J . Am. Chem. SOC.1990, 112, 5324-5340
5324
Ab Initio Study of the Vibrational Spectra of N9-H and N7-H Adenine and 9-Methyladenine Joanna Wi6rkiewicz-Kuczerat and Martin Karplus* Contribution from the Department of Chemistry, Harvard University, I 2 Oxford Street, Cambridge, Massachusetts 02138. Received June 28, 1989
Abstract: The structures and vibrational spectra of adenine in two tautomeric forms (N9-H and N7-H) and 9-methyladenine have been calculated at the Hartree-Fock level with a 4-21G basis set and are in good agreement with experimental structural data. The ab initio normal modes have been used to interpret experimental vibrational data for adenine and 9-methyladenine isolated in an argon matrix, in the crystalline solid and in solution. Experimental band assignments of the spectra in the low-temperature matrix and in the polycrystalline state have been analyzed and several reassignments have been proposed. Overall the agreement between the experimental argon matrix and calculated results is very good; for the scaled ab initio frequencies the deviation from experiment is 3% for the entire frequency range. The 4-21G geometries and force constants for adenine and 9-methyladenine have been used to calculate the vibrational spectra of N-deuterated derivatives of the studied systems. These results have proved to be helpful in analyzing experimental band assignments in spectra of deuterated adenine derivatives and in verifying the assignments for the undeuterated molecules.
1. Introduction
presence of the rare N7-H tautomer. The compound 9methyladenine is a model for adenine in adenosine and its derivatives. As a test of the accuracy of 4-21G assignments, the vibrational spectra of deuterated derivatives of adenine and 9-methyladenine have been calculated by using the optimized geometries and force constants of the undeuterated parent molecule. These results prove to be useful in the assignments of matrix or vapor-phase experiments on isotopic derivatives of adenine. They are also used in
The biological importance of the nucleic acid bases is widely recognized. Numerous experimental and theoretical studies of the structure and vibrations of these molecules have been made.'-2' However, for adenine in particular, a full understanding of the internal motions is not yet available. Adenine and its derivatives are particularly interesting nucleic acid compounds because of their multiple roles, including that of nucleic acid building blocks, reaction catalysts, and energy-storing molecules.22 Vibrational data for adenine and its derivatives include IR ( I ) Ferenczy, G.; Harsinyi, L.; Rowndai, B.; Hargittai, I. J . Mol. Srrucr. low-temperature argon matrix spectra of adenine and 91986, 140, 71. meth~ladenine,~ IR and Raman spectra of polycrystalline ade(2) Fan, K.;,Boggs, J. E. THEOCHEM 1986, 139, 283. (3) Harsanyi, L.; Csiszir, P.; CsiszBr, A.; Boggs, J. E.Inf. J . Quantum nine"*23and 9-methyladenine,12 and Raman spectra of adenine ~ ' ~ 1986, 29, 799. and adenosine 5'-monophosphate (AMP) in s o l u t i ~ n . * ~ * ~ ~Chem. (4) SzczGSniak. M.; Szczepaniak, K.; Kwiatkowski, J. S.; KuBulat, K.; Low-temperature rare gas matrix isolation spectroscopy yields Person, W.B. J . A m . Chem. Soc. 1988, 110,8319. relatively sharp and well-defined bands for monomeric molecules (5) Kuczera, K.; SzczqSniak, M.; Szczepaniak, K. J. Mol. Sfrucr. 1988, 172, 73. with minimal influence of intermolecular interactions. Thus, in (6) Kuczera, K.; SzczqSniak, M.; Szczepaniak, K. J. Mol. Srrucr. 1988, the absence of gas-phase data, low-temperature matrix isolation 172. 89. spectroscopy provides particularly suitable information for com(7) Kuczera, K.; Szcz$Sniak, M.; Szczepaniak, K. J. Mol. Sfrucr. 1988, parison with quantum mechanical and force field results. It may 172, 103. (8) Nishimura, Y.; Tsuboi, M. Chem. Phys. 1985, 98, 71. also serve as a reference for the analysis of molecular spectra in (9) Stepanian, S. G.;Sheina, G.G.; Radchenko, E. D.; Blagoi, Yu. P. J . solution and in crystals and for the study of intermolecular soMol. Sfrucr. 1985, 131, 333. lute-solute and solute-solvent interactions. (IO) Nowak, M. J.; Lapinski, L.; Kwiatkowski, J. S. Chem. Phys. Lerr. Ab initio calculations have proven to be of assistance in the 1989, 157, 14. ( I I ) Majoube, M. J. Raman Specrrosc. 1985, 16, 98. interpretation of vibrational spectra of complex molecules. Such (12) Savoie, R.; Pokier, D.; Prizant, L.; Beauchamp, A. L. J . Raman calculations have been recently reported for u r a ~ i l , ~cytosine:** *~J~ Specfrosc. 1981, 11, 481. and g ~ a n i n e . 'Here ~ we report the results of calculations of the ( I 3) Letellier, R.; Ghomi, M.; Taillandier, E. Eur. Eiophys. J . 1987, 14, vibrational spectra of adenine and its derivatives at the 4-21G level 243. (14) Livramento, J.; Thomas, G. J. J . A m . Chem. SOC.1974, 96, 6529. with the GAUSSIAN 82 program. The 4-21G basis set has been used (IS) Livramento, J.; Thomas, G.J. Eiochemisfry 1975, 14, 5210. previously to calculate the vibrational frequencies of benzene2s,z6 ( I 6) Tsuboi. M.; Takahashi, S.; Harada, I. In Physicochemicol Properties and ~ r a c i land ~ , ~yielded a deviation of the theoretical frequencies of Nucleic Acids; Duchesne, J., Ed.; Academic Press: New York, 1973; Vol. from the experimental values of about 10%. Analyses of ab initio 2, p 91. (17) Kyogoku, Y.; Higushi, S.; Tsuboi, M. Specfrochim. Acra 1967, ,423, calculations have shown that the size of the basis set used and 969. the level of the correlation correction affects the calculated vi(18) LautiE, A.; Novak, A. J . Chim. Phys. 1974, 71, 415. brational frequencies.26 The 4-21G basis set employed in this work (19) Latajka, Z.; Person, W. 8.; Morokuma, K. THEOCHEM 1986, 135, is a compromise between the size of the systems studied and the 253. (20) Szczepaniak, K.; SzczGniak, M. J. Mol. Srrucr. 1987, 156, 29. desired accuracy of the results. There exist a number of semi(21) Sheina, G. G.; Stepanian. S. G.;Radchenko, E. D.; Blagoi, Yu. P. J . empirical calculations for adenine and related compound^,^^-^^ Mol. Srrucf. 1987, 158, 275. although no vibrational studies were performed. (22) Saenger, W. Principles of Nucleic Acid Sfrucrure; Springer-Verlag: Geometry optimization and frequency calculations have been New York, 1984. (23) Majoube, M. J. Mol. Sfrucr. 1986, 143, 427. made for three systems: the N9-H and N7-H tautomers of ad(24) CsiszAr, P.; Harsinyi, L.; Boggs, J. E. Inr. J . Quantum Chem. 1988, enine, and 9-methyladenine (Figure 1). Both N9-H and N,-H 33, 1. tautomeric forms of adenine have been included in the analysis (25) Pulay, P.; Fogarasi, G.;Boggs, J. E. J . Chem. Phys. 1981, 74, 3999. of the spectrum of adenine in the argon matrix9 to test for the (26) Guo, H.; Karplus, M. J . Chem. Phys. 1988, 89, 4235. 'On leave from the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Rakowiecka 36, 02-532 Warsaw, Poland,
0002-78631901 I5 I2-5324$02.50/0
(27) Sygula, A.; Buda, A. J. Mol. Srrucr. 1985, 121, 133. (28) Pullman, B.; Pullman, A. Adu. Hererocycl. Chem. 1971, 13, 77. (29) Boyd, D. B. J. A m . Chem. SOC.1972, 94.64. (30) Jordan, F.; Sostman, H. D. J. A m . Chem. SOC.1972, 94, 7898.
0 1990 American Chemical Society
J . Am. Chem. Soc.. Vol. 112, No. 13, 1990 5325
Vibrational Spectra of Adenine and 9-Methyladenine 14
14
\
\
\,
N9-H Adenine
14\
/15
ilo
i3
N7-H Adenine
/I5
i
lo
Table 1. 4-21G Optimized Structures of N9-H Adenine, N7-H Adenine, and 9-Methyladenine adenine crystal N9-H N7-H 9-methyl- mean coordinate' adenine adenine adenine valueb SDc Bond Lengths, A 1.338 0.012 1.3381 1.3450 1.3386 1.332 0.014 1.3157 1.3251 1.3256 1.342 0.009 1.3389 1.3359 1.3352 1.382 0.010 1.3818 1.3817 1.3881 1.3964 1.409 0.005 1.3978 1.3964 1.349 0.01 1 1.3365 1.3252 1.3364 1.385 0.010 1.3975 1.3901 1.3991 1.2950 1.312 0.007 1.2933 1.3732 1.367 0.016 1.2978 1.3881 1.3900 1.376 0.009 1.3925 1.3660 1.3688 1.337 0.015 1.3414 1.3556 1.3408 1.4596 1.0679 1.0673 1.0678
1.0637
1.0644
1.0645
0.9936 0.9949 0.9957 0.9957
0.9963 0.9929
9-Methyladenine
Figure 1. Atom numbering in N,-H and N7-H tautomers of adenine and 9-methyladenine.
0.9956 0.9957 1.0804 1.0806 1.0806
-
Bond Anales. dea 119.78 119.77 120.3 2 126.59 126.62 126.08 1 13.23 113.27 1 14.84 125.26 125.14 122.92 118.57 117.16 1 17.26 117.93 117.47 1 17.97 109.85 110.13 105.71 104.97 105.25 106.01 1 12.87 113.12 I 12.28 105.68 106.16 106.85 128.60 127.60 129.37 132.60 135.71 132.99 119.31 119.35 1 18.08 122.73 122.72 124.45 125.66 128.18 116.27 116.16 116.31
a more qualitative way to confirm band assignments from other phases and to correct misassignments. The method used is outlined in section 2 below. Section 3 presents the results and discusses their significance. The conclusions are given in section 4. 2. Methods The calculations were carried out a t the Hartree-Fock level with the Pople split-valence shell 4-21G basis set." Geometry optimization was performed with the GAUSSIAN 82 program32 with no constraint on the planarity of the molecules. In previous studies molecules with amino groups have been found to be slightly n~nplanar.~'For the two adenine tautomers considered in this work a planar geometry was found to be the most stable at the 4-21G level. In 9-methyladenine the optimized geometry was also practical1 planar, with negligible deviations from nonplanarity (less than 0.001 for atoms other than the methyl hydrogens). The calculated geometric parameters are listed in Table I, together with average results from a series of crystallographic structures for adenine and its derivative^.^' The second derivative matrices for the Cartesian displacements were obtained by numerical differentiation of the analytical gradient at the equilibrium geometry. The Cartesian matrices were transformed to internal coordinates with the aid of the program M O L V I B , ~which was also used to assign normal modes. The potential energy distribution matrix PED)' was calculated as follows:
x
where L is the transformation matrix between the internal (symmetry) coordinates and normal coordinates; LTand L-l denote the transpose and the inverse of L, respectively. The nonredundant internal coordinates used in this work are given in Tables 11 and 111. The internal coordinates for the imidazole ring have been found from a redundancy a n a l y ~ i s . ] ~For - ~ ~the pyrimidine ring, internal coordinates given by Pulay et aLZ5for benzene are used. The out-of-plane ring deformation about the central C4-C5 bond (Figure I ) is described by coordinate 39 in Table 11. (31) Binkley, J. S.; Pople, J. A.; Hehre, W. J. J . Am. Chem. Soc. 1980, 102, 939. (32) Binkley, J. S.; Frisch, M.J.; DeFrees, D. J. E.; Raghavachari, K.; Whiteside, R. S.; Schlegel, H. B.; Fluder, E. M.;Pople, J. A. GAUSSIAN 82; Carnegie Mellon University: Pittsburgh, PA, 1982. (33) Taylor, R.; Kennard, 0. J. Mol. Struct. 1982. 78, I . (34) Kuczera, K.; Wibrkiewicz-Kuczera, J. MOLVIB-program for molecular vibrational spectroscopy. 1988. (35) Keresztury, G.; Jalsovszky, G.J . Mol. Sfruct. 1971, 10, 304. (36) Wilson, E.B., Jr.; Decius, J. C.; Cross, P. C. Molecular Vibrations; McGraw-Hill: New York, 1950. (37) Kuczera, K. J . Mol. Struct. 1987, 160, 159.
117.07
1 1 7.76
117.15
125.85
121.71
125.80
121.87
125.18
121.33
118.8 129.0 110.8 126.9 116.9 117.6 110.7 103.9 113.8 105.9 127.4 132.3 119.0 123.4
0.8 0.6 0.6 0.8 0.6 0.6 0.5 0.7 0.7 0.5 0.6 0.7 0.8 1.0
128.04 125.95 125.54 127.62 118.93 120.74 120.33
117.55 123.29 119.16
118.94 120.72 120.35 108.83 1 10.06 1 10.06 109.49 109.49 108.91
Dihedral Angles, deg 180.0
60.0 -60.0 OAtom numbering as in Figure 1. bAverage value from 21 crystal structures of adenine and its derivatives from ref 33. 'SD, standard deviation of distribution. 9-methyladenine the atom numbering is slightly different from that in adenine (see Figure I ) . Consequently the adenine Coordinates listed in this table corresponding to 9-methyladenine are given in parentheses. They are C2-H12,Cs-H,,, NI-C~-H~I,N&-Hi,, N7C8-Hl,, and N9-C8-H13.
c;-N;-c ;-H
The evaluation of the vibrational frequencies of adenine and methyladenine at the 4-21G level required 39 and 48 h, respectively, on a
5326 J. Am. Chem. SOC.,Vol. 112, No. 13. 1990 Table 11. Vibrational Coordinates for N9-H and N7-H Adenine no.' definition* 1
Widrkiewicz- Kuczera and Karplus N' 1.o 1 .o 1 .o 1 .o 1 .o 1 .O 1 .o
description
symbol
6 7 8 9 IO II 12 13 14 15 16 17 18 19c 20 21 22 23
2.0-112 2.0-1/2 2.0-112 2.0-'/2 6.0-'/, 2.04/2 6.0-l/,
str NIOHIS str N9H str C2H str C8H str C6Nlostr C5C6str C4C, str N3C4 str C2N, str NIC, str N l C 6 str C,N, str N7C8 Str CsN9 str C4N9str C2H bend CBH bend N9H bend C 6 H I 0bend NH, sciss NH, rock 6-membered ring def I
24
1 2.0-'/,
6-membered ring def I1
25 26
2.0-I 6-membered ring def 40.0-1/2 5-membered ring def
27 288 298
Mf
2 36
4 5
I .o 1 .o 1 .o
I .o
1 .o 1 .o 1 .o 1.o I .O
N10H14
111
5-membered ring def I C2H wag CBH wag N9H wag C6N10 wag 2.0-I/, N H 2 tors 2.0-l/, NH, wag 6.0-1/2 oopl 6-membered rinl def I 2.0-I oopl 6-membered ring def I1 1 2.0-l/, oopl 6-membered ring def 111 40.0-'/2 oopl 5-membered ring def I
Mf
oopl 5-membered ring def I1
2.0'12 oopl butterfly ring def x(r6) in-plane vibrations; 28-39, out-of-plane vibrations. bAtom numbering as in Figure I . ' N is the normalizing factor. dN7-H 3, N,H str, and u(N7H) for N7-H adenine. C(CB-N7-H13)- (C5-N7-HI3), N7H bend, and B(N7H) for N,-H adenine. f M = [ I O 32c2(c2- 1 ) ] - l j 2 ; c = [ 5 (9 - 4(51/2))1/21/8 = cos2 ( 7 r / 5 ) . gThe out-of-plane coordinate is defined according to ref 36. hAngle between N7-HI3 bond and C5-Cs-N7 plane, N,H wag, and +(N,H) for N7adenine.
' 1-27,
CRAY X - M P most of the time was used for numerical evaluation of the second derivatives. The vibrational spectra of N-deuterated adenine and N-deuterated 9-methyladenine were obtained by the Wilson GF method.x The 4-21G optimized geometry and force constant matrix of the parent molecule were used, with the assumption that they are not affected by isotopic substitution.36 Different scaling factors would be needed to correct the systematic overestimation of diagonal force constants obtained from Hartree-Fcck calculations and the more complex pattern of the off-diagonal terms. A range of scaling factors has been used previously for different internal ~ ~ r a c i l , Lpyrrole$I ~ * ~ ~ maleimide$2 coordinates in b e n ~ e n e ?pyridine,391q and imidazole.43 Accumulation of a b initio calculation results and experimental gas-phase and matrix data for different pyrimidine and purine bases should lead to a more systematic adjustment of scaling factors and test the transferability of these factors among related mo(38) Widrkiewicz-Kuczera, J.; Karplus, M.,to be submitted for pubiication. (39) Pongor, G.; Fogarasi, G.;Boggs, J. E. J . Mol. Specfrosc. 1985, 114, 445. (40) Pongor, G.; Fogarasi, G.;Boggs, J. E. J . Am. Chem. Soc. 1985, 107, 6487. (41) Xie. Y.; Fan, K.; Boggs, J. E. Mol. Phys. 1986, 58, 401. (42) Csiszir, P.;Csfisdr, A.; Harsinyi, L.; Boggs, J. E. J . Mol. Strucr. 1986, 136, 323. (43) Fan, K.; Xie, Y . ; Boggs, J. E. THEOCHEM 1986, 136, 339.
+
+
lecular fragments. The calculated frequencies of all normal modes were
all scaled by a factor of 0.91, which brings the calculated and experimental frequencies of the reliably assigned u(NH,) and u(N9H) [or u(N7H)] vibrations in the argon matrix spectrum into close agreement. With the single scaling factor used here, the overall deviation between scaled calculated frequencies and the experimental values from the argon matrix is less than 3%. The root mean square (rms) deviation of the scaled calculated frequencies from the experimental values is less than 2% for in-plane modes, and 5% for out-of-plane modes; only a few bands assigned to out-of-plane deformations are observed experimentally, however. Ab initio 4-21G force constants for N9-H and N,-H adenine and 9-methyladenine will be given elsewhere.3s
3. Results and Discussion
3.1. Equilibrium Geometries, Dipole Moments, and Tautomerization Energy. T h e 4-21G minimized geometry for N,-H and NT-H tautomers of adenine a n d 9-methyladenine are presented in Table I, together with crystallographic d a t a for adenine.33 T h e calculated bond lengths a n d bond angles agree very well with the crystallographic structures of neutral adenine derivatives. T h e 4-21G dipole moments a r e 2.37.7.52, a n d 2.57 D for N9-H adenine, N,-H adenine, a n d 9-methyladenine, respectively. Experimental dipole moments a r e not available for adenine tautomers; t h e calculated values m a y however be compared with t h e
Vibrational Spectra of Adenine and 9-Methyladenine Table 111. Vibrational Coordinates for 9-Methyladenine no.' definitionb same as 1-2 for adenine 1-2 3 4 5 6 7-16
C2-H12 C8-H
I3
J . Am. Chem. Soc., Vol. 112, No. 13, 1990 5327 NC I .o
1 .o
description C2H str C8H str
same as 6 for adenine N9-C11 1 .O N 9 C l Istr same as 7-16 for adenine 17 (NI-C~-HIZ)- (N,-C~-H,I) 2.0-112 C2H bend 18 ( N ~ - C B - H ] ~- )(N7-Cs-Hi9) 2.0-112 C8H bend 19 same as 20 for adenine 20 ( C ~ - N ~ - C I I-) ( C ~ - N ~ - C I I ) 2.0-112 N9CII bend same as 21-27 for adenine 21-27 3.0-1/2 CH, str 28 ( C I I - H I ~+ ) ( C I I - H I ~-)I-(Cii-Hid 6 .O-Il2 CH, str 29 ~ ( C I I - H I-~ ()C I I - H I ~-) ( C I I - H I ~ 30 ( H I ~ - C I I - H I 4~ )( H I ~ - ~ I I - H+I (~H)I ~ - C I I - H I B -) 6 .O-Il2 CH, bend (N9-Cii-Hlc.) - (N9-Cii-Hi7) - (N9-Cii-Hia) 6.0"/2 CH, bend 31 2( H I 7-C I1-H I8) - ( H 16-cI I-H I 7) - ( H I6-c I 1-H I 8) 32 ~ ( N ~ - C I , - H I-&( N ~ - C I I - H I , )- ( N ~ - C I I - H I ~ ) 6.0-1/2 CH, bend 33 (Cii-Hid - ( C I I - H I ~ ) 2.0-1 1 2 CH, str 34 ( H I ~ - C ~ I - H-I ~(H16-Cll-H17) ) 2.0412 CH, bend 35 (N9-Cii-His) - (Ng-Cii-Hi7) 2.0412 CH, bend 36d angle between C2-HI2 bond and NI-N,-C2 plane C2H wag 3Id angle between C8-H13bond and N7-N9-C8 plane CgH wag 38 same as 31 for adenine 3 9d angle between N9-C,, bond and C4-C8-N9 plane N9Cll wag same as 32-39 for adenine 40-47 48 ( C ~ - N ~ - C I I - H I+~ () C B - N ~ - C I I - H I ~+) ( C B - N ~ - C I I - H I ~ ) 3.0-1/2 CH, tors a 1-27, in-plane vibrations; 28-35, stretching and deformation motions of the methyl group; 36-48, out-of-plane vibrations. in Figure I . N is the normalizing factor. dThe out-of-plane coordinate is defined according to ref 36.
experimental dipole moments of purine (2.92 D in ethyl acetate) and hypoxanthine (3.16 D in acetic acid).@ The calculated dipole moment of 9-methyladenine may be compared with the dipole moment of 9-n-butyladenine (3.0 D in CClq).45 The large difference between the dipole moments of the two tautomers arises from the change in the component parallel to the C4-Cs bond. The atomic populations other than at N7, N9, and the tautomeric hydrogen are essentially the same; in the N9-H tautomer, they are N7 (-0.66), N9 (-0.57), HI3 (0.39) and in the N7-H tautomer, N7 (-l.O), N9 (-0.64), HI3 (0.37). There is a resulting shift in the center of charge along the C4-C5bond direction corresponding to a change in the contributions from the three atoms to the dipole moment. The N9-H tautomer was found to be favored by AEo = A P C F = 10.6 kcal mol-' over the N7-H tautomer at the 4-21G level after correcting for zero-point vibrations. The energy difference between the two tautomers calculated at the 6-3 1G* for geometries optimized at the 3-21G level is 9.8 kcal mol-l.lo A value of 6 kcal mol-' has been previously calculated by using the MNDO method.27 The energy difference between the N7-H and N9-H tautomers calculated here suggests that the N7-H tautomer is unlikely to be observed in the gas phase or low-temperature matrices by IR spectroscopy. However, in the low-temperature argon m a t r i ~ the , ~ experimental spectrum appears to be a superposition of vibrations of both tautomers (see section 3.2). From a comparison of the calculated dipole moment for the N,-H and N7-H tautomers it is expected that the relative tautomeric populations in various media will depend on the polarity of the solvent; i.e., the population of the N7-H tautomer is expected to increase with the polarity of the medium. Experimental estimates of the population of the N7-H tautomer range from 15% in DMSO at 37 "C from chemical shifts in the carbon N M R spectrum of adenine46 to 22% in water at 20 OC from T-jump relaxation measurement^;^^ these values would correspond to a free energy difference of I . 1 and 0.7 kcal mol-], respectively. 3.2. Vibrational Spectra. 3.2.1. Adenine. The calculated vibrational spectra of N9-H and N7-H tautomers of adenine are
+
(44) Aaron, J.-J.; Gaye, M. D.; Pbrklnyi, C.; Cho, N . S.; von Szentpily, L . L. J . Mol. Struct. 1987, 156, 119. (45) DeVoe, H.; Tinoco, I . , Jr. J . Mol. Bioi. 1962, 4, 500. (46) Chenon, M.-T.; Pugmire, R. J.; Grant, D. M.; Panzica, R. P.; Townsend, L. B. J . Am. Chem. Soc. 1975, 97,4636. (47) Dreyfus, M.; Dobin, G.; Bensaude, 0.; Dubuis, J. E. J . Am. Chem. SOC.1975, 97, 2369.
symbol v(C2H) v(C,H) ~(Cdii) B(C2H) B(C8H) 4(N9C11) u(CH,) A' u(CH,) A' 8(CH3) A' 8(CH,) A' 6(CH,) A' v(CH,) A" b(CH3) A" 6(CHg) A" Y(C~H) Y(CEH) ?w9CIl) t(CHJ bAtom numbering as
presented in Table IV together with the argon matrix spectrum of adenine9 and the Raman spectrum of polycrystalline adenine." I n the 3600-1000-~m-~region, all but u(CH) vibrations in the argon matrix and v(NH2) and u(NH) vibrations in the crystal are observed in the experimental spectra. Below 1000 cm-I most in-plane vibrations are observed in both the low-temperature matrix and crystal spectra. Only three lines corresponding to calculated 6 ( r ) and P(C6Nlo)modes were missing from the experimental spectrum. For only one calculated frequency assigned to 6(r) deformations no appropriate band is observed in the crystal spectrum. For out-of-plane vibrations only 5 of the expected 12 modes for each tautomer are observed in the Ar matrix spectrum; 6 bands in the crystal spectrum have been assigned to out-of-plane modes. 3600-3000-~m-~ Range. In this region bands connected with the stretching vibrations v(NH) and v(CH) appear. The frequencies calculated at 3922 and 3910 cm-' corresponding to stretching vibrations of the NH2 group in the N7-H and N9-H tautomers, respectively, were scaled to 3566 and 3555 cm-'. The scaling factor (see section 2) was chosen to obtain close agreement between the calculated and experimental frequencies of the reliably assigned v(NH2) and v(NH) vibrations. The experimental bands at 3564 and 3556 cm-l in the Ar matrix spectrum are assigned to antisymmetric -NH2 stretching vibrations in the N7-H and N9-H tautomers, respectively. The experimental assignment9 was based on a comparison of the spectrum of adenine in the Ar matrix with spectra of N-deuterated adenine derivatives, with spectra of molecules containing similar molecular fragments (pyrimidine and imidazole), and on empirical force field calculations. The bands at 3447 and 3440 cm-' in the Ar matrix spectrum are assigned to symmetric stretching vibrations of the amino group. The calculated frequency difference between the N9-H and N7-H tautomers is 9-1 1 cm-I, in accord with the 7-8-cm-' band splitting observed experimentally. NH stretching (scaled) frequencies have been calculated at 351 I and 3502 cm-I for the N7-H and N9-H tautomers, respectively. The calculated frequencies are close to the experimental bands at 3497 and 3488 cm-' in the Ar matrix spectrum. The calculated frequency difference of 9 cm-l between the N9-H and N7-H tautomers is in agreement with the 8-cm-' band splitting in the experimental spectrum. The calculated (scaled) lines at 3 153, 3 147, 3 105, and 3 101 cm-' corresponding to C8-H and C2-H stretching modes are not observed in the IR spectrum due to their low intensity. The
Wi6rkiewicz-Kuczera and Karplus
5328 J . Am. Chem. SOC.,Vol. 112. No. 13, 1990 Table IV. Vibrational Frequencies in Adenine (in cm-l) (Contribution in '70) N9-H adenine calc
scaled'
descrptnb
N7-H adenine calc 3922
scaled" 3566
3910
descrptnb
adenine in Ar matrix exP 3564
descrptn u(NH2)as
3556 3861
351 I
3790
3446
385 I
3497 3488 3447 3440
3780 3468 3410 1804
polycrystalline adenine (Raman) descrptn exP
3101
1640
346 1 3415
3147 3105
181 1
I646
u ( C ~ H (99) ) 6(NH2) (91) 1761
1644 1637 1632
3125
U(C8H)
3038
u(CIH)
1675
6(NH2)
1612
u(r)
+ 6(r)
1597
u(r)
+ 6(r)
1510
u(r)
1482 1462
+ /3(N9H) u ( r ) + 0(C2H)
1418
u(r)
+ P(N9H)
1370
v(r)
+ P(N9H) + @(C,H)
1331
u(r)
1307
P(C2H)
+ u(r)
1248
B(C8H)
+ u(r)
1235
6(NH2) + v ( r )
I602
1753 1618 1738 1612 1706
1551
1639
1641
1492
1481
I624
1622
1475
1473 sh 1472
1598
I552
+ P(CH) + BKH)
1421 1418 1526
1388
1519
1494
1358
1343
1468
1335
1333
1328
1442
131 I
I429
1325
1288
I394
121 1
u ( C ~ N (22) ~) r(NH2) (34)
u(r)
1388
1345
1463
1332
u(r) u(r)
1394
1267
1246 sh
P(CH)
1345
1223
1239
u(C-NH2)
1227
B(NH)
+ @(CH)
Vibrational Spectra of Adenine and 9- Methyladenine Table IV (Continued) N9-H adenine calc scaleda descrptn* I309 1 I90 1210
1101
1 I34 1 I32
1031 1029
1084
986
1032 I025 989
938 932 899
965
877
833
J . Am. Chem. Soc., Vol. 112, No. 13, 1990 5329
N7-H adenine
polycrystalline adenine (Raman)
exo
eXD
scaleda 1158
1 I79
1072
1061
P(CH)
1170
1064
1017
u(r)
1 I28 1077
1026 979
1066 1033
968 939
958
6(r)
918
y(CH)
888
y(CH)
849
6(r)
802
6(r)
655
6(r)
986
897
954
868
820
745
165
696
descrotn'
adenine in Ar matrix
calc I274
descrotn
+ 6(r)
758
76 1
692
757
688
680
72 1
655
650 (IR) 718
67 I
descrotn
653
610
640
582
584
53 I
58 I 577
529 525
66 1
60 1
660
600
622
565
580
528
562
51 I
559
508
612
6(r)
592 582
w(NH2) w(NH2)
566
w(NH2)
512
y(NH)
w(NH2)
Wibrkiewicz- Kuczera and Karplus
5330 J . Am. Chem. SOC., Vol. 112, No. 13. 1990 Table IV (Continued) adenine in Ar
calc
N9-H adenine scaleda descrptnb
557
506
354
322
29 I
265
253
230
203
185
N,-H adenine
calc
scaled"
362
3 29
34 1
310
312
284
248
225
I84
167
descrpt nb
x(r2 "The
exp
matrix descrptn
polycrystalline adenine (Raman) exp
descrptn
(10)
scaling factor is 0.91. "Contributions greater than 10% are given.
calculated frequency splitting for v(CH) modes in the N,-H and from N H 2 bending deformations is calculated. Our assignment N9-H tautomers is 4-6 cm-I. The weak bands at 3125 and 3038 of this band to v ( r ) vibrations is supported by the frequencies cm-' in the Raman spectrum may be assigned to Cs-H and C2-H obtained for adenine-d3 and the experimental spectrum of adestretching vibrations of the N9-H adenine tautomer. The calnine-d3 (see section 3.2.4) in this region, in which a band at 1610 culated frequencies for C8-H and C2-H stretching modes in cm-' is found. We do not find that ring bending modes contribute adenine are also in accord with the presence of a band at 3 126 to the 16 12-cm-' Raman band, as suggested by Majoube" on the cm-' in the Ar spectrum of imidazole, and at 3020 cm-' in the basis of empirical force field calculations. The bands at I598 and 1597 cm-' in the Ar and Raman spectra, spectrum of ~ y r i m i d i n e . ~ The 4-2 1G assignments for the 3600-3000-~m-~frequency respectively, may be assigned to v(r) vibrations of the pyrimidine range are in agreement with those from earlier empirical force ring. Here again no contributions from ring bending modes to field calculation^.^^"*^^ The rms deviation of the scaled 4-21G the 1597-cm-' Raman band are obtained at the 4-21G level. The frequencies from the experimental values is 0.2%. band at 1481 cm-' in the Ar spectrum and the band at 1482 cm-' 2000-1630-~m-~Range. The bands at 1644 and 1637 cm-' in in the Raman spectrum are predicted to be associated with v(r) the Ar spectrum are assigned to the scissoring mode of the N H 2 modes of the imidazole ring, with a contribution from the @(C&) group in the N7-H and N9-H tautomers, respectively. The mode;in the case of the N7-H tautomer a small contribution from calculated 6-cm-' frequency difference for the two tautomers is the N7-H bending deformation is also found. The P(N,H) in accord with the experimental band splitting of 7 cm-'. bending mode in the N9-H tautomer is predicted to contribute The band at 1675 cm-I in the Raman spectrum may be assigned to lower frequency vibrations. The assignment of these two bands to the b(NH2) mode in the N9-H tautomer. The large difference to v ( r ) vibrations of the five-membered ring is supported by the between the calculated and observed frequencies may be the result presence of a band at 1480 cm-' in the Ar spectrum of imida~ole.~ of intermolecular interactions in the crystal; N H 2 vibrations have The band at 1472 cm-' in the Ar spectrum and the band at 1462 been shown to be particularly sensitive to the e n v i r ~ n m e n t . ~ . ~ ~ cm-l in the Raman spectrum correspond to C2H bending deforThe 4-2 1G assignments in the 2000-1 630-cm-l frequency range mations, with a contribution from v ( r ) modes of the pyrimidine are in agreement with earlier experimental a s ~ i g n m e n t s . ~ J ' * ' ~ ring and v(C6Nlo)in the amino group. The calculated contri1630-1250-cm-' Range. Ring stretching vibrations [v(r)] of butions to normal modes in the 1420-1 350-cm-' range are different both the pyrimidine and imidazole rings, with contributions from for the N9-H and N7-H tautomers. Our calculations suggest the the stretching mode v(C6Nlo) in the amino group, deformation assignment of the band at 1418 cm-' in the Raman spectrum to modes P(C,H) and P(C2H), and bending modes P(NH) are /3(C2H) and v ( r ) modes of the six-membered ring, and not to predicted in this region. The difference between frequencies v(C6Nlo),as proposed by Majoube;" our assignment is supported calculated for the N9-H and N7-H tautomers in this region is by the presence of a band at 1400 cm-' in the Ar spectrum of 0-29 cm-I; it is interesting to note that the frequency splitting pyrimidine. We propose to assign the band at 1388 cm-I in the calculated for pyrimidine ring stretching modes (8-29 cm-l) is Ar spectrum to P(NH) deformations, and not to ring stretching larger than that calculated for stretching vibrations of the imidmodes.9 The unassigned bands at 1345 and 1343 cm-' in the Ar azole ring (2-7 cm-I). spectrum may correspond to v ( r ) and /3(C2H) deformations, with Our calculations suggest the assignment of the bands at 1618 a contribution from P(N9H) in the N9-H tautomer, for which the cm-l in the A t spectrum and at 1612 cm-I in the Raman spectrum calculated (scaled) frequencies are 1381 and 1358 cm-I. to pyrimidine ring stretching modes. Contrary to the experimental The 4-21G frequencies calculated in this region of the spectrum assignment of the band in the Ar matrix spectrum, no contribution are in agreement with experimental values. Several new assignments or reassignments of the experimental bands both in the argon matrix and in the crystal are proposed. 1250-1050-cm-' Range. The experimental bands in this region (48) SzczSSniak. M . ; Nowak, M . J.; Rostkowska, H.; Szczepaniak. K.; are predicted to correspond to rocking modes of the -NH2 group, Person, W . B.; Shugar, D. J . Am. Chem. SOC.1983, 105, 5969.
Vibrational Spectra of Adenine and 9- Methyladenine ring stretching deformations, and ring bending deformations. Lines calculated at 1223 and 121 1 cm-' corresponding to the r(NH2) and u ( r ) modes in the N7-H and Ng-H tautomers, respectively, suggest the experimental bands at 1239 and 1227 cm-l in the Ar spectrum be assigned to these modes, rather than u(C6N10) and P(NH), as proposed by Sheina et al.9 on the basis of empirical force field calculations. The calculated frequency difference for the r(NH2) mode in the Ng-H and N7-H tautomers is 12 cm-I, in agreement with the band splitting observed experimentally. The bands at 1126 and 1061 cm-l in the Ar spectrum, and at 1 164 and 1 126 cm-' in the Raman spectrum, are predicted to correspond to ring stretching modes, with contributions from ring bending modes for the lower frequency. Reassignments of several bands in this region in the argon matrix spectrum are proposed on the basis of 4-21G calculations. The frequencies calculated here are in good agreement with experimental values. Overall, for frequencies calculated in the 3600-1 050-cm-I spectral region, the rms deviation from values in the Ar matrix spectrum is 1.5%. 1050-150-cm-'Range. In this region vibrations associated with both in-plane and out-of-plane deformation modes are expected in the spectrum. In-Plane Modes. The bands at 1017 cm-I in the Ar spectrum and at 1023 cm-I in the Raman spectrum are associated with stretching deformations of the five-membered ring, with contributions from N-H bending modes. The presence of a band at 1056 cm-' in the Ar spectrum of imidazole supports this assignment, as opposed to the assignment of the band at 1023 cm-' to the r(NH2) mode by Maj0ube.I' Lines due to rocking deformations of the -NH2 group, with contributions from ring stretching modes, are calculated at 986 and 979 cm-l for the N9-H and N7-H tautomers, respectively. These modes may be associated with the band at 940 cm-l in the Raman spectrum. This assignment seems to be in better accord with the IR spectrum of pyrimidine, in which no bands have been observed around 950 cm-l, rather than the assignment to 6(r) modes of the six-membered ring suggested by Majoube." It is not clear whether the band at 958 cm-l in the Ar spectrum should be associated with the rocking mode of the amino group or bending deformations of the five-membered ring. There is no corresponding band in the spectrum of imidazole, which would point to the assignment of the band to r(NH2) vibrations; on the other hand, a band is observed at 969 cm-I in the spectrum of deuterated adenine, which suggests the line corresponds to 6(r) deformations. The band at 898 cm-' in the Raman spectrum is associated with ring bending deformations of the five-membered ring. This assignment is supported by the presence of a band at 900 cm-l in the spectrum of imidazole. Below 900 cm-l one vibration with dominant u(r) character is predicted for each tautomer. The calculated frequencies at 696 and 692 cm-' for the N7-H and N9-H tautomers, respectively, may be associated with the bands at 655 and 722 cm-' in the Ar and Raman spectra, respectively. Three modes with dominant ring bending character are calculated below 900 cm-I. The lines calculated at 877 and 868 cm-I for the N9-H and N7-H tautomers, respectively, corresponding to bending deformations of the pyrimidine ring, may be associated with the band at 849 cm-I in the Ar spectrum. The calculated frequencies for 6(r) deformation vibrations at 610 cm-l (N,-H tautomer) and 600 cm-l (N7-H tautomer) correspond to the bands at 6 12 and 620 cm-l in the Ar and Raman spectra, respectively. The bands at 566 and 558 cm-' in the Ar and Raman spectra, respectively, may be assigned to pyrimidine ring bending deformations for which the calculated frequency is 529 cm-' for the Ng-H tautomer, and 528 cm-' for the N7-H tautomer. The calculated lowest frequency in-plane vibrations correspond to C-N bending deformations of the amino group; the bands at 535 and 330 cm-' in the Raman spectrum may be associated with the b(C6N 10) mode. As was the case for frequencies above 1000 cm-', several new assignments or reassignments have been proposed in this region of the spectrum. The rms deviation of the scaled 4-21G frequencies for in-plane vibrations from experimental values in the
J . Am. Chem. SOC.,Vol. 112, No. 13, 1990 5331 argon matrix spectrum below 1000 cm-l is 5%, somewhat larger than for higher frequencies. Out-of-Plane Modes. Not all predicted out-of-plane vibrational modes are observed in the experimental spectra. Frequencies associated with out-of-plane bending C2-H deformations are predicted to occur at 1031 and 1026 cm-I, and C8-H wagging modes at 938 and 968 cm-' in the Ng-H and N7-H tautomers, respectively. These bands are not observed in the IR spectrum. The band at 888 cm-' in the Ar spectrum may be assigned to out-of-plane deformations of the pyrimidine and imidazole rings for which frequencies at 899 and 897 cm-' for the Ng-H and N7-H tautomers, respectively, have been calculated. The band at 870 cm-l in the Raman spectrum may also be assigned to out-of-plane ring deformations in the Ng-H tautomer. On the basis of empirical force field calculations, Sheina et aL9 assigned the band at 888 cm-l to C-H wagging vibrations, while Majoubell and Letellier et al.I3 suggested the Raman band at 870 cm-' is associated with N-H wagging modes. Vibrations associated with out-of-plane C6-Nlo bending deformations in the amino group and ring deformations are predicted around 750 cm-' (758 cm-' for N9-H adenine and 745 cm-' for N7-H adenine). These bands are not observed in the IR spectrum. The Raman band at 797 cm-l associated by Majoube" with y(C2H) vibrations, and by Letellier et aI.l3 with X(r) modes, is assigned here to y(C6N and X(r) deformations. In the 700-500-~m-~ range out-of-plane ring deformation modes are predicted, as well as out-of-plane deformations of the -NH2 group and out-of-plane N-H bending deformations. Five outof-plane deformation vibrations are predicted for the N9-H tautomer in the 700-500-cm-' range: two ring deformation modes, one N-H wagging mode, and two out-of-plane deformation modes of the -NH2 group. Four out-of-plane deformation modes are predicted for the N7-H tautomer: two ring deformation modes, one N-H wagging mode, and one out-of-plane deformation mode of the -NH2 group. For vibrations arising mainly from ring deformation modes the calculated frequency splitting between corresponding modes in the N9-H and N7-H tautomers is 19-35 cm-'. Out-of-plane deformations of the imidazole ring in the N9-H tautomer are predicted to give rise to a line at 688 cm-I. The band at 680 cm-' in the Raman spectrum may be tentatively assigned to this mode. The corresponding vibration in the N7-H tautomer is predicted to lie at 653 cm-I. A vibration corresponding mainly to out-of-plane deformation modes of the pyrimidine ring is predicted at 601 cm-l for the N7-H tautomer, and at 582 cm-I for the N9-H tautomer. The calculated frequency for the 7(N9H) mode in the N9-H tautomer is 655 cm-' and lies 100 cm-l higher than the corresponding y(N7H) mode in the N7-H tautomer. This mode may be associated with the band at 650 cm-' in the IR spectrum of polycrystalline adenine, assigned to wagging deformations of the amino group." Deformation modes of the -NH2 group in N9-H adenine are predicted to give rise to lines at 531 and 525 cm-l with an equal contribution from torsional and wagging deformations. It is interesting to note that the corresponding wagging and torsion deformations of the amino group in the N7-H tautomer are predicted to have significantly different frequencies: they are calculated at 508 and 3 IO cm-I. The larger frequency difference calculated for the N7-H tautomer may be the result of intramolecular interactions between the amino group in c6 position and the N7-H group. Out-of-plane deformation modes of the amino group, rather than y(CH) as proposed by Sheina et may be associated with the bands at 582, 566, and 512 cm-I in the Ar spectrum. Letellier et aI.l3 associated the bands at 660 and 640 cm-' in the IR spectrum of polycrystalline adenine" with wagging deformations of the amino group, and the band at 650 cm-' with C8H wagging deformations; this assignment is contradicted by the presence of identical bands in the spectrum of N- and C8-deuterated adenine." The three remaining calculated frequencies below 350 cm-' corresponding to out-of-plane ring deformation modes in each tautomer are associated with vibrations of the pyrimidine and imidazole rings, as well as butterfly-type deformation of the whole
Wicirkiewicz- Kuczera and Karplus
5332 J . Am. Chem. Soc., Vol. 112, No. 13, 1990 Table V. Vibrational Freauencies in 9-Methvladenine (in cm-I) (Contributions in '70) 9-methyladenine polycrystalline 9-methyladenine in Ar matrix 9-methyladenine (Raman) calc scaleda descriptd exp descrptn exP descrptn 3557 u(NH2)as 3355 u(NH2) 3910 3443 3438
3780
3301 329 I 3223 1644 1636 1632 1628 1622
8(NH2)as
I749
1615
u(r)
1725
1610 1596
u(r)
1680 1662
151 1 1483
u(r)
+ P(CH)
1654 1621
1476 1467
u(r)
+ @(CH)
I608
1449 1443 1435 1425 1411
1639
b(NH2) (91)
AMP (Raman) descrptn
v(NH2)s
3459 3407
I803
exP
3280
u(NH2)
3146 3104 3091 3031 2986 2956 2917 2808
v(NH2) u ( C ~ H + ) v(C~H) ) u(C2H) u(NH2) + v ( C ~ H + u(CH~) u(CH,) u(CH,)
1680
6(NHZ)
1600 1580 1573
u(r)
+ b(NH2)
u(r)
+ F(r)
+
u(r) t b(NH2)s
+ I(NH2)
1526 1517
1580
u(r)
+ 6(r)
1508
u(r)
+ B(C8H)
1485
u(r)
+ j3(C2H)
1337
u(r)
+ fl(C2H)
1308
@(C2H) u(r)
1489 1470
@(CH) + u(r) B(CH) + u(r)
b(CH3)
1442
b(CH3)as
h(CH3) u(r) + B(CH) u(r) B(CH)
1414
b(r)
1370
u(r)
1373
u(r)
1358 1344 1328 1325
b(CH3) 1349 1343
u(r)
+ B(C,H)
1431
1295
u(CH)
1328 1308
b(r) u(r)
+ @(CH)
1389
1254
P(CH)
1256
b ( r ) + v(r)
1366
1237
u(N-CH~)
1251
r(NH2)
+ u(r) + u(N-CHJ
1314
1234
u(C-NHJ
1218
P(C8H)
+ Y(T)
1555 1499
1450
+
u(r)
+ u(r)
I294
1 I95
1271 1148
1085
u(r)
1047
6(CH,)
1 I33
1044
B(CH)
I I33 1071
944
u(r)
I029 986
894
y(CH)
+ 6(r)
905
+ P(C2H)
+ u(N-CH,)
950 1019
r(NH,)
+
+ 6(CH3)
J . Am. Chem. SOC.,Vol. 112, No. 13, 1990 5333
Vibrational Spectra of Adenine and 9- Methyladenine Table V (Continued)
calc 969
9-methyladenine scaledu descriptnb 881 dN,Cd (11)
9-methyladenine in Ar matrix exp descrptn
polycrystalline 9-methyladenine (Raman) exp descrptn
843
84 1
6(r)
exP 912
AMP (Raman) descrptn b(r) + u(r)
727
6(CH3)+ u(r)
r(CH)
829
754
799
80 1
729
744
770
700
718
75 I
683
644
585
624
568
582
529
562
58 1
529
542
b(r)
580
528
530
6(r)
573
522
360
327
355
335
305
312
297
270
245
229
208
205
227
206
6r
155 130 1 I3 90 64 49 -79
