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Xu X, Liu A, Liu S, Ma Y, Zhang X, Zhang M, Zhao J, Sun S, Sun X. Application of molecular dynamics simulation in self-assembled cancer nanomedicine. Biomater Res 2023; 27:39. [PMID: 37143168 PMCID: PMC10161522 DOI: 10.1186/s40824-023-00386-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Self-assembled nanomedicine holds great potential in cancer theragnostic. The structures and dynamics of nanomedicine can be affected by a variety of non-covalent interactions, so it is essential to ensure the self-assembly process at atomic level. Molecular dynamics (MD) simulation is a key technology to link microcosm and macroscale. Along with the rapid development of computational power and simulation methods, scientists could simulate the specific process of intermolecular interactions. Thus, some experimental observations could be explained at microscopic level and the nanomedicine synthesis process would have traces to follow. This review not only outlines the concept, basic principle, and the parameter setting of MD simulation, but also highlights the recent progress in MD simulation for self-assembled cancer nanomedicine. In addition, the physicochemical parameters of self-assembly structure and interaction between various assembled molecules under MD simulation are also discussed. Therefore, this review will help advanced and novice researchers to quickly zoom in on fundamental information and gather some thought-provoking ideas to advance this subfield of self-assembled cancer nanomedicine.
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Affiliation(s)
- Xueli Xu
- School of Science, Shandong Jianzhu University, Jinan, 250101, China
| | - Ao Liu
- School of Science, Shandong Jianzhu University, Jinan, 250101, China
| | - Shuangqing Liu
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Yanling Ma
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Xinyu Zhang
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Meng Zhang
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Jinhua Zhao
- School of Science, Shandong Jianzhu University, Jinan, 250101, China
| | - Shuo Sun
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, 02115, USA
| | - Xiao Sun
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China.
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2
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Han Y, Zhang T, Guo X, Jiao T. Insights into the mechanism of electrostatic field promoting ozone mass transfer in water: A molecular dynamics perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157710. [PMID: 35908697 DOI: 10.1016/j.scitotenv.2022.157710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/17/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Ozone is the main role of ozone-based advanced oxidation process for organic wastewater treatment, which is usually added in water by aeration. However, the low solubility of ozone in water seriously affects the degradation efficiency. In this article, the external electrostatic field (EF) was proposed to improve the ozone solubility in water. The mass transfer characteristics of ozone in a gas-liquid two-phase system under EF were studied by molecular dynamics (MD) simulation. The microscopic mechanism of ozone mass transfer in water promoted by external EF was revealed by analyzing Gibbs dividing surface (GDS) interface structure, interfacial water molecular orientation, surface tension, liquid phase viscosity, hydrogen bond network and ozone self-diffusion coefficient. Our findings reveal that EF can enhance the thickness of GDS region (from 0.4648 nm to 0.4996 nm when EF is 0.2 V/nm) as well as its ozone content. The dipole moment orientation of water molecules also tends to point in the EF direction due to the influence of EF, making the difference in dipole moment orientation of water molecules in the first and second layers of GDS region gradually disappear. In addition, compared with the absence of EF, the existence of external EF can decrease the surface tension (from 77.6162 mN/m to 73.3480 mN/m when EF is 0.2 V/nm) at the gas-liquid interface and the viscosity of liquid phase (from 0.293 mPa·s to 0.162 mPa·s when EF is 0.2 V/nm), break the network of hydrogen bond in liquid phase, and increase the mobility of ozone (self-diffusion coefficient of ozone changes from 1.3232 × 10-6 cm2·s-1 to 1.8812 × 10-6 cm2·s-1 when EF is 0.2 V/nm). All these properties changes indicate that the presence of external EF enhances the ability of ozone to penetrate the interface of the two-phase system, and then improves the ozone mass transfer efficiency in water.
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Affiliation(s)
- Yong Han
- State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao, Hebei 066004, PR China; School of Electrical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, PR China.
| | - Teng Zhang
- School of Electrical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, PR China
| | - Xiaoqiang Guo
- School of Electrical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, PR China
| | - Tifeng Jiao
- State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao, Hebei 066004, PR China.
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3
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Wang C, Ou L. Molecular dynamics investigation of the liquid-gas interface behavior: Simulations of the sodium oleate/sodium abietate/water system. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2021.128086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Yousefi R, Lynch GC, Galbraith M, Pettitt BM. Contributions of higher-order proximal distribution functions to solvent structure around proteins. J Chem Phys 2021; 155:104110. [PMID: 34525817 DOI: 10.1063/5.0062580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein myoglobin in the P6 crystal unit cell. Molecular dynamics simulations are performed, and solvent density distributions around the solute molecules are compared with the results from different pDF reconstruction models. It is shown that the next-nearest-neighbor modification significantly improves the reconstruction of the solvent number density distribution in concave regions and between solute molecules. The probability densities are then used to calculate the solute-solvent non-bonded interaction energies including van der Waals and electrostatic, which are found to be in good agreement with the simulated values.
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Affiliation(s)
- Razie Yousefi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| | - Gillian C Lynch
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| | - Madeline Galbraith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
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5
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McGachy L, Heyda J, Tomas J, Čejková J. Decanol pattern formation over a sessile aqueous decanoate droplet. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.126541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Zelič K, Katrašnik T. Thermodynamically consistent derivation of chemical potential of a battery solid particle from the regular solution theory applied to LiFePO 4. Sci Rep 2019; 9:2123. [PMID: 30765797 PMCID: PMC6375981 DOI: 10.1038/s41598-019-38635-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/27/2018] [Indexed: 11/18/2022] Open
Abstract
The chemical potential of lithium in LixFePO4 active cathode nanoparticles and the surface free energy between LixFePO4 and electrolyte were determined with the novel thermodynamically consistent application of the regular solution theory. Innovative consideration of crystal anisotropy accounts for the consistent determination of the dependency of the chemical potential on the mechanistically derived enthalpy of mixing and the phase boundary gradient penalty. This enabled the analytic, thermodynamically consistent determination of the phase boundary thickness between LiFePO4 and FePO4, which is in good agreement with experimental observations. The obtained explicit functional dependency of the surface free energy on the lithium concentration enables adequate simulation of the initiation of the phase transition from FePO4 to LiFePO4 at the surface of active cathode particles. To validate the plausibility of the newly developed approaches, lithium intercalation into the LixFePO4 nanoparticles from electrolyte was modeled by solving the Cahn-Hilliard equation in a quasi-two-dimensional domain.
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Affiliation(s)
- Klemen Zelič
- University of Ljubljana, Faculty of Mechanical Engineering, Laboratory for Internal Combustion Engines and Electromobility, Ljubljana, SI-1000, Slovenia.
| | - Tomaž Katrašnik
- University of Ljubljana, Faculty of Mechanical Engineering, Laboratory for Internal Combustion Engines and Electromobility, Ljubljana, SI-1000, Slovenia
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7
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Peng H, Firouzi M. Evaluation of interfacial properties of concentrated KCl solutions by molecular dynamics simulation. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2017.11.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Ergin G, Lbadaoui-Darvas M, Takahama S. Molecular Structure Inhibiting Synergism in Charged Surfactant Mixtures: An Atomistic Molecular Dynamics Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14093-14104. [PMID: 29160707 DOI: 10.1021/acs.langmuir.7b03346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Synergistic and nonsynergistic surfactant-water mixtures of sodium dodecyl sulfate (SDS), lauryl betaine (C12B), and cocoamidopropyl betaine (CAPB) systems are studied using molecular simulation to understand the role of interactions among headgroups, tailgroups, and water on structural and thermodynamic properties at the air-water interface. SDS is an anionic surfactant, while C12B and CAPB are zwitterionic; CAPB differs from C12B by an amide group in the tail. While the lowest surface tensions at high surface concentrations in the SDS-C12B synergistic system could not be reproduced by simulation, estimated partitioning between surface and bulk shows trends consistent with synergism. Structural analysis shows the influence of the SDS headgroup pulling C12B to the surface, resulting in closely packed structures compared to their respective homomolecular-surfactant systems. The SDS-CAPB system, on the other hand, is nonsynergistic when the surfactants are mixed on account of the tilted structure of the CAPB tail. The translational excess entropy due to the tailgroup interactions discriminates between the synergistic and nonsynergistic systems. The implications of such interactions on surfactant effects in complex, multicomponent atmospheric aerosols are discussed.
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Affiliation(s)
- Gözde Ergin
- Atmospheric Particle and Research Laboratory, School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Mária Lbadaoui-Darvas
- Atmospheric Particle and Research Laboratory, School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Satoshi Takahama
- Atmospheric Particle and Research Laboratory, School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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9
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Benavides AL, Portillo MA, Chamorro VC, Espinosa JR, Abascal JLF, Vega C. A potential model for sodium chloride solutions based on the TIP4P/2005 water model. J Chem Phys 2017; 147:104501. [DOI: 10.1063/1.5001190] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. L. Benavides
- Departamento de Ingeniería Física, División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, Col. Lomas del Campestre, CP 37150 León, Mexico
| | - M. A. Portillo
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - V. C. Chamorro
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J. R. Espinosa
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J. L. F. Abascal
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C. Vega
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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10
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Kim K, Kwon T, Sung BJ, Kim C. Effect of methane-sugar interaction on the solubility of methane in an aqueous solution. J Colloid Interface Sci 2017; 500:113-118. [PMID: 28402843 DOI: 10.1016/j.jcis.2017.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/27/2017] [Accepted: 04/02/2017] [Indexed: 10/19/2022]
Abstract
In this study, the effect of methane-sugar interaction on the solubility of methane in an aqueous solution at ambient pressure was investigated. Various sugars, such as fructose, glucose, sucrose, maltose, and raffinose, were used, and depending on the type and concentration of sugar, the methane solubility increased from 21.72mg/L (in pure water) to 24.86mg/L. Sugars with a low hydrogen-bonding number between the water and sugar molecules exhibited a large enhancement in methane solubility. The solute partitioning model and molecular dynamics simulations were employed to verify the results obtained for the experimental solubility of methane in aqueous sugar solutions.
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Affiliation(s)
- Kwangmin Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Taejin Kwon
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Choongik Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea.
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11
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Chiba S, Furuta T, Shimizu S. Kirkwood–Buff Integrals for Aqueous Urea Solutions Based upon the Quantum Chemical Electrostatic Potential and Interaction Energies. J Phys Chem B 2016; 120:7714-23. [DOI: 10.1021/acs.jpcb.6b05611] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Shuntaro Chiba
- Education
Academy of Computational Life Sciences, Tokyo Institute of Technology, J3-141 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Tadaomi Furuta
- School
of Life Science and Technology, Tokyo Institute of Technology, B-62 4259
Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Seishi Shimizu
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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12
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Ploetz EA, Rustenburg AS, Geerke DP, Smith PE. To Polarize or Not to Polarize? Charge-on-Spring versus KBFF Models for Water and Methanol Bulk and Vapor–Liquid Interfacial Mixtures. J Chem Theory Comput 2016; 12:2373-87. [DOI: 10.1021/acs.jctc.5b01115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elizabeth A. Ploetz
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ariën S. Rustenburg
- AIMMS
Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical
Sciences, Faculty of Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Daan P. Geerke
- AIMMS
Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical
Sciences, Faculty of Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Paul E. Smith
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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13
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Grechnikov AA. Analytical capabilities of surface-assisted laser desorption/ionization in the determination of low-molecular-weight volatile compounds. JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1134/s1061934815090051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Bogár F, Bartha F, Násztor Z, Fábián L, Leitgeb B, Dér A. On the Hofmeister Effect: Fluctuations at the Protein–Water Interface and the Surface Tension. J Phys Chem B 2014; 118:8496-504. [DOI: 10.1021/jp502505c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ferenc Bogár
- MTA-SZTE
Supramolecular and Nanostructured Materials Research Group of Hungarian
Academy of Sciences, University of Szeged, H-6720 Szeged, Hungary
| | - Ferenc Bartha
- Department
of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary
| | - Zoltán Násztor
- Department
of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - László Fábián
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - Balázs Leitgeb
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
- Department
of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - András Dér
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
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15
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Shimizu S, Matubayasi N. Preferential Solvation: Dividing Surface vs Excess Numbers. J Phys Chem B 2014; 118:3922-30. [DOI: 10.1021/jp410567c] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seishi Shimizu
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10
5YW, United Kingdom
| | - Nobuyuki Matubayasi
- Division
of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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16
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Cummings OT, Wick CD. Interfacial behavior of simple inorganic salts at the air-water interface investigated with a polarizable model with electrostatic damping. J Chem Phys 2013; 139:064708. [DOI: 10.1063/1.4817775] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ploetz EA, Smith PE. Local Fluctuations in Solution: Theory and Applications. ADVANCES IN CHEMICAL PHYSICS 2013; 153:311-372. [PMID: 24683278 DOI: 10.1002/9781118571767.ch4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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18
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Grechnikov AA, Borodkov AS, Alimpiev SS, Nikiforov SM, Simanovsky YO. Gas-phase basicity: Parameter determining the efficiency of laser desorption/ionization from silicon surfaces. JOURNAL OF ANALYTICAL CHEMISTRY 2012. [DOI: 10.1134/s1061934812110056] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Abstract
An extension of the traditional Kirkwood-Buff (KB) theory of solutions is outlined which provides additional fluctuating quantities that can be used to characterize and probe the behavior of solution mixtures. Particle-energy and energy-energy fluctuations for local regions of any multicomponent solution are expressed in terms of experimentally obtainable quantities, thereby supplementing the usual particle-particle fluctuations provided by the established KB inversion approach. The expressions are then used to analyze experimental data for pure water over a range of temperatures and pressures, a variety of pure liquids, and three binary solution mixtures - methanol and water, benzene and methanol, and aqueous sodium chloride. In addition to providing information on local properties of solutions it is argued that the particle-energy and energy-energy fluctuations can also be used to test and refine solute and solvent force fields for use in computer simulation studies.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
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20
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Morris VK, Ren Q, Macindoe I, Kwan AH, Byrne N, Sunde M. Recruitment of class I hydrophobins to the air:water interface initiates a multi-step process of functional amyloid formation. J Biol Chem 2011; 286:15955-63. [PMID: 21454575 DOI: 10.1074/jbc.m110.214197] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Class I fungal hydrophobins form amphipathic monolayers composed of amyloid rodlets. This is a remarkable case of functional amyloid formation in that a hydrophobic:hydrophilic interface is required to trigger the self-assembly of the proteins. The mechanism of rodlet formation and the role of the interface in this process have not been well understood. Here, we have studied the effect of a range of additives, including ionic liquids, alcohols, and detergents, on rodlet formation by two class I hydrophobins, EAS and DewA. Although the conformation of the hydrophobins in these different solutions is not altered, we observe that the rate of rodlet formation is slowed as the surface tension of the solution is decreased, regardless of the nature of the additive. These results suggest that interface properties are of critical importance for the recruitment, alignment, and structural rearrangement of the amphipathic hydrophobin monomers. This work gives insight into the forces that drive macromolecular assembly of this unique family of proteins and allows us to propose a three-stage model for the interface-driven formation of rodlets.
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Affiliation(s)
- Vanessa K Morris
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
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21
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Ploetz EA, Bentenitis N, Smith PE. Kirkwood-Buff integrals for ideal solutions. J Chem Phys 2010; 132:164501. [PMID: 20441282 DOI: 10.1063/1.3398466] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Kirkwood-Buff (KB) theory of solutions is a rigorous theory of solution mixtures which relates the molecular distributions between the solution components to the thermodynamic properties of the mixture. Ideal solutions represent a useful reference for understanding the properties of real solutions. Here, we derive expressions for the KB integrals, the central components of KB theory, in ideal solutions of any number of components corresponding to the three main concentration scales. The results are illustrated by use of molecular dynamics simulations for two binary solutions mixtures, benzene with toluene, and methanethiol with dimethylsulfide, which closely approach ideal behavior, and a binary mixture of benzene and methanol which is nonideal. Simulations of a quaternary mixture containing benzene, toluene, methanethiol, and dimethylsulfide suggest this system displays ideal behavior and that ideal behavior is not limited to mixtures containing a small number of components.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
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22
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Smith PE. The effect of urea on the morphology of NaCl crystals: A combined theoretical and simulation study. FLUID PHASE EQUILIBRIA 2010; 290:36-42. [PMID: 20383314 PMCID: PMC2850219 DOI: 10.1016/j.fluid.2009.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
It has been known for over a century that the presence of cosolvents such as urea and formamide can alter the morphology of NaCl crystals grown from solution. To help understand this effect we have been developing a theoretical approach based on the Kirkwood-Buff (KB) theory of solutions, and have combined this with computer simulations of the interation of urea with different crystal faces of NaCl. In this way one can predict the effect of urea on the thermodynamic stability of different NaCl faces, with atomic level detail provided by the simulations. We observe that urea is preferentially excluded from 100 and 111 crystal faces, but is less excluded from 111 faces which present chloride ions at the surface. The results indicate that the 111 face is stabilized in urea solutions and promotes the formation of octahedral over cubic NaCl crystals. The approach is totally general and can be applied to understand a variety of interfacial properties. Furthermore, we apply KB theory to study several other issues regarding the simulation of crystal growth.
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Affiliation(s)
- Paul E Smith
- Department of Chemistry, 213 CBC Building, Kansas State University, Manhattan, KS 66506-0401, Tel: 785-532-5109, ,
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23
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D’Auria R, Tobias DJ. Relation between Surface Tension and Ion Adsorption at the Air−Water Interface: A Molecular Dynamics Simulation Study. J Phys Chem A 2009; 113:7286-93. [PMID: 19438204 DOI: 10.1021/jp810488p] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Raffaella D’Auria
- Department of Chemistry and AirUCI Environmental Molecular Sciences Institute, University of California, Irvine, Irvine, California 92697-2025
| | - Douglas J. Tobias
- Department of Chemistry and AirUCI Environmental Molecular Sciences Institute, University of California, Irvine, Irvine, California 92697-2025
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Pegram LM, Record MT. Using surface tension data to predict differences in surface and bulk concentrations of nonelectrolytes in water. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2009; 113:2171-2174. [PMID: 19436772 PMCID: PMC2680307 DOI: 10.1021/jp8073305] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Recently, we developed a quantitative interpretation of surface tension increments (STI) of salts, acids, and bases in terms of the solute (or salt ion) partitioning model (SPM). Here, we obtain an analogous SPM-based interpretation of surface tension increments of nonelectrolytes, which yields local-bulk partition coefficients (K(p)) quantifying the accumulation or exclusion of these solutes in the local region near the air-water surface, and the amount of water per unit area of that region (b1σ). Sucrose exhibits the largest positive STI (approximately 1.4 ergs cm(-2) Osm(-1)). Assuming that K(p) = 0 for sucrose (i.e. that it is completely excluded from the surface of water), these STI provide a minimum estimate of b1σ of 0.20 H(2)O/Å(2), or a minimum thickness of the surface region of approximately two layers of water at bulk density. This is the same value as obtained previously from analysis of surface tension and hydrocarbon solubility increments of Na(2)SO(4) and also for the interaction of glycine betaine with anionic carboxylate surface, indicating that this quantity is not a function of the type of solute or surface investigated and therefore that it may represent the molecular thickness of the region. Partition coefficients of other nonelectrolytes investigated range from moderately excluded (e.g urea) to moderately accumulated (e.g. glycerol, ethylene glycol); strongly accumulated surface active solutes (e.g. mono-substituted alcohols) were not included in this analysis. Partition coefficients for many salt ions obtained from STI and hydrocarbon solubility increments fall in a rank order which corresponds to the Hofmeister series for protein folding and protein solubility, indicating a common pattern of accumulation or exclusion of salt ions at the air-water surface and nonpolar surfaces of dissolved hydrocarbons and proteins; no such patterns are observed for nonelectrolytes.
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Affiliation(s)
- Laurel M. Pegram
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - M. Thomas Record
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Mountain RD. An Internally Consistent Method for the Molecular Dynamics Simulation of the Surface Tension: Application to Some TIP4P-Type Models of Water. J Phys Chem B 2008; 113:482-6. [DOI: 10.1021/jp8012514] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raymond D. Mountain
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320
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Pegram LM, Record MT. Quantifying accumulation or exclusion of H +, HO -, and Hofmeister salt ions near interfaces. Chem Phys Lett 2008; 467:1-8. [PMID: 23750042 PMCID: PMC3673785 DOI: 10.1016/j.cplett.2008.10.090] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recently, surface spectroscopies and simulations have begun to characterize the non-uniform distributions of salt ions near macroscopic and molecular surfaces. The thermodynamic consequences of these non-uniform distributions determine the often-large ion-specific effects of Hofmeister salts on a very wide range of processes in water. For uncharged surfaces, where these nonuniform ion distributions are confined to the first few layers of water at the surface, a two-state approximation to the distributions of water and ions, called the salt ion partitioning model (SPM) has both molecular and thermodynamic signiicance. Here, we summarize SPM results quantifying the local accumulation of H+, exclusion of HO-, and range of partitioning behavior of Hofmeister anions and cations near macroscopic and molecular interfaces. These results provide a database to interpret or predict Hofmeister salt effects on aqueous processes in terms of structural information regarding amount and composition of the surface exposed or buried in these processes.
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Affiliation(s)
- L. M. Pegram
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - M. T. Record
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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