Molecular Structure of Guanine-Quartet Supramolecular Assemblies in

7520

Langmuir 2008, 24, 7520-7527

Molecular Structure of Guanine-Quartet Supramolecular Assemblies in a Gel-State Based on a DFT Calculation of Infrared and Vibrational Circular Dichroism Spectra Vladimı´r Setnicˇka,† Jakub Novy´,† Stanislav Bo¨hm,† Nampally Sreenivasachary,‡ Marie Urbanova´,*,† and Karel Volka† Institute of Chemical Technology, Technicka´ 5, 166 28 Prague 6, Czech Republic, and ISIS, UniVersite´ Louis Pasteur, CNRS UMR 7006, BP 70028, 67083 Strasbourg, France ReceiVed February 26, 2008. ReVised Manuscript ReceiVed April 4, 2008 The infrared (IR) and vibrational circular dichroism (VCD) spectra of guanosine-5′-hydrazide (G-1), a powerful hydrogelator, have been measured and analyzed on the basis of ab initio modeling. B3LYP/6-31G** DFT calculations predict that G-1, forming a clear solution in deuterated DMSO, is present in monomeric form in this solvent, whereas strong gelation in a phosphate buffer is due to the formation of a guanine-quartet structure, (G-1)4, in which the four G-1 are linked by hydrogen-bonded guanine moieties and stabilized by an alkali metal cation. The B3LYP/6-31G** IR and VCD spectra of the nearly planar G-quartet, whose structure is slightly distorted from the C4h symmetry, in which the G-bases interact via four Hoogsteen-type hydrogen bonds and a sodium cation is positioned in the middle of the G-quartet, are in very good agreement with the experimental spectra, indicating that this structure is the predominant structure in the gel state. The geometric parameters are discussed. This study is the first to use IR and VCD spectroscopies coupled with DFT calculations to elucidate the structure of a supramolecular species in a gel state and shows the VCD spectroscopy as a powerful method for investigating the structure of complex supramolecular self-assemblies where the use of other structural methods is limited.

Introduction Structural studies of guanine (G) derivatives assembled into cyclic tetrameric entities, guanine quartets,1–3 have attracted particular attention because these play a critical role in a variety of biologically important cellular processes,4–7 including nucleic acid transcription, replication, and recombination, in synthetic ion channels for ion transport across membranes,8,9 and in chromosomic telomers as potential therapeutic targets for cancer therapy10–12 and in other diseases.13,14 Molecules forming G-quartets are also of great significance in supramolecular chemistry15,16 and nanotechnology.17,18 They have been used as * To whom correspondence should be addressed. Phone: (+420) 220443036. Fax: (+420) 220444334. E-mail: [email protected]. † Institute of Chemical Technology. ‡ Universite´ Louis Pasteur. (1) Gellert, M.; Lipsett, M. N.; Davies, D. R. Proc. Natl. Acad. Sci. U.S.A. 1962, 48, 2013–2018. (2) Davis, J. T. Angew. Chem., Int. Ed. 2004, 43, 668–698. (3) Davis, J. T.; Spada, G. P. Chem. Soc. ReV. 2007, 36, 296–313. (4) Neidle, S.; Parkinson, G. N. Curr. Opin. Struct. Biol. 2003, 13, 275–283. (5) Gottarelli, G.; Spada, G. P.; Garbesi, A. In ComprehensiVe Supramolecular Chemistry; Sauvage, J. P., Hosseini, M. W., Eds.; Pergamon: Oxford, 1996; Vol. 9, pp 483-506. (6) Guschlbauer, W.; Chantot, J.-F.; Thiele, D. J. Biomol. Struct. Dyn. 1990, 8, 491–511. (7) Monchaud, D.; Teulade-Fichou, M. P. Org. Biomol. Chem. 2008, 6, 627– 636. (8) Matile, S.; Som, A.; Sorde, N. Tetrahedron 2004, 60, 6405–6435. (9) Chen, L.; Sakai, N.; Moshiri, S. T.; Matile, S. Tetrahedron Lett. 1998, 39, 3627–3630. (10) Oganesian, L.; Bryan, T. M. BioEssays 2007, 29, 155–165. (11) Qi, H. Y.; Lin, C. P.; Fu, X.; Wood, L. M.; Liu, A. A.; Tsai, Y. C.; Chen, Y. J.; Barbieri, C. M.; Pilch, D. S.; Liu, L. F. Cancer Res. 2006, 66, 11808–11816. (12) Read, M. A.; Wood, A. A.; Harrison, J. R.; Gaowan, S. M.; Kelland, L. R.; Dosanjh, H. S.; Neidle, S. J. Med. Chem. 1999, 42, 4538–4546. (13) Wyatt, J. R.; Vickers, T. A.; Roberson, J. L.; Buckheit, R. W.; Klimkait, T.; Debaets, E.; Davis, P. W.; Rayner, B.; Imbach, J. L.; Ecker, D. J. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 1356–1360. (14) Gilbert, D. E.; Feigon, J. Curr. Opin. Struct. Biol. 1999, 9, 305–314. (15) Lehn, J.-M. Science 2002, 295, 2400–2403. (16) Lehn, J.-M. Proc. Natl. Acad. Sci. U.S.A. 2005, 99, 4763–4768. (17) Alberti, P.; Mergny, J. L. Cell. Mol. Biol. 2004, 50, 241–253.

low molecular weight gelling agents (gelators) of nonpolar19 and polar1,20–22 solvents, as well as in polymeric films23 and biosensors.24 Most of the above-mentioned applications utilize the ability of G-containing molecules to form highly ordered supramolecular species, G-quartets, mostly arising from the association of four G-bases into a cyclic Hoogsteen hydrogenbonding arrangement,2,6 in which each G-base forms two H-bonds with the neighboring G-base: the inner loop of hydrogen bonds is made up of C6dO6 · · · H1-N1 interactions, whereas the amino groups of the G-bases are involved in the outer N2-H2 · · · N7 hydrogen bonds. However, other G-quartet geometries have also been proposed.25,26 The stability of G-quartet structures depends on several factors: (i) the presence of monovalent cations, (ii) the substituents on or the sequence of the G-containing molecule, (iii) the concentration of the molecules, and (iv) the temperature. We have recently studied22 the influence of some of these factors on the structure of guanosine-5′-hydrazide, G-1 (Scheme 1), which was found21 to be a powerful hydrogelator in the presence of alkali metal cations, forming remarkably stable dynamic hydrogels. It was proposed that gelation of the sample is caused by the formation of highly organized supramolecular aggregates consisting of G-quartets, (G-1)4, that may be subsequently stacked into columns, [(G-1)4]n, by binding of monovalent metal cations (18) He, Y.; Liu, H. P.; Chen, Y.; Tian, Y.; Deng, Z. X.; Ko, S. H.; Ye, T.; Mao, C. D. Microsc. Res. Tech. 2007, 70, 522–529. (19) Sato, T.; Seko, M.; Takasawa, R.; Yoshikawa, I.; Araki, K. J. Mater. Chem. 2001, 11, 3018–3022. (20) Ghoussoub, A.; Lehn, J.-M. Chem. Commun. 2005, 5763–5765. (21) Sreenivasachary, N.; Lehn, J.-M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 5938–5943. (22) Setnicˇka, V.; Urbanova´, M.; Volka, K.; Nampally, S.; Lehn, J. M. Chem. Eur. J. 2006, 12, 8735–8743. (23) Arnal-Herault, C.; Pasc, A.; Michau, M.; Cot, D.; Petit, E.; Barboiu, M. Angew. Chem., Int. Ed. 2007, 46, 8409–8413. (24) He, F.; Tang, Y. L.; Wang, S.; Li, Y. L.; Zhu, D. B. J. Am. Chem. Soc. 2005, 127, 12343–12346. (25) Gu, J.; Leszczynski, J.; Bansal, M. Chem. Phys. Lett. 1999, 311, 209–214. (26) Van Mourik, T.; Dingley, A. J. Chem. Eur. J. 2005, 11, 6064–6079.

10.1021/la800611h CCC: $40.75  2008 American Chemical Society Published on Web 06/14/2008

Guanine-Quartet Supramolecular Assemblies Scheme 1. Schematic (a) and DFT Optimized (b) Structures of Guanosine-5′-hydrazide G-1

between the (G-1)4 species. To reach this conclusion, we used22 the chiroptical spectroscopies: electronic circular dichroism (ECD)27 in the UV/vis region, which had previously been employed to good effect in the study of guanosine assemblies,5,28,29 and vibrational circular dichroism (VCD)30–32 in the mid-IR spectral region, which has recently been applied in supramolecular chemistry.22,33–35 In particular, VCD, which has hitherto been applied for structural studies of relatively small36–39 and medium-sized36,39–41 organic molecules or small biomolecules,32,42–44 seems to be a very efficient tool because of the large number of resolved, relatively localized (corresponding to specific bond types) transitions, rather than the few, broad, overlapping vibronic bands that are observed in ECD. In addition, VCD has the advantage of exquisite sensitivity to molecular structure for chiral conformations36 and VCD spectra can be reliably calculated45 using methods available in commercial programs, for instance, the Gaussian program package.46 We have utilized these advantages in studying the structure of G-1 supramolecular assemblies. Guanine derivatives have been the (27) Berova, N.; Nakanishi, K.; Woody, R. W. Circular Dichroism: Principles and Applications, 2nd ed.; John Wiley and Sons: New York, 2000. (28) Gottarelli, G.; Mezzina, E.; Spada, G. P.; Carsughi, F.; Di Nicola, G.; Mariani, P.; Sabatucci, A.; Bonazzi, S. HelV. Chim. Acta 1996, 79, 220–234. (29) Sprecher, C. A.; Johnson, W. C., Jr Biopolymers 1977, 16, 2243–2264. (30) Stephens, P. J. J. Phys. Chem. 1985, 89, 748–752. (31) Nafie, L. A.; Freedman, T. B. In Circular Dichroism: Principles and Applications, 2nd ed.; Berova, N., Nakanishi, K., Woody, R. W., Eds.; John Wiley and Sons: New York, 2000; pp 97-132. (32) Keiderling, T. A. In Circular Dichroism: Principles and Applications, 2nd ed.; Berova, N., Nakanishi, K., Woody, R. W., Eds.; John Wiley and Sons: New York, 2000; pp 621-666. (33) Urbanova´, M.; Malonˇ, P. In Analytical Methods in Supramolecular Chemistry; Schalley, C., Ed.; Wiley VCH: Weinheim, 2007; pp 265-304. (34) Kra´l, V.; Pataridis, S.; Setnicˇka, V.; Za´ruba, K.; Urbanova´, M.; Volka, K. Tetrahedron 2005, 61, 5499–5506. (35) Urbanova´, M.; Setnicˇka, V.; Devlin, F. J.; Stephens, P. J. J. Am. Chem. Soc. 2005, 127, 6700–6711. (36) Freedman, T. B.; Cao, X. L.; Dukor, R. K.; Nafie, L. A. Chirality 2003, 15, 743–758. (37) Stephens, P. J.; McCann, D. M.; Devlin, F. J.; Smith, A. B. J. Nat. Prod. 2006, 69, 1055–1064. (38) Qu, X.; Lee, E.; Freedman, T. B.; Nafie, L. A. Appl. Spectrosc. 1996, 50, 649–657. (39) Polavarapu, P. L. Chem. Rec. 2007, 7, 125–136. (40) Stephens, P. J.; Pan, J. J.; Devlin, F. J.; Urbanova´, M.; Ha´jı´cˇek, J. J. Org. Chem. 2007, 72, 2508–2524. (41) Setnicˇka, V.; Urbanova´, M.; Bourˇ, P.; Kra´l, V.; Volka, K. J. Phys. Chem. A 2001, 105, 8931–8938. (42) Bourˇ, P.; Navra´tilova´, H.; Setnicˇka, V.; Urbanova´, M.; Volka, K. J. Org. Chem. 2002, 67, 161–168. (43) Shanmugam, G.; Polavarapu, P. L. Proteins: Struct., Funct., Bioinf. 2006, 63, 768–776. (44) Novy´, J.; Urbanova´, M.; Volka, K. J. Mol. Struct. 2005, 748, 17–25. (45) Crawford, T. D. Theor. Chem. Acc. 2006, 115, 227–245. (46) Gaussian 03, rev. C.02.; Gaussian, Inc.: Pittsburgh, PA, 2004; www. gaussian.com.

Langmuir, Vol. 24, No. 14, 2008 7521

subject of previous studies by vibrational spectroscopy (IR and Raman) where the extensive assignment of the vibrational modes has been done.47–52 In this paper, we discuss in more detail the structural features. To gain more insight into the geometries of the species formed, structural modeling has been performed by means of density functional theory (DFT). Our primary goal has been to determine whether a cyclic tetramer of G-1, a G-quartet, is indeed formed in the gel state in sodium phosphate/D2O buffer, as suggested in our previous experimental report,22 and, if so, to characterize its structure. To the best of our knowledge, this is the second report35 that describes the structure of supramolecular entities using DFT IR and VCD spectra calculation and the first one to describe a molecular structure in a gel state, where commonly used structural techniques as X-ray and NMR have not been efficient. We therefore believe that this study shows the very great potential of VCD spectroscopy and may substantially extend the applicability of this technique as an alternative way to investigate the structure of complex chiral supramolecular entities.

Experimental Section Materials. Guanosine-5′-hydrazide, G-1, was synthesized in the laboratory of Prof. Jean-Marie Lehn and characterized by the methods described previously.21 G-1, although insoluble in pure water, was found to form stable white opaque hydrogels in the presence of monovalent metal cations at near-neutral pH values.21 The properties of these hydrogels have already been studied under various physicochemical conditions (concentration, temperature, and solvent) using different spectral methods, including chiroptical spectroscopy.22 G-1 is also readily soluble in deuterated dimethyl sulfoxide, DMSO-d6, forming a transparent colorless solution, easily achieving a concentration sufficiently high for IR and VCD measurements.22 D2O (99.9% D, Isosar) and DMSO-d6 (99.8% D, Isosar) were used as solvents. Sodium deuteroxide (NaOD, 99.5% D) and deuterated phosphoric acid (D3PO4, 99% D) were purchased from Aldrich and used to prepare 0.5 mol L-1 deuterated sodium phosphate/ D2O buffer solution (pD ) 6.1). Methods. The samples for IR absorption and VCD measurements were prepared in two different solvents, first by mixing G-1 at a concentration of 12.0 g L-1 (∼38 mmol L-1) with 0.5 mol L-1 deuterated sodium phosphate/D2O buffer (pD ) 6.1). Because of the low solubility of G-1 at room temperature, the mixture was heated until dissolution. The level of H-D exchange of G-1, caused by deuterated solvents, was not systematically studied in our experiment. The solution was placed on a CaF2 window and then covered by a second window separated by a 25 µm spacer. Finally, the demountable cell A 145 (Bruker) was assembled in the steel cell holder, and IR and VCD spectra were recorded when the sample had cooled to room temperature and was fully gelated. Spectral homogeneity of the samples inside the cell was checked by the same IR and VCD patterns for various cell positions. In addition, the hydrogels were prepared repeatedly, giving very good reproducibility of the VCD spectra. Additional experiments were performed in DMSO-d6 solution. G-1 was dissolved in DMSO-d6 at a concentration of 17.0 g L-1 (∼55 mmol L-1). The sample was then introduced by filling holes in the A 145 cell equipped with a 100 µm Teflon spacer. IR and VCD spectra were acquired at room temperature on an IFS-66/S FT-IR spectrometer equipped with the VCD/IRRAS module (47) Toyama, A.; Hanada, N.; Ono, J.; Yoshimitsu, E.; Takeuchi, H. J. Raman Spectrosc. 1999, 30, 623–630. (48) Pelmenschikov, A.; Hovorun, D. M.; Shishkin, O. V.; Leszczynski, J. J. Chem. Phys. 2000, 113, 5986–5990. (49) Delabar, J. M.; Majoube, M. Spectrochim. Acta, Part A 1978, 34, 129– 140. (50) Lane, M. J.; Thomas, G. J. Biochemistry 1979, 18, 3839–3846. (51) Floria´n, J. J. Phys. Chem. 1993, 97, 10649–10658. (52) Dhaouadi, Z.; Ghomi, M.; Coulombeau, C.; Coulombeau, C.; Jobic, H.; Mojzesˇ, P.; Chinsky, L.; Turpin, P. Y. Eur. Biophys. J. 1993, 22, 225–236.

7522 Langmuir, Vol. 24, No. 14, 2008

Setnicˇka et al.

PMA 37 (Bruker) by a procedure described elsewhere.53 VCD spectra were measured for sample and solvent under identical experimental conditions as an average of six blocks of 3380 scans (each block accumulated for 30 min) at 4 cm-1 spectral resolution and processed with a zero-filling factor of 4. Baseline correction was performed afterward. The presented vibrational spectra are expressed in molar absorptivity ε (L mol-1 cm-1) per one G-1 molecule. Molecular Modeling. Ab initio DFT calculations were carried out on an Altix 350 computer (Silicon Graphics) equipped with 28 Intel Itanium2 processors operating at 1.5 GHz and with 120 GB RAM using the program Gaussian 03.46 The B3LYP hybrid functional54,55 was used throughout, together with the 6-31G** basis set. First, the geometry of the G-1 monomer was optimized. Then, the various geometries of the dimer (G-1)2 were optimized on the basis of the structure of the monomer, and finally, the structural features found for the monomer and dimer were used to build up the G-quartets, (G-1)4. Their structures were optimized in the presence and absence of the monovalent metal cation Na+. All minimumenergy structures (G-1)n were checked by the vibrational analysis and were found to represent energy minima. Harmonic vibrational frequencies, dipole strengths, and rotational strengths were obtained from Hessians (force fields), atomic polar tensors (APTs), and atomic axial tensors (AATs).56,57 AATs were calculated using gauche-invariant atomic orbitals (GIAOs); as a result, rotational strengths are origin-independent. IR and VCD spectra were obtained from vibrational frequencies, dipole strengths, and rotational strengths assuming Lorentzian band shapes with a 10 cm-1 half-width of the peak. The calculated frequencies were scaled by a factor of 0.95. Assignments of characteristic vibrations and depictions of the calculated structures were provided by means of the MOLEKEL program.58

Results and Discussion Experimental IR and VCD Spectra of G-1. The IR and VCD spectra of G-1 measured for a solution in DMSO-d6 and for a hydrogel in sodium phosphate/D2O buffer at concentrations of 55 and 38 mmol L-1, respectively, are shown in Figure 1. Substantially different spectra are observed in the two media. The difference is especially large between the VCD spectra. Overall, the VCD of the hydrogel measured in sodium phosphate/ D2O buffer is much larger compared to that of the solution in DMSO-d6. In our previous study,22 the features observed in the IR and VCD spectra were empirically assigned to particular vibrations. In the region 1500-1400 cm-1, the broad IR band centered at 1461 cm-1 results from hydrogen-deuterium (H-D) exchange of D2O, leading to H-O-D. This region is therefore deleted for clarity in Figure 1. It has been suggested previously22 that strong enhancement of the VCD signal observed in a gel state originates from the formation of highly ordered supramolecular species, G-quartets, whereas the very weak VCD of G-1 in DMSO-d6 solution indicates the presence of monomeric molecules. In fact, the C, N skeleton of the guanine base in G-1 is planar except for peripheral hydrogens that are slightly inflexed and cause slight distortion from entire planarity. However, such nonplanarity is generally small and thus G alone is considered to be optically inactive,59 especially in UV region where the skeleton is the principal chromophore. In monomeric G-1, the guanine moiety is attached to the 1′-carbon of the chiral ribose; therefore, a VCD (53) Urbanova´, M.; Setnicˇka, V.; Volka, K. Chirality 2000, 12, 199–203. (54) Becke, A. D. J. Chem. Phys. 1993, 98, 5648–5652. (55) Lee, C. T.; Yang, W. T.; Parr, R. G. Phys. ReV. B 1988, 37, 785–789. (56) Devlin, F. J.; Stephens, P. J.; Cheeseman, J. R.; Frisch, M. J. J. Phys. Chem. A 1997, 101, 6322–6333. (57) Devlin, F. J.; Stephens, P. J.; Cheeseman, J. R.; Frisch, M. J. J. Phys. Chem. A 1997, 101, 9912–9924. (58) Flu¨kinger, P., Lu¨thi, H. P., Portmann, S., Weber, J. MOLEKEL, rev. 4.3.; Swiss Center for Scientific Computing: Manno, Switzerland, 2000.

Figure 1. Experimental IR and VCD spectra of G-1 obtained from (a) a solution in DMSO-d6 (dashed lines, 55 mmol L-1) and (b) a gel state in deuterated sodium phosphate/D2O buffer (solid lines, 38 mmol L-1). Molar absorptivity and concentrations are expressed per G-1.

Figure 2. B3LYP/6-31G** VCD spectrum of the monomeric G-1 and the experimental VCD spectrum measured in DMSO-d6 (55 mmol L-1). The spectra are offset for clarity.

signal can be induced in the guanine vibrational modes. Unfortunately, such a signal, if present at all, is rather weak, reflecting the inherent molecular chirality of G-1 (Figure 1, spectrum in DMSO-d6). Its strong enhancement, as observed in the spectrum in sodium phosphate/D2O buffer, is due to a coupling of vibrational modes between particular molecules during the self-assembly process (for instance, gelation) and may be attributed to the formation of highly ordered supramolecular species.22,34,60 To rationalize these empirical observations, we present here the results of an ab initio DFT study. (59) Johnson, W. C. In Circular Dichroism: Principles and Applications, 2nd ed.; Berova, N., Nakanishi, K., Woody, R. W., Eds.; John Wiley and Sons: New York, 2000; p 703-718. (60) Setnicˇka, V.; Urbanova´, M.; Pataridis, S.; Kra´l, V.; Volka, K. Tetrahedron: Asymmetry 2002, 13, 2661–2666.

Guanine-Quartet Supramolecular Assemblies

Langmuir, Vol. 24, No. 14, 2008 7523

Figure 3. B3LYP/6-31G** structures of the dimer (G-1)2 in top (upper structures) and side view (lower structures): (a and b) G-G, N1-carbonyl, symmetric structure and (c) G-G, N1-carbonyl, N7-amino structure.

It was reasonable, of course, to hypothesize that the aggregation of G-1 in a gel state may involve not only tetramerization, but also the presence of less ordered species such as monomers, dimers, and other intermediates, as indicated by MS.22 Therefore, we calculated the IR and VCD spectra of the particular (G-1)n species that may be present in a gel state, with emphasis on G-quartets as a most favorable species, and we discuss here their geometries and structural parameters. Structure of Monomeric G-1. At the start of our work, we optimized the structure of the G-1 monomer, representing the building block of the supramolecular entities studied, at the B3LYP/6-31G** level. Before doing so, we took into account the substantial flexibility of the hydrazide chain, which can easily be rotated not only about the single bond C4′-C5′ but also about the other bonds C5′-N6′ and N6′-N7′. As a consequence, the hydrazide chain can occupy a wide range of conformations and can be strongly puckered. Therefore, we optimized several starting geometries, mostly differing in the dihedral angle N6′-C5′C4′-C3′. All of the hydrazide dihedrals were relaxed during the calculation. The structure of the lowest-energy conformer is shown in Scheme 1. While the guanine C, N skeleton is nearly planar (180° ( 1°), the peripheral hydrogens are distorted from planarity, typically less than 5°. The highest distortion, about 30°, was calculated for hydrogens at N2. The ribose moiety is puckered in a C3′-exo envelope, confirming the nonplanarity of the five-membered furanose ring.61 Not surprisingly, the molecule adopts an anti conformation of the glycosidic bond between the sugar and base due to its higher stability than found for the syn conformation.62 The glycosidic dihedral angle χ about the single bond C1′-N9, defined by atoms O4′-C1′-N9-C4, can, in principle, adopt a wide range of values.62 We have found that its value is close to 165°. The other dihedrals of the monomeric G-1 describing the ribose and hydrazide conformations are as follows: δ(C5′-C4′-C3′-O3′) ) -75.9°, γ(O5′-C5′-C4′-C3′) ) -123.2°, β (N6′-C5′-C4′-C3′) ) 57.6°, and R (N7′-N6′C5′-C4′) ) -174.1°. Our calculations also revealed the presence of two intramolecular hydrogen bonds, N3 · · · H(O2′) and O3′ · · · H(N6′), characterized by bond lengths of 1.855 and 2.217 Å, respectively. The other guanine atom distances and angles are in good agreement with DFT63 and experimental X-ray61,64 data published previously. Having optimized the geometry of G-1, harmonic vibrational frequencies were calculated at the B3LYP/6-31G** level. The VCD spectrum obtained is presented in Figure 2 together with (61) Saenger, W. Principles of Nucleic Acid Structure; Springer Verlag: New York, 1984. (62) Neidle, S. Nucleic Acid Structure and Recognition; Oxford University Press: Oxford, 2002; Chapter 4. (63) Gu, J.; Leszczynski, J. J. Phys. Chem. A 2000, 104, 6308–6313. (64) Taylor, R.; Kennard, O. J. Mol. Struct. 1982, 78, 1–28.

Table 1. Calculated Fundamental Frequencies (cm-1) of Monomeric G-1 and Their Assignment to the Experimental Bands in the Spectral Region 1800-1400 cm-1 a mode

Vcalc

Vexp

assignment, remarks

1 2 3 4 5 6 7

1690 1638 1573 1541 1497 1467 1443

1687 1673 1596 1547 1506 1466 1434

V(C6dO6), G-ring V(C5′dO5′), sugar δ(H-N7′-H), hydrazide δ(H-N2-H) + V(C2-N2), G-ring δ(H-N2-H) + V(C2-N3), G-ring V(C4-C5) + V(C4-N3) + V(C2-N1), G-ring V(C4-N9) + V(C8-N7) + V(C4-N3), G-ring

a

Numbered bands correspond to those in Figure 2.

Table 2. B3LYP/6-31G** Structural Parameters of Dimeric Conformation c of (G-1)2a parameter bond lengths O6 · · · H1 N3 · · · H(C2′) O3′ · · · H(N6′) N7 · · · H(N2) bond angles C6-O6 · · · H1 N1-H1 · · · O6 N2-H · · · N7 dihedral angles C6-O6 · · · H1-N1 N2-H · · · N7-C5 χ (O4′-C1′-N9-C4) δ (C5′-C4′-C3′-O3′) γ (O5′-C5′-C4′-C3′) β (N6′-C5′-C4′-C3′) R (N7′-N6′-C5′-C4′)

conformation c 1.871 1.767/1.854 2.221/2.205 1.897 129.8 170.9 172.8 -157.3 -178.4 156.3/161.1 -76.2/-75.4 -121.3/-123.5 59.0/57.0 -172.0/-172.9

a The structure assignment c corresponds to Figure 3. Bond lengths in Å bond angles and dihedrals in degrees are given for both G-1 units, if they are different. Atom numbering is as in Scheme 1.

the experimental spectrum of G-1 measured in DMSO-d6 solution. The experimental spectrum is the same as that presented in Figure 1; only the vertical scale has been expanded. As mentioned above, DMSO-d6 was used as the solvent, which disrupts intermolecular hydrogen bonds owing to its hydrogen-bond-accepting character and therefore prevents self-organization of G-1. This hypothesis was confirmed by a very good agreement of the simulated and experimental spectra, in spite of a noisy experimental spectrum caused by the weak inherent chirality of G-1 resulting in very weak VCD signals. Moreover, the combined experimental and theoretical approach allowed a consistent assignment of the fundamental modes in the range 1800-1400 cm-1, as listed in Table 1. It should be noted that especially vibrational modes with substantial participation of the guanine core are delocalized and overlapped, so we assigned specific modes only to the most pronounced motions (the same is valid throughout the text for the other species).

7524 Langmuir, Vol. 24, No. 14, 2008

Setnicˇka et al.

Figure 4. B3LYP/6-31G** structures of the G-quartet (G-1)4 in top and side view. The conformations differ in the different orientations of the ribose moieties, as indicated schematically.

The detailed analysis of vibrational spectra of guanine derivatives48–50 often coupled with the potential energy distribution (PED)51,52 has been published previously. In our case, the signs of all of the VCD bands and their relative intensities were correctly predicted and the frequencies were typically calculated with errors smaller than 1%. Only for modes 2 and 3, originating in the ribose and hydrazide moieties, did the errors increase to about 2%. Such an increase may be attributed to the higher local flexibility of the hydrazide chain and sugar compared to the rigid guanine moiety. Taken together, the DFT geometry optimization and the VCD spectra calculation revealed that the G-1 conformer described above is the predominant one in DMSO-d6 solution and thus confirmed our empirical observation22 suggesting that G-1 is present in monomeric form when dissolved in DMSO-d6. A very good agreement between the calculated and experimental spectra allows us to characterize the structure of the G-1 monomer with atomic resolution. This step is very important for successful modeling of more complex supramolecular species, as shown below. DFT-Calculated Geometry of the Dimer, (G-1)2. The next step in modeling the structure of complex entities, G-quartets, involved DFT geometry optimization of the dimers, (G-1)2, formed by the association of two G-1 species held together by noncovalent intermolecular forces. We used the optimized structure of G-1, described in the previous paragraph, to build up and further optimize various dimeric structures with the different geometries that may occur naturally. Structures a and b (Figure 3) represent the geometrically simplest possible dimers, in which the guanine moieties interact through Watson-Crick edges, creating the conformation described in the literature as trans Watson-Crick/Watson-Crick.65 Both structures a and b show a trans glycosidic bond orientation and N1-carbonyl, symmetric base-pairing geometry.61,65 They differ in the orientation of the sugar moieties characterized by the position of the O4′ atom with respect to the G-G plane, as shown in the side views in Figure 3. While both the sugars are oriented by the O4′ atoms lying above the G-G plane in conformer a, one ribose lies above and one lies below the plane in conformer b. Unfortunately, the trans Watson-Crick/Watson-Crick structure of both the conformers a and b precludes the formation of the stable cyclic tetramer that we set out to study. Therefore, we

used the structural data mentioned above to build up and geometryoptimize a new dimeric conformation, c, having a cis Watson-Crick/Hoogsteen orientation65 of the guanine moieties. Unlike a and b, conformation c may serve as a building block for the construction of G-quartets.2,5,6 Its structure is shown in Figure 3 and the geometrical parameters are summarized in Table 2. Conformer c, having a cis glycosidic bond orientation, is held together by two (N1-carbonyl and N7-amino)61,65 hydrogen bonds. The lengths of other hydrogen bonds are also specified in Table 2. Interestingly, the guanine planes in c are more distorted from planarity, by about 25°, than calculated for a and b (