Infrared, 1H and 13C NMR spectra, structural charcterization and DFT calculations of novel adenine-cyclodiphosp(V)azane derivatives

Article abstract of DOI:10.1016/j.saa.2011.08.035

Adenine tetrachlorocyclodiphospha(V)zane derivatives (III_a-c) were prepared by the reaction of hexachlorocyclodiphospha(V)zane derivatives (I_a-c) and adenine (II) as precursors. The synthesized compound's and their structures (III

Full text of DOI:10.1016/j.saa.2011.08.035

Spectrochimica Acta Part A 83 (2011) 304–313
Contents lists available at SciVerse ScienceDirect
Spectrochimica Acta Part A: Molecular and
Biomolecular Spectroscopy
journal homepage: www.elsevier.com/locate/saa
Infrared, 1H and 13C NMR spectra, structural charcterization and DFT calculations
of novel adenine-cyclodiphosp(V)azane derivatives
Tarek A. Mohameda,∗, Wajdi M. Zoghaibb, Ibrahim A. Shaabana,1, Rabei S. Faraga,
Abd Elnasser M.A. Alajhaza
a Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City 11884, Cairo, Egypt
b Department of Chemistry, Sultan Qaboos University, P.O. Box 36, Al Khod, Muscat, Oman
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 29 July 2011
Received in revised form 21 August 2011
Accepted 22 August 2011
Adenine tetrachlorocyclodiphospha(V)zane derivatives (IIIa–c) were prepared by the reaction of hex-
achlorocyclodiphospha(V)zane derivatives (Ia–c
) and adenine (II) as precursors. The synthesized
compound’s and their structures (IIIa–c) were firmly characterized (based on the presence of an inversion
center) using FT-IR (4000–200 cm−1), UV–vis. (190–800 nm), 1H, 13C NMR and Mass spectral measure-
ments in addition to C, H, N, P elemental analysis. The compounds (IIIa–c) were found to be a 1:2 molar
ratio of (Ia–c) and adenine (II) adducts, respectively. Confident and complete vibrational assignments are
proposed for nearly all fundamental vibrations, along with detailed interpretation for all observed signals
in both 1H and 13C NMR spectra of the investigated phospha(V)zanes (IIIa–c). In addition, unconstrained
geometry optimization of IIIa–c were carried out by means of DFT-B3LYP/3-21G(d) calculations to provide
new insight into the structural parameters and molecular geometries of compounds IIIa–c. The results
are reported herein and compared with similar molecules whenever appropriate.
Keywords:
Adenine-cyclodiphospha(V)zanes
Vibrational assignments
1H NMR
13C NMR and theoretical calculations
© 2011 Elsevier B.V. All rights reserved.
1. Introduction
and vibrational assignment for all observed frequencies. Moreover,
little computational studies have been extended to cyclodiphosp-
Cyclodiphosphazane derivatives are an important family of
inorganic heterocyclic compounds containing a saturated four-
membered P2N2 ring which gained considerable interest in
synthesis and structural investigations [1–3]. This is due to the
organic and inorganic properties of theses compounds particu-
larly the ability of the inorganic rigid P–N framework to combine
with organic substituents. Moreover, the ability of these com-
pounds to form transition metal complexes with remarkable
chemical and biological properties is also of great interest [4–7]. The
high reactivity of hexachlorocyclodiphospha(V)zane toward nucle-
ophilic substitution provides for chlorine atom(s) substitution by
nucleophiles. Therefore, several cyclodiphospha(V)zanes contain-
ing active methylene, alcohols, thiols [3,8], aromatic and aliphatic
amines [9–11] have already been synthesized and characterized.
However, no one article provides a comprehensive interpretation
hazanes [12].
We aimed at synthesizing novel adenine-cyclodiphospha-
(V)zane derivatives via amination of hexachlorocyclodiphos-
pha(V)zane derivatives with adenine hoping the derivatives
possess some important biological features. Furthermore, the
synthesized compound’s structures were characterized using ele-
mental analysis and spectroscopic measurement including IR,
UV, Mass Spec, 1H and 13C NMR. In the context of our most
recent work on P3N3Cl6 [13] and adenine [14] we carried out
computational calculations for IIIa–c using Density Functional
Theory (DFT) [15] in order to provide an efficient approach to
their structures configurationally and structural parameters as
well.
2. Experimental
2.1. Materials
∗
Corresponding author at: University of Nizwa, College of Arts and Sciences, Post
Code 616, P.O. Box 33, Nizwa, Oman. Tel.: +202 38503918; fax: +202 22629356.
Adenine, actonitrile, dimethylformamide (DMF), and dimethyl-
sulfoxide (DMSO) were purchased from Aldrich Chemical Com-
pany. All reagents with 99% purity grade were used without further
purification.
E-mail address: tarek ama@hotmail.com (T.A. Mohamed).
Taken in part from the Master Thesis of Ibrahim A. Shaaban which was submitted
to Chemistry Department, Faculty of Science, Al Azhar University, Nasr City, Cairo
11884, Egypt.
1
1386-1425/$ – see front matter © 2011 Elsevier B.V. All rights reserved.
doi:10.1016/j.saa.2011.08.035

T.A. Mohamed et al. / Spectrochimica Acta Part A 83 (2011) 304–313
305
Fig. 1. Synthesis of adenine-cyclodiphosph(V)azane derivatives (IIIa–c).
2.2. Synthesis of adenine-tetrachlorocyclodiphospha(V)zanes
(IIIa–c
a Magnex Scientific superconducting magnet, and Top Spin 1.3 soft-
ware. Tetramethylsilane (TMS) was used as an internal reference.
To identify and ascertain the NH peaks in 1H NMR spectra of the
compounds under investigation, D2O was added to the NMR sample
with vigorous shaking to either reduce or eliminate the NH signal
(proton deuterium exchange). To reduce the signal to noise ratio,
10,000 scans were acquired for 13C NMR measurements and 16
scans for 1H NMR analysis with a 5 s relaxation delay time using a
10 k data point file. The 1H and 13C chemical shifts of compounds
(IIIa–c) are listed in Tables 3 and 4, respectively.
)
The hexachlorocyclodiphosphazane compounds (Ia–c) were pre-
pared using the provided scheme (Fig. 1) and purified using known
procedures [16]. Solid adenine (1.35 g, 0.01 mol) was added in
small portions to a well stirred solution of 0.005 mol hexachlorocy-
clodiphosphazane derivatives (Ia–c) in 100 mL acetonitrile for 0.5 h.
The hot reaction mixture was refluxed for 2 h in a fume hood with
continuous stirring while evolving HCl gas. The reaction mixture
was filtered and the resulting solid was washed several times with
acetonitrile and diethyl ether before drying under vacuum.
2.3. Instrumentation
2.3.1. Elemental analysis
Carbon, hydrogen and nitrogen elemental analyses were carried
out at the Micro Analytical Center, Cairo University, Giza, Egypt.
While, the phosphorus percent was determined gravimetrically
as phosphorous ammonium molybdate using Voy’s method [17].
Analytical data for the adenine-tetrachlorocyclodiphosphazane
derivatives (IIIa–c) are listed in Table 1.
2.3.2. IR and UV–vis spectra
The mid-infrared spectra (4000–200 cm−1) of solid adenine and
the synthesized compounds (IIIa–c) were recorded on a Perkin
Elmer Spectrum 100 FT-IR Spectrometer using CsI disk technique
(Fig. 2). To improve the S/N ratio, forty scans were collected uti-
lizing 0.5 cm−1 resolution. The observed IR bands of adenine and
the compounds (IIIa–c) are listed in Table 2. The ultraviolet–visible
spectra (190–800 nm) were measured using a Perkin Elmer Lambda
35 spectrophotometer with the samples dissolved in DMF (Fig. 3).
2.3.3. Mass spectra
Mass spectra (Supplement Fig. S-1) for compounds (IIIa–c) were
acquired on a Quattro Ultima Pt (Waters Corp., Milford, MA, USA),
Tandem Quadrupole mass spectrometer using chemical ionization
technique. Samples were initially dissolved in DMSO and serial
dilutions were carried out in 50/50 (v/v) acetonitrile/water. The
samples were infused using a Harvard syringe pump (Harvard, CA,
USA) at a flow rate of 10 ␮L per minute into the mass spectrometer.
2.3.4. NMR spectra
1H (Fig. 4) and 13C (Fig. 5) NMR spectral measurements were
performed with the samples (IIIa–c) dissolved in DMSO-d6 at 25 ◦C
using a Bruker Avance 400 MHz NMR spectrometer equipped with
Fig. 2. FT-IR solid spectrum of adenine and adenine-cyclodiphosph(V)azane deriva-
tives in CsI; (A) adenine; (B) IIIa; (C) IIIb; (D) IIIc.

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T.A. Mohamed et al. / Spectrochimica Acta Part A 83 (2011) 304–313
Table 1
Analytical and physical data of adenine-cyclodiphosph(V)azane derivatives (IIIa–c).
Comp. No. Reactants (mol, g)
Hexachlorocyclodiphosph(V)azane
Molecular
formula
m.p.
(◦C)
Color
(%Yield)
Elemental analysis; found/calculated
%C
%H
%N
%P
derivatives and adenine
IIIa
IIIb
IIIc
[(C6H6)NPC13]2(Ia): adenine (II)
(0.01, 4.57): (0.02, 2.70)
[(p-CH3C6H5)NPC13]2 (Ib): adenine (II)
(0.01, 4.85): (0.02, 2.70)
[(p-ClC6H5)NPC13]2 (Ic): adenine (II)
(0.01, 5.26): (0.02, 2.70)
C22H18Cl4N12P2 283–285
(654 g/mol)
C24H22Cl4N12P2 260–263
(682 g/mol)
C22H16Cl6N12P2 272–275
(723 g/mol)
White
39.74/40.39
41.81/42.25
36.50/36.54
3.01/2.77
3.12/3.25
2.50/2.23
26.00/25.69
25.00/24.64
24.01/23.24
9.22/9.47
8.84/9.08
8.34/8.57
80.20%
Greenish
81.80%
White
76.90%
3. Computational procedure
heavy atoms other than carbon and hydrogen which require Unix
systems or work stations. Energy minima with respect to the
nuclear coordinates were obtained by the simultaneous relaxation
of all geometrical parameters for molecules (IIIa–c) using Pulay’s
gradient method [21] with Gaussian-98 computational package
[22] running on a PC, 2.0 GHz Pentium processor, 2 MB Ram. The
bond lengths, bond angles, dihedral angles and selected structural
parameters (SPs) are presented in Table 5. 1H (Table 3) and 13C
(Table 4) chemical shifts for adenine-cyclodiphospha(V)zanes
In order to obtain structural details about the prepared
adenine-tetrachlorocyclodiphospha(V)zane derivatives (IIIa–c),
unconstrained geometry optimizations were performed while
excluding the inversion center for compounds IIIa–c using DFT [15]
calculations. The calculations were carried out with B3LYP method
in which Becke’s non-local exchange [18] and the Lee–Yang–Parr
correlation functiona [19] were applied with a 3-21G(d) basis set
[20]. We could not implement larger basis sets owing to the lack
of advanced computational facilities and the presence of eighteen
(IIIa–c
) were also predicted using Chem Draw Ultra v8
[23].
Table 2
Vibrational assignments of adenine-cyclodiphosph(V)azane derivatives (IIIa–c) compared with adenine.a
IIIa(Y= H)
IIIb(Y= p-CH3)
IIIc (Y= p-Cl)
Vibrational assignment
Adenine [14]
PCl2 wag
PCl2 Scissor
N−H wag
δwag. NH2
N−H wag
209 vs
217 s
209 vs
228 s
225 vs
254 w
254 m
251 sh
250 w
337 s
265 sh
271 vw
284 sh
267 vw
Pyrimidine ring puckering
325 sh
335 m,s
326 sh
335 s
321 sh
335 s
Benzene ring puckering
P−Cl stretch
387 w
371 w
382 w
392 sh
425 br, sh
425 w, br
410 w
420 sh
PNP in plane deformation
Imidazole NH wagging
473 m, s
497 m
465 w
486 sh
492 s
450 br, sh
496 m, br
513 sh
543 s
522 sh
502 sh
513 sh
Pyrimidine ring puckering
NPN in plane deformation
Imidazole ring puckering
535 vs
563 w
535 vs
539 sh
535 s
541 sh
563 w
570 sh
563 w
621 s, sh
667 s, br
609 sh
620 s
610 s
619 m
619 m
Imidazole ring in plane
deformation
637 s
655 sh
637 s
543 sh
637 m
650 sh
683 m
723 vs
683 s
680 m
700 sh
681 m
C−N wagging
Pyrimidine ring breath
C−Cl inplane deformation
Benzene C−H wagging
711 s
719 sh
711 s
720 sh
711 m
720 sh
744 m, br
742 s
755 sh
774 m, sh
753 m, br
776 m
754 m, br
783 vw, sh
Pyrimidine ring in plane bending
797 m
789 m,sh,spl.
800 sh
789 w, sh
791 vw, sh

T.A. Mohamed et al. / Spectrochimica Acta Part A 83 (2011) 304–313
307
Table 2 (Continued )
IIIa(Y= H)
IIIb(Y= p-CH3)
IIIc (Y= p-Cl)
Vibrational assignment
Adenine [14]
Methyl rocking
811 s
Imidazole C−H wagging
Pyrimidine ring bending
Imidazole ring bending
Pyrimidine C−H wagging
846 m, s
872 s
913 vs
939 vs
(860 br, sh)b
(858 m, br)
(858 m, br)
893 s
(870 sh, br)
(870 sh, br)
898 m
(860 br,sh)
898 m
946 s
946 s
965 sh
946 s
982 m, br
1015 sh, br
1029 sh
999 br
1017 w, sh
1021 w, sh
984 w, sh
1016 m
Benzene C=C−C stretches
C−Cl stretch
1067 sh, w
1096 m
NH2 rocking
1025 s
1126 s
Methyl rock
1075 m
1112 w
1121 sh
Imidazole CN ring stretch
1112 max, br
1123 max, br
1113 max, sh
1119 max, sh
1140 sh
1170 sh
1137 m
1173 m
1138 sh
1156 sh
P−N stretch
P−N stretch
1185 m
1193 sh
1186 m
1202 sh
1185 s
1200 sh
1253 vs
1309 vs
1242 s
1242 s
1242 s, br
Imidazole C−H in plane bending
Methyl in plane deformation
Benzene C−H in plane bending
Pyrimidine C−N stretch
1259 s
1288 sh
1306 w
1285 vw, sh
1306 w
1319 w
1281 sh
1305 m
1335 vs
1368 s
1331 m
1331 m
1331 m
Imidazole ring stretch (ν CN)
C−N stretch
Benzene C=C−C stretches
1382 sh
1399 w, sh
1384 m
1398 m
1398 m, sh
1420 vs
1413 m
1421 sh
1413 s
1419 sh
1413 vs
1418 sh
Pyrimidine C−H in plane bending
Methyl in plane deformation
Pyrimidine CC ring stretch
Imidazole CN ring stretch
1441 m
1466 w, br
1496 s
1451 s
1506 w
1465 w, br
1493 m
1467 w, br
1493 vs
1508 sh
1520 vw, sh
1550 vw, sh
1574 m
1531 vw
1556 w, sh
1576 s
1539 sh, br
1576 s
Benzene C=C−C stretches
Pyrimidine CN and CC ring
stretch
1603 vs
1675 vs
1602 sh
1592 w
1611 vs, br
1611 m
1611 vs
1651 w, sh
1654 vw, sh
NH2 Scissor
N−H in plane bending
1701 vs, br
1789 vw
1702 vs, br
1790 w
1698 v.br
1789 w
(2955 s, br)
(2955 s, br)
3033 s, br
3085 sh
(2954 s, br)
(2954 s, br)
3033 s, br
3138 sh
(2953 s, br)
(2953 s, br)
3033 s, br
(3102 vbr)
Benzene C−H stretch
Pyrimidine C−H stretch
Benzene C−H stretch
Imidazole C−H stretch
NH2 symmetric stretch
N−H stretch
2980 s
3119 vs
3296 vs
(3253 s, sh)
(3253 s, sh)
(3255 s)
(3255 s)
3315 sh, br
3375 sh
3347 sh
3426 vw
Imidazole N−H stretch
NH2 antisymmetric stretch
a
Vibrational assignment of adenine taken from Ref. [14].
Bands between brackets are used for two fundamentals modes.
b
4. Result and discussion
4.1. Electronic absorption spectral analysis
Analytical data and selected physical properties of the prepared
adenine-cyclodiphospha(V)zane derivatives (IIIa–c) are presented
in Table 1. Comparison of calculated and experimental elemental
analysis percentages indicates that the composition of compounds
(IIIa–c) coincides well with the structures proposed.
Electronic absorption bands (Fig. 3) observed in the 193–262 nm
range were assigned to ␲ → ␲* transitions within the benzene
and purine rings [24]. However, the recorded absorption bands
at 268, 268 and 268 nm were attributed to the n → ␲* (adenine
moiety) transition of IIIa, IIIb and IIIc, respectively, in agreement

308
T.A. Mohamed et al. / Spectrochimica Acta Part A 83 (2011) 304–313
Table 3
Characteristic 1H NMR chemical shift (ı, ppm) of adenine-cyclodiphosph(V)azane compounds (IIIa–c).
IIIa (Y= H)
Calc.b Obs.
IIIb (Y= p-CH3)
Calc.b Obs.
IIIc (Y= p-Cl)
Calc.b Obs.
Types of hydrogen atomsa
4.0
(9.01 br)c
4.0
8.92 brc
4.0
(8.87 br) c
H(a) (exocyclic N−H)
H(b) (N−H imidazole)
H(c) (C−H pyrimidine)
H(d) (C−H imidazole)
13.65 (9.01 br)c
13.65 9.19 brc
13.65
8.16
7.86
(8.87 br) c
8.37 (s)
8.16
7.86
8.42 (s)
8.41 (s)
8.16
7.86
8.42 (s)
8.41 (s)
8.36 (s)
6.72 (doublet)
6.74
7.06 (doublet)
7.0 9
6.63
7.27d
6.51
7.158d
6.57
H(e) (C−H o-benzene)
7.20
6.81
7.38e
7.30e
6.98
7.19d
7.24
H(f) (C−H m-benzene)
H(g) (C−H p-benzene)
H(g) (C−H Methyl)
2.34
2.22 (s)
0.59
Correlation Coeff. (R2)
0.56
0.58
a
b
c
For hydrogen atoms numbering, see Fig. 1.
1H NMR were calculated by Chem. Office [23].
These signals were disappeared after adding D2O.
d
e
These signals are well resolved to doublet upon the addition of D2O, see Fig. 4.
These signals are well resolved to triplet upon the addition of D2O, see Fig. 4.
Table 4
Characteristic 13C NMR chemical shift (ı, ppm) of adenine-cyclodiphosph(V)azane derivatives (IIIa–c).
Types of carbon atomsa
IIIa (Y H)
IIIb (Y p-CH3)
IIIc (Y p-Cl)
Calc.b
Obs.
Calc.b
Obs.
21.35
Calc.b
Obs.
C10 (Methyl group)
C7 (o-benzene)
C4 (purine)
C9 (p-benzene)
C8 (m-benzene)
C5 (imidazole)
C1 (purine)
21.3
116.2
119.4
131.2
129.8
138.7
144.8
143.7
151.2
152.4
0.9983
116.3
119.4
122.4
129.5
138.7
144.8
146.7
151.2
152.4
0.9488
115.17
123.63
128.49
130.59
133.27
144.27
146.21
149.98
152.18
115.31
123.88
131.01
129.69
138.67
146.08
144.32
149.96
152.10
117.7
119.5
124.3
129.7
144.7
144.8
144.8
153.9
152.4
0.9916
115.49
118.99
123.8
129.68
143.90
(146.82)c
(146.82)
152.46
150.22
C6 (benzene)
C3 (purine)
C2 (pyrimidine)
Correlation Coeff. (R2)
a
For carbon atoms numbering, see Fig. 1.
b
13C NMR were calculated by Chem Draw Ultra [23].
c
Signal between brackets was assigned to two different carbons.
with those reported for adenine [25]. The reported bands between
270 and 290 nm [3,26,27] are characteristic of delocalized electrons
within the phospha(V)azo four-membered ring (dimeric structure).
Therefore the observed bands at 275, 273 and 273 nm were for
compounds IIIa, IIIb and IIIc, respectively.
4.2. Mass spectral analysis
The recorded mass spectrum of adenine-cyclodiphospha-
(V)zane (IIIa; calculated formula weight is 654 amu) is provided
in Supplement Fig. S-1A. Fragment ion peaks of 2–100% abun-
dances are attributed to the corresponding fragmentation patterns
resulting from bond cleavage at different positions in adenine-
cyclodiphospha(V)zane derivatives (IIIa–c). Supplement Figs. S-2,
S-3 and S-4 summarize the calculated/found molecular weight of
compounds IIIa–c and the proposed fragmentation pathways corre-
sponding to their masses and relative intensities. As can be deduced
from Supplement Figs. S-2, S-3 and S-4, the recorded peak intensi-
ties are directly proportional to fragment stability.
The decomposition and the common fragmentation features
of IIIa are presented in Supplement Fig. S-2. The parent peak
appeared at m/z = 656 (3%) is attributed to 37Cl isotope (M+2).
The most intense ion (base peak) at m/z = 460 (100%) is attributed
to fragment [C20H18N10P2]+. In addition, the observed peaks at
m/z = 460.8 (27%), 442 (55.1%), 399.5 (14%) and 376.5 (44.2%) best
describe [C16H17ClN11P2]+, [C14H15Cl2N9P2]+, [C8H9Cl3N9P2]+ and
Fig. 3. Ultraviolet spectrum of adenine-cyclodiphosph(V)azane derivatives; (A) IIIa;
(B) IIIb; (C) IIIc.

T.A. Mohamed et al. / Spectrochimica Acta Part A 83 (2011) 304–313
309
Table 5
B3LYP structural parameters for adenine-cyclodiphosph(V)azane derivatives (IIIa–c) utilizing 3-21G(d) basis set.
Structural parametera
IIIa (Y H)
IIIb (Y p-CH3)
IIIc (Y p-Cl)
Bond lengths in Å
P1–N2 N3–P4
P1–N3 N2–P4
P1–Cl40 P4–Cl38
P1–Cl39 P4–Cl37
N2–C5 N3–C11
1.811
1.671
2.056
2.239
1.442
1.393–1.398
1.081–1.082
1.810
1.670
2.056
2.240
1.440
1.392–1.403
1.081–1.085
1.440
1.706
1.388
1.025
1.338
1.356
1.349
1.342
1.407
1.402
1.080
1.385
1.397
1.326
1.397
1.013
1.076
1.097
1.813
1.670
2.056
2.236
1.439
1.391–1.368
1.082
C
C (benzene ring)
C–H (benzene ring)
C10–C57 C16–C61
P1–N23 P4–N17
1.705
1.389
1.026
1.338
1.356
1.349
1.342
1.407
1.402
1.080
1.384
1.397
1.326
1.397
1.013
1.076
1.700
1.391
1.026
1.337
1.358
1.348
1.342
1.407
1.401
1.080
1.380
1.397
1.326
1.396
1.013
1.076
N17–C18 N23–C24
N
C
N
C
17–H
18–N33 C24–N29
33–C21 N29–C27
21–N34 C27–N30
34–C20 N30–C26
N23–H (exocyclic NH)
N
C
C
C
C
20–C19 C25–C26
19–C18 C25–C24
21–H C27–H (pyrimidine CH)
20–N35 C26–N32
N
35–C22 N32–C28
C
22–N36 C28–N31
N
N
36–C19 N31–C25
32–H N35–H (imidazole NH)
C
22–H C28–H (imidazole CH)
C57–H 61–H (methyl CH)
C
C10–Cl58 C6–Cl57
1.761
N31· · ·HN23 N36· · ·. . .HN17
2.640b
2.639b
2.630b
Bond angles in◦
P1–N2–P4 P1–N3–P4
N2–P1–N3 N2–P4–N3
Cl39–P1–Cl40 Cl37–P4–Cl38
P1–N23–C24 P4–N17–C18
P1–N23–H P4–N17–H
100.6
79.4
90.2
100.6
79.4
90.3
100.8
79.2
90.3
129.8
113.5
121.2
119.3
119.1
126.8
112.7
125.6
116.4
104.5
130.0
113.5
121.3
119.3
119.1
126.8
112.7
125.6
116.4
104.5
112.5
107.0
116.5
125.4
125.5
118.5–120.8
119.3–120.7
111.0
108.4
129.3
129.1
129.8
113.5
121.3
119.4
119.0
126.7
112.8
125.6
116.4
104.9
N
23–C24–N29 N17–C18–N33
C
25–C24–N29 C19–C18–N33
C24–N29–C27 C18–N33–C21
N29–C27–N30 N33–C21–N34
C27–N30–C26 C21–N34–C20
N
30–C26–C25 N34–C20–C19
C
C
26–C25–C24 C20–C19–C18
25–N31–C28 C19–N36–C22
N
31–C28–N32 N36–C22–N35
112.5
107.0
112.5
107.0
C28–N32–C26 C22–N35–C20
N29–C27–H N33–C21–H
116.2
125.4
125.5
119.9–120.2
119.4–120.1
116.2
125.3
125.5
119.1–121.0
119.5–120.8
C
26–N32–H C20–N35–H
N31–C28–H N36–C22–H
C
C
C–C (benzene ring)
C–H (benzene ring)
C10–C57–H C16–C61–H
H–C27–H H–C61–H
P1–N3–C11 P4–N2–C5
P4–N3–C11 P1–N2–C5
Dihedral angles in◦
129.3
129.1
129.1
129.2
N2–P1–N3–P4
00.0
00.0
00.0
N17–P4–N2–P1 N23–P1–N2–P4
P1–N23–C24–N29 P4–N17–C18–N33
C7–C5–N2–P1
92.1
4.5
91.2
91.9
3.5
90.7
92.2
5.6
91.7
C12–C11–N3–P4
88.4
88.5
88.3
P1–N23–H–C24 P4–N17–H–C18
Benzene ring
Purine ring
159.9
0.15–0.4
0.13–1.29
160.5
0.17–0.52
0.1–1.2
159.2
0.07–0.68
0.23–1.04
a
For atom numbering, see Fig. 6.
Represent intramolecular hydrogen bonding, see Fig. 6.
b
[C14H13ClN7P2]+ fragment ions, respectively, beside lesser intense
fragment peaks with intensities ranging from 3 to 10%.
The calculated formula mass of compound IIIb is 682 amu a
peak appearing at m/z = 684 (9.1%) is due to the 37Cl isotope (M+2)
whereas the observed peak at m/z = 376.6 (100%) is attributed to
fragment ion [C14H13ClN7P2]+ (Supplement Fig. S-3). The fragment
at m/z = 609.9 (22.4%) is due to ion [C24H21Cl2N12P2]+ resulting from
Cl2 and H loss from the parent molecule. The ion peak recorded at
m/z = 527 (22.4%) belongs to fragment [C19H18Cl3N8P2]+ owing to
bond cleavage between the purine moiety and the exocyclic N–H in
addition to loss of HCl. On the other hand, the moderately intense
ion peaks observed at m/z = 502 (50.3%), and 366.8 (33.9%) are safely
assigned to [C18H19Cl3N7P2]+, and [C11H10Cl3N4P2]+ fragments,
respectively.

310
T.A. Mohamed et al. / Spectrochimica Acta Part A 83 (2011) 304–313
The mass spectrum of adenine-cyclodiphospha(V)zane (IIIc;
723 amu) validates the proposed structural formula, Supplement
Fig. S-1C. molecular ion peak at m/z = 722 (8%) corre-
A
sponds to the molecular ion (M−1). The observed fragment at
m/z = 353 (100%, base peak) fits [C16H15N6P2]+ ion fragment,
whereas the moderately intense peak (73%) at m/z = 446.7 is
assigned to [C11H13Cl4N7P2]+ ion fragment. The mass spectrum
of IIIc reveals a series of peaks at m/z = 670, 622, 564.8, 541,
etc. corresponding to various fragment ions as explained in
Supplement Fig. S-4.
4.3. 1H and 13C NMR spectral interpretations
The characteristic 1H and 13C NMR spectral data for compounds
IIIa–c and their assignments are listed in Tables 3 and 4, respec-
tively. Linear correlations between theoretical and experimental
13C chemical shift results for compounds IIIa–c are reported with
a correlation coefficient R2 equal to 0.9488, 0.9983 and 0.9916,
respectively. However, unsatisfactory correlation coefficients were
found between observed/calculated 1H chemical shifts.
4.3.1. 1H NMR
The 1H NMR spectra of adenine-cyclodiphospha(V)zane deriva-
tives; IIIa–c (Fig. 4) were recorded in DMSO-d6 with tetramethylsi-
lane (TMS) as an internal standard. The intense singlet at 4.0 ppm
is attributed inherent water to (D–O–H) in DMSO-d6. The observed
chemical shifts of the three investigated compounds (IIIa–c) were
found to be somewhat similar owing to the high symmetry of com-
pounds IIIa–c. In the 1H NMR spectra of IIIa and IIIc, the two different
N–H singlets (exocyclic N–H and imidazole N–H) were nearly over-
lapped and therefore assigned to the observed broad signals at
9.01 and 8.87 ppm, respectively (Fig. 4). For IIIb, the two distinct
peaks at 8.92 and 9.19 ppm are assigned to exocyclic N–H and imi-
dazole N–H, respectively. Addition of D2O to the previous 3 NMR
solutions with vigorous shaking results in diminishing the above
mentioned signals due to hydrogen deuterium magnetic exchange.
On the other hand, the observed broadness may be attributed to the
nuclear quadruple broadening of nitrogen [28]. The singlets at 8.42,
8.42 and 8.37 ppm are assigned to the pyrimidine ring C–H, for IIIa,
IIIb and IIIc, respectively. The imidazole ring C–H was assigned to
the observed singlets at 8.41, 8.41 and 8.36 ppm in the 1H NMR
spectra of IIIa, IIIb and IIIc, respectively. The 1H NMR spectrum
of IIIa exhibits a doublet and two triplets in the spectral range
7.25–7.40 ppm which correspond to o-, m- and p-benzene(C–H e, f
and g, respectively). But in case of IIIb and IIIc, only two doublets
were observed in the 6.72–7.20 ppm range which is attributed to
o- and m-benzene C–H protons. On the other hand, the observed
singlet at 2.22 ppm in the IIIb spectrum is characteristic of methyl
group protons [28].
Fig. 4. 1H NMR spectra (ı, ppm) in DMSO-d6 solvent; (A) IIIa; (B) IIIb; (C) IIIc.
4.3.2. 13C NMR
The 13C NMR spectra of adenine-cyclodiphospha(V)zane deriva-
tives (IIIa–c) dissolved in DMSO-d6 are provided in Fig. 5. The
observed 13C peak at 40 ppm is due DMSO-d6 [28]. The 13C peak
of tetramethylsilane (TMS) was used as the internal standard. In
view of the fact that adenine-cyclodiphospha(V)zanes (IIIa–c) have
an inversion center, the number of observed 13C peaks is supposed
to be less than the number of carbon atoms present in the molecule.
The 13C NMR spectrum of IIIa (Fig. 5A) displays nine signals. The
signals observed at 115.17, 128.49, 130.59 ppm are characteristic
of benzene ortho-(C7), para-(C9) and meta-(C8) positions, respec-
tively [28]. The benzene carbon atoms attached to the nitrogen
atoms of phospha(V)azo ring (C6) were assigned to the recorded
signal at 146.21 ppm. On the other hand, the remaining five 13C
signals were due to ten carbon atoms of the two purine rings as
seen in Table 4. Ten signals at different chemical shifts appeared
Fig. 5. 13C NMR spectra (ı, ppm) in DMSO-d6 solvent; (A) IIIa; (B) IIIb; (C) IIIc.

T.A. Mohamed et al. / Spectrochimica Acta Part A 83 (2011) 304–313
311
Fig. 6. B3LYP/3-21G(d) optimized structure of adenine-cyclodiphosph(V)azane derivatives; (A) Y H for IIIa; (B) Y p-CH3 for IIIb; (C) Y p-Cl for IIIc.
in the 13C NMR spectrum of IIIb as seen in Fig. 5B. The intense
4.5. Vibrational assignment
peak observed at 21.35 ppm corresponds to the methyl group (C10
)
The mid-FT-IR (4000–200 cm−1) for solid samples of adenine-
cyclodiphospha(V)zane derivatives (IIIa–c) are shown in Fig. 2.
The recorded wavenumbers and their assignment are collected
in Table 2. The assignment of adenine-cyclodiphospha(V)zanes
(IIIa–c) fundamentals are mainly dependant on our recent vibra-
tional interpretation of adenine [14]. Moreover, our focus is
carbon atom [28]. The peaks observed at 123.88 and 149.96 ppm
are attributed to C4 and C3 purine ring atoms, respectively. The
imidazole carbon atom (C5) is assigned to the recorded signal at
138.67 ppm [14]. On the other hand, 13C NMR spectrum of IIIc
exhibits eight peaks only rather than nine which may be due
to the fact that two carbons are predicted at the same chemi-
cal shift (Table 4 and Fig. 5C). Therefore, the observed peak at
146.82 ppm is attributed to C1 (purine ring) and also to C6 (ben-
zene ring) supported by the calculated 13C chemical shifts as seen
later.
on the
ꢀ C C (benzene ring), ꢀ P–N, ꢀ P–Cl, ı PNP, ı
NPN and ı PCl2 vibrational motion. The symmetry coordinates
describing the vibration modes are also given in Ref. [14]. A
large number of fundamentals were expected in the investi-
gated adenine-cyclodiphospha(V)zane derivatives owing to 3N-6.
On the other hand owing to the symmetry of the synthe-
sized compounds (IIIa–c), these fundamentals are lesser than
expected.
In the IR spectrum of the adenine-cyclodiphospha(V)zane
derivatives(IIIa–c) as seen in Fig. 2, the splitting of the observed
bands of imidazole, pyrimidine and benzene rings are due to
the existence of two molecules of adenine and benzene in the
prepared compounds. In addition, the observed bands in the
2980–1795 cm−1 range were attributed to either combination
bands or overtones.
4.4. Structural parameters
B3LYP/3-21g(d) structural parameters for compounds IIIa–c are
listed in Table 5, whereas atom numbering is given in Fig. 6.
All compounds (IIIa–c) retain inversion center (Ci symmetry)
in agreement with earlier crystallographic studies where most
trans-cyclodiphosphazane molecules were found constrained to
Ci symmetry in the solid phase [29–31]. In addition, the sum of
calculated internal angles in (P–N)2 four memberd ring is 360◦
which agree precisely with the observed X-ray data for trans-
[ClP(O)NBut]2 [31]. Therefore, the phospha(V)azo four-membered
ring is planar. In addition the calculated P–N bond lengths of (P–N)2
4.5.1. NH Fundamentals
were in agreement within 0.06–0.01 A to X-ray values of trans-
Around 3000 cm−1 the observed IR bands in adenine-
cyclodiphospha(V)zane derivatives; IIIa–c (Fig. 2) show extensive
broadness compared to those observed in adenine (Fig. 2A)
which reflects larger hydrogen bonding interaction in cyclophos-
pha(V)zanes (IIIa–c). Their NH stretches undergo shift to lower
frequency ∼3253 cm−1. Unfortunately this region is off scale for
IIIc, thus a maximum center around 3102 cm−1 was chosen. These
bands represent all NH stretches as seen in Fig. 2.
˚
[C15H14N2PS]2 [32].
The benzene ring makes a 91.16 and 88.45◦dihedral angle with
the phospha(V)azo ring which indicates that the benzene ring is
perpendicular to the phospha(V)azo ring. On the other hand, the
phosphorus atom displays distorted trigonal bipyrimidal geometry
owing to the four-membered ring strain. While the nitrogen atoms
(N17 and N23) of exocyclic N–H are slightly triagonal pyramidal with
a dihedral angle of (P1–N23–H–C24 P4–N17–H–C18) ∼ 160◦.
On the other hand, the equilibrium intramolecular distances r
(N31· · ·HN23 N35· · ·HN17) in the optimized structures of IIIa–c are
The adenine NH2 wag was assigned earlier [14] to the recorded
weak IR band at 250 cm−1, therefore the corresponding NH wag
of the adenine-cyclodiphospha(V)zane derivatives (IIIa–c) better
match the observed IR bands in the 271–251 cm−1 range as seen in
Table 2. In addition, the imidazole ring NH wag was assigned
to the observed shoulders at 522 and 486 cm−1 for IIIa and IIIb,
respectively. Adenine NH2 scissor mode was assigned to the
˚
0.11 A shorter than the sum of Van der Waal contact radii for nitro-
˚
gen and hydrogen atoms (2.75 A) [33]. This indicates the formation
of intramolecular hydrogen bonding between N31 and HN23 also
between N35 and HN17 in all three molecules IIIa–c
.

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T.A. Mohamed et al. / Spectrochimica Acta Part A 83 (2011) 304–313
band at 1675 cm−1(vs) [14]. However four N–H in plane bend-
ing fundamentals were expected in the prepared compounds
IIIa–c at the observed bands in 1698–1789 cm−1 range. The broad-
ness of these bands may represent more hydrogen bonding
interaction in cyclophospha(V)zanes (IIIa–c) compared to ade-
nine.
zene rings ıip C–H of IIIa–c in contrast to the absence of bands in
that region for adenine IR spectra as seen in Fig. 2A.
The observed very strong IR band at 939 cm−1 for adenine has
been assigned to the pyrimidine ring C–H wagging [14]. Conse-
quently, the observed strong bands at 946 cm−1 for IIIa–c correlated
to pyrimidine ring C–H wagging. However, the imidazole ring C–H
wag in the 846–870 cm−1 range overlapped with pyrimidine ring
bending modes. The benzene ring C–H wagging modes in IIIa–c
were assigned to the observed bands in the 742–783 cm−1 range
of 450-500 cm-1 in agreement with earlier literature [14,37].
The C–N stretching modes for imidazole and pyrimidine rings
in adenine were observed at 1126(s) and 1309(vs) cm−1, respec-
tively. Therefore the recorded bands in the 1112–1123 cm−1 and
1305–1306 cm−1 ranges were assigned to ꢀC–N of imidazole and
pyrimidine in IIIa–c, respectively. In addition, benzene ring con-
jugated C C–C stretches were observed in the 982–1100 cm−1
spectral range for the phospha(V)zanes (IIIa–c) along with the
recorded bands in the 1382–1399 cm−1 range which is supported
by the absence of these bands in the adenine IR spectrum as seen
in Fig. 2A. The pyrimidine ring puckering mode of adenine was
recorded at 337 cm−1 compared to medium to strong band at
335 cm−1 for adenine-cyclodiphospha(V)zane derivatives (IIIa–c).
In addition, the imidazole ring puckering is observed at 621 cm−1 in
adenine. Therefore, the recorded bands in the 609–620 cm−1 range
would fit the imidazole ring puckering modes in IIIa–c. However, the
observed bands in the 371–392 cm−1 range were consistent with
the benzene ring puckering modes.
4.5.2. CH3 fundamentals
For each methyl group (C3v local symmetry) there are ꢀas
(stretch), ꢀs, ıas (bending), ıs, ꢁ (rock) and ꢂ fundamentals [34]. The
methyl stretches (ꢀC–H) in compound IIIb are hidden under a very
broad band observed around 3000 cm−1. In addition, the observed
IR bands in spectrum of IIIb (Fig. 2C) at 1441(m) and 1259(s) cm−1
were assigned to the methyl groups bending modes in consistency
with Ref. [34]. Similar spectral features are also observed the IR
spectrum of adenine as well as compounds IIIa and IIIc. However,
the two methyl rocking modes of IIIb are expected in the region
of 1000–1100 and 850–800 cm−1[34], thus we concluded that the
two methyl rocks (ꢁ CH3) for compound IIIb are attributed to the
observed IR bands at 1075(m) and 811(s) cm−1 (Fig. 2C), see Table 2.
4.5.3. P–Cl, P–N and C–Cl fundamentals
Comparing the infrared spectra of adenine and adenine-
cyclodiphospha(V)zane derivatives (IIIa,b), the observed band in
the range of 217–225 cm−1 is definitely belongs to the PCl2 scissor-
ing mode, whereas a very strong bands observed at 209 cm−1 are
assigned to the PCl2 wagging modes. However the PCl2 wagging
of IIIc seems to be shifted below 200 cm−1, therefore not observed
herein. On the other hand, the predicted PCl2 twisting and rocking
modes match those reported earlier at 100 and 50 cm−1, respec-
tively [35], these bands are beyond our experimental capability to
detect.
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.saa.2011.08.035.
The P–Cl stretching mode is observed in the 410–425 cm−1
range in agreement with Ref. [35]. The P–N stretching modes were
assigned to the observed bands in the 1137–1202 cm−1 range, an
assignment supported by the absence of these bands in the ade-
nine IR spectrum (Fig. 2A) and compared to the 900–1200 cm−1
for P–O stretch [35]. On the other hand, the observed IR bands in
the ranges were assigned to the P–N–P and N–P–N bending modes,
in agreement with assignments given for phosphorus compounds
[35].
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