A comparative study of the metal−glycine bonding for the biologically relevant Cu+ and Cu2+ pair is presented. The structure and vibrational frequencies for several coordination modes of Cu+ and Cu2+ to glycine have been determined using the hybrid three-parameter B3LYP density functional approach. Single-point calculations have also been carried out at the modified coupled pair functional (MCPF) and single- and double- (triple) excitation coupled cluster (CCSD(T)) levels of theory and using larger basis sets. Calculations have shown that the metal−glycine bonding and the energy ordering of the different conformers are very different in Cu+-glycine than in Cu2+-glycine. Whereas for Cu+-glycine, the ground state structure is found to have a bidentated η2-N,O coordination in which Cu+ interacts with the nitrogen of the amino group and the carbonyl oxygen, the ground state structure of Cu2+-glycine is the η 2 -O,O (CO2 -) one, derived from the interaction of the metal cation with the CO2 - terminus of the zwitterionic glycine. In this case, the results seem to indicate that glycine acquires an important radical character that changes the relative metal affinities of the different basic sites, which favors the interaction of the metal cation with the CO2 group compared with other coordinations.

Correlated calculations show the proton-transferred OH−H3O+ isomer to be the ground-state structure of the (H2O)2 + dimer ion, with the C 2 h hemibond structure being ca. 8 kcal/mol less stable. Modern density functionals however favor the hemibond structure, overestimating the strength of the three-electron bond by ca. 17 kcal/mol. The wrong prediction of the relative stability of the two isomers is attributed to overestimation by the exchange functionals of the self-interaction part of the exchange energy in the hemibond ion due to its delocalized electron hole. It is cautioned that this erroneous behavior of the density functionals for exchange, if unrecognized, may lead to wrong predictions for ground-state structures of systems with a three-electron bond.

Single and double proton-transfer reactions in Watson−Crick Guanine−Cytosine (GC) and Adenine−Thymine (AT) radical cations have been studied using the hybrid density functional B3LYP method. Calibration calculations for the formamidine−formamide dimer, a model system of AT, have shown that B3LYP compares well to the high level ab initio correlated method CCSD(T), both for the neutral and cationic systems. The single proton-transfer reaction is favorable in both the GC and AT radical cations; it takes place from the ionized monomer (guanine and adenine, respectively), which increases its acidity, to the neutral fragment. For the two systems, GC and AT, the nonproton transferred and single proton transferred structures are almost degenerate (ΔE = 1.2 kcal/mol), and the process presents low energy barriers (4.3 kcal/mol for GC and 1.6 kcal/mol for AT). The double proton-transfer reaction is less favorable than the single one, in contrast to what is observed for the neutral systems. The relative stability of the different structures can be understood considering two factors:  the relative stability of the asymptotes from which they derive and the number and sequence of the strong and weak hydrogen bonds formed. For the same number of strong short hydrogen bonds, the most stable structures are those in which the strong H-bonds are neighbors. Based on these considerations, a prediction for other pairings is reported.

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.

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Cobalt cations are open shell systems with several possible electronic states arising from the different occupations of the 3d and 4s orbitals. The influence of these occupations on the relative stability of the coordination modes of the metal cation to glycine has been studied by means of theoretical methods. The structure and vibrational frequencies have been determined using the B3LYP method. Single-point calculations have also been carried out at the CCSD(T) level. The most stable structure of Co(+)-glycine is bidentate, with the Co(+) cation interacting with the amino group and the carbonyl oxygen of neutral glycine, and the ground electronic state being (3)A. For Co(2+)-glycine, the lowest energy structure corresponds to the interaction of the metal cation with the carboxylate group of the zwitterionic glycine, the ground electronic state being (4)A''.

A detailed exploration of the three proposed mechanisms (associative, dissociative, and interchange) for the activation of Grubbs–Hoveyda-type precatalysts is performed, using DFT (B3LYP) calculations. The effects induced by the nature of the reacting alkene, the bulk of the chelating alkoxy group, and the presence of substituents in the Hoveyda ligand are taken into account. Results show that, while the associative mechanism has always high energy barriers, neither the dissociative nor the interchange mechanism can be ruled out for the first step of the activation process. In fact, the preference for one or the other mechanism seems to be influenced, to a large extent, by the nature of the chelating alkoxy group in such a way that small OR groups tend to favor the interchange pathway. Moreover, for all considered Grubbs–Hoveyda-type precatalysts, the highest transition structure corresponds to the Hoveyda ligand decoordination at the end of the cross-metathesis process. It is worth noting that this is observed regardless of the initial alkene coordination pathway (dissociative or interchange), precursor nature, and substrate and, thus, the rate-determining transition structure in all considered cases is the final alkene decoordination process. In contrast, the highest transition structure for the activation process of the phosphine-containing complexes is the initial phosphine dissociation, for which the reacting alkene is not yet involved. Overall, although the interchange mechanism may also have a role, the present calculations show that the different sign of the experimentally measured activation entropies is more likely associated with a change in the nature of the rate-determining transition structure rather than in a change of the nature of the elementary steps.

The ground and low-lying states of Cu2+−H2O have been studied using different density functional and post-Hartree−Fock methods. CCSD(T) results indicate that Cu2+−H2O has C 2 v symmetry and that the ground electronic state is a 2A1 state. At this level of theory the relative order of the electronic states is 2A1 < 2B1 < 2B2 < 2A2. However, density functional results show that the relative stabilities of these states vary depending on the degree of mixing of exact Hartree−Fock (HF) and density functional (DF) exchange. For pure generalized gradient approximation (GGA) functionals and also for hybrid functionals with percentages of HF mixing up to ∼20−25%, the 2B1 state becomes more stable than the 2A1 one. Moreover, with these functionals a C s (2A‘) structure is found to be the ground-state structure of Cu2+−H2O. This is attributed to the fact that, for C 2 v (2B1) and C s (2A‘), GGA functionals provide a delocalized picture of the electron hole, which is overstabilized due to a bad cancellation of the self-interaction part by the exchange-correlation functional. Among the different functionals tested, the one that provides better results compared to CCSD(T) is the BHLYP one.