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Moucca F.,University of Ontario Institute of Technology | Moucca F.,rkinje University | Lisal M.,rkinje University | Lisal M.,Czech Institute of Chemical Process Fundamentals | Smith W.R.,University of Ontario Institute of Technology
Journal of Physical Chemistry B | Year: 2012

We extend the osmotic ensemble Monte Carlo (OEMC) molecular simulation method (Moucča et al. J. Phys Chem. B2011, 115, 7849-7861) for directly calculating the aqueous solubility of electrolytes and for calculating their chemical potentials as functions of concentration to cases involving electrolyte hydrates and mixed electrolytes, including invariant points involving simultaneous precipitation of several solutes. The method utilizes a particular semigrand canonical ensemble, which performs simulations of the solution at a fixed number of solvent molecules, pressure, temperature, and specified overall electrolyte chemical potential. It avoids calculations for the solid phase, incorporating available solid chemical potential data from thermochemical tables, which are based on well-defined reference states, or from other sources. We apply the method to a range of alkali halides in water and to selected examples involving LiCl monohydrate, mixed electrolyte solutions involving water and hydrochloric acid, and invariant points in these solvents. The method uses several existing force-field models from the literature, and the results are compared with experiment. The calculated results agree qualitatively well with the experimental trends and are of reasonable accuracy. The accuracy of the calculated solubility is highly dependent on the solid chemical potential value and also on the force-field model used. Our results indicate that pairwise additive effective force-field models developed for the solution phase are unlikely to also be good models for the corresponding crystalline solid. We find that, in our OEMC simulations, each ionic force-field model is characterized by a limiting value of the total solution chemical potential and a corresponding aqueous concentration. For higher values of the imposed chemical potential, the solid phase in the simulation grows in size without limit. © 2012 American Chemical Society.


Moucka F.,University of Ontario Institute of Technology | Moucka F.,rkinje University | Lisal M.,rkinje University | Lisal M.,Czech Institute of Chemical Process Fundamentals | And 6 more authors.
Journal of Physical Chemistry B | Year: 2011

We present a new and computationally efficient methodology using osmotic ensemble Monte Carlo (OEMC) simulation to calculate chemical potential-concentration curves and the solubility of aqueous electrolytes. The method avoids calculations for the solid phase, incorporating readily available data from thermochemical tables that are based on well-defined reference states. It performs simulations of the aqueous solution at a fixed number of water molecules, pressure, temperature, and specified overall electrolyte chemical potential. Insertion/deletion of ions to/from the system is implemented using fractional ions, which are coupled to the system via a coupling parameter λ that varies between 0 (no interaction between the fractional ions and the other particles in the system) and 1 (full interaction between the fractional ions and the other particles of the system). Transitions between λ-states are accepted with a probability following from the osmotic ensemble partition function. Biasing weights associated with the λ-states are used in order to efficiently realize transitions between them; these are determined by means of the Wang-Landau method. We also propose a novel scaling procedure for λ, which can be used for both nonpolarizable and polarizable models of aqueous electrolyte systems. The approach is readily extended to involve other solvents, multiple electrolytes, and species complexation reactions. The method is illustrated for NaCl, using SPC/E water and several force field models for NaCl from the literature, and the results are compared with experiment at ambient conditions. Good agreement is obtained for the chemical potential-concentration curve and the solubility prediction is reasonable. Future improvements to the predictions will require improved force field models. © 2011 American Chemical Society.


Fuentes-Paniagua E.,University of Alcalá | Fuentes-Paniagua E.,CIBER ISCIII | Hernandez-Ros J.M.,University of Alcalá | Sanchez-Milla M.,University of Alcalá | And 11 more authors.
RSC Advances | Year: 2014

Cationic carbosilane dendrimers of generations 1-3 have been synthesized employing thiol-ene click chemistry. The obtained dendrimers present three different types of ammonium functions, two of them with the charge at the surface, -NH3 + and -NMe3 +, and other with the charge internalized by the presence of ethylalcohol moieties, -[NMe2(CH2CH2OH)]+. The influence of -NMe3 + and -[NMe2(CH2CH 2OH)]+ in dendrimer structure have been studied by molecular dynamics. The antibacterial properties of these families of dendrimers have been evaluated against Gram-positive (Staphylococcus aureus CECT 240) and Gram-negative (Escherichia coli CECT 515) bacterial strains, and the results have been compared with those obtained for related cationic carbosilane dendrimers functionalized by hydrosilylation reactions. These data show the relevance of the sulfur atom versus the silicon atom close to the dendrimer surface and the outer charge versus the inner charge. Finally, the stability of the most active first generation dendrimers vs. pH and temperature has also been studied. © 2014 The Royal Society of Chemistry.


Petrus P.,rkinje University | Lisal M.,rkinje University | Lisal M.,Czech Institute of Chemical Process Fundamentals | Brennan J.K.,U.S. Army
Langmuir | Year: 2010

We present a dissipative particle dynamics simulation study on nanostructure formation of symmetric and asymmetric diblock copolymers confined between planar surfaces. We consider symmetric and slightly asymmetric diblock copolymers that form lamellar nanostructures in the bulk, and highly asymmetric diblock copolymers that form cylindrical nanostructures in the bulk. The formation of the diblock copolymer nanostructures confined between the planar surfaces is investigated and characterized by varying the separation width and the strength of the interaction between the surfaces and the diblock copolymers. Both the slit width and the surface interaction strongly influence the phase diagram, especially for the asymmetric systems. For the symmetric and slightly asymmetric diblock copolymer systems, the confinement primarily affects the orientation of the lamellar domains and only marginally influences the domain morphologies. These systems form parallel lamellar phases with different number of lamellae, and perpendicular and mixed lamellar phases. In a narrow portion of the phase diagram, these systems exhibit a parallel perforated lamellar phase, where further insight into the appearance of this phase is provided through free-energy calculations. The confined highly asymmetric diblock copolymer system shows, in addition to nanostructures with parallel and perpendicular cylinders, noncylindrical structures such as parallel lamellae and parallel perforated lamellae. The formation of the various confined nanostructures is further analyzed by calculating structural characteristics such as the mean square end-to-end distance of the diblock copolymers and the nematic order parameter. © 2010 American Chemical Society.


Petrus P.,rkinje University | Petrus P.,Czech Institute of Chemical Process Fundamentals | Lisal M.,Czech Institute of Chemical Process Fundamentals | Brennan J.K.,U.S. Army
Langmuir | Year: 2010

We present a dissipative particle dynamics simulation study on the formation of nanostructures of symmetric diblock copolymers confined between planar surfaces with and without nanopattems. The nanopatterned surface is mimicked by alternating portions of the surface that interact differently with the diblock copolymers. The formation of the diblock.-copolymer nanostructures confined between the planar surfaces is investigated and characterized by varying the separation width and the strength of the interaction between the surfaces and the diblock copolymers. For surfaces with nanopattems, we also vary both the mutual area and location of the nanopatterns, where we consider nanopatterns on the opposing surfaces that are vertically (a) aligned, (b) staggered, and (c) partially staggered. In the case of planar slits without nanopattems, we observe the formation of perpendicular and parallel lamellar phases with different numbers of lamellae. In addition, the symmetric diblock copolymers self-assemble into adsorbed layer and adsorbed layer-parallel lamellar phases and a mixed lamellar phase when the opposing surfaces of the planar slits are modeled by different types of wall beads. In the case of nanopatterned planar slits, we observe novel nanostructures and attempt to rationalize the diblock copolymer self-assembly on the basis of the behavior that we observed in the planar slits without nanopattems. In particular, we investigate the applicability of predicting the structures formed in the nanopatterned slits by a superposition of the observed structures in slits without nanopatterns. © 2009 American Chemical Society.


Lisal M.,Czech Institute of Chemical Process Fundamentals | Lisal M.,rkinje University
Journal of Chemical Physics | Year: 2013

We present molecular-level insight into the liquid/gas interface of two chiral room-temperature ionic liquids (RTILs) derived from 1-n-butyl-3- methylimidazolium bromide ([bmim][Br]); namely, (R)-1-butyl-3-(3-hydroxy-2- methylpropyl)imidazolium bromide (hydroxypropyl) and 1-butyl-3-[(1R)-nopyl] imidazolium bromide (nopyl). We use our currently developed force field which was validated against the experimental bulk density, heat of vaporization, and surface tension of [bmim][Br]. The force field for the RTILs adopts the Chemistry at Harvard Molecular Mechanics (CHARMM) parameters for the intramolecular and repulsion-dispersion interactions along with the reduced partial atomic charges based on ab initio calculations. The net charges of the ions are around ±0.8e, which mimic the anion to cation charge transfer and many-body effects. Molecular dynamics simulations in the slab geometry combined with the intrinsic interface analysis are employed to provide a detailed description of the RTIL/gas interface in terms of the structural and dynamic properties of the interfacial, sub-interfacial, and central layers at a temperature of 300 K. The focus is on the comparison of the liquid/gas interface for the chiral RTILs with the interface for parent [bmim][Br]. The structure of the interface is elucidated by evaluating the surface roughness, intrinsic atomic density profiles, and orientation ordering of the cations. The dynamics of the ions at the interfacial region is characterized by computing the survival probability, and normal and lateral self-diffusion coefficients in the layers. © 2013 AIP Publishing LLC.


Siperstein F.R.,University of Manchester | Lisal M.,Czech Institute of Chemical Process Fundamentals | Lisal M.,rkinje University | Brennan J.K.,U.S. Army
Collection of Czechoslovak Chemical Communications | Year: 2010

Adsorption isotherms of methane and nitrogen in porous titanium silicate ETS-4 (Engelhard titanium silicate) are calculated using grand canonical Monte Carlo (GCMC) simulations. Self-diffusion coefficients are determined using molecular dynamics (MD) simulations. Properties for pure gases were determined for two of the ideal ETS-4 polymorphs (ABAB-AA and ABAB-AC) dehydrated at different temperatures (423 and 573 K), taking into account only the framework atoms of the structure and ignoring the non-framework cations and water molecules. It was observed that equilibrium properties are slightly dependent on the structure selected for idealized polymorphs. However, it is not sufficient to explain the differences in adsorption capacity observed experimentally, which can only be explained with the combination of two polymorphs. In polymorphs with straight channels, self-diffusion in the direction of the main channel is two orders of magnitude larger than through the small rings that connect the main channels with some small cages. The trends observed in the self-diffusion coefficient with loading confirmed that crossing an eight-membered ring is an activated process. © 2010 Institute of Organic Chemistry and Biochemistry.


Popescu L.M.,National RandD Institute for Non Ferrous and Rare Metals | Piticescu R.M.,National RandD Institute for Non Ferrous and Rare Metals | Rusti C.F.,National RandD Institute for Non Ferrous and Rare Metals | Maly M.,rkinje University | And 4 more authors.
Materials Letters | Year: 2011

The present paper reports on an innovative route for the preparation of new hybrid nanostructured thin films based on hydroxyapatite and functionalized polyurethane. Hybrid nanopowders based on hydroxyapatite and functionalized polyurethane have been synthesized by a hydrothermal method with high pressure and low temperature conditions and further used for spin coating deposition. Biocompatible thin films with a thickness of about 50 nm have been deposited onto Si/SiO2/Ti/Au substrates and their properties recommend them suitable as possible electrodes for the fabrication of impedance biosensors. Hybrid materials with improved properties are obtained, combining the mechanical properties of polyurethane with biocompatible properties of hydroxyapatite (bioactivity and osteoconductivity). The presence of functional groups in polyurethane structure ensures the existence of strong interactions between components and an increased affinity of the thin films for further protein bonding in biosensor design. Hybrid nanostructured thin films based on hydrothermally synthesized hydroxyapatite-polyurethane nanopowders could enhance the amount of immobilized biomolecules in the construction of an impedance biosensor for diagnosis and therapy of bone diseases. © 2011 Elsevier B.V.


Moreno N.,National University of Colombia | Perilla J.E.,National University of Colombia | Colina C.M.,Pennsylvania State University | Lisal M.,Czech Institute of Chemical Process Fundamentals | Lisal M.,rkinje University
Molecular Physics | Year: 2015

Dissipative particle dynamics, a meso-scale particle-based model, was used to study the aggregation of mucins in aqueous solutions. Concentration, strength of the mucin-water interactions, as well as the effects of size, shape, and composition of the model molecules were studied. Model proteins were represented as rod-like objects formed by coarse-grained beads. In the first model, only one type of beads formed the mucin. It was found that all the surfaces were available to form aggregates and the conformation of the aggregates was a function of the strength of the mucin-water interaction. With this model, the number of aggregates was unaffected by the initial position of the mucins in the simulation box, except for the lowest mucin concentration. In a more refined mucin model, two kinds of beads were used in the molecule in order to represent the existence of cysteine-like terminal groups in the actual molecule. With this new scheme, aggregation took place by the interaction of the terminal groups between model molecules. The kinetic analysis of the evolution of the number of aggregates with time was also studied for both mucin models. © 2015 Taylor & Francis.


Sirk T.W.,U.S. Army | Slizoberg Y.R.,U.S. Army | Brennan J.K.,U.S. Army | Lisal M.,Czech Institute of Chemical Process Fundamentals | And 2 more authors.
Journal of Chemical Physics | Year: 2012

We develop an alternative polymer model to capture entanglements within the dissipative particle dynamics (DPD) framework by using simplified bond-bond repulsive interactions to prevent bond crossings. We show that structural and thermodynamic properties can be improved by applying a segmental repulsive potential (SRP) that is a function of the distance between the midpoints of the segments, rather than the minimum distance between segments. The alternative approach, termed the modified segmental repulsive potential (mSRP), is shown to produce chain structures and thermodynamic properties that are similar to the softly repulsive, flexible chains of standard DPD. Parameters for the mSRP are determined from topological, structural, and thermodynamic considerations. The effectiveness of the mSRP in capturing entanglements is demonstrated by calculating the diffusion and mechanical properties of an entangled polymer melt. © 2012 American Institute of Physics.

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