Pina Colarusso et al- The infrared spectra of uracil, thymine, and adenine in the gas phase

8/3/2019 Pina Colarusso et al- The infrared spectra of uracil, thymine, and adenine in the gas phase

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E L S E V I E R

25 A pril 1997

Chemical Physics Letters 269 (1997 ) 39-48

CH EM I C A LPH YS I C SLE ' r ' r ERS

T h e infrared spectra of uraci l , thymine, and adeninein the gas phase

Pina Colarusso, KeQing Zhang, Bujin Guo, Peter E BernathDepartment of Chemistry, University of W aterloo, Waterloo, Ontario, Canada N2G 3G1

Received 14 Decem ber 1996; in final form 28 Janua ry 1997

A b s t r a c tTh e infrared spectra of gas-p hase uracil, thymine, and adenine have been recorded fro m 100 to 3700 cm - I at a resolutionof 1 cm -l . Th e vibrational ba nd positions and qualitative band intensities are reported and co mp ared to published m atrixdata as well as to theoretical calculations. Ou r work suggests that gas-ph ase emission spectroscopy is a sensitive techniquefor recording spec tra of organic and biological m olecules. 199 7 Elsevier Science B.V.

1 . I n t r o d u c t i o n

S p e c t r o s c o p i c i n v e s t i g a t i o n s o f t h e n u c l e i c a c i d( N A ) b a s e s c o n t a i n e d i n n o n - i n t e r a c t i n g e n v i r o n -m e n t s m a y h e l p c l a r i fy t h e r o l e o f th e s e m o l e c u l e s i nb i o l o g i c a l s y s t e m s . T h e s p e c t r a o f t h e i s o la t e d b a s e s,f o r e x a m p l e , m a y s e r v e a s r e f e r e n c e d a t a f o r t h e i n -t e r p r et a t io n o f r e su l t s o b t a i n e d i n m o r e c o m p l e x s u r -r o u n d i n g s . I n d e e d , g a s - p h a s e i n f r a r e d s t u d ie s o f o n ec l a s s o f b i o l o g i c a l m o l e c u l e s , t h e m e t a l l o p o r p h y r i n s ,h a v e i n d i c a t e d t h a t i t m a y b e p o s s i b l e t o d i s t i n g u i s hb e t w e e n t h e r m a l a n d s o l v e n t e f f e c t s o n t h e o p t i c a lspe c t r a o f t he se m o le c u le s [ 1 ,2 ] .

T h e s p e c t r o s c o p y o f t h e i s o la t e d N A b a s e s a l s o m a yb e u s e d t o p r o b e t h e m o l e c u l a r u n d e r p i n n i n g o f p o i n tm u t a t i o n s . I t b e e n p r o p o s e d [ 3 , 4 ] t h a t m u t a t i o n s o c -c u r w h e n m i n o r t a u t o m e r s o f t he N A b a s e s fo r m n o n -s t a nda r d ba se pa i r s ; i f l e f t unc o r r e c t e d , t he m ispa i r sm a y l e a d t o c h a n g e s i n t h e g e n e t ic c o d e . W h e t h e r t h eN A b a s e s t a u t o m e r i z e t o m i n o r f o r m s c a n b e s t u d i e db y a n a l y z i n g t h e s p e c t r a o f t h e i s o l a te d m o n o m e r s .

T w o t e c h n i q u e s t h a t a p p r o x i m a t e i s o l a t e d c o n d i -

t i o n s a r e m a t r i x a n d g a s - p h a s e s p e c t r o s c o p y . A l t h o u g hm a t r ix t e c hn ique s y i e ld spe c t r a t ha t a r e e x t r e m e lywe l l - r e so lve d , t he v ib r a t iona l ba nds c a n e xh ib i t sp l i t -t i ngs o r sh i f t s , a r i s ing f r om d i f f e r e nc e s in t he loc a le n v i r o n m e n t a n d i n t h e t y p e o f m a t r i x , r e s p e c t i v e l y .G a s - p h a s e s p e c t r o s c o p y , i n t u r n , i s h a m p e r e d b y t h el o w v a p o r p r e s s u re s a n d t h e p r o p e n s i t y t o w a r d d e -c o m p o s i t i o n e x h i b i t e d b y t h e N A b a s e s . I t is c l e a r t h a tr e s u l t s f r o m b o t h g a s - p h a s e a n d m a t r i x a p p r o a c h e she lp to e luc ida t e t he spe c t r a l p r ope r t i e s o f t he NAbases .

I n th i s Le t t e r , we p r e se n t su r ve y spe c t r a o f u r a c i l ,t hym ine , a nd a de n ine in t he in f r a r e d . The spe c t r a e x -t e n d f r o m 1 0 0 t o 3 7 0 0 c m - l , a r e g i o n t h a t i n cl u d e sm o s t o f t h e f u n d a m e n t a l m o d e s o f v i b r a t i o n f o r t h eN A b a s es . W e c o m p a r e t h e g a s - p h a s e re s u l t s w i th p u b -l i she d e xpe r im e n ta l a nd the o r e t i c a l s tud ie s .

P r e v ious inve s t iga t ions in t he in f r a r e d r e g ion in -c l u d e b o t h g a s - p h a s e a n d m a t r i x - p h a s e w o r k . T h ea b s o r p t i o n s p e c t r a o f g a s - p h a s e u r a c i l , m e t h y l a t e du r a c i l s , a n d m e t h y l a t e d a d e n i n e s h a v e b e e n r e p o r t e din the C =O a nd N H s t r e t c h ing r e g ions [ 5 ] . R e c e n t ly ,

0009-2614/97/$17.00 ~) 1997 Elsevier Science B.V. All rights reserved.P II S 0 0 09 - 26 1 4 ( 9 7 ) 0 0 2 4 5 - 5


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40 P C o l a r u s s o e t a l . /C h e m i c a l P h y s i c s L et t er s 2 6 9 ( 1 9 9 7 ) 3 9 - 4 8V i a n t e t a l. r e po r t e d a n a na l y s i s o f a r o t a t i ona l l yr e s o l v e d s p e c t r u m o f t h e ( P 6 C 2 = O , C 4 ) s t re t c h inu r a c i l ; t h e s p e c t r u m w a s r e c o r d e d b y e x c i t i n g t h em o l e c u l e s w i t h a n i n f r a r ed d i o d e l a s e r in a s u p e r s o n i cj e t e x p a n s i o n [ 6 ] . T h e i n f r a r e d sp e c t r a o f u ra c il [ 7 -1 3 ] a n d d e u t e r a t e d u r a c i l [ 1 0 ] , t h y m i n e [ 7 , 1 1 - 1 5 ] ,a n d a d e n i n e [ 1 6 - 1 9 ] h a v e a l so b e e n r e p o r t e d i n r a r ega s m a t r i c e s .

A s f o r m a n y p o l y a t o m i c m o l e cu l e s, t h e t h o r o u g ha s s i g n m e n t o f N A i n f r a re d s p e c t r a r e q u i r es a n i n te r -p l a y b e t w e e n t h e o r e ti c a l p r e d i c t i o n s a n d e x p e r i m e n t a lr e s u l ts . S o m e r e c e n t t he o r e t i c a l t r e a t m e n t s o f t he i n -f r a r e d s pe c t r u m o f u r a c il i nc l ude c a l c u l a t i ons a t theH a r t r e e - F oc k l e ve l u s i ng a 6 - 31G * * ba s i s s e t [ 12 , 20 ]a s w e l l a s c a l c u l a t i ons ba s e d on de ns i t y f unc t i ona lm e t h o d s [ 2 1 ] . F o r t h y m i n e , s i m i l a r p r e d i c t io n s o f t h ev i b r a t i ona l s pe c t r a ha ve be e n c a r r i e d ou t a t t he S C Fl e ve l u s i n g 6 - 3 1 G * * [ 1 2 ] a n d 6 - 3 1 G ( d ) [ 1 5 ] b a s i ss e ts . M o r e c u r r e n t w o r k o n a d e n i n e i n c l u d e s H a r t r e e -F o c k c a l c u l a t i o n s w i t h a 6 - 3 1 G ( d , p ) b a s is s e t [ 1 7 , 1 8 ]a nd a de ns i t y f unc t i ona l i nve s t i ga t i on [ 19 ] .

08H ~ ~ / HN~ ~ ~

7 IH

U r a c i l

08H\N ~ ~

7 IHThymine

H~N/HH~N 41~9~

HA d e n i n e

H

Fig. 1. Uracil, thymine, and ad enine. The atom num bering followsRefs. [12,2 0] for uracil, Ref. [121 for thymine, and R ef. [19]for adenine.

2 . E x p e r i m e n tU r a c i l , t h y m i n e , a n d a d e n i n e w e r e h e a t e d i n a tu b e

f u r n a c e i n s e p a r a t e e x p e r i m e n t s . A p p r o x i m a t e l y 3 0 go f e a c h c o m p o u n d w e r e p l a c e d i n th e c e n tr a l p o r t io no f a s t a i n l e s s s t e el t ube l i ne d w i t h py r e x . T he s t a in l e s ss te e l t u b e w a s s e a l e d w i t h K R S - 5 ( a b o v e 3 5 0 c m - 1 )o r p o l y e t h y l e n e ( b e l o w 4 0 0 c m - l ) w i n d o w s a t b o the n d s , a n d t h e n e v a c u a t ed . N e x t , 1 0 - 1 5 T o r r o f a r g o nw e r e i n t r o d u c e d i n t o t h e t u b e ; a b u f f e r g a s s u c h a s a r -g o n w a s n e c e s s a r y t o p r e v e n t d e p o s i t io n o f t h e c o m -p o u n d o n t h e w i n d o w s .

T h e c e n t ra l r e g i o n o f t h e tu b e w a s c o n t a i n e d i n ac o m m e r c i al f u r n ac e ( C M R a p i d - T e m p ) . T h e t em p e r -a t u r e o f t h e f u r n a c e w a s r a is e d a t a r a te o f 1 0 C perm i n u t e . S p e c t r a o f t h e N A b a s e s w e r e r e c o r d e d f r o m2 0 0 t o 3 2 5 C i n b o t h e m i s s i o n a n d a b s o r p t i o n . T h eb l a c k b o d y s o u r c e i n t h e a b s o r p t i o n m e a s u r e m e n t s , ag i o b a r , w a s p l a c e d a t o n e e n d o f t h e t ub e . F o r b o t h t h ee m i s s i o n a n d a b s o r p t i o n m e a s u r e m e n t s , t h e i n f r a r e dr a d i a ti o n w a s d i r e c t e d w i t h a m i r r o r f r o m t h e o t h e r e n do f t h e t u b e t h r o u g h a n e x t e r n al p o r t o f a F o u r i e r t r an s -f o r m s p e c t ro m e t e r ( B r u k e r I F S 1 2 0 H R ) . T h e r eg i o n sb e t w e e n t h e t u b e a n d t h e p o r t a s w e l l a s b e t w e e n t h et u b e a n d t h e g l o b a r w e r e p u r g e d w i t h d r y N 2 i n o r -

d e r t o m i n i m i z e a t m o s p h e ri c c o n t a m i n a t i o n f r o m C O 2a n d H 2 0 .

I n t h e s p e c tr o m e t e r , t h e b e a m o f i n f r a r e d r a d i a t io nw a s d iv i d ed b y a G e c o a t e d K B r b e a m s p l i tt e r ( 4 0 0 -4 8 0 0 c m - 1 ) o r a 3 . 5 / z m M y l a r b e a m s p l i t te r ( 1 0 0 -7 2 0 c m - 1 ) . L i q u i d - n it r o g e n c o o l e d I n : S b ( 1 8 5 0 -9 0 0 0 c m - I ) a n d M C T ( 8 0 0 - 1 8 5 0 c m - l ) d e t e c to r s a sw e l l a s l i q u id h e l i u m - c o o l e d S i : B ( 3 0 0 - 1 5 0 0 c m - 1a n d b o l o m e t e r ( b e l o w 3 5 0 c m - 1 ) d e t e c t o r s w e r e u s e dt o m e a s u r e t h e i n f r a r e d r a d i a ti o n . E a c h i n t e r f e r o g r a m ,c o r r e s p o n d i n g to t w o h u n d r e d c o - a d d e d s c a n s , w a sc o l l e c te d a t a re s o l u t i o n o f 1 c m - l ; t h e F o u r i e r t ra n s -f o r m w a s c a r r i e d o u t b y t h e B r u k e r O p u s s o f t w a r e .T h e f i n a l s p e c t r u m w a s o b t a i n e d b y t a k i n g t h e r a t i oo f th e r aw s p e c t r u m t o th e b a c k g r o u n d s p e c t r u m t h a tw a s r e c o r d e d w i t h o u t a s a m p l e i n t h e t u b e . I n o r d e rt o c h e c k f o r d e c o m p o s i t i o n p r o d u c t s , m a s s s p e c t r a o ft h e s a m p l e w e r e r e c o r d e d b e f o r e a n d a f t e r e a c h r u n .

3 . R e s u l t s a n d d i s c u s s i o nT h e s p e c t r a o f t h e t h re e N A b a s e s w e r e r e c o r d e d a s

a f u n c t i o n o f t e m p e r a tu r e . F o r e a c h c o m p o u n d , t h e v i -b r a t io n a l b a n d s b e g a n t o a p p e a r a t t e m p e r a t u r e s a b o v e2 0 0 C . A l t h o u g h w e r e c o r d e d s p e c t r a in b o t h e m i s s i o n


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P C o l a r u s s o e t a l . / C h e m i c a l P h y s i c s L e tt e r s 2 6 9 ( 1 9 9 7 ) 3 9 - 4 8 4 1

==

I L ~ i 4 - I I - i i3 2 0 0 3 3 0 0 3 4 0 0 3 5 0 0 3 6 0 0 3 7 0 0 3 8 0 0W a v e n u m b e r ( c m ~)

Fig. 2. The infrared spectra of gas-phase uracil, thymine, andadenine measured with an lnSb detector. The temperature was325C for uracil and adenine and 300C for thymine.

I b i I i ~ - - - t500 600 700 800Wavenumber cm')

Fig. 4. The infrared spectra of gas-phase uracil, thymine, andadenine obtained with an Si : B detector. The temperature was325C for uracil and adenine and 300C for thymine.

. . . . .

? ~/~ Zracil1 0 0 0 1 2 0 0 1 4 0 0 1 6 0 0 1 8 1 )0

W a v e n u m b e r ( c m ' )Fig. 3. The infrared spectra of gas-phase uracil, thymine, andadenine obtained with an MCT detector. The temperature was325C for uracil and adenine and 300C for thymine.

and in absorption, we report the emission results be-cause the technique yielded a superior signal-to-noiseratio for most modes, especially in the wavenumberregion below 1000 cm -I . We found si milar resultsin the infrared spectra of polycyclic aromatic com-pounds [22].

The infrar ed spectra, illustrated in Figs. 2-5 , weremeasured at 325C for uracil and adenine, and at300C for thymine. Mass spectra of uracil, thymine,and adenine recorded before and after each run con-

-ta5

N

t I I I ~ I I i q - -5 0 100 150 200 250 300Wavenumber cm")

Fig. 5. The infrared spectra of gas-phase adenine obtained with abolometer detector. The temperature was 325C.firmed that no appreciable decomposition occurredduring the runs. We were unsuccessful in our attemptsto record the gas-phase spectra of cytosine and gua-nine, the two other major NA bases, because the com-pounds have low vapor pressures and d ecompose read-ily when heated.

The gas-phase band pos itions and qualitative inten-sities are summarized in Tables 1-3. The error in thereported gas-phase va lues is approxi matel y -t-2 cm -t .For comparison, we have also inc luded matrix and the-oretical values that have appeared in publ ishe d reports.


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42 P . C o l a ru s s o e t a l . / C h e m i c a l P h y s i c s L e t te r s 2 6 9 ( 1 9 9 7 ) 3 9 - 4 8Table 1Uracil. Comparison of the gas-phase, matrix, and theoretical results. Band positions are in units of cm -l . For the theoretical results, theabsolute intensities follow in parentheses, in units of km /m olGas Matrix

ReL [13] ReL [12]Theory Approximate modeRef. [21] a Re~. [12,201 b de sc rip tio n e~. [12,20]

3484s 3484.3 ) 3485 3582(138) 3511(134) uN1H3479 ~ 34803472.8 34743436s 3434.5 3435 3539(74) 3477(99) uN3H3124m 3227(6) 3087(1) uC5H3184(0) 3054(4) uC6H1897m 1791.5 17921774.3 } 17751770.2 17711756vs 1763.7 1764

1762.81761.41757.5 1758 18 13 (70 5) 18 11 (45 9) uC20, uC401741 / 17421733.2 17331731.31730.3 17301728.21717.3 / 17191706.4 1706 17 6 8( 66 9) 1795(1218) uC40, uC2 01705.31703(sh)vs 1703.51698.4 1699168716811641s 1644 1644 1678 (30) 1662(1 26) uC5C616091515m 15175171474.2 }1471.91467.61465.0 14661461s 1458.5 145914251422

1472 1521 (107) 14 82 (1 4 7) ]3N1H, uC6NI

1400s 1399.6 1 1399 1424 (81) 1401(8 2)1396.7 J 1405(17) 1399(103)1387s 1388.7 1389 1357 (1.4) 1377(1 7)1386.3 }1371(sh)m 13801356 (sh)m 1359.3 13591313.3 } 13141306.2 13071302.8 13031217.4 1217 1260(14) 1212(17) uN3C4, ~C5 H1187s 1185 ~ 11921184.4 ) 1185 1179(6 9) 1175(1 15) flC6H, flN1H1172s 1183.5 1176

flN3H, uC2N3flN3H, vN3C4flC6H, flC5H


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P Colarusso et al./Chemical Physics Letters 269 (1997) 39-48 43T ab l e 1 - - c on t i n u e dGas Matrix

Ref. [13]Theory

Ref. 112] Ref . [21] a Re~ . [12,20] bA p p r ox im at e m od edescription Re~. [12,20]

1082m

9 9 0 ( s h ) w9 7 2 ( s h ) w952w802w757w717vw692vw660w

545w

512w395w374vw

1102.41075.51068.7987.5981.5958.3

80 4756.5759.2717.4662.1659.5657.355 955 6551.2536.4516.5

110210761069 1083(8) 1057(20) vC 6N I, BC 5H1065987 994(6) 998(0 .06) yC6H982 960(6) 969(7) yr ing958 926( 1 ) 947 (6) vr ing94 48 0 4 7 8 6 ( 6 6 ) 8 1 4 ( 1 0 3 ) y C5 H, y C 4 079 27 5 7 7 7 8 ( 2 ) 7 7 6 ( 1 0 5 ) y C 2 0759 747(37) 746(4) vr ing717 697(22) 723(5) yC4 0, yC5H662 663(67) 658(98) yN3H

55 955 555 054 553 651 651 439 3391

580(32) 548(5) Br ing , BCO5 4 5 ( 5 ) 5 3 0 ( 7 4 ) T NI H529(2) 533(7) BCO , Br ing505(19) 505(24) Br ing388(20) 387(32) r ing deform, yC 40376(22) 383(31 ) f lC4 0, f lC 20160 (0) 162( 1 ) ring de form137(2) 151 ( l ) r ing de form

Abbreviations: v, stretch; B, bend; T, wag; R, r ing; sh, shoulder; vs, very strong; s, strong; m, medium; w, weak; vw, very weak.a Density functional , local density approximation;b Hartree-Fock, 6-31G** basis .T h e c a l c u l a t e d i n t e n s it i e s, w h i c h f o l l o w t h e t h eo r e t ic a lw a v e n u m b e r s i n p a re n t h e se s , a r e i n un i t s o f k m / m o l .T h e a s s i g n m e n t s o f s o m e m o d e s d i ff e r a m o n g t h eq u o t e d t h e o r e t i c a l w o r k ; t o r e m a i n c o n s i s t e n t , w e l is tt h e m o d e d e s c r i p t i o n s o f R e f . [ 1 2 ] f o r u r a ci l a n dt h y m i n e a n d R e f . [ 1 9 ] f o r a d e n i n e . F o r s im p l i c i t y , t h ed e s c r i p t io n s i n c l u d e o n l y t h e d o m i n a n t m o d e c o n t r i-b u t i o n s .

A o n e - t o - o n e c o m p a r i s o n o f o u r r es u l ts w i t h t hep r e v i o u s m a t r i x a n d t h e o r e t i c a l r e s u l t s i s n o t a l w a y sp o s s i b l e b e c a u s e s o m e o f t h e g a s - p h a s e b a n ds c o n -t a in t w o o r m o r e v i b r a t i o na l m o d e s . T o o b s e r v e m o s to f t h e v i b r a t i o n a l m o d e s , i t i s n e c e s s a r y t o h e a t t h em o l e c u l e s t o a b o u t 3 0 0 C . A t s u c h el e v a t e d t em p e r -a t u r e s , r o t a t i o n a l b r o a d e n i n g c a u s e s s o m e o f t h e v i -b r a t i o n a l m o d e s t o o v e r l a p . I n a d d i t i o n , t h e g a s - p h a s e

s p ec t ra a l m o s t c e r t a in l y c o n t a i n c o m b i n a t i o n a n d o v e r -t o n e t r a n s it i o n s o f t h e l o w e r - w a v e n u m b e r v i b r a t io n a lm o d e s . O n e e x a m p l e i s t h e ba n d o b s e r v e d a t 5 7 6 c m - li n t h e a d e n i n e s p e c t r u m , wh i c h i s n o t p r e d i c t e d t o b ea fu n d a m e n t a l m o d e [ 1 9 ] .

W e d i d n o t o b s e r v e a n y e v i d e n c e o f t h e t a u t o m e r -i z a t i o n o f u r a c i l o r t h y m i n e t o t h e e n o l f o r m o r o fa d e n i n e t o t h e i m i n o f o r m , f i n d i n g s t h a t a g r e e w i t hp r e v i o u s i n f r a r e d m a t r i x e x p e r i m e n t s . I f t h e e n o l t a u -t o m e r we r e p r e s e n t i n e i t h e r u r a c i l a n d t h y m i n e , a nO H s tr e tc h w o u l d b e e x p e c t e d a b o v e 3 5 0 0 c m - 1 . T h ei m i n o f o r m o f a d e n i n e w o u l d e x p e c t t o s h o w a b an dn e a r 3 3 2 0 c m - 1 ; s u c h a b a n d w a s n o t o b s er v e d , a l -t h o u g h i t c o u l d b e o b s c u r e d b y t h e s t r o n g N H s t re t c h-i n g m o d e s i n t h e re g i o n . O u r e x p e r i m e n t s , o f c o u r s e ,d o n o t p r e c lu d e t h e e x i s t e n c e o f m i n o r t a u t o m e r s: t h e y


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44 P. Colarusso et al. /Chemical Physics Letters 269 (1997) 39-48

Table 2Thymine. Compar isonthe ab solute in tensi t ies

of the g as-phase, matrix, a nd theoretical results. Band positions are in units of cm -1 . For the theoretical results,follow in parentheses , in uni ts of km/m ol

G as Matr ixR e~ [ I l l R e f . [ 1 2 ]

Theory A pprox im a te m odeRef. [ 121 a des cript ion Ref. [ 121

3484s3437s3076m298429411772vs

1725vs

t668s1518m1463s

1409s1393s

1178s

1078m1031vw

3480 3480 3513(131) uN IH3434 3434 3477(99) vN 3H2992 3049(6 ) vC 6H2971 2943(23 ) vM e2 9 4 0 2 9 3 7 ( 1 9 ) v M e2 8 55 2 8 7 6 ( 3 1 ) v M e1768 176917591752 ~ 1805(720) vC 20

f747174217311725 }1712 1713 1784(9 49) uC 4017011684 1683 1693(8 7) uC5C6166815101472 1472 1485(163) ~ N IH

1455 14671455 1461(1 ) ~ M e1451 1451 }1437 1437 1440 (5) ~M e1433 1433 }14231419

14141405 1406 1412(1 34)1388 1389 1404(1 5)

1395 1396(10)1367

1357 1357 1360 (6) BC6H13461315130812971221 1221 1214(1 1) ~C6 H, pC2N312081198 119811901183 1184 1166 (154)11431140 113910961087 1087 1128(2 8) uC6N I1046 1056(0 . 4 ) ~ M e1005 1005 1002 (3) BM e

vC 2N 3, B N 1H~ M e~ N 3 H

uC 5C I I , uC 6N 1


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P . C o l a r u s s o e t a l . / C h e m i c a l P h y s i c s L e t te r s 2 6 9 ( 1 9 9 7 ) 3 9 - 4 8 45Tab le 2 - - co n t in u edGas Matrix

Ref . I l l ] Ref. 112]TheoryRef. [12] a

Approximate modedescription Ref. [ 121

963vw 959 959 948(8)931vw 936 936885w 890 890 934(17)804vw 800 785(7)78 5767w 764 764 778(146)755w 754 754 764(1)726 727 705 (4)689vw 662 662 658(92)658w 659 660541w 545 540541 545 }462vw 455

39 439128 0

pN1C2-,/C6H/3RIy C 2 0y C4 0 , y C2 0~C4C5yN3H

593(2) /3C20, /3C40536(7) /3R3,/3R2522(89) yNIH446 (23 ) /3R2387(24) R I, R2, R3 deform385(31 ) /3C20, /3C40291(0.2) yC5C I 1267(3) /3C5C11152(0.3) Me deform148(0.5) Me deform106(0.03) R2 deform

Abbreviations: ~,, stretch;/3, bend; 3', wag; R, ring; Me, in methyl; sh, shoulder; vs, veryweak.a Hartree-Foc k, 6-3 IG** basis.strong; s, strong; m, m edium; w, weak; vw, very

m a y b e p r e s e n t i n c o n c e n t r a t i o n s b e l o w t h e d e t e c t i o nt h r e s h o l d ( o n t h e o r d e r o f 1 % ) .W h e r e a d i r e c t c o m p a r i s o n i s p o s s i b l e , t h e a g r e e -m e n t b e t w e e n t h e g a s - p h a s e a n d m a t r i x - p h a s e b a n dp o s i t i o n s i s w i t h i n 1 0 c m - ~ . I n a d d i t i o n , t h e t h e o r e t i -c a l c a l c u l a t i o n s p r e d i c t t h e v i b r a t i o n a l b a n d p o s i t i o n st o a r e a s o n a b l e a c c u r a c y . B o t h t h e H a r t r e e - F o c k a n dd e n s i t y f u n c t i o n a l m e t h o d s y i e l d c o m p a r a b l e r e s u l t sf o r u r a c i l a n d a d e n i n e , a l t h o u g h o n e a p p r o a c h m a yl e a d t o b e t t e r r e s u l t s f o r a s p e c i f i c v i b r a t i o n a l m o d e .

A s i l l u s t r a t e d i n F i g . 5, t h e g a s - p h a s e s p e c t r u m o fa d e n i n e e x h i b i t s t h r e e s t r o n g m o d e s a t 1 6 2 , 2 0 4 , a n d2 7 0 c m - l a n d a w e a k m o d e a t 2 4 4 c m - l . T h e b a n dp o s i t i o n s a r e i n g o o d a g r e e m e n t w i t h t h e d e n s i ty f u n c-t i o n a l c a l c u l a t i o n , w h i c h p r e d i c t s m o d e s a t 1 62 , 2 0 5,2 4 4 , a n d 2 6 9 c m - l [ 1 9 ] . T h e q u a l i t a t i v e i n t e n s i ti e so f t h e g a s - p h a s e m o d e s , h o w e v e r , d o n o t m a t c h t h ep r e d i c t e d i n t e n s i t i e s q u i t e s o w e l l . O f t h e f o u r m o d e s ,t h e o n e a t 2 4 4 c m - l s h o u l d b e th e s t r o ng e s t , w i t h ap r e d i c t e d a b s o l u t e i n t e n s it y o f 1 77 k m / m o l . I n s te a d ,t h e m o d e a t 2 4 4 c m - l i s e x t r e m e l y w e a k i n t h e g a s -

p h a s e s p e c t r u m . F u r t h e r m o r e , t h e c a l c u l a t i o n p r e d i c t st h e m o d e a t 1 61 c m - 1 t o b e v e r y w e a k , b u t i t is o b -s e r v e d t o h a v e a m o d e r a t e i n t e n s i t y .

T h e w a v e n u m b e r r e g i on b e l o w 1 0 00 c m - l , w h i c hi n c l u d e s m o s t o f th e w a g a n d t o r s i o n m o d e s , m a y s e r v ea s a c o n v e n i e n t f i n g e r p r i n t r e g i o n f o r t h e N A b a s e s .A s c a n b e e x p e c t e d , t h e s p e c t r a o f u r a c il a n d t h y m i n ea r e v e r y s i m i l a r a b o v e b e c a u s e t h e i r s t ru c t u r e s d i f -f e r o n l y b y a m e t h y l g r o u p b o n d e d t o a r i n g c a r b o n .T h e s p e c t r a b e l o w 1 0 0 0 c m - 1 , h o w e v e r , c o n t a i n a f e wm o d e s t h a t m a k e t h e s p e c t r a d i s t i n g u i s h a b l e , a s s e e ni n F i g . 4 . I t c a n a l s o b e n o t e d t h a t a d e n i n e h a s s e v -e r a l c le a r l y de f i n e d m o d e s i n t h e s a m e r e g i o n . M o r e -o v e r, t h e v i b r a t i o n a l m o d e s a r e w e l l - s e p a r a t e d i n t h el o w e r w a v e n u m b e r r e g i o n a n d t h e o v e r l a p o f t h e v a r -i o us m o d e s i s m i n i m a l c o m p a r e d t o t he m i d - i n f r a r e d( M C T d e t e c t o r ) r e g i o n .

T h e s p e c t r a o f t h e i s o l a t e d b a s e s m a y h e l p g u i d et h e i n t e r p r e t a ti o n o f r e s u l t s o b t a i n e d i n i n t e r a c t i n g e n -v i r o n m e n t s , s u c h a s i n s o l v e n t s o r i n m o l e c u l a r c l u s -t e rs [ 2 3 ] . S e l e c t e d v i b r a t i o n a l b a n d s c o u l d b e m o n i -


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46 P. Colarusso e t a l . / Chemica l Phys ic s L e t ters 269 (1997 ) 39 -4 8

Table 3Adenine. Co mparison of the gas-phase, matrix, and theoretical results. Band positions are in units of cm - I. For the theoretical results, theabsolute intensities follow in parentheses, in units of km/molGas Matr ix Theory Approximate mo de

Ref. [191 Ref. [17] a Ref. I19 ] b description ReL [19 ]3565 3601 3676 (53)3557 }3555

3552m 35523506 ) 3530 3589 (80)3503

3501s 35023498349434893448 ) 3471 3540 (90)3441

3434s 34383061m 3057 3082 3195 (1)3041 3026 3115 (30)1903w 191016931659165116451639 1635 1641(597)1625vs 1626633 }

16181612 1639 1617(108)1599 1602 1584(7)1482 1549 1502(15)1468s 1474 1485 1487(57)14211415s 1419 1419 1416(18)1389 1404 1400(11)1358134 6(sh)m 1345 1350(38)13341326s 1328 1346 1342(30)1330

1280s 1290 1269 1317(67)1246 1228 1250(30)12401234s 1229 1213 1228(11)11331126w 1127 1120 1129(20)10781065 (sh)w 1061 1065(17)

1053(sh)w 10321050

vNH2 ant isym

v N9 H

uNH2symv C 8 Hv C2 H

/3NH2 scissu C6 NI 0 , u C5 C6

uN3C4~ N H 2 s c i s sv N7 C8v C 6 N I , f l C 2 HuC4C5, vC4N9f lN9H, f lC2HuN9C8u N I C 2uC2N3B C 8 H~ N H 2 r o c k , u C 5N 7p C4 N9uC8N9


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P. Colarusso et al./Chemical Physics Letters 269 (1997) 39-48 47Tab le 3 - - co n t in u edGas Matrix

Ref. [191Theory Approximate modeRef. [17] a Ref. [19] b description Re f. [19]

1018m957vw926vw

847w801w748w

650vw600vw576vw563w

515w506m497(sh)vw

10171005 996 1000(5) flNH2 rock958 1009 953 (2) yC2H927 922 925(15) fir4887 882 882(13) fiR1869848 904 831(4) ~C8H802 809 793(14) R1 deform71 769 868 767 8

702 713(3) ~N3C4

694 672(3) yC6N 10655 652 658 (6) r4 deform, r5 deform610 601 607( 1 r5 deform591583 }566 557 568(64) R1, R2 deform, yN9H515 528(13) twist NH2517 521(8) R3 deform513 500 514(61 ) yN9H503 505 504(5) twist NH2

298 298(0.5) R3 deform270m 276 271 269(22) flC6N10244vw 242 244(177) inv NH2214 205(90) Rr torsion208m 215162m 168 162(2) R2 deform93

Abbreviations: ~,, stretch; fl, bend; y , wa g; R, six-mem bered in ring; r, five-membered ring; sh, shoulder; vs, very strong; s, in strong; m,medium; w, weak; vw, very weak.a Hartree-Fock, 6-31G(d,p) basis,b Density functional, local density approximation.t o r e d f o r c h a n g e s i n p o s i t i o n a n d i n t e n s i t y as i n d i c a -t o r s o f t h e f o r m a t i o n o f i n t e r m o l e c u l a r b o n d s . I n t h eu r a c i l a n d t h y m i n e s p e c t ra , t h e b a n d s t h a t a r e a s s o c i -a t e d w i t h t h e v a r i o u s m o t i o n s o f t h e C O g r o u p s c o u l dp r o v e t o b e u s e f u l m a r k e r b a n d s . F o r i n s t an c e , t h e r e l-a t i ve i n t e n s i t i e s o f t h e C O b a n d s i n t h e s p e c t r u m o ft h y m i n e o l i g o m e r s d i s s o lv e d in D 2 0 a r e a ff e c te d w h e nb a s e p a i r i n g w i t h a d e n i n e o c c u r s [ 2 4 ] . I n t h e a d e n i n es p e c t r u m , i t i s p r o b a b l e t h a t t h e b a n d s a s s o c i a t e d w i t ht h e N H 2 m o d e s m a y b e s e n s i t i v e t o t h e f o r m a t i o n o fi n t e r m o l e c u l a r b o n d s .

T h e e x p e r i m e n t s r e p o r t e d h e r e h a v e l e d t o th e i n -

f r a re d s p e c t r a o f u r a c i l, t h y m i n e , a n d a d e n i n e o v e rt h e w a v e n u m b e r r e g i o n t h a t c o n t a i n s t h e f u n d a m e n t a lm o d e s o f v i b r a t i o n o f th e s e m o l e c u l e s . A l t h o u g h t h el o w v a p o r p re s s u r e s a n d e a s e o f d e c o m p o s i t i o n p r e s e n to b s t a c l e s t o g a s - p h a s e w o r k , i t i s p o s s i b l e t o o b t a i ns p e c t r a b y h e a t in g t h e m o l e c u l e s a n d r e c o r d i n g t h e i n -f r a re d e m i s s i o n . T h e v i b r a t i o n a l b a n d s o f t h e i s o l a t e dm o l e c u l e s m a y b e u s e d a s m a r k e r b a n d s f o r s t u d i e sc a r r i e d o u t i n i n t e r a c t i n g e n v i r o n m e n t s . I n p a r t i c u l a r ,t h e l o w e r f re q u e n c y b a n d s , c o r r e s p o n d i n g t o t h e r i n gt o r s i o n s a n d f u n c t i o n a l g r o u p w a g s , m a y b e s u i t a b l ef o r i d e n t i f y i n g t h e N A b a s e s i n m o r e c o m p l e x s y s t e m s .


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48 P Colarusso et al. /Chemical Physics Letters 269 (1997) 39-48Acknowledgements

W e t h a n k t h e N a t i o n a l S c i e n c e s a n d E n g i n e e r i n gR e s e a r c h C o u n c i l o f C a n a d a ( N S E R C ) f o r t h e s u p p o r to f t h is r e se a rc h . The a u th o r s wo u ld l i ke to t ha nk Dr .H . H u n z i k e r f o r b r i n g i n g s o m e u s e f u l r e f e r e n c e s t othe i r a t t e n t ion .

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Pina Colarusso et al- The infrared spectra of uracil, thymine, and adenine in the gas phase