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Chubak I, Alon L, Silletta EV, Madelin G, Jerschow A, Rotenberg B. Quadrupolar 23Na + NMR relaxation as a probe of subpicosecond collective dynamics in aqueous electrolyte solutions. Nat Commun 2023; 14:84. [PMID: 36604414 PMCID: PMC9816157 DOI: 10.1038/s41467-022-35695-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
Nuclear magnetic resonance relaxometry represents a powerful tool for extracting dynamic information. Yet, obtaining links to molecular motion is challenging for many ions that relax through the quadrupolar mechanism, which is mediated by electric field gradient fluctuations and lacks a detailed microscopic description. For sodium ions in aqueous electrolytes, we combine ab initio calculations to account for electron cloud effects with classical molecular dynamics to sample long-time fluctuations, and obtain relaxation rates in good agreement with experiments over broad concentration and temperature ranges. We demonstrate that quadrupolar nuclear relaxation is sensitive to subpicosecond dynamics not captured by previous models based on water reorientation or cluster rotation. While ions affect the overall water retardation, experimental trends are mainly explained by dynamics in the first two solvation shells of sodium, which contain mostly water. This work thus paves the way to the quantitative understanding of quadrupolar relaxation in electrolyte and bioelectrolyte systems.
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Affiliation(s)
- Iurii Chubak
- Sorbonne Université CNRS, Physico-Chimie des électrolytes et Nanosystèmes Interfaciaux, F-75005, Paris, France
| | - Leeor Alon
- New York University School of Medicine, Department of Radiology, Center for Biomedical Imaging, 660 First Avenue, New York, NY, 10016, USA
- Center for Advanced Imaging Innovation and Research, Department of Radiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Emilia V Silletta
- Universidad Nacional de Córdoba, Facultad de Matemática, Astronomía, Física y Computación, Medina Allende s/n, X5000HUA, Córdoba, Argentina
- Instituto de Física Enrique Gaviola, CONICET, Medina Allende s/n, X5000HUA, Córdoba, Argentina
| | - Guillaume Madelin
- New York University School of Medicine, Department of Radiology, Center for Biomedical Imaging, 660 First Avenue, New York, NY, 10016, USA
- Center for Advanced Imaging Innovation and Research, Department of Radiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Alexej Jerschow
- New York University, Department of Chemistry, 100 Washington Square E, New York, NY, 10003, USA.
| | - Benjamin Rotenberg
- Sorbonne Université CNRS, Physico-Chimie des électrolytes et Nanosystèmes Interfaciaux, F-75005, Paris, France.
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2
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Chatzidaki MD, Papavasileiou KD, Papadopoulos MG, Xenakis A. Reverse Micelles As Antioxidant Carriers: An Experimental and Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:5077-5085. [PMID: 28481539 DOI: 10.1021/acs.langmuir.7b00213] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Water-in-oil microemulsions with biocompatible components were formulated to be used as carriers of natural antioxidants, such as hydroxytyrosol (HT) and gallic acid (GA). The system was composed of a mixture of natural surfactants, lecithin and monoglycerides, medium chain triglycerides, and aqueous phase. A dual approach was undertaken to study the structure and dynamics of these complicated systems. First, experimental data were collected by using adequate techniques, such as dynamic light scattering (DLS) and electron paramagnetic resonance (EPR) spectroscopy. Following this, a coarse-grained molecular dynamics (CGMD) study based on the experimental composition using the MARTINI force field was conducted. The simulations revealed the spontaneous formation of reverse micelles (RMs) starting from completely random initial conformations, underlying their enhanced thermodynamic stability. The location of the bioactive molecules, as well as the structure of the RM, were in accordance with the experimental findings. Furthermore, GA molecules were found to be located inside the water core, in contrast to the HT ones, which seem to lie at the surfactant interfacial layer. The difference in the antioxidants' molecular location was only revealed in detail from the computational analysis and explains the RM's swelling observed by GA in DLS measurements.
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Affiliation(s)
- Maria D Chatzidaki
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation , 116 35 Athens, Greece
| | - Konstantinos D Papavasileiou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation , 116 35 Athens, Greece
- National Center for Scientific Research "Demokritos", Institute of Nanoscience and Nanotechnology , Aghia Paraskevi Attikis, 153 10 Athens, Greece
| | - Manthos G Papadopoulos
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation , 116 35 Athens, Greece
| | - Aristotelis Xenakis
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation , 116 35 Athens, Greece
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4
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Damjanović M, Morita T, Horii Y, Katoh K, Yamashita M, Enders M. How Ions Arrange in Solution: Detailed Insight from NMR Spectroscopy of Paramagnetic Ion Pairs. Chemphyschem 2016; 17:3423-3429. [DOI: 10.1002/cphc.201600804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Marko Damjanović
- Institute of Inorganic Chemistry Heidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany), Tel: +49-6221-54-6247, Fax: +49-6221-54-161-6247
| | - Takaumi Morita
- Department of Chemistry Graduate School of Science Tohoku University 6-3 Aramaki-Aza-Aoba Sendai 980-8578 Japan
| | - Yoji Horii
- Department of Chemistry Graduate School of Science Tohoku University 6-3 Aramaki-Aza-Aoba Sendai 980-8578 Japan
| | - Keiichi Katoh
- Department of Chemistry Graduate School of Science Tohoku University 6-3 Aramaki-Aza-Aoba Sendai 980-8578 Japan
| | - Masahiro Yamashita
- Department of Chemistry Graduate School of Science Tohoku University 6-3 Aramaki-Aza-Aoba Sendai 980-8578 Japan
| | - Markus Enders
- Institute of Inorganic Chemistry Heidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany), Tel: +49-6221-54-6247, Fax: +49-6221-54-161-6247
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5
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Carof A, Salanne M, Charpentier T, Rotenberg B. On the microscopic fluctuations driving the NMR relaxation of quadrupolar ions in water. J Chem Phys 2016; 143:194504. [PMID: 26590539 DOI: 10.1063/1.4935496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) relaxation is sensitive to the local structure and dynamics around the probed nuclei. The Electric Field Gradient (EFG) is the key microscopic quantity to understand the NMR relaxation of quadrupolar ions, such as (7)Li(+), (23)Na(+), (25)Mg(2+), (35)Cl(-), (39)K(+), or (133)Cs(+). Using molecular dynamics simulations, we investigate the statistical and dynamical properties of the EFG experienced by alkaline, alkaline Earth, and chloride ions at infinite dilution in water. Specifically, we analyze the effect of the ionic charge and size on the distribution of the EFG tensor and on the multi-step decay of its auto-correlation function. The main contribution to the NMR relaxation time arises from the slowest mode, with a characteristic time on the picosecond time scale. The first solvation shell of the ion plays a dominant role in the fluctuations of the EFG, all the more that the ion radius is small and its charge is large. We propose an analysis based on a simplified charge distribution around the ion, which demonstrates that the auto-correlation of the EFG, hence the NMR relaxation time, reflects primarily the collective translational motion of water molecules in the first solvation shell of the cations. Our findings provide a microscopic route to the quantitative interpretation of NMR relaxation measurements and open the way to the design of improved analytical theories for NMR relaxation for small ionic solutes, which should focus on water density fluctuations around the ion.
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Affiliation(s)
- Antoine Carof
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 Place Jussieu, F-75005 Paris, France
| | - Mathieu Salanne
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 Place Jussieu, F-75005 Paris, France
| | - Thibault Charpentier
- CEA, IRAMIS, NIMBE, LSDRM, UMR CEA-CNRS 3685, F-91191 Gif-sur-Yvette Cedex, France
| | - Benjamin Rotenberg
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 Place Jussieu, F-75005 Paris, France
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6
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Bradley-Shaw JL, Camp PJ, Dowding PJ, Lewtas K. Glycerol Monooleate Reverse Micelles in Nonpolar Solvents: Computer Simulations and Small-Angle Neutron Scattering. J Phys Chem B 2015; 119:4321-31. [DOI: 10.1021/acs.jpcb.5b00213] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joshua L. Bradley-Shaw
- School
of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, Scotland
| | - Philip J. Camp
- School
of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, Scotland
| | | | - Ken Lewtas
- School
of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, Scotland
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7
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Carof A, Salanne M, Charpentier T, Rotenberg B. Accurate Quadrupolar NMR Relaxation Rates of Aqueous Cations from Classical Molecular Dynamics. J Phys Chem B 2014; 118:13252-7. [DOI: 10.1021/jp5105054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antoine Carof
- Sorbonne
Universités,
UPMC Univ. Paris 06, UMR 8234 PHENIX, 75005 Paris, France
- CNRS, UMR
8234
PHENIX, 75005 Paris, France
| | - Mathieu Salanne
- Sorbonne
Universités,
UPMC Univ. Paris 06, UMR 8234 PHENIX, 75005 Paris, France
- CNRS, UMR
8234
PHENIX, 75005 Paris, France
| | - Thibault Charpentier
- CEA, IRAMIS, NIMBE,
LSDRM, UMR CEA-CNRS 3299, F-91191 Gif-sur-Yvette cedex, France
| | - Benjamin Rotenberg
- Sorbonne
Universités,
UPMC Univ. Paris 06, UMR 8234 PHENIX, 75005 Paris, France
- CNRS, UMR
8234
PHENIX, 75005 Paris, France
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8
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Tomkins J, Hanna G. Signatures of nanoconfinement on the linear and nonlinear vibrational spectroscopy of a model hydrogen-bonded complex dissolved in a polar solvent. J Phys Chem B 2013; 117:13619-30. [PMID: 24079369 DOI: 10.1021/jp407469f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The one-dimensional IR (1D-IR) absorption and IR pump-probe spectra of a hydrogen stretch in a model hydrogen-bonded complex dissolved in a polar solvent confined in spherical hydrophobic cavities of different sizes were simulated using ground-state mixed quantum-classical dynamics. Due to a thorough analysis of key properties of the complex and solvent from equilibrium trajectory data, we were able to gain insight into the microscopic details underlying the spectra. Both the 1D-IR and IR pump-probe spectra manifested the effects of confinement on the relative stabilities of the covalent and ionic forms of the complex through pronounced changes in their peak intensities and numbers. However, in contrast to the 1D-IR spectra, the time-resolved pump-probe spectra were found to be uniquely sensitive to the changes in the molecular dynamics as the cavity size is varied. In particular, it was found that the variations in the time evolutions of the peak intensities in the pump-probe spectra reflect the differences in the solvation dynamics associated with the various forms of the complex in different locations within the cavities. The ability to detect these differences underscores the advantage of using pump-probe spectroscopy for studying nanoconfined systems.
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Affiliation(s)
- Joseph Tomkins
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
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9
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Aidas K, Ågren H, Kongsted J, Laaksonen A, Mocci F. A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+in aqueous solution. Phys Chem Chem Phys 2013; 15:1621-31. [DOI: 10.1039/c2cp41993a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Mudzhikova GV, Brodskaya EN. Computer simulation of reverse micelles and water-in-oil microemulsions. COLLOID JOURNAL 2012. [DOI: 10.1134/s1061933x1203009x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Chowdhary J, Ladanyi BM. Molecular simulation study of water mobility in aerosol-OT reverse micelles. J Phys Chem A 2011; 115:6306-16. [PMID: 21548627 DOI: 10.1021/jp201866t] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this work, we present results from molecular dynamics simulations on the single-molecule relaxation of water within reverse micelles (RMs) of different sizes formed by the surfactant aerosol-OT (AOT, sodium bis(2-ethylhexyl)sulfosuccinate) in isooctane. Results are presented for RM water content w(0) = [H(2)O]/[AOT] in the range from 2.0 to 7.5. We show that translational diffusion of water within the RM can, to a good approximation, be decoupled from the translation of the RM through the isooctane solvent. Water translational mobility within the RM is restricted by the water pool dimensions, and thus, the water mean-squared displacements (MSDs) level off in time. Comparison with models of diffusion in confined geometries shows that a version of the Gaussian confinement model with a biexponential decay of correlations provides a good fit to the MSDs, while a model of free diffusion within a sphere agrees less well with simulation results. We find that the local diffusivity is considerably reduced in the interfacial region, especially as w(0) decreases. Molecular orientational relaxation is monitored by examining the behavior of OH and dipole vectors. For both vectors, orientational relaxation slows down close to the interface and as w(0) decreases. For the OH vector, reorientation is strongly affected by the presence of charged species at the RM interface and these effects are especially pronounced for water molecules hydrogen-bonded to surfactant sites that serve as hydrogen-bond acceptors. For the dipole vector, orientational relaxation near the interface slows down more than that for the OH vector due mainly to the influence of ion-dipole interactions with the sodium counterions. We investigate water OH and dipole reorientation mechanisms by studying the w(0) and interfacial shell dependence of orientational time correlations for different Legendre polynomial orders.
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Affiliation(s)
- Janamejaya Chowdhary
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, USA
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12
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Vasquez VR, Williams BC, Graeve OA. Stability and Comparative Analysis of AOT/Water/Isooctane Reverse Micelle System Using Dynamic Light Scattering and Molecular Dynamics. J Phys Chem B 2011; 115:2979-87. [DOI: 10.1021/jp109202f] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- V. R. Vasquez
- Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - B. C. Williams
- Kazuo Inamori School of Engineering, Alfred University, Alfred, New York 14802, United States
| | - O. A. Graeve
- Kazuo Inamori School of Engineering, Alfred University, Alfred, New York 14802, United States
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13
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Pieniazek PA, Lin YS, Chowdhary J, Ladanyi BM, Skinner JL. Vibrational Spectroscopy and Dynamics of Water Confined inside Reverse Micelles. J Phys Chem B 2009; 113:15017-28. [DOI: 10.1021/jp906784t] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Piotr A. Pieniazek
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Yu-Shan Lin
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Janamejaya Chowdhary
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Branka M. Ladanyi
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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14
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Nevidimov AV, Razumov VF. Molecular dynamics simulations of AOT reverse micelles' self-assembly. Mol Phys 2009. [DOI: 10.1080/00268970903203736] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Mitchell-Koch KR, Thompson WH. Infrared spectra of a model phenol-amine proton transfer complex in nanoconfined CH3Cl. J Phys Chem B 2008; 112:7448-59. [PMID: 18517239 DOI: 10.1021/jp076714e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The vibrational spectra of a model phenol-amine proton transfer complex dissolved in CH3Cl solvent confined in a 12 A radius spherical hydrophobic cavity were calculated using mixed quantum-classical molecular dynamics simulations. The reaction free energy of the proton transfer complex was varied in order to explore the contributions to the vibrational absorption band from product and reactant species. The vibrational spectra of the model proton transfer complex resulted in motionally narrowed spectral linewidths with two distinct peaks for products and reactants in cases where the system undergoes chemical exchange. It was found that the n=1 and n=2 vibrational excited states combine to form diabatic states such that the spectra have contributions from both n=0 --> n=1 and n=0 --> n=2 transitions. A strong relationship between the instantaneous vibrational frequency and a collective solvent coordinate was found that assists in understanding the origin of the spectral features.
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16
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17
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Rosenfeld DE, Schmuttenmaer CA. Dynamics of Water Confined Within Reverse Micelles. J Phys Chem B 2006; 110:14304-12. [PMID: 16854137 DOI: 10.1021/jp060552p] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report structural and dynamical properties of water confined within reverse micelles (RMs) ranging in size from R = 10 A to R = 23 A as determined from molecular dynamics simulations. The low-frequency infrared spectra have been calculated using linear response theory and depend linearly on the fraction of bulklike water within the RMs. Furthermore, these spectra show nearly isosbestic behavior in the region near 660 cm(-1). Both of these characteristics are present in previously measured experimental spectra. The single dipole spectra for interfacial trapped, bound, and bulklike water within the RMs have also been calculated and show region-dependent frequency shifts. Specifically, the bound and trapped water spectra have a peak at lower frequencies than that for the inner core water. We therefore assign the low-frequency band in the IR spectra to bound and trapped interfacial water. Finally, region-dependent hydrogen bonding profiles and spatial distribution functions are also presented.
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Affiliation(s)
- Daniel E Rosenfeld
- Department of Chemistry, Yale University, 225 Prospect St., P.O. Box 208107, New Haven, CT 06520-8107, USA
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18
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Mudzhikova GV, Brodskaya EN. Molecular Dynamics Simulation of Surfactant Microaggregates in the Apolar Medium of n-Octane. COLLOID JOURNAL 2005. [DOI: 10.1007/s10595-005-0118-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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20
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Pal S, Vishal G, Gandhi KS, Ayappa KG. Ion exchange in reverse micelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:767-778. [PMID: 15641853 DOI: 10.1021/la048771u] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The distribution and dynamics of alkali cations inside Na-AOT reverse micelles have been investigated using Monte Carlo and molecular dynamics simulations. Water is modeled using the extended simple point charge (SPC/E) model. Simulations were carried out for alkali salts of Li+, Na+, K+, and Cs+ placed into the aqueous core of the reverse micelle, for situations corresponding to one and three molecules of added salt. In all cases, we observe that the larger K+ and Cs+ ions exchange with the Na+ counterion; however, the smaller Li+ ion prefers to remains solvated within the core of the reverse micelle. Our study reveals that the oil-water interface of the Na-AOT reverse micelle has the greatest selectivity toward Cs+ followed by K+ and Li+. A model based on enthalpic contributions illustrates that the solvation energies of the different cations in water control the ion-exchange process. The hydration number of the first water shell for Li+ situated in the aqueous core of the reverse micelle with radius R = 14.1 A was similar to that observed at infinite dilution in bulk water.
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Affiliation(s)
- Sandeep Pal
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
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21
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Cesare Marincola F, Denisov VP, Halle B. Competitive Na(+) and Rb(+) binding in the minor groove of DNA. J Am Chem Soc 2004; 126:6739-50. [PMID: 15161302 DOI: 10.1021/ja049930z] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. Here, we present new (23)Na and (87)Rb magnetic relaxation dispersion (MRD) data that demonstrate competitive and long-lived binding of Na(+) and Rb(+) ions in the minor groove of the B-DNA duplex [d(CGCGAATTCGCG)](2). The Na(+)/Rb(+) selectivity of the minor groove is found to be weak, consistent with local structural flexibility. The ion occupancies derived from the MRD data are substantially higher than previously reported, suggesting that groove-bound ions significantly influence the energetics and structural polymorphism of DNA in vivo. For example, in the presence of 0.20 M Na(+) and 0.56 M Rb(+) at 4 degrees C, the ApT site in the minor groove is occupied by a Rb(+) ion, a Na(+) ion, or a water molecule 40, 10, and 50% of the time, respectively. In the absence of Rb(+), the Na(+) occupancy increases to 50%. At 4 degrees C, the mean residence time of groove-bound ions is 0.2 +/- 0.1 micros for Rb(+) and 10 ns to 100 micros for Na(+). A shorter correlation time of 2 ns is attributed to counterions bridging cross-strand phosphate groups.
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22
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Mocci F, Laaksonen A, Lyubartsev A, Saba G. Molecular Dynamics Investigation of23Na NMR Relaxation in Oligomeric DNA Aqueous Solution. J Phys Chem B 2004. [DOI: 10.1021/jp047744+] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Li S, Shepherd TD, Thompson WH. Simulations of the Vibrational Relaxation of a Model Diatomic Molecule in a Nanoconfined Polar Solvent. J Phys Chem A 2004. [DOI: 10.1021/jp048361e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Shenmin Li
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045-7582, and Department of Chemistry/Physics, Westminster College, Salt Lake City, Utah 84105
| | - Tricia D. Shepherd
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045-7582, and Department of Chemistry/Physics, Westminster College, Salt Lake City, Utah 84105
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045-7582, and Department of Chemistry/Physics, Westminster College, Salt Lake City, Utah 84105
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24
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25
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Chen P. Electrostatic attraction between ionic reverse micelles with dielectric discontinuity. J Chem Phys 2002. [DOI: 10.1063/1.1516596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Affiliation(s)
- Anne-Laure Rollet
- Département de Recherche Fondamentale sur la Matière Condensée, SI3M, Groupe Polymères Conducteurs Ioniques, CEA-Grenoble 17, rue de Martyrs, 38054 Grenoble Cedex 9, France
| | - Olivier Diat
- Département de Recherche Fondamentale sur la Matière Condensée, SI3M, Groupe Polymères Conducteurs Ioniques, CEA-Grenoble 17, rue de Martyrs, 38054 Grenoble Cedex 9, France
| | - Gérard Gebel
- Département de Recherche Fondamentale sur la Matière Condensée, SI3M, Groupe Polymères Conducteurs Ioniques, CEA-Grenoble 17, rue de Martyrs, 38054 Grenoble Cedex 9, France
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27
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Faeder J, Ladanyi BM. Solvation Dynamics in Aqueous Reverse Micelles: A Computer Simulation Study. J Phys Chem B 2001. [DOI: 10.1021/jp010632n] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James Faeder
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Branka M. Ladanyi
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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28
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Delville A. Influence of Specific Site Binding on the Interactions between Charged Colloids: A ( N, V, T) Monte Carlo Study. J Phys Chem B 2000. [DOI: 10.1021/jp001090x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Delville
- CRMD, CNRS, 1B rue de la Férollerie, 45071 Orléans, Cedex 02, France
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Hedin N, Furó I, Eriksson PO. Fast Diffusion of the Cl- Ion in the Headgroup Region of an Oppositely Charged Micelle. A 35Cl NMR Spin Relaxation Study. J Phys Chem B 2000. [DOI: 10.1021/jp001453t] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Hedin
- Division of Physical Chemistry, Department of Chemistry, Royal Institute of Technology, SE-100 44 Stockholm, Sweden, and AstraZeneca Structural Chemistry Laboratory, SE-431 83 Mölndal, Sweden
| | - I. Furó
- Division of Physical Chemistry, Department of Chemistry, Royal Institute of Technology, SE-100 44 Stockholm, Sweden, and AstraZeneca Structural Chemistry Laboratory, SE-431 83 Mölndal, Sweden
| | - P. O. Eriksson
- Division of Physical Chemistry, Department of Chemistry, Royal Institute of Technology, SE-100 44 Stockholm, Sweden, and AstraZeneca Structural Chemistry Laboratory, SE-431 83 Mölndal, Sweden
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30
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Faeder J, Ladanyi BM. Molecular Dynamics Simulations of the Interior of Aqueous Reverse Micelles. J Phys Chem B 2000. [DOI: 10.1021/jp993076u] [Citation(s) in RCA: 382] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Faeder
- Department of Chemistry, Colorado State University, Ft. Collins, Colorado 80523
| | - B. M. Ladanyi
- Department of Chemistry, Colorado State University, Ft. Collins, Colorado 80523
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31
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Abstract
Recent studies by x-ray crystallography, NMR, and molecular simulations have suggested that monovalent counterions can penetrate deeply into the minor groove of B form DNA. Such groove-bound ions potentially could play an important role in AT-tract bending and groove narrowing, thereby modulating DNA function in vivo. To address this issue, we report here (23)Na magnetic relaxation dispersion measurements on oligonucleotides, including difference experiments with the groove-binding drug netropsin. The exquisite sensitivity of this method to ions in long-lived and intimate association with DNA allows us to detect sequence-specific sodium ion binding in the minor groove AT tract of three B-DNA dodecamers. The sodium ion occupancy is only a few percent, however, and therefore is not likely to contribute importantly to the ensemble of B-DNA structures. We also report results of ion competition experiments, indicating that potassium, rubidium, and cesium ions bind to the minor groove with similarly weak affinity as sodium ions, whereas ammonium ion binding is somewhat stronger. The present findings are discussed in the light of previous NMR and diffraction studies of sequence-specific counterion binding to DNA.
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Affiliation(s)
- V P Denisov
- Physical Chemistry 2, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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32
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Hedin N, Furó I. Accurate intensities of broad NMR lines from composite pulse experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 142:32-36. [PMID: 10617433 DOI: 10.1006/jmre.1999.1883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Accurate determination of integral intensities of broad lines is difficult when spin relaxation during the applied pulses cannot be neglected and/or when ringing of the tank circuit interferes with the signal. Here we present an extension of the analytical solution of the generalized Bloch equations (G. A. Morris and P. B. Chilvers, J. Magn. Reson. A 107, 236 (1994)), which is then used to evaluate the signal intensity obtained in a composite pulse experiment designed to cancel ringing effects. Comparing intensities of broad and narrow (81)Br spectral lines tests and proves the accuracy of this approach.
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Affiliation(s)
- N Hedin
- Department of Chemistry, Royal Institute of Technology, Stockholm, SE-100 44, Sweden
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33
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Brovchenko I, Paschek D, Geiger A. Gibbs ensemble simulation of water in spherical cavities. J Chem Phys 2000. [DOI: 10.1063/1.1289246] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Affiliation(s)
- N. Hedin
- Division of Physical Chemistry, Department of Chemistry, Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - I. Furó
- Division of Physical Chemistry, Department of Chemistry, Royal Institute of Technology, SE-10044 Stockholm, Sweden
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35
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Montoro JCG, Abascal JLF. The Radial Boundary of Polyelectrolyte Solutions Containing Asymmetrical Salts. MOLECULAR SIMULATION 1999. [DOI: 10.1080/08927029908022065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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36
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Lundberg P, Kuchel PW. Diffusion of solutes in agarose and alginate gels: 1H and 23Na PFGSE and 23Na TQF NMR studies. Magn Reson Med 1997; 37:44-52. [PMID: 8978631 DOI: 10.1002/mrm.1910370108] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cells immobilized in gels experience potential metabolic restrictions in the form of reduced diffusion rates of metabolites and ions and their possible selective adsorption on the gel matrix. Diffusion and relaxation characteristics of common solutes in agarose and barium alginate gels were investigated at 37 degrees C by using 1H PFGSE and 23Na TQF NMR spectroscopy. Glucose, glycine, alanine, lactate, sodium ions, and HDO were studied. There were no selective interactions between any of the metabolites and the gel materials but the diffusion coefficients were uniformly reduced. The effects of metabolite diffusion and utilization, in gel beads and threads containing cells, were simulated by using a reaction diffusion model incorporating the measured diffusion coefficients. Metabolism is expected to be very significantly limited by diffusion of solutes to and from the cells that are centrally located within gel threads or spheres of radius approximately 2.0 mm, which is a commonly used size.
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Affiliation(s)
- P Lundberg
- Department of Physical Chemistry, University of Umeå, Sweden
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37
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Gil Montoro JC, Abascal JLF. A Modulated Bulk as a Fuzzy Boundary for the Simulation of Long-Ranged Inhomogeneous Systems. MOLECULAR SIMULATION 1995. [DOI: 10.1080/08927029508022026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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38
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Furó I, Halle B. Micelle size and orientational order across the nematic-isotropic transition: A field-dependent nuclear-spin-relaxation study. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 51:466-477. [PMID: 9962665 DOI: 10.1103/physreve.51.466] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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39
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Quist PO, Halle B. Curvature defects in a lamellar phase revealed by nuclear-spin-relaxation anisotropy. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 47:3374-3395. [PMID: 9960390 DOI: 10.1103/physreve.47.3374] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Quist PO, Blom I, Halle B. Anisotropic 23Na spin relaxation in liquid crystals. Determination of all nine spectral densities for a hexagonal lyotropic phase. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0022-2364(92)90261-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Quist P, Halle B, Furó I. Micelle size and order in lyotropic nematic phases from nuclear spin relaxation. J Chem Phys 1992. [DOI: 10.1063/1.461892] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Quist P, Halle B, Furó I. Nuclear spin relaxation in a hexagonal lyotropic liquid crystal. J Chem Phys 1991. [DOI: 10.1063/1.461506] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Einarsson L, Nordenskjold L, Rupprecht A, Furó I, Wong TC. 7Li and 133Cs spin relaxation in macroscopically oriented Li- and Cs-DNA fibers. ACTA ACUST UNITED AC 1991. [DOI: 10.1016/0022-2364(91)90028-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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47
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