Syntheses, spectral and chiral properties and DNA interactions of multi-heterocyclic di- And trinuclear boron complexes

Article abstract of DOI:10.1039/d0nj04474a

Tetrahedrally coordinated multi-heterocyclic boron complexes are stable, but much less investigated inorganic ring systems. In the present study, a series of dinuclear (2aI-2cI and 2aII-2cII) and trinuclear (3aI-3cI and 3aII-3cII) boron complexes were synthesized from SalenH2 type symmetrical bulky ligands [HOArCHN-R-NCHArOH; R = (CH2)n, n = 2 (1a), 3 (1b) and 4 (1c)], arylboronic acids (phenylboronic acid and 4-formylphenylboronic acid), and boric acid for the investigation of their spectral, stereogenic and DNA cleavage activities. The Salen-boron complexes have two equivalent chiral B-centers, giving rise to diastereoisomers. The stereogenic properties of these complexes were investigated by nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopies. The stereoisomers were compared with each other for two different architectural types and a total of 12 Salen-boron complexes with seven- to nine-membered [(B-O-B)-(N-R-N)] heterocycles. The combination of NMR and CD spectra of the complexes shows that the boron complexes (2bI and 3bII) and (2bII and 3bI) from the (CH2)3 precursor give only a cis-meso (RS/SR) isomer and only one trans-enantiomer (RR or SS), respectively. The complexes (2cI, 3cI and 3cII) from the (CH2)4 precursor give only one enantiomer (RR or SS), whereas the boron complexes (2aI, 2aII, 3aI and 3aII) from the (CH2)2 precursor and (2cII) from the (CH2)4 precursor form two diastereoisomers as one enantiomer (RR or SS) and one meso (RS/SR). Furthermore, the DNA cleavage activities of the adducts were determined using agarose gel electrophoresis and UV absorption in order to compare the cleavage efficiency of the boron complexes depending on the type of complexes (dinuclear or trinuclear) and the number of members in the heterocyclic frameworks. In this assay, the seven-membered trinuclear boron complex (3bII) showed the highest cleavage efficiency. This journal is

Full text of DOI:10.1039/d0nj04474a

NJC
View Article Online
View Journal | View Issue
PAPER
Syntheses, spectral and chiral properties and DNA
interactions of multi-heterocyclic di- and
trinuclear boron complexes†
Cite this: New J. Chem., 2020,
44, 20966
a
a
b
Selen Bilge Koçak, *a O¨ zgecan Kaya,
Zeynel Kılıç,
Burak Coban,
b
c
Ufuk Yildiz
and Bunyemin Ços-ut
¨
Tetrahedrally coordinated multi-heterocyclic boron complexes are stable, but much less investigated
inorganic ring systems. In the present study, a series of dinuclear (2aI–2cI and 2aII–2cII) and trinuclear
(3aI–3cI and 3aII–3cII) boron complexes were synthesized from SalenH2 type symmetrical bulky ligands
[HOArCHQN–R–NQCHArOH; R = (CH2)n, n = 2 (1a), 3 (1b) and 4 (1c)], arylboronic acids (phenylboronic
acid and 4-formylphenylboronic acid), and boric acid for the investigation of their spectral, stereogenic
and DNA cleavage activities. The Salen-boron complexes have two equivalent chiral B-centers, giving
rise to diastereoisomers. The stereogenic properties of these complexes were investigated by nuclear
magnetic resonance (NMR) and circular dichroism (CD) spectroscopies. The stereoisomers were
compared with each other for two different architectural types and a total of 12 Salen-boron complexes
with seven- to nine-membered [(B–O–B)–(N–R–N)] heterocycles. The combination of NMR and CD
spectra of the complexes shows that the boron complexes (2bI and 3bII) and (2bII and 3bI) from
the (CH2)3 precursor give only a cis–meso (RS/SR) isomer and only one trans-enantiomer (RR or SS),
respectively. The complexes (2cI, 3cI and 3cII) from the (CH2)4 precursor give only one enantiomer (RR
or SS), whereas the boron complexes (2aI, 2aII, 3aI and 3aII) from the (CH2)2 precursor and (2cII) from
the (CH2)4 precursor form two diastereoisomers as one enantiomer (RR or SS) and one meso (RS/SR).
Furthermore, the DNA cleavage activities of the adducts were determined using agarose gel
electrophoresis and UV absorption in order to compare the cleavage efficiency of the boron complexes
depending on the type of complexes (dinuclear or trinuclear) and the number of members in the
heterocyclic frameworks. In this assay, the seven-membered trinuclear boron complex (3bII) showed
the highest cleavage efficiency.
Received 6th September 2020,
Accepted 27th October 2020
DOI: 10.1039/d0nj04474a
rsc.li/njc
other than carbon, such as stereogenic nitrogen,2 phosphorus,3
silicon,4 and sulfur5 atoms, rather less attention has been paid
1. Introduction
Stereoisomerism is of well-recognized importance in many realms to studying the features of compounds with tetrahedrally-
such as in the life sciences due to the different activity of individual coordinated boron. This is not only primarily because the
stereoisomers in biological systems.1 Although considerable tetrahedrally-coordinated boron atom with a labile nature is
research has been devoted to investigating enantiomerism in configurationally stable only under certain conditions,6 but also
compounds with tetrahedrally-coordinated main group elements partly because tetrahedrally-coordinated boron is incorporated in a
chiral environment created by enantiomerically pure ligands7 or
counterions.8 The reactions for the synthesis of some complexes
a
˘
occur in a diastereoselective manner9 or a manner producing a
mixture of diastereomers.10 Boron turns out to be a stable stereo-
genic center in complexes obtained from Schiff base ligands and
aryl boronic acids. However, the Schiff base boron complexes
either contain fixed carbon stereocenters in chiral Schiff base
ligands or are racemic.11 Diastereomerically and enantiomerically
pure complexes were synthesized by taking advantage of the
interactions between chiral Schiff base ligands derived from aro-
Department of Chemistry, Ankara University, Tandogan, 06100 Ankara, Turkey.
E-mail: sbilge@science.ankara.edu.tr; Fax: +90-312-2232395;
Tel: +90-312-2126720-1021
b
¨
Department of Chemistry, Zonguldak Bulent Ecevit University, Incivez,
67100 Zonguldak, Turkey
c Department of Chemistry, Gebze Technical University, 41400 Gebze-Kocaeli,
Turkey
† Electronic supplementary information (ESI) available: Schematic presentation of
the syntheses of dinuclear (2aI–2cI and 2aII–2cII) and trinuclear (3aI–3cI and 3aII–
3cII) boron complexes, IR and 11B NMR spectra for all the complexes, 1H and 13
C
NMR and HSQC spectra of the complexes except 2cI. See DOI: 10.1039/d0nj04474a matic aldehydes and chiral aminoethanols, and arylboronic acids.12
20966 | New J. Chem., 2020, 44, 20966--20981 This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020

View Article Online
Paper
NJC
On the other hand, in the studies of boron complexes with Schiff coordinated multi-heterocyclic dinuclear (2aI–2cI and 2aII–2cII)
base ligands, stereogenism only at the boron atom is much less and trinuclear (3aI–3cI and 3aII–3cII) boron complexes.
common. The first example of one such optically pure stable Schiff
base boron complex was reported by Hutton and coworkers.13 The
absolute configuration of stereogenic boron in enantiomeric Schiff
base boron complexes was assigned by the evident accordance of
2. Experimental
2.1. Materials
measured and calculated circular dichroism (CD) for the first time
by Braun and coworkers.14 As part of the research on Schiff base
Commercial-grade reagents were used without further purification,
and solvents were dried and distilled by standard methods. The
solvents and salicylaldehyde were purchased from Merck, while
aliphatic amines, boric acid, phenylboronic acid and 4-formylphenyl
boronic acid were purchased from Fluka. All reactions were
boron complexes we have described the preparation and structural
characterization of a series of dinuclear (2aI–2cI and 2aII–2cII) and
trinuclear (3aI–3cI and 3aII–3cII) Salen-boron complexes (Table 1)
that contain two equivalent stereogenic boron centers, and which
conducted under an argon atmosphere and monitored using
give rise to diastereoisomers (Schemes 1 and 2). The Salen-boron
thin-layer chromatography (TLC) on Merck DC Alufolien Kiesel-
complexes are the only examples of compounds in which the
gel 60 B254 sheets.
chirality is imparted exclusively by two boron stereocenters, and
there is no paper reporting the CD spectrum of an enantiomer
and a diastereoisomer of a boron complex with two equivalent
2.2. Physical methods
stereogenic boron centers. We therefore have reason for studying Melting points were measured with a Gallenkamp apparatus
dinuclear (2aI–2cI and 2aII–2cII) and trinuclear (3aI–3cI and using a capillary tube. Microanalyses (C, H, N) were performed
3aII–3cII) boron complexes.
using a Leco CHNS-932 elemental analyzer at the Central
Additionally, boron-based compounds possess various and Instrumental Analysis Laboratory in the Faculty of Pharmacy
1
useful biological activities, including hypolipidemic, antiosteo- at Ankara University. H (400 MHz) and 13C (100 MHz) NMR,
porosis, antineoplastic,15 antibacterial, antifungal, antiviral, anti- and HSQC spectra were recorded on a Varian Mercury 400 MHz
parasitic, anti-inflammatory,16 anticancer,17,18 and DNA binding FT spectrometer. 11B NMR spectra were obtained using an
and cleavage19 activities. Research along these lines is under Agilent 600 MHz PremiumCOMPACT NMR spectrometer at
development in laboratories, and some of these compounds are the Çankırı Karatekin University Research Center. FTIR spectra
even used as FDA-approved drugs.20,21 We therefore decided to of the compounds were recorded on a Shimadzu Infinity FTIR
examine the DNA cleavage activities of the novel tetrahedrally spectrometer. ESI-MS mass spectra were obtained on an Agilent
Table 1 Formulae of the dinuclear [(2aI–2cI) and (2aII–2cII)] and trinuclear [(3aI–3cI) and (3aII–3cII)] boron complexes
Compound
R
R0
—
Diastereomeric ratioa
—
(1a)
(1b)
(1c)
—
—
—
—
(2aI)
H
65 : 35
96 : 4
(2aII)
CHO
(2bI)
(2bII)
(2cI)
H
—
CHO
H
—
—
(2cII)
CHO
86 : 14
(3aI)
H
53 : 47
52 : 48
(3aII)
CHO
(3bI)
H
—
—
(3bII)
CHO
(3cI)
H
—
—
(3cII)
CHO
a
Determined by 1H NMR (400 MHz) examination of the crude reaction mixtures.
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020
New J. Chem., 2020, 44, 20966--20981 | 20967

View Article Online
NJC
Paper
Scheme 1 Possible stereoisomers for the dinuclear [(2aI–2cI) and (2aII–2cII)] boron complexes.
Scheme 2 Possible stereoisomers for the trinuclear [(3aI–3cI) and (3aII–3cII)] boron complexes.
1100 MSD spectrometer. The ultra-violet (UV) absorption 10 nm minꢀ1 with a spectral bandwidth of 1 nm and data
and CD spectra of the boron complexes were obtained with a resolution of 0.2 nm. The solvent was DMSO and pathlengths of
Jasco J720 spectropolarimeter, flushed with N2, and scanned at the cells were 1 cm and 0.2 cm. CD spectra are presented with
20968 | New J. Chem., 2020, 44, 20966--20981 This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020

View Article Online
Paper
NJC
respect to the normalized absorbance, A(265.6 nm) = 1, in a Anal. calc. for C30H28B2N2O3 (%): C, 74.11; H, 5.80; N, 5.76.
1 cm cell.
Found; C, 74.01; H, 5.90; N, 5.84%. IR (KBr, cmꢀ1): n 3063;
3040 (C–H arom.), 1649 (CQN), 1609 (CQC), 1560 (N–B), 1300
(O–B). ESI-MS (fragments were based on 11B, Ir %): m/z 297
{[OHArCHQN–(CH2)4–NQCHArOHH]+, 48}.
2.3. Syntheses
2.3.1. Syntheses of the compounds (1–3 and 2aI, 2bI, 3aI
and 3bI). The SalenH2 ligands {N,N0-bis(salicylidene)-1,3-pro-
panediamine (1a), N,N0-bis(salicylidene)-1,3-propanediamine
(1b) and N,N0-bis(salicylidene)-1,4-butanediamine (1c)} were
prepared according to the published procedure in which sali-
cylaldehyde was reacted with 1,2-diaminoetane, 1,3-diamino-
propane and 1,4-diaminobutane in dry MeOH, respectively.22
The dinuclear boron complexes (2aI and 2bI) were prepared
according to a published procedure in which one equimolar
amount of SalenH2 ligands (1a and 1b) was reacted with two
equimolar amounts of phenylboronic acid in toluene, respectively,
using a Dean–Stark trap.23 The trinuclear boron complexes (3aI
and 3bI) were synthesized using a method in which one equimolar
amount of SalenH2 ligands (1a and 1b), two equimolar amounts of
boric acid and two equimolar amounts of phenylboronic acid were
refluxed in acetonitrile, respectively, using a Dean–Stark trap
according to the published procedure.24 The spectroscopic data
of the dinuclear (2aI and 2bI) and trinuclear (3aI and 3bI) boron
complexes were reported,23,24 but the stereochemistry and DNA
interaction studies of 2aI, 2bI, 3aI and 3bI were discussed in this
paper for comparison purposes.
2.3.2.2. 2aII. Complex 2aII was prepared from SalenH2 (1a)
(0.22 g, 0.84 mmol) and 4-formylphenylboronic acid (0.25 g,
1.67 mmol) (6 h). Two diastereomers were obtained in a ratio of
approximately 96 : 4. Yield: 0.34 g (79%). mp: 263 1C. Anal. calc.
for C30H24B2N2O5 (%): C, 70.08; H, 4.71; N, 5.45. Found; C,
68.96; H, 4.87; N, 5.36%. IR (KBr, cmꢀ1): n 3055; 3024 (C–H
arom.), 2822; 2724 (H–CO), 1703 (HCQO), 1645 (CQN), 1599
(CQC), 1557 (N–B), 1308 (O–B). ESI-MS (fragments were based
on 11B, Ir %): m/z 515 {[MH]+, 100}.
2.3.2.3. 2bII. Complex 2bII was prepared from SalenH2 (1b)
(0.24 g, 0.84 mmol) and 4-formylphenylboronic acid (0.25 g,
1.67 mmol) (6 h). Yield: 0.30 g (75%). mp: 230 1C. Anal. calc. for
C
31H26B2N2O5 (%): C, 70.83; H, 4.98; N, 5.33. Found; C, 69.64;
H, 5.16; N, 5.01%. IR (KBr, cmꢀ1): n 3067; 3030 (C–H arom.),
2820; 2724 (H–CO), 1699 (HCQO), 1637 (CQN), 1595 (CQC),
1559 (N–B), 1300 (O–B). ESI-MS (fragments were based on 11B,
Ir %): m/z 527 {[MH]+, 100}.
2.3.2.4. 2cII. Complex 2cII was prepared from SalenH2 (1c)
(0.25 g, 0.84 mmol) and 4-formylphenylboronic acid (0.25 g,
1.67 mmol) (6 h). Two diastereomers were obtained in a ratio of
approximately 86 : 14. Yield: 0.38 g (80%). mp: 220 1C. Anal. calc.
for C32H28B2N2O5 (%): C, 70.89; H, 5.20; N, 5.17. Found; C, 69.86;
H, 5.55; N, 4.24%. IR (KBr, cmꢀ1): n 3071; 3034 (C–H arom.),
2830; 2733 (H–CO), 1692 (HCQO), 1641 (CQN), 1597 (CQC),
1559 (N–B), 1304 (O–B). ESI-MS (fragments were based on 11B,
Ir %): m/z 297 {[OHArCHQN–(CH2)4–NQCHArOHH]+, 28}.
2.3.3. Synthesis of the new trinuclear boron complexes
2aI. Two diastereomers were obtained in a ratio of approxi-
mately 65 : 35. IR (KBr, cmꢀ1): n 3051 (C–H arom.), 1638 (CQN),
1609 (CQC), 1557 (N–B), 1317 (O–B). ESI-MS (fragments were
based on 11B, Ir %): m/z 459 {[MH]+, 100}.
2bI. IR (KBr, cmꢀ1): n 3065; 3048 (C–H arom.), 1643 (CQN),
1608 (CQC), 1559 (N–B), 1319 (O–B). ESI-MS (fragments were
based on 11B, Ir %): m/z 473 {[MH]+, 100}.
3aI. Two diastereomers were obtained in a ratio of approxi- (3cI, 3aII, 3bII and 3cII). The trinuclear boron complexes (3cI,
mately 53 : 47. IR (KBr, cmꢀ1): n 3060; 3030 (CꢀH arom.), 1641 3aII, 3bII and 3cII) were prepared by similar methods; there-
(CQN), 1611 (CQC), 1559 (N–B), 1302 (O–B). ESI-MS (fragments fore, the experimental procedure of the preparation was only
were based on 11B, Ir %): m/z 269 {[OHArCHQN–(CH2)2–NQ described in detail for the first case.
CHArOHH]+, 100}.
2.3.3.1. 3cI. A mixture of SalenH2 (1c) (0.61 g, 2.05 mmol)
3bI. IR (KBr, cmꢀ1): n 3045; 3025 (C–H arom.), 1641 (CQN), and boric acid (0.25 g, 4.10 mmol) in acetonitrile (15 mL) was
1611 (CQC), 1560 (N–B), 1300 (O–B). ESI-MS (fragments were based refluxed until a yellow precipitate formed. Then a solution of
on 11B, Ir %): m/z 283 {[OHArCHQN–(CH2)3–NQCHArOHH]+, 100}. phenylboronic acid (0.25 g, 2.05 mmol) in acetonitrile (20 mL)
2.3.2. Synthesis of the new dinuclear boron complexes (2cI, was added without isolation of the dinuclear intermediate
2aII, 2bII and 2cII). The dinuclear boron complexes (2cI, 2aII, (Fig. S1, ESI†) and the mixture was refluxed for 16 h using a
2bII and 2cII) were prepared by similar methods; therefore, the Dean–Stark trap with argon being passed over the reaction
experimental procedure of the preparation was only described mixture. The yellow precipitate was filtered, washed with hot
in detail for the first case.
acetonitrile, and dried in air. Yield: 0.33 g (36%). mp: 245 1C.
Anal. calc. for C24H23B3N2O5 (%): C, 63.79; H, 5.13; N, 6.20.
Found; C, 63.75; H, 5.08; N, 6.18%. IR (KBr, cmꢀ1): n 3055; 3030
(C–H arom.), 1641 (CQN), 1609 (CQC), 1559 (N–B), 1300 (O–B).
ESI-MS (fragments were based on 11B, Ir %): m/z 297
{[OHArCHQN–(CH2)4–NQCHArOHH]+, 100}.
2.3.2.1. 2cI. SalenH2 (1c) (0.3 g, 1.03 mmol) in toluene
(50 mL) was slowly added during 0.5 h to a solution of phenyl-
boronic acid (0.25 g, 2.05 mmol) in boiling toluene (100 mL)
with argon being passed over the reaction mixture. The mixture
was refluxed for 6 h and then cooled to room temperature. After
1 h of reflux, the solution was concentrated with a Dean–Stark
2.3.3.2. 3aII. Complex 3aII was prepared from SalenH2 (1a)
trap. The yellow precipitate was filtered, washed with hot (1.00 g, 3.70 mmol), boric acid (0.46 g, 7.50 mmol) and 4-formyl-
toluene, and dried in air. Yield: 0.17 g (35%). mp: 225 1C. phenylboronic acid (0.56 g, 3.70 mmol) (14 h). Two diastereomers
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020
New J. Chem., 2020, 44, 20966--20981 | 20969

View Article Online
NJC
Paper
were obtained in a ratio of approximately 52 : 48. Yield: 1.24 g 2.5. UV titrations
(74%). mp: 4300 1C. Anal. calc. for C23H19B3N2O6 (%): C, 61.14;
Solutions of calf thymus DNA (CT-DNA; purchased from Sigma)
in 50 mM ammonium acetate (pH = 7.4) had a UV-vis absorbance
ratio A260/A280= 1.9, indicating that the DNA was sufficiently free
of protein. The concentration of DNA was determined spectro-
photometrically using a molar absorptivity of 6600 Mꢀ1 cmꢀ1
(260 nm).27 Double-distilled water was used to prepare buffers.
Stock solutions of CT-DNA were stored at 4 1C and not used after
4 days. UV-vis spectra were recorded on a Carry WinUV 100 Bio
Varian spectrophotometer. The complexes were dissolved in
minimum amounts of DMSO before preparing stock solutions.
The absorption titrations of the dinuclear (2bI and 2bII) and
trinuclear (3bI and 3bII) boron complexes were performed in the
buffer. The concentration of the boron complexes was fixed
H, 4.24; N, 6.30. Found; C, 61.11; H, 4.26; N, 6.16%. IR
(KBr, cmꢀ1): n 3050; 3028 (C–H arom.), 2820; 2730 (H–CO),
1701 (HCQO), 1641 (CQN), 1611 (CQC), 1560 (N–B), 1302
(O–B). ESI-MS (fragments were based on 11B, Ir %): m/z 269
{[OHArCHQN–(CH2)2–NQCHArOHH]+, 100}.
2.3.3.3. 3bII. Complex 3bII was prepared from SalenH2 (1b)
(0.66 g, 2.30 mmol), boric acid (0.28 g, 4.60 mmol) and
4-formylphenylboronic acid (0.35 g, 2.30 mmol) (14 h). Two
diastereomers were obtained in a ratio of approximately 52 : 48.
Yield: 0.52 g (49%). mp: 4300 1C. Anal. calc. for C24H21B3N2O6
(%): C, 61.88; H, 4.54; N, 6.01. Found; C, 61.85; H, 4.60; N,
6.04%. IR (KBr, cmꢀ1): n 3060; 3030 (C–H arom.), 2849; 2725 (20 mM). The increments of the 3 mM DNA stock solution were
(H–CO), 1694 (HCQO), 1641 (CQN), 1609 (CQC), 1560 (N–B), added to the complex solutions. The complex solutions were
1300 (O–B). ESI-MS (fragments were based on 11B, Ir %): m/z 283
thoroughly mixed after every addition and incubated for 10 min
before the absorption spectra were recorded.
{[OHArCHQN–(CH2)3ꢀNQCHArOHH]+, 100}.
2.3.3.4. 3cII. Complex 3cII was prepared from SalenH2 (1c)
(0.97 g, 3.30 mmol), boric acid (0.48 g, 6.60 mmol) and
3. Results and discussion
4-formylphenylboronic acid (0.50 g, 3.30 mmol) (12 h). Yield:
0.58 g (37%). mp: 4300 1C. Anal. calc. for C25H23B3N2O6 (%): C,
62.57; H, 4.83; N, 5.84. Found; C, 62.50; H, 4.79; N, 5.80%. IR
(KBr, cmꢀ1): n 3060; 3030 (C–H arom.), 2880; 2820 (H–CO), 1705
(HCQO), 1641 (CQN), 1609 (CQC), 1560 (N–B), 1302 (O–B).
ESI-MS (fragments were based on 11B, Ir %): m/z 297
{[OHArCHQN–(CH2)4–NQCHArOHH]+, 49}.
3.1. Chemistry
SalenH2 type symmetrical bulky ligands are useful for the synthesis
of boron complexes because the boron atoms form strong covalent
bonds with the phenolic oxygens and coordinate covalent bonds
with the azomethine nitrogens. Arylboronic acids (phenylboronic
acid and 4-hydroxyphenylboronic acid) and SalenH2 ligands
[HOArCHQN–R–NQCHArOH; R = (CH2)n, n = 2 (1a), n = 3 (1b)
and n = 4 (1c)] underwent condensation reactions in a 2 : 1
stoichiometry in toluene to obtain dinuclear boron complexes
2.4. DNA cleavage activity
Plasmid DNA (Thermo Scientifict pBR322 Plasmid DNA SD0041, with a boraxane group (PhB–O–BPh) (2aI–2cI and 2aII–2cII).
0.5 mg mLꢀ1) was used in the gel electrophoresis experiments and Trinuclear boron complexes with a boroxine group (B–O–B)–
diluted 25 times before use. It was run on 1% agarose gel in a (O2BPh) (3aI–3cI and 3aII–3cII) were synthesized through the
tris(hydroxymethyl)aminomethane-borate-EDTA (TAE) running combination of boric acid/arylboronic acid (phenylboronic acid
buffer solution. DMSO was often used to prepare solutions of and 4-hydroxyphenylboronic acid) and SalenH2 ligands (1a–1c)
compounds with low water solubility for investigating DNA in acetonitrile without isolation of the dinuclear intermediates
interactions.25 In several studies, it has been shown that (Fig. S1, ESI†). A Dean Stark trap was used to separate the water
using minimum amounts of DMSO for the preparation of the formed during the condensation. The dinuclear boron com-
stock solutions has no effect on nucleic acids.26 The reaction plexes contain two tetrasubstituted boron atoms, while the
mixtures were prepared (20 mL) in 50 mM ammonium acetate trinuclear boron complexes contain two tetrasubstituted and
buffer, pH 7.4 at 0 1C, containing 10 mL of plasmid DNA and additionally a trisubstituted boron atom. The boron complexes
10 mL of the complex at two different concentrations by contain central seven- (2aI, 2aII, 3aI and 3aII), eight- (2bI, 2bII,
preparing [DNA]/[complex] ratios of 0.8 and 8. They were 3bI and 3bII) and nine- (2cI, 2cII, 3cI and 3cII) membered
incubated at 37 1C for 24 h in the dark. From the reaction [(B–O–B)–(N–R–N)] heterocyclic ring motifs with an oxygen atom
mixtures, 10 mL aliquots of complex-DNA mixtures were loaded bridging two boron atoms and two azomethine nitrogens forming
onto 1% agarose gel with a loading buffer (0.1% bromophenol N–B bonds with the boron atoms.
blue, 0.1% xylene cyanol), and electrophoresis was performed
On the other hand, the choice of the SalenH2 type symmetrical
on a Thermo Midi-cell Primo horizontal electrophoresis system bulky ligands (1a–1c) is important because stereochemically con-
in 0.05 M tris base, 0.05 M glacial acetic acid and 1 mM EDTA trolled reactions may be achieved. Moreover, it is crucial to arrange
(TAE buffer, pH = 8.0) for 5 h at 35 V with a Thermo EC250-90 the configurations of tetrahedrally-coordinated boron atoms to
power supply. The gel was stained with ethidium bromide form controlled stereogenic centers. The condensation reaction
solution (0.5 mg mLꢀ1) for 30 min. It was rinsed with water between the SalenH2 ligands (1a–1c) and arylboronic acids
for 20 min and then visualized under UV light. The experiments (phenylboronic acid and 4-formylphenylboronic acid) and boric
were repeated three times. Untreated DNA was used as a acid/arylboronic acids provides two tetrasubstituted boron
control.
atoms, [B(Nimine)(OB)(OPh)(Ph)], which are centers of chirality.
20970 | New J. Chem., 2020, 44, 20966--20981 This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020

View Article Online
Paper
NJC
Therefore, a notable feature of all the boron complexes is the stereoisomers. When we compared the stereoisomers of all
presence of two equivalent stereogenic B-centers and each is seven-membered boron complexes (2aI, 2aII, 3aI and 3aII) with
potentially capable of existing as two pairs of diastereoisomers the eight-membered counterparts (2bI, 2bII, 3bI and 3bII) regard-
of RS/SR (meso) and RR/SS (racemic) configurations. The stereo- less of whether the complexes are dinuclear or trinuclear, we
isomer distributions and the expected and the isolated isomers indeed find the seven-membered complexes to be a mixture of
of the complexes are presented in Schemes 1 and 2. As is known, the two diastereoisomers, but the eight-membered ones to be one
four optical isomers (RR, SS, RS and SR) are expected from two of the two diastereoisomers. That situation could be significantly
stereogenic centers. According to Schemes 1 and 2, only one attributed to the fact that eight-membered heterocycles are highly
racemic (RR/SS) and one meso (RS or SR) mixture must form flexible structures compared to seven-membered ones. In other
since two phenyl groups are bonded to B-atoms in the trans and words, the seven-membered heterocycles may possess consider-
cis fashion, respectively, for the dinuclear (2aI–2cI and 2aII–2cII) ably locked-conformations with respect to the eight-membered
and trinuclear (3aI–3cI and 3aII–3cII) boron complexes. The heterocycles. But, perhaps more significantly, it is not always easy
SS/RR forms with a trans-configuration of the B-phenyl groups have to determine which of the two possible diastereomers are likely to
C2 symmetry while the RS/SR meso form with a cis-configuration of form with higher yields than the other ones, due to the molecular
the B-phenyl groups has a molecular plane.
symmetry of the diastereomers (cis or trans with respect to the
It is noteworthy that the most important result is obtained B-phenyl groups) (Schemes 1 and 2). To determine which
from the CD and NMR spectra of the boron complexes. The CD diastereomer is preferred for the boron complexes, an X-ray
spectra of the complexes are depicted in Fig. 1–3 together with crystallographic study should be undertaken. Unfortunately, in the
the UV spectra. In the UV spectra of the complexes, two bands present study suitable crystals of the new boron complexes could
are observed; namely the first band (270–280 nm) is attributed not be grown in order to understand their preferred configuration.
to the p - p* transitions of aromatic rings. The second band
Despite the preference for either cis- or trans-configurations
between 350 and 370 nm involves n - p* transitions of the being possible, the formation of cis-isomers (RS/SR meso stereo-
imine groups, which disappear completely in the CD spectra. isomer) appears to be much more likely than the formation of
The CD spectra of two dinuclear (2aI and 2aII) and two tri- trans-isomers (RR or SS enantiomers) during the reaction.
nuclear (3aI and 3aII) boron complexes from the (CH2)2 pre- However, in the cis-configured seven-membered C2B2N2O hetero-
cursor, one dinuclear (2bII) and one trinuclear (3bI) boron cycles, the two salicylidene groups are oriented parallel to each
complex from the (CH2)3 precursor and two dinuclear (2cI other, and the proximity between them would be repulsive due to
and 2cII) and two trinuclear (3cI and 3cII) boron complexes p–p and and steric interactions. Hence, the trans-configuration is
from the (CH2)4 precursor show negative and positive Cotton likely to emerge as a consequence of the twisting of the seven-
effects, which is good evidence that the complexes consist of membered ring. Thus, the yields of the trans-isomers ought to be
only one enantiomer, RR or SS. However, one dinuclear (2bI) larger than those of the cis-isomers. In the case of eight mem-
and one trinuclear (3bII) boron complex from the (CH2)3 bered heterocycles with a propylene bridge between the two
precursor do not display negative and positive Cotton effects, imino groups, as the number of members in the (B–O–B)–
which indicates that the complexes have a cis–meso (RS/SR) (N–R–N) heterocyclic ring increases, p–p interactions between
isomer. When we consider all of the reactions, according to the the two salicyclidene groups decrease and only one configuration
NMR results, the dinuclear (2bI and 2bII) and trinuclear (3bI (cis or trans) becomes preferred (meso for 2bI and 3bII, enantio-
and 3bII) boron complexes with the (CH2)3 precursor have been meric for 2bII and 3bI). The molecular structure of eight-
found to be only one diastereomer. On the other hand, the membered dinuclear boron complex 2bI synthesized diastereo-
dinuclear (2aI and 2aII) and trinuclear (3aI and 3aII) boron selectively was determined in the literature.23 The X-ray study
complexes with the (CH2)3 precursor and the dinuclear boron demonstrated that the cis-configuration was preferred over the
complex (2cII) with the (CH2)4 precursor were diastereomeric trans-configuration and in this case a boat conformation was
mixtures, and we have been unable to separate the diastereo- formed, with the two imino-nitrogen atoms at the bow/stern
isomers from any of the reactions. Contrary to this observation, positions for 2bI. Taken together, this result is consistent with
23
Sanchez et al. and Vargas et al.24 conclude that only one our findings from the CD spectrum of 2bI in solution.
´
diastereomer has been formed for dinuclear 2aI and trinuclear
According to our result, trinuclear complexes 3aI and 3aII
3aI. The findings from the evaluation of NMR (Tables 2 and 3) contain an approximately equimolar mixture (50/50) of the two
and CD spectra (Fig. 1–3) together show that the boron com- diastereomers (meso and enantiomeric forms). It shows that
plexes with seven- (2aI, 2aII, 3aI and 3aII) and nine- (2cII) the probabilities for the B–O bond to be the cis- or trans-
membered heterocycles form two diastereoisomers as one configurations are equal and the conformation of the seven-
enantiomer (RR or SS) and one meso (RS/SR), whereas the boron membered C2B2N2O heterocycle is stable for both configurations.
complexes (2bI and 3bII) and (2bII and 3bI) with an eight- These two configurations must form according to the effect on B
membered heterocycle give only a meso (RS/SR) isomer and only during the reaction with H3BO3. The seven-membered (B–O–B)–
one enantiomer (RR or SS), respectively, and the boron complexes (N–R–N) heterocyclic ring is more flexible than the six-membered
(3cI and 3cII) with a nine-membered heterocycle give only one BOPhCN ring. Even if the six-membered BOPhCN ring having a
enantiomer (RR or SS). Therefore, the number of members in the planar CQN bond and a phenyl group is rigid and there is
heterocycles seems to have an effect on the formation of electron delocalization here, the seven-membered (B–O–B)–(N–R–N)
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020
New J. Chem., 2020, 44, 20966--20981 | 20971

View Article Online
NJC
Paper
Fig. 1 (a) UV and (b) CD spectra of seven-membered dinuclear (2aI and 2aII) and trinuclear (3aI and 3aII) boron complexes. The spectra in the 400 to
250 nm region are from 1 cm path length cells, and for those in the 400 to 250 nm region the path lengths are 0.2 cm.
heterocyclic ring may be twisted. Therefore, accommodation of the probability of being both cis- and trans-configurations seems
the B–N bonds in the seven-membered ring can regulate the con- to be 50%. Considering the dinuclear intermediate given in
formation, and the seven-membered B2C2N2O heterocyclic ring may Fig. S1 (ESI†), it may be possible to be both cis- and trans-
have different conformations. According to these conformations, configurations depending on the state of OH. On the other
20972 | New J. Chem., 2020, 44, 20966--20981
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020

View Article Online
Paper
NJC
Fig. 2 (a) UV and (b) CD spectra of eight-membered dinuclear (2bI and 2aII) and trinuclear (3bI and 3bII) boron complexes. The spectra in the 400 to
250 nm region are from 1 cm path length cells, and for those in the 400 to 250 nm region the path lengths are 0.2 cm.
hand, the eight-membered (B–O–B)–(N–R–N) ring is not rigid
Vargas et al.24 conclude that the seven- and eight-membered
and a single conformation is adopted by the ring. Thus, the (B–O–B)–(N–R–N) heterocyclic rings have different conformations
conformation of the ring remained twisted, not rotated for based on X-ray crystallography and theoretical calculations.
trinuclear complexes 3bI (enatiomeric) and 3bII (meso).
For example, the seven-membered B2C2N2O heterocycle in the
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020
New J. Chem., 2020, 44, 20966--20981 | 20973

View Article Online
NJC
Paper
Fig. 3 (a) UV and (b) CD spectra of nine-membered dinuclear (2bI and 2aII) and trinuclear (3cI and 3cII) boron complexes. The spectra in the 400 to
250 nm region are from 1 cm path length cells, and for those in the 400 to 250 nm region the path lengths are 0.2 cm.
experimentally determined and theoretically calculated structures of However, in this literature, the issue of stereoisomerism was not
3aI possesses twisted-chair and chair conformations, respectively, discussed.24 As a result, the trinuclear derivatives can have
while the eight-membered B2C3N2O heterocycle in the theoretically different configurations depending on their (B–O–B)–(N–R–N)
calculated structure of 3bI prefers a chair–chair conformation. heterocyclic ring conformations.
20974 | New J. Chem., 2020, 44, 20966--20981 This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020

View Article Online
Paper
NJC
Table 2 11B NMR data (d6-DMSO) of the dinuclear (2aI–2cI and 2aII–2cII)
and trinuclear (3aI–3cI and 3aII–3cII) boron complexes (d in ppm)
chiral compounds can crystallize spontanaously from the race-
mic or diastereomeric mixtures. In recent years, this situation has
also been observed in some cyclotri29 and cyclotetra30 phospha-
zene derivatives.
All of the boron complexes have relatively high melting
points and are stable to air. They (1 ꢁ 10ꢀ2 g) are insoluble, but
decompose in about 2 days in 5 mL of water at room temperature.
In boiling water the complexes easily and completely decompose
in about 5 min. Moreover, they are practically insoluble in most
polar and nonpolar organic solvents, but are sparingly soluble in
DMSO. Especially 2cI dissolves very poorly in DMSO. Hence, its 1H
and 13C NMR spectra were not recorded. The boron complexes
seem to be stable in DMSO at room temperature for more than
three weeks but small quantities of decomposition products are
observed in the NMR spectra.
Compound
dBX
Compound
dBX
dBY
(2aI)
(2bI)
(2cI)
(2aII)
(2bII)
(2cII)
3.94
3.99
4.13
3.48
3.63
1.77
(3aI)
(3bI)
(3cI)
(3aII)
(3bII)
(3cII)
1.96
1.55
1.57
1.93
1.44
1.61
19.71
19.93
19.86
19.73
19.79
19.88
The elemental analyses of the compounds are consistent
with the structures, and fragments were observed under electro-
Moreover, the CHO group leads to the formation of one of spray ionization mass spectrometry (ESI-MS) conditions. All the
the enantiomers of dinuclear complex 2bII, and a meso isomer in dinuclear boron complexes except 2cI and 2cII give protonated
trinuclear complex 3bII for the (CH2)3 chain precursor. As a result, molecules [MH]+, which are the parent peaks in relative intensity. In
these compounds are likely to be conformationally-locked, and the mass spectra of the trinuclear boron complexes, the molecular
hence they are essentially chiral as they do not convert to their ion peak does not appear, but the fragments corresponding to Schiff
mirror images in the solid state. In the literature, a nice paper28 bases [[HOArCHQN–(CH2)n–NQCHArOHH]+] appear at m/z 269
asserts that one enantiomer of some conformationally-locked for 3aI and 3aII, 283 for 3bI and 3bII and 297 for 3cI and 3cII.
Table 3 1H NMR data (d6-DMSO) of dinuclear boron complexes (2aI, 2bI and 2aII–2cII) (d in ppm, J in Hz, s: singlet, d: doublet, dd: doublet of doublets,
t: triplet, dt: doublet of triplets, b: broad, and m: multiplet)
2aI
A
2bI
2aII
A
2bII
2cII‡
H
B
meso
B
Enantiomeric
A
B
NCH2CH2
—
—
1.96 (m,1H) (a)
2.48 (m,1H) (b)
—
—
2.02 (m,1H) (a) 1.48 (m,4H)
2.35 (m,1H) (b)
1.61 (m,4H)
NCH2
3.45 (d,2H) (a) 3.72 (d,2H) (a) 3.49 (t,4H)
3.81 (m,2H) (a)
3.85 (m,2H) (b)
*
3.44 (m,2H) (a) 3.34 (m,2H) (a) 3.00 (m,2H) (a)
3.53 (m,2H) (b) 3.49 (m,2H) (b) 3.19 (m,2H) (b)
3
3.75 (d,2H) (b) 3.87 (d,2H) (b) JHH = 6.0
2JHaHb = 10
—
2JHaHb = 8.2
—
CHO
HCQN
ArH
—
9.92 (s,2H)
8.58 (s,2H)
—
7.72 (d,4H)
7.66 (d,4H)
7.29 (d,2H)
6.73 (t,2H)
7.39 (ti,2H)
6.63 (d,2H)
—
—
8.0
7.2
1.6
7.6
*
9.82 (s,2H) 9.93 (s,2H)
8.61 (s,2H) 8.60 (s,2H)
—
9.88 (s,2H)
8.40 (s,2H)
—
10.0 (s,2H)
8.64 (s,2H)
—
8.56 (s,2H)
H1 6.91 (d,2H)
H2 7.14 (t,4H)
H3 7.17 (dd,4H)
H7 7.40 (dd,2H)
H8 6.85 (t,2H)
H9 7.55 (dt,2H)
H10 6.84 (d,2H)
8.49 (s,2H)
6.95 (d,2H)
7.11 (t,4H)
7.45 (dd,4H)
7.25 (dd,2H)
6.69 (dt,2H)
7.36 (dt,2H)
6.59 (d,2H)
7.2
1.6
8.0
7.8
1.8
8.53 (s,2H)
7.13 (m,2H)
7.21 (t,4H)
7.57 (d,4H)
7.05 (d,2H)
6.48 (t,2H)
7.15 (m,2H)
6.36 (d,2H)
7.2
*
7.0
8.0
1.4
—
7.85 (d,4H) 7.76 (m,4H)
7.97 (d,4H) 7.76 (m,4H)
7.47 (d,2H) 7.07 (dd,2H)
7.22 (t,2H) 6.50 (dt,2H)
7.56 (t,2H) 7.17 (dt,2H)
7.15 (d,2H) 6.38 (d,2H)
—
—
8.0
8.0
*
7.69
7.6
7.83
7.71
7.17 (d)
6.91
7.52
6.85 (d)
—
**
7.6
7.2
**
**
**
7.24 (d)
6.53 (b,2H)
6.9
6.28 (b,2H)
—
**
**
7.2
**
**
**
**
3J1–2
4J1–3
3J2–3
3J7–8
4J7–9
3J8–9
4J8–10
3J9–10
7.6
1.6
8.0
8.2
1.4
7.8
*
—
—
*
7.6
1.6
7.4
0.8
8.4
7.9
1.2
7.6
*
7.9
*
8.0
7.6
8.4
8.8
8.4
**
A designates a major diastereoisomer. A: meso and B: enantiomeric or A: enantiomeric and B: meso forms, ‡poor solubility, * not determined, ** not
calculated. The notations a and b are used to show nonequivalent nuclei in NMR spectra.
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020
New J. Chem., 2020, 44, 20966--20981 | 20975

View Article Online
NJC
Paper
These fragments show that the major fragmentation pathway signal at 19.93–19.71 ppm is typical for a trisubstituted boron
involves the initial cleavage of the O–B and N–B bonds for the atom. Therefore, a trisubstituted boron atom is more acidic
trinuclear boron complexes. The ion peak at m/z 297 corresponding than the other two. The chemical shifts are indicative of tetra-
to [[HOArCHQN–(CH2)4–NQCHArOHH]+] is also attributed to the and trisubstituted boron atoms and these shifts are in agrement
cleavage of O–B and N–B bonds in two dinuclear complexes 2cI and with findings in the literature for tetra- and trisubstituted boron
2cII from the (CH2)4 chain precursor.
atoms.31
The 1H and 13C NMR spectral data establish the symmetrical
nature of the boron complexes. The 1H (Fig. S26–S36, ESI†) and
3.2. IR spectroscopy
The IR spectra of the boron complexes (Fig. S2–S13, ESI†) show 13C NMR (Fig. S37–S47, ESI†) resonances of the boron com-
that the nCQN stretching frequencies (1638–1649 cmꢀ1) are plexes are summarized in Tables 3–5, respectively. The assign-
shifted to higher wavenumbers (Dn = 12–30 cmꢀ1) compared to ments were made unambiguously by HSQC (Fig. S48–S58,
the free SalenH2 ligands [1a (1618 cmꢀ1), 1b (1625 cmꢀ1) and 1c ESI†). The 1H and 13C NMR spectra reflect the differences
(1624 cmꢀ1)]. This is due to the N - B coordination, which between the two sets of isolated boron complexes. The spectra
serves to increase the electron density in the CQN bonds. In of 2bI, 2bII, 3bI and 3bII [R = (CH2)3] show one set of signals
addition, compared with the IR spectra of the SalenH2 ligands, corresponding to only one diastereoisomer. However, the spectra
the IR spectra of the complexes display new absorption bands of 2aI, 2aII, 3aI and 3aII [R = (CH2)2] and 2cII [R = (CH2)4] show
appearing at 1557–1562 cmꢀ1 and 1300–1319 cmꢀ1 indicating greater complexity due to doubling of the signals for the diaster-
the existence of N–B and O–B bonds, respectively.
eoisomers. In the 1H NMR spectra of 2aI, 2aII, 2cII, 3aI and 3aII,
the two sets of signals corresponding to the meso and enantio-
meric isomers are readily assigned to HCQN (2aI, 2aII, 2cII, 3aI),
3.3. NMR spectroscopy
The existence of N–B and O–B bonds was established by 11B CHO (2aII, 2cII, 3aII), H3 (2aII, 3aI), H7 (2aI, 2aII, 3aII) and H9
NMR (Fig. S14–S25, ESI†). It is not understandable from the 11
B
(2aI, 2aII) and integration of the signals is consistent with the
NMR spectra whether the complexes contain a diastereomer populations of the two isomers in ratios of 65 : 35 (2aI), 96 : 4
mixture or not. For the dinuclear boron complexes (2aI–2cI and (2aII), 86 : 14 (2cII), 53 : 47 (3aI), and 52 : 48 (3aII) (Tables 3 and 4).
2aII–2cII), the signals at 4.13–1.77 ppm are characteristic of the The disappearance of the singlet signals at 13.4 (1a), 13.5 (1b) and
tetrasubstituted boron atoms (Table 2). For the trinuclear 13.6 (1c) ppm assigned to the Ar–OH protons of the SalenH2
1
complexes (3aI–3cI and 3aII–3cII), this signal is slightly high- ligands (1a–1c) in the H NMR spectra of the boron complexes
field-shifted Dd = 2.56–0.16 ppm and additionally a less intense indicates that the phenolic oxygen atoms are covalently bonded
Table 4 1H NMR data (d6-DMSO) of trinuclear boron complexes (3aI–3cI and 3aII–3cII) (d in ppm, J in Hz, s: singlet, d: doublet, t: triplet, and
m: multiplet)
3aI
3bI‡
3cI‡
3aII
3bII‡
3cII‡
H
A
B
Enantiomeric
Enantiomeric
A
B
meso
Enantiomeric
NCH2CH2
NCH2
CHO
HCQN
ArH
—
—
2.53 (m,2H)
3.85 (t,4H)
—
1.77 (m,4H)
3.76 (m,4H)
—
—
—
2.23 (m,2H)
3.81 (m,8H)
9.91 (s,2H)
8.62 (s,2H)
—
7.59 (d,2H)
7.69 (d,2H)
7.47 (d,2H)
6.90–6.80
7.48 (t,2H)
6.90–6.80
—
1.93 (m,4H)
3.80 (m,8H)
9.92 (s,2H)
8.67 (s,2H)
—
7.60 (d,2H)
7.87 (d,2H)
7.55–7.41
6.97–6.80
7.55–7.41
6.97–6.80
—
3.98 (m,4H)
—
4.07 (m,4H)
—
4.06 (m,4H)
9.82 (s,2H)
3.99 (m,4H)
9.91 (s,2H)
8.63 (s,4H)
7.18 (d,2H)
7.17 (t,4H)
8.61 (s,2H)
7.13 (d,1H)
7.25 (m,2H)
7.47 (d,2H)
7.73 (m,2H)
6.82 (m,2H)
7.41 (m,2H)
6.88 (d,2H)
6.4
8.0
**
**
7.6
8.65 (s,2H)
7.11 (m,1H)
7.21 (m,2H)
7.39 (d,2H)
7.68 (m,2H)
6.82 (t,2H)
7.40 (m,2H)
6.85 (m,2H)
**
7.2
7.6
7.2
**
8.63 (s,4H)
H1
H2
H3
H7
H8
H9
H10
—
—
7.42 (d,4H)
7.54 (d,2H)
7.53 (d,4H)
6.96 (t,2H) 6.91 (t,2H)
7.52 (t,4H)
6.84 (d,2H) 6.90 (d,2H)
6.0
8.4
8.8
7.6
7.8
7.57 (d,2H)
7.68 (d,2H)
7.53 (d,2H)
7.47 (d,2H)
7.65 (d,2H)
6.91 (t,4H)
7.50 (t,4H)
6.90 (d,4H)
3J1–2
3J2–3
3J7–8
3J8–9
3J9–10
—
8.0
7.6
—
7.6
8.0
8.4
7.8
7.6
7.6
7.6
7.6
8.0
8.0
8.0
**
**
**
7.6
7.2
‡
A designates a major diastereoisomer. A: meso and B: enantiomeric or A: enantiomeric and B: meso forms, poor solubility, ** not calculated.
20976 | New J. Chem., 2020, 44, 20966--20981 This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020

View Article Online
Paper
NJC
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020
New J. Chem., 2020, 44, 20966--20981 | 20977

View Article Online
NJC
Paper
to the boron atoms. The same result was confirmed by the IR by HPLC on a chiral column. However, the solubility problem of
spectra. the boron complexes in common organic solvents is the biggest
The singlet signals due to azomethine protons (HCQN) obstacle to this study. In addition, to our knowledge, no report
[8.59 (1a), 8.58 (1b) and 8.56 (1c) ppm in the free SalenH2 has appeared in the literature on the performance to separate
ligands] are shifted towards higher fields for 2aI and 2bI, and diastereoisomers or enantiomers of boron complexes derived
lower fields for 2aII, 2bII, 2cII, 3aI, 3bI, 3cI, 3aII, 3bII and 3cII, from arylboronic acids and imine ligands and stereogenic only
confirming the involvement of azomethine nitrogen in the at B-atom/atoms.
formation of the boron complexes. Upfield shifts are expected
for the dHCQN values of the boron complexes, compared to
3.5. Interactions of DNA with the compounds
those of the SalenH2 ligands (1a–1c). This situation depends on
3.5.1. Agarose gel electrophoresis. When circular plasmid
the electron density around the HCQN bonds increasing by DNA is subjected to electrophoresis, relatively fast migration is
electron delocalization throughout the six-membered BOPhCN observed in the intact supercoiled form (Form I). If a scission
rings after the N - B coordination, and this is in agreement occurs on one strand (nicked circular), then the supercoil form
with observations on similar structures.32 However, this is relaxes to generate a slower-moving open circular form
observed for dinuclear boron complexes 2aI and 2bI. The (Form II). If both strands are cleaved, a linear form (Form III)
downfield shifts for the dHCQN values of the dinuclear 2aII that migrates between forms I and II is generated.34 The cleaving
and 2bII and trinuclear 3aII and 3cII boron complexes can be activities of the complexes against pBR322 plasmid DNA were
attributed to the electronic changes induced by the p-CHO tested by agarose gel electrophoresis study. Two concentrations
group in the B-phenyl moiety, which has an electron with- of the complexes were tried. In Fig. 4, C is the control line where
drawing effect. The existence of stereogenic centers at the two no compounds have been added to the pBR322 plasmid DNA.
boron atoms gives rise to diastereotopic signals for the methylene There is mainly one large band of supercoiled DNA (Form I) and
hydrogens (Dd = 0.04–0.30 ppm for NCH2 and Dd = 0.33–0.52 ppm a low amount of the nicked DNA (Form II) above it. Form II
for NCH2CH2).
becomes larger with a scission. When multiple scissions
The 13C NMR spectra of the seven- (2aI, 2aII, 3aI and 3aII) occurred in both strands, fast-moving small DNA pieces
and nine- (2cII) membered heterocycles exhibit two sets of (Form III) were formed for 2bI, 2aII, 2bII and 3bII. While the
signals, which correspond to the meso and enantiomeric iso- strongest activity was found in the complexes from the (CH2)3
mers (Fig. S48, S50, S52, S53, S56, ESI† and Table 4). The NMR precursor, no activity was observed in the complexes from the
signals of the aromatic ipso carbon atoms (C4) for the boron (CH2)4 precursor. The scission activities can be put into order as
complexes except 3aI and 3aII were not detectable, which may 3bII 4 2bII 4 2bI 4 2aII 4 3cII. The Schiff bases and starting
be due to the fast relaxation caused by the magnetic interaction materials showed no activity against pBR322 plasmid DNA at a
with the boron nuclei.33
very high [DNA]/[complex] ratio (Fig. 5).
Consequently as explained above, the 1H and 13C NMR
3.5.2. UV titrations. The complexes with the (CH2)3 pre-
spectra of some of the complexes indicate that there are only cursor (2bI, 2bII, 3bI and 3bII) were titrated with DNA solutions
a meso (cis) (RS/SR) isomer and two enantiomers (RR/SS) in the for the evaluation of changes in the UV spectra (Fig. 6) because
racemic (trans) mixtures. It is understood that both isomers do of their high cleavage activities against pBR322. When the DNA
not form equally. One might expect to separate the diastereo- concentration increases, the degree of hypochromism also
isomers or enantiomers of these boron complexes into components increases according to the UV spectra of the complexes, indicating
Fig. 4 The electrophoretograms of pBR322 plasmid DNA (15 mM) in the presence of the complexes at two concentrations where the [DNA]/[complex]
ratios are 0.8 and 8, respectively, in 50 mM ammonium acetate buffer, pH 7.4. ‘‘C’’ is for control; only DNA, no compounds added.
20978 | New J. Chem., 2020, 44, 20966--20981
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020

View Article Online
Paper
NJC
complex 3bII into the DNA grooves. For better evaluation and
comparison between the complexes, the binding constants Kb were
calculated:
[DNA]/(eA ꢀ ef) = [DNA]/(eB ꢀ ef) + 1/Kb(eB ꢀ ef)
where [DNA] is in base pairs, eA is the absorption coefficient of the
complex for each measurement, and ef and eB are the absorptivity
values of the free and the fully bound form of the complex. The
binding constant Kb is given by the ratio of the slope to the intercept
in the [DNA]/(eA ꢀ ef) vs. [DNA] plot. The calculated binding
constants were found to be around 104 Mꢀ1, comparable to recent
spiro-cyclotriphosphazenes containing 4-hydroxyphenylethyl pen-
dant arms.35 According to Table 6, the highest binding constant
among the boron complexes with seven-membered heterocycles was
observed for 3bII, similar to its cleavage activity. On the other hand,
Fig. 5 The electrophoretograms of pBR322 plasmid DNA (15 mM) in
50 mM ammonium acetate buffer, pH 7.4, in the presence of the Schiff
bases and the starting materials. Lane 1 is for the control; only DNA, no
compounds added. Lanes 2–7 are for 1a, 1b, 1c, boric acid, phenylboronic
acid and 4-formylphenylboronic acid, respectively. The [DNA]/[com-
pound] ratios are 12.
a mode of groove binding. In addition to the hypochromism, the lowest binding value belongs to complex 3bI, which has no
a bathochromic shift (2–3 nm) indicated a stronger insertion of activity against pBR322 plasmid DNA in the electrophoresis study.
Fig. 6 The change in the absorption spectra of complexes from the (CH2)3 precursor (2bI, 2bII, 3bI and 3bII) (20 mM) in 50 mM ammonium acetate
buffer on the addition of CT-DNA: 0–32 mM. The arrows show the absorbance change with an increase in DNA concentration. The insets show plots of
DNA concentration divided by the difference between the apparent absorption coefficient (eA) and the absorption coefficient of the free complexes (ef)
versus DNA concentration.
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020
New J. Chem., 2020, 44, 20966--20981 | 20979

View Article Online
NJC
Paper
Table 6 Binding constants of the complexes for double-stranded DNA
(calf-thymus DNA)
Eventually, the complexes have moderate binding constants
(Table 6) for the double-stranded DNA with the groove binding
mode. There is a paper on DNA cleavage activity studies of boric
acid complexes obtained from the reaction of citric, glucuronic
and salicylic acids with boric acid in the literature.19 The paper
concluded that there was an intercalative interaction between
the boric acid complexes and DNA. This result is consistent
with the findings of the present study.
Complexes
2bI
2bII
3bII
3bI
Kb (ꢁ 104 Mꢀ1
)
0.50
0.62
1.50
0.14
The stability of SalenH2 ligands in aqueous solutions was
always debated.36 DNA titration of SalenH2 ligand 1b was also
performed and a similar interaction pattern was observed (Fig. 7a).
When the compound was studied without DNA addition in the
titration conditions at room temperature, a new formation takes
place within a short time after the compound is introduced into
the buffer solution (Fig. 7b). Once the new species occurred in the
solution it was again titrated with DNA for new possible inter-
actions. However, there was no change in the UV spectrum of the
‘‘decomposed’’ SalenH2 ligand (Fig. 7c), indicating that the decom-
position products did not interact with DNA. The electrophoresis
study of the other SalenH2 ligands (1a and 1c) gave similar results.
4. Conclusions
The synthesis, spectroscopic characterization and stereoisomerism
of two different architectural types of tetrahedrally coordinated
multi-heterocyclic boron compounds, namely di- and trinuclear
boron complexes, were studied and compared with each other.
These complexes have two equivalent chiral B-centers, giving rise
to diastereoisomers. According to the 13C and 1H NMR spectra of
the complexes, it was understood that two dinuclear (2bI and 2bII)
and two trinuclear (3bI and 3bII) boron complexes from the (CH2)3
precursor and two trinuclear (3cI and 3cII) from the (CH2)4
precursor were present as only one diastereomer, whereas two
dinuclear (2aI and 2aII) and two trinuclear (3aI and 3aII) boron
complexes from the (CH2)2 precursor and one dinuclear (2cII)
complex from the (CH2)4 precursor were found to be diastereo-
meric mixtures. More reliable results were obtained by the combi-
nation of the NMR and CD spectra of the complexes. On the other
hand, CD spectroscopy is a potential tool for determining which of
the diastereoisomers in the diastereomeric boron complexes is
present and whether the boron complex contains only a single
diastereoisomer or a mixture of diastereoisomers.
Furthermore, when all DNA interaction studies were con-
sidered together, the seven-membered boron complexes from
the (CH2)3 precursor were found to be the most effective ones in
each architectural type of the boron complexes. Whether it is a
dinuclear or trinuclear boron complex or whether there is a
CHO group in the phenyl ring or not, the number of methylene
groups in the (CH2)n chain precursors or the number of
members in the [(B–O–B)–(N–R–N)] heterocyclic ring was found
to have a significant impact on the DNA cleavage activity. When
compared to the DNA cleavage ability of dinuclear (2bI and
2bII) and trinuclear (3bI and 3bII) boron complexes with an
eight-membered heterocycle, cleavage was found to be the most
efficient in the presence of trinuclear boron complex 3bII. This
result can be explained by the fact that trinuclear boron
complex 3bII contains a planar phenyl ring and a CHO group
compared to the dinuclear complexes, and this part may
increase the groove binding mode of DNA by van der Waals
interactions.
In addition, in the trinuclear boron complexes, two boron
atoms have tetrahedral and one boron atom has trigonal planar
geometry. Considering that the trigonal planar boron atom may
still act as a Lewis acid, the trinuclear boron complexes might
be useful as a catalyst for asymmetric synthesis.
Fig. 7 The change in the absorption spectra of 1b (20 mM) in 50 mM
ammonium acetate buffer at pH 7.4 (a) on the addition of CT-DNA:
0–32 mM. The arrows show the absorbance change with an increase in
DNA concentration. (b) (The stability titration) After 1b is introduced into
the solution the absorption peak at 400 nm started to decrease and
completely disappeared at the 20th minute. However, the peak at
320 nm increased. (c) (After decomposition) No change can be seen upon
addition of DNA.
As a result, this study answers the following questions:
(1) The extent to which the reaction is stereospecific at the
20980 | New J. Chem., 2020, 44, 20966--20981 This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020

View Article Online
Paper
NJC
14 M. Braun, S. Schlecht, M. Engelmann, W. Frank and
S. Grimme, Eur. J. Org. Chem., 2008, 5221–5225.
15 L.-M. Chen, J. Liu, J.-C. Chen, S. Shi, C.-P. Tan, K.-C. Zheng
and L.-N. Ji, J. Mol. Struct., 2008, 881, 156–166.
16 F. Yang, M. Zhu, J. Zhang and H. Zhou, MedChemCommun,
2018, 9, 201–211.
two equivalent chiral boron centers, and what factors determine
the major diastereoisomer produced by reaction of a SalenH2
ligand. (2) The influence of the formyl group CHO attached to
the benzene ring on the formation of diastereoisomers and DNA
cleavage.
17 J. Zhang, F. Yang, Z. Qiao, M. Zhu and H. Zhou, Bioorg. Med.
Chem. Lett., 2016, 26, 5797–5801.
Conflicts of interest
18 F. Ali, N. S. Hosmane and Y. Zhu, Molecules, 2020, 25, 828.
There are no conflicts to declare.
¨
19 A. Arslantas, A. K. Devrim, M. Sudagidan and D. A. Kose,
J. Chem., 2013, 406161.
Acknowledgements
20 R. C. Kane, P. F. Bross, A. T. Farrell and R. Pazdur, Oncol-
ogist, 2003, 8, 508–513.
21 A. Markham, Drugs, 2014, 74, 1555–1558.
22 A. Natsagdorj, PhD thesis, Ankara University, Department of
Chemistry, 2002.
Selen Bilge Koçak is grateful to the Ankara University Scientific
Research Projects (BAP) (Project No. 13B4240011). Zeynel Kılıç
thanks Turkish Academy of Sciences (TUBA) for partial support
¨
of this work.
´
¨
´
23 M. Sanchez, H. Hopfl, M.-E. Ochoa, N. Farfan, R. Santillan
and S. Rojas, Inorg. Chem., 2001, 40, 6405–6412.
´
¨
´
24 G. Vargas, I. Hernandez, H. Hopfl, M.-E. Ochoa, D. Castillo,
References
´
N. Farfan, R. Santillan and E. Gomez, Inorg. Chem., 2004, 43,
1 S. Dutta and A. J. Geliman, Chem. Soc. Rev., 2017, 46, 7787–7839.
8490–8500.
2 F. A. Davis and R. H. Jenkins Jr., in Asymmetric Synthesis: 25 A. N. Wein, A. T. Stockhausen, K. I. Hardcastle, M. R.
Synthesis and Utilization of Compounds with Chiral Nitrogen
Centers, ed. J. D. Morrison and J. W. Scott, Academic Press,
San Diego, 1984, ch. 4, vol. 4.
Saadein, S. Peng, D. Wang, D. M. Shin, Z. Chen and
J. F. Eichler, J. Inorg. Biochem., 2011, 105, 663–668.
˙
26 Q. I. Zhou and P. Yang, Inorg. Chim. Acta, 2006, 359, 1200–1206.
3 A. Uslu and S. Yes-ilot, Coord. Chem. Rev., 2015, 291, 27 U. Yildiz, A. Sengul, I. Kandemir, F. Comert, S. Akkoç and
28–67. B. Coban, Bioorg. Chem., 2019, 87, 70–77.
4 J. R. Jagannathan, J. C. Fettinger, J. T. Shaw and A. K. Franz, 28 E. Pidcock, Chem. Commun., 2005, 3457–3459.
¨
˙
˘
29 N. Asmafiliz, I. Berberoglu, M. Ozgu¨r, Z. Kılıç, H. Kayalak,
J. Am. Chem. Soc., 2020, 142, 11674–11679.
´
´
¨
5 S. Otocka, M. Kwiatkowska, L. Madalinska and P. Kiełbasinski,
L. Açık, M. Tu¨rk and T. Hokelek, Inorg. Chim. Acta, 2019,
Chem. Rev., 2017, 117, 4147–4181.
495, 118949.
¨
6 E. Vedejs, S. C. Fields, R. Hayashi, S. R. Hitchcock, D. R. 30 G. Elmas (nee Egemen), A. Okumus-, Z. Kılıç, T. Hokelek,
˘
Powell and M. R. Schrimpf, J. Am. Chem. Soc., 1999, 121,
L. Açık, H. Dal, N. Ramazanoglu and L. Y. Koç, Inorg. Chem.,
2460–2470.
2012, 51, 12841–12856.
´
7 S. Thormeier, B. Carboni and D. E. Kaufmann, J. Organomet. 31 V. Barba, E. Gallegos, R. Santillan and N. Farfan,
Chem., 2002, 657, 136–145.
J. Organomet. Chem., 2001, 622, 259–264.
8 D. J. Owen, D. VanDerveer and G. B. Schuster, J. Am. Chem. 32 A. Gonzalez-Hernandez, A. Leon-Negrete, J. M. Galvan-Hidalgo,
´
´
´
´
´
Soc., 1998, 120, 1705–1717.
E. Gomez and V. Barba, J. Mol. Struct., 2020, 1207, 127779.
´
9 H. I. Beltran, L. S. Zamudio-Rivera, T. Mancilla, R. Santillan 33 M. M. Reichvilser, C. Heinzl and P. Klufers, Carbohydr. Res.,
´
and N. Farfan, J. Organomet. Chem., 2002, 657, 194–204.
2010, 345, 498–502.
¨
10 E. Vedejs, R. W. Chapman, S. Lin, M. Mu¨ller and 34 N. S. Bas-terzi, S. Bilge Koçak, A. Okumus-, Z. Kılıç, T. Hokelek,
¨
D. R. Powell, J. Am. Chem. Soc., 2000, 122, 3047–3052.
11 S. Schlecht, W. Frank and M. Braun, Beilstain J. Org. Chem.,
2011, 7, 615–621.
O. Çelik, M. Tu¨rk, Y. Koç, L. Açık and B. Aydın, New J. Chem.,
2015, 39, 8825–8839.
35 S. Pektas-, S. Bilge Koçak, N. S. Bas-terzi, Z. Kılıç, C. T. Zeyrek,
¨
12 S. Schlecht, W. Frank and M. Braun, Eur. J. Org. Chem., 2010,
3721–3731.
B. Coban, U. Yildiz and O. Çelik, Inorg. Chim. Acta, 2018,
474, 51–65.
13 P. F. Kaiser, J. M. White and C. A. Hutton, J. Am. Chem. Soc., 36 E. H. Cordes and W. P. Jencks, J. Am. Chem. Soc., 1962, 84,
2008, 130, 16450–16451. 832–837.
This journal is ©The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2020
New J. Chem., 2020, 44, 20966--20981 | 20981