1
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Jang T, Lee S, Pang Y. Anomalous proton transfer of a photoacid HPTS in nonaqueous reverse micelles. Phys Chem Chem Phys 2024; 26:11283-11294. [PMID: 38456549 DOI: 10.1039/d3cp05710k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The proton transfer reaction is one of the fundamental chemical reactions where the reaction dynamics strongly depend on solvent properties such as acidity or basicity. A photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS) shows a sharp decrease of pKa (7.7 → 0.5) upon photoexcitation, and the excited-state proton transfer (ESPT) occurs with ultrafast time constants of 2.5 and 89 ps in bulk aqueous solution. However, the two-step proton transfers via the contact ion pair formation and the proton diffusion are strongly limited inside the nanopools of reverse micelles (RMs). The confinement in small RMs strongly impeded the proton transfer reactions. In this work, we report the ESPT of HPTS confined in methanol-in-oil RMs by steady-state and time-resolved electronic spectroscopy. Interestingly, HPTS shows substantial deprotonation in the excited state only in small RMs, while the ESPT of HPTS does not occur in bulk methanol solution due to the low basicity of aliphatic alcohols. The kinetic analysis of time-resolved fluorescence and transient absorption measurements will compare the proton transfer dynamics of HPTS in the water-in-oil and methanol-in-oil RMs. The ESPT of photoacids, especially in the nonaqueous RMs, can be crucial in understanding many important chemical reactions involving proton transfer in the confined environments of cells and membranes.
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Affiliation(s)
- Taehyung Jang
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.
| | - Sebok Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.
| | - Yoonsoo Pang
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.
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2
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Vuorte M, Lokka A, Scacchi A, Sammalkorpi M. Dioctyl sodium sulfosuccinate surfactant self-assembly dependency of solvent hydrophilicity: a modelling study. Phys Chem Chem Phys 2023; 25:27250-27263. [PMID: 37791412 DOI: 10.1039/d3cp02173d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The self-assembly of dioctyl sodium sulfosuccinate (AOT) model surfactant in solvent environments of differing polarity is examined by means of dissipative particle dynamics (DPD) bead model parametrized against Hildebrand solubility parameters from atomistic molecular dynamics (MD) simulations. The model predicts that in hydrophobic solvents (e.g. dodecane) the surfactant forms small (Nagg ∼ 8) reverse micellar aggregates, while in a solvent corresponding to water lamellar assembly takes place, in good agreement with literature structural parameters. Interestingly, solvents of intermediate polarity lead to formation of large, internally structured aggregates. In these, the surfactant headgroups cluster within the aggregate, surrounded by a continuous phase formed by the hydrocarbon tails. We show that the partitioning of the headgroups between the aggregate surface layer and the inner clustered phase depends primarily on solvent polarity, and can be controlled by the solvent, but also system composition. Finally, we compare the DPD assembly response to simplified effective interaction potentials derived at dilute concentration limit for the interactions. The comparison reveals that the simplified effective potential descriptions provide good level of insight on the assembly morphologies, despite drastic, isotropic interactions simplification involved.
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Affiliation(s)
- Maisa Vuorte
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Aapo Lokka
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Alberto Scacchi
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Applied Physics, School of Science, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
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3
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Dynamics in tris(pentafluoroethyl)trifluorophosphate (FAP) anion based ionic liquids: A 2D-IR study with tungsten hexacarbonyl. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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5
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Bhat A, Harris MT, Jaeger VW. Structural Insights into Self-Assembled Aerosol-OT Aggregates in Aqueous Media Using Atomistic Molecular Dynamics. J Phys Chem B 2021; 125:13789-13803. [PMID: 34898216 DOI: 10.1021/acs.jpcb.1c07136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In water, the surfactant dioctyl sulfosuccinate (Aerosol-OT or AOT) exhibits diverse aggregate structures, ranging from micelles to lamella. An atomic-level understanding, however, of the formation and structure of these aggregates is lacking. Herein, using atomistic molecular dynamics (MD) with microsecond-long simulations, self-assembly of AOT in water is studied for concentrations of 1, 7.2, and 20 wt % at 293 K and for 7.2 wt % at 353 K. Assembly proceeds through stepwise association and dissociation of single AOT molecules, and the fusion and fission of AOT clusters. At 293 K, AOT self-assembles into either (i) spherical micelles (1 wt %), (ii) biphasic systems consisting of rod-like and prolate spheroidal micelles (7.2 wt %), or (iii) bilayers (20 wt %). We hypothesize that the observed rod-like structure is a precursor to lamellar microdomains found experimentally in biphasic dispersions. Increasing temperature to 353 K at 7.2 wt % results in a system consisting of prolate micelles but no rod-like micelles. Simulated phase behavior agrees with previously published experimental observations. Individual aggregates formed during self-assembly are identified using graph theory. Structural metrics of these aggregates like the radius of gyration, shape anisotropy, and prolateness are presented. Trends in structural metrics quantitatively reflect how shapes and sizes of AOT aggregates vary with surfactant concentration and temperature. These simulations provide deeper insight into open questions in the scientific community and demonstrate a method to generate physics-based micelle structures that can be used to rationalize experimental observations.
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Affiliation(s)
- Anuradha Bhat
- Division of Environmental and Ecological Engineering, Purdue University, Potter Engineering Center, 500 Central Drive, West Lafayette, Indiana 47907, United States
| | - Michael T Harris
- Davidson School of Chemical Engineering, Purdue University, Forney Hall of Chemical Engineering 1060, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Vance W Jaeger
- Department of Chemical Engineering, University of Louisville, Ernst Hall, Room 312, 216 Eastern Parkway, Louisville, Kentucky 40292, United States
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6
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Dutta R, Ghosh M, Pyne A, Sarkar N. Insight into the Dynamics of Different Fluorophores in the Interior of Aerosol OT Lamellar Structures in the Presence of Sugars: From Picosecond-to-Femtosecond Study. J Phys Chem B 2018; 123:117-129. [DOI: 10.1021/acs.jpcb.8b10609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rupam Dutta
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Meghna Ghosh
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Arghajit Pyne
- 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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7
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Kiefer LM, Kubarych KJ. Two-dimensional infrared spectroscopy of coordination complexes: From solvent dynamics to photocatalysis. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Zang J, Feng M, Zhao J, Wang J. Micellar and bicontinuous microemulsion structures show different solute–solvent interactions: a case study using ultrafast nonlinear infrared spectroscopy. Phys Chem Chem Phys 2018; 20:19938-19949. [DOI: 10.1039/c8cp01024b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Using aqueous and organic probes to simultaneously explore the structural dynamics of reverse micellar and bicontinuous microemulsion structures.
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Affiliation(s)
- Jinger Zang
- Beijing National Laboratory for Molecular Sciences
- Molecular Reaction Dynamics Laboratory
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Minjun Feng
- Beijing National Laboratory for Molecular Sciences
- Molecular Reaction Dynamics Laboratory
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences
- Molecular Reaction Dynamics Laboratory
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences
- Molecular Reaction Dynamics Laboratory
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
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9
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Kundu A, Verma PK, Cho M. Role of Solvent Water in the Temperature-Induced Self-Assembly of a Triblock Copolymer. J Phys Chem Lett 2017; 8:3040-3047. [PMID: 28613892 DOI: 10.1021/acs.jpclett.7b01008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Water-soluble triblock copolymers have received much attention in industrial applications and scientific fields. We here show that femtosecond mid-IR pump-probe spectroscopy is useful to study the role of water in the temperature-induced self-assembly of triblock copolymers. Our experimental results suggest two distinct subpopulations of water molecules: those that interact with other water molecules and those involved in the hydration of a triblock copolymer surface. We find that the vibrational dynamics of bulk-like water is not affected by either micellation or gelation of triblock copolymers. The increased population of water interacting with ether oxygen atoms of the copolymer during the unimer to micelle phase transition is important evidence for the entropic role of water in temperature-induced micelle formation at a low copolymer concentration. In contrast, at the critical gelation temperature and beyond, the population of surface-associated water molecules interacting with ether oxygen atoms decreases, which indicates important enthalpic control by water. The present study on the roles of water in the two different phase transitions of triblock copolymers sheds new light on the underlying mechanisms of temperature-induced self-aggregation behaviors of amphiphiles that are ubiquitous in nature.
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Affiliation(s)
- Achintya Kundu
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Pramod Kumar Verma
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
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10
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Welbourn RJL, Bartholomew F, Gutfreund P, Clarke SM. Neutron Reflectometry of an Anionic Surfactant at the Solid-Liquid Interface under Shear. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:5982-5990. [PMID: 28530832 DOI: 10.1021/acs.langmuir.7b00530] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Neutron reflectometry with in situ rheology is used to measure the shear response of an adsorbed anionic surfactant (sodium bis(2-ethylhexyl) sulfosuccinate, AOT) at the alumina-water interface. A low surfactant concentration is measured where a single bilayer adsorbs at the interface as well as a higher concentration where a multilamellar structure forms. The low concentration structure does not change with the imposed shear (oscillatory or steady). However, the lamellar phase shows a loss of structure under both steady and oscillatory shear. There are differences between the steady and oscillatory cases, which are discussed, with both showing a strong dependence on the strain amplitude.
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Affiliation(s)
- Rebecca J L Welbourn
- BP Institute and Department of Chemistry, University of Cambridge , Madingley Rise, Madingley Road, Cambridge, U.K
| | - Felicity Bartholomew
- BP Institute and Department of Chemistry, University of Cambridge , Madingley Rise, Madingley Road, Cambridge, U.K
| | | | - Stuart M Clarke
- BP Institute and Department of Chemistry, University of Cambridge , Madingley Rise, Madingley Road, Cambridge, U.K
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11
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Nishida J, Yan C, Fayer MD. Enhanced nonlinear spectroscopy for monolayers and thin films in near-Brewster’s angle reflection pump-probe geometry. J Chem Phys 2017. [DOI: 10.1063/1.4977508] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Jun Nishida
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Chang Yan
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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12
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Roy S, Skoff D, Perroni DV, Mondal J, Yethiraj A, Mahanthappa MK, Zanni MT, Skinner JL. Water Dynamics in Gyroid Phases of Self-Assembled Gemini Surfactants. J Am Chem Soc 2016; 138:2472-5. [DOI: 10.1021/jacs.5b12370] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Santanu Roy
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - David Skoff
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Dominic V. Perroni
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Jagannath Mondal
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Mahesh K. Mahanthappa
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - James L. Skinner
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
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13
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Abstract
Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.
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Affiliation(s)
- Amanda L Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405, USA.
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14
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Welbourn RJL, Lee SY, Gutfreund P, Hughes A, Zarbakhsh A, Clarke SM. Neutron reflection study of the adsorption of the phosphate surfactant NaDEHP onto alumina from water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3377-84. [PMID: 25761046 DOI: 10.1021/la504837s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The adsorption of a phosphorus analogue of the surfactant AOT, sodium bis(2-ethylhexyl) phosphate (NaDEHP), at the water/alumina interface is described. The material is found to adsorb as an essentially water-free bilayer from neutron reflection measurements. This is similar to the behavior of AOT under comparable conditions, although AOT forms a thicker, more hydrated layer. The NaDEHP shows rather little variation with added salt, but a small thickening of the layer on increasing the pH, in contrast to the behavior of AOT.
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Affiliation(s)
- Rebecca J L Welbourn
- †BP Institute and Department of Chemistry, University of Cambridge, Madingley Rise, Madingley Road, Cambridge, UK
| | - Seung Yeon Lee
- †BP Institute and Department of Chemistry, University of Cambridge, Madingley Rise, Madingley Road, Cambridge, UK
| | | | - Arwel Hughes
- §ISIS, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, UK
| | | | - Stuart M Clarke
- †BP Institute and Department of Chemistry, University of Cambridge, Madingley Rise, Madingley Road, Cambridge, UK
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15
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Cai K, Du F, Liu J, Su T. Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:701-710. [PMID: 25260065 DOI: 10.1016/j.saa.2014.08.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/05/2014] [Accepted: 08/24/2014] [Indexed: 06/03/2023]
Abstract
The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the CO bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China.
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Jia Liu
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Tingting Su
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
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16
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Maj M, Ahn C, Kossowska D, Park K, Kwak K, Han H, Cho M. β-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes. Phys Chem Chem Phys 2015; 17:11770-8. [DOI: 10.1039/c5cp00454c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump–probe spectroscopy.
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Affiliation(s)
- Michał Maj
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
| | - Changwoo Ahn
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
| | - Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
| | - Kwanghee Park
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
| | - Kyungwon Kwak
- Department of Chemistry
- Chung-Ang University
- Seoul 156-756, Korea
| | - Hogyu Han
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
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17
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Peran I, Oudenhoven T, Woys AM, Watson M, Zhang TO, Carrico I, Zanni MT, Raleigh DP. General strategy for the bioorthogonal incorporation of strongly absorbing, solvation-sensitive infrared probes into proteins. J Phys Chem B 2014; 118:7946-53. [PMID: 24749542 PMCID: PMC4317048 DOI: 10.1021/jp5008279] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/19/2014] [Indexed: 11/28/2022]
Abstract
A high-sensitivity metal-carbonyl-based IR probe is described that can be incorporated into proteins or other biomolecules in very high yield via Click chemistry. A two-step strategy is demonstrated. First, a methionine auxotroph is used to incorporate the unnatural amino acid azidohomoalanine at high levels. Second, a tricarbonyl (η(5)-cyclopentadienyl) rhenium(I) probe modified with an alkynyl linkage is coupled via the Click reaction. We demonstrate these steps using the C-terminal domain of the ribosomal protein L9 as a model system. An overall incorporation level of 92% was obtained at residue 109, which is a surface-exposed residue. Incorporation of the probe into a surface site is shown not to perturb the stability or structure of the target protein. Metal carbonyls are known to be sensitive to solvation and protein electrostatics through vibrational lifetimes and frequency shifts. We report that the frequencies and lifetimes of this probe also depend on the isotopic composition of the solvent. Comparison of the lifetimes measured in H2O versus D2O provides a probe of solvent accessibility. The metal carbonyl probe reported here provides an easy and robust method to label very large proteins with an amino-acid-specific tag that is both environmentally sensitive and a very strong absorber.
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Affiliation(s)
- Ivan Peran
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Tracey Oudenhoven
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396, United States
| | - Ann Marie Woys
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396, United States
| | - Matthew
D. Watson
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Tianqi O. Zhang
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396, United States
| | - Isaac Carrico
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396, United States
| | - Daniel P. Raleigh
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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18
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Fogarty A, Laage D. Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation. J Phys Chem B 2014; 118:7715-29. [PMID: 24479585 PMCID: PMC4103960 DOI: 10.1021/jp409805p] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 12/27/2013] [Indexed: 02/08/2023]
Abstract
Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.
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Affiliation(s)
- Aoife
C. Fogarty
- Department
of Chemistry, UMR ENS-CNRS-UPMC 8640, École
Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
| | - Damien Laage
- Department
of Chemistry, UMR ENS-CNRS-UPMC 8640, École
Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
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19
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Kel O, Tamimi A, Fayer MD. The Influence of Cholesterol on Fast Dynamics Inside of Vesicle and Planar Phospholipid Bilayers Measured with 2D IR Spectroscopy. J Phys Chem B 2014; 119:8852-62. [DOI: 10.1021/jp503940k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Oksana Kel
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Amr Tamimi
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
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20
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Novel polymer-free iridescent lamellar hydrogel for two-dimensional confined growth of ultrathin gold membranes. Nat Commun 2014; 5:3313. [DOI: 10.1038/ncomms4313] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 01/22/2014] [Indexed: 11/08/2022] Open
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21
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Agzenai Y, Lindman B, Alfredsson V, Topgaard D, Renamayor CS, Pacios IE. In Situ X-ray Polymerization: From Swollen Lamellae to Polymer–Surfactant Complexes. J Phys Chem B 2014; 118:1159-67. [DOI: 10.1021/jp411894e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yahya Agzenai
- Dpt. CC
y TT Fisicoquímicas, Facultad de Ciencias, UNED, P° Senda
del Rey 9, 28040 Madrid, Spain
- Physical Chemistry, Lund University, Box
124, SE-221 00 Lund, Sweden
| | - Björn Lindman
- Physical Chemistry, Lund University, Box
124, SE-221 00 Lund, Sweden
| | - Viveka Alfredsson
- Physical Chemistry, Lund University, Box
124, SE-221 00 Lund, Sweden
| | - Daniel Topgaard
- Physical Chemistry, Lund University, Box
124, SE-221 00 Lund, Sweden
| | - Carmen S. Renamayor
- Dpt. CC
y TT Fisicoquímicas, Facultad de Ciencias, UNED, P° Senda
del Rey 9, 28040 Madrid, Spain
| | - Isabel E. Pacios
- Dpt. CC
y TT Fisicoquímicas, Facultad de Ciencias, UNED, P° Senda
del Rey 9, 28040 Madrid, Spain
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22
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Mukherjee SS, Skoff DR, Middleton CT, Zanni MT. Fully absorptive 3D IR spectroscopy using a dual mid-infrared pulse shaper. J Chem Phys 2013; 139:144205. [PMID: 24116612 PMCID: PMC4108792 DOI: 10.1063/1.4824638] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/25/2013] [Indexed: 12/27/2022] Open
Abstract
This paper presents the implementation of 3D IR spectroscopy by adding a second pump beam to a two-beam 2D IR spectrometer. An independent mid-IR pulse shaper is used for each pump beam, which can be programmed to collect its corresponding dimension in either the frequency or time-domains. Due to the phase matching geometry employed here, absorptive 3D IR spectra are automatically obtained, since all four of the rephasing and non-rephasing signals necessary to generate absorptive spectra are collected simultaneously. Phase cycling is used to isolate the fifth-order from the third-order signals. The method is demonstrated on tungsten hexacarbonyl (W(CO)6) and dicarbonylacetylacetonato rhodium (I), for which the eigenstates are extracted up to the third excited state. Pulse shaping affords a high degree of control over 3D IR experiments by making possible mixed time- and frequency-domain experiments, fast data acquisition and straightforward implementation.
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Affiliation(s)
- Sudipta S Mukherjee
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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23
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Bakulin AA, Cringus D, Pieniazek PA, Skinner JL, Jansen TLC, Pshenichnikov MS. Dynamics of water confined in reversed micelles: multidimensional vibrational spectroscopy study. J Phys Chem B 2013; 117:15545-58. [PMID: 23980543 DOI: 10.1021/jp405853j] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Here we perform a comprehensive study of ultrafast molecular and vibrational dynamics of water confined in small reversed micelles (RMs). The molecular picture is elucidated with two-dimensional infrared (2D IR) spectroscopy of water OH stretch vibrations and molecular dynamics simulations, bridged by theoretical calculations of linear and 2D IR vibrational spectra. To investigate the effects of intermolecular coupling, experiments and modeling are performed for isotopically diluted (HDO in D2O) and undiluted (H2O) water. We put a separation of water inside RMs into two subensembles (water-bound and surfactant-bound molecules), observed by many before, on a solid theoretical basis. Water molecules fully attached to the lipid interface ("shell" water) are decoupled from one another and from the central water nanopool ("core" water). The environmental fluctuations are largely "frozen" for the shell water, while the core waters demonstrate much faster dynamics but still not as fast as in the bulk case. A substantial nanoconfinement effect on the dynamics of the core water is observed after disentanglement of the shell water contribution, which is fully confirmed by the simulations of 2D IR spectra. Current results provide new insights into interaction between biological objects like membranes or proteins with the surrounding aqueous bath, and highlight peculiarities in vibrational energy redistribution near the lipid surface.
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Affiliation(s)
- Artem A Bakulin
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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24
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Zhang Z, Wells KL, Seidel MT, Tan HS. Fifth-order three-dimensional electronic spectroscopy using a pump-probe configuration. J Phys Chem B 2013; 117:15369-85. [PMID: 23808641 DOI: 10.1021/jp4046403] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the theoretical details and experimental demonstration of fifth-order three-dimensional (3D) electronic spectroscopy using a pump-probe beam geometry. This is achieved using a pulse shaper and appropriate phase cycling schemes. We show how 8-step and 27-step phase cycling schemes can measure purely absorptive 3D spectra as well as 3D spectra for the individual fifth-order processes that contribute to the purely absorptive spectrum. 3D spectra as a function of two separate controllable waiting time periods can be obtained. The peak shapes and positions of the peaks in the experimental measurement correspond well to theory.
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Affiliation(s)
- Zhengyang Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University , 21 Nanyang Link, Singapore 637371
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25
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Kel O, Tamimi A, Thielges MC, Fayer MD. Ultrafast Structural Dynamics Inside Planar Phospholipid Multibilayer Model Cell Membranes Measured with 2D IR Spectroscopy. J Am Chem Soc 2013; 135:11063-74. [DOI: 10.1021/ja403675x] [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)
- Oksana Kel
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Amr Tamimi
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Megan C. Thielges
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
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