Clustering Of Solvent Molecules Research Articles

Ion Formation from Rapidly Heated Aqueous Droplets by Droplet-Assisted Ionization.

When aqueous droplets travel through a temperature-controlled capillary from atmospheric pressure into a vacuum, they undergo aerodynamic and/or thermal breakup to give charged progeny droplets that subsequently produce gas-phase molecular ions from solutes that were in the original droplets. This phenomenon is the basis of droplet-assisted ionization, a method that was recently developed for online characterization of aerosols by mass spectrometry. The conditions allowing initial droplets to break up into progeny droplets were studied by computational fluid dynamics (CFD) with a droplet evaporation model. The CFD results were then used to interpret experimental measurements of ion current vs capillary wall temperature. For capillary wall temperatures below about 150 °C, the abilities of droplets to undergo either aerodynamic or thermal breakup are strongly temperature dependent. Above this temperature, the mode of initial droplet breakup becomes temperature independent, and the temperature dependence of the ion signal intensity can be explained in relation to ion formation from charged progeny droplets. Activation energies for ion formation fall into two main categories: ∼41 kJ mol-1 for droplets containing predominantly nonionic solutes, which matches the enthalpy of vaporization for water and suggests a charge residue process for ion formation, and ∼24 kJ mol-1 for droplets containing salts, which suggests an ion evaporation process where the ion is ejected from the droplet surface within a cluster of solvent molecules.

A First Principle Model of Differential Ion Mobility: the Effect of Ion-Solvent Clustering.

The use of differential mobility spectrometry (DMS) as a separation tool prior to mass analysis has increased in popularity over the years. However, the fundamental principles behind the difference between high- and low-field mobility is still a matter of debate-especially regarding the strong impact of solvent molecules added to the gas phase in chemically modified DMS environments. In this contribution, we aim to present a thorough model for the determination of the ion mobility over a wide range of field strengths and subsequent calculation of DMS dispersion plots. Our model relies on first principle calculations only, incorporating the modeling of the "hard-sphere" mobility, the change in CCS with field strength, and the degree of clustering of solvent molecules to the ion. We show that all three factors have to be taken into account to qualitatively predict dispersion plots. In particular, type A behavior (i.e., strong clustering) in DMS can only be explained by a significant change of the mean cluster size with field strengths. The fact that our model correctly predicts trends between differently strong binding solvents, as well as the solvent concentration and the background gas temperature, highlights the importance of clustering for differential mobility.

Structures of clusters surrounding ions stabilized by hydrogen, halogen, chalcogen, and pnicogen bonds

Four H-binding HCl and HF molecules position themselves at the vertices of a tetrahedron when surrounding a central Cl−. Halogen bonding BrF and ClF form a slightly distorted tetrahedron, a tendency that is amplified for ClCN which forms a trigonal pyramid. Chalcogen bonding SF2, SeF2, SeFMe, and SeCSe occupy one hemisphere of the central ion, leaving the other hemisphere empty. This pattern is repeated for pnicogen bonding PF3, SeF3 and AsCF. The clustering of solvent molecules on one side of the Cl− is attributed to weak attractive interactions between them, including chalcogen, pnicogen, halogen, and hydrogen bonds. Binding energies of four solvent molecules around a central Na+ are considerably reduced relative to chloride, and the geometries are different, with no empty hemisphere. The driving force maximizes the number of electronegative (F or O) atoms close to the Na+, and the presence of noncovalent bonds between solvent molecules.

Three dimensional nanoscale analysis reveals aperiodic mesopores in a covalent organic framework and conjugated microporous polymer.

The integrated analytical approach developed in this study offers a powerful methodology for the structural characterisation of complex molecular nanomaterials. Structures of a covalent organic framework based on boronate esters (COF-5) and a conjugated microporous polymer (Aza-CMP) have been investigated by a combination of several electron microscopy techniques elucidating the three-dimensional topology of the complex polycrystalline (COF) and non-crystalline (CMP) materials. Unexpected, aperiodic mesoporous channels of 20-50 nm in diameter were found to be penetrating the COF and CMP particles, which cannot be detected by X-ray diffraction techniques. The mesopores appear to be stable under a range of different conditions and accessible to gas molecules, exhibiting a particular bonding capability with CO2 in the case of the CMP. The mesoporosity is unrelated to the intrinsic chemical structures of the COF or CMP but rather it reflects the mechanisms of polymer particle formation in a polycondensation reaction. The mesopores may be templated by clusters of solvent molecules during the COF or CMP synthesis, leaving cavities within the polymer particles. The unexpected mesoporosity discovered in COF and CMP materials begs for re-assessment of the nature of framework materials and may open new opportunities for applications of these molecular materials in gas sorption or catalysis.

Structural and functional characterization of EIAV gp45 fusion peptide proximal region and asparagine-rich layer

Equine infectious anaemia virus (EIAV) and human immunodeficiency virus (HIV) are members of the lentiviral genus. Similar to HIV gp41, EIAV gp45 is a fusogenic protein that mediates fusion between the viral particle and the host cell membrane. The crystal structure of gp45 reported reveals a different conformation in the here that includes the fusion peptide proximal region (FPPR) and neighboring asparagine-rich layer compared with previous HIV-1 gp41 structures. A complicated hydrogen-bond network containing a cluster of solvent molecules appears to be critical for the stability of the gp45 helical bundle. Interestingly, viral replication was relatively unaffected by site-directed mutagenesis of EIAV, in striking contrast to that of HIV-1. Based on these observations, we speculate that EIAV is more adaptable to emergent mutations, which might be important for the evolution of EIAV as a quasi-species, and could potentially contribute to the success of the EIAV vaccine.

Putting the squeeze on cavities in liquids: Quantifying pressure effects on solvation using simulations and scaled-particle theory

Extensive molecular simulations of the Lennard-Jones fluid are performed to examine the response of the excess chemical potential of cavitylike solutes to applied pressure. Solutes as large as ten times the solvent diameter are considered. The simulations are analyzed using the revised scaled-particle theory developed by Ashbaugh and Pratt to evaluate the thermodynamics of cavity solvation and curvature dependent interfacial properties well into the compressed liquid portion of the solvent phase diagram. The revised theory provides a quantitatively accurate description of the solvent-solute contact correlation function for all solutes and state points considered. The main structural effect of increasing pressure is to push the solvent molecules up against the solute surfaces, counteracting the dewetting that is observed at lower pressures along the solvent saturation curve. Decomposing the excess chemical potential of cavities into volume and surface-area contributions shows that pressure differentially affects the interfacial free energies of molecular versus macroscopic solutes. The interfacial free energy of surfaces of molecular dimension monotonically decreases with applied pressure, while that of surfaces larger than a small cluster of solvent molecules exhibit a maximum with increasing pressure, which may play a role in pressure-induced disaggregation of molecular assemblies. Moreover, since the pressure dependence of the interfacial free energy is thermodynamically linked to the excess adsorption of solvent on the solute surface, the former is potentially a measurable macroscopic indicator of microscopic wetting∕dewetting phenomena, implicated in hydrophobic interactions between macroscopic hydrophobic particles. Finally, some inferences about pressure-dependent solvation processes in water are made by using the revised theory to analyze previously published simulation data.

Solvation of 5‐fluorouracil in supercritical CO2

AbstractThe solvation properties of 5‐fluorouracil in supercritical carbon dioxide (SC‐CO2) is investigated by means of molecular dynamics computer simulations using a force field that treats all atoms explicitly. Solvation shell distribution functions and solvent density maps around the solute were computed at different supercritical temperatures in the range 308–328 K and densities varying from 0.117 to 0.94 g/cm3. At the lowest density, we detect a strongly inhomogeneous local density augmentation effect manifested as the clustering of solvent molecules above and below the solute molecular plane and around its carbonyl and NH groups. The free‐energy benefit for a CO2 molecule to be in the first solvation shell relative to the bulk is roughly twice the thermal energy at such conditions. The distribution of the relative orientation of CO2 with respect to the solute suggests that local bond multipolar solute–solvent interactions are responsible for the solvent density enhancement in these systems. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches

Kwac and Cho [J. Chem. Phys. 119, 2247 (2003)] have recently developed a combined electronic structure/molecular dynamics approach to vibrational spectroscopy in liquids. The method involves fitting ab initio vibrational frequencies for a solute in a cluster of solvent molecules to a linear combination of the electrostatic potentials on the solute atoms due to the charges on the solvent molecules. These authors applied their method to the N-methylacetamide-D/D(2)O system. We (S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, [J. Chem. Phys. 120, 8107 (2004)]) have recently explored a closely related method, where instead of the electrostatic potential, the solute vibrational frequencies are fit to the components of the electric fields on the solute atoms due to the solvent molecules. We applied our method to the HOD/D(2)O and HOD/H(2)O systems. In order to make a direct comparison of these two approaches, in this paper we apply their method to the water system, and our method to the N-methylacetamide system. For the water system we find that the electric field method is superior to the potential approach, as judged by comparison with experiments for the absorption line shape. For the N-methylacetamide system the two methods are comparable.

A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels.

Urease catalyzes the hydrolysis of urea, the final step of organic nitrogen mineralization, using a bimetallic nickel centre. The role of the active site metal ions and amino acid residues has not been elucidated to date. Many pathologies are associated with the activity of ureolytic bacteria, and the efficiency of soil nitrogen fertilization with urea is severely decreased by urease activity. Therefore, the development of urease inhibitors would lead to a reduction of environmental pollution, to enhanced efficiency of nitrogen uptake by plants, and to improved therapeutic strategies for treatment of infections due to ureolytic bacteria. Structure-based design of urease inhibitors would require knowledge of the enzyme mechanism at the molecular level. The structures of native and inhibited urease from Bacillus pasteurii have been determined at a resolution of 2.0 A by synchrotron X-ray cryogenic crystallography. In the native enzyme, the coordination sphere of each of the two nickel ions is completed by a water molecule and a bridging hydroxide. A fourth water molecule completes a tetrahedral cluster of solvent molecules. The enzyme crystallized in the presence of phenylphosphorodiamidate contains the tetrahedral transition-state analogue diamidophosphoric acid, bound to the two nickel ions in an unprecedented mode. Comparison of the native and inhibited structures reveals two distinct conformations of the flap lining the active-site cavity. The mode of binding of the inhibitor, and a comparison between the native and inhibited urease structures, indicate a novel mechanism for enzymatic urea hydrolysis which reconciles the available structural and biochemical data.

What size RNA loop holds bulk solvent?

The loss in conformational entropy that results from the closure of a loop in a polymer chain has been derived in cases where the effects of discrete solvent structure inside the loop can be neglected. We show that a pronounced entropic contribution is encountered as the discrete clustering of solvent molecules inside the loop affects the conformations of the chain, forcing the orientation of individual residues. An algorithm for RNA structure prediction incorporating such effects is implemented and tested.

Distribution of Solvent Molecules Around Apolar Side-chains in Protein Crystals

We have analysed the distribution of solvent sites within 5·0 Å of the apolar side-chains alanine, valine, leucine, isoleucine and phenylalanine based on experimental data from 24 high-resolution protein structures. Clustering of solvent molecules into specific regions can be seen superimposed on a broad background of sites. The non-random nature of these distributions is confirmed by quantitative analysis of the solvent sites according to a spherical polar (r, θ and φ) co-ordinate system with the apolar atom of interest at the centre. One of the general features of these solvent sites is that they peak at around 4·0 Å from an apolar protein carbon atom. Preferences in orientation (θ and φ) are also seen in the solvent distributions especially around the alanine CB atom and the phenylalanine ring. Most (around 75%) of the solvent sites around apolar groups are also within hydrogen bonding distance of protein (main chain) polar groups which leads to a distribution dependent on the local secondary structure. The remaining 25% of solvent sites are referred to as "non-polar" water molecules and their crystallographic temperature factors are higher than average by between 15% to 28%. For alanine and phenylalanine there are enough data to show that water molecules not within hydrogen bonding distance of protein polar atoms also cluster into specific regions. However, the main conclusion appears to be that the hydrophobic hydration in protein crystals is correlated with hydration of polar groups and thus depends on the local environment as well as on the stereochemistry of the apolar atoms.

Real-time path-integral simulation of vibrational transition probabilities of small molecules in clusters: Theory and application to Br2 in Ar

A discretized real-time Feynman path integral is applied to a system containing a diatomic in a small cluster of solvent molecules. The system considered consists of Br2 in Ar. An adiabatic separation of variables is assumed. The solvent as well as the Br2 center of mass are gathered into a vector called bath or solvent coordinates. The forced oscillator approximation is used to analytically obtain the vibrational contribution to the transition amplitude. The discretized real-time propagators (bath dependent only, since the vibrational part is carried out analytically) are highly oscillatory and, therefore, not suitable for Monte Carlo calculations. The coarse-graining technique introduced by Filinov and developed by Freeman and Doll, and Miller is employed to make the integrals more suitable for Monte Carlo calculations. The computations are carried out for five different times. For each time, we study the convergence of the technique for a range of Gaussian widths used as conditioning functions. We also examine the convergence as a function of the number of points in the discretized description of the solvent path.

The molecular basis of temperature effects in supercritical extraction

AbstractThe behavior of solute partial molar enthalpies in dilute supercritical mixtures gives rise to the well‐known phenomenon of retrograde solubility (equilibrium solubility decreasing with increasing temperature at constant pressure). A mechanistic interpretation of this phenomenon in terms of the formation of large clusters of solvent molecules around solute molecules is consistent with experimentally observed retrograde behavior. Cluster formation occurs as a consequence of the unbounded increase in the solvent's compressibility arbitrarily close to the latter's critical point. At infinite dilution, the solute's partial molar volume and enthalpy grow linearly with cluster size. This means that the negative divergence of these quantities is simply a macroscopic manifestation of a “condensation” in which an increasing number of solvent molecules cluster around solute molecules. Arbitrarily close to the solvent's critical point, scaling relationships show that the decay of both solvent‐solvent and solute‐solvent correlation functions exhibits the same radial dependence. This functionality is thus solute‐independent, and is determined exclusively by the proximity to the solvent's critical point. The locus along which thermal effects associated with cluster formation are maximized is arbitrarliy close to the solvent's critical isochore as the latter's critical point is approached.

Mass spectrometry of biogenic catecholamine ion pairs by direct liquid introduction

dihydroxyphenylacetic acid with n-octylsulphonate has been investigated by direct liquid introduction in an acidic buffer currently used for their high-performance liquid chromatographic separation. In order to follow the fate of the ion pairs, they were first studied by desorption/chemical ionization as dichloromethane extracts or in the buffer. The results show that characteristic spectra of the solutes can be obtained by direct liquid introduction provided that the interface between the chromatographic system and the mass spectrometer permits the desolvation of the ion pairs from the cluster of solvent molecules.

Electrohydrodynamic ionization mass spectrometry: Review of instrumentation, mechanisms and applications

Electrohydrodynamic ionization is a technique whereby ions are generated directly from a liquid surface by application of an electric field. Mass spectrometry can be used to characterize these ions and the necessary instrumentation is described. Ions may be generated from liquid metals and also from organic liquids if an ionic electrolyte is dissolved. Singly charged atomic ions are emitted from liquid metals whereas doped organic liquids generate solvated cations or anions attached to clusters of solvent molecules. Two different ionization mechanisms are distinguished and electrohydrodynamic interaction of the electric field with the liquid surface is discussed. The applications of electrohydrodynamic ionization mass spectrometry are reviewed; in particular, chemical analysis of liquids and dissolved materials is described. The technique can also be used for the study of solution chemistry.

The kinetics of solvent reorientation in hydroxylated solvents from the exciting-wavelength dependence of chromophore emission spectra

The disappearance of the exciting-wavelength dependence of the phosphorescence spectra of polar, aromatic chromophores in supercooled glycol–water mixtures is utilized to monitor the kinetics of solvent reorientation. Reorientation times in the nanosecond to second range are obtained for (3:2 v/v) glycerol–water and (1:1 v/v) ethylene glycol–water at 140–240 °K. The results suggest that the process is one involving a cluster of solvent molecules and in which the chromophore plays a relatively passive role. Steady-state data and direct measurements of phosphorescence shifts as a function of time indicate that the solvent reorientation process is nonexponential in nature. The decay function derived from the temperature dependence of the steady state data is consistent with the decays observed directly as a function of time. Interpretation of this nonexponential decay in terms of a summation of rate processes leads to a distribution dominated by two reorientation rate constants. The relative contributions of the slow and faster reorientation rate constants in addition to their activation parameters differ for the glycerol–water and ethylene glycol–water mixtures.

Sorption properties of polypropylene

AbstractThe sorption properties of atactic polypropylene (APP) and isotactic polypropylene (IPP) were studied by equilibrium sorption of various organic solvents. The variation of the Flory‐Huggins interaction parameter χ for the APP‐CCl4 system at 25°C was expressed as a function of the volume fraction v2 of polymer by the relation: x = 0.113 exp {1.879 v2}. The average molecular weight Mc of the polymer chains between successive crystallites for IPP subjected to different thermal treatments was calculated to be 250 to 350 by the equation of Flory and Rehner. From the variation of Mc with solvent concentration, we estimated the number fraction of polymer chains actually contributing to elastic deformation. The clustering function for solvent in the polymer calculated by the method of Zimm and Lundberg decreased linearly from a positive value to −1 with increasing solvent concentration. Clustering of solvent molecules was found to occur more easily in APP than in IPP.

Kinetics of hydrogen isotope exchange reactions. Part XIX. Effect of added solutes on aliphatic tritium exchange of t-butyl alcohol(2-methylpropan-2-ol) under the influence of β-radiation, and related experiments

The effect of added solutes (AgClO4, CdSO4, CuSO4, NiSO4, and H2O2) on the tritium exchange in the methyl groups of t-butyl alcohol is to decrease the exchange rate very sharply, the silver salt having the most pronounced influence. The inhibitors do not totally suppress the exchange. The results suggest that there are two exchange routes the major one of which is susceptible to inhibition by electron scavengers while the minor one is not. As a working hypothesis it is suggested that the major exchange route involves reaction between the hydrated electron and t-butyl alcohol. This results in the formation of a solvated electron containing one molecule of t-butyl alcohol in the cluster of solvent molecules in which the electron is trapped with consequent hydrogen exchange between the molecules of the cluster. The minor route is envisaged as the direct formation of this mixed solvent cluster by the action of radiation. The scavenger effects suggest that the second-order rate constant for the reaction between t-butyl alcohol and the hydrated electron is ca. 108 l mol–1 s–1. Since this reaction does not destroy the solvated electron, the high value deduced is not incompatible with the low rate constants obtained for the destruction of the hydrated electron by alcohols from pulse-radiolysis studies.