Indian Journal of Pure & Applied Physics Vol. 4 1 . April 2003. pp. 258-26 1

Spectral and normal coordinate analysis of 5,6-dihydro-5-methyl uracil

V Krishnakumar & R Ramasamy*

Post Graduate Department of Applied Physics. Nehru Memorial Col lege, Puthanampatti 621 007

*Department of Physics, Shanmugha College of Engineering, Tirumalaisamudram 6 1 3 402

Received 25 June 2002; accepted 1 0 March 2003

�he FfIR sp.ectrum of 5.6-dihydro-5-methyl uracil has been recorded in the region 4000- 1 00 em' ! and the normal coordinate analysIs has been carried out by assuming Cs point group symmetry. All the normal modes of vibrations are assigned and calculations of potential energy distribution are also perfonned.

[Keywords: Nonnal coordinate analysis, Vibrational spectra. Dihydromethyl uracil . Potential energy]

1 Introduction

The vibrational spectra of uraci l and its derivatives have been the subject of several investigations. Though a large number of spectral data are available for these biomolecules, differences in the interpretation of the results obtained are still considerable. This is obviously due to the complexity of the spectra and nature of the substituents . Uraci l and it derivatives belong to the N-heterocyclic group and they play an important role in deriving the properties of various nucleic acid constituents ! " . In the present investigation, a complete study of vibrational spectra of 5,6-dihydro-5-methyl uracil has been carried out. The normal coordinate analysis and potential energy distribution calculations have also been performed.

2 Experimental Details

Spectroscopical ly pure 5,6-dihydro-5-methyl uracil was obtained from Sigma Chemical Co, USA, and used as such. The FfIR spectrum was recorded on BRUCKER IFS 66V model FfIR spectrophotometer, using KBr polyethylene pellets in the region 4000- 1 00 cm!.

3 Normal Coordinate Analysis

The molecular structure of 5,6-dihydro-5-methyl uraci l and its mid FfIR spectrum are shown in Fig. I (a). The far FfIR spectrum of the title compound is shown in Fig. l (b). The molecule is assumed to have C point group symmetry by treating CH, and CHz as point masses. The 30 normal modes of vibrations are distributed to 2 1 a' and 9a" group. The

a' and a" group represent the in-plane and out-of­plane vibrations, respectively. The evaluation of potential energy constants are made on the basis of General Valence Force Field, by applying Wilson 's FG matrix mechanism4• The structural parameters required for the computation are obtained from the closely related systems. The vibrational secular equations have been solved using computer programsS with s implex optimization procedure. The initial set of force constants required to solve the vibrational secular determinants were taken from the l iterature. The force constants obtained in this study, have also been refined by adopting a non-linear, least square-fit technique. In the refinement process, all the fundamental frequencies are used to refine 29 valence force constants. The refinement converged smoothly in three cycles. An average error of 1 2.6 cm! between the observed and calculated frequencies was estimated. The best-fit force constants are presented in Table I .

4 Results and Discussion

The bonding properties of uracil a nd its 1C substituent derivatives are influenced by the rearrangement of electrons during substitution and addition reactions. The values of the principal force constants obtained in this study are quite comparable with the characteristic values". The values of the potential energy constants between the carbon atoms 1. and .", are found to be 4.224 and 3 .601 m.dyne k!, respectively . This decreasing trend shows that, the force between the carbon atoms within the ring are strong, as compared to that

KRISHNA KUMAR & RAMASAMY: SPECTRA OF 5,6-DIHYDRO-5-METHYL URACIL 259

of the carbon atoms at the 5'h substituent position. Interaction force constants are slowly introduced in the force constant refinement process in order to minimize the difference between the observed and calculated frequencies.

Table I - Potential energy constants of 5,6-dihydro-5-ethyl uracil

[ In units of m.dyne k I , m.dyne rad· 1 and m.dyne k l rad-2]

Type of Para-constants meter

Diagonal constants

Stretching fo fd j, f.. iT fr

Bending fu h fr h fill fer fa fr

I nteraction constants

Stretch-stretch fos

Stretch-bend

fss fsT fs, fll fill

Bend-bend .f"u fup fuy frill

5 Vibrational Analysis

Coordinates i nvolved

N - H C - H C - N C - C c = o C - C

CNC

CCC

NCC

NCO

CCO CNH

CCH

NCN

NH CN CN CN CN CO CN CC CC CC CC CH

NH CNC

CO NCN

CO NCC

CH CCC

CC CCC

CNC CNC CNC CCC

CNC NCC CCN NCN

Value

5.4 1 8 4.532 4.968 4.224 7.569 3.60 1

1 .564

1 . 306

0.835

0.75 1

0.682 1 .341 0.485

0.247

1 . 1 94 0.966 0.793 0.654 0.236 0.275

0. 1 78

0. 1 65

0. 1 64

0. 1 36

0. 1 27

0.065

0.02 1

0.046 0.038

An attempt has been made in the study, to interpret the vibrational spectrum of the title compound, based on the results of the normal coordinate analysis. The potential energy distribution and eigen-vector calculations are also

made, to check the validity of the assignment proposed in this study.

Table 2 - V ibrational assignments of fundamental frequencies (in em- I ) of 5 ,6-dihydro-5-methyl uracil

Spe- FTIR Calcula-cies obser- ted fre-

a'

a'

a'

a'

a'

a'

a'

a'

a'

a'

a'

(l'

a'

a'

d

a'

a'

a'

a'

a"

a"

a"

a"

a"

a"

a'

a'

a"

a"

a"

ved fre- quency quency & intensity

3388 w

33 1 4m

3084 m

2996 w

2980 w 2933 w 2890 w 2839 w 1 946 w 1 758 w

1 742 w

1 7 1 5 w

1 602 w

1 495 ms 1 463 m

1 422 ms

1 4 1 7 m 1 390 ms

1 338 m

1 267 w

1 238 vs

1 1 28 m 1 1 05 w 1 0 1 9 w

1 007 w 867 w

821 ms

756 m 694 m

679 w

650 w

5 1 3 w

453 m

45 1 m 4 1 4 m 356 m

294 w 234 m

1 85 m 1 34 w

3383

3302

3072

2982

1 755

1 739

1 7 1 2

1 596

1 487 1 455 1 4 1 6

1 384

1 333

1 263

1 232

1 0 1 4

948 8 1 6

692

677

647

5 1 1 426

4 1 2

342

242 221

1 77

1 1 0

Assignments (% PED)

N - H stretching (98)

N - H stretching (98)

C - H stretching (96) C - H stretching (94)

CH, asymmetric stretching CHJ symmetric stretching CHI asymmetric stretching CH2 symmetric stretching 1 267 + 679 C=O stretching (89)

c=o stretching (li7)

C=O stretching (liD)

C-N stretching ( 84) C-C stretching (79)

C-C stretching (76)

C-N stretching (8 1 ) CHI scissoring C-N stretching (77)

N-H in-plane bending (72)

N-H i n-plane bending (70)

C-H i n-plane bending (74)

CH2 Wagging CH, rocking C-H in-plane bending (69) C-C-C trigonal bending (66)

C-C-C in-plane bending (68)

Ring breathing mode

CHI rocking N-H out-or-plane bending (62)

N-H out-or-plane bending (64)

C-H out-of-plane bending (58)

CoN out-or-plane bending ( 6 1 ) C-C-C out-or-plane bending (57)

CH, torsion C-C out-or-plane bending (64)

C-N-C in-plane bending (72)

N-C-O in-plane bending ( 7 1 ) C-N-H out-or-plane bending (64)

C-N-C out-of-planc bending (6 1 )

N-C-O out-ot-plane bending (57)

vs- very strong. s - strong, m - medium. w - weak

5.1 N-H Vibrations

In al l the heterocyclic compounds, the N-H stretching vibration7 occur in the region 3500-3000

260 INDIAN J PURE & APPL PHYS, VOL 4 1 , APRIL 2003

...-.. � C1> u

2 '8 U) <=; ", . .....

1 0 0

8 0

6 0

'"' 0 o I I H f-

20 I-' ' N / C ........... C/

I I -CH3

0

4000 3500

c C H 0"::;' '-- N / 2 I H

3 000 2 5 0 0 2000 1 500 1000 500

Fig. I (a) - Molecular structure of 5.6-dihydro-5-methyl urat:il and its mid FTIR spet:trum

65

5 5 -----� "--'

<L> 45 <.> � C<l � ·S '" 3 5 � E-<

25

15 500 450 400 350 300 250 200 150 ( 00

Wavenumber (em-I) Fig. I (b) - Far FTIR spectrum of 5.6-dihydro-5-methyl uradl

em" . Hence, the IR bands observed, in this study, at 3388 and 33 1 4 em' have been designated to N-H stretching modes of vibrations, The in-plane and out-of-plane bending vibrations of N-H group are presented in Table 2.

5.2 C-H Vibrations

The characteristic region for the ready identification of C-H stretching vibration i s in between 3 1 00-3000 cm' . The IR bands appeared at 3084 and 2996 cm" are assigned to C-H stretching vibrations for the title compound.

5.3 Methyl Group Vibrations

Fox & MartinX have assigned the symmetric and asymmetric stretching modes of methyl group at

2872 and 2962 em" in the molecules contaInIng methyl group. In the vibrational studies of 5-methyl-2-thio uracil Yadav et al.,� have identified the CH,1 symmetric and asymmetric bands at 2820 and 2920 cm" , respectively. In view of the above findings, in the present study, the IR bands at 2980 and 2933 cm' ( are assigned to CH.1 asymmetric and symmetric stretching vibrations. The rocking, torsion modes of methyl group are also found at 1 1 05 and 45 1 cnr ' , respecti vel y.

5.4 Carbonyl Vibrations

Although the two C=O groups of uracil derivatives are chemically in different positions, they seem to be interacting with each other within the uracil molecule "' , The interaction of the carbonyl

KRISHNAKUMAR & RAMASAMY: SPECTRA OF 5,6-DIHYDRO-5-METHYL URACIL 26 1

group with a hydrogen-donor group does not produce such drastic and characteristic changes in the frequency of the C=O stretch, as does by interaction of N-H stretch . A great deal of structural information can be derived from the exact position of the carbonyl stretching absorption peak. The large force constant value obtained for C=O bond indicates that, the extensive coupling interactions taking place among the C=O stretching coordinates.

In cyclic ketones, the bond angle C-O-C influences the stretching frequency of the carbonyl group. The carbonyl frequency is also affected by the adjacent C-C stretching modes. The interaction of C=O bond with adjacent C-C bond increases the energy required for C=O stretching and this increases the carbonyl stretching frequency in strained ring compounds. This behaviour of the carbonyl group is another manifestation of the steric effect.

Krishnakumar et al" identified the c=o stretching mode at 1 685 cml in 5,6-diamino uracil . In 5-iodo uracil and in 5-methyl uracil the c=o stretching modes are identified at ] 645 and 1 6 1 4 cml , respectively by Susi & Ardl2. On referring to the above findings, and on the basis of the results of the normal coordinate analysis, the IR bands appeared at 1 758, 1 742 and 1 7 ] 5 cm- I have been designated to C=O stretching modes for 5 ,6-dihydro-5-methyl uraci l in this study.

5.5 CHz Vibrations

The stretching assignments proposed, in this study, for CH2 group are presented in Table 2.

Further, the scissoring, wagging and rocking modes of CH2 group are identified at 1 4 1 7, 1 1 28 and 756 cml, respectively.

Acknowledgement

The authors are thankful to RSIC, Indian Institute of Technology, Chennai, for spectral facilities.

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