Gas-Phase Experimental and Theoretical Studies of Adenine, Imidazole, Pyrrole, and Water Non-Covalent Complexes S. Carles, F. Lecomte, J. P. Schermann, and C. Desfranc ¸ ois* Laboratoire de Physique des Lasers UMR CNRS 7538, Institut Galile ´ e, UniVersite ´ Paris-Nord, F-93430 Villetaneuse, France ReceiVed: June 15, 2000; In Final Form: September 12, 2000 We present both experimental and theoretical gas-phase studies of several noncovalent complexes of elementary molecules of biological interest: adenine, imidazole, pyrrole, and water. By means of charge-transfer collisions between those complexes and laser-excited atoms, dipole-bound cluster anions are observed. This Rydberg electron transfer (RET) spectroscopic technique is used to experimentally determine the very weak excess electron binding energies of the complex anions. Theoretical calculations which rely on a homemade semiempirical intermolecular force field allow for the determination of the structures of the low-lying equilibrium configurations of the neutral complexes. The electrostatic properties of these configurations (dipole moments, quadrupole moments, etc.) lead to predicted excess electron binding energies which are compared to the experimental values. This comparison provides a test of the validity of the employed methods, as discussed in the case of the five studied complexes: adenine-imidazole, adenine-pyrrole, adenine-water, pyrrole-water, and imidazole-water. 1. Introduction Interactions between proteins and nucleic acid bases are of great importance in living systems since they govern the mechanisms of molecular recognition essential for gene expres- sion and control. Most of the knowledge about protein-DNA and protein-RNA complexes has been established by NMR and X-ray diffraction studies but model compounds have been also investigated by means of theoretical 1 and experimental studies conducted in the gas phase. 2 There is currently a large interest in the design of artificial ligands 3,4 which are capable of recognition of unique sites of DNA. 5 Those molecules would specifically bind to sequences of base pairs precisely identified in the deciphered human genome and provide tools for control of gene expression. Among artificial ligands, hairpin polyamides containing pyrrole, 3-hydroxypyrrole, and imidazole can dis- tinguish all four Watson-Crick base pairs in the minor groove of DNA. Molecular modeling studies of those artificial ligands 4 have been performed using force-fields parameters. The starting structures were then derived from NMR structures of large complexes containing imidazole, pyrrole, and poly-desoxy- nucleosides. A distance-dependent dielectric constant and a layer of water molecules were added in order to mimic biological conditions. As shown by an analysis of protein-nucleic acid base recognition sites, water molecules are indeed nearly always present in those sites and can establish bridges which mediate shape complementarity. 6 We here employ a very different and more microscopic approach in order to investigate the interactions between pyrrole, imidazole, and adenine. Our aim is to obtain gas-phase experimental data which can be directly compared either to ab initio quantum chemistry calculations or to empirical force fields. To take into account the ubiquitous presence of water in biological systems, we also consider the hydrated complexes of those molecules. We use Rydberg electron transfer (RET) spectroscopy, 7 a method which takes advantage of the rather large polarity of most molecules of biological interest and relies on the determination of dipole moment configurations of the complex by comparison between experimental data and results of semiempirical calculations. 8,9 As compared to usual UV optical spectroscopic techniques in the gas phase, 10-12 this method does not require the presence of a chromophore molecule with a well-defined UV spectroscopy in the complex. However, as discussed below, it requires that the studied complex possesses a large enough polarity together with a negative valence electron affinity. The principle of this method is briefly described in the next section, and the comparison between experimental and theoretical results of the noncovalent complexes of adenine, imidazole, pyrrole, and water is given in Section 3. 2. Rydberg Electron Transfer Spectroscopy 2.1. Method. We will here consider neutral noncovalent complexes of polar molecules which valence electron affinities are negative. This means that, upon attachment of an excess electron, no stable valence negative ions of those complexes can be formed. However, due to the existence of primarily a large enough total permanent electric dipole moment 13 and secondarily of a quadrupole moment and polarizability, 14 a very weakly bound (in the meV range) excess electron can be accommodated by the electrostatic field in a very diffuse orbital (in the nanometer range), mostly located outside the molecular frame. As it has been shown in many previous studies, 15 the formation of a stable so-called dipole-bound (or multipole- bound) anion only releases very little internal energy into the complex, so that fragmentation is very unlikely to occur, even for weakly bound noncovalent complexes. For the same reasons, the structure of the created dipole-bound anion is generally very similar to that of its neutral parent. However, this may not be * Author to whom correspondence should be addressed at Laboratoire de Physique des Lasers, Institut Galile ´e, Villetaneuse, 93430, France. Fax: (33) 1 4940 3200. E-mail: desfranc@galilee.univ-paris13.fr. 10662 J. Phys. Chem. A 2000, 104, 10662-10668 10.1021/jp002157j CCC: $19.00 © 2000 American Chemical Society Published on Web 10/28/2000