Anharmonic Vibrational Signatures of DNA Bases and Watson-Crick Base Pairs

Transcription

1 CHINESE JOURNAL OF CHEMICAL PHYSICS VOLUME 22, NUMBER 6 DECEMBER 27, 2009 ARTICLE Anharmonic Vibrational Signatures of DNA Bases and Watson-Crick Base Pairs Gui-xiu Wang, Xiao-yan Ma, Jian-ping Wang Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing , China (Dated: Received on August 5, 2009; Accepted on September 29, 2009) Changes of molecular structure and associated charge distributions, and changes of anharmonic vibrational parameters from DNA base monomers to the Watson-Crick base pairs, have been investigated at the density functional theory level. Through examination of the NH 2, N H, and C=O stretching vibrational modes that are involved in the multiple H-bonds in the base pairs, sensitivity of their diagonal and off-diagonal anharmonicities, as well as anharmonic vibrational couplings, to the structure change are predicted. Our results reveal the intrinsic connection between the anharmonic vibrational potentials, H-bonding, and electrostatic interactions in DNA bases. Key words: Anharmonic vibration, Anharmonicity, Coupling, Two-dimensional infrared spectroscopy, DNA base I. INTRODUCTION Selective pairing between adenine-thymine (A-T) and guanine-cytosine (G-C) through multiple intermolecular H-bonds forms the well known Watson-Crick base dimers, which are basic building blocks of DNA double helical structures [1,2]. Conventional vibrational spectroscopic techniques such as linear infrared (IR) have been employed to elucidate the 3D structures of DNA [3 12]. Using structurally sensitive IR probes, for example, the C=O and N H stretching vibrations, information about base isomers can be obtained from argon and/or nitrogen matrix isolation [3 7] or gas-phase [8 12] IR experiments. The principle behind the IR method is that a vibrational mode is intrinsically connected to a set of nucleus displacements in a given molecular system [13]. An IR spectrum reflects essentially an eigenmode characteristics of the molecular system whose intermode interactions are already encoded into the spectrum. However, because of spectral congestion and the complication of intermode interactions, to extract parameters for the vibrational potential functions directly from linear IR spectra has been known to be very difficult. Fortunately, femtosecond nonlinear IR techniques such as pump/probe and two-dimensional (2D) IR in particular [14,15], have shown the capability to overcome the obstacles; a number of parameters for the vibrational potential functions, including diagonal Part of the special issue for the Chinese Chemical Society s 11th National Chemical Dynamics Symposium. Author to whom correspondence should be addressed. jwang@iccas.ac.cn, Tel.: , FAX: and off-diagonal anharmonicities, and vibrational couplings, can be retrieved simultaneously from a 2D IR spectrum, thus allowing one to study the structure and structural dynamics of the DNA in great details. The 2D IR studies of the DNA base oligomers [16,17] and IR pump/probe studies of nucleic acid base pairs [7,18] in condensed phases have been reported very recently. Ab initio computations, molecular dynamics (MD) simulations of DNA oligomers, and 2D IR spectra simulations in cm 1 region have also been reported in recent years [17,19 21]. Since the vibrational modes in all molecules are essentially anharmonic, it is of great importance to evaluate the anharmonic properties of the vibrational modes of DNA, starting from the bases and base pairs. The importance of anharmonic corrections in predicting vibrational frequency of the A-T and G-C base pairs have been pointed out earlier [22,23], however, systematic assessment of multiple anharmonic parameters on the basis of ab initio computations is still missing. Further, by combining the experimental findings and computational predictions together, one expects to be able to obtain a detailed picture of the force fields determining the 3D molecular structures and dynamics of DNA. Here we examine the anharmonic properties of DNA bases and their Watson-Crick pairs at the density functional theory (DFT) level (B3LYP/ G ). Figure 1 shows the Watson-Crick A-T and G-C pairs. The A-T pair is connected via two intermolecular H-bonds mainly: A N6 H6 O4 T and T N3 H3 N1 A, while the G-C base pair is connected via three intermolecular H-bonds: G N1 H1 N3 C, G N2 H2 O2 C, and C N4 H4 O6 G. We compare changes of bond geometries and charge distributions from the base monomers to the paired struc- 563

2 564 Chin. J. Chem. Phys., Vol. 22, No. 6 Gui-xiu Wang et al. FIG. 1 DNA Watson-Crick base pairs with atom numbering. (a) A-T. (b) G-C. H-bond distance (in Å, top) and bond-order (down) are given. tures. The strength of the formed H-bonds is analyzed in terms of bond order and orbital hyperconjugation interactions. We then present a comparison of the computed anharmonic frequencies with experimental measurements for the four bases and their dimers, to demonstrate the necessity of anharmonic corrections in frequency calculations. We examine the diagonal and offdiagonal anharmonicities of key vibrational modes associates with multiple intermolecular H-bonds that are essential for DNA helical stabilization. Efforts have been made to reveal the intrinsic connection between the anharmonic properties and the H-bonded base dimeric structures. II. COMPUTATIONAL METHODS DNA base A, T, G, and C monomers and their Watson-Crick pairs A-T and G-C were optimized without geometry constraint at the level of B3LYP/ G. Harmonic and anharmonic normal-mode frequency calculations were carried out for the optimized structures. A tight convergence was forced during the optimization, which was also needed for the followed anharmonic frequency calculations. All optimized structures have no imaginary harmonic frequency except cytosine. In the case of cytosine, one imaginary frequency has been found (154.8i cm 1 ). This belongs to the NH 2 out-of-plane vibration of the amino group. The extremely low planarization barrier of the amino group accounts for the easily happened imaginary frequency, which is well known for cytosine even at MP2/cc-pVTZ level of theory (275i cm 1 ) [24]. Intermolecular binding energies in the case of A-T and G-C were corrected for basis set superposition error (BSSE) using the standard counterpoise correction protocol [25]. No imaginary frequencies were found for the two dimer systems. The natural bond orbital (NBO) calculation [26,27] were also performed. The anharmonic frequency computations were carried at the same level of theory. Details of such calculations can be found in recent works [28,29]. Diagonal and off-diagonal anharmonicities of the 3N 6 normal modes (with N being the number of atoms), defined as ii =2ν i ν 2i and ij =ν i +ν j ν i+j respectively, were obtained. Here ν i, ν 2i, and ν i+j are the anharmonic fundamental and overtone transition frequencies for the ith mode, and the anharmonic combination transition frequency for the ith and jth modes, respectively. For A, T, G, and C monomer, and A-T and G-C dimer, the wall-clock time spent for the anharmonic frequency computations was 130, 110, 180, 70, 3280, and 3400 h respectively, using a 2-CPU 2.33 GHz computer. Since it is an all-mode anharmonic frequency computation, the computation cost increases exponentially. All calculations were carried out using Gaussian 03 [30]. Furthermore, pairwise anharmonic vibrational coupling (β ij ) between two vibrational modes of the same type was evaluated by de-mixing the wave functions of the two coupled modes, using a procedure described previously [31]. III. RESULTS AND DISCUSSION A. Geometry of DNA base pairs In the Watson-Crick A-T and G-C pairs shown in Fig.1, optimal bond distances and bond-orders are labeled for comparison for the multiple H-bonds. Higher bond-order suggests stronger H-bond, which is usually accompanied by shorter bond distance. Theory predicts A N1 H3 T has a stronger H-bond than A H6 O4 T in the A-T pair, where the A H2 O2 T H-bond is the weakest. For the G-C pair, differences in the NBO bond order for the three H-bonds are clearly shown, suggesting a compromise made between lowering the energy of the system and forming the multiple H-bonds. Further, the formation enthalpies for the A-T and G-C pairs are predicted to be and kj/mol after BSSE corrections, respectively, clearly demonstrating the difference of H-bond strengths in the two base pairs. The computed enthalpies are very close to the gas-phase experimental values ( and kj/mol) [32]. Figure 2 shows the optimized Watson-Crick A-T and G-C pairs with key structural differences indicated with respect to individual bases. There are several structural features worth mentioning: bond-length and bondangle, planarity of the H-bonded dimer, and charge redistributions. These properties change to some extent from base monomer to base pair. Bond-length and bond-angle variations are clearly seen in both the A-T and G-C pairs. The largest bond-length increase is seen in r N3 H3 of the base T (0.032 Å), while the largest bong-angle increase is seen

3 Chin. J. Chem. Phys., Vol. 22, No. 6 DNA Bases and Watson-Crick Base Pairs A (a) T (-0.003) (-0.062) A (+0.035) (+0.012)(+0.004) (+0.018) (+0.013) (+0.040) (a) (-0.056) (-0.008) (-0.025) T G C FIG. 2 Geometrical deformations of interfacial groups in the Watson-Crick base pairs with respect to individual bases. (a) A-T. (b) G-C. Bond-length change (in Å) and bondangle change (in degree) are given. (b) (-0.085) (+0.011) (+0.024) (-0.022) (+0.042) (-0.057) (+0.019) (+0.012) (-0.003) (-0.059) G (+0.053) (+0.043) (b) (+0.022) FIG. 3 Partial atomic charge distributions of interfacial atoms in the Watson-Crick base pairs and their charge variations (parentheses) with respect to those of the base monomers. (a) A-T. (b) G-C. Charges are in Coulomb (C). C in H2 N2 C2 in the base G (4.70 ). In particular, for the G-C pair, the two peripherally and symmetrically arranged NH O=C hydrogen bonds have clearly different deformations with respect to their monomeric states. The smallest bond-length and bond-angle variations are seen for the A C2H and T C2O species, indicating the presence of the weakest H-bond between the two species. Geometric changes occurred in the H-bonding participants certainly facilitate the formation of multiple H-bonds. However, the three formed H-bonds, for example, in the G-C pair, have somewhat different bond-lengths and bond-orders, indicating that the triple H-bonds can not be simultaneously optimized between two rigid molecules, in order for the system to reach a global energy minimum [33]. Structural planarity, seen in both the A-T and G-C pairs, clearly plays an important role in stabilizing the paired geometries. The conjugation between the partially double bonded C N and the well-conjugated sixnumber ring within adenine and guanine bases themselves, as well as the formation of multiple intermolecular H-bonds, are responsible for the coplanar structure of the two base pairs. For guanine, the amino in its monomeric form has a pyramidal NH 2 group with dihedral angles φ H2 N2 C2 N3 = Such a pyramidal structure becomes planar in the G-C dimer, indicating another significant structural change from the base monomer to dimer. The charge redistributions from monomer to dimer are found to be closely related to the structural changes. The NBO analysis yielded atomic charge distributions for the interfacial atoms in the two base pairs are given in Fig.3, along with the charge variations in comparison with the corresponding monomers. Clearly, quite significant charge transfer occurs. Changes of the charge distributions certainly indicate changes of the electrostatic interactions between two H-bonded base monomers. Further analysis using the NBO approach shows a hyperconjugative interaction between the H-bond acceptor orbital and the H-bond donor anti-bond orbital (also a type of charge transfer), which is believed to be the intrinsic nature of the H-bond [34]. For example, hyperconjugation occurs between the lone-pair obital of the O atom in cytosine and the anti-bonding orbital σ of the N2H2 group of guanine. Similar conclusion has been reached in an earlier study [35]. B. Anharmonic frequencies The computed anharmonic frequencies without any scaling factor are compared with argon and nitrogenmatrix [3 7], as well as in gas-phase [8 12] IR measurements. The results of NH 2 symmetric (ν s ) and asymmetric (ν a ) stretching modes, the N H, and C=O stretching modes that are involved in intermolecular H- bonds are listed in Table I. The interfacial C H and free N H stretching frequencies are also listed. Remarkable agreement between computed frequencies and experimental values is shown in Table I. The relative intensities between experiments and computations are also found to be in reasonable agreement. The harmonic and anharmonic frequencies of some of these modes and a few other modes are given in Table II. It can be seen clearly that without anharmonic corrections the vibrational frequencies would be significantly higher than experimental observables. Together, these results suggest

4 566 Chin. J. Chem. Phys., Vol. 22, No. 6 Gui-xiu Wang et al. TABLE I Comparison of the calculated anharmonic frequencies (ν i, in cm 1 ), transition intensities (I i, in km/mol), with corresponding experimental values ν exp (cm 1 ) and I exp (in relative intensity) given in parenthesis. System Mode ν i (ν exp) I i (I exp) A ν NH2, a (3565 a ) 65.4 (84 a ) ν N9H (3490 a ) 89.6 (135 a ) ν NH2, s (3448 a ) (110 a ) ν C2H (3041 a, 3093 b ) 18.3 (3 b ) T ν N1H (3479 c, 3480 d ) (130 c ) ν N3H (3432 c, 3434 d ) 66.5 (110 c ) ν C2O (1767 c ) (617 c ) ν C4O (1711 c ) (492 c ) G ν NH2, a (3503 e, 3506 f ) 41.1 ν N9H (3497 e, 3490 f ) 78.8 ν N1H (3449 e, 3456 f ) 54.1 ν C6O (1736 e ) C ν NH2, a (3565 g ) 56.0 (81 g ) ν N1H (3471 g ) 61.2 (143 g ) ν NH2, s (3441 g ) (209 g ) ν C2O (1720 g ) (872 g ) A-T ν NH2, s (3215 h ) ν C2O (1716 h ) ν C4O (1665 h ) G-C ν G:NH2, a (3352 i ) ν C:NH2, a (3532 i ) 95.4 ν G:NH2, s (3426 i ) ν N9H (3510 i ) 73.0 ν G:C6O (1706 j ) ν C:C2O (1639 j ) 34.7 a=asymmetric stretching; s=symmetric stretching. I exp was obtained by normalizing the total integrated absorbance of all absorption bands to that of the computed intensities (same for all entries). a Argon- and nitrogen-matrix [3]. b Argon-matrix [4]. c Argon-matrix [5]. d Gas-phase [11]. e Gas-phase [9]. f Gas-phase [8]. g N 2-matrix [6]. h N 2-matrix [7]. i Gas-phase [10]. j Gas-phase [12] the DFT predicted anharmonic frequencies for the DNA bases are reasonable. C. Diagonal anharmonicities The diagonal anharmonicities, ii, of the bases are predicted to be highly structure dependent. The computed ii are listed in Table II for the vibrational modes TABLE II Harmonic frequency (ω i, in cm 1 ), anharmonic frequency (ν i, in cm 1 ) and diagonal anharmonicity ( ii, in cm 1 ) of selected modes in the DNA base monomers and pairs. System Mode ω i ν i ii A ν N9H a ν NH ν C2H T ν N1H ν N3H ν C2O ν C4O G ν N9H ν N1H ν NH ν C6O C ν N1H ν NH ν C2O A-T ν A:N9H ν T:N1H ν A:NH ν A:C2H ν T:N3H ν T:C2O ν T:C4O G-C ν G:N9H ν C:N1H ν G:NH ν G:N1H ν C:NH ν G:C6O ν C:C2O a All NH 2 modes in this table are referred to the symmetric vibrational NH 2. that may be involved in H-bonds. The results of the base monomers and base pairs are compared. The N H and C H vibrational modes are highly anharmonic, which can be seen from their large ii values. Theory predicted ii of ν T:N3H is cm 1 in monomeric T, which is in reasonable agreement with recent solutionphase experimental results of the N H stretching mode in free uracil (155±15 cm 1 ) [18] and in formamide (129 cm 1 ) [36]. A dramatic increase of ii is predicted for this mode (392.6 cm 1 ) when participating in the strongest H-bond in the A-T base pair. A recent solution-phase IR pump/probe experiment of adenineuracil pair showed a similarly increased ii (230 cm 1 ) for the H-bonded N H stretching mode [18]. The ii of the symmetric NH 2 stretching mode increases significantly from free A, G, and C monomers to corre-

5 Chin. J. Chem. Phys., Vol. 22, No. 6 DNA Bases and Watson-Crick Base Pairs 567 A (a) T A (b) T that for cytosine the vibrational parameters of the key groups are well predicted (e.g. for the C=O stretching mode, ν i = cm 1 and ii =17.1 cm 1 as seen in Table I and II respectively), suggesting that the existence of one imaginary frequency does not affect significantly the results of these key modes. Further, one anharmonic frequency computation at the level of HF/6-31+G yields no imaginary frequency (data not shown). In this case, ii =15.5 cm 1 was predicted for the C=O stretching mode, which is in reasonable agreement with the DFT result. G C G C (c) (d) FIG. 4 C=O stretching modes with delocalized motions in the Watson-Crick base pairs. (a) ν T:C2O= cm 1, (b) ν T:C4O= cm 1, (c) ν G:C6O= cm 1, and (d) ν C:C2O= cm 1. sponding H-bonded dimers. These results suggest that the potential surface of the high-frequency motions can be easily influenced by structural variations. However, only slight increase of the ii of the ν A:C2H mode is seen from base monomer to dimer, indicating an insignificant influence of the structural change on this mode. This is in agreement with the NBO analysis of the H-bond order given above. The carbonyl stretching modes show relatively smaller ii values in general in comparison with the high-frequency modes. The ii value of ν C=O mode in free base G and C is around 18 cm 1, which is reasonably predicted in comparison with experimental results of cytidine and guanosine base monomers (9 and 14 cm 1 respectively) by a recent 2D IR study [16]. In the monomeric form, two carbonyl stretching modes (ν T:C2O and ν T:C4O ) in thymine differ in their ii by 9.8 cm 1, primarily due to vibrational coupling effect. Based on a simple exciton model, anharmonic vibrational coupling between the same type of mode would change the magnitude of the diagonal anharmonicities, as have been shown in peptides [29]. In the H-bonded base pairs, the ii of C=O stretching modes are found to vary quite substantially. For example, the values of ii become 23.7 and 2.7 cm 1 for the two ν C=O modes in the A-T pair, 13.2 and 3.9 cm 1 for the G-C pair. These computed results reflect the intrinsic delocalization nature of this type of normal modes, whose delocalized motions are clearly seen in Fig.4. Further, it is very likely that the ii of the ν C=O modes in the bases would behave similarly to that of the amide-i modes in peptides [14,29,37,38], since the latter is also primarily C=O stretching. Together, these results show that the vibrational modes in the DNA base pairs have structurally sensitive diagonal anharmonicities, which shall be useful to characterize the structure and dynamics of the DNA bases and DNA helices. In addition, we find D. Off-diagonal anharmonicities between intramolecular modes Table III lists the values of the off-diagonal anharmonicity ij of various modes in the base monomers and base pairs. Changes of the ij values from monomer to dimer are found to be closely related to the structural changes of the DNA bases. For base A and T, negative ij of selected intramolecular pair of modes all become positive in the H-bonded A-T pair, with large magnitude of change found in certain cases. For base T, subtle differences present in bond-length and bond-angles between N3H/C2O and N3H/C4O, however, their ij values are quite different from each other. The two ij values also increase dramatically in the A-T pair. These results show the structural sensitivity of the ij of the NH/CO pair in the DNA bases. In the A-T pair, the ij of the C2O and C4O stretching modes, is found to be only 2.4 cm 1, which is due to the remote distance between the two groups, and also possibly due to the insulating effect from the central strongly H-bonded N3H group (see Fig.4). Additionally, large frequency splitting between the two modes ( cm 1 versus cm 1, see Table II) in the A- T pair is also responsible for the small ij. Clearly the variation of the sign and magnitude of the off-diagonal anharmonicities of these interfacial vibrational modes, although may belonging to the same base, could be significantly influenced by the structural deformations due to base pairing. Similar structural dependence of the off-diagonal anharmonicities is also seen in guanine and cytosine monomers and also in the formed G-C pair. For example, in the G-C pair, the N2H2 bond of the amino group in guanine pointing to O2 of cytosine is constrained by H-bond. Nearly parallel orientation of the N2H2 and N1H bonds and closer bond distance in guanine are seen in the G-C structure, which favor the intermode interactions and thus has an increased ij (12.0 cm 1 ) in comparison with the case of free guanine (6.9 cm 1 ). Further, inspection of the other two intramolecular ij (one in guanine and one in cytosine) reveals an interesting aspect. The negative and small ij of the NH 2 /C2O pair in cytosine monomer becomes positive with larger magnitude in the G-C dimer, while the positive and

6 568 Chin. J. Chem. Phys., Vol. 22, No. 6 Gui-xiu Wang et al. TABLE III Off-diagonal anharmonicities ( ij, in cm 1 ), bond-angle (θ ij, in degree) and intermode distance (r ij, between bond-mid points, in Å) of selected pair of modes in the DNA base monomers and pairs. System Mix-mode ij θ ij r ij A NH a 2 /C2H T N3H/N1H C2O/C4O N3H/C2O N3H/C4O G N9H/N1H NH 2/N1H N1H/C6O C NH 2/C2O A T NH 2(A)/C2H(A) N3H(T)/N1H(T) C2O(T)/C4O(T) N3H(T)/C2O(T) N3H(T)/C4O(T) N9H(A)/N3H(T) N9H(A)/N1H(T) C2H(A)/C2O(T) C2H(A)/C4O(T) NH 2(A)/N3H(T) NH 2(A)/C4O(T) G C NH 2(G)/N1H(G) N9H(G)/N1H(G) N1H(G)/C6O(G) NH 2(C)/C2O(C) N1H(G)/N1H(C) N9H(G)/N1H(C) N1H(G)/ NH 2(C) NH 2(G)/C2O(C) NH 2(C)/C6O(G) C6O(G)/C2O(C) a All NH 2 modes in this table are referred to the symmetric vibrational NH 2. small ij of the N1H/C6O pair in guanine monomer becomes negative with increased magnitude in the G-C dimer. These results clearly show structural sensitivity of the intramolecular ij. E. Off-diagonal anharmonicities between intermolecular modes Structural dependent intermolecular off-diagonal anharmonicities in the case of N H/N H, C=O/C=O, and N H/C=O stretching modes are found. Two typical NH/NH pairs, N6H6(A)/N3H(T) and N1H(G)/ N4H4(C), have their ij values equal to 29.8 and cm 1 respectively. The two NH/NH pairs have very similar geometry, both having two NH bond directions being in nearly antiparallel orientations. However, their off-diagonal interactions are quite different, which must be associated with their being in different H-bonding environment. Each base pair has a C8 ring that involves the N H/N H pair (Figs. 1 3). The H-bond strengths in the two C8 rings are different. For example, N4H4(C) group participates in a stronger H-bond with shorter intermode distance seen for the N1H(G)/N4H4(C) pair in the G-C geometry, in comparison with those in a similar C8 structure in the A-T dimer. The only pair of intermolecular interacting C=O/C=O in the G-C dimer has a moderate ij (7.9 cm 1 ). Almost antiparallel bond directions favor the intermode interaction, even though the intermode distance is close to 5 Å in this case. Three pairs of N H/C=O stretching modes, NH 2 (A)/C4O(T), NH 2 (G)/C2O(C), and NH 2 (C)/C6O(G), show clearly structural dependent ij values. The H-bonding geometries, bond-angles and bond mid-point distances vary significantly from case to case, resulting in the observed difference in their ij. It is noticed that the relative strength of these ij is nicely anticorrelated with the intermode distance (Table III): the larger the ij, the shorter the distance. In addition, in spite of the highly localized nature of the C H stretching mode, and that there is only very weak H-bonding associated with the C H species, the ij values of both C2H/C2O and C2H/C4O stretching modes in the A-T pair are non-negligible and quite different, also reflecting the geometric difference of the two cases. Overall, the observed changes in the intra- and intermolecular ij could be ascribed to the change of electrostatic interactions, and to the cooperativity effect of the H-bonding interaction. Change of the electrostatic interactions between the H-bonded species is seen by the change of their charge redistributions from monomer to dimer. The H-bond cooperatively in the G-C pair may yield averaged bond elongation and averaged frequency redshift in the associated N H stretching modes. Smaller N H stretching frequencies permit vibrational resonance to occur, which may also be, for instance, the reason for the increased N1H(G)/NH 2 (C) off-diagonal anharmonicity in the G-C pair. F. Anharmonic vibrational couplings The delocalization characterizations of the vibrational modes in base monomers and pairs were examined. Due to the vibrational state delocalization, the transition intensity, frequency of a set of local modes would change, accompanying the mixing of their wave functions. Here we decouple the normal modes and obtain the local modes and inter-mode coupling using the wave function demixing approach [31]. The obtained

7 Chin. J. Chem. Phys., Vol. 22, No. 6 DNA Bases and Watson-Crick Base Pairs 569 local mode (zero-order) frequencies represent the transition energy without the perturbation from the specific coupling contribution. This forms a local mode basis that leads to the vibrational excitonic picture (eigenstates). The result of the C=O stretchings were given in Table IV, and those of the N-H stretching modes were given in Table V. In Table IV it can be seen that the coupling constant β ij of two C=O stretching modes in thymine is 5.4 cm 1, which is of very similar interaction strength revealed by the corresponding off-diagonal anharmonicity ( 4.3 cm 1 ). Similar correspondence between β ij and ij are also seen in other pair of C=O stretching modes. In the case of the G-C pair, the computed C=O/C=O intermode coupling is of the same order of magnitude as seen in a recent 2D IR experiment (ca. 10 cm 1 ) [17]. This is in agreement with the general understanding that magnitude of the off-diagonal anharmonicity is intrinsically connected to strength of intermode coupling [29]. In the case of N H stretching modes, the correspondence between β ij and ij seems to be also valid, even though the coupling strengths are much weaker than those found in case of C=O modes. In addition, it is found that all the zero-order frequencies are almost the same as their corresponding normal modes, again showing the weak interactions between N H stretching modes. Further, the calculated ij and β ij is dependent on the bond angles and bond distances, which is clearly shown in Table III, IV, and V. IV. CONCLUSION Anharmonic vibrational frequencies, anharmonicities as well as couplings in the DNA base monomers and their Watson-Crick pairs are evaluated at the DFT level using the hybrid functional B3LYP with G basis set. Several key vibrational modes, including the NH 2, N H, C=O, as well as the C H stretching modes, are considered because they are believed to be involved in the multiple H-bonds in the base pairs. By comparing the calculated anharmonic frequencies with those identified by argon and nitrogen matrix isolation and gasphase IR experiments, we find that DFT can predict vibrational frequencies of the above mentioned stretching modes reasonably. By comparing the calculated anharmonicities for base monomers and dimers, we find that both the diagonal and off-diagonal anharmonicities are structurally sensitive. Our results suggest that computations can be used to obtain anharmonic parameters for DNA bases and base pairs. The computed anharmonicities and couplings are predicted to be sensitive to molecular structure, suggesting that both can serve as structural probes for the DNA bases. Such computations can, actually provide a complete set of anharmonic parameters, which are useful to aid 2D IR spectral interpretation and further to guide 2D IR experiments. Our current work involves TABLE IV Calculated normal mode frequency (ω i, in cm 1 ), local mode frequency (ωi 0, in cm 1 ), transition intensity (I i, in km/mol), vibrational coupling constant (β ij, in cm 1 ), and off-diagonal anharmonicity ( ij, in cm 1 ) for the C=O stretching modes in DNA base monomers and pairs. Species Mode ω i I i ωi 0 β ij ij T C4O C2O A-T C4O C2O G-C C2O(C) C6O(G) TABLE V Calculated normal mode frequency (ω i, in cm 1 ), local mode frequency (ω 0 i, in cm 1 ), transition intensity (I i, in km/mol), vibrational coupling constant (β ij, in cm 1 ), and off-diagonal anharmonicity ( ij, in cm 1 ) for the N H stretching modes in DNA base monomers and pairs. Species Mode ω i I i ωi 0 β ij ij T N3H N1H G N1H N9H A-T N3H(T) a 0.4 N1H(T) N9H(A) G-C N1H(G) a 0.6 N1H(C) N9H(G) a From top to down, the β values are defined for modes listed in line 1 and 2, 1 and 3, and 2 and 3 respectively. examining the anharmonic properties of the H-bonded DNA base oligomers in larger sizes, where base stacking effect shall play a role. Such computations shall be feasible using lower-level theories with smaller basis sets. Our recent studies [29,39] have shown that the anharmonic parameters of the amide-i mode could be reasonably predicted at the level of HF/6-31+G. One expects a similar performance of this choice of method for the DNA molecules. Our results also suggest that structural deformation and associated changes in the electrostatic and H-bonding interactions from the base monomers to base pairs are responsible for the change in the anharmonic parameters. Because the anharmonicity is determined by the quartic and cubic force constants in the vibrational potentials, change of anharmonicity from monomer to dimer certainly indicates an increased number of modes involved in the potential functions, and also indicates the change in chemical environment and hence change in the anharmonic force fields. This

8 570 Chin. J. Chem. Phys., Vol. 22, No. 6 Gui-xiu Wang et al. is also true for both the diagonal anharmonicity and the intra- and intermolecular off-diagonal anharmonicities. V. ACKNOWLEDGMENT This work was supported by the National Natural Science Foundation of China (No and No ), the National High-Tech Research and Development Program of China (No.2007AA02Z139), and the Hundred Talent Fund of the Chinese Academy of Sciences. [1] G. A. Jeffrey and W. Saenger, Hydrogen Bonding in Biological Structures, 1st Edn., Berlin: Springer, 569 (1991). [2] G. R. Desiraju and T. Steiner, The Weak Hydrogen Bond in Structural Chemistry and Biology, 1st Edn., Oxford: Oxford University Press, 526 (1999). [3] M. J. Nowak, L. Lapinski, J. S. Kwiatkowski, and J. Leszczynski, J. Phys. Chem. 100, 3527 (1996). [4] K. Schoone, J. Smets, L. Houben, M. K. Van Bael, L. Adamowicz, and G. Maes, J. Phys. Chem. A 102, 4863 (1998). [5] K. Szczepaniak, M. M. Szczesniak, and W. B. Person, J. Phys. Chem. 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