- Email: [email protected]
Inelastic neutron scattering, Raman spectroscopy and periodic DFT study of purine
Vibrational Spectroscopy 35 (2004) 173–177
Inelastic neutron scattering, Raman spectroscopy and periodic DFT study of purine Stewart F. Parkera,*, Richard Jeansb, Robin Devonshireb a
b
ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield S3 7HF, UK
Received 10 October 2003; received in revised form 12 January 2004; accepted 14 January 2004 Available online 5 March 2004
Abstract The inelastic neutron scattering (INS) spectrum of purine at 20 K has been recorded and compared to that derived from ab initio DFT calculations for the isolated molecule in both its N7–H and N9–H tautomers as well as a periodic DFT calculation using the complete unit cell. For the isolated molecule calculations modest agreement is found for the N7–H tautomer and poor agreement with the N9–H tautomer consistent with the known crystal structure. Much better agreement is found with a periodic DFT calculation of the complete unit cell that explicitly includes the intermolecular interactions, in particular, the hydrogen bonding and the factor group splitting. The lattice mode region is observed by INS and Raman spectroscopies for the first time and assignments are made. # 2004 Elsevier B.V. All rights reserved. Keywords: Inelastic neutron scattering; Purine; Periodic DFT
1. Introduction Purine (see Fig. 1) is the parent compound of the purine bases whose derivatives include the biologically important molecules adenine and adenosine. In solution, purine exists in equilibrium between the N9–H and N7–H tautomers [1]. In the solid state, X-ray crystallography [2] indicates that it is present exclusively as the N7–H tautomer. The infrared and Raman spectra of purine, including isotopic derivatives, have been extensively investigated in solution [3], in argon matrices [4] and in the solid state [5,6]. The assignments have been supported by ab initio calculations [4,5] for the isolated molecule but only at the Hartree– Fock level. For inelastic neutron scattering (INS) spectroscopy, the scattered intensity depends on the number of scattering centres, the amplitude of vibration and the inelastic scattering cross-section [7]. Thus it is straightforward to obtain the INS spectrum from ab initio calculations, which provides a stringent test of the model and unambiguous assignments. Previous work [8–11] has shown that density functional theory (DFT) provides much better results than Hartree– Fock. The cross-section is large for hydrogen and small for *
Corresponding author. Tel.: þ44-1235-446182; fax: þ44-1235-445720. E-mail address: [email protected] (S.F. Parker). 0924-2031/$ – see front matter # 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.vibspec.2004.01.003
virtually all other elements, so modes involving substantial hydrogen motion dominate the spectrum, additionally, there are no selection rules and the low energy region is readily accessible. The purpose of the present work was to obtain the INS spectrum of purine and compare it to ab initio calculations to confirm the assignments. To support the work, we have also obtained the Raman spectrum of solid state purine in the lattice mode region for the first time.
2. Experimental The INS spectrum of purine (Aldrich, 98%, used asreceived) was recorded using the TOSCA spectrometer [12] at the pulsed neutron source ISIS (Chilton, UK). Neutrons exchange both energy and momentum when scattered inelastically, however, the design of TOSCA is such that there is a unique value for the momentum transfer at each energy transfer. The INS spectrum is available from the INS [13] database at http://www.isis.ac.uk/insdatabase. The Raman spectrum of purine was obtained with a Renishaw 2000 spectrometer using 0.5 mW of 514.5 nm as the excitation source. To obtain spectra in the lattice mode region, the laser notch filter and the imaging capability of the instrument are replaced by the NEXT filter accessory. The key component is a grating so the spectrometer is essentially converted into a double monochromator. In the present
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S.F. Parker et al. / Vibrational Spectroscopy 35 (2004) 173–177
Fig. 1. The two tautomeric forms of purine.
instance, this allows spectra to be obtained to as low as 20 cm1 Raman shift. Ab initio DFT calculations on the isolated molecule in its N7–H and N9–H tautomers were carried out using GAUSSIAN’98 [14] with the 6-31G basis set and the B3LYP functional. Periodic DFT was carried out on the N7–H tautomer using DMOL3 [15] as implemented in the Materials Studio package by Accelrys. The BLYP functional was used together with the DNP basis set which includes polarisation d-functions on all non-hydrogen atoms and polarisation p-functions on all hydrogen atoms to include hydrogen bonding effects. Both GAUSSIAN’98 and DMOL3 optionally calculate the vibrational spectrum and give the atomic displacements in each mode. This output (without scaling) was used to calculate the INS spectra with the programme aCLIMAX [16].
3. Results and discussion Fig. 2 shows the measured INS spectrum of purine and compares it to the spectra derived from the DFT calculation
Fig. 2. Comparison of observed and calculated INS spectra of purine. Top: isolated molecule calculation of the N7–H tautomer, middle: experimental INS spectrum, bottom: isolated molecule calculation of the N9–H tautomer.
for the isolated molecule in its N7–H and N9–H tautomers. It is apparent that the predicted INS spectra of the tautomers are clearly different so enabling them to be distinguished, however, the agreement with the experimental spectrum is only modest. In particular, the correspondence of the predicted and observed intensities in the 800–1000 cm1 region is poor. As might be hoped, the pattern of intensities is a better match for the N7–H tautomer, although the result is hardly convincing. The poor agreement results from the failure of the isolated molecule approximation. The hydrogen bonding strongly changes both the position and intensity of many of the modes. This is most graphically shown by the N–H outof-plane bend which is observed at 470 cm1 for the matrix isolated molecule [4] (predicted at 615 cm1) and observed here at 870 cm1. Close inspection of the experimental spectrum shows that several of the bands are doubled, this is particularly clear with the pair at 230/252 and at 454/ 469 cm1. The splitting occurs because there are four molecules in the orthorhombic cell thus factor group splitting is inherently present. Each mode will give four-factor group modes, in all previous work this has been neglected because the observed infrared and Raman frequencies are generally close and only one of the factor group components has significant intensity in either spectroscopy. In INS spectroscopy all the components are allowed and all have similar intensity. The limitations of the isolated molecule approximation can be overcome by the use of periodic DFT calculations on the complete unit cell. The results for the N7–H tautomer are shown in Fig. 3 and it is apparent that the agreement is much improved. In particular, the lattice mode region below 200 cm1 is present and approximately correct, the factor group splitting is present and the N–H out-of-plane bend is correctly predicted at 880 cm1. The close correspondence of the observed and calculated spectra provides good evidence for the validity of the model and allows a complete set of assignments to be made. Table 1 compares the observed and calculated frequencies and a description, based on visualisation of the mode. The assignments are in good agreement with those of Majoube et al. [5] except for the C–H out-of-plane bends. These modes typically have a large amplitude of motion of the hydrogen so give strong INS features. In the present case
S.F. Parker et al. / Vibrational Spectroscopy 35 (2004) 173–177
175
Fig. 3. INS spectra of purine (top) and the spectrum calculated by periodic DFT (middle). The stick diagram is the calculated spectrum for the fundamentals only.
Table 1 Frequencies (200–1600 cm1) and descriptions for the internal modes of the N7–H conformer of purine in the solid state INSa (cm1)
230 270 423 452 567 613 625 650 788 800 888 900 929 929
(w)/251 (w) (s) (m) (m)/468 (m) (w) (m) (m) (w) (w) (vw) (m, br) (m, br) (s) (s)
978 (s) 1097 (w) 1141 (w) 1195 1266 1308 1336 1398 1422 1422 1489
a b
(w) (w) (w) (w) (w) (w) (w) (w)
Descriptionb
Calculated Position (cm1)
Average intensity
230/231/231/234 267/267/270/278 422/424/428/431 449/451/473/475 558/564/565/567 600/601/602/604 617/621/624/624 642/647/657/664 781/785/786/791 791/792/792/792 882/883/890/892 894/895/900/900 916/919/924/924 924/925/934/935 936/936/965/966 986/986/992/992 1087/1093/1094/1094 1129/1131/1134/1139 1180/1183/1184/1185 1221/1222/1223/1224 1266/1266/1271/1272 1300/1303/1305/1307 1329/1331/1331/1334 1379/1384/1384/1392 1430/1432/1435/1437 1441/1443/1449/1450 1498/1505/1507/1510 1534/1535/1549/1552 1591/1591/1593/1593
1.0 2.0 1.5 1.2 0.4 1.0 1.5 0.6 0.6 0.5 3.1 3.5 3.4 4.0 2.4 4.1 1.5 3.0 0.8 1.2 1.0 1.6 1.4 2.2 2.4 1.9 3.0 1.0 1.0
For the numbering scheme, see Fig. 1. s: strong, m: medium, w: weak, v: very, br: broad. n: stretch, d: in-plane bend, g: out-of-plane bend, t: torsion, þ: ‘‘in-phase with’’, : ‘‘out-of-phase with’’.
tC8N7 tN3C2 tC4C5 þ tC2N1 tC4C5 tC2N1 dN3C4N9 dC6C5N7 dN1C6C5 dC2N3C4 tC8N9 tN3C2 tC2N1 þ tC8N9 dN3C2N1 dC4C5N7 dC2N3C4 þ dC2N1C6 tN3C4 dC2N1C6 gN7H dC2N1C6 þ gN7H gC8H gC2H þ gC6H dC5N7C8 þ d42N9C8 gC2H gC6H nC2N1 nC8N7 nC5N7 nC8N9 nC8N9 þ nN7C8 nC4N9 þ dC6H nC2N3 dC6H dC2H þ dC8H þ nN7C8 dN7H dC8H þ nC8N9 – dC2H dN7H þ dC2H dC6H nN3C4 nC4C5 nC5C6
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S.F. Parker et al. / Vibrational Spectroscopy 35 (2004) 173–177
Fig. 4. The lattice mode region of purine. From top to bottom: Raman spectrum, experimental INS spectrum, INS spectrum calculated by periodic DFT, stick diagram calculated by periodic DFT for the fundamentals.
they are readily assignable to the intense bands at 929 and 978 cm1. The DFT calculation shows that the 978 cm1 band is the out-of-phase out-of-plane bend of the hydrogens on C2 and C6 and that the corresponding in-phase mode and the out-of-plane bend of the hydrogen on C8 are not resolved in the 929 cm1 band. The stick diagram in Fig. 3 shows the individual modes. For the internal modes, the factor group splitting decreases with increasing energy, generally it is the out-of-plane modes that show the largest splitting. For the external modes, shown in more detail in Fig. 4, 12 librational modes, nine optic translational and three acoustic translational modes are expected. The calculated profile has maxima at 28, 61 cm1, a shoulder at 73, 104 cm1, a tail to 140 cm1 and a band at 188 cm1. The observed INS bands are at 80, 98 cm1, a tail to 140 cm1 and a weak band at 174 cm1. Inspection of the eigenvectors shows that the highest energy feature at 174 cm1 is a b-axis translation, the band at 98 cm1 tailing to 140 cm1 is due to librations about the a-axis which is parallel to the ‘‘long’’ axis of the molecule. In the isolated molecule this has the lowest moment of inertia so would be expected to have the highest librational frequency. The next group of modes peaking at 61 cm1 is of mixed translational and librational nature. The lowest energy modes are translational modes. In the Raman spectrum five modes are apparent at 113 (s, br), 102 (s, br), 67 (s), 58 (w) and 48 (s) cm1. The spectrum was recorded at room temperature so the frequencies would be expected to be higher than either the INS or the calculated spectrum since both of these are obtained at (effectively) 0 K. Librations are generally stronger in the Raman spectrum than translations and the two modes at 113 and 102 cm1 are undoubtedly librations. The presence of strong modes at 48 and 67 cm1 is consistent with the mixed
libration/translation nature of the modes predicted by DMOL3. Finally, we note that all attempts to obtain a converged solution for the N9–H tautomer in the solid state were unsuccessful, consistent with the N7–H tautomer being the stable form in the solid state.
4. Conclusions In this work we have shown that the hydrogen bonding and factor group splitting present in the solid state structure of purine has to be explicitly considered in order to correctly assign the spectrum. Comparison of the calculated and observed INS spectra confirms the validity of the analysis and allows unambiguous assignments in the 0–2000 cm1 region to be made. The ability to make this comparison is the great strength of INS spectroscopy and at present is the only form of vibrational spectroscopy that allows quantitative use of the intensity information to validate ab initio results. For the internal modes, the work has largely confirmed previous assignments except for the C–H out-of-plane bending modes which give very weak infrared and Raman bands but strong INS features. The lattice mode region is observed and assigned for the first time. The low symmetry results in extensive mixing of the librational and translational modes.
Acknowledgements The Rutherford Appleton Laboratory (Chilton, UK) is thanked for access to neutron beam facilities.
S.F. Parker et al. / Vibrational Spectroscopy 35 (2004) 173–177
References [1] M.T. Chenon, R.J. Pugmire, D.M. Grant, R.P. Panzica, L.B. Townsend, J. Am. Chem. Soc. 97 (1975) 4636. [2] D.G. Watson, R.M. Sweet, R.E. Marsh, Acta Crystallogr. 19 (1965) 573. [3] M. Majoube, Ph. Millie´ , L. Chinsky, P.Y. Turpin, G. Vergoten, J. Mol. Struct. 355 (1995) 147. [4] M.J. Maciej, H. Rostkowska, L. Lapinski, J.S. Kwiatkowski, J. Leszcyn˜ ski, J. Phys. Chem. 98 (1994) 2813. [5] M. Majoube, M. Henry, G. Vergoten, J. Raman Spectrosc. 233 (1994) 233. [6] X. Cao, G. Fischer, Spectrosc. Acta 55A (1999) 2329. [7] P.C.H. Mitchell, S.F. Parker, A.J. Ramirez-Cuesta, J. Tomkinson, Inelastic Neutron Scattering in Chemistry, World Scientific, Singapore, 2004. [8] Y. He, J. Gra¨ fenstein, E. Kraka, D. Cremer, Mol. Phys. 98 (2000) 1639. [9] S.F. Parker, K.P.J. Williams, D. Steele, H. Herman, Phys. Chem. Chem. Phys. 5 (2003) 1508. [10] B.S. Hudson, J. Phys. Chem. A 105 (2001) 3949. [11] A. Navarro, M. Ferna´ ndez-Go´ mez, J.J. Lo´ pez-Gonza´ lez, M. Paz Ferna´ ndez-Liencres, E. Martı´nez-Torres, J. Tomkinson, G.J. Kearley, J. Phys. Chem. A 103 (1999) 5833.
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[12] D. Colognesi, M. Celli, F. Cilloco, R.J. Newport, S.F. Parker, V. Rossi-Albertini, F. Sacchetti, J. Tomkinson, M. Zoppi, Appl. Phys. A 74 (Suppl.) (2002) S64. [13] S.F. Parker, D.J. Champion, Int. J. Vibr. Spectrosc. 3 (1999). http:// www.ijvs.com/volume3/edition3/section1.htm. [14] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.A. Montgomery Jr., R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, J.L. Andres, C. Gonzalez, M. Head-Gordon, E.S. Replogle, J.A. Pople, GAUSSIAN’98, Revision A.3, Gaussian Inc., Pittsburgh, PA, 1998. [15] B. Delley, J. Chem. Phys. 113 (2000) 7756. [16] A.J. Ramirez-Cuesta, Comp. Phys. Comm. 157 (2004) 226.
Inelastic neutron scattering, Raman spectroscopy and periodic DFT study of purine Stewart F. Parkera,*, Richard Jeansb, Robin Devonshireb a
b
ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield S3 7HF, UK
Received 10 October 2003; received in revised form 12 January 2004; accepted 14 January 2004 Available online 5 March 2004
Abstract The inelastic neutron scattering (INS) spectrum of purine at 20 K has been recorded and compared to that derived from ab initio DFT calculations for the isolated molecule in both its N7–H and N9–H tautomers as well as a periodic DFT calculation using the complete unit cell. For the isolated molecule calculations modest agreement is found for the N7–H tautomer and poor agreement with the N9–H tautomer consistent with the known crystal structure. Much better agreement is found with a periodic DFT calculation of the complete unit cell that explicitly includes the intermolecular interactions, in particular, the hydrogen bonding and the factor group splitting. The lattice mode region is observed by INS and Raman spectroscopies for the first time and assignments are made. # 2004 Elsevier B.V. All rights reserved. Keywords: Inelastic neutron scattering; Purine; Periodic DFT
1. Introduction Purine (see Fig. 1) is the parent compound of the purine bases whose derivatives include the biologically important molecules adenine and adenosine. In solution, purine exists in equilibrium between the N9–H and N7–H tautomers [1]. In the solid state, X-ray crystallography [2] indicates that it is present exclusively as the N7–H tautomer. The infrared and Raman spectra of purine, including isotopic derivatives, have been extensively investigated in solution [3], in argon matrices [4] and in the solid state [5,6]. The assignments have been supported by ab initio calculations [4,5] for the isolated molecule but only at the Hartree– Fock level. For inelastic neutron scattering (INS) spectroscopy, the scattered intensity depends on the number of scattering centres, the amplitude of vibration and the inelastic scattering cross-section [7]. Thus it is straightforward to obtain the INS spectrum from ab initio calculations, which provides a stringent test of the model and unambiguous assignments. Previous work [8–11] has shown that density functional theory (DFT) provides much better results than Hartree– Fock. The cross-section is large for hydrogen and small for *
Corresponding author. Tel.: þ44-1235-446182; fax: þ44-1235-445720. E-mail address: [email protected] (S.F. Parker). 0924-2031/$ – see front matter # 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.vibspec.2004.01.003
virtually all other elements, so modes involving substantial hydrogen motion dominate the spectrum, additionally, there are no selection rules and the low energy region is readily accessible. The purpose of the present work was to obtain the INS spectrum of purine and compare it to ab initio calculations to confirm the assignments. To support the work, we have also obtained the Raman spectrum of solid state purine in the lattice mode region for the first time.
2. Experimental The INS spectrum of purine (Aldrich, 98%, used asreceived) was recorded using the TOSCA spectrometer [12] at the pulsed neutron source ISIS (Chilton, UK). Neutrons exchange both energy and momentum when scattered inelastically, however, the design of TOSCA is such that there is a unique value for the momentum transfer at each energy transfer. The INS spectrum is available from the INS [13] database at http://www.isis.ac.uk/insdatabase. The Raman spectrum of purine was obtained with a Renishaw 2000 spectrometer using 0.5 mW of 514.5 nm as the excitation source. To obtain spectra in the lattice mode region, the laser notch filter and the imaging capability of the instrument are replaced by the NEXT filter accessory. The key component is a grating so the spectrometer is essentially converted into a double monochromator. In the present
174
S.F. Parker et al. / Vibrational Spectroscopy 35 (2004) 173–177
Fig. 1. The two tautomeric forms of purine.
instance, this allows spectra to be obtained to as low as 20 cm1 Raman shift. Ab initio DFT calculations on the isolated molecule in its N7–H and N9–H tautomers were carried out using GAUSSIAN’98 [14] with the 6-31G basis set and the B3LYP functional. Periodic DFT was carried out on the N7–H tautomer using DMOL3 [15] as implemented in the Materials Studio package by Accelrys. The BLYP functional was used together with the DNP basis set which includes polarisation d-functions on all non-hydrogen atoms and polarisation p-functions on all hydrogen atoms to include hydrogen bonding effects. Both GAUSSIAN’98 and DMOL3 optionally calculate the vibrational spectrum and give the atomic displacements in each mode. This output (without scaling) was used to calculate the INS spectra with the programme aCLIMAX [16].
3. Results and discussion Fig. 2 shows the measured INS spectrum of purine and compares it to the spectra derived from the DFT calculation
Fig. 2. Comparison of observed and calculated INS spectra of purine. Top: isolated molecule calculation of the N7–H tautomer, middle: experimental INS spectrum, bottom: isolated molecule calculation of the N9–H tautomer.
for the isolated molecule in its N7–H and N9–H tautomers. It is apparent that the predicted INS spectra of the tautomers are clearly different so enabling them to be distinguished, however, the agreement with the experimental spectrum is only modest. In particular, the correspondence of the predicted and observed intensities in the 800–1000 cm1 region is poor. As might be hoped, the pattern of intensities is a better match for the N7–H tautomer, although the result is hardly convincing. The poor agreement results from the failure of the isolated molecule approximation. The hydrogen bonding strongly changes both the position and intensity of many of the modes. This is most graphically shown by the N–H outof-plane bend which is observed at 470 cm1 for the matrix isolated molecule [4] (predicted at 615 cm1) and observed here at 870 cm1. Close inspection of the experimental spectrum shows that several of the bands are doubled, this is particularly clear with the pair at 230/252 and at 454/ 469 cm1. The splitting occurs because there are four molecules in the orthorhombic cell thus factor group splitting is inherently present. Each mode will give four-factor group modes, in all previous work this has been neglected because the observed infrared and Raman frequencies are generally close and only one of the factor group components has significant intensity in either spectroscopy. In INS spectroscopy all the components are allowed and all have similar intensity. The limitations of the isolated molecule approximation can be overcome by the use of periodic DFT calculations on the complete unit cell. The results for the N7–H tautomer are shown in Fig. 3 and it is apparent that the agreement is much improved. In particular, the lattice mode region below 200 cm1 is present and approximately correct, the factor group splitting is present and the N–H out-of-plane bend is correctly predicted at 880 cm1. The close correspondence of the observed and calculated spectra provides good evidence for the validity of the model and allows a complete set of assignments to be made. Table 1 compares the observed and calculated frequencies and a description, based on visualisation of the mode. The assignments are in good agreement with those of Majoube et al. [5] except for the C–H out-of-plane bends. These modes typically have a large amplitude of motion of the hydrogen so give strong INS features. In the present case
S.F. Parker et al. / Vibrational Spectroscopy 35 (2004) 173–177
175
Fig. 3. INS spectra of purine (top) and the spectrum calculated by periodic DFT (middle). The stick diagram is the calculated spectrum for the fundamentals only.
Table 1 Frequencies (200–1600 cm1) and descriptions for the internal modes of the N7–H conformer of purine in the solid state INSa (cm1)
230 270 423 452 567 613 625 650 788 800 888 900 929 929
(w)/251 (w) (s) (m) (m)/468 (m) (w) (m) (m) (w) (w) (vw) (m, br) (m, br) (s) (s)
978 (s) 1097 (w) 1141 (w) 1195 1266 1308 1336 1398 1422 1422 1489
a b
(w) (w) (w) (w) (w) (w) (w) (w)
Descriptionb
Calculated Position (cm1)
Average intensity
230/231/231/234 267/267/270/278 422/424/428/431 449/451/473/475 558/564/565/567 600/601/602/604 617/621/624/624 642/647/657/664 781/785/786/791 791/792/792/792 882/883/890/892 894/895/900/900 916/919/924/924 924/925/934/935 936/936/965/966 986/986/992/992 1087/1093/1094/1094 1129/1131/1134/1139 1180/1183/1184/1185 1221/1222/1223/1224 1266/1266/1271/1272 1300/1303/1305/1307 1329/1331/1331/1334 1379/1384/1384/1392 1430/1432/1435/1437 1441/1443/1449/1450 1498/1505/1507/1510 1534/1535/1549/1552 1591/1591/1593/1593
1.0 2.0 1.5 1.2 0.4 1.0 1.5 0.6 0.6 0.5 3.1 3.5 3.4 4.0 2.4 4.1 1.5 3.0 0.8 1.2 1.0 1.6 1.4 2.2 2.4 1.9 3.0 1.0 1.0
For the numbering scheme, see Fig. 1. s: strong, m: medium, w: weak, v: very, br: broad. n: stretch, d: in-plane bend, g: out-of-plane bend, t: torsion, þ: ‘‘in-phase with’’, : ‘‘out-of-phase with’’.
tC8N7 tN3C2 tC4C5 þ tC2N1 tC4C5 tC2N1 dN3C4N9 dC6C5N7 dN1C6C5 dC2N3C4 tC8N9 tN3C2 tC2N1 þ tC8N9 dN3C2N1 dC4C5N7 dC2N3C4 þ dC2N1C6 tN3C4 dC2N1C6 gN7H dC2N1C6 þ gN7H gC8H gC2H þ gC6H dC5N7C8 þ d42N9C8 gC2H gC6H nC2N1 nC8N7 nC5N7 nC8N9 nC8N9 þ nN7C8 nC4N9 þ dC6H nC2N3 dC6H dC2H þ dC8H þ nN7C8 dN7H dC8H þ nC8N9 – dC2H dN7H þ dC2H dC6H nN3C4 nC4C5 nC5C6
176
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Fig. 4. The lattice mode region of purine. From top to bottom: Raman spectrum, experimental INS spectrum, INS spectrum calculated by periodic DFT, stick diagram calculated by periodic DFT for the fundamentals.
they are readily assignable to the intense bands at 929 and 978 cm1. The DFT calculation shows that the 978 cm1 band is the out-of-phase out-of-plane bend of the hydrogens on C2 and C6 and that the corresponding in-phase mode and the out-of-plane bend of the hydrogen on C8 are not resolved in the 929 cm1 band. The stick diagram in Fig. 3 shows the individual modes. For the internal modes, the factor group splitting decreases with increasing energy, generally it is the out-of-plane modes that show the largest splitting. For the external modes, shown in more detail in Fig. 4, 12 librational modes, nine optic translational and three acoustic translational modes are expected. The calculated profile has maxima at 28, 61 cm1, a shoulder at 73, 104 cm1, a tail to 140 cm1 and a band at 188 cm1. The observed INS bands are at 80, 98 cm1, a tail to 140 cm1 and a weak band at 174 cm1. Inspection of the eigenvectors shows that the highest energy feature at 174 cm1 is a b-axis translation, the band at 98 cm1 tailing to 140 cm1 is due to librations about the a-axis which is parallel to the ‘‘long’’ axis of the molecule. In the isolated molecule this has the lowest moment of inertia so would be expected to have the highest librational frequency. The next group of modes peaking at 61 cm1 is of mixed translational and librational nature. The lowest energy modes are translational modes. In the Raman spectrum five modes are apparent at 113 (s, br), 102 (s, br), 67 (s), 58 (w) and 48 (s) cm1. The spectrum was recorded at room temperature so the frequencies would be expected to be higher than either the INS or the calculated spectrum since both of these are obtained at (effectively) 0 K. Librations are generally stronger in the Raman spectrum than translations and the two modes at 113 and 102 cm1 are undoubtedly librations. The presence of strong modes at 48 and 67 cm1 is consistent with the mixed
libration/translation nature of the modes predicted by DMOL3. Finally, we note that all attempts to obtain a converged solution for the N9–H tautomer in the solid state were unsuccessful, consistent with the N7–H tautomer being the stable form in the solid state.
4. Conclusions In this work we have shown that the hydrogen bonding and factor group splitting present in the solid state structure of purine has to be explicitly considered in order to correctly assign the spectrum. Comparison of the calculated and observed INS spectra confirms the validity of the analysis and allows unambiguous assignments in the 0–2000 cm1 region to be made. The ability to make this comparison is the great strength of INS spectroscopy and at present is the only form of vibrational spectroscopy that allows quantitative use of the intensity information to validate ab initio results. For the internal modes, the work has largely confirmed previous assignments except for the C–H out-of-plane bending modes which give very weak infrared and Raman bands but strong INS features. The lattice mode region is observed and assigned for the first time. The low symmetry results in extensive mixing of the librational and translational modes.
Acknowledgements The Rutherford Appleton Laboratory (Chilton, UK) is thanked for access to neutron beam facilities.
S.F. Parker et al. / Vibrational Spectroscopy 35 (2004) 173–177
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