When solutes are small compared to the size of the ions in an ionic liquid, energetic heterogenei... more When solutes are small compared to the size of the ions in an ionic liquid, energetic heterogeneities associated with charge enhanced (stiff) and charge depleted (soft) nanoenvironments are sampled. In a recent article [J. C. Araque et al., J. Phys. Chem. B 119(23), 7015-7029 (2015)], we explored large deviations from Stokes-Einstein translational diffusion caused by such a heterogeneity. The current article is set to explore the effect of soft and stiff solvent environments (i.e., structure) on OH-bond rotations in the case of water and small alcohols in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (Im1,2 (+)NTf2 (-)). Is solute rotational dynamics heterogeneous? If so, are solute rotations and translations coupled in the sense that stiff and soft solvent environments hinder or speed up both types of dynamics? For the systems studied here, there appears to be a clear connection between translations, rotations, and stiff/soft solvent environments. We also discuss interesting asymmetries of the correlation between solutes with anions and cations.
In a recent communication [J. J. Hettige et al., J. Chem. Phys. 140, 111102 (2014)], we investiga... more In a recent communication [J. J. Hettige et al., J. Chem. Phys. 140, 111102 (2014)], we investigated the anomalous temperature dependence of the X-ray first sharp diffraction peak (or prepeak) in the tetradecyltrihexylphosphonium bis(trifluoromethylsulfonyl)-amide ionic liquid. Contrary to what was expected and often observed, the first sharp diffraction peak in this system was shown to increase in intensity with increasing temperature. This implies higher intermediate-range periodicity at a higher temperature. Is this counter-intuitive behavior specific to the combination of cation and anion? The current work analyzes the structural behavior of the same cation coupled with six different anions ranging from the small and spherically symmetric Cl(-) to the more structurally complex and charge-diffuse NTf2 (-). In all cases, the same temperature behavior trend for the prepeak is observed independent of anionic nature. We will show that the intensity increase in the prepeak region is a...
- 12:48 PM 321b. Cooperativity Mechanisms and Hybridization Free-Energy Landscapes of Model Oligo... more - 12:48 PM 321b. Cooperativity Mechanisms and Hybridization Free-Energy Landscapes of Model Oligonucleotides In Solution. Juan C. Araque 1 , Athanassios Z. Panagiotopoulos 2 , and Marc A. Robert 1 . (1) Department of ...
- 9:12 AM 404c. Understanding the Self-Assembling Mechanisms of Model DNA-Linked Nanoparticles by... more - 9:12 AM 404c. Understanding the Self-Assembling Mechanisms of Model DNA-Linked Nanoparticles by Monte Carlo Simulations. Juan C. Araque 1 , Athanassios Z. Panagiotopoulos 2 , and Marc A. Robert 1 . (1) Department ...
In more than one way pure ionic liquids (ILs) can be seen as mixtures. By definition they are com... more In more than one way pure ionic liquids (ILs) can be seen as mixtures. By definition they are comprised of cationic and anionic components and they also possess dual charge and apolar characteristics. We recently uncovered interesting dynamical behavior [Araque et al., J. Phys. Chem. B 119(23), 7015 (2015)] that can be ascribed to this duality. For small neutral solutes local friction can be high in certain regions and much lower in others. It is only reasonable to ask whether this interesting behavior is unique to ILs or is also common in certain conventional solvent mixtures such as dimethylsufoxide/glycerol for which the viscosity can be tuned to be similar. We make the case that the latter scenario is correct and that whereas viscous conventional solvent mixtures are structurally very different from ILs, dynamically they are not. From the perspective of a solute that is small, both ILs and viscous conventional solvent mixtures display frictionally stiff and soft regions associated with cage and jump diffusive regimes. In the case of ILs these are associated with charge-enhanced and charge-depleted liquid regions, whereas in the case of the conventional solvents by the distinct frictional properties of the two components.
We characterize the spontaneous development of morphologically complex phases in binary blends co... more We characterize the spontaneous development of morphologically complex phases in binary blends composed of an asymmetric diblock copolymer and a homopolymer with affinity to the minority block. The addition of homopolymer to a well-segregated copolymer melt has a drastic effect in the formation of microstructured bicontinuous phases, i.e., having periodic dividing interfaces without self-intersections. Such phases are of technological relevance for applications in which nanoporous materials with high internal surface area and periodic connectivity are desirable, e.g., templates for high conductivity composites, photonic materials and photovoltaic systems (solar cells). We use particle-based simulations to explore regions of the phase diagram, as function of the homopolymer volume fraction and the homopolymer/copolymer size ratio, where mainly triply periodic phases are predicted to be stable using self-consistent field theory calculations. The stability regions of the phases spontan...
Modern room temperature ionic liquids are structurally defined by symmetries on different length ... more Modern room temperature ionic liquids are structurally defined by symmetries on different length scales. Polar-apolar alternation defines their nanoscale structural heterogeneity, whereas positive-negative charge alternation defines short length scale order. Much progress has been made in the past few years as it pertains to the theoretical interpretation of X-ray scattering experiments for these liquids. Our group has contributed to the development of theoretical interpretation guidelines for the analysis of their structure function. Perhaps less well developed is our understanding of how transport and dynamics in general couple to the very unique structure of ionic liquids which are often dynamically and structurally heterogeneous. This article attempts to present our most current understanding of ionic liquid structure in general and its coupling to transport and dynamics in minimally technical terms for the benefit of the broadest audience.
The deviations from Stokes-Einstein hydrodynamics of small solutes are more pronounced in ionic l... more The deviations from Stokes-Einstein hydrodynamics of small solutes are more pronounced in ionic liquids than in conventional solvents (J. Phys. Chem. B 2013 117 (39), 11697). Small neutral solutes diffuse much faster than expected, whereas small charged solutes diffuse much slower. This article attempts to establish a link between the local friction experienced by tracer solutes and the polar/apolar structure of ionic liquids. We find that small neutral solutes probe locally "stiff" (mostly charged, high electrostriction) regions and locally "soft" (mostly apolar, low electrostriction) regions. These regions of high and low friction are associated with cage and jump regimes. Enhanced neutral tracer mobility in the low friction regions associated with the cationic apolar component has an important bearing on the large positive deviations from Stokes-Einstein behavior. In contrast, diminished charged tracer mobility involves long caging dynamics separated by jump events often triggered by the loss and recovery of counterions.
Nucleic acid hybridization describes a thermodynamic transition in which a single-stranded DNA mo... more Nucleic acid hybridization describes a thermodynamic transition in which a single-stranded DNA molecule associates with its complementary sequence. A comprehensive understanding of the thermodynamic behavior of this process can be achieved by computer simulation. However, the collective behavior of DNA hybridization in solution and on grafted surfaces exhibits disparate time and length scales that make atomistic simulations technically unfeasible. We
We propose a coarse-grained lattice model of short DNA strands to investigate the microscopic pat... more We propose a coarse-grained lattice model of short DNA strands to investigate the microscopic pathways and mechanisms of oligonucleoides hybridization in solution. The extent to which hybridization in solution conforms to two-state thermodynamics is also analyzed. Monte Carlo simulations with parallel tempering are performed to estimate the equilibrium population of single- and double-stranded states and the associated free-energy landscapes. Sequence
The high specificity and selectivity of DNA hybridization makes nucleic acid recognition a powerf... more The high specificity and selectivity of DNA hybridization makes nucleic acid recognition a powerful tool for bottom-up assembling approaches. Here, we propose a coarse-grained model to address the question of how nanoparticles tethered with single stranded DNA self-assemble in solution. Our approach employs a computationally efficient discretization of hard-core interactions and a high-coordination lattice, in combination with parallel tempering and
We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) z... more We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) zeolite membranes with differing surface chemistries. Using molecular dynamics, we have studied the flow of water under hydrostatic pressure through a fully hydrated LTA zeolite film (~2.5 nm thick) capped with hydrophilic and hydrophobic moieties. Pressure drops in the 50-400 MPa range were applied across the membrane, and the flux of water was monitored for at least 15 ns of simulation time. For hydrophilic membranes, water molecules adsorb at the zeolite surface, creating a highly structured fluid layer. For hydrophobic membranes, a depletion of water molecules occurs near the water/zeolite interface. For both types of membranes, the water structure is independent of the pressure drop established in the system and the flux through the membranes is lower than that observed for the bulk zeolitic material; the latter allows an estimation of surface barrier effects to pressure-driven water transport. Mechanistically, it is observed that (i) bottlenecks form at the windows of the zeolite structure, preventing the free flow of water through the porous membrane, (ii) water molecules do not move through a cage in a single-file fashion but rather exhibit a broad range of residence times and pronounced mixing, and (iii) a periodic buildup of a pressure difference between inlet and outlet cages takes place which leads to the preferential flow of water molecules toward the low-pressure cages.
Triphilic ionic liquids (containing polar, apolar, and fluorinated components) that can hydrogen ... more Triphilic ionic liquids (containing polar, apolar, and fluorinated components) that can hydrogen bond present a new paradigm in ionic liquid structural morphology. In this study we show that butylammonium pentadecafluorooctanoate and its nonfluorinated analogue butylammonium octanoate form disordered bicontinuous phases where a network of charge alternating hydrogen bonds continuously percolate through the whole liquid. These systems show order on multiple length scales, the largest length scale given by the percolating network. Separation between filaments in the network gives rise to a prepeak or first sharp diffraction peak. In the case of the fluorinated system, shorter range order occurs due to apolar-fluorinated alternation that decorates the surface of each individual filament. The backbone of the filaments is the product of the shortest organized length scale, namely, charge alternating hydrogen bonds. Liquid structure obtained via molecular dynamics simulations is used to compute coherent X-ray scattering intensities, and a full picture of the liquid landscape is developed. A careful mathematical analysis of the simulation data proposed here reveals individual molecular correlations that importantly contribute to each feature of the experimental structure function.
Proceedings of SPE Latin American and Caribbean Petroleum Engineering Conference, 2003
... Ggc = gas cap volume at current pressure (mmscf) Sgbt = gas saturation at breakthrough (fract... more ... Ggc = gas cap volume at current pressure (mmscf) Sgbt = gas saturation at breakthrough (fraction) Bga = gas formation volume factor at current pressure (cf ... gas oil ratio (scf/stb) Rs = solution gas oil ratio (scf/stb) Bw = water formation volume factor (rb/stb) qw = water production ...
When solutes are small compared to the size of the ions in an ionic liquid, energetic heterogenei... more When solutes are small compared to the size of the ions in an ionic liquid, energetic heterogeneities associated with charge enhanced (stiff) and charge depleted (soft) nanoenvironments are sampled. In a recent article [J. C. Araque et al., J. Phys. Chem. B 119(23), 7015-7029 (2015)], we explored large deviations from Stokes-Einstein translational diffusion caused by such a heterogeneity. The current article is set to explore the effect of soft and stiff solvent environments (i.e., structure) on OH-bond rotations in the case of water and small alcohols in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (Im1,2 (+)NTf2 (-)). Is solute rotational dynamics heterogeneous? If so, are solute rotations and translations coupled in the sense that stiff and soft solvent environments hinder or speed up both types of dynamics? For the systems studied here, there appears to be a clear connection between translations, rotations, and stiff/soft solvent environments. We also discuss interesting asymmetries of the correlation between solutes with anions and cations.
In a recent communication [J. J. Hettige et al., J. Chem. Phys. 140, 111102 (2014)], we investiga... more In a recent communication [J. J. Hettige et al., J. Chem. Phys. 140, 111102 (2014)], we investigated the anomalous temperature dependence of the X-ray first sharp diffraction peak (or prepeak) in the tetradecyltrihexylphosphonium bis(trifluoromethylsulfonyl)-amide ionic liquid. Contrary to what was expected and often observed, the first sharp diffraction peak in this system was shown to increase in intensity with increasing temperature. This implies higher intermediate-range periodicity at a higher temperature. Is this counter-intuitive behavior specific to the combination of cation and anion? The current work analyzes the structural behavior of the same cation coupled with six different anions ranging from the small and spherically symmetric Cl(-) to the more structurally complex and charge-diffuse NTf2 (-). In all cases, the same temperature behavior trend for the prepeak is observed independent of anionic nature. We will show that the intensity increase in the prepeak region is a...
- 12:48 PM 321b. Cooperativity Mechanisms and Hybridization Free-Energy Landscapes of Model Oligo... more - 12:48 PM 321b. Cooperativity Mechanisms and Hybridization Free-Energy Landscapes of Model Oligonucleotides In Solution. Juan C. Araque 1 , Athanassios Z. Panagiotopoulos 2 , and Marc A. Robert 1 . (1) Department of ...
- 9:12 AM 404c. Understanding the Self-Assembling Mechanisms of Model DNA-Linked Nanoparticles by... more - 9:12 AM 404c. Understanding the Self-Assembling Mechanisms of Model DNA-Linked Nanoparticles by Monte Carlo Simulations. Juan C. Araque 1 , Athanassios Z. Panagiotopoulos 2 , and Marc A. Robert 1 . (1) Department ...
In more than one way pure ionic liquids (ILs) can be seen as mixtures. By definition they are com... more In more than one way pure ionic liquids (ILs) can be seen as mixtures. By definition they are comprised of cationic and anionic components and they also possess dual charge and apolar characteristics. We recently uncovered interesting dynamical behavior [Araque et al., J. Phys. Chem. B 119(23), 7015 (2015)] that can be ascribed to this duality. For small neutral solutes local friction can be high in certain regions and much lower in others. It is only reasonable to ask whether this interesting behavior is unique to ILs or is also common in certain conventional solvent mixtures such as dimethylsufoxide/glycerol for which the viscosity can be tuned to be similar. We make the case that the latter scenario is correct and that whereas viscous conventional solvent mixtures are structurally very different from ILs, dynamically they are not. From the perspective of a solute that is small, both ILs and viscous conventional solvent mixtures display frictionally stiff and soft regions associated with cage and jump diffusive regimes. In the case of ILs these are associated with charge-enhanced and charge-depleted liquid regions, whereas in the case of the conventional solvents by the distinct frictional properties of the two components.
We characterize the spontaneous development of morphologically complex phases in binary blends co... more We characterize the spontaneous development of morphologically complex phases in binary blends composed of an asymmetric diblock copolymer and a homopolymer with affinity to the minority block. The addition of homopolymer to a well-segregated copolymer melt has a drastic effect in the formation of microstructured bicontinuous phases, i.e., having periodic dividing interfaces without self-intersections. Such phases are of technological relevance for applications in which nanoporous materials with high internal surface area and periodic connectivity are desirable, e.g., templates for high conductivity composites, photonic materials and photovoltaic systems (solar cells). We use particle-based simulations to explore regions of the phase diagram, as function of the homopolymer volume fraction and the homopolymer/copolymer size ratio, where mainly triply periodic phases are predicted to be stable using self-consistent field theory calculations. The stability regions of the phases spontan...
Modern room temperature ionic liquids are structurally defined by symmetries on different length ... more Modern room temperature ionic liquids are structurally defined by symmetries on different length scales. Polar-apolar alternation defines their nanoscale structural heterogeneity, whereas positive-negative charge alternation defines short length scale order. Much progress has been made in the past few years as it pertains to the theoretical interpretation of X-ray scattering experiments for these liquids. Our group has contributed to the development of theoretical interpretation guidelines for the analysis of their structure function. Perhaps less well developed is our understanding of how transport and dynamics in general couple to the very unique structure of ionic liquids which are often dynamically and structurally heterogeneous. This article attempts to present our most current understanding of ionic liquid structure in general and its coupling to transport and dynamics in minimally technical terms for the benefit of the broadest audience.
The deviations from Stokes-Einstein hydrodynamics of small solutes are more pronounced in ionic l... more The deviations from Stokes-Einstein hydrodynamics of small solutes are more pronounced in ionic liquids than in conventional solvents (J. Phys. Chem. B 2013 117 (39), 11697). Small neutral solutes diffuse much faster than expected, whereas small charged solutes diffuse much slower. This article attempts to establish a link between the local friction experienced by tracer solutes and the polar/apolar structure of ionic liquids. We find that small neutral solutes probe locally "stiff" (mostly charged, high electrostriction) regions and locally "soft" (mostly apolar, low electrostriction) regions. These regions of high and low friction are associated with cage and jump regimes. Enhanced neutral tracer mobility in the low friction regions associated with the cationic apolar component has an important bearing on the large positive deviations from Stokes-Einstein behavior. In contrast, diminished charged tracer mobility involves long caging dynamics separated by jump events often triggered by the loss and recovery of counterions.
Nucleic acid hybridization describes a thermodynamic transition in which a single-stranded DNA mo... more Nucleic acid hybridization describes a thermodynamic transition in which a single-stranded DNA molecule associates with its complementary sequence. A comprehensive understanding of the thermodynamic behavior of this process can be achieved by computer simulation. However, the collective behavior of DNA hybridization in solution and on grafted surfaces exhibits disparate time and length scales that make atomistic simulations technically unfeasible. We
We propose a coarse-grained lattice model of short DNA strands to investigate the microscopic pat... more We propose a coarse-grained lattice model of short DNA strands to investigate the microscopic pathways and mechanisms of oligonucleoides hybridization in solution. The extent to which hybridization in solution conforms to two-state thermodynamics is also analyzed. Monte Carlo simulations with parallel tempering are performed to estimate the equilibrium population of single- and double-stranded states and the associated free-energy landscapes. Sequence
The high specificity and selectivity of DNA hybridization makes nucleic acid recognition a powerf... more The high specificity and selectivity of DNA hybridization makes nucleic acid recognition a powerful tool for bottom-up assembling approaches. Here, we propose a coarse-grained model to address the question of how nanoparticles tethered with single stranded DNA self-assemble in solution. Our approach employs a computationally efficient discretization of hard-core interactions and a high-coordination lattice, in combination with parallel tempering and
We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) z... more We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) zeolite membranes with differing surface chemistries. Using molecular dynamics, we have studied the flow of water under hydrostatic pressure through a fully hydrated LTA zeolite film (~2.5 nm thick) capped with hydrophilic and hydrophobic moieties. Pressure drops in the 50-400 MPa range were applied across the membrane, and the flux of water was monitored for at least 15 ns of simulation time. For hydrophilic membranes, water molecules adsorb at the zeolite surface, creating a highly structured fluid layer. For hydrophobic membranes, a depletion of water molecules occurs near the water/zeolite interface. For both types of membranes, the water structure is independent of the pressure drop established in the system and the flux through the membranes is lower than that observed for the bulk zeolitic material; the latter allows an estimation of surface barrier effects to pressure-driven water transport. Mechanistically, it is observed that (i) bottlenecks form at the windows of the zeolite structure, preventing the free flow of water through the porous membrane, (ii) water molecules do not move through a cage in a single-file fashion but rather exhibit a broad range of residence times and pronounced mixing, and (iii) a periodic buildup of a pressure difference between inlet and outlet cages takes place which leads to the preferential flow of water molecules toward the low-pressure cages.
Triphilic ionic liquids (containing polar, apolar, and fluorinated components) that can hydrogen ... more Triphilic ionic liquids (containing polar, apolar, and fluorinated components) that can hydrogen bond present a new paradigm in ionic liquid structural morphology. In this study we show that butylammonium pentadecafluorooctanoate and its nonfluorinated analogue butylammonium octanoate form disordered bicontinuous phases where a network of charge alternating hydrogen bonds continuously percolate through the whole liquid. These systems show order on multiple length scales, the largest length scale given by the percolating network. Separation between filaments in the network gives rise to a prepeak or first sharp diffraction peak. In the case of the fluorinated system, shorter range order occurs due to apolar-fluorinated alternation that decorates the surface of each individual filament. The backbone of the filaments is the product of the shortest organized length scale, namely, charge alternating hydrogen bonds. Liquid structure obtained via molecular dynamics simulations is used to compute coherent X-ray scattering intensities, and a full picture of the liquid landscape is developed. A careful mathematical analysis of the simulation data proposed here reveals individual molecular correlations that importantly contribute to each feature of the experimental structure function.
Proceedings of SPE Latin American and Caribbean Petroleum Engineering Conference, 2003
... Ggc = gas cap volume at current pressure (mmscf) Sgbt = gas saturation at breakthrough (fract... more ... Ggc = gas cap volume at current pressure (mmscf) Sgbt = gas saturation at breakthrough (fraction) Bga = gas formation volume factor at current pressure (cf ... gas oil ratio (scf/stb) Rs = solution gas oil ratio (scf/stb) Bw = water formation volume factor (rb/stb) qw = water production ...
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