The subtle trans-gauche equilibrium in the ethanol molecule is affected by hydrogen bonding. The resulting conformational complexity in ethanol dimer manifests itself in three hydrogen-bonded OH stretching bands of comparable infrared intensity in supersonic helium expansions. Admixture of argon or nitrogen promotes collisional relaxation and is shown to enhance the lowest frequency transition. Global and local harmonic frequency shift calculations at MP2 level indicate that this transition is due to a gauche-gauche dimer, but the predictions are sensitive to basis set and correlation level. Energetically, the homochiral gauche-gauche dimer is predicted to be the most stable ethanol dimer conformation. The harmonic MP2 predictions are corroborated by perturbative anharmonicity contributions and CCSD(T) energies. Thus, a consistent picture of the subtle hydrogen bond energetics and vibrational dynamics of the ethanol dimer is starting to emerge for the first time.

In this review, we present a brief summary of the theoretical methods most frequently used in gas-phase ion chemistry. In subsequent sections, the performance of these methods is analyzed, paying attention to the reliability of geometries, vibrational frequencies, energies, and entropies. The possible pathologies of the different methods, in the form of instabilities of the wave function or spin contamination problems, are discussed. Several examples are presented to illustrate the usefulness of ab initio or density functional theory (DFT) methods to predict the existence of elusive molecules and/or to characterize non-conventional structures, and to rationalize the charge redistributions normally associated with ion-molecule interactions and which result in bond-weakening or bond-reinforcement effects. Finally, the role of non-classical structures in ion-molecule interactions is also illustrated with different examples.

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High-level G2(MP2) ab initio and B3LYP/6-311+G(3df,2p) density functional calculations have been carried out for a series of β-chalcogenovinylaldehydes, HC(X)−CHCH−CYH (X = O, S; Y = Se, Te). Our results indicate that for X = O, S and Y = Se, the O−H···Se and the S−H···Se intramolecular hydrogen bonds compete in strength with the O···Se and the S···Se interaction, while the opposite is found for the corresponding tellurium-containing analogues. The different strength of O−H···Se and O···H−Se intramolecular hydrogen bonds explains why the chelated enolic and keto forms of selenovinylaldehyde are very close in energy, although enol-tautomers are estimated to be about 10 kcal mol-1 more stable than keto-tautomers. The situation is qualitatively similar for selenothiovinylaldehyde, although the S−H···Se and S···H−Se intramolecular hydrogen bonds (IHBs) are weaker and much closer in strength, and the energy gap between enethiol- and thione-tautomers also smaller. The relative strengths of the X−H···Te and X···H−Te (X = O, S) IHBs, are very similar to those of the corresponding selenium analogues. However, there are dramatic differences as far as the X···Y (X = O, S; Y = Se, Te) interactions are concerned, which for Se-derivatives are rather small, while for Te-compounds are very strong. An analysis of these chalcogen-chalcogen interactions indicates that both, the electrostatic and the dative contributions are smaller for Se- than for Te-derivatives. In the latter, the electrostatic component clearly dominates when X = O, while the opposite is found for sulfur-containing derivatives. We have also shown that these two components are entangled in some manner, in the sense that strong electrostatic interactions favor the nO−σ*YH (or nS−σ*YH) dative interaction. The proton-transfer processes in species with IHBs were also investigated.

The complexes between BeX2 (X = H, F, Cl, OH) with different Lewis bases have been investigated through the use of B3LYP, MP2, and CCSD(T) approaches. This theoretical survey showed that these complexes are stabilized through the interaction between the Be atom and the basic center of the base, which are characterized by electron densities at the corresponding bond critical points larger than those found in conventional hydrogen bonds (HBs). Actually, all bonding indices indicate that, although these interactions that we named "beryllium bonds" are in general significantly stronger than HBs, they share many common features. Both interactions have a dominant electrostatic character but also some covalent contributions associated with a non-negligible electron transfer between the interacting subunits. This electron transfer, which in HBs takes place from the HB acceptor lone-pairs toward the σYH* antibonding orbital of the HB donor, in beryllium bonds goes from the lone pairs of the Lewis base toward the empty p orbital of Be and the σBeX* antibonding orbital. Accordingly, a significant distortion of the BeX2 subunit, which in the complex becomes nonlinear, takes place. Concomitantly, a significant red-shifting of the X-Be-X antisymmetric stretching frequencies and a significant lengthening of the X-Be bonds occur. The presence of the beryllium bond results in a significant blue-shifting of the X-Be-X symmetric stretch.

The gas-phase proton affinities of 2- and 4-thiouracil and 2,4-dithiouracil have been measured by means of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. High-level ab initio calculations, in the framework of the G2(MP2) theory, have been carried out to establish the nature of the protonation site. Thiouracils behave as bases of rather similar moderate strength in the gas phase, the 2,4-dithiouracil being the most basic of the three. In all cases, the protonation takes place at the heteroatom attached to position 4, hence although, in general, thiocarbonyls are stronger bases than carbonyls in the gas phase, 2-thiouracil behaves as an oxygen base. For 2-thiouracyl and 2,4-dithiouracil, the most stable protonated conformer is the enol−enethiol form that cannot be formed by either direct protonation of the corresponding neutral or a unimolecular tautomerization of the oxygen or sulfur protonated species. We have shown that alternative mechanisms involving the formation of hydrogen bonded dimers between the protonated form and the neutral form, followed by appropriate proton transfers within the dimer, can be invoked to explain the formation of the most stable conformer.

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