Noncovalent attachment of psoralen derivatives with DNA: Hartree-Fock and density functional studies on the probes.

Article abstract of DOI:10.1016/S1386-1425(03)00038-6

Two psoralen derivatives (probes) were prepared. Their geometries were optimized at the Hartree-Fock (HF) and Density Functional (B3LYP) levels employing 6-31G** and cc-pVDZ basis sets. Their interaction with DNA was investigated using spectrophotometric and computational techniques. Both of them have shown strong binding to calf thymus DNA. The red-shift and hypochromism that detected in the spectrum were taken as an evidence for the strong interaction between these probes and DNA. The spectrophotometric DNA titration data were treated by two different methodologies to calculate the intercalation affinity. Half-reciprocal plots gave binding constants of 5.5065 x 10(4) and 6.4727 x 10(4) for 8-butoxypsoralen (8-BOP) and 8-hexoxypsoralen (8-HOP), respectively. Schatchard plots gave a comparable intercalation binding constants and also the surface binding constants along with the number of intercalated probe molecules per base pair. The interaction between these probes and DNA were studied theoretically. The energy of interaction was computed using molecular mechanics method. Strength of interaction of these probes with different types of DNA was computed and compared. Calculated energies of interaction were compared with the observed intercalation affinities. HOMO and LUMO energies were computed and used to account for the strength of interaction.

Full text of DOI:10.1016/S1386-1425(03)00038-6

Spectrochimica Acta Part A 59 (2003) 2635ꢀ2644
/
www.elsevier.com/locate/saa
Noncovalent attachment of psoralen derivatives with DNA:
Fock and density functional studies on the probes
Hartreeꢀ
/
Tarek M. El-Gogary a,*, Eman M. El-Gendy b
a Chemistry Department, Faculty of Science (Domyat), Mansoura University, Domyat AL-Gideda, Egypt
b Department of Home Economy, Faculty of Specific Education, Mansoura University, Mansoura, Egypt
Received 14 October 2002; received in revised form 13 January 2003; accepted 13 January 2003
Abstract
Two psoralen derivatives (probes) were prepared. Their geometries were optimized at the Hartreeꢀ
/Fock (HF) and
Density Functional (B3LYP) levels employing 6-31G** and cc-pVDZ basis sets. Their interaction with DNA was
investigated using spectrophotometric and computational techniques. Both of them have shown strong binding to calf
thymus DNA. The red-shift and hypochromism that detected in the spectrum were taken as an evidence for the strong
interaction between these probes and DNA. The spectrophotometric DNA titration data were treated by two different
methodologies to calculate the intercalation affinity. Half-reciprocal plots gave binding constants of 5.5065ꢁ
/
104 and
6.4727ꢁ
/
104 for 8-butoxypsoralen (8-BOP) and 8-hexoxypsoralen (8-HOP), respectively. Schatchard plots gave a
comparable intercalation binding constants and also the surface binding constants along with the number of
intercalated probe molecules per base pair. The interaction between these probes and DNA were studied theoretically.
The energy of interaction was computed using molecular mechanics method. Strength of interaction of these probes
with different types of DNA was computed and compared. Calculated energies of interaction were compared with the
observed intercalation affinities. HOMO and LUMO energies were computed and used to account for the strength of
interaction.
# 2003 Elsevier B.V. All rights reserved.
Keywords: Intercalation; Spectrophotometric titration; DNA; Psoralens; Ab initio DFT calculations
1. Introduction
for many years in the experiments of vitiligo and
psoriasis [1,2]. Various biological targets are likely
to be involved in the therapeutic effects of such
compounds. Their anti-proliferative effects are
usually related to their ability to undergo photo-
cycloaddition reactions with pyrimidine DNA-
bases, and particularly with thymine, leading to
the formation of monofunctional and bifunctional
adducts [3]. Psoralens, as furocoumarin deriva-
tives, have been actively investigated with regard
Psoralens are naturally occurring and/or syn-
thetic substances which are used in treatment of
skin diseases. Psoralen derivatives have been used
* Corresponding author. Tel.:
57403868.
E-mail address: tarekelgogary@hotmail.com (T.M. El-
Gogary).
ꢂ
/
20-5743003; fax:
ꢂ/20-
1386-1425/03/$ - see front matter # 2003 Elsevier B.V. All rights reserved.
doi:10.1016/S1386-1425(03)00038-6

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T.M. El-Gogary, E.M. El-Gendy / Spectrochimica Acta Part A 59 (2003) 2635ꢀ2644
/
to their ability to act as dermal photosensitizing
agents and as probes of DNA [4,5]. The biological
activity of psoralen is primarily due to the result of
the covalent bonding they have with DNA. This
process is believed to start with non-covalent
intercalative binding to the DNA helix [6].
The aim of this work is to synthesize a more
hydrophobic DNA probes namely, 8-butoxypsor-
alen (8-BOP) and 8-hexoxypsoralen (8-HOP),
study their geometries and electronic structures
by sophisticated ab-initio computational methods
and to investigate the strength of their non-
covalent binding with calf thymus DNA.
2. Experimental
Fig. 1. Synthesis of 8-MOP (3), and 8-HOP (4); reaction
scheme.
2.1. Instrumentations
2.2.1.2. Preparation of 8-butoxypsoralen (9-
butoxy-7H-furo[3,2-g] [1]benzopyran-7-one) (3).
A solution of xanthotoxol (2) Fig. 1, (4 g, 0.02
mol), n-butyl bromide (4 g, 0.023 mol) and
potassium carbonate anhydrous (8 g) in acetone
(30 ml), was refluxed for 6 h. The inorganic salt
that separated was filtered off. The acetone solu-
tion was evaporated under reduced pressure to
give a gummy material, which was recrystallized
from a mixture of (ethyl acetate: n-hexane, 3:7) to
give yellow powders of 8-BOP (3), Fig. 1. In
Spectrophotometric titration was performed on
PerkinꢀElmer Lambda2 spectrophotometer in
/
Tris buffer at the physiological pH. IR measure-
ments were recorded in KBr disc using Nicolet 205
FT-IR spectrophotometer. NMR spectra were
obtained in CDCl3 using Varian 300 MHz NMR
machine.
2.2. Materials
2.2.1. Synthesis
approximately 60% yield, m.p.ꢃ
IR (KBr): nꢄ ꢃ
3050, 2960, 2860, 1690, 1617,
1540, 1220 cmꢄ1
1H-NMR (CDCl3): d 1.0 (t, 2H, Jꢃ
CH3), 1.6 (pen., 2H, Jꢃ8 Hz, 3?-CH2), 1.9 (hex,
2H, Jꢃ8 Hz, 2?-CH2), 4.52 (t, 2H, Jꢃ8 Hz,
OCH2), 6.4 (d, 1H, Jꢃ10 Hz, 6-H), 6.83 (d, 1H,
Jꢃ2.5 Hz, 3-H), 7.37 (s, 1H, 4-H), 7.7 (d, 1H, Jꢃ
2.5 Hz, 2-H) and 7.8 (d, 1H, Jꢃ10 Hz, 5-H).
/
87 8C.
/
2.2.1.1. Demethylation of xanthotoxin (9-methoxy-
.
7H-furo[3,2-g] [1] benzopyran-7-one)(1) [7ꢀ
A mixture of xanthotoxin, supplied by Sigma (1)
(Fig. 1), (4.4 g, 0.02 mol) and pyridineꢀHCl (11.5
g, 0.1 mol) was fused on an oil bath for 3 h at
(180ꢀ200 8C). The reaction mixture was poured
into crushed ice to dissolve the excess of pyridineꢀ
/9].
/
8 Hz, 4?-
/
/
/
/
/
/
/
/
/
/
HCl, the residue was filtrated off, and recrystal-
lized from glacial acetic acid to give pale yellow
powder of xanthotoxol (9-hydroxy-7H-furo[3,2-g]
[1]benzopyran-7-one) (2). In approximately 50%
2.2.1.3. Preparation of 8-hexoxypsoralen (9-
hexoxy-7H-furo[3,2-g] [1]benzopyran-7-one)
yield, m. p.ꢃ
1H-NMR (CDCl3): d 6.3 (br., 1H, OH), 6.39 (d,
1H, Jꢃ10 Hz, 6-H), 6.84 (d, 1H, Jꢃ2.5 Hz, 3-H),
7.30 (s, 1H, 4-H), 7.73 (d, 1H, Jꢃ2.5 Hz, 2-H) and
7.83 (d, 1H, Jꢃ10 Hz, 5-H).
/
220 8C ([10] m. p. 220 8C).
(4). A solution of xanthotoxol 2, Fig. 1, (4 g,
0.02 mol), was reacted and worked up as above
using n-hexyl bromide (4.5 g, 0.02 mol) to give 9-
hexyloxy-psoralin (4), Fig. 1. In approximately
/
/
/
/
60% yield, m.p.ꢃ55 8C.
/

T.M. El-Gogary, E.M. El-Gendy / Spectrochimica Acta Part A 59 (2003) 2635ꢀ
/2644
2637
IR (KBr): nꢄ ꢃ
1540, 1220 cmꢄ1
1H-NMR (CDCl3): d 0.9 (t, 2H, Jꢃ
CH3), 1.4 (com. PAT., 6H, 4CH2), 3.8 (t, 2H, Jꢃ
Hz, OCH2), 6.39 (d, 1H, Jꢃ10 Hz, 6-H), 6.81 (d,
1H, Jꢃ2.5 Hz, 3-H), 7.37 (s, 1H, 4-H), 7.73 (d,
1H, Jꢃ2.5 Hz, 2-H) and 7.81 (d, 1H, Jꢃ10 Hz, 5-
H).
/
3050, 2960, 2860, 1690, 1600,
bound and the free probe. Hence the fraction of
.
the bound probe is proportional to the fractional
decrease in extinction coefficient. To this end it is
necessary to discuss how the experimental data
were interpreted.
In an extreme simplification, the reaction system
now in question can be expressed as follows:
/
8 Hz, 6?-
/8
/
/
/
/
Free probeꢂfree site on DNA
ꢃbound probe
(1)
(2)
2.2.2. DNA preparation
Calf-thymus DNA (CT DNA) obtained from
Sigma Chemical Company was purified by the
The affinity constant K is given by:
Kꢃ[bound probe]=[free probe][free site]
literature method [11] involving phenolꢀchloro-
/
form in extraction followed by ethanol precipita-
tion. The purified CT DNA was dissolved in
buffer and used for spectrophotometric titration.
The DNA concentration were determined by using
an extinction coefficient of 6600 Mꢄ1 cmꢄ1 at 260
nm and expressed in terms of base molarity [12].
where [free probe] etc. mean the concentrations of
free probe etc. This is written as:
KꢃCb=(nꢅDꢄCb)C
(3)
where C is the concentration of the free probe, Cb
is the concentration of the bound probe, D is the
concentration of the DNA base pair, n* is the
number of sites per base pair. Let us introduce
binding ratio r defined as:
2.3. Spectrophotometric titration studies
2.3.1. McGhee and von Hippel treatment
rꢃCb=D
(4)
When DNA is added to a solution of a probe
which intercalates into DNA there is a progressive
decrease in the molar extinction coefficient of the
probe at the lmax of the free probe as the
proportion of DNA is increased. This occurs up
to a limiting concentration of DNA after which,
there is no decrease in the extinction coefficient; at
this point the probe is fully bound to DNA.
Therefore, if the absorbance is recorded at this
lmax at various probe/DNA ratios, extinction
coefficients obtained at these ratios may be
calculated. The fraction of probe bound can thus
be calculated, at any particular concentrations of
DNA and probe. From this it is possible to
determine the affinity of the probe for DNA.
This method is quantitative, giving information on
the affinity rather than on the nature of the
binding.
so that Cbꢃ
fore:
/
rD. Then, Kꢃ
/
r/(n*ꢄ
/
r)C and, there-
r=CꢃK(nꢅꢄr)
(5)
The plot of r/C against r is called the Scatchard
plot [13]. On the basis of this simplified theory
[14,15] the plot should result in a straight line, and
the inclination should give the affinity constant K.
As was pointed out by McGhee and von Hippel,
[16], however, the last above equation (Eq. (5))
involves a serious defect in enumerating the
number of free sites along the DNA duplex.
Here the number of free sites is assumed to be
always proportional to the number of unoccupied
base pairs. McGhee and von Hippel [16] properly
estimated the probability Pg of occurrence of the
gap containing g base pairs, and then the number
of the free sites. They finally derived the following
equation to replace Eq. (5):
For the spectrophotometric titration method to
be valid it is essential that both the free probe and
the bound probe obey BeerꢀLambert’s law over
/
r=CꢃK(1ꢄnr) [(1ꢄnr)=(1ꢄ(nꢄ1)r)]nꢄ1
(6)
the probe concentrations used for the assay. A
clear isosbestic point must also be present, since
this indicates that there are only two spectro-
photometrically distinct forms of the probe; the
where n is the number of base pairs occupied by
one probe molecule bound to DNA duplex. When
r/C was plotted against r (Scatchard plot) using

2638
T.M. El-Gogary, E.M. El-Gendy / Spectrochimica Acta Part A 59 (2003) 2635ꢀ2644
/
this equation it came out as a curved line instead of
a straight line. This curvature was because the
Scatchard plot will only be linear if there is a single
type of non-interacting site. In the case of interac-
tion of probes with DNA there are at least two
radically different binding sites available. The
probes can either bind externally to the phosphate
residues or can intercalate into DNA [17]. The
affinity constants (K) for interaction at the two
sites usually are different; K for external binding is
usually about 104 compared with 106 for inter-
calation [18]. The two sites may be treated
separately on the binding curve.
In order to determine r and r/C, the fraction of
bound probe (a) is determined. In order to
estimate a it was necessary to determine the
extinction due to free probe (of), the extinction
due to bound probe (ob), and the extinction of the
sample after each addition of DNA (oobs). The
extinction of free probe was obtained from the
absorbance of the free probe, extinction of the
sample under test is obtained from the absorbance
of the probe/DNA mixture. The extinction of
bound probe was estimated from a plot of oobs
versus D/Ct, where Ct is the total probe concen-
tration [19]. The fraction of probe bound after
each addition of DNA was calculated by method
of Peacocke and Skerret [20], Eq. (7):
fitted to the equation, with a slope equal to 1/Do
K). The binding
constant (K) was determined from the ratio of the
and an y-intercept equal to 1/(Do ×
/
slope to y-intercept.
3. Computations
Calculations on the probes were performed
within GUASSIAN 98 [22] program package. Equili-
brium geometries of the probes were determined
and confirmed by a subsequent calculation of
force constants and vibration analysis. Calcula-
tions were performed using the closed-shell
HartreeꢀFock (HF) method and Becke’s three
/
parameter density functional theory (DFT)
method [23] in combination with the Lee, Yang
and Parr correlation functional [24] (B3LYP). The
split valence basis set 6-31G** [25,26] and Dun-
ning’s correlation consistent double-zeta basis set
(cc-pVDZ) [27ꢀ29] were used with the above
/
methods. A Pentium III computer machine with
900 MHz processor and 256 RAM was utilized to
run all the calculations. Calculations on probe/
DNA ware performed using HYPERCHEM pakage
version 6.03 of Hypercube, Inc. 2000. The geome-
try of probe/DNA complexes were optimized using
molecular mechanics method. AM1 orbitals of the
probes and energy have been computed for the
complexes.
aꢃ(of ꢄoobs)=(of ꢄob)
r and r/C can now be calculated from a since: Cꢃ
(1ꢄa)Ct and rꢃa Ct/D.
(7)
/
/
/
4. Results and discussion
2.3.2. Half-reciprocal treatment
4.1. Spectrophotometric DNA titration
The binding constant for the probe/DNA com-
plex was determined by the half-reciprocal plot
method [21].
The binding constant (K) for a given complex
with CT DNA was obtained from a plot of D/Doab
versus D according to the equation:
The absorption spectra of 8-BOP and 8-HOP
with CT DNA were obtained in Tris buffer at the
physiological pH in different probeꢀDNA ratios
/
at room temperature. The changes in the electronic
absorption spectra induced by increasing amounts
of calf thymus DNA to a solution of the probe,
show a decrease in the absorbance of the probe
(hypochromicity) especially at lmax of the free
probe. Furthermore, a red-shift was also observed
as compared with the free probe absorption
maximum. These changes in absorption spectra
are common features of probes upon binding to
D=oab ꢃD=oꢂ1=(Do × K)
where D is the concentration of DNA in base
molarity, ?oabꢃoaꢄof and ?oꢃobꢄof where ob,
(8)
/
/
/
/
and of are respective extinction coefficient of the
complex in the presence and absence of DNA. The
apparent extinction coefficient, oa, was obtained
by calculating Aobsd/[complex]. The data were

T.M. El-Gogary, E.M. El-Gendy / Spectrochimica Acta Part A 59 (2003) 2635ꢀ
/2644
2639
Fig. 2. Half-reciprocal plot of 8-HOP with CT DNA in Tris
buffer.
Fig. 3. Scatchard plot of 8-HOP with CT DNA in Tris buffer.
binding of psoralen probes to CT DNA are
reported in Table 1. Affinity of intercalation
binding of psoralen probes to CT DNA, could
DNA and are suggested to be due to strong
interactions between the electronic states of the
probe and those of the DNA bases [30]. This
allows an electronic redistribution of the bound
probe, leading usually to spectral modifications
such as hypochromicity and red-shifts of the
absorption bands [31,32]. Upon binding of these
probes to CT DNA, the observed hypochromicity
and red-shifts are consistent with a strong inter-
action of these probes to CT DNA.
be ranked as follows: 8-HOPꢀ
/
8-BOPꢀ8-MOP.
/
This indicates that these probes have higher DNA
affinity than the well-known probes 8-MOP and
khellin Table 1. In order of decreasing surface
binding affinity constant of the probes to CT
DNA they could be ranked also as: 8-HOPꢀ
/
8-
BOPꢀ8-MOP. The computed log P values, re-
/
ported in Table 2, reveal that the hydrophobicity
shows the same sequence as the intercalation
constant values which is an expected result.
The spectrophotometric titration data were
employed to calculate the binding constants using
another mathematical treatment the so-called half-
reciprocal method which is recently used [33]. Fig.
3 shows the half-reciprocal plot for the binding of
8-HOP to CT DNA. Table 2 gives the binding
constants of the studied psoralens with CT DNA
using the latter method. Comparing the resulting
binding constants shows consistency of the two
methods.
The spectrophotometric titration data for the
probes bound to CT DNA were analyzed accord-
ing to the McGhee and von Hippel model (see
Section 2.2) and plotted as a Scatchard representa-
tion. Fig. 2 shows the Scatchard plot for the
binding of 8-HOP to CT DNA. Similar Scatchard
plots were obtained for other systems.
Values of intercalation affinity constants (Ki),
surface binding constants (Ks), numbers of base
pairs bound per probe molecule for intercalation
binding (ni), numbers of base pairs bound per
probe molecule for surface binding (ns), frequency
of binding sites (1/ni) and (1/ns) and log P for the
Table 1
Schatchard results of intercalation and surface binding of psoralen probes to CT DNA; ‘k’ is refereed to affinity constants and ‘n’ is
refereed to numbers of base pairs bound per probe molecule where subscripts ‘i’ and ‘s’ stand for intercalation and surface, respectively
Complex
ki
ks
ni
ns
1/ni
1/ns
8-MOP
8-BOP
8-HOP
456.29
9.87
7.23
22.21
0.138
0.176
0.252
0.045
0.061
0.079
643699
812499
/
219
7529
9389
/
18
5.689
3.979
/
1.2
16.359
12.689
/
2.9
/301
/26
/0.87
/2.2

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T.M. El-Gogary, E.M. El-Gendy / Spectrochimica Acta Part A 59 (2003) 2635ꢀ2644
/
Table 2
Intercalation affinity constants (Ki), numbers of base pairs bound per probe molecule (ni), frequency of binding sites (1/ni) and
octanolꢀwater partition coefficient, log P, for the binding of psoralen probes to CT DNA
/
Complex
Ki (Mꢄ1
)
ni
1/ni
log Pa
Half-reciprocal
Scatchard
Khellinb
8-MOP
8-BOP
ꢀ
/
132
456.29
10.44
7.23
0.096
0.138
0.176
0.252
ꢄ
/
3.33
2.34
1.13
0.34
301.36
550659
647279
ꢄ
/
/
189
244
643699
812499
/
236
5.689
3.979
/
1.5
ꢄ
/
8-HOP
/
/348
/
0.79
ꢄ/
a
Computed using the QSAR module in the HYPERCHEM
Ref. [46].
.
b
As going from psoralen to 8-HOP the number of
methylene groups increases and so that the hydro-
fobicity increases as experiments and calculations
show. The increased hydrophobicity of these
compounds results in easier intercellular penetra-
tion and may also result in improved tumor
localization and enhanced phototoxicity [34], Fig.
3.
initio calculations were found of the level HF/3-
21G [43] and HF/6-31G* [44].
Probe structures were build using HYPERCHEM
program and converted to Guassian input z-
matrix format using BABELWIN [45]. Equilibrium
geometries of the probes were determined and
confirmed by a subsequent calculation of force
constants and vibration analysis. Geometry opti-
mization were performed using the closed-shell
HartreeꢀFock method (RHF) and Becke’s three
/
4.2. Molecular modeling
parameter DFT method [23] in combination with
the Lee, Yang and Parr correlation functional [24]
(B3LYP). Different basis sets were used with these
methods namely, the split valence 6-31G** [25,26]
4.2.1. Probes geometrical features
Although there are some reported semi-empiri-
cal calculations [35ꢀ42] on psoralens, only few ab
/
Table 3
Selected geometricala parameters and total energy calculated with HF and density functional methods using different basis sets for 8-
BOP molecule
Description
RHF/6-31G**
B3LYP/6-31G**
B3LYP/cc-pVDZ
R1-2
R10-11
1.3288
1.3323
1.3516
1.3536
1.354
1.3571
R5-13
R5-14
1.3517
1.1839
1.3967
1.2082
1.3995
1.2062
R9-18
R11-12
1.3453
1.3567
1.3583
1.3758
1.3581
1.3764
R22-21
R25-22
1.5158
1.5293
1.5201
1.534
1.519
1.5323
A11-10-7
A13-5-1
D7-8-9-18
D21-18-9-8
D23-21-18-9
D25-22-21-18
E (au)
105.6101
116.3811
177.1941
99.7657
59.9136
179.8538
106.0917
115.8298
176.4875
123.9874
310.8962
180.5278
106.0003
115.8984
176.4625
124.5409
311.1928
180.7469
ꢄ875.6339821
/
ꢄ880.92569211
/
ꢄ/880.957302313
aR, bond length; A, bond angle and D, dihedral angle. Atom numbering conventions in Fig. 6.

T.M. El-Gogary, E.M. El-Gendy / Spectrochimica Acta Part A 59 (2003) 2635ꢀ
/2644
2641
Table 4
Selected geometricala parameters and total energy calculated with HF and density functional methods using different basis sets for 8-
HOP molecule
Description
RHF/6-31G**
B3LYP/6-31G**
B3LYP/cc-pVDZ
R1-2
R10-11
1.3289
1.3323
1.3516
1.3536
1.354
1.3571
R5-13
R5-14
1.3516
1.1839
1.3961
1.2084
1.3992
1.2063
R9-18
R11-12
1.3452
1.3567
1.3576
1.3762
1.3575
1.3763
R22-21
R25-22
1.5161
1.5307
1.5203
1.5353
1.5192
1.5337
A11-10-7
A13-5-1
D7-8-9-18
D21-18-9-8
D23-21-18-9
D25-22-21-18
E (au)
105.6059
116.3837
177.2121
99.644
106.0899
115.8391
177.0388
126.8124
314.7377
181.0089
105.9912
115.9033
176.9495
126.8038
315.1698
181.4435
300.0587
180.5185
ꢄ
/
953.707912580
ꢄ959.557460280
/
ꢄ/959.585168075
aR, bond length; A, bond angle and D, dihedral angle. Atom numbering conventions in Fig. 7.
Fig. 4. Computed frontier orbitals of psoralen probes.

2642
T.M. El-Gogary, E.M. El-Gendy / Spectrochimica Acta Part A 59 (2003) 2635ꢀ2644
/
and Dunning’s correlation consistent double-zeta
basis set (cc-pVDZ) [27ꢀ29]. Some geometrical
Table 5
Computed total energy of the DNA/psoralens complexes using
MM
/
parameters computed with RHF and B3LYP
using two different basis sets were presented in
Tables 3 and 4 for 8-BOP and 8-HOP, respectively.
The numbering scheme for the psoralens in this
section is shown in Figs. 4 and 5. Geometrical
values; bond lengths, bond angles and dihedral
angles, of the HF level are generally smaller than
those from DFT. Geometrical values for 8-BOP
and 8-HOP using B3LYP/6-31G** are generally
about 1.835% larger than those using HF/6-
31G**. Bond lengths of 8-BOP and 8-HOP using
B3LYP/cc-pVDZ are about 2.360% larger than
that computed with HF/6-31G**. Comparing the
DFT geometries shows close values of bond
lengths and angles within only about 0.219%
difference. This indicates the unreliability of the
HF geometry and the consistency of the DFT
methods. The computed total energy at different
level is shown in Tables 3 and 4 which again
accounts for the reliability of the DFT methods as
a minimum energy geometry.
Complex
Total energy (kcal molꢄ1
)
PAT_ps
ꢄ
/
21.455
22.447
9.864
PAT_ps2*
PAT_MOP
PAT_MOP2
PAT_BOP
PAT_BOP2
PAT_HOP
PAT_HOP2
PCG_ps
ꢄ
/
ꢄ/
ꢄ
/
20.333
12.338
21.633
15.286
25.576
15.891
13.605
18.670
10.564
22.162
13.259
20.001
17.104
ꢄ
/
ꢄ
/
ꢄ
/
ꢄ
/
ꢄ
/
PCG_ps2
ꢄ
/
PCG_MOP
PCG_MOP2
PCG_BOP
PCG_BOP2
PCG_HOP
PCG_HOP2
ꢄ
/
ꢄ
/
ꢄ
/
ꢄ
/
ꢄ
/
ꢄ/
*2 here indicate that the probe has been optimized alone in
the presence of the DNA (i.e. initial position is in the
intercalation site), PAT, (Poly[dA] ×
(Poly[dG] × Poly[dC]) and ps, psoralen.
/
Poly[dT]), PCG,
/
polydeoxyadenylic
(Poly[dA] × Poly[dT]) and, polydeoxyguanylic
acidꢀpolydeoxycytidylic acid (Poly[dG] ×
Poly[dC]). Energy of interaction of the different
probe/DNA complexes is displayed in Table 5. In
this work the non-bonded intermolecular energy
between the oligonucleotide and the psoralen was
considered:
acidꢀ
/
polythymidylic
acid
/
4.2.2. Probe/DNA interaction
/
/
Probe/DNA interactions were investigated using
molecular mechanics and quantum mechanics
methods. Psoralen (Ps) and 8-methoxypsoralen
(8-MOP) were also computed for comparison.
For simplicity, only four nucleotides were used
and their geometries were optimized using mole-
cular mechanics. Two types of oligonucleotides
(DNA) were selected, for such a study, namely,
Einteraction ꢃEcomplex ꢄ EDNA ꢄEpsoralen
Two methods were used, optimization of the
probe/DNA complex and optimizing the position
of the probe in the presence of the DNA followed
by the optimization process of the complex as a
whole. The latter results in a more stable complex
and a stronger interaction. With (Poly[dA] ×
/
Poly[dT]) the strength of interaction as predicted
from molecular mechanics method could be
ranked as Psꢀ
/
8-HOPꢀ
/
8-BOPꢀ8-MOP which
/
is in an excellent agreement with the experimen-
tally determined affinity constants. On the other
hand, with (Poly[dG] ×
interaction as predicted from molecular mechanics
method could be ranked as Psꢀ8-BOPꢀ8-
/
Poly[dC]) the strength of
Fig. 5. Optimized geometry of PAT/8-BOP intercalation com-
plex.
/
/

T.M. El-Gogary, E.M. El-Gendy / Spectrochimica Acta Part A 59 (2003) 2635ꢀ
/2644
2643
the intercalated portion of the molecule, which
interacts with the DNA base pairs. This is again
agrees well with the experimental results. The
optimized geometry of the probe/DNA complex
is shown in Fig. 7.
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