Indian Journal of Pure & Applied Physics Vol. 44, September 2006, pp. 653-660 Vibrational spectra and thermodynamics of biomolecule: 5-chlorocytosine V K Rastogi 1 , M A Palafox 2 , Kamil Lang 3 , S K Singhal 1 , R K Soni 4 & Rekha Sharma 5 1 Department of Physics, CCS University, Meerut 250 004 2 Departamento de Quimica-Fisica I, Facultad de Ciencias Quimicas, Universidad Complutense, Madrid-28040, Spain 3 Department of Kinetics, Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Czech Republic 4 Department of Chemistry, CCS University, Meerut 250 004 5 Department of Physics, Meerut College, Meerut 250 004 Received 11 November 2005; revised 9 May 2006; accepted 12 June 2006 The laser Raman and IR spectra of biomolecule 5-chlorocytosine have been recorded in solid phase. The vibrational spectra have been analysed assuming planar geometry and C s point group symmetry for the molecule and observed fundamentals have been assigned to different normal modes of vibrations. The studies indicate that the features that are characteristic of the vibrational spectra of cytosine and its derivatives are retained by the spectrum of 5-chlorocytosine and it exists in amino-oxo form in solid phase. The validity of empirical relation ν s = 345.5 + 0.876 ν asym suggests the equivalence of the two NH bonds of the NH 2 group. The observed fundamental frequencies are used to calculate the thermodynamic functions, namely, the enthalpy, entropy, heat capacity and the free energy were also computed in the temperature range 200-1000K using the rigid-rotor harmonic oscillator approximation. For this purpose, the fundamental wavenumbers obtained in the present study were taken, while the structural parameters were taken from literature. Keywords: Vibrational spectra, 5-chlorocytosine, Laser Raman spectra IPC Code: G01J3/28 1 Introduction The largest and most fascinating molecules, found in living organisms today are the nucleic acid molecules. All the evidences indicate that the nucleic acids are the molecules that exert primary control over the basic life processes in all organisms. Whatever may be the nucleic acid, on hydrolysis it is found to comprise two other kinds of molecules besides sugar molecules. These are (i) phosphoric acid and (ii) nitrogen bases:pyrimidines and purines (Fig. 1). The pyrimidine bases are all derivatives of the parent compound pyrimidine. The important pyrimidine bases found in the nucleic acid comprise cytosine, uracil and thymine (Fig. 2). Thus, for the interpretation of the vibrational spectrum of DNA, it is necessary first to assign precise frequencies of the bands observed in the spectra of nucleic bases and their derivatives. Of these, uracil and cytosine derivatives are most useful and have been found to exhibit interesting biological and chemeotherapeutic properties. A survey of large number of synthetic pyrimidines having interesting biological properties reveals that in such compounds, the position of importance are C-5 and C-6 positions. The vibrational spectra of uracil and its derivatives have been studied by a number of researchers, recent studies being those of Harsányi et al. 1 , Barnes et al. 2 , Wojick 3 , Stepanian et al. 4 and Rastogi et al 5,6 . Cytosine has been studied intensively by infrared spectroscopy in the free Fig. 1—Structure of (a) pyrimidine (b) purine Fig. 2—Structure of three pyrimidines: cytosine, thymine and uracil