Effects of Hydrogen Bonding on Vibrational Normal Modes of Pyrimidine

Jun 8, 2010 - software package.60 Given the floppy nature of the pyrimidine/. (H2O)n clusters, rather strict convergence criteria ..... pyridine,66,67...
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J. Phys. Chem. A 2010, 114, 6803–6810

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Effects of Hydrogen Bonding on Vibrational Normal Modes of Pyrimidine Austin A. Howard, Gregory S. Tschumper,* and Nathan I. Hammer* Department of Chemistry and Biochemistry, UniVersity of Mississippi, UniVersity, Mississippi 38677 ReceiVed: February 9, 2010; ReVised Manuscript ReceiVed: May 13, 2010

The effects of weak intermolecular interactions on 10 vibrational normal modes of pyrimidine are investigated by Raman spectroscopy and electronic structure computations. Hydrogen-bonded networks of water induce a shift to higher energy in certain normal modes of pyrimidine with increasing water concentration, while other modes are relatively unaffected. Pyrimidine molecules also exhibit weak C-H · · · N interactions and shifted normal modes upon crystallization. The selective nature of the shifting of normal modes to higher energy allows for definitive assignments of the nearly degenerate ν8a and ν8b modes with polarized Raman spectroscopy. Natural bond orbital (NBO) analyses indicate that when water molecules donate hydrogen bonds to the nitrogen atoms of pyrimidine, there is significant charge transfer from pyrimidine to water, much of which can be accounted for by substantial decreases in the populations of the nitrogen lone pair orbitals. Despite the overall decrease of electron density in pyrimidine upon complexation with water, there are concomitant changes in NBO populations that polarize the π-electron system toward the proton acceptor N atoms, as well as contractions of the bonds associated with the N-C-N and C-C-C regions of the pyrimidine ring. Introduction Noncovalent interactions dictate the physical properties of molecular systems from nanoscale self-assembled architectures to biological building blocks.1-11 They are prevalent in nature and contribute to important processes such as molecular recognition and self-assembly. Hydrogen bonding is perhaps the most extensively investigated class of noncovalent interactions due to its importance in the chemical and physical properties of water as well as its impact on the structure and function of biomolecules including amino acids, nucleotides, monosaccharides, and the polymers formed from these molecules.12 Hydrogen bonding also plays a dominant role in determining crystal structure; solvation phenomena; reaction dynamics in liquids; nonlinear optical responses in solid state materials; surface and electrode chemistry; and the macroscopic properties of gases and condensed phase materials. Hydrogen bonding has been investigated since the 19th century, even before the term “hydrogen bond” was coined in the 1930s.5,13,14 The most common and widely studied class of interactions involves moderately strong hydrogen bonding and includes N-H · · · N, N-H · · · O, O-H · · · N, O-H · · · O, and other similar interactions between neutral fragments with distances typically ranging from approximately 1.5 to 2.2 Å.5 This class of interactions is observed in neutral biological molecules, and electrostatic interactions dominate the resulting structures and physical observables. Weaker C-H · · · N, C-H · · · O, and C-H · · · S interactions (sometimes referred to as weak hydrogen bonds) are typically longer than 2.2 Å. These weaker interactions are not as directional as the stronger varieties of hydrogen bonding but still have a pronounced effect on observables, such as, on average, a 10% shift of peak positions in the vibrational spectrum of the neat molecular liquid. A number of collections1,3,5,14-25 highlight and summarize the extensive literature and detail the structures involved with and * To whom correspondence should be addressed. E-mail: tschumpr@ olemiss.edu (G. S. T.), [email protected] (N. I. H.).

the experimentally observed effects of noncovalent interactions. In addition, these references highlight many instances where vibrational spectroscopy helps elucidate the structures of interaction in specific molecular systems. Vibrational spectroscopy, both infrared and Raman, are powerful tools for the study of the effects of weak intermolecular interactions such as hydrogen bonding. Changes in the vibrational spectra of interacting molecules allow us to ascertain exactly which atoms and bonds are affected and to what extent they are affected. The typical vibrational spectral signature of a hydrogen bond is an increase in peak intensity as well as a shift to lower energy due to the stretching mode of the donor molecule, corresponding to an elongated bond. Although not technically accurate, this spectral phenomenon is commonly referred to as a red shift. Hydrogen bonds have been investigated using Raman spectroscopy since the 1950s, when Puranik investigated hydrogen bonding between donors and carbonyl acceptors26-28 and found the first evidence in a Raman spectrum for hydrogen bonds to nitrogen.29 Vibrational spectroscopy has also been employed to investigate hydrogen bonding in terms of thermodynamic and kinetic properties including association constants,30 rate constants,31 and formation enthalpies.32 Here, we present a Raman spectroscopic study of hydrogen bonding between pyrimidine molecules and between pyrimidine and water. The crystal spectrum of pyrimidine has been previously studied by vibrational spectroscopy, and normal modes were found to exhibit a shift to higher energy when compared to the liquid-phase Raman spectra.33-36 This type of change in the vibrational spectrum is more commonly referred to as a blue shift. Past liquid phase studies have found a blue shift of the most prominent peak in pyrimidine’s Raman spectrum, that due to the ring-breathing mode ν1, to accompany hydrogen bonding. In fact, blue-shifted normal modes in both pyrimidine37 and pyridine38 in mixtures with water were first reported in the 1960s. Recently, Schlucker et al. studied the evolution of ν1 as a function of water concentration in pyrimidine/water mixtures.39 Through a combined experimental and computational study, they

10.1021/jp101267w  2010 American Chemical Society Published on Web 06/08/2010

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showed a good correlation between the calculated blue shifts of the ν1 mode and the O-H · · · N hydrogen-bond distances between the water molecules hydrogen bonded to the central pyrimidine molecule. Here, we present a comprehensive study of the effects of hydrogen bonding by water on 10 normal modes of pyrimidine (ν16a, ν16b, ν6b, ν6a, ν1, ν9a, ν15, ν3, ν8a, and ν8b in the notation of Lord et al.40) in order to better understand the origin of the shifting of these modes to higher energy. As in the recent report by Schlucker et al., we employ polarization-resolved linear Raman spectroscopy of pyrimidine/water mixtures to study the effects of water solvation on the location of the normal modes. For comparison, we also examine the effects of C-H · · · N intermolecular interactions on the normal modes by pressurizing liquid pyrimidine until it crystallizes. Polarized Raman spectra were also employed to definitively assign vibrational modes to Raman peaks for which conflicting assignments have been made in the past.33-37,40-50 To uncover the mechanism of pyrimidine’s blue-shifting Raman peaks, we have performed natural bond orbital (NBO) population analyses on a low energy structure of pyrimidine hydrogen bonded to water to investigate the shifts in electron density contributing to the observed peak shifts. NBO analyses have been employed previously to elucidate the transfer of charge from acceptor to donor in a hydrogen-bonded complex.51 Hobza et al. have also used NBO analysis to qualitatively explain the phenomenon of the blue-shifting hydrogen bond in terms of charge shifts among NBOs, in which the stretching peak of the donor molecule is blue-shifted as opposed to red-shifted, that is, the bond is shortened rather than lengthened.12 We analyze changes in the electron density in the central nitrogen and carbon atoms as well as in the carbon-carbon and carbon-nitrogen bonds as the hydrogen-bonded water networks are extended. Because NBOs use localized bonds and lone pairs as “basic units of molecular structure”,51 they can be related to the forms of the normal modes studied, and changes in electron populations can demonstrate whether a molecule’s intramolecular bonds are strengthened or weakened in various hydrogen-bonded complexes. Methods Experimental Methods. Commercially obtained pyrimidine (Sigma-Aldrich) was used without further purification. The excitation source was the 514.5 nm line of a Coherent Innova 200 Ar+ laser. A 514.5 nm laser line filter (Thorlabs) and halfwave plate (Thorlabs) were placed in front of the sample. The half-wave plate was employed to rotate the laser polarization from horizontal to vertical before exciting the sample. Spectra were obtained using laser powers ranging from 100 mW to 1 W and local heating effects were not observed. Since spectral features did not change with increasing power, spectra obtained with 1 W excitation at the sample are presented here. Spectra were collected using a Labview-controlled Jobin-Yvon Ramanor HG2-S Raman spectrometer employing a 90° scattering geometry relative to the incident laser. The spectrometer is equipped with a double grating (2000 grooves/mm) monochromator and a photomultiplier tube detector. A scan speed of 0.2 cm-1/s and slit width of 1.6 µm were used for each scan. Polarized Raman spectra were collected by placing linear polarizing film (Edmund Optics) between the sample and the monochromator.52 A depolarization ratio of the totally symmetric band in carbon tetrachloride was obtained to verify the depolarization ratio setup. Spectra were obtained for pyrimidine/water mixtures of 6 different concentrations including χH2O ) 0.00, 0.15, 0.30, 0.50, 0.70, and 0.90. Each mixture was prepared using Fisherbrand

Howard et al. microliter pipettes. Water was purified beforehand using a Barnstead Nanopure Diamond ultrapure water system and each mixture was placed for a short time in a sonicator to ensure homogeneity. Spectra of neat pyrimidine were also recorded as a function of applied pressure using a custom high pressure apparatus described previously.53 Computational Methods Density functional theory (DFT) computations were performed to investigate the minimum energy structures and vibrational spectra of small pyrimidine/(H2O)n clusters (n ) 0-2). In 2007, Schlucker et al. optimized 10 different pyrimidine/water clusters up to n ) 6 at the B3LYP/6-31++G(d, p) level of theory,39 and those structures were used as starting geometries here. In this work, full geometry optimizations were performed with the B3LYP density functional using appropriate basis sets of double- and triple-ζ quality with polarization and diffuse functions, specifically the 6-31+G(d, 2p) and 6-311++ G(2df, 2pd) split valence basis sets. Harmonic vibrational frequencies (including infrared and Raman intensities) were computed for each optimized structure. NBO54 analyses were also performed on select clusters to provide insight into the origin of the observed blue shifts in the vibrational frequencies. Dissociation energies were computed both with and without a Boys-Bernardi counterpoise (CP) correction55,56 for basis set superposition error (BSSE).57 For every fragment in a given complex, the energy was computed in the full basis set of the complex, and relaxation effects were computed in the corresponding fragment basis set. Full details of this procedure can be found in a recent review.58 Finally, the IEFPCM implicit solvent model59 was also used to examine changes in the vibrational frequencies of pyrimidine between the gas phase and an aqueous environment. All computations were performed with the Gaussian 09 software package.60 Given the floppy nature of the pyrimidine/ (H2O)n clusters, rather strict convergence criteria were adopted. The electronic energy was converged to at least 1 × 10-9 Eh by employing a threshold of 10-10 for the rms change in the density matrix during the self-consistent field procedure. For geometry optimizations, residual Cartesian forces on every atom are less than 8 × 10-6 Eh bohr-1. Furthermore, a dense numerical integration grid was used for all of the DFT calculations: a pruned grid composed of 99 radial shells and 590 angular points per shell. The default solvent parameters for water were used in the IEFPCM self-consistent reaction field calculations. Results and Discussion Raman Spectroscopy of Pyrimidine Water Mixtures. Shown in Figure 1 is a Raman spectrum of liquid pyrimidine. The region encompassing 1600-3000 cm-1 contains no fundamentals.36,45,46,49 A number of Raman-allowed overtones and combination bands are evident, however, including the ν15 overtone at 2315 cm-1 and the overlapped ν3 + ν15 and ν1 + ν19 combination bands at 2385 cm-1.61 Shown in Figure 2a are Raman spectra of pyrimidine/water mixtures showing the effects of increasing water content on ν1. The position of the ν1 peak in a 90% water (by mole fraction) solution was found to blue shift by 14 cm-1 from its position in neat pyrimidine. This shift occurs gradually and continually with successive dilutions. These findings agree with those of Schlucker et al. in both qualitative and quantitative behavior of the ν1 peak.39 In addition to the ν1 peak, we have investigated the behavior of several other peaks in pyrimidine’s Raman spectrum under similar conditions and found the peaks due to other fundamentals to behave quite

Vibrational Normal Modes of Pyrimidine and H-Bonds

Figure 1. Raman spectrum of liquid pyrimidine.

differently both in terms of shift (as a function of water concentration) and in magnitude of overall shift at the maximum dilution. Shown in Figure 2b are the Raman spectra for the pyrimidine/ water mixtures in the region of the modes ν6a, an in-plane CCC/

J. Phys. Chem. A, Vol. 114, No. 25, 2010 6805 NCN bending mode (i.e., the CCC and NCN angles change), and ν6b, an in-plane CNC/CNC bending mode. The spectrum for the χ ) 0.15 mixture shows a peak at 626 cm-1 in addition to a small shoulder at 630 cm-1. The initial peak at 626 cm-1 disappears, and the shoulder continually shifts with further dilution. This behavior is very similar to that observed in ν1. Schlucker et al. attributed such peak shapes to the addition of multiple hydrogen-bonded arrangements. The final position of the ν6b peak in the χ ) 0.90 spectrum is at 639 cm-1, showing that this peak shifts less than the ν1 peak (9 cm-1 versus 14 cm-1). The ν6a peak initially at 682 cm-1 exhibits a smaller blue shift (approximately 3 cm-1), shifting by only slightly more than 1 cm-1 up to the χ ) 0.50 mixture. Furthermore, the peak exhibits no shoulder at any of the concentrations shown, unlike the ν6b and ν1 peaks. Figure 3a shows the evolution of ν8a (a CN stretch) and ν8b (a CC and CN stretch mode) with increasing water content. The ν8a peak shifts by approximately 1 cm-1 up to the χ ) 0.50 mixture and by a total of 6 cm-1 in the most dilute pyrimidine solution. However, ν8b, observed as only a shoulder in the

Figure 2. Raman spectra of pyrimidine/water mixtures showing (a) ν1 and (b) ν6a and ν6b. Shown at the right of each spectrum is the amount of water (by mole fraction) present in each sample.

Figure 3. (a) Raman spectra showing the evolution of ν8a and ν8b as the concentration of water is increased and (b) polarized Raman spectra showing ν8a, ν8b, ν3, ν15, and ν9a in neat pyrimidine and a pyrimidine/water mixture with a 0.90 mol fraction of water.

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Figure 4. Evolution of ν16b, ν16a, ν3, ν9a, and ν15 with increasing water content.

Raman spectrum of neat pyrimidine, shifts by approximately 12 cm-1 such that the peak is very clearly resolved in the χ ) 0.90 spectrum. The neat pyrimidine and most dilute pyrimidine mixture spectra have been fit to Lorentzian curves to show more clearly the positions of ν8a and ν8b in the two samples. Figure 3b shows polarized Raman spectra of ν9a, ν15, ν3, ν8a, and ν8b for neat pyrimidine and a pyrimidine/water mixture with χ ) 0.90. Raman scattered light polarized perpendicularly to the incident laser polarization should be less intense compared with the scattered light polarized parallel to the incident laser light for modes of a1 symmetry.62 Figure 3b shows that the peaks assigned to ν8a and ν9a are due to modes of a1 symmetry because of the loss of intensity when the collected light is polarized perpendicularly to the laser light vs parallel to the laser. The assignment of ν8a and ν8b has been in question in the past,37,46-48 and this polarization Raman study serves to confirm this assignment. Figure 4a shows the Raman spectra of the pyrimidine/water mixtures in the region of the ν16a and ν16b peaks and Figure 4b shows Raman spectra of ν9a, ν15, and ν3. ν16b is puckering involving C1 and C6, and ν16a is out-of-plane CN puckering. Both peaks are shifted by slightly less than 3 cm-1. ν9a, a NCN bending mode, behaves similarly to ν8a. The peak is shifted by 1 cm-1 in the χ ) 0.50 spectrum and shifts by a total of 5 cm-1. The ν15 peak, due to in-plane CH bending, shows a much more regular shift at approximately 1 cm-1 in each successive dilution but a similar overall shift. ν3, another in-plane CH bending mode, exhibits a steady shift of approximately 3 cm-1 as the concentration of water is increased. Of these five modes, only ν15 demonstrates a significant shift with increasing water concentration. Table 1 summarizes the experimental blue shifts of the 10 normal modes studied here. Effect of Pressure on Pyrimidine Normal Modes. Shown in Figure 5 are Raman spectra of pyrimidine with increasing applied pressure and at reduced temperature. Increasing the pressure of the liquid forces the molecules closer together until it eventually crystallizes. Spectra below the freezing point are also included for comparison. As pressure is increased, some of the peaks sharpen; some modes are observed to shift to higher wavenumbers; some disappear; and others split into multiple peaks. Both infrared33,34 and Raman35,36 spectra of crystalline pyrimidine have previously been reported. Pyrimidine crystallizes in the orthorhombic Pna21 space group with C2V symmetry

TABLE 1: Experimental Shifts of Selected Pyrimidine Normal Modes mode symmetry original location (cm-1) maximum shift (cm-1) ν16b ν16a ν6b ν6a ν1 ν9a ν15 ν3 ν8a ν8b

b1 a2 b2 a1 a1 a1 b2 b2 a1 b2

351 401 626 681 990 1139 1159 1228 1564 1571

+2 +2 +13 +5 +14 +5 +9 +3 +6 +12

and has four molecules in its unit cell.63,64 For this reason many of the normal modes are observed to split into multiple Raman allowed peaks. This effect is illustrated by both ν16a and ν8a. Most interesting, however, are the rather large blue shift (15 cm-1), the sharpening of ν3 (Figure 5c) and the sharpening of the CH stretching modes (Figure 5e). This sharpening of the CH stretches was first noted by Sbrana in 1966, who remarked that the CH stretching fundamentals were much easier to identify in the crystalline state than the liquid,33 and it has been attributed to reduced molecular motion as the pyrimidine molecules are “locked-in” to well-defined positions in the crystal. The structure of crystalline pyrimidine is shown in Figure 6 and is characterized by weak C-H · · · N interactions,63,64 reminiscent of those found in planar configurations of the dimer.65 The modes that are most perturbed upon crystallization are those that involve more than one of these interactions. ν3 is the inplane CH bending motion in which all hydrogens participate. The large blue shift in ν3 and the sharpening of the CH stretching modes are likely a direct result of the nearest neighbor C-H · · · N interactions. The behavior of ν3 in the crystalline state differs significantly from that observed when pyrimidine is hydrogen bonded with water, in which only a 3 cm-1 shift was observed. This points to different origins of the blue-shifting of normal modes of pyrimidine in these different environments. Computational Results Overall, results obtained with the 6-31+G(d, 2p) and 6-311++G(2df, 2pd) basis sets are very similar. Therefore, only data obtained with the larger basis set will be discussed here.

Vibrational Normal Modes of Pyrimidine and H-Bonds

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Figure 5. Raman spectra of pyrimidine at atmospheric pressure (bottom spectra), with applied pressure (middle spectra), and at reduced temperature (top spectra) showing (a) ν16b and ν16a; (b) ν6b and ν6a; (c) ν9a, ν15, and ν3; (d) ν8a and ν8b; and (e) CH stretching modes.

Figure 6. Intermolecular interactions and distances (in Å) present in the pyrimidine crystal structure.63,64

The B3LYP/6-31+G(d, 2p) results can be found in the Supporting Information. Structures and Energetics. The structures of four small pyrimidine/(H2O) n clusters (n ) 1, 2) are shown in Figure 7. All structures are minima. The pyrimidine monomer and the 1 + 1 pyrimidine/(H2O)2 complex have C2V and C2 symmetry, respectively, and all other structures belong to the C1 point group. The 1 + 0, 1 + 1, and 2 + 0-side minima appear to be the PW, PW2(1+1), and PW2(2+0) structures examined by Schlucker,39 but the 2 + 0-front complex was not considered in that work. Cartesian coordinates of the optimized structures are provided in the Supporting Information. The dissociation energies (De) of these clusters computed with the B3LYP functional and the 6-311++G(2df, 2pd) basis set are listed at the top of Table 2. BSSE has a relatively modest effect on De and does not exceed 0.84 kcal mol-1 (or ≈7%).

CP corrections have an even smaller effect on the relative energies of the pyrimidine/(H2O)2 structures (e0.15 kcal mol-1). When water donates a hydrogen bond to the N atom of the ring, the interaction is quite significant. The De of the 1 + 0 structure (5.65 kcal mol-1) is larger than that of the water dimer computed at the same level of theory (4.88 kcal mol-1). For n ) 2, there is a clear preference to add the second water molecule next to the first, as in the 2 + 0 motifs, rather than donating a hydrogen bond to the other N atom on the other side of the ring (i.e., the 1 + 1 configuration). In the 2 + 0 arrangements, a C-H · · · O interaction is present along with the more conventional O-H · · · N and O-H · · · O hydrogen bonds. The 2 + 0-side minimum is the most stable pyrimidine/(H2O)2 configuration. The 2 + 0-front orientation is only 1.09 kcal mol-1 less stable, whereas the 1 + 1 structure lies more than 3 kcal mol-1 above the global minimum. Cooperative (or nonpairwise additive) effects58 are largely responsible for the stability of the 2 + 0 structures. The 3-body contributions to De are 0.04, 2.25, and 2.60 kcal mol-1 for the 1 + 1, 2 + 0-front, and 2 + 0-side configurations, respectively. For comparison, the 3-body effects in the water trimer account for 2.76 kcal mol-1 of the total binding energy, which is 15.07 kcal mol-1 when computed at the same level of theory. Vibrational Frequencies and NBO Analysis. The computed blue shifts for the 10 vibrational modes of interest are also listed in Table 2 for each of the four pyrimidine/(H2O)n explicit solvent models shown in Figure 7. The shifts for the ν1 ring-breathing mode computed in this work at the B3LYP/6-311++G(2df, 2pd) level of theory are within 1 cm-1 of those previously reported from B3LYP computations with the smaller 6-31++G(d, p) basis set.39 That earlier work identified a linear correlation between the O-H · · · N hydrogen bond distance and magnitude of the ν1 shift. All four microsolvation models (Figure 7) examined in this work nicely reproduce the observed shift for the ν1 mode of +14 cm-1 (+8, +15, +10, and +10 for the 1

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Howard et al. TABLE 2: Dissociation Energies (kcal mol-1) and Calculated Blue Shifts (cm-1) of Pyrimidine/Water Clusters at the B3LYP/6-311++G(2df, 2pd) Level of Theory structures 1 + 0 1 + 1 2 + 0-front 2 + 0-side IEFPCM expt De DCP e ν16b ν16a ν6b ν6a ν1 ν9a ν15 ν3 ν8a ν8b

Figure 7. Minimum energy structures and intermolecular distances (in Å) of pyrimidine with 1 and 2 water molecules optimized at the B3LYP/6-311++G(2df, 2pd) level of theory.

+ 0, 1 + 1, 2 + 0-front, and 2 + 0-side structures, respectively). The IEFPCM results are also reported in Table 2. Unfortunately, this implicit solvent model does not reproduce the observed shifts. The computed values are too small and/or in the wrong direction. As such, results obtained with the implicit solvent model will not be discussed further. Analysis of NBO populations can provide insight into the origin of effects of this nature in weakly bound noncovalent complexes, and population changes induced by intermolecular interactions (e.g., the formation of a hydrogen bond) on the order of 0.001 electrons (or 1 me-) are generally considered to be chemically significant.51 In fact, during the preparation of this manuscript Li and co-workers published a theoretical study of the ring-breathing modes of pyridine that included an NBO analysis to help understand the blue shifts induced by complexation with various haloforms (CHF3, CHCl3, and CHBr3).66

5.65 5.35 +2 +14 +5 +4 +8 +2 +2 +4 -2 +9

10.94 10.35 +6 +19 +12 +7 +15 +5 +3 +8 +2 +12

13.25 12.42 +5 -4 +10 +0 +10 -3 +5 -1 -2 +15

14.35 13.50 +5 -4 +7 +4 +10 +8 +2 +12 -2 +15

+1 -2 +1 -3 +1 -5 -2 -3 -4 +2

+2 +2 +13 +5 +14 +5 +9 +3 +6 +12

Their NBO analysis showed that charge transfer (from pyridine to the haloform) and hyperconjugation (between the N lone pair orbital and the σ* antibonding orbitals associated with the ortho and meta C atoms) can help explain the observed wavenumber shifts. Upon complexation, the population of the σ* orbital decreases by ≈ -1 me-, which leads to a contraction of the corresponding CC bonds in pyridine. The role of charge transfer and intermolecular hyperconjugation in the pyrimidine/H2O system can actually be traced back to work by Del Bene who, in 1975, made the interesting observation that despite the occurrence of significant charge transfer from the proton acceptor to the proton donor through the σ electron system, the negative charge on the N atom actually increases due to polarization of the π cloud.67 Table 3 lists the NBO population changes for one resonance form of pyrimidine that have a magnitude of at least 1 mewhen the 1 + 1 complex forms. The C2 symmetry of the 1 + 1 model simplifies the correlation of orbitals with those from the C2V from pyrimidine to the two water molecules, much of which can be accounted for by the concomitant population decrease of -11 me- in each of the N lone pair orbitals, n(N2) and n(N3). As with pyridine,66,67 hyperconjugation leads to substantial polarization of the π-electron cloud toward the proton acceptor but only modest changes in the σ bonding and antibonding orbitals. Both the π and π* populations associated with the CCC region of the pyrimidine ring decrease by at least -15 me-. The populations of all other π orbitals increase by +4 to +15 me-, and the largest increases are associated with the NCN section of the ring. In contrast, formation of the hydrogen bonds has relatively little effect on the σ and σ* orbitals; the populations do not change by more than (3 me-. Nevertheless, the interaction consistently induces population decreases on the order of -1 or -2 me- in σ* orbitals between the atoms in the ortho and meta positions relative to the N atom(s) in pyridine66 and pyrimidine. Changes in the CC and CN bond lengths induced by hydrogen bond formation are provided in Table 4. The data are reported to four decimal places to facilitate comparison; the precision is not intended to reflect the accuracy of the computed geometrical parameters. There is a qualitative correlation between the NBO population changes in Table 3 and the bond length changes for the 1 + 1 complex in Table 4. Summing the bonding and antibonding contributions, as one would to determine bond order for a simple homonuclear diatomic molecule, reveals a net bonding increase of +10 me- for the NCN region and +4 mefor the CCC region, whereas there is a a net bonding decrease of -4 me- for the N2 C4 and N3 C5 sections. Although an

Vibrational Normal Modes of Pyrimidine and H-Bonds TABLE 3: Population Changes (in me-) of the B3LYP/ 6-311++G(2df, 2pd) Natural Bond Orbitals of Pyrimidine up Complexation with 2 Water Molecules to Form the 1 + 1 Structurea orbital

change

orbital

change

σ (C1 N2) σ (C1 N3) π (C1 N3) σ (C1 H7) σ (N2 C4) π (N2 C4) σ (N3 C5) σ (C4 C6) σ (C4 H8) σ (C5 C6) π (C5 C6) σ (C5 H9) σ (C6 H10) n(N2) n(N3)

0 0 +15 0 0 +4 0 0 -1 0 -15 -1 0 -11 -11

σ* (C1 N2) σ* (C1 N3) π* (C1 N3) σ* (C1 H7) σ* (N2 C4) π* (N2 C4) σ* (N3 C5) σ* (C4 C6) σ* (C4 H8) σ* (C5 C6) π* (C5 C6) σ* (C5 H9) σ* (C6 H10) Rydberg (C1) Rydberg (C4) Rydberg (C5)

-1 -1 +7 -2 +1 +6 +1 -2 -3 -2 -17 -3 -1 -2 -1 -1

a

See Figure 7a for atom numbers.

TABLE 4: Changes (in Å) of the CC and CN Bond Lengths of Pyrimidine at the B3LYP/6-311++G(2df, 2pd) Level of Theory That Occur upon Complexation with 1 or 2 Water Moleculesa bond

pyrimidineb

1+0

1+1

R(C1 N2) R(C1 N3) R(N2 C4) R(N3 C5) R(C4 C6) R(C5 C6)

1.3321 1.3321 1.3332 1.3332 1.3874 1.3874

+0.0006 -0.0023 +0.0017 +0.0004 -0.0013 +0.0002

-0.0017 -0.0017 +0.0023 +0.0023 -0.0011 -0.0011

2 + 0-front 2 + 0-side +0.0055 -0.0008 +0.0009 -0.0008 -0.0023 +0.0006

+0.0012 -0.0035 +0.0051 +0.0012 -0.0006 -0.0006

a

See Figure 7(a) for atom numbers. Data given to 4 decimal places to facilitate comparison. b Bond lengths of isolated pyrimidine provided as reference values.

oversimplification, this analysis of NBO population changes is, nevertheless, qualitatively consistent with the contraction of the C1-N2 and C1-N3 bonds by -0.0017 Å and of the C4-C6 and C5-C6 bonds by -0.0011 Å as well as the elongation of the N2-C4 and N3-C5 bonds by +0.0023 Å in the 1 + 1 complex. Of course, the actual bonding in pyrimidine is more complicated, as is the connection to the observed spectroscopic shifts. The vibrational potential energy distribution (PED) of pyrimidine is quite complex.68 For example, even the totally symmetric ν1 ring-breathing mode is composed of more than a symmeterized linear combination of CC and CN stretches; the second largest contribution actually comes from the wagging motion of H8 and H9. This heavy mixing is common to almost every mode and makes it difficult to connect local changes in NBO populations with bond lengths to shifts in the vibrational spectrum. Furthermore, significant changes to the PED of pyrimidine are observed when a single hydrogen bond is formed with a water molecule.68 The semiquantitative agreement between the computed and experimentally observed vibrational wavenumber shifts extends beyond ν1 to several other modes, especially those with large shifts (J10 cm-1). As can be seen from the data in Table 2, however, a few modes are problematic, and no single pyrimidine/(H2O)n cluster can qualitatively reproduce the observed shifts for all 10 modes. Consider, for example, ν16a and ν16b, both of which shift by +2 cm-1 experimentally. For the latter mode, the DFT calculations are in excellent agreement, giving blue shifts that range from +2 to +6 cm-1 for the four

J. Phys. Chem. A, Vol. 114, No. 25, 2010 6809 pyrimidine/(H2O)n complexes. In contrast, the calculated ν16a shifts are far too large for the 1 + 0 and 1 + 1 complexes (+14 and +19 cm-1, respectively), whereas the computed shifts are in the wrong direction for the 2 + 0-front and 2 + 0-side structures (both red-shifted by -4 cm-1). Some of these differences could be attributed to comparing results from gas-phase electronic structure computations to condensed-phase experimental data. However, Albert and Quack recently measured the first high-resolution rotationally resolved gas-phase infrared spectrum of pyrimidine,69 and the gas-phase vibrational bands are within a few wavenumbers of previous liquid-phase studies. In addition, Maes and co-workers68 earlier reported FTIR spectra for pyrimidine and pyrimidine/water complexes in matrix isolation. Their results for isolated pyrimidine are within a few wavenumbers of the liquid spectra for most modes, and the magnitude of the spectral shifts for the isolated complexes agree well with the results obtained here for 0.50 mol fraction mixtures. For example, they observed a 6 cm-1 shift for both ν1 and ν8b, while not observing a shift for ν8a. In addition, they actually observed a slight red-shift in ν16a whereas we observed only a slight blue-shift. These small deviations between the gas phase, liquid phase, and Ar matrix suggest that the microsolvation models adopted here and elsewhere39 should provide a good description of hydrated pyrimidine. Clearly, certain modes are extremely sensitive to the specific hydrogen bonding environment. We are currently investigating this phenomenon using two approaches: (1) larger explicit models of solvation (more water molecules interacting with pyrimidine), and (2) a combination of explicit and implicit solvation models. Conclusions A combined experimental and theoretical approach has examined 10 blue-shifted vibrational normal modes of watersolvated pyrimidine. Whereas certain modes exhibit experimental blue shifts on the order of 12-14 cm-1, others are relatively unaffected by the presence of water. This selective blue shifting helped definitively assign the ν8a and ν8b modes. NBO computations reveal that charge transfer from pyrimidine to water substantially decreases the populations of the nitrogen lone pair orbitals. The formation of the O-H · · · N hydrogen bonds also significantly alters the populations of the π and π* orbitals of pyrimidine and induces the contraction of the C1-N2, C1-N3, C4-C6, and C5-C6 bonds by more than 0.001 Å as well as the elongation of the N2-C4 and N3-C5 bonds by more than 0.002 Å. These population and structural changes provide some insight into the electronic origins of the selective nature of the blue-shifting observed for pyrimidine. Many modes are quite sensitive to the specific hydration environment, and a completely satisfactory solvent model has yet to be found. The IEFPCM implicit solvent model cannot reproduce the observed shifts. Although simple explicit solvent models are much better, none of the four simple hydrated structures examined in this study could reproduce the wavenumber shifts of all 10 modes. We are currently exploring the effects of larger explicit solvation models as well as combined implicit and explicit models on these sensitive normal modes. Acknowledgment. This work has been supported, in part, by the National Science Foundation (EPS-0903787, CHE0955550, and CHE-0957317). Some of the computations were performed using resources at the Mississippi Center for Supercomputing Research.

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