A new theoretical prediction of the infrared spectra of cytosine tautomers

Specrrochimica Ada. Vol. 48A. Printed in Great Britain

o%w.s539/9255.00+0.00

No. 6. pp. 811418.1992 0

1992 Pergamon

Press Ltd

A new theoretical prediction of the infrared spectra of cytosine tautomers IAN R. GOULD, MARK

A. VINCENTand IAN H. HILLIER*

Department of Chemistry, University of Manchester, Manchester Ml3 9PL, U.K.

and LESZEK LAPINSKI

and MACIJZJJ. NOWAK

Institute of Physics, Polish Academy of Sciences, Al. Lotnik6w 32/46, M-668 Warsaw, Poland (Received 28 October 1991; accepted 20 November

1991)

Abstract-The infrared spectra of the cytosine amino-ox0 and amino-hydroxy tautomers predicted theoretically at the ab initio Hartree-Fock level with a 6-31G** basis set are reported. These are compared with the experimental spectra obtained in an argon low-temperature matrix. The IR spectra computed at this level reproduce the experimental spectra closer than the previous predictions.

possibility of the proper and reliable theoretical simulation of the IR spectra of medium size compounds is of great importance to the identification of the products of chemical (or photochemical) reactions taking part in low temperature matrices [ 11. Up to now, the IR spectra of polyatomic molecules have been usually interpreted by comparison with ab inifio calculations performed at the Hartree-Fock level with split-valence basis sets without any polarization functions. Inaccurate prediction of the out-of-plane modes was a major drawback of these calculations. The results of such calculations were useful in interpretation procedures, but were still not sufficiently precise to be used as references in spectroscopical identification of compounds. Very recently the infrared spectra of 6azauraci1, Sazauracil [2], uracil [3], and two tautomers of 2-pyridinone [4] have been predicted at the HF/6-31G** level. The theoretical spectra, calculated with this basis set, were found to agree with the experimental ones quite well for both in-plane and out-of-plane modes. The good agreement between theoretical HF/6-31G** and experimental spectra raised hope that such calculations could be used for analytical purposes. Cytosine, with its non-planar amino group provides certainly a more demanding challenge for the calculations. Previous ab inifio theoretical prediction of the harmonic vibrational frequencies and infrared intensities of the tautomers of cytosine was performed at the HF/3-21G level by KWIATKOWSKI [5]. We investigate here if a HF/6-31G** theoretical prediction of the IR spectrum of this molecule containing an amino group can reproduce the experimental spectrum with sufficiently good accuracy to perform a reliable assignment.

THE

AMINO-OX0

AMINO-HYOROXY

Scheme 1. * Author to whom correspondence should be addressed. 811

812

IAN R. GOULD

etal.

H H 099 N4.991 II.349

Fig. 1. Calculated structure (HF/6-31G**) of the amino-hydroxy tautomer of cytosine.

The matrix isolation technique is practically a unique experimental method for studying the spectral properties of isolated molecules of cytosine. Because of the low volatility of the compound and its thermal decomposition at higher temperatures, the gas-phase measurements would be very difficult. Cytosine, when isolated in neon, argon and nitrogen low temperature matrices adopts mainly amino-hydroxy and amino-ox0 tautomeric forms and possibly a very few per cent of cytosine molecules exist in the imino-oxo form [5-S]. The spectra of amino-oxo and amino-hydroxy tautomers of matrix isolated cytosine were previously reported by RADCHENKOet al. [6], SZCZESNIAKet al. [5] and NOWAK ef al. [7]. The IR spectra of cytosine must be first separated into the spectra of particular tautomers to be interpreted. A method for the separation of the IR spectra of cytosine tautomers, based on the phototautomeric reaction, was developed in this laboratory. Successful separation of the spectra of the tautomers has been performed

1252 c &~;2&6\H 11531 H

Cl230

Fig. 2. Calculated structure (HF/6-31G**) of the amino-ox0 tautomer of cytosine.

813

Infrared spectra of cytosine Table 1. Internal coordinates used in the normal modes analysis for cytosine tautomers (atom numbering as in Scheme 1)

&=r,., sz=r2.3 .%=r3.4 s4=

r4.5

&=r5.6 &

=

r6, 1

&=r2.7 &=r4.8 h=b.ll %O =

rb. I2

(amino-ox0 form) h. 13 S,i = r,, ,3 (amino-hydroxy form) St2= (2-l”) (r8.9+ r8.10)

SI,

=

&3=Cm”2)

hu-ci.l~)

S14=(6-“~)

(82.6.1-&3.2+84.2.3-85.3.4+/%.4.5-&1.6)

s,5=w”2)

(B,.3.2-B2.4.3+B4.6.s-81.5.6)

&=W”2)

(81.7.2-83.7.2)

SIR=v”2)

(B3.*.4-BS.R.4)

s19=(2-“*)

(84.,1.s-Bb.11.5)

s20=(2-“2)

(/95.12.6-81.12.6)

s21=(2~“2)

(/%.4.8-/%0.4.*)

S2~=(6~“~)

(~BV.ID.X-~~.~.~-B,O.~.R)

SD= (2-l”) (& 13,1-fi2. 13, ,) &3=82.13.7

SX=(~-I’*) %=(112)

(5,.2.3.4-~2.3.4.5+t3.4.5.6-t4.s.6.I+t~.6.1.2-t6.1.2.3)

(-~,.2.3.4+~~2.3.4.5-~3.4.5.6-~4.5.h.1+2~J.b.1.2-~6.,.2.3)

(amino-ox0 form)

S27=Y13.2.1.h

SZ7= (2-l”) (r,3.7.2.I + S2,=(W =

(amino-ox0 form) (amino-hydroxy form)

(5,,2.3.4-t3.4.S.6+r4.S.6.1-56.1.2.3)

s2b=(12-“2)

s29

+283.5.4-86.4.5-81.5.6)

(282.6.1-83.1.2-~4.2.3

sI,=(112)

r13.7.2.3)

(amino-hydroxy

form)

(4.*.4.3+~Y.n.4.s+7.IO.X.4.3+~1l1.X.4.s) Y4.r.

R. I,,

&I=Y7.1.2.3 &I

=

Yx. 3.4.5

S32=~11.4.5.h &3=YIZ.s.h.I

Y NlC2 v C2N3 v N3C4 v c4c.5 v CSC6 v C6Nl vco v CN8 v C5H v C6H Y NlH vOH v NH2 sym v NH2 antisym B Rl B R2 B R3 DC0 B CN8 /?ICSH /3 C6H Rock NH2 Scis NH* j3 NlH BOH t Rl t R2 r R3 y NlH sOH Twist NH2 Inv NH2 YCO y CN8 y CSH y C6H

Key: r,,, is the distance between atoms A, and A,. p,,,.k is the angle between vectors AkA, and At Aj Y,.,.~.,is the angle between the vector AiAiand the plane defined by atoms A,, At, AI. T,,,,~,, is the dihedral angle between the plane defined by A,, A,, Ak and the plane defined by A, Akr A, atoms.

in our previous works [7,9] and in the work of SZCZESNIAK et al. [5]. Because the noble gas environment interacts only very weakly with the matrix isolated molecules, their IR spectra may be treated as a good approximation to the spectra of strictly non-interacting molecules.

COMPUTATIONAL

We have previously reported the results of geometry optimization calculations at the HF/6-31G** level of the amino-hydroxy, amino-oxo and imino-oxo forms of cytosine [lo], followed by the inclusion of zero-point vibrational energy effects, and of correlation calculated at the MP2 level. These calculations predict the amino-hydroxy form to be the most stable, followed by the amino-ox0 form, in agreement with spectral studies [5-81. The calculated bond lengths and bond angles of the amino-hydroxy and amino-ox0 tautomers are summarized in Figs 1 and 2. In both molecules, the ring is effectively planar whilst the amino groups are predicted to be somewhat non-planar. When

814

IAN R. GOULD

etal.

compared with the experimental crystallographic data for the amino-ox0 tautomer [ll], the standard deviation of our calculated structure is 0.02 A for bond lengths and 1.5” for bond angles. The CADPAC [12] code has been used to calculate the analytical energy derivatives. The calculated wavenumbers of all the normal modes were scaled by a single factor of 0.9. In order to express normal mode forms in the molecule fixed coordinate system we define a set of internal coordinates (Table 1). These are the same as previously used by KWIATKOWSKI [5] except for the coordinates describing the amino group, which were chosen in a similar way as in Ref. [13]. The force constant matrices with respect to Cartesian coordinates were transformed to internal coordinates and the potential energy distribution matrices [14,15] were calculated. Potential energy distribution components (PEDs) greater than 10% are given in Tables 2 and 3. VIBRATIONAL ASSIGNMENT

The experimental IR spectra of the monomeric amino-ox0 and amino-hydroxy tautomers of cytosine isolated in an argon matrix are compared with the theoretically Table 2. The experimental wavenumbers (c). integral intensities (I) and assignments to the normal modes (Q) of the bands observed in Ar and N2 matrices compared with theoretically calculated wavenumbers, absolute intensities (A’h) and potential energy distribution (PED) of the absorption bands of the amino-hydroxy tautomer of cytosine

Mode no.

Ql

Experimental Ar matrix (cnLr) (ril.)

3592

Calculated HF/6-31G** A’h (km/mol) (crL’)

168

3746

139

PED W) v

OH (100)

Q2

3564

98

3593

62

Y NH2 antisym (100)

03

3446

154

3468

93

v NH2 sym (99)

Q4

3051

8

v C5H (93)

Q5

3014

25

v C6H (93) v C5C6 (25). v C2N3 (2l), p C6H (12)

Q6

1622

645

1643

674

Q7

1589

64

1616

84

Q8

1575 1570 1561

21 52 62

1605

467

v N3C4 (21) v NlC2 (19) v C4C5 (18). v C6Nl (11)

09

1496 1493

73

1498

61

B C5H (21) scis NH2 (12). v N3C4 (ll), v CN8 (10)

010

1439 1427 1418

276 285 14

1459

536

Qll

1379 1374

67 20

1377

29

Q12

1333 1320

49 72

1318

156

j3 C6H (39). j3 OH (14) v CN8 (14)

1303

12

1292

7

1257 1252 1224 1211 1196

26 7 35 21 124

1231

117

/3 OH (38) v C6Nl (19) /5 C6H (11)

Q13

scis NH2 (78). v CN8 (12)

v CO (25) j3 C6H (15). v NlC2 (14) vC5C6(16),~CN8(14),vC0(13),j3R1 v C6Nl (10)

(12),bCSH(12),

Infrared spectra of cytosine

815

Table 2 (continued)

Mode no.

Experimental Ar matrix Q I (cm-‘) (rel.)

1187

1

29

1100

70

60

1084

37

Q14 Q15

1110 1108

Q16

1083

1019

Q17

17

W)

v NlC2 (22) YC6Nl (20). YN3C4(17). v C2N3(16) B C5H (23) rock NH2 (17),

v C5C6 (15), /3 C6H (10)

Rock NH2 (20), /3 C5H (20), v C5C6 (18). v C6Nl (11) y C6H (IOl), y C5H (10)

980

955

3

973

4

807

69

822

117

790

17

773

9

720

2

y CO (39). y CN8 (36). y CH5 (20)

587

0.4

#J R3 (72), v CO (14) /J R2 (77), v CN8 (10)

980

Q19 Q20 Q21

Q23

0.03

PED

30

Q18

022

Calculated HF/6-31G** (cmY_‘) (knZo*)

781 710

30 8

024

B RI (34), v NlC2 (21), v C2N3 (17) v C4C5 (37), rock NH2 (21), B Rl (ll),

v CO (10)

y CO (57), t Rl (46). y C5H (18) y C5H (52), y CN8 (41) /l Rl (22). v C4C5 (20), v CN8 (12), v CO (11)

Q25

557

21

546

5

Q26

520

221

528

132

Q27

507

67

501

10

Twist NH2 (37), j3 CO (28), B CN8 (15)

028

498

42

491

3

Twist NH2 (34), fi CO (32), B CN8 (11)

029

443

13

443

15

t R3 (43), Twist NH2 (34). r Rl (19)

Q30

343

11

/3 CN8 (55), /¶ CO (20)

r OH (91)

337

11

031

224

179

Inv NH2 (53), r R3 (15), T Rl (14)

032

214

151

InvNH,(39),yCO(21),rR3(14),rR2(13),tR1(10)

033

194

4

t R2 (97), r R3 (25)

rel.: relative. Internal coordinates are defined in Table 1. Calculated wavenumbers scaled by a factor of 0.9.

calculated frequencies (scaled by the factor 0.9) and infrared intensities in Tables 2 and 3. The bands observed in the high frequency region (3700-3400 cm-‘) originate from the stretching vibrations of OH, NH2 and NH groups. The present assignment of the bands observed in this region of the experimental spectrum is the same as those previously published [5,7], which were based on a HF/3-21G calculation. The present HF/6-31G** calculation predicts the proper sequence of v OH and v NH2 antisymmetric bands in the amino-hydroxy form, while the HF/3-21G calculation predicts the reversed sequence. To come to the proper assignment, given in the paper of SZCZESNIAK er al. [5], experimental arguments have been used. The frequencies of the bands in this region calculated at the HF/6-31G** level are systematically higher than their counterparts calculated with the 3-21G basis set and, while scaled by the factor of 0.9, they are still overestimated in comparison with experimental values. In the frequency region 1700-700 cm-’ most bands are due to the stretching vibrations of the ring mixed with CH bending. Those bands are usually quite well predicted theoretically and their assignment seems reliable. The results of present calculations (frequencies, intensities and PEDs) are not much different for these bands from those obtained previously at the HF/3-21G level [5]. For the amino-ox0 form this concerns the modes Q7, Q9, QlO, Q12, Q13, Q15 and Q22 (from Table 3) corresponding to the modes 7,9, 10, 12, 14, 15 and 23 from Ref. [5]. For the amino-hydroxy form the modes are Q6, Q8, QlO, Q14, Q22 (Table 2) and their counterparts-modes 7, 8, 10, 14,22 in

816

IAN R. GOULD

etal.

Ref. [5]. The assignment of the band of the carbonyl group stretching (mode Q6), which is the most intense band in the spectrum of the amino-oxo form, was obvious. The somewhat problematic assignment of the bands due to the scissoring NH* vibrations in both tautomers, given in the previous works [5,7], is supported by the present calculation. Contrary to the HF/3-21G prediction, the present calculation gives proper sequence of the strong ring stretching band (Q6) and the weaker NH1 scissoring band (Q7) in the hydroxy form. The normal modes with considerable contributions of the #I OH vibration (Q12, Q13-hydroxy form) are quite well predicted in the present as well as in the previous calculation (modes 12 and 13 in Ref. [S]). The splitting of those bands observed in the experimental spectrum is typical for /I OH modes in heterocyclic compounds [4,16,17]. In the lower frequency range the bands due to both “in-plane” and “out-of-plane” vibrations are present. The “in-plane” vibrations in this region originate from ring bending vibrations and the bending vibrations of CO and CN8 groups. These bands are well predicted, as is usual for calculations performed at this level, except for the modes Q27, Q28 in the hydroxy form and Q26, Q27 in the 0x0 form, in which the “in-plane” vibrations are coupled with the twisting vibration of the amino group. The coupling of the twisting vibrations of amino-groups with the “in-plane” vibrations is rather unexpected. This certainly could not be predicted by the HF/3-21G calculation in which the Table 3. The experimental wavenumbers (V). integral intensities (I) and assignments to the normal modes (Q) of the bands observed in Ar and N, matrices compared with theortically calculated wavenumbers, absolute intensities (Alh) and potential energy distribution (PED) of the absorption bands of amino-ox0 tautomer of cytosine

Mode no.

Experimental Ar matrix li I (cm-‘) (rel.)

Calculated HF16-31G** lj Alh (cm-‘) (kmlmol)

PED W)

Ql

3564

122

3602

70

02

3472

123

3504

107

Y NlH (100)

Q3

3441

192

3472

112

Y NH2 sym (99)

3066

4

Y C5H (82) v C6H (17)

3043

4

v C6H (82) v C5H (18)

1784

873

v co (77)

1670

675

Y C5C6 (39). v N3C4 (18). p C6H (11) Scis NH2 (82)

Q4 QS

06

07 08

1784 1779 1754 1749 1733 1719

25 25 78 133 111 782

1673 1666 1656 1648

149 124 384 59

1598 1551

312 54

1611

176

Y NH2 antisym (99)

Q9

1539

113

1558

303

v N3C4 (27), v C4C5 (14), j3 NlH (13). v C5C6 (10)

010

1475

242

1473

127

jz?C5H(18).~C6H(17),v’N3C4(15),~CN8(15),~C6N1(

011

1423

30

1420

163

/!INlH (41). v C4C5 (12)

Q12

1337

66

1331

83

p C6H (20). v CN8 (20), j5 C5H (18), v C5C6 (13)

Q13

1244

28

1252

23

v C2N3 (45) v CN8 (14) v N3C4 (10)

Q14

1196 1125

49

1179

77

@C6H (31), v C6Nl (19). /5 C5H (17) /9 NlH (16)

1097

4

Q15

B C5H (34) v C6Nl (28), v C5C6 (14)

:13)

Infrared spectra of cytosine

817

Table 3 (continued)

Mode no. Q16

Experimental Ar matrix Q I (cm-‘) (rel.) 1090 1088

56

Calculated HF/6-31G** G

A’”

(cm-‘)

(kmlmol)

1088

41

PED (70) Rock NH2 (44),/I CO (12), v

NlC2 (10)

Q17

997

0.03

y C6H (98), y C5H (15)

Q18

964

0.7

B Rl (55), v C4C5(23)

Q19

911

3

vN1C2(30),rockNH2(16),vC4C5(16),vC2N3(11),~R1(10)

747

34

716

39

636 623

64 8

Q24

614

85

599

Q25

575

76

563

3

B R3 (75)

4

Twist NH2 (58) p R2 (12)

7

100

Rl (23) y CN8 (22)

y NlH (82)

Q26

568

58

530

Q27

535

24

526

5

fi R2 (39) twist NH2 (21) fi CO (17)

523

7

B co (32) B ~2 (27)

390

28

Q30

352

4

031

199

15

Q28 029

400

23

032 033

235

244

142

1

86

271

7

R3 (46).

7

Rl (20).

7 RZ

(14), y CN8 (11)

,LlCN8 (61) ,5 CO (14) 7

R3 (46)

T R2 (88)

7

Rl (38)

7 R3

(11)

Inv NH, (93)

rel.: relative. Internal coordinates are defined in Table 1. Calculated wavenumbers scaled by a factor of 0.9. For sake of comparison with the theoretical data the experimental intensities have been scaled using two different factors for amino-oxo and amino-hydroxy form; the ratio of those factors was 2.35.

optimized structures of the 0x0 tautomers of cytosine are planar and the NH2 torsions and “in-plane” modes may not be coupled because of symmetry. The description of the “out-of-plane” modes is improved in the present calculation in comparison with the previous HF/3-21G one. In particular the frequencies of the wagging modes of the CO and CH group (e.g. Q20, Q21, Q23 in the amino-ox0 form or Q20, Q21, Q23 in the amino-hydroxy form) are predicted much better in the present calculation in which a basis set augmented with polarization functions has been used. The forms of these normal vibrations also change considerably in comparison with the previous HF/3-21G calculation of the normal modes of cytosine tautomers. The predicted frequencies of the bands originating from ring “out-of-plane” deformations (mode Q33 in the aminohydroxy and Q32 in the amino-ox0 form) are not so sensitive to the quality of the basis set used. The OH torsonal vibration was predicted well, both in the present and in the previous calculation (Q26 and mode 27 in Ref. [5]). The present calculation provides new information on the nature of the modes which involve vibrations of the amino group performed along twisting and inversional coordinates. With the symmetry plane removed the prediction of the bands in the spectral range 600-450 cm-’ changed considerably. In this spectral region the HF/6-31G**

IAN

818

R.

GOULD

et al.

calculation predicts the bands due to twisting NH2 vibrations coupled with CO, CN8 or ring bending vibrations. The present calculation predicts at frequencies lower than 250 cm-’ intense bands due to the vibrations of NH2 performed along an inversional coordinate. For the amino-oxo tautomer of cytosine and for several other heterocyclic compounds (adenine [18], 1-methylcytosine and 54uoro, 24hiocytosine [19]) with an amino group attached to the ring we observed strong bands in this region of the experimental spectra. Hence this prediction seems to be qualitatively correct. The calculated frequencies of the “inversional” modes of the amino group in the cytosine tautomers are still not accurate. In the experimental spectrum of cytosine the only strong bands below 250 cm-’ are due to the amino-ox0 form and the bands originating from the “inversional” vibrations in the amino-hydroxy tautomer must be placed below the observed spectral range (i.e. below 200 cm-‘). Theory, however, predicts rather that the bands due to the “inversional” vibrations in the hydroxy tautomer may be observed. It seems then, that it may be necessary to account at least for the electronic correlation, and may be also for anharmonic effects, to describe with sufficient accuracy the vibrations of the amino group attached to the heterocyclic ring. Acknowledgements-We

thank

the SERC (U.K.) for

support

of this research

under grant No.

GRIE26921.

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