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Published: Apr 2020

Published: Apr 2020

Redox probe transport through supported lipid bilayers and nanopore‐confined lipid assemblies on silica thin films is examined using electrochemical impedance spectroscopy (EIS). These supported lipid systems are emerging biomimetic separation and sensor platforms. The ability to quantify the accessibility of the pore structure of the mesoporous silica thin films is demonstrated, which is essential for the incorporation of carriers into the lipids for selective solute transport. Redox probe molecules with varying hydrophilicity are used to compare ion transport in supported lipid pore‐spanning bilayers (enveloped bilayers) and novel lipid filled pores of mesoporous silica thin films. The films feature orthogonally oriented 8–10 nm cylindrical nanopores formed by deposition of P123‐templated silica sols onto chemically modified fluorine‐doped tin oxide. Nanopore accessibility is confirmed by EIS with hydrophilic probe 1,1′‐ferrocenedimethanol (FDM). Filling the pores with lipid 1,2‐dipalmitoyl‐sn‐glycero‐3‐phosphocholine results in a superior barrier (with roughly 1/9 the permeability) to transport of FDM compared to fragile enveloped lipid bilayers deposited by vesicle fusion. The pore‐confined lipids not only provide a better barrier to FDM, but also a better pathway for the transport across the films of a hydrophobic redox probe 1,1′‐dioctadecyl‐4,4′‐bipyridinium dibromide, with an ideal transport selectivity of 11 compared to FDM.

Authors: Maruyama, Ippei, et al

Published: Jan 2021

Authors: Maruyama, Ippei, et al

Published: Jan 2021

Published: Sep 2018

Published: Sep 2018

The SAFT-γ Mie group-contribution equation of state [Papaioannou J. Chem. Phys. 2014, 140, 054107] is used to develop a transferable coarse-grained (CG) force-field suitable for the molecular simulation of linear alkanes. A heterogroup model is fashioned at the resolution of three carbon atoms per bead in which different Mie (generalized Lennard-Jones) interactions are used to characterize the terminal (CH3–CH2–CH2−) and middle (−CH2–CH2–CH2−) beads. The force field is developed by combining the SAFT-γ CG top-down approach [Avendaño J. Phys. Chem. B 2011, 115, 11154], using experimental phase-equilibrium data for n-alkanes ranging from n-nonane to n-pentadecane to parametrize the intermolecular (nonbonded) bead–bead interactions, with a bottom-up approach relying on simulations based on the higher resolution TraPPE united-atom (UA) model [Martin; , Siepmann J. Phys. Chem. B 1998, 102, 2569] to establish the intramolecular (bonded) interactions. The transferability of the SAFT-γ CG model is assessed from a detailed examination of the properties of linear alkanes ranging from n-hexane (n-C6H14) to n-octadecane (n-C18H38), including an additional evaluation of the reliability of the description for longer chains such as n-hexacontane (n-C60H122) and a prototypical linear polyethylene of moderate molecular weight (n-C900H1802). A variety of structural, thermodynamic, and transport properties are examined, including the pair distribution functions, vapor–liquid equilibria, interfacial tension, viscosity, and diffusivity. Particular focus is placed on the impact of incorporating intramolecular interactions on the accuracy, transferability, and representability of the CG model. The novel SAFT-γ CG force field is shown to provide a reliable description of the thermophysical properties of the n-alkanes, in most cases at a level comparable to the that obtained with higher resolution models.

Published: Mar 2015

Published: Mar 2015

In this work, we develop coarse-grained (CG) force fields for water, where the effective CG intermolecular interactions between particles are estimated from an accurate description of the macroscopic experimental vapour–liquid equilibria data by means of a molecular-based equation of state. The statistical associating fluid theory for Mie (generalised Lennard-Jones) potentials of variable range (SAFT-VR Mie) is used to parameterise spherically symmetrical (isotropic) force fields for water. The resulting SAFT-γ CG models are based on the Mie (8-6) form with size and energy parameters that are temperature dependent; the latter dependence is a consequence of the angle averaging of the directional polar interactions present in water. At the simplest level of CG where a water molecule is represented as a single bead, it is well known that an isotropic potential cannot be used to accurately reproduce all of the thermodynamic properties of water simultaneously. In order to address this deficiency, we propose two CG potential models of water based on a faithful description of different target properties over a wide range of temperatures: our CGW1-vle model is parameterised to match the saturated-liquid density and vapour pressure; our other CGW1-ift model is parameterised to match the saturated-liquid density and vapour–liquid interfacial tension. A higher level of CG corresponding to two water molecules per CG bead is also considered: the corresponding CGW2-bio model is developed to reproduce the saturated-liquid density and vapour–liquid interfacial tension in the physiological temperature range, and is particularly suitable for the large-scale simulation of bio-molecular systems. A critical comparison of the phase equilibrium and transport properties of the proposed force fields is made with the more traditional atomistic models.

Published: Feb 2013

Published: Feb 2013

In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, and E. A. Müller, J. Phys. Chem. B2011, 115, 11154] we introduced the SAFT-γ force field for molecular simulation of fluids. In our approach, a molecular-based equation of state (EoS) is used to obtain coarse-grained (CG) intermolecular potentials that can then be employed in molecular simulation over a wide range of thermodynamic conditions of the fluid. The macroscopic experimental data for the vapor–liquid equilibria (saturated liquid density and vapor pressure) of a given system are represented with the SAFT-VR Mie EoS and used to estimate effective intermolecular parameters that provide a good description of the thermodynamic properties by exploring a wide parameter space for models based on the Mie (generalized Lennard-Jones) potential. This methodology was first used to develop a simple single-segment CG Mie model of carbon dioxide (CO2) which allows for a reliable representation of the fluid-phase equilibria (for which the model was parametrized), as well as an accurate prediction of other properties such as the enthalpy of vaporization, interfacial tension, supercritical density, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thomson coefficient, and speed of sound). In our current paper, the methodology is further applied and extended to develop effective SAFT-γ CG Mie force fields for some important greenhouse gases including carbon tetrafluoride (CF4) and sulfur hexafluoride (SF6), modeled as simple spherical molecules, and for long linear alkanes including n-decane (n-C10H22) and n-eicosane (n-C20H42), modeled as homonuclear chains of spherical Mie segments. We also apply the SAFT-γ methodology to obtain a CG homonuclear two-segment Mie intermolecular potential for the more challenging polar and asymmetric compound 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), a novel replacement refrigerant with promising properties. The description of the fluid-phase behavior and the prediction of the other thermophysical properties obtained by molecular simulation using our SAFT-γ CG Mie force fields are found to be of comparable quality (and sometimes superior) to that obtained using the more sophisticated all-atom (AA) and united-atom (UA) models commonly employed in the field. We should emphasize that though the focus of our current work is on simple homonuclear models, the SAFT-γ methodology is based on a group contribution methodology which is naturally suited to the development of more sophisticated heteronuclear models.

From Paper: SAFT- <i>γ</i> force field for the simulation of molecular fluids: 3. Coarse-grained models of benzene and hetero-group models of <i>n</i> -decylbenzene

Published: Jun 2012

From Paper: SAFT- <i>γ</i> force field for the simulation of molecular fluids: 3. Coarse-grained models of benzene and hetero-group models of <i>n</i> -decylbenzene

Published: Jun 2012

In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C.S. Adjiman, G. Jackson, and E.A. Müller, J. Phys. Chem. B 115, 11154 (2011)] our methodology for the development of accurate coarse-grained (CG) SAFT-γ force fields for the computer simulation of molecular fluids was introduced with carbon dioxide as a particular case study. The procedure involves the use of a molecular-based equation of state to obtain effective intermolecular parameters (from experimental fluid phase equilibrium data) appropriate for molecular simulation over a wide range of fluid conditions. We now extend the methodology to develop coarse-grained models for benzene (C6H6) that can be used in fluid phase simulations. Our SAFT-γ CG force fields for benzene consist of a simple single-segment spherical model, and a rigid three-segment ring structure of tangent spherical groups interacting via Mie (generalized Lennard-Jones) segment–segment interactions. The description of the fluid phase behaviour of benzene with our simplified CG force fields is found to be comparable to that obtained with the more sophisticated models commonly used in the field; a marked improvement is seen with our SAFT-γ models for the vapour pressure, particularly at lower temperatures. These models of benzene together with the previously developed SAFT-γ three-segment chain model of n-decane are used to develop hetero-group force fields for n-decylbenzene, in the spirit of a group contribution methodology. In our approach, the parameters of the phenyl and n-decyl groups are obtained transferably from the individual models of benzene and n-decane, respectively, and the unlike energetic parameters between the phenyl and decyl segments can be obtained from vapour–liquid equilibria data for n-decylbenzene using the SAFT-γ equation of state. The resulting CG hetero-group models are found to describe the fluid properties of n-decylbenzene over a wide range of conditions, exemplifying how our approach can be used as a group contribution methodology. This is the first example of the development of hetero-group SAFT-γ force fields for molecules formed from Mie segments of different size, energy, softness/hardness, and range.

Published: Sep 2011

Published: Sep 2011

An application of the “top-down” concept for the development of accurate coarse-grained intermolecular potentials of complex fluids is presented. With the more common “bottom-up” procedure, coarse-grained models are constructed from a suitable simplification of a detailed atomistic representation, and small adjustments to the intermolecular parameters are made by comparison with limited experimental data where necessary. In contrast, in the top-down approach, a molecular-based equation of state is used to obtain an effective coarse-grained intermolecular potential that reproduces the macroscopic experimental thermophysical properties over a wide range of conditions. These coarse-grained intermolecular potentials can then be used in conventional molecular simulation to obtain properties (such as structure or dynamics) that are not directly accessible from the equation of state or at extreme conditions where the theory is expected to fail. To demonstrate our procedure, a coarse-grained model for carbon dioxide (CO2) is obtained from a recent implementation of the statistical associating fluid theory of variable range (SAFT-VR) employing a Mie (generalized Lennard-Jones) potential; the parameters of this single-site Mie model of CO2 are estimated by optimizing the equation of state’s description of the experimental vapor-pressure and saturated liquid density data. This approach is only viable because of the excellent agreement of the SAFT-VR Mie EoS with simulation data. Our single-site SAFT-γ coarse-grained model for CO2 is used in Monte Carlo molecular simulation to assess the adequacy of the description of the fluid-phase behavior and properties that were not used to develop the potential model such as the enthalpy of vaporization, interfacial tension, density profiles, supercritical densities, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule–Thompson coefficient, and speed of sound). The accuracy of the description with the single-site SAFT-γ model of CO2 is found to be of similar quality to that of more sophisticated intermolecular potentials such as a six-site (three LJ centers and three charged sites) all-atom model. The SAFT-γ top-down approach to coarse-graining resolves a key challenge with coarse-graining techniques: the provision of a direct robust link between the microscopic and macroscopic scales.

Published: Jan 2009

Published: Jan 2009

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed‐up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.

Published: Mar 2013

Published: Mar 2013

Authors: Deepali Sharma, Suvardhan Kanchi, Krishna Bisetty

Published: Dec 2019

Authors: Deepali Sharma, Suvardhan Kanchi, Krishna Bisetty

Published: Dec 2019

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