DFT calculations show that in the gas phase, the adenine molecule, a DNA base, is an almost planar molecule consisting of five and six membered ring with an amino group –NH2 connected to it via a sp3 hybridization; this results in the two hydrogen
atoms slightly tilted out of the plane at a shallow angle of 14° according to our DFT calculation. Displayed in Figure 3.2 is the configuration of a single molecule in top view, denoted as A; Ā is its enantiomeric motif, obtained by reflecting A in mirror plane perpendicular to the page. Because of the nearly planar configuration, the adenine molecule is considered as prochiral and belongs to a Cs point group. Two
mirror-related adsorbed species, resulting from the two modes of adsorption by either face-up or face down [1], can be generated upon adsorption on surfaces.
Fig. 3.2: Adenine molecule in configuration A, Ā is obtained by reflecting A in a mirror plane perpendicular to the page. The six possible adenine pairs of nearest N and H atoms, referred as bonding site, that can participate in the formation of two adjacent hydrogen bonds between the two molecules are indicated [27]; the approximate dimension of an adenine molecule is also indicated, it is about 6.4 Å in length and 5.1 Å in width.
Adenine is capable of forming hydrogen bonded pairs arising from the existence of the N atoms and CH or NH groups; generally, a stable molecular dimer is characterised by at least one pair of double hydrogen bonds [28, 29]. Based on this principle, six pairs of adenine hydrogen bonding sites are identified in the adenine
molecule [10, 27], as described in Figure 3.2. Each bonding site refers to the neighbouring hydrogen bond donor, CH or NH groups, and acceptors, N atoms, and is capable of connecting with the site from another molecule in the formation of double hydrogen bonds. Hence, a total of 21 adenine dimers can be obtained; nine pairs are hetero-chiral, AĀ, where one of the molecules should be flipped to facilitate the formation of double hydrogen bonds between two corresponding sites, and twelve are homo-chiral, i.e. AA or ĀĀ. The corresponding double hydrogen bond connected dimer is denoted as AnAm orAnĀm, where n, m refers to the hydrogen bonding sites
involved. The chirality of each adenine dimer is determined by considering the individual chirality of the two molecules composing the dimer. Among these dimers, six AnAn possess C2 symmetry where double hydrogen bonding forms between the
same binding sites, and the large dipole moment is cancelled in these cases [1]. As a result, stable centro-symmetric pairs are usually adopted as the most common pairs in the construction of gas-phase overlayer networks.
Here, we present the relaxed geometries of the six centro-symmetric adenine pairs, in order of stability from high to low, Figure 3.3. All the relaxed pairs exhibit very near-planar geometries; the dimer, denoted as A5A5, has the highest stabilization energy, it is connected with other less energetically favourable dimers in the construction of adenine dimer chains observed on the Cu(110) surface [1]. Here, the structure of each pair is optimized using DFT methods with the B3LYP functional and the 6-31G basis set. It is assumed that the B3LYP functional gives a better description of the system containing hydrogen bond [30].
Fig. 3.3: Six centro-symmetric adenine pairs and the corresponding stabilization energies are given. Each molecule of the pair denotes the same hydrogen binding sites. The structures are optimized using DFT methods B3LYP functional with 6-31G basis sets. The adenine pair is denoted asAnAm, where n
and m indicate explicitly the hydrogen bonding sites of the two molecules engaged in each pair.
There have been different calculation results reported concerning the stabilization energies of the six centro-symmetric pairs, which might be due to the different functions used in the geometric optimization. However, all pairs are in the same energetic order and show the same almost planar geometries [1, 27]. The stabilization energies of all 21 gas-phase adenine pairs have been calculated by Kelly, et al.using the PBE and the B3LYP GGA functionals [27], the corresponding relaxed geometries are presented. According to their results, the Estab,which is defined as the total energy
of the relaxed dimer minus the total energy of the individual monomers relaxed separately for all the dimers, is in the range of -0.03 eV to -0.86 eV [10]; the
deformation energies are small, indicating that the atomic relaxation in each dimer is not significant, hence, it can be neglected to give a good approximation during adsorption. Dimers involving the electronegative nitrogen atoms are expected to be more energetically favourable than those including the less electronegative carbon atoms. In addition, the strength of the hydrogen bonds can be approximately evaluated by considering the corresponding hydrogen bond length and the angle between the two molecules. Stable dimers are supposed to have shorter hydrogen bond lengths and an angle of nearly 180º [10].
As we come to build up the structural models for the observed STM structure, several factors must be taken into consideration. Firstly, the geometry of the adenine pair chosen should match well the molecular features imaged in STM. Secondly, the relative stability of each adenine pair involved in the suggested building blocks has to be accounted for. This can be evaluated theoretically by the corresponding stabilization energy, referred as Estab[31]; hence, a stable dimer always has negative
stabilization energy. Lastly, in order to satisfy all the necessary links between the molecules comprising the networks with the presence of the substrate, both the favourable and less favourable pairs need to be considered [16].