Synthesis of novel anthraquinones: Molecular structure, molecular chemical reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs

Article abstract of DOI:10.1016/j.molstruc.2016.10.098

Anthraquinones are well-known anticancer drugs. Anthraquinones anticancer drugs carry out their cytotoxic activities through their interaction with DNA, and inhibition of topoisomerase II activity. Anthraquinones (AQ5 and AQ5H) were synthesized and studied with 1,5-DAAQ by computational and experimental tools. The purpose of this study is to shade more light on mechanism of interaction between anthraquinone DNA affinic agents and different types of DNA. This study will lead to gain of information useful for drug design and development. Molecular structures were optimized using DFT B3LYP/6-31 + G(d). Depending on intramolecular hydrogen bonding interactions four conformers of AQ5 were detected within the range of about 42 kcal/mol. Molecular reactivity of the anthraquinone compounds was explored using global and condensed descriptors (electrophilicity and Fukui functions). NMR and UV–VIS electronic absorption spectra of anthraquinones/DNA were investigated at the physiological pH. The interaction of the anthraquinones (AQ5 and AQ5H) were studied with different DNA namely, calf thymus DNA, (Poly[dA].Poly[dT]) and (Poly[dG].Poly[dC]). UV–VIS electronic absorption spectral data were employed to measure the affinity constants of drug/DNA binding using Scatchard analysis. NMR study confirms qualitatively the drug/DNA interaction in terms of peak shift and broadening.

Full text of DOI:10.1016/j.molstruc.2016.10.098

Journal of Molecular Structure xxx (2016) 1e11
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: http://www.elsevier.com/locate/molstruc
Synthesis of novel anthraquinones: Molecular structure, molecular
chemical reactivity descriptors and interactions with DNA as antibiotic
and anti-cancer drugs
,
, *
Jamelah S. Al-Otaibi a b, Tarek M. EL Gogary c
a Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11951, Saudi Arabia
b Deanship of Scientific Research, Princess Nora Bint Abdul Rahman University, Saudi Arabia
c Department of Chemistry, Faculty of Science, Jazan University, Jazan, Saudi Arabia
a r t i c l e i n f o
a b s t r a c t
Article history:
Anthraquinones are well-known anticancer drugs. Anthraquinones anticancer drugs carry out their
cytotoxic activities through their interaction with DNA, and inhibition of topoisomerase II activity. An-
thraquinones (AQ5 and AQ5H) were synthesized and studied with 1,5-DAAQ by computational and
experimental tools. The purpose of this study is to shade more light on mechanism of interaction be-
tween anthraquinone DNA affinic agents and different types of DNA. This study will lead to gain of in-
formation useful for drug design and development. Molecular structures were optimized using DFT
B3LYP/6-31 þ G(d). Depending on intramolecular hydrogen bonding interactions four conformers of AQ5
were detected within the range of about 42 kcal/mol. Molecular reactivity of the anthraquinone com-
pounds was explored using global and condensed descriptors (electrophilicity and Fukui functions). NMR
and UVeVIS electronic absorption spectra of anthraquinones/DNA were investigated at the physiological
pH. The interaction of the anthraquinones (AQ5 and AQ5H) were studied with different DNA namely, calf
thymus DNA, (Poly[dA].Poly[dT]) and (Poly[dG].Poly[dC]). UVeVIS electronic absorption spectral data
were employed to measure the affinity constants of drug/DNA binding using Scatchard analysis. NMR
study confirms qualitatively the drug/DNA interaction in terms of peak shift and broadening.
© 2016 Elsevier B.V. All rights reserved.
Received 29 August 2016
Received in revised form
30 October 2016
Accepted 31 October 2016
Available online xxx
Keywords:
Anthraquinone
Anti-cancer
Reactivity descriptors
NMR
Scatchard analysis
1. Introduction
other hand, they can cause inhibition of topoisomerase II activity,
leading to DNA damage. The development of novel potent che-
Quinone-containing compounds are a series of widespread
compounds found in nature. Quinones and quinone-derivatives are
important class of molecules, having high importance in dye in-
dustry, biology and pharmaceutical chemistry [1e7].These com-
pounds are known to perform many biochemical and physiological
processes in living organisms. Anthraquinones, as a group of nat-
ural quinones, are widely used in treatment of cancer [8e11]. An-
thraquinones anticancer drugs carry out their cytotoxic activities
through their interaction with DNA, preferentially at guanine/
cytocine rich sites [12]. This interaction is believed to cause sig-
nificant conformational changes in the DNA leading to inhibition of
the DNA replication [12]. This may lead to DNA damage. On the
motherapeutics and design of small drug molecules that selectively
target DNA, with high binding constants, has led to the discovery of
many anticancer, antibiotic, and antiviral drugs [13e21]. Most DNA-
targeted molecules start their binding with double helix DNA non-
covalently which subsequently may developed to covalent binding.
Non-covalent binding may include
p-stacking, hydrogen bonding,
electrostatic, charge transfer, and hydrophobic interactions [12]. All
these interactions may contribute to the drug/DNA interaction
mechanism so that the main objective of this study is to explore the
dominant interaction. This information is crucial for design and
development of new anthraquinone antibiotic and anticancer
drugs.
Of the anthraquinones, the ones having hydroxy and amino
substituents have been extensively investigated, to understand
their biochemical activity [22e34]. For this study the following
amino and hydroxy anthraquinone derivatives (Scheme 1), 1,5-bis
{[2-(methylamino)ethyl]amino}-4,8-dihydroxy anthracene-9,10-
* Corresponding author. Department of Chemistry, Faculty of Science, Damietta
University, New Damietta City, Egypt.
E-mail address: tarekelgogary@yahoo.com (T.M. EL Gogary).
http://dx.doi.org/10.1016/j.molstruc.2016.10.098
0022-2860/© 2016 Elsevier B.V. All rights reserved.
Please cite this article in press as: J.S. Al-Otaibi, T.M. EL Gogary, Synthesis of novel anthraquinones: Molecular structure, molecular chemical
reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs, Journal of Molecular Structure (2016), http://dx.doi.org/
10.1016/j.molstruc.2016.10.098

2
J.S. Al-Otaibi, T.M. EL Gogary / Journal of Molecular Structure xxx (2016) 1e11
O
NH2
NH2
O
AQ5
AQ5H
1,5-DAAQ
Scheme 1. Studied anthraquinones.
solution (1%, 1000 cm3). The mixture was neutralised to pH 7
with 5 M sodium hydroxide. The titled compound was extracted
from the aqueous phase with CH2Cl2 and concentrated. Column
chromatography (SiO2, (9:1 CH2Cl2/MeOH) gave AQ5 (1.2 g,
dione, (AQ5), and 1,5-bis{[2-(methylamino)ethyl]amino}anthra-
cene-9,10-dione, (AQ5H) and 1,5-diaminoanthraquinone were
chosen for this study.
20%). Rf(9:1 CH2Cl2/MeOH):0.17. 1H NMR
d
(CDCl3): 13.99 (s, 2H),
2. Experimental details
9.8 (t, 2H), 7.2 (d, 2H), 7.0 (d, 2H), 3.42 (q, 4H), 2.65 (t, 4H), 2.33
(s, 12H). 13C NMR
d (CDCl3): 186.5, 154.9, 137, 135, 115, 114, 58.1,
The UVeVIS absorption spectra were measured using a Perkin
Elmer Lambda-16 UVeVIS Spectrophotometer. NMR spectra were
recorded in CDCl3 using a Bruker AC250 at 30 ꢀC utilizing these
experimental parameters: 250 MHz, 5.9 T, 5 mm multinuclear
broadband probe, Receiver Gain RG ¼ 8, Pulse Width PW ¼ 4,
Relaxation Delay RD ¼ 2 and Number of Scan NS ¼ 8. DNA con-
centrations per nucleotide were determined spectrophotometri-
cally using the molar absorption coefficient: ε 260 ¼ 6600 Mꢁ1 cmꢁ1
to be 1.061 ꢂ 10ꢁ4 M. NMR spectra of drug/DNA mixtures were
measured at 30 ꢀC. Two or three mixture solutions were produced
by accurate dilution from the stock solutions keeping AQs con-
centration constant while varying the concentration of the DNA,
were run and compared with the spectra of pure drug. The chem-
ical shift of the AQs bands were measured with reference to the
TMS band as internal standard.
45.5, 40.95. Mass spectrum, m/z 413 (mþ þ 1). Anal. Calcd. For
C22H28O4N4.0.5H2O: C, 62.7; H, 6.7; N, 13.3. Found: C, 62.7; H,
6.9; N, 13.3. UVeVIS Lambda max 642, 600, 238.
3. Computations
All computations were done using G09 suit of programs [38].
Molecular geometry of anthraquinone compounds were optimized
in the gas phase at DFT B3LYP/6-31 þ G(d,p) level of theory. A
frequency job was performed on the optimized geometry to
confirm a minimum energy structure. Fukui functions were calcu-
lated using DMol3 module [39,40] employing B3LYP/DND method
implemented in Material studio program [41].
Calf thymus DNA, polydeoxyadenylic acid-polythymidylic acid
(Poly[dA].Poly[dT]) and polydeoxyguanylic acid-polydeoxycytidylic
acid (Poly[dG].Poly[dC]) were purchased from Sigma Chemical Co
and were used without further purification. 1,4-DAAQ and D2O
(99.9% D) were purchased from Aldrich. Trizma base (Tris[hydrox-
ymethyl] aminomethane) and NaCl were supplied from Sigma and
used for buffer preparation without further purification.
Synthesis of anthraquinone drugs
1,5-bis {[2-(methylamino)ethyl]amino}-4,8-dihydroxy anthra-
cene-9,10-dione, (AQ5), and 1,5-bis{[2-(methylamino)ethyl]amino}
anthracene-9,10-dione, (AQ5H) were synthesized according to the
following method [35e37]:
4. Results and discussion
4.1. Computational work
4.1.1. Molecular geometry
Since there is no reported experimental molecular geometrical
data for AQ5 and AQ5H, we calculated the geometry of AQ5, AQ5H
and 1,5-DAAQ at B3LYP/6-31 þ G(d). Based on possibility of intra
molecular hydrogen bonding formation, four minimum energy
conformers, Conf-1, Conf-2, Conf-3 and Conf-4, of AQ5 were studied
and displayed in Fig.1. Conf-1 allows four intra-molecular hydrogen
bonds while Conf-2 allows three intra-molecular hydrogen bonds
and Conf-3 and Conf-4 allow two and one intra molecular hydrogen
bonds respectively (see Fig. 1). The relative total energies differ-
ences are shown in Fig. 1. Conf-1 with four intra molecular
hydrogen bonds is the most stable structure separating from Conf-
4, with only one hydrogen bond, by 41.858 kcal/mol. Conf-2 with
three hydrogen bonds is the next stable structure with energy
difference 15.762 kcal/mol and Conf-3, with two hydrogen bonds, is
separating from Conf-1 by 27.045 kcal/mol. Conformer with no
intra molecular hydrogen bonds was also studied however, an
optimized minimum structure has not been obtained.
AQ5H synthesis
1 1,5-dichloroanthraquinone (15 g, 54 mmol) was dissolved in
N,N-dimethylethylenediamine (47.6 g, 540 mmol) and refluxed
for 18 h. The reaction was monitored by TLC (9:1 CH2Cl2/MeOH).
The mixture was cooled to room temperature and diluted with
water to precipitate the title compound. The filtered solid was
recrystallized from methanol to afford AQ5H (15.8 g, 89%) as a
crystalline solid. Rf(9:1 CH2Cl2/MeOH): 0.60. 1H NMR
d (CDCl3):
9.8 (t, 2H), 7.6 (m, 4H), 6.9 (m, 2H), 3.4 (q, 4H), 2.7 (t, 4H), 2.4 (s,
12H). Mass spectrum, m/z 381 (mþ þ 1).
Optimized geometry of AQ5 conformers are shown in Fig. 1. All
optimized geometrical parameters of AQ5, Conf-1-4, are repre-
sented in Tables S1eS4 in the Supplementary Material. Vibrational
frequencies for AQ5 Conf-1 were computed to confirm the mini-
mum energy structure and given in Table S5 in Supplementary
Materials.
AQ5 synthesis
2 The AQ5H (6 g,15.8 mmol) was dissolved in 65 g of concentrated
sulphuric acid and cooled to ꢁ10 ꢀC. Anhydrous sodium chlorate
(6.5 g, 61.6 mmol) was added in portions over 1.5 h and the
mixture then stirred for 3 h at room temperature. The blue so-
lution was added slowly to cold sodium hydrogen sulfite
In Conf-1, the carbonyls bond lengths C7]O15 and C10 ¼ O16 are
identical and calculated as 1.273 Å. The reason for being the same
Please cite this article in press as: J.S. Al-Otaibi, T.M. EL Gogary, Synthesis of novel anthraquinones: Molecular structure, molecular chemical
reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs, Journal of Molecular Structure (2016), http://dx.doi.org/
10.1016/j.molstruc.2016.10.098

J.S. Al-Otaibi, T.M. EL Gogary / Journal of Molecular Structure xxx (2016) 1e11
3
Fig. 1. Optimized Structure of AQ5 Conf-1-5, AQ5H and 1,5-DAAQ showing atomic numeration and H-bonding.
Please cite this article in press as: J.S. Al-Otaibi, T.M. EL Gogary, Synthesis of novel anthraquinones: Molecular structure, molecular chemical
reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs, Journal of Molecular Structure (2016), http://dx.doi.org/
10.1016/j.molstruc.2016.10.098

4
J.S. Al-Otaibi, T.M. EL Gogary / Journal of Molecular Structure xxx (2016) 1e11
length is because of the symmetry of the molecule and the
engagement of the O15 and O16 with two intramolecular hydrogen
bonds. Formation of hydrogen bond results in more polarization of
the carbonyl group and hence decreasing duple bond character
which affect the elongation of the bond. Bond lengths of the two
DN is summarized in Table 1. Inspection of the calculated charge,
as shown in the Table shows that the charge transfer takes place
from DNA base pairs (AT and GC) to anthraquinones. The higher
transferred charge with GC reflects the extent of interaction be-
tween anthraquinone and DNA base pair which is in agreement
with our previous experimental studies [12]. AQ5 and AQ5H are
electron acceptors to A, C, and G while they are electron donors
toward T. 1,5-DAAQ has an electron accepting nature toward all
hydrogen bonds, O17H28/O15 and N18H29/O15 are 1.626 and
1.784 Å respectively. The former hydrogen bond is stronger than the
latter. This could be attributed to the higher electronegativity of the
O atom with respect to N atom. The angle C5eC4eC10 is computed
to 121.2ꢀ while the corresponding angle C2eC3eC7 is calculated is
computed 118.9ꢀ. The later angle is decreased to permit effective
hydrogen bond interaction. The same argument is true for the angle
C7eC8eC14 (121.2ꢀ) and the angle C10eC9eC11 (118.9ꢀ) where the
contraction of the later angle facilitates the OeH/O hydrogen
bond formation. The ring system in Conf-1 is fully planar as
Table 2
Condensed Fukui Functions ((fk0) (fkþ) and (fkꢁ) indices of AQ5.
Fukui Indices for
radical attack fk0
Fukui Indices for
nucleophilic attack
fkþ
Fukui Indices for
electrophilic attack
fkꢁ
appeared from the values of the dihedral angles, C7eC8eC9eC10
,
Mulliken Hirshfeld Mulliken Hirshfeld Mulliken Hirshfeld
C
C
11eC9eC8eC14
10eC16 which are almost 0.0 and 180.0ꢀ (see Table S1).
In AQ5H (Table S6 in Supplementary Materials), the hydrogen
, C2eC3eC4eC5, C3eC4eC10eO16 and C8eC9e
C (1)
C (2)
C (3)
C (4)
C (5)
C (6)
C (7)
C (8)
C (9)
C (10)
C (11)
C (12)
C (13)
C (14)
O (15) 0.035
O (16) 0.036
O (17) 0.054
N (18) 0.045
C (19)
C (20)
0.028
0.028
0.014
0.015
0.021
0.029
0.028
0.016
0.014
0.027
0.029
0.026
0.03
0.041
0.036
0.017
0.016
0.027
0.043
0.025
0.017
0.018
0.025
0.036
0.041
0.043
0.027
0.037
0.038
0.051
0.045
0.008
0.004
0.006
0.005
0.003
0.025
0.022
0.025
0.022
0.014
0.014
0.010
0.014
0.005
0.001
0.010
0.004
0.006
0.010
0.004
0.000
0.051
0.045
0.008
0.004
0.001
0.004
0.003
0.014
0.014
0.013
0.011
0.000
0.005
0.009
0.001
0.006
0.009
0.006
0.001
0.038
0.022
0.011
0.006
0.025
0.033
0.045
0.005
0.011
0.044
0.023
0.037
0.034
0.023
0.054
0.055
0.043
0.029
ꢁ0.017
0.002
0.001
ꢁ0.01
ꢁ0.008
0.049
0.045
0.049
0.047
0.015
0.015
0.017
0.026
0.009
ꢁ0.005
0.017
0.006
0.01
0.051
0.030
0.014
0.010
0.027
0.049
0.043
0.010
0.014
0.043
0.030
0.051
0.050
0.027
0.056
0.056
0.040
0.031
0.006
0.003
0.004
0.005
0.002
0.028
0.024
0.028
0.024
0.013
0.012
0.009
0.013
0.004
ꢁ0.001
0.009
0.003
0.005
0.010
0.003
ꢁ0.001
0.041
0.031
0.006
0.003
0.001
0.004
0.003
0.013
0.012
0.012
0.010
ꢁ0.001
0.004
0.009
0.000
0.006
0.009
0.006
0.001
0.018
0.034
0.016
0.025
0.017
0.025
0.011
0.026
0.018
0.01
0.034
0.016
0.025
0.016
0.016
0.016
0.065
0.062
ꢁ0.021
ꢁ0.001
0.003
ꢁ0.012
ꢁ0.01
0.043
0.04
0.031
0.042
0.020
0.023
0.027
0.037
0.008
0.024
0.021
0.008
0.043
0.030
0.037
0.027
0.018
0.019
0.061
0.060
0.010
0.006
0.007
0.006
0.004
0.022
0.020
0.022
0.020
0.015
0.017
0.012
0.016
0.005
0.002
0.010
0.004
0.007
0.011
0.005
0.000
0.061
0.059
0.010
0.005
0.002
0.005
0.003
0.015
0.017
0.014
0.013
0.000
0.006
0.009
0.001
0.006
0.010
0.006
0.001
bond N19eH20/O10 is 1.805 Å with an angle N19eH20eO10 136.4
and hydrogen bond N41eH36/O15 is 1.816 Å with an angle
N
41eH3eO15 135.4ꢀ as shown from Fig. 1. In 1,5-DAAQ, the amino
group is planar as shown from Fig. 1. The intra molecular hydrogen
bonds 17eH23/O15 and 25eH27/O16 are 1.873 with
N
N
Å
a
hydrogen bond angle 129.7ꢀ as shown from Fig. 1. This similarity of
the hydrogen bonds strength and geometry results from the sym-
metry of the molecule. Vibrational frequencies for AQ5H were
computed to confirm the minimum energy structure and given in
Table S7 in Supplementary Materials.
0.019
4.1.2. Chemical reactivity
Chemical reactivity descriptors were computed to explore the
readability of anthraquinones to interact with DNA. The density of
electrons on an atom is an important property that contains all the
information about the molecular systems. Descriptors of chemical
reactivity are good tools for predicting and understanding reac-
tivity of compounds. These descriptors initially developed within
the density functional theory framework.
ꢁ0.019
0.001
N (21) 0.002
C (22)
C (23)
ꢁ0.011
ꢁ0.009
H (24) 0.046
H (25) 0.043
H (26) 0.046
H (27) 0.043
H (28) 0.015
H (29) 0.018
H (30) 0.02
H (31) 0.029
H (32) 0.011
H (33) ꢁ0.002
H (34) 0.018
H (35) 0.007
H (36) 0.011
H (37) 0.021
H (38) 0.008
H (39) ꢁ0.003
O (40) 0.054
N (41) 0.045
0.043
0.04
0.015
0.02
Global quantities as chemical potential (
chemical hardness (ƞ), chemical softness (S), and electrophilicity
) of anthraquinones were calculated according to the equations
m), electronegativity (c),
(u
0.023
0.031
0.013
0.002
0.019
0.008
0.013
0.022
0.01
ꢁ0.002
0.065
0.061
ꢁ0.02
0.001
ꢁ0.004
ꢁ0.009
ꢁ0.01
0.015
0.02
0.029
0.025
ꢁ0.002
0.013
0.018
0.001
0.013
0.019
0.013
0
presented elsewhere [42] and presented in Table 1. From the results
in Table 1, it may be observed that the global softness decreases in
the order AQ5 > AQ5H > 1,5-DAAQ. AQ5 has the highest global
electrophilicity (7.312) and highest softness (0.439). Softness of a
molecule is a measure of its polarizability and hence, its reactivity.
In terms of softness, the reactivity of the anthraquinones goes in the
order AQ5 > AQ5H > 1,5-DAAQ.
The calculated charge transfer DN between two systems A and B
(the studied anthraquinones and DNA bases and DNA base pairs)
was computed according to the equation [42e44]:
0.02
0.007
ꢁ0.003
0.043
0.029
ꢁ0.017
0.003
ꢁ0.004
ꢁ0.008
ꢁ0.009
0.015
0.015
0.025
0.019
ꢁ0.006
0.01
C (42)
C (43)
ꢁ0.019
0.002
N (44) ꢁ0.004
Table 1
C (45)
C (46)
ꢁ0.009
ꢁ0.01
Calculated global quantities: chemical potential (
(ƞ), softness (S), and electrophilicity ( ) and charge transfer
anthraquinones and DNA bases and base pairs.
m
), electronegativity (
c), hardness
u
DN between the studied
H (47) 0.015
H (48) 0.018
H (49) 0.027
H (50) 0.022
H (51) ꢁ0.004
H (52) 0.012
H (53) 0.018
H (54) 0.000
H (55) 0.013
H (56) 0.018
H (57) 0.013
H (58) 0.000
m
c
ƞ
S
u
EHOMO
ELUMO
DEL-H
AQ5
AQ5H
ꢁ4.082 4.082 1.140 0.439 7.312 ꢁ5.222 ꢁ2.943 2.279
ꢁ4.193 4.193 1.435 0.348 6.128 ꢁ5.628 ꢁ2.759 2.870
1,5-DAAQ ꢁ4.349 4.349 1.537 0.325 6.150 ꢁ5.886 ꢁ2.811 3.075
0.017
ꢁ0.001
0.012
0.018
0.012
0
A
G
C
T
AT
GC
AQ5
AQ5H
1,5-DAAQ
ꢁ0.258
ꢁ0.508
ꢁ0.851
ꢁ0.744
ꢁ1.025
ꢁ1.367
ꢁ0.298
ꢁ0.539
ꢁ0.864
0.317
0.111
ꢁ0.215
ꢁ0.546
ꢁ0.802
ꢁ1.126
ꢁ0.820
ꢁ1.085
ꢁ1.385
Please cite this article in press as: J.S. Al-Otaibi, T.M. EL Gogary, Synthesis of novel anthraquinones: Molecular structure, molecular chemical
reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs, Journal of Molecular Structure (2016), http://dx.doi.org/
10.1016/j.molstruc.2016.10.098

J.S. Al-Otaibi, T.M. EL Gogary / Journal of Molecular Structure xxx (2016) 1e11
5
Table 3
Condensed Fukui Functions ((fk0) (fkþ) and (fkꢁ) indices of AQ5H.
Table 4
Condensed Fukui Functions ((fk0) (fkþ) and (fkꢁ) indices of 1,5-DAAQ.
Fukui Indices for
radical attack fk0
Fukui Indices for
nucleophilic attack
fkþ
Fukui Indices for
electrophilic attack
fkꢁ
Fukui Indices for
radical attack fk0
Fukui Indices for
nucleophilic attack
fkþ
Fukui Indices for
electrophilic attack
fkꢁ
Mulliken Hirshfeld Mulliken Hirshfeld Mulliken Hirshfeld
Mulliken Hirshfeld Mulliken Hirshfeld Mulliken Hirshfeld
C (1)
C (2)
C (3)
C (4)
C (5)
C (6)
C (7)
C (8)
C (9)
0.015
0.015
0.032
0.012
0.032
0.016
0.012
0.038
0.034
0.021
0.015
0.032
0.019
0.033
0.017
0.022
0.047
0.045
0.052
0.021
0.048
0.048
0.037
0.052
0.024
0.022
0.025
0.046
0.015
0.009
0.015
0.011
0.006
0.003
0.006
0.012
0.006
0.010
0.008
0.005
0.004
0.011
0.006
0.001
0.013
0.037
0.025
0.023
0.023
0.043
0.002
0.003
0.002
0.008
0.013
0.014
0.004
0.004
0.009
0.006
0.003
0.003
0.006
0.009
0.000
0.021
0.005
0.053
0.02
0.053
0.003
0.018
0.037
0.022
0.079
0.02
0.022
0.037
0.025
0.08
0.047
0.038
0.05
0.023
0.014
ꢁ0.017
0.026
0.017
0.002
ꢁ0.006
0.008
0.001
ꢁ0.01
0.017
0.01
0.006
ꢁ0.008
0.02
0.006
ꢁ0.003
0.012
0.025
0.05
0.047
0.038
0.024
0
0.006
0.003
ꢁ0.02
0.021
0.023
ꢁ0.003
ꢁ0.009
0.016
0.01
0.005
ꢁ0.007
0.01
0.017
ꢁ0.004
0.022
0.011
0.055
0.024
0.055
0.011
0.024
0.049
0.035
0.079
0.022
0.035
0.049
0.047
0.079
0.025
0.021
0.028
0.026
0.011
0.006
0.013
0.008
0.002
ꢁ0.001
0.003
0.003
0.004
0.009
0.005
0.003
0.002
0.010
0.003
ꢁ0.001
0.010
0.047
0.028
0.025
0.021
0.026
0.001
0.002
0.001
0.006
0.010
0.011
0.002
0.004
0.008
0.005
0.003
0.003
0.005
0.008
ꢁ0.001
0.009
0.024
0.01
0.004
0.012
0.03
0.007
0.039
0.046
0.025
0.006
0.05
0.038
0.005
0.025
0.041
0.038
0.043
0.07
0.022
ꢁ0.023
0.035
0.027
ꢁ0.004
0.008
0.018
0.015
ꢁ0.015
0.023
0.02
0.012
ꢁ0.013
0.025
0.017
0.002
0.02
0.005
0.045
0.04
0.042
0.061
ꢁ0.002
0.01
0.020
0.019
0.008
0.015
0.011
0.024
0.019
0.046
0.055
0.025
0.020
0.060
0.047
0.028
0.025
0.022
0.023
0.022
0.066
0.019
0.012
0.018
0.013
0.009
0.006
0.008
0.020
0.009
0.012
0.011
0.007
0.006
0.013
0.009
0.002
0.016
0.028
0.023
0.021
0.025
0.060
0.002
0.004
0.003
0.010
0.015
0.016
0.006
0.005
0.009
0.007
0.004
0.004
0.007
0.009
0.000
C (1)
C (2)
C (3)
C (4)
C (5)
C (6)
C (7)
C (8)
C (9)
C (10)
C (11)
C (12)
C (13)
C (14)
O (15) 0.057
O (16) 0.057
N (17) 0.054
H (18) 0.053
H (19) 0.045
H (20) 0.054
H (21) 0.054
H (22) 0.053
H (23) 0.023
H (24) 0.038
N (25) 0.054
H (26) 0.045
H (27) 0.023
H (28) 0.038
0.018
0.041
0.012
0.019
0.013
0.04
0.035
0.018
0.013
0.034
0.013
0.041
0.016
0.039
0.041
0.053
0.023
0.019
0.026
0.053
0.034
0.019
0.023
0.034
0.026
0.053
0.041
0.053
0.057
0.057
0.059
0.029
0.026
0.030
0.030
0.029
0.020
0.029
0.059
0.026
0.020
0.029
0.027
0.024
0.018
0.006
0.017
0.038
0.057
0.005
0.018
0.056
0.017
0.039
0.026
0.023
0.084
0.084
0.028
0.054
0.042
0.054
0.055
0.054
0.018
0.034
0.028
0.042
0.018
0.034
0.049
0.038
0.025
0.013
0.024
0.052
0.057
0.013
0.025
0.057
0.024
0.052
0.049
0.038
0.083
0.083
0.035
0.031
0.023
0.030
0.031
0.031
0.015
0.024
0.035
0.023
0.015
0.024
0.008
0.057
0.006
0.032
0.008
0.042
0.013
0.031
0.008
0.012
0.009
0.043
0.007
0.055
0.03
0.033
0.068
0.021
0.026
0.029
0.055
0.011
0.025
0.021
0.011
0.029
0.054
0.033
0.067
0.03
0.031
0.082
0.027
0.029
0.029
0.029
0.027
0.025
0.034
0.083
0.029
0.025
0.035
O (10) 0.052
C (11)
C (12)
C (13)
C (14)
O (15) 0.052
H (16) 0.044
H (17) 0.038
H (18) 0.047
N (19) 0.046
H (20) 0.018
0.013
0.036
0.038
0.015
0.03
0.08
0.052
0.049
0.054
0.054
0.052
0.027
0.042
0.081
0.048
0.028
0.042
C (21)
H (22) 0.03
H (23) 0.022
ꢁ0.02
C (24)
ꢁ0.001
H (25) 0.001
H (26) 0.013
N (27) 0.008
C (28)
ꢁ0.012
H (29) 0.02
H (30) 0.015
H (31) 0.009
C (32)
H (33) 0.023
H (34) 0.012
H (35)
H (36) 0.016
C (37) 0.015
H (38) 0.048
H (39) 0.043
H (40) 0.04
N (41) 0.042
C (42)
H (43) 0.008
H (44) 0.005
condensed Fukui function, favors the higher reactivity. Tables 2e4
show the condensed Fukui functions and local softness as calcu-
lated based on Mullikin and Hirchfeld charges for AQ5, AQ5H and
1,5-DAAQ. Isosurface maps for Fukui functions of electrophilic,
nucleophilic and radical attack are given in Fig. 2. Isosurface maps
show that AQ5 acts better as nucleophilic and free radical attack
than electrophilic attack. Ring system in AQ5 has no electrophilic
centers, these centers are shown on oxygen and nitrogen atoms. On
the other hand, nucleophilic and free radical attack are shown on
the ring system. From the results of Table 2, the reactivity for the
radical attack was found on C1, C6, C11, C12, C13, O15, O16, O17,
N18, O40 and N41. Among these atoms the reactivity of radical
attack could be ranked as N17 ¼ O40 > N41 ¼ N18 > C6 ¼
C13 > C12 ¼ C1 > O16 > O15. For nucleophilic attack, the most
reactive sites are O15 and O16 (0.056). The order of reactivity to-
ward nucleophilic attack could be ranked as O16 ¼ O15 > C1 ¼
C12 > C13 > C1 > C6 > C7 ¼ C10 > N18. On the other hand, for
electrophilic attack, the most reactive site is O17(0.061),
N40(0.061), N18(0.060) and N41(0.059). The reactivity order to-
ꢁ0.011
0
ꢁ0.001
0.007
ꢁ0.025
0.029
0.03
C (45)
ꢁ0.023
H (46) 0.025
H (47) 0.026
N (48) ꢁ0.002
0
C (49)
ꢁ0.01
ꢁ0.011
0.017
0.013
0.007
ꢁ0.008
0.014
0.019
ꢁ0.003
H (50) 0.017
H (51) 0.012
H (52) 0.006
C (53)
ꢁ0.007
H (54) 0.012
H (55) 0.018
H (56) ꢁ0.004
ward electrophilic attack could be ranked as N40
¼
O17 > N18 > N41 > C11 > C2 > C6¼C13 > C1 > C5¼C14 > C8 > C9.
From Table 3, it is clear that AQ5H is more reactive than AQ5 when
comparing values (Mullikin and Hirshfeld) of condensed Fukui
functions for electrophilic and nucleophilic attack as shown, also,
from Fig. 2. For electrophilic attack, the highest Fukui function value
is accommodated on N19 (0.066). the order of the electrophilic
attack is N19 (0.066) > N42 ¼ C12 (0.060) > C9 (0.055) > C13
(0.047) > C8 (0.046). For nucleophilic attack the most nucleophilic
site is O15 (Fukui function value is 0.079) and the tendency for
bases and base pairs. Comparing AQ5 and AQ5H with 1,5-DAAQ
confirm that the order of interaction, taking the amount of charge
transferred as
DAAQ > AQ5H > AQ5. Values of
confirm the importance of the charge transfer mechanism for the
course of drug/DNA interaction.
a
measure of interaction strength, is 1,5-
N, as shown in Table 1 clearly,
D
Fukui [45] introduced a qualitative approach of chemical reac-
tivity in the form of what we call Frontier Orbital Theory. Later, this
theory was demonstrated [46,47] in the framework of DFT. In a
molecular system, the atomic site, which possesses highest
nucleophilic attack decreases as O15 (0.079)
>
C3¼C5
(0.055) > C8¼C13 (0.049) > C14 ¼ C37 (0.047). AQ5H has larger
tendency for nucleophilic attack (0.079 on O19) than AQ5 (0.056 on
O15). For free radical attack, there are many reactive sites with
Please cite this article in press as: J.S. Al-Otaibi, T.M. EL Gogary, Synthesis of novel anthraquinones: Molecular structure, molecular chemical
reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs, Journal of Molecular Structure (2016), http://dx.doi.org/
10.1016/j.molstruc.2016.10.098

6
J.S. Al-Otaibi, T.M. EL Gogary / Journal of Molecular Structure xxx (2016) 1e11
moderate Fukui function values. The susceptibility of the free
radical attack decreases as O15 (0.052) > C12 ¼ C13 (0.048) > C8
(0.047) > N19 (0.046) > C9 (0.045) > C14 ¼ C37 (0.037) > C5 (0.033).
For 1,5-DAAQ (Table 4), the free radical reactivity decreases in the
order, N17 ¼ N25 (0.059) > O15 ¼ O16 (0.057) > C2¼C6¼C12 ¼ C14
(0.053) > C1¼C13 (0.041) >C7¼C10 (0.034). The tendency for
[50,51].
The energy values of HOMO are computed as ꢁ5.222, ꢁ5.628
and ꢁ5.886 eV and LUMO are ꢁ2.943, ꢁ2.759 and ꢁ2.811 eV, and
the energy gap values are 2.279, 2.870 and 3.075 eV for AQ5, AQ5H
and 1,5-DAAQ, respectively. Computed values of DELeH shows that
AQ5 is more reactive than AQ5H which is more reactive than 1,5-
DAAQ. This is in accord with the calculated chemical softness
0.439, 0.348 and 0.325 for AQ5, AQ5H and 1,5-DAAQ respectively.
Anthraquinones are electron acceptors toward DNA bases and
nucleophilic attack in 1,5-DAAQ decreases as O15
¼
O16
(0.083) > C7¼C10 (0.057) > C6¼C12 (0.052) > C1¼C13 (0.049) > C2
0.038) > N17 ¼ N25 (0.035). The most electrophilic site is O17and
O40 and the order decreases as O17 ¼ O40 (0.061) > N18
(0.060) > N41 (0.059) > C11 (0.043) >C2 (0.042) > C6 (0.037).
base pair as appeared from the computed
DN negative values in
Table 1. So that, the anthraquinones LUMO energy is the deter-
mining factor in their interaction with DNA and hence, the order of
reactivity of these anthraquinones with DNA could be ranked as
1,5-DAAQ > AQ5H > AQ5. This is consistent with values of calcu-
4.2. Frontier orbital analysis
lated charge transfer
AQ5H and 1,5-DAAQ respectively toward AT base pair
and ꢁ0.820, ꢁ1.085 and ꢁ1.385 toward GC base pair.
D
N of ꢁ0.546, ꢁ0.802, and ꢁ1.126 for AQ5,
Highest occupied molecular orbital (HOMO) and lowest unoc-
cupied molecular orbital (LUMO) for AQ5, AQ5H and 1,5-DAAQ are
calculated and presented in Fig. 3. HOMO and LUMO, as frontier
molecular orbitals, are considered as very important molecular
parameters for the stability and chemical reactivity of the species
[48,49]. HOMO and LUMO energies, and LUMOeHOMO energy gap
(DELeH), in eV, are displayed in Table 1. The lower the HOMO energy
the more readily of that orbital to participate in chemical reaction
by donating electrons. LUMO energy, on the other hand, determine
HOMO and LUMO plots of AQ5, AQ5H and 1,5-DAAQ are pre-
sented in Fig. 3. As can be seen in Fig. 3, the HOMO of AQ5 is
delocalized mainly on the carbon CeC bonds, OH and NH(R) groups.
Carbonyl groups and CeH bonds show anti-bonding nature where
no electron projection at these regions. LUMO of AQ5 is being
participated mainly from the ring carbons and oxygen atoms of the
C]O and OeH groups. It is clear from Fig. 3 that, the LUMO of AQ5
shows antibonding character over the CeH bonds both in the ring
and side chain.
the ability to accept an electron in
a chemical change.
LUMOeHOMO energy gap reflects the chemical hardnessesoftness
and polarizability of the molecule and hence its biological activity
Fig. 2. Isosurface maps for Fukui functions of electrophilic, nucleophilic and radical attack for AQ5, AQ5H and 1,5-DAAQ.
Please cite this article in press as: J.S. Al-Otaibi, T.M. EL Gogary, Synthesis of novel anthraquinones: Molecular structure, molecular chemical
reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs, Journal of Molecular Structure (2016), http://dx.doi.org/
10.1016/j.molstruc.2016.10.098

J.S. Al-Otaibi, T.M. EL Gogary / Journal of Molecular Structure xxx (2016) 1e11
7
Fig. 3. HOMO and LUMO plots of AQ5, AQ5H and 1,5-DAAQ.
The HOMO of AQ5H is delocalized on the ring carbon atoms
4.3. Experimental study
except the carbonyl carbons and carbons meta to the side chain
which show anti-bonding character. LUMO of the AQ5H is distrib-
uted on the ring system and the carbonyl oxygen. Both side chains
show anti-bonding nature.
The HOMO of 1,5-DAAQ is delocalized on the amino groups and
terminal ring carbon atoms except the carbons located meta to the
amino group. Carbonyl carbons and CeH bonds show anti-
bonding character. The LUMO are delocalized on the ring car-
bons and oxygen and nitrogen atoms. CeH bonds show anti-
bonding character.
The anthraquinone drug/DNA intercalation complexes have
been investigated using different experimental techniques [52e54]
including NMR spectroscopy [55,56] and modeled using compu-
tational quantum chemistry [21,57e59].
In this work the anthraquinone drug/DNA interactions have
been discussed. Three types of DNA were used, namely calf thymus
DNA, polydeoxyadenylic acid-polythymidylic acid (Poly[dA].Poly
[dT]) and polydeoxyguanylic acid-polydeoxycytidylic acid (Poly
[dG].Poly[dC]). AQ5 and AQ5H were experimentally investigated
Please cite this article in press as: J.S. Al-Otaibi, T.M. EL Gogary, Synthesis of novel anthraquinones: Molecular structure, molecular chemical
reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs, Journal of Molecular Structure (2016), http://dx.doi.org/
10.1016/j.molstruc.2016.10.098

8
J.S. Al-Otaibi, T.M. EL Gogary / Journal of Molecular Structure xxx (2016) 1e11
Table 5
1H NMR chemical shift differences,
D
(Hz) for different drug protons in their mixtures with DNA.
System
Drug: DNA
N(CH3)2
ArHNCH2
Ara
D
Broadening
D
Broadening
D
Broadening
AQ5/calf thymus
AQ5H/calf thymus
1:0.5
1:1
1:0.25
ꢁ0.16
ꢁ0.05
ꢁ0.29
e
e
✓
ꢁ0.13
ꢁ0.37
1.19
e
e
✓
1.89
2.46
7.99
12.02
6.76
too broad
2.27
3.38
3.69
5.54
2.97
7.73
10.11
8.02
5.61
1.63
1.21
2.60
0.74
1.5
e
e
✓
1:0.5
1:0.25
1:0.5
ꢁ0.21
ꢁ0.03
ꢁ0.20
ꢁ0.27
✓
e
e
✓
too broad
ꢁ0.52
ꢁ6.62
0.54
✓
e
e
✓
✓
e
e
✓
AQ5/P(dA).P(dT)
AQ5H/P(dA).P(dT)
1:0.25
1:0.5
e
✓
ꢁ0.22
✓
✓
AQ5/P(dG).P(C)
1:0.5
1:1
1:0.25
ꢁ0.61
ꢁ0.68
ꢁ0.18
e
e
✓
ꢁ0.15
0.08
ꢁ0.11
e
e
✓
e
e
✓
AQ5H/P(dG).P(C)
1:0.5
ꢁ0.30
✓
ꢁ0.15
✓
✓
3.24
0.90
a
Aromatic protons in AQ5 exhibit identical shifts. For AQ5H the shifts for protons at positions 2&6, 3&7 and 4&8 are presented sequentially.
while the low solubility of 1,5-DAAQ does not allow such investi-
gation. This study has been done using NMR and UVeVIS
spectroscopy.
spectra of AQ5 and AQ5/P(dG).P(dC) showing the broadening of the
methyl peak.
Different drug NMR signals in the spectra of drug/calf thymus
DNA mixtures were compared with that of the corresponding drug
in its pure solution. It was observed that the side chain protons
were always shifted downfield whereas the aromatic protons show
up-field shift, except for drug/calf thymus. Aromatic protons show
4.4. NMR studies
The NMR spectra of drug/DNA mixtures were obtained in D2O
buffer at pH ¼ 7.2 in different drug/DNA ratios. Different drug NMR
signals in the spectra of drug/DNA mixtures were compared with
that of the corresponding drug in its pure solution. Generally two
observations were obtained, the first is the peak shift and the
second is the peak broadening. NMR spectra of AQ5 and AQ5H, with
calf thymus DNA, (Poly[dA].Poly[dT]) and (Poly[dG].Poly[dC]) were
obtained in D2O buffer at pH ¼ 7.2 in different drug/DNA ratios at
30 ꢀC in presence of TMS as an internal standard. Table 5 gives the
degree of peak shift (in Hz, defined as (chemical shift unbound)-
(chemical shift bound)) and the presence of the broadening for
different drug/DNA ratios of the studied drugs with different DNA.
Delta shift value would show the change in the electronic envi-
ronment compared to unbound.
more shift
(
D
z
1.00e12.00) than side chain protons
(D
z ꢁ0.03: ꢁ7.00). This indicates that the mode of interaction is
intercalation in nature. The intercalated ring system interacts more
effectively with the DNA bases. The methyl protons N(CH3)2 of
AQ5H (zꢁ0.21: ꢁ0.29) is more shifted than that of AQ5
(zꢁ0.03: ꢁ0.20). The hydroxyl groups of the intercalated drug in
AQ5 form intermolecular hydrogen bonding that leads to locating
of the N(CH3)2 outside the interaction zone hence lower shift is
observed. In case of intercalated AQ5H the N(CH3)2 group is present
within the interaction site which results in higher shift. Another
interesting observation is the peak broadening which depends on
The chemical shifts of proton environments in the AQs were
observed to change upon interaction with DNA (Table 5). These
shifts can be interpreted in terms of the mode of binding and the
orientation of the complexed species. Interaction with DNA
through charge transfer complex formation will place electron
density within the LUMO of the acceptor, and the change in
1
0.2
0.1
0.0
chemical shift (D) for a given environment should relate closely to
its position within the LUMO. Conversely, if there is no apparent
link between the chemical shift changes and positions of the
different environments within the LUMO, then a non charge
transfer stacking interaction is the most likely mode of binding.
2
Here the extent of the chemical shift change (D) is dependant on
the strength of the interaction and on the electronics of the envi-
ronment within the drug/DNA. For AQ5/DNA and AQ5H/DNA, all
proton environments are significantly altered. The smallest values
500
600
700
of
D
are observed for the equivalent proton positions 1,4,5 and 8.
and LUMO density indicates that
nm
The close correlation between
D
Fig. 4. The electronic absorption spectra of 1) free AQ5H ([AQ5H] ¼ 1.379 ꢂ 10ꢁ5 M), 2)
AQ5H/p(dG).p(dC) complex ([AQ5H] ¼ 6.435 ꢂ 10ꢁ6 M, [DNA] ¼ 1.760 ꢂ 10ꢁ4 M).
charge transfer is the principle mode of binding in this complex.
Fig. S1 in the Supplementary Materials represents the H NMR
Please cite this article in press as: J.S. Al-Otaibi, T.M. EL Gogary, Synthesis of novel anthraquinones: Molecular structure, molecular chemical
reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs, Journal of Molecular Structure (2016), http://dx.doi.org/
10.1016/j.molstruc.2016.10.098

J.S. Al-Otaibi, T.M. EL Gogary / Journal of Molecular Structure xxx (2016) 1e11
9
0.24
0.22
0.20
0.18
0.16
0.14
0.12
0.10
0.08
0.06
protons of 6&7 positions is larger than that of protons of 2&3. The
magnitude of the shift of the protons of AQ5 and AQ5H suggests
that these drugs are AT selective, which is consistent with the re-
sults from the spectrophotometric titration as shown below.
Considering the magnitude of the shift as a measure of the drug/
DNA interaction, AQ5H shows stronger interaction than AQ5 as can
be seen from Table 5. This result is consistent with the results of the
computed charge transfer of AT and GC as shown above (Table 1).
4.5. UVeVIS studies
The interactions between three types of DNA (calf thymus DNA,
(Poly[dA].Poly[dT]) and, (Poly[dG].Poly[dC])) and anthraquinone
drugs (AQ5 and AQ5H) were investigated in Tris buffer at pH ¼ 7.2
by absorption spectroscopy.
0
1
2
3
4
5
6
The absorption spectra of AQ5 and AQ5H with DNA were ob-
tained in Tris buffer at the physiological pH in different drug/DNA
ratios at room temperature. Fig. 4 shows the absorption spectra of
AQ5H/p(dG).p(dC) system as an example. Similar spectra were
obtained for other systems. As can be seen from the spectra the
changes in the uvevis spectra induced by excess amounts of DNA to
the drug solution, show hypochromicity in the absorbance of the
drug. Furthermore, a shift to higher wavelength was also observed
as compared to the free drug. The degree of the red shift (in nm) is
16, 16, 17, 11, 7, 10 nm for AQ5/calf thymus DNA, AQ5/p(dA).p(dT),
AQ5/p(dG).p(dC), AQ5H/calf thymus DNA, AQ5H/p(dA).p(dT), and
AQ5H/p(dG).p(dC) respectively. Table S8 in Supplementary Mate-
rial gives the degree of the red shift (in nm) observed in the spectra
of the drugs with DNA. The modifications of these absorption
spectra are common features of drugs upon binding to DNA due to
strong interactions between the electronic states of the DNA bases
with the drug [60]. This leads to an electronic redistribution of the
bound drug, leading usually to spectral changes (red-shifts and
hypochromicity) [61,62].
The absorption titration data for these drugs with DNA were
employed to calculate the affinity constants and number of base
pairs occupied by a bound drug molecule. The experiments were
done in triplicates to estimate the uncertainity in the measured
parameters. Fig. 5 shows the uncertainity (as a standard deviation)
in the absorbance values at 598 nm against DNA/drug ratio for the
system AQ5H/p(dG).p(dC). The absorbance titration data for the
drugs bound to DNA were analyzed according to the MC Ghee and
Von Hippel model [63] and plotted as a Scatchard representation.
[DNA]/[drug]
Fig. 5. Absorbance at 598 nm of the system AQ5H/P(dG).P(dC) against [DNA]/[drug]
ratio. Uncertainity in absorbance values is displayed. Solid line shows a theoretical
curve based on the best fit of the absorbance data to the first order exponential decay
function.
1000000
800000
600000
400000
200000
0
0.3
0.4
0.5
0.6
0.7
0.8
r
Fig. 6. Scatchard plot of AQ5H bound to P(dG).P(dC). Solid line shows a theoretical
curve based on smoothing to adjacent averaging.
Fig.
p(dG).p(dC).
The curvature of the Scatchard plot is a confirmation of the
presence of two types of binding modes of the drug to DNA, i.e.
intercalation and surface binding. The data points in the Scatchard
plots can be divided into two portions and treated separately to
determine the binding parameters for each mode of binding. The
least squares method was used to fit the data points (linearly) of
each data point portion of the Scatchard plot. Affinity constants (K)
6 shows the Scatchard plot for the binding of AQ5H/
the drug/DNA ratio. The degree of broadening increases with
increasing of DNA concentration. At high DNA concentration the
drug peaks are too broad to be seen at all. On the other hand, at low
DNA concentration there is an equilibrium between the bound and
the free drug, and an average-positioned signal was observed.
The order of shift of the aromatic and side chain protons of AQ5
and AQ5H is P(dG).P(dC) < P(dA).P(dT). The shift in the aromatic
Table 6
Affinity constants (K)a and numbers of base pairs bound per drug molecule (n)b for the binding of AQs drugs with DNA.
Drug/DNA
K1
n1
K2
n2
AQ5/calf thymus
AQ5H/calf thymus
AQ5/P(dA).P(dT)
AQ5H/P(dA).P(dT)
AQ5/P(dG).P(dC)
AQ5H/P(dG).P(dC)
2.8 ꢂ 107 5 ꢂ 105
2.1 ꢂ 107 1.2 ꢂ 106
3.0 ꢂ 107 2.4 ꢂ 104
7.1 ꢂ 106 1.4 ꢂ 105
1.39 ꢂ 107 1.6 ꢂ 106
6.0 ꢂ 106 1.4 ꢂ 106
14.29 0.002
10.0 0.001
10.00 0.000
5.73 0.001
2.5 0.001
6.3 ꢂ 105 1. x103
1.7 ꢂ 105 2.8 ꢂ 103
7.3 ꢂ 104 11314
4.2 ꢂ 105 22243
3.3 ꢂ 105 50968
4.7 ꢂ 105 5364
8.33 0.0
2.86 0.04
0.90 0.16
4.20 0.005
1.1 0.07
10.0 0.002
5.9 0.002
a
K1 intercalation binding affinity constant, K2 surface binding affinity constant.
b
n1 number of drug molecules intercalated per base pair, n2 number of drug molecules surface binding per base pair.
Please cite this article in press as: J.S. Al-Otaibi, T.M. EL Gogary, Synthesis of novel anthraquinones: Molecular structure, molecular chemical
reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs, Journal of Molecular Structure (2016), http://dx.doi.org/
10.1016/j.molstruc.2016.10.098

10
J.S. Al-Otaibi, T.M. EL Gogary / Journal of Molecular Structure xxx (2016) 1e11
and number of base pairs occupied by a bound drug molecule (n)
were calculated from the slope and the intercept with the X-axis,
respectively, and are displayed in Table 6 where K1 and n1 are for
intercalation mode and K2 and n2 for surface binding mode. In or-
der of decreasing intercalation affinity constant of the drugs to all
types of DNA, the drugs ranked as follows: AQ5 > AQ5H. This result
is consistent with the measured red shift in the UVeVIS spectra of
the drug/DNA solutions as shown in Table S8 in the Supplementary
Material. However, in order of decreasing surface binding affinity
constant of the drugs to calf thymus DNA the drugs ranked as fol-
lows: AQ5H > AQ5. AQ5/P(dA).P(dT) shows the most stable com-
plex (3.0 ꢂ 107 Mꢁ1). AQ5 shows largest tendency and selectivity to
AT sites. This is consistent with the NMR investigations which show
highest chemical shift with P(dA).P(dT) as displayed in Table 5.
However, this result is inconsistent with the calculated charge
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Appendix A. Supplementary data
Supplementary data related to this article can be found at http://
dx.doi.org/10.1016/j.molstruc.2016.10.098.
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