101
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Abstract
The field of nanoscience has produced more hype than probably any other branch of materials science and engineering in its history. Still, the potentials of this new field largely lay undiscovered ahead of us; what we have learnt so far with respect to the peculiarity of physical processes on the nanoscale is only the tip of an iceberg. Elaborated in this critical review is the idea that the surge of interest in physical chemistry of phenomena at the nanoscale presents a natural consequence of the spatial refinement of the human ability to controllably manipulate the substratum of our physical reality. Examples are given to illustrate the sensitivity of material properties to grain size on the nanoscale, a phenomenon that directly contributed to the rise of nanoscience as a special field of scientific inquiry. Main systemic challenges faced by the present and future scientists in this field are also mentioned. In part, this perspective article resembles standing on the constantly expanding seashore of the coast of nanoscience and nanoengineering and envisioning the parts of the island where the most significant advances may be expected to occur and where, therefore, most of the attention of scientist in this field is to be directed: (a) crossing the gap between life science and materials science; (b) increasing experimentation sensitivity; (c) crisscrossing theory and experiments; and (d) conjoining top-down and bottom-up synthetic approaches. As for materials and the application areas discussed, a special emphasis is placed on calcium phosphate nanoparticles and their usage in controlled drug delivery devices and other applications of biomedical relevance. It is argued that the properties of nanoparticles as drug carriers often comprise the critical determinant for- the efficacy of the drug therapy. Therefore, the basic properties of nanoparticles to be optimized for the purpose of maximizing this efficacy are discussed: size, size distribution, morphology, polymorphic nature, crystallinity, biocompatibility, biodegradability, drug elution profiles, and aggregation propensity.
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Affiliation(s)
- Vuk Uskoković
- Therapeutic Micro and Nanotechnology Laboratory, Department of Bioengineering and Therapeutic Sciences, University of California, 1700 4th Street, San Francisco, CA 94158-2330, USA.
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102
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Singh PK, Kuroda DG, Hochstrasser RM. An ion's perspective on the molecular motions of nanoconfined water: a two-dimensional infrared spectroscopy study. J Phys Chem B 2013; 117:9775-84. [PMID: 23855349 DOI: 10.1021/jp406725a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The vibrational population relaxation and hydration shell dynamics of the symmetric tricyanomethanide (TCM) anion are investigated in a sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle as a function of the water pool radius. Two-dimensional infrared (IR) spectroscopy in combination with linear absorption and ultrafast IR pump-probe spectroscopy is utilized in this study. Spectroscopic measurements show that the anion has two bands in the 2160-2175 cm(-1) region, each with its own spectroscopic signatures. Analysis of the vibrational dynamics shows that the two vibrational bands are consistent with the anion located either at the interface or in the water pool. The sensitivity of the TCM anion to the environment allows us to unequivocally monitor the vibrational and hydration dynamics of the anion in those two different environments. A TCM anion located at the interface does not show any significant variation of the vibrational dynamics with the water pool size. On the contrary, the TCM anion inside the water pool exhibits a large and nonlinear variation of the vibrational lifetime and the frequency-frequency correlation time with the pool radius. Moreover, for the solvated anion in water pools of 49 Å in radius (W0 = 30), the vibrational lifetime reaches the values observed for the anion in bulk water while the frequency-frequency correlation time shows a characteristic time higher than that observed in the bulk. In addition, for the first time a model is developed and used to explain the observed nonlinear variation of the spectroscopic observables with the pool size. This model attributes the changes in the vibrational dynamics of the TCM anion in the water pool to the slow and radius-dependent water dynamics present in the confined environment of a reverse micelle.
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Affiliation(s)
- Prabhat K Singh
- Ultrafast Optical Processes Laboratory, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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103
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Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin. Chem Phys 2013; 430:88-97. [PMID: 24039330 DOI: 10.1016/j.chemphys.2013.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Hemoglobin is an appropriate tool with which to probe hydration effects. We describe both a protocol for hemoglobin encapsulation in reverse micelles and a facile method using PEG and cosolvents to manipulate water content. Hydration properties are probed using the water-sensitive fluorescence from Hb bound pyranine and covalently attached Badan. Protein dynamics are probed through ligand recombination traces derived from photodissociated carbonmonoxy hemoglobin on a log scale that exposes the potential role of both α and β solvent fluctuations in modulating protein dynamics. The results open the possibility of probing hydration level phenomena in this system using a combination of NMR and optical probes.
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104
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Gruenbaum SM, Tainter CJ, Shi L, Ni Y, Skinner JL. Robustness of Frequency, Transition Dipole, and Coupling Maps for Water Vibrational Spectroscopy. J Chem Theory Comput 2013; 9:3109-17. [DOI: 10.1021/ct400292q] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. M. Gruenbaum
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - C. J. Tainter
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - L. Shi
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - Y. Ni
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - J. L. Skinner
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
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105
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Rana MK, Chandra A. Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet. J Chem Phys 2013; 138:204702. [DOI: 10.1063/1.4804300] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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106
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Lv W, Wu R. The interfacial-organized monolayer water film (MWF) induced "two-step" aggregation of nanographene: both in stacking and sliding assembly pathways. NANOSCALE 2013; 5:2765-2775. [PMID: 23429907 DOI: 10.1039/c3nr33447c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A computational investigation was carried out to understand the aggregation of nanoscale graphene with two typical pathways of stacking assembly and sliding assembly in water. The interfacial-organized monolayer water film (MWF) induced "two-step" aggregation of nanographene in both stacking and sliding assembly pathways was reported for the first time. By means of potential mean forces (PMFs) calculation, no energy barrier was observed during the sliding assembly of two graphene nanosheets, while the PMF profiles could be impacted by the contact forms of nanographene and the MWF within the interplate of two graphene nanosheets. To explore the potential physical basis of the "hindering role" of self-organized interfacial water, the dynamical and structural properties as well as the status of hydrogen bonds (H-bonds) for interfacial water were investigated. We found that the compact, ordered structure and abundant H-bonds of the MWF could be taken as the fundamental aspects of the "hindering role" of interfacial water for the hydrophobic assembly of nanographene. These findings are displaying a potential to further understand the hydrophobic assembly which mostly dominate the behaviors of nanomaterials, proteins etc. in aqueous solutions.
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Affiliation(s)
- Wenping Lv
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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107
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Das A, Patra A, Mitra RK. Do the Physical Properties of Water in Mixed Reverse Micelles Follow a Synergistic Effect: A Spectroscopic Investigation. J Phys Chem B 2013; 117:3593-602. [DOI: 10.1021/jp3102833] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arindam Das
- Unit for Nano Science & Technology, Department of Chemical Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700098, India
| | - Animesh Patra
- Unit for Nano Science & Technology, Department of Chemical Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700098, India
| | - Rajib Kumar Mitra
- Unit for Nano Science & Technology, Department of Chemical Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700098, India
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108
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Kumar SKK, Tamimi A, Fayer MD. Dynamics in the interior of AOT lamellae investigated with two-dimensional infrared spectroscopy. J Am Chem Soc 2013; 135:5118-26. [PMID: 23465101 DOI: 10.1021/ja312676e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics inside the organic regions of aerosol-OT (AOT)/water mixtures in the lamellar mesophase, bicontinuous cubic (BC) phase, and in an analogous molecule without the charged sulfonate headgroup are investigated by observing spectral diffusion, orientational relaxation and population relaxation using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy and IR pump-probe experiments on the asymmetric CO stretch of a vibrational probe, tungsten hexacarbonyl (W(CO)6). The water layer thickness between the bilayer planes in the lamellar phase was varied. For comparison, the dynamics of W(CO)6 in the normal liquid bis(2-ethylhexyl) succinate (EHS), which is analogous to AOT but has no charged sulfonate headgroup, were also studied. The 2D IR experiments measure spectral diffusion, which results from the structural evolution of the system. Spectral diffusion is quantified by the frequency-frequency correlation function (FFCF). In addition to a homogeneous component, the FFCFs are biexponential decays with fast and slow time components of ∼12.5 and ∼150 ps in the lamellar phase. Both components of the FFCF are independent of the number of water molecules per headgroup for the lamellae, but they slow somewhat in the BC phase. The dynamics in the ordered phases are in sharp contrast to the dynamics in EHS, which displays fast and slow components of the FFCF of 5 and 80 ps, respectively. As the hydration level of AOT increases, vibrational lifetime decreases, suggesting some change in the local environment of W(CO)6 with water content.
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Affiliation(s)
- S K Karthick Kumar
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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109
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Guchhait B, Biswas R, Ghorai PK. Solute and Solvent Dynamics in Confined Equal-Sized Aqueous Environments of Charged and Neutral Reverse Micelles: A Combined Dynamic Fluorescence and All-Atom Molecular Dynamics Simulation Study. J Phys Chem B 2013; 117:3345-61. [DOI: 10.1021/jp310285k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Biswajit Guchhait
- Department
of Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt
Lake, Kolkata 700098, India
| | - Ranjit Biswas
- Department
of Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt
Lake, Kolkata 700098, India
| | - Pradip K. Ghorai
- Indian Institute of Science Education and Research, Kolkata, Mohanpur Campus, Nadia 741252,
India
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110
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Son H, Kwon Y, Kim J, Park S. Rotational Dynamics of Metal Azide Ion Pairs in Dimethylsulfoxide Solutions. J Phys Chem B 2013; 117:2748-56. [DOI: 10.1021/jp312055f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hyewon Son
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - YoungAh Kwon
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Jinwoo Kim
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Sungnam Park
- Department of Chemistry, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy
Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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111
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Patra A, Luong TQ, Mitra RK, Havenith M. Solvent dynamics in a reverse micellar water-pool: a spectroscopic investigation of DDAB–cyclohexane–water systems. Phys Chem Chem Phys 2013. [DOI: 10.1039/c2cp42560b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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112
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Singh PK, Nath S. Ultrafast torsional dynamics in nanoconfined water pool: Comparison between neutral and charged reverse micelles. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.08.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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113
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Chaladze R, Gvaramia M, Kurtanidze M, Bezarashvili G, Rukhadze M. Study of Influence of Salt Additives on Mixed Reverse Micelles via Reverse Microemulsion Chromatography and UV–visible Spectroscopy. CHEM LETT 2012. [DOI: 10.1246/cl.2012.1035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Rusudan Chaladze
- Department of Chemistry, Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University
| | - Manuchar Gvaramia
- Department of Chemistry, Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University
| | - Manoni Kurtanidze
- Department of Chemistry, Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University
| | - George Bezarashvili
- Department of Chemistry, Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University
| | - Marina Rukhadze
- Department of Chemistry, Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University
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114
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Kosmella S, Koetz J. Polymer-modified w/o microemulsions - with tunable droplet-droplet interactions. Curr Opin Colloid Interface Sci 2012. [DOI: 10.1016/j.cocis.2012.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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115
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van der Loop TH, Panman MR, Lotze S, Zhang J, Vad T, Bakker HJ, Sager WFC, Woutersen S. Structure and dynamics of water in nonionic reverse micelles: A combined time-resolved infrared and small angle x-ray scattering study. J Chem Phys 2012; 137:044503. [DOI: 10.1063/1.4736562] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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116
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Correa NM, Silber JJ, Riter RE, Levinger NE. Nonaqueous Polar Solvents in Reverse Micelle Systems. Chem Rev 2012; 112:4569-602. [DOI: 10.1021/cr200254q] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Mariano Correa
- Departamento de Química, Universidad Nacional de Río Cuarto, Agencia
Postal #3, C.P. X5804BYA Río Cuarto, Argentina
| | - Juana J. Silber
- Departamento de Química, Universidad Nacional de Río Cuarto, Agencia
Postal #3, C.P. X5804BYA Río Cuarto, Argentina
| | - Ruth E. Riter
- Department of Chemistry, Agnes Scott College, Decatur, Georgia 30030-3770, United
States
| | - Nancy E. Levinger
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872,
United States
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117
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Vartia AA, Thompson WH. Solvation and Spectra of a Charge Transfer Solute in Ethanol Confined within Nanoscale Silica Pores. J Phys Chem B 2012; 116:5414-24. [DOI: 10.1021/jp210737c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anthony A. Vartia
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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118
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Hoarfrost ML, Tyagi MS, Segalman RA, Reimer JA. Effect of Confinement on Proton Transport Mechanisms in Block Copolymer/Ionic Liquid Membranes. Macromolecules 2012. [DOI: 10.1021/ma202741g] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Megan L. Hoarfrost
- Department of Chemical and Biomolecular
Engineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Madhu S. Tyagi
- NIST Center for Neutron Research, Gaithersburg, Maryland 20899, United States
- Department of Materials Science
and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Rachel A. Segalman
- Department of Chemical and Biomolecular
Engineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Jeffrey A. Reimer
- Department of Chemical and Biomolecular
Engineering, University of California,
Berkeley, Berkeley, California 94720, United States
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119
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Setua P, Ghatak C, Rao VG, Das SK, Sarkar N. Dynamics of Solvation and Rotational Relaxation of Coumarin 480 in Pure Aqueous-AOT Reverse Micelle and Reverse Micelle Containing Different-Sized Silver Nanoparticles Inside Its Core: A Comparative Study. J Phys Chem B 2012; 116:3704-12. [PMID: 22380919 DOI: 10.1021/jp203043k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Palash Setua
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West
Bengal, India
| | - Chiranjib Ghatak
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West
Bengal, India
| | - Vishal Govind Rao
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West
Bengal, India
| | - S. K. Das
- Variable Energy Cyclotron Centre, 1/AF, Bidhan Nagar,
Kolkata 700064, West Bengal, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West
Bengal, India
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120
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Rao VG, Ghosh S, Ghatak C, Mandal S, Brahmachari U, Sarkar N. Designing a New Strategy for the Formation of IL-in-Oil Microemulsions. J Phys Chem B 2012; 116:2850-5. [DOI: 10.1021/jp2110488] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Vishal Govind Rao
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Surajit Ghosh
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Chiranjib Ghatak
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Sarthak Mandal
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Udita Brahmachari
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
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121
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Skinner JL, Pieniazek PA, Gruenbaum SM. Vibrational spectroscopy of water at interfaces. Acc Chem Res 2012; 45:93-100. [PMID: 22032305 DOI: 10.1021/ar200122a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding liquid water's behavior at the molecular level is essential to progress in fields as disparate as biology and atmospheric sciences. Moreover, the properties of water in bulk and water at interfaces can be very different, making the study of the hydrogen-bonding networks therein very important. With recent experimental advances in vibrational spectroscopy, such as ultrafast pulses and heterodyne detection, it is now possible to probe the structure and dynamics of bulk and interfacial water in unprecedented detail. We consider here three aqueous interfaces: the water liquid-vapor interface, the interface between water and the surfactant headgroups of reverse micelles, and the interface between water and the lipid headgroups of aligned multi-bilayers. In the first case, sum-frequency spectroscopy is used to probe the interface. In the second and third cases, the confined water pools are sufficiently small that techniques of bulk spectroscopy (such as FTIR, pump-probe, two-dimensional IR, and the like) can be used to probe the interfacial water. In this Account, we discuss our attempts to model these three systems and interpret the existing experiments. For the water liquid-vapor interface, we find that three-body interactions are essential for reproducing the experimental sum-frequency spectrum, and presumably for the structure of the interface as well. The observed spectrum is interpreted as arising from overlapping and canceling positive and negative contributions from molecules in different hydrogen-bonding environments. For the reverse micelles, our theoretical models confirm that the experimentally observed blue shift of the water OD stretch (for dilute HOD in H(2)O) arises from weaker hydrogen bonding to sulfonate oxygens. We interpret the observed slow-down in water rotational dynamics as arising from curvature-induced frustration. For the water confined between lipid bilayers, our theoretical models confirm that the experimentally observed red shift of the water OD stretch arises from stronger hydrogen bonding to phosphate oxygens. We develop a model for heterogeneous vibrational lifetime distributions, and we implement the model to calculate isotropic and anisotropic pump-probe decays. We then compare these results with experimental data. Clearly, recent experimental advances in vibrational spectroscopy have led to beautiful new results, providing information about the structure and dynamics of water at interfaces. These experimental and concomitant theoretical advances (particularly the unified theoretical framework of non-linear response functions) have greatly contributed to our understanding of this unique and important substance.
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Affiliation(s)
- J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - P. A. Pieniazek
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - S. M. Gruenbaum
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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122
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Abstract
Water is a critical component of many chemical processes, in fields as diverse as biology and geology. Water in chemical, biological, and other systems frequently occurs in very crowded situations: the confined water must interact with a variety of interfaces and molecular groups, often on a characteristic length scale of nanometers. Water's behavior in diverse environments is an important contributor to the functioning of chemical systems. In biology, water is found in cells, where it hydrates membranes and large biomolecules. In geology, interfacial water molecules can control ion adsorption and mineral dissolution. Embedded water molecules can change the structure of zeolites. In chemistry, water is an important polar solvent that is often in contact with interfaces, for example, in ion-exchange resin systems. Water is a very small molecule; its unusual properties for its size are attributable to the formation of extended hydrogen bond networks. A water molecule is similar in mass and volume to methane, but methane is a gas at room temperature, with melting and boiling points of 91 and 112 K, respectively. This is in contrast to water, with melting and boiling points of 273 and 373 K, respectively. The difference is that water forms up to four hydrogen bonds with approximately tetrahedral geometry. Water's hydrogen bond network is not static. Hydrogen bonds are constantly forming and breaking. In bulk water, the time scale for hydrogen bond randomization through concerted formation and dissociation of hydrogen bonds is approximately 2 ps. Water's rapid hydrogen bond rearrangement makes possible many of the processes that occur in water, such as protein folding and ion solvation. However, many processes involving water do not take place in pure bulk water, and water's hydrogen bond structural dynamics can be substantially influenced by the presence of, for example, interfaces, ions, and large molecules. In this Account, spectroscopic studies that have been used to explore the details of these influences are discussed. Because rearrangements of water molecules occur so quickly, ultrafast infrared experiments that probe water's hydroxyl stretching mode are useful in providing direct information about water dynamics on the appropriate time scales. Infrared polarization-selective pump-probe experiments and two-dimensional infrared (2D IR) vibrational echo experiments have been used to study the hydrogen bond dynamics of water. Water orientational relaxation, which requires hydrogen bond rearrangements, has been studied at spherical interfaces of ionic reverse micelles and compared with planar interfaces of lamellar structures composed of the same surfactants. Water orientational relaxation slows considerably at interfaces. It is found that the geometry of the interface is less important than the presence of the interface. The influence of ions is shown to slow hydrogen bond rearrangements. However, comparing an ionic interface to a neutral interface demonstrates that the chemical nature of the interface is less important than the presence of the interface. Finally, it is found that the dynamics of water at an organic interface is very similar to water molecules interacting with a large polyether.
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Affiliation(s)
- Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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123
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Fenn EE, Fayer MD. Extracting 2D IR frequency-frequency correlation functions from two component systems. J Chem Phys 2011; 135:074502. [PMID: 21861571 DOI: 10.1063/1.3625278] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The center line slope (CLS) method is often used to extract the frequency-frequency correlation function (FFCF) from 2D IR spectra to delineate dynamics and to identify homogeneous and inhomogeneous contributions to the absorption line shape of a system. While the CLS method is extremely efficient, quite accurate, and immune to many experimental artifacts, it has only been developed and properly applied to systems that have a single vibrational band, or to systems of two species that have spectrally resolved absorption bands. In many cases, the constituent spectra of multiple component systems overlap and cannot be distinguished from each other. This situation creates ambiguity when analyzing 2D IR spectra because dynamics for different species cannot be separated. Here a mathematical formulation is presented that extends the CLS method for a system consisting of two components (chemically distinct uncoupled oscillators). In a single component system, the CLS corresponds to the time-dependent portion of the normalized FFCF. This is not the case for a two component system, as a much more complicated expression arises. The CLS method yields a series of peak locations originating from slices taken through the 2D spectra. The slope through these peak locations yields the CLS value for the 2D spectra at a given T(w). We derive analytically that for two component systems, the peak location of the system can be decomposed into a weighted combination of the peak locations of the constituent spectra. The weighting depends upon the fractional contribution of each species at each wavelength and also on the vibrational lifetimes of both components. It is found that an unknown FFCF for one species can be determined as long as the peak locations (referred to as center line data) of one of the components are known, as well as the vibrational lifetimes, absorption spectra, and other spectral information for both components. This situation can arise when a second species is introduced into a well characterized single species system. An example is a system in which water exists in bulk form and also as water interacting with an interface. An algorithm is presented for back-calculating the unknown FFCF of the second component. The accuracy of the algorithm is tested with a variety of model cases in which all components are initially known. The algorithm successfully reproduces the FFCF for the second component within a reasonable degree of error.
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Affiliation(s)
- Emily E Fenn
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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124
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Abstract
In many situations, form biology to geology, water occurs not as the pure bulk liquid but rather in nanoscopic environments, in contact with interfaces, interacting with ionic species, and interacting with large organic molecules. In such situations, water does not behave in the same manner as it does in the pure bulk liquid. Water dynamics are fundamental to many processes such as protein folding and proton transport. Such processes depend on the dynamics of water's hydrogen bonding network. Here, the results of ultrafast infrared experiments are described that shed light on the influences of nanoconfinement, interfaces, ions, and organic molecules on water hydrogen bond dynamics.
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Affiliation(s)
- Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California
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125
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Bakulin AA, Pshenichnikov MS. Reduced coupling of water molecules near the surface of reverse micelles. Phys Chem Chem Phys 2011; 13:19355-61. [PMID: 21959913 DOI: 10.1039/c1cp22235j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on vibrational dynamics of water near the surface of AOT reverse micelles studied by narrow-band excitation, mid-IR pump-probe spectroscopy. Evidence of OH-stretch frequency splitting into the symmetric and asymmetric modes is clearly observed for the interfacial H(2)O molecules. The polarization memory of interfacial waters is preserved over an exceptionally extended >10 ps timescale which is a factor of 100 longer than in bulk water. These observations point towards negligibly small intermolecular vibrational coupling between the water molecules as well as strongly reduced water rotational mobility within the interfacial water layer.
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Affiliation(s)
- Artem A Bakulin
- Department of Physical Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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126
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Fenn EE, Wong DB, Giammanco CH, Fayer MD. Dynamics of Water at the Interface in Reverse Micelles: Measurements of Spectral Diffusion with Two-Dimensional Infrared Vibrational Echoes. J Phys Chem B 2011; 115:11658-70. [DOI: 10.1021/jp206903k] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emily E. Fenn
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Daryl B. Wong
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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127
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Sengupta A, Khade RV, Hazra P. How Does the Urea Dynamics Differ from Water Dynamics inside the Reverse Micelle? J Phys Chem A 2011; 115:10398-407. [DOI: 10.1021/jp206069z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abhigyan Sengupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411021, Maharashtra, India
| | - Rahul V. Khade
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411021, Maharashtra, India
| | - Partha Hazra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411021, Maharashtra, India
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128
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Pramanik R, Sarkar S, Ghatak C, Rao VG, Sarkar N. Solvent and rotational relaxation study in ionic liquid containing reverse micellar system: A picosecond fluorescence spectroscopy study. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.07.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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129
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Nucci NV, Marques BS, Bédard S, Dogan J, Gledhill JM, Moorman VR, Peterson RW, Valentine KG, Wand AL, Wand AJ. Optimization of NMR spectroscopy of encapsulated proteins dissolved in low viscosity fluids. JOURNAL OF BIOMOLECULAR NMR 2011; 50:421-30. [PMID: 21748265 PMCID: PMC4174299 DOI: 10.1007/s10858-011-9528-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/28/2011] [Indexed: 05/20/2023]
Abstract
Comprehensive application of solution NMR spectroscopy to studies of macromolecules remains fundamentally limited by the molecular rotational correlation time. For proteins, molecules larger than 30 kDa require complex experimental methods, such as TROSY in conjunction with isotopic labeling schemes that are often expensive and generally reduce the potential information available. We have developed the reverse micelle encapsulation strategy as an alternative approach. Encapsulation of proteins within the protective nano-scale water pool of a reverse micelle dissolved in ultra-low viscosity nonpolar solvents overcomes the slow tumbling problem presented by large proteins. Here, we characterize the contributions from the various components of the protein-containing reverse micelle system to the rotational correlation time of the encapsulated protein. Importantly, we demonstrate that the protein encapsulated in the reverse micelle maintains a hydration shell comparable in size to that seen in bulk solution. Using moderate pressures, encapsulation in ultra-low viscosity propane or ethane can be used to magnify this advantage. We show that encapsulation in liquid ethane can be used to reduce the tumbling time of the 43 kDa maltose binding protein from ~23 to ~10 ns. These conditions enable, for example, acquisition of TOCSY-type data resolved on the adjacent amide NH for the 43 kDa encapsulated maltose binding protein dissolved in liquid ethane, which is typically impossible for proteins of such size without use of extensive deuteration or the TROSY effect.
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Affiliation(s)
- Nathaniel V. Nucci
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - Bryan S. Marques
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - Sabrina Bédard
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - Jakob Dogan
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - John M. Gledhill
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - Veronica R. Moorman
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - Ronald W. Peterson
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - Kathleen G. Valentine
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - Alison L. Wand
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - A. Joshua Wand
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
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130
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McPhee JT, Scott E, Levinger NE, Van Orden A. Cy3 in AOT Reverse Micelles II. Probing Intermicellar Interactions Using Fluorescence Correlation Spectroscopy. J Phys Chem B 2011; 115:9585-92. [DOI: 10.1021/jp2001282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeffrey T McPhee
- Colorado State University, Department of Chemistry, Fort Collins, Colorado 80523, USA
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131
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132
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Tian J, García AE. Simulations of the confinement of ubiquitin in self-assembled reverse micelles. J Chem Phys 2011; 134:225101. [PMID: 21682536 PMCID: PMC3133568 DOI: 10.1063/1.3592712] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 04/30/2011] [Indexed: 11/14/2022] Open
Abstract
We describe the effects of confinement on the structure, hydration, and the internal dynamics of ubiquitin encapsulated in reverse micelles (RM). We performed molecular dynamics simulations of the encapsulation of ubiquitin into self-assembled protein/surfactant reverse micelles to study the positioning and interactions of the protein with the RM and found that ubiquitin binds to the RM interface at low salt concentrations. The same hydrophobic patch that is recognized by ubiquitin binding domains in vivo is found to make direct contact with the surfactant head groups, hydrophobic tails, and the iso-octane solvent. The fast backbone N-H relaxation dynamics show that the fluctuations of the protein encapsulated in the RM are reduced when compared to the protein in bulk. This reduction in fluctuations can be explained by the direct interactions of ubiquitin with the surfactant and by the reduced hydration environment within the RM. At high concentrations of excess salt, the protein does not bind strongly to the RM interface and the fast backbone dynamics are similar to that of the protein in bulk. Our simulations demonstrate that the confinement of protein can result in altered protein dynamics due to the interactions between the protein and the surfactant.
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Affiliation(s)
- Jianhui Tian
- Department of Physics, Applied Physics and Astronomy and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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133
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Morales CM, Thompson WH. Molecular-level mechanisms of vibrational frequency shifts in a polar liquid. J Phys Chem B 2011; 115:7597-605. [PMID: 21608988 DOI: 10.1021/jp201591c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A molecular-level analysis of the origins of the vibrational frequency shifts of the CN stretching mode in neat liquid acetonitrile is presented. The frequency shifts and infrared spectrum are calculated using a perturbation theory approach within a molecular dynamics simulation and are in good agreement with measured values reported in the literature. The resulting instantaneous frequency of each nitrile group is decomposed into the contributions from each molecule in the liquid and by interaction type. This provides a detailed picture of the mechanisms of frequency shifts, including the number of surrounding molecules that contribute to the shift, the relationship between their position and relative contribution, and the roles of electrostatic and van der Waals interactions. These results provide insight into what information is contained in infrared (IR) and Raman spectra about the environment of the probed vibrational mode.
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Affiliation(s)
- Christine M Morales
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, USA
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134
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Fenn EE, Wong DB, Fayer MD. Water dynamics in small reverse micelles in two solvents: two-dimensional infrared vibrational echoes with two-dimensional background subtraction. J Chem Phys 2011; 134:054512. [PMID: 21303143 DOI: 10.1063/1.3532542] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water dynamics as reflected by the spectral diffusion of the water hydroxyl stretch were measured in w(0) = 2 (1.7 nm diameter) Aerosol-OT (AOT)/water reverse micelles in carbon tetrachloride and in isooctane solvents using ultrafast 2D IR vibrational echo spectroscopy. Orientational relaxation and population relaxation are observed for w(0) = 2, 4, and 7.5 in both solvents using IR pump-probe measurements. It is found that the pump-probe observables are sensitive to w(0), but not to the solvent. However, initial analysis of the vibrational echo data from the water nanopool in the reverse micelles in the isooctane solvent seems to yield different dynamics than the CCl(4) system in spite of the fact that the spectra, vibrational lifetimes, and orientational relaxation are the same in the two systems. It is found that there are beat patterns in the interferograms with isooctane as the solvent. The beats are observed from a signal generated by the AOT/isooctane system even when there is no water in the system. A beat subtraction data processing procedure does a reasonable job of removing the distortions in the isooctane data, showing that the reverse micelle dynamics are the same within experimental error regardless of whether isooctane or carbon tetrachloride is used as the organic phase. Two time scales are observed in the vibrational echo data, ~1 and ~10 ps. The slower component contains a significant amount of the total inhomogeneous broadening. Physical arguments indicate that there is a much slower component of spectral diffusion that is too slow to observe within the experimental window, which is limited by the OD stretch vibrational lifetime.
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Affiliation(s)
- Emily E Fenn
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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135
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Falcone RD, Baruah B, Gaidamauskas E, Rithner CD, Correa NM, Silber JJ, Crans DC, Levinger NE. Layered Structure of Room-Temperature Ionic Liquids in Microemulsions by Multinuclear NMR Spectroscopic Studies. Chemistry 2011; 17:6837-46. [DOI: 10.1002/chem.201002182] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 01/26/2011] [Indexed: 11/09/2022]
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136
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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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137
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Esai Selvan M, Calvo-Muñoz E, Keffer DJ. Toward a Predictive Understanding of Water and Charge Transport in Proton Exchange Membranes. J Phys Chem B 2011; 115:3052-61. [DOI: 10.1021/jp1115004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Myvizhi Esai Selvan
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996-2200, United States
| | - Elisa Calvo-Muñoz
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996-2200, United States
| | - David J. Keffer
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996-2200, United States
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 120-749, Republic of Korea
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138
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Furse KE, Corcelli SA. Effects of an unnatural base pair replacement on the structure and dynamics of DNA and neighboring water and ions. J Phys Chem B 2011; 114:9934-45. [PMID: 20614919 DOI: 10.1021/jp105761b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Incorporating small molecule probes into biomolecular systems to report on local structure and dynamics is a powerful strategy that underlies a wide variety of experimental techniques, including fluorescence, electron paramagnetic resonance (EPR), and Forster resonance energy transfer (FRET) measurements. When an unnatural probe is inserted into a protein or DNA, the degree to which the presence of the probe has perturbed the local structure and dynamics it was intended to study is always an important concern. Here, molecular dynamics (MD) simulations are used to systematically study the effect of replacing a DNA base pair with a fluorescent probe, coumarin 102 deoxyriboside, at six unique sites along an A-tract DNA dodecamer. While the overall structure of the DNA oligonucleotide remains intact, replacement of A*T base pairs leads to widespread structural and dynamic perturbations up to four base pairs away from the probe site, including widening of the minor groove and increased DNA flexibility. New DNA conformations, not observed in the native sequence, are sometimes found in the vicinity of the probe and its partner abasic site analog. Strong correlations are demonstrated between DNA surface topology and water mobility.
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Affiliation(s)
- K E Furse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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139
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Zhu R, Lu R, Yu A. Photophysics and locations of IR125 and C152 in AOT reverse micelles. Phys Chem Chem Phys 2011; 13:20844-54. [DOI: 10.1039/c1cp21946d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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140
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Calvo-Muñoz EM, Selvan ME, Xiong R, Ojha M, Keffer DJ, Nicholson DM, Egami T. Applications of a general random-walk theory for confined diffusion. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:011120. [PMID: 21405674 DOI: 10.1103/physreve.83.011120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Indexed: 05/30/2023]
Abstract
A general random walk theory for diffusion in the presence of nanoscale confinement is developed and applied. The random-walk theory contains two parameters describing confinement: a cage size and a cage-to-cage hopping probability. The theory captures the correct nonlinear dependence of the mean square displacement (MSD) on observation time for intermediate times. Because of its simplicity, the theory also requires modest computational requirements and is thus able to simulate systems with very low diffusivities for sufficiently long time to reach the infinite-time-limit regime where the Einstein relation can be used to extract the self-diffusivity. The theory is applied to three practical cases in which the degree of order in confinement varies. The three systems include diffusion of (i) polyatomic molecules in metal organic frameworks, (ii) water in proton exchange membranes, and (iii) liquid and glassy iron. For all three cases, the comparison between theory and the results of molecular dynamics (MD) simulations indicates that the theory can describe the observed diffusion behavior with a small fraction of the computational expense. The confined-random-walk theory fit to the MSDs of very short MD simulations is capable of accurately reproducing the MSDs of much longer MD simulations. Furthermore, the values of the parameter for cage size correspond to the physical dimensions of the systems and the cage-to-cage hopping probability corresponds to the activation barrier for diffusion, indicating that the two parameters in the theory are not simply fitted values but correspond to real properties of the physical system.
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Affiliation(s)
- Elisa M Calvo-Muñoz
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
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141
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Sarangi MK, Dey D, Basu S. Influence of heterogeneity of confined water on photophysical behavior of acridine with amines: a time-resolved fluorescence and laser flash photolysis study. J Phys Chem A 2010; 115:128-35. [PMID: 21155585 DOI: 10.1021/jp107610k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photophysical behavior of acridine (Acr) shows facilitated water-assisted protonation equilibrium between its deprotonted (Acr* ∼ 10 ns) and protonated forms (AcrH(+*) ∼ 28 ns) within confined region of ordered water molecules inside AOT/H(2)O/n-heptane reverse micelles (RMs). The time-resolved-area-normalized-emission spectra confirm both Acr* and AcrH(+*), while time-resolved-emission spectra depict time evolution between them. Quenching of AcrH(+*) with N,N-dimethylaniline (DMA) is a purely diffusion-controlled bimolecular quenching with linear Stern-Volmer (S-V) plot, while nonlinearity arises with triethylamine (TEA) that forms ground state complex with AcrH(+) (AcrH(+)··H(2)O··TEA) indicating both static and dynamic quenching. Transient intermediates, DMA(•+) and AcrH(•) infer photoinduced electron transfer from DMA to Acr, while those from AcrH(+)··H(2)O··TEA complex suggest water mediated excited-state proton transfer (ESPT) between AcrH(+) and TEA. The ESPT becomes faster in larger RMs due to enhanced mobility of hydronium ions in AcrH(+)··H(2)O··TEA, which reduces in smaller RMs as water becomes much more constrained owing to stronger complexation by excess confinement.
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Affiliation(s)
- Manas Kumar Sarangi
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India
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142
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Mamontov E, Faraone A, Hagaman EW, Han KS, Fratini E. A Low-Temperature Crossover in Water Dynamics in an Aqueous LiCl Solution: Diffusion Probed by Neutron Spin−Echo and Nuclear Magnetic Resonance. J Phys Chem B 2010; 114:16737-43. [DOI: 10.1021/jp108497b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. Mamontov
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6473, United States, National Institute of Standards and Technology Center for Neutron Research, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States, Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, United States, and CSGI and Department of
| | - A. Faraone
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6473, United States, National Institute of Standards and Technology Center for Neutron Research, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States, Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, United States, and CSGI and Department of
| | - E. W. Hagaman
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6473, United States, National Institute of Standards and Technology Center for Neutron Research, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States, Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, United States, and CSGI and Department of
| | - K. S. Han
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6473, United States, National Institute of Standards and Technology Center for Neutron Research, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States, Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, United States, and CSGI and Department of
| | - E. Fratini
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6473, United States, National Institute of Standards and Technology Center for Neutron Research, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States, Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, United States, and CSGI and Department of
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143
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Wojciechowski M, Szymczak P, Cieplak M. The influence of hydrodynamic interactions on protein dynamics in confined and crowded spaces-assessment in simple models. Phys Biol 2010; 7:046011. [PMID: 21119219 DOI: 10.1088/1478-3975/7/4/046011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We consider several systems that are confined within a softly repulsive sphere. The first one is a model protein, crambin, which is described by a structure-based coarse grained model. We demonstrate that the folding process is accelerated by the hydrodynamic interactions (HI) in a way that depends on the radius of the sphere. The tighter the encompassing sphere, the smaller the effect, independent of the nature of the starting conformations. The second system is a protein surrounded by protein-like softly repulsive spheres that make the confined space crowded. In this case, the HI shorten the folding times in a way which depends on the degree of crowdedness only weakly. The third system is a collection of spheres that are meant to represent molecules. We show that confinement increases association times. We also observe that the HI either facilitate or obstruct association of two spheres depending on the crowding conditions. The dependence of the association time on crowdedness in the confining sphere is qualitatively distinct from that derived by Wieczorek and Zielenkiewicz for a cube with the periodic boundary conditions.
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144
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Rather SR, Yadav R, Sen P. Microviscosity inside a nanocavity: a femtosecond fluorescence up-conversion study of malachite green. J Phys Chem B 2010; 114:13988-94. [PMID: 20949966 DOI: 10.1021/jp1037238] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Femtosecond fluorescence up-conversion measurements of malachite green (MG) have been carried out to confirm the relaxation pathway and subsequently to probe the microviscosity of water trapped in a nanoconfined environment using an AOT (sodium dioctylsulfosuccinate, aerosol-OT) reverse micelle as a model system. The experimental results reveal a strong dependence of S(1) state relaxation dynamics of MG on solvent viscosity while a very weak dependence has been observed for the S(2) state relaxation. The time-dependent density functional theory (TD-DFT) calculations have been used to construct potential energy surfaces of MG by pursuing an intramolecular rotation along the torsional coordinate of the phenyl rings. On synchronization with the experimental observations, the computational results comprehend the existence of a conical intersection along the S(1) and S(0) potential energy surfaces, which leads to mixed vibrational levels of S(1) and S(0) characteristics. The results suggest that the conical intersection is along the torsional coordinate of N,N-dimethyl substituted phenyl ring. Correlating the observed dynamics of MG in a confined system with the relaxation time of MG in different glycerol-water mixtures, we assert the determination of the microviscosity of water inside the AOT reverse micelle. The data confer that the microviscosity of water in an AOT water pool of w(0) = 2 (9 cP) is almost 9 times higher than the bulk water. As we increase the w(0) from 2 to 40, the microviscosity decreases monotonically to 5.68 cP, and the decrease is observed to be exponential in nature.
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Affiliation(s)
- Shahnawaz R. Rather
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208 016, UP, India
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145
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Debnath A, Mukherjee B, Ayappa KG, Maiti PK, Lin ST. Entropy and dynamics of water in hydration layers of a bilayer. J Chem Phys 2010; 133:174704. [DOI: 10.1063/1.3494115] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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146
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Vodolazkaya NA, Mchedlov-Petrossyan NO, Salamanova NV, Surov YN, Doroshenko AO. Molecular spectroscopy studies of solvent properties of dispersed ‘water pools’: Fluorescein and 2,7-dichlorofluorescein in reversed AOT-based microemulsions. J Mol Liq 2010. [DOI: 10.1016/j.molliq.2010.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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147
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Acik M, Mattevi C, Gong C, Lee G, Cho K, Chhowalla M, Chabal YJ. The role of intercalated water in multilayered graphene oxide. ACS NANO 2010; 4:5861-5868. [PMID: 20886867 DOI: 10.1021/nn101844t] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A detailed in situ infrared spectroscopy analysis of single layer and multilayered graphene oxide (GO) thin films reveals that the normalized infrared absorption in the carbonyl region is substantially higher in multilayered GO upon mild annealing. These results highlight the fact that the reduction chemistry of multilayered GO is dramatically different from the single layer GO due to the presence of water molecules confined in the ∼1 nm spacing between sheets. IR spectroscopy, XPS analysis, and DFT calculations all confirm that the water molecules play a significant role interacting with basal plane etch holes through passivation, via evolution of CO(2) leading to the formation of ketone and ester carbonyl groups. Displacement of water from intersheet spacing with alcohol significantly changes the chemistry of carbonyl formation with temperature.
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Affiliation(s)
- Muge Acik
- Department of Materials Science and Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
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148
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Asaro F, Benedetti A, Freris I, Riello P, Savko N. Evolution of the nonionic inverse microemulsion-acid-TEOS system during the synthesis of nanosized silica via the sol-gel process. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:12917-12925. [PMID: 20604556 DOI: 10.1021/la101737x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The cyclohexane-igepal inverse microemulsion, comprehensively established for the synthesis of silica nanoparticles in an ammonia-catalyzed sol-gel process, was alternatively studied with an acid-catalyzed sol-gel process. Tetraethyl orthosilicate (TEOS) was used as the silica precursor, while two different aqueous phases containing either HNO(3) or HCl at two different concentrations, 0.1 and 0.05 M, were examined in the presence and in the absence of NaF, a catalyst of the condensation step. The evolution of the overall reacting system, specifically hydrolysis and polycondensation of reaction intermediates, was monitored in situ by time-resolved small-angle X-ray scattering. No size variation of the inverse micelles was detected throughout the sol-gel process. Conversely, the density of the micellar core increased after a certain time interval, indicating the presence of the polycondensation product. The IR spectra of the reacting mixture were in agreement with such a hypothesis. (1)H and (13)C NMR measurements provided information on the soluble species, the surfactant, and TEOS. The TEOS consumption was well fitted by means of an exponential decay, suggesting that a first-order kinetics for TEOS transpires in the various systems examined, with rate constants dependent not only on the acid concentration but also on its nature (anion specific effect), on the presence of NaF, and on the amount of water in the core of the inverse micelle. The self-diffusion coefficients, determined by means of PGSTE NMR, proved that a sizable amount of the byproduct ethanol was partitioned inside the inverse micelles. Characterization of the final product was carried out by means of thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and transmission electron microscopy (TEM), which concurrently confirmed that the silica isolated from the inverse nonionic microemulsion is not significantly different from the product of a bulk acid-catalyzed sol-gel synthesis. TEM micrographs illustrated particles with diameters smaller than the diameter of the inverse micelles as determined by SAXS, due to a shrinkage effect, in addition to nanostructured aggregates in the range 20-100 nm.
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Affiliation(s)
- F Asaro
- Department of Chemical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy.
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149
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Nagata Y, Mukamel S. Vibrational sum-frequency generation spectroscopy at the water/lipid interface: molecular dynamics simulation study. J Am Chem Soc 2010; 132:6434-42. [PMID: 20394423 PMCID: PMC3151577 DOI: 10.1021/ja100508n] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sum-frequency generation (SFG) spectrum from the water/[1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine] (DMPC) interface in the OH stretching mode region of water is simulated and shows three spectral peaks which are assigned to different environments. The weak 3590 cm(-1) peak is attributed to a few water molecules coupled to the glycerol backbone of DMCP. The 3470 cm(-1) feature comes from the top water layer adjacent to the hydrophilic headgroup of DMPC. The 3290 cm(-1) peak arises from the near-bulk water nonadjacent to DMPC. The stretching mode corresponding to the 3290 cm(-1) peak is strongly coupled to the neighboring water molecules. In contrast, the 3470 cm(-1) mode is decoupled from the surrounding water molecules, and the orientation of water is governed by DMPC. This decoupling explains the slow relaxation dynamics of water measured in the time-resolved SFG experiment. Despite the similarity of the SFG spectra, the peak origins of water/lipid and water/vapor interfaces are different.
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Affiliation(s)
- Yuki Nagata
- University of California Irvine, Irvine, California, 92617, USA
| | - Shaul Mukamel
- University of California Irvine, Irvine, California, 92617, USA
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150
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Sasmal DK, Mojumdar SS, Adhikari A, Bhattacharyya K. Deuterium Isotope Effect on Femtosecond Solvation Dynamics in an Ionic Liquid Microemulsion: An Excitation Wavelength Dependence Study. J Phys Chem B 2010; 114:4565-71. [DOI: 10.1021/jp910948w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dibyendu Kumar Sasmal
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Supratik Sen Mojumdar
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Aniruddha Adhikari
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Kankan Bhattacharyya
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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