Identification of hydrolysis products of AlCl(3)*6H(2)O in the presence of sulfate by electrospray ionization time-of-flight mass spectrometry and computational methods

ElectroSpray Ionization-Mass Spectrometry (ESI-MS) and computational methods (DFT, MP2, and COSMO) were used to investigate the hydrolysis products of aluminium chloride as a function of sulfate concentration at pH 3.7. With the aid of computational chemistry, structural information was deduced from the chemical compositions observed with ESI-MS. Many novel types of hydrolysis products were noted, revealing that our present understanding of aluminium speciation is too simple. The role of counterions was found to be critical: the speciation of aluminium changed markedly as a function of sulfate concentration. Ab initio calculations were used to reveal the energetically most favoured structures of aluminium sulfate anions and cations selected from the ESI-MS results. Several interesting observations were made. Most importantly, the bonding behaviour of the sulfate group changed as the number of aqua ligands increased. The accompanying structural rearrangement of the clusters revealed the highly active role of sulfate as a ligand. The gas phase calculations were expanded to the aquatic environment using a conductor-like screening model. As expected, the bonding behaviour of the sulfate group in the minimum energy structures was distinctly different in the aquatic environment compared to the gas phase. Together, these methods open a new window for research in the solution chemistry of aluminium species.     

Conformational analysis of hydroxymatairesinol in aqueous solution with molecular dynamics

Molecular dynamics simulations were performed on the naturally occuring lignan hydroxymatairesinol (HMR) using the GROMACS software. The aim of this study was to explore the conformational behavior of HMR in aqueous solution adopting the TIP4P model. The topology of HMR was constructed by hand and HMR was modeled with the OPLS‐AA force field implemented in GROMACS. The five torsional angles in HMR were properly analyzed during the simulations. Correlations through certain patterns were observed between the angles. The determining property for the conformation preferred in aqueous solution was found to be the dipole moment and not the lowest energy in gas phase. The solvation effects on HMR was also studied by quantum chemical calculations applying the COnductorlike Screening MOdel (COSMO), the results of which were compared with results from a previous study using the Polarized Continuum Model (PCM). In the present work, COSMO was found to give more credible relative energies than PCM. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009     

Theoretical study of the oxidation of histidine by singlet oxygen

Herein we present a theoretical study of the reaction of singlet oxygen with histidine performed both in the gas phase and in aqueous solution. The potential energy surface of the reactive system was explored at the B3LYP/cc-pVTZ level of theory and the electronic energies were refined by means of single-point CCSD(T)/cc-pVTZ(-f) calculations. Solvent effects were taken into account by using a solvent continuum model (COSMO) and by adding explicit water molecules. The results show that the first step in the reaction mechanism corresponds to a nearly symmetric Diels-Alder addition of the singlet oxygen molecule to the imidazole ring to yield an endoperoxide, in agreement with experimental evidence. The intermediate formed can evolve along two different reaction paths leading to two isomeric hydroperoxides and, eventually, to open-chain or internally cyclised oxidised products. Water plays a significant role in stabilising the reaction structures by solvation and by acting as a bifunctional catalyst in the elimination/addition reaction steps. Our results explain why substituents at the N1-imidazole ring can hamper the evolution of the initial endoperoxide and result in Gibbs energy barriers in solution similar to those experimentally measured and suggest a likely route to the formation of peptide aggregates during the oxidation of histidine by singlet molecular oxygen.     

A theoretical study of neighboring-group participation in thione-to-thiol rearrangement of xanthates. molecular orbital calculation using a conductor-like screening model (COSMO) approach.

The transition structures of the thione-to-thiol rearrangement of O-(2-dimethylaminoethyl and 2-methylthio-) S-methyl xanthates in several solvents were located by semiempirical molecular orbital method (PM3) using the conductor-like screening model (COSMO) approach. Each transition state transforms into the ion-pair intermediate with a three-membered ring structure (aziridinium or thiiranium), indicating that the rearrangement proceeds through an ionic intermediate with the anchimeric assistance of the neighboring group. The intermediary structures in gas phase are also analyzed by ab initio and density functional theory calculations.     

Density functional studies of the hydrolysis of aluminum (chloro)hydroxide in water with CPMD and COSMO

Car-Parrinello molecular dynamics (CPMD) and the static density functional method (DFT) with a conductor-like screening model (COSMO) were used to investigate the chemistry of aluminum (chloro)hydroxide in water. With these methods, the stability, reactivity, and acidic nature of the chosen chlorohydrate were able to be determined. Constrained molecular dynamics simulations were used to investigate the binding of chlorine in an aquatic environment. According to the results, aluminum preferred to be 5-fold-coordinated. In addition, the activation energy barriers for the dissociation of chlorine atoms from the original chlorohydrate structure were able to be determined. The actual values for the barriers were 14 +/- 3 and 40 +/- 5 kJ mol (-1). The results also revealed the acidity of the original cationic dimer. DFT with COSMO was used to determine free energy differences for the reactions detected in the molecular dynamic simulations. In conclusion, new results and insight into the aquatic chemistry of the aluminum (chloro)hydroxides are provided.     

Environment-induced stabilization of hydrogen-bonded dimers in crystal of lysine (5-methyl-1H-[1,2,4]triazol-3ylsulfanyl)-acetate

Crystal and molecular structure of lysine (5-methyl-1H-[1,2,4]triazol-3-ylsulfanyl)-acetate was determined and intermolecular interactions between ions in crystal were investigated by quantum-chemical methods (MP2 and B3LYP-D). COSMO solvation method was used to account crystal field effects. While the gas-phase calculations significantly overestimate attraction between similarly charged and repulsion between oppositely charged ions, COSMO method provides results which are consistent with interaction energies estimated from AIM analysis of electron density distribution. Also, all hydrogen-bonded dimers found in crystal are intrinsically stable if modeled with COSMO method, contrary to gas phase calculations.     

Anchor points for the unified Brønsted acidity scale: the rCCC model for the calculation of standard Gibbs energies of proton solvation in eleven representative liquid media

The COSMO cluster-continuum (CCC) solvation model is introduced for the calculation of standard Gibbs solvation energies of protons. The solvation sphere of the proton is divided into an inner proton-solvent cluster with covalent interactions and an outer solvation sphere that interacts electrostatically with the cluster. Thus, the solvation of the proton is divided into two steps that are calculated separately: 1) The interaction of the proton with one or more solvent molecules is calculated in the gas phase with high-level quantum-chemical methods (modified G3 method). 2) The Gibbs solvation energy of the proton-solvent cluster is calculated by using the conductor-like screening model (COSMO). For every solvent, the solvation of the proton in at least two (and up to 11) proton-solvent clusters was calculated. The resulting Gibbs solvation energies of the proton were weighted by using Boltzmann statistics. The model was evaluated for the calculation of Gibbs solvation energies by using experimental data of water, MeCN, and DMSO as a reference. Allowing structural relaxation of the proton-solvent clusters and the use of structurally relaxed Gibbs solvation energies improved the accordance with experimental data especially for larger clusters. This variation is denoted as the relaxed COSMO cluster-continuum (rCCC) model, for which we estimate a 1σ error bar of 10 kJ mol(-1) . Gibbs solvation energies of protons in the following representative solvents were calculated: Water, acetonitrile, sulfur dioxide, dimethyl sulfoxide, benzene, diethyl ether, methylene chloride, 1,2-dichloroethane, sulfuric acid, fluorosulfonic acid, and hydrogen fluoride. The obtained values are absolute chemical standard potentials of the proton (pH=0 in this solvent). They are used to anchor the individual solvent specific acidity (pH) scales to our recently introduced absolute acidity scale.     

Theoretical and experimental studies of cationized uracil complexes in the gas phase

Cationized uracil clusters were generated in the gas phase by electrospray ionization (ESI). Mass spectrometry experiments showed that with particular experimental conditions, decameric uracil clusters are magic number clusters. MS/MS experiments demonstrated that the structure of these decameric uracil clusters depends substantially on the size and the charge of the cation. On the basis of the ab initio and density functional theory (DFT) quantum chemistry calculations, structures for these decameric clusters were proposed. These structures are in agreement with the experimental mass spectra of modified nucleobases. Theoretical calculations showed that complexes experimentally observed using ESI-MS techniques, are not naturally the most stable in the gas phase.     

Size selective spectroscopy of Se microclusters

The electronic structure and photofragmentation in outer and inner valence regions of Se(n) (n ≤ 8) clusters produced by direct vacuum evaporation have been studied with size-selective photoelectron-photoion coincidence technique by using vacuum-ultraviolet synchrotron radiation. The experimental ionization potentials of these clusters were extracted from the partial ion yield measurements. The calculations for the possible geometrical structures of the Se(n) microclusters have been executed. The ionization energies of the clusters have been calculated and compared with the experimental results. In addition, theoretical fragment ion appearance energies were estimated. The dissociation energies of Se(n) clusters were derived from the recurrent relation between the gas phase enthalpies of the formation of corresponding cationic clusters and experimental ionization energies.     

Structures and energetics of electrosprayed uracil(n)Ca2+ clusters (n = 14-4) in the gas phase

Clusters of uracil (U) about a calcium dication, U(n)Ca(2+) (n = 14-4), have been studied in the gas phase by both experimental and theoretical methods. Temperature dependent blackbody infrared radiative dissociation (BIRD) experiments were performed on U(n)Ca(2+) clusters with n = 14-5 and the observed Arrhenius parameters are reported here. Master equation modeling of the BIRD kinetics data was carried out to determine threshold dissociation energies. Initial geometry calculations were performed using the B3LYP density functional and 3-21G(d) basis set. A sample of ten conformations per cluster was obtained through a simulated annealing study. These structures were optimized using B3LYP/6-31G(d) level of theory. Fragment-based hybrid many body interaction (HMBI) MP2/6-311++G(2df,2p)/Amoeba calculations were performed on representative conformations to determine theoretical binding energies. Results were examined in relation to cluster size (n). A significant increase in the energy required to remove uracil from U(6)Ca(2+) when compared to larger clusters supports previous reports that the calcium ion is coordinated by six uracil molecules in the formation of an inner shell. For clusters larger than n = 6, an odd-even alternation in threshold dissociation energies was observed, suggesting that the outer shell uracil molecules bind as dimers to the inner core. Proposed binding schemes are presented. Multiple structures of U(5)Ca(2+) are suggested as being present in the gas phase where the fifth uracil may be either part of the first or second solvation shell.     

AM1 and PM3 Study of Tautomerism of Hypoxanthine in the Gas and Aqueous Phases

Heats of formation, entropies, Gibbs free energies, relative tautomerisation energies, tautomeric equilibrium constants, dipole moments, and ionization potentials for the eight possible tautomers of hypoxanthine have been studied using semiempirical AM1 and PM3 quantum-chemical calculations at the SCF level in the gas and aqueous phases, with full geometry optimization. The COSMO solvation model was employed for aqueous solution calculations. The calculations show that the two keto tautomers H17 and H19 are the predominant species at room temperature in the gas and aqueous phase. However, the tautomer H17 is the more dominant species in gas phase, while the H19 tautomer is the more dominant species in the aqueous phase. Comparison with available experimental data provides support for the results derived from theoretical computations. The entropy effect on the Gibbs free energy of hypoxanthine is very small and there is little significance for the tautomeric equilibria of the base. The enthalpic term is dominant in the determination of the equilibrium constant.     

Ab initio rigid water: effect on water structure, ion hydration, and thermodynamics

We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ( approximately 8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 A longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.     

An ab initio study of water clusters in gas phase and bulk aqueous media: (H2O)n,n=1–12

Geometries of several clusters of water molecules including single minimum energy structures of n‐mers (n=1–5), several hexamers and two structures of each of heptamer to decamer derived from hexamer cage and hexamer prism were optimized. One structural form of each of 11‐mer and 12‐mer were also studied. The geometry optimization calculations were performed at the RHF/6‐311G* level for all the cases and at the MP2/6‐311++G** level for some selected cases. The optimized cluster geometries were used to calculate total energies of the clusters in gas phase employing the B3LYP density functional method and the 6‐311G* basis set. Frequency analysis was carried out in all the cases to ensure that the optimized geometries corresponded to total energy minima. Zero‐point and thermal free energy corrections were applied for comparison of energies of certain hexamers. The optimized cluster geometries were used to solvate the clusters in bulk water using the polarized continuum model (PCM) of the self‐consistent reaction field (SCRF) theory, the 6‐311G* basis set, and the B3LYP density functional method. For the cases for which MP2/6‐311++G** geometry optimization was performed, solvation calculations in water were also carried out using the B3LYP density functional method, the 6‐311++G** basis set, and the PCM model of SCRF theory, besides the corresponding gas‐phase calculations. It is found that the cage form of water hexamer cluster is most stable in gas phase among the different hexamers, which is in agreement with the earlier theoretical and experimental results. Further, use of a newly defined relative population index (RPI) in terms of successive total energy differences per water molecule for different cluster sizes suggests that stabilities of trimers, hexamers, and nonamers in gas phase and those of hexamers and nonamers in bulk water would be favored while those of pentamer and decamer in both the phases would be relatively disfavored. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 90–104, 2001     

Theoretical study of benzonitrile clusters in the gas phase and their adsorption onto a Au(111) surface

We made theoretical calculations for a benzonitrile molecule and its clusters in the gas phase and as adsorbed on the Au(111) surface, to explain the observation by scanning tunneling microscope, that is, the trimer formation of cyanophenyl porphyrins adsorbed onto the Au(111) surface. With regard to the gas-phase species, ab initio calculations showed that (1) the benzonitrile dimer has a single stable structure that is planar and antiparallel; (2) the trimer has two isoenergetic stable structures, that is, a planar and cyclic structure and an antiparallel and nonplanar one; (3) the clusters are more stable, at low temperatures, than the monomer. For the adsorbed species, we made quantum mechanical/molecular mechanical calculations in which the interaction between the adsorbates and the surface is evaluated in a molecular-mechanical way by using analytical potential functions and an image charge model. Because the stable structures were found to be similar to those in the gas phase, the cluster formation of adsorbed cyanophenyl porphyrins was attributed to the interaction between cyanophenyl groups, which is barely affected by adsorbate-surface interaction. It was also found that the adsorbed cyclic benzonitrile trimer is more stable than the monomer and the dimer because the relative stability is dependent on enthalpy alone. We therefore concluded that the preferential formation of trimers by the adsorbed cyanophenyl porphyrins is due to the negligible contribution of entropy to the relative stability of the adsorbed species and that the adsorption hardly changes the situation found in the gas phase.     

Thermochemical properties of HxNO molecules and ions from ab initio electronic structure theory

Coupled-cluster calculations through noniterative triple excitations were used to compute optimized structures, atomization energies at 0 K, and heats of formation at 0 and 298 K for NH2O, HNOH, NH2O-, NH2OH+, NH3OH+, HNO-, and HON. These molecules are important in the gas-phase oxidation of NH3, as well as its solution-phase chemistry. The O-H, N-H, and N-O bond energies of these molecules are given and compared. The N-H and O-H bond energies are quite low, and, for NH2OH, the O-H bond is weaker than the N-H bond (by 7.5 kcal/mol). The energetics for a variety of ionic chemical processes in the gas phase, including the electron affinities of NH2O and HNO, the proton affinities of NH2O and NH2OH, and the acidities of NH2OH and NH2O, are given. The compounds are weak bases and weak acids in the gas phase. Solvation effects were included at the PCM and COSMO levels. The COSMO model gave better values than the PCM model. The relative values for pKa for NH2O and NH2OH are in good agreement with the experimental values, showing both compounds to be very strong bases in aqueous solution with NH2OH being the stronger base by 1.8 pK units at the COSMO level, compared to the experimental pK difference of 1.1+/-0.3 pK units. We predict that NH2OH+ will not be formed in aqueous solution, because it is a very strong acid. Based on the known acidity of NH3OH+, we predict pKa(NH2OH+)=-5.4 at the COSMO level, which is in good agreement with the experimental estimate of pKa(NH2OH+)=-7+/-2.     

Investigations on mixed water-clusters: Gas phase titration with cyclopentanone and identification of some isomers by time-of-flight mass spectrometry

Mixed-clusters of water with cyclopentanone have been investigated using high resolution time-of-flight mass spectrometry. These clusters are synthesized in a gas-aggregation source at comparatively higher temperature. They contain water-cluster at the core and cyclopentanone molecules hydrogen bonded through ketone oxygen with the dangling OH available at the core. Thus these mixed-clusters may also be considered as the products of a titration in gas phase. The growth reaction reveals that all clusters are protonated. From the configuration of dimer and tetramer, it is suggested that the proton resides as an Eigen ion in the core. The protonated mixed-clusters containing six, seven and eight water molecules substantiate the hydronium contained hexa, hepta and octamer water-cluster structures predicted by [KJ(H₃O)⁺] model calculations. For clusters with 9–19 water molecules, the core appears to have configurations that give less than the predicted number of dangling bonds. In large size clusters having more than 20 water molecules, the water-core appears to have open configuration like the melted structures obtained as a result of increase in temperature.     

Gas phase synthesis of Au clusters deposited on titanium oxide clusters and their reactivity with CO molecules

Titanium oxide clusters were formed in the gas phase by the laser ablation of a Ti rod in the presence of oxygen in a He gas. Not only stoichiometric but also nonstoichiometric titanium oxide clusters, Ti(n)O(2n+x)(+) (n = 1-22 and x = -1-3), were formed. The content of oxygen atoms depends strongly on a partial pressure of oxygen. Gold clusters, Au(m) (m = 1-4), were generated by the laser ablation, which were then deposited on Ti(n)O(2n+x) clusters. The formation of Au(m)Ti(n)O(2n+x)(+) follows electron transfer from Au(m) to Ti(n)O(2n+x)(+). The reactivity of Au(m)Ti(n)O(2n+x)(+) cluster ions with CO was examined for different m, n, and x by the mass spectrometry. It was found that Au(m) on Ti(n)O(2n-1)(+) are less reactive than those on the other Ti(n)O(2n+x)(+) (x = 0 and 1). In addition, the reactivity is highest when Au(m) (m = 1 and 3) is on the stoichiometric titanium oxide (x = 0), whereas the reactivity is also high when Au(2) is on the oxygen-rich titanium oxide (x = 1). The reactivity was found to relate to geometrical structures of Au(m)Ti(n)O(2n+x)(+), which were studied by density functional calculations.     

Photoelectron spectroscopic study of iron-pyrene cluster anions

Iron-pyrene cluster anions, [Fe(m)(pyrene)(n)](-) (m = 1-2, n = 1-2) were studied in the gas phase by photoelectron spectroscopy, resulting in the determination of their electron affinity and vertical detachment energy values. Density functional theory calculations were also conducted, providing the structures and spin multiplicities of the neutral clusters and their anions as well as their respective electron affinity and vertical detachment energy values. The calculated magnetic moments of neutral Fe(1)(pyrene)(1) and Fe(2)(pyrene)(1) clusters suggest that a single pyrene molecule could be a suitable template on which to deposit small iron clusters, and that these in turn might form the basis of an iron cluster-based magnetic material. A comparison of the structures and corresponding photoelectron spectra for the iron-benzene, iron-pyrene, and iron-coronene cluster systems revealed that pyrene behaves more similarly to coronene than to benzene.     

Tautomerism and proton transfer in photoionized acetaldehyde and acetaldehyde–water clusters

Understanding the gas‐phase chemistry of acetaldehyde can be challenging because the molecule can assume several tautomeric forms, namely keto, enol and carbene. The two last forms are the most stable ionic forms. Here, insight into the gas‐phase cluster ion chemistry of homogeneous acetaldehyde and mixed water–acetaldehyde clusters is provided by mass spectrometry/vacuum ultraviolet photoionization combined with density functional theory calculations. (AA)_nH⁺ clusters (AA = acetaldehyde) and mixed (AA)_nH₃O⁺ clusters were detected using tunable vacuum ultraviolet photoionization. Barrierless proton transfers were observed during the geometry optimization of the most stable dimer structures and helped to explain the cluster ion chemistry induced by photoionization, namely the formation of deprotonated tautomers and protonated keto tautomers. Water was found to catalyze the keto–enol and keto–carbene isomerizations and facilitate the proton transfer from the ionized enol or carbene part of the cluster to the neutral keto part, resulting in protonated keto structures. The production of protonated keto structures was identified to be the main fragmentation channel following ionization of the homogeneous acetaldehyde cluster and a channel for ionized mixed clusters as well. These findings are significant for a broad range of fields, including current atmospheric models, because acetaldehyde is one of the most prominent organic species in the troposphere and ions play a crucial role in aerosol formation. Copyright © 2014 John Wiley & Sons, Ltd.