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Comparison is made of the interaction of NO2 with Cu+ ions in the gas phase and inside zeolites using density functional theory (B3LYP functional). The zeolite is represented by a tritetrahedra model embedded in the periodic structure of zeolite ZSM-5 and by a free space cluster model. Both models yield virtually the same results. Cu+ is coordinated to two oxygen atoms of the zeolite framework only. For the complexes with NO2, several minima and transition structures on the potential energy surfaces are localized. The naked Cu+ ion preferentially binds NO2 in the η1-O trans mode, while in zeolites the Cu+ site binds NO2 in a 2η-O,O coordination. For the 2η-O,O structure the binding is three to four times stronger in the zeolite (43 kcal/mol) than in the gas phase which is due to a three-body zeolite frameworkCu+ ion−NO2 interaction. d10−s1d9 promotion leads to a more favorable orbital interaction between Cu+ and NO2 in the 2A‘‘ state and, due to reduced repulsion, to a stronger electrostatic interaction between Cu+ and the zeolite framework.

Cu+-exchanged Si/Al 11:1 chabazite has been studied ab initio using the periodic CRYSTAL03 computer code with Hartree−Fock and the hybrid B3LYP Hamiltonians to characterize the structures and energetics of the Cu+ ion sitting preference and its interaction with H2. Two sites (I and IV) have been found to be stable for Cu+ ion:  site I, the most stable one, envisaging coordination in a six-membered zeolite ring and site IV in which the Cu+ ion sits in the largest eight-membered ring. Interaction of H2 gives adsorption energies at B3LYP of −13 and −56 kJ/mol for sites I and IV, respectively. The B3LYP bathochromic harmonic H2 frequency shifts are 847 and 957 cm-1 for adsorption at sites I and IV, respectively, in good agreement with the shifts measured (1030 and 1081 cm-1) in the Cu−ZSM-5 system in which Cu+ ion is, respectively, three and bi-coordinated by the oxygen atoms of the zeolite framework. Analysis of the components of the adsorption energy, carried out within the cluster approach, revealed that charge transfer from the Cu(3dπ) orbital through the antibonding H2(σu) and orbital polarization play a significant role in the H2 adsorption energy, and cause the large bathochromic H2 frequency shift.

The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C') in DNA have been studied through complete DFT optimization of different structures of G-C and G-C' dimers (i.e., G-C/C-G and G-C'/C'-G), using four different functionals. Our results show that stacking leads to an increase of the O(6)...H-N(4) hydrogen bond length and to a simultaneous decrease of the N(2)-H...O(2) one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.

Ribosomes transform the genetic information encoded within genes into proteins. In recent years, there has been much progress in the study of this complex molecular machine, but the mechanism of peptide bond formation and the origin of the catalytic power of this ancient enzymatic system are still an unsolved puzzle. A quantum-mechanical study of different possible mechanisms of peptide synthesis in the ribosome has been carried out using the M06-2X density functional. The uncatalyzed processes in solution have been treated with the SMD solvation model. Concerted and two-step mechanisms have been explored. Three main points suggested in this work deserve to be deeply analyzed. First, no zwitterionic intermediates are found when the process takes place in the ribosome. Second, the proton shuttle mechanism is suggested to be efficient only through the participation of the A2451 2'-OH and two crystallographic water molecules. Finally, the mechanisms in solution and in the ribosome are very different, and this difference may help us to understand the origin of the efficient catalytic role played by the ribosome.

An isolable heterocyclic silylene (4) with two different π-donating substituents, namely a classical amino group and a more electropositive and stronger carbon-based π-donating phosphonium ylide, was synthesized and fully characterized. The combination of these two different π-donating substituents confers high thermal stability and an unusual nucleophilic character on silylene 4. Therefore, silylene 4 behaves as a strong donor ligand toward transition metals with a donating character comparable to N-heterocyclic carbenes, in contrast to classical N-heterocyclic silylenes, which generally present a weak donating character.

Improved methodologies are provided to synthesize (1R,2S)-2-aminocyclobutane-1-carboxylic acid derivatives and their incorporation into beta-peptides of 2-8 residues bearing different N-protecting groups. The conformational analysis of these oligomers has been carried out by using experimental techniques along with theoretical calculations. This study shows that these oligomers adopt preferentially a strand-type conformation in solution induced by the formation of intra-residue six-membered hydrogen-bonded rings, affording cis-fused [4.2.0]octane structural units that confer high rigidity on these beta-peptides. Moreover, all of them are prone to self-assemble producing nano-sized fibres, as evidenced by TEM, AFM and SPFM, and, in some instances, they also form gels. These techniques and molecular modelling allowed us to suggest an aggregation model for the assembly structures in which a parallel molecular-arrangement is preferred and the conformation is similar to that observed in solution. According to this model, both hydrogen-bonding and hydrophobic interactions would account for formation of the assemblies.