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Crystal growth, structural and spectroscopic analysis of hypoxanthinium chloride monohydrate
Spectrochimica Acta Part A 67 (2007) 750–755
Crystal growth, structural and spectroscopic analysis of hypoxanthinium chloride monohydrate S. Kalyanaraman a , V. Krishnakumar b,∗ , K. Ganesan c a
Department of Physics, Sri Paramakalyani College, Alwarkurichi 627412, India b Department of Physics, Periyar University, Salem 636011, India c Department of Physics, T.B.M.L. College, Porayar 609307, India Received 14 May 2006; accepted 28 July 2006
Abstract Protonated form of hypoxanthinium chloride monohydrate single crystal has been grown from dilute hydrochloric acid. Single crystal X-ray analysis was carried out and the titled crystal belong to the monoclinic P21 /c space group. Hypoxanthine is protonated at N(1) with the hypoxanthine cations, linked to chlorine anion via weak bifurcated N–H· · ·Cl hydrogen bonds and interconnected by hydrogen bonding contacts of the type N–H· · ·O. Infrared, Raman and UV spectroscopic tools were applied to characterize hypoxanthinium chloride monohydrate. By applying group theoretical methods the internal and external modes of vibrations of the title crystal have been identified and discussed. © 2006 Elsevier B.V. All rights reserved. Keywords: Single crystal XRD; Hydrogen bonding; IR and Raman spectral analysis
1. Introduction Hypoxanthine, a naturally occurring oxopurine is an intermediate product of purine metabolism formed by enzymatical degradation of nucleic acids. The hypoxanthine ring is a very important structure in purine nucleotide biochemistry, since adenine and guanine rings arise from it in living things [1]. Neutral hypoxanthine involves three acidic protons, two of which are attached to the N(1) and N(3) pyrimidine nitrogens, while the third is attached to the N(7) imidazole nitrogen. Protonation has an important effect on hydrogen bonding in nucleic acid bases on the variety of base-pairing schemes in which they participate [2]. Hypoxanthine is protonated at N(1) and N(9) in the solid [3] or aqueous solution [4,5]. In metal complexes of hypoxanthine, the ligand binds the metal ion through N(7) when unidentate and through N(3), N(7) or N(3), N(9) when bidentate [6–9]. The present work was aimed at the synthesis of a zinc chloride complex of hypoxanthine in dilute hydrochloric acid. The single crystal XRD measurements revealed the absence of zinc coordination with hypoxanthine, which may be due to the inappropriate stoichiometry. However, protonation at the N(1) site was con-
∗
Corresponding author. Tel.: +91 427 2345766x214; fax: +91 427 2345124. E-mail address: vkrishna [email protected] (V. Krishnakumar).
1386-1425/$ – see front matter © 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.saa.2006.07.053
firmed after a thorough examination with a modified hydrogen bonding profile. Hence, we present the single crystal examination of hypoxanthinium chloride monohydrate and a detailed spectroscopic analysis in support of protonation and hydrogen bonding. In 1969, Sleteen and Jensen [10] had undertaken the single crystal examination of the title crystal. With the availability of sophisticated software and statistical algorithms, now a day the crystal structure analysis has been carried out more precisely even for giant molecules. The crystal data reported in this study confirm the crystal structure of hypoxanthinium chloride monohydrate and they are also in agreement with the literature. Group theoretical methods have been employed to identify the internal and external modes of vibrations present in the title crystal. 2. Experimental synthesis Hypoxanthine purchased from Lancaster chemicals (UK) has been dissolved in dilute hydrochloric acid and kept for slow evaporation. Small plate like crystals started to grow within a week. Repeated recrystallization yields good quality single crystals suitable for X-ray and spectroscopic analysis. The following chemical reaction gives the required title compound. C5 H4 N4 O + HCl + H2 O → C5 H5 ON4 + Cl− H2 O
S. Kalyanaraman et al. / Spectrochimica Acta Part A 67 (2007) 750–755 Table 1 Crystal data and structure refinement Empirical formula Formula weight Temperature Wavelength Crystal system Space group Unit cell dimensions Volume Z Density (calculated) Absorption coefficient F(0 0 0) Crystal size θ range for data collection Index ranges Reflections collected Independent reflections Completeness to θ = 30.80◦ Absorption correction Refinement method Data/restraints/parameters Goodness-of-fit on F2 Final R indices [I > 2 (I)] R indices (all data) Extinction coefficient Largest different peak and hole
C5 H7 ClN4 O2 190.60 301(2) K ˚ 0.71073 A Monoclinic P2(1)/c ˚ 90◦ ; b = 17.7595(13) A, ˚ a = 4.8347(4) A, ˚ 90◦ 94.568(2)◦ ; c = 9.0219(7) A, ˚3 772.18(10) A 4 1.639 mg/m3 0.458 mm−1 392 0.3 mm × 0.25 mm × 0.2 mm 2.29–30.80◦ −6 ≤ h ≤ 6, −24 ≤ k ≤ 25, −12 ≤ l ≤ 9 3844 1499 [R(int) = 0.0300] 62.3% None Full-matrix least-squares on F2 1499/6/129 1.088 R1 = 0.0475, wR2 = 0.1195 R1 = 0.0558, wR2 = 0.1233 0.001(5) ˚ −3 0.415 and −0.300 eA
3. Crystallographic measurements 3.1. Crystal data X-ray diffraction data were collected on the Bruker Smart diffractometer, using graphite monochromated Mo K␣ ˚ radiation. The unit cell dimensions were calcu(λ = 0.71073 A) lated by the least squares fit to 25 automatic centered reflections (2θ range: 9–14◦ ). The data collection was monitored with these at regular intervals of time for the orientation of intensity. Relevant crystallographic data, together with data collection and structural refinement details are listed in Table 1. Diffraction measurements were based on phi and omega scan method. The structure was solved by Patterson syntheses using the program SHELXS-97 [11]. Full-matrix least squares refinement was carried out with SHELXL-97 [12]. Diagrams were drawn using an ORTEP H [13] programs. The least square refinement followed by differences map led to the location of all the 12 non-H atoms and their final atomic coordinates and equivalent isotropic displacement parameters are listed in Table 2. The calculated thermal anisotropic displacement parameters of the non-H atoms are listed in Table 3. The hydrogen atom positions were obtained by difference Fourier map. The positional and isotropic displacement parameters of hydrogen atoms were found to vary during refinement. The hydrogen coordinates and their isotropic displacement parameters are listed in Table 4. The packing diagram of hypoxanthinium chloride monohydrate is shown in Fig. 1. Numbering of atoms of
751
Table 2 Atomic coordinates (×104 ) and equivalent isotropic displacement parameters ˚ 2 × 103 ) (A
Cl(1) O(1) C(1) N(1) C(2) N(2) C(3) C(4) N(3) C(5) N(4) O(2)
x
y
z
U(eq)
1916(1) 2757(3) 4502(4) 5266(4) 7179(5) 8579(4) 7914(4) 6009(4) 8967(4) 7729(5) 5939(4) 2447(4)
5314(1) 7270(1) 7165(1) 6452(1) 6307(1) 6816(1) 7524(1) 7725(1) 8185(1) 8758(1) 8499(1) 9039(1)
7786(1) 7425(2) 6528(2) 6088(2) 5094(2) 4428(2) 4829(2) 5802(2) 4316(2) 4959(2) 5873(2) 7731(2)
49(1) 36(1) 27(1) 32(1) 34(1) 32(1) 26(1) 25(1) 31(1) 34(1) 31(1) 46(1)
U(eq) is defined as one-third of the trace of the orthogonalized Uij tensor.
hypoxanthinium chloride monohydrate is given in the ORTEP diagram of Fig. 2, while the bond length and angles are listed in Table 5. 3.2. H-bonding The N–H· · ·N types of H-bonding present in the neutral form [14] have been disrupted in the protonated form. This may be due to the presence of Cl anion and water molecule. The breaking of N–H· · ·N bonds led to N–H· · ·Cl, C–H· · ·Cl, O–H· · ·Cl and O–H· · ·N types of bonds. These types of H-bonding changed the pattern of motifs in the protonated form and the triclinic structure in the neutral form changes to monoclinic structure in the protonated form. The complex hydrogen-bonding network of this system has two types of motifs that bind the adjacent molecules. The first type of motif has been labeled as R33 (11) that means 11 atoms with 3 donors and 3 acceptors are participating in the hydrogen bonding network and the second type of hydrogen bonding has been labeled as R23 (9) (9 atoms with 3 donors and 2 acceptors) using graph set analysis [15]. These two types of motifs are interconnected by the O–H· · ·Cl hydrogen bonding as shown in Fig. 1. Table 3 ˚ 2 × 103 ) Anisotropic displacement parameters (A
Cl(1) O(1) C(1) N(1) C(2) N(2) C(3) C(4) N(3) C(5) N(4) O(2)
U11
U22
U33
U23
U13
U12
57(1) 37(1) 27(1) 33(1) 35(1) 31(1) 24(1) 24(1) 29(1) 37(1) 33(1) 48(1)
30(1) 38(1) 32(1) 29(1) 32(1) 33(1) 30(1) 30(1) 35(1) 31(1) 31(1) 37(1)
64(1) 36(1) 25(1) 34(1) 35(1) 32(1) 25(1) 24(1) 29(1) 35(1) 31(1) 57(1)
3(1) 1(1) 1(1) 1(1) −3(1) −3(1) 1(1) 0(1) 0(1) 0(1) 0(1) 7(1)
29(1) 21(1) 7(1) 13(1) 11(1) 12(1) 9(1) 8(1) 13(1) 10(1) 12(1) 28(1)
−6(1) −2(1) 0(1) −2(1) 1(1) 2(1) 0(1) 0(1) −4(1) −2(1) 2(1) 6(1)
The anisotropic displacement factor −2p2 [h2 a*2 U11 + · · · + 2hka* b* U12 ].
exponent
takes
the
form:
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S. Kalyanaraman et al. / Spectrochimica Acta Part A 67 (2007) 750–755
Table 4 ˚ and angles (◦ ) Bond lengths (A) O(1)–C(1) C(1)–N(1) C(1)–C(4) N(1)–C(2) C(2)–N(2) N(2)–C(3) C(3)–C(4) C(3)–N(3) C(4)–N(4) N(3)–C(5) C(5)–N(4) O(1)–C(1)–N(1) O(1)–C(1)–C(4) N(1)–C(1)–C(4) C(2)–N(1)–C(1) N(2)–C(2)–N(1) C(2)–N(2)–C(3) N(2)–C(3)–C(4) N(2)–C(3)–N(3) C(4)–C(3)–N(3) C(3)–C(4)–N(4) C(3)–C(4)–C(1) N(4)–C(4)–C(1) C(5)–N(3)–C(3) N(4)–C(5)–N(3) C(5)–N(4)–C(4)
1.229(2) 1.387(2) 1.423(2) 1.363(2) 1.304(2) 1.354(2) 1.369(2) 1.375(2) 1.376(2) 1.336(2) 1.325(2) 122.61(17) 126.98(18) 110.41(16) 124.76(16) 125.27(17) 112.18(16) 126.80(17) 126.98(16) 106.21(15) 108.09(16) 120.57(17) 131.34(16) 108.28(15) 110.07(16) 107.35(16)
Symmetry transformations used to generate equivalent atoms.
Fig. 2. ORTEP drawing of hypoxanthinium chloride monohydrate. Thermal ellipsoids drawn at 50% probability level. Table 5 ˚ 2 × 103 ) Hydrogen coordinates (×104 ) and isotropic displacement parameters (A
H(1) H(2D) H(3) H(5) H(4) H(2A) H(2B)
x
y
z
U(eq)
4,570(80) 7,512 10,210 8,073 5,200(300) 1,380(110) 1,300(100)
5988(14) 5806 8224 9265 8830(50) 8630(20) 9500(19)
6540(30) 4872 3689 4790 6650(100) 8150(50) 7500(50)
72(10) 43(7) 55(9) 77(10) 690(90) 160(20) 105(15)
4. Factor group analysis The hypoxanthinium chloride monohydrate belongs to P21 /c space group with Z = 4, the number of molecules per unit cell. The 57 atoms in the unit cell give rise to 225 (k = 0) optical modes, which can be characterized according to the C2h factor group of the crystal using standard group theoretical methods [16]. The representation corresponding to the total degrees of freedom, Γ total , is given by [57Ag + 57Au + 57Bg + 57Bu ] among which the three acoustic modes are Au + 2Bu . The 225 optical modes are further divided into internal and external modes, whose irreducible representations are given by 42Ag + 42Au + 42Bg + 42Bu and 15Ag + 15Au + 15Bg + 15Bu , respectively. All the fundamental lattice vibrations of the hypoxanthinium cation, chloride anion and the water molecule, as predicted by the group theoretical method has been listed in Table 6, along with the lattice vibrations of the individual atoms of the present crystal to cross-check the correctness of the predictions. 5. Recording of spectra
Fig. 1. The packing diagram of hypoxanthinium chloride monohydrate.
The infrared spectra were recorded with a BRUKER IFS 6 V vacuum FT spectrometer in the range 400–4000 cm−1 with a KBr pellet and extended to Far-IR region with CsI window in the
S. Kalyanaraman et al. / Spectrochimica Acta Part A 67 (2007) 750–755
753
Table 6 Summary of the factor group analysis of hypoxanthinium chloride monohydrate Factor 4 group, C2h , species
Ag (R) Bg (R) Au (IR) Bu (IR)
4(C5 H5 Cl N4 O), C1 sites
4(H2 O), C1 sites
Cl, C1
General, C1 sites
I
E
I
E
E
C
H
N
O
Cl
39 39 39 39 156
3T, 3R 3T, 3R 3T, 3R 3T, 3R 12T, 12R
3 3 3 3 12
3T, 3R 3T, 3R 3T, 3R 3T, 3R 12T, 12R
3T 3T 3T 3T 12T
15 15 15 15 60
21 21 21 21 84
12 12 12 12 48
6 6 6 6 24
3 3 3 3 12
Optical modes
Acoustic modes
57 57 56 55 225
1 2 3
I refers to internal modes; E refers to external modes.
cies with the predicted vibrational assignments are listed in Table 7. 6.2. Analysis of spectra
Fig. 3. FT-IR spectrum of hypoxanthinium chloride monohydrate.
range 100–700 cm−1 . The FT-Raman spectra of the sample was recorded in the range 50–3500 cm−1 at room temperature using the BRUKER RFS 100/s Spectrophotometer which employs 1064 nm Nd-YAG laser excitation with 4 cm−1 resolution. 6. Vibrational analysis 6.1. Spectrum and band assignments The FT-IR and FT-Raman spectra of the compound were depicted in Figs. 3–5, respectively and the observed frequen-
Fig. 4. Far-IR spectrum of hypoxanthinium chloride monohydrate.
6.2.1. 3500–2900 cm−1 region IR bands observed at higher frequencies show two strong peaks at 3402 and 3369 cm−1 that are assigned to ν(OH) vibrations [17], which are exclusively absent in the neutral form of hypoxanthine [18–20]. However, a Raman spectrum does not show the ν(OH) vibrations, as these vibrations are usually very weak in Raman. The spectral lines assigned to ν(NH) and ν(CH) bands have shifted to higher region by about 40 cm−1 in the present system. It clearly indicates that the stretching of NH and CH bonds upon protonation has shifted the frequency to a higher region. Another possible cause for the stretching may be due to the occurrence of N–H· · ·Cl and C–H· · ·Cl hydrogen bonds in the atomic sites of the pyrimidine and imidazole rings. 6.2.2. 1700–1500 cm−1 region The strong and broad line at 1655 cm−1 in IR and a very strong line at 1670 cm−1 in Raman are assigned to ν(C O) bands. An appreciable shift found in ν(C O) type bands than the characteristic frequency may be due to the N–H· · ·O type of intermolecular hydrogen bonds that prevail between adjacent molecules. The medium shoulder at 1635 cm−1 in IR and
Fig. 5. FT-Raman spectrum of hypoxanthinium chloride monohydrate.
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S. Kalyanaraman et al. / Spectrochimica Acta Part A 67 (2007) 750–755
Table 7 Assignment of various vibrational modes of hypoxanthinium hydrochloride monohydrate Wave number (cm−1 ) IR
Assignment Raman
Hypoxanthinium chloride monohydrate 3654 w 3402 s 3369 vs 3182 vs 3148 w 3090 ms, sh 3071 w 3000 ms 2915 ms 2760 w 1655 vvs 1670 s 1635 m, sh 1608 m 1575 m, sh 1573 m 1508 ms 1515 m 1458 s 1455 s 1427 s 1374 ms 1369 m 1290 ms 1306 ms 1235 ms 1253 ms 1141 m 1131 w 1104 m 1106 m 979 w 927 s 882 mw 890 w 815 m 791 m 710 s 663 ms 600 ms 618 w 547 w 547 m 522 ms 521 w 426 w 411 w 367 w 334 s 329 w 310 w 232 mw 197 s 184 m 153 m 133 m 127 s
ν(OH) ν(OH) ν(OH) ν(NH), ν(CH) ν(NH), ν(CH) ν(NH), ν(CH) ν(C O), δ(OH) δH–O–H ν(C C), ν(C N) ν(C–N), δ(NH), ν ring ν(C–N), δ(NH), ν ring ν(C–N), δ(NH), ν ring ν(C–N), δ(CH) ν ring, δ(CH) δ(NH) δ(NH) ν ring, ν ring ν ring, δ(CH) δ(CH) ν ring, δ ring ν ring, δ ring ν ring, δ ring νhypoxanthine τ(NH) νhypoxanthine νhypoxanthine νhypoxanthine νhypoxanthine νhypoxanthine Lattice Lattice Lattice Lattice
1608 cm−1 in Raman may be attributed to H–O–H bonding [17]. Hence the presence of strong hydrogen bonding found in the Xray studies has been reflected in the vibrational spectral studies also. 6.2.3. 1500–50 cm−1 region There is no much appreciable change in the frequencies of ring vibrations, which is quite obvious. If at all if there is any minor change in the frequency that could be due to the C–N–C angle in the inner ring. However, changes in the single bonded stretching and bending vibrations of the exocyclic atoms can be predicted. All these vibrations have been categorically assigned in analogy with the literature [21,22]. The region 600–200 cm−1 is exclusively the ligand field region and the bands observed in this region are assigned to hypoxanthine ring stretching and they agree well with the values collected from the literature [18–20]. There are several strong peaks below 200 cm−1 observed both in IR and Raman, which are attributed to the combinations of translational and librational motions of hypoxanthine and translations of water molecules.
Fig. 6. Optical transmission spectrum of hypoxanthinium chloride monohydrate.
7. Optical transmission studies The transmission spectrum of hypoxanthinium chloride monohydrate shown in Fig. 6 was recorded using a Varian Cary 5E UV–vis-NIR spectrophotometer in the range 200–800 nm with high resolution. The crystal has been transparent throughout the UV–vis region. The absorbance in this region is nearly 2 units. The less absorbance behavior in the entire visible region also confirms the colorless nature and the quality of the crystal. 8. Conclusion Good quality single crystals of hypoxanthinium chloride monohydrate were grown in dilute hydrochloric acid using slow evaporation technique. The grown crystals were characterized by single crystal X-ray analysis and spectroscopic methods. Both the analyses confirm the protonation and the change in the crystal structure of the hypoxanthinium chloride monohydrate from the neutral form of hypoxanthine. The hydrogen-bonded motifs were identified and labeled using graph set analysis. The internal and external modes of vibrations were predicted by group theoretical means and the assignments of IR and Raman bands proposed in this study clearly justify the predictions. The UV spectrum of the title compound clearly shows the quality and transparency of the material. Acknowledgements The authors are thankful to IISC, Bangalore, IIT Madras, Chennai, and IGCAR, Kalpakkam for spectral facilities. The authors would like to place on record their gratitude to Prof. J.J. Vittal, Department of Chemistry, University of Singapore for taking single crystal X-ray measurements. One of the authors (S. Kalyanaraman) is thankful to University Grants Commission, New Delhi for awarding Teacher research fellowship and indebted to the Management and Principal of Sri Paramakalyani College, Alwarkurichi, India for their constant support and encouragement.
S. Kalyanaraman et al. / Spectrochimica Acta Part A 67 (2007) 750–755
References [1] A.L. Lehninger, Bioquimica: Las Bases Moleculares de la Estructura y function Celular, 6th ed., Omega, Barcelona, 1980. [2] R. Taylor, O. Kennard, J. Mol. Struct. 78 (1982) 1. [3] H.W. Schmalle, G. Hanggi, E. Dubler, Acta Cryst. C 44 (1988) 732. [4] D. Lichtenberg, F. Bergmann, Z. Neiman, Isr. J. Chem. 10 (1972) 805. [5] D. Lichtenberg, F. Bergmann, Z. Neiman, Isr. J. Chem. Soc. C 9 (1971) 1676. [6] E. Dubler, G. Hanggi, W. Bensch, J. Inorg. Biochem. 29 (1987) 269. [7] E. Dubler, G. Hanggi, H.W. Schmalle, Acta Cryst. C 43 (1987) 1872. [8] M.E. Kastner, K.F. Coffey, M.J. Clarke, S.E. Edmonds, K. Eriks, J. Am. Chem. Soc. 103 (1981) 5747. [9] E. Sletten, Acta Cryst. B 26 (1970) 1609. [10] J. Sleteen, L.H. Jensen, Acta Cryst. B 25 (1969) 1608. [11] G. Sheldrick, SHELXS-97 Program for Crystal Structure Solution, Instit¨ut f¨ur Anorganische Chemie der Universit¨at, Tammanstrasse 4, D-3400, Gottingen, Germany, 1997.
755
[12] G. Sheldrick, SHELXL-97 Program for Crystal Structure Refinement, Instit¨ut f¨ur Anorganische Chemie der Universit¨at, Tammanstrasse 4, D3400 Gottingen, Germany, 1997. [13] C.K. Johnson, ORTEP-II. A Fortran Thermal-Ellipsoid Program, Report ORNL-5138, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 1976. [14] H.W. Schmalle, G. Hanggi, E. Dubler, Acta Cryst. C 44 (1988) 732. [15] M.C. Etter, J.C. MacDonald, Acta Cryst. B 46 (1990) 256. [16] W.G. Fateley, F.R. Dollish, N.T. McDevitt, F.F. Bentley, Infrared and Raman Selection Rules for Molecular and Lattice Vibrations—The Correlation Method, Wiley–Interscience, New York, 1972. [17] I. Nakagawa, T. Shimanouchi, Spectrochim. Acta 20 (1964) 429. [18] E.R. Blout, M. Fields, J. Am. Chem. Soc. 72 (1950) 479. [19] C.P. Beetz Jr., G. Ascarelli, Spectrochim. Acta 36A (1980) 299. [20] P. Piperaki, N. Katsaros, D. Katakis, Inorg. Chim. Acta 67 (1982) 37. [21] C.M. Mikulski, S. Grossman, C.J.A. Lee, N.M. Karayannis, Trans. Metal. Chem. 12 (1987) 21. [22] W. Beck, N. Kottmair, Chem. Ber. 109 (1976) 970.
Crystal growth, structural and spectroscopic analysis of hypoxanthinium chloride monohydrate S. Kalyanaraman a , V. Krishnakumar b,∗ , K. Ganesan c a
Department of Physics, Sri Paramakalyani College, Alwarkurichi 627412, India b Department of Physics, Periyar University, Salem 636011, India c Department of Physics, T.B.M.L. College, Porayar 609307, India Received 14 May 2006; accepted 28 July 2006
Abstract Protonated form of hypoxanthinium chloride monohydrate single crystal has been grown from dilute hydrochloric acid. Single crystal X-ray analysis was carried out and the titled crystal belong to the monoclinic P21 /c space group. Hypoxanthine is protonated at N(1) with the hypoxanthine cations, linked to chlorine anion via weak bifurcated N–H· · ·Cl hydrogen bonds and interconnected by hydrogen bonding contacts of the type N–H· · ·O. Infrared, Raman and UV spectroscopic tools were applied to characterize hypoxanthinium chloride monohydrate. By applying group theoretical methods the internal and external modes of vibrations of the title crystal have been identified and discussed. © 2006 Elsevier B.V. All rights reserved. Keywords: Single crystal XRD; Hydrogen bonding; IR and Raman spectral analysis
1. Introduction Hypoxanthine, a naturally occurring oxopurine is an intermediate product of purine metabolism formed by enzymatical degradation of nucleic acids. The hypoxanthine ring is a very important structure in purine nucleotide biochemistry, since adenine and guanine rings arise from it in living things [1]. Neutral hypoxanthine involves three acidic protons, two of which are attached to the N(1) and N(3) pyrimidine nitrogens, while the third is attached to the N(7) imidazole nitrogen. Protonation has an important effect on hydrogen bonding in nucleic acid bases on the variety of base-pairing schemes in which they participate [2]. Hypoxanthine is protonated at N(1) and N(9) in the solid [3] or aqueous solution [4,5]. In metal complexes of hypoxanthine, the ligand binds the metal ion through N(7) when unidentate and through N(3), N(7) or N(3), N(9) when bidentate [6–9]. The present work was aimed at the synthesis of a zinc chloride complex of hypoxanthine in dilute hydrochloric acid. The single crystal XRD measurements revealed the absence of zinc coordination with hypoxanthine, which may be due to the inappropriate stoichiometry. However, protonation at the N(1) site was con-
∗
Corresponding author. Tel.: +91 427 2345766x214; fax: +91 427 2345124. E-mail address: vkrishna [email protected] (V. Krishnakumar).
1386-1425/$ – see front matter © 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.saa.2006.07.053
firmed after a thorough examination with a modified hydrogen bonding profile. Hence, we present the single crystal examination of hypoxanthinium chloride monohydrate and a detailed spectroscopic analysis in support of protonation and hydrogen bonding. In 1969, Sleteen and Jensen [10] had undertaken the single crystal examination of the title crystal. With the availability of sophisticated software and statistical algorithms, now a day the crystal structure analysis has been carried out more precisely even for giant molecules. The crystal data reported in this study confirm the crystal structure of hypoxanthinium chloride monohydrate and they are also in agreement with the literature. Group theoretical methods have been employed to identify the internal and external modes of vibrations present in the title crystal. 2. Experimental synthesis Hypoxanthine purchased from Lancaster chemicals (UK) has been dissolved in dilute hydrochloric acid and kept for slow evaporation. Small plate like crystals started to grow within a week. Repeated recrystallization yields good quality single crystals suitable for X-ray and spectroscopic analysis. The following chemical reaction gives the required title compound. C5 H4 N4 O + HCl + H2 O → C5 H5 ON4 + Cl− H2 O
S. Kalyanaraman et al. / Spectrochimica Acta Part A 67 (2007) 750–755 Table 1 Crystal data and structure refinement Empirical formula Formula weight Temperature Wavelength Crystal system Space group Unit cell dimensions Volume Z Density (calculated) Absorption coefficient F(0 0 0) Crystal size θ range for data collection Index ranges Reflections collected Independent reflections Completeness to θ = 30.80◦ Absorption correction Refinement method Data/restraints/parameters Goodness-of-fit on F2 Final R indices [I > 2 (I)] R indices (all data) Extinction coefficient Largest different peak and hole
C5 H7 ClN4 O2 190.60 301(2) K ˚ 0.71073 A Monoclinic P2(1)/c ˚ 90◦ ; b = 17.7595(13) A, ˚ a = 4.8347(4) A, ˚ 90◦ 94.568(2)◦ ; c = 9.0219(7) A, ˚3 772.18(10) A 4 1.639 mg/m3 0.458 mm−1 392 0.3 mm × 0.25 mm × 0.2 mm 2.29–30.80◦ −6 ≤ h ≤ 6, −24 ≤ k ≤ 25, −12 ≤ l ≤ 9 3844 1499 [R(int) = 0.0300] 62.3% None Full-matrix least-squares on F2 1499/6/129 1.088 R1 = 0.0475, wR2 = 0.1195 R1 = 0.0558, wR2 = 0.1233 0.001(5) ˚ −3 0.415 and −0.300 eA
3. Crystallographic measurements 3.1. Crystal data X-ray diffraction data were collected on the Bruker Smart diffractometer, using graphite monochromated Mo K␣ ˚ radiation. The unit cell dimensions were calcu(λ = 0.71073 A) lated by the least squares fit to 25 automatic centered reflections (2θ range: 9–14◦ ). The data collection was monitored with these at regular intervals of time for the orientation of intensity. Relevant crystallographic data, together with data collection and structural refinement details are listed in Table 1. Diffraction measurements were based on phi and omega scan method. The structure was solved by Patterson syntheses using the program SHELXS-97 [11]. Full-matrix least squares refinement was carried out with SHELXL-97 [12]. Diagrams were drawn using an ORTEP H [13] programs. The least square refinement followed by differences map led to the location of all the 12 non-H atoms and their final atomic coordinates and equivalent isotropic displacement parameters are listed in Table 2. The calculated thermal anisotropic displacement parameters of the non-H atoms are listed in Table 3. The hydrogen atom positions were obtained by difference Fourier map. The positional and isotropic displacement parameters of hydrogen atoms were found to vary during refinement. The hydrogen coordinates and their isotropic displacement parameters are listed in Table 4. The packing diagram of hypoxanthinium chloride monohydrate is shown in Fig. 1. Numbering of atoms of
751
Table 2 Atomic coordinates (×104 ) and equivalent isotropic displacement parameters ˚ 2 × 103 ) (A
Cl(1) O(1) C(1) N(1) C(2) N(2) C(3) C(4) N(3) C(5) N(4) O(2)
x
y
z
U(eq)
1916(1) 2757(3) 4502(4) 5266(4) 7179(5) 8579(4) 7914(4) 6009(4) 8967(4) 7729(5) 5939(4) 2447(4)
5314(1) 7270(1) 7165(1) 6452(1) 6307(1) 6816(1) 7524(1) 7725(1) 8185(1) 8758(1) 8499(1) 9039(1)
7786(1) 7425(2) 6528(2) 6088(2) 5094(2) 4428(2) 4829(2) 5802(2) 4316(2) 4959(2) 5873(2) 7731(2)
49(1) 36(1) 27(1) 32(1) 34(1) 32(1) 26(1) 25(1) 31(1) 34(1) 31(1) 46(1)
U(eq) is defined as one-third of the trace of the orthogonalized Uij tensor.
hypoxanthinium chloride monohydrate is given in the ORTEP diagram of Fig. 2, while the bond length and angles are listed in Table 5. 3.2. H-bonding The N–H· · ·N types of H-bonding present in the neutral form [14] have been disrupted in the protonated form. This may be due to the presence of Cl anion and water molecule. The breaking of N–H· · ·N bonds led to N–H· · ·Cl, C–H· · ·Cl, O–H· · ·Cl and O–H· · ·N types of bonds. These types of H-bonding changed the pattern of motifs in the protonated form and the triclinic structure in the neutral form changes to monoclinic structure in the protonated form. The complex hydrogen-bonding network of this system has two types of motifs that bind the adjacent molecules. The first type of motif has been labeled as R33 (11) that means 11 atoms with 3 donors and 3 acceptors are participating in the hydrogen bonding network and the second type of hydrogen bonding has been labeled as R23 (9) (9 atoms with 3 donors and 2 acceptors) using graph set analysis [15]. These two types of motifs are interconnected by the O–H· · ·Cl hydrogen bonding as shown in Fig. 1. Table 3 ˚ 2 × 103 ) Anisotropic displacement parameters (A
Cl(1) O(1) C(1) N(1) C(2) N(2) C(3) C(4) N(3) C(5) N(4) O(2)
U11
U22
U33
U23
U13
U12
57(1) 37(1) 27(1) 33(1) 35(1) 31(1) 24(1) 24(1) 29(1) 37(1) 33(1) 48(1)
30(1) 38(1) 32(1) 29(1) 32(1) 33(1) 30(1) 30(1) 35(1) 31(1) 31(1) 37(1)
64(1) 36(1) 25(1) 34(1) 35(1) 32(1) 25(1) 24(1) 29(1) 35(1) 31(1) 57(1)
3(1) 1(1) 1(1) 1(1) −3(1) −3(1) 1(1) 0(1) 0(1) 0(1) 0(1) 7(1)
29(1) 21(1) 7(1) 13(1) 11(1) 12(1) 9(1) 8(1) 13(1) 10(1) 12(1) 28(1)
−6(1) −2(1) 0(1) −2(1) 1(1) 2(1) 0(1) 0(1) −4(1) −2(1) 2(1) 6(1)
The anisotropic displacement factor −2p2 [h2 a*2 U11 + · · · + 2hka* b* U12 ].
exponent
takes
the
form:
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Table 4 ˚ and angles (◦ ) Bond lengths (A) O(1)–C(1) C(1)–N(1) C(1)–C(4) N(1)–C(2) C(2)–N(2) N(2)–C(3) C(3)–C(4) C(3)–N(3) C(4)–N(4) N(3)–C(5) C(5)–N(4) O(1)–C(1)–N(1) O(1)–C(1)–C(4) N(1)–C(1)–C(4) C(2)–N(1)–C(1) N(2)–C(2)–N(1) C(2)–N(2)–C(3) N(2)–C(3)–C(4) N(2)–C(3)–N(3) C(4)–C(3)–N(3) C(3)–C(4)–N(4) C(3)–C(4)–C(1) N(4)–C(4)–C(1) C(5)–N(3)–C(3) N(4)–C(5)–N(3) C(5)–N(4)–C(4)
1.229(2) 1.387(2) 1.423(2) 1.363(2) 1.304(2) 1.354(2) 1.369(2) 1.375(2) 1.376(2) 1.336(2) 1.325(2) 122.61(17) 126.98(18) 110.41(16) 124.76(16) 125.27(17) 112.18(16) 126.80(17) 126.98(16) 106.21(15) 108.09(16) 120.57(17) 131.34(16) 108.28(15) 110.07(16) 107.35(16)
Symmetry transformations used to generate equivalent atoms.
Fig. 2. ORTEP drawing of hypoxanthinium chloride monohydrate. Thermal ellipsoids drawn at 50% probability level. Table 5 ˚ 2 × 103 ) Hydrogen coordinates (×104 ) and isotropic displacement parameters (A
H(1) H(2D) H(3) H(5) H(4) H(2A) H(2B)
x
y
z
U(eq)
4,570(80) 7,512 10,210 8,073 5,200(300) 1,380(110) 1,300(100)
5988(14) 5806 8224 9265 8830(50) 8630(20) 9500(19)
6540(30) 4872 3689 4790 6650(100) 8150(50) 7500(50)
72(10) 43(7) 55(9) 77(10) 690(90) 160(20) 105(15)
4. Factor group analysis The hypoxanthinium chloride monohydrate belongs to P21 /c space group with Z = 4, the number of molecules per unit cell. The 57 atoms in the unit cell give rise to 225 (k = 0) optical modes, which can be characterized according to the C2h factor group of the crystal using standard group theoretical methods [16]. The representation corresponding to the total degrees of freedom, Γ total , is given by [57Ag + 57Au + 57Bg + 57Bu ] among which the three acoustic modes are Au + 2Bu . The 225 optical modes are further divided into internal and external modes, whose irreducible representations are given by 42Ag + 42Au + 42Bg + 42Bu and 15Ag + 15Au + 15Bg + 15Bu , respectively. All the fundamental lattice vibrations of the hypoxanthinium cation, chloride anion and the water molecule, as predicted by the group theoretical method has been listed in Table 6, along with the lattice vibrations of the individual atoms of the present crystal to cross-check the correctness of the predictions. 5. Recording of spectra
Fig. 1. The packing diagram of hypoxanthinium chloride monohydrate.
The infrared spectra were recorded with a BRUKER IFS 6 V vacuum FT spectrometer in the range 400–4000 cm−1 with a KBr pellet and extended to Far-IR region with CsI window in the
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Table 6 Summary of the factor group analysis of hypoxanthinium chloride monohydrate Factor 4 group, C2h , species
Ag (R) Bg (R) Au (IR) Bu (IR)
4(C5 H5 Cl N4 O), C1 sites
4(H2 O), C1 sites
Cl, C1
General, C1 sites
I
E
I
E
E
C
H
N
O
Cl
39 39 39 39 156
3T, 3R 3T, 3R 3T, 3R 3T, 3R 12T, 12R
3 3 3 3 12
3T, 3R 3T, 3R 3T, 3R 3T, 3R 12T, 12R
3T 3T 3T 3T 12T
15 15 15 15 60
21 21 21 21 84
12 12 12 12 48
6 6 6 6 24
3 3 3 3 12
Optical modes
Acoustic modes
57 57 56 55 225
1 2 3
I refers to internal modes; E refers to external modes.
cies with the predicted vibrational assignments are listed in Table 7. 6.2. Analysis of spectra
Fig. 3. FT-IR spectrum of hypoxanthinium chloride monohydrate.
range 100–700 cm−1 . The FT-Raman spectra of the sample was recorded in the range 50–3500 cm−1 at room temperature using the BRUKER RFS 100/s Spectrophotometer which employs 1064 nm Nd-YAG laser excitation with 4 cm−1 resolution. 6. Vibrational analysis 6.1. Spectrum and band assignments The FT-IR and FT-Raman spectra of the compound were depicted in Figs. 3–5, respectively and the observed frequen-
Fig. 4. Far-IR spectrum of hypoxanthinium chloride monohydrate.
6.2.1. 3500–2900 cm−1 region IR bands observed at higher frequencies show two strong peaks at 3402 and 3369 cm−1 that are assigned to ν(OH) vibrations [17], which are exclusively absent in the neutral form of hypoxanthine [18–20]. However, a Raman spectrum does not show the ν(OH) vibrations, as these vibrations are usually very weak in Raman. The spectral lines assigned to ν(NH) and ν(CH) bands have shifted to higher region by about 40 cm−1 in the present system. It clearly indicates that the stretching of NH and CH bonds upon protonation has shifted the frequency to a higher region. Another possible cause for the stretching may be due to the occurrence of N–H· · ·Cl and C–H· · ·Cl hydrogen bonds in the atomic sites of the pyrimidine and imidazole rings. 6.2.2. 1700–1500 cm−1 region The strong and broad line at 1655 cm−1 in IR and a very strong line at 1670 cm−1 in Raman are assigned to ν(C O) bands. An appreciable shift found in ν(C O) type bands than the characteristic frequency may be due to the N–H· · ·O type of intermolecular hydrogen bonds that prevail between adjacent molecules. The medium shoulder at 1635 cm−1 in IR and
Fig. 5. FT-Raman spectrum of hypoxanthinium chloride monohydrate.
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Table 7 Assignment of various vibrational modes of hypoxanthinium hydrochloride monohydrate Wave number (cm−1 ) IR
Assignment Raman
Hypoxanthinium chloride monohydrate 3654 w 3402 s 3369 vs 3182 vs 3148 w 3090 ms, sh 3071 w 3000 ms 2915 ms 2760 w 1655 vvs 1670 s 1635 m, sh 1608 m 1575 m, sh 1573 m 1508 ms 1515 m 1458 s 1455 s 1427 s 1374 ms 1369 m 1290 ms 1306 ms 1235 ms 1253 ms 1141 m 1131 w 1104 m 1106 m 979 w 927 s 882 mw 890 w 815 m 791 m 710 s 663 ms 600 ms 618 w 547 w 547 m 522 ms 521 w 426 w 411 w 367 w 334 s 329 w 310 w 232 mw 197 s 184 m 153 m 133 m 127 s
ν(OH) ν(OH) ν(OH) ν(NH), ν(CH) ν(NH), ν(CH) ν(NH), ν(CH) ν(C O), δ(OH) δH–O–H ν(C C), ν(C N) ν(C–N), δ(NH), ν ring ν(C–N), δ(NH), ν ring ν(C–N), δ(NH), ν ring ν(C–N), δ(CH) ν ring, δ(CH) δ(NH) δ(NH) ν ring, ν ring ν ring, δ(CH) δ(CH) ν ring, δ ring ν ring, δ ring ν ring, δ ring νhypoxanthine τ(NH) νhypoxanthine νhypoxanthine νhypoxanthine νhypoxanthine νhypoxanthine Lattice Lattice Lattice Lattice
1608 cm−1 in Raman may be attributed to H–O–H bonding [17]. Hence the presence of strong hydrogen bonding found in the Xray studies has been reflected in the vibrational spectral studies also. 6.2.3. 1500–50 cm−1 region There is no much appreciable change in the frequencies of ring vibrations, which is quite obvious. If at all if there is any minor change in the frequency that could be due to the C–N–C angle in the inner ring. However, changes in the single bonded stretching and bending vibrations of the exocyclic atoms can be predicted. All these vibrations have been categorically assigned in analogy with the literature [21,22]. The region 600–200 cm−1 is exclusively the ligand field region and the bands observed in this region are assigned to hypoxanthine ring stretching and they agree well with the values collected from the literature [18–20]. There are several strong peaks below 200 cm−1 observed both in IR and Raman, which are attributed to the combinations of translational and librational motions of hypoxanthine and translations of water molecules.
Fig. 6. Optical transmission spectrum of hypoxanthinium chloride monohydrate.
7. Optical transmission studies The transmission spectrum of hypoxanthinium chloride monohydrate shown in Fig. 6 was recorded using a Varian Cary 5E UV–vis-NIR spectrophotometer in the range 200–800 nm with high resolution. The crystal has been transparent throughout the UV–vis region. The absorbance in this region is nearly 2 units. The less absorbance behavior in the entire visible region also confirms the colorless nature and the quality of the crystal. 8. Conclusion Good quality single crystals of hypoxanthinium chloride monohydrate were grown in dilute hydrochloric acid using slow evaporation technique. The grown crystals were characterized by single crystal X-ray analysis and spectroscopic methods. Both the analyses confirm the protonation and the change in the crystal structure of the hypoxanthinium chloride monohydrate from the neutral form of hypoxanthine. The hydrogen-bonded motifs were identified and labeled using graph set analysis. The internal and external modes of vibrations were predicted by group theoretical means and the assignments of IR and Raman bands proposed in this study clearly justify the predictions. The UV spectrum of the title compound clearly shows the quality and transparency of the material. Acknowledgements The authors are thankful to IISC, Bangalore, IIT Madras, Chennai, and IGCAR, Kalpakkam for spectral facilities. The authors would like to place on record their gratitude to Prof. J.J. Vittal, Department of Chemistry, University of Singapore for taking single crystal X-ray measurements. One of the authors (S. Kalyanaraman) is thankful to University Grants Commission, New Delhi for awarding Teacher research fellowship and indebted to the Management and Principal of Sri Paramakalyani College, Alwarkurichi, India for their constant support and encouragement.
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References [1] A.L. Lehninger, Bioquimica: Las Bases Moleculares de la Estructura y function Celular, 6th ed., Omega, Barcelona, 1980. [2] R. Taylor, O. Kennard, J. Mol. Struct. 78 (1982) 1. [3] H.W. Schmalle, G. Hanggi, E. Dubler, Acta Cryst. C 44 (1988) 732. [4] D. Lichtenberg, F. Bergmann, Z. Neiman, Isr. J. Chem. 10 (1972) 805. [5] D. Lichtenberg, F. Bergmann, Z. Neiman, Isr. J. Chem. Soc. C 9 (1971) 1676. [6] E. Dubler, G. Hanggi, W. Bensch, J. Inorg. Biochem. 29 (1987) 269. [7] E. Dubler, G. Hanggi, H.W. Schmalle, Acta Cryst. C 43 (1987) 1872. [8] M.E. Kastner, K.F. Coffey, M.J. Clarke, S.E. Edmonds, K. Eriks, J. Am. Chem. Soc. 103 (1981) 5747. [9] E. Sletten, Acta Cryst. B 26 (1970) 1609. [10] J. Sleteen, L.H. Jensen, Acta Cryst. B 25 (1969) 1608. [11] G. Sheldrick, SHELXS-97 Program for Crystal Structure Solution, Instit¨ut f¨ur Anorganische Chemie der Universit¨at, Tammanstrasse 4, D-3400, Gottingen, Germany, 1997.
755
[12] G. Sheldrick, SHELXL-97 Program for Crystal Structure Refinement, Instit¨ut f¨ur Anorganische Chemie der Universit¨at, Tammanstrasse 4, D3400 Gottingen, Germany, 1997. [13] C.K. Johnson, ORTEP-II. A Fortran Thermal-Ellipsoid Program, Report ORNL-5138, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 1976. [14] H.W. Schmalle, G. Hanggi, E. Dubler, Acta Cryst. C 44 (1988) 732. [15] M.C. Etter, J.C. MacDonald, Acta Cryst. B 46 (1990) 256. [16] W.G. Fateley, F.R. Dollish, N.T. McDevitt, F.F. Bentley, Infrared and Raman Selection Rules for Molecular and Lattice Vibrations—The Correlation Method, Wiley–Interscience, New York, 1972. [17] I. Nakagawa, T. Shimanouchi, Spectrochim. Acta 20 (1964) 429. [18] E.R. Blout, M. Fields, J. Am. Chem. Soc. 72 (1950) 479. [19] C.P. Beetz Jr., G. Ascarelli, Spectrochim. Acta 36A (1980) 299. [20] P. Piperaki, N. Katsaros, D. Katakis, Inorg. Chim. Acta 67 (1982) 37. [21] C.M. Mikulski, S. Grossman, C.J.A. Lee, N.M. Karayannis, Trans. Metal. Chem. 12 (1987) 21. [22] W. Beck, N. Kottmair, Chem. Ber. 109 (1976) 970.