Solvated Fluorophore Dataset Notes¶

Solvents¶

Solvent	$\varepsilon_0$	$n$	$\alpha$	$\beta$	$\gamma\:(mN/m)$ $293.15K$	$\gamma\:(cal\cdot mol^{-1})$ $(mN/m\times 1.439)$	$\phi$	$\psi$	Price
N-Hexane	1.88	1.3749	0.00	0.00	18.35	26.41	0.00	0.00
Toluene	2.37	1.4969	0.00	0.14	27.94	40.21	0.86	0.00
Anisole	4.22	1.517	0.00	0.29	35.37	50.90	0.75	0.00
Diethyl ether	4.24	1.3473	0.00	0.41	17.15	24.68	0.00	0.00
$\ce{CH3Cl}$	4.71	1.4458	0.15	0.02	27.10	39.00	0.00	0.50
THF	7.43	1.4072	0.00	0.48	27.37	39.39	0.00	0.00	$150-240/L
DCM	8.93	1.4241	0.10	0.05	27.84	40.06	0.00	0.67
Ocanol	9.86	1.430	0.37	0.48	26.02	37.44	0.00	0.00	$100-190/L
EtOH	24.85	1.3614	0.37	0.48	22.28	32.06	0.00	0.00
ACN	35.69	1.3441	0.07	0.32	28.37	40.82	0.00	0.00
DMF	37.22	1.4305	0.00	0.74	36.73	52.85	0.00	0.00
DMSO	46.83	1.4793	0.00	0.88	43.36	62.40	0.00	0.00

There’s no point in doing water, since SMD uses its own parameters for it and apart from nile red, nothing will fluoresce in it.

Should we use octanol? I wanted a low dialectric, h-bonding solvent, but maybe Michelle’s comments suggest not to add more h-bonding solvents.

The Initial Proposed dataset¶

Fluorophore	Class	Other notes	Price
Rhodamine 6G	Rhodamine
Rhodamine 123(?)	Rhodamine
AlexaFluor 532	Rhodamine-like	In azide form
NDI (of some description)	NDI
Naphthalamide (of some description)	NDA
Prodan/	Prodan		Prodan $245/25mg
DAPI	DAPI	“Someone in bio will have some”	$128/10mg
FITC	Fluorescein	Can we just use fluorescein?	$66 USD/100mg
Coumarin 343/519	Coumarin
Texas Red	Rhodamine-like	“Alison will have some”	$256/5mg
Nile Red	Oxazine
BODIPY 493/503	BODIPY	Toby wants this to be investigated	$467/500mg
Merocyanine 540	Cyanine
Dansyl	Naphthalene	Which dansyl?	Hydrazine $68/250mg Amide $150/1g Chloride $160/1g
Azulene	Azulene	$S_2\to S_0$ emitter	$55/50mg

Indigo Carmine			$87/25g
Cascade Blue	Pyrene		$208/1g

After Consultation with Michelle¶

Notes form meeting

Suggestions to the dataset¶

Add quinones and anthroquinones,
Add aza-indole
Remove merocynainie
remove anything that can internally hydrogen bond and any solvents that will hydrogen bond
We Don’t want s1-s0 gap being too small - biradicals
Find species in the dataset that enolise - we don’t really want this
make sure there’s a few ct molecules, but not too many * [ ] Probably want a subset of CT molecules
Need to consider how much of the emisison state is populated

Suggestions for the process¶

Cluster continuum will remove some of the issues with h-bonding - “That would be more satisfactory”
For a benchmarking referecne, photoelectron spectra in gas phase to determine the $t_1 \to s_0$ gap
For casscf - basis set def2-tzvp
For dft - use cam-b3lyp - not too small of a basis set * Need to consider more roots. the errors are going to be much worse in higher roots. * This brings a bigger question - should we be comparing the WHOLE spectra, instead of just the lower states/0-0 transition * Probably need caspt2 results with casscf geoms

To read up on¶

Papers by jackerman
El-sayad rules
- The rate of intersystem crossing is relatively large if the radiationless transition involves a change of orbital type
  - e.g. $^1\pi,\pi^* \to ^3n,\pi^*$ is faster than $^1\pi,\pi^* \to ^3\pi,\pi^*$

Danny jacoman’s work benchmarking dft
Marco garavelli’s work

To investigate¶

Check the difference between wb97x-dx and wb97x

If I had a system…

I’d look at the structure and look and look at the solvent, and specifically use cluster continuum.
I’d look at molecules that don’t internally hydrogen bond
I’d use the best method I could, and if that’s not MR, I’d use a selection of DFT functionals
I’d then try to find the combination of method and solvation method that gives the best results.

We have regularly come to the conclusion that SMD does a good job and that wb97-xd does a decent job - if there’s no hydrogen bonding involved. ” I don’t believe for a moment in accurate quantitative”

The Revision Process:¶

Fluorophore	Internal/H-Bonding acceptor/donor	Protonation sites	$pK_a$	Do I want it
Rhodamine 6g				They seem to be non-fluorescent in their closed form though…
Rhodamine 123
Rhodamine 800				?
AlexaFluor 532				(Internal h-bonding)

NDI
Naphthalamide
Prodan		2?
DAPI		?	4.31	?
Coumarin 343/519		1-3
7-amino-4-methylcoumarin (coumarin 120)		1-2	3.37	?

Texas Red	→	many	many	(too many protonation states)
Nile Red		1	4.08
BODIPY 493/503	?
Dansyl Amide			4.63/9.97
Azulene		0
Indigo Carmine		2	12-13
Fluorescein				(cyclises)
FITC				(cyclises)
Merocyanine				(too many conformers)
Cascade Blue				(too many protonation states)

1-aminoanthroquinone		1		$76/100g
aza-indole			4.59	(complexes and tautiomerises) unless we only use aprotic solvents

anthracene?		0

Rejected¶

Fluorophore	Toby owns	Needs digging up	Needs purchasing	CT	Class	Other notes	Price
7-azaindole					indole		$47.80/1g

New Dataset¶

Fluorophore	Class	Other notes	Price
Rhodamine 800	Rhodamine		$216/250mg
NDI (of some description)	NDI
Naphthalamide (of some description)	NDA
Prodan	Prodan		$245/25mg
DAPI	DAPI	“Someone in bio will have some”	$128/10mg
Coumarin 153	Coumarin
Nile Red	Oxazine
BODIPY 493/503	BODIPY	Toby wants this to be investigated	$467/500mg
Dansyl Amide	Naphthalene		$150/1g
Azulene	Azulene	$S_2\to S_0$ emitter	$55/50mg
Indigo Carmine			$87/25g
1-aminoantrhaquinone	anthraquinone		$76.30/100g

Other option¶

Fluorophore	Toby owns	Needs digging up	Needs purchasing	Class	Other notes	Price
Anthracene				anthracene	Can see the fine structure, only soluble in low-polar solvents	$42.2/1g

Fluorophore Specific Notes¶

Notes of concern¶

Rhodamine 800
- Concentrations need to be kept low to prevent aggregation
- Seems to be poorly handled by TD-DFT, but I think this should be okay
- The $\ce{ClO4-}$ might have some chemical interactions that should lead us to exclude this species.
7-Azaindole
- Forms clusters in solution and tautomerises with any protic solvent facilitate it
BODIPY - all varieties and cyanine dyes (N-B-N, N-B-O and O-B-O)
- Have strong MR character from double-excitation that leaved the adiabaitc TD-DFT approach with large errors 0.3-0.5 eV

Finalised!¶

Fluorophore	Solvated Dataset	Gas Dataset	Class	$m$-diagnostic	$D_{CT}\:(\AA)$	$t\:(\AA)$
Azulene	Yes	Yes	Azulene	0.120	0.967	-0.859
Rhodamine 800	Yes	No	Xanthene	0.076	1.074	-0.436
1-aminoanthraquinone	Yes	No	Quinone	0.063	2.914	1.377
Coumarin 153	Yes	Yes	Coumarin	0.087	1.877	-0.271
Nile Red	Yes	No	Oxazine	0.078	1.592	-1.376
BODIPY 493/503	Yes	No	Cyanine	0.087	0.453	-0.941
N-propyl-4-hydroxyl-1,8-naphthalamide	Yes	No	Naphthalamide	0.071	0.626	-1.197
DAPI	Yes	No	Phenylindole	0.082	1.959	-1.249
Dansyl Amide	Yes	No	Dansyl	0.071	1.660	-0.087
Boron subphthalocyanine chloride	Yes	No	Cyanine	0.096	0.398	-1.830
α-Sexithiophene	Yes	No	Polymeric thiophene	0.079	0.002	-5.353
Rhodamine 575	No	Yes	Xanthene	0.050	0.741	-1.228
Fluorescein	No	Yes	Xanthene	0.074	3.756	2.358
8-methoxy-BODIPY	No	Yes	Cyanine	0.089	0.770	-1.209

Fluorophore	Price	Quantity	Shop	Item Number	Notes
Already have
Nile Red
Naphthalamide
Rhodamine 800	$170.10	250mg	Sigma	8370
Coumarin 153	$57.96	100mg	Sigma	546186
BODIPY 503	$368.10	500mg	Sigma	790389
Azulene	$44.01	50mg	Sigma	37879
1-aminoanthraquinone	$60.21	100g	Sigma	A39009
DAPI	$287.13	10mg	ThermoFisher	62247
Dansyl Amide	$117.90	1g	Sigma	218898
Boron subphthalocyanine chloride	$104.03	50mg	Biosynth	FB179000
α-Sexithiophene	$26 USD	100mg	TCI	S0504	?
Total	~$1248.31 AUD

Rejected species Types¶

Fluoresceins - internal cyclisation - require pH modification

Rejected species¶

7-azaindole
indigo species - Tautomerise freely and have a very high triplet yield

Rhodamine 800BODIPY 493/503Azulene1-aminoanthraquinone7-azaindole

It’s always depicted with the perchlorate ion, but I’m not sure if that’s significant for its fluorescence, or if it’s just the common counterion.

DOI: 10.1016/j.jlumin.2012.08.017

Has a relatively small stokes shift, with mostly two identifiable emission peaks though the tail extends all the way to 950 nm
Is VERY red
Φ of ~0.25 in ethanol

DOI: 10.1007/s11664-018-6367-6

Has a pretty small solvatochromic effect
Concentration dependent, with 23nm redshifting ocurring as aggregates form (mM or greater)

DOI: 10.1002/qua.25780

“Why the lowest electronic excitations of rhodamines are overestimated by time-dependent density functional theory”

They seem to have large double excitation character, even in their singlet states, so MR and highly correlated methods can capture this, but TD-DFT struggles a bit.
Has a “partial” CT character? (0.37e over 1.791Å)
Not entirely sure how much I trust all of this without using cLR/VEM though.

They used modest basis sets for their testing 6-31+G(d,p)
Haven’t specified integration grids, which makes me think they used the G09 default (pruned 75,302) which probably isn;t sufficient for all their functionals
Used the same B3LYP-D3 geom for all their functionals

DOI: 10.1007/s00894-022-05034-w

TD-DFT paper in water. B3PW91/6-31++G(d,p)/IEFPCM
Has an H-bonding site on the nitrile that needs attention

DOI: 10.1021/ct500775r DOI: 10.1021/ar500447q

In general, these seem to have double-excitation character in the lowest ES, making the adiabatic approximation of TD-DFT a big ask.
Not CT species
Very large Φ
Looks like have a large MR character
- Need either correlated or MR methods to model
- Might not be the most appropriate for a TD-DFT datadset

REALLY useful thesis on Azulene

DOI: 10.1016/0009-2614(74)85131-6

Has mostly single fluorescence ($s_2 \to s_0$) unless substituted
Energy gap between $s_2$ and $s_1$ is large enough that $s_2 \to s_2$ non-radiative relaxation is too slow to compete with $s_2 \to s_0$ fluorescence

10.1039/c5cp01826a

Conical intersection between $s_1$ and $s_0$
Small amounts of $S_1$ emission can be detected as $t_1 \to s_1 \to s_0$

DOI: 10.3390/ijms222111926

Both absorbance and emission are highly solvatochromic - large Stokes shifts
Φ decreases with increasing solvent polarity (0.15 in n-hexane to <0.03 in DMSO)
Charge Transfer species
Amine can either be twisted (TICT) or planar (PICT) - low energy barrier
Excited state intramolecular proton transfer not considered possible in $s_1$

Timing

560 ps fluorescence lifetime
4.7 ps vibrtational relaxation in the ICT state
150-180 ps ICT dynamics

DOI: 10.1021/acs.jpca.7b11675

CAM-B3LYP/6-31G(d,p) (no diffuse functions?)
LR IEF-PCM ACN

Results

Identified the $s_1$ state as the “crucial state”, as it’s the lowest optically allowed excited state with a “relatively large oscilaltor strength”
In the $s_1$ state, it looks like the amino group wants to be perpendicular to the rings of the molecule
In polar solvents, it looks like they quench emission by enhancing ISC from $s_1 \to t_2$. I’m guessing this is die to a competition between intramolecular H-bonding and solvent-solute H-bonding

<iframe style="width: 100%; height: 300px;" frameborder="0" src="https://embed.molview.org/v1/?mode=balls&cid=9222&bg=white"></iframe>

DOI: [10.1021/jp9630232](https://doi.org/10.1021/jp9630232)

* Forms clusters in solution with water and alcohols that have different $\lambda_{max}^{em}$
* Water will pronate this species... not sure if other solvents can do this, as it seems to be largely cluster-shape dependent

![Screenshot 2022-11-21 at 1.34.54 pm](Screenshot 2022-11-21 at 1.34.54 pm.png){class="center"}

Timing

* 910 ps fluorescence lifetime in water at pH=7

DOI: [10.1021/j100178a023](https://doi.org/10.1021/j100178a023)

* It also seemingly tautomerises when excited, so I think we should rule out this species unless we go for aprotic only solvents