Analysis of uracil hydration by means of vibrational spectroscopy and density functional calculations

Journal of Molecular Structure 565±566 (2001) 469±473

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Analysis of uracil hydration by means of vibrational spectroscopy and density functional calculations M.-P. Gaigeot, C. Kadri, M. Ghomi* Laboratoire de Physicochimie BiomoleÂculaire et Cellulaire, UPRESA CNRS 7033, Case Courrier 138, Universite Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05, France Received 31 August 2000; accepted 29 September 2000

Abstract Interaction of water molecules (up to seven) with uracil (RNA base) through the ®rst hydration shell has been analysed by means of density functional theory (DFT) calculations at the B3LYP/6-31G p level. Water molecules in uracil 1 2H2O and uracil 1 4H2O complexes interact with adjacent N±H and CyO chemical groups of the base. In addition to these groups, water molecules are also H-bonded to the uracil C±H groups in the uracil 1 7H2O complex. It has been shown that the formation of water dimer and water trimer around uracil is necessary to complete its ®rst hydration shell. Harmonic vibrational calculations have been performed after full geometry optimisation of each compound. A discussion has then been undertaken on the vibrational analysis of uracil in going from gas phase to solution state on the basis of available observed vibrational spectra and those calculated for isolated uracil and uracil 1 nH2O complexes. q 2001 Elsevier Science B.V. All rights reserved. Keywords: Uracil; Nucleic acids; Hydration; DFT calculations; Vibrational spectra

1. Introduction Water is the natural medium of all biological molecules, participating in different processes involving the living cell. Particularly, several structural features that are necessary for the biological functions of nucleic acids, such as DNA double helix formation or RNA folding, are dependent on their interactions with surrounding water. The hydration of nucleic acids is controlled by the interaction of water molecules with various hydrophilic sites such as phosphates, bases and sugars [1]. Water is a highly polar molecule which can be simultaneously an acceptor and a donor of H-bond via the interactions occurring * Corresponding author. Tel.: 133-1-44277555; fax: 133-144277560. E-mail address: [email protected] (M. Ghomi).

through its oxygen or hydrogen atoms, respectively, with the nucleic acid constituents. As far as the nucleic acid bases are concerned, due to their chemical structure the majority of the H-bond interactions between them and water are of the following types: CyO´´´H, N±H´´´O and N´´´H±O. In this work, we focus our attention on uracil (RNA base) which is the structurally simplest base of nucleic acids and can mainly interact with water molecules through its H1, O2, H3 and O4 sites (Fig. 1). The main purpose of this paper is to analyse the hydrogen bonding features of uracil with up to seven water molecules. Stable con®gurations of uracil±water complexes will be taken into consideration by means of full geometry optimisation. Calculated vibrational spectra of uracil and uracil± water complexes are also discussed on the basis of available vibrational spectra observed in gas phase and aqueous solutions of uracil.

0022-2860/01/$ - see front matter q 2001 Elsevier Science B.V. All rights reserved. PII: S 0022-286 0(00)00848-6

470 M.-P. Gaigeot et al. / Journal of Molecular Structure 565±566 (2001) 469±473 Fig. 1. Graphical representation of uracil, water and water dimer (top) and uracil 1 2H2O, uracil 1 4H2O and uracil 1 7H2O complexes (bottom) obtained by geometry optimisation at the B3LYP/6-31G p theoretical level. Water molecules are numbered (W1±W7) with a counter-clockwise rotation around uracil molecule. Hydrogen bond distances, i.e. hydrogen±acceptor distances (in angstroms) and hydrogen bond angles, i.e. donor±hydrogen±acceptor angles, (in degrees) are also displayed.

M.-P. Gaigeot et al. / Journal of Molecular Structure 565±566 (2001) 469±473

471

Table 1 Energy data for uracil, water, water dimer and uracil±water complexes calculated at the B3LYP/6-31G p level. See also Fig. 1 (Ee: electronic energy, Ev: zero-point vibrational energy (ZPVE)) Compound

Ee (a.u.)

Ev (kcal/mol)

Compound

Ee (a.u.)

Ev (kcal/mol)

uracil Water monomer Water dimer

2 414.808042 2 76.407023 2 152.826619

54.86 13.26 28.84

Uracil 1 2H2O Uracil 1 4H2O Uracil 1 7H2O

±567.666058 2 720.531515 2 949.800405

86.33 118.40 164.98

2. Theoretical details All quantum mechanical computations have been performed on NEC supercomputers or on IBM workstations using the gaussian98 package [2]. Theoretical calculations have been performed at the DFT level by means of the B3LYP non-local exchangecorrelation functional and 6-31G p basis set. For a

given molecular compound, geometry optimisation allowed the electronic energy (Ee) to be obtained. Harmonic vibrational calculations also allowed us to verify whether the optimised geometry corresponds to a molecular minimum and not to a transition state by the absence of any imaginary frequency. The assignment of the calculated modes has then been performed by means of potential energy distribution (PED).

Table 2 Comparison between the calculated and observed wavenumbers (cm 21) of uracil. See Fig. 1 for the atom numbering in uracil (Exp. IR spectrum of uracil in gas phase [5]. Calc. harmonic vibrations of isolated uracil calculated at the B3LYP/6-31G p level. v : out of-plane wagging, t : torsion) Exp.

Calc.

Assignments (PED%)

3450

3641

N1±H (99)

3427 3101

3605 3271

N3±H (99) C5±H (96)

974 841

969 817

3076

3230

C6±H (96)

810

773

1734 1688

1848 1811

C2yO2 (73) C4yO4 (75)

769 672

758 732

1632

1693

C5yC6 (54); N1C6H (12)

633

691

1480

1513

N1±C6 (23); HN1C2 (20); HN1C6 (15) C5C6H (15); N1C6H (11); C4N3H (10) C2N3H (19); N1±C2 (13)

588

563

556

558

C4N3H (24); C2N3H (10); C2±N3 (10) C4C5H (19); C6C5H (15); N1±C6 (12) C2±N3 (23); N3±C4 (20); N1C6H (14) N1±C6 (25); C6yC5±H (23); C5yC6 (11) N1C6C5 (13); C2N1C6 (10)

527

519

411

395

377

385

185

170

1431 1396

1415

1380

1391 1239

1228

1204

1089

1096

999

992

Exp.

Calc.

Assignments (PED%)

970

v (C6H) (49); t (C5C6) (25); v (C5H) (12) N1±C2 (14); C4±C5 (10) v (C5H) (40); v (C4O4) (33); t (C4C5) (12); v (C6H) (10) C4±C5 (27); N1±C2 (19): ring breathing mode v (C2O2) (71); v (C4O4) (33); v (C6H) (20); t (C5C6) (15); v (C2O2) (11) v (N3H) (36); t (N3C4) (27); t (C2N3) (22) t (C6N1) (32); v (N1H) (28); t (N1C2) (27) N1C2O2 (22); N1C2N3 (17)

541

149

C5C4O4 (21); N3C2O2 (17); N3C4C5 (10) N3C4C5 (19); N3C4O4 (17); C2N1C6 (12); C4C5C6 (11) v (N1H) (28); v (C5H) (22); t (C5C6) (15) N3C2O2 (18); C5C4O4 (17); N3C4O4 (16); N1C2O2 (14) t (C4C5) (26); v (N1H) (25); t (N1C2) (15); t (N3C4) (14) v (N3H) (43); t (C2N3) (18); t (N3C4) (13)

472

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Table 3 Comparison between the calculated vibrational wavenumbers (cm 21) of uracil±water complexes with those observed in aqueous solutions of uracil. See also Fig. 1 and Table 2. Only the vibrational modes assigned mainly to the uracil molecule are reported (Exp. Raman and IR spectra observed in the aqueous solutions of uracil [6]. Calc. theoretical wavenumbers obtained at the B3LYP/6-31G p level. n : bond±stretch, d : angle bending, v : out of-plane wagging, t : torsion) Calc. uracil 1 2H2O

uracil 1 4H2O

uracil 1 7H2O

3411 3332 3269 3231 1815 1777 1684 1553 1488 1456 1414 1257 1249 1111 977 1009 995 826 930 817 789 757 718 581 562 532 421 434 186 183

3114 3063 3270 3230 1802 1766 1692 1600 1533 1470 1417 1276 1254 1121 1011 1060 998 994 970 819 796 763 728 571 548 521 433 435 188 181

3189 3060 3174 3231 1800 1714 1671 1565 1527 1467 1437 1285 1272 1151 1059 1000 994 951 921 895 801 768 749 584 557 517 451 439 185 181

3. Results and discussion Table 1 and Fig. 1 show the calculated energies and graphical representation of the molecular compounds analysed in the present work, respectively. Recent ab initio calculations on uracil 1 1H2O [3,4] have shown that the two lowest energy con®gurations of this complex are those including a water molecule making two simultaneous H-bonds either with the (H1 and O2) atom pair, or with the (H3 and O4) atom pair of uracil. We have thus used these preferential sites in our studies on uracil 1 2H2O (Fig. 1). Hydrogen bonding geometrical data of uracil 1 2H2O are reported in Fig. 1. It should be

Assignments

n (N1±H) n (N3±H) n (C5±H) n (C6±H) n (C2yO) n (C4yO) n (CyC); n (C4yO); d (C±H) d (N±H); n ring n ring n ring d (C±H); d (CyO) d (C±H); n ring n ring d (C±H); n ring v (C±H); t ring d (N±H); d ring d ring; n ring v (N±H); t ring v (C±H); t ring; v (CyO) v (C±H) ring breathing mode v (CyO); v (C±H) v (CyO); t ring d (CyO); d ring d ring d (N±H); d ring v (C±H); v (N±H) d (CyO) v (N±H); t ring v (N±H); d N±H)

Exp. Raman

1708 1677 1637 1496 1413 1387 1232 1091 997

IR

1710 1675 1640 1506 1448 1414 1391 1222

1000 993

782 573 553 536 423 401

mentioned that N±H and CyO bonds are lengthened Ê upon uracil±water complexation. We by ,0.01 A also attempted to cover the above-mentioned uracil sites by four water molecules organised as two water dimers, leading to uracil 1 4H2O complex (Fig. 1). The existence of a water dimer instead of water monomer on each uracil atom pair leads to the formation of linear H-bonds between water molecules and uracil. In addition, stronger H-bonds (as revealed by shorter hydrogen bond distances) are obtained in the uracil 1 4H2O complex in comparison with those found in uracil 1 2H2O (Fig. 1). Intermolecular geometrical parameter changes of water dimers bound to uracil compared to those obtained in free

M.-P. Gaigeot et al. / Journal of Molecular Structure 565±566 (2001) 469±473

water dimer, should also be stressed (Fig. 1). At last, we could optimise the geometry of a uracil surrounded by seven water molecules. Indeed, uracil 1 7H2O complex is derived from uracil 1 4H2O to which a water dimer has been added on the (O4, H5) atom pair, along with a water monomer making a hydrogen bond with the H6 atom and another one with the water molecule bound to the H1 atom. Thus, all the hydrogen donor and acceptor sites of uracil are occupied through hydrogen bonding with water molecules. It should be mentioned that the uracil C±H bonds give rise to longer H-bond distances compared to those formed on the N±H and CyO bonds. Harmonic vibrational modes calculated for isolated uracil can satisfactorily assign those observed in the gas phase [5] with n exp/n cal ratios greater than 0.93 in the whole spectral region (Table 2). Table 3 shows the theoretical harmonic modes and their brief assignments corresponding mainly to the uracil ring vibrational motions as found in uracil 1 nH2O (n ˆ 2,4,7) complexes. The observed wavenumbers in Raman and infrared spectra of the aqueous solution of uracil [6] are also reported for comparison. The vibrational modes which are highly affected by the presence of the surrounding water molecules are n (N±H), n (CyO) and v (N±H) (Table 3). Among these vibrations, only the n (CyO) modes can be analysed by the Raman and IR spectra recorded in aqueous phase (Table 3). N±H bond-stretchings undergo strong wavenumber downshifts of about 500 cm 21, in going from isolated uracil to uracil 1 7H2O (Table 3). n (C±H) modes are less affected by H-bonding. Moreover, the difference in the behaviour of n (C5±H) and n (C6±H) as far as their wavenumber shifts are concerned, can be explained by the differences in the corresponding C±H´ ´ ´O hydrogen bond distances (Fig. 1). The higher is the number of water molecules in interaction with carbonyl groups, the larger are the wavenumber downshifts on the n (CyO) vibrations, leading to a gradual improvement of the agreement between the observed and calculated wavenumbers (Tables 2 and 3). v (N±H) vibrations are considerably shifted to higher wavenumbers (Dn , 260 cm 21) from isolated uracil to uracil 1 7 H2O.

473

4. Conclusions We have analysed in this work the structural and vibrational characteristics of the ®rst hydration shell of uracil through realistic molecular models. Particularly, uracil 1 7H2O complex can be considered as a ®rst theoretical attempt made up to now to mimic the ®rst hydration shell of uracil. However, the present calculations can be considered as a ®rst stage in understanding uracil±water complexation and further investigations using diffuse orbitals are now in progress in order to improve the hydrogen bonding features discussed above. Acknowledgements The authors would like to thank IDRIS (Orsay, France), CINES (Montpellier, France) and CCR (Jussieu, Paris, France) calculation centers for the computational facilities. References [1] G.A. Jeffrey, W. Saenger, Hydrogen Bonding in Biological Structures, Springer, New York, 1991. [2] 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 Inc., Pittsburgh PA, 1998. [3] T. van Mourik, D.M. Benoit, S.L. Price, D.C. Clary, Phys. Chem. Chem. Phys. 2 (2000) 1281. [4] M.T. Nguyen, A.K. Chandra, Th. Zeegers-Huyskens, J. Chem. Soc., Faraday Trans. 94 (1998) 1277. [5] S. Nunziante-Cesaro, unpublished results as quoted in: L. HarzaÁnyi, P. CsaÁszaÁr, A. CsaÁszaÁr, J.E. Boggs, Int. J. Quantum Chem. 29 (1986) 799. [6] A. Aamouche, M. Ghomi, C. Coulombeau, H. Jobic, L. Grajcar, M.H. Baron, V. Baumruk, P.Y. Turpin, C. Henriet, G. Berthier, J. Phys. Chem. 100 (1996) 5224.