Antiaromaticity,	s-Indacene,	and	Molecular	Electronics		

by		

Isabella	S.	Demachkie	

		

A	dissertation	accepted	and	approved	in	partial	fulfillment	of	the			

requirements	for	the	degree	of		

Doctor	of	Philosophy			

in	Chemistry	

		

Dissertation	Committee:		

David	Johnson,	Chair		

Christopher	Hendon,	Advisor		

Victoria	DeRose,	Core	Member		

Benjamín	Alemán	Institutional	Representative		

	
	

University	of	Oregon		
	

Winter	2025	
	
	
	
	
	
	
	
	
	



 

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©	2025	Isabella	S.	Demachkie	
This work is openly licensed via CC BY 4.0. 

	

	 	



 

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DISSERTATION	ABSTRACT	
	
Isabella	S.	Demachkie	
	
Doctor	of	Philosophy	in	Chemistry	
	
Title:	Antiaromaticity,	s-Indacene,	and	Molecular	Electronics	
	
	
	 Almost	 100	 years	 ago,	 the	 publication	 of	 Hückel’s	 [4n	 +2]	 𝜋-electrons	 rule	 for	

identifying	aromatic	compounds	piqued	the	interest	of	theorists	and	experimentalists	alike.	

F.	London	published	his	quantum	theory	of	 interatomic	currents	 in	aromatic	compounds,	

commonly	referred	to	as	London	diamagnetism	only	one	year	later.	The	idea	in	a	nutshell,	is	

that	the	delocalized	ring	current	of	𝜋-electrons	found	in	aromatic	molecules	behaves	like	a	

conductive	metal	wire.	In	the	1950’s	R.	Breslow,	proposed	the	idea	of	antiaromatic	[4n]	𝜋-

electron	molecules,	 (formally	 referred	 to	 as	 pseudo	 aromatic)	 as	 potentially	much	more	

conductive	 molecular	 wires.	 Significant	 developments	 in	 synthetic	 organic	 chemistry	

methodology	and	techniques	over	the	last	75	years	have	facilitated	the	study	and	isolation	

of	a	multitude	of	antiaromatic	and	aromatic-antiaromatic	hybrid	molecules.	The	valuable	

molecular	properties	associated	with	this	class	of	molecules	(such	as	a	small	HOMO-LUMO	

gap,	 amphoteric	 redox	 properties,	 and	 low	 energy	 absorbance)	 has	 motivated	 further	

investigation	 due	 to	 their	 potential	 materials	 applications	 in	 organic	 electronics.	

Antiaromatic	 molecules	 have	 maintained	 a	 fundamentally	 interesting	 status	 within	 the	

chemistry	community	because	they	are	extremely	reactive,	difficult	to	isolate,	and	possess	

interesting	electronic	properties.	

	 In	 this	 dissertation	 I	 will	 discuss	 conductive	 materials	 composed	 of	 organic	

molecules,	conductivity	as	 it	applies	to	molecular	circuits,	molecular	wires,	 the	structure-

property	 relationships	 of	 antiaromatic	 heterocycle-fused-s-indacene	 derivatives,	 and	 the	

synthesis	 and	 study	 of	 donor-acceptor	 heterocycles	 fused	 across	 s-indacene	 in	 a	 set	 of	

structural	isomers.	Chapter	I	is	a	historical	review	of	conductive	organic	materials,	electrical	

conduction	in	molecular	wires,	and	explanation	of	the	relationship	between	paratropic	ring	

current	strength	and	diradical	character	in	antiaromatic	molecules.	Chapter	II	describes	the	

synthetic	methodology	of	s-indacene	derivatives	developed	by	the	Haley	 lab,	 the	effect	of	



 

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heterocycle	 fusion	 on	 the	magnetic	 properties	 of	 s-indacene,	 and	 rationalization	 of	 such	

based	on	physical	organic	principals	and	the	rule	of	topological	charge	stabilization.	Chapter	

III	details	the	synthesis	and	effects	of	asymmetric	donor-acceptor	heterocycle	fusion	on	the	

s-indacene	 core	 and	 explains	 the	 potential	 impact	 of	 this	 work	 with	 reference	 to	

superconductivity.	 Chapter	 IV	 is	 a	 conclusion.	 This	 dissertation	 includes	 previously	

published	and	unpublished	co-authored	material.	

	
	
	

	 	



 

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CURRICULUM	VITAE	
	
NAME	OF	AUTHOR:		Isabella	S.	Demachkie	
	
GRADUATE	AND	UNDERGRADUATE	SCHOOLS	ATTENDED:	
	
	 University	of	Oregon,	Eugene	
	 University	of	California	at	Santa	Cruz,	Santa	Cruz	
	
DEGREES	AWARDED:	
	
	 Doctor	of	Philosophy,	Chemistry,	2025	University	of	Oregon	
	 Bachelor	of	Science,	Chemistry,	2017,	University	of	California	at	Santa	Cruz	
	 	
AREAS	OF	SPECIAL	INTEREST:	
	
	 Physical	Organic	Chemistry	
	 Intermolecular	forces	and	Supramolecular	Assembly	
	 Materials	Science	
	 						Conductive	Organic	Materials	
	
PROFESSIONAL	EXPERIENCE:	
	
	 Graduate	Employee,	University	of	Oregon,	2019-2025	
	 Nanopore	Research	Associate,	Two	Pore	Guys	Inc.,	2018-2019	
	 	
GRANTS,	AWARDS,	AND	HONORS:	

	 Research	Scholarship,	Synthesis	and	Study	of	Novel	Helicene	Compounds,	Deutscher	
	 Akademischer	Austauschdienst	(DAAD),	2024	

	 Research	Training	Fellowship,	Indenoflourene	Cyclophanes,	National	Science	
	 Foundation	(NSF),	2021	

	 Dean’s	Academic	Honors,	University	of	California	at	Santa	Cruz,	2017		

PUBLICATIONS:	
	
I.	S.	Demachkie,	M.	P.	Miller,	G.	I.	Warren,	J.	E.	Barker,	E.	T.	Strand,	L.	N.	Zakharov,	M.	M.	
Haley,	Angew.	Chem.	Int.	Ed.	2024,	64,	e202420989.	

G.I.	Warren,	K.	Młodzikowska-Pieńko,	S.	Jalife,	I.	S.	Demachkie,	J.	I.	Wu,	M.	M.	Haley,	R.	
Gershoni-	Poranne,	Chem.	Sci.,	2025,	16,	575-583.		



 

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T.	A.	Shear,	L.	J.	Zocchi,	I.	S.	Demachkie,	H.	J.	Trubenstein,	L.	N.	Zakharov,	D.	W.	Johnson.	
Expanding	Eur.	J.	Org.	Chem.	2022,	26,	e202200056.		

	
	
	



 

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ACKNOWLEDGMENTS	
	
	

	 I	would	first	and	foremost	like	to	thank	my	parents,	family,	and	friends	in	California,	

Washington,	Germany,	and	New	Zealand	 for	being	with	me	 from	far	away,	 I	never	would	

have	made	it	this	far	without	your	relentless	support.	I	love	you	guys.		

	 I	would	like	to	thank	Prof.	Chris	Hendon	for	graduating	me	and	reading	weird	verbose	

drafts	of	the	same	10	paragraphs,	patiently	listening	to	lose	ideas,	and	tolerating	me	and	my	

relationship	with	the	moon.	The	happiest	I’ve	been	in	grad	school	has	been	the	last	year	I	got	

to	spend	with	Robin,	Eoghan,	Casey,	Brian,	Parker,	Doran,	Byoung-Yong,	Tekalign	and	all	the	

undergrads	at	the	coffee	bar	and	in	your	student	office.	Thank	you	for	advising	me	through	

the	end	of	my	degree.	Thank	you	to	Dr.	Josh	Barker,	who	mentored	me	through	the	beginning	

of	my	PhD	journey,	 taught	me	how	to	make	my	favorite	molecules	 in	 the	world,	and	that	

presentations,	papers,	posters,	and	dissertations	are	most	efficiently	done	with	a	lot	of	candy	

and	an	impending	deadline.		Thank	you	from	the	bottom	of	my	heart	to	Josh	and	Prof.	Jeremy	

Bard,	I	will	be	forever	grateful	for	everything	you	guys	did	for	me	my	first	and	second	years,	

it’s	been	a	bumpy	road,	and	I	never	would	have	made	it	without	you.	Thank	you	to	Augie	

Witkowski	and	Allison	Van	Cleve,	I	wouldn’t	have	even	made	it	through	first	year	without	

you	two.	Thank	you	to	Efrain,	Nolan,	Gabby,	Michael,	Megan,	Nathan,	and	all	the	undergrads	

and	REU	students	for	4	years	of	comradery	in	the	Haley	lab.	Thank	you	to	Prof.	Mike	Haley	

and	Prof.	Darren	Johnson	for	an	interesting	4	years,	funding,	and	conferences,	I	will	always	

appreciate	 it.	Thank	you	to	Prof.	Victoria	DeRose	for	sticking	with	me	to	the	end,	and	my	

whole	committee;	Prof.	David	Johnson,	Prof.	Christopher	Hendon,	Prof.	Victoria	DeRose,	Prof.	

Benjamin	 Aleman	 for	 being	 very	 understanding	with	 deadlines	 and	 letting	me	 graduate.	

Thank	 you	 to	 Prof.	 Mike	 Pluth,	 for	 positive	 feedback	 when	 I	 really	 needed	 it,	 and	 Prof.	

Ramesh	Jasti	and	the	Jasti	Lab	for	the	good	times	along	the	way.	Thank	you	to	Helen,	Leah,	

Zoe,	Kathy,	Jannet,	Carissa,	Christi,	Casey,	Nanette,	Natalie,	and	Seth,	this	department	would	

collapse	without	you.	I	must	thank	the	University	of	Oregon	for	the	facilities,	the	US	taxpayer	

for	the	NSF	funding,	and	the	Germans	(and	Prof.	Oliver	Dumele)	for	the	DAAD	scholarship	

and	3	months	in	Berlin!	



 

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	 Thank	 you	 to	 Diana	 Gentry,	 for	 my	 first	 research	 opportunity	 at	 NASA,	 my	 first	

conference,	 and	 being	 a	 truly	 inspirational	 woman	 in	 STEM.	 I	 would	 like	 to	 thank	 Prof.	

Bakthan	Singaram,	Prof.	Gabriella	Amberchan,	and	Prof.	Chad	Higa	for	showing	me	the	magic	

of	organic	synthesis	and	taking	a	chance	on	a	curious	undergrad.	Thank	you,	Prof.	William	

Dunbar	and	Dr.	Andrew	Smith,	for	my	first	industry	research	opportunity	at	Two	Pore	Guys.	

Thank	you,	David	Klech	and	Primrose	Pisares,	(and	my	high	school	and	college	XC	teams)	for	

coaching	and	mentoring	me,	and	making	me	strong.	I	would	like	to	thank	my	undergraduate	

institution,	UC	Santa	Cruz	and	all	my	professors	for	a	strong	foundation	and	well-rounded	

chemistry	 education.	 This	 work	 was	 supported	 by	 the	 National	 Science	 Foundation,	 by	

grants	NRT	DGE-2022168,	CHE-1954389,	and	CHE-2246964	

	

	 	

	 	



 

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DEDICATION	
	

This	dissertation	is	dedicated	to	all	the	women	in	STEM	who	came	before	me	and	blazed	a	

trail,	those	who	hiked	it	with	me,	those	we	lost	along	the	way,	and	those	who	will	follow	in	

our	footsteps.	Watch	out	for	snakes.	

	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	



 

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TABLE	OF	CONTENTS	

Chapter	 Page	
	
I.	INTRODUCTION	............................................................................................................................		 15	

	 1.0	Preamble	...............................................................................................................................		 15	

	 1.1	A	Brief	and	Selective	History	of	Organic	Conductive	Materials	.....................		 16	
	
	 1.2	Molecular	Wires	.................................................................................................................		 19	

	 1.3	[4n]	𝜋-electron	Molecules	along	the	AADCC	..........................................................		 25	

	 1.4	Rational	Design	and	Synthesis	of	s-Indacene	Hybrids	......................................		 32	

II.	STRUCTURE	PROPERTY	RELATIONSHIPS	OF	S-INDACENE	HYBRIDS	...............		 35	

	 2.1	Introduction	.........................................................................................................................		 35	

	 2.2	The	Heterocycle	Effect	.....................................................................................................		 37	

	 2.3	The	Donor	Acceptor	Topological	Charge	Argument	..........................................		 41	

III.	DONOR	ACCEPTOR-FUSED-S-INDACENE-DERIVATIVES	........................................		 48	

	 3.1	Introduction	.........................................................................................................................		 48	

	 3.2	Results	and	Discussion	....................................................................................................		 51	

	 3.2.1	Molecular	Design	and	Solid-State	Structures	.............................................		 51	

	 3.2.2	Optical	and	Electrochemical	Properties	.......................................................		 55	

	 3.2.3	Magnetic	Properties	..............................................................................................		 61	

IV.	CONCLUSION	...............................................................................................................................		 69	

	 4.1	Molecular	Electronics	......................................................................................................		 69	

	 4.2	Conclusion	............................................................................................................................		 71	

APPENDIX	............................................................................................................................................		 72	

REFERENCES	CITED	........................................................................................................................		 165	



 

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LIST	OF	FIGURES	
	
Figure	 Page	
	
	
1.	 Figure	1.1	Conductive	HMTSF-TCNQ	molecules	........................................................		 17	
	
2.	 Figure	1.2	Electrical	conduction	in	𝜋-stacked	benzene	rings	..............................		 19	
	
3.	 Figure	1.3	Structural	explanations	of	benzene	...........................................................		 20	

4.	 Figure	1.4	Aromatic	vs.	Antiaromatic	charge	density		............................................		 22	

5.	 Figure	1.5	The	AADCC	from	CBD	to	s-Indacene	.........................................................		 28	

6.	 Figure	1.6	The	AADCC	from	s-Indacene	to	DCPA	......................................................		 30	

7.	 Figure	1.7	General	retrosynthesis	of	s-Indacene	derivatives	...............................		 33	

8.	 Figure	2.1	Reported	benzoheterocycle-fused-s-indacene	derivatives	.............		 38	

9.	 Figure	2.2	Isoelectronic,	unreported,	and	imaginary	analogs	.............................		 39	

10.	Figure	2.3	GIMIC	plots	and	resonance	structures	.....................................................		 40	

11.	Figure	2.4	Topological	charge	and	donor	acceptor	resonance	structures	.....		 42	

12.	Figure	2.5	Further	arrow	pushed	resonance	structures	........................................		 43	

13.	Figure	2.6	Asymmetric	donor	acceptor	resonance	structures	............................		 45	

14.	Figure	2.7	Induced	charge	transfer	in	UV-vis	studies	..............................................		 46	

15.	Figure	3.1	Fusion	orientations	...........................................................................................		 49	

16.	Figure	3.2	8	new	asymmetric	s-indacene	derivatives	.............................................		 50	

17.	Figure	3.3	X-ray	crystal	structures	and	bond	length	alternation	.......................		 54	

18.	Figure	3.4	Absorbance	spectra	..........................................................................................		 57	

19.	Figure	3.5	Solvatochromic	UV-vis	studies	....................................................................		 58	

20.	Figure	3.6	Cyclic	Voltammograms	....................................................................................		 61	



 

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21.	Figure	3.7	NICS	scans	.............................................................................................................		 63	

22.	Figure	3.8	1H	NMR	spectra	..................................................................................................		 67	

23.	Figure	3.9	1H	NMR	spectra	in	cyclohexane	...................................................................		 68	

	

	

	

	

	

	

	

	

	

	

	

	



 

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LIST	OF	TABLES	
	
Table	 Page	
	
	
1.	 Table	1.	Electrochemical,	optical,	and	HOMO-LUMO	gaps	.....................................		 59	
	
2.	 Table	2.	NICS	and	1H	NMR	shifts	.......................................................................................		 64	



 

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LIST	OF	SCHEMES	
	
Scheme	 Page	
	
	
1.	 Scheme	1.	General	5	step	synthesis	for	s-indacene	derivatives.	.........................		 36	
	
3.	 Scheme	2.	Synthesis	of	IBFBTs	and	IBFBTS	.................................................................		 53	

	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	
	



 

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CHAPTER	I	
INTRODUCTION	

This	chapter	was	written	by	me	with	helpful	input	from	Doran	Pennington	and	Prof.	Chris	
Hendon.	

	
1.0	Preamble	

The	 ability	 for	 a	material	 to	 transfer	 electrical	 charge	 (electrons)	 is	 conductivity,	

which	 is	 an	 inherent	 property	 of	 the	 element	 or	 alloy	 the	 material	 is	 composed	 of	 and	

therefor	has	limited	ability	to	be	tuned	(increased	or	decreased	ability	to	transfer	charge).	In	

this	context,	conductive	materials	 typically	refer	 to	metal	and	metal	alloy-based	materials	

with	a	0	eV	band	gap.	A	superconducting	material	is	a	conductive	material	that	beyond	some	

critical	temperature,	has	zero	electrical	resistance.	Semiconducting	materials	are	defined	by	

their	small	(<4	eV)	band	gap,	and	insulating	materials	have	large	band	gaps	(>4	eV).	Most	

materials	composed	of	organic	molecules	(plastics)	are	insulating	or	semiconducting	(based	

on	 their	 fundamental	 material	 properties)	 with	 low	 conductivities	 (<10-8	 mho/cm)	 that	

decrease	 with	 decreasing	 temperature,	 unlike	 traditional	 metal	 based	 semiconducting	

materials.	The	benefits	 of	 organic	materials	 over	 traditional	metal	 based	 semiconducting	

materials	 include	 flexibility,	 transparency,	 and	 weight	 to	 name	 a	 few.	 Semiconducting	

materials	 made	 from	 organic	 molecules	 (organic	 conductors)	 come	 in	 an	 ever-growing	

variety,	 because	 of	 their	 promise	 of	 designer	 properties	 and	 accessed	 through	 synthetic	

modification.	 Despite	 their	 potential,	 the	 implementation	 of	 organic	 conductors	 into	

commercially	 available	 devices	 is	 just	 getting	 started.	 Continued	 progress	 in	 this	 area	

necessitates	 an	 improved	 understanding	 of	 the	 relationship	 between	 the	 fundamental	

molecular	 properties	 these	 organic	 molecules,	 and	 the	 desired	 properties	 of	 resulting	

materials	such	as	temperature	dependent	conductivity.		

	 The	following	is	a	tangentially	related	PhD	dissertation	on	antiaromaticity,	s-indacene	

derivatives,	and	molecular	electronics.		

	

	

	

	

	



 

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1.1	A	brief	and	selective	overview	of	the	history	of	organic	electronics	
	 In	 the	 fall	 of	 1948,	 a	 sassy	 retort	 from	Fritz.	 London	 titled,	On	 the	 Problem	of	 the	

Molecular	Theory	of	Superconductivity,	pointed	out	the	assumptions	and	paradoxes	that	lead	

to	 Heisenberg’s	 electronic	 superlattice	 theory.1	 London	 proposed	 that	 instead,	

superconductivity	should	be	characterized	as	a	condensed	state	in	momentum	space	and	is	

based	 on	 second	 order	 perturbation	 rather	 than	 first.2	 This	 idea	 of	 molecular	

superconductivity	 in	 combination	 with	 his	 theory	 of	 the	 diamagnetic	 susceptibility	 of	

conjugated	 hydrocarbons,3	 lead	 to	 a	 flurry	 of	 publications	 throughout	 the	 late	 50’s	 and	

1960’s	centered	around	the	idea	that	the	electron	delocalization	found	in	the	conjugated	𝜋-

bonds	 of	 organic	molecules	 could	 be	 considered	 as	 a	 form	 of	 conductivity	 and	 could	 (in	

theory)	be	 thought	of	 as	molecular	wires.	 Polyacetylene	 (polyethylene,	 repeating	units	 of	

C2H2)	is	the	simplest	version	of	a	molecular	wire	and	is	the	basis	of	2/5	of	the	most	common	

plastics	 used	 today.	 Plastics	 are	 typically	 insulators	 which	 do	 not	 conduct	 electricity.	

Nevertheless,	 at	 the	 end	 of	 the	 1970’s	 a	 collaborative	 cross-disciplinary	 effort	 between	

Hideki	Shirakawa	(polymer	chemistry),	Alan	MacDiarmid	(inorganic	chemistry),	and	Alan	

Heeger	(physics),	demonstrated	that	by	using	halogen	mediated	doping,	free	electrons	and	

holes	 could	 be	 introduced	 rendering	 the	 formally	 insulating	 polyethylene	 polymer	

conductive.4	 This	 seminal	 publication	 earned	 its	 authors	 the	Nobel	 prize	 in	Chemistry	 in	

2000,	 and	 paved	 the	 way	 for	 the	 field	 of	 conductive	 polymer	 (CP)	 chemistry,	 which	 is	

sustained	 today.	 The	 effective	 limit	 of	 the	 doping	 approach	 is	 the	 formation	 of	 polarons	

(sometimes	called	bipolarons,	meaning	the	recombination	of	charges).	Past	a	certain	amount	

of	doping	 too	many	 free	charges	are	 too	close	 together,	so	 they	start	recombining,	which	

decreases	 conductivity	 because	 conductivity	 requires	 the	 separation	 of	 charges.	 More	

information	 about	 the	 development	 of	 novel	 CPs,	 and	 the	 broad	 range	 of	 applications	 in	

organic	electronics	and	biomedical	applications,	can	be	found	in	several	reviews	and	texts	

that	the	reader	is	encouraged	to	check	out	if	interested.5,6,7	

In	1964	Little	proposed	a	 theoretical	 infinite,	 linear,	𝜋-conjugated	chain	appended	

with	polarizable	side	chains	as	a	CP	with	room	temperature	superconductivity.	In	a	nutshell,	



 

17 
 

 

the	idea	was	that	molecular	conductivity	requires	the	exchange	of	electron	density	in	one	

direction	to	facilitate	conductivity	along	a	perpendicular	axis.	8	This	design	would	likely	be	

quite	difficult	produce	because	wave	functions	of	the	pendant	groups	are	supposed	to	match	

the	oscillation	of	the	chain.	The	theoretical	chain	Little	proposes	is	of	infinite	length,	but	the	

oscillation	of	a	real	chain	would	be	dependent	on	chain	length.	Assuming	chain	growth	could	

be	controlled,	the	design	of	pendant	groups	with	matching	wave	functions	would	have	to	be	

chain	 length	 specific	 and	would	 require	 substantial	 (if	 not	 unending)	 optimization	when	

considering	the	other	requirements	of	reality	such	as	solubility	and	synthetic	feasibility.		

Organic	 conductors	 composed	of	 individual	 organic	molecules	 (as	 opposed	 to	CPs	

composed	of	repeating	monomers),	promise	increased	tunability	due	to	the	lack	of	required	

polymerizable	 functional	 groups,	 and	 (increased	 hope	 for)	 crystallinity.	 Polymerizable	

monomers	 are	 challenging	 to	 modify	 synthetically	 because	 of	 the	 physical	 space	 the	

functional	groups	require,	as	well	as	the	limited	reaction	conditions	they	can	tolerate.	The	

obstacles	present	in	designing	organic	conductors	composed	of	individual	molecules	with	

interesting	electronic	properties	are	that	they	are	often	extremely	air	sensitive	(pentacene	

and	pentacene	derivatives),	as	well	as	the	𝜋-stacking	(in	order	to	 facilitate	proper	orbital	

alignment)	 requirements	 in	 the	 solid	 state.9	 Air	 sensitivity	 can	 often	 be	 reduced	 with	

synthetic	modification,	but	engineering	the	crystal	packing	of	organic	molecules	remains	a	

dark	art.		

Figure	 1.1:	 (a)	 Conductive	 organic	 donor	 (HMTSF)	 and	 acceptor	 (TCNQ)	molecules.	 (b)	
Donor-acceptor	interactions	between	molecules	and	interchain	coupling	in	the	ab	plane.	(c)	
Orientation	of	HMTSF-TCNQ	donor	acceptor	pairs	projected	along	the	a	axis.	Single	crystal	
conductivity	measurements	are	strongest	along	the	c	axis.		

CN

CNNC

NC

Se

Se Se

Se

TCNQHMTSF

(a)

CNNC

NC CN

Se Se

SeSe

CNNC

NC CN

Se Se

SeSe

a
b

(b)

CN
CN

NC
NC

Se
Se

Se
Se

CN
CN

NC
NC

Se
Se

Se
Se

CN
CN

NC
NC

Se
Se

Se
Se

CN
CN

NC
NC

Se
Se

Se
Se

CN
CN

NC
NC

Se
Se

Se
Se

b
c

(c)

CNNC

NC CN

Se Se

SeSe

CNNC

NC CN

Se Se

SeSe



 

18 
 

 

	 Chemists	at	duPont	uirst	reported	electrical	conductivities	(as	high	as	100	mho/cm)	

in	salts	of	7,7,8,8-tetracyanoquinodimethane	(TCQN)	in	the	early	‘60s.10	A	short	while	later,	

materials	 chemists	 at	 Bell	 Labs	 and	 Johns	 Hopkins	 had	 developed	 several	 derivatives	 of	

tetrathiofulvalenium-7,7,8,8-tetracyanoquinodimethane	(TTF-TCNQ)	donor	acceptor	pairs,	

and	by	1972	the	uirst	room	temperature	organic	conductor	was	reported,	with	conductivity	

increasing	as	temperature	decreases,	to	a	maximum	(104	mho/cm)	at	59	K.11	Finally,	in	1975	

Poehler	 and	 coworkers	 reported	 hexamethylene-tetraselenafulvalenium-7,7,8,8-

tetracyanoquinodimethane	 (HMTSF-TCNQ),	 the	 uirst	organic	 conductor	 to	 exhibit	metallic	

conductivity	at	all	temperatures	(Figure	1.1).12		Perhaps	the	most	valuable	insight	from	these	

studies	was	the	realization	that	conductivity	was	strongest	in	the	direction	perpendicular	to	

the	donor-acceptor	interactions,	through	space	via	end-to-end	orbital	overlap	(𝜋-stacking)	

between	the	aromatic	rings.	The	authors	also	note	temperature	dependent	phase	transitions	

(metallic	to	insulating	states)	in	several	TTF-TCQN	derivatives	because	of	a	peierls	distortion	

caused	by	the	strong	interactions	in	only	one	crystallographic	direction.	HMTSF-TCNQ,	the	

only	derivative	that	exhibited	metallic	like	conductivity	at	all	temperatures,	is	the	largest	of	

the	 donor	 molecules	 and	 has	 the	 strongest	 interchain	 coupling	 (interactions	 in	 two	

crystallographic	 directions).	 Weak	 interactions	 between	 chains	 of	 alternating	 molecules	

establishes	 the	 fermi	 level	 of	 the	 system.	 The	 highest	 occupied	 wave	 functions	 of	 the	

individual	molecules	are	the	𝜋-orbitals	of	aromatic	rings	perpendicular	to	the	plane	of	the	

molecule.	𝜋-stacking	between	layers	(c	direction)	allows	for	end	to	end	𝜋	orbital	overlap	of	

the	highest	energy	orbitals	facilitating	electrical	conduction	vertically	through	the	stacks	of	

molecules.	 	 These	 results	 corroborated	 Little’s	 theory,	 albeit	 not	with	 a	 linear	 chain,	 but	

between	the	pz	orbitals	of	aromatic	ring	systems,	perpendicular	to	the	direction	of	the	donor	

acceptor	 and	 interchain	 coupling	 interactions.	 These	 results	 imply	 the	 mechanism	 of	

conductivity	in	the	𝜋-stacking	direction	between	aromatic	ring	systems	is	analogous	to	the	

right-hand	rule	for	determining	electromagnetic	force	(EMF),	Figure	2.	A	helpful	review	of	

the	theory	behind	magnetoelectricity,	and	progress	in	the	area	of	multiferroics	in	condensed	

matter	physics	can	be	found	in	the	perspectives	referenced.13,14	

	



 

19 
 

 

	
Figure	1.2.	(a)	Benzene	and	pz	orbitals	with	x,	y,	and	z	axes	defined.	(b)	𝜋-stacked	benzene	
rings	with	 clockwise	 ring	 current	 in	 green	 and	 induced	magnetic	 field	 in	 pink.	 Electrical	
conduction	flows	vertically	along	the	magnetic	field	lines.	(c)	The	right-hand-rule	dictates	
that	 a	 clockwise	 current	 in	 the	 x-y	 plane	will	 induce	 a	 perpendicular	magnetic	moment,	
which	is	in	the	negative	z-direction.	
	
1.2	Molecular	Wires	

	 224	years	ago,	one	of	the	most	influential	scientists	of	all	time	was	born	in	a	village	

called	Newington	Butts	(now	London	England).	Michael	Faraday	was	a	self-made	chemist	

and	 physicist	 with	 very	 little	 formal	 education,	 who	 single	 handedly	 discovered	

electromagnetic	rotation,	induction,	and	diamagnetism,	and	was	an	early	pioneer	in	the	field	

of	 electrochemistry	 (among	 other	 scientific	 achievements).	 Faraday	 visualized	 magnetic	

fields	 as	 “magnetic	 curves…	 which	 would	 be	 depicted	 by	 iron	 filings”	 which	 induction	

occurred	along.	After	10	years	of	work,	in	1831	he	was	able	to	prove	through	demonstration	

that	an	electric	current	can	be	induced	by	moving	a	magnet,	by	turning	an	electromagnet	on	

and	 off,	 or	 by	moving	 a	wire	 in	 earth’s	magnetic	 field.	 These	 demonstrations	 converted	

mechanical	energy	into	electrical	energy,	which	paved	the	way	for	the	first	electric	generator	

and	 transformer.15,16	 Between	 discovering	 electromagnetic	 rotation	 in	 1821	 and	 proving	

induction	 in	 1831,	 Faraday	worked	 for	 Humphrey	Davey	 as	 a	 chemist	 and	was	 the	 first	

person	to	isolate	benzene	(from	the	condensed	gases	of	pyrolyzed	whale	oil)	in	1825.17	

	 Several	other	people	synthesized	and	accessed	benzene	in	different	ways	throughout	

Europe	and	about	40	years	after	Faraday’s	 initial	report,	Kekulé	proposed	two	resonance	

structures	 oscillating	 at	 equilibria	 to	 explain	 the	 reactivity	 of	 benzene,	 which	 informed	

Thiele’s	 visual	 depiction	 (later	 popularized	 by	 Pauling)	 of	 the	 delocalized	 structure	 of	

y

x

z
(a) (b) (c)

i

B0

Ele
ctr
ica
lc
on
du
cti
on



 

20 
 

 

benzene	we	all	know	today	(Figure	1.3).18	100	years	of	synthesis,	study,	and	daydreaming	

about	 benzene	 and	 various	 benzene	 derivatives	 finally	 culminated	 in	Hückle’s	 [4n+2]	 π-

electrons	rule	for	the	identification	of	aromatic	molecules	in	1931.19	

Figure	 1.3:	 a)	 Kekulé's	 explanation	 for	 the	 6-membered	 cyclic	 structure	 of	 benzene.	 b)	
Thiele’s	 suggestion	 of	 a	 hexacentric	 delocalized	 electronic	 structure	 to	 explain	 aromatic	
stability.	c)	Hückel’s	rules	for	monocyclic	aromatic	molecules	based	on	the	MO	diagram	for	
benzene.	

	 Aromatic	 molecules	 are	 defined	 by	 their	 unusual	 stability.	 In	 other	 words,	 the	

difference	between	 the	observed	heats	of	 formation	of	benzene	and	cyclohexatriene	 (the	

hypothetical	 unconjugated	 resonance	 structure	 of	 benzene),	 is	 the	 resonance	 energy	 of	

benzene.20	This	resonance	energy	manifests	as	the	delocalization	of	[4n+2]	π-electrons	in	

planar,	 conjugated,	 cyclic	molecules.	With	Hückle’s	 aromaticity	 criteria	 in	hand,	one	year	

later	London	published	a	quantum	theory	of	interatomic	currents	in	aromatic	compounds	

based	on	Bloch’s	approximation	method	and	molecular	orbital	bonding	theory,	commonly	

referred	to	as	“London	diamagnetism”.3	In	the	1950’s	Pople’s	ring	current	model	elaborated	

on	London’s	theory	to	include	the	relationship	between	the	strength,	size,	and	shape	of	the	

ring	 current	 and	 corresponding	 induced	 magnetic	 field	 generated.21	 The	 works	 of	 the	

aforementioned	(and	many	more	unmentioned)	chemists	and	physicists	in	the	19th	and	early	

20th	 centuries	 provided	 the	 foundation	 for	 some	 really	 exciting	 ideas	 in	 the	 mid	 20th	

century.22	

	 In	 the	 early	 1960’s	 several	 theories	 emerged	 with	 the	 same	 core	 idea,	 that	 the	

electron	 delocalization	 found	 in	 the	 conjugated	𝜋-bonds	 of	 aromatic	molecules	 could	 be	

thought	of	as	a	form	of	conductivity	and	could	be	described	as	looped	molecular	wires.23	In	

1965,	Ronald	Breslow,	an	organic	chemist	at	Columbia	University,	first	proposed	the	concept	

of	antiaromaticity,	based	on	cyclobutadiene’s	molecular	orbital	 configuration.24	Breslow’s	

E

“oscillates	between”
Kekulé	1872

“hexacentric”
Thiele	1899

[4n	+	2]	!-electrons
Hückel	1931

(c)(b)(a)



 

21 
 

 

work	in	this	area	largely	focused	on	differentiating	antiaromaticity	from	psuedoaromaticity,	

and	developing	experimental	methods	to	quantify	antiaromatic	character.25,26,27	This	led	to	

the	 widely	 accepted	 theory	 that	 reduced	 aromaticity	 or	 molecules	 with	 pronounced	

antiaromatic	 character	 should	 be	 more	 conductive	 as	molecular	 wires.	 What	 I	 think	 is	

convoluted	is	the	relationship	between	the	direction	of	the	ring	current	and	the	direction	of	

electrical	 conduction	 measurable	 with	 single	 molecule	 conductance	 studies.	 The	

development	of	the	field	of	molecular	electronics	necessitates	a	functional	understanding	of	

the	relationship	between	the	electronic	structure	of	a	given	molecule	and	conductivity.	

Chemistry,	Physics,	and	(I’m	sure)	all	fields	of	study	to	some	extent,	have	their	own	

language,	 so	words	 like	 conductivity	mean	 different	 things	 in	 different	 contexts.	 Physics	

defines	conductance	(𝜎)	as	the	reciprocal	of	resistivity	(𝜌),	and	is	measured	in	siemens	per	

meter	(S/m).	Conductivity	is	generally	defined	as	the	ability	of	some	material	to	conducts	

electricity,	so	S	=	amperes/volts	(A/V).	A	material	with	a	conductivity	of	1	S	would	exhibit	a	

conductance	increase	of	1	amp	per	every	1	volt	increase	across	some	length	of	that	material	

(m).	 Electrochemistry	 measures	 conductivity	 of	 molecules	 or	 electrolytes	 in	 solution	 as	

voltage	over	impedance,	which	can	also	be	used	to	study	to	kinetics	of	charge	transfer	in	that	

solution.	Charge	transfer	between	molecules	in	solution	is	driven	by	potential	energy	which	

comes	 from	 the	 separation	 of	 charges	 (further	 apart,	 greater	 potential	 energy).28,29	

Molecular	conductivity	can	be	measured	and	defined	in	a	variety	of	ways,	one	of	which	is	

single	molecule	conductance	studies	where	a	molecule	is	held	between	two	electrode	tips	

with	 an	 applied	 current.	 Breslow’s	 work	 focused	 on	 diamino	 functionalized	 aromatic	

polycyclic	ring	systems,	which	are	typically	thought	of	as	2-dimesional	in	the	direction	the	

conductivity	is	measured.	So,	the	conductivity	of	the	molecule	is	determined	as	reciprocal	of	

the	 change	 in	 current	 (resistance)	 between	 the	 electrodes.	 This	 method	 measures	 the	

conductivity	 parallel	 to	 the	 plane	 of	 the	 molecule,	 which	 could	 also	 be	 described	 as	

intramolecular	charge	transfer.	

When	a	looped	metal	wire	(and	in	theory	a	molecular	wire),	is	subjected	to	an	applied	

magnetic	field,	an	electrical	current	is	induced	in	the	wire,	which	in	turn	produces	an	induced	

magnetic	 field.	 The	 direction	 of	 induced	 current	 in	metal	wire	 is	 dependent	 only	 on	 the	

relative	orientation	of	the	applied	magnetic	field	and	the	direction	the	metal	wire	is	being	



 

22 
 

 

moved,	while	the	direction	of	induced	current	in	a	molecular	wire	also	depends	on	the	type	

of	molecular	wire	(Figure	1.4).30	Importantly,	in	all	cases,	the	direction	of	electrical	current	

follows	the	path	of	the	wire,	and	conductance	between	wires	flows	along	the	magnetic	field	

lines	of	the	induced	magnetic	field,	the	strength	of	which	is	proportional	to	the	flux	of	the	

induced	magnetic	field?	Charge	transfer	(or	conductivity)	within	molecules	relies	on	orbital	

overlap,	 so	 if	 the	highest	 occupied	wave	 functions	of	 the	 individual	molecules	 are	 the	𝜋-

orbitals	of	aromatic	rings	perpendicular	to	the	plane	of	the	molecule,	charge	transfer	should	

be	 strongest	 in	 the	 direction	 of	maximum	 orbital	 overlap	 (end-to-end),	 which	would	 be	

perpendicular	to	the	plane	of	the	molecule,	not	parallel	to	it.	

Figure	1.4	(a)	Left,	6	𝜋-electron	diatropic	ring	current	of	benzene	illustrated	in	green.	Right,	
the	 volume	 of	 benzene	 (approximated	 as	 V=!√!

#
(a2	 ∙h),	 when	 a	 =	 the	 bond	 lengths	 of	

delocalized	benzene,	and	h	=	the	diameter	of	a	carbon	atom)	illustrated	in	pink.		(b)	Left,	4	
𝜋-electron	paratropic	ring	current	of	cyclobutadiene	illustrated	in	green.	Right,	the	volume	
of	cyclobutadiene	(approximated	as	V=a2	∙h),	illustrated	in	pink.	
	

This	 is	why	 the	way	molecular	 conductivity	 is	 defined	 is	 important.	 Antiaromatic	

molecules	have	stronger	ring	currents	(destabilizing	resonance	energies)31	because	of	the	

greater	 charge	 density	 in	 cyclic	 structures	 with	 [4n]	𝜋-electrons	 (Figure	 1.4).21,32	 When	

single	 molecule	 conductance	 studies	 include	 aromatic	 analogs,	 the	 single	 molecule	

6 !-e-

4	!-e- V	≅ 2.9	Å3

V	≅ 8.7	Å3

(a)

(b)



 

23 
 

 

conductance	is	higher	in	the	antiaromatic	molecules.33	When	𝜋-stacked	aromatic	rings	are	

measured	as	the	junction	in	scanning	tunneling	microscope-based	break-junctions	(STM-BJ)	

studies,	conductance	decreases	with	increasing	rings,	ohmic	behavior.34	in	the	HOMO	energy	

level	of	aromatic	and	antiaromatic	ring	systems	are	typically	the	𝜋-bonding	orbitals	of	the	

conjugated	ring.	

	 The	 direction	 of	 conductivity	 that	 would	 be	 significantly	 greater	 in	 materials	

composed	 of	 antiaromatic	 molecular	 subunits	 (relative	 to	 analogous	 aromatic	 subunits)	

would	 be	 in	 the	 direction	 of	 𝜋	 -stacking	 between	 the	 pz	 orbitals	 of	 vertically	 aligned	

molecular	 subunits.35	 As	 a	 conducting	 layer	 between	 other	 materials,	 the	 valence	 band	

(HOMO)	will	be	higher	in	energy	in	antiaromatic	molecules,	which	should	be	closer	to	the	

fermi	 level	 of	 inorganic	 conductive	 materials.36	 The	 Breslow	 groups	 initial	 STM-BJ	

publication	 in	 the	 early	 2000’s,	 included	 a	 correlation	 between	 the	 relative	 aromatic	

character	of	a	set	of	molecular	wires	and	oxidation	potentials	as	measured	by	solution	state	

CV.37,38	However	this	correlation	is	frequently	mis-cited,	and	later	proved	to	be	limited	to	

aromatic	molecules.	In	the	groups	2010	publication,	several	derivatives	of	biphenylene	were	

investigated	and	no	correlation	between	oxidation	potential	and	molecular	conductivity	as	

measured	 by	 in	 single	molecule	 conductance	 studies	 was	 found.39	 Although	 the	 authors	

stated	 that	 the	 antiaromatic	 character	 of	 biphenylene	 was	 not	 prominent	 (because	

biphenylene	is	not	antiaromatic),	so	the	study	was	inconclusive.	The	body	of	work	generated	

by	the	Haley	lab	over	the	last	12	years	proves	that	increasing	antiaromatic	character	(in	a	

family	 of	 structural	 isomeric	 s-indacene	 hybrids)	 has	 no	 correlation	 with	 increased	 or	

decreased	oxidation	potential,	and	instead	correlates	with	decreasing	reduction	potential	as	

measured	 by	 solution	 state	 CV.40	 The	 difference	 in	 electrochemical	 property	 trends	 in	

aromatic	 and	 antiaromatic	 molecules	 reminds	 me	 of	 p-type	 and	 n-type	 doped	

semiconductors.	 The	 concept	 of	 antiaromaticity	 is	 difficult	 to	 articulate,	 which	 makes	

identification	 of	 structure	 property	 relationships	 in	 this	 class	 of	 molecules	 a	 unique	

challenge.	

	 Computational	 studies	with	 decreasingly	 aromatic	 3-coordinate	 subunits	 (organic	

linkers)	 in	metal-organic-frameworks	 (MOFs)	 indicate	 conductivity	 (based	 on	 computed	

band	 gaps)	 increases	 between	 layers	 (𝜋	 -stacking	 direction)	with	 decreasing	 aromaticity	



 

24 
 

 

(increasing	NICS	values)	of	 the	 linkers.41,42,43	Single	crystal	conductivity	measurements	of	

conductive	MOFs	 corroborate	 this	 with	 consistent	 highest	 conductivity	measured	 in	 the	

direction	 of	 𝜋	 -stacking	 between	 the	 organic	 linkers.44,45	 The	 strength	 of	 conduction	 is	

determined	 by	 the	 identity	 (and	 corresponding	 HOMO	 energy	 level)	 of	 the	 linker.42,46,47,	

Single	molecule	conductance	studies	are	not	a	direct	way	of	measuring	relative	strengths	of	

aromatic	or	antiaromatic	ring	current	conductivity	in	fused	ring	systems.48			

Conductance	 increases	 with	 decreasing	 aromatic	 character	 in	 single	 molecule	

conductance	studies	because	as	the	ring	current	gets	weaker	(from	benzene	to	naphthalene	

to	anthracene),	the	molecule’s	resistance	to	charge	transfer	in	and	out	the	current	decreases.	

Likewise,	 single	 molecule	 conductance	 studies	 with	 antiaromatic	 molecules	 have	 been	

described	 as	 possessing	 anti-ohmic	 resistance.	 The	 term	 anti-ohmic	 refers	 to	 Ohm’s	 law	

which	dictates	that	the	resistance	of	a	conductive	wire	should	increase	with	increasing	wire	

length,	so	anti-ohmic	means	the	relationship	is	inverse.	It’s	a	term	that	is	relevant	for	linear	

(cumulene-like)	 molecular	 wires,	 but	 in	 this	 context	 it	 is	 a	 convoluted	 way	 of	 saying;	

molecules	composed	of	fused	ring	systems	do	not	behave	like	linear	stretches	of	metal	wires,	

instead	they	behave	like	looped	metal	wires	(rings)	when	they	are	composed	of	one	or	a	few	

rings.	As	the	number	of	rings	increases,	the	ring	current	in	the	single	molecule	junction	gets	

weaker	 (regardless	 of	 direction),	 the	 voltage	 across	 the	 length	 of	 the	 molecule	 remains	

constant,	and	conductivity	along	the	length	of	the	molecule	experiences	less	resistance	as	it	

passes	through	the	molecules	ring	current	(becomes	more	wire	like).49,50,51	It	is	interesting	

that	both	 aromatic	 and	antiaromatic	molecules	become	more	 conductive	with	 increasing	

conjugation,	 because	 would	 be	 anti-ohmic	 behavior.	 They	 also	 both	 poses	 increased	

diradical	 character	 with	 increased	 conjugation.	 As	 acenes	 get	 progressively	 longer,	 they	

become	increasingly	air	sensitive	because	of	cycloaddition	reactions	with	O2.	Antiaromatic	

molecules	 are	 significantly	 less	 air	 sensitive,	 because	 their	 reactivity	 is	 fundamentally	

different.52	 Unfortunately,	 the	 limiting	 factor	 for	 synthesizing	 novel	 extended	 acene	 like	

structures	(aromatic,	antiaromatic,	or	hybrid)	is	solution	processability	(solubility).		

	

	

	



 

25 
 

 

1.3 [4n]	𝝅-Electron	Molecules	along	the	Antiaromatic-Diradical	Character	Continuum	
	 Antiaromaticity	is	defined	by	in	the	Gold	Book	of	the	international	Union	of	Pure	and	

Applied	Chemistry	(IUPAC),53	based	on	Minkin’s	definition	as	“antiaromaticity	(antithetical	

to	 aromaticity)	 ….	 In	 contrast	 to	 aromatic	 compounds,	 antiaromatic	 ones	 are	 prone	 to	

reactions	causing	changes	in	their	structural	type,	and	display	tendency	to	alternation	of	bond	

lengths	 and	 fluxional	 behavior	 (see	 fluxional	 molecules)	 both	 in	 solution	 and	 in	 the	 solid.	

Antiaromatic	molecules	possess	negative	(or	very	low	positive)	values	of	resonance	energy	and	

a	small	energy	gap	between	their	highest	occupied	and	lowest	unoccupied	molecular	orbitals.	

In	antiaromatic	molecules,	an	external	magnetic	field	induces	a	paramagnetic	electron	current.	

Whereas	benzene	represents	the	prototypical	aromatic	compound,	cyclobutadiene	exemplifies	

the	compound	with	most	clearly	defined	antiaromatic	properties.”	54	

	 Assuming	 the	 electronic	 nature	 of	 antiaromatic-aromatic-hybrid	molecules	 can	 be	

accurately	described	as	being	along	a	continuum,	the	following	is	how	I	would	explain	it.	I	

prefer	 to	define	 the	 classes	of	 cyclic,	 conjugated	organic	molecules	as:	 formally	aromatic,	

formally	 antiaromatic,	 and	 nonaromatic	 molecules	 based	 on	 structural	 criterial	 alone.	 A	

molecule	is	aromatic	or	antiaromatic	if	it	belongs	to	the	corresponding	formal	class	(based	

on	planarity	and	number	of	𝜋-electrons)	AND	has	a	detectable	diatropic	or	paratropic	ring	

current.	Therefore,	aromaticy	and	antiaromaticy	are	not	properties	themselves,	unless	those	

terms	 are	 synonymous	 with	 diatropic	 and	 paratropic	 ring	 current	 respectively.	 Planar,	

conjugated,	cyclic	molecules	with	[4n]	𝜋-electrons	exist	on	a	size	dependent	continuum	of	

antiaromatic	to	diradical	character	continuum	(AADCC).		

For	the	remainder	of	this	discussion,	the	following	terms	will	be	defined	as	such:	

1. Formally	aromatic:	A	class	of	organic	molecules	which	are	conjugated,	cyclic,	and	planar	

with	[4n+2]	π-electrons,	and	behave	like	increasingly	conductive	molecular	wires	with	

increasing	aromatic	character.	

2. Aromatic:	A	subset	of	formally	aromatic	molecule	which	displays	empirical	evidence	of	a	

diatropic	ring	current,	behave	like	moderately	conductive	molecular	wires.		



 

26 
 

 

3. Formally	 antiaromatic:	 A	 class	 of	 organic	molecules	which	 are	 conjugated,	 cyclic,	 and	

planar	with	[4n]	π-electrons,	and	behave	like	increasingly	conductive	molecular	wires	

with	increasing	antiaromatic	character.	

4. Antiaromatic:	 A	 subset	 of	 formally	 antiaromatic	 molecules	 which	 displays	 empirical	

evidence	of	a	paratropic	ring	current,	behave	like	highly	conductive	molecular	wires.	

5. Nonaromatic:	A	molecule	missing	one	or	more	criteria	that	define	the	classes	of	formally	

aromatic	and	formally	antiaromatic	molecules,	should	not	behave	like	a	molecular	wire.	

	 	

	 The	 first	 highly	 coveted	 antiaromatic	 synthetic	 target	 (which	maintains	 its	 status	

today	 the	 defining	 example	 of	 antiaromaticity)	 was	 cyclobutadiene	 (CBD).	 CBD	 (C4H4)	

delocalizes	4	π-electrons	in	a	conjugated,	planar,	square	shaped	ring,	resulting	in	a	strongly	

destabilizing	 paratropic	 ring	 current.	 Unsubstituted	 CBD	was	 finally	 tamed	 by	 Cram	 and	

coworkers	in	1988,	and	evidence	of	a	paratropic	ring	current	can	be	found	in	the	1H	NMR	

spectra	 which	 exhibits	 a	 sharp	 peek	 at	 2.3	 ppm	 (below	 the	 expected	 range	 for	 isolated	

alkenes).55	However,	when	tetra-substituted	with	t-butyl	groups,	Masamune	et	al.	found	4	

bands	by	IR	spectroscopy,	disproving	a	D4h	symmetry	(i.e.	no	delocalization,	no	ring	current),	

making	 (along	 with	 several	 other	 examples)	 substituted	 CBD	 formally	 antiaromatic.56	

Interest	permitting,	the	reader	is	directed	to	a	comprehensive	review	of	the	early	work	on	

cyclobutadiene,	 and	 it’s	 various	 substituted	 derivatives	 which	 informed	 the	 community	

about	the	reactivity	and	electronic	structure	of	this	strange	little	molecule,	and	motivates	the	

study	of	antiaromatic	molecules	in	perpetuity.57	Cyclooctatetraene	(COT)	is	nonaromatic,	not	

formally	antiaromatic	because	 it	 is	not	planar.	 It	 is	 cyclic,	 conjugated,	and	contains	4n	π-

electrons,	but	the	ring	current	does	not	exist	because	the	molecule	forms	a	tub	shape.	It	is	

(relatively)	 stable	 and	 can	 be	 isolated	 in	 it’s	 unsubstituted	 form	 as	 liquid	 at	 room	

temperature.58	COT	can	be	planarized	through	aromatic	ring	fusion,	at	which	point	it	does	

exhibit	evidence	of	a	weak	 local	antiaromatic	ring	current,	but	 the	native	(unsubstituted)	

molecule	 is	 nonaromatic.59	 On	 the	 other	 hand,	 pentalene	 (the	 bicyclic	 analog	 of	 COT)	 is	

antiaromatic.	Pentalene	contains	the	same	number	of	π-electrons	and	carbons	as	COT	but	

has	two	less	hydrogens	and	is	planar.	Pentalene	has	been	isolated	in	a	variety	of	substituted	

forms	 and	 shows	 empirical	 evidence	 of	 a	 paratropic	 ring	 current.60,61These	 definitions	



 

27 
 

 

primarily	rely	on	structural	and	magnetic	properties	because	the	structural	criteria	can	be	

described	 numerically	 (by	 π-electron	 count)	 and	 with	 symmetry	 labels.62,63	 Magnetic	

properties	are	definitive	because	they	are	experimentally	quantified	and	are	directly	related	

to	the	direction	and	strength	of	the	ring	current.16,21,30,64	The	magnetic	properties	define	the	

relative	antiaromatic	 character	of	molecules	along	 this	 spectrum.	The	 trends	 in	magnetic	

properties	as	measured	by	proton	NMR	for	a	set	core	length,	align	with	expected	energetic	

property	 trends	 as	measured	 by	 UV-vis	 and	 solution	 state	 cyclic	 voltammetry	 (CV).	 The	

HOMO-LUMO	gap	(can	be	approximated	by	the	optical	gap,	which)	decreases	with	increasing	

antiaromatic	character	(ring	current	strength).	If	antiaromatic	molecules	can	be	thought	of	

as	 molecular	 wires,	 and	 ring	 current	 strength	 is	 proportional	 to	 conductivity,	 then	 the	

susceptibility	of	the	wire	to	electromagnetic	forces	should	be	related	on	the	conductivity	of	

the	wire.	More	specifically,	an	electronic	current	is	more	easily	induced	in	wires	with	strong	

ring	 currents	 (more	 antiaromatic	 character)	 by	 magnetic	 fields,	 and	 more	 sensitive	 to	

electromagnetic	 radiation	 (absorbs	 more	 broadly	 and	 lower	 energy	 light).	 The	 detailed	

description	 of	 the	 continuum	 is	 important	 because	 energetic	 molecular	 properties	

(decreasing	 HOMO-LUMO	 gap)	 trend	 with	 increasing	 n	 and	 corresponding	 decreasing	

antiaromatic	character.	Energetic	measurements	should	only	ever	be	used	to	compare	the	

effects	of	synthetic	modification	of	a	single	structure,	for	example	the	optical	gap	decreases	

from	anti-IDBF	to	syn-IDBF	because	the	syn-fusion	of	benzofuran	increases	the	paratropic	

ring	current	strength	more	than	the	anti-fusion	of	the	same	heterocycle	to	the	same	core	(s-

indacene).65,66	The	HOMO-LUMO	gap	decreases	from	syn-IDBF	to	syn-IIDBF	with	decreasing	

paratropic	ring	current	strength	because	conjugation	increases	from	IDBF	to	IIDBF.62,67,68,69		

	 A	small	HOMO-LUMO	gap	is	a	characteristic	of	antiaromatic	molecules	but	cannot	be	

a	 definitive	 criterion	 for	 antiaromaticity,	 because	 lots	 of	 aromatic	 molecules	 have	 small	

HOMO-LUMO	 gaps,	 and	 small	 is	 relative.	 Additionally,	 based	 on	 molecular	 orbital	

calculations	at	the	TPSSh/def2tzvp	level	of	theory,	the	HOMO-LUMO	gap	varies	considerably	

along	 the	AADC.	The	HOMO-LUMO	gap	decreases	 from	CBD	 to	pentalene,	 increases	 to	 s-

indacene,	 and	 then	decreases	 to	DCPN	and	DCPA	 (Figure	1.5	 and	1.6).	 The	pseudo-Jahn-

Teller	(pJT)	distortion	associated	with	weakly	antiaromatic	molecules	is	a	result	of	the	small	



 

28 
 

 

HOMO-LUMO	gap	and	refers	to	the	pseudo	degenerate	HOMO	and	HOMO-1	energy	levels	in	

s-indacene	and	beyond	on	the	AADC.	Jahn-Teller	distortion	is	the	molecular	equivalent	of	a	

peierls	distortion,	 the	effects	of	which	 increase	with	 increasing	density	of	states	near	 the	

fermi	level	in	materials,	and	analogously	density	of	molecular	orbital	energy	levels	near	the	

HOMO-LUMO	gap	in	molecules.	The	distortion	in	molecules	with	[4n]	π-electrons	is	pseudo	

because	the	(D4h	or	D2h	for	CBD,	and	D2h	or	C2h	for	pentalene	and	beyond	depending	on	the	

method	 of	 calculation)	 symmetry	 does	 not	 have	 any	 degenerate	 orbitals,	 in	 contrast	 to	

benzene	(Figure	1.5	b,	c).	The	pJT	distortion	occurs	in	molecules	with	increasing	n	along	the	

AADCC	to	stabilizes	the	HOMO-1	bond-alternant	ground	state	(valence	tautomer),	to	avoid	

forbidden	transitions	to	higher	energy	and	increasingly	antiaromatic	states.	

Figure	 1.5.	 (a)	 AADCC	 from	 CBD	 to	 s-indacene	 depicted	 with	 molecular	 orbitals.	 (b)	
Benzene’s	D6h	symmetry	results	in	degenerate	orbitals	(for	contrast).	(c)	pseudo-Jahn-Teller	
distortion	of	s-indacene	depicted	as	an	energy	barrier	between	two	bond-alternant	ground	
states	with	a	delocalized	transition	state,	next	to	benzene	which	has	a	delocalized	ground	
state	 in	 an	 energetic	 well	 between	 two	 bond	 alternant	 resonance	 structures.	 Molecular	
orbital	calculations	preformed	at	the	TPSSh/def2tzvp	level	of	theory	with	isosurface	values	
at	0.015	a.u.	
	
	 It	is	well	established	that	as	the	number	of	𝜋-electrons	increase	within	the	class	of	

formally	 antiaromatic	 molecules,	 the	 strength	 of	 the	 paratropic	 ring	 current	 decreases	

HOMO-2	(B1u)	-9.745	eV

HOMO-1	(B2u)	-8.851	eV

HOMO	(B2g)	
-4.492	eV

LUMO	(B1g)	-2.430	eV

LUMO+1	(Ag)	
1.948 eV

HOMO-2	(B2g)	-8.168	eV

HOMO	(B1u)	-4.710	eV

LUMO+1	(B2g)	0.795	eV

HOMO-1	(B1g)	-6.572	eV

LUMO	(B3u)	-3.402	eV

LUMO+1	(Ag)	1.82	eV

HOMO-2	(B3u)	-7.287	eV

HOMO	(B2g)	-5.159	eV

LUMO	(B1g)	-3.394	eV

LUMO+1	(B3u)	-1.068	eV

HOMO-1	(Au)	-5.515	eV

LUMO+2	(B3g)	1.374	eV

HOMO-1	(E2g)	
-6.641	eV

HOMO	(E2g)
-6.614	eV

LUMO	(E1g)	
-0.626	eV

LUMO+1	(E1g)	
-0.626	eV

Increasing	antiaromaticity

s-Indacene

Benzene

PentaleneCyclobutadiene

(a)
(b)

(c)



 

29 
 

 

(increasing	the	stability	of	the	delocalized	state).70	The	LUMO+1	state	(which	is	above	the	

vacuum	in	these	calculations,	and	are	meant	to	be	qualitative)	for	CBD	and	pentalene	looks	

like	delocalized	ring	currents	that	becomes	increasingly	wobbly	with	increasing	n	and	is	no	

longer	continuous	in	s-indacene	(LUMO+2).	With	increasing	n,	the	ring	current	gets	larger	

and	weaker,	the	stability	of	the	delocalized	state	increases,	dropping	from	the	LUMO+2	of	s-

indacene	(above	the	vacuum)	to	the	LUMO+2	of	DCPN	(below	the	vacuum)	and	then	back	up	

to	the	LUMO+3	of	DCPA.	This	 is	a	visual	representation	of	 the	antiaromaticity	cutoff	at	s-

indacene.	 Also	 at	 this	 point	 on	 the	 continuum,	 the	HOMO	 and	HOMO-1	 reverse,	 and	 the	

transition	from	the	HOMO	to	the	LUMO+1	(diradical	state)	is	facilitated	by	the	decreasing	

HOMO-LUMO	gap	which	trends	with	increasing	conjugation	and	diradical	character	from	s-

indacene	to	dicyclopenta[b,g]anthracene	(Figure	1.6).71,72	The	antiaromaticity	cut-off	at	s-

indacene	 aligns	 with	 Berger	 and	 Viel’s	 interpretation	 of	 symmetry	 criteria	 for	

antiaromaticity.	Pentalene	(n	=2)	and	s-indacene	(n=3)	are	still	S2	symmetric	(in	terms	of	Kae	

cyclic-based	point	 groups)	 and	 are	 antiaromatic,	 but	 dicyclopenta[b,g]naphthalene	DCPN	

(n=4)	 and	 dicyclopenta[b,g]anthracene	 DCPA	 (n=5)	 are	 diradicaloids,	 and	 are	 S2n+2	

symmetric.63	



 

30 
 

 

	
Figure	1.6	AADCC	from	s-indacene	to	DCPA.	Molecular	orbital	calculations	preformed	at	
the	TPSSh/def2tzvp	level	of	theory	with	isosurface	values	at	0.015	a.u.	
	
	 The	continuum	begins	at	cyclobutadiene	(4	𝜋-electrons,	n=1),	which	has	significant	

antiaromatic	character	in	its	unsubstituted	form,	but	any	thermodynamic	(aryl	ring	fusion)	

or	 kinetic	 (sterically	 bulky	 groups	 i.e.	 t-butyl)	 render	 it	 formally	 antiaromatic.	 	 This	 is	

because	stabilization	of	the	ground	state	(valence	tautomers	of	D2h	symmetry)	result	 in	a	

larger	activation	barrier	and	making	the	delocalized	structure	less	frequently	occupied.	This	

differentiation	between	antiaromatic	and	formally	antiaromatic	is	particularly	important	for	

CBD	derivatives	because	of	the	bond	length	alternation	(BLA)	discussions	in	the	literature.	

BLA	 (in	 combination	 with	 the	 remaining	 structural	 criteria)	 is	 evidence	 of	 a	 formally	

antiaromatic	 ground	 state,	 (or	 a	 frozen	 transition	 state)73	 but	 not	 antiaromaticity.	 For	

example,	multiple	reports	of	aromatic	ring	fused	CBDs	(in	the	absence	of	protons	on	the	4-

membered	ring),	cite	highly	alternating	bond	lengths	and	crystal	structure	bond	angles	as	

HOMO-2	(B3u)	-7.287	eV

HOMO	(B2g)	
-5.159	eV

LUMO	(B1g)	
-3.394	eV

LUMO+1	(B3u)	
-1.068	eV

HOMO-2	(Au)	
-6.713	eV

HOMO-1	(B3u)
-5.448	eV

HOMO	(B1g)	
-4.95	eV

LUMO	(Au)	
-3.394	eV

LUMO+1	(B2g)	
-1.869	eV

LUMO+2	(B3u)	
-0.268	eV

HOMO-1	(Au)
-5.515	eV

HOMO-2	(Au)	
-6.137	eV

HOMO-1	(B2g)
-5.619	eV

HOMO	(B1g)	
-4.59	eV

LUMO	(Au)	
-3.417	eV

LUMO+1	(B3u)	-2.439	eV

LUMO+2	(B2g)	-0.841	eV

LUMO+3	(B3u)	-0.111	eV

Increasing	diradical	character

s-Indacene
Dicyclopenta[b,g]naphthalene	

(DCPN)
Dicyclopenta[b,g]anthracene	

(DCPA)



 

31 
 

 

evidence	 of	 strong	 antiaromatic	 character.74	 There	 is	 no	 reason	 to	 believe	 some	 novelly	

substituted	phenanthrene	fused	CBD	derivative	would	be	antiaromatic,	when	every	other	

example	reported	is	only	formally	antiaromatic	because	any	substitution	of	CBD	stabilizes	

the	bond	alternant	ground	state	making	the	delocalized	transition	state	inaccessible.75,76	If	it	

doesn’t	delocalize	it’s	not	antiaromatic.	Maybe	I’m	biased,	I	just	think	zirconacene	chemistry	

is	too	perplexing	for	CBD	derivatives.77			

	 A	 recent	 report	 from	 the	 Yasuda	 group	 describes	 taming	 the	 pseudo-Jahn-Teller	

distortion	effect	 in	a	pair	of	dibenzothieno[a,f]pentalene	isomers	via	fusion	orientation	of	

the	thiophene	moieties.	The	authors	attribute	the	decreased	energy	barrier	(Ea‡	of	less	than	

1	kcal/mol)	 to	 the	decreased	aromatic	character	of	 the	 fused	thiophene	rings	(relative	 to	

benzene),	stabilizing	the	transient	C2v-symmetric	structure.	This	could	also	be	thought	of	as	

destabilizing	the	bond	alternant	ground	state,	resulting	in	more	pronounced	antiaromatic	

character	 in	 the	 hybrid	 molecules	 because	 of	 the	 increased	 time	 spent	 in	 the	

transition/excited	state.78	A	similar	phenomena	(opposite	approach,	increasing	the	Ea‡)	has	

also	been	observed	in	s-indacene	and	dicyclopenta[b,g]naphthalene	derivatives,	(syn-IDBTS	

and	IIDBTS).	Thermodynamic	stabilization	of	the	ground	state	was	increased	upon	oxidation	

of	 the	 fused	 (aromatic)	 benzothiophene	 moieties	 to	 (nonaromatic)	 benzothiophene-S,S-

dioxides,	 causing	 in	 an	 increased	 HOMO-LUMO	 gap	 (based	 on	 experimental	 optical	 and	

electrochemical	gaps).	This	was	described	by	the	authors	as	“decreasing	the	antiaromaticity	

via	 late-stage	modification”.	 Anyway,	 the	 result	was	 evidence	 of	 valence	 tautomerization	

(post	 oxidation)	 in	 the	 crystal	 structures,	 where	 the	 bond	 alternation	 pattern	 in	 the	 s-

indacene	core	reversed.	1H	and	13C	NMR	peaks	are	sharp	at	room	temperature	and	indicate	

a	significant	Ea‡,	and	upfield	shifted	1H	core	proton	peaks	post	oxidation	corroborates	the	

claim	of	decreased	antiaromatic	character.	The	observation	that	this	is	due	to	spending	less	

time	in	the	transition	state	is	not	mentioned	but	fits	with	the	reported	data.79		

	 Thermally	accessible	diradical	character	is	present	in	several	derivatives	of	DCPN	and	

DCPA	 reported	 by	 the	 Haley	 lab.80,81,82	 The	 trends	 in	 the	 optical	 and	 electrochemical	

properties	of	DCPN	and	DCPA	derivatives	indicate	increased	conjugation	is	responsible	for	

decreased	HOMO-LUMO	gaps,	because	1H	NMR	data	(corroborated	by	NICS	scans)	implies	

the	deshielding	effects	of	the	paratropic	ring	current	decrease	from	s-indacene	to	DCPN	to	



 

32 
 

 

DCPA	in	heterocycle	fused	and	hydrocarbon	derivatives.62,81,69,83,84,85	Further	information	on	

the	 structure	 property	 relationships	 of	 formally	 antiaromatic	 molecules	 past	 the	

antiaromaticity	cutoff	 (n	>	3)	on	the	antiaromatic-diradical	character	can	be	 found	 in	 the	

impending	review	article	from	the	Haley	group	at	the	University	of	Oregon.		

	

1.4 Rational	Design	and	Synthesis	of	s-Indacene	Hybrids	
	 s-Indacene	 occupies	 a	 unique	 intersection	 of	 the	 antiaromaticity-diradicaloid	

continuum,	 at	 the	 point	 of	 maximum	 ring	 current	 size	 and	 the	 end	 of	 the	 accessibly	

antiaromaticity.	The	size	of	the	ring	current	is	inversely	related	to	the	strength	of	the	ring	

current,	 so	 compared	 to	 cyclobutadiene	 and	 pentalene,	 s-indacene	 is	 relatively	 stable.	

Relatively	being	the	key	word,	s-indacene	cannot	be	isolated	in	its	native	form	because	it	will	

readily	react	with	oxygen	to	 form	Janus	dione	 in	addition	 to	other	degradation	pathways	

under	ambient	conditions.86	However,	through	the	power	of	organic	synthesis,	s-Indacene	

can	be	effectively	stabilized	through	aromatic	ring	fusion	to	the	outer	five-membered	rings,	

and	the	reactive	apical	carbons	can	be	kinetically	blocked	with	bulky	substituents.		

	 The	indeofluorene	project	began	with	reports	of	hydrocarbon	structural	isomers	of	

indenofluorene,	which	identified	the	optimal	12	𝜋-electron	scaffold	to	study	the	structure	

property	relationships	of	antiaromatic-hybrid	molecules	as	s-indacene.87,88	s-Indacene	can	

be	thermodynamically	stabilized	by	fusion	of	aryl	rings	to	the	outside	of	the	5-membered	

rings	of	the	core,	the	most	basic	form	of	which	would	be	symmetric	fusion	of	benzene	rings	

to	 make	 indeno[1,2b]fluorene	 (IF).89	 	 Initial	 investigations	 into	 the	 structure	 property	

relationships	of	IF	involved	tuning	through	addition,	by	altering	the	identity	of	the	protecting	

group	at	 the	apical	 carbons.90	This	 tuning	direction	was	not	very	effective	 in	altering	 the	

electronic	 or	magnetic	 properties	 of	 the	molecule	 but	 does	 control	 solid	 state	 packing.91	

Relatively	quickly,	the	Haley	lab	moved	from	tuning	by	addition	to	tuning	by	fusion	through	

several	 different	 methods	 including	 𝜋-extension	 of	 the	 s-indacene	 core,	 𝜋-extension	 of	

peripheral	aromatics,	and	the	inclusion	of	heterocycles	in	the	core	and	peripheral	aromatics	



 

33 
 

 

in	an	extremely	thorough	effort	to	probe	the	structure	property	relationships	of	this	strange	

class	of	molecules	(Figure	1.7).	40,92,93		

Figure	1.7.	 (a)	general	retrosynthesis	of	 IF	derivatives.	 (b)	Tuning	through	fusion	occurs	
within	the	first	set	of	synthetic	steps.	Arrows	1	and	3	illustrate	tuning	through	𝜋-extension	
and	 heterocycle	 incorporation	 of	 the	 peripheral	 aromatics,	 respectively.	 Arrows	 2	 and	 4	
illustrate	𝜋-extension	of	the	core	and	desymmetrization	of	the	core,	respectively.	(c)	Tuning	
by	addition	for	arrow	1	occurs	as	a	variable	lithiation	addition	to	the	diketone	intermediate.	
Tuning	 by	 addition	 for	 arrow	 2	 refers	 to	 pendant	 functional	 groups	 attached	 to	 the	
peripheral	aromatics,	which	occurs	before	the	first	step	of	the	synthesis.	
	
	 𝜋-Extension	 of	 the	 core	 by	 n=2,	 which	 lead	 to	 the	 synthesis	 and	 isolation	 of	

fluoreneofluorenes	 (FF)83,94	 and	 eventually	 by	 n=4	 to	 diarenoanthracene	 (Dian).95,96	 The	

most	notable	impact	of	𝜋-extension	of	the	core	on	the	molecular	properties	is	the	increasing	

diradical	character	with	increased	core	conjugation	(relative	to	s-indacene	core	IFs),	which	

provided	 valuable	 insight	 about	 the	 antiaromatic-diradical	 continuum.	 The	 study	 (and	

further	synthetic	modification)97,98,99,100,68,101	of	extended	diradicaloid	scaffolds	based	on	the	

original	s-indacene	IF	core	is	essentially	a	separate	project	at	this	point	and	is	for	that	reason	

outside	 the	 scope	 of	 this	 discussion.102,103	 	𝜋-Extension	 of	 the	 peripheral	 aromatics	 from	

benzene	to	naphthalene,	had	some	minor	 impact	on	the	molecular	properties,	which	was	

attributed	 to	 the	change	 in	bond	order	along	 the	 fusion	bonds	of	 s-indacene.	Heterocycle	

incorporation	into	the	peripheral	aromatic	stabilizing	groups	has	by	far	in	a	way	been	the	

most	impactful	method	of	synthetic	modification	for	tuning	the	molecular	properties	of	this	

family	 of	 molecules.98,62	 I	 am	 skipping	 past	 several	 impressive	 projects	 that	 combined	

multiple	modifications	 (such	 as	𝜋-extended	 heterocycle	 peripheral	 aromatics).104,105	 The	

R

R
n

X

X

1
3

2

4

EtO O

OEtO OEtO

EtO O

2 Ar
Bpin

Ar

Ar

R

R
X

Y
O

O

Ar

Ar

Ar

Ar

R

R

R

R

1
2

(a)

(b) (c)



 

34 
 

 

impact	of	heterocycle	incorporation	is	dramatic	and	clearly	illustrated	by	the	breadth	of	NICS	

values	(representative	of	paratropic	ring	strength),	but	the	structure	property	relationships	

across	all	heterocycle-fused-s-indacene	has	yet	to	be	explained	(in	a	way	that	 includes	𝜋-

accepting	heteroatoms).106,62,81	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	



 

35 
 

 

CHAPTER	II	
HETEROCYCLE	FUSED	S-INDACENE	HYBRIDS	

	

The	 experimental	 work	 in	 this	 chapter	 was	 performed	 by	 Isabella	 S.	 Demachkie	 and	 is	

unpublished.	The	computational	work	in	this	chapter	was	performed	by	Dr.	Said	Jalifo	Jacobo	

with	the	help	of	Prof.	Judy	I.	Wu	and	is	unpublished.	This	chapter	was	written	by	me	with	

computational	assistance	from	Dr.	Said	Jalifo	Jacobo,	and	helpful	input	from	Brian	Diamond,	

Parker	Brodale,	and	Prof.	Chris	Hendon.			

2.1	Introduction	
	 Aromaticity	 is	 a	 fundamental	 concept	 in	 organic	 chemistry	 which	 explains	 the	

stability	of	benzene	and	other	molecules	with	4n+2	π-electrons	in	a	planar,	conjugated	ring.	

Initially	proposed	by	Ronald	Breslow	in	1965,	the	term	antiaromaticity	refers	to	a	class	of	

organic	molecules	with	4n	π-electrons	in	a	planar,	conjugated	ring.[1-4]	Antiaromaticity	is	the	

“opposite”	of	aromaticity	in	that	the	delocalized	ring	current	(in	an	applied	magnetic	field)	

is	 diatropic	 (clockwise)	 for	 aromatic	 molecules,	 and	 paratropic	 (counterclockwise)	 for	

antiaromatic	molecules.	Antiaromatic	molecules	are	fundamentally	interesting	because	they	

are	 extremely	 reactive	 in	 a	 unique	 way,	 are	 nearly	 impossible	 to	 isolate	 in	 their	

unsubstituted	form.	However,	significant	work	undertaken	by	various	groups	has	resulted	

in	a	library	of	aromatic-antiaromatic	hybrids	based	on	cyclobutadiene,107,108	pentalene,109–

111	and	indacene,40,112		among	others.	This	work	has	been	in	part,	motivated	by	the	molecular	

properties	 associated	 with	 antiaromatic	 molecules	 such	 as	 a	 small	 HOMO-LUMO	 gap,	

concomitant	 red-shifted	 absorption,	 amphoteric	 redox	 properties,	 and	 induced	

magnetism.113	These	properties	are	desirable	for	applications	in	organic	electronics	such	as	

organic	field	effect	transistors	(OFETs),	organic	photovoltaics	(OPVs),	and	organic	solar	cells	

(OSCs),	 among	 other	 potential	 future	 possibilities.	 They	 are	 fundamentally	 interesting	

because	 when	 fused	 between	 diatropic	 aromatic	 rings,	 a	 paratropic	 antiaromatic	 ring	

current	 is	 induced	 by	 polarization.	 The	 paratropic	 ring	 current	 is	 detectable	 by	 1H	NMR	

spectroscopy,	and	the	relative	strengths	of	the	ring	current	(in	isomers	of	the	same	aromatic-

antiaromatic-aromatic	system)	are	accurately	illustrated	by	NICS𝜋ZZ1.7	plots.21,30,93		



 

36 
 

 

	 The	strength	of	 the	 induced	paratropic	 ring	current	 can	be	 tuned	 through	organic	

synthesis.	The	Haley	lab	has	spent	the	last	15	years	systematically	synthetically	tuning	the	s-

indacene	 scaffold	 (and	 extended	 quinoidal	 analogs	 along	 the	 antiaromaticity-diradical	

character	 continuum	 (ADCC)).	 Tetra-iododo-dibenzo[a,g]s-indacene,	 first	 reported	 by	

Swager	and	coworkers	in	1994,	was	not	incredibly	stable,	but	provided	the	inspiration	and	

basis	 for	 tetrayne-indeno[1,2b]fluorene,	which	 is	reasonably	stable	and	 	was	reported	by	

Chase	 et	 al	 a	 short	 16	 years	 later.86,114	 There	 were	 other	 successful	 synthetic	 routes	

developed	in-between	the	two,	which	deserve	recognition,	but	are	omitted	for	brevity.	Over	

the	last	15	years,	the	Haley	lab	has	developed	a	synthetic	route	that	is	robust	and	adaptable	

enough	to	facilitate	a	systematic	study	of	the	structure	property	relationships	of	s-indacene	

through	an	isomeric	study	of	aryl-fused-s-indacene	hybrid	molecules.	For	an	in-depth	review	

of	 the	 various	 synthetic	 methods	 developed	 by	 the	 Haley	 lab,	 please	 refer	 to	 Gabrielle	

Warren’s	 dissertation.115	 The	 general	 synthesis	 is	 as	 follows:	Beginning	with	 diethyl	 2,5-	

dihaloterephthalate,	 two	 equivalents	 of	 arylboronic	 acids	 or	 arylboronate	 esters	 can	 be	

Suzuki	 cross-coupled	 either	 simultaneously	 or	 sequentially	 (to	 introduce	 asymmetry),	 to	

yield	 the	 diester	 intermediate.	 The	 diester	 is	 then	 saponified	 and	 then	 undergoes	 a	

subsequent	Friedel-Crafts	alkylation	or	(acylation	depending	on	coupling	partners)	to	form	

the	 dione.	 Following	 the	 ensuing	 lithiation	 addition,	 a	 tin-mediated	 reductive	

dearomatization	yields	the	antiaromatic	s-indacene-aromatic-hybrid	product	(Scheme	1).	

		
Scheme	1.	General	5	step	synthesis	for	s-indacene	derivatives	from	commercially	available	
starting	materials	
	

While	the	synthesis	is	robust,	the	purification	of	the	final	products	is	not	for	the	faint	of	heart.	

Organotin	 compounds	 (the	 inevitable	 biproducts	 and	 degradation	 products	 of	 the	 final	

 i. COCl2, DMF 
DCM, rt, N2 8 h

OEtO

EtO O

Y

X

L2Pd, K3PO4

Toluene, Water, 
110 °C, N2, 

12 h

Ar1
B(OR)2

Ar2
B(OR)2

EtO2C

CO2EtAr1

Ar2

EtOH, Water,
90 °C, 3 days

KOH

HO2C

CO2HAr1

Ar2

ii. AlCl3, DCM, 
N2, rt, 12 h

O

O

Ar1

Ar2 THF, -78 °C - rt, 
N2, 12 h

Li-R
Ar1

Ar2

HO R

HO R

Ar1

Ar2

R

R
Toluene

rt, N2, 12 h

SnCl2

1 2

3 4 5



 

37 
 

 

reaction)	 are	 notoriously	 toxic.	 Making	 cool	 molecules	 usually	 requires	 skill	 and	 strong	

reagents,	so	you	(usually)	get	to	pick	your	poison	and	how	many	times	you	poison	yourself.	

I	never	ran	mine	with	heat,	and	I	obsessively	cleaned	my	starting	material,	but	 increased	

exposure	 frequency	 is	 inherent	 to	 late-stage	 synthetic	 optimization	 projects.	 Despite	 the	

potential	health	risks,	 I	appreciate	 the	structural	diversity	of	 the	 library	of	molecules	 the	

synthetic	methodology	has	facilitated.	

	 Through	a	large	library	of	antiaromatic-hybrid	molecules,	physical	organic	intuition,	

topological	charge	 theory,	and	experimental	and	computational	data	 I	have	developed	an	

understanding	of	the	structure	property	relationships	of	molecules	on	the	ADCC.81,62,93,106It	

is	understood	that	all	the	molecular	properties	and	the	structure	are	all	one	thing	defined	by	

the	linear	combination	of	wave	functions	for	each	particle.	Structure	and	properties	are	just	

how	the	molecule	 interacts	with	different	 things,	so	 talking	about	 it	as	a	cause-and-effect	

relationship	is	silly	because	quantum	mechanics	is	real.	But	the	physical	organic	principals	

that	explain	reactivity	and	reaction	mechanisms	are	also	real.	It	all	fits	together,	so	it	really	

doesn’t	matter,	you	can	explain	it	both	ways.	

	

2.2	The	Heterocycle	Effect	
	 The	s-indacene	scaffold	can	be	tuned	through	2	major	methods,	tuning	by	addition	

and	 tuning	 through	 fusion.	Step	5	 (Scheme	1)	 is	 tolerant	of	a	variety	of	alkyl	and	phenyl	

lithiates.	116,117,118	The	reactivity	of	at	the	apical	carbons	requires	sterically	bulky	protecting	

groups,	 so	 mesityl-like	 R	 groups	 are	 most	 kinetically	 stabilizing,	 and	 TIPS	 ethynyl-like	

groups	facilitate	the	best	solid-state	packing	for	the	conducting	layer	of	organic	electronic	

devices.36,119	 Tuning	 by	 addition	 does	 not	 have	 a	 significant	 impact	 on	 the	 magnetic	 or	

electronic	molecular	properties,	other	than	fluorinated	phenyl	groups,	which	were	reported	

to	have	reduced	the	electrochemical	gap	by	up	to	0.2	eV.120	Tuning	through	fusion	described	

several	 different	 synthetic	modifications	 including	𝜋-extension	of	 the	 s-indacene	 core,	𝜋-

extension	 of	 peripheral	 aromatics,	 and	 the	 inclusion	 of	 heterocycles	 in	 the	 core	 and	

peripheral	 aromatics.	 The	 most	 effective	 of	 which	 is	 the	 fusion	 of	 heterocycles	 as	 the	

peripheral	 aromatics.	 The	 complete	 collection	 of	 benzoheterocycle-fused-s-indacenes	

published	by	the	Haley	lab,	can	be	seen	below	in	Figure	2.1.	The	defining	molecular	property	



 

38 
 

 

of	 antiaromatic	 molecules	 is	 the	 energetically	 destabilizing	 paratropic	 ring	 current.	 The	

relative	 strength	 of	 the	 ring	 current	 (antiaromatic	 character/antiaromaticity)	 can	 be	

approximated	by	the	shielding	effect	on	the	protons	on	the	periphery	of	the	ring	caused	by	

the	 ring	 current’s	 induced	 magnetic	 field.	 The	 shielding	 effect	 can	 be	 measured	

experimentally	by	1H	NMR	and	accurately	predicted	and	ranked	by	NICS	plots.	When	NICS	

plots	are	computed	at	B97-2/6-311+G**//M11/6-311+G**73,93	

Figure	2.1.	 All	 14	 reported	benzoheterocycle-fused-s-indacene	hybrids	 by	 the	Haley	 lab.	
Pink	brackets	highlight	the	symmetric	IDBTs	(1	and	2)	and	oxidized	IDBTS	analogs	(3	and	
4).	Green	brackets	highlight	the	asymmetric	IBFBTs	(7	-	10)	and	oxidized	IBFBTS	analogs	
(11	-	14).	

The	effect	of	the	fusion	orientation	heterocycles	(1-14)	on	the	antiaromatic	character	has	

been	partially	explained	with	reference	to	Gimarc’s	rule	of	topological	charge	stabilization,	

which	can	be	summarized	as:	In	a	non-isoelectronic	structure,	there	is	a	preferred	(lowest	

energy)	arrangement	of	 topological	 charge.121	Natural	population	analysis	 (NPA)	 charges	

provided	by	the	Wu	group	in	a	collaborative	publications	with	the	Haley	lab	reported	the	

points	of	highest	topological	charge	are	at	2	and	6	positions	of	s-indacene.62,79	The	original	

NPA	calculations	of	the	IDBT	(1	and	2)	and	IDBF	(5	and	6)	suggested	that	the	syn-fusion	(for	

this	subset)	was	more	destabilizing	because	it	enforced	a	less	negative	partial	charge	on	the	

2	and	6	carbons	of	the	s-indacene	core,	which	agreed	with	the	experimental	data	and	NICS	

calculations	 for	 all	 four	 molecules.	 It	 was	 thought	 that	 the	 syn-IDBF	 (5)	 was	 more	

destabilizing	 than	 the	 syn-IDBT(1)	 because	 oxygen	 is	 a	 better	 donor	 than	 sulfur	 due	 to	

O

S

R

RS

O R

R

O

S

R

R

7 109

S

O

R

R

8

O

S

R

RS

O R

R

O

S

R

R

11 1413

S

O

R

R

12

O O

O
O

O
O

O
O

S

S

R

RS

S R

R

1 2

S

S

R

RS

S R

R

3 4

O O

O O

O
O

O
O

O

O

R

R

O

O R

R

5

6

[O] [O]



 

39 
 

 

atomic	size	and	orbital	alignment	with	sp2	hybridized	carbon	atoms.	Everything	was	great	

and	made	sense	until	Justin	oxidized	the	IDBTs.	The	IDBTSs	(3	and	4)	flipped	trend	in	fusion	

orientation	 effect	 and	 made	 no	 sense	 with	 the	 topological	 charge	 rational.	 The	

benzothiophene-S,S-dioxide	heterocycles	should	be	less	donating	than	benzothiophene,	so	

the	IDBTSs	should	have	just	had	less	antiaromatic	character	than	the	IDBTs	but	the	reason	

for	the	trend	reversal	written	off	as	“being	dominated	by	the	clar-sextet	effect”.79In	a	more	

recent	computational	study,	Warren	et.	al.,	explain	that	when	fused	in	the	syn	orientation,	

O,S,	 and	 N-containing	 heterocycles	 follow	 a	 trend	 of	 increasing	 paratropic	 ring	 current	

strength	(antiaromaticity)	with	increasing	donor	strength	(N>O>S).	With	𝜋-extension	of	the	

peripheral	 benzenes	 of	 the	 fused	 heterocycles,	 the	 strength	 of	 the	 donor	 effect	 of	 the	

heteroatoms	decreases.106		 Elaborating	 on	 this	 explanation,	 I	 would	 agree	 that	 the	 syn-

fusion	of	heterocycles	to	the	s-indacene	core	are	better	oriented	to	donate,	but	I	would	add	

that	 the	anti-fusion	 of	 the	 same	heterocycle	 is	 better	 oriented	 to	withdraw	 from/donate	

holes	to	the	paratropic	ring	current,	because	the	current	it	directional.	Electrons	and	holes	

each	flow	in	one	direction,	so	depending	on	whether	electrons	or	holes	are	being	donated,	

either	 the	 syn	 or	 anti	 fusion	 orientation	 accelerates	 the	 ring	 current.	 Strong	 𝜋-donors	

primarily	donate	 electron	density,	 regardless	 of	 fusion,	 and	 strong	𝜋-acceptors	primarily	

withdraw	electron	density	(donate	holes),	regardless	of	fusion	orientation.	These	structure	

property	 relationships	 are	 depicted	 by	 calculated	 benzocyclopentadiene-anion-fused-s-	

indacenes	(isoelectronic	analogs,	IDCPDAs	19,	20)			

HN

NH

R

R
H
N

N
H

R

R

23 24

HB

BH

R

R
H
B

B
H

R

R

25 26

HC

CH

R

R
H
C

C
H

R

R

21 22

HC

CH

R

R
H
C

C
H

R

R

19 20



 

40 
 

 

Figure	2.2.	Top	row,	 imaginary	 isoelectronic	analogs	 left	 to	right;	syn-IDCPDA	(19),	anti-
IDCPDA	 (20),	 syn-IDCPDC	 (21),	 anti-IDCPDC	 (22).	 Bottom	 row	 left	 to	 right;	 unreported	
indole-fused	 s-indacenes	 syn-IDI	 (23),	 anti-IDI	 (24),	 and	 imaginary	 borole-fused-s-
indacenes	syn-IDB	(25),	anti-IDB	(26).	

indacenes	 (isoelectronic	 analogs,	 IDCPDAs	 19,	 20)	 for	 the	 𝜋-donating-heterocycle-fused	

molecules	 (1,2,5,6,7-10,	23	 and	24),	 and	benzocyclopentadiene-cation-fused-s-indacenes	

(isoelectronic	 analogs,	 IDCPDCs	21,	22)	 for	 the	𝜋-accepting-heterocycle-fused	molecules	

(3,4,	11-14,	25	and	26)	seen	above	in	Figure	2.2.		

	 The	impact	of	these	effects	on	the	ring	current	are	illustrated	by	the	Gauge-Including	

Magnetically	Induced	Current	(GIMIC)	plots,	NICS(1)zz		ring	values,	and	Natural	Population	

Analysis	(NPA)	backed	resonance	structures	below	(Figure	2.3e).	

	

Figure	2.3.	(a)	GIMIC	plots	of	𝜋-donating	isoelectronic	analogs	(syn-IDBCH-	and	anti-IDBCH-
)	and	(b)	GIMIC	plots	of	𝜋-accepting	isoelectronic	analogs	(syn-IDBCH+	and	anti-IDBCH+)	
computed	at	M11/6-311G**	level	of	theory.	(c)	NICS(1)zz	values	of	𝜋-donating	isoelectronic	
analogs	and	(d)	s-indacene	and	(e)	𝜋-accepting	isoelectronic	analogs	computed	at	the	B97-
2/6-311+G(d,p)	 level	 of	 theory	 based	 on	 M11/6-311+G**	 optimized	 structures,	 with	
resonance	 structures	 supported	 by	 NPA	 calculations.	 𝜋-Electron	 density	 at	 the	 2	 and	 6	
carbons	in	(c),	(d),	and	(e)	are	calculated	using	extended	Hückel	theory.		

GIMIC	plots	 generated	 using	M11/6-311G**	 geometry	 optimized	 structures,	which	when	

placed	in	an	integration	plane,	produce	directional	current	flow	to	the	left	or	right	of	each	

(a)

(b)

(c)

(e)

(d)



 

41 
 

 

grid	point.	Because	tropicity	is	a	non-local	property,	and	every	molecule	with	a	ring	current	

contains	a	paratropic	(negative	by	convention)	and	diatropic	(positive	by	convention),	the	

streamlines	(spaghetti	plots	which	are	the	basis	of	the	GIMIC	plots)	illustrate	the	dominant	

current.122	 Syn-fusion	 of	 CH-	 induces	 the	 strongest	 paratropic	 ring	 current	 (ring	 A	 NICS	

value)	in	the	s-indacene	core,	followed	by	anti-fusion	of	CH-,	followed	by	anti-fusion	of	CH+,	

then	finally	syn-fusion	of	CH+.	Fusion	of	CH-	(𝜋-donors)	donates	electron	density	to	the	s-

indacene	core,	accelerating	the	paratropic	ring	current.	The	effect	is	stronger	in	the	syn-fused	

orientation	 and	weaker	 in	 the	anti-fused	 orientation,	which	 can	 be	 rationalized	with	 the	

ideas	of	linear	vs	cross	conjugation	for	𝜋-donating	heterocycles	and	arrow	pushing	rational	

proposed	by	Warren	 et.	 al.98	 Conversely,	anti-fusion	of	 CH+	 (𝜋-withdrawing/hole-donor)	

accelerates	and	globalizes	the	ring	current,	which	is	backed	by	the	NPA-generated	resonance	

structure	(Figure	2.3e)	and	highly	negative	NICS	value	for	ring	A.	Syn-fusion	of	CH+	results	

in	localized	ring	current	on	the	5-membered	ring	of	the	heterocycle	(to	stabilize	the	positive	

charge),	which	reduces	ring	current	strength	of	 the	s-indacene	core.	NICS(1)zz	values	 for	

rings	 A	 and	 B	 are	 interpreted	 as	 ring	 current	 strength,	where	 positive	 values	 indicate	 a	

paratropic	 ring	 current	 and	 negative	 values	 indicate	 a	 diatropic	 ring	 current,	 with	

unsubstituted	s-indacene	for	reference	(Figure	2.3d).	The	𝜋-Electron	density	at	the	2	and	6	

carbons	in	(c),	(d),	and	(e)	relates	to	a	topological	charge	stabilization	argument	discussed	

further	in	the	following	section.	

2.3	The	Donor-Acceptor	Topological	Charge	Argument	
	 The	 difference	 in	 fusion-dependent	 magnetic	 property	 trends	 for	 the	 𝜋-donating	

heterocycle-fused	s-indacene	derivatives	is	explained	by	an	arrow	pushing	and	resonance	

structure	rational,	but	the	effects	of	the	𝜋-withdrawing/hole-donating	heterocycle-fused	s-

indacene	 derivatives	 are	 not.	 Both	 can	 be	 explained	 by	 applying	 donor/acceptor	

assignments	to	the	s-indacene	core	and	both	peripheral	heterocycles,	in	combination	with	

the	 rules	 of	 topological	 charge	 stabilization.	 The	 symmetrically	 fused	 𝜋-donating	

heterocycles	 act	 as	donors,	 and	 the	 s-indacene-core	 acts	 as	 an	 acceptor	 in	 a	D-A-D	 triad.	

Increased	 electron	 density	 (donated	 by	 the	 heterocycles)	 is	 pulled	 by	 the	𝜋-accepting	 s-

indacene	 core	 toward	 it’s	 points	 of	 preferred	 highest	 topological	 charge	 (C2	 and	 C6	



 

42 
 

 

positions).	When	the	𝜋-donating	heterocycles	are	syn-fused,	the	preferred	topological	charge	

arrangement	 for	 s-indacene	 is	 obstructed	 by	 the	 topological	 charge	 preferences	 of	 the	

heterocycle,	increasing	the	strength	of	the	paratropic	(counterclockwise)	current	toward	the	

C2	 and	C6	positions	 of	 s-indacene.	When	 the	𝜋-donating	 heterocycles	 are	 fused	anti,	 the	

preferred	topological	charge	arrangement	for	s-indacene	is	enforced,	which	does	not	induce	

a	pull,	and	is	relatively	stabilizing.	The	symmetrically	fused	𝜋-accepting	heterocycles	act	as	

acceptors,	and	the	s-indacene-core	acts	as	a	donor	in	a	A-D-A	triad.	When	the	𝜋-accepting	

heterocycles	are	syn-fused,	the	preferred	topological	charge	arrangement	for	s-indacene	is	

obstructed	by	the	topological	charge	preferences	of	the	heterocycle,	but	the	reversed	bond	

dipole	between	the	heteroatom	and	C2/6	atom	pulls	electron	density	from	the	s-indacene	

ring	current	decreasing	the	strength	of	the	paratropic	(counterclockwise)	current.	When	the	

𝜋-accepting	heterocycles	are	anti-fused,	the	preferred	topological	charge	arrangement	for	s-

indacene	 is	 enforced	 by	 the	 topological	 charge	 preferences	 of	 the	 heterocycle,	 but	 the	

reversed	bond	dipole	between	the	heteroatom	donates	holes	to	the	s-indacene	ring	current	

increasing	the	strength	of	the	diatropic	(clockwise)	current	(Figure	2.4).		

Figure	 2.4.	 (a)	 and	 (b)	 Topological	 charge	 points	 of	 high	 electron	 density	 (C2/6	 of	 s-
indacene)	are	marked	with	black	circles,	syn-fusion	are	highlighted	in	green	and	anti-fusions	
are	highlighted	in	green,	and	bond	dipoles	represented	by	arrows	to	and	from	𝜋-donor	and	
acceptor	heteroatoms.	(c)	Top,	syn-fusion	of		𝜋-donor	heterocycles	result	in	an	antiaromatic	
resonance	 structure.	 Bottom,	 anti-fusion	 of	 	 𝜋-donor	 heterocycles	 result	 in	 an	 aromatic	
resonance	structure.	(d)	Top,	syn-fusion	of		𝜋-acceptor	heterocycles	result	in	an	antiaromatic	
resonance	structure	with	electron	deficient	s-indacene	core.	Bottom,	anti-fusion	of		𝜋-donor	
heterocycles	result	in	a	globally	antiaromatic	resonance	structure	with	double	fulvalene-like	
rings.	
	

D

D

Mes

Mes

D

D Mes

Mes

D

D
Mes

Mes
D

D

Mes

Mes

A

A

Mes

Mes

A

A Mes

Mes

A

A
Mes

Mes
A

A

Mes

Mes

D D A A

(a)

(c)

(b)

(d)



 

43 
 

 

	 The	proposed	arrow	pushing	and	resulting	resonance	structures	for	the	𝜋-donating	

heterocycles	above	and	those	found	in	the	computational	study	by	Warren	et.	al	both	agree	

with	 previously	 published	 experimental	 and	 computational	 results	 (for	 1,	 2,	 5,	 6)	 and	

unpublished	 results	 for	19	and	20.	 However,	 the	 above	 proposed	 rationalizations	 above	

differ	in	that	they	include	donation	from	both	heteroatoms	to	the	core	in	a	D-A-D	triad,	are	

backed	by	Gimarc’s	rule	of	topological	charge	stabilization,	GIMIC	plots,	and	calculations	of	

𝜋-electron	 density	 at	 C2/6	 using	 extended	 Hückel	 theory	 (Figure	 2.3).	 Additionally,	 this	

expansion	 includes	 the	𝜋-accepting	 heterocycles	 and	 can	 be	 extrapolated	 to	 include	 the	

asymmetric	 heterocycle-fused-s-indacene	 derivatives	 (7-14)	 as	 well	 (Figure	 2.6).	 A	 final	

argument	 in	 favor	of	 this	 expanded	 rational	 is	provided	by	 further	 arrow	pushing	of	 the	

resonance	 structures	 for	 the	 .𝜋-accepting	 heterocycles	 to	 the	 “bond-flipped”	 structures	

found	 in	 the	 crystal	XRD	data	 for	3	 and	4,	 and	geometry	optimizations	of	11-14	 (Figure	

2.5).79,123	

Figure	2.5.	Arrow	pushing	through	to	bond-localized	ground	state	structures	reflected	in	
the	 previously	 published	 data	 for	 all	 s-indacene	 derivatives	 with	 fused	 𝜋-acceptor	
heterocycles,	(a)	syn-fusion	and	(b)	anti-fusion.	
	
	 To	quote	Gimarc,	“From	a	pattern	of	charge	densities	once	can	see	immediately	what	

is	 favorable	 of	 destabilizing	 about	 a	 particular	 arrangement	 of	 atoms.”	 The	 resonance	

structures	 from	 the	 initial	 arrow	 push	 (Figures	 2.4	 and	 2.5)	 are	 representative	 of	 the	

delocalized	excited	state,	and	reflect	the	ring	current	densities	depicted	in	the	GIMIC	plots	

because	 the	 delocalized	 (antiaromatic)	 state	 is	 stabilized	 by	 a	magnetic	 field.	𝜋-Electron	

density	at	the	2	and	6	carbons	(C2/6)	calculated	using	extended	Hückel	theory,	can	be	used	

to	 explain	 the	 relative	 strength	 of	 each	 fusion	 type	 and	 donor	 type.	 Syn-fusion	 of	 the	𝜋-

donating	heterocycles	opposes	the	preferred	topological	charge	arrangement	for	s-indacene,	

which	destabilizes	the	molecule	and	increases	the	strength	of	the	paratropic	ring	current	in	

A

A

Mes

Mes

A

A Mes

Mes

A

A
Mes

Mes
A

A

Mes

Mes

A

A

Mes

Mes

A

A
Mes

Mes

(a)

(b)



 

44 
 

 

the	delocalized	state.	The	negative	charge	preferentially	held	at	C2/6	by	native	s-indacene	is	

decreased	(opposed)	by	the	syn-fusion	of		𝜋-donating	heterocycles	in	order	with	donating	

character	 (N>O>CH->S),	 and	 increased	 (enforced)	 by	 the	 anti-fusion	 of	 𝜋-donating	

heterocycles	 in	 order	 with	 electronegativity	 (O>N>S>CH-)	 (Figure	 S34,	 appendix).	 The	

negative	 charge	 preferentially	 held	 at	 held	 at	 C2/6	 by	 native	 s-indacene	 is	 decreased	

(opposed)	by	 the	 syn-fusion	 and	anti-fusion	of	𝜋-accepting	heterocycles	 in	order	with	𝜋-

accepting	ability.	CH+	is	the	strongest	𝜋-acceptor	with	a	formal	positive	charge,	followed	by	

BH	with	an	empty	p-orbital	and	trigonal	planar	geometry	(well	situated	to	withdraw	from	

the	 sp2	 hybridized	 carbons).	 SO2	 is	 the	weakest	𝜋-acceptor	 because	 it	 is	 larger	 than	 the	

carbon	 atoms	 and	 further	 bent	 out	 of	 orbital	 alignment	 with	 the	 planar	 ring	 by	 it’s	

tetrahedral	geometry.	These	statements	are	corroborated	by	previously	reported	NICS1.7𝜋zz	

calculations,	 which	 as	 previously	 mentioned,	 are	 representative	 of	 the	 pz	 orbital	

contributions	to	the	ring	current	and	magnetic	properties	of	the	molecules.	They	are	also	

reflected	in	the	NICS(1)zz	calculations,	which	include	more	of	the	sigma	contributions,	which	

is	relevant	because	inductive	effects	occur	through	sigma	bonds.		



 

45 
 

 

	 The	 arrow	 pushing	 rational	 for	 the	 donor-acceptor-fused-s-indacenes	 (11-14)	 in	

seen	below	in	Figure	2.6,	can	be	related	to	bipolar	junction	transistors	through	a	figurative	

analogy.	The	relative	energy	levels	of	the	calculated	HOMO	(𝜋-electron	donation)	and	LUMO	

(𝜋-electron	accepting)	for	the	heterocycles	and	s-indacene	core	can	be	thought	of	as	a	

	Figure	2.6.	(a)	syn-syn	IBFBTS	(11)	has	the	least	favorable	zwitterionic	resonance	structure	
with	the	negative	charge	localized	on	the	apical	carbon	because	the	alternative	is	to	break	
the	aromaticity	of	the	outer	benzene	ring	on	the	sulfone	side.	(b)	syn-anti	IBFBTS	(12),	and	
(c)	anti-syn	IBFBTS	(13).	(d)	anti-anti	IBFBTS	(14)	passes	through	the	most	favorable	center	
zwitterionic	resonance	structure.	The	right	most	resonance	structure	for	all	four	isomers	is	
reflected	in	the	bond	length	alternation	calculations	found	in	the	appendix.	Syn-fusions	are	
highlighted	in	green,	and	anti-fusions	are	highlighted	in	pink.		
	
potential	energy	gradient	in	across	a	transistor.	In	this	analogy,	the	donor	heterocycle	is		

always	syn-fused	and	 it	donates	 from	the	HOMO,	 the	acceptor	heterocycle	 is	always	anti-

fused,	 and	 accepts	 from	 the	 LUMO.	 The	 s-indacene	 core	 is	 either	 a	 donor	 or	 acceptor	

depending	on	the	fusion	of	the	heterocycles,	so	11	is	a	D-A-D	triad	from	the	furan	to	sulfone,	

12	is	a	D-A-A,	13	is	A-D-D,	and	14	is	A-D-A.		

(a)

(b)

(c)

(d)

SO

Mes

Mes

O
O

S

O

Mes

Mes

OO
S

O

OO

O S

Mes

Mes

O
O

Mes

Mes

O S

Mes

Mes

O O
SO
OO

Mes

Mes

S

O

OO

Mes

Mes

S

O

Mes

Mes

O
O S

O
Mes

Mes O
O

O S

Mes

Mes

O O

SO

Mes

Mes

O
O

S

O

Mes

Mes

OO



 

46 
 

 

	 The	 transistor	 analogy	would	 be	11	 as	 a	N-P-N	 junction,	with	 a	 steeper	 potential	

energy	gradient	on	one	side,	but	would	not	transfer	charge	well	from	N	to	N.	12	would	be	a	

N-P	junction	with	a	constant	negative	potential	gradient	and	would	transfer	charge	well	from	

N	to	P.	13	would	be	a	reversible	P-N	junction,	and	would	transfer	charge	well	if	the	sulfone	

could	𝜋-donate	(increased	e-	doping	of	the	N,	or	increased	hole	doping	of	the	P	side).	There	

is	some	experimental	evidence	to	suggest	charge	transfer	is	induced	with	the	addition	of	acid	

or	water	in	DMF	for	13.	Addition	water	could	provide	additional	electron	density	to	the	syn-

fused	sulfone	through	dipole-dipole	interactions	(additional	e-	doping	of	the	N	side	of	the	

junction),	facilitating	charge	transfer	from	the	core	to	the	furan	side,	which	is	stabilized	by	

hydrogen	 bonding	 between	 the	 oxygen	 of	 the	 furan	 moiety	 and	 water	 (additional	 hole	

doping	of	the	P	side).	Addition	of	acid	in	this	analogy	would	be	reversing	the	P	and	N	sides	

of	the	junction.	Hole	doping	of	the	formerly	N	side	(syn-fused	sulfone)	to	induce	e-	donation	

from	the	 formerly	P	side	of	 the	 junction	 (anti-fused	 furan)	 facilitates	 inductive	withdraw	

stabilized	by	H+	in	solution	at	the	partial	negative	charge	on	the	oxygen	atom	of	the	sulfone	

(Figure	2.7).		

Figure	2.7.	(a)	addition	of	formic	acid	in	DMF	induces	a	solvatochromic	shift,	reminiscent	of	
those	in	12	and	14.	(b)	addition	of	water	in	DMF	induces	a	bathochromic	shift,	presumably	
in	the	opposite	direction	across	the	molecule	(sulfone	to	furan).	
	
14	would	be	a	P-N-P	junction,	with	a	steeper	potential	energy	gradient	to	one	side,	which	

could	 induce	 a	 steady	 gradient	 from	 P	 to	 P.	 This	 analogy	 is	 reasonable	 because	 the	

amphoteric	 redox	 properties	 of	 s-indacene	 based	molecules	 imply	 the	 core	 could	 act	 as	

either	a	donor	(N-type)	or	acceptor	(P-type),	but	the	trend	of	decreasing	reduction	potentials	

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

300 400 500 600 700 800

N
or

m
al

iz
ed

 A
bs

or
ba

nc
e 

(a
.u

.)

Wavenumber (nm)

40 uL AS Sulfone

+ 10uL acid

+ 50 uL acid

+ 90 uL acid

+ 150 uL acid

+ 200 uL acid

+ 300 uL acid

+ 400 uL acid

+ 500 uL acid

+ 600 uL acid

+ 700 uL acid

+ 800 uL acid

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

300 400 500 600 700 800

N
or

m
al

iz
ed

 A
bs

or
ba

nc
e 

(a
.u

.)

Wavenumber (nm)

70 uL AS Sulfone

+ 10 uL di water

+ 50 uL di water

+ 100 uL di water

+ 200 uL di water

+ 300 uL di water

+ 400 uL di water

+ 500 uL di water

+ 600 uL di water

+ 800 uL di water

+ 1000 uL di water

SO

Mes

Mes

O
O

O S
O

O

Mes

Mes HH(a) (b)
SO

Mes

Mes

O
O

SO

Mes

Mes

O
O

HO
HOH2

OH2 OH2



 

47 
 

 

with	increasing	antiaromaticity	imply	they	are	better	acceptors	than	donors.	This	offers	a	

possible	 explanation	 for	 the	 lack	 of	 charge	 transfer	 observed	 in	11,	 if	 the	 N	 part	 of	 the	

junction	 offers	 a	 local	 energy	 well	 (strong	 binding	 energy)	 charge	 donated	 from	 the	

heterocycles	 will	 collect	 in	 the	 core	 instead	 of	 transferring	 across	 the	 molecule.	 And	

rationalizes	the	strength	of	the	charge	transfer	observed	in	14	(along	with	the	pro-aromatic	

resonance	structure),	which	has	an	anti-fused	(withdrawing	in	the	analogy)	donor	moiety.	

The	remainder	of	the	experimentally	observed	properties	of	these	molecules	(11-14)	and	

their	 unoxidized	 asymmetric	 precursors	 (7-10)	 are	 discussed	 at	 length	 in	 the	 following	

chapter.	

	 If	we	think	about	structure	property	relationships	in	the	context	of	Hammett	values,	

we	could	think	of	it	as	a	cause-and-effect	relationship,	and	maybe	we	can	relate	all	of	this	to	

pKa	 values	 at	 some	 point	 in	 the	 future.	 If	 the	 defining	 characteristic	 of	 antiaromatic	

molecules	is	the	magnetic	properties	(paratropic	ring	current),	and	the	property	is	the	effect,	

then	the	structure	is	the	cause.		

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	

	



 

48 
 

 

CHAPTER	III	

DONOR/ACCEPTOR-FUSED-S-INDACENE	DERIVATIVES	

This	chapter	includes	previously	published	and	co-authored	materials	from	Demachkie,	I.	S.;	

Miller,	 M.	 P.;	 Warren,	 G.	 I.;	 Barker,	 J.	 E.;	 Strand,	 E.	 T.;	 Zakharov,	 L.	 N.;	 Haley,	 M.	 M.	

Intramolecular	Charge	Transfer	in	Antiaromatic	Donor/Acceptor-Fused	s-Indacenes.	Angew.	

Chem.	 Int.	 Ed.	 2024,	 e202420989.	 This	 manuscript	 was	 written	 by	 me	 with	 editorial	

assistance	from	Dr.	Josh	Barker,	Dr.	Gabrielle	Warren,	and	Prof.	Michael	M.	Haley.	The	project	

in	this	chapter	was	initially	conceived	by	Dr.	Josh	Barker.	The	synthetic	adaptation	to	make	

isolation	of	 the	 target	molecules	possible	 and	 investigative	methods	were	 conceived	 and	

carried	out	by	me,	along	with	the	entirety	of	published	and	unpublished	experimental	work.	

The	 computational	 work	 in	 this	 chapter	 was	 performed	 by	 Michael	 Miller	 and	 me,	

crystallographic	measurements	were	performed	by	Lev	N.	Zakharov.		

3.1	Introduction	

	 Antiaromaticity	refers	to	a	class	of	organic	molecules	with	4n	π-electrons	in	a	planar,	

conjugated	ring.24,25,124,125	s-Indacene	(12	π-electrons	in	a	planar,	conjugated	3-ring	scaffold)	

can	be	effectively	stabilized	through	aromatic	ring	fusion	to	the	outer	five-membered	rings,	

and	the	reactive	apical	carbons	can	be	kinetically	blocked	with	bulky	substituents.	A	general	

modification	 (oxidation).126	 Previous	 studies	 have	 incorporated	 heterocycles	

(benzothiophene,	 benzofuran)	 as	 part	 of	 the	 outer	 aromatic	 rings,	 e.g.,	 1-6	 (Figure	

3.1c).62,79,127	 By	 varying	 the	 fusion	 orientation	 (Figure	 3.1b)	 from	 anti-	 (where	 the	

heteroatom	is	fused	on	the	opposite	side	of	the	scaffold	from	the	apical	carbon	of	the	five-

membered	ring)	to	syn-	(where	the	heteroatom	is	on	the	same	side	as	the	apical	carbon),	we	

could	further	tune	molecular	properties	within	a	set	of	regioisomers.	synthetic	method	for	

s-indacene	 derivatives	 permits	 fine-tuning	 of	 molecular	 properties	 through	 early-stage	

(identity	 of	 the	 fused	 peripheral	 aromatics)	 or	 late-stage	 synthetic	 modification	

(oxidation).126	 Previous	 studies	 have	 incorporated	 heterocycles	 (benzothiophene,	

benzofuran)	as	part	of	the	outer	aromatic	rings,	e.g.,	1-6	(Figure	3.1c).62,79,127	By	varying	the	

fusion	orientation	(Figure	3.1b)	from	anti-	(where	the	heteroatom	is	fused	on	the	opposite	

side	of	 the	scaffold	 from	the	apical	carbon	of	 the	 five-membered	ring)	 to	 syn-	 (where	the	



 

49 
 

 

heteroatom	 is	 on	 the	 same	 side	 as	 the	 apical	 carbon),	 we	 could	 further	 tune	molecular	

properties	within	a	set	of	regioisomers.	

Figure	3.1.	(a)	Generic	and	abbreviated	s-indacene	retrosynthesis	for	tuning	by	fusion.	(b)	
Generic	 benzoheterocycle-fused	 s-indacene	 with	 labelled	 apical	 carbons;	 syn-fusion	 is	
highlighted	in	blue	and	anti-fusion	is	highlighted	in	red.	(c)	Previously	reported	symmetric	
benzoheterocycle-fused	s-indacenes.	
	

Many	of	the	same	properties	that	make	antiaromatic	compounds	attractive	for	organic	

electronics	are	also	associated	with	donor-acceptor	(D/A)	molecules.	Incorporation	of	D/A	

motifs	 is	 a	 popular	 design	 strategy	 in	 improving	 aromatic	 scaffolds	 for	 use	 in	 organic	

electronics	because	it	can	facilitate	intramolecular	charge	transfer	(ICT),128,129	which	is	the	

functional	 basis	 for	 many	 semiconducting	 and	 optoelectronic	 devices.130,131	 ICT	 is	 a	

fundamental	process	in	photochemistry	where	upon	excitation,	electron	density	flows	from	

a	donor	group	through	a	covalently	linked	s-	or	π-bridge	to	an	acceptor	group.132	ICT	results	

in	molecular	properties	such	as	an	extension	of	the	absorption	spectrum,	a	decrease	in	the	

HOMO-LUMO	energy	gap,	and	amphoteric	redox	behavior.	ICT	can	be	tuned	by	the	identity	

and	 strength	 of	 the	 donor	 and	 acceptor	 groups,	 the	 length	 of	 the	 π-bridge,	 bond	 length	

alternation	 in	 the	 π-bridge,	 and	 the	 ways	 in	 which	 the	 donor,	 bridge,	 and	 acceptor	 are	

connected.133,134	Conductivity	is	defined	as	the	ratio	of	current	density	in	a	material	to	the	

electric	 field.	 ICT	 is	 the	 flow	of	electron	density	 from	a	donor	group	through	a	covalently	

XX

R

R

apical carbon

apical carbon

Ar

Ar

R

R

EtO2C

CO2Et
Ar

Ar

X

X

X

XR

R

R

R

(a)

(b)

(c)

1: x = S, 3: x = SO2, 5: x = O 2: x = S, 4: x = SO2, 6: x = O



 

50 
 

 

linked	s-	 or	 π-bridge	 to	 an	 acceptor	 group	 within	 a	 molecule.	 The	 corrolation	 between	

antiaromaticity	 and	 conductivity	 has	 been	 investigated	 via	 single	 molecule	 conductance	

measurements	several	times	across	different	systems.	To	the	best	of	our	knowledge	this	is	

the	 first	 study	 that	 has	 been	 able	 to	 correlate	 increasing	 antiaromaticity	with	 increasing	

intramolecular	charge	transfer.		

Several	 groups	 have	 incorporated	 donor	 and/or	 acceptor	 groups	 onto	 antiaromatic	

scaffolds,	but	almost	always	as	either	a	D-A-D	or	A-D-A	 triad	with	 the	paratropic	core	as	

either	the	acceptor	or	donor	unit.135–141	Molecular	property	tuning	is	limited	to	the	identity	

of	the	donor	or	acceptor	groups,	and	evidence	of	ICT	has	been	weak.	Recently,	the	London	

group	appended	donor	and	acceptor	groups	on	two	 isomers	of	monobenzopentalene	and	

observed	some	evidence	of	donor-acceptor	character,	although	this	was	not	the	focus	of	the	

work.142	Das	and	co-workers	were	able	to	desymmetrize	an	indeno[2,1-c]fluorene	(IF)	with	

donor-	and	acceptor-functionalized	R	groups,	with	one	derivative	showing	modest	evidence	

of	 charge	 transfer	 (~10	 nm	 solvatochromic	 shift),	 which	 is	 noteworthy	 considering	 the	

limited	conjugation	between	the	planar	core	and	the	orthogonal	aryl	groups;	however,	the	

authors	 noted	 the	 synthesis	was	 difficult.143	To	 the	 best	 of	 our	 knowledge,	 there	 are	 no	

published	examples	of	antiaromatic	molecules	with	fused	donor	and	acceptor	groups.	

	 Recent	 studies	 focused	 on	 novel	 D/A	 aromatic	 topologies	 suggest	 electronic	

interactions	between	the	donor	and	acceptor	groups	may	be	greatly	enhanced	if	 they	are	

fused	coplanar	to	the	π-conjugated	bridge;	however,	such	structures	have	proven	elusive.[36]		

Figure	3.2.	Eight	new	unsymmetrical	benzoheterocycle-fused	s-indacenes,	IBFBTs	7-10	and	
IBFBTSs	11-14;	colored	5-membered	rings	denote	the	four	possible	substitution	patterns	of	
asymmetric	heterocycle	fusion	on	the	s-indacene	core	(green	syn-fusion,	pink	anti-fusion.	



 

51 
 

 

	 Herein,	we	report	the	synthesis	and	characterization	of	a	 family	of	unsymmetrical,	

antiaromatic	indacenobenzofuran-benzothiophenes	(IBFBTs	7-10,	Figure	3.2).	

Late-stage	oxidation	transforms	the	thiophene	into	an	acceptor	motif,	furnishing	all	four	D/A	

isomers	(IBFBTSs	11-14)	that,	depending	on	the	fusion	orientation	of	the	benzofuran	donor	

and	benzothiophene-S,S-dioxide	acceptor,	show	varying	degrees	of	antiaromaticity	and	ICT	

character.	The	previously	reported	sets	of	symmetric	benzoheterocycle-fused	s-indacenes	

(1-6)62,79,127	provide	standards	for	the	impact	of	each	heterocycle	and	its	fusion	orientation	

on	the	antiaromaticity	and	molecular	properties	of	the	s-indacene	scaffold,	thus	permitting	

a	thorough,	rationally	designed	study	of	desymmetrization	of	the	paratropic	s-indacene	core,	

as	well	as	any	interplay	between	antiaromaticity	and	ICT.	Notably,	analogous	studies	with	

benzoheterocycles	 fused	 to	 aromatic	 motifs	 such	 as	 naphthalene	 (10	 π-electrons)	 or	

anthracene	 (14	π-electrons),	most	 comparable	 to	 s-indacene,	have	not	been	 reported.	As	

Anthony	 showed	 in	 2004,	 creating	 heterocycle-fused	 acenes	 is	 a	 significant	 synthetic	

challenge,	as	the	double	Aldol	condensation	to	generate	the	eventual	anthracene	core	leads	

to	an	inseparable	syn/anti	mixture.144		While	Tykwinski	was	able	to	prepare	isomerically-

pure	 syn-thiophene145	 and	 syn-benzothiophene	 regioisomers,	 their	 syntheses	 were	

considerably	more	involved.145	 Importantly,	none	of	the	routes	are	amenable	to	installing	

different	 heterocycles	on	 either	 side	of	 the	 aromatic	 core,	 thus	highlighting	 the	precision	

synthetic	chemistry	used	to	construct	11-14.	

	

3.2	Results	and	Discussion	
3.2.1	Molecular	Design	and	Solid-State	Structures.		
	 The	synthesis	of	symmetric	IFs	and	their	benzoheterocycle	analogues	(1-6,	Figure	1a)	

typically	 begins	 with	 a	 Pd-mediated	 Suzuki	 cross-coupling	 of	 arylboronic	 acids	 or	

arylboronate	 esters	 to	 diethyl	 2,5-dibromoterephthalate.	 This	 modular	 route	 is	 readily	

adaptable	 to	 desymmetrization,	 as	 we	 previously	 disclosed	 using	 diethyl	 2-bromo-5-

chloroterephthalate	(19)	with	Pd(PPh3)4	as	the	catalyst	to	gain	regioselectivity	in	the	initial	

cross-coupling	 step	with	 phenylboronic	 acid.146	 For	 this	 current	 family	 of	molecules,	 the	

bromo/chloro	 reactivity	 difference	 in	 the	 initial	 oxidative	 addition	 step	 on	 19	 was	

insufficient,	as	a	small	amount	of	double-coupled	product	was	also	produced,	which	proved	

exceedingly	 difficult	 to	 separate	 from	 the	 desired	 mono-coupled	 material.	 Rather,	 the	



 

52 
 

 

revised	synthesis	(In	2)	begins	with	an	aromatic	Finkelstein	reaction	to	convert	19	to	the	

more	reactive	diethyl	2-chloro-5-iodoterephthalate	(20).	Suzuki	cross-coupling	with	either	

3-	 (15)	 or	 2-benzothiopheneboronic	 acid	 pinacolate	 ester	 (16)	 using	 third	 generation	

Buchwald	pre-catalyst	yielded	chlorides	21	and	22,	respectively,	with	no	evidence	of	double-

coupled	 material.	 Each	 chloride	 was	 then	 cross-coupled	 with	 3-benzofuranboronic	 acid	

pinacolate	 ester	 (17)	 or	 2-benzofuranboronic	 acid	 (18)	 to	 furnish	 diesters	 23-26	 in	

moderate	to	good	yields.	Each	diester	was	subsequently	saponified	and	subjected	to	Friedel-

Crafts	acylation	to	afford	the	poorly	soluble	diketones	27-30.	Nucleophilic	addition	of	the	

mesityl	units	to	each	dione	introduced	the	protecting	groups	for	the	apical	carbons,	followed	

by	 a	 SnCl2-mediated	 reductive	 dearomatization	 to	 give	 the	 four	 asymmetric	 IBFBT	

regioisomers	7-10.	Because	of	 the	 rapid	decomposition	of	anti-IDBF	6	 to	 its	 ring-opened	

form,62	we	were	unsure	of	 the	 stability	of	anti/anti-IBFBT	10;	 however,	 inclusion	of	 one	

benzothiophene	provides	a	stabilizing	effect.	All	four	parent	isomers	are	stable	for	months	

at	–20	°C	and	up	to	several	weeks	at	20	°C.	 IBFBTs	7-10	were	subsequently	subjected	to	

mCPBA	oxidation	to	yield	their	sulfone	analogues	(IBFBTSs)	11-14	in	modest	yields.	All	four	

sulfones	are	acid	sensitive,	which	is	partially	responsible	for	the	lowered	yields.	Similar	to	

anti-IDBF	6,	anti/anti-IBFBTS	14	began	to	decompose	upon	oxidation	and	is	extremely	acid	

sensitive,	 as	 the	 stabilizing	 effect	 of	 the	 thiophene	 in	 10	 is	 significantly	 reduced	 upon	

oxidation.	



 

53 
 

 

	

Scheme	2.	Synthesis	of	IBFBTs	7-10	and	late-stage	oxidation	to	IBFBTSs	11-14.	
	

Several	 groups	have	utilized	asymmetry	as	a	means	of	 creating	a	dipole	moment	and	

exploiting	this	property	to	influence	solubility,	solid-state	packing,	and	polarizability;147,148	

thus,	 we	 sought	 insight	 into	 the	 molecular	 structures	 of	 the	 asymmetric	 s-indacene	

derivatives	via	single-crystal	X-ray	diffraction	(XRD).	Slow	evaporation	of	a	CHCl3	solution	

of	10	gave	deep	violet	crystals,	whereas	layering	pentanes	over	CH2Cl2	provided	dark	blue	

crystals	of	8.	The	XRD	structure	of	10	(Figure	3.3a)	r