Theoretical calculations and vibrational study of hypoxanthine in aqueous solution

Journal of Molecular Structure 744–747 (2005) 749–757 www.elsevier.com/locate/molstruc

Theoretical calculations and vibrational study of hypoxanthine in aqueous solution M. Ferna´ndez-Quejo, M. de la Fuente*, R. Navarro Facultad de Ciencias, Department of Ciencias y Te´cnicas Fisicoquı´micas, Universidad Nacional de Educacio´n a Distancia, C/Senda del Rey, 9, Madrid 28040, Spain Received 8 September 2004; accepted 11 October 2004 Available online 13 December 2004

Abstract The vibrational analysis of the two predominant tautomers of hypoxanthine (HX) in solution, the keto-N1–H/N7–H (HX/N7H) and N1–H/N9–H (HX/N9H) forms, have been carried out by means of DFT calculations, applying the B3LYP hybrid density functional and four basis sets namely 6-31G(d,p), 6-31CCG(d,p), 6-11G(d,p) and 6-311CCG(d,p). The influence of the solvent was considered using the Tomasi’s Polarized Continuum Model (PCM). Comparison with experimental data provides support for the quality of results derived from theoretical computations. The assignment of the vibrational spectra of the hypoxanthine in aqueous solution has been performed in the light of information makes available from the previous experimental and theoretical studies, the observed isotopic shifts in the spectra of deuterated derivatives and from the theoretical normal modes computed from SCRF/DFT calculations. The interpretation of the vibrational spectra gives experimental evidences for the coexistence of the two tautomers, HX/N7H HX/N9H, in aqueous solution. q 2004 Elsevier B.V. All rights reserved. Keywords: Hypoxanthine; FT-IR; Vibrational analysis; SCRF/DFT calculations

1. Introduction Hypoxanthine (HX) is a purine nitrogenous base which is a metabolic intermediate of nucleic acid. Also it is found as a minor purine base in transfer RNA [1]. It can be form by deamination of guanine and is the base moiety of nucleosides like 2 0 -deoxyinosine, a nucleoside with important applications, such as being incorporated into oligonucleotides used in PCR, or being used as hybridisation probe for the detection or analysis of a target DNA strand containing ambiguities. These applications are due to its property of binding with weak hydrogen bonds to any of the four natural DNA bases [2]. There are different potential tautomeric forms for hypoxanthine. Tautomerism determines the specific pattern of hydrogen-bond donors and acceptors available to a specific molecule, which is very important in biochemical and pharmacological research [3,4].

* Corresponding author. Tel.: C34 91 3987 207; fax: C34 91 3986 697. E-mail address: [email protected] (M. de la Fuente). 0022-2860/$ - see front matter q 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2004.10.092

Different experimental and theoretical techniques have been applied to study the relative stability, structure and hydration effects of different tautomers of HX. Thus, in gas phase, it has been suggested from the IR spectra of isolated molecules [5] that the keto form predominates. Ultraviolet photoelectron spectra [6] and quantum mechanical calculations at MP2/6-31CG(d,p)//HF/6-31G(d) [4] and MP2/6-31G(d,p) [7] levels and DFT with BP/DZVP [8], B3LYP/6-31CG(d,p)//HF/6-31G(d) [4], MP2/ 6-31GCCG(d,p)//B3LYP/6-31GCCG(d,p) [9,10] and B3LYP/6-311CCG(d,p) [11] functional levels indicate that HX, in gas phase, exists mainly in two keto tautomeric forms, N1–H/N7–H (HX/N7H) and N1–H/ N9–H (HX/N9H) (Fig. 1), the former being the dominant species. In solution, 13C NMR spectroscopic studies in DMSO [12] also indicate that the HX/N7H form is more favoured, while in aqueous medium, UV spectroscopic studies suggest, although do not prove, that hypoxanthine are present predominantly as the HX/N9H tautomer [13]. SCRF/MST calculations performed at AM1 and HF/ 6-31G(d) levels [4] and SCRF/COSMO calculations at

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M. Ferna´ndez-Quejo et al. / Journal of Molecular Structure 744–747 (2005) 749–757

Fig. 1. The hypoxanthine molecule. Molecular structure for ketoN1H/N9H (HX/N9H) and keto-N1H/N7H (HX/N7H) tautomers.

AM1 and PM3 levels [14] of HX, as well as calculations at MP2/6-31G(d,p) [7] and DFT/6-311G(d,p) [11] levels of mono- and dihydrated tautomers show that, under aqueous solvation, a mixture of HX/N7H and HX/N9H species is expected, being the HX/N9H form more favoured than the HX/N7H form. However, calculations at most reliable B3LYP/6-311CCG(d,p) level of the dihydrated species and at MP2/6-31GCCG(d,p)//B3LYP/6-31GCCG(d,p) level of the monohydrated species predict higher stability for the HX/N7H form [9–11]. In crystal, hypoxanthine occurs as the HX/N9H tautomeric form [15]. In the present work a interpretation of the vibrational spectra of the hypoxanthine in aqueous solution is proposed, since a structural determination in this medium is required for a full understanding of the biochemical reactions in which this purine is involved. The assignment of the vibrational spectra is performed in the light of information provides from the previous experimental and theoretical studies, the observed isotopic shifts in the spectra of deuterated derivatives and by means of the theoretical normal modes computed from SCRF/DFT calculations.

Fig. 2. FT-IR spectra of: (A) HX-d2 in solid phase, (B) HX in solid phase and (D) HX-d2 in aqueous solution; and its second derivatives (-d2A/dn2) (C and E).

2.1. FT-IR spectra

2. Experimental The hypoxanthine was purchased from Sigma Chemical Co. and was used as supplied. Its water solubility is very poor at room temperature, probably this is the reason because of the experimental studies in aqueous medium are not as prolific as would be expected. Nevertheless, its solubility is sufficient to obtained FT-IR spectra of good quality (Fig. 2). In order to activate the solution process, an aqueous solution 0.02 mol dmK3 of this compound were prepared dissolving the commercial product in 2H2O (Scharlau, 99.999%) and heating up to 90 8C. The saturated solution at room temperature, conveniently filtered, was used to record the FT-IR spectra. In these conditions, N1 and N7 or N9-deuterium substitution is expected [16]. The presence of C8-deuterated species are neglected, which is verified by means of 1H NMR. The solid product from this solution (N1- and N7- or N9-deuterated hypoxanthine, HX-d2) was also obtained by freeze-drying.

The FT-IR spectra were recorded in a Bomem-DA3.02 interferometer operating under a vacuum (pressure %133.3 Pa). About 3000 interferograms were co-added for the mid-IR spectra of the solution in Specac vacuum tight cell of 34 mm path length with BaF2 windows. The effective apodized resolution was sZ1.77 cmK1 (RESZ2.0 cmK1 and Hamming apodizing function). A high sensitivity MCT detector was used. The FT-IR spectra of polycrystalline samples, HX and HX-d2 in KBr, were also recorded, in order to compare this information with data from the solution phase and the theoretical vibrational modes. About 1000 interferograms were co-added for these mid-IR spectra, using an effective apodized resolution of sZ0.89 cmK1 (RESZ 1.0 cmK1 and Hamming apodizing function) and a DTGS detector. The experiments were carried out at room temperature. The second derivatives of the recorded spectra (Savitzky–Golay algorithm) [17] were calculated to resolve the bands containing more than one component, using Grams/AI package [18].

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2.2. Calculations The quantum mechanical calculations were carried out using GAUSSIAN 03 package [19]. The geometry of hypoxanthine was optimised with no restriction by using density functional theory with the hybrid B3LYP functional. To analyse the effect of the basis set extension on vibrational modes, four different split valence Gaussian basis sets, i.e. 6-31G(d,p), 6-31CCG(d,p), 6-311G(d,p) and 6-311CCG(d,p), have been employed. The basis sets were applied as they are stored internally in GAUSSIAN 03. The vibrational wavenumbers and absolute intensities were calculated within the harmonic approximation at the same level of theory for the optimised geometries. Local minima were verified by establishing that the matrix of energy second derivatives (Hessian) has only positive eigenvalues. In aqueous-phase calculations the Tomasi’s Polarized Continuum Model (PCM) [20] was used as is implemented in GAUSSIAN 03 by default (using integral equation formalism model, IEF-PCM) [21]. The vibrational mode descriptions were made on the basis of the normal modes calculated as displacements in redundant internal coordinates (option FreqZIntModes, GAUSSIAN 03), as well as on calculated nuclear displacements associated with the vibrational wavenumbers, and by means of the visualization of the vibrational normal modes for the different optimised structures using the GaussView 3.0 program [22]. Only those degrees of freedom which dominate the vibrational form were used for assigning a normal vibration. The B3LYP method was chosen because different studies have shown that the data obtained with this level of theory are in good agreement with those obtained by other more cost computationally methods as MP2 calculations [23,24] and it predicts vibrational frequencies of DNA bases better than the HF and MP2 methods [25,26]. All quantum mechanical computations have been performed on a HP Integrity rx2600 server, with 2 Intelw Itaniumw 2 processors, clock frequency 1.5 GHz, 6 MB cache, 2 GB memory and Red Hat Enterprise Linux AS 2.1 operating system, at Computational Chemistry Laboratory from Universidad Nacional de Educacio´n a Distancia (Lab-QC, UNED) [27].

3. Results and discussion

751

modes were calculated also in gas phase with the same basis sets, in order to notice the solvent effect on the wavenumbers. Comparing the results from each basis set in gas phase and with SCRF calculations, for both tautomers, it is possible to observe an important approach to the experimental values of condensed phase when PCM solvation model is considered. The highest wavenumbers are the most notably influenced for the solvent effect, specially those vibrational modes in which polar groups are involved. Fundamental contributions of stretching modes are expected at these wavenumbers (Tables 3 and 4). Less effects are observed at lower wavenumbers. Thus, vibrational modes between 1650 and 1200 cmK1 appear at lower wavenumber (up to 27 cmK1), or they do not change, in SCRF calculations, in relation to computed wavenumber in gas phase. Below 1200 cmK1, either unaffected wavenumbers are found, or they appear at higher wavenumber (up to 32 cmK1). Table 5 takes into account of these effects on the computed vibrational modes with the 6-311CCG(d,p) basis set of HX/N9H tautomer. A similar trend is observed in all calculations. 3.2. Effect of basis set on calculated vibrational modes Regarding the applied basis sets, differences up to 33 cmK1 are achieved in going from the 6-31G(d,p) to the 6-311G(d,p) basis set (Tables 1 and 2). Most of the main alterations bring in a decrease of the wavenumbers. The addition of diffuse function to the basis sets also provokes changes up to 54 cmK1 of some vibrational modes. Once again, a lower wavenumber is achieved in most of the variations. The stretching modes of polar groups (N–H and C]O) are the most affected by the application of diffuse function. The comparison of the experimental bands with the theoretical modes reveals that the results with 6-311CCG(d,p) are the most consistent. For instance, the band about 1670 cmK1 in FT-IR spectra from Fig. 2, may be assigned to the vibrational mode calculated at 1680/ 1683 cmK1. This band, common for all of the base moieties of the nucleic acids presenting keto group, have been traditionally assigned to coupling of the carbonyl bond to the rings bond strectching [16,28], and it is usually one of the worst theoretically predicted modes. The rest of the vibrational bands analysed in the present study may also be interpreted, to a great extent, on the basis of these calculations (PCM/6-311CCG(d,p)), as it will be discussed below.

3.1. Effect of PCM solvation model on calculated vibrational modes

3.3. Vibrational analysis

The 36 vibrational modes calculated for the two predominant tautomers of HX in aqueous solution, i.e. HX/N9H and HX/N7H [4,7,9–15] are shown in Tables 1 and 2. Four different basis sets have been employed, i.e. 6-31G(d,p), 6-31CCG(d,p), 6-311G(d,p) and 6-311CC G(d,p) applying PCM solvation model. The vibrational

The FT-IR recorded spectra of HX in aqueous solution (2H2O), where the HX-d2 species are expected, in 1800– 1300 cmK1 region, as well as the FT-IR spectra for the solid samples (HX and HX-d2) are shown in Fig. 2. This has been the region analysed since, at these wavenumbers, the IR vibrational modes from 2H2O do not interfere.

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Table 1 Calculate B3LYP wavenumbers, with different basis sets and PCM solvation model, for HX/N7H tautomer 6-31G(d,p) (n/cmK1)

6-31CCG(d,p) (n/cmK1)

6-311G(d,p) (n/cmK1)

6-311CCG(d,p) (n/cmK1)

Vibrational modes (fundamental contributions) a

3306 3275 3192 3136 1744 1629 1554 1547 1468

3270 3234 3186 3136 1693 1614 1551 1539 1460

3274 3246 3166 3111 1715 1615 1542 1536 1453

3255 3224 3161 3111 1683 1607 1542 1532 1450

1440 1411 1399 1349 1291 1204 1139 1115 1084 947 947

1438 1409 1399 1346 1288 1207 1142 1117 1090

1438 1399 1390 1339 1278 1196 1135 1111 1080

948 946 902 887 781 729 713 670 633 614 566 549 547

954 950 898 891 806 745 709 676 638 611 569

1436 1399 1391 1339 1279 1200 1137 1113 1085 952 948

71% n(N7–H) 73% n(N1–H) 73% n(C8–H) 75% n(C2–H) 12% n(C6]O), 12% n(C6C5), 11% d(N1–H) 17% d(C2–H), 13% d(N1–H), 10% n(C2N3) 11% n(C4C5), 10% n(N3C4), 8% d(N1–H) 14% d(N7–H), 14% d(C8–H), 10% d(C2–H), 8% d(N1–H) 20% d(C8–H), 10% d(N7–H), 8% n(N7C8), 8% d(N1–H), 8% n(C8N9) 26% d(N1–H), 18% d(N7–H) 22% d(C2–H), 9% d(N7–H) 13% d(N7–H), 13% d(N1–H) 26% d(C2–H), 11% n(C4N9) 25% d(C8–H), 10% n(C8N9), 9% d(N7–H) 16% d(C8–H), 12% d(N7–H), 8% d(N1–H) 20% d(N1–H), 11% n(N1C2) 24% d(N7–H), 16% d(C8–H), 11% n(N7C8) 13% d(N7–H), 10% d(C8–H), 9% d(C2–H), 8% n(N1C6) 60% d imidazol ring 58% g(C2–H), 11% t(N1C6) 60% d imidazol ring 22% d(N1C2N3), 14% d(C2N1C6), 10% d(C2N3C4) 63% g(C8–H), 10% t(C5N7) t rings 29% g(N1–H), 15% t(C5C6), 9% t(C4C5) Rings breathing 47% g(N1–H), 17% t(N7C8), 8% t(N1C6) 27% g(N1–H), 23% t(N7C8), 19% t(C5N7) 14% d C6]O t rings 9% d(C5C6O6), 9% d(C4C5C6), 8% d(N3C4C5) 57% g(N7–H) 9% d(C5C6O6), 9% d(C4C5C6), 8% d(N3C4C5) 11% d(N1C6C5), 9% d(C2N3C4) 22% d(C6]O), 11% d(C6C5N7), 8% d(N3C4N9) t rings t rings t rings

898 882 786 730 712 675 636 610 566 548 546 515 310 284 198 162

521 316 283 199 165

554 548 518 312 283 196 158

903 887 787 735 712 670 631 616 566 550 548 523 316 279 195 158

n: stretching; d: bending; t: torsion; g: out of plane motion. a Vibrational modes descriptions corresponding to 6-311CCG(d,p) calculation. They are similar with the other basis sets. Only contributions greater than 7% are reported.

In order to interpret the FT-IR spectra of HX-d2 in aqueous solution, structure optimisation and vibrational analysis calculations were performed for the N1- and N9- or N7–H deuterated form of HX, using 6-311CCG(d,p) basic set with PCM solvation model. The results of the theoretical vibrational analyses, in the 1800–1300 cmK1 range, of the four HX forms considered, i.e. HX/N9H, HX/N7H, HX-d2/N9D and NX-d2/N7D are shown in Table 6. Scaling factors have not been used. In this table, the corresponding IR bands of HX-d2 in aqueous solution, as well as of HX and HX-d2 samples in solid phase have also been reported. Raman peak wavenumber of HX in solid phase [29] and of HX and HX-d2 in aqueous solution [16] are also included. In this latter previous study, the Resonance Raman spectra of

HX and its deuterated species, with 257 and 281 nm of laser excitation wavelengths, were reported [16]. The assignment of the spectra were performed according to the Wilson GF method by using an empirical harmonic valence force field, and the spectra were assumed to be a result of the HX/N9H tautomeric contributions. From the present considerations, i.e. in aqueous solution, a mixture of HX/N7H and HX/N9H species is expected, while in solid phase HX/N9H species occurs, a interpretation of the vibrational spectra have been performed. As can be observed in Table 6, the theoretical values correspond, to a great extent, with the experimental data. Thus, the Resonance Raman peak at 1691–1687 cmK1, of HX in aqueous solution (predicted at 1683 cmK1 in HX/ N7H and 1680 cmK1 in HX/N9H), is assigned to both

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Table 2 Calculate B3LYP wavenumbers, with different basis sets and PCM solvation model, for HX/N9H tautomer 6-31G(d,p) (n/cmK1)

6-31CCG(d,p) (n/cmK1)

6-311G(d,p) (n/cmK1)

6-311CCG(d,p) (n/cmK1)

Vibrational modes (fundamental contributions) a

3307 3276 3193 3138 1743 1620 1595 1531 1475 1434 1406 1378 1360 1296 1195 1141 1094 1090 948 942 895 861 789 729 707 672 655 609 580 546 541 511

3269 3234 3187 3137 1689 1608 1589 1524 1469 1431 1402 1378 1355 1294 1198 1143 1099 1090 949 944 900 867 784 725 709 668 653 615 577 546 544 518

3275 3246 3166 3113 1715 1607 1582 1520 1466 1426 1396 1364 1353 1286 1187 1137 1088 1082 955 944 896 870 814 740 704 674 659 611 588 551 541 513

3254 3224 3163 3112 1680 1602 1581 1516 1463 1425 1394 1367 1352 1286 1191 1139 1093 1084 950 947 902 867 793 728 707 668 652 616 578 547 544 518

321 282 205 161

326 281 206 165

322 281 205 156

326 278 202 158

71% n(N9–H) 72% n(N1–H) 74% n(C8–H) 75% n(C2–H) 14% n(C6]O), 13% n(C6C5), 13% d(N1–H) 21% d(C2–H), 11% d(N1–H), 11% n(C2N3) 15% d(N9–H), 10% d(C8–H), 9% n(N3C4) 16% d(C8–H), 13% d(N1–H), 8% n(C4C5) 20% d(N1–H), 13% d(C8–H), 8% n(N7C8) 17% d(C2–H), 15% d(N1–H), 10% d(N9–H) 22% d(N9–H), 9% d(C2–H), 9% d(N1–H), 9% d(C8–H), 8% n(C8N9) 10% n(C5N7), 10% d(C2–H), 10% d(N1–H), 8% n(C5C6) 25% d(C2–H), 12% d(C8–H), 11% d(N9–H) 24% d(C8–H), 15% d(N9–H), 9% d(C2–H) 17% d(C8–H), 10% d(N1–H), 8% d(N9–H) 19% d(N1–H), 10% n(N1C2) 10% d(C2–H), 10% n(N1C6), 9% d(N9–H), 8% d(C8–H) 28% d(N9–H), 12% d(C8–H), 12% n(C8N9) 60% g(C2–H), 11% t(N1C6) 59% d imidazol ring 22% d(N1C2N3), 13% d(C2N1C6), 10% d(C2N3C4) 62% g(C8–H), 11% t(C4N9) t rings 35% g(N1–H), 12% t(C5C6), 11% t(C4N9), 11% t(C4C5) Rings breathing 25% g(N1–H), 22% t(C8N9), 11% t(N7C8), 8% t(C4C5) 42% g(N1–H), 10% t(C4N9), 8% t(C5C6) 13% d(C6]O) 61% g(N9–H) t rings 10% d(C5C6O6), 9% d(C4C5C6), 8% d(C6C5N7) 10% d(N1C6C5), 9% d(N3C4N9), 9% d(C2N3C4), 9% d(N3C4C5), 8% d(N1C6O6) 20% d(C6]O), 11% d(C6C5N7), 8% d(N3C4N9) t rings t rings t rings

n: stretching; d: bending; t: torsion; g: out of plane motion. a Vibrational modes descriptions corresponding to 6-311CCG(d,p) calculation. They are similar with the other basis sets. Only contributions greater than 7% are reported.

Table 3 Calculate B3LYP wavenumbers with different basis sets for HX/N7H tautomer in gas phase and with PCM solvation model 6-31G(d,p) (n/cmK1) GAS

6-31G(d,p) (n/cmK1) PCM

6-31CC G(d,p) (n/cmK1) GAS

6-31CC G(d,p) (n/cmK1) PCM

6-311G(d,p) (n/cmK1) GAS

6-311G(d,p) (n/cmK1) PCM

6-311CC G(d,p) (n/cmK1) GAS

6-311CC G(d,p) (n/cmK1) PCM

Vibrational modes (fundamental contributions)

3662 3608 3264 3190 1811

3306 3275 3192 3136 1744

3655 3602 3268 3198 1774

3270 3234 3186 3136 1693

3644 3594 3243 3169 1789

3274 3246 3166 3111 1715

3641 3593 3245 3173 1767

3255 3224 3161 3111 1683

n (N7–H) n(N1–H) n(C8–H) n(C2–H) n(C6]O)Cn ringsC d exocyclic groups

n: stretching; d: bending.

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Table 4 Calculate B3LYP wavenumbers with different basis sets for HX/N9H tautomer in gas phase and with PCM solvation model 6-31G(d,p) (n/cmK1) GAS

6-31G(d,p) (n/cmK1) PCM

6-31CC G(d,p) (n/cmK1) GAS

6-31CC G(d,p) (n/cmK1) PCM

6-311G(d,p) (n/cmK1) GAS

6-311G(d,p) (n/cmK1) PCM

6-311CC G(d,p) (n/cmK1) GAS

6-311CC G(d,p) (n/cmK1) PCM

Vibrational modes (fundamental contributions)

3662 3605 3263 3195 1833

3307 3276 3193 3138 1743

3655 3599 3267 3202 1799

3269 3234 3187 3137 1689

3646 3590 3241 3174 1815

3275 3246 3166 3113 1715

3642 3589 3243 3178 1794

3254 3224 3163 3112 1680

n(N9–H) n(N1–H) n(C8–H) n(C2–H) n(C6]O)Cn ringsC d exocyclic groups

n: stretching; d: bending.

species. This peak arises from coupling of the carbonyl bond to the ring bonds stretching and bending of N1–H. It moves towards 1674–1673 cmK1 under N–H deuteration (observed IR and Raman spectra), being predicted at 1676 and 1672 cm K1 for HX/N7D and HX/N9D, respectively. Raman peaks at 1594–1590 cmK1 of HX (predicted at 1607–1602 cmK1) shift to 1578–1676 cmK1 (observed in IR and Raman spectra). These latter vibrational bands are predicted at 1593 and 1591 cmK1 for HX/N7H and HX/N9H, respectively. Therefore, they are attributed, again, to both species. It is worthwhile to mention that there are some vibrational modes which could be characteristic bands for each tautomer. Then, some experimental bands could represent each one of the two different tautomers. Thus, the vibrational band predicted at 1581 cmK1 for HX/N9H tautomer, with fundamental contributions of N9–H bending, appears in Raman spectra at 1580 cmK1. On the other hand, a band at 1537 cmK1 appear in the IR spectra of HX-d2 in 2 H2O, which could be related to the vibrational band predicted at 1538 cmK1 for the HX-d2/N7D tautomer. The assignment of these vibrational bands, as well as for the rest of the bands observed in the spectra en aqueous solution in 1800–1300 cmK1 range, has been summarised in Table 6. The most likely correspondences with the vibrational bands from the spectra recorded in solid phase are also reported.

4. Conclusions Comparing the results from vibrational analysis in gas phase and with SCRF calculations, it possible to observe a important approach to the experimental values of condensed phase when PCM solvation model is considered. The comparison of the experimental bands with the theoretical wavenumbers reveals that the inclusion of the solvent reaction field in quantum-chemical theory is obligatory for accurate results in solution. Regarding the basis sets applied, the diffuse function is shown to have an appreciable effect on the calculated wavenumber. The results which has been obtained with 6-311CCG(d,p) basis set are most consistent with the experimental data. The interpretation of the vibrational spectra gives experimental evidences for

the coexistence of two tautomers of HX, i.e. HX/N7H and HX/N9H, in aqueous solution. HX/N7H tautomer can be represented for the IR band at 1537 cmK1 of the HX-d2 spectra, while the Raman peak at 1580 cmK1 of HX in aqueous solution look like be originated by vibrational modes of HX/N9H species. Table 5 Calculate B3LYP/6-311CCG(d,p) wavenumbers for HX/N9H tautomer in gas phase and with PCM solvation model GAS (n/cmK1)

PCM (n/cmK1)

Solvent effect D (n/cmK1)

3642 3589 3243 3178 1794 1624 1587 1522 1477 1431 1401 1369 1352 1293 1186 1134 1076 1055 948 933 901 835 784 729 699 668 649 608 568 537 525 509 322 266 200 148

3254 3224 3163 3112 1680 1602 1581 1516 1463 1425 1394 1367 1352 1286 1191 1139 1093 1084 950 947 902 867 793 728 707 668 652 616 578 547 544 518 326 278 202 158

K388 K365 K80 K66 K114 K22 K7 K6 K14 K5 K6 K3 0 K7 4 5 17 29 2 14 1 32 9 0 8 0 4 9 10 9 19 9 3 12 2 10

Table 6 Observed (IR and Raman) and calculate (PCM/B3LYP/6-311CCG(d,p)) wavenumbers for HX/N9H and HX/N7H and its dideuterated derivatives (HX-d2/N9D and HX-d2/N7D) Vibrational modes (fundamental contributions)

HX experimental wavenumbers (n/cmK1)

N7H

N9H

Raman 257 nm aq. sol. [16]

Raman 281 nm aq. sol. [16]

Raman solid phase [29]

FT-IR solid phase

n(C6]O), n(C6C5), d(N1–H)

1683

1680

1691m,br

1687w

1678m

1668vs

d(C2–H), d(N1–H), n(C2N3)

1607

1602

1594s

1590sh

d(N9–H), d(C8–H), n(N3C4) n(C4C5), n(N3C4), d(N1–H)

1581

1580s

1571m

HX HX-d2 experimental wavenumbers (n/cmK1)

HX-d2 PCM/B3LYP 6-311CCG(d,p) (n/cmK1)

FT-IR solid phase

FT-IR 2 H2O solution

Raman 257 nm aq. sol. [16]

Raman 281 nm aq. sol. [16]

N7D

N9D

1671vs

1673vs

1674m,br

1673m.br

1676

1672

n(C6]O), n(C6C5)

1580w

1578m

1576s

1576sh

1593

1591

d(C2–H), n(C2N3)

1564

d(C8–H), n(N3C4), d(N9-D) n(N3C4), n(C4C5), d(C8–H)

1504

d(C8–H), d(C2–H)

1443

d(C2–H), d(C8–H), n(N7C8) d(C8–H), n(C8N9)

1579m

1542

1567w 1550w

d(N7–H), d(C8–H), d(C2–H), d(N1–H) d(C8–H), d(N1–H), n(C4C5)

1552m

1554vs

1537m

1548s

1538

1495w

1498s

1498s

1429w

1429m

1430w

1532 1516

1516m

1507s

1514vw 1490vw 1468vw

d(N1–H), d(C8–H), n(N7C8) d(C8–H), d(N7–H), n(N7C8), d(N1–H), n(C8N9)

1463

1460s

1460s

1463vs

1508

1467w

1450

1428w

1422w

1439 d(N1–H), d(N7–H) d(C2–H), d(N1–H), d(N9–H) d(C2–H), d(N7–H) d(N9–H), d(C2–H), d(N1–H), d(C8–H), n(C8N9)

1436

1439m,sh 1425

1399

1435s

1421m

1395m 1394

1392w

1375w d(N7–H), d(N1–H)

Vibrationalmodes (fundamental contributions)

M. Ferna´ndez-Quejo et al. / Journal of Molecular Structure 744–747 (2005) 749–757

HX PCM/B3LYP 6-311CCG(d,p) (n/cmK1)

1389w 1374vw

1397 1380

d(C2–H) d(C2–H), d(N1-D), n(C5N7)

1391 (continued on next page) 755

d(C2–H), d(N1-D), d(N9-D) or d(N7D), n(N1C2) d(C8–H), d(N1-D) d(N1-D), d(C2–H), n(N1C2), n(C4N9) 1335

The authors wish to thank to the Vicerrectorado de Investigacio´n de la Universidad Nacional de Educacio´n a Distancia, Spain (Project 2002) and the Ministerio de Ciencia y Tecnologı´a (Project BQU2002-02875) for support of this research.

1328

d(C2–H), d(N9-D) or d(N7-D), n(C4N9), n(N7C8)

Acknowledgements

1336m,sh

1334

1317

References

1320vw 1321w

1342s,sh 1334vw 1348vw 1348w

n: stretching; d: bending.

1339

1352 d(C2–H), d(C8–H), d(N9–H) d(C2–H), n(C4N9)

1340m

1344w

1352w

1365w 1371w 1367 n(C5N7), d(C2–H), d(N1–H), n(C5C6)

N9H

Raman 281 nm aq. sol. [16]

Raman solid phase [29] Raman 257 nm aq. sol. [16] N7H

FT-IR solid phase

FT-IR solid phase

1368w

1353w

FT-IR 2 H2O solution

1359s

Raman 257 nm aq. sol. [16]

1357s

Raman 281 nm aq. sol. [16]

N7D

1365

N9D

Vibrationalmodes (fundamental contributions) HX-d2 PCM/B3LYP 6-311CCG(d,p) (n/cmK1) HX HX-d2 experimental wavenumbers (n/cmK1) HX experimental wavenumbers (n/cmK1) HX PCM/B3LYP 6-311CCG(d,p) (n/cmK1) Vibrational modes (fundamental contributions)

Table 6 (continued)

1365

M. Ferna´ndez-Quejo et al. / Journal of Molecular Structure 744–747 (2005) 749–757

756

[1] L. Stryer, Biochemistry, third ed., Freeman, New York, 1988. [2] Howard Huge Medical Institute. http://bpf.med.harvard.edu/Pages/ techs/O/IDT/Internal_Modifications.html, 2002. [3] W. Saenger, Principles of Nucleic Acid Structure, Springer, New York, 1984. [4] B. Hernandez, F.J. Luque, M. Orozco, J. Org. Chem. 61 (1996) 5964. [5] G.G. Sheina, S.G. Stepanyan, E.D. Radchenko, Y. Blagoi, J. Mol. Struct. 158 (1987) 275. [6] J. Lin, C. Yu, S. Peng, I. Akiyama, K. Li, L.K. Lee, P.R. LeBreton, J. Phys. Chem. 84 (1980) 1006. [7] M.K. Shukla, J. Leszczynski, J. Phys. Chem. A 104 (2000) 3021. [8] M.E. Costas, R. Acevedo-Chavez, J. Phys. Chem. A 101 (1997) 8309. [9] R. Ramaekers, A. Dkhissi, L. Adamowicz, G. Maes, J. Phys. Chem. A 106 (2002) 4502. [10] R. Ramaekers, G. Maes, L. Adamowicz, A. Dkhissi, J. Mol. Struct. 560 (2001) 205. [11] M.K. Shukla, J. Leszczynski, J. Mol. Struct. (Theochem) 529 (2000) 99. [12] M.T. Chenon, R.J. Pugmire, D.M. Grant, R.P. Panzica, L.B. Townsend, J. Am. Chem. Soc. 97 (1975) 4636. [13] D. Lichtenberg, F. Bergmann, Z. Neiman, Israel J. Chem. 10 (1972) 805. [14] P.U. Civcir, Struct. Chem. 12 (2001) 15. [15] H. Schmalle, G. Haenggi, E. Dubler, Acta Crystallogr. C C44 (1988) 732. [16] J. Ulicny, M. Ghomi, A. Tomkova, P. Miskovsky, P.Y. Turpin, L. Chinsky, Eur. Biophys. J. 23 (1994) 115. [17] A. Savitzky, M.J.E. Golay, Anal. Chem. 36 (1964) 1627. [18] Grams/AI, v. 7.01, Thermo Galactic, 2002. [19] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery, Jr., T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. AlLaham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, J.A. Pople, GAUSSIAN 03, Revision B.05 Gaussian, Inc., Pittsburgh, PA, 2003. [20] S. Miertus, E. Scrocco, J. Tomasi, Chem. Phys. 55 (1981) 117; S. Miertus, J. Tomasi, Chem. Phys. 65 (1982) 239; M. Cossi, V. Barone, R. Cammi, J. Tomasi, Chem. Phys. Lett. 255 (1996) 327; M.T. Cance`s, B. Mennucci, J. Tomasi, J. Chem. Phys. 107 (1997) 3032; V. Barone, M. Cossi, J. Tomasi, J. Chem. Phys. 107 (1997) 3210; M. Cossi, V. Barone, B. Mennucci, J. Tomasi, Chem. Phys. Lett. 286 (1998) 253; V. Barone, M. Cossi, J. Tomasi, J. Comp. Chem.

M. Ferna´ndez-Quejo et al. / Journal of Molecular Structure 744–747 (2005) 749–757 19 (1998) 404; V. Barone, M. Cossi, J. Phys. Chem. A 102 (1998) 1995; B. Mennucci, J. Tomasi, J. Chem. Phys. 106 (1997) 5151; B. Mennucci, J. Tomasi, J. Chem. Phys. 106 (1997) 5151; J. Tomasi, B. Mennucci, E. Cance`s, J. Mol. Struct. (Theochem) 464 (1999) 211. [21] S. Miertus, E. Scrocco, J. Tomasi, Chem. Phys. 55 (1981) 117; S. Miertus, J. Tomasi, Chem. Phys. 65 (1982) 239; M. Cossi, V. Barone, R. Cammi, J. Tomasi, Chem. Phys. Lett. 255 (1996) 327; M.T. Cance`s, B. Mennucci, J. Tomasi, J. Chem. Phys. 107 (1997) 3032; M. Cossi, V. Barone, B. Mennucci, J. Tomasi, Chem. Phys. Lett. 286 (1998) 253; B. Mennucci, J. Tomasi, J. Chem. Phys. 106 (1997) 5151; B. Mennucci, E. Cance`s, J. Tomasi, J. Phys. Chem. B 101 (1997) 10506; J. Tomasi, B. Mennucci, E. Cance`s, J. Mol. Struct. (Theochem) 464 (1999) 211; M. Cossi, V. Barone, M.A. Robb, J. Chem. Phys. 111 (1999) 5295; R. Cammi, B. Mennucci, J. Tomasi, J. Phys. Chem. A 104 (2000) 5631; M. Cossi, V. Barone, J. Chem. Phys. 112 (2000) 2427; M. Cossi, V. Barone, J. Chem. Phys. 115 (2001) 4708; M. Cossi, N. Rega, G. Scalmani, V. Barone, J. Chem.

[22] [23] [24] [25] [26] [27] [28] [29]

757

Phys. 114 (2001) 5691; M. Cossi, G. Scalmani, N. Rega, V. Barone, J. Chem. Phys. 117 (2002) 43; M. Cossi, N. Rega, G. Scalmani, V. Barone, J. Comp. Chem. 24 (2003) 669. GaussView 3.0, Gaussian, Inc., Pittsburgh, PA, 2003. Y. Podolyan, Y.V. Rubin, J. Leszczynski, Int. J. Quantum Chem. 83 (2001) 203. O.V. Shishkin, L. Gorb, J. Leszczynski, Chem. Phys. Lett. 330 (2000) 603. A. Pelmenschikov, D.M. Hovorun, O.V. Shishkin, J. Leszczynski, J. Chem. Phys. 113 (2000) 5986. M.J. Nowak, L. Lapinski, J.S. Kwiatkowski, J. Leszczynski, Comput. Chem. 2 (1997) 140 (Singapore). Laboratorio de Quı´mica Computacional (Lab-QC)-UNED. http://www.uned.es/lab-qc, 2004. M. de la Fuente, R. Navarro, J. Mol. Struct. 687 (2004) 7. J. Chowdhury, K.M. Mukherjee, T.N. Misra, J. Raman Spectrosc. 31 (2000) 427.