1
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Carpentier R, Lambert S, Brunetti E, Jabin I, Bartik K. Specific Binding of Primary Ammoniums in Aqueous Media by Homooxacalixarenes Incorporated into Micelles. J Org Chem 2022; 87:12749-12758. [PMID: 36149399 DOI: 10.1021/acs.joc.2c01318] [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
The development of artificial receptors for efficient recognition of analytes in water is a challenging task. Homooxacalix[3]arene-based receptor 1, which is selective toward primary ammoniums in organic solvents, was transferred into water following two different strategies: direct solubilization and micellar incorporation. Extensive 1H NMR studies showed that recognition of ammoniums is only observed in the case of micellar incorporation, highlighting the beneficial effect of the microenvironment of the micellar core. The selectivity of the system for primary ammoniums over secondary and tertiary ones was also maintained. The hydrophobic effect plays an important role in the recognition properties, which are counterion-dependent due to the energy penalty for the dissociation of certain ammonium salts in the apolar micellar core. This study shows that the straightforward self-assembly process used for the encapsulation of artificial receptors in micelles is an efficient strategy for developing water-soluble nanosized supramolecular recognition systems.
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Affiliation(s)
- Romain Carpentier
- Université libre de Bruxelles (ULB), Ecole polytechnique de Bruxelles, Engineering of Molecular NanoSystems, Avenue F.D. Roosevelt 50, CP165/64, B-1050 Brussels, Belgium.,Université libre de Bruxelles (ULB), Laboratoire de Chimie Organique, Avenue F.D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
| | - Simon Lambert
- Université libre de Bruxelles (ULB), Ecole polytechnique de Bruxelles, Engineering of Molecular NanoSystems, Avenue F.D. Roosevelt 50, CP165/64, B-1050 Brussels, Belgium.,Université libre de Bruxelles (ULB), Laboratoire de Chimie Organique, Avenue F.D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
| | - Emilio Brunetti
- Université libre de Bruxelles (ULB), Ecole polytechnique de Bruxelles, Engineering of Molecular NanoSystems, Avenue F.D. Roosevelt 50, CP165/64, B-1050 Brussels, Belgium.,Université libre de Bruxelles (ULB), Laboratoire de Chimie Organique, Avenue F.D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
| | - Ivan Jabin
- Université libre de Bruxelles (ULB), Laboratoire de Chimie Organique, Avenue F.D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
| | - Kristin Bartik
- Université libre de Bruxelles (ULB), Ecole polytechnique de Bruxelles, Engineering of Molecular NanoSystems, Avenue F.D. Roosevelt 50, CP165/64, B-1050 Brussels, Belgium
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2
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Javan Nikkhah S, Vandichel M. Modeling Polyzwitterion-Based Drug Delivery Platforms: A Perspective of the Current State-of-the-Art and Beyond. ACS ENGINEERING AU 2022; 2:274-294. [PMID: 35996394 PMCID: PMC9389590 DOI: 10.1021/acsengineeringau.2c00008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Drug delivery platforms
are anticipated to have biocompatible and
bioinert surfaces. PEGylation of drug carriers is the most approved
method since it improves water solubility and colloid stability and
decreases the drug vehicles’ interactions with blood components.
Although this approach extends their biocompatibility, biorecognition
mechanisms prevent them from biodistribution and thus efficient drug
transfer. Recent studies have shown (poly)zwitterions to be alternatives
for PEG with superior biocompatibility. (Poly)zwitterions are super
hydrophilic, mainly stimuli-responsive, easy to functionalize and
they display an extremely low protein adsorption and long biodistribution
time. These unique characteristics make them already promising candidates
as drug delivery carriers. Furthermore, since they have highly dense
charged groups with opposite signs, (poly)zwitterions are intensely
hydrated under physiological conditions. This exceptional hydration
potential makes them ideal for the design of therapeutic vehicles
with antifouling capability, i.e., preventing undesired
sorption of biologics from the human body in the drug delivery vehicle.
Therefore, (poly)zwitterionic materials have been broadly applied
in stimuli-responsive “intelligent” drug delivery systems
as well as tumor-targeting carriers because of their excellent biocompatibility,
low cytotoxicity, insignificant immunogenicity, high stability, and
long circulation time. To tailor (poly)zwitterionic drug vehicles,
an interpretation of the structural and stimuli-responsive behavior
of this type of polymer is essential. To this end, a direct study
of molecular-level interactions, orientations, configurations, and
physicochemical properties of (poly)zwitterions is required, which
can be achieved via molecular modeling, which has become an influential
tool for discovering new materials and understanding diverse material
phenomena. As the essential bridge between science and engineering,
molecular simulations enable the fundamental understanding of the
encapsulation and release behavior of intelligent drug-loaded (poly)zwitterion
nanoparticles and can help us to systematically design their next
generations. When combined with experiments, modeling can make quantitative
predictions. This perspective article aims to illustrate key recent
developments in (poly)zwitterion-based drug delivery systems. We summarize
how to use predictive multiscale molecular modeling techniques to
successfully boost the development of intelligent multifunctional
(poly)zwitterions-based systems.
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Affiliation(s)
- Sousa Javan Nikkhah
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Republic of Ireland
| | - Matthias Vandichel
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Republic of Ireland
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3
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Singh A, Doan LC, Lou D, Wen C, Vinh NQ. Interfacial Layers between Ion and Water Detected by Terahertz Spectroscopy. J Chem Phys 2022; 157:054501. [DOI: 10.1063/5.0095932] [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
Dynamic fluctuations in hydrogen-bond network of water occur from femto- to nano-second timescale and provides insights into structural/dynamical aspects of water at ion-water interfaces. Employing terahertz spectroscopy assisted with molecular dynamics simulations, we study aqueous chloride solutions of five monovalent cations, namely, Li, Na, K, Rb and Cs. We show that ions modify the behavior of surrounding water molecules and form interfacial layers of water around them with physical properties distinct from that of bulk water. Small cations with high charge densities influence the kinetics of water well beyond the first solvation shell. At terahertz frequencies, we observe an emergence of fast relaxation processes of water with their magnitude following the ionic order Cs>Rb>K>Na>Li, revealing an enhanced population density of weakly coordinated water at ion-water interface. The results shed light on the structure breaking tendency of monovalent cations and provide insights into the properties of ionic solutions at the molecular level.
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Affiliation(s)
- Abhishek Singh
- Physics, Virginia Polytechnic Institute and State University, United States of America
| | - Luan C Doan
- Virginia Polytechnic Institute and State University, United States of America
| | - Djamila Lou
- Virginia Polytechnic Institute and State University, United States of America
| | - Chengyuan Wen
- Virginia Polytechnic Institute and State University - National Capital Region, United States of America
| | - Nguyen Q Vinh
- Department of Physics, Virginia Polytechnic Institute and State University, United States of America
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4
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Tang C, Wang Y, Cheng J, Chang C, Hu J, Lü J. Probing terahertz dynamics of multidomain protein in cell-like confinement. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121173. [PMID: 35334430 DOI: 10.1016/j.saa.2022.121173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
The development of meaningful descriptions of multidomain proteins exhibiting complex inter-domain dynamics modes is a key challenge for understanding their roles in molecular recognition and signalling processes. Here we developed a generally applicable approach for probing the low frequency collective hydration dynamics of multidomain proteins that uses terahertz spectroscopy of a protein molecule confined in a phospholipid reverse micelles environment (named Droplet THz). With the combination of normal mode analysis, we demonstrated the binding of calcium ions modulates the local inter-domain motion of the human coagulant factor VIII protein in a concentration-dependent manner. These findings highlight the Droplet THz as a valuable tool for dissecting the ultrafast dynamics of domain motion in the multidomain proteins and suggest a modulating mechanism of calcium ions on the structural flexibility and function of human coagulant proteins.
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Affiliation(s)
- Chao Tang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China; Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yadi Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China; Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; College of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Jie Cheng
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China; Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chao Chang
- Advanced Interdisciplinary Technology Research Center, National Innovation Institute of Defense Technology, Beijing 100071, China.
| | - Jun Hu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China; Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Junhong Lü
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China; Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; College of Pharmacy, Binzhou Medical University, Yantai 264003, China.
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5
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Nishida K, Anada T, Tanaka M. Roles of interfacial water states on advanced biomedical material design. Adv Drug Deliv Rev 2022; 186:114310. [PMID: 35487283 DOI: 10.1016/j.addr.2022.114310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 12/15/2022]
Abstract
When biomedical materials come into contact with body fluids, the first reaction that occurs on the material surface is hydration; proteins are then adsorbed and denatured on the hydrated material surface. The amount and degree of denaturation of adsorbed proteins affect subsequent cell behavior, including cell adhesion, migration, proliferation, and differentiation. Biomolecules are important for understanding the interactions and biological reactions of biomedical materials to elucidate the role of hydration in biomedical materials and their interaction partners. Analysis of the water states of hydrated materials is complicated and remains controversial; however, knowledge about interfacial water is useful for the design and development of advanced biomaterials. Herein, we summarize recent findings on the hydration of synthetic polymers, supramolecular materials, inorganic materials, proteins, and lipid membranes. Furthermore, we present recent advances in our understanding of the classification of interfacial water and advanced polymer biomaterials, based on the intermediate water concept.
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Affiliation(s)
- Kei Nishida
- Institute for Materials Chemistry and Engineering Kyushu university, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan; Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Japan(1)
| | - Takahisa Anada
- Institute for Materials Chemistry and Engineering Kyushu university, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering Kyushu university, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan.
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6
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Doan LC, Dahanayake JN, Mitchell-Koch KR, Singh AK, Vinh NQ. Probing Adaptation of Hydration and Protein Dynamics to Temperature. ACS OMEGA 2022; 7:22020-22031. [PMID: 35785325 PMCID: PMC9245114 DOI: 10.1021/acsomega.2c02843] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Protein dynamics is strongly influenced by the surrounding environment and physiological conditions. Here we employ broadband megahertz-to-terahertz spectroscopy to explore the dynamics of water and myoglobin protein on an extended time scale from femto- to nanosecond. The dielectric spectra reveal several relaxations corresponding to the orientational polarization mechanism, including the dynamics of loosely bound, tightly bound, and bulk water, as well as collective vibrational modes of protein in an aqueous environment. The dynamics of loosely bound and bulk water follow non-Arrhenius behavior; however, the dynamics of water molecules in the tightly bound layer obeys the Arrhenius-type relation. Combining molecular simulations and effective-medium approximation, we have determined the number of water molecules in the tightly bound hydration layer and studied the dynamics of protein as a function of temperature. The results provide the important impact of water on the biochemical functions of proteins.
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Affiliation(s)
- Luan C. Doan
- Department
of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jayangika N. Dahanayake
- Department
of Chemistry, Faculty of Science, University
of Kelaniya, Kelaniya 11600, Sri Lanka
| | | | - Abhishek K. Singh
- Department
of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Nguyen Q. Vinh
- Department
of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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7
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Reid KM, Singh AK, Bikash CR, Wei J, Tal-Gan Y, Vinh NQ, Leitner DM. The origin and impact of bound water around intrinsically disordered proteins. Biophys J 2022; 121:540-551. [PMID: 35074392 PMCID: PMC8874019 DOI: 10.1016/j.bpj.2022.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/14/2021] [Accepted: 01/13/2022] [Indexed: 12/29/2022] Open
Abstract
Proteins and water couple dynamically over a wide range of time scales. Motivated by their central role in protein function, protein-water dynamics and thermodynamics have been extensively studied for structured proteins, where correspondence to structural features has been made. However, properties controlling intrinsically disordered protein (IDP)-water dynamics are not yet known. We report results of megahertz-to-terahertz dielectric spectroscopy and molecular dynamics simulations of a group of IDPs with varying charge content along with structured proteins of similar size. Hydration water around IDPs is found to exhibit more heterogeneous rotational and translational dynamics compared with water around structured proteins of similar size, yielding on average more restricted dynamics around individual residues of IDPs, charged or neutral, compared with structured proteins. The on-average slower water dynamics is found to arise from excess tightly bound water in the first hydration layer, which is related to greater exposure to charged groups. The more tightly bound water to IDPs correlates with the smaller hydration shell found experimentally, and affects entropy associated with protein-water interactions, the contribution of which we estimate based on the dielectric measurements and simulations. Water-IDP dynamic coupling at terahertz frequencies is characterized by the dielectric measurements and simulations.
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Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Abhishek K. Singh
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia
| | | | - Jessica Wei
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Nguyen Q. Vinh
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia,Corresponding author
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada,Corresponding author
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8
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Cui H, Vedder M, Schwaneberg U, Davari MD. Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents. Methods Mol Biol 2022; 2397:179-202. [PMID: 34813065 DOI: 10.1007/978-1-0716-1826-4_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biocatalysis in organic solvents (OSs) is very appealing for the industry in producing bulk and/or fine chemicals, such as pharmaceuticals, biodiesel, and fragrances. The poor performance of enzymes in OSs (e.g., reduced activity, insufficient stability, and deactivation) negates OSs' excellent solvent properties. Molecular dynamics (MD) simulations provide a complementary method to study the relationship between enzymes dynamics and the stability in OSs. Here we describe computational procedure for MD simulation of enzymes in OSs with an example of Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO) cosolvent with software GROMACS. We discuss main essential practical issues considered (such as choice of force field, parameterization, simulation setup, and trajectory analysis). The core part of this protocol (enzyme-OS system setup, analysis of structural-based and solvation-based observables) is transferable to other enzymes and any OS systems. Combining with experimental studies, the obtained molecular knowledge is most likely to guide researchers to access rational protein engineering approaches to tailor OS resistant enzymes and expand the scope of biocatalysis in OS media. Finally, we discuss potential solutions to overcome the remaining challenges of computational biocatalysis in OSs and briefly draw future directions for further improvement in this field.
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Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Markus Vedder
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany.
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9
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Singh AK, Wen C, Cheng S, Vinh NQ. Long-range DNA-water interactions. Biophys J 2021; 120:4966-4979. [PMID: 34687717 DOI: 10.1016/j.bpj.2021.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/14/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ∼8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ∼18 Å from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA.
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Affiliation(s)
- Abhishek K Singh
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia
| | - Chengyuan Wen
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia
| | - Shengfeng Cheng
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia; Macromolecules Innovation Institute, Blacksburg, Virginia; Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia
| | - Nguyen Q Vinh
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia; Macromolecules Innovation Institute, Blacksburg, Virginia; Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia.
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10
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Jang J, Kim S, Eom K. NaCl increases the dielectric constant of nanoconfined water in phospholipid multilamellar vesicle by enhancing intermolecular orientation correlation rather than rotational freedom of individual molecules. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Tarasov AS, Rakhmatullin IZ, Shurshalova GS, Klochkov AV, Il’yasov KA, Klochkov VV. The Affect of Gadolinium Ion on Micelles and Reverse Micelles by NMR Spectroscopy. BIONANOSCIENCE 2021. [DOI: 10.1007/s12668-020-00813-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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12
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Cui H, Zhang L, Eltoukhy L, Jiang Q, Korkunç SK, Jaeger KE, Schwaneberg U, Davari MD. Enzyme Hydration Determines Resistance in Organic Cosolvents. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03233] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Lingling Zhang
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Lobna Eltoukhy
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Qianjia Jiang
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Seval Kübra Korkunç
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Wilhelm Johnen Strasse, Jülich 52426, Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, Jülich 52426, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstrasse 50, Aachen 52074, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
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13
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Charkhesht A, Lou D, Sindle B, Wen C, Cheng S, Vinh NQ. Insights into Hydration Dynamics and Cooperative Interactions in Glycerol–Water Mixtures by Terahertz Dielectric Spectroscopy. J Phys Chem B 2019; 123:8791-8799. [DOI: 10.1021/acs.jpcb.9b07021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Das K, Roy B, Satpathi S, Hazra P. Impact of Topology on the Characteristics of Water inside Cubic Lyotropic Liquid Crystalline Systems. J Phys Chem B 2019; 123:4118-4128. [DOI: 10.1021/acs.jpcb.9b01559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Konoya Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Bibhisan Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Sagar Satpathi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Partha Hazra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pashan, Pune, India 411008
- Centre for Energy Science, Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, India 411008
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15
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Dahanayake JN, Shahryari E, Roberts KM, Heikes ME, Kasireddy C, Mitchell-Koch KR. Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics. J Chem Inf Model 2019; 59:2407-2422. [PMID: 30865440 DOI: 10.1021/acs.jcim.9b00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions on the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.
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Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Elaheh Shahryari
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Kirsten M Roberts
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Micah E Heikes
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Chandana Kasireddy
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Katie R Mitchell-Koch
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
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16
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Functional Hydration Behavior: Interrelation between Hydration and Molecular Properties at Lipid Membrane Interfaces. J CHEM-NY 2019. [DOI: 10.1155/2019/4867327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Water is an abundant commodity and has various important functions. It stabilizes the structure of biological macromolecules, controls biochemical activities, and regulates interfacial/intermolecular interactions. Common aspects of interfacial water can be obtained by overviewing fundamental functions and properties at different temporal and spatial scales. It is important to understand the hydrogen bonding and structural properties of water and to evaluate the individual molecular species having different hydration properties. Water molecules form hydrogen bonds with biomolecules and contribute to the adjustment of their properties, such as surface charge, hydrophilicity, and structural flexibility. In this review, the fundamental properties of water molecules and the methods used for the analyses of water dynamics are summarized. In particular, the interrelation between the hydration properties, determined by molecules, and the properties of molecules, determined by their hydration properties, are discussed using the lipid membrane as an example. Accordingly, interesting water functions are introduced that provide beneficial information in the fields of biochemistry, medicine, and food chemistry.
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17
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Singh P, Mukherjee D, Singha S, Sharma VK, Althagafi II, Ahmed SA, Mukhopadhyay R, Das R, Pal SK. Probing relaxation dynamics of a cationic lipid based non-viral carrier: a time-resolved fluorescence study. RSC Adv 2019; 9:35549-35558. [PMID: 35528090 PMCID: PMC9074709 DOI: 10.1039/c9ra06824d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/18/2019] [Indexed: 01/11/2023] Open
Abstract
Lipid vesicles composed of cationic dioctadecyldimethylammonium bromide (DODAB) and neutral 1-monooleoyl-rac-glycerol (MO) are promising non-viral carriers of nucleic acids for delivery into cells. Among them, higher cell transfection efficiency was displayed by DODAB-rich vesicles than those enriched with MO. Structural relaxation of these mixed lipid vesicles plays a key role in their cell transfection efficiency because structural organization of the DODAB-rich vesicles are different from that of the MO-rich vesicles. Polarization-gated anisotropy in conjunction with picosecond resolved emission transients of a novel fluorophore 6-acetyl-(2-((4-hydroxycyclohexyl)(methyl)amino)naphthalene) (ACYMAN) has been employed to probe relaxation dynamics in pure DODAB vesicles, and in mixed vesicles of DODAB with varying content of MO. Both orientational relaxation of ACYMAN and relaxation dynamics of its local environment are retarded significantly in mixed lipid vesicles with increasing MO content, from a mole fraction (χMO) of 0.2 to that of 0.8 which is consistent with increased rigidity of the MO-rich (χMO > 0.5) vesicles relative to the DODAB-rich (χMO < 0.5) vesicles. Therefore, higher structural rigidity of the MO-rich vesicles (χMO > 0.5) gives rise to their lower cell transfection efficiency than the more flexible DODAB-rich (χMO < 0.5) vesicles as observed in previous in vivo studies (Biochim. Biophys. Acta, Biomembr., 2014, 1838, 2555–2567). Lipid vesicles composed of cationic dioctadecyldimethylammonium bromide (DODAB) and neutral 1-monooleoyl-rac-glycerol (MO) are promising non-viral carriers of nucleic acids for delivery into cells.![]()
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Affiliation(s)
- Priya Singh
- Department of Chemical, Biological & Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700106
- India
| | - Dipanjan Mukherjee
- Department of Chemical, Biological & Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700106
- India
| | - Subhankar Singha
- Centre of Health Science &Technology
- JIS Institute of Advanced Studies
- Kolkata
- India
| | - V. K. Sharma
- Solid State Physics Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
| | - Ismail I. Althagafi
- Chemistry Department
- Faculty of Applied Sciences
- Umm Al-Qura University
- 21955 Makkah Al-Mokarramma
- Saudi Arabia
| | - Saleh A. Ahmed
- Chemistry Department
- Faculty of Applied Sciences
- Umm Al-Qura University
- 21955 Makkah Al-Mokarramma
- Saudi Arabia
| | - R. Mukhopadhyay
- Solid State Physics Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
| | - Ranjan Das
- Department of Chemistry
- West Bengal State University
- Kolkata 700126
- India
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700106
- India
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18
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Khademi M, Barz DPJ. Dielectric relaxation spectroscopy of aqueous micellar electrolyte solutions: A novel application to infer Dukhin number and zeta potential of a micelle. Electrophoresis 2018; 40:710-719. [DOI: 10.1002/elps.201800293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/14/2018] [Accepted: 08/29/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Mahmoud Khademi
- Department of Chemical Engineering; Queen's University; Kingston Ontario Canada
| | - Dominik P. J. Barz
- Department of Chemical Engineering; Queen's University; Kingston Ontario Canada
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19
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Mortara L, Lima FDS, Cuccovia IM, Nazet A, Horinek D, Buchner R, Chaimovich H. Specific Ion Effects on Zwitterionic Micelles Are Independent of Interfacial Hydration Changes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11049-11057. [PMID: 30126270 DOI: 10.1021/acs.langmuir.8b02115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Zwitterionic micelles adsorb anions and several techniques were used to determine the specificity of this interaction. Although at a lower intensity, this adsorption can be compared to those observed in cationic micelles, which showed that interfacial dehydration is a fundamental property for the geometry and size of micelles. Because there is no information on the interfacial hydration of zwitterionic micelles, we used dielectric relaxation spectroscopy (DRS) together with molecular dynamics (MD) simulations to evaluate the importance of surface dehydration promoted by the binding of anions at the micellar interface (sodium bromide, sodium methanesulfonate, sodium trifluoroacetate, and sodium triflate) in N-dodecyl- N, N-dimethyl-3-ammonio-1-propanesulfonate (DPS) micelles. Our results, showing good agreement between DRS and MD simulations, strongly suggest that specific ion effects on zwitterionic micelles are unrelated to global changes in the interfacial hydration and depend on specific interactions of the headgroups with selected anions.
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Affiliation(s)
- Laura Mortara
- Departamento de Química, Instituto de Química , Universidade de São Paulo , São Paulo 05508-000 , Brazil
| | - Filipe da Silva Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza , Universidade Federal de Pernambuco , Recife 50740-540 , Brazil
| | - Iolanda Midea Cuccovia
- Departamento de Bioquímica, Instituto de Química , Universidade de São Paulo , São Paulo 05508-000 , Brazil
| | - Andreas Nazet
- Institut für Physikalische und Theoretische Chemie , Universität Regensburg , D-93040 Regensburg , Germany
| | - Dominik Horinek
- Institut für Physikalische und Theoretische Chemie , Universität Regensburg , D-93040 Regensburg , Germany
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie , Universität Regensburg , D-93040 Regensburg , Germany
| | - Hernan Chaimovich
- Departamento de Bioquímica, Instituto de Química , Universidade de São Paulo , São Paulo 05508-000 , Brazil
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20
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Dahanayake JN, Mitchell-Koch KR. How Does Solvation Layer Mobility Affect Protein Structural Dynamics? Front Mol Biosci 2018; 5:65. [PMID: 30057902 PMCID: PMC6053501 DOI: 10.3389/fmolb.2018.00065] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations. Data was obtained for the enzyme in acetonitrile, cyclohexane, n-butanol, and tert-butanol, in addition to water. Protein dynamics and solvation shell dynamics are characterized regionally: for each α-helix, β-sheet, and loop or connector region. Correlations are seen between solvent mobility and protein flexibility. So, does local viscosity explain the relationship between protein structural dynamics and solvation layer dynamics? Halle and Davidovic presented a cogent analysis of data describing the global hydrodynamics of a protein (tumbling in solution) that fits a model in which the protein's interfacial viscosity is higher than that of bulk water's, due to retarded water dynamics in the hydration layer (measured in NMR τ2 reorientation times). Numerous experiments have shown coupling between protein and solvation layer dynamics in site-specific measurements. Our data provides spatially-resolved characterization of solvent shell dynamics, showing correlations between regional solvation layer dynamics and protein dynamics in both aqueous and organic solvents. Correlations between protein flexibility and inverse solvent viscosity (1/η) are considered across several protein regions and for a rather disparate collection of solvents. It is seen that the correlation is consistently higher when local solvent shell dynamics are considered, rather than bulk viscosity. Protein flexibility is seen to correlate best with either the local interfacial viscosity or the ratio of the mobility of an organic solvent in a regional solvation layer relative to hydration dynamics around the same region. Results provide insight into the function of aqueous proteins, while also suggesting a framework for interpreting and predicting enzyme structural dynamics in non-aqueous solvents, based on the mobility of solvents within the solvation layer. We suggest that Kramers' theory may be used in future work to model protein conformational transitions in different solvents by incorporating local viscosity effects.
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21
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Charkhesht A, Regmi CK, Mitchell-Koch KR, Cheng S, Vinh NQ. High-Precision Megahertz-to-Terahertz Dielectric Spectroscopy of Protein Collective Motions and Hydration Dynamics. J Phys Chem B 2018; 122:6341-6350. [PMID: 29791154 DOI: 10.1021/acs.jpcb.8b02872] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of the hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here, we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The dielectric relaxation spectra reveal several polarization mechanisms at the molecular level with different time constants and dielectric strengths, reflecting the complexity of protein-water interactions. Combining the effective-medium approximation and molecular dynamics simulations, we have determined collective vibrational modes at terahertz frequencies and the number of water molecules in the tightly bound and loosely bound hydration layers. High-precision measurements of the number of hydration water molecules indicate that the dynamical influence of proteins extends beyond the first solvation layer, to around 7 Å distance from the protein surface, with the largest slowdown arising from water molecules directly hydrogen-bonded to the protein. Our results reveal critical information of protein dynamics and protein-water interfaces, which determine biochemical functions and reactivity of proteins.
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Affiliation(s)
| | | | - Katie R Mitchell-Koch
- Department of Chemistry , Wichita State University , Wichita , Kansas 67260 , United States
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22
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Phukon A, Sahu K. How do the interfacial properties of zwitterionic sulfobetaine micelles differ from those of cationic alkyl quaternary ammonium micelles? An excited state proton transfer study. Phys Chem Chem Phys 2017; 19:31461-31468. [DOI: 10.1039/c7cp06339c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The interface of a zwitterionic sulfobetaine micelle is more packed and less hydrated compared to a cationic alkyl-ammonium micelle with an identical alkyl tail.
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Affiliation(s)
- Aparajita Phukon
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati 781039
- India
| | - Kalyanasis Sahu
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati 781039
- India
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