Journal of Molecular Structure 834–836 (2007) 311–317 www.elsevier.com/locate/molstruc 0022-2860/$ - see front matter  2006 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2006.09.037 DFT calculations and vibrational (FT-IR, FT-Raman) spectra on an uracilyl-pyridinium salt A. Schmidt a , A.S. Lindner a , F.J. Ramírez b,¤ a Institute of Organic Chemistry, Clausthal University of Technology, Leibnizstrasse 6, D-38678 Clausthal-Zellerfeld, Germany b Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, Málaga 29071, Spain Received 28 July 2006; received in revised form 13 September 2006; accepted 22 September 2006 Available online 17 November 2006 Abstract In the present article we have studied the structural and vibrational properties of the N-protonated derivative of a cross-conjugated heterocyclic mesomeric betaine formed by an uracilyl and a dimethylamino substituted pyridinium group. Fourier transform infrared and Raman spectra were recorded from solid samples. Quantum chemistry density functional theory calculations were performed at the B3PW91/6-31G ¤¤ level. Geometrical parameters, charge distribution and natural bond orders were calculated for the ground-state mini- mum energy structure. The optimized geometry was found twisted with respect to the two aromatic planes. The pyridinium ring presents a quinoid structure, while the uracilyl ring only presents a localized double-bond, which is far from the carbonyl groups. The molecule is strongly polar along the longest molecular axis, being largely originated by the charge separation between the heterocycles. A force Weld and normal coordinate calculation was performed in order to correctly assign the measured infrared and Raman bands. Assignments sug- gest the existence of centro-symmetrical structures in solid state bonded by the CBO and N–H groups of the uracilyl ring. The calculated force constants in vibrational internal coordinates are in agreement with the structural parameters.  2006 Elsevier B.V. All rights reserved. Keywords: Uracilyl-pyridinium; DFT; Structure; Infrared; Raman 1. Introduction Mesomeric betaines (MB) form a class of conjugated molecules which can exclusively be presented by dipolar canonical formulae in which an odd number of positive and negative charge is delocalized within a common -electron system. Numerous MB have been identiWed as alkaloids. Examples are Nigellicine, from Nigella sativa [1], pyridino- line or pyridinebetaines [2,3]. It has been demonstrated that some MB can serve as modiWed nucleobases [4]. Some oth- ers are being currently studied as potential non-linear opti- cal materials with promising applications [5]. The study of modiWed nucleobases and related model compounds has become an important topic in modern bioorganic chemis- try. ModiWed nucleobases establish alternative base-pairing and -stacking interactions, thus providing us molecular properties which can be useful to design new chemical drugs against a wide number of diseases. The physico-chemical and biochemical properties of MB are signiWcantly inXuenced by the type of conjugation, which is modulating the internal charge separation [6]. In consequence, the study of the structural properties of a MB is essential in order to establish reliable structure–activity relationships that allow us to explain and predict the poten- tial applications of these molecules. In a recent work [7], and as a part of a wider project aimed to study modiWed nucleobases that are members of the class of heterocyclic MB [8–11], we reported the synthesis and crystal data of uracilium salts and their corresponding MB. NMR experi- ments were also performed in order to examine -stacking interactions and hydrogen bonding capabilities. The pres- ent paper is focused on the structural and vibrational * Corresponding author. Tel.: +34 952132258; fax: +34 952132000. E-mail addresses: schmidt@ioc.tu-clausthal.de (A. Schmidt), ramirez@uma.es (F.J. Ramírez).