Easy and accurate computation of energy barriers for carbocation solvation: an expeditious tool to face carbocation chemistry.

An expeditious procedure for the challenging computation of the free energy barriers (ΔG≠) for the solvation of carbocations is presented. This procedure is based on Marcus Theory (MT) and the popular B3LYP/6-31G(d)//PCM method, and it allows the easy, accurate and inexpensive prediction of these barriers for carbocations of very different stability. This method was validated by the fair mean absolute error (ca. 1.5 kcal mol-1) achieved in the prediction of 19 known experimental barriers covering a range of ca. 50 kcal mol-1. Interestingly, the new procedure also uses an original method for the calculation of the required inner reorganization energy (Λi) and free energy of reaction (ΔG). This procedure should pave the way to face computationally the pivotal issue of carbocation chemistry and could be easily extended to any bimolecular organic reaction.

Prediction of the near-IR spectra of ices by ab initio molecular dynamics.

A method to predict the near-infrared spectra of amorphous solids by means of ab initio molecular dynamics is presented. These solids can simulate molecular ices. To test the method, mixtures of methane, water and nitrogen are generated as amorphous samples of various concentrations. The full theoretical treatment includes as a first step, the optimization of their geometrical structure for a range of densities, after which, the most stable systems are taken as initial structures for molecular dynamics, performed at 200 K in trajectories of 4 ps duration with a 0.2 fs time step. All the dynamics are carried out using the first principles method, solving the quantum problem for the electrons using density-functional theory (DFT), and integrating the DFT forces, following the Born-Oppenheimer dynamics. After the dynamics, near-IR spectra are predicted by the Fourier transform of the macroscopic polarization autocorrelation function. The calculated spectra are compared with the experimental spectra of ice mixtures of CH4 and H2O recorded in our laboratory, and with some spectra recorded by the New Horizons mission on Pluto.

Vibrational spectra and physico-chemical properties of astrophysical analogs.

We undertake in this paper a theoretical study based on DFT methodology of amorphous solids formed by methane, water and nitrogen in a ratio of 1 : 3 : 3. By varying the size of the cell containing this mixture of molecules, we study the effect of the corresponding cell volume and density on the predicted IR spectra, in particular on the hydrogen bond modes. Also the relative stability of the structures as a function of the density is studied. We have enclosed a large density range, from a very low value that simulates a gas-phase mixture, to values corresponding to solids under fairly high internal stress, with an intermediate range that could be expected to cover the values of mixtures at astronomical conditions. The variation of the energy at constant temperature with the volume of the unit cell fits well to a Morse function, which allows finding an equation of state for the material in the range of volumes studied here.

Proton transfer and autoionization in HNO3·HCl·(H2O)n particles.

The structure and spectroscopic properties of clusters of HNO(3)·HCl·(H(2)O)(n), with n = 1 to 6, have been calculated at the MP2/aug-cc-pVDZ level of theory. Altogether 22 different clusters have been found as stable structures, with minima in their potential energy surfaces. The clusters can be grouped in families with the same number of water molecules, and with close aggregation energies within each family. The addition of each new water molecule increments the aggregation energy of the clusters by a nearly constant value of 76.2 ± 0.1 Hartree. The proton transfer parameter and the coordination number of HNO(3) and HCl in each cluster have been evaluated, and the wavenumber shifts for the X(-)-H(+) vibration from the corresponding mode in the isolated molecules have also been predicted. These values allow classification of the acidic species in the clusters into three types, characterized by the strength of the hydrogen bond and the degree of ionization. A correspondence is found between the coordination number of HNO(3) and the magnitude of the X(-)-H(+) vibrational shift.

Ab initio study of hydroxyl torsional barriers and molecular properties of mono- and di-iodotyrosine.

Phenol rings with one or two iodine atoms bonded to ortho carbons are the essential organic source of iodine for living organisms. The salvage of this halogen fundamental for a variety of biological functions is accomplished through enzymatic processes that rely on recognition of mono- and di-iodotyrosine (MIT and DIT, respectively). Ab initio quantum calculations are used to investigate molecular properties of MIT and DIT associated with their recognition by cognate proteins. Energies, electron density properties, atomic charges, and electrostatic potentials are analyzed in relation with the presence of one or two iodine atoms and internal rotation of hydroxyl hydrogen. The formation of an intramolecular hydrogen bond at some conformations has little effect on the properties that might affect the recognition and further deiodination of MIT and DIT. Polarizability of iodine and the reactive nature of iodinated tyrosines as nucleophilic targets are the essential features revealed in this work.

Clusters of atmospheric relevance: H(2)O/HCl/HNO(3). Prediction of IR & MW spectra.

Theoretical calculations at the B3LYP/aug-cc-pVQZ level are performed on ternary clusters of water, hydrogen chloride and nitric acid to predict their IR and MW spectra. The main IR spectral features and their changes in a set of 15 selected clusters are analyzed in terms of the different hydrogen bonding characteristics of the aggregates. The formation of these clusters in laboratory experiments and their possible identification based on their infrared and microwave spectral properties are discussed. Based on a calculation of the Gibbs free-energy of formation of the clusters from their monomers, the population distribution of the molecules at atmospherically relevant temperatures is evaluated, and the IR spectra of the composed mixture are predicted. The variations of specific spectral features with temperature are assessed, and the possible observation of these features is proposed as a means to detect the existence of these clusters, as well as an indication of the temperature of the corresponding atmospheric sample.

Characterization of two types of intermolecular interactions on halogen monoxide monohydrates.

Monohydrates of halogen monoxides ClO.H2O and BrO.H2O have been studied by means of DFT (B3LYP) and ab initio (MP2) correlated calculations with aug-cc-pVnZ basis sets ranging from triple- up to quintuple-zeta. These complexes might be formed in the troposphere and stratosphere and participate in chemical reactions involved in ozone depletion. Two stable structures are found that differ in the intermolecular interaction which takes place, namely: conventional XO...HOH hydrogen bond and OX...OH2 halogen bond. We demonstrate that both types of interactions participate in the formation of these complexes yet all the computational methods tested predict a slightly greater stability for the latter OX...O link. Both intermolecular interactions are characterized upon analyzing electron density distribution, charge transfer effects, and electron localization domains. These analyses reveal the central role played by electron redistribution. Because of this, the greater spatial extent of the electron density in Cl or Br as compared to H could be the main cause to yield a slightly greater stability for the O-X...O halogen bond with respect to the O...H-O hydrogen bond.

An Experimental and Computational Study about the Effect of a Spirocyclopropane Group on the Solvolysis Rates of Bridgehead Triflates.

7',7'-Dimethylspiro[cyclopropane-1,2'-norbornan]-1'-yl triflate (9) was obtained and its solvolysis rates in buffered 60% aqueous ethanol were determined at different temperatures. The solvolytic behavior of 9 and other bridgehead derivatives (13-17, see Table 1) was studied by force-field, semiempirical and ab initio [B3LYP/6-31g(d)] methods. Cation 9(+) is a slightly pyramidal cyclopropylcarbinyl cation in a nearly perpendicular conformation, showing an sp(2)-like hybridization. Its high electron demand provokes an enhancement of the sigma-participation of the C(5)-C(6) and C(4)-C(7) bonds. The introduction of a cyclopropyl group adjacent to the bridgehead cation leads to an increase of the strain energy. This fact has two opposite effects on the solvolysis rate: (a) the strain energy hinders the flattening of the cation and, hence, originates a rate depression, and (b) the strained C-C bonds are prone to stabilize the cation at C(1) by sigma-delocalization, which provokes a rise of the solvolysis rate. Both effects are accounted for only by the B3LYP/6-31g method. The claimed electron-withdrawal effect of the cyclopropyl group as a basis for the small k(17)/k(16) rate ratio is not confirmed by our calculations.

Variation of atomic charges on proton transfer in strong hydrogen bonds: the case of anionic and neutral imidazole-acetate complexes.

The variation of atomic charges upon proton transfer in hydrogen bonding complexes of 4-methylimidazole, in both neutral and protonated cationic forms, and acetate anion, is investigated. These complexes model the histidine (neutral and protonated)-aspartate pair present in active sites of proteases where strong N--H...O hydrogen bonds are formed. Three procedures (Merz-Kollman scheme, Natural Population Analysis, and Atoms in Molecules Method) are used to compute atomic charges and explore their variation upon H-transfer in the gas phase and in the presence of two continuum media with dielectric constants 5 (protein interiors) and 78.39 (water). The effect of electron correlation was also studied by comparing Hartree-Fock and MP2 results for both complexes in the gas phase. Greater net charge interchanged upon H-transfer is observed in the anionic complex with respect to the neutral complex. Raising the polarity of the medium increases the amount of net charge transfer in both complexes, although the neutral system exhibits a larger sensitivity to the presence of solvent. Charge transfer associated to N--H...O and N...H--O bonds reveal the ionic contribution to the interaction depending on the number of charged subunits but the presence of solvent affects little this quantity. The lack of electron correlation overestimates all the charges as well as their variations and so uncorrelated calculations should be avoided.

Environmental effects on proton transfer in a strong hydrogen bond dimer: the 4-methyl-imidazole-aspartate case.

Proton transfer in hydrogen bond dimers formed by acetate anion plus 4-methyl-imidazole, in both neutral and protonated forms, is studied by means of ab initio correlated calculations at the MP2/6-311++G(d,p) level of theory. These two dimers are selected as systems displaying a short and strong hydrogen bond with possible low barriers to proton transfer, also these systems resemble the dyad formed by histidine aspartate which is present in a variety of enzymes whose catalytic mechanisms involve the formation of short hydrogen bonds in the active site. The purpose of this job is twofold: we focus here on the effect of the polarity of the surrounding medium on the hydrogen bond, and on the other hand we analyse the relevance of the intermonomeric distance for the low barrier to proton transfer between the partners of the dimer. We have carried out an investigation for a number of intermonomeric distances and it was found that polar solvents and short intermonomeric distances lower the barrier, enhancing in that way the proton transfer between neutral imidazole and acetate. However, the binding energy of the dimer does not follow necessarily the same pattern. In the case of protonated imidazole no double well is found at all in the potential energy curve (not even in polar media) and barrierless proton transfer to acetate occurs at the shortest intermonomeric distances.