Molecular Vibrations of Solvated Uracil. Ab Initio Reaction Field

J. Phys. Chem. B 1997, 101, 10923-10938

10923

Molecular Vibrations of Solvated Uracil. Ab Initio Reaction Field Calculations and Experiment Predrag Ilich, Craig F. Hemann, and Russ Hille* Department of Medical Biochemistry, The Ohio State UniVersity, Columbus, Ohio 43210 ReceiVed: February 20, 1997; In Final Form: August 12, 1997X

Harmonic vibrational frequencies and transition strengths in uracil have been calculated in self-consistent reaction fields of low ( ) 1.53) and high ( ) 78.54) dielectric constant using ab initio Hartree-Fock and density functional theory methods at the 6-31+G* level of theory. Uniformly scaled frequencies calculated in low dielectric medium agree well with infrared spectra of uracil in argon matrix, ∆ν(avg) ) 2.2 cm-1, although only partial agreement is obtained for individual matrix-induced frequency shifts and intensity changes. Reaction field calculations with a tighter spherical cavity or solute cavity determined by the isodensity polarizable continuum method yield better match with experiment for certain vibrations. In a polar protic medium, the vibrational analysis is extended beyond neutral uracil to its (de)protonation derivatives selected by reaction field calculations. Unscaled vibrational frequencies, as well as infrared and Raman intensities of the uracil-4-ol cation, neutral uracil, uracil N1-anion, and uracil N1,3-dianion calculated in continuous high dielectric medium are found to agree fairly well with vibrational spectra of uracil in aqueous media recorded over a wide pH range. The deficiencies of the reaction field model, like hydrogen bonding and ion-solvent interactions, are highlighted and their contributions quantitatively estimated.

Introduction As an essential constituent of numerous biologically relevant compounds (e.g., cytosine, folic acid, flavin), pyrimidine-2,4dione, the most stable form of uracil (I), has been a frequent subject of vibrational spectroscopic and theoretical studies. The

high-resolution infrared and Raman spectra of crystalline uracil1,2 and of uracil isolated in solid gas matrices3-6 have been assigned with the help of empirical,7 semiempirical,8 and lowlevel ab initio9-11 calculations. Higher level ab initio calculations,12-14 particularly those employing density functional (DF) theory methods,15-17 have significantly narrowed the gap between the observed and the calculated vibrational frequencies and transition strengths. Our interest in uracil vibrations originates from the resonance Raman spectroscopic and mechanistic studies of the oxidative hydroxylation catalyzed by xanthine oxidase.18-25 Pyrimidine-2,4-dione is a structural element of substrates for xanthine oxidase (both purines and pteridines) as well as one of its cofactors (flavin adenine dinucleotide). A first step in gaining a greater understanding of these species25 depends in part on knowledge of uracil vibrations in different ionization states and in media of different polarities. Only a few experimental studies have addressed the assignment of uracil vibrational spectra in aqueous media at room temperature.2,26-29 Empirical30,31 and semiempirical32 * Corresponding author. E-mail: [email protected]. X Abstract published in AdVance ACS Abstracts, November 15, 1997.

S1089-5647(97)00628-7 CCC: $14.00

force fields for the crystalline phase and frequency-scaling procedures have been developed to account for the uracil vibrational frequencies observed in argon matrix,2 crystalline phase,2,33 and in aqueous solution;2 aside from the most recent reports15 molecular orbital (MO) calculations of harmonic vibrations have been performed only for isolated uracil in vacuo. The recent numerical analysis of the effects of different media by Paglieri et al.16 does not attempt to compare theoretical and experimental data, and a comparative analysis of experimental and theoretical vibrational spectra of solvated uracil ions has not been reported to date. In the present study we apply two types of reaction field models in continuous media of low and high dielectric constant to calculate the optimized geometries and harmonic normal modes of solvated uracil in the cation, neutral, monoanion and dianion forms. We first assess the performance of the method by comparing the vibrational frequencies and transition strengths of uracil, calculated with two ab initio Gaussian formalisms, two basis sets, and two low dielectric constant reaction fields, with six different sources of infrared and Raman spectra reported for uracil in argon matrix. We show that for a major part of the uracil vibrational spectrum the correlation between theory and experiment is comparable to uncertainties among experimental data. Detailed analysis of argon matrix-induced frequency shifts and transition strength changes in uracil vibrational spectra show only moderate correlation between theory and experiment. We extend this analysis to aqueous medium, by assuming large variations in pH and the existence of uracil in different protonation states. We show by vibrational calculations in two types of reaction fields that neutral uracil, uracil-4-ol cation, uracil N1-anion and uracil N1,3-dianion are the most probable species in aqueous medium over the pH 0.7-13.0 region. On the basis of these calculations we create a series of simulated spectra by coalescing the stoichiometrically weighted calculated infrared and Raman vibrational lines of individual uracil species and compare those with experimental infrared and Raman spectra recorded at different pH values. Although detailed interpretation of experiment in terms of fundamental © 1997 American Chemical Society

10924 J. Phys. Chem. B, Vol. 101, No. 50, 1997 frequencies and absolute intensities remains difficult (due to sample self-association, inhomogeneous band-broadening, solvent vibrational interference, hydrogen bonding with solvent, and other factors not accounted for in our theoretical model), we show that major vibrational spectroscopic features observed for uracil in aqueous media over the pH 0.74-13.0 range are fairly well-reproduced from the first-principles calculations. Materials and Methods Experiment. Uracil was purchased from Aldrich (98% pure, lot 06609KF) and used without further purification. Infrared spectra were collected on a Mattson Sirius 100 FTIR interferometer at 1.0 cm-1 resolution. Double-sided interferograms were signal-averaged 4096 times for all spectra. Triangular apodization of the interferogram was performed using the real part of the Fourier transform to obtain a single-beam spectrum. Each sample and solvent (H2O) single-beam spectrum was ratioed against a 4096-scan background single-beam spectrum of air to obtain an absorbance spectrum. A scaled subtraction of the sample and solvent absorbance spectra was done to remove solvent bands using software provided by Mattson Instruments, Inc. A liquid nitrogen cooled, photovoltaic mercury cadmium telluride detector (Infrared Associates, Inc.) was used to observe the spectra and an intermediate aperture was adjusted to keep the interferogram intensity in a range resulting in less than 1% detector nonlinearity (for this detector, a peak-to-peak voltage of not greater than 5 V). The sample temperature was maintained at 15 °C using a water-jacketed sample holder connected to a NESLAB Endocal RTE-9 refrigerated circulating bath. Barium fluoride and (for samples at extreme pH) zinc selenide windows were used with inert spacers providing a nominal path length of 8 µm. Raman spectra were obtained for room temperature aqueous samples in 5 mm diameter quartz test tubes held in a standard NMR tube spinner that was fitted with a customized Teflon sleeve. Excitation at 647 nm was provided by a Coherent 599 standing wave dye laser using DCM dye. The dye laser was pumped by a Coherent INNOVA 307 argon ion laser using multiline output. The excitation beam from the dye laser was passed through a Pellin-Broca prism stage to remove extraneous light prior to illumination of the sample. Backscattered photons from the sample were collected at approximately 60° relative to the excitation beam with an optical arrangement providing a 2-fold magnification at the entrance slit of a Chromex 500IS single-stage 0.5 meter imaging spectrograph equipped with a 1200 groove/mm holographic grating. Rayleigh scattered photons were rejected mechanically at the spectrograph slit by adjusting the slit height and optically by using a holographic notch filter (Kaiser Optical Systems, Inc.) that was angle-tuned for maximum spectral coverage. The detector was a Princeton Instruments, Inc. LN/CCD-1024TKB liquid nitrogen cooled, 1024 by 1024 pixel array charge-coupled device (CCD). The detector controller was interfaced to a Gateway2000 486/33C computer with hardware provided by the manufacturer. The detector control software used was the CCD Spectrometric Multichannel Analysis (CSMA) software version 2.2a provided by Princeton Instruments, Inc. Spectra were calibrated using a software package based on the ASYST scientific software development package (Asyst Software Technologies) and further developed in the laboratory of Dr. Terry Gustafson at The Ohio State University. A solution of neat ethyl acetate and a 1:1 mixture of benzene and CCl4 provided a sufficient number of calibration lines over the range 250-1800 cm-1. A quadratic fit to these points served as the calibration function for converting from pixel number on the CCD to wavenumber shift.

Ilich et al. Raman band center frequencies were determined using the PEAKFIT program (Jandel Scientific) running on a PC/DOS platform. Calculation. The uracil vibrational frequencies and transition strengths were obtained in double harmonic approximation34,35 using ab initio Gaussian methods36 within the Hartree-Fock (HF) and hybrid Hartree-Fock/density functional theory37-39 formalisms; the latter employed Becke’s 3-parameter exchange functional40,41 combined with Lee, Yang, and Parr’s correlation functional42 (B3LYP). Standard basis sets were employed;43 the 6-31+G* basis set44 was the highest used for the HF calculations (labeled “H62”) and the HF/DF B3LYP calculations. The latter formalism is labeled “B62”, by analogy to “B2”, employed by Gill et al.45 Several lower level basis sets, consisting of 3, 4, or 6 primitive Gaussians, with or without diffuse and polarization functions on non-hydrogen atoms, were also used; of these we mention the 4-31G,46 employed within the HF/DF B3LYP formalism, and labeled “B4”. For the purpose of this presentation we will refer to different ab initio Gaussian formalisms and levels of theory as “methods”. The solute-solvent interaction was evaluated using the Kirkwood-Onsager reaction field (RF) formalism,47,48 as first implemented by Beens and Weller49 and later expanded by Wong et al.50 The radius of the solute spherical cavity was determined from the molecular volume inside the electron density contour of 0.001 qe/bohr.3 Alternatively, the solute cavity was determined using the method described by Wiberg et al.,51,52 by which a solute is enveloped in a closed surface that is an image of its electron density preset at a certain level, usually at 0.001 to 0.0004 qe/bohr3.52 All reaction field calculations were carried out for two media: (i) a low dielectric constant continuum, ) 1.53, approximating argon matrix (at T ) 82 K53), and a high dielectric constant continuum, ) 78.54, approximating bulk water at room temperature. The labels for the reaction field calculations in “argon matrix” acquired a suffix “A”, and in “water” a “W”: thus, for example, B4A, H62W. All calculations were performed with the GAUSSIAN-94 set of programs54 on a CRI Cray Y-MP8/864 supercomputer running the UNICOS operating system. Numerical and graphical processing of the GAUSSIAN-94 results were completed on a DEC VAX station 3200 running the VMS operating system (P. Ilich, unpublished FORTRAN software). Results and Discussion In the first part (A) of this section we evaluate the performance of the reaction field HF/DF B3LYP method, employing the 6-31+G*44 (B62, B62A) and 4-31G46 (B4 and B4A) Gaussian basis sets. As no complete vapor-phase uracil vibrational spectrum has been reported to date, we have compared the vibrational frequencies and infrared transition strengths calculated in low dielectric constant reaction field with respect to six sources of uracil vibrational spectra in the argon matrix.3-6,12,55 The results of the calculation and experimental data are given in Tables 1 and 2 and Figure 1. In the second part (B), we analyze the performance of a low dielectric constant Kirkwood-Onsager reaction field by comparing the calculated and experimental frequency shifts for uracil in argon matrix (and for maleimide in argon matrix, where data for uracil are lacking). The effects of the different-size spherical cavity (SC) solute model are compared with those obtained with the isodensity polarizable continuum (IPC) model in Table 3, while the performance of different methods is summarized in Table 4. The major part of section C is partitioned into four subsections. In C.1 we analyze the prototropic equilibria (Scheme 1)

Molecular Vibrations of Solvated Uracil

J. Phys. Chem. B, Vol. 101, No. 50, 1997 10925

TABLE 1: Uracil in Argon Matrix: Calculated and Experimental Wavenumbers and Mode Assignmentsa B3-LYP/4-31G/ ) 1.53

experiment

mode

freq

ints

(cm-1)

Q1 Q2

3516 3487

102 56

Q3 Q4 Q5 Q6 Q7 Q8

3182 3133 1719 1689 1630 1463

1 3 568 609 11 43

Q9

1398

15

Q10

1389

40

Q11

1352

142

Q12

1233

13

Q13

1178

101

Q14

1067

11

Q15

977

6

Q16 Q17

942 755

6 2

Q18

548

9

Q19

529

3

Q20 Q21 Q22

513 372 945

23 24 1

Q23 Q24

806 780

215 45

Q25

705

13

Q26

680

48

Q27

622

85

Q28 Q29 Q30

404 178 168

14 1 3

3485 [3,6] 3482 [4] 3490 [5] 3435 [3,6] 3433 [4] 3440 [5] 3444 [55] 3084 [3] 3130 [4] 2970 [4] 3085 [1] 1761/1764 [3] 1762/1764 [6] 1706 [3,6] 1707 [5] 1643 [3,5,6] 1644 [4] 1472 [3,6] 1473 [4] 1471 [5] 1399 [3,12] 1461/1389 [4] 1400 [5,6] 1398 [55] 1389 [3,6] 1400 [4] 1388[5] 1360 [3,5] 1359 [6] 1389/1283 [4] 1217 [3,6,55] 1219 [4] 1216 [5] 1184 [3,55] 1186 [4] 1185 [5,6] 1073 [3,5] 1076 [4] 1075 [6] 1069 [55] 1001 [3] 963 [4] 978,980 [6] 982 [12] 958 [3,4,6] 960 [5] 761 [3] 719 [4] 759 [5,6,55] 559 [3,55] 557/551 [4] 562 [6] 536 [3,55] 539 [5] 537 [4,6] 516 [3,4,6,55] 520 [5] 391 [3] 393 [4] 395 [6] 842 [3] 970/960 [5] 987,980 [6] 958 [55] 804 [3,6,55] 806 [4,5] 757 [3,6,55] 769 [4] 759 [5] 718 [3,6] 685 [4] 720 [5] 717.4 [55] 662 [3,6] 664 [4] 665 [5] 659 [55] 551 [3,6,55] 585,557 [4] 554 [5] 393 [12] 397-427 [1,2,58] 194 [58]

B3-LYP/6-31+G*/ ) 1.53 description

freq

ints

symm

νN1H

3534

117

a′

νN3H νC5H νC6H νC2O νC4O νC5C6 βN1H

3501 3180 3145 1758 1723 1635 1470

63 1 3 687 925 76 93

a′ a′ a′ a′ a′ a′ a′

νR + βN3H νR βN3H

1392

11

a′

1379

98

a′

1355

66

a′

1208

12

a′

1174

123

a′

1067

6

a′

966

8

a′

948 752

12 3

a′ a′

544

6

a′

528

6

a′

508 375 963

24 24 0

a′ a′ a′′

γC4O, γCH γC2O + def

806 737

60 53

a′′ a′′

γCO, γC5H

720

12

a′′

N3H def, γNH

675

93

a′′

N1H oop def, γN1H

568

51

a′′

γCO, R torsion oop R

395 168 148

27 0 1

a′′ a′′ a′′

βC5H νR, νR+βN1H νR + βCH, βC5H ip βC6H, νR βC6H + νR + βN3H, νR/βNH, βC5H oop βC6H νR+βNH, βNH ip βCH, νR βR ip def, βR νR +βN3H, νR, νR, Br νCC, νCN, Br βR + βC4O, R ip def R oop def R def βC2O + βR R ip def, R def, βR βCO ip, βCO γC6H, γR

a The calculated and observed frequencies, freq, are given in cm-1 and the calculated strengths, ints, are in km/mol. β and ν denote in-plane bending and stretching modes, respectively, and γ denotes out-of-plane bending modes. ip means “in-phase” and oop means “out-of-phase” (bending, stretching, etc.). R denotes the uracil ring, and def stands for ring deformation. The modes Q1-Q21 are assigned to in-plane vibrations and are of a′ symmetry, symm, while the modes Q22-Q30 denote the out-of-plane displacements and are of a′′ symmetry. The frequencies calculated by the B4A method are uniformly scaled by 0.9666 (in-plane modes) and 0.9262 (out-of-plane modes); those calculated with the B62A method are scaled by 0.9739 and 0.9923, respectively.

of uracil in aqueous media and suggest, on the basis of the high dielectric constant ( ) 78.54) reaction field calculations, four most plausible uracil species in aqueous medium (Figure 2). In C.2 we present (Figure 3) and analyze (Figures 4 and 5) the vibrational frequency shifts and infrared transition strength and Raman scattering intensity changes induced by (de)protonation of uracil. Solvent shifts and intensity changes expected in a protic medium of high dielectric constant are analyzed in subsection C.3, while in C.4 we compare the simulated infrared and Raman spectra of mixtures of different uracil protonation species with infrared and Raman spectra recorded in aqueous media over the pH range 0.74-13.0 (Figure 6). We conclude this study with assignment of experimental infrared and Raman spectra at four different pH values (Table 5) and a detailed analysis of three vibrational spectroscopic regions: 1400-1700

cm-1, 1150-1350 cm-1, and 650-850 cm-1 (subsections C.4.1, C.4.2, and C.4.3 and Figure 7a,b,c). A. Low Dielectric Medium. The calculated vibrational frequencies, uniformly scaled, and absolute infrared transition strengths for uracil in low dielectric continuous medium ( ) 1.53) are given in Table 1 along with the frequencies of infrared and Raman bands of uracil in argon matrix, reported by Barnes et al.,3 Szczesniak et al.,4 Maltese et al.,5 and Graindourze et al.6 Additional experimental data are found in the more recent argon matrix spectra reported by Les et al.12 and Ivanov et al.55 In the case of the lowest uracil vibrational bands, difficult to observe by infrared and Raman spectroscopy in argon matrix, the calculations were compared with the infrared and Raman spectra of polycrystalline uracil, as reported by Susi and Ard1 and by Florian and Hourda,33 the infrared crystalline powder

10926 J. Phys. Chem. B, Vol. 101, No. 50, 1997

Figure 1. (a) The calculated harmonic vibrational transitions of uracil in low dielectric medium ( ) 1.53) enveloped in Gaussians (fwhm ) 10 cm-1) and (b) the average of six experimental sets (refs 3-6, 12, and 55) of infrared spectra of uracil in argon matrix, enveloped in the same width Gaussians.

spectra reported by Beetz et al.56 and Shimanouchi and Harada,57 and the inelastic electron-tunneling spectra (IETS) of uracil adsorbate reported by Clark and Coleman.58 (In Supporting Information Table 1B are plotted all harmonic vibrational modes in uracil, calculated by the B62A method, along with representative skeletal distortions of benzene, caculated by the HF/ DF B3LYP 6-31G* method in vacuo.) The differences between the observed and calculated vibrational frequencies for several modes are considerable even after scaling. The discrepancies are particularly pronounced for the highly anharmonic stretching vibrations, ∆ν(NH) ≈ 31 to 49 cm-1 and ∆ν(C5H5) ≈ 75 cm-1, and also for some low-energy vibrations that are poorly supported by experimental data. If, instead of “harmonization” of the vibrational frequencies and transition strengths59 at the highest and lowest ends of the spectrum, we limit our analysis to the experimentally most amenable range, 300-1800 cm-1, and apply a bilinear scaling of the calculated frequencies, the theoretical and experimental sets of vibrational lines are brought to a good agreement (Figure 1). The experimental band intensities in Figure 1 have been derived by a simple “averaging” of the experimental absorption data reported by Szczesniak et al.,4 Les et al.,12 and Ivanov et al.55 and also by including, as weighting factors, the semiquantitative band intensity descriptions (“strong”, “weak”, etc.) by Barnes et al.3 and Maltese et al.5 In this “unified” representation the line strengths of the experimentally observed bands have been given the following numerical values: “very strong”, 500200; “strong”, 200-100; “medium strong”, “medium”, and “medium weak”, 100-40; and “weak” and “very weak”, 205. These values, together with the reported band strengths and qualitative descriptions thereof are given in Table 2. In the case of several bands, e.g., the νCH, the νCO, and the two bands

Ilich et al. around 393-394 cm-1, the experimental data4,12 are apparently insufficient to support any definitive quantitative measure of the band strength, and the values assigned in Table 2 are somewhat arbitrary, admittedly biased by the calculations. With the exception of the Q9 vibration, observed around 1397 cm-1, and the low-energy Q28 vibration that has not been observed experimentally, the transition strengths of the calculated and observed uracil vibrations are fairly well matched. Better matching of certain vibrational frequencies and strengths in uracil can be obtained2 by the method of internal force matrix adjustments;60-63 however, this method has also been known to create additional uncertainties in the spectral interpretation.64,65,2 In the case of deuterated uracils (data not shown), larger discrepancies between the theoretical and experimental transition strengths also point to the inadequacies of the BornOppenheimer approximation in the calculations of harmonic oscillator energies with different masses. As noted early by Crawford,66 derived analytically by Nakagawa and Shimanouchi,67 and demonstrated in a quantitative way by Gussoni,68 Chaem and Krimm,69 and a number of other investigators, the changes in the harmonic eigenvector matrix (normal modes) can lead to large errors in the calculated transition vibrational strengths and second-order intensities. On the other hand, within the realm of pure ab initio calculations, the use of larger basis sets, diffuse functions70 (as, for example, in the 6-31+G* basis set in our calculations), and, in particular, density functional methods,71,72 has resulted in a considerable improvement of calculated vibrational transition strengths and has in a number of compounds, like uracil, attained or surpassed experimental uncertainties. In summarizing the results in low dielectric medium, we conclude that the vibrational frequencies and infrared transition strengths obtained from the unscaled force constant matrix calculated by the B62A method agree fairly well with experiment, as can be seen in Table 1, Figure 1, and Table 2. The same is true of the frequencies of the in-plane vibrations calculated by the B4A method while the infrared transition strengths and the out-of-plane vibrational frequencies calculated by the B4A method agree less well with experiment. The latter is a known consequence43 of the poor representation of certain regions of molecular energy gradient surface (tangent space) with basis sets containing smaller number of primitive Gaussians, for example, the 3-2112,13,73,74 and 4-21.75 Despite these limitations it should be noted that, within the hybrid HF/DF formalisms, the vibrational frequencies and transition strengths in uracil and analogous compounds, calculated at the 4-31G level, are much closer to experiment than in a number of reported vibrational calculations at the Hartree-Fock level with considerably larger basis sets.12,14 B. Effects of a Low Dielectric Medium. A comparison of the uracil vibrational frequencies and line strengths calculated in the Kirkwood-Onsager dipole reaction field of a low dielectric continuum with those calculated in vacuo exhibits two sets of reaction field-induced effects: small frequency shifts and significant increases in transition strengths. The average relative frequency shifts, ∆ν/ν ) (νvacuum - νargon)/νvacuum, are under 1%, in good agreement with the argon matrix-induced vibrational shifts observed in a variety of molecules.76,77 The calculated increase in the absolute intensity depends on the method of calculation, size and shape of the solute cavity, and the particular vibrational mode under consideration; the average transition strength per mode is expected to be higher by about 10% in comparison to vacuum. No intensity measurements have been reported for uracil; however, in diatomic78 and smaller polyatomic molecules76,79 the intensities of stretching vibrations



TABLE 2: Uracil IR Spectrum in Argon Matrix: Averaged Experimental Frequencies, Experimental and Assigned Band Strengthsa band

frequency (cm-1)

mode and symmetry

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

3485.22 3435.42 3107.00 2970.00 1760.40 1715.26 1643.50 1470.00 1397.20 1390.90 1362.20 1217.20 1184.70 1071.70 982.30 978.20 958.10 804.70 759.60 759.20 718.00 661.70 557.10 553.40 536.90 516.40 393.00 392.50 0.00 0.00

Q01(XY) Q02(XY) Q03(XY) Q04(XY) Q05(XY) Q06(XY) Q07(XY) Q08(XY) Q09(XY) Q10(XY) Q11(XY) Q12(XY) Q13(XY) Q14(XY) Q22(Z) Q15(XY) Q16(XY) Q23(Z) Q17(XY) Q24(Z) Q25(Z) Q26(Z) Q18(XY) Q27(Z) Q19(XY) Q20(XY) Q28(Z) Q21(XY) Q29(Z) Q30(Z)

exptb 125 100 15 {{15}} {672} {375} 100 125 {38} 138 {83} 13 {413} 50 13 25 175 14 125 {14} 100 25 {13} 25 125 25

exptc

exptd

194 122 1

69 48

{{1632}} {{1632}} 60 115 {79} {79} 31 9 144 11 {11} {11} 11 69 5 39 13 100 7 63 9 38 {{548/sh}} {{548/sh}}

{273} {137} 17 44 31 10 1.5 1 58 3 4 22 1 12 33 24 4 14

expte

assigned intensity

exptf

s s

m m

{vs} {vs} m ms vs m vw w vs w vw

{vs} {s} m m m mw vw m w {{vw}}

w s

m

s w s w m w m

m w m w m mw m

125 100 5 5 750 500 80 100 80 60 15 5 150 20 5 10 15 100 5 60 10 100 15 40 15 60

m

{m}

40

a The experimental frequencies of six sets of infrared spectra of uracil in argon matrix (refs 3-6, 12, 55), the individual experimental line strengths or their semiquantitative descriptions, and the “average” line strengths (km/mol) assigned on the basis of experimental data. The data in double braces were considered questionable and were left out. b Szczesniak et al. (ref 4). c Les et al. (ref 12). d Ivanov et al. (ref 55). e Barnes et al. (ref 3). f Maltese et al. (ref 5).

in the argon matrix have been reported to increase by a factor ranging from 15% to almost 10-fold in comparison to those in the vapor phase. As for bending modes in uracil and smaller molecules, we predict little or no intensity increase, as is generally true for smaller molecules.76,79 Matrix-induced frequency shifts are more difficult to generalize than the changes in transition strengths. The principal reason is the dearth of experimental data: the reported uracil vaporphase vibrational spectra are either limited to a single band80 or contain a reference to few bands but not the spectra,4 or the few vibrational bands in the spectrum are too broadened for a comparison with theoretical predictions.81 Furthermore, the occasionally referenced,2,10,82 supposedly complete, vapor-phase vibrational spectrum of uracil has never been published. For this reason we have included in our analysis a uracil proxy, maleimide, whose vapor and argon matrix vibrational spectra are more complete.83-86 Another difficulty in this type of analysis is that vibrational frequency shifts in a concentrated sample of polar protic compounds in solid gas matrices are likely to be induced in larger part by self-association rather than by matrix enclosure, as pointed out by Barnes et al.3 Having stated this, we restrict our analysis to several vibrations whose shifts are summarized in Table 3. The predicted frequency shifts for the NH stretching vibrations (B62A and B4A columns) are only qualitatively supported in deuterated maleimide. (On the other hand, it is puzzling that the reported matrix-induced shifts for νNH are of opposite sign in uracil4 and in maleimide.83) The predicted small blue shifts (B62A) for νCH are in accord with previous reaction field calculations50 but experimental support is scarce due to the low strengths of these transitions and paucity of spectroscopic

TABLE 3: Vibrational Shifts in Uracil Induced by Argon Matrixa vibration ∆ν (cm-1) ∆ν (cm-1) ∆ν (cm-1) ∆ν (cm-1) ∆ν (cm-1) type B62A B4A B4A tight other calc experiment νN1H νN3H νNH νND νCH νCO νCO a νCO νCO s νCO νCdC

-2.4 -10.9 +0.5b +0.5b -0.2 -1.1 +3.2 +5.6 +0.6b +8.5b +1.9 +1.1b

+2.4c -1.5c

-0.2 -9.8

+3.0 -12.4

+2.4 +3.8 +2.6 +3.4

+2.0 +6.0 +8.9

+12.2c +11.4c

+1.6

+3.7

+4.0

+4 [4] +12 [4] -4 [83] +5 [83]

+3 [4,80] +5 [83] +12 [83] +6b [83]

a

The calculated vibrational frequency shifts in uracil, induced by reaction field of dielectric constant ) 1.53 (columns two through five), compared to those in vacuo, and the experimental argon matrixinduced frequency shifts compared to those from the vapor phase observed in uracil and maleimide; see text for additional explanation. b Maleimide. c ICPM calculations (uracil).

data.87,88 Good qualitative agreement has been obtained for νCdO in uracil and for the strongly coupled symmetric (A1) and antisymmetric (B1) carbonyl stretching vibrations in maleimide; the same can be said for the νCdC vibration in maleimide. In addition to the standard reaction field calculations, employing the spherical cavity determined in the prescribed way,50 we have also carried out calculations with different reaction field parameters. In the self-consistent reaction field (SCRF) expression for the solute-solvent interaction (1),47-49 the operator g that couples the transpose of the molecular dipole


Ilich et al.

TABLE 4: Comparison of the Experimental and Calculated Frequency Ratios, Average Frequency Differences and Absolute Average Frequency Differences, and Execution Times for Uracila method

medium

XY-fac

Z-fac

∆σ

|∆σ| (cm-1)

CPU [h:m:s]

B3LYP/6-31+G*/SCRF B3LYP/6-31+G* HF/6-31G/SCIPCM(N) HF/6-31G/(N) B3LYP/4-31G/SCRF B3LYP/4-31G/SCIPCM(N) B3LYP/4-31G

) 1.53 vacuum ) 1.53 vacuum ) 1.53 ) 1.53 vacuum

0.9842 0.9843 0.8994 0.8995 0.9764 0.9751 0.9764

0.9912 0.9983 0.8977 0.9009 0.9065 0.9065 0.9125

2.24 2.61 4.69 5.76 -0.06 -0.76 0.06

8.34 8.38 12.41 15.57 13.59 14.44 13.14

07:32:12 04:44:27 10:02:25 04:10:54 01:51:23 10:49:21 01:00:03

a Summary of the performance of vibrational calculations for uracil in low dielectric medium and in vacuo. The XY-fac and Z-fac are multiplicative factors applied to the in-plane and out-of-plane calculated vibrational frequencies, respectively, obtained by comparison to the averaged experimental frequencies. ∆σ are the average differences between the calculated (after scaling) and experimental frequencies, and |∆σ| are the absolute values of these differences (proportional to average linear dispersions). The CPU execution times refer to the GAUSSIAN-94 calculations on a CRI Cray Y-MP8/864 or a computer of similar capabilities.

moment observable (µT) with its iteratively upgraded value is a simple scalar expression in dielectric constant of the continuum () and the radius (a0) of the solute spherical cavity:

H′ ∝ µT g µ

(1)

g ) ( - 1)/{(2 + 1)a03}

(2)

The nominal size of the spherical cavity for uracil, calculated with the HF/DF B3LYP/4-31G method has a radius a0 ) 3.87 A. When the cavity radius in reaction field calculations is contracted by 20%, to 3.10 A, the predicted frequency shifts become closer to experiment (the “B4A tight” column in Table 3). The predicted matrix-induced shift for νN1H (but not for the νN3H!) changes sign and becomes comparable to the reported value.4 One may think of these effects in terms of the “tight-cage” solvation model of Pimentel and Charles.89 A similar trend is observed in the reaction field calculations employing the isodensity polarizable continuum model of solute cavity,51,52 though the predicted red shift for νCdO is closer to experimental argon matrix shifts for alkyl carbonyls.90 In addition to the stretching vibration shifts presented in Table 3, a number of in-plane and out-of-plane vibration shifts exhibit different degrees of agreement between the theory and experiment. Apparently, there is a slight prevalence in the calculations toward matrix-induced blue-shift for the out-of-plane vibrational frequencies in maleimide (no data for uracil reported) and smaller molecules, in general agreement with experiment.91 In summary, we present the frequency-scaling factors, average dispersion, and cumulative average dispersions between the calculated and experimental vibrational frequencies and typical execution times for several methods of calculations, Table 4. Overall, the best agreement with experiment is obtained with B62A method; better agreement with experiment for certain vibrations is obtained by “tight-shell” calculations and the reaction field calculations employing the isodensity polarizable continuum model for the solute cavity.51,52 However, in the present implementation in the GAUSSIAN-94 set of programs, the latter method is apparently too time-consuming. C. High Dielectric Medium. Bulk solvent effects on uracil vibrations in aqueous medium have been evaluated by the Kirkwood-Onsager47-50 reaction field model in a high dielectric medium, ) 78.54. As specific hydrogen-bonding interactions between a solute and solvent are absent in the dipole reaction field model, we have attempted to simulate electrostatic interaction between solvent and more polar molecular domains in solute by varying the size of the solute cavity. The reaction field calculations with the spherical cavity model have been performed with the following “cage” sizes: tight cage (a0′ ) 0.85a0), nominal cage (a0), and loose cage (a0′ ) a0/0.85). Alternatively, the solute cavity has been calculated using the

isodensity polarizable continuum model.51,52 While a particular cavity size or shape in reaction field calculations can be more or less suitable in simulating solvent-induced vibrational effects in water, an ingredient clearly missing in this model is the ability of the solvent to exchange protons with the solute. This is particularly important in the case of uracil which can exist either as an acid or as a base in aqueous media. Furthermore, the acid/base properties of pyrimidine-2,4-dione are even more important in bicyclic (e.g., purine, pteridine) and tricyclic derivatives (e.g., flavin) of this ring where, due to the overall increase in amphoteric character, the gap between protonation and deprotonation equilibria is reduced by several orders of magnitude in comparison to uracil. We account for this solvent property by externally introducing a number of uracil species in different protonation states, Scheme 1. C.1. Protonation States: Relative Stabilities. In vacuo calculations with the semiempirical AM1 method93 and ab initio Gaussian methods at several levels of theory54 of the four uracil cations give two groups, with the N1H2- and N3H2-iminium cations predicted to be considerably less stable than the O2Hand O4H-cations. The ordering of the latter two species poses an interesting problem. According to in vacuo calculations (AM1, ab initio Gaussian (U)HF and HF/DF B3LYP at the 3-21G, 4-31G, and 6-31+G* levels) protonation should occur predominantly at O4, with the ratio of the equilibrium constants associated with the formation of uracil-4-ol cation and uracil2-ol cation, Keq(O4)/Keq(O2), estimated to be approximately 108. The electron energy gap between the two cations in vacuo, ∆EE ∼ 10-12 kcal/mol, is well in the range of reaction field solvation energies. As the dipole moment of the uracil-2-ol cation (∼8 D) in vacuo is predicted to be higher than that for the uracil-4-ol cation (∼6 D) one would expect the gap between the electronic energies of the two cations in vacuo to narrow significantly in a highly polar medium. According to the B62W calculations in high dielectric medium, ) 78.54, with uracil imbedded in the loose cage, ∆EE is predicted to decrease by 3 kcal/mol. Further reaction field calculations with gradually decreased solute cavity (or increased dielectric constant) predict a collapse of the energy gap with a concomitant increase in the difference between the induced dipole moments in the two cations. The evolution of both properties is seen in Figure 2a, where the angle subtended with the x-axis is proportional to the energy gap and the length of the line is proportional to the dipole moment difference between two cationic species in equivalent environments. The energy levels of the two species could eventually reverse and, according to the B62W calculations with the tight cage model, the uracil-O2H+ is in fact expected to constitute about 95% of the cation form in highly acidic aqueous medium. Solvent stabilization predicted by the reaction field calculations with the IPC model51,52 is about 1



SCHEME 1. Four Steps of the Consecutive Deprotonation of Uracil Cationa

a

The energy differences within the same group of species (cations, anions) are from the B62 calculations; the pKa values are from ref 92.

Figure 2. Mutual positions on the energy-dipole moment surface of the uracil-2-ol and uracil-4-ol cations (a) and uracil N3- and N1-anions (b) calculated with the B62W method. The total electronic energies are obtained by adding -260 000 kcal/mol to the energy for the cations and -259 000 kcal/mol to the energy for the anions.

order of magnitude larger than that predicted by the SC model (Figure 2a). Significant narrowing (but no reversal) of the energy gap between the uracil-4-ol and uracil-2-ol cations imbedded in a continuous medium of high dielectric constant

( ) 78.54) is predicted by the calculations with the IPC model. Thus, uracil-4-ol is expected to remain the predominant form in aqueous medium, with the Keq(O4)/Keq(O2) ratio ranging from 2 × 104 (IPCM B4W calculations) to 1.4 × 104 (IPCM B62W calculations). A similar situation is encountered in the case of the N1- and N3-anions. According to the in vacuo ab initio calculations the N1-anion is more stable, by 17.6 kcal/mol (UHF/3-21G method) to 14.01 kcal/mol (HF/DF B3LYP/6-31+G* method), than the N3-species. The large difference between the dipole moments, µ(N1-anion) ) 2.4[D] and µ(N3-anion) ) 8.1[D], suggests that this gap will be narrowed in a polar medium due to the different magnitudes of the dipole-dipole interactions between solute and solvent. As in the case of the monoketopyrimidine-ol cations, the reaction field SC model calculations with uracil anion imbedded in the tight solvation cage predict a reversal of the energy gap and a predominance of the N3anion. Calculations with the loose cage and the nominal cage predict narrowing of the energy gap, with a strong inverse dependence on the solute cavity radius (see eq 2) but no reversal of the order of the electronic energies seen in vacuo. Deprotonation at N1, with equilibrium constant Keq(N1), should be the dominant path of ionization of neutral uracil in alkaline aqueous media. The latter result is supported by the reaction field calculations with the IPC model, with the equilibrium constant ratio, Keq(N1) /Keq(N3) ≈ 5 × 104. It is instructive to note the far smaller extent of solvent stabilization of the N1-anion (Figure 2b) than in case of the N3-anion (as well as the uracil OHcations, Figure 2a). This is a straightforward consequence of the differences between the dipole moments of the two anions. On the basis of these calculations the protonation Scheme 1 can be reduced to the following sequence:

4-ol cation T neutral uracil T N1-anion T N1,3-dianion (3) C.2. Protonation States: Vibrational Spectra. To provide a more complete set of experimental data on uracil vibrations in aqueous media at different pH values we have recorded both the infrared and scattering Raman spectra. Accordingly, we have calculated the vibrational frequencies and both the infrared


Ilich et al.

Figure 3. Vibrational spectra of the uracil cation, neutral uracil, anion, and dianion, calculated by the B62W method (infrared) and the H62W method (Raman). The transition lines are enveloped in Gaussians of 35 cm-1 fwhm (infrared) and 15 cm-1 fwhm (Raman) to visually simulate the experimental spectra.

transition strengths and Raman scattering intensities for the four uracil species given in (3). The reaction field calculations of vibrational frequencies and infrared transition strengths have been carried out using the B62W method. As second-order transition moments evaluated within the DF formalism94 are not available within the GAUSSIAN-94 set of programs,54 Raman scattering intensities have been obtained from a separate set of calculations using the HF/6-31+G* method (H62W). The calculated infrared and Raman frequencies and transition intensities of the fundamental vibrations in the uracil cation (23 a′ and 10 a′′ modes), neutral uracil (21 a′ and 9 a′′ modes), the anion (18 a′ and 8 a′′ modes), and the dianion (17 a′ and 7 a′′ modes) are presented in Figure 3. Given the inferior performance of the Hartree-Fock method in predicting vibrational frequencies when uncorrected for electron correlation effects (e.g., H62W), we have, following the usual procedure,95,96 uniformly scaled the Raman vibrational frequencies of the four uracil species (3) by factors ranging from 0.89 to 0.92, derived from a comparison with the vibrational frequencies calculated by the B62W method. The infrared vibrational frequencies calculated by the B62W method are presented unscaled. Protonation of uracil at O4, creating a closed shell cation, is expected to induce relatively small red shifts, ∆ν ≈ 25 cm-1, in NH and CH stretching vibrations (vide infra) and small to

moderate blue shifts in most of the in-plane and out-of-plane bending and ring-deformation vibrations, in comparison to neutral uracil. The overall increase in frequency, 0.44%, and force constant, 0.70%, is expected to become only slightly attenuated in a continuous polar medium. Similar effects, induced by N- and C-protonation, have been predicted for imidazole and N- and C-alkyl pyrroles by ab initio Gaussian calculations within the HF/DF B3LYP formalism at the 6-31G*, 6-31+G*, and 6-311G** levels of theory (P. Ilich, R. Hille, and J. O. Alben, unpublished calculations). Small blue shifts, 1-2 cm-1, have been observed in the ultraviolet resonance Raman (UVRR) spectra of the amide (imide) II band, in the 1476-1486 cm-1 region in X-Pro dipeptides at pH 1.5, in comparison to the spectra of zwitterion forms at neutral pH.97 Strong support for the prediction that a number of vibrational bands shift to higher energy in closed shell cations upon protonation is found in the vibrational spectra of p-cresol and anisole. When dissolved in strong, proton-donating haloacetic acids, the phenol oxygen in both species becomes protonated and a significant blue shift of the tyrosine 8b98 and several other skeletal vibrations is observed.99 Small red shifts, ∆ν ≈ 11-16 cm-1, are predicted for the N-H stretching vibration in the anion and moderate to large red shifts, ∆ν ≈ 38-190 cm-1, for the C-H stretching



Figure 4. Changes of the average infrared absorption strength, frequency, and force constant of the in-plane vibrational modes (0, O, 4, B62W method) and Raman scattering intensities (3, H62W method) with deprotonation of uracil from the cation to the dianion.

vibrations in the anion and dianion in comparison to neutral uracil; however, this part of the spectrum has not been experimentally assessed. The largest frequency shifts induced by a change in the protonation state, in the vibrational spectroscopic region under consideration, are expected in the carbonyl stretching region of uracil anions (Figure 3). The C2dO, C4dO, and C5dC6 stretching vibrations, spanning the 1670-1780 cm-1 region in neutral uracil, are expected to shiftsnot necessarily in the same ordersto the 1560-1680 cm-1 region in the anion and to 1425-1580 cm-1 in the dianion. This effect is so large that, on average, all in-plane frequencies in uracil and (even more pronounced) reduced-mass normalized force constants are expected to exhibit a steady decrease on going from neutral species to dianion (Figure 4). Red shifts of 40-60 cm-1 in the same vibrational region have been observed by Nishimura et al.28 in the Raman spectra of N1-substituted uracil ring in 5′-uridine monophosphate at high pH (one should note, however, that the deprotonated ring of uridine monophosphate is an N3-anion, while we are considering here the N1anion; the spectra of the two anions are expected to differ in several details). Large red shifts have also been recorded by the UVRR spectra of tyrosinate anion in proteins [100] and tyrosine analogues at high pH.101,102 Although a large red shift in phenolate anions is observed for a skeletal mode 8b98 rather than in the carbonyl stretching vibrations, as in uracil, both shifts have the same origin: the expansion of the valence electron spatial domain in a negatively charged species, with a concomitant decrease in bond alternancy and force constants in comparison to the neutral compound. Concomitant with the decrease in vibrational energies induced by deprotonation, steady increases in infrared transition strengths and Raman scattering intensities are expected for the in-plane vibrational modes (Figure 4). The magnitude of the intensity increase predicted by the reaction field calculations, however, should be carefully gauged with respect to the solvation parameters used in the calculations. The overall increase in intensity is roughly inversely proportional with the third power of the solute cavity radius and, particularly in the case of vibrational transitions localized to a distinctly polar atomic pair, e.g., νCdO in anionic species, the predicted intensity increase can be quite large. In the case of out-of-plane vibrations, infrared and Raman transition intensities are predicted to have distinctly opposite trends to

Figure 5. Correlation (full line) and approximate correlation (dotted line) among vibrational modes in uracil-4-ol cation (+), neutral uracil (n), uracil N1-anion (-) and uracil N1,3-dianion ()), calculated by the H62W method. The vibrational frequencies are linearly scaled with respect to the B62W results, while the line heights correspond to square roots of the calculated Raman intensities in order to visualize weak transitions.

those for the in-plane vibrations while frequencies and force constants do not exhibit any simple dependence on the degree of uracil protonation (data not shown). These significant effects notwithstanding, a number of vibrational modes in uracil are not significantly affected by changes in the protonation state. Not surprisingly, these include strong ring vibrations and vibrations localized on the C5-C6 fragment. The lowest energy in-plane vibration, which we assign to the Q23 mode in the cation, predicted at 376 cm-1, Q21 at 390 cm-1 in neutral uracil, Q19 at 390 cm-1 in the anion, and Q17 at 415 cm-1 in the dianion, retains the approximate relative position in the spectrum in all four species (Figure 5). Similarly, the large amplitude-low frequency in-plane ring deformations of the benzene e2g symmetry parentage show little change with stepwise deprotonation and accumulation of negative charge. Examples are the modes Q21 predicted at 541 cm-1 and Q22 at 523 cm-1 in the cation, closely associated to the modes Q19 predicted at 557 cm-1 and Q20 at 524 cm-1 in neutral uracil, and to the modes Q17 predicted at 558 cm-1 and Q18 at 524 cm-1 in the anion. These modes correspond to the blue-shifted vibrational modes Q14 predicted at 670 cm-1 and Q16 at 540 cm-1, respectively, in the dianion, which are of similar skeletal deformation patterns. Interestingly, all of these low-frequency skeletal modes in uracil are expected to shift toward higher energy to varying degrees, following the loss of one, two, or three protons. The ring-breathing vibration (mode Q17 in neutral uracil, predicted at 780 cm-1), which is the strongest band in the scattering Raman spectrum of uracil in water (ref 2; also Figure 6) is expected to change little with

10932 J. Phys. Chem. B, Vol. 101, No. 50, 1997 the protonation and deprotonation of the ring; we assign it to the Q19 mode, predicted at 785 cm-1 in the cation, Q15 at 798 cm-1 in the anion (largest shift), and Q15 at 776 cm-1 in the dianion (Figure 5). Similarly, slight shifts toward lower energy with little change in the relative position in the spectrum are expected for the in-plane triangular vibration, assigned to the Q17 mode predicted at 1025 cm-1 in the cation, Q15 at 1009 cm-1 in neutral uracil, Q14 at 974 cm-1 in the anion, and Q12 at 950 cm-1 in the dianion. Proximal to this band, in all four uracil species (3), we expect to find the highest energy out-ofplane vibration, characterized by a highly localized C5-H5/ C6-H6 out-of-phase bending. This vibration is assigned to the mode Q24 predicted at 1049 cm-1 in the cation, Q22 at 1023 cm-1 in neutral uracil, Q20 at 1020 cm-1 in the anion, and Q18 at 974 cm-1 in the dianion. The in-plane bending vibrations, assigned to the Q8 through Q14 modes in the 1000-1500 cm-1 region of neutral uracil,2-6,12,28,55 are affected by changes in the protonation state of uracil to different degrees. Though the asymmetric ring distortions of the benzene e1u and e2g parentage are preserved in most vibrations, only a few pairwise relations can be established between similar modes in any two uracil species. For example, the in-plane N1-H bending mode Q10, predicted at 1506 cm-1 in the cation, is analogous to the Q8 mode predicted at 1540 cm-1 in neutral uracil but is only remotely related (by the ring distortion pattern) to the Q7 mode predicted at 1488 cm-1 in the anion. More pronounced are the vibrational frequency differences among uracil ionic species that result from the shifts of the center of mass due to the loss of protons giving rise to several specific effects. First, the order of the νC2dO and νC4dO vibrations (predicted at 1659 and 1693 cm-1, respectively) in the anion are reversed in comparison to neutral uracil. Second, both carbonyl stretching vibrations shift below the νC5dC6 vibration (predicted at 1579 cm-1) in the dianion. Third, novel coupling patterns between the CdO and C5dC6 stretching modes are predicted to evolve in the anionic species (e.g., the Q6 mode, predicted at 1567 cm-1 in the dianion). Smaller effects are also evident in the amplitudes of already existing vibrational patterns. For example, little contribution of the Kekule-type symmetric ring distortion (q14 mode of the b2u symmetry in benzene) is expected in the uracil vibrations in vacuo and in low dielectric media. In the reaction field calculations with different sizes of solute cages in high dielectric medium, a weak Kekule component is predicted for the Q14 mode at 1198 cm-1 in the cation, but a significant Kekule-type distortion is found in the Q12 mode predicted at 1259 cm-1 in neutral uracil; in the anion, this is the dominant vibrational motion in the Q11 mode predicted at 1158 cm-1. Finally, altogether new vibrational modes emerge that involve the hydroxylate group in the cation. Examples are the coupled νC5dC6 and νC4-O4(H) motions in Q7 predicted at 1648 cm-1 and Q8 predicted at 1609 cm-1 (reminiscent of the Y8b mode in neutral tyrosine) and the outof-plane partial rotation of H4 around the C4-O4 bond in the Q30 mode predicted at 565 cm-1. In summary, we note that both the protonation of uracil to give the cation and, to an even larger extent, deprotonation of uracil to give the anion and, subsequently, dianion, are expected to give rise to significant changes in intensity and, in particular, vibrational frequencies of uracil species. The major expected effects, e.g., the intensity increase of the 785 cm-1 band in the Raman of the cation and the large red shift in the CdO stretching region in negatively charged species, should be readily observable in the vibrational spectra of uracil in polar media and, likely, its C- and N-substituted derivatives as well as bi-

Ilich et al. and tricyclic heterocycles containing pyrimidine dione as a constituent element. As we show in C.4.1, C.4.2, and C.4.3, these predictions for uracil are well supported by experiment. C.3. Effects of Aqueous Medium. Like in the argon matrix, the vibrational energies and transition strengths of uracil in water are perturbed by solute dipole-solvent dipole (or induced dipole) interaction. In addition, the vibrations of uracil in water are affected by selective and spatially asymmetric hydrogenbonding (HB) interactions. Furthermore, in uracil ions, the vibrations are also perturbed by charge-molecule interactions, similar in nature to HB interactions but less spatially selective. Only the first type of perturbations is represented in the reaction field calculations and, as expected, a number of vibrational effects predicted for uracil in a spherical cavity model imbedded in a continuum of dielectric constant 79 are qualitatively similar to the perturbations predicted in a medium of dielectric constant 1.5. These are (i) an overall increase in transition strengths, (ii) a predominant red shift of the in-plane vibrational frequencies, and (iii) a predominant blue shift of the out-of-plane vibrational frequencies, relative to the spectrum of isolated species in vacuo. The expected increase of the transition strengths in high dielectric medium is considerably larger and not as monotonic as in the argon matrix, ranging from 40% to 176%, depending on the solute cavity radius (by comparison, a 5% to 25% increase is expected in low dielectric medium, see section B). The predicted shifts of N1H and N3H stretching vibrations, though larger than those in low dielectric medium, are also predicted to be of opposite sign. The CH stretching vibrations are expected to be blue-shifted, though not nearly as much as predicted by the calculations of formaldehyde vibrations in acetonitrile.50 The largest frequency shiftsstoward lower energiessare expected for the O4-H stretching vibrations in the cation, ∆ν ) 91 cm-1. The predicted CdO stretching shift in neutral uracil and the anions in bulk water ( ) 78.54), ∆ν(average) ) 43 cm-1, compares well with the 14-38 cm-1 red shifts observed50,103 for the CdO stretching vibration in smaller carbonyl compounds in acetonitrile ( ) 35.9) and dimethyl sulfoxide ( ) 46.68), in comparison to vapor phase ( ) 1.0). By constrast, the in-plane bending modes, spanning the intermediate region ∼1050 cm-1 to ∼1550 cm-1 (950 cm-1 to 1350 cm -1 in the dianion) are not expected to exhibit significant frequency shifts in a high dielectric medium; this is probably true for the C5H and C6H vibrations. An increase in transition strengths in high dielectric medium, in comparison to vapor phase, is expected for some vibrations in this region; examples are Q10, predicted at 1301 cm-1 in the anion, and Q15, predicted at 1173 cm-1 in the cation (both are in-plane modes consisting of N3H, C5H, and C6H bending superimposed on Kekule-type symmetric ring distortion). The same is true to a lesser extent for the analogous vibration Q13, predicted at 1228 cm-1 in neutral uracil (an out-of-phase N1H and C6H bending superimposed to a hybrid, b2u(Kekule)-e2g skeletal distortion). This prediction is well supported by experiment: a strong band is observed at 1288 and 1289 cm-1 in the vibrational spectrum of uracil in aqueous medium at high pH while a 1173 cm-1 band is evident in the infrared spectrum of neutral uracil in water (but poorly resolved in the FTIR spectrum of uracil at low pH, vide infra). The out-of-plane modes are predicted to shift toward higher energies but not uniformly. One of the largest shifts toward higher energy, ∆ν ) 69 cm-1 in comparison to vacuum, is predicted for Q30, the out-of-plane vibration of the hydroxyl proton in the uracil cation. By contrast, the modes of predominant out-of-plane N-H bending character, γN3H, assigned to Q28 at 689 cm-1 in the cation, to Q26 at 654 cm-1 in neutral uracil, and to Q24 at 662 cm-1 in

Molecular Vibrations of Solvated Uracil the anion, is expected to shift toward lower energies in comparison to vacuum. Unfortunately, there is no way at present to confirm the latter two predictions experimentally. Hydrogen-bonding interactions between uracil and water are expected to induce additional red shifts of uracil vibrations. The largest HB effect is expected for the O4-H stretching due to the strong proton-donating tendency of this pair; in addition to the 91 cm-1 red shift predicted by ab initio calculations on the basis of solute dipole-solvent dipole interactions we expect a 30-60 cm-1 red shift on the basis of the observed vibrational shifts in small water104 and methanol clusters.105,106 It is our opinion also that the calculated red shift (∆ν ) 16 ( 2 cm-1) underestimates the actual shift for the C4-O4(H) hydroxyl stretching vibrations in the uracil cation in water (predicted at 1568 and 1609 cm-1); the actual red shift is likely to be 2- to 3-times larger due to the strong proton-donating character of the hydroxyl proton. A similar-type perturbation, of smaller magnitude, is expected to originate from the proton-donating (uracil)N-H f O(water) interactions. An additional red shift will be induced in both the N1H and N3H stretching vibrations; more in N1H than in N3H due to the larger predicted acidity of the former (see C.1). On the other hand, only a small additional red shift is expected for the carbonyl stretching vibrations, given the proton-accepting nature of this complex, CdO r H(water). Another effect caused by uracil-water HB interactions, smaller in magnitude than the selected stretching vibrational shifts but more pervasive in the overall vibrational patterns, will be caused by effective changes in the mass of the hydrogen-bonded amino hydrogens and carbonyl oxygens. As we have noticed in the deuterated uracils (data not shown), variations in the mass of the exonuclear atoms can cause considerable mixing of both stretching and bending modes that are pure in unsubstituted uracil. If we consider uracil as a partially conjugated cyclic N-(N-methylene)formamido-trans-acetamide, then similar effects observed in peptides provide guidance for further refinement of the vibrational analysis of uracil species in aqueous media. The hydrogen-bonding effects, causing shifts in vibrational frequencies as well as changes in transition strengths and local dipole directions in the CdO stretching and C-O-H and NH stretching and bending vibrations in oligopeptides in solvent or in the crystal phase, have been particularly well documented by Krimm and co-workers.107,108 We conclude by noting that, while expected to be significant for some vibrational modes, the solvation effects are more difficult to evaluate experimentally than the effects caused by changes in the protonation state of uracil. This is due to two major reasons: first, the difference in the band-broadening mechanisms precludes direct comparison of the band centroids in the vapor and dense phases, and second, the differential solvation effects for the several uracil species are within the experimental uncertainty since little additional solvent relaxation is expected for uracil ions in comparison to neutral uracil. The latter is due to low charge density and nonspecific interactions with bulk solvent, as has been clearly demonstrated by the IR spectra of small charged water clusters.109 C.4. Vibrational Spectra in Water at pH 0.74-13.0: Experiment and Calculations. The infrared and Raman spectra of uracil have been recorded at four pH values: 0.74, 4.7 (5.1, Raman), 11.4, and 13.0. Given the large span between the first two acid dissociation constants, pK1 ∼ 0.5 and pK2 ) 9.5, respectively,92 a sample of pure neutral uracil, at pH 4.7 (5.1), and of reasonably pure anion, at pH 11.4 with molar composition 0.97(anion):0.02(dianion):0.01(neutral), can be easily prepared. Due to the sensitivity of the cells and windows

J. Phys. Chem. B, Vol. 101, No. 50, 1997 10933 used in infrared spectroscopy to extreme pH we could record only the spectrum of the cation in a mixture with neutral uracil at pH 0.74, with a nominal molar fraction 0.64(neutral):0.36(cation), and the spectrum of the dianion in a mixture with the anion at pH 13.0, with a molar composition 0.56(anion):0.44(dianion). The molar fractions of the anionic species were calculated by assuming a value for pK3 of 13.1 (the literature value is “>13”92). To these experimental infrared and Raman spectra (Figure 6) we compare the composite spectra obtained as weighted sums of the vibrational transition lines for each of the four uracil species (3) as calculated by the B62W method and enveloped in Gaussian curves. The assignments of the experimental spectroscopic features (bands, clusters of bands, and shoulders), obtained by reference to the calculated frequencies of pure uracil species, are given in Table 5. It is evident that the simulated infrared spectra differ from experiment in a number of features. Most conspicuous is the poor matching between the predicted and observed CdO stretching vibrational bands in the 1600-1750 cm-1 region in both the infrared and Raman spectra. This is not unexpected, in view of a number of unfavorable conditions associated with the experimental measurements in this part of the spectrum, for example, the high congestion in this spectroscopic region due to a number of combination and Fermi resonance bands,3-6,12,55 strong inhomogeneous broadening of the fundamental CdO stretching bands in aqueous medium, and (most of all) the presence of a solvent fundamental vibration. The effects due to inhomogeneous broadening can be addressed by a solvation model that incorporates the intrinsically inhomogeneous nature of the immediate chromophore environment, either in bulk water or, more plausibly, within a biopolymer. Construction of small uracil-water clusters and evaluation of the electronic energy profile of these complexes, as Smets et al. have partially addressed [110], would constitute the first step in this approach; an actual simulation of this type would consist of a large number of vibrational calculations carried out for uracil “dressed” in clusters of differently arranged water molecules. This approach, used in the simulation of electronic transition spectra in hydrated chromophores [111], is at present not practical within a framework of a relatively high-level ab initio calculation. The above notwithstanding, a large portion of the observed bands can be assigned to a vibrational mode of one of the uracil species present at the nominal pH by matching the observed frequencies andsto a lesser extentsthe strengths with the calculated vibrational transitions in the four uracil species (Table 5). While a number of bands in the experimental infrared and Raman spectra are not well matched by either frequency or intensity with the features in the simulated spectra, major characteristics of the vibrational spectra of the mixture of uracil species at different pH values appear to be correctly predicted by the calculations. A brief analysis of three characteristic groups of bands, (i) the CdO and CdC stretching region; (ii) the in-plane bending, 1150-1300 cm-1 region; and (iii) the 780-790 cm-1 ring-breathing region, clearly illustrates this point. C.4.1. The CdO, CdC Stretching Region. The CdO and CdC stretching vibrations, assigned to Q9-Q6 in the cation and to Q7-Q5 in neutral uracil, are expected in the 15501780 cm-1 region; in the anion these vibrations are assigned to Q8-Q6 and expected in the 1570-1685 cm-1 region. In the dianion, four fundamental vibrations of this type are expected in the 1425-1580 cm-1 region and assigned to Q6-Q3. When the calculated transition lines in this vibrational region are enveloped in broad Gaussian curves and arranged in order of ascending pH the unmistakable trend is a large shift toward


Ilich et al.

Figure 6. Experimental and simulated infrared and Raman spectra of mixtures of uracil species in aqueous media at given pH values. The infrared spectra were calculated with the B62W method and the Raman spectra with the H62W method; the spherical cavity model was used in both series of calculations.

lower energy as negative charge accumulates on the uracil nucleus. According to our calculations, and as indicated in the correlation scheme (Figure 5), three types of changes are predicted to occur in this spectral region as the pH increases: (i) the overall energies of CdO stretching vibrations (and also most in-plane vibrations) decrease with the accumulation of negative charge (see Figure 4), (ii) the νC2dO (Q6, predicted at 1784 cm-1 for the cation) and Q5 (predicted at 1780 cm-1 for neutral uracil) swap with νC4dO as the highest carbonyl stretching band in the monoanion (Q4, predicted at 1685 cm-1), and (iii) both carbonyl stretching vibrations shift below the CdC stretching vibration in the dianion (Q3, predicted at 1425 cm-1). No features in this region of the infrared spectrum appear to be sufficiently discernible to be assigned with certainty, although we note that the shift of the apparent maximum of the broad peak at 1711 cm-1 at pH < 7 by 70-90 cm-1 to lower energy, as the pH increases, and a concomitant increase of the height of the band envelope in the 1350-1510 cm-1 region clearly supports the predicted spectral changes (Figure 7a). C.4.2. The In-Plane Bending, 1100-1300 cm-1 Region. The second most intense Raman band (after the ring-breathing vibration at 784 cm-1) in the mixture of uracil cation and neutral

uracil at pH 0.74 is the band observed at 1232 cm-1; it gradually loses strength and evolves into a single, higher energy band at 1292 cm-1 and the indistinct tandem peak observed at 1209 and 1188 cm-1 at pH 13.0 (Figure 6). According to H62W calculations, the vibration in neutral uracil corresponds to a symmetric, in-plane, Kekule-type ring deformation Q12, at 1259 cm-1 (1240 cm-1 by the B62W calculations); it is apparently of the same symmetry parentage as the Q14 vibration in the cation, expected at 1198 cm-1 (1230 cm-1 by the B62W calculations). We assign these two transitions to the Raman band observed at 1232 cm-1 at pH < 9. When neutral uracil loses the proton at N1, the Q12 vibration is expected to shift to lower energy by 103 cm-1 and is assigned to the Q11 mode in the anion, a strong vibration of the Kekule-type symmetry, expected at 1156 cm-1 (Figure 5). Further deprotonation results in this vibration acquiring more energy to give the Q9 mode in the dianion, expected at 1185 cm-1 (1200 cm-1 by B62W calculations). We assign these two transitions, Q11 in the anion and Q9 in the dianion, to the tandem observed at 1185 (1188) cm-1 and 1208 (1209) cm-1 at pH > 10. On the other hand, the occurrence of the higher frequency band at 1292 cm-1 in the vibrational spectrum of the uracil anion is apparently not



TABLE 5: Assignments of the Observed Bands in the Infrared and Raman Spectra of Uracil Species at Given pH Valuesa pH 0.75 ( 0.1

pH 4.9 ( 0.2

assigned

observed

419 (Ra)

414 Q31 (+) 407 Q28 (n)

421 (Ra)

407 Q28

535 (Ra)

523 Q22 (+) 516 Q20 (n)

535 (Ra)

516 Q20

552 (Ra)

542 Q21 (+) 550 Q19 (n)

555 (Ra)

550 Q19

557 (Ra)

575 (Ra)

576 Q20 (+) 564 Q18 (n)

576 (Ra)

564 Q18

784 (Ra)

785 Q19 (+) 768 Q17 (n)

784 (Ra)

768 Q17

999 (Ra)

1092 (Ra)

1225 (IR) 1232 (Ra) 1262 (IR)

985 Q18 (+) 1033 Q17 (+) 985 Q16 (n) 994 Q15 (n)

1087 Q14 (n)

1198 Q14 (+) 1240 Q12 (n)

1002 (Ra)

assigned

pH 11.4 ( 0.1

observed

assigned

426 (Ra)

413 Q19 (-) 413 Q17 ())

pH 13.2 ( 0.2 observed

assigned

430 (Ra)

453 Q22 ())

567 Q17 (-) 550 Q19 (n) 540 Q16 ())

556 (Ra)

567 Q17 (-) 540 Q16 ())

586 (Ra)

580 Q16 (-) 564 Q18 (n) 580 Q15 ())

586 (Ra)

580 Q16 (-) 580 Q15 ())

788 (Ra) 798 (Ra)

764 Q15 (-) 768 Q17 (n) 779 Q13 ())

788 (Ra) 798 (Ra)

764 Q15 (-) 779 Q13 ())

982 (Ra)

970 Q14 (-)

981 (Ra)

970 Q14 (-) 952 Q12 ())

1031 (Ra)

1013 Q20 (-)

1032 (Ra)

1021 Q11 ()) 1007 Q18 ())

1098 (Ra)

1100 Q12 (-)

1100 (Ra)

1100 Q12 (-) 1096 Q10 ())

1185 (Ra) 1208 (Ra)

1200 Q11 (-)

1188 (Ra) 1209 (Ra)

1166 Q9 ())

1291 Q10 (-)

1292 (Ra)

1293 Q8 ()) 1291 Q10 (-)

1345 (IR)

1346 Q7 ()) 1343 ( 15 Q9 (-)

994 Q15 985 Q16

1083 (IR) 1089 (Ra)

1092 ( 5 Q14

1173 (IR)

1201 Q13

1225 (IR) 1226 (Ra) 1261 (IR)

observed

1240 Q12

1211 (IR) 1287 (Ra) 1288 (IR)

1276 (IR)

1383 (Ra)

1390 Q12 (+) 1405 Q11 (n)

1383 (Ra)

1395 ( 10 Q11

1415 (Ra) 1416 (IR) 1460 (IR)

1415 ( 5 Q11 (+) 1428 ( 7 Q10 (n) 1456 Q10 (+)

1412 (Ra) 1416 (IR)

1428 ( 7 Q10

1360 (Ra) 1364 (IR)

1361 Q9 (-)

1363 (Ra) 1365 (IR) 1379 (Ra)

1349 Q7 ()) 1361 Q9 (-) 1379 Q6 ())

1394 (IR)

1388 Q8 (-)

1395 (IR)

1388 Q8 (-)

1473 (Ra) 1480 (IR)

1468 ( 4 Q5 ())

1471 (Ra) 1476 (IR) 1503 (Ra)

1502 ( 6 Q10 (+) 1513 ( 6 Q8 (n)

1618 (IR)

1609 Q8 (+)

1500 (Ra)

1519 Q8

1507 (IR)

1501 Q6 (-) 1513 ( 6 Q8 (n)

1507 (IR)

1501 Q6 (-)

1555 (Ra)

1567 Q3 ())

1557 (Ra)

1567 Q3 ())

1643 Q5 (-)

1643 (IR)

1643 Q5 (-)

1621 (IR) 1617 (IR) 1643 (IR) 1676 (Ra) 1678 (IR) 1704 (IR) 1711 (Ra)

1649 ( 2 Q7 (+) 1663 ( 4 Q7 (n) 1719 ( 3 Q6 (n)

1676 (Ra) 1677 (IR) 1706 (Ra) 1712 (IR)

1663 ( 4 Q7 1719 ( 3 Q6

a The assignments are based on the 33 harmonic modes of the uracil cation (+), 30 modes of neutral uracil (n), 27 modes of the anion (-), and 24 modes of the dianion ()). The modes that are not labeled refer to neutral uracil (n).

caused by a large blue shift of the Q12 vibration in neutral uracil, as hypothesized by Nishimura et al.28 Instead, it is more likely that by deprotonation of neutral uracil to the monoanion the in-plane Q11 vibration (characterized by in-phase bending of the H1, H3, H5, and H6 atoms superimposed to a ring distortion of the benzene e2g symmetry parentage and expected at 14271385 cm-1 by the B62W calculations) shifts to a lower energy

vibration Q10 in the anion, expected at 1289 cm-1. The large drop in vibrational frequency, ∆ν ) 1427 cm-1(Q11, neutral uracil) - 1289 cm-1(Q10, the anion) ) 138 cm-1, is due mostly to the loss of the βN1H1 component and partial evolution of the vibration to a high-amplitude, low-energy skeletal deformation in the anion (the difference is only half as large according to the B62W calculations, ∆ν ) 1385 - 1314 ) 71 cm-1). We


Ilich et al.

Figure 7. (a) The expected frequency and intensity changes of the CdO and CdC stretching region in the infrared spectra of uracil in aqueous medium, induced by pH increase from 0.74 to 13.0; the transition lines calculated using the B62W method are enveloped into 65 cm-1 fwhm Gaussian curves. (b) The expected changes in the midrange, in-plane bending vibrations in the Raman spectra of uracil in the 0.74-13.0 pH region; the transition lines calculated using the H62W method are enveloped into 15 cm-1 fwhm Gaussian curves. (c) Simulated evolution of the ringbreathing vibration in the uracil Raman spectra; all parameters are the same as in (b).

assign this vibration to the Raman band observed at 1289 (1292) cm-1 at pH > 10. The Raman intensity of the Q10 transition in the anion, as predicted by the Hartree-Fock calculations (H62W), is apparently too low; the fact that any feature at all is seen at this position in the simulated spectrum at high pH is most likely due to the emergence of an unrelated band in the dianion (Q8), predicted at 1298 cm-1 (Figure 7b). C.4.3. The Ring-Breathing Vibrations. The strongest band in the experimental scattering Raman spectra of uracil species in the pH 0.7-13.0 region is expected at 782 ( 2 cm-1 in uracil4-ol cation and neutral uracil, in very good agreement with the observed peak at 784 cm-1. At pH > 10 the band apparently broadens and acquires a higher energy component, and at pH 13.0 it appears to be split into two bands, at 788 and 798 cm-1, that cannot be resolved under the experimental conditions. Our calculations suggest a simple explanation for this behavior: the ring-breathing vibration, assigned to the Q19 mode and predicted at 784 cm-1 in the cation, assigned to the Q17 mode and predicted at 780 cm-1 in neutral uracil, and assigned to the Q13 mode and predicted at 780 cm-1 in the dianion, shifts by 1214 cm-1 toward higher energy in N1-anion (blue shifts of 4-7 cm-1 are also predicted for the three lowest in-plane, ring deformation vibrations, with the loss of protons in the uracil ring). In the pH 9-13 region neutral uracil, the anion, and the dianion are all presentsalbeit in different proportionssand since the band splitting between Q15 in the anion and Q17 in neutral uracil, on one hand, and between Q15 in the anion and Q13 in the dianion, on the other hand, is smaller than the experimental bandwidth (∼15 cm-1) the observed band appears to be broadened although no additional broadening is expected to occur (Figure 7c). Conclusions We have analyzed and assigned infrared and scattering Raman spectra of uracil in aqueous media at pH 0.74-13.0 with the help of ab initio reaction field vibrational calculations of uracil and its most stable (de)protonation derivatives: uracil-4-ol cation, uracil N1-anion, and uracil N1,3-dianion. We have first evaluated the theoretical method by comparing the vibrational frequencies and infrared transition strengths calculated using the HF and hybrid, HF/DF methods, two Gaussian basis sets, and two reaction field models as implemented in the GAUSSIAN-94 set of programs54 with six sets of uracil infrared spectra

in an argon matrix.3-6,12,55 On the basis of this analysis we draw the following conclusions: (i) The uniformly scaled vibrational frequencies calculated by the ab initio Gaussian HF/DF B3LYP methods37,40-42 at the 6-31+G* level of theory44 in a reaction field of low dielectric constant ( ) 1.53) agree well with experiment (average frequency dispersion is 2.2 cm-1). The calculated transition strengths show good though not quantitative agreement with averaged experimental band intensities; larger dispersion exists among individual experimental data sets. A lower degree of agreement between theory and experiment is found for the transition strengths and vibrational frequencies calculated within the HF/DF B3LYP formalism at the 4-31G level of theory; however, both the line strengths and vibrational energies are superior to HF calculations at higher levels of theory, e.g., 6-31G*.12-14 (ii) Vibrational calculations using the Kirkwood-Onsager dipole reaction field47-50 are found to approximate several experimentally observed solvent effects, for example, a red shift of stretching vibrations localized to a strong dipolar atomic pair (e.g., CdO), a blue shift of most of the out-of-plane vibrations (e.g., the Q8-Q14 modes at 1050-1600 cm-1 in neutral uracil), and a significant increase of infrared transition strengths of stretching vibrational modes in solution compared to vapor phase. Detailed quantitative comparisons could not be carried out for two reasons: in low dielectric constant medium ( ) 1.53) the magnitude of the predicted effects is within the uncertainty of the method while in simulated aqueous medium ( ) 78.54) band-broadening, solvent interference, and hydrogenbonding effects in experimental spectra are comparable to or larger than the solvent effects predicted solely by dipole reaction field perturbations. Comparison of vibrational frequencies calculated using the spherical cavity and the isodensity polarizable continuum model with vibrational spectra in the argon matrix suggests a somewhat better performance of the latter algorithm for evaluation of effective solute cavity, but the execution times are found to be up to 1 order of magnitude longer. (iii) Several features observed in the infrared and scattering Raman spectra of uracil in aqueous media, for example, the pronounced red shift of the carbonyl stretching region (∼1710 cm-1 f ∼1640 cm-1) at pH > 9, the loss of intensity of the Raman active ring-breathing band at 784 cm-1 at pH > 1, the

Molecular Vibrations of Solvated Uracil apparent splitting of the same band at pH > 9, and the disappearance of the Raman active 1262 cm-1 band at neutral pH and appearance of new bands around 1200 cm-1 and 1290 cm-1 at pH > 9 will be useful in the analysis and identification of protonation states of the uracil nucleus. (iv) Comparison of the calculated uracil vibrational frequencies and strengths in an inert medium with those of neutral uracil and uracil ions in a polar medium indicates that changes in the uracil protonation state induce larger effects than does the presence of a medium with high dielectric constant; within the limitations outlined in (ii) this is supported by experiment. Furthermore, little variation in the solvation frequency shifts and intensity changes are expected to be found among differently charged uracil species, in good agreement with the solvent perturbation observed in small aqueous clusters of metal ions.109 Although a number of simulated and observed vibrational bands do not match in energy and intensity (particularly those calculated with the H62W method), our analysis shows that major gross effects and a large proportion of individual effects observed in the vibrational spectra of uracil in aqueous medium in the pH 0.74-13.0 region are well reproduced by calculations. Acknowledgment. We thank Dr. J. O. Alben (Ohio State University, Columbus, Ohio) for access to FTIR spectrometers, Dr. W. A. Oertling (East Washington University, Cheney, Washington) for useful comments, and a reviewer for constructive criticism. The work was supported by the NIH, through Grant AR 38917 (to C.R.H.), and by Ohio Supercomputer Center, through the Grants PAS874.1, 2 & 3. Supporting Information Available: Table 1B contains the uracil harmonic modes calculated by the ab initio Gaussian SCRF HF/DF B3LYP method at the 6-31+G* level of theory (B62A). The benzene in-plane skeletal modes, represented without hydrogen atoms, are calculated by the ab initio Gaussian HF/DF B3LYP method at the 6-31G* level of theory in vacuo (3 pages). Ordering information is given on any current masthead page. References and Notes (1) Susi, H.; Ard, J. S. Spectrochim. Acta 1970, 27A, 1549. (2) Aamanouche, A.; Ghomi, M.; Coulombeau, C.; Jobic, H.; Grajcar, L.; Baron, M. H.; Baumruk, V.; Turpin, P. Y.; Henriet, C.; Berthier, G. J. Phys. Chem. 1996, 100, 5224. (3) Barnes, A. J.; Stuckey, M. A.; Le Gall, L. Spectrochim. Acta 1984, 4OA, 419. (4) Szczesniak, M.; Nowak, M. J.; Rostkowska, H.; Szczepaniak, K.; Person, W. B.; Shugar, D. J. Am. Chem. Soc. 1983, 105, 5969. (5) Maltese, M.; Passerini, S.; Nunziante-Cesaro, S.; Dobos; Harsanyi, L. J. Mol. Struct. 1984, 116, 49. (6) Graindourze, M.; Smets, J.; Zeergers-Huyskens, Th.; Maes, G. J. Mol. Struct. 1990, 222, 345. (7) Susi, H.; Scherer, J. R. Spectrochim. Acta 1969, 25A, 1243. (8) Harsanyi, L.; Csaczar, P. Acta Chim. Acad. Sci. Hung. 1983, 113, 257. (9) Nishimura, Y.; Tsuboi, M.; Kato, S.; Morokuma, K. J. Am. Chem. Soc. 1981, 103, 1354. (10) Csaczar, P.; Harsanyi, L.; Boggs, J. E. Int. J. Quantum Chem. 1988, 33, 1. (11) Chin, S.; Scott, I.; Szczepaniak, K.; Person, W. B. J. Am. Chem. Soc. 1984, 106, 3415. (12) Les, A.; Adamowicz, L.; Nowak, M. J.; Lapinski, L. Spectrochim. Acta 1992, 48A, 1385. (13) Rostkowska, H.; Nowak, M. J.; Lapinski, L.; Bretner, M.; Kulikowski, T.; Les, A.; Adamowicz, L. Biochim. Biophys. Acta 1993, 1172, 239. (14) Gould, I. R.; Vincent, M. A.; Hiller, I. H. J. Chem. Soc., Perkin Trans. 2 1992, 69. (15) Estrin, A.; Paglieri, L.; Corongiu, G. J. Phys. Chem. 1994, 98, 653. (16) Paglieri, L.; Corongiu, G.; Estrin, D. Int. J. Quantum Chem. 1995, 56, 615. (17) Rauhut, G.; Pulay, P. J. Phys. Chem. 1995, 99, 3093. (18) Hille, R.; Massey, V. J. Biol. Chem. 1986, 261, 1241.

J. Phys. Chem. B, Vol. 101, No. 50, 1997 10937 (19) Hille, R. Chem. ReV. (Washington, D.C.) 1996, 96, 2757. (20) Hille, R.; Sprecher, H. J. Biol. Chem. 1987, 262, 10914. (21) Hille, R.; Massey, V. J. Biol. Chem. 1991, 266, 17401. (22) McWhirter, R. B.; Hille, R. J. Biol. Chem. 1991, 266, 23724. (23) Hille, R. Biochemistry 1991, 30, 8522. (24) Oertling, W. A.; Hille, R. J. Biol. Chem. 1990, 265, 17446. (25) Davis, M. D.; Olson, J. S.; Palmer, G. J. Biol. Chem. 1982, 257, 14730. (26) Angell, C. L. J. Chem. Soc. 1961, 504. (27) Lord, R. C.; Thomas, G. J., Jr. Spectrochim. Acta 1967, 23A, 2591. (28) Nishimura, Y.; Hirakawa, A. Y.; Tsuboi, M. AdV. Infrared & Raman Spectroscopy; Clark, R. J. H., Hester, R. E., Eds.; Wiley: New York, 1978; Vol. 5, Chapter 4. (29) Tsuboi, M.; Nishimura, Y.; Hirakawa, A. Y.; Peticolas, W. In Biological Applications of Raman Spectroscopy; Spiro, T. G., Ed.; Wiley: New York, 1987; Vol. 2, Chapter 3. (30) Bandekar, J.; Zundel, G. Spectrochim. Acta 1983, 39A, 343. (31) Espinoza-Mueller, A. W.; Bravo, A. N. J. Mol. Struct. 1982, 90, 187. (32) Bowman, W. D.; Spiro, T. G. J. Chem. Phys. 1980, 73, 5482. (33) Florian, J.; Hrouda, V. Spectrochim. Acta 1993, 49A, 921. (34) Pople, J. A.; Krishnan, R.; Schlegel, H. B.; Binkley, J. S. Int. J. Quantum Chem. Quantum. Chem. Symp. 1979, 13, 269. (35) Komornicki, A.; McIver, J. W. J. Chem. Phys. 1979, 70, 2014. (36) Boys, S. F. Proc. R. Soc. (London) 1950, A200, 542. (37) Kohn, W.; Becke, A. D.; Parr, R. G. J. Phys. Chem. 1996, 100, 12974 (38) Andzelm, J.; Wimmer, E. J. Chem. Phys. 1992, 96, 1280. (39) Johnson, B. G.; Gill, P. M. W.; Pople, J. A. J. Phys. Chem. 1993, 98, 5612. (40) Becke, A. D. J. Chem. Phys. 1993, 98, 5648. (41) Becke, A. D. Phys. ReV. 1988, A38, 3098. (42) Lee, C.; Yang, W.; Parr, R. G. Phys. ReV. 1988, 37B, 785. (43) Hehre, W. J.; Radom, L.; Scheleyer, P. v. R.; Pople, J. A. Ab initio Molecular Orbital Theory; Wiley: New York, 1985; Chapter 4. (44) Clark, T.; Chandrasekhar, J.; Spitznagel, G. W.; Schleyer, P. v. R. J. Comput. Chem. 1983, 4, 293. (45) Gill, P. M. W.; Johnson, B. G.; Pople, J. A.; Frisch, M. J. Chem. Phys. Lett. 1992, 197, 499. (46) Ditchfield, R.; Hehre, W. J.; Pople, J. A. J. Chem. Phys. 1971, 54, 724. (47) Kirkwood, J. G. J. Chem. Phys. 1934, 2, 351. (48) Onsager, L. J. Am. Chem. Soc. 1936, 58, 1486. (49) Beens, H.; Weller, A. Chem. Phys. Lett. 1969, 3, 666. (50) Wong, M. W.; Wiberg, K. B. J. Chem. Phys. 1991, 95, 8991. (51) Wiberg, K. B.; Rablen, P. R.; Rush, D. J.; Keith, T. A. J. Am. Chem. Soc. 1995, 117, 4261 and references therein. (52) Frisch, M. J.; Frisch, Ae.; Foresman, J. B. Gaussian 94 User’s Reference; Gaussian, Inc.: Pittsburgh, PA, 1994-1995; pp 144-146. (53) CRC Handbook of Chemistry and Physics; Weast, R. C., Ed.; CRC Press: Boca Raton, FL, 1990; p E-44. (54) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; HeadGordon, M.; Gonzalez, C.; Pople, J. A. Gaussian 94, ReVision C.3; Gaussian, Inc.: Pittsburgh, PA. (55) Ivanov, A. Yu.; Plokhotnichenko, A. M.; Radchenko, E. D.; Sheina, G. G.; Blagoi, Yu. P. J. Mol. Struct. 1995, 372, 91. (56) Beetz, C. P., Jr.; Ascarelli, G. Spectrochim. Acta 1980, 36A, 299. (57) Shimanouchi, T.; Harada, I. J. Chem. Phys. 1964, 41, 2651. (58) Clark, J. M.; Coleman, R. V. J. Chem. Phys. 1980, 73, 2156. (59) Bludsky, O.; Bak, K.; Joergensen, P.; Spirko, V. J. Chem. Phys. 1995, 103, 10110. (60) Duncan, J. L. In Molecular Spectroscopy. A Specialis Report; The Chemical Society: London, U.K., 1975; Vol. 3, pp 104-162. (61) Pulay, P.; Fogarasi, G.; Pongor, G.; Boggs, J. E.; Vargha, A. J. Am. Chem. Soc. 1983, 105, 7037 and references therein. (62) Popyshev, V. I.; Panchenko, Yu. N.; Bock, Ch. W.; Pongor, G. J. Chem. Phys. 1991, 94, 1247. (63) Dasgupta, S.; Goddard, W. A., III J. Chem. Phys. 1984, 90, 7207. (64) Zerbi, G. In Vibrational Spectroscopy - Modern Trends; Barnes, A. J., Orville-Thomas, W. J., Eds.; Elsevier: Amsterdam, The Netherlands, 1977; Chapter 17. (65) Redington, R. L. J. Mol. Spectry. 1977, 65, 171. (66) Crawford, B., Jr. J. Chem. Phys. 1952, 20, 977. (67) Nakagawa, I.; Shimanouchi, T. J. Chem. Soc. Jpn. 1959, 80, 128. (68) Gussoni, M. AdV. Infrared and Raman Spectroscopy; Clark, R. J. H., Hester, R. E., Eds.; Heyden: London, U.K., 1980; Vol. 6, Chapter 2. (69) Chaem, T. C.; Krimm, S. J. Chem. Phys. 1985, 82, 1631. (70) Yamaguchi, Y.; Frisch, M.; Gaw, J.; Schaeffer, H. F., III.; Binkley, J. S. J. Chem. Phys. 1986, 84, 2262.

10938 J. Phys. Chem. B, Vol. 101, No. 50, 1997 (71) Dobbs, K. D.; Dixon, D. A. J. Phys. Chem. 1994, 98, 4498. (72) Ho, Y.-P.; Yang, Yu-C.; Klippenstein, S. J.; Dunbar, R. C. J. Phys. Chem. 1995, 99, 12115. (73) Fulara, J.; Nowak, M. J.; Lapinski, L.; Les, A.; Adamowicz, L. Spectrochim. Acta 1991, 47A, 595. (74) Nowak, J.; Lapinski, L.; Fulara, J.; Les, A.; Adamowicz, L. J. Phys. Chem. 1992, 96, 1562. (75) Harsanyi, L.; Csaczar, P.; Csaczar, A.; Boggs, J. E. Int. J. Quantum Chem. 1986, 29, 799. (76) Kolomiitsova, T. D.; Shchepkin, D. N. AdV. Spectroscopy; Clark, R. J. H., Hester, R. E., Eds.; Wiley: New York, 1993; Vol. 23, pp 89-132. (77) Jodl, H. In Chemistry and Physics of Matrix-Isolated Species; Andrews, L., Moskovits, M., Eds.; North-Holland: Amsterdam, The Netherlands, 1989; Chapter 12. (78) Jiang, G. J.; Person, W. B.; Brown, K. G. J. Chem. Phys. 1975, 62, 1201. (79) Sennikov, P. G.; Raldugin, D. A.; Nabiev, Sh. Sh.; Revin, V. A.; Khodziev, B. S. Spectrochim. Acta 1996, A52, 453. (80) Viant, M. R.; Fellers, R. S.; McLaughlin, R. P.; Saykally, R. J. J. Chem. Phys. 1995, 103, 9502. (81) Nowak, M. J.; Szczepaniak, K.; Barski, A.; Shugar, D. Z. Naturforsch. 1978, 33C, 876. (82) Bardi, G.; Bencivenni, L.; Ferro, D.; Martini, B.; Nunziante-Cesaro, S.; Teghil, R. Thermochim. Acta 1980, 40, 275 and ref 1 therein. (83) Barnes, A. J.; Le Gall, L.; Madec, C.; Lauransan, J. J. Mol. Struct. 1977, 38, 109. (84) Woldbaek, T.; Klaboe, P.; Nielsen, C. J. J. Mol. Struct. 1975, 27, 283. (85) Le Gall, L.; Lauransan, J.; Saumugne, P. Can. J. Spectrosc. 1975, 20, 136. (86) Giorgini, M. G.; Fortunate, B.; Mirone, P. Atti. Soc. Nat. Mater. Modena 1975, 106, 89. (87) Goodman, M. A.; Sweany, R. L.; Flury, R. L., Jr. J. Phys. Chem. 1983, 87, 7. (88) Murchison, C. B.; Overend, J. Spectrochim. Acta 1971, 27A, 1509. (89) Pimentel, G. S.; Charles, S. W. Pure Appl. Chem. 1963, 7, 111 and references therein. (90) Reva, I. D.; Plokhotnichenko, A. M.; Radchenko, F. D.; Sheina, G. G.; Blagoi, Yu. P. Spectrochim. Acta 1994, 50A, 1107. (91) Downs, A. J.; Hawkins, M. AdV. Raman Infrared Spectroscopy; Clark, R. J. H., Hester, R. E., Eds.; Wiley: New York, 1983; Vol. 10, pp 1-109.

Ilich et al. (92) Dawson, R. M. C.; Elliott, D. C.; Elliott, W. H.; Jones, K. M. Data for Biochemical Research; Oxford Sci. Publ.: Clarendon, Oxford, U.K., 1990; p 98. (93) Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902. (94) Stirling, A. J. Chem. Phys. 1996, 104, 1254. (95) Pople, J. A.; Schlegel, H. B.; Krishnan, R.; Defrees, D. J.; Binkley, J. S.; Frisch, M. J.; Whiteside, R. A.; Hour, R. F.; Hehre, W. J. Int. J. Quantum Chem., Quantum. Chem. Symp. 1981, 15, 269. (96) Pople, J. A.; Scott, A. P.; Wong, M. W.; Radom, L. Isr. J. Chem. 1993, 33, 345. (97) Harhay, G. P.; Hudson, B. S. J. Phys. Chem. 1991, 95, 3511. (98) Harada, I.; Takeuchi, H. AdV. Infrared & Raman Spectroscopy; Clark, R. J. H., Hester, R. E., Eds.; Wiley: Chichester, U.K., 1996; Vol. 13, Chapter 3. (99) Rodgers, K. R.; Su, C.; Subramaniam, S.; Spiro, T. G. J. Am. Chem. Soc. 1992, 114 (4), 3697. (100) Hildebrandt, P.; Copeland, R. A.; Spiro, T. G.; Otlewski, J.; Laskowski, M.; Prendergast, F. G. Biochemistry 1988, 27, 5426. (101) Rava, R. P.; Spiro, T. G. J. Phys. Chem. 1985, 89, 1856. (102) Kim, M.; Matthies, R.; Hoft, W. D.; Hellingwater, K. J. Biochemistry 1995, 34, 12669. (103) Koiling, O. W. J. Phys. Chem. 1992, 96, 6217. (104) Yeh, L. I.; Okumura, M.; Myers, J. D.; Lee, Y. T. J. Chem. Phys. 1989, 91, 7319. (105) Huisken, F.; Kulcke, A.; Lausch, C.; Lisy, J. M. J. Chem. Phys. 1991, 95, 3924. (106) Schrems, O. J. Mol. Struct. 1986, 141, 451. (107) Qian, W.; Krimm, S. Biopolymers 1994, 34, 1377 and references therein. (108) Krimm, S.; Bandekar, J. AdV. Prot. Chem.; Anfinsen, C. B., Edsall, J. T., Richards, F. M., Eds.; Academic: Orlando, FL, 1986; Vol. 38, pp 183-364. (109) Weinheimer, C. J.; Lisy, J. M. J. Phys. Chem. 1996, 100, 15305. (110) Smets, J.; McCarty, W. J.; Adamowicz, L. J. Phys. Chem. 1996, 100, 14655. (111) Ilich, P.; Haydock, C.; Prendergast, F. G. Chem. Phys. Lett. 1989, 158, 129.

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