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Locating saddle points on free energy surfaces is key in characterizing multistate transition events in complicated molecular-scale systems. Because these saddle points represent transition states, determining minimum free energy pathways to these saddles and measuring their free energies relative to their connected minima are further necessary, for instance, to estimate transition rates. In this work, we propose a new multistring version of the climbing string method in collective variables to locate all saddles and corresponding pathways on free energy surfaces. The method uses dynamic strings to locate saddles and static strings to keep a history of prior strings converged to saddles. Interaction of the dynamic strings with the static strings is used to avoid the convergence to already-identified saddles. Additionally, because the strings approximate curves in collective-variable space, and we can measure free energy along each curve, identification of any saddle's two connected minima is guaranteed. We demonstrate this method to map the network of stationary points in the 2D and 4D free energy surfaces of alanine dipeptide and alanine tripeptide, respectively. [ABSTRACT FROM AUTHOR]

Solvent density fluctuations play a crucial role in liquid-vapor transitions in solvophobic confinement and can also be important for understanding solvation of polar and apolar solutes. In the case of ionic liquids (ILs), density fluctuations can be used to understand important processes in the context of nanoscale aggregation and colloidal self-assemblies. In this article, we explore the nature of density fluctuations associated with capillary evaporation of the IL 1-ethyl-3-methylimidazolium tetrafluoroborate ([EMIM][BF4]) in the confined region of model solvophobic nanoscale sheets by using molecular dynamics simulations combined with non-Boltzmann sampling techniques. We demonstrate that density fluctuations of the confined IL play an important role in capillary evaporation, suggesting analogies to dewetting transitions involving water. Significant changes in the interfacial structure of the IL are also detailed and suggested to underlie a non-classical (non-parabolic) dependence of the free energy barrier to evaporation on the degree of confinement. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are utilized here to explore the nanoscale morphology and the nature of hydrogen bonding in the equimolar mixtures of butylammonium nitrate protic ionic liquid with ethanol, propanol, and butanol. The X-ray scattering experimental study of Greaves et al. [Phys. Chem. Chem. Phys. 13, 13 501 (2011)] has evidenced that alkylammonium nitrate plus alcohol mixtures possess nanoscale structural order which becomes more pronounced as the chain length of the alcohol increases. Our analysis carried out using simulated total and partial X-ray scattering structure functions quantifies the basis of these observations. The partial structure functions highlight the off-phase density correlations of alcohol with both cation and anion in the low-q region. We demonstrate that the chain lengthening of alcohols offers significant variation in the structuring of the polar and apolar moieties in the mixtures. The inspection based on radial distribution functions manifests the non-linear hydrogen bonds of cations with nitrate anions as well as alcohol molecules. The alcohol's hydroxyl group prefers to form linear hydrogen bonds with anions and with other alcohol molecules. Incremented chain length of alcohol improves the extent of hydrogen bonding but does not alter their geometry. Spatial distribution functions delineate similar preferences. It shows stronger directional preferences of the hydroxyl group of alcohols than cation in the vicinity of an anion. Enhanced pair correlations associated with the terminal methyl carbons suggest aggregation of butanol chains in apolar domains. Triplet correlation functions (TCFs) are also used to evaluate the orientational preferences of the present polar moieties in the mixtures. Information based on TCFs for distribution of polar head group of cations and anions unveils the dominance of equilateral configurations over the less frequent isosceles configurations in all the three mixtures. [ABSTRACT FROM AUTHOR]

The extent to which solvent-mediated effective interactions between nanoparticles can be predicted based on structure and associated thermodynamic estimators for bulk solvents and for solvation of single and pairs of nanoparticles is studied here. As a test of the approach, we analyse the strategy for creating temperature-independent solvent environments using a series of homologous chain fluids as solvents, as suggested by an experimental paper [M. I. Bodnarchuk et al., J. Am. Chem. Soc. 132, 11967 (2010)]. Our conclusions are based on molecular dynamics simulations of Au140(SC10H21)62 nanoparticles in n-alkane solvents, specifically hexane, octane, decane and dodecane, using the TraPPE-UA potential to model the alkanes and alkylthiols. The 140-atom gold core of the nanocrystal is held rigid in a truncated octahedral geometry and the gold-thiolate interaction is modeled using a Morse potential. The experimental observation was that the structural and rheological properties of n-alkane solvents are constant over a temperature range determined by equivalent solvent vapour pressures. We show that this is a consequence of the fact that long chain alkane liquids behave to a good approximation as simple liquids formed by packing of monomeric methyl/methylene units. Over the corresponding temperature range (233-361 K), the solvation environment is approximately constant at the single and pair nanoparticle levels under good solvent conditions. However, quantitative variations of the order of 10%-20% do exist in various quantities, such as molar volume of solute at infinite dilution, entropy of solvation, and onset distance for soft repulsions. In the opposite limit of a poor solvent, represented by vacuum in this study, the effective interactions between nanoparticles are no longer temperature-independent with attractive interactions increasing by up to 50% on decreasing the temperature from 361 K to 290 K, accompanied by an increase in emergent anisotropy due to correlation of mass dipoles on the two nanoparticles. One expects therefore that during self-assembly using solvent evaporation, temperature can be used as a structure-directing factor as long as good solvent conditions are maintained. It also suggests that disordered configurations may emerge as solvent quality decreases due to increasing role of short-range attractions and ligand fluctuation-driven anisotropy. The possibilities of using structural estimators of various thermodynamic quantities to analyse the interplay of ligand fluctuations and solvent quality in self-assembly as well as to design solvation environments are discussed. [ABSTRACT FROM AUTHOR]

Pd-doped chabazite (Pd/CHA) offers unique opportunities to adsorb and desorb NO x in the target temperature range for application as a passive NO x adsorber (PNA). The ability of Pd/CHA to trap NO x emissions at low temperatures (<200 °C) is facilitated by the binding of NO x species at various Pd sites available in the CHA framework. Density functional theory (DFT) simulations are performed to understand Pd speciation in CHA and the interaction of NO with Pd/CHA to explain the mechanisms of NO adsorption, oxidation, and desorption processes. The calculations are used to elucidate the important role of Pd 1+ cationic species, anchored at 6MR-3NN, in providing a strong ( E b = -272 kJ/mol) NO adsorption site in Pd/CHA. For NO release, the redox transformation of Pd species comes into play and Pd 1+ species are suggested to transform into cationic Pd 2+ , [PdOH] + , or [Pd-O-Pd] 2+ species, all of which show significantly reduced NO binding (-116, -153, and -117 kJ/mol, respectively) as compared to Pd 1+ . This enables NO desorption at the operating temperature of a downstream catalyst for subsequent catalytic reduction.