Acetonitrile real gas phase behavior from quasi-ideal gas to nanodroplets: A microscopical view.

We have applied a recently developed general purpose acetonitrile force field based on first-principles calculations to simulate acetonitrile in the gas phase at different temperatures and densities. These conditions range from nearly ideal to real gas phase behavior and condensation. The molecular dynamics simulation results agree fairly well with the experimental studies available in the literature on the gas samples. The structural analysis of aggregates and their associated interaction energies is examined and related to the early model proposed on molecular association and equilibrium determining the non-ideal behavior. The formation of dimers is mainly responsible for the non-ideal behavior of the gas at very low density, confirming suggested models based on previous experimental studies. However, when the density of the sample rises, the level of aggregation increases and the simple concept of dimerization does not hold anymore. The real behavior adopted by the gas is related to the distribution of molecular structures observed. The macroscopical view of a real gas as a generic interparticle interaction system without a defined form may then be rationalized on the basis of a defined molecular association originated by a distribution of aggregates at the low density regime. The sample with the highest density (∼1.4 × 103 mol m-3) at the lowest temperature exhibits a massive aggregation where most of the acetonitrile (ACN) molecules in the simulation box form a big cluster. Its radial distribution function is similar to that of the liquid ACN. This strongly inhomogeneous distribution in the box can be considered a condensation in the gas phase under specific density-T conditions. This formation opens the door to the potential tuning of its solvent properties as a function of its size in these nanodroplets that in turn are controlled by the density-T conditions.

A novel approach using nonlinear surfaces for dynamic aperture optimization in MBA synchrotron light sources.

MBA cell-based synchrotron light sources have enabled an unprecedented increase in beam coherence and brightness, greatly benefiting the scientific disciplines that rely on X-ray techniques. However, controlling the electron dynamics is a theoretical and technological challenge, due to the large number of parameters to adjust and constraints to satisfy when designing modern synchrotrons. Having versatile tools for the description and manipulation of electron dynamics could favor the design of these accelerators and lead to progress on several fronts in the understanding of matter. In this paper, a formalism based on the use of nonlinear geometric surfaces represented by polynomial quasi-invariants, to analyze and optimize the dynamic aperture of electrons in MBA storage rings, is introduced. The formalism considers on- and off-momentum particle dynamics. Within the optimization scheme, different objective functions defined in terms of the nonlinear surfaces, which are minimized using genetic algorithm methods, are proposed. A remarkable horizontal dynamic aperture exceeding 19 mm is obtained for the design particle of a synchrotron model with 86 pm [Formula: see text] rad emittance along with a dynamic aperture above 5 mm for momentum deviations of ± 3[Formula: see text]. According to the results presented, this formalism could be greatly useful for manipulating the dynamical properties of electrons in synchrotrons light sources close to the diffraction limit.

Increasing beam stability zone in synchrotron light sources using polynomial quasi-invariants.

The objective of this article is to propose a scheme to increase the stability zone of a charged particles beam in synchrotrons using a suitable objective function that, when optimized, inhibits the resonances onset in phase space and the dynamic aperture of electrons in storage rings can be improved. The proposed technique is implemented by constructing a quasi-invariant in a neighborhood of the origin of the phase space, then, by using symbolic computation software, sets of coupled differential equations for functions involved in nonlinear dynamics are obtained and solved numerically with periodic boundary conditions. The objective function is constructed by proposing that the innermost momentum solution branch of the polynomial quasi-invariant approaches to the corresponding ellipse of the linear dynamics. The objective function is optimized using a genetic algorithm, allowing the dynamic aperture to be increased. The quality of results obtained with this scheme are compared with particle tracking simulations performed with available software in the field, showing good agreement. The scheme is applied to a synchrotron light source model that can be classified as third generation due to its emittance.

A molecular dynamics study proposing the existence of statistical structural heterogeneity due to chain orientation in the POPC-cholesterol bilayer.

We performed molecular dynamics simulations of a lipid bilayer consisting of POPC and cholesterol at temperatures from 283 to 308K and cholesterol concentrations from 0 to 50% mol/mol. The purpose of this study was to look for the existence of structural differences in the region delimited by these parameters and, in particular, in a region where coexistence of liquid disordered and liquid ordered phases has been proposed. Our interest in this range of concentration and temperature responds to the fact that polyene ionophore activity varies considerably along it. Two force fields, CHARMM36 and Slipids, were compared in order to determine the most suitable. Both force fields predict non-monotonic behaviors consistent with the existence of phase transitions. We found the presence of lateral structural heterogeneity, statistical in nature, in some of the bilayers occurring in this range of temperatures and sterol concentrations. This heterogeneity was produced by correlated ordering of the POPC tails and not due to cholesterol enrichment, and lasts for tens of nanoseconds. We relate these observations to the action of polyenes in these membranes.

Morphology and dynamics of domains in ergosterol or cholesterol containing membranes.

The effect of cholesterol and ergosterol on supported lipid bilayers composed of 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and egg sphingomyelin (eSM) in a 1/1 M ratio was studied using atomic force microscopy. The addition of ergosterol or cholesterol to these membranes considerably modifies both the structure and the dynamics of the domains present in them. The height of the eSM enriched domains increases with concentration of both sterols, but more markedly with ergosterol. The height of the POPC enriched domains increases with concentration in a similar manner for both sterols. This effect is larger for eSM than for POPC when ergosterol, not cholesterol, is present. Domain coverage increases with both sterols at 5 mol% but decreases at 20 mol% and almost disappears at 40 mol%. The size of the eSM enriched domains decreases with sterol concentration, more markedly with cholesterol. Bilayer rupture forces show that overall stiffness increases with the addition of 5 mol% cholesterol, but only for the eSM enriched domains with ergosterol at the same concentration. At larger sterol concentrations the stiffness of both regions becomes reduced. At 40 mol% sterol concentration, both membranes present the same rupture force value. To gain mechanistic insight into these observations we performed Quantum Mechanical calculations and Molecular Dynamics simulations of the sterol molecules. We found that conformational freedom for the sterol molecules is quite different. This difference might be behind the observed phenomena. Finally, the different action of sterols on membrane properties is related to the sterol-dependent ionophoretic activity of polyene antibiotics.

Experimental and Theoretical Studies on the Implications of Halide-Dependent Aqueous Solvation of Sm(II).

The addition of water to samarium(II) has been demonstrated to have a significant impact on the reduction of organic substrates, with the majority of research dedicated to the most widely used reagent, samarium diiodide (SmI2). The work presented herein focuses on the reducing capabilities of samarium dibromide (SmBr2) and demonstrates how the modest change in halide ligand results in observable mechanistic differences between the SmBr2-water and the SmI2-water systems that have considerable implications in terms of reactivity between the two reagents. Quantum chemical results from Born-Oppenheimer molecular dynamics simulations show significant differences between SmI2-water and SmBr2-water, with the latter displaying less dissociation of the halide, which results in a lower coordination number for water. Experimental results are consistent with computational results and demonstrate that the coordination sphere of SmBr2 is saturated at lower concentrations of water. In addition, coordination-induced bond-weakening of the O-H bond is demonstrably different for water bound to SmBr2, leading to an estimated O-H bond-weakening of at least 83 kcal/mol, nearly 10 kcal/mol larger than the bond-weakening observed in SmI2-H2O. Experimental results also demonstrate that the use of alcohols in place of water with SmBr2 leads to substrate reduction, albeit several orders of magnitude slower than for SmBr2-water. The difference in rates resulting from the change in proton donor is attributed to a rate-limiting proton-coupled electron transfer in SmBr2-water and a sequential electron transfer then proton transfer in SmBr2-alcohol systems, where electron transfer is rate-limiting.

Hydration of CH3HgOH and CH3HgCl compared to HgCl2, HgClOH, and Hg(OH)2: A DFT microsolvation cluster approach.

We address the aqueous microsolvation of the CH3HgCl and CH3HgOH molecules using a stepwise hydration scheme including up to 33 water molecules and compare our results with the previously studied HgCl2, HgClOH, and Hg(OH)2 complexes. Optimized geometries and Gibbs free energies were obtained at the B3PW91/aug-RECP(Hg)-6-31G(d,p) level. At least 33 water molecules were required to build the first solvation shell around both methylmercury compounds. Optimized geometries were found having favorable interactions of water molecules with Hg, Cl, and the OH moiety. Born-Oppenheimer molecular dynamics simulations were performed on the largest CH3HgX(X = Cl, OH)-(H2O)33 clusters at the same level of theory. Born-Oppenheimer molecular dynamics simulations at T = 300 K (ca. 0.62 kcal/mol) revealed the presence of configurations with hydrogen-bonded networks that include the OH moiety in CH3HgOH and exclude both the Hg and Cl in CH3HgCl, favoring a clathrate-type structure around the methyl moiety. The comparison to the microsolvated HgClOH, Hg(OH)2, and HgCl2 molecules showed that, in all cases, the water molecules easily move away from Cl, thus supporting the idea that HgCl2 behaves as a non-polar solute. The theoretical (LIII edge) X-ray absorption near edge structure spectra are obtained and found in good agreement with experimental data, especially for the CH3HgCl species.

Aqueous Solvation of SmI3: A Born-Oppenheimer Molecular Dynamics Density Functional Theory Cluster Approach.

We report the results of Born-Oppenheimer molecular dynamics (BOMD) simulations on the aqueous solvation of the SmI3 molecule and of the bare Sm3+ cation at room temperature using the cluster microsolvation approach including 37 and 29 water molecules, respectively. The electronic structure calculations were done using the M062X hybrid exchange-correlation functional in conjunction with the 6-31G** basis sets for oxygen and hydrogen. For the iodine and samarium atoms, the Stuttgart-Köln relativistic effective-core potentials were utilized with their associated valence basis sets. When SmI3 is embedded in the microsolvation environment, we find that substitution of the iodine ions by water molecules around Sm(III) cannot be achieved due to an insufficient number of explicit water molecules to fully solvate the four separate metal and halogen ions. Therefore, we studied the solvation dynamics of the bare Sm3+ cation with a 29-water molecule model cluster. Through the Sm-O radial distribution function and the evolution of the Sm-O distances, the present study yields a very tightly bound first rigid Sm(III) solvation shell from 2.3 to 2.9 Å whose integration leads to a coordination number of 9 water molecules and a second softer solvation sphere from 3.9 to 5 Å with 12 water molecules. No water exchange processes were found. The theoretical EXAFS spectrum is in excellent agreement with the experimental spectrum for Sm(III) in liquid water. The strong differences between the solvation patterns of Sm(III) vs Sm(II) are discussed in detail.

X-ray accelerated photo-oxidation of As(III) in solution.

We performed near edge X-ray absorption spectroscopy (XANES) measurements on the arsenic K-edge of As(III) in solution under acidic and basic conditions, after exposure of the solutions to air. Spectra were recorded for increasing exposure times to the X-rays used to perform absorption spectroscopy measurements. We did not find changes for the solution under acidic conditions, whereas we observed significant changes in the case of solution under alkaline conditions. To interpret these changes, we compared the obtained spectra with XANES spectra of As(III) and As(V) solutions under alkaline conditions, not exposed to air, and used as standards. Principal component fits using these standards indicate an accelerated conversion of As(III) to As(V) due to the exposure to X-rays.

Interpretation of X-ray absorption spectra of As(III) in solution using Monte Carlo simulations.

We performed X-ray absorption spectroscopy measurements on the arsenic K-edge of As(III) in solution under acidic conditions. Extended X-ray absorption fine structure (EXAFS) and X-ray near edge structure (XANES) spectra were compared with theoretical calculations which use local atomic structure configurations, either derived from density functional theory (DFT) energy minimization (EM) calculations or based on classical Monte Carlo (MC) simulations, for a As(OH)3 cluster surrounded by water molecules. The nearest arsenic-oxygen distances obtained from the fit of the XAFS spectra are consistent with the distances present in configurations derived from Monte Carlo simulations but not with those obtained from DFT-EM calculations. Calculations of XANES using either DFT-EM or the average configuration obtained from MC simulations do not reproduce the XANES spectra in the vicinity of the absorption edge. However, specific local atomic structural configurations of the As(OH)3 and water molecules, obtained from MC simulations, which show some ordering of water molecules up to 5 Å from the arsenic, reproduce qualitatively the experimental spectra. These results highlight the capability of XANES to yield information about hydration of ions in solution.

Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: the hydration of Cf³âº.

This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H2O)n](m+)(H2O)ℓ clusters (n going from 6 to 10 and ℓ from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H2O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R(Cf-O) in the range 2.43-2.48 Å, whereas the fourth one is closer to 9 with R(Cf-O) = 2.54 Å. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.

A refined potential for hydroxylamine clusters and the liquid phase.

A detailed study including ab initio calculations and classic Monte-Carlo simulations of hydroxylamine in the gas and liquid phases is presented. A classical interaction potential for hydroxylamine, which includes polarizability, many-body effects, and intramolecular relaxation, was constructed. The results of the simulation were compared to the available experimental data in order to validate the model. We conclude that liquid hydroxylamine has a multitude of hydrogen bonds leading to a large density where the existence of cis conformers and clusters of these conformers is possible. This explains the occurrence of the classical [R. Nast and I. Z. Foppl, Z. Anorg. Allg. Chem. 263, 310 (1950)] scheme for the molecule's decomposition at room temperature and its large exothermicity and instability.

Liquid methanol Monte Carlo simulations with a refined potential which includes polarizability, nonadditivity, and intramolecular relaxation.

Monte Carlo simulations of liquid methanol were performed using a refined ab initio derived potential which includes polarizability, nonadditivity, and intramolecular relaxation. The results present good agreement between the energetic and structural properties predicted by the model and those predicted by ab initio calculations of methanol clusters and experimental values of gas and condensed phases. The molecular level picture of methanol shows the existence of both rings and linear polymers in the methanol liquid phase.

A new nonsymmetric as (OH)3 species. Comparison with the known C3 species and themochemistry at the HF, DFT(B3LYP), MP2, MP4, and CCSD(T) levels of theory.

A new nonsymmetric As(OH)(3) species that is more stable than the C(3) structure is found at HF, Density Functional Theory (B3LYP), MP2, MP4 and CCSD(T) levels with the Stuttgart RECP-basis for As and the aug-cc-pvdz/pvtz extended basis sets. Transition state (TS) geometries are close to the C(3) one. Energy differences and interconversion barriers become smaller with increasing inclusion of electronic correlation. However, for MP4 and CCSD(T) descriptions, these differences increase by more than 100% when basis set goes from the AVDZ to AVTZ quality. Zero point energy (ZPE) corrections are essential and have been taken into account at all levels of theory; although this leads to barrier collapse at the B3LYP, MP2, MP4 and CCSD(T) levels, the C(1) isomer remains more stable than the C(3) one. MP2/AVTZ infrared spectra are also given for the C(1) and C(3) isomers as guiding data for future IR studies in the gas phase.

Ion hydration in nanopores and the molecular basis of selectivity.

Using a simple model, it is shown that the cost of constraining a hydrated potassium ion inside a narrow pore is smaller than the cost of constraining hydrated sodium or lithium ions in pores of radius around 1.5 A. The opposite is true for pores of radius around 2.5 A. The reason for the selectivity in the first region is that the potassium ion allows for a greater distortion of its hydration shell and can therefore maintain a better coordination, and the reason for the reverse selectivity in the second region is that the smaller ions retain their hydration shells in these pores. This is relevant to the molecular basis of ion selective channels, and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes.

Water liquid-vapor equilibria predicted by refined ab initio derived potentials.

Coexistence properties for water near the critical point using several ab initio models were calculated using grand canonical Monte Carlo simulations with multiple histogram reweighting techniques. These models, that have proved to yield a good reproduction of the water properties at ambient conditions, perform rather well, improving the performance of a previous ab initio model. It is also shown that bulk geometry and dipole values, predicted by the simulation, can be used and a good approximation obtained with a polarizable rigid water model but not when polarization is excluded.

Water models based on a single potential energy surface and different molecular degrees of freedom.

Up to now it has not been possible to neatly assess whether a deficient performance of a model is due to poor parametrization of the force field or the lack of inclusion of enough molecular properties. This work compares several molecular models in the framework of the same force field, which was designed to include many-body nonadditive effects: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration [B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002), H. Saint-Martin, B. Hess, and H. J. C. Berendsen, J. Chem. Phys. 120, 11133 (2004)], (b) a polarizable and classically flexible molecule [H. Saint-Martin, J. Hernandez-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys. 113, 10899 (2000)], (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal is to determine how significant the different molecular properties are. The results indicate that all factors--nonadditivity, polarizability, and intramolecular flexibility--are important. Still, approximations can be made in order to diminish the computational cost of the simulations with a small decrease in the accuracy of the predictions, provided that those approximations are counterbalanced by the proper inclusion of an effective molecular property, that is, an average molecular geometry or an average dipole. Hence instead of building an effective force field by parametrizing it in order to reproduce the properties of a specific phase, a building approach is proposed that is based on adequately restricting the molecular flexibility and/or polarizability of a model potential fitted to unimolecular properties, pair interactions, and many-body nonadditive contributions. In this manner, the same parental model can be used to simulate the same substance under a wide range of thermodynamic conditions. An additional advantage of this approach is that, as the force field improves by the quality of the molecular calculations, all levels of modeling can be improved.