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Nishimura Y, Nakai H. Species-selective nanoreactor molecular dynamics simulations based on linear-scaling tight-binding quantum chemical calculations. J Chem Phys 2023; 158:054106. [PMID: 36754823 DOI: 10.1063/5.0132573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Here, extensions to quantum chemical nanoreactor molecular dynamics simulations for discovering complex reactive events are presented. The species-selective algorithm, where the nanoreactor effectively works for the selected desired reactants, was introduced to the original scheme. Moreover, for efficient simulations of large model systems with the modified approach, the divide-and-conquer linear-scaling density functional tight-binding method was exploited. Two illustrative applications of the polymerization of propylene and cyclopropane mixtures and the aggregation of sodium chloride from aqueous solutions indicate that species-selective quantum chemical nanoreactor molecular dynamics is a promising method to accelerate the sampling of multicomponent chemical processes proceeding under relatively mild conditions.
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Affiliation(s)
- Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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2
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Le HM, Kumar S, May N, Martinez-Baez E, Sundararaman R, Krishnamoorthy B, Clark AE. Behavior of Linear and Nonlinear Dimensionality Reduction for Collective Variable Identification of Small Molecule Solution-Phase Reactions. J Chem Theory Comput 2022; 18:1286-1296. [PMID: 35225611 DOI: 10.1021/acs.jctc.1c00983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identifying collective variables (CVs) for chemical reactions is essential to reduce the 3N-dimensional energy landscape into lower dimensional basins and barriers of interest. However, in condensed phase processes, the nonmeaningful motions of bulk solvent often overpower the ability of dimensionality reduction methods to identify correlated motions that underpin collective variables. Yet solvent can play important indirect or direct roles in reactivity, and much can be lost through treatments that remove or dampen solvent motion. This has been amply demonstrated within principal component analysis (PCA), although less is known about the behavior of nonlinear dimensionality reduction methods, e.g., uniform manifold approximation and projection (UMAP), that have become recently utilized. The latter presents an interesting alternative to linear methods though often at the expense of interpretability. This work presents distance-attenuated projection methods of atomic coordinates that facilitate the application of both PCA and UMAP to identify collective variables in the presence of explicit solvent and further the specific identity of solvent molecules that participate in chemical reactions. The performance of both methods is examined in detail for two reactions where the explicit solvent plays very different roles within the collective variables. When applied to raw molecular dynamics data in solution, both PCA and UMAP representations are dominated by bulk solvent motions. On the other hand, when applied to data preprocessed by our attenuated projection methods, both PCA and UMAP identify the appropriate collective variables (though varying sensitivity is observed due to the presence of explicit solvent that results from the projection method). Importantly, this approach allows identification of specific solvent molecules that are relevant to the CVs and their importance.
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Affiliation(s)
- Hung M Le
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Sushant Kumar
- Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Nathan May
- Department of Mathematics and Statistics, Washington State University, Vancouver, Washington 98686, United States
| | - Ernesto Martinez-Baez
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Ravishankar Sundararaman
- Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Bala Krishnamoorthy
- Department of Mathematics and Statistics, Washington State University, Vancouver, Washington 98686, United States
| | - Aurora E Clark
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
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3
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Blazquez S, Conde MM, Abascal JLF, Vega C. The Madrid-2019 force field for electrolytes in water using TIP4P/2005 and scaled charges: Extension to the ions F−, Br−, I−, Rb+, and Cs+. J Chem Phys 2022; 156:044505. [DOI: 10.1063/5.0077716] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- S. Blazquez
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - M. M. Conde
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain
| | - J. L. F. Abascal
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C. Vega
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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4
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Zhang X, Kindt JT. Free energy of micellization of dodecyl phosphocholine (DPC) from molecular simulation: Hybrid PEACH-BAR method. J Comput Chem 2021; 42:2221-2232. [PMID: 34561897 DOI: 10.1002/jcc.26751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/08/2021] [Accepted: 09/05/2021] [Indexed: 11/06/2022]
Abstract
A new method to extract the free energy of aggregation versus aggregate size from molecular simulation data is proposed and applied to a united atom model of the zwitterionic surfactant dodecyl phosphocholine in water. This system's slow dissociation rate and low critical micelle concentration (CMC of approximately 1-2 mM) make extraction of cluster free energies directly from simulation results using the "partition-enabled analysis of cluster histogram" (PEACH) method impractical. The new approach applies PEACH to a model with weakened attractions between aggregants, which allows sampling of a continuous range of cluster sizes, then recovers the free energy of aggregation under the original fully-attractive force field using the BAR free energy difference method. PEACH-BAR results are compared with free energy differences calculated via umbrella sampling, and are used to make predictions of CMC, average cluster size, and SAXS scattering profiles that are in fair agreement with experiment.
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Affiliation(s)
- Xiaokun Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| | - James T Kindt
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
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5
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Patel LA, Yoon TJ, Currier RP, Maerzke KA. NaCl aggregation in water at elevated temperatures and pressures: Comparison of classical force fields. J Chem Phys 2021; 154:064503. [PMID: 33588550 DOI: 10.1063/5.0030962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The properties of water vary dramatically with temperature and density. This can be exploited to control its effectiveness as a solvent. Thus, supercritical water is of keen interest as solvent in many extraction processes. The low solubility of salts in lower density supercritical water has even been suggested as a means of desalination. The high temperatures and pressures required to reach supercritical conditions can present experimental challenges during collection of required physical property and phase equilibria data, especially in salt-containing systems. Molecular simulations have the potential to be a valuable tool for examining the behavior of solvated ions at these high temperatures and pressures. However, the accuracy of classical force fields under these conditions is unclear. We have, therefore, undertaken a parametric study of NaCl in water, comparing several salt and water models at 200 bar-600 bar and 450 K-750 K for a range of salt concentrations. We report a comparison of structural properties including ion aggregation, hydrogen bonding, density, and static dielectric constants. All of the force fields qualitatively reproduce the trends in the liquid phase density. An increase in ion aggregation with decreasing density holds true for all of the force fields. The propensity to aggregate is primarily determined by the salt force field rather than the water force field. This coincides with a decrease in the water static dielectric constant and reduced charge screening. While a decrease in the static dielectric constant with increasing NaCl concentration is consistent across all model combinations, the salt force fields that exhibit more ionic aggregation yield a slightly smaller dielectric decrement.
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Affiliation(s)
- Lara A Patel
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Tae Jun Yoon
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Robert P Currier
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Katie A Maerzke
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Zhu Z, Duan X, Li Q, Wu R, Wang Y, Li B. Low-Noise Nanopore Enables In-Situ and Label-Free Tracking of a Trigger-Induced DNA Molecular Machine at the Single-Molecular Level. J Am Chem Soc 2020; 142:4481-4492. [PMID: 32069050 DOI: 10.1021/jacs.0c00029] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Solid-state nanopores have shown special high potential in a label-free molecular assay, structure identification, and target-index at the single-molecular level, even though frustrating electrical baseline noise is still one of the major factors that limit the spatial resolution and signaling reliability of solid-state nanopores, especially in small target detection. Here we develop a significant and easy-operating noise-reduction approach via mixing organic solvents with high dielectric constants into a traditional aqueous electrolyte. The strategy is generally effective for pores made of different materials, such as the most commonly used conical glass (CGN) or SiNx. While the mechanism should be multisourced, MD simulations suggest the noise reduction may partially arise from the even ionic distribution caused by the addition of higher dielectric species. Among all solvents experimentally tested, the two with the highest dielectric constants, formamide and methylformamide, exhibit the best noise reduction effect for target detection of CGN. The power spectral density at the low-frequency limit is reduced by nearly 3 orders with the addition of 20% formamide. Our work qualifies the reliability of solid-state nanopores into much subtler scales of detection, such as dsDNAs under 100 bp. As a practical example, bare CGN is innovatively employed to perform in-situ tracking of trigger-responsive DNA machine forming oligomers.
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Affiliation(s)
- Zhentong Zhu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiaozheng Duan
- State Key Lab of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
| | - Qiao Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yesheng Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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Abstract
In this study, molecular dynamic simulations are employed to investigate the homogeneous nucleation mechanism of NaCl crystal in solutions. According to the simulations, the dissolved behaviors of NaCl in water are dependent on ion concentrations. With increasing NaCl concentrations, the dissolved Na+ and Cl- ions tend to be aggregated in solutions. In combination with our recent studies, the aggregate of dissolved solutes is mainly ascribed to the hydrophobic interactions. Different from the two-step mechanism, no barrier is needed to overcome the formation of the aggregate. In comparison with the classical nucleation theory (CNT), because of the formation of solute aggregate, this lowers the barrier height of nucleation and affects the nucleation mechanism of NaCl crystal in water.
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Tsironi I, Schlesinger D, Späh A, Eriksson L, Segad M, Perakis F. Brine rejection and hydrate formation upon freezing of NaCl aqueous solutions. Phys Chem Chem Phys 2020; 22:7625-7632. [DOI: 10.1039/c9cp05436g] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studying the freezing of saltwater on a molecular level is of fundamental importance for improving freeze desalination techniques.
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Affiliation(s)
- Ifigeneia Tsironi
- Department of Physics
- AlbaNova University Center
- Stockholm University
- 114 19 Stockholm
- Sweden
| | - Daniel Schlesinger
- Department of Environmental Science & Bolin Centre for Climate Research
- Stockholm University
- 114 18 Stockholm
- Sweden
| | - Alexander Späh
- Department of Physics
- AlbaNova University Center
- Stockholm University
- 114 19 Stockholm
- Sweden
| | - Lars Eriksson
- Department of Materials and Environmental Chemistry
- Stockholm University
- 106 91 Stockholm
- Sweden
| | - Mo Segad
- Department of Materials and Environmental Chemistry
- Stockholm University
- 106 91 Stockholm
- Sweden
| | - Fivos Perakis
- Department of Physics
- AlbaNova University Center
- Stockholm University
- 114 19 Stockholm
- Sweden
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9
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Karmakar T, Piaggi PM, Parrinello M. Molecular Dynamics Simulations of Crystal Nucleation from Solution at Constant Chemical Potential. J Chem Theory Comput 2019; 15:6923-6930. [DOI: 10.1021/acs.jctc.9b00795] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Tarak Karmakar
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - Pablo M. Piaggi
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
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