Vibrational analysis of I2*- x nCO2 clusters (n = 1-10): a first principle study on microsolvation

Structure, stability, and vibrational IR and Raman spectra of I(2)(*-) x nCO(2) clusters (n = 1-10) are reported based on first-principle electronic structure calculations. Several close-lying minimum energy structures are predicted for these solvated clusters following the quasi Newton-Raphson procedure of geometry optimization. Search strategy based on Monte-Carlo simulated annealing is also applied to find out the global minimum energy structures of these clusters. Successive addition of solvent CO(2) molecules to the negatively charged diatomic solute, I(2)(*-), is fairly symmetrical. Energy parameters of these solvated clusters are calculated following second-order Moller-Plesset perturbation (MP2) as well as coupled cluster theory with 6-311+G(d) set of basis function (I atom is treated with 6-311G(d) set of basis function). The excess electron in these solvated clusters is observed to be localized mainly over the two I atoms. Average interaction energy between the anionic solute, I(2)(*-), and a solvent CO(2) molecule is approximately 129 meV in I(2)(*-) x nCO(2) clusters, and the average interaction energy between two solvent CO(2) molecules is approximately 85 meV in the case of neutral (CO(2))(n) clusters at MP2 level of theory. IR spectra show similar features in all these solvated clusters, depicting a strong band at approximately 2330 cm(-1) for C-O stretching and a weak band at approximately 650 cm(-1) for CO(2) bending modes. Degeneracy of the bending mode of a free solvent CO(2) unit gets lifted when it interacts with the charged solute I(2)(*-) to form a molecular cluster because of the change in structure of solvent CO(2) units. The vibrational band at the bending region of CO(2) in the Raman spectra of these anionic clusters shows a characteristic feature for the formation of I(2)(*-) x nCO(2) clusters showing a Raman band at approximately 650 cm(-1).     

A theory of elementary photophysical processes with the participation of excess electrons in polar liquids

The main concepts of the new theory of processes with the participation of excess electrons in polar liquids are considered. The theory takes into account that (1) polar liquids are electrostatically inhomogeneous (local potentials on molecules are different) and (2) a molecule can accept an electron for a short time to produce an anion in an unstable state with a certain energy and lifetime. A discrete model of a substance consisting of molecules with constant dipole moments is used. Excess electrons in a liquid are described by energy distribution density, and the behavior of electrons, by quantum mechanics equations. The experimental data on the photoionization of water and aqueous solutions of salts and the low threshold energy of photons (～6.5 eV) at which solvated electrons appear in water are explained. The absorption spectra of water with excess electrons at the first and subsequent time moments after their photogeneration are reproduced theoretically. The dependence of the photoemission of solvated electrons from potassium-ammonia solutions on the energy of photons is interpreted. The continuous spectrum of spontaneous radiation of solvated electrons in liquid ammonia and water is calculated. The optical absorption spectra of solvated electrons in such polar liquids as water and ammonia are reproduced.     

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 A r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1-0.2 Debye in keeping with previously reported work.     

Hydrogen bond dynamics at water/organic liquid interfaces

Hydrogen bond dynamics at the neat interface between water and a series of organic liquids are studied with molecular dynamics computer simulation. The organic liquids are nonpolar (carbon tetrachloride), weakly polar (1,2-dichloroethane), and polar (nitrobenzene). The effect of surface polarity and surface roughness is examined. The dynamics are expressed in terms of the hydrogen bond population autocorrelation functions and are found to be nonexponential and strongly dependent on the nature of the organic phase. In particular, at all interfaces, the dynamics are slower at the interface than in the bulk and sensitive to the location of the water molecules along the interface normal.     

Solvation of perfluorooctane and octane in water, methanol, acetonitrile, and aqueous mixtures of methanol and acetonitrile

Molecular dynamics simulations are used to examine the local solvation structure of single octane and perfluorooctane molecules in liquid water, methanol, acetonitrile, and aqueous mixtures of methanol and acetonitrile. The motivation is to obtain baseline information about the solvation of perfluorooctane by liquids used as the mobile phase in liquid chromatography and how it differs from the solvation of octane. While octane is uniformly solvated by both water and the second component, perfluorooctane is solvated by methanol and acetonitrile with the exclusion of water from the first solvation layer when the solvent is a mixture.     

Mechanism of pyridine protonation in water clusters of increasing size

This work presents a theoretical mechanistic study of the protonation of pyridine in water clusters, at the B3LYP/cc-pVDZ theory level. Clusters from one to five water molecules were used. Starting from previously determined structures, the reaction paths for the protonation process were identified. For complexes of pyridine with water clusters of up to three water molecules just one transition state (TS) links the solvated and protonated forms. It is found that the activation energy decreases with the number of water molecules. For complexes of four and five water molecules two transition states are found. For four water molecules, the first TS links the starting solvated structure with a new, less stable, solvated form through a concerted proton transfer between a ring of water molecules. The second TS links the new solvated structure to the protonated form. Thus, protonation is a two-step process. For the five water molecules cluster, the new solvated structure is more stable than the starting one. This structure exhibits two double hydrogen bonds involving the pyridinic nitrogen and several water molecules. The second TS links the new structure with the protonated form. Now the process occurs in one step. In all cases considered, the proton transfers involve an interconversion between covalent and hydrogen bonds. For four and five water molecules, the second TS is structurally and energetically very close to the protonated form. As evidenced by the vibration frequencies, this is due to a flat potential energy hypersurface in the direction of the reaction coordinate. Determination of DeltaG at 298.15 K and 1 atm shows that the protonation of pyridine needs at least four water molecules to be spontaneous. The complex with five water molecules exhibits a large DeltaG. This value yields a pKa of 2.35, relatively close to the reported 5.21 for pyridine in water.     

The photo-dissociation of the pyrrole-ammonia complex--the role of hydrogen bonding in Rydberg states photochemistry

The photochemistry of the pyrrole-ammonia cluster is analyzed theoretically. Whereas in neat pyrrole the dominant photochemical reaction is H-atom cleavage, recent experiments show that in pyrrole-ammonia clusters the major reaction is H-transfer to form the NH(4) radical (solvated by ammonia molecules in the case of large clusters) and the pyrrolyl radical. A mechanism involving the hydrogen-bonded Rydberg state is offered to account for these results and verified computationally. Two minima are located on the lowest excited singlet PES. Both of them are Rydberg states, one leads to the formation of NH(4) and pyrrolyl radicals, the other is connected to the πσ* state through a relatively high barrier, leading to a 3-body dissociation reaction to form a pyrrolyl radical, ammonia and an H-atom. The former is the energetically and statistically preferred one.     

On the structure of water—alcohol and ammonia—alcohol protonated clusters

Collision-induced dissociation (CID) of protonated ammonia-alcohol and water-alcohol heteroclusters was studied using a triple quadrupole mass spectrometer with a corona discharge atmospheric pressure ionization source. CID results suggested that the ammonia-alcohol clusters had NH: at the core of the cluster and that hydrogen-bonded alcohol molecules solvated this central ion. In contrast, CID results in water-alcohol clusters showed that water loss was strongly favored over alcohol loss and that there was a preference for the charge to reside on an alcohol molecule. The results also indicated that a loose chain of hydrogen-bonded molecules was formed in the water-alcohol clusters and that there appeared to be no rigid protonation site or a fixed central ion. (J Am Soc Mass     

X-ray structural studies on microscopic mixing in binary mixtures of dimethyl sulphoxide with acetonitrile and N,N-dimethylformamide

The liquid structures of binary acetonitrile (AN)–dimethyl sulphoxide (DMSO) and N,N-dimethylformamide (DMF)–DMSO mixtures were investigated by the X-ray scattering method. Comparison of the X-ray scattering data of AN–DMSO liquid mixtures with those of neat AN and DMSO revealed that the intermolecular AN–DMSO interactions are practically not detected; that is, the X-ray scattering data of the liquid mixtures are well reproduced by summing up those of neat AN and DMSO weighted by their mole fractions. The same applies for DMF–DMSO mixtures. Thus, each component solvent molecule independently forms self-assembled clusters in the liquid mixtures, the structures of which are the same as those in the neat liquids. The clusters are mixed to form macroscopically homogeneous liquid mixtures. The thermodynamic quantities on mixing process for the AN–DMSO, DMF–DMSO and AN–DMF systems in the literature are well elucidated on the basis of the microscopic structure of the liquid mixtures.     

Non-nuclear attractor of electron density as a manifestation of the solvated electron

Two or more polar molecules can trap an excess electron either in a dipole-bound fashion where it is located outside of the cluster (dipole-bound electron) or inside the cluster (solvated electron). The topology of the electron density in dipole-bound and solvated-electron clusters has been examined for the paradigm (HF)3- cluster. As spatial confinement of the excess electron increases, a non-nuclear maximum (or attractor) of the electron density eventually forms, which suggests that the solvated electron can be described as a topological atom with its own set of physicochemical properties.     

Electron trapping by polar molecules in alkane liquids: cluster chemistry in dilute solution

Experimental observations are presented on condensed-phase analogues of gas-phase dipole-bound anions and negatively charged clusters of polar molecules. Both monomers and small clusters of such molecules can reversibly trap conduction band electrons in dilute alkane solutions. The dynamics and energetics of this trapping have been studied using pulse radiolysis-transient absorption spectroscopy and time-resolved photoconductivity. Binding energies, thermal detrapping rates, and absorption spectra of excess electrons attached to monomer and multimer solute traps are obtained, and possible structures for these species are discussed. "Dipole coagulation" (stepwise growth of the solute cluster around the cavity electron) predicted by Mozumder in 1972 is observed. The acetonitrile monomer is shown to solvate the electron by its methyl group, just as the alkane solvent does. The electron is dipole-bound to the CN group; the latter points away from the cavity. The resulting negatively charged species has a binding energy of 0.4 eV and absorbs in the infrared. Molecules of straight-chain aliphatic alcohols solvate the excess electron by their OH groups; at equilibrium, the predominant electron trap is a trimer or a tetramer, and the binding energy of this solute trap is ca. 0.8 eV. Trapping by smaller clusters is opposed by the entropy that drives the equilibrium toward the electron in a solvent trap. For alcohol monomers, the trapping does not occur; a slow proton-transfer reaction occurs instead. For the acetonitrile monomer, the trapping is favored energetically, but the thermal detachment is rapid (ca. 1 ns). Our study suggests that a composite cluster anion consisting of a few polar molecules imbedded in an alkane "matrix" might be the closest gas-phase analogue to the core of solvated electron in a neat polar liquid.     

Microscopic hydration of the sodium chloride ion pair

Hydration of ion pairs is an essential process in various physicochemical phenomena occurring in solutions. Isolated clusters of an ion pair solvated with finite number of waters have been considered as a model system for the critical evaluation of microscopic interactions involved in the process, and theoretical studies have contributed exclusively to the subject up to now. Here we report the first experimental characterization of structure and internal dynamics of hydrated ion pairs, NaCl-(H2O)n (n = 1-3). The measurements of their rotational spectra have proven that the clusters have cyclic forms, in which Na+ and Cl- ions are strongly interacted with the O and H atoms of the solvent molecules, respectively. The Na-Cl distance shows a pronounced increase with the successive addition of water molecules. The separation for n = 3 approaches the value predicted for the contact ion-pair state in aqueous solution by recent molecular dynamics simulations.     

Molecular dynamics study of 2-nitrophenyl octyl ether and nitrobenzene

The pure organic liquids nitrobenzene (NB) and 2-nitrophenyl octyl ether (NPOE) have been studied by means of molecular dynamics simulations. Both solvents are extremely important in various interfacial processes, mainly connected with ion transfer taking place across the interface with water. Thermodynamic (mass density, enthalpy of vaporization, isothermal compressibility, dipole moment) and dynamic (viscosities and self-diffusion coefficients) properties of both liquids have been calculated and are in very good agreement with the experimental data. In the case of NB, several potentials have been tested and the obtained results compared and discussed. In most cases, the OPLS all-atom potential gives results that are in better agreement with available experimental values. Atomic radial distribution functions, dihedral and angle distributions, as well as dipole-orientation correlation functions are used to probe the structure and interactions of the bulk molecules of both organic solvents. These were seen to be very similar in terms of structure and thermodynamics, but quite distinct in terms of dynamic behavior, with NPOE showing a much slower dynamic response than NB. A simulation study of the simple Cl- and K+ ions dissolved in both solvents has been also undertaken, revealing details about the diffusion and solvation mechanisms of these ions. It was found that in both liquids the positive potassium ion is solvated by the negative end of the molecular dipole, whereas the negative chloride ion is solvated by the positive end of the dipole.     

Enhanced stability of the model mini‐protein in amino acid ionic liquids and their aqueous solutions

Using molecular dynamics simulations, the structure of model mini‐protein was thoroughly characterized in the imidazolium‐based amino acid ionic liquids and their aqueous solutions. Complete substitution of water by organic cations and anions further results in hindered conformational flexibility of the mini‐protein. This observation suggests that amino acid‐based ionic liquids are able to defend proteins from thermally induced denaturation. We show by means of radial distributions that the mini‐protein is efficiently solvated by both solvents due to a good mutual miscibility. Amino acid‐based anions prevail in the first coordination sphere of positively charged sites of the mini‐protein whereas water molecules prevail in the first coordination sphere of negatively charged sites of the mini‐protein. © 2015 Wiley Periodicals, Inc.     

Parallel variable selection of molecular dynamics clusters as a tool for calculation of spectroscopic properties

Clusters of a solute and a few solvent molecules obtained from molecular dynamics (MD) are a powerful tool to study solvation effects by advanced quantum chemical (QC) methods. For spectroscopic properties strongly dependent on the solvation, however, a large number of clusters are needed for a good convergence. In this work, a parallel variable selection (PVS) method is proposed that in some cases efficiently reduces the number of clusters needed for the averaging. The mass, charge, or atomic density MD distributions are used as a secondary variable to preselect the most probable cluster geometries used for averaging of solute spectral properties. When applied to nuclear magnetic resonance chemical shift of a model alcohol, the method allowed one to significantly reduce the total computational time, by a factor of 10. Even larger savings were achieved for the modeling of Raman and Raman optical activity spectra of (S)‐lactamide molecule dissolved in water. The results thus suggest that the PVS method can be generally used for simulations of spectroscopic properties of solvated molecules and makes multiscale MD/QC computations more affordable. © 2012 Wiley Periodicals, Inc.     

Ionic Liquids Made with Dimethyl Carbonate: Solvents as well as Boosted Basic Catalysts for the Michael Reaction

This article describes 1) a methodology for the green synthesis of a class of methylammonium and methylphosphonium ionic liquids (ILs), 2) how to tune their acid–base properties by anion exchange, 3) complete neat‐phase NMR spectroscopic characterisation of these materials and 4) their application as active organocatalysts for base‐promoted carbon–carbon bond‐forming reactions. Methylation of tertiary amines or phosphines with dimethyl carbonate leads to the formation of the halogen‐free methyl‐onium methyl carbonate salts, and these can be easily anion‐exchanged to yield a range of derivatives with different melting points, solubility, acid–base properties, stability and viscosity. Treatment with water, in particular, yields bicarbonate‐exchanged liquid onium salts. These proved strongly basic, enough to efficiently catalyse the Michael reaction; experiments suggest that in these systems the bicarbonate basicity is boosted by two orders of magnitude with respect to inorganic bicarbonate salts. These basic ionic liquids used in catalytic amounts are better even than traditional strong organic bases. The present work also introduces neat NMR spectroscopy of the ionic liquids as a probe for solute–solvent interactions as well as a tool for characterisation. Our studies show that high catalytic efficacy of functional ionic liquids can be achieved by integrating their green synthesis, along with a fine‐tuning of their structure. Demonstrating that ionic liquid solvents can be made by a truly green procedure, and that their properties and reactivity can be tailored to the point of bridging the gap between their use as solvents and as catalysts.     

Formation of solvated ions in the atmospheric interface of an electrospray ionization triple-quadrupole mass spectrometer

A simple method capable of generating and investigating various solvent clusters and solvated ions was developed. The technique opens a door to studying these complexes on commercially available instruments. Formation of the desired solvated ion in the gas phase was achieved by introducing the appropriate volatile solvent vapour into the curtain gas stream. Capabilities of the technique are illustrated by generating alkali, alkaline earth and transition metal cations solvated by various volatile compounds such as water, methanol and acetonitrile. Depending on the ligands and on the experimental conditions, clusters of 2-100 molecules may be observed. Isotope labelling suggests that these are formed by a re-solvation process in the curtain gas region.     

Janus and ternary particles generated by microfluidic synthesis: design, synthesis, and self-assembly

This paper reports a microfluidic method for fast continuous synthesis of Janus particles and three-phase particles with narrow size distribution. Synthesis of particles included emulsification of monomer liquids and in-situ photoinitiated polymerization of multiphase droplets. We show the strategy for precise control over the structure of Janus particles and their structure-dependent assembly in clusters. We demonstrate an asymmetric chemical modification of the surface of JPs by conjugating them with protein molecules. The Janus and ternary particles were synthesized from largely immiscible liquids and had a sharp interface between the constituent phases.     

Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer

The relative stabilities of glycine tautomers involved in the intramolecular proton transfer are investigated computationally by considering glycine-water complexes containing up to five water molecules. The supermolecule results are compared with continuum calculations. Specific solute-solvent interactions and solvent induced changes in the solute wave function are considered using the natural bond orbitals (NBO) method. The stabilization of the zwitterion upon solvation is explained by the changes in the wave functions localized on the forming and breaking bonds as well as by the different interaction energies in the zwitterionic and neutral clusters. Only the neutral species exist in mono- and dihydrated clusters and in the gas phase. In the smaller clusters, zwitterions are mainly stabilized by conformational effects, whereas in larger clusters, in particular when glycine is solvated on both sides of its heavy atom backbone, polarization effects dominate the stability of a given tautomer. Generally, the strength of the solute-solvent interactions is governed by the intermolecular charge transfer interactions. As the solvation progresses, the hypothetical gaseous zwitterion is better solvated than the gaseous neutral, making zwitterion to neutral tautomerization progressively less exothermic for clusters containing up to three water molecules, and endothermic for larger clusters. The neutral isomer does not exist for some solvent arrangements with five water molecules. Only solvent arrangements in which water molecules do not interact with the reactive proton are considered. Hence, the experimentally observed double well potential energy surface may be due to such an interaction or to a different reaction mechanism.