Hydrogen bonded supramolecular assembly in N6-benzyladeninium nitrate and N6-benzyladeninium 3-hydroxy picolinate: A synthetic cytokinin

Article abstract of DOI:10.1007/s10870-011-0014-x

N ⁶-benzyladeninium nitrate, (1), C₁₂H ₁₂N₅ ⁺ NO₃ ^- crystallizes in P2 ₁/c, with a = 15.0035(13), b = 5.3788(5), c = 16.8954(13) A, β = 107.331(6)°, Z = 4 and N ⁶-benzyladeninium 3-hydroxy picolinate, (2), C₁₂H₁₂N₅ ⁺ C₆H₄NO₃ ^-, crystallizes in P1, with a = 8.3017(4), b = 14.6170(7), c = 14.7909 (8) A, α = 78.801 (4), β = 81.979 (4),γ = 88.849 (4)°, Z = 4. In both the salts, the cation exists as N(7)H tautomer with protonation at the N₃ atom. The dihedral angle of 76.64 (16)° for (1), 67.91(12)° for (cation A) and 68.27 (13)° for (cation B) in (2), between the adenine plane and phenyl ring plane, the distal orientation of the N6 substituent with respect to the imidazole ring and the free N1 position, make these benzyladeninium cations meet all the requirements necessary for cytokinin activity. The crystal structures are stabilized by N-H???N, N-H???O, C-H???O hydrogen bonds and C-H???π stacking interaction between symmetry related benzyladenine molecule.

Full text of DOI:10.1007/s10870-011-0014-x

J Chem Crystallogr (2011) 41:864–867
DOI 10.1007/s10870-011-0014-x
ORIGINAL PAPER
Hydrogen Bonded Supramolecular Assembly in N6-
Benzyladeninium Nitrate and N6-Benzyladeninium 3-Hydroxy
Picolinate: A Synthetic Cytokinin
•
Jeyaraman Selvaraj Nirmalram
•
Duraisamy Tamilselvi Packianathan Thomas Muthiah
Received: 19 November 2010 / Accepted: 31 January 2011 / Published online: 15 February 2011
Ó Springer Science+Business Media, LLC 2011
Abstract N6-benzyladeninium nitrate, (1), C12H12N5
(N6-furfuryladenine) and benzyladenine have been found to
?
-
NO3
crystallizes in P21/c, with a = 15.0035(13),
markedly influence the biological activity. Zeatin and
kinetin are naturally occurring cytokinins, whereas ben-
zyladenine is a synthetic cytokinin.The crystal structures of
cytokinins have been investigated in a variety of crystalline
environments; N6-benzyladenine [2], N6-furfuryladenine
[3], N6-benzyladenine hydrochloride [4], N6-benzyladenine
hydrobromide [5], N6-benzyladenine sulphosalicylate
monohydrate [6], N6-furfuryladenine hydrochloride [7],
copper complex of N6-furfuryladenine [8] and a copper
complex of N6-benzyladenine [9]. The aim of the present
study is to understand the conformations and supramolec-
ular architectures of N6-benzyladeninium nitrate and
N6-benzyladeninium 3-hydroxy picolinate.
˚
b = 5.3788(5), c = 16.8954(13) A, b = 107.331(6)°, Z = 4
and N6-benzyladeninium 3-hydroxy picolinate, (2), C12H12
N5? C6H4NO3-, crystallizes in P1, with a = 8.3017(4), b =
˚
14.6170(7), c = 14.7909 (8) A, a = 78.801 (4), b =
81.979 (4),c = 88.849 (4)°, Z = 4. In both the salts, the
cation exists as N(7)H tautomer with protonation at the N3
atom. The dihedral angle of 76.64 (16)° for (1), 67.91(12)° for
(cation A) and 68.27 (13)° for (cation B) in (2), between the
adenine plane and phenyl ring plane, the distal orientation of
the N6 substituent with respect to the imidazole ring and the
free N1 position, make these benzyladeninium cations
meetalltherequirementsnecessaryforcytokininactivity.The
crystal structures are stabilized by N–HÁÁÁN, N–HÁÁÁO,
C–HÁÁÁO hydrogen bonds and C–HÁÁÁp stacking interaction
between symmetry related benzyladenine molecule.
Experimental
Keywords N6-benzyladenine salts Á Crystal structure Á
Cytokinin activity Á Supramolecular architecture
Crystals were prepared by dissolving; N6-benzyladenine
(Loba Chemie, India) in methanol and addition of 0.5 ml of
dilute nitric acid for (1) and 3-hydroxy picolinic acid
(Aldrich) in 20 ml of water in 1:1 ratio for (2). The
resultant solution was heated for 15 min over a water bath
and kept for slow evaporation. After a few days, colorless
crystals were obtained (The quality of the crystals obtained
was poor. Our efforts to crystallize these compounds in a
variety of solvents were not fruitful).
Introduction
Cytokinins are well known plant growth substances [1],
which play a vital role in the development process of
plants. They occur abundantly in plant tissues, root tips,
xylum sap developing fruits, tumour tissues and germi-
nating seeds. Among different classes of cytokinins,
adenine type aromatic cytokinins like zeatin, kinetin
Data collection: APEX2 [10]; cell refinement: SAINT
[10]; data reduction: SAINT [10]; program(s) used to solve
structure: SHELXS97 [11]; program(s) used to refine
structure: SHELXL97 [11]; molecular graphics: PLATON
[12]; software used to prepare material for publication:
PLATON [12]. All hydrogen atoms were positioned geo-
metrically and were refined using riding model. The N–H
J. S. Nirmalram Á D. Tamilselvi Á P. T. Muthiah (&)
School of Chemistry, Bharathidasan University, Tiruchirappalli
620 024, Tamilnadu, India
˚
and C–H bond lengths are 0.86 and 0.93–0.97 A,
e-mail: tommtrichy@yahoo.co.in
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J Chem Crystallogr (2011) 41:864–867
865
˚
respectively [Uiso(H) = 1.2Ueq(parent atom)]. Crystallo-
graphic details and hydrogen bonding geometries for the
compounds are given in Tables 1 and 2, respectively.
Table 2 Hydrogen bonding geometry (A, °) for compounds 1 and 2
D–HÁÁÁA
D–H
HÁÁÁA
DÁÁÁA
D–HÁÁÁA
Compound 1
N3–H3ÁÁÁN9i
0.86
0.86
0.86
0.93
0.93
0.97
0.93
0.93
2.00
2.00
1.90
2.35
2.56
2.42
2.54
2.55
2.846 (5)
2.824 (5)
2.745 (5)
3.235 (6)
3.386 (6)
2.869 (5)
2.867 (6)
3.468 (7)
168
160
165
160
149
108
101
171
N6–H6ÁÁÁO1
Results and Discussion
N7–H7ÁÁÁO2
C8–H8ÁÁÁO2ii
The probable tautomeric forms assumed by adenines and
adenine based cytokinins in normal and acidic conditions
have been reviewed [13]. As expected the benzyladenine
molecule of the title compounds exist as N(7)H tautomer
with protonation at the N3 atom. The evidence for the
presence of the H atoms on these sites is further confirmed
by the changes in bond angles at N1, N3, N7 and N9. The
internal angles at N1 and N9 do not differ largely, whereas
N3 and N7 show a significant change. The dihedral angle
of 76.4 (2)° for (1), 67.91(12)° for (cation A) and 68.27
(13)° for (cation B) in (2), between the adenine plane and
phenyl ring plane, the distal orientation of the N6 sub-
stituent with respect to the imidazole ring and the free N1
position, are the salient features reported as the require-
ments necessary for cytokinin activity [3, 14–17]. The
molecular geometry of these compounds, in terms of bond
length and bond angles are in good agreement with the
crystal structures of N6-benzyladenine hydrochloride [4],
N6-benzyladenine hydrobromide [5], and N6-benzyladenine
copper complex [9].
C8–H8ÁÁÁO3ii
C10–H10AÁÁÁN1
C12–H12ÁÁÁN6
C15–H15ÁÁÁO1iii
Compound 2
O3B–H3B1ÁÁÁO2B
O3A–H3A1ÁÁÁO2A
N3A–H3AÁÁÁO1Biv
N3A–H3AÁÁÁN17Biv
N3B–H3BÁÁÁO1A
N3B–H3BÁÁÁN17A
N6A–H6AÁÁÁO2A
N6B–H6BÁÁÁO2B
N7A–H7AÁÁÁO1A
N7B–H7BÁÁÁO1B
C2A–H2AÁÁÁO1Biv
C2B–H2BÁÁÁO1A
0.82
0.82
0.86
0.86
0.86
0.86
0.86
0.86
0.86
0.86
0.93
0.93
1.81
1.83
2.52
1.97
2.52
1.92
1.96
1.97
1.79
1.79
2.54
2.54
2.536 (3)
2.548 (3)
2.967 (3)
2.811 (3)
2.963 (3)
2.766 (3)
2.789 (3)
2.802 (3)
2.642 (3)
2.645 (3)
3.017 (4)
3.012 (4)
146
146
113
168
113
169
162
162
173
173
113
112
Symmetry codes: (i) = 2 - x, -1/2 ? y, 3/2 - z; (ii) = 2 - x,
2 - y, 1 - z; (iii) = 1 - x, -1/2 ? y, 1/2 - z; (iv) = x, -1 ? y, z
Table 1 Crystal data and
Compound reference
1
2
structure refinement for
compounds 1 and 2
?
-
?
-
Chemical formula
C12H12N5 NO3
288.28
C12H12N5 C6H4NO3
364.37
Formula mass
Crystal system
Monoclinic
15.0035(13)
5.3788(5)
16.8954(13)
90.00
Triclinic
8.3017(4)
14.6170(7)
14.7909(8)
78.801(4)
81.979(4)
88.849(4)
1743.37(15)
296 (2)
˚
a/A
˚
b/A
˚
c/A
a/°
b/°
c/°
107.331(6)
90.00
3
˚
Unit cell volume/A
1301.57(19)
296
Temperature/K
Space group
P21/c
P 1
No. of formula units per unit cell, Z
No. of reflections measured
No. of independent reflections
Rint
4
4
6478
18163
1130
3575
0.0446
0.0484
Final R1 values (I [ 2r(I))
Final wR(F2) values (I [ 2r(I))
Final R1 values (all data)
Final wR(F2) values (all data)
Goodness of fit on F2
0.0386
0.0427
0.0981
0.1071
0.0572
0.0641
0.1116
0.1242
0.958
1.008
123

866
J Chem Crystallogr (2011) 41:864–867
The asymmetric unit of (1) contains one N6-benzylade-
nine cation and a nitrate anion (Fig. 1). The 21 screw
related N6-benzyladenine cations are linked by N(3)–
HÁÁÁN(9) hydrogen bonds. The nitrate ion forms an inter-
esting network of hydrogen bonds with the benzyl adenine
cation. The N6H and N7H of the benzyl adenine cation
form a cyclic ring motif with graph set [18] R22(9) with the
oxygen atoms (O1 and O2) of the nitrate anion through
N–HÁÁÁO hydrogen bonds. This type of motif is very much
similar to the fork like interaction observed in aminopy-
rimidine carboxylates [19, 20]. Interestingly there exists a
C–HÁÁÁO interaction involving the C8–H8 of the benzyl
adenine cation with the O2 and O3 atom of the nitrate
anion. The three centered hydrogen bond R21(4) bridges the
symmetry related benyladenine nitrate pairs. This
arrangement leads to the creation of a new dimeric unit
with motif R24(10), facilitated by a bifurcated hydrogen
Fig. 1 ORTEP view of the compound (1) with 30% probability
displacement ellipsoids
Fig. 2 A view of the
supramolecular interactions in
compound (1). Dashed lines
indicate hydrogen bonds and H
atoms not involved in hydrogen
bonding have been omitted for
clarity
Fig. 3 ORTEP view of the compound (2) with 30% probability displacement ellipsoids
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J Chem Crystallogr (2011) 41:864–867
867
Fig. 4 View of the chain along the b axis for compound (2)
Acknowledgments JSN thanks the UGC-SAP, India, for the award
of RFSMS. The authors thank the D.S.T-India (FÁI.S.T programme)
for the use of Bruker SMART APEX II diffractometer at the School
of Chemistry, Bharathidasan University, Tiruchirappalli, Tamilnadu,
India.
bond donor and a bifurcated acceptor (O2). The combi-
nation of R22(9) and R24(10) leads to the formation of an
array of hydrogen bonds. Two such dimeric units thus
formed are linked via C–HÁÁÁO hydrogen bonds as shown in
(Fig. 2). The crystal structure is further stabilized by
C–HÁÁÁp interaction between the symmetry related benzy-
ladenine molecule.
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CCDC-795111 for (1) and 795105 for (2) contains the sup-
plementary crystallographic data for this paper. These data
can be obtained free of charge athttp://www.ccdc.cam.ac.uk/
conts/retrieving.html [or from the Cambridge Crystallo-
graphic Data Centre (CCDC), 12 Union Road, Cambridge
CB2 IEZ, UK; fax: C44 (0) 1223-336033; e-mail:
deposit@ccdc.cam.ac.uk].
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