1
|
Yonetani Y. Dielectric continuum model examination of real-space electrostatic treatments. J Chem Phys 2021; 154:044103. [PMID: 33514106 DOI: 10.1063/5.0033053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Electrostatic interaction is long ranged; thus, the accurate calculation is not an easy task in molecular dynamics or Monte Carlo simulations. Though the rigorous Ewald method based on the reciprocal space has been established, real-space treatments have recently become an attractive alternative because of the efficient calculation. However, the construction is not yet completed and is now a challenging subject. In an earlier theoretical study, Neumann and Steinhauser employed the Onsager dielectric continuum model to explain how simple real-space cutoff produces artificial dipolar orientation. In the present study, we employ this continuum model to explore the fundamental properties of the recently developed real-space treatments of three shifting schemes. The result of the distance-dependent Kirkwood function GK(R) showed that the simple bare cutoff produces a well-known hole-shaped artifact, whereas the shift treatments do not. Two-dimensional mapping of electric field well explained how these shift treatments remove the hole-shaped artifact. Still, the shift treatments are not sufficient because they do not produce a flat GK(R) profile unlike ideal no-cutoff treatment. To test the continuum model results, we also performed Monte Carlo simulations of dipolar particles. The results found that the continuum model could predict the qualitative tendency as to whether each electrostatic treatment produces the hole-shaped artifact of GK(R) or not. We expect that the present study using the continuum model offers a stringent criterion to judge whether the primitive electrostatic behavior is correctly described or not, which will be useful for future construction of electrostatic treatments.
Collapse
Affiliation(s)
- Yoshiteru Yonetani
- Quantum Beam Science Research Directorate and Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| |
Collapse
|
2
|
Falcón-González JM, Contreras-Aburto C, Lara-Peña M, Heinen M, Avendaño C, Gil-Villegas A, Castañeda-Priego R. Assessment of the Wolf method using the Stillinger-Lovett sum rules: From strong electrolytes to weakly charged colloidal dispersions. J Chem Phys 2020; 153:234901. [PMID: 33353329 DOI: 10.1063/5.0033561] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Ewald method has been the cornerstone in molecular simulations for modeling electrostatic interactions of charge-stabilized many-body systems. In the late 1990s, Wolf and collaborators developed an alternative route to describe the long-range nature of electrostatic interactions; from a computational perspective, this method provides a more efficient and straightforward way to implement long-range electrostatic interactions than the Ewald method. Despite these advantages, the validity of the Wolf potential to account for the electrostatic contribution in charged fluids remains controversial. To alleviate this situation, in this contribution, we implement the Wolf summation method to both electrolyte solutions and charged colloids with moderate size and charge asymmetries in order to assess the accuracy and validity of the method. To this end, we verify that the proper selection of parameters within the Wolf method leads to results that are in good agreement with those obtained through the standard Ewald method and the theory of integral equations of simple liquids within the so-called hypernetted chain approximation. Furthermore, we show that the results obtained with the original Wolf method do satisfy the moment conditions described by the Stillinger-Lovett sum rules, which are directly related to the local electroneutrality condition and the electrostatic screening in the Debye-Hückel regime. Hence, the fact that the solution provided by the Wolf method satisfies the first and second moments of Stillinger-Lovett proves, for the first time, the reliability of the method to correctly incorporate the electrostatic contribution in charge-stabilized fluids. This makes the Wolf method a powerful alternative compared to more demanding computational approaches.
Collapse
Affiliation(s)
- José Marcos Falcón-González
- Unidad Profesional Interdisciplinaria de Ingeniería, Campus Guanajuato, Instituto Politécnico Nacional, Av. Mineral de Valenciana No. 200, Col. Fraccionamiento Industrial Puerto Interior, C.P. 36275 Silao de la Victoria, Guanajuato, Mexico
| | - Claudio Contreras-Aburto
- Facultad de Ciencias en Física y Matemáticas, Universidad Autónoma de Chiapas, 29050 Tuxtla Gutiérrez, Mexico
| | - Mayra Lara-Peña
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Mexico
| | - Marco Heinen
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Mexico
| | - Carlos Avendaño
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M13 9PL, United Kingdom
| | - Alejandro Gil-Villegas
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Mexico
| | - Ramón Castañeda-Priego
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Mexico
| |
Collapse
|
3
|
Stenqvist B, Aspelin V, Lund M. Generalized Moment Correction for Long-Ranged Electrostatics. J Chem Theory Comput 2020; 16:3737-3745. [PMID: 32315176 PMCID: PMC7588037 DOI: 10.1021/acs.jctc.9b01003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
Describing
long-ranged electrostatics using short-ranged pair potentials
is appealing because the computational complexity scales linearly
with the number of particles. The foundation of the approach presented
here is to mimic the long-ranged medium response by cancelling electric
multipoles within a small cutoff sphere. We propose a rigorous and
formally exact new method that cancels up to infinitely many multipole moments and is free of operational damping parameters
often required in existing theories. Using molecular dynamics simulations
of water with and without added salt, we discuss radial distribution
functions, Kirkwood–Buff integrals, dielectrics, diffusion
coefficients, and angular correlations in relation to existing electrostatic
models. We find that the proposed method is an efficient and accurate
alternative for handling long-ranged electrostatics as compared to
Ewald summation schemes. The methodology and proposed parameterization
are applicable also for dipole–dipole interactions.
Collapse
Affiliation(s)
- Björn Stenqvist
- Division of Physical Chemistry, Department of Chemistry, Lund University, 221 00 Lund, Sweden.,Division of Theoretical Chemistry, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Vidar Aspelin
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Mikael Lund
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, 221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
| |
Collapse
|
4
|
Purton JA. Diffusion in gadolinium doped ceria thin films: a combined Monte Carlo and molecular dynamics study. Phys Chem Chem Phys 2019; 21:9802-9809. [PMID: 31026005 DOI: 10.1039/c8cp07136e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The mobility of oxygen ions at surfaces and interfaces in solid oxide fuel materials is controversial. Experiments are complex and conflicting results for grain boundary and surface O2- diffusion have been obtained. Thus, it is not clear what the necessary conditions are to optimise O2- diffusion during the manufacturing process. To aid the interpretation of experimental results, combined Monte Carlo and molecular dynamics simulations were applied to model thin films of CeO2 on binary oxide substrates. The objective of this work is to determine the effects of both tensile lattice strain and segregation on the calculated diffusion coefficients. The distribution of Gd3+ and O2- ions has been interpreted as evidence for the formation of a space charge layer at both the interface and surface. The space charge layer impacts the calculated diffusion coefficients at the thin film surface. Moderate tensile strain in the CeO2 thin film has little influence on the segregation of Gd3+ ions.
Collapse
Affiliation(s)
- John A Purton
- Scientific Computing Department, Daresbury Laboratory, Keckwick Lane, Warrington, UK.
| |
Collapse
|
5
|
Mehta NA, Levin DA. Electrospray molecular dynamics simulations using an octree-based Coulomb interaction method. Phys Rev E 2019; 99:033302. [PMID: 30999539 DOI: 10.1103/physreve.99.033302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Indexed: 06/09/2023]
Abstract
A new octree-based Coulomb interaction model is developed to model the electrospray of ionic liquids (ILs) in molecular dynamics. Using an octree-based method, Coulomb interactions are categorized as intra- and interleaf Coulomb interactions based on a criterion related to the Bjerrum length of the IL. The octree-based method is found capable of reproducing Coulomb energy in agreement with established and computationally more expensive models, such as the direct Coulomb and the damped shifted force (DSF) method in the absence of an external electric field. In the presence of an external electric field, the octree-based method produces distinctly different results compared to that obtained by the direct Coulomb method. The time required to form Taylor's cone was shorter for the octree method compared to the direct Coulomb approach. While no emission larger than monomers was observed from the direct Coulomb simulation, emission of larger species such as dimers and trimers was observed when the octree-based Coulomb interaction model was used. Furthermore, the octree-based model forms a smaller ion emission cone compared to that from the direct Coulomb method.
Collapse
Affiliation(s)
- Neil A Mehta
- The University of Illinois Urbana-Champaign, IL 61801, USA
| | | |
Collapse
|
6
|
Waibel C, Feinler MS, Gross J. A Modified Shifted Force Approach to the Wolf Summation. J Chem Theory Comput 2018; 15:572-583. [PMID: 30418767 DOI: 10.1021/acs.jctc.8b00343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Wolf method for calculation of electrostatic interactions in molecular simulations is known to describe the energy well, whereas the forces have discontinuities. For a more reliable description of the forces this method can be extended with a shifted force approach. This leads to a good description of the forces and precise molecular dynamics simulation, but the description of the energy becomes poorer. In this study we propose a modification of a shifted force extension to describe the energy as well as the forces in better agreement to reference data as determined from the Ewald summation. We show that vapor-liquid phase equilibria (VLE) calculated with Monte Carlo simulations in the grand canonical ensemble and dynamic properties calculated with molecular dynamics simulations can be calculated reliably using this modification to describe the electrostatic interactions.
Collapse
Affiliation(s)
- Christian Waibel
- Institute of Thermodynamics and Thermal Process Engineering , University of Stuttgart , Pfaffenwaldring 9 , 70569 Stuttgart , Germany
| | - Mathias Simon Feinler
- Institute of Thermodynamics and Thermal Process Engineering , University of Stuttgart , Pfaffenwaldring 9 , 70569 Stuttgart , Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering , University of Stuttgart , Pfaffenwaldring 9 , 70569 Stuttgart , Germany
| |
Collapse
|
7
|
Hens R, Vlugt TJH. Molecular Simulation of Vapor-Liquid Equilibria Using the Wolf Method for Electrostatic Interactions. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2018; 63:1096-1102. [PMID: 30258248 PMCID: PMC6150682 DOI: 10.1021/acs.jced.7b00839] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023]
Abstract
The applicability of the Wolf method for calculating electrostatic interactions is verified for simulating vapor-liquid equilibria of hydrogen sulfide, methanol, and carbon dioxide. Densities, chemical potentials, and critical properties are obtained with Monte Carlo simulations using the Continuous Fractional Component version of the Gibbs Ensemble. Saturated vapor pressures are obtained from NPT simulations. Excellent agreement is found between simulation results and data from literature (simulations using the Ewald summation). It is also shown how to choose the optimal parameters for the Wolf method. Even though the Wolf method requires a large simulation box in the gas phase, due to the lack of screening of electrostatics, one can consider the Wolf method as a suitable alternative to the Ewald summation in VLE calculations.
Collapse
|
8
|
Waibel C, Gross J. Modification of the Wolf Method and Evaluation for Molecular Simulation of Vapor–Liquid Equilibria. J Chem Theory Comput 2018; 14:2198-2206. [DOI: 10.1021/acs.jctc.7b01190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Waibel
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| |
Collapse
|
9
|
Crack nucleation criterion and its application to impact indentation in glasses. Sci Rep 2016; 6:23720. [PMID: 27079431 PMCID: PMC4832188 DOI: 10.1038/srep23720] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/14/2016] [Indexed: 01/29/2023] Open
Abstract
Molecular dynamics (MD) simulations are used to directly observe nucleation of median cracks in oxide glasses under indentation. Indenters with sharp angles can nucleate median cracks in samples with no pre-existing flaws, while indenters with larger indenter angles cannot. Increasing the tip radius increases the critical load for nucleation of the median crack. Based upon an independent set of simulations under homogeneous loading, the fracture criterion in the domain of the principal stresses is constructed. The fracture criterion, or “fracture locus”, can quantitatively explain the observed effects of indenter angle and indenter tip radius on median crack nucleation. Our simulations suggest that beyond the maximum principal stress, plasticity and multi-axial stresses should also be considered for crack nucleation under indentation, even for brittle glassy systems.
Collapse
|
10
|
Vlugt TJH, García-Pérez E, Dubbeldam D, Ban S, Calero S. Computing the Heat of Adsorption using Molecular Simulations: The Effect of Strong Coulombic Interactions. J Chem Theory Comput 2015; 4:1107-18. [PMID: 26636364 DOI: 10.1021/ct700342k] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular simulations are an important tool for the study of adsorption of hydrocarbons in nanoporous materials such as zeolites. The heat of adsorption is an important thermodynamic quantity that can be measured both in experiments and molecular simulations, and therefore it is often used to investigate the quality of a force field for a certain guest-host (g - h) system. In molecular simulations, the heat of adsorption in zeolites is often computed using either of the following methods: (1) using the Clausius-Clapeyron equation, which requires the partial derivative of the pressure with respect to temperature at constant loading, (2) using the energy difference between the host with and without a single guest molecule present, and (3) from energy/particle fluctuations in the grand-canonical ensemble. To calculate the heat of adsorption from experiments (besides direct calorimetry), only the first method is usually applicable. Although the computation of the heat of adsorption is straightforward for all-silica zeolites, severe difficulties arise when applying the conventional methods to systems with nonframework cations present. The reason for this is that these nonframework cations have very strong Coulombic interactions with the zeolite. We will present an alternative method based on biased interactions of guest molecules that suffers less from these difficulties. This method requires only a single simulation of the host structure. In addition, we will review some of the other important issues concerning the handling of these strong Coulombic interactions in simulating the adsorption of guest molecules. It turns out that the recently proposed Wolf method ( J. Chem. Phys. 1999, 110 , 8254 ) performs poorly for zeolites as a large cutoff radius is needed for convergence.
Collapse
Affiliation(s)
- T J H Vlugt
- Process & Energy Laboratory, Delft University of Technology, Leeghwaterstraat 44, 2628CA Delft, The Netherlands, Department of Physical, Chemical, and Natural Systems, University Pablo de Olavide, Ctra. Utrera km 1, 41013 Sevilla, Spain, Chemical and Biological Engineering Department, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, and Condensed Matter and Interfaces, Utrecht University, P.O. Box 80000, 08 TA Utrecht, The Netherlands
| | - E García-Pérez
- Process & Energy Laboratory, Delft University of Technology, Leeghwaterstraat 44, 2628CA Delft, The Netherlands, Department of Physical, Chemical, and Natural Systems, University Pablo de Olavide, Ctra. Utrera km 1, 41013 Sevilla, Spain, Chemical and Biological Engineering Department, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, and Condensed Matter and Interfaces, Utrecht University, P.O. Box 80000, 08 TA Utrecht, The Netherlands
| | - D Dubbeldam
- Process & Energy Laboratory, Delft University of Technology, Leeghwaterstraat 44, 2628CA Delft, The Netherlands, Department of Physical, Chemical, and Natural Systems, University Pablo de Olavide, Ctra. Utrera km 1, 41013 Sevilla, Spain, Chemical and Biological Engineering Department, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, and Condensed Matter and Interfaces, Utrecht University, P.O. Box 80000, 08 TA Utrecht, The Netherlands
| | - S Ban
- Process & Energy Laboratory, Delft University of Technology, Leeghwaterstraat 44, 2628CA Delft, The Netherlands, Department of Physical, Chemical, and Natural Systems, University Pablo de Olavide, Ctra. Utrera km 1, 41013 Sevilla, Spain, Chemical and Biological Engineering Department, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, and Condensed Matter and Interfaces, Utrecht University, P.O. Box 80000, 08 TA Utrecht, The Netherlands
| | - S Calero
- Process & Energy Laboratory, Delft University of Technology, Leeghwaterstraat 44, 2628CA Delft, The Netherlands, Department of Physical, Chemical, and Natural Systems, University Pablo de Olavide, Ctra. Utrera km 1, 41013 Sevilla, Spain, Chemical and Biological Engineering Department, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, and Condensed Matter and Interfaces, Utrecht University, P.O. Box 80000, 08 TA Utrecht, The Netherlands
| |
Collapse
|
11
|
Ojeda-May P, Pu J. Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations. J Chem Phys 2015; 143:174111. [PMID: 26547162 PMCID: PMC4636498 DOI: 10.1063/1.4934880] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 10/19/2015] [Indexed: 11/14/2022] Open
Abstract
The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.
Collapse
Affiliation(s)
- Pedro Ojeda-May
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, USA
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, USA
| |
Collapse
|
12
|
Bidault X, Chaussedent S, Blanc W. A simple transferable adaptive potential to study phase separation in large-scale xMgO-(1-x)SiO2 binary glasses. J Chem Phys 2015; 143:154501. [PMID: 26493909 DOI: 10.1063/1.4932984] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A simple transferable adaptive model is developed and it allows for the first time to simulate by molecular dynamics the separation of large phases in the MgO-SiO2 binary system, as experimentally observed and as predicted by the phase diagram, meaning that separated phases have various compositions. This is a real improvement over fixed-charge models, which are often limited to an interpretation involving the formation of pure clusters, or involving the modified random network model. Our adaptive model, efficient to reproduce known crystalline and glassy structures, allows us to track the formation of large amorphous Mg-rich Si-poor nanoparticles in an Mg-poor Si-rich matrix from a 0.1MgO-0.9SiO2 melt.
Collapse
Affiliation(s)
- Xavier Bidault
- Laboratoire de Photonique d'Angers (LPhiA)-UPRES EA 4464, Université d'Angers, 2 Bd Lavoisier, 49045 Angers Cedex 01, France
| | - Stéphane Chaussedent
- Laboratoire de Photonique d'Angers (LPhiA)-UPRES EA 4464, Université d'Angers, 2 Bd Lavoisier, 49045 Angers Cedex 01, France
| | - Wilfried Blanc
- CNRS, Laboratoire de Physique de la Matière Condensée (LPMC)-UMR 7336, Université de Nice-Sophia Antipolis, Parc Valrose, 06100 Nice Cedex 2, France
| |
Collapse
|
13
|
Fanourgakis GS. An Extension of Wolf’s Method for the Treatment of Electrostatic Interactions: Application to Liquid Water and Aqueous Solutions. J Phys Chem B 2015; 119:1974-85. [DOI: 10.1021/jp510612w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- George S. Fanourgakis
- Computation-based Science
and Technology Research Center (CaSToRC), The Cyprus Institute, P.O. Box 27456, 1645 Nicosia, Cyprus
| |
Collapse
|
14
|
Fukuda I, Kamiya N, Nakamura H. The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems. J Chem Phys 2014; 140:194307. [PMID: 24852538 DOI: 10.1063/1.4875693] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 174107 (2013)], the zero-multipole (ZM) summation method was proposed for efficiently evaluating the electrostatic Coulombic interactions of a classical point charge system. The summation takes a simple pairwise form, but prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large energetic noises and significant artifacts. The purpose of this paper is to judge the ability of the ZM method by investigating the accuracy, parameter dependencies, and stability in applications to liquid systems. To conduct this, first, the energy-functional error was divided into three terms and each term was analyzed by a theoretical error-bound estimation. This estimation gave us a clear basis of the discussions on the numerical investigations. It also gave a new viewpoint between the excess energy error and the damping effect by the damping parameter. Second, with the aid of these analyses, the ZM method was evaluated based on molecular dynamics (MD) simulations of two fundamental liquid systems, a molten sodium-chlorine ion system and a pure water molecule system. In the ion system, the energy accuracy, compared with the Ewald summation, was better for a larger value of multipole moment l currently induced until l ≲ 3 on average. This accuracy improvement with increasing l is due to the enhancement of the excess-energy accuracy. However, this improvement is wholly effective in the total accuracy if the theoretical moment l is smaller than or equal to a system intrinsic moment L. The simulation results thus indicate L ∼ 3 in this system, and we observed less accuracy in l = 4. We demonstrated the origins of parameter dependencies appearing in the crossing behavior and the oscillations of the energy error curves. With raising the moment l we observed, smaller values of the damping parameter provided more accurate results and smoother behaviors with respect to cutoff length were obtained. These features can be explained, on the basis of the theoretical error analyses, such that the excess energy accuracy is improved with increasing l and that the total accuracy improvement within l ⩽ L is facilitated by a small damping parameter. Although the accuracy was fundamentally similar to the ion system, the bulk water system exhibited distinguishable quantitative behaviors. A smaller damping parameter was effective in all the practical cutoff distance, and this fact can be interpreted by the reduction of the excess subset. A lower moment was advantageous in the energy accuracy, where l = 1 was slightly superior to l = 2 in this system. However, the method with l = 2 (viz., the zero-quadrupole sum) gave accurate results for the radial distribution function. We confirmed the stability in the numerical integration for MD simulations employing the ZM scheme. This result is supported by the sufficient smoothness of the energy function. Along with the smoothness, the pairwise feature and the allowance of the atom-based cutoff mode on the energy formula lead to the exact zero total-force, ensuring the total-momentum conservations for typical MD equations of motion.
Collapse
Affiliation(s)
- Ikuo Fukuda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Narutoshi Kamiya
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
15
|
Electrostatic properties of water models evaluated by a long-range potential based solely on the Wolf charge-neutral condition. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.12.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
16
|
Fukuda I, Kamiya N, Yonezawa Y, Nakamura H. Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water. J Chem Phys 2012; 137:054314. [PMID: 22894355 DOI: 10.1063/1.4739789] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011)], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 Å for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we treated. We discussed the origin of this difference between the two schemes and the dependence of this fact on the physical system. The use of the zero damping-factor will enhance the efficiency of practical computations, since the complementary error function is not employed. In addition, utilizing the zero damping-factor provides freedom from the parameter choice, which is not trivial in the zero-charge scheme, and eliminates the error function term, which corresponds to the time-consuming Fourier part under the periodic boundary conditions.
Collapse
Affiliation(s)
- Ikuo Fukuda
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | | | | | | |
Collapse
|
17
|
Nguyen TD, Carrillo JMY, Dobrynin AV, Brown WM. A Case Study of Truncated Electrostatics for Simulation of Polyelectrolyte Brushes on GPU Accelerators. J Chem Theory Comput 2012; 9:73-83. [DOI: 10.1021/ct300718x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Trung Dac Nguyen
- National Center
for Computational
Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
| | - Jan-Michael Y. Carrillo
- Polymer Program,
Institute of
Materials Science and Department of Physics, University of Connecticut,
Storrs, Connecticut 06269, United States
| | - Andrey V. Dobrynin
- Polymer Program,
Institute of
Materials Science and Department of Physics, University of Connecticut,
Storrs, Connecticut 06269, United States
| | - W. Michael Brown
- National Center
for Computational
Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
| |
Collapse
|
18
|
The Wolf method applied to the type I methane and carbon dioxide gas hydrates. J Mol Graph Model 2012; 38:455-64. [DOI: 10.1016/j.jmgm.2012.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/29/2012] [Accepted: 10/05/2012] [Indexed: 11/23/2022]
|
19
|
Fukuda I, Nakamura H. Non-Ewald methods: theory and applications to molecular systems. Biophys Rev 2012; 4:161-170. [PMID: 23293678 PMCID: PMC3428531 DOI: 10.1007/s12551-012-0089-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 06/21/2012] [Indexed: 11/29/2022] Open
Abstract
Several non-Ewald methods for calculating electrostatic interactions have recently been developed, such as the Wolf method, the reaction field method, the pre-averaging method, and the zero-dipole summation method, for molecular dynamics simulations of various physical systems, including biomolecular systems. We review the theories of these approaches and their potential applications to molecular simulations, and discuss their relationships.
Collapse
Affiliation(s)
- Ikuo Fukuda
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | | |
Collapse
|
20
|
Yonezawa Y. A long-range electrostatic potential based on the Wolf method charge-neutral condition. J Chem Phys 2012; 136:244103. [DOI: 10.1063/1.4729748] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
21
|
Hansen JS, Schrøder TB, Dyre JC. Simplistic Coulomb Forces in Molecular Dynamics: Comparing the Wolf and Shifted-Force Approximations. J Phys Chem B 2012; 116:5738-43. [DOI: 10.1021/jp300750g] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. S. Hansen
- DNRF Centre “Glass and Time”, IMFUFA,
Department of Science, Systems and Models, Roskilde University, Postbox 260, DK-4000 Roskilde, Denmark
| | - Thomas B. Schrøder
- DNRF Centre “Glass and Time”, IMFUFA,
Department of Science, Systems and Models, Roskilde University, Postbox 260, DK-4000 Roskilde, Denmark
| | - Jeppe C. Dyre
- DNRF Centre “Glass and Time”, IMFUFA,
Department of Science, Systems and Models, Roskilde University, Postbox 260, DK-4000 Roskilde, Denmark
| |
Collapse
|
22
|
Viveros-Méndez PX, Gil-Villegas A. Computer simulation of sedimentation of ionic systems using the Wolf method. J Chem Phys 2012; 136:154507. [DOI: 10.1063/1.4704743] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
23
|
Fukuda I, Yonezawa Y, Nakamura H. Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle. J Chem Phys 2011; 134:164107. [PMID: 21528950 DOI: 10.1063/1.3582791] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose a novel idea, zero-dipole summation, for evaluating the electrostatic energy of a classical particle system, and have composed an algorithm for effectively utilizing the idea for molecular dynamics. It conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. The resulting energy formula is nevertheless represented by a simple pairwise function sum, which enables facile application to high-performance computation. By following a heuristic approach to derive the current electrostatic energy formula, we developed an axiomatic approach to construct the method consistently. Explorations of the theoretical details of our method revealed the structure of the generated error, and we analyzed it by comparisons with other methods. A numerical simulation using liquid sodium chloride confirmed that the current method with a small damping factor yielded sufficient accuracy with a practical cutoff distance region. The current energy function also conducts stable numerical integration in a liquid MD simulation. Our method is an extension of the charge neutralized summation developed by Wolf et al. [J. Chem. Phys. 110, 8254 (1999)]. Furthermore, we found that the current method becomes a generalization of the preaveraged potential method proposed by Yakub and Ronchi [J. Chem. Phys. 119, 11556 (2003)], which is based on a viewpoint different from the neutrality. The current study presents these relationships and suggests possibilities for their further applications.
Collapse
Affiliation(s)
- Ikuo Fukuda
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | | | | |
Collapse
|
24
|
Docherty H, Dyer PJ, Cummings PT. The importance of polarisability in the modelling of solubility: quantifying the effect of charged co-solutes on the solubility of small non-polar solutes. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.553225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
25
|
Yonezawa Y, Fukuda I, Kamiya N, Shimoyama H, Nakamura H. Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method. J Chem Theory Comput 2011; 7:1484-93. [DOI: 10.1021/ct100357p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasushige Yonezawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ikuo Fukuda
- Computational Science Research Program, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Narutoshi Kamiya
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiromitsu Shimoyama
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
26
|
Jiménez-Serratos G, Avendaño C, Gil-Villegas A, González-Tovar E. Computer simulation of charged hard spherocylinders at low temperatures. Mol Phys 2011. [DOI: 10.1080/00268976.2010.524171] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
27
|
Makó É, Rutkai G, Kristóf T. Simulation-assisted evidence for the existence of two stable kaolinite/potassium acetate intercalate complexes. J Colloid Interface Sci 2010; 349:442-5. [DOI: 10.1016/j.jcis.2010.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 05/06/2010] [Accepted: 05/07/2010] [Indexed: 11/27/2022]
|
28
|
Brommer P, Beck P, Chatzopoulos A, Gähler F, Roth J, Trebin HR. Direct Wolf summation of a polarizable force field for silica. J Chem Phys 2010; 132:194109. [DOI: 10.1063/1.3396084] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
|
29
|
|
30
|
DeMille RC, Molinero V. Coarse-grained ions without charges: reproducing the solvation structure of NaCl in water using short-ranged potentials. J Chem Phys 2009; 131:034107. [PMID: 19624181 DOI: 10.1063/1.3170982] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A coarse-grained model of NaCl in water is presented where the ions are modeled without charge to avoid computationally challenging electrostatics. A monatomic model of water [V. Molinero and E. B. Moore, J. Phys. Chem. B 113, 4008 (2009)] is used as the basis for this coarse-grain approach. The ability of Na(+) to disrupt the native tetrahedral arrangement of water molecules, and of Cl(-) to integrate within this organization, is preserved in this mW-ion model through parametrization focused on water's solvation of these ions. This model successfully reproduces the structural effect of ions on water, referenced to observations from experiments and atomistic molecular dynamics simulations, while using extremely short-ranged potentials. Without Coulomb interactions the model replicates details of the ion-water structure such as distinguishing contact and solvent-separated ion pairs and the free energy barriers between them. The approach of mimicking ionic effects with short-ranged interactions results in performance gains of two orders of magnitude compared to Ewald methods. Explored over a broad range of salt concentration, the model reproduces the solvation structure and trends of diffusion relative to atomistic simulations and experimental results. The functional form of the mW-ion model can be parametrized to represent other electrolytes. With increased computational efficiency and reliable structural fidelity, this model promises to be an asset for accessing significantly longer simulation time scales with an explicit solvent in a coarse-grained system involving, for example, polyelectrolytes such as proteins, nucleic acids, and fuel-cell membranes.
Collapse
Affiliation(s)
- Robert C DeMille
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
| | | |
Collapse
|
31
|
Simulation and experimental study of intercalation of urea in kaolinite. J Colloid Interface Sci 2009; 334:65-9. [DOI: 10.1016/j.jcis.2009.03.022] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 02/09/2009] [Accepted: 03/09/2009] [Indexed: 11/22/2022]
|
32
|
Kikugawa G, Apostolov R, Kamiya N, Taiji M, Himeno R, Nakamura H, Yonezawa Y. Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. J Comput Chem 2009; 30:110-8. [DOI: 10.1002/jcc.21035] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
33
|
Shi Q, Liu P, Voth GA. Coarse-graining in Interaction Space: An Analytical Approximation for the Effective Short-ranged Electrostatics. J Phys Chem B 2008; 112:16230-7. [DOI: 10.1021/jp807205q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qiang Shi
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S. 1400 E. Rm. 2020, Salt Lake City, Utah 84112-0850
| | - Pu Liu
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S. 1400 E. Rm. 2020, Salt Lake City, Utah 84112-0850
| | - Gregory A. Voth
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S. 1400 E. Rm. 2020, Salt Lake City, Utah 84112-0850
| |
Collapse
|
34
|
Nagata Y, Lennartz C. Atomistic simulation on charge mobility of amorphous tris(8-hydroxyquinoline) aluminum (Alq3): Origin of Poole–Frenkel–type behavior. J Chem Phys 2008; 129:034709. [DOI: 10.1063/1.2949506] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
|
35
|
Mendoza FN, López-Lemus J, Chapela GA, Alejandre J. The Wolf method applied to the liquid-vapor interface of water. J Chem Phys 2008; 129:024706. [DOI: 10.1063/1.2948951] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
36
|
Dyer PJ, Docherty H, Cummings PT. The importance of polarizability in the modeling of solubility: Quantifying the effect of solute polarizability on the solubility of small nonpolar solutes in popular models of water. J Chem Phys 2008; 129:024508. [DOI: 10.1063/1.2953324] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
37
|
Izvekov S, Swanson JMJ, Voth GA. Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials. J Phys Chem B 2008; 112:4711-24. [PMID: 18366209 DOI: 10.1021/jp710339n] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A short-range effective potential for long-range electrostatic interactions in homogeneously disordered condensed phase systems has been determined with a novel approach to coarse-graining in interaction space. As opposed to coarse-graining the system resolution, this approach "coarsens" the system's interactions by mapping multiple configurations of an accurate long-range atomistic potential onto a more efficient, short-range effective potential with a force-matching (FM) method. Developing an empirical potential in this manner is fundamentally different from existing strategies because it utilizes condensed-phase (as opposed to gas-phase) atomistic interactions to determine general pair potentials defined on distance meshes (as opposed to fitting predetermined functional forms). The resulting short-range ( approximately 10 A) effective potential reproduces structural, dynamical, and many thermodynamic properties of liquid water, ions in water, and hydrophobes in water, with unprecedented accuracy. The effective potential is also shown to be transferable to a nonaqueous molten salt system. With continued development, such effective potentials may provide an accurate and highly efficient alternative to Ewald-based long-range electrostatics methods.
Collapse
Affiliation(s)
- Sergei Izvekov
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | | | | |
Collapse
|
38
|
Chowdhary J, Ladanyi BM. Water/hydrocarbon interfaces: effect of hydrocarbon branching on single-molecule relaxation. J Phys Chem B 2008; 112:6259-73. [PMID: 18324803 DOI: 10.1021/jp0769025] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water/hydrocarbon interfaces are studied using molecular dynamics simulations in order to understand the effect of hydrocarbon branching on the dynamics of the system at and away from the interface. A recently proposed procedure for studying the intrinsic structure of the interface in such systems is utilized, and dynamics are probed in the usual laboratory frame as well as the intrinsic frame. The use of these two frames of reference leads to insight into the effect of capillary waves at the interface on dynamics. The systems were partitioned into zones with a width of 5 A, and a number of quantities of dynamical relevance, namely, the residence times, mean squared displacements, the velocity auto correlation functions, and orientational time correlations for molecules of both phases, were calculated in the laboratory and intrinsic frames at and away from the interface. For the aqueous phase, translational motion is found to be (a) diffusive at long times and not anomalous as in proteins or micelles, (b) faster at the interface than in the bulk, and (c) faster upon reduction of the effect of capillary waves. The rotational motion of water is (a) more anisotropic at the interface than in the bulk and (b) dependent on the orientation of the covalent O-H bond with respect to the plane of the interface. The effect of hydrocarbon branching on aqueous dynamics was found to be small, a result similar to the effect on the interfacial water structure. The hydrocarbon phase shows a larger variation for all dynamical probes, a trend consistent with their interfacial structure.
Collapse
Affiliation(s)
- Janamejaya Chowdhary
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, USA
| | | |
Collapse
|
39
|
Chowdhary J, Ladanyi BM. Surface fluctuations at the liquid-liquid interface. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:031609. [PMID: 18517397 DOI: 10.1103/physreve.77.031609] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Indexed: 05/26/2023]
Abstract
Within the capillary-wave model (CWM), the liquid-vapor interface is a hypothetical two-dimensional surface whose deviations from planarity are represented as long wavelength capillary waves. We modify the CWM for liquid-liquid interfaces and treat them as two harmonically interacting surfaces (model 1). Corrections to the model are proposed to prevent the usual divergence of the capillary-wave broadening in the thermodynamic limit by introducing a surface-bulk coupling (model 2) and to incorporate the curvature of the two surfaces (model 3). Expressions for the capillary-wave contribution to the surface tension of the interface are obtained. Molecular dynamics simulations are performed for two series of water-hydrocarbon interfacial systems (a) n -pentane, 2-methyl pentane, and 2,2,4-trimethyl pentane (constant chain length) and (b) n -octane, 2-methyl heptane, and 2,2,4-trimethyl pentane (constant molecular mass). A simple procedure to identify the molecular sites at the surface is utilized for a molecular representation of the surface. The distribution of these surface sites as well as the wave-vector dependence of surface fluctuations are analyzed in order to extract the parameters required for model 2. A small length scale is identified above which surface fluctuations correspond to capillary-wave fluctuations thereby connecting the molecular and mesoscopic scales. This approach is applied to all interfacial systems studied here and predictions based on the parameters found to be in good agreement with independent simulation results for surface tension and interfacial widths. Hydrocarbon branching has a small effect on model parameters.
Collapse
Affiliation(s)
- Janamejaya Chowdhary
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA.
| | | |
Collapse
|
40
|
Avendaño C, Gil-Villegas A, González-Tovar E. Computer simulation of charged hard spherocylinders. J Chem Phys 2008; 128:044506. [DOI: 10.1063/1.2823736] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
41
|
Mahajan SS, Subbarayan G, Sammakia BG. Estimating thermal conductivity of amorphous silica nanoparticles and nanowires using molecular dynamics simulations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:056701. [PMID: 18233784 DOI: 10.1103/physreve.76.056701] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 06/24/2007] [Indexed: 05/25/2023]
Abstract
In several recent applications, including those aimed at developing thermal interface materials, nanoparticulate systems have been proposed to improve the effective behavior of the system. While nanoparticles by themselves may have low conductivities relative to larger particles owing to interfacial resistance, their use along with larger particles is believed to enhance the percolation threshold leading to better effective behavior overall. One critical challenge in using nanoparticulate systems is the lack of knowledge regarding their thermal conductivity. In this paper, the thermal conductivity of silica clusters (or nanoparticles) as well as nanowires is determined using molecular dynamics (MD) simulations. The equilibrium MD simulations of nanoparticles using Green-Kubo relations are demonstrated to be computationally very expensive and unsuitable for such nanoscaled systems. A nonequilibrium MD method adapted from the study of Müller-Plathe is shown to be faster and more accurate. The method is first demonstrated on bulk amorphous silica (using both cubic and orthorhombic simulation cells) and silica nanowires. The thermal conductivity values are compared to those reported in the literature. The mean thermal conductivity values for bulk silica and silica nanowire were estimated to be 1.2 W/mK and 1.435 W/mK, respectively. To model nanoparticles, the Müller-Plathe technique is adapted by dividing the cluster into concentric shells so as to capture the naturally radial mode of heat transfer. The mean thermal conductivity value of a 600-atom silica nanoparticle obtained using this approach was 0.589 W/mK. This value is approximately 50-60% lower than those of bulk silica or silica nanowire.
Collapse
Affiliation(s)
- Sanket S Mahajan
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907-2088, USA
| | | | | |
Collapse
|
42
|
Chemical potential calculations by thermodynamic integration with separation shifting in adaptive sampling Monte Carlo simulations. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.07.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
43
|
Kristóf T, Csányi É, Rutkai G, Merényi L. Prediction of adsorption equilibria of water–methanol mixtures in zeolite NaA by molecular simulation. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020600934179] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
44
|
Chowdhary J, Ladanyi BM. Water−Hydrocarbon Interfaces: Effect of Hydrocarbon Branching on Interfacial Structure. J Phys Chem B 2006; 110:15442-53. [PMID: 16884266 DOI: 10.1021/jp060440y] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulation are performed for the water/hydrocarbon system to study the effect of hydrocarbon branching on interfacial properties. The following two series of hydrocarbons are considered: (1) n-pentane, 2-methyl pentane, and 2,2,4-trimethyl pentane (constant chain length) and (2) n-octane, 2-methyl heptane, and 2,2,4-trimethyl pentane (constant molecular mass). With a simple algorithm for identification of surface sites and mapping nonsurface sites to these surface sites, intrinsic profiles were constructed with respect to the surface layer. Intrinsic density profiles for water and hydrocarbons with respect to the hydrocarbon and water surface, respectively, resemble density profiles of liquids in the presence of a wall. Order parameters were used to study orientation of molecules with respect to the surface normal and the hydrogen bond network was characterized in terms of the number of hydrogen bonds per water molecule and percentage of hydrogen bonded molecules in the first coordination shell. The corresponding intrinsic profiles were obtained. The O-H bond for surface water was found to have two preferential orientations, pointing toward the hydrocarbon phase and parallel to the interface. Hydrocarbon molecules in series 1 orient along the interface with the more branched molecule better aligned. For molecules in series 2, the larger molecular length reduces the alignment of molecules along the interface.
Collapse
Affiliation(s)
- Janamejaya Chowdhary
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA.
| | | |
Collapse
|
45
|
Avendaño C, Gil-Villegas A. Monte Carlo simulations of primitive models for ionic systems using the Wolf method. Mol Phys 2006. [DOI: 10.1080/00268970600551155] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
46
|
Ma Y, Garofalini SH. Modified Wolf electrostatic summation: Incorporating an empirical charge overlap. MOLECULAR SIMULATION 2005. [DOI: 10.1080/08927020500262598] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
47
|
Ma Y, Garofalini SH. Application of the Wolf damped Coulomb method to simulations of SiC. J Chem Phys 2005; 122:094508. [PMID: 15836151 DOI: 10.1063/1.1858860] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A multibody interatomic potential is developed for bulk SiC using a modification of the Wolf et al. summation technique [D. Wolf, P. Keblinski, S. R. Phillpot, and J. Eggebrecht, J. Chem. Phys. 110, 8254 (1999)] for the electrostatic interaction. The technique is modified to account for the short-range nonpoint charge effect. The nonelectrostatic interaction is modeled by a simple Morse-stretch term. This potential is then applied to beta-SiC to calculate various bulk properties using molecular dynamics simulations. The simulated x-ray diffraction pattern, radial distribution functions, lattice constant, elastic constants, and defect energy agree well with experimental data.
Collapse
Affiliation(s)
- Y Ma
- Interfacial Molecular Science Laboratory, Department of Materials Science and Engineering, Rutgers University, Piscataway, New Jersey 08854, USA
| | | |
Collapse
|
48
|
Demontis P, Stara G, Suffritti GB. Dynamical behavior of one-dimensional water molecule chains in zeolites: Nanosecond time-scale molecular dynamics simulations of bikitaite. J Chem Phys 2004; 120:9233-44. [PMID: 15267860 DOI: 10.1063/1.1697382] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nanosecond scale molecular dynamics simulations of the behavior of the one-dimensional water molecule chains adsorbed in the parallel nanochannels of bikitaite, a rare lithium containing zeolite, were performed at different temperatures and for the fully and partially hydrated material. New empirical potential functions have been developed for representing lithium-water interactions. The structure and the vibrational spectrum of bikitaite were in agreement both with experimental data and Car-Parrinello molecular dynamics results. Classical molecular dynamics simulations were extended to the nanosecond time scale in order to study the flip motion of water molecules around the hydrogen bonds connecting adjacent molecules in the chains, which has been observed by NMR experiments, and the dehydration mechanism at high temperature. Computed relaxation times of the flip motion follow the Arrhenius behavior found experimentally, but the activation energy of the simulated system is slightly underestimated. Based on the results of the simulations, it may be suggested that the dehydration proceeds by a defect-driven stepwise diffusion. The diffusive mechanism appears as a single-file motion: the molecules never pass one another, even at temperatures as high as about 1000 K, nor can they switch between different channels. However, the mean square displacement (MSD) of the molecules, computed with respect to the center of mass of the simulated system, shows an irregular trend from which the single-file diffusion cannot be clearly evidenced. If the MSDs are evaluated with respect to the center of mass of the molecules hosted in each channel, the expected dependence on the square root of time finally appears.
Collapse
Affiliation(s)
- Pierfranco Demontis
- Dipartimento di Chimica, Università degli studi di Sassari, Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | | | | |
Collapse
|
49
|
Ribeiro MCC. Molecular Dynamics Study on the Glass Transition in Ca0.4K0.6(NO3)1.4. J Phys Chem B 2003. [DOI: 10.1021/jp034566w] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mauro C. C. Ribeiro
- Laboratório de Espectroscopia Molecular, Instituto de Química, Universidade de São Paulo C.P. 26077, CEP 05513-970, São Paulo, SP, Brazil
| |
Collapse
|
50
|
Zahn D, Schilling B, Kast SM. Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation. J Phys Chem B 2002. [DOI: 10.1021/jp025949h] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|