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Study of hydrogen bonds in 1-methyluracil by DFT calculations of oxygen, nitrogen, and hydrogen quadrupole coupling constants and isotropic chemical shifts
Chemical Physics Letters 438 (2007) 304–307 www.elsevier.com/locate/cplett
Study of hydrogen bonds in 1-methyluracil by DFT calculations of oxygen, nitrogen, and hydrogen quadrupole coupling constants and isotropic chemical shifts q Mahmoud Mirzaei, Nasser L. Hadipour
*
Department of Chemistry, Tarbiat Modares University (TMU), P.O. Box 14115-175, Tehran, Iran Received 7 February 2007; in final form 22 February 2007 Available online 12 March 2007
Abstract Hydrogen bonds (HB) properties were studied in 1-methyluracil (1MU) by DFT calculations of solid-state NMR parameters including quadrupole coupling constants and isotropic chemical shifts at oxygen, nitrogen, and hydrogen nuclei. To perform the calculations, the neutron diffraction crystalline structures of 1MU at 15 and 123 K were obtained from literature and heptameric clusters including the most HB interacting molecules with the target one were created and considered. The calculated results reveal different contributions of various nuclei to HB in the cluster where O4 and N3 have the major contributions. Ó 2007 Elsevier B.V. All rights reserved.
1. Introduction The pioneering work of Watson and Crick [1] indicated the HB importance in the stabilization of nucleobase pairs. Further studies have also demonstrated this importance in the nucleic acids and their derivatives [2–4], e.g., uracil which is the characteristic RNA nucleobase [5–7]. Earlier, Wu et al. [8,9] performed experimental and computational 17 O NMR studies on uracil. Recently, Kelly et al. [10] studied the homopairing possibility of uracil the results of which were in agreement with the previous trends about formation of nanoscale assemblies of DNA and RNA bases on various surfaces [11,12]. Hobza et al. [13–15] also extensively studied on uracil and the related structures. However, to this point, neither experimental solid-state NMR nor systematic
q
M.M. dedicates this work to Mohammad Reza Khalili Zanjani, Ph.D. Student of Analytical Chemistry at TMU, who died unexpectedly at the age of 26 when working in the research laboratory. He will stay with us in memory through his words and works and we will miss him sincerely. * Corresponding author. Fax: +98 0 21 8800 9730. E-mail addresses: [email protected] (M. Mirzaei), hadipour. [email protected] (N.L. Hadipour). 0009-2614/$ - see front matter Ó 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.cplett.2007.03.011
computational studies have been available for 1-methyluracil (1MU), the simplest uracil N1 derivative. Present work systematically studies HB properties in the real crystalline 1MU by DFT calculations of solid-state NMR parameters including quadrupole coupling constants and isotropic chemical shifts at oxygen, nitrogen and hydrogen nuclei. This work is based on some reasons. First, since electric field gradient (EFG) and chemical shielding (CS) tensors at quadrupole and magnetic nuclei, respectively, are very sensitive to the HB effects, solid-state NMR spectroscopy is among the most versatile techniques to study HB properties in nucleic acids [16–20]. Second, since the nucleobase derivatives are very complex, studying the simplest forms is an advantage to investigate the backbone nucleobase properties due to derivation. 1MU is the simplest uracil N1 derivative. Third, the neutron diffraction single crystalline 1MU at various temperatures was available [21], therefore, the real crystalline clusters could be considered in NMR calculations. Forth, in addition to classical HB type of N-H. . .O@C, a non-classical one of CH. . .O@C is also existed in crystalline 1MU, therefore, its characterization is interesting. Fifth, to this point, there have been no systematic experimental and theoretical NMR data available for 1MU, therefore, this systematic
M. Mirzaei, N.L. Hadipour / Chemical Physics Letters 438 (2007) 304–307
305
The calculated CS tensors in the PAS (r33 > r22 > r11) at O, 15N, and 1H nuclei were converted to the isotropic chemical shielding, riso, by Eq. 3. Furthermore, the 17O and 15N isotropic chemical shift, diso, were also evaluated by Eq. 4 where the absolute oxygen chemical shielding scale of 287.5 ppm which is specific to water in water at 300 K [25] and that of 135.8 ppm for nitrogen in nitromethane [26] were used as the references in the equation. The results are listed in Table 3.
17
riso ¼ ðr11 þ r22 þ r33 Þ=3 diso ðppmÞ ¼ riso;ref riso;sample
ð3Þ ð4Þ
3. Results and discussion 3.1. Electric field gradient tensors
Fig. 1. The seven-molecule cluster of 1MU. Dashed lines show HB.
computational work could predict NMR data for 1MU for the first time. To these aims, 17O, 15N/14N and 2H/1H NMR parameters were systematically calculated in the available 1MU structures at 15 and 123 K [21], Fig. 1. 2. Computational procedure NMR calculations were performed by GAUSSIAN 98 package [22] employing B3LYP and B3PW91 DFT methods and 6-311++G** standard basis where the gaugeincluded atomic orbital (GIAO) approach [23] was used to calculate the CS tensors. Since the coordinates of 1MU were obtained from available neutron diffraction study at 15 and 123 K [21] (from now 1MU-15 and 1MU-123), no geometry optimization was needed in this study. NMR parameters were calculated in two 1MU models: one, crystalline monomers 1MU-15 and 1MU-123, and two, seven-molecule clusters 1MU-15 and 1MU-123. The cluster model includes the most possible HB interacting molecules with the target one. The calculated EFG tensors in the principal axis system (PAS) (jqzzj > jqyyj > jqxxj) at 17O, 14N and 2H nuclei were converted to quadrupole coupling constant, CQ, and asymmetry parameter, gQ, by Eqs. 1,2. CQ means the interaction energy of electric quadrupole moment, eQ, and the EFG tensors at quadrupole nucleus while gQ measures the EFG tensors deviation from the cylindrical symmetry at this site. Those nuclei with nuclear spin angular momentum, I, greater than one-half are quadrupole. The standard Q values reported by pyykko¨ [24] are used in Eq. 1, Q(17O) = 25.58 mb, Q(14N) = 20.44 mb, and Q(2H) = 2.86 mb. Table 2 exhibits the converted calculated 17O, 14 N and 2H EFG tensors to the experimentally measurable parameters, CQ and gQ. C Q ðMHzÞ ¼ e2 Qqzz h1 gQ ¼ jðqxx qyy Þ=qzz j
ð1Þ ð2Þ
The target molecule in cluster contributes to two HB types, N-H. . .O@C and C-H. . .O@C, which the latter one is non-classic, Fig. 1 and Table 1. A quick look at Table 2 reveals different HB effects on the EFG tensors at various 17 O, 14N and 2H nuclei. However, no significant difference is shown between the structures at low 15 and 123 K, whereas Amini et al. [27] calculated different EFG tensors for the structures at higher temperature. 1MU has urea and amide oxygen types, O2 and O4, respectively, [28,29] where their chemical environments are different in the cluster. O2 contributes to C-H. . .O@C but O4 contributes to either C-H. . .O@C or N-H. . .O@C, therefore, their EFG tensors are not similarly influenced by HB, CQ(17O2) reduces 0.18 MHz and CQ(17O4) reduces 0.35 MHz from monomer to the target molecule. In agreement with these changes, gQ increases 0.13 and 0.35 at O2 and O4, respectively. It is noted that HB significantly influences on the EFG tensors at O2 and O4 where this influence is major for O4 and minor for O2. The methyl group restricts N1 from contributing to HB while N3 interacts through N-H. . .O=C in the cluster. Although, because of side effects, CQ(14N1) reduces 0.4 MHz form monomer to the target molecule, but the negligible change of gQ reveals the cylindrical symmetry of EFG tensors at N1. On the other hand, CQ(14N3) reduces 0.8 MHz and gQ Table 1 The intermolecular HB geometry of 1-Methyluracila Intermolecular HB geometry rH5. . .O2 rH6. . .O2 rH6. . .O4 rN3. . .O4 rH3. . .O4 rH11. . .O4
Cluster at 15 K ˚ 2.593 A ˚ 2.359 A ˚ 2.766 A ˚ 2.806 A ˚ 1.764 A ˚ 2.321 A
Cluster at 123 K ˚ 2.600 A ˚ 2.372 A ˚ 2.775 A ˚ 2.812 A ˚ 1.772 A ˚ 2.337 A
\N3-H3 O4 \C5-H5 O2 \C6-H6 O2 \C1-H11 O4
179.37° 115.64° 123.94° 176.38°
179.40° 115.71° 123.95° 176.39°
a
See Fig. 1, data are from Ref. [21].
306
M. Mirzaei, N.L. Hadipour / Chemical Physics Letters 438 (2007) 304–307 Table 3 17 O, 15N and 1H CS tensors
Table 2 17 O, 14N and 2H EFG tensors Nucleus
O2 O4 N1 N3 H3 H5 H6 H11
CQa (MHz)
gQa
Nucleus
Monomerb
Clusterc
Monomerb
Clusterc
9.01; 8.97 (8.86; 8.82) 10.13; 10.09 (10.04; 10.0) 3.95; 3.96 (3.90; 3.90) 3.77; 3.76 (3.70; 3.69) 215.6; 219.1 (216.7; 220.2) 216.5; 217.7 (217.9; 219.0) 204.4; 204.1 (205.8; 205.4) 211.3; 215.4 (212.7; 216.8)
8.83; 8.80 (8.68; 8.65) 8.46; 8.46 (8.29; 8.30) 3.55; 3.57 (3.51; 3.52) 2.99; 3.0 (2.96; 2.97) 180.7; 184.7 (181.8; 185.8) 215.2; 216.4 (216.6; 217.8) 193.7; 193.6 (195.3; 195.1) 195.7; 200.2 (197.1; 201.6 )
0.34; 0.33 (0.36; 0.35) 0.14; 0.13 (0.15; 0.14) 0.01; 0.01 (0.01; 0.01) 0.12; 0.12 (0.12; 0.12) 0.16; 0.16 (0.16; 0.16) 0.09; 0.09 (0.09; 0.09) 0.10; 0.10 (0.09; 0.09) 0.10; 0.10 (0.10; 0.10)
0.41; 0.40 (0.43; 0.42) 0.49; 0.47 (0.51; 0.49) 0.04; 0.04 (0.03; 0.03) 0.54; 0.53 (0.53; 0.53) 0.23; 0.23 (0.22; 0.22) 0.08; 0.08 (0.08; 0.08) 0.06; 0.06 (0.05; 0.05) 0.12; 0.12 (0.12; 0.12)
O2 O4 N1 N3 H3 H5 H6 H11
disoa (ppm) Monomerb
Clusterc
298; 296 (295; 293) 391; 389 (388; 386) 244; 245 (247; 248) 212; 212 (216; 216) 23.8; 23.9 (23.7; 23.8) 26.3; 26.3 (26.2; 26.2) 24.9; 25.0 (24.8; 24.8) 29.4; 29.5 (29.3; 29.4)
277; 276 (274; 273) 299; 298 (295; 295) 231;233 (235; 236) 210; 211 (214; 214) 18.6; 18.8 (18.6; 18.7) 25.6; 25.6 (25.4; 25.5) 22.6; 22.7 (22.5; 22.6) 26.8; 27.0 (26.7; 26.9)
a The results in parenthesis are for B3PW91 and others are for B3LYP. In each row, the first number is for 1MU-15 and the second one for 1MU123. The CQ(2H) are in kHz. b Crystalline monomer. c The target molecule in cluster.
a The results in parenthesis are for B3PW91 and others are for B3LYP. In each row, the first number is for 1MU-15 and the second one for 1MU123. For H, riso (ppm) is reported. b Crystalline monomer. c The target molecule in cluster.
increases 0.4 from monomer to the target molecule which means the contribution of N3 to N-H. . .O@C in the cluster. Since H nuclei have poor electrostatic distribution, HB has less influence on their EFG tensors. H3 contributes to NH. . .O@C and its EFG tensors are influenced from monomer to the target molecule, CQ(2H3) reduces 35 kHz and gQ increases 0.07. H5 and H6 both contribute to C-H. . .O@C but H6 has two HB interactions which the calculated EFG results reveal that rather than H5, the EFG tensors at H6 are more influenced by HB, CQ(2H6) reduces 11 kHz, whereas CQ(2H5) reduces 1 kHz. H11 belongs to – CH3 group placing in the planar sheet of the cluster and contributes to C-H. . .O@C, CQ(2H11) reduces 15 kHz from monomer to the target molecule. This magnitude of reduction reveals more significant contribution of H11 to CH. . .O@C rather than H5 and H6. But it is noted that H3 has the major contribution to HB in the cluster.
that because N1 is restricted by –CH3 to contribute to HB, its CS tensors are almost remained unchanged but although N3 contributes to N-H. . .O@C, its CS tensors are not either significantly influenced by HB. For hydrogen nuclei, riso(1H3) reduces 5 ppm from monomer to the target molecule because of N-H. . .O@C. The change of riso(1H5) is negligible, however, riso(1H6) and riso(1H11) reduce 2 and 2.5 ppm, respectively. As mentioned earlier, because of poor electrostatic environment of H, a 2 ppm reduction of riso can reveal the contribution of H6 and H11 to C-H. . .O@C in the cluster.
3.2. Chemical shielding tensors The calculated CS tensors at 17O, 15N and 1H nuclei in two considered 1MU models are listed in Table 3. A quick look at the results reveals that parallel to the EFG tensors, the CS tensors are also influenced by HB. Furthermore, in agreement with the EFG results, no significant difference is shown in the calculated CS tensors of the structures at two low temperatures. From monomer to the target molecule in cluster, diso(17O2) and diso(17O4) reduce 20 and 90 ppm, respectively. Remembering from the previous section, the changes of EFG and CS tenors at oxygen nuclei are parallel to each other revealing the advantage of calculating both tensors for oxygen to study HB properties. It is noted
4. Conclusions We performed a computational work to study HB properties in 1MU by evaluation of solid-state NMR parameters. Some remarkable trends are concluded from the calculated results. First, O4 contributes to either NH. . .O@C or C-H. . .O@C, whereas O2 contributes to just C-H. . .O@C where the contribution of O4 to HB is major while that of O2 is minor. Second, EFG tensors at N1 and N3 nuclei are influenced by HB, however, the HB effects on the CS tensors at these nuclei are negligible. Third, among the hydrogen nuclei, H3, H6 and H11 have the major role of contributing to HB. Forth, the EFG tensors are more sensitive to HB effects rather than the CS tensors. Acknowledgements The authors gratefully thank Tarbiat Modres University Research Council for financial supports.
M. Mirzaei, N.L. Hadipour / Chemical Physics Letters 438 (2007) 304–307
References [1] J. Watson, H.C. Crick, Nature 171 (1953) 737. [2] A.J. Dingley, R.D. Peterson, S. Grzesiek, J. Feigon, J. Am. Chem. Soc. 127 (2005) 14466. [3] H.E. Herbert, M.D. Halls, H.P. Hratchian, K. Raghavachari, J. Phys. Chem. B 110 (2006) 3336. [4] K.C. Hunter, L.R. Rutledge, S.D. Wetmore, J. Phys. Chem. A 109 (2005) 9554. [5] P.D. Burrow, G.A. Gallup, A.M. Schear, S. Denifl, S. Ptasinska, T. Ma¨rk, P. Scheier, J. Chem. Phys. 124 (2006) 124310. [6] S. Tonzani, C.H. Greene, J. Chem. Phys. 124 (2006) 054312. [7] A. Martı´nez, J. Chem. Phys. 123 (2005) 024311. [8] R. Ida, M. De Clerk, G. Wu, J. Phys. Chem. A 110 (2006) 1065. [9] G. Wu, S. Dong, R. Ida, N. Reen, J. Am. Chem. Soc. 124 (2002) 1768. [10] R.E.A. Kelly, L.N. Kantorovich, J. Phys. Chem. B 110 (2006) 2249. [11] R. Otero, M. Scho¨ck, L.M. Molina, E. Laegsgaard, I. Stensgaard, B. Hammer, F. Besenbacher, Angew. Chem., Int. Ed. 44 (2005) 2270. [12] T. Uchihashi et al., Appl. Surf. Sci. 157 (2000) 244. [13] I. Da˛bkowska, P. Jurecˇka, P. Hobza, J. Chem. Phys. 122 (2005) 204322. [14] M. Hanus, M. Kabelac, D. Nachtigallova, P. Hobza, Biochemistry 44 (2005) 1701.
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[15] F. Ryja´cˇek, O. Engkvist, J. Vacek, M. Kratochvı´l, P. Hobza, J. Phys. Chem. A 105 (2001) 1197. [16] J.N.S. Evans, Biomolecular NMR Spectroscopy, Oxford University Press, New York, 1995. [17] K. Wu¨thrich, NMR of Proteins and Nucleic Acids, Wiley, New York, 1986. [18] T.P. Das, E.L. Han, Nuclear Quadrupole Resonance Spectroscopy, Academic Press, New York, 1958. [19] F.A. Bovey, Nuclear Magnetic Resonance Spectroscopy, Academic Press, San Diego, 1988. [20] M. Mirzaei, N.L. Hadipour, J. Phys. Chem. A 110 (2006) 4833. [21] R.K. McMullan, B.M. Craven, Acta Cryst. B 45 (1989) 270. [22] M.J. Frisch et al., GAUSSIAN 98 Revision A.7, Gaussian, Inc., Pittsburgh, PA, 1998. [23] K. Wolinski, J.F. Hinton, P. Pulay, J. Am. Chem. Soc. 112 (1990) 8251. [24] P. Pyykko¨, Mol. Phys. 99 (2001) 1617. [25] R.E. Wasylishen, D.L. Bryce, J. Chem. Phys. 117 (2002) 10061. [26] C.J. Jameson, J. Mason, in: J. Mason (Ed.), Multinuclear NMR, Plenum Press, New York, 1987, p. 56. [27] S.K. Amini, N.L. Hadipour, F. Elmi, Chem. Phys. Lett. 391 (2004) 95. [28] K. Yamada, S. Dong, G. Wu, J. Am. Chem. Soc. 122 (2000) 11602. [29] S. Dong, R. Ida, G. Wu, J. Phys. Chem. A 104 (2000) 11194.
Study of hydrogen bonds in 1-methyluracil by DFT calculations of oxygen, nitrogen, and hydrogen quadrupole coupling constants and isotropic chemical shifts q Mahmoud Mirzaei, Nasser L. Hadipour
*
Department of Chemistry, Tarbiat Modares University (TMU), P.O. Box 14115-175, Tehran, Iran Received 7 February 2007; in final form 22 February 2007 Available online 12 March 2007
Abstract Hydrogen bonds (HB) properties were studied in 1-methyluracil (1MU) by DFT calculations of solid-state NMR parameters including quadrupole coupling constants and isotropic chemical shifts at oxygen, nitrogen, and hydrogen nuclei. To perform the calculations, the neutron diffraction crystalline structures of 1MU at 15 and 123 K were obtained from literature and heptameric clusters including the most HB interacting molecules with the target one were created and considered. The calculated results reveal different contributions of various nuclei to HB in the cluster where O4 and N3 have the major contributions. Ó 2007 Elsevier B.V. All rights reserved.
1. Introduction The pioneering work of Watson and Crick [1] indicated the HB importance in the stabilization of nucleobase pairs. Further studies have also demonstrated this importance in the nucleic acids and their derivatives [2–4], e.g., uracil which is the characteristic RNA nucleobase [5–7]. Earlier, Wu et al. [8,9] performed experimental and computational 17 O NMR studies on uracil. Recently, Kelly et al. [10] studied the homopairing possibility of uracil the results of which were in agreement with the previous trends about formation of nanoscale assemblies of DNA and RNA bases on various surfaces [11,12]. Hobza et al. [13–15] also extensively studied on uracil and the related structures. However, to this point, neither experimental solid-state NMR nor systematic
q
M.M. dedicates this work to Mohammad Reza Khalili Zanjani, Ph.D. Student of Analytical Chemistry at TMU, who died unexpectedly at the age of 26 when working in the research laboratory. He will stay with us in memory through his words and works and we will miss him sincerely. * Corresponding author. Fax: +98 0 21 8800 9730. E-mail addresses: [email protected] (M. Mirzaei), hadipour. [email protected] (N.L. Hadipour). 0009-2614/$ - see front matter Ó 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.cplett.2007.03.011
computational studies have been available for 1-methyluracil (1MU), the simplest uracil N1 derivative. Present work systematically studies HB properties in the real crystalline 1MU by DFT calculations of solid-state NMR parameters including quadrupole coupling constants and isotropic chemical shifts at oxygen, nitrogen and hydrogen nuclei. This work is based on some reasons. First, since electric field gradient (EFG) and chemical shielding (CS) tensors at quadrupole and magnetic nuclei, respectively, are very sensitive to the HB effects, solid-state NMR spectroscopy is among the most versatile techniques to study HB properties in nucleic acids [16–20]. Second, since the nucleobase derivatives are very complex, studying the simplest forms is an advantage to investigate the backbone nucleobase properties due to derivation. 1MU is the simplest uracil N1 derivative. Third, the neutron diffraction single crystalline 1MU at various temperatures was available [21], therefore, the real crystalline clusters could be considered in NMR calculations. Forth, in addition to classical HB type of N-H. . .O@C, a non-classical one of CH. . .O@C is also existed in crystalline 1MU, therefore, its characterization is interesting. Fifth, to this point, there have been no systematic experimental and theoretical NMR data available for 1MU, therefore, this systematic
M. Mirzaei, N.L. Hadipour / Chemical Physics Letters 438 (2007) 304–307
305
The calculated CS tensors in the PAS (r33 > r22 > r11) at O, 15N, and 1H nuclei were converted to the isotropic chemical shielding, riso, by Eq. 3. Furthermore, the 17O and 15N isotropic chemical shift, diso, were also evaluated by Eq. 4 where the absolute oxygen chemical shielding scale of 287.5 ppm which is specific to water in water at 300 K [25] and that of 135.8 ppm for nitrogen in nitromethane [26] were used as the references in the equation. The results are listed in Table 3.
17
riso ¼ ðr11 þ r22 þ r33 Þ=3 diso ðppmÞ ¼ riso;ref riso;sample
ð3Þ ð4Þ
3. Results and discussion 3.1. Electric field gradient tensors
Fig. 1. The seven-molecule cluster of 1MU. Dashed lines show HB.
computational work could predict NMR data for 1MU for the first time. To these aims, 17O, 15N/14N and 2H/1H NMR parameters were systematically calculated in the available 1MU structures at 15 and 123 K [21], Fig. 1. 2. Computational procedure NMR calculations were performed by GAUSSIAN 98 package [22] employing B3LYP and B3PW91 DFT methods and 6-311++G** standard basis where the gaugeincluded atomic orbital (GIAO) approach [23] was used to calculate the CS tensors. Since the coordinates of 1MU were obtained from available neutron diffraction study at 15 and 123 K [21] (from now 1MU-15 and 1MU-123), no geometry optimization was needed in this study. NMR parameters were calculated in two 1MU models: one, crystalline monomers 1MU-15 and 1MU-123, and two, seven-molecule clusters 1MU-15 and 1MU-123. The cluster model includes the most possible HB interacting molecules with the target one. The calculated EFG tensors in the principal axis system (PAS) (jqzzj > jqyyj > jqxxj) at 17O, 14N and 2H nuclei were converted to quadrupole coupling constant, CQ, and asymmetry parameter, gQ, by Eqs. 1,2. CQ means the interaction energy of electric quadrupole moment, eQ, and the EFG tensors at quadrupole nucleus while gQ measures the EFG tensors deviation from the cylindrical symmetry at this site. Those nuclei with nuclear spin angular momentum, I, greater than one-half are quadrupole. The standard Q values reported by pyykko¨ [24] are used in Eq. 1, Q(17O) = 25.58 mb, Q(14N) = 20.44 mb, and Q(2H) = 2.86 mb. Table 2 exhibits the converted calculated 17O, 14 N and 2H EFG tensors to the experimentally measurable parameters, CQ and gQ. C Q ðMHzÞ ¼ e2 Qqzz h1 gQ ¼ jðqxx qyy Þ=qzz j
ð1Þ ð2Þ
The target molecule in cluster contributes to two HB types, N-H. . .O@C and C-H. . .O@C, which the latter one is non-classic, Fig. 1 and Table 1. A quick look at Table 2 reveals different HB effects on the EFG tensors at various 17 O, 14N and 2H nuclei. However, no significant difference is shown between the structures at low 15 and 123 K, whereas Amini et al. [27] calculated different EFG tensors for the structures at higher temperature. 1MU has urea and amide oxygen types, O2 and O4, respectively, [28,29] where their chemical environments are different in the cluster. O2 contributes to C-H. . .O@C but O4 contributes to either C-H. . .O@C or N-H. . .O@C, therefore, their EFG tensors are not similarly influenced by HB, CQ(17O2) reduces 0.18 MHz and CQ(17O4) reduces 0.35 MHz from monomer to the target molecule. In agreement with these changes, gQ increases 0.13 and 0.35 at O2 and O4, respectively. It is noted that HB significantly influences on the EFG tensors at O2 and O4 where this influence is major for O4 and minor for O2. The methyl group restricts N1 from contributing to HB while N3 interacts through N-H. . .O=C in the cluster. Although, because of side effects, CQ(14N1) reduces 0.4 MHz form monomer to the target molecule, but the negligible change of gQ reveals the cylindrical symmetry of EFG tensors at N1. On the other hand, CQ(14N3) reduces 0.8 MHz and gQ Table 1 The intermolecular HB geometry of 1-Methyluracila Intermolecular HB geometry rH5. . .O2 rH6. . .O2 rH6. . .O4 rN3. . .O4 rH3. . .O4 rH11. . .O4
Cluster at 15 K ˚ 2.593 A ˚ 2.359 A ˚ 2.766 A ˚ 2.806 A ˚ 1.764 A ˚ 2.321 A
Cluster at 123 K ˚ 2.600 A ˚ 2.372 A ˚ 2.775 A ˚ 2.812 A ˚ 1.772 A ˚ 2.337 A
\N3-H3 O4 \C5-H5 O2 \C6-H6 O2 \C1-H11 O4
179.37° 115.64° 123.94° 176.38°
179.40° 115.71° 123.95° 176.39°
a
See Fig. 1, data are from Ref. [21].
306
M. Mirzaei, N.L. Hadipour / Chemical Physics Letters 438 (2007) 304–307 Table 3 17 O, 15N and 1H CS tensors
Table 2 17 O, 14N and 2H EFG tensors Nucleus
O2 O4 N1 N3 H3 H5 H6 H11
CQa (MHz)
gQa
Nucleus
Monomerb
Clusterc
Monomerb
Clusterc
9.01; 8.97 (8.86; 8.82) 10.13; 10.09 (10.04; 10.0) 3.95; 3.96 (3.90; 3.90) 3.77; 3.76 (3.70; 3.69) 215.6; 219.1 (216.7; 220.2) 216.5; 217.7 (217.9; 219.0) 204.4; 204.1 (205.8; 205.4) 211.3; 215.4 (212.7; 216.8)
8.83; 8.80 (8.68; 8.65) 8.46; 8.46 (8.29; 8.30) 3.55; 3.57 (3.51; 3.52) 2.99; 3.0 (2.96; 2.97) 180.7; 184.7 (181.8; 185.8) 215.2; 216.4 (216.6; 217.8) 193.7; 193.6 (195.3; 195.1) 195.7; 200.2 (197.1; 201.6 )
0.34; 0.33 (0.36; 0.35) 0.14; 0.13 (0.15; 0.14) 0.01; 0.01 (0.01; 0.01) 0.12; 0.12 (0.12; 0.12) 0.16; 0.16 (0.16; 0.16) 0.09; 0.09 (0.09; 0.09) 0.10; 0.10 (0.09; 0.09) 0.10; 0.10 (0.10; 0.10)
0.41; 0.40 (0.43; 0.42) 0.49; 0.47 (0.51; 0.49) 0.04; 0.04 (0.03; 0.03) 0.54; 0.53 (0.53; 0.53) 0.23; 0.23 (0.22; 0.22) 0.08; 0.08 (0.08; 0.08) 0.06; 0.06 (0.05; 0.05) 0.12; 0.12 (0.12; 0.12)
O2 O4 N1 N3 H3 H5 H6 H11
disoa (ppm) Monomerb
Clusterc
298; 296 (295; 293) 391; 389 (388; 386) 244; 245 (247; 248) 212; 212 (216; 216) 23.8; 23.9 (23.7; 23.8) 26.3; 26.3 (26.2; 26.2) 24.9; 25.0 (24.8; 24.8) 29.4; 29.5 (29.3; 29.4)
277; 276 (274; 273) 299; 298 (295; 295) 231;233 (235; 236) 210; 211 (214; 214) 18.6; 18.8 (18.6; 18.7) 25.6; 25.6 (25.4; 25.5) 22.6; 22.7 (22.5; 22.6) 26.8; 27.0 (26.7; 26.9)
a The results in parenthesis are for B3PW91 and others are for B3LYP. In each row, the first number is for 1MU-15 and the second one for 1MU123. The CQ(2H) are in kHz. b Crystalline monomer. c The target molecule in cluster.
a The results in parenthesis are for B3PW91 and others are for B3LYP. In each row, the first number is for 1MU-15 and the second one for 1MU123. For H, riso (ppm) is reported. b Crystalline monomer. c The target molecule in cluster.
increases 0.4 from monomer to the target molecule which means the contribution of N3 to N-H. . .O@C in the cluster. Since H nuclei have poor electrostatic distribution, HB has less influence on their EFG tensors. H3 contributes to NH. . .O@C and its EFG tensors are influenced from monomer to the target molecule, CQ(2H3) reduces 35 kHz and gQ increases 0.07. H5 and H6 both contribute to C-H. . .O@C but H6 has two HB interactions which the calculated EFG results reveal that rather than H5, the EFG tensors at H6 are more influenced by HB, CQ(2H6) reduces 11 kHz, whereas CQ(2H5) reduces 1 kHz. H11 belongs to – CH3 group placing in the planar sheet of the cluster and contributes to C-H. . .O@C, CQ(2H11) reduces 15 kHz from monomer to the target molecule. This magnitude of reduction reveals more significant contribution of H11 to CH. . .O@C rather than H5 and H6. But it is noted that H3 has the major contribution to HB in the cluster.
that because N1 is restricted by –CH3 to contribute to HB, its CS tensors are almost remained unchanged but although N3 contributes to N-H. . .O@C, its CS tensors are not either significantly influenced by HB. For hydrogen nuclei, riso(1H3) reduces 5 ppm from monomer to the target molecule because of N-H. . .O@C. The change of riso(1H5) is negligible, however, riso(1H6) and riso(1H11) reduce 2 and 2.5 ppm, respectively. As mentioned earlier, because of poor electrostatic environment of H, a 2 ppm reduction of riso can reveal the contribution of H6 and H11 to C-H. . .O@C in the cluster.
3.2. Chemical shielding tensors The calculated CS tensors at 17O, 15N and 1H nuclei in two considered 1MU models are listed in Table 3. A quick look at the results reveals that parallel to the EFG tensors, the CS tensors are also influenced by HB. Furthermore, in agreement with the EFG results, no significant difference is shown in the calculated CS tensors of the structures at two low temperatures. From monomer to the target molecule in cluster, diso(17O2) and diso(17O4) reduce 20 and 90 ppm, respectively. Remembering from the previous section, the changes of EFG and CS tenors at oxygen nuclei are parallel to each other revealing the advantage of calculating both tensors for oxygen to study HB properties. It is noted
4. Conclusions We performed a computational work to study HB properties in 1MU by evaluation of solid-state NMR parameters. Some remarkable trends are concluded from the calculated results. First, O4 contributes to either NH. . .O@C or C-H. . .O@C, whereas O2 contributes to just C-H. . .O@C where the contribution of O4 to HB is major while that of O2 is minor. Second, EFG tensors at N1 and N3 nuclei are influenced by HB, however, the HB effects on the CS tensors at these nuclei are negligible. Third, among the hydrogen nuclei, H3, H6 and H11 have the major role of contributing to HB. Forth, the EFG tensors are more sensitive to HB effects rather than the CS tensors. Acknowledgements The authors gratefully thank Tarbiat Modres University Research Council for financial supports.
M. Mirzaei, N.L. Hadipour / Chemical Physics Letters 438 (2007) 304–307
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