2.1. Document parsing with OCR tools#
An important part of data extraction pipelines is often converting inputs into a form that the text-based pipelines can use.
In many cases, this conversion involves that image inputs (e.g., scans of a paper) must be converted into text. This involves multiple steps:
characters must be recognized, this is known as OCR (Optical Character Recognition),
the layout and reading order must be understood,
relevant blocks of text must be extracted, cleaned and combined.
In the past, this was often done using tools specialized for each of these steps (e.g., tesseract, LayoutParser). New tools such as nougat or marker, however, allow to perform the entire process end-to-end.
As an example we will demonstrate the conversion of a PDF to plain text that can be sent to an LLM using the docTR tool.
import matextract # noqa: F401
import os
from doctr.io import DocumentFile
from doctr.models import ocr_predictor
docTR internally uses different modules for text detection (identifying sequences of characters) and then text recognition (converting the detected elements to text).
def convert_pdf_with_doctr(pdf_path, det_arch="db_resnet50", reco_arch="crnn_vgg16_bn"):
model = ocr_predictor(det_arch=det_arch, reco_arch=reco_arch, pretrained=True)
model = ocr_predictor(pretrained=True)
# PDF
doc = DocumentFile.from_pdf(pdf_path)
# Analyze
result = model(doc)
return result.render()
As an example, the PDF downloaded in the data mining notebook was converted into markdown files.
pdf_dir = "../obtaining_data/PDFs"
specific_pdf_file = "10.26434_chemrxiv-2024-1l0sn.pdf"
# Check if the specific file exists in the directory
pdf_path = os.path.join(pdf_dir, specific_pdf_file)
text = convert_pdf_with_doctr(pdf_path)
print(text)
Linear Amine-Linked Oligo-BODIPYS: Convergent Access via
Sebastian H. Rôttger, [a] Lukas J. Patalag,o) Felix Hasenmaile,a Lukas Milbrandt,o) Burkhard
Buchwald-Hartwig Coupling
Butschke,cl Peter G. Jonesld] and Daniel B. Werz*la)
[a] S.H. Rôttger, Dr. F. Hasenmaile, Prof. Dr. D.B. Werz
Institute of Organic Chemistry
AlbertstraBe 21, 79104 Freiburg (Breisgau), Germany
E-mail: daniel. wer@chemeunltelbupde
[b] Dr. L. J. Patalag, L. Milbrandt
Technische Universitât Braunschweig
Institute of Organic Chemistry
Hagenring 30, 38106 Braunschweig, Germany
[c] Dr. B. Butschke
Abert.ludwgsUnkerstat Freiburg
Institute of Inorganic and Analytical Chemistry
AlbertstraBe 21, 79104 Freiburg (Breisgau), Germany
[d] Prof. Dr. P. G. Jones
Technische Universitât Braunschweig
Institute of Inorganic and. Analytical Chemistry
Hagenring 30, 38106 Braunschweig, Germany
DFG Cluster of Excellence livMats @FIT and Aber.uowgsUnversiat Freiburg
Abstract: A convergent route towards nitrogen-bridged BODIPY
oligomers has been developed. The synthetic key step is a
Buchwald-Hartwig cross-coupling reaction of an a-amino-
synthesis provide control of the oligomer size, but the facile
preparative procedure also enables easy access to this type of
dyes. Furthermore, functionalized examples were accessible via
Various BODIPY oligomer
pocbolag
BODIPY and the
brominated derivatives.
Introduction
halide.
respective
Not only does the selective
- - - EN
cooe
The family of BODIPY dyes, first reported in 1968 by Treibs and
Kreuzer,"l has gained major interest in research in the past
decades because of their fairly simple preparative access, their
flexibility in terms of possible modifications and their useful
properties such as outstanding attenuation coefficients and also
high fluorescence quantum yields.2) Hence, they are already
widely applied for imaging, e.g. as biomarkers for medical
purposes, and have also proven to be applicable in other fields,
for instance as various types of photosensitizers and organic light-
emitting diodes (OLEDs).3) Various types of oligo-BODIPYS have
already shown the capability to enhance such desirable
properties and thus have been the focus of much recent
preparative chemistry. Alkylene bridged or directly connected
BThiswork
symmetric & unsymmetric dimers
and
functionalized examples
BODIPYS have been known for several years (Figure 1A (top).141 Figure 1. A) Various C-C bridged (top) and heteroatom bridged (bottom)
BODIPY oligomers. B) Linearly amine-linked BODIPY oligomers (this work).
Residual substituents of the BODIPY core were omitted for clarity.
1
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These types of connectivity have also been converted to extended ANomenclature
m-systems by oxidative follow-up reactions, allowing a higher level
of conjugation and hence strong bathochromic shifts.5) The
installation of heteroatoms has however been a challenge for
some time. In 2014, Shinokubo et al. presented linearly connect a: Pyrrole substitution pattern
monomers through an azo-bridge at the B-position (Figure 1A Br:
(d).61 Linear connectivity at the a-position using heteroatoms DM (24-Dimethy-yrole): R'= R3= Me,R2= H Ar 4-BuPh:
such as sulfur has been achieved through a similarly iterative EDM GEny*24-dimelhypymol; R' R3 Me, R2=E Et
process by the groups of Hao and Jiao (Figure 1A (e).7
Furthermore, cyclic amine-linked oligo-BODIPYS have already tri: Trimer tet: Tetramer
been synthesized in a one-pot reaction in 2022 by Song et al., DPecurorsynlaess
utilizing Buchwald-Hartwig conditions (Figure 1A (0).181
We present a novel type of BODIPY oligomers, connected
via N-bridges in a linear fashion (Figure 1B). Utilizing both
symmetric and unsymmetric BODIPY monomers as building
blocks has paved the way to selectively synthesize oligomers with
various chain lengths. Both symmetric and unsymmetric dimers
were synthesized starting from unsymmetric mondfunctionalized
monomer units. Additionally, the chain length of these oligo-
BODIPYS was extended using the functionalized monomer Br-Ar-
R3
R2
31
F
a-b-c-d
b(monomers & dimers):
d (monomers only):
Substituent x
R Br, R2 R3= H meso-substitution (R")
T
c: Grade of oligomerization
mono: Monomer di; Dimer
1)n-BuLi, 2,6-dimethyl-
aniline, benzaldehyde 4-iso-butyl
Et0,rt,5h
HN. 2)imidazole, TBSCI
CH2Clz. r, 1h
TFA, 4-iso-butyl-
benzaldehyde CH2Cl.rt,24h
H IN
7: 68%
1)NBS, THF, -78 "C, 1h
2)DDQ, .-78 C thenr rt, 1h
3)PfNEt, BFxOEL2
CH2Cl. rt, 30min
o
NCS o
HN. THF, rt,3-7d HN
2: 529/R"- Ar)
1) M
R2
Me
5; R2=H H
6: R2=Et, POCI3
CH,Clyln-hexane (2:1)
0°Ct thenrt, 16h
2)NEls. BF,-OEl2
0°Ct then rt, 1h
Me
R2.
Me
DM-Me-mono-Ct 49%
DM-Ar-mono-CH EDM-Ar-mono-CH: 83% 91%
Pd(OAc),
(E)-BINAP Cs,CO3
PhMe, 80 "C,3-22h
3:559( (R" Me)
4: 56%(R" Ar)
mono-Br and the dimer Br-Ar-di
Results and Discussion
(Scheme 1).
In contrast to the aforementioned cyclic amine-linked examples, [8]
we have focused on selectively synthesizing open-chained
oligomers and addressing their specific properties. Variation of
the BODIPY core has been shown to have a considerable impact
on the respective reaction times and yields. To dimerize Br-Ar-mono-Br
selectively when forming the nitrogen bridge, monofunctionalized
a-chlorinated BODIPY monomers were used. The key step in
obtaining such unsymmetric BODIPYS (in contrast to the usual
mirror plane through the meso position and boron center) was a
Bischler-Napieralski type reaction of the respective chlorinated
acylpyrrole and alkylpyrrole, following an established procedure
developed by Dehaen and coworkers.9 Converting the a-chloro- C)Oligomerization
BODIPY into the respective amine and performing a Buchwald-
Hartwig coupling of both led to N-bridged BODIPY dimers, in
which alkylpyrroles such as 2,4-dimethylpyrrole (5) and
cryptopyrrole (6) serve as capping units on the BODIPY core.
Terminal a-brominated examples provide an option for further
versatile functionalization. During the investigation of meso
substitution patterns, the 4-iso-buty/phenyl moiety has been
shown to overcome solubility issues, while maintaining
crystallizability (albeit sometimes with disorder problems),
whereas dimer syntheses are made easier by an increasing level
of alkyl-substitution on the pyrrole motif. For a simplified overview
of the BODIPY scope, compounds are labeled according to the
systematic nomenclature shown in Scheme 1A.
The synthetic strategy began with pyrrole (1) for both kinds
of monomers. To obtain monochlorinated BODIPYs, it was first
converted into the respective 2-benzoylpyrrole 2 for the meso aryl
examples.10 TBS protection of the benzyl alcohol by- product in
the crude simplified the purification later on.1) This species and
2-acetylpyrrole were then chlorinated using NCS in THF at room
temperature to obtain a-chlorinated 2- -acylpyrroles 3 and 4.!12]
NH3(7 N in! MeOH)
60-C, 30r min- 7 d
R3 R"
R2. N
R' F B F NH2
DM-Me-mono-NH, 47%
DM-Ar-mono-NH, EDM-Ar-mono-NH, 58% 58%
Br-Ar-mono-NH, quant.
EDM-Ar-
mono-NH2 or
Br-Ar-
mono-NHz
Pd(OAc),
(H)-BINAP
PhMe, Cs,COs 80 *C,1-5h
38%
R"
R3
B. F
R
R1
DM-MelAr-di DM-Me-di: 30% 25%
Br-Ar- DM-Ar-di: EDM-Ar-di: 40% 68%
mono- Br
-Br-Ar-di: 44%
F-B
Ar
F
R3
R'
EDM-tri: Br-tri: 82% 5%
NH
d 0
Ar
8
I E e
R3
Aminated dilutedi in BODIPYS CH2Clz
- -
R
Ar.
Ar
HN
Br-tet: EDM-tet: 1.4% 55%
Scheme 1. A) Nomenclature for BODIPYS. B) Synthetic route towards
monomers. C) Oligomerization to dimers, trimers and tetramers.
2
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We preferred chlorination over the analogous bromination since thus causing one of the peripheral cores to be tilted by as much
the by-products were easier to separate from the desired as 29° with regard to the plane of the residual two units. Moreover,
products. To arrive finally at the monofunctionalized BODIPY one molecule of CH2Cl2 is adjacent to the cavity, indicating
monomers, acylpyrroles 3 and 4 were then converted with the hydrogen bonding to the BF2 units. Furthermore, the C-N-C bond
respective alkylpyrroles 5 and 6 in the presence of POCI3 in angles of the N-bridges range between 123° and 127°, showing
CHaCln-hexane (2:1), followed by the established procedure for deviation from the theoretical value of 120° for sp?-hybridized
BODIPY syntheses from the in situ formed dipyrrin using nitrogen. Within the resulting cavity, the minimum distance
triethylamine and BF3*OEt2, with yields up to 91% over 2 steps. between fluorine and the bridging nitrogen atom amounts to 2.9 A
To obtain higher oligomers, bisfunctionalized monomers had to and 3.4 A for the opposing BF2 units for the dimer. The trimer in
be synthesized prior to amination. For symmetrically comparison shows larger distances of the two closest fluorine
bisfunctionalized monomer Br-Ar-mono-Br, an excess of pyrrole atoms of two different BF2 groups (3.9 A) and as much as 5.2À
(1) was converted into dipyrromethane 7 using 4-iso- for the two peripheral BODIPY units (Figure 2C). For more details
butylbenzaldhyde with catalytic amounts of TFA in CH2Cl2 in 68% see the Supporting Information.
yield.13) Stepwise addition of NBS in small portions to a solution
of 7 in THF at -78 C for selective bromination, followed by A)
oxidation with DDQ, gave the crude dipyrrin, which was used in
the following step after filtration. The actual BODIPY synthesis
was subsequently conducted in a similar manner as for the
unsymmetric monomers. However, Pr2NEt was found to give
higher yields for less substituted dipyrrins. Thus, using this tertiary C)
amine base, in lieu of triethylamine, together with BF3-OEtz gave
Br-Ar-mono-Br in 38% yield over three steps. Bromination was
necessary in this case because the corresponding chlorinated
derivative of an a-amino-BODIPY showed no oligomerization
beyond the dimer under the same conditions. Additionally,
purification was not an obstacle, in contrast to the aforementioned
brominated acylpyrroles. Preparative details of the chlorinated
amino-BODIPY are given in the Supporting Information. The
respective d-amino-BODIPYS were then synthesized by stirring
halogenated BODIPYS in an ammonia solution in MeOH (7 N) in
a sealed tube at 60 oC to furnish the target compounds in up to
58% yieldf for chlorinated derivatives and even in quantitative yield
for the brominated example (Scheme 1B). For Buchwald- Hartwig
coupling of a-chloro- and a-amino-BODIPYS, one equivalent of D)
each was converted with Pd(OAc)2, (+)-BINAP and Cs2CO3 in
PhMe at 80 C.1141 Interestingly, the reaction times and yields
showed a trend of improvement with increasing level of
substitution of the BODIPY core with up to 68% yields. While
these dimer syntheses were straightforward by simply stirring all
of the components together, synthesis of Br-Ar-di required slow
addition of Br-Ar-mono-NH2 to a heated solution of the remaining
starting material was recovered. As for the dimers synthesized via
manner with the respective bromides (Br-Ar-di for EDM-
B)
)
reagents. Such a procedure ensured selectivity by maintaining an Figure 2. Molecular structures of DM-Me-di A) front view, B) top view andl EDM-
excess of Br-Ar-mono-Br to avoid further oligomerization. The tri C) front view and D) top view. Hydrogen atoms were omitted for clarity.
the chlorides, synthesis of trimers and tetramers was achieved in The photophysical behavior of the dimers shows a strong
tet), with a remarkable decrease of the reaction time. Throughout respective monomers (from AA max = 510 nm to 659 nm for the
the reaction of Br-Ar-mono-Br with EDM-Ar-mono-Bir, formation EDM examples) and also significantly increased attenuation
of the respective intermediate dimer was observed within coefficients 6 (Figure 3). An excerpt of the respective data is given
30 minutes, while full conversion took an additional 60 minutes. below (Table 1). The presence of a second absorption region at
It was possible to obtain crystals from the dimers and from approximately 500 nm (S2 state) indicates a Davydov splitting as
EDM-tri. For all dimers, the BODIPY cores are mutually slightly a result of an excitonic coupling process. The unusual double-
twisted (-12°, see Figure 2B). The small twist angle, however, peak shape may suggest some conformational instabilities. In this
implies a certain amount of conjugation through the central context, the absorption profile is expanded to three absorption
nitrogen atom. In contrast, EDM-tri shows a stronger deviation events at the trimer, corresponding to three excitonic states
from planarity, which is probably attributable to steric hindrance, excited at 752 nm (S1), 562 nm (S2), and 470 nm (S3),
reaction yielded 44% of the functionalized dimer, while 45% of the Ellipsoids correspond to 50% probability levels.
bathochromic shift of the main
same
band
absorption
compared to the
respectively. Notably, the S2 state exhibits the highest oscillator
3
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strength, attributed to the significant geometrical deviation from Table 1. Absorption and emission data of EDM- -BODIPYS.al
linearity, gradually leading to a helical superstructure for higher
homologs (Figure 4). This trend is accentuated for the tetramers,
where the absorption signature becomes intricate. However, the
intensified coiling in this case, where the terminal BODIPY units
start overlapping and thus forming a looped superstructure,
results in an exceptionally weak Si+-So excitation at 820 nm. The
remaining states of the exciton manifold are hardly assignable
because of the amount and overlap of absorption bands, yet they mono-NH2
are responsible for the absorptions at 633 nm and 521 nm. The
simulated through TDDFT computations and accurately mirrors
the experimentally observed absorption band intensities for all
oligomer species (Figure 4). The emission strength decreases
gradually along the oligomeric series. While the monomers exhibit
fluorescence quantum yields @F of up to 0.53 in CH2Cl2, these
tetramers, emission is hardly detectable (CPF << 0.01).
Compound AAmax AFmax 4PIcm-1 s[103 M- @
[nm] [nm]
510
534
881
525
539
495
659
cm-"'l
121
59
EDM-Ar-
mono-CI
EDM-Ar-
0.04
0.01
oscillator strength distribution of the exciton manifold was EDM-Ar-di 482, 510, 671
271 47,40, 134 0.01
EDM-tri 562, 757 778 357lb)
EDM-tet 521,633 n.d.Icl
97, 76
111,114
0.01
values decrease to QF < 0.01 for the dimer and trimer. For the [a] Absorption and emission spectra were recorded in solutions of CH2Cl2 at
room temperature. [b] AAmax is not responsible for AFmax. Stokes shift 40 was
calcd. using the respective 2Amax2. [c] Not detecteddetermined. Further
spectroscopic data is given in the Supporting Information.
The frontier orbitals of the oligomeric series integrate the lobe
patterns found for the monomeric building blocks. All BODIPY
units are characterized by an electron-depleted meso position at
the HOMO and also by the cyanine-like relocalization of electron
density to this position during excitation (Figure 4).
Cyclic voltammograms of amine-linked oligomers and the
respective monomers for the EDM-series are shown below
(Figure 5). In general, the larger the molecules, the easier the
oxidation; however, most of them are oxidized irreversibly. The
monomeric primary amine and the trimer show irreversible
oxidation, unlike the respective chloride and the dimer. However,
the chlorinated monomer has only one reversible reduction
potential at -1.28 V, whereas the dimer shows two reduction
150 - Absorption
EDM EDM- -Ar -Ar -mono-NH, mono-cI
EDMr EDM Ar-di
EDM- tet
100
50
Emissien
EDM EDM- -Ar-mono-NH, Ar mono-CI
EDM-Ar-di EDM-tri
450 500 550 600 650 700 750 800 850
Wavelength. AInm]
Figure 3. Absorption and emission spectra of EDM- BODIPYS. Absorption and potentials, at -1.25 V and at -1.64 V.
emission spectra were recorded in solutions of CH2Cl2 at room temperature.
Dimer
&
HOMO (-6.07 ev)
&
CDD S1
Trimer
Tetramer
LUMO (-2.04e evy
HOMO (5.85€ ev)
LUMO
(2.15ev]
HOMO (-5.71ev)
LUMO (2.20ev]
CDD S2
S1: 2.20eV(516nm) /f=1.11 S2: 3.046 ev (407 nm)/f=0.54
CDD_S2
(S1: 2154V57mm/F-02
CDD_ S3
CDD S2
S1:1 1.94eV/(641 inmy/f-0.080
CDD_
S2:2.75ev (451nm)/f=1.45 $3:3.07e ev (403nm)/f-0.34 S2: 2.45eV (508nm)/t-1.12 S3: 2.89eV (430nm)/f-1.55
Figure 4. Frontier orbitals and minimum energy structures of oligomeric series. Geometrical optimizations at the DFT level M052X-D3De2TZVP) in vacuo.
Oscillator strengths (fvalues) obtained from corresponding TDDFT computations (0B97XD/De121ZVP)- The input structures were truncated at the meso phenyl
residues (iso-butyl groups).
4
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Thei trimer shows almost irreversible oxidation potentials at 0.69 V Acknowledgements
and 1.33 V and also reduction at -1.69 V. EDM-tet, however,
shows several oxidation and reduction potentials within the range We thank the Deutsche Forschungsgemeinschat (DFG, German
of t 2.00 V, which are mostly irreversible (Figure 5). Attempts to Research Foundation, WE2932/14-1) and livMats Cluster of
oxidize the obtained oligomers did not provide quinodiimine Excellence under Germany's Excellence Strategy (EXC-2193/1-
analogs as for the cyclic derivates.8)
390951807) for funding. S.H.R. thanks Adrian Bauschke and
Susanne Klein (both TU Braunschweig) for their support and
Boumahdi Benkmil (University of Freiburg) for X-ray diffraction
analysis as well as Dr. Ulrich Papke (TU Braunschweig) for the
HRMS measurements and discussions thereof.
Keywords: BODIPY . dyes amines . oligomers Buchwald-
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-3
-2
-1
0
1
2
3
EDM-tet
EDM-tri
Hartwig coupling
EDM-Ar-
mono- NH,
EDM-Ar-
mono-CI
1
2
3
-3
-2
-1
Potential [VI vs. SCE
5.
Ed.: 2022, 61, e2021168.
D. T.
Sysak,
Figure Cyclic voltammograms. Cyclic voltammetry (IUPAC convention) was
measured of 4 mM solutions in CH2Cl2 with TBAPF6 (0.4 M) in reference to a
saturated calomel electrode (SCE) with a scan rate of 200 mV/s (clockwise,
starting from 0 V) in steps of 1 mV at room temperature.
Conclusion
Ins summary, we have successfully developed a method to access
linearly amine-linked BODIPYS using Buchwald-Hartwig
conditions. Terminal Br substituents allowed elongation of the
chain by two further BODIPY subunits. X-ray structure analyses
revealed conjugation of the various subunits via the linking
nitrogen atom. Absorption spectra show significantly increased
attenuation coefficients for the oligomers in comparison to the
respective monomers, and also strong bathochromic shifts. DFT
calculations provided an insight into the electronic properties and
showed a decreasing HOMO/LUMO gap as well as increasing
oscillator strengths (fvalues) of the excited states with increasing
level of oligomerization. The computed orbital energies are also
closely consistent with cyclovoltammetric investigations,
demonstrating a more facile oxidation and reduction with
22, 7694-7698.
increasing chain length.
Supporting Information
The Supporting
Information
Tang,
is available free of charge and
contains detailed experimental procedures, analytical, X-ray
crystallographic and absorption and emission data, and 'H, 13C,
19F and 11B NMR spectra of all new compounds.
Chem. 2023, 88, 14368-14376.
5
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with open("raw_text.txt", "w") as f:
f.write(text)
Important
To review the quality and accuracy of the conversion at least partially afterward is crucial. If the OCR-tool is not able to convert the relevant parts correctly, one should think about using a different method.
The obtained text contains some errors. Most obvious one is that the text still contains page numbers of other characters that are not relevant for the main text.
More advanced approaches such as nougat or marker minimize those errors.
Conversion of PDF to Markdown using Nougat
Converting PDFs to Markdown using nougat is not much more difficult and can be accomplished by installing nougat with pip install nougat-ocr.
After that, a conversion can be performed directly on the command line using
```
nougat path/to/file.pdf -o output_directory
```
In the output directory, the converted files will be stored as Markdown files with the extension mmd.
However, even those more advanced techniques will still make mistake and will struggle to handle very old tables. To deal with those cases, one could use a vision model or an agentic approach to minimize those errors.
Afterward the received files should be cleaned, as shown in the document cleaning notebook.