to it. Its OL is 3 and is denoted as OL 3. The OL of vinyl chloride is 2, the
intended vinyl chloride carbon has a pi-bond and a hetero atom bond to it.
Alternatively, the OL is determined by half of the difference in oxidation state between the intended functional group
carbon(s) and the corresponding alkane carbon(s). For example, the oxidation state for a carboxylic carbon is +3 and
the oxidation state of an ethane carbon is -3, the difference is 6 and the OL is 3. By this rule, the alkenes and alkynes
functional carbons obtain a mean OL. The OL of an individual carbon of a multiple carbon-carbon bond is also its
difference in oxidation state to the oxidation state of the corresponding alkane carbon. Electronegative atoms on
multiple carbon-carbon bonds ask for an appropriate larger or branched corresponding alkane. For example, the
corresponding alkane carbon for the carbon of the carbon-halogen bond in vinyl chloride is the methylene of
propane. The OL of a benzene carbon (OL 2) is the same as the OL of the corresponding alkyne carbon. Note that
benzene can be regarded as a trimer of ethyne.
4.0. Abbreviations
BORKS Basic Organic Reaction Knowledge Space
OL(s) Oxidation Level(s)
NECA Neon Electron Configuration Analogy
18 Supplemental Information for
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Cited Literature
1. Struyf, J. J. Chem. Educ. 2009, 86 (2), 190-193.
2. Soloveichik, S.; Krakauer, H. J. Chem. Educ. 1966, 43, 532-535.
3. Clayden, J.; Greeves, N.; Warren, S. Organic Chemistry, 2 nd
. ed.,
Oxford University Press: London, 2012.
4. Charonnat, J. Chemistry 333 http://www.csun.edu/~hcchm007/333oloc.pdf (accessed June 2014).
5. Hendrickson, J.B. J. Chem. Educ. 1978, 55, 216-221.
6. Struyf, J. The Chem. Educator 2007, 12, 1-9.
7. Struyf, J. J. Chem. Educ. 2011, 88 (7), 937-943.
8. Struyf, J. J. Chem. Educ., 2012, 89 (6), 819–820.
9. March, J. Advanced Organic Chemistry, 250-252, 4th
edition, John Wiley, New York: 1992.
10. Bordwell pKa Table, http//www.chem.wisc.edu/areas
19 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
Fig. 1. The Neon Electron Configuration Analogy (NECA)
Reproduced with permission The Chemical Educator, http://chemeducator.org
The 1s shell discusses the fundamentals of organic structures:
• The molecular structure of organic compounds
• Physical properties and their relationship to intermolecular forces
The second shell presents organic reactions and mechanisms
The 2s subshell discusses the fundamentals of reactions and mechanisms
• Oxidation level based reaction schemes
• Acid-base reactions and introduction to mechanisms
The 2p subshell concerns the mechanistic applications (three pairs of reaction mechanisms)
1. • Nucleophilic substitution (and competitive elimination)
• Nucleophilic addition (and consecutive elimination)
2. • Electrophilic substitution
• Electrophilic addition
3. • Free radical substitution
• Free radical addition
20 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
Table 1. Single bonded functional group classes and their ionic forms in relation to the
periodic table.
Haloniums
Amines RNR1R2
primary: RNH2
secondary: RNHR' tertiary: RNR'R"
(Cyclo)Alkyl and Aryl Halides
RH(Cyclo)Alkanes
RO
+ R X
R'
C- R N
- R O-
OxoniumsAmmoniumsCarbocations
Carbanions Amine Anions
Beta Anions
ROR1
ROH R1 is H and
if R is (cyclo)alkyl: Alcoholsif R is aryl: Phenolsif R is 1-alkenyl: EnolsROR' R1 is R': Ethers
if R is (cyclo)alkyl: Alkoxidesif R is aryl: Phenoxidesif R is 1-alkenyl: Enolates
C-
C X
HN
H
H
HO
H H X
RN
R2
R1
RO
R1
R X
C+ N
+R
HC
H
HH
C
Group IVA Group VA Group VIA Group VIIA
Reproduced with permission of the Journal of Chemical Education
21 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
Table 2. Related Properties for Selected Compounds of the Compared Homologous Series
Alkyl C-0 Alkyl C-1 Alkyl C-2 Alkyl C-4 Alkyl C-6 Alkyl C-8
BPincr BP BPincr BP BPincr BP BPincr BP BPincr BP BPincr BP Mean Aincr Mean µ
Homologous Series K °C K °C K °C K °C K °C K °C 10-6
m3
mol-1 D
n-Alkanamides 458 205 395 213 309 221 236 236 182 251 141 267 8,7 3,78
n-Alkanoic Acids 353 101 300 118 230 141 187 186 154 223 129 255 6,3 1,67
n-Alkanoic Anhydrides 229 140 171 170 131 200 102 228 11,0 3,20
1-Nitro-n-alkanes 284 101 203 114 148 147 110 179 84 210 5,8 3,56
Di-n-alkyl Disulfides 198 110 155 154 125 194 100 226 16,1 2,02
n-Alkanenitriles 278 26 264 82 186 97 142 141 116 185 99 224 4,4 3,85
n-Alkanoyl Chlorides 233 51 169 80 129 128 105 174 90 215 10,5 2,50
n-Alkan-1-ols 353 100 248 65 167 79 118 117 89 158 69 195 1,6 1,67
1-Iodo-n-alkanes 217 -35 225 42 161 72 131 131 112 181 100 226 13,0 1,84
Methyl n-Alkanoates 214 32 146 57 103 102 82 151 67 193 6,4 1,74
n-Alkan-2-ones 145 56 103 102 83 152 70 195 4,8 2,71
n-Alkanals 232 -21 203 21 137 49 104 103 84 153 65 191 5,0 2,57
1-Bromo-n-alkanes 186 -67 186 4 127 38 102 102 86 155 75 201 7,8 2,04
Di-n-alkyl Sulfides 126 37 93 92 73 142 60 186 8,0 1,54
n-Alkane-1-thiols 192 -61 189 6 124 35 99 99 82 151 73 199 8,0 1,51
1-Amino-n-alkanes 219 -33 176 -6 105 17 78 78 62 131 54 180 3,5 1,30
1-Chloro-n-alkanes 168 -85 159 -24 101 12 79 78 66 135 56 182 4,9 1,97
n-Alkyl Ethynes 169 -84 159 -23 97 8 72 71 56 125 48 174 7,2 0,81
n-Alkyl Ethenes 149 -104 135 -47 82 -6 64 63 52 121 45 171 8,9 0,41
Di-n-alkyl Ethers 66 -23 35 35 22 91 16 142 2,0 1,24
1-Fluoro-n-alkanes 273 20 104 -78 51 -38 33 33 23 92 17 143 -0,1 1,90
n-Alkanes BP (°C) -252,5 -182,5 -88,6 -0,5 69,0 125,7
BP (K) 20,7 90,7 184,6 272,7 342,2 398,9
A (10-6
m3 mol
-1) 1.8a 6.5a 11.2a 20.5a 29,9 39,2
In the n-Alkanes, Alkyl C-0 BP is boiling point µ is dipole moment A is molar refractivity a is an extrapolated
corresponds to H2 incr is increment D is Debye unit value
Reproduced with permission of the Journal of Chemical Education
22 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
Figure 2. Overview of Some Boiling Point Curves
Reproduced with permission of the Journal of Chemical Education
23 Supplemental Information for
“A Hierarchical Structure for an Organic Chemistry Course”
OL=0
OL=1
OL=2
OL=3-10
0
10
20
30
40
50 Alk
an
es,
50
Alk
enes,
44
Ary
l A
mm
oniu
ms,
4,5
Alk
yl A
mm
oniu
ms,
10,8
Phenols
, 10
Alc
oho
ls, 16
Alk
oxoniu
ms,
-2
Alk
ynes
; 25
Imin
es;
31
Ald
eh
ydes;
17
Keto
nes;
19
Nit
rile
s, 2
5A
ryl
Carb
oxyli
c A
cid
s, 4
,19
Alk
yl
Carb
oxy
lic A
cid
s , 4,7
5
pKa
Fig. 4. A 3-D graph corresponding to Reaction scheme 1 showing the pKa values of the
functional groups.