1
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Vo T. Theory and simulation of ligand functionalized nanoparticles - a pedagogical overview. SOFT MATTER 2024; 20:3554-3576. [PMID: 38646950 DOI: 10.1039/d4sm00177j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Synthesizing reconfigurable nanoscale synthons with predictive control over shape, size, and interparticle interactions is a holy grail of bottom-up self-assembly. Grand challenges in their rational design, however, lie in both the large space of experimental synthetic parameters and proper understanding of the molecular mechanisms governing their formation. As such, computational and theoretical tools for predicting and modeling building block interactions have grown to become integral in modern day self-assembly research. In this review, we provide an in-depth discussion of the current state-of-the-art strategies available for modeling ligand functionalized nanoparticles. We focus on the critical role of how ligand interactions and surface distributions impact the emergent, pre-programmed behaviors between neighboring particles. To help build insights into the underlying physics, we first define an "ideal" limit - the short ligand, "hard" sphere approximation - and discuss all experimental handles through the lens of perturbations about this reference point. Finally, we identify theories that are capable of bridging interparticle interactions to nanoscale self-assembly and conclude by discussing exciting new directions for this field.
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Affiliation(s)
- Thi Vo
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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2
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Guerrero-García GI, Bhuiyan LB, Outhwaite CW, González-Tovar E. Charge asymmetric electrolytes around a rigid cylindrical polyelectrolyte: A generalization of the capacitive compactness. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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3
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Size and/or charge asymmetry effects in coulombic fluids in the presence of external fields: From simple electrolytes to molten salts. Biophys Chem 2022; 282:106747. [DOI: 10.1016/j.bpc.2021.106747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/27/2022]
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4
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Abstract
JACFC is a Java web application (http://neuronanobiophysics.utsa.edu/) that provides both experts and non-experts in the field suitable tools for elucidating the molecular mechanisms modulating the electrical signal propagation, stability, and bundle formation of microtubules and actin filaments under different molecular (wild type, isoforms, mutants) and environmental (physiological and pathological) conditions. This acknowledgment might reveal the potential role of cytoskeleton filaments in neuronal activities, including molecular-level processing of information and neural regeneration. Molecular understanding of the polyelectrolyte properties of bionanowires, is also crucial for development of reliability, highly functioning small devices with biotechnological applications such as bionanosensors and computing bionanoprocessors.
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Affiliation(s)
- Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249, United States of America
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5
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Patra CN. Size and charge correlations in spherical electric double layers: a case study with fully asymmetric mixed electrolytes within the solvent primitive model. RSC Adv 2020; 10:39017-39025. [PMID: 35518397 PMCID: PMC9057371 DOI: 10.1039/d0ra06145j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/05/2020] [Indexed: 11/21/2022] Open
Abstract
Size and charge correlations in spherical electric double layers are investigated through Monte Carlo simulations and density functional theory, through a solvent primitive model representation. A fully asymmetric mixed electrolyte is used for the small ions, whereas the solvent, apart from being a continuum dielectric, is also treated as an individual component. A partially perturbative density functional theory is adopted here, and for comparison, a standard canonical ensemble Monte Carlo simulation is used. The hard-sphere free energy is treated within a weighted density approach and the residual ionic contribution is estimated through perturbation around the uniform density. The results from both methods corroborate each other quantitatively over a wide range of physical parameters. The importance of structural correlations is envisaged through the size and charge asymmetry of the supporting electrolytes that includes the solvent as a component. Size and charge correlations in spherical electric double layers are investigated through Monte Carlo simulations and density functional theory, through a solvent primitive model representation.![]()
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Affiliation(s)
- Chandra N Patra
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre Mumbai 400 085 India
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6
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Taylor Z, Marucho M. The Self-Adaptation Ability of Zinc Oxide Nanoparticles Enables Reliable Cancer Treatments. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E269. [PMID: 32033506 PMCID: PMC7075113 DOI: 10.3390/nano10020269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 11/26/2022]
Abstract
Optimal procedures for reliable anti-cancer treatments involve the systematic delivery of zinc oxide nanoparticles, which spread through the circulatory system. The success of these procedures may largely depend on the NPs' ability of self-adapting their physicochemical properties to overcome the different challenges facing at each stage on its way to the interior of a cancerous cell. In this article, we combine a multiscale approach, a unique nanoparticle model, and available experimental data to characterize the behavior of zinc oxide nanoparticles under different vessels rheology, pH levels, and biological environments. We investigate their ability to prevent aggregation, allow prolonged circulation time in the bloodstream, avoid clearance, conduct themselves through the capillarity system to reach damaged tissues, and selectively approach to target cancerous cells. Our results show that non-functionalized spherical zinc oxide nanoparticles with surface density N = 5.89 × 10-6 mol/m2, protonation and deprotonation rates pKa = 10.9 and pKb = -5.5, and NP size in the range of 20-50 nm are the most effective, smart anti-cancer agents for biomedical treatments.
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Affiliation(s)
- Zane Taylor
- Department of Applied Physics and Materials Science, California Institute of Technology, Pasadena, CA 91125, USA;
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
| | - Marcelo Marucho
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
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7
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Zhou S. Role of neutral and non-hard sphere interaction in differential capacitance of electrical double-layer. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Marucho M. A Java Application to Characterize Biomolecules and Nanomaterials in Electrolyte Aqueous Solutions. COMPUTER PHYSICS COMMUNICATIONS 2019; 242:104-119. [PMID: 31827306 PMCID: PMC6905646 DOI: 10.1016/j.cpc.2019.03.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The electrostatic, entropic and surface interactions between a macroion (nanoparticle or biomolecule), surrounding ions and water molecules play a fundamental role in the behavior and function of colloidal systems. However, the molecular mechanisms governing these phenomena are still poorly understood. One of the major limitations in procuring this understanding is the lack of appropriate computational tools. Additionally, only experts in the field with an extensive background in programming, who are trained in statistical mechanics, and have access to supercomputers are able to study these systems. To overcome these limitations, in this article, we present a free, multiplatform, portable Java software, which provides experts and non-experts in the field an easy and efficient way to obtain an accurate molecular characterization of electrical and structural properties of aqueous electrolyte mixture solutions around both cylindrical- and spherical-like rigid macroions under multiple conditions. These properties include the normalized ions and water density profile distributions, the mean electrostatic potential, the integrated charge, the zeta potential, the electrostatic potential energy, the particle crowding entropy energy, the ion-ion electrostatic direct correlation energy, and the ionic potential of mean force. The Java software does not require outstanding skills and comes with detailed user-guide documentation. The application is based on the so-called Classical Density Functional Theory Solver (CSDFTS), which was successfully applied to a variety of rod-like biopolymers, rigid-like globular proteins, nanoparticles, and nano-rods. CSDFTS implements several electrolyte and macroion models, uses different levels of approximation and takes advantage of high performance Fortran90 routines and optimized libraries. These features enable the software to run on single processor computers at low-to-moderate computational cost depending on the computer performance, the grid resolution, and the characterization of the macroion and the electrolyte solution, among other factors. As a unique feature, the software comes with a graphical user interface (GUI) that allows users to take advantage of the visually guided setup of the required input data to properly characterize the system and configure the solver. Several examples on nanomaterials and biomolecules are provided to illustrate the use of the GUI and the solver performance.
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Affiliation(s)
- Marcelo Marucho
- , website: https://www.utsa.edu/physics/faculty/MarceloMarucho.html
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9
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Sun LZ, Zhou Y, Chen SJ. Predicting Monovalent Ion Correlation Effects in Nucleic Acids. ACS OMEGA 2019; 4:13435-13446. [PMID: 31460472 PMCID: PMC6705202 DOI: 10.1021/acsomega.9b01689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 07/18/2019] [Indexed: 05/14/2023]
Abstract
Ion correlation and fluctuation can play a potentially significant role in metal ion-nucleic acid interactions. Previous studies have focused on the effects for multivalent cations. However, the correlation and fluctuation effects can be important also for monovalent cations around the nucleic acid surface. Here, we report a model, gMCTBI, that can explicitly treat discrete distributions of both monovalent and multivalent cations and can account for the correlation and fluctuation effects for the cations in the solution. The gMCTBI model enables investigation of the global ion binding properties as well as the detailed discrete distributions of the bound ions. Accounting for the ion correlation effect for monovalent ions can lead to more accurate predictions, especially in a mixed monovalent and multivalent salt solution, for the number and location of the bound ions. Furthermore, although the monovalent ion-mediated correlation does not show a significant effect on the number of bound ions, the correlation may enhance the accumulation of monovalent ions near the nucleic acid surface and hence affect the ion distribution. The study further reveals novel ion correlation-induced effects in the competition between the different cations around nucleic acids.
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Affiliation(s)
- Li-Zhen Sun
- Department
of Applied Physics, Zhejiang University
of Technology, Hangzhou 310023, China
- Department
of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Yuanzhe Zhou
- Department
of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department
of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
- E-mail:
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10
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Zhou S. Effects of interionic non-hard sphere neutral interaction and solvent crowding on differential capacitance curve of electrical double layer. J Chem Phys 2019. [DOI: 10.1063/1.5110660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- S. Zhou
- School of Physics and Electronics, Central South University, Changsha, Hunan 410083, China
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11
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González-Tovar E, Lozada-Cassou M, Bhuiyan LB, Outhwaite CW. Comparison of zeta potentials and structure for statistical mechanical theories of a model cylindrical double layer. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.12.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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12
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Hunley C, Uribe D, Marucho M. A multi-scale approach to describe electrical impulses propagating along actin filaments in both intracellular and in vitro conditions. RSC Adv 2018; 8:12017-12028. [PMID: 30761211 PMCID: PMC6369918 DOI: 10.1039/c7ra12799e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
An accurate and efficient characterization of the polyelectrolyte properties for cytoskeleton filaments are key to the molecular understanding of electrical signal propagation, bundle and network formation, as well as their potential nanotechnological applications. In this article, we introduce an innovative multi-scale approach able to account for the atomistic details of a protein molecular structure, its biological environment, and their impact on electrical impulses propagating along wild type actin filaments. The formulation includes non-trivial contributions to the ionic electrical conductivity and capacitance coming from the diffuse part of the electrical double layer of G-actins. We utilize this monomer characterization in a non-linear inhomogeneous transmission line prototype model to account for the monomer–monomer interactions, dissipation and damping perturbations along the filament length. A novel, simple, accurate, approximate analytic expression has been obtained for the transmission line model. Our results reveal the propagation of electrical signal impulses in the form of solitons for the range of voltage stimulus and electrolyte solutions typically present for intracellular and in vitro conditions. The approach predicts a lower electrical conductivity with higher linear capacitance and non-linear accumulation of charge for intracellular conditions. Our results show a significant influence of the voltage input on the electrical impulse shape, attenuation and kern propagation velocity. The filament is able to sustain the soliton propagation at almost constant kern velocity for the in vitro condition, whereas the intracellular condition displays a remarkable deceleration. Additionally, the solitons are narrower and travel faster at higher voltage input. As a unique feature, this multi-scale theory is able to account for molecular structure conformation (mutation) and biological environment (protonations/deprotonations) changes often present in pathological conditions. It is also applicable to other highly charged rod-like polyelectrolytes with relevance in biomedicine and biophysics. An innovative analytic solution accounting for the molecular structure, its biological environment, and their impact on electrical impulses along microfilaments.![]()
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Affiliation(s)
- Christian Hunley
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003
| | - Diego Uribe
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003
| | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003
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13
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Reindl A, Bier M, Dietrich S. Electrolyte solutions at curved electrodes. II. Microscopic approach. J Chem Phys 2017; 146:154704. [DOI: 10.1063/1.4979948] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Abstract
The accurate characterization of the electrical double layer properties of nanoparticles is of fundamental importance for optimizing their physicochemical properties for specific biotechnological and biomedical applications. In this article, we use classical solvation density functional theory and a surface complexation model to investigate the effects of the pH and the nanoparticle size on the structural and electrostatic properties of an electrolyte solution surrounding a spherical silica oxide nanoparticle. The formulation has been particularly useful for identifying dominant interactions governing the ionic driving force at a variety of pH levels and nanoparticle sizes. As a result of the energetic interplay displayed between electrostatic potential, ion-ion correlation and particle crowding effects on the nanoparticle surface titration, rich, non-trivial ion density profiles and mean electrostatic potential behavior have been found.
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Affiliation(s)
- Christian Hunley
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003, USA.
| | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003, USA.
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15
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Sushko ML, Thomas DG, Pabit SA, Pollack L, Onufriev AV, Baker NA. The Role of Correlation and Solvation in Ion Interactions with B-DNA. Biophys J 2016; 110:315-326. [PMID: 26789755 DOI: 10.1016/j.bpj.2015.12.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/30/2015] [Accepted: 12/07/2015] [Indexed: 01/28/2023] Open
Abstract
The ionic atmospheres around nucleic acids play important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle x-ray scattering can provide important insights into the structure and energetics of such atmospheres but are time- and resource intensive. In this article, we use classical density functional theory to explore the balance among ion-DNA, ion-water, and ion-ion interactions in ionic atmospheres of RbCl, SrCl2, and CoHexCl3 (cobalt hexamine chloride) around a B-form DNA molecule. The accuracy of the classical density functional theory calculations was assessed by comparison between simulated and experimental anomalous small-angle x-ray scattering curves, demonstrating that an accurate model should take into account ion-ion correlation and ion hydration forces, DNA topology, and the discrete distribution of charges on the DNA backbone. As expected, these calculations revealed significant differences among monovalent, divalent, and trivalent cation distributions around DNA. Approximately half of the DNA-bound Rb(+) ions penetrate into the minor groove of the DNA and half adsorb on the DNA backbone. The fraction of cations in the minor groove decreases for the larger Sr(2+) ions and becomes zero for CoHex(3+) ions, which all adsorb on the DNA backbone. The distribution of CoHex(3+) ions is mainly determined by Coulomb and steric interactions, while ion-correlation forces play a central role in the monovalent Rb(+) distribution and a combination of ion-correlation and hydration forces affect the Sr(2+) distribution around DNA. This does not imply that correlations in CoHex solutions are weaker or stronger than for other ions. Steric inaccessibility of the grooves to large CoHex ions leads to their binding at the DNA surface. In this binding mode, first-order electrostatic interactions (Coulomb) dominate the overall binding energy as evidenced by low sensitivity of ionic distribution to the presence or absence of second-order electrostatic correlation interactions.
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Affiliation(s)
- Maria L Sushko
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Dennis G Thomas
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Alexey V Onufriev
- Department of Computer Science and Department of Physics, Virginia Tech, Blacksburg, Virginia
| | - Nathan A Baker
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, Washington; Division of Applied Mathematics, Brown University, Providence, Rhode Island.
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16
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Warshavsky V, Marucho M. Polar-solvation classical density-functional theory for electrolyte aqueous solutions near a wall. Phys Rev E 2016; 93:042607. [PMID: 27176352 DOI: 10.1103/physreve.93.042607] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 01/10/2023]
Abstract
A precise description of the structural and dielectric properties of liquid water is critical to understanding the physicochemical properties of solutes in electrolyte solutions. In this article, a mixture of ionic and dipolar hard spheres is considered to account for water crowding and polarization effects on ionic electrical double layers near a uniformly charged hard wall. As a unique feature, solvent hard spheres carrying a dipole at their centers were used to model water molecules at experimentally known concentration, molecule size, and dipolar moment. The equilibrium ionic and dipole density profiles of this electrolyte aqueous model were calculated using a polar-solvation classical density-functional theory (PSCDFT). These profiles were used to calculate the charge density distribution, water polarization, dielectric permittivity function, and mean electric potential profiles as well as differential capacitance, excess adsorptions, and wall-fluid surface tension. These results were compared with those corresponding to the pure dipolar model and unpolar primitive solvent model of electrolyte aqueous solutions to understand the role that water crowding and polarization effects play on the structural and thermodynamic properties of these systems. Overall, PSCDFT predictions are in agreement with available experimental data.
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Affiliation(s)
- Vadim Warshavsky
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio Texas 78249-5003, USA
| | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio Texas 78249-5003, USA
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17
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Patra CN. A three-component model on the structure of colloidal solution with size-asymmetric electrolytes. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1143126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Chandra N. Patra
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
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18
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Ion-ion correlation, solvent excluded volume and pH effects on physicochemical properties of spherical oxide nanoparticles. J Colloid Interface Sci 2015; 462:325-33. [PMID: 26476201 DOI: 10.1016/j.jcis.2015.10.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 01/08/2023]
Abstract
One major source of complexity in the implementation of nanoparticles in aqueous electrolytes arises from the strong influence that biological environments has on their physicochemical properties. A key parameter for understanding the molecular mechanisms governing the physicochemical properties of nanoparticles is the formation of the surface charge density. In this article, we present an efficient and accurate approach that combines a recently introduced classical solvation density functional theory for spherical electrical double layers with a surface complexation model to account for ion-ion correlation and excluded volume effects on the surface titration of spherical nanoparticles. We apply the proposed computational approach to account for the charge-regulated mechanisms on the surface chemistry of spherical silica (SiO2) nanoparticles. We analyze the effects of the nanoparticle size, as well as pH level and electrolyte concentration of the aqueous solution on the nanoparticle's surface charge density and Zeta potential. We validate our predictions for 580Å and 200Å nanoparticles immersed in acid, neutral and alkaline mono-valent aqueous electrolyte solutions against experimental data. Our results on mono-valent electrolyte show that the excluded volume and ion-ion correlations contribute significantly to the surface charge density and Zeta potential of the nanoparticle at high electrolyte concentration and pH levels, where the solvent crowding effects and electrostatic screening have shown a profound influence on the protonation/deprotonation reactions at the liquid/solute interface. The success of this approach in describing physicochemical properties of silica nanoparticles supports its broader application to study other spherical metal oxide nanoparticles.
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19
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Wu YY, Zhang ZL, Zhang JS, Zhu XL, Tan ZJ. Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA. Nucleic Acids Res 2015; 43:6156-65. [PMID: 26019178 PMCID: PMC4499160 DOI: 10.1093/nar/gkv570] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 05/20/2015] [Indexed: 01/30/2023] Open
Abstract
Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Co(NH3)6 (3+) (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive. However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become 'internal binding' into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit 'external binding' to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.
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Affiliation(s)
- Yuan-Yan Wu
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Zhong-Liang Zhang
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Jin-Si Zhang
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiao-Long Zhu
- Department of Physics, School of Physics & Information Engineering, Jianghan University, Wuhan 430056, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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20
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Barrios-Contreras EA, González-Tovar E, Guerrero-García GI. The dominance of small ions in the electric double layer of size- and charge-asymmetric electrolytes: a mean-field study on the charge reversal and surface charge amplification. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1018853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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