Infrared matrix isolation and ab initio quantum mechanical studies of purine and adenine

Spectrochimica Acfa. Vol. 47A. hinted in Great Britain

No.

1. pp. 87-103.

1991 0

Infrared matrix isolation and ab initio quantum purine and adenine

0584-8539/91 s3.oo+o.w 1991 Pergamon Press plc

mechanical studies of

MAC~EJJ. NOWAK* and LESZEK LAPINSKI Institute of Physics, Polish Academy of Sciences, Al. Lotnikbw 32/46, 02-668 Warsaw, Poland

and J~ZEF S. KWIATKOWSKI Institute of Physics, N. Copernicus University, Grudziadzka 5, 87-100 Toruri, Poland

and JERZY LESZCZYNSKI Department

of Chemistry, The University of Alabama at Birmingham, UAB Station, Birmingham, AL 35294,U.S.A. (Received

19 June 1990; accepted 18 July 1990)

Abstract-Results are presented from ab initio SCF (3-21G) calculations for the geometries of the N(9)H and N(7)H tautomers of purine and adenine and vibrational spectra (wavenumbers and intensities) of the N(9)H forms. All these results are compared with available geometries from crystallographic studies and with reported infrared spectra of the molecules isolated in inert gas low-temperature matrices. The N(9)H=N(7)H tautomerism of the molecules in question is also briefly discussed.

DURING the last few years, several attempts have been made to predict the tautomeric stabilities and vibrational spectra of the nucleic acid bases and their derivatives by means of both i.r. matrix isolation spectroscopy and ab inifio quantum mechanical methods. Most of these studies deal with the pyrimidinic nucleic acid bases (uracils and thiouracils, cils, thymine, cytosine, 5fluorocytosine and 5methylcytosine, isocytosine). Here we shall discuss the structure and vibrational spectra of adenine and its parent molecule, purine. Purine, being the iV-heterocyclic compound with the pyrrolic nitrogen atom >N-H, exhibits the prototropic tautomerism connected with the position of the hydrogen (proton)-the proton may eithei remain at the nitrogen N(9) atom or migrate to other six- or five-membered ring nitrogen atoms. The most widely investigated tautomerism in purine is related to the rearrangement of the proton between the nitrogens of the imidazole ring, i.e. the N(9)H=N(7)H tautomerism (Scheme 1; in N(7)H tautomers the hydrogen H( 12) is located at the N(7) nitrogen). This type of tautomerism is also extensively studied in adenine (6-aminopurine). The other type of the prototropic tautomerism of adenine connected with the rearrangement of the proton between the NH2 group and the ring nitrogen atoms (amino-imino tautomerism) is not discussed here. Recently, we have reinvestigated the vibrational spectra of both purine and adenine isolated in inert matrices (argon, nitrogen and neon) at low temperatures [l]. Contrary to the previous interpretation of the i.r. spectra of the molecules suggesting that they exist as a mixture of two tautomeric forms N(9)H and N(7)H in comparable amounts [2] we have stated that the observed i.r. absorption is due to one tautomeric form of either purine or adenine. This result has been confirmed by ab initio quantum mechanical calculations of the relative internal energies of purine and adenine tautomers which * Author to whom correspondence

should be addressed. 87

MACIEJ J. NOWAKetal.

88

H,, H PURINE

H 14

12

N(9)H

PURINE

Ni7)H

Nl9)H

ADENINE

N(7)H

H

'N'

I ‘0

AOENINE

E

predicted the N(9)H form to be the most stable one in both cases [l, 31. During our study [l], the i.r. spectra of purine and adenine molecules were measured. In the present paper we report the i.r. spectra of purine and adenine, and compare those with the spectra predicted at the ab initio SCF level using the 3-21G basis set. The discussion of the molecular structure of N(9)H and N(7)H tautomers of the molecules is also presented, based on a comparison of the predicted 3-21G optimized geometries of the tautomers with available experimental geometries. A brief discussion of the tautomerism N(9)H*N(7)H in the molecules in question is also given.

EXPERIMENTAL

The low-temperature matrices were obtained in a liquid helium continuous flow cryostat. The preparation procedure for matrices has been described in detail elsewhere [4]. The matrix gas (Ne, Ar, NJ was mixed with the vapour of the investigated compound (adenine or purine), which came from a small heated glass furnace containing the compound. This furnace was placed inside the cryostat chamber ca 3 cm from the cold CsI window. The gas mixture was deposited on a CsI cold window mounted to the cold finger of the cryostat. The glass furnace during preparation of the matrix was heated up to 385 K (purine) and 450 K (adenine). At these temperatures the thermal decomposition of adenine or purine did not occur. The temperature of the CsI window, on which the matrix was formed, was about 5-7 K. This was not sufficiently low to prevent diffusion during neon matrix preparation, hence in the neon matrix some associates were present. The guest to host ratio in the matrix was controlled by changing the flow-rate of a matrix gas and the temperature of the glass furnace. They were adjusted experimentally to avoid associations in a matrix. Typical time of matrix deposition was 2-3 h. The i.r. spectra were taken on a Perkin-Elmer 580 grating spectrometer working in a mode with l-3cm-’ spectral resolution. Integral absorbances of the bands were obtained via numerical integration. Adenine and purine were obtained from Fluka Chemie AG (Switzerland). Matrix gases: neon, argon and nitrogen (spectral grade) were obtained from VEB Technische Gase Leipzig (Germany). No traces of water or other contaminants were detected in the spectra.

DETAILS OF CALCULATIONS

Geometry optimization for two tautomers of both purine and adenine has been performed at the ab initio SCF level with the 3-21G basis set [5] by the use of the

Infrared spectra of purine and adenine Table 1. Optimized

Bond*

WWW C(2)-N(3) N(3)-C(4) C(4)-C(5) C(5)-C(6) C(6)-N(1) C(4)-N(9) C(5)-N(7) N(7)-C(8) C(8)-N(9) C(2)-H( 11) C(6)-H( 10) C(8)-H(13) N(9)-H( 12) N(7)-H( 12) C(6)-N( 10) N( lO)-H( 14) N( lO)-H( 15)

(3-21G) bond lengths (A) for purine and adenine experiment

Tautomer Calc. Purine Adenine 1.3383 1.3366 1.3291 1.3245 1.3195 1.3322 1.3960 1.3812 1.3777 1.3951 1.3305 1.3338 1.3686 1.3673 1.3995 1.3956 1.2923 1.2926 1.3877 1.3892 1.0663 1.0675 1.0669 1.0637 1.0634 0.9953 0.9951 1.3390 0.9960 0.9961

Tautomer Calc. Purine Adenine

N(9)H A$

=p.t

- 0.0017

1.338

1.353

- 0.0046

1.332

1.327

0.0127

1.342

I.346

- 0.0148

1.382

1.394

0.0174

1.409

1.413

0.0033

1.349

1.358

- 0.0013

1.376

1.377

- 0.0039

1.385

1.380

0.0003

1.312

1.321

0.0015

1.367

1.374

0.0012

1.084 -

-

-

-0.0003

-

-0.0002

-

-

-

-

-

-

1.337 -

1.079

1.336 1.008 0.993

1.3425 1.3432 1.3230 1.3145 1.3229 1.3358 1.3994 I .3878 1.3794 1.3961 1.3251 1.3230 1.3932 1.3902 1.3791 1.3875 1.3792 1.3730 1.2942 1.2965 1.0660 1.9670 1.0698 1.0639 1.0641 0.9948 0.9939 1.3538 0.9932 0.9967

89 tautomers

and comparison

N(7)H A0

with

Exp.S 1.349

I.349

1.339

1.324

1.337

1.336

1.407

I .398

1.393

1.385

1.330

I .330

I.379

I .369

1.373

1.375

1.327

1.337

1.311

1.313

1.06

0.97

1.00

0.93

0.95

1.06

-

-

0.89

0.84

-

-

0.0007 - 0.0085 0.0129 -0.0116 0.0167 -0.0021 - 0.0030 0.0084 - 0.0062 0.0023 0.0010

0.0002 -0.0009

-

-

* For the numbering of atoms in purine see Scheme 1.

t The first data are the mean values of bond lengths (or bond angles in Table I) of adenine residues based on an analysis of a number of crystallographic structures [13]. (Comp. also [14].) The second data are the bond lengths corrected for thermal motion (or bond angles) of adenine residue of the complex 9-methyladenine : lmethylthymine from neutron diffraction studies [15]. (For the X-ray crystallographic structure of this complex see Ref. [16].) $ Two independent structures of the N(7)H tautomer of purine from a crystallographic study [ 17). $ The difference between the bond length of adenine and the corresponding bond of purine.

GAUSSIAN 86 program [6] at the Alabama Supercomputer Center. The optimization has been carried out under the assumption that the tautomers are planar. As far as the SCF calculations with the 3-21G basis set are concerned, in all cases reported here, the optimized planar geometry corresponds to a minimum (not to a saddle point) on the potential energy hypersurface. This was confirmed by the subsequent calculations of the i.r. frequencies, which are all positive. If there were any energy-lowering out-of-plane distortions of the molecule, then they would manifest themselves in the calculations by the appearance of imaginary frequencies. The planarity of the real structure of the molecules in question, particularly adenine, deserves some comment. Molecules with amino groups are found, in general, to be nonplanar; this is also the case for amino

90

MACIEJJ.NOWAK etal.

tautomers of the nucleic acid bases [7-91. However, we may expect that the deviations from nonplanarity for the systems are small (compare the discussion given for the structure of cytosine [8]). Force constant matrix F,, both for in-plane and out-of-plane Cartesian displacement was obtained analytically using the GAMESS program [lo]. The nonredundant internal symmetry coordinates were defined as recommended by PULAY et al.[ 111. The list of these coordinates is given in Table 3. Transformation of F, to the force constant matrix in internal symmetry coordinates allowed ordinary normal coordinates calculations to be carried out as described by SCHACHTSCHNEIDER [ 121.The calculated wavenumbers of all normal modes were scaled by a single factor of 0.9. The intensities of the corresponding modes have been calculated automatically by the use of the GAMESS program.

Table 2. Optimized

(3-21G)

Tautomer Calc. Purine Adenine

Angle*

125.35 126.44 114.74 113.43 124.45 125.09 116.58 117.22 119.44 117.93 119.45 119.88 109.38 110.11 105.79 105.50 105.48 105.36 112.81 112.19 106.53 106.84 117.29 116.43 118.43 -

N(l)-C(2)-N(3) C(2)-N(3)-C(4) N(3)-C(4)-C(5) C(4)-C(5)-C(6) C(5)-C(6)-N(1) C(6)-N(

1)-C(2)

C(4)-C(5)-N(7) C(5)-C(4)-N(9) C(5)-N(7)-C(8) N(7)-C(S)-N(9) C(8)-N(9)-C(4) N(l)-C(2)-H(11) N( l)-C(6)-H( C(4)-N(9)-H( C(5)-N(7)-H( N(9)-C(8)-H( N( l)-C(6)-N(

bond angles

10)

125.83 125.52 -

12) 12)

N(9)H Al

10)

for tautomers experiment

of purine

and adenine

Tautomer Calc. Purine Adenine

Exp.t

-

-

-

125.10 125.92 116.21 114.98 122.16 122.89 118.19 118.50 118.83 117.50 119.52 120.21 105.53 105.79 109.44 109.38 106.28 105.00 113.21 113.03 105.54 105.80 117.13 116.24 117.99 -

-0.31

-

-

-

-

-

0.21

-

1.09

129.0

129.7

- 1.31

110.8

110.6

0.64

126.9

127.0

0.64

116.9

116.9

- 1.51

117.6

117.6

0.43

118.8

118.2

0.73

110.7

110.6

- 0.29

105.7

105.6

-0.12

103.9

104.4

- 0.62

113.8

113.2

0.31

105.9

106.2 114.4

- 0.86

-

121.7

127.28 128.03 125.27 125.28 -

119.0

118.10 -

C(6)-N(

IO)-H( 14)

119.42 -

-

121.0

lO)-H(

120.77 -

-

C(6)-N(

123.41 -

118.88

-

-

121.4

117.44

15)

* For the numbering t,$ See footnotes

BThe difference A(i)-B(j)-C(k)-the

of atoms

and comparison

N(7)H A$

with

Exp.S 127.9

128.5

113.0

113.4

123.9

123.1

117.9

118.5

118.9

119.1

118.4

117.5

105.1

105.5

109.6

109.6

106.5

106.3

115.1

114.1

103.8

104.6

121.9

114.4

118.7

113.9

0.82 - 1.23 0.73 0.31 - 1.33 0.69 0.26 -0.05 -0.28 -0.18 0.26 -0.89 -

121.68 121.89 -

13)

(degrees)

see Scheme

119.0

126.6

121.4

125.3

0.01 -

-

1.

t and $ in Table I. between the bond angle of adenine and the corresponding angle between the bonds A(i)-B(j) and C(k)-B(j).

118.X 0.75

angle of purine.

-

Infrared spectra of purine and adenine RESULTS

AND

91

DISCUSSION

Molecular geometries The optimized geometries (the bond lengths and bond angles) for N(9)H and N(7)H tautomers of purine and adenine are shown in Tables 1 and 2 where they are compared with the available experimental crystallographic data. A comparison of the isolated molecule optimization should really be made with the gas phase data (so far not available

B 8 f i? 8

$ C

o., 0.: 0.f

JI,

?!

t C

0.01

I

3500

1700

3400 CM-’

1600

1500

1400

CM-'

A

Y f

0.4 -

0.0.

1300

1200

1100

1000 CM-'

1

,

I

I

1000

900

800

700

I

600 CM-’

Fig. 1. Infrared absorption spectra of purine isolated in; matrices.

(A)

neon, (B) argon, (C) nitrogen

92

MACIEJ J. NOWAK ef al.

0.01 I

I

600

500

I

I

400

1

300 CM-’

Fig. 1 (continued)

for the molecules in question). The constraints imposed by molecular packing in the crystal will enevitably lead to distortions. For instance, uncertainties in the accurate crystallographic determination of H-atom positions are well known, and the lengths are frequently 0.1-0.2 A shorter than those in the gas phase. The experimental data are available for N(9)-substituted derivatives of adenine, while for purine itself the geometry of its N(7)H tautomer is known. It is seen from Tables 1 and 2 that in general the geometries predicted for the N(9)H tautomer of adenine and N(7)H tautomer of purine agree well with the experimental data. In the case of the bond

3600

3500

Fig. 2. Infrared

3400 absorption

cm” spectra

1700 of adenine

isolated

matrices.

1600

1500

l&O0 cm-’

in; (A) neon, (9) argon, (C) nitrogen

93

Infrared spectra of purine and adenine

0.0 L 1300

1200

1100

1000

1000

900

800

700

cm-’

cm-’

600

500

400

300

cm-’

Fig. 2 (continued)

lengths between the heavy atoms, the greatest discrepancies between the predicted and experimental data are in general not higher than 0.02-0.03 A. The N(7)-C(8) bond of purine is exceptionally predicted to be longer by 0.04-0.05 8, as compared to experimental values. The predicted bond lengths involving hydrogen atoms are calculated to be longer even by 0.1-O. 15 A in comparison with X-ray crystallographic data for purine. In the case of adenine however, for which the experimental data from neutron diffraction studies are known, the discrepancies between the computed and experimental C-H and N-H bond lengths are significantly smaller (not higher than -0.02 A). The predicted bond angles between the heavy atoms differ from the experimental values generally not more than 1-2” (except the bond angles N(l)C(2)N(3) and C(2)N(3)C(4) where the differences are 1.5-2 times larger), but the predicted bond angles involving the hydrogen atoms differ from the X-ray crystallographic values even by 4-8”. It is also seen from Tables 1 and 2 that the changes caused by the NH, substitution at the C(6) atom of purine are generally small. Tautomerism N(9)H*N(7)H

in purine and adenine

Several experimental studies of both purine and adenine in polar or non-polar solvents (for a list of original papers see Refs [l, 3,18 1) clearly indicate that purine exists in

MACIEJ 3.

94

NOWAK

et al.

Table 3. Internal coordinates used in the normal modes analysis for purine and adenine

Six-membered ring stretchings S,=r,.z s2=r2.3 s3=r3,4 S4 = r4.5 s5=%6 s6 = r6, I

Five-membered S7= r4.9

ring stretchings

&=r5.7 S9=

r7.8

SIO = r8.9

CH and NH stretchings %I= r9.12 $2

=

b.

vNgH VC*H

13

VC2H

S13 = r2. II

Purine Adenine Adenine Adenine

S14 = r6. 10 St4 = r6, 10 X4

= r10.14

SC=r 10.15 Six-membered

vclY vC6N

%H,4 “N10ii15

ring in-plane deformations

~,5=(6-“2)(B2.6,1

-8,.3.2+84.2.3-85.3.4+~6.4.5-85.1.6)

s,,=(12-“2)(2s2,6,,-B3,1,2-B4,2,3+2B3,s,4-86.4,5-81.5.6) s,,=(3)(8,.3.2-82.4.3+84,6.5-81.5.6)

Five-membered ring in-plane deformations S~a=~I+~a2+~b2~~“2~B~.s.~+a~8~.~,~+8~,~.s~+b~B~,~,~+8~.s,~~1 s~9=[2(U-b)2+2(1-U)2]-1’2[(U-~)(~s.9.4-87,9.8)-(1-a)(~4.7.5-~s.s.7)1

Bending CH and NH s,=(2-“2)(8~.,,.2-83.,,.2) s2,=(2-“2)(84.12.9-BS.12.9) s2,=(2-“2)(B9.,3.~-87.13,8) s23=(2-“2)(81,10.6-85.10,6) ~,=(2-“2)(~,.,0.6-~S,lO.6) ~;3=(~-“2~~~~,4.15.10-814.6.~o-~15.6.10~ ~3=(2-L’2)(814.6.10-~IS.6.10)

Purine Adenine Adenine Adenine

solvents as a mixture of two N(9)H and N(7)H tautomers in varying concentrations. (For instance, while for purine itself in water the concentrations of the two forms are almost the same, in dimethyl sulphoxide the purine N(9)H tautomer predominates over the purine N(7)H tautomer by a factor of 2.) In the crystalline state, purine has the structure N(7)H [17], while the structure of adenine itself in the crystalline state is not known. As for the isolated purine and adenine (i.e. monomers non-interacting with the molecules of a medium), the available experimental data are very rare. As far as we are aware, the N(9)HeN(7)H tautomerism of these molecules isolated in inert low-temperature matrices has been investigated by i.r. spectroscopy [l, 21. As has already been stated, the interpretation of the i.r. spectra of purine and adenine as presented in Ref. [2] was rather doubtful, and according to our interpretation, the observed vibrational spectra of the molecules are due to one of their tautomeric forms. Based on the available experimental spectra we were unable to specify the dominating tautomer of the molecules. However, an analysis of the recent ab inifio calculations of the relative internal energies of purine and adenine tautomers [3] and a qualitative estimate of the effect of environment on the change of the relative stabilities of the tautomers allowed to suggest that the N(9)H tautomer of purine and the N(9)H tautomer of adenine is the dominating form in inert matrices or in vapour phase. Our conclusion concerning the tautomerism of adenine in

95

Infrared spectra of purine and adenine Table 3 (continued) Out-of-plane Wagging CH, NH and torsions NH2 ~24=Yl1.2.3.1

YC2H

Gs=Y12.9,8.4

YN~H YCsH

S26= Y13.s.7.9

Purine Adenine Adenine Adenine

s27= YlO.6.1.5

S27=YIo.6.1.5 ~~,=(2-1'2)(~,4.10,6,1+~14,10,6.5) $=(2-1'2)(%.,0.6,1 + %10,6,5)

Six-membered

YCdC

Ycdr,o %ou14 %lHI5

ring torsions

Five-membered ring torsions SjI = (I+ 2a2 + 2bZ)-1’2[r4.~.r.s+ b(rs.9.4.5 +

r7.8.9.4) +a(r9.4.~.7+r~.7.8.9)1

~32=[(a-b)2+(1-a)2]~"2[(R-b)(t~,7,~,~-~~.4.~~7)+(~-a)(~7.~.9.4-~~.P.4.5)l Two

rr4 rr5

rings relative torsion rRr

s33=(2-"2)(~6.5.4,9-r77.5.4.3)

Where, r,., is the distance between atoms A, and AI. ,!?,,,,k is the angle between vectors AkAi and AkAj. Y,,,,~,, is the angle between the vector A,Ai and the plane defined by atoms Aj, At. A,. r r,,*k,,is the dihedral angle between the plane defined by Ai, Aj, Ak and the plane defined by A,, Ak, A, atom. a = cos 144”= - 0.8090; b = cos 72” = 0.3090.

matrices

is

in full agreement with the studies of adenine in gaseous phase. Very recently,

BROWN etal. [19] measured and analysed the microwave spectrum of adenine in a cw seeded supersonic beam. From the comparison of the experimental rotational constants with those obtained using ab initio SCF (3-21G) calculations they also concluded that N(9)H tautomer is the most stable. The relative internal energies of the N(9)H and N(7)H tautomers of purine and adenine have been computed for the geometries of their tautomers optimized at the SCF (km/mall 0.

O_

O_

-1

lSO0

1300

1100

900

700

500

300 cm-’

Fig. 3. Comparison between the ab initiocalculated i.r. spectrum of purine and the experimental spectrum of the Ar matrix isolated purine presented in the “stick” form in the 1700-2OOcm-’ spectral range. Experimental integral absorbances are normalized in the same way as in the Table 5. Theoretical spectral positions of the bands are scaled by the factor 0.9. Numbers refer to the normal modes as in Table 4.

MACIEJ

96

J. NOWAK

et

al.

(km/m0 30

27 7

2c0-E:

z

1010.

17

10

5

l(.

Y a u

29

15

36 37 38 39

IS

, 1700

!,

,

1500

,

1300

,

,

1100

(

, 900

,

, 700

,

, 500

I II

,

,I

I

II ,

300 cm-'

Fig. 4. Comparison between the a6 initio calculated i.r. spectrum of adenine and the experimental spectrum of the Ar matrix isolated adenine presented in the “stick” form in the 1700-200 cm-’ spectral range. Experimental integral absorbances are normalized in the same way as in the Table 7. Experimental band signed with an arrow and placed at 1633 cm-’ is two times more intense than presented in the figure. Theoretical spectral positions of the bands art scaled by the factor 0.9. Numbers refer to the normal modes as in Table 6.

level with 3-21G basis set as the contribution of the relative SCF energies with 6-31G* basis set [5] and the relative zero-point vibrational energies calculated at the SCF level with 3-21G basis set (the calculated wavenumbers have been scaled by a constant factor The predicted relative internal energy of purine tautomers of 0.9). (A,!?‘=AESCF+AEvib(o)=(21.7+0.6)kJmol-1= 22.3 kJ mol-‘) indicates that the energy difference between the N(9)H and N(7)H tautomer is so large that the tautomer N(7)H is unlikely to be present in the vapour phase (or in inert matrices) in sufficient amounts to same is be detected spectroscopically. The the case for adenine (AE”=AESCF+AEvib(o)=(42.6-2.4) kJ mol-‘=40.2 kJ mol-‘). As we see, on going from the vapour to solution in polar media, the relative stability of the N(9)H and N(7)H purine tautomers as well as of adenine is changed significantly. A qualitative explanation of this behaviour can be given by considering the simple Onsager-Kirkwood reaction field model (e.g. see Ref. [20]), according to which, in the first approximation, the tautomers with higher dipole moments are more strongly stabilized in the polar media than those with lower dipole moments. Thus the purine N(7)H tautomer with a dipole moment p = 5.98 D is more strongly stabilized by polar medium than the purine N(9)H tautomer with p= 3.64 D. The same is the case for adenine for which the dipole moments of their N(7)H and N(9)H tautomers are 7.5 and 2.4 D, respectively. As a result, the energy difference of about 22 kJ mol-’ for the isolated purine tautomers decreases to almost 0 kJ mol-’ for the tautomers of both molecules interacting with the molecules of the polar medium. In a similar way we can explain qualitatively the behaviour of N(9)H and N(7)H amino tautomers of adenine. The relative internal energy for isolated tautomers of the base is AE” = 40.2 kJ mol-’ [3] in favour of the adenine N(9)H form, but on going from the vapour phase to polar medium the adenine N(7)H tautomer with p= 7.54 D is more strongly stabilized by polar medium than the tautomer adenine N(9)H with p = 2.38 D, and in polar medium both tautomers exist in almost the same proportions. Infrared absorption spectra The i.r. spectra of purine and adenine isolated in Ne, Ar and Nz matrices are presented in Figs 1 and 2. The wavenumbers of the maxima of the absorption bands together with

Infrared spectra of purine and adenine

97

integral absorbances are collected in Tables 5 and 7. Tables 5 and 7 also contain a proposed assignment to the calculated normal modes. Since the thickness of matrices and the guest to host ratio are unknown, only the relative intensities of the bands are given there. The spectra registered in various matrix media do not differ in their general pattern, but most of the frequencies, intensities and splitting patterns of the bands depend (more or less) on the matrix. Such behaviour is called “matrix effect”. As can be seen in Figs 1 and 2 and in Tables 5 and 7, the nitrogen matrix influenced the spectrum the most, and the N-H modes were the most sensitive to environment. The ab initioSCF (3-21G) calculations of the force constants were performed to obtain frequencies, potential energy distributions of the normal modes and absolute intensities of the corresponding i.r. absorption bands of purine and adenine. The results are collected in Tables 4 and 6. These calculations were performed in order to make an assignment of the observed absorption bands. But, since numerous approximations are implemented in the method, the resulting assignments, based on comparison between experiment and theory should be treated with scepticism, especially for the molecules of high complexity (purine has 33 and adenine 39 normal modes). For this reason the assignments given in Tables 5 and 7 are not unequivocal in the case of many bands. For the sake of better illustration of how the theoretical spectra fit the experimental, we compared them (in a “stick spectrum” form) in Figs 3 and 4. As can be seen in the figures, the spectra consist of many densely spaced absorption bands. Hence, taking into Table 4. Ab initio SCF (3-21G) calculated wavenumbers (9), absolute intensities (A), and potential energy distributions of the i.r. spectrum of purine Mode No.

“,: g: :: g;

go

Qll

Q12 Q13 Q14

Q15 Q16 Q17

Qls 919 020 Q21 Q22 Q23 Q24 Q25 Q26 Q27 Q28 Q29 Q30 031 032 Q33

(c:~‘)

3442 3109 3100 3076 159.5 1552 1480 1434 1375 1367 1324 1256 1249 1158 1104 1075 1061 1018 1003 957 918 898 878 777 689 663 655 622 559 469 427 273 247

A

(km mol-‘) 146 0.1 20 8 103 74 33 19 53 20 45 46 54 2 54 3 3 27 20 0.1 0.02 52 18 19 189 6 4 55 5 4 14 4 6

Potential energy distribution %“(99) vc&98) v&96) %“(97) v,,c,(26)> vcscAl5) ~~~~(24). vc,cF(17), vN,c,(12) Nc”(49). BC”i1(19) &“(45). vCbN,(17)7 JM10) f&(39). vc,cJlO) bNyH(38h

,&2”(21h

/%XH(2Q)r

vN,Cs

vCxNy(12),

vC,,,W%

i3N9H(12)r

&,dll)

BC&W.

vC,~,(16)3

vC5N,(13).

fL(39)r

/f&(11)

VC,N,W)

vN,C#7),

,%S(13)v

~~,(36).

vN,C,(22h

ycd76h

i%dO)

(15) /%H(ll)? BRI(l0)

vN,C,(12)r vC2N,(12).

vC2,+(12)*

vW,(lo)*

8r4(l”)

vC,N,(lo)

YWI(W

vC,N,(73).

&Htlg)

YC,HWL

y,Ht15)

YC”H(95) i3,4(45).

VQd33)

~Rd46)r

dW

. +$‘&13).

vC,C,03),

vNaC,(lo)r

vC~N,(lo)~h(lO)

Internal coordinates are defined in Table 3. Wavenumbers scaled by the factor 0.9. SA(A1

47:1-G

MACIEJJ.

98

NOWAK et al.

Table 5. Experimental frequencies (Q), relative integral absorbances* (I) and approximate assignments to the normal modes (as in Table 4) of the absorption bands of isolated purine observed in rare gas matrices Matrix Ar

Ne C (cm-‘) 351 lsh 3505sh 3500

(FL.)

155

li (cm-‘) 3493 3489sh >

Assignment (Number of the normal mode from Table 4)

N2

&I.)

188

D (cm-‘) 3482sg

3477 >

&I.)

Ql

269

1738

16

1738

1631 1620

10 2

1625

13 9

1610

100

1609

90

1609

79

1591

4

1598

I4

Overtone

Q5 or Q6

1587

116

1584 1577

IO1 3

1586 1579

83 14

Q6 or Q5

1500 1489

5 15

1500 1488

3 19

1487

8

1451

12

1454

22 14

Q7

1453 1406 1402

22 73

1403 1401

24 80

1404

72

1389 1382

11 23

1385 1378

8 15

1367

20

Qlo

1335 1331

75 19

1333

89

1333

94

Qll

1314

4

1289

40

1289

31

1293

34

1257

16

1256

14

1259

11

1228 1222

40 36 10

1228 1221

67 3 8

1230 1225 1210

34 20 9

6

1183 1102

8 4

1073 1068

13 7

33 16

924

15

1207 1182 1105

8 12

1024

8 8 37

923

19

903 895 871 824 798 788

15 11 8 3 I6 18 4

1061 1057

668 650 608 561 508 437 409

10 30 6 117 I7 5

1206 1180 1101 1060 1057 1034 919 903

10 12 2

Q8 Q9

? Q12 or Q13

Q13 or Q12 ? Q14 Ql5 Q16 Ql8

10

908

3

896 871 823 796 788

14 7 4 14 17

899

16

649 607

I1 27

562 513 438 409

5 139 19 4

Q21, Ql9, Q23, Q22, 920 !

798 789

10 16

614

62

Q28

162 19

~29 ~25 Q31

~24

Q26 or Q27

561 441

* For better comparison of experiment with theory the integrated absorbances of absorption bands are normalized in such a way that the sum of integrated absorbances of all normal modes observed experimetnally was equalized to the sum of absolute intensities obtained in calculations.

account - 10% accuracy in the theoretical determination of the band frequencies, we may understand the reason for the doubts in attributing experimental bands to certain

99

Infrared spectra of purine and adenine

theoretical modes. The additional difficulty is the fact that the frequencies of out-ofplane modes are usually highly overestimated in theoretical calculations. Of course, it was taken into acount when the assignment (Tables 5 and 7) was performed. The most spectacular cases of such overestimation are the modes Q25 in purine and Q27 in adenine, both connected with the out-of-plane deformation of N(9)H group, where the differences between theoretical (scaled by 0.9) and experimental spectral positions are 176 and 181 cm-‘, respectively. In the case of purine (Fig. 3) the general pattern of the absorption bands obtained in the theoretical spectrum is not very dissimilar from those obtained in the matrix spectrum. Correlation between positions and intensities of theoretical and experimental bands is not so poor. But in the case of adenine (Fig. 4) the calculated and matrix spectra differ much more. The differences of positions and, mainly, differences in intensities of the bands make the experimental and theoretical spectral patterns much more dissimilar than in the case of purine. The probable cause of such discrepancies is the presence of the

Table 6. A6 initio SCF (3-21G) calculated wavenumbers (c), absolute intensities (A), and potential energy distributions of the i.r. spectrum of adenine

No.

g: :: ::

;x’ $0 Qll

Ql2 Q13 Q14 Ql5 Ql6

Q17 Q18 Q19 Q20 Q21 922 023 ~24 925

Q26 ~27 Q28 Q29

Q30 Q31 ~32 Q33 Q34 935 936 Q37 Q38 Q39

(cICI)(km L’) 3520 3467 3404 3122 3069 1625 1583 1568 1477 1466 1400 1370 1320 1291 1257 1205 1185 1095 1031 1022 980 955 926 924 873 779 694 689 657 606 584 536 529 527 504 326 265 237 I87

Internal coordinates 0.9.

Potential

energy distribution

79 140 122 2 29 322 234 316 1 152 0.06 3 9 90 44 17 164 12 6 37 2 42 18 47 16 0.2 289 2 68 2 1 279 19 4 5 4 14 I2 10 are defined

in Table 3. Wavenumbes

scaled by the factor

MACIEJJ. NOWAKet al.

100

Table 7. Experimental frequencies (C), relative integral absorbances* (I) and approximate assignments to the normal modes (as in Table 6) of the absorption bands of isolated adenine observed in rare gas matrices Matrix Ar

Ne 3 (cm-‘)

(FL.)

3569

79

3517

sh

s (cm-‘) 3565 3557

NZ

Assignment (Number of the normal mode from Table 6)

3 (cm-‘)

(FL.)

116

3556

131

186

3486 3477 >

286

Q2

153

3442

207

Q3

(Ll.)

Ql Association

3503

110

3498 3489 >

3453

108

3448 3441 >

4

Q4? QS?

3041

8 4

3066 3057 1694

13

1693

15

Overtone?

1664

142

1659

13

Association

1651

192

1651

9

1645

32

46

1648

104

1641 1636

554

1645 1639 1633 1626I

618

1637

528

Q6

1619 1613 1607I

363

1619 1612>

302

1615

216

Q7 or Q8

1598

29

1599

67

1597

98

Q8 or Q7

1572

16

1476

98

1484sh 1476 >

88

1451

13

1426sh 1420 1390

1482 1474

15 98 4

Association

82

1452 1422 1419

67

1420

57

14

1389

62

1398 1389

1361

6

1344

18 14

1358 1345

18 8 7

1335 1329 1299 1290 1247 1241 1229

Q9 Q10 Association

3

1354

1334

28 11

1345 1342I

33

60 34 54

1328

56

1329

58

1290

94

1294

6

1246

13

25 12

1240 1229

38 17

1243sh 1240

,

96

Association Qll? Q12? Association

Q13, Q14, Q15. Ql6. Qt7

75

amino group in the adenine molecule. The NH2 group may not be planar itself and may be twisted out-of-plane of the rings, in contrast to the totally planar geometry optimized at SCF (3-21G) level of theory. The i.r. Ar matrix spectra of purine and adenine were reported earlier by RADCHENKO et al. [2]. Their spectra do not differ from those obtained in this work in the limit of accuracy of used spectrophotometers. The main discrepancy in our spectrum is the lack of the band found by RADCHENKO at 3480 cm-’ (with a shoulder at 3477 cm-‘) in the case of purine.

101

Infrared spectra of purine and adenine Table 7 (conhumf) Matrix Ar

Ne C (cm-‘)

(IL.)

4 (cm-‘)

N2

(IL.)

Assignment (Number of the normal mode from Table 6)

v (cm-‘)

(IL.)

1124

34

Q18?

1075

31

QlS?

9 8 2

1133 1127 1078

9 1

19

1061

17

26

1032

37

1008

17

1017 1005

5 12

10%

13

961

3

958

4

961

4

Q2l

931 928

22

927

17

931

22

Q22

887

10

887

11

887

6

Q24

862 849

1 7

869 848

2

861

12

Q25 (?)

804 722 716 696

14

802

8 13

804

9

~25 (9 Q26 (‘9

717

6

716

12

698

4

705

2

686 667

3

688

3

6%

3

1 6

678 655

1 9

683 663

2 2

583

75

566

49

648 610 591 583 566

3

608

10 7

546

32

508

66

513

127

586

201

~27

497

6

503

5

515

7

035

311 274

3 20

276

16

280

8

Q37

261

5

239

72

242

91

118

Q38

207

28

214

104

1133 1127 1074 1065sh 1061 1023

655 649

10 8 2

10

8

Q20 Q19?

p28

? Association

610

3

136 63

036

319 313 > 220

7

* For better comparison of experiment with theory the integrated absorbances of absorption bands are normalized in such a way that the sum of integrated absorbances of all normal modes observed experimentally was equalized to the sum of absolute intensities obtained in calculations. sh--Shoulder.

The 3600-3000

cm-’ spectral region

In this range the absorptions of the stretching vibrations of N-H, NH2 and C-H groups are expected. The v(N(9)H) absorption is placed at 3493 cm-’ (Ar) in case of purine, and at 3498 cm-’ (Ar) in adenine. The stretchings of amino group of adenine are at 3565 cm-’ (antisymmetric) and 3448 cm-’ (symmetric) in the Ar matrix. A detailed description of the matrix spectra in this range is performed in our previous paper [l]. We proved there that the splitting of the bands in this region is due to the matrix effect. We excluded the possibility that the splitting is a manifestation of the coexistence of two tautomers [l]. Our statement was based on the finding that the splittings depend on the matrix (Ne, Ar,

102

MACIEJ J. NOWAK et al.

N2) and disappear after annealing. During annealing only the crystalline structure of the matrix was changing, whereas the change of tautomeric form was not possible. In heterocyclic compounds the C-H stretching vibration absorption bands are usually very weak. In the cases discussed here, those absorptions are expected in the 3100-3000 cm-’ spectral range (see Tables 5 and 7). Some very weak absorptions were detected only in the Ar matrix. They may be due to the C-H stretching or to overtones.

The 1700-200 cm-’ spectral region The i.r. absorption spectra of purine and adenine in this region are mainly due to vibrations of atoms forming pyrimidine or imidazole rings. The proper assignment of such bands to normal modes, only on the basis of experimental data, is practically not possible. Therefore the assignment, performed in this work, is based on the comparison of the observed spectra with the results of the calculations. More characteristic are the bands due to the modes in which participate the vibrations of the N-H and NH2 groups. In the spectrum of adenine, the most intense absorption band appears at 1626 cm-‘. Since there is no such strong band in the spectrum of purine, we attributed it as due to the scissoring vibration of the NH* group. The band at 1034 cm-’ (Ar) of purine spectrum and the band at 1032 cm-’ (Ar) of the adenine spectrum are both very sensitive to the matrix environment. In the N2 matrix those bands disappeared. They probably shifted towards higher frequencies and became very broad and disappeared in the backgrund of the spectrum. Such features are characteristic for the bands connected with N-H deformation, hence we attributed the bands discussed here to Q18 (purine) and Q20 (adenine) modes. Also the bands of the out-of-plane deformation modes change their frequency considerably when we take into consideration Ar or N2 matrices. The relatively strong bands at 513 cm-’ (Ar) found in the purine and adenine spectra exhibit such features and therefore we attributed them to Q25 and Q27 modes (the modes with the contribution of the y(N(9)H) vibration) in purine and adenine spectra, respectively. CONCLUSIONS

The main conclusions from our previous paper [l] and from this study are as follows: (1) Both adenine and its parent compound purine exist in one tautomeric form in an inert matrix environment. This is confirmed by ab initio calculations [3] at the SCF (631G*//3-21G) level with the zero-point vibrational contributions from the computed vibrational wavenumbers at the SCF (3-21G) level (scaled by one factor 0.9). These calculations predict the N(9)H tautomers for both adenine and purine to be the most energetically stable ones. (2) The geometries of two tautomeric forms of the molecules predicted at the SCF (321G) level agree satisfactorily with the available experimental data. (3) Calculations at the SCF (3-21G) level appear to be useful for an interpretation of the general features of the i.r. matrix spectra of the isolated molecules. However, in several cases the calculated frequencies and intensities do not reproduce the experimental data sufficiently close. Acknowledgemenrs-This the project

work was supported

CPBP 01 .W. The experimental

11.05 provided

by the Polish Academy

JL would like to thank the Alabama the calculations

presented

in part by the Ministry

of National

Education

(Poland)

within

part of this work was financed by the grants CPBP 01.12 and CPBR

of Sciences. Supercomputer

Network

for generous allotment

of computer

time for

here.

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L. Lapinski

[2] E. D. Radchenko, (1984);

and J. S. Kwiatkowski,

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Phys. Let?. 157, 14 (1989).

G. G. Sheina and Yu. P. Blagoi,

Biofirika

(Russian)

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Infrared spectra of purine and adenine

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S. G. Stepanian, G. G. Sheina, E. D. Radchenko and Yu. P. Blagoi, 1. Molec. Struct. 131,333 (1985); G. G. Sheina, E. D. Radchenko, S. G. Stepanian and Yu. P. Blagoi, Studia Biophys. 114, 123 (1986). [3] J. S. Kwiatkowski and J. Leszczynski, 1. Molec. Struct. (Theo&em); to be published; J. S. Kwiatkowski and W. B. Person, in D. Beveridge and R. Lavery (Editors), Theoreticul Biochemistry and Molecular Biophysics: A Comprehensive Survey. Adenine Press, Guilderland, NY, U.S.A. (1990). [4] M. Szczesniak, M. J. Nowak, H. Rostkowska, K. Szczepaniak, W. B. Person and D. Shugar, J. Am. Chem. Sot. 105,5%9 (1983). [S] W. J. Hehre, L. Radom, P. von R. Schleyer and J. A. Pople, Ab Initio Molecular Orbital Theory. Wiley, New York (1986). [6] M. J. Frisch, J. S. Binkley, H. B. Schlegel, K. Raphavachari, C. F. Melius, L. Martin, J. J. P. Stewart, F. W. Bobrowicz, C. M. Rohlfing, L. R. Kahn, D. J. E. DeFrees, R. Seeger, R. S. Whiteside, D. J. Fox, E. M. Fluder and J. A. Pople, Carnegie Mellon Quantum Chemistry Publishing Unit, Pittsburgh, PA, U.S.A. (1984). [7] J. S. Kwiatkowski, B. Lesyng, M. H. Palmer and W. Saenger, Z. Naturforsch. 37~. 937 (1982). [8] M. H. Palmer, J. R. Wheeler, J. S. Kwiatkowski and B. Lesyng, J. Molec. Struct. (Theochem) 92, 283 (1983); I. R. Gould and I. H. Hillier, Chem. Phys. Len. 161, 185 (1989). [9] A. Sygula and A. Buda, J. Molec. Struct. 121, 133 (1985). [lo] M. Duppis, D. Spangler and J. J. Wendolski, NRCC Software Catalog, University of California, Berkeley, CA, 1980 (Program QCOl); M. W. Schmidt, J. A. Boatz, K. K. Baldrige, S. Kosecki, M. S. Gordon, S. T. Elbert and B. Lam, QCPE Bulletin 7, 115 (1987). [Ill P. Pulay, G. Fogarasi, F. Pang and J. E. Boggs, J. Am. Chem. Sot. 101,255O (1979); G. Fogarasi and P. Pulay, in J. R. Durig (Editor), Vibrational Spectra and Structure, Vol. 14, p. 125. Elsevier, Amsterdam (1985). [12] H. J. Schachtschneider, Technical Report, Shell Development Co., Emerville, CA (1969). [13] R. Taylor and 0. Kennard, 1. Molec. Struct. 78, 1 (1982). [14] D. Voet and A. Rich, Progr. Nucleic Acid Rex Molec. Biol. 10, 183 (1970). [15] M. N. Frey, T. F. Koetzke, M. S. Lehmann and W. C. Hamilton, J. Chem. Phys. 59, 915 (1973) [16] K. Hoogsten, Acta Crystallogr. 16, 907 (l%3). [17] D. G. Watson, R. M. Sweet and R. E. Marsh, Acta Crystallogr. 19, 573 (1965). [18] D. Shugar and A. Psoda, in W. Saenger (Editor), Landolt-Bornstein-New Series-Biophysics of Nucleic Acids. Springer-Verlag, New York, in press. [19] R. D. Brown, P. D. Godfrey, P. McNaughton and A. P. Pierlot, Chem. Phys. Left. 156, 61 (1989). [20] M. Berndt and J. S. Kwiatkowski, in G. Naray-Szabo (Editor), Theoretical Biochemistry of Biological Systems, p. 349. Elsevier, Amsterdam (1986).