Download I find troublesome Dewar`s statement that our

Structural Ontology and Chemical Epistemology:
The case of the p-complex
Dr. Eamonn F. Healy
Professor of Chemistry
St. Edward’s University
Austin, Tx.
“I find troublesome Dewar’s statement that
our formulation of the ethylene bromonium ion
involves a ring but his doesn’t. All that is
meant by a three membered ring is a
triangular arrangement of 3 atoms.”
– Saul Winstein (1950)
“The exclusive anionoid reactivity of olefines
can then be explained if the intermediate
‘cyclic’ cation is in fact a p-complex in which
a bromous cation is linked to the p-electrons of
the C=C bond….the corresponding reaction
with an anion is impossible since ethylene has
no vacant electron orbital of low energy and
cannot therefore act as an electron acceptor
without actual fission of the p-bond”
– Michael J. S. Dewar (1949)
   ci  i
i
where
 i   n j j
j
   ni i
i
where
i 
atoms
n c 
i
j
j
j
Structural Ontology:
The Molecular bond
“…Dewar’s contribution represented an outstanding leap of the imagination.”
- D. Michael Mingos (2001)
“…Chatt got credit for the idea by showing that I was right and he was wrong!”
- Michael Dewar (1988)
Chemical Epistemology:
The Potential Energy Surface
Organic mechanism:
The Constructivist approach
Unified Mechanistic Concept of Electrophilic Aromatic
Nitration: Convergence of Computational Results and
Experimental Data, Olah et al JACS (2009)
Organic mechanism:
The Principled approach
Sir Robert Robinson
Sir Christopher K. Ingold
(1924)
(1926)
“. . . these ideas constituted, in the
writer's opinion, his most important
contribution to knowledge.. .“
- Robinson (1976)
“They represent, in my opinion, a very fine
effort, especially on the theoretical side, and
the theory is certainly one of organic chemistry
and not of aromatic substitution only.”
- Ingold (1926)
“The new work made it inescapably clear that the
old order in organic chemistry was changing, the
art of the subject diminishing, its science
increasing: no longer could one just mix things:
sophistication in
physical chemistry was the base from which all
chemists, including the organic chemist, must
start.”
- Chem. Rev. (1934)
J. Chem. Soc.,(1925)
J. Chem. Soc.,(1926)
J. Chem. Soc.,(1927)
J. Chem. Soc.,(1926)
Organic mechanism:
Principled vs Constructivist
Direct Observation of the Wheland
Intermediate in Electrophilic Aromatic
Substitution – Jay K. Kochi JACS (2000)
Using electrophilic carriers EY where Y=OH, OAc, NO3, Cl and Py as a source of electrophilic E+, electron
donor acceptor (EDA) complexes are formed with a variety of electron-rich aromatic hydrocarbons, followed
by thermal or photochemical activation to yield aromatic substitution:
KEDA
NO2Y
+
NO2YNO
, ArH
2Y , ArH
ArH
 ( 25o C ) or
o C)
h ( -40.....(5)
+
ArNO2
Irradiating these EDA complexes at the wavelength associated with the charge-transfer band and using
picosecond time-resolved spectroscopy to follow the result Kochi has
identified the following mechanism:
h
NO 2Y , ArH
hCT
NO 2Y , ArH
fast
NO 2Y-. ArH+.
NO 2..
NO 2
ArH+.+.
ArH
Y- -
Y
-. -. ArH
+. +.
NONO
2Y 2YArH
. +. ArHY
+.NO 2. NO ArH
2
H
+ Ar +
Y- ArNO
NOHY
2
2
CT
fast
Y-+
NO 2Y-. ArH+.
.....(7)
NO 2.
ArH+.
ArNO 2
.....(8)
+
f ast
.....(9)
ArNO2
Y-
..
..
..
HY
+
YH
HY
Transient absorption spectra obtained at 0.5, 1.5,
4.2, and 18ms (top to bottom) following the
charge-transfer excitation of themesitylene/NO+
EDA complex in dichloromethane at -60°C with
a10-ns laser pulse at 355nm. The spectra consist
of the two overlapping absorption bands of
mesitylene cation radical (centered at 470nm) and
nitrosomesitylenium cation (centered at 430nm).
Charge Transfer Mechanism for Electrophilic Aromatic Nitration
and Nitrosation via the Convergence of ab Initio Molecular-Orbital
and Marcus-Hush Theories with Experiments
- Head-Gordon and Kochi JACS (2003)
Structure and Dynamics of Reactive Intermediates in
Reaction Mechanisms. s– and p-Complexes in Electrophilic
Aromatic Substitutions– Jay K Kochi JOC (2000)
Superposition of the X-ray structures of
hexamethylbenzene complexes with various
electrophiles showing the continuous transition
from the heptamethylbenzenium s-complex to
the hexamethylbenzene/nitrosonium p-complex
depending on the electrophile.
Electron Transfer in Electrophilic Aromatic Nitration and Nitrosation:
Computational Evidence for the Marcus Inverted Region
- Yirong Mo JOTC (2013)
( x1 , y1.......z N )   N ( x, y, z )
N
“Well I tend not to be interested in the more
abstruse aspects of quantum mechanics. I take a sort
of Bridgmanian attitude toward them. Bridgman
with his ideas about operational significance of
everything would say that a question that does not
have operational significance, that does not lead to
an experiment of some sort or an observation, isn’t
significant. I never have been bothered by the
detailed or penetrating discussions about
interpretation of quantum mechanics.”
- Interview of Linus Pauling by John L. Heilbron
(1964)
‘2 may be taken as
the measure of density of an
“electron gas” representing the
average electron distribution
over a comparatively long
period’, and since this
distribution represents all we
can know about the electron,
‘the failure to localize the
electrons more exactly
is of little practical importance’
“Modern chemistry and molecular biology are the
products of quantum mechanics…The concept of the - Electronic Theory of Organic
chemical bond is the most valuable concept in
Chemistry (1949)
chemistry. Its development over the past 150 years
has been one of the greatest triumphs of the human
intellect.”
- J. Chem. Ed. (1992)
The theory of resonance was not only 'claimed to be'
a direct consequence of quantum mechanics, it was
a direct consequence of quantum mechanics.
- Proc. R. Soc. Lond. (1977)
“Ingold spent so much time (1932-1946) on this
project, he was a victim of the preoccupation
that theoretical physics was going to solve the
problems of chemistry, including that of
predicting chemical reactivity.
He was fascinated by seeing how the transition
state concept had been transformed by Eyring
into an “activated complex”. He hypothesized
then that one might use the electronic spectra of
polyatomic molecules, hoping that one of the
electronically excited states was identical to the
reactive state. Actually, the spectroscopic studies
on molecules such as acetylene and
formaldehyde had shown that in the excited state
these molecules have different geometries from
those in the ground state. If one could identify
the molecular geometry of benzene and
determine the energy associated with its reactive
state, it would become possible to discuss
quantitatively the aromatic reactivity problem.”
- C. K. INGOLD AND THE ACTIVATED
COMPLEX GEOMETRY
Giorgio Montaudo (2010)
Structural Ontology:
Visualizing the molecular wavefunction
Atoms in Molecules from the exact one-electron wavefunction
- Geoffrey Hunter Can. J. Chem. (1996)
Given the experimental electron density, re , for an N-electron system, the
wavefunction:
e
 1e   r
N
satisfies the one-electron Schrödinger equation:
(
2
. 2  U r , R ) 1e  E R  1e
2me
where ER is the total electronic energy
Ur,R is the effective potential for the motion of the single electron,
Since:
 re  N[1e ]2
then
 re  2 N1e 1e
and
 re
 re
2
 1e
 1e
Therefore a semi-log plot of the experimental electron density gradient, ,
will display the topology of the one-electron wavefunction .
Structural Ontology:
The s-complex and the molecular bond
Studies of [(C5Me5)Os(L)H2(H2)+]
Complexes. - ChristopherL.Gross
Organometallics (2007)
H
H
M
A
 e  e
1.654
H1
1.632
1.654
H2
Hb
1.015
Ha
 e  e
 e  e
A
 e  e
1.716
1.645
1.649
H1
H2
Hb
1.074
Ha
C
 e  e
1.605
1.631
H1
H2
1.600
Hb 1.306
Ha
 e  e
 e
as compared to
 e  e
 e  e
C
1.605
1.631
H1
H2
1.600
 e
Hb 1.306
Ha
 e
Synthesis, Structural Diversity, Dynamics, and Acidity of
[MH3(PR3)4]+ (M = Fe, Ru, Os; R= Me, Et) Complexes
Dmitry G. Gusev JACS (1997)
 e  e
1.865
H1
1.561
H3
H2
“There is a remarkable asymmetry of bonding in the Fe(H2) demonstrated by all three (calculated and
experimental) structures. This was explained invoking a weak attractive interaction between the cis-H and H2 ligands (between H1 and H2 in the Figure). The theoretical report on [FeH(H2)(PH3)4] + also mentions
that those hydrogens in the positions of H3 and H2 look as if they retained “memory” on their chemical
origin, i.e., that one of H3 appears as a proton coordinating onto a classical hydride−iron bond. This
structural feature however still remains speculative”
Dmitry G. Gusev et al (1997)
Atoms in Molecules
2  e
1.865
H1
1.561
H3
H2
 e  e
“In addition, models involve commitments
which are properly described as involving more
than belief in the model as a good computing
device. Potential energy surfaces are a prime
example. Yes, such surfaces allow us to
calculate. They are also entities which we
cannot observe in principle. But that does not
entail that they are not physically significant.
Energy minima and slopes are real…In short, I
believe we must endorse models as a locus of
epistemological and ontological commitment.”
- (1996)
A final characteristic feature of many
constructive theories is the presence of
entities not given by the fundamental theory.
Critics can defend the use of
constructive theories because they give
information about these explanatory
entities. The potential energy surface is such
an entity. The surface was (and is)
inaccessible to experiment.
- (2000)
The Electronic Theory of
Organic Chemistry
A Quantum Mechanical Discussion of Orientation
of Substituents in Aromatic Molecules
G. W. Wheland, Linus Pauling
J. Am. Chem. Soc., 1935, 57 (11), pp 2086–2095
CCCLXXXVIII.—The nature of the alternating
effect in carbon chains. Part XXII. An attempt
further to define the probable mechanism of
orientation in aromatic substitution
Christopher Kelk Ingold, Florence Ruth Shaw
J. Chem. Soc., 1927, 2918-2926
Learning to Predict Chemical Reactions –
Pierre Baldi J. Chem. Inf. Model (2011)
“While mechanistic reaction representations are approximations quite far from the Schrodinger
equation, we expect them to be closer to the underlying reality and therefore more useful than overall
[rules-based molecular graph] transformations. Furthermore, we expect them also to be easier to
predict than overall transformations due to their more elementary nature. In combination, these
arguments suggest that working with mechanistic steps may facilitate the application of statistical
machine learning approaches as well as their capability to generalize. “