1
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Gómez S, Bottari C, Egidi F, Giovannini T, Rossi B, Cappelli C. Amide Spectral Fingerprints are Hydrogen Bonding-Mediated. J Phys Chem Lett 2022; 13:6200-6207. [PMID: 35770492 PMCID: PMC9272440 DOI: 10.1021/acs.jpclett.2c01277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The origin of the peculiar amide spectral features of proteins in aqueous solution is investigated, by exploiting a combined theoretical and experimental approach to study UV Resonance Raman (RR) spectra of peptide molecular models, namely N-acetylglycine-N-methylamide (NAGMA) and N-acetylalanine-N-methylamide (NALMA). UVRR spectra are recorded by tuning Synchrotron Radiation at several excitation wavelengths and modeled by using a recently developed multiscale protocol based on a polarizable QM/MM approach. Thanks to the unparalleled agreement between theory and experiment, we demonstrate that specific hydrogen bond interactions, which dominate hydration dynamics around these solutes, play a crucial role in the selective enhancement of amide signals. These results further argue the capability of vibrational spectroscopy methods as valuable tools for refined structural analysis of peptides and proteins in aqueous solution.
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Affiliation(s)
- Sara Gómez
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Cettina Bottari
- Elettra
Sincrotrone Trieste S.C.p.A., S. S. 14 Km 163.5 in Area Science Park, I-34149, Trieste, Italy
| | - Franco Egidi
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Tommaso Giovannini
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Barbara Rossi
- Elettra
Sincrotrone Trieste S.C.p.A., S. S. 14 Km 163.5 in Area Science Park, I-34149, Trieste, Italy
- Department
of Physics, University of Trento, via Sommarive 14, I-38123 Povo, Trento, Italy
| | - Chiara Cappelli
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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2
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Lupi L, Bracco B, Sassi P, Corezzi S, Morresi A, Fioretto D, Comez L, Paolantoni M. Hydration Dynamics of Model Peptides with Different Hydrophobic Character. Life (Basel) 2022; 12:life12040572. [PMID: 35455063 PMCID: PMC9031890 DOI: 10.3390/life12040572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022] Open
Abstract
The multi-scale dynamics of aqueous solutions of the hydrophilic peptide N-acetyl-glycine-methylamide (NAGMA) have been investigated through extended frequency-range depolarized light scattering (EDLS), which enables the broad-band detection of collective polarizability anisotropy fluctuations. The results have been compared to those obtained for N-acetyl-leucinemethylamide (NALMA), an amphiphilic peptide which shares with NAGMA the same polar backbone, but also contains an apolar group. Our study indicates that the two model peptides induce similar effects on the fast translational dynamics of surrounding water. Both systems slow down the mobility of solvating water molecules by a factor 6–8, with respect to the bulk. Moreover, the two peptides cause a comparable far-reaching spatial perturbation extending to more than two hydration layers in diluted conditions. The observed concentration dependence of the hydration number is explained considering the random superposition of different hydration shells, while no indication of solute aggregation phenomena has been found. The results indicate that the effect on the dynamics of water solvating the amphiphilic peptide is dominated by the hydrophilic backbone. The minor impact of the hydrophobic moiety on hydration features is consistent with structural findings derived by Fourier transform infrared (FTIR) measurements, performed in attenuated total reflectance (ATR) configuration. Additionally, we give evidence that, for both systems, the relaxation mode in the GHz frequency range probed by EDLS is related to solute rotational dynamics. The rotation of NALMA occurs at higher timescales, with respect to the rotation of NAGMA; both processes are significantly slower than the structural dynamics of hydration water, suggesting that solute and solvent motions are uncoupled. Finally, our results do not indicate the presence of super-slow water (relaxation times in the order of tens of picoseconds) around the peptides investigated.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, 00146 Rome, Italy;
| | - Brenda Bracco
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (S.C.); (D.F.)
| | - Assunta Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Daniele Fioretto
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (S.C.); (D.F.)
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 060123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 060123 Perugia, Italy
- Correspondence: (L.C.); (M.P.)
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
- Correspondence: (L.C.); (M.P.)
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3
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Laity PR, Holland C. Seeking Solvation: Exploring the Role of Protein Hydration in Silk Gelation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020551. [PMID: 35056868 PMCID: PMC8781151 DOI: 10.3390/molecules27020551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 02/05/2023]
Abstract
The mechanism by which arthropods (e.g., spiders and many insects) can produce silk fibres from an aqueous protein (fibroin) solution has remained elusive, despite much scientific investigation. In this work, we used several techniques to explore the role of a hydration shell bound to the fibroin in native silk feedstock (NSF) from Bombyx mori silkworms. Small angle X-ray and dynamic light scattering (SAXS and DLS) revealed a coil size (radius of gyration or hydrodynamic radius) around 12 nm, providing considerable scope for hydration. Aggregation in dilute aqueous solution was observed above 65 °C, matching the gelation temperature of more concentrated solutions and suggesting that the strength of interaction with the solvent (i.e., water) was the dominant factor. Infrared (IR) spectroscopy indicated decreasing hydration as the temperature was raised, with similar changes in hydration following gelation by freezing or heating. It was found that the solubility of fibroin in water or aqueous salt solutions could be described well by a relatively simple thermodynamic model for the stability of the protein hydration shell, which suggests that the affected water is enthalpically favoured but entropically penalised, due to its reduced (vibrational or translational) dynamics. Moreover, while the majority of this investigation used fibroin from B. mori, comparisons with published work on silk proteins from other silkworms and spiders, globular proteins and peptide model systems suggest that our findings may be of much wider significance.
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4
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Corezzi S, Bracco B, Sassi P, Paolantoni M, Comez L. Protein Hydration in a Bioprotecting Mixture. Life (Basel) 2021; 11:life11100995. [PMID: 34685367 PMCID: PMC8537178 DOI: 10.3390/life11100995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/10/2021] [Accepted: 09/18/2021] [Indexed: 11/16/2022] Open
Abstract
We combined broad-band depolarized light scattering and infrared spectroscopies to study the properties of hydration water in a lysozyme-trehalose aqueous solution, where trehalose is present above the concentration threshold (30% in weight) relevant for biopreservation. The joint use of the two different techniques, which were sensitive to inter-and intra-molecular degrees of freedom, shed new light on the molecular mechanism underlying the interaction between the three species in the mixture. Thanks to the comparison with the binary solution cases, we were able to show that, under the investigated conditions, the protein, through preferential hydration, remains strongly hydrated even in the ternary mixture. This supported the water entrapment scenario, for which a certain amount of water between protein and sugar protects the biomolecule from damage caused by external agents.
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Affiliation(s)
- Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy;
| | - Brenda Bracco
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.)
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.)
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.)
- Correspondence: (M.P.); (L.C.)
| | - Lucia Comez
- CNR-IOM at Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy
- Correspondence: (M.P.); (L.C.)
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5
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Liu H, Xiang S, Zhu H, Li L. The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation. Molecules 2021; 26:molecules26175403. [PMID: 34500836 PMCID: PMC8434405 DOI: 10.3390/molecules26175403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/01/2022] Open
Abstract
The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.
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Affiliation(s)
- Hangxin Liu
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
| | - Shuqing Xiang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
| | - Haomiao Zhu
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
- Correspondence: (H.Z.); (L.L.)
| | - Li Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
- Correspondence: (H.Z.); (L.L.)
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6
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Stasiulewicz M, Panuszko A, Śmiechowski M, Bruździak P, Maszota P, Stangret J. Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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7
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Tan P, Huang J, Mamontov E, García Sakai V, Merzel F, Liu Z, Ye Y, Hong L. Decoupling between the translation and rotation of water in the proximity of a protein molecule. Phys Chem Chem Phys 2020; 22:18132-18140. [PMID: 32761039 DOI: 10.1039/d0cp02416c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The interaction between water and biomacromolecules is of fundamental interest in biophysics, biochemistry and physical chemistry. By combining neutron scattering and molecular dynamics simulations on a perdeuterated protein at a series of hydration levels, we demonstrated that the translational motion of water is slowed down more significantly than its rotation, when water molecules approach the protein molecule. Further analysis of the simulation trajectories reveals that the observed decoupling results from the fact that the translational motion of water is more correlated over space and more retarded by the charged/polar residues and spatial confinement on the protein surface, than the rotation. Moreover, around the stable protein residues (with smaller atomic fluctuations), water exhibits more decoupled dynamics, indicating a connection between the observed translation-rotation decoupling in hydration water and the local stability of the protein molecule.
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Affiliation(s)
- Pan Tan
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Eugene Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Victoria García Sakai
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, UK
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, SI 1000 Ljubljana, Slovenia
| | - Zhuo Liu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yiyang Ye
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Yahya A, Tan L, Perticaroli S, Mamontov E, Pajerowski D, Neuefeind J, Ehlers G, Nickels JD. Molecular origins of bulk viscosity in liquid water. Phys Chem Chem Phys 2020; 22:9494-9502. [DOI: 10.1039/d0cp01560a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The shear viscous response of water is closely associated with changes in network connectivity on the sub ps timescale. The bulk viscous response is shown here to be associated with local density fluctuations and rotational motion around 1–3 ps.
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Affiliation(s)
- Ahmad Yahya
- Department of Chemical and Environmental Engineering
- University of Cincinnati
- Cincinnati
- USA
| | - Luoxi Tan
- Department of Chemical and Environmental Engineering
- University of Cincinnati
- Cincinnati
- USA
| | - Stefania Perticaroli
- Shull Wollan Center—a Joint Institute for Neutron Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Eugene Mamontov
- Neutron Scattering Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Daniel Pajerowski
- Neutron Scattering Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Joerg Neuefeind
- Neutron Scattering Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Georg Ehlers
- Neutron Technologies Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Jonathan D. Nickels
- Department of Chemical and Environmental Engineering
- University of Cincinnati
- Cincinnati
- USA
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9
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Abstract
Brillouin spectroscopy and imaging are emerging techniques in analytical science, biophotonics, and biomedicine. They are based on Brillouin light scattering from acoustic waves or phonons in the GHz range, providing a nondestructive contactless probe of the mechanics on a microscale. Novel approaches and applications of these techniques to the field of biomedical sciences are discussed, highlighting the theoretical foundations and experimental methods that have been developed to date. Acknowledging that this is a fast moving field, a comprehensive account of the relevant literature is critically assessed here.
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Affiliation(s)
- Francesca Palombo
- School
of Physics and Astronomy, University of
Exeter, Stocker Road, EX4 4QL Exeter, U.K.
| | - Daniele Fioretto
- Department
of Physics and Geology, University of Perugia, via Alessandro Pascoli, I-06123 Perugia, Italy
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10
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Corezzi S, Paolantoni M, Sassi P, Morresi A, Fioretto D, Comez L. Trehalose-induced slowdown of lysozyme hydration dynamics probed by EDLS spectroscopy. J Chem Phys 2019; 151:015101. [DOI: 10.1063/1.5099588] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Assunta Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
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11
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Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results. Int J Pharm 2018; 540:65-77. [PMID: 29412151 DOI: 10.1016/j.ijpharm.2018.01.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 11/20/2022]
Abstract
The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey of the fundamental backgrounds of concentration dependence and experimental solubility results show some peculiar behavior of aqueous solutions with several types of similar solutes. Secondly, the use of a variety of experimental spectroscopic devices, operating under different experimental conditions of dimension and frequency, has produced a large amount of structural and dynamic data on aqueous solutions showing the richness of the information produced, depending on where and how the experiment is carried out. Finally, the use of molecular dynamics computational work is presented to highlight how the different types of solute functional groups and surface topologies organize adjacent water molecules differently. The highly valuable contribution of computer simulation studies in providing molecular explanations for experimental deductions, either of a thermodynamic or spectroscopic nature, is shown to have changed the current knowledge of many aqueous solution processes. While this paper is intended to provide a collective view on the latest literature results, still the presentation aims at a tutorial explanation of the potentials of the three methodologies in the field of aqueous solutions of pharmaceutical molecules.
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12
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Perticaroli S, Comez L, Sassi P, Morresi A, Fioretto D, Paolantoni M. Water-like Behavior of Formamide: Jump Reorientation Probed by Extended Depolarized Light Scattering. J Phys Chem Lett 2018; 9:120-125. [PMID: 29243934 DOI: 10.1021/acs.jpclett.7b02943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Water is a strong self-associated liquid with peculiar properties that crucially depend on H-bonding. As regards its molecular dynamics, only recently has water reorientation been successfully described based on a jump mechanism, which is responsible for the overall H-bonding exchange. Here, using high-resolution broad-band depolarized light scattering, we have investigated the reorientational dynamics of formamide (FA) as a function of concentration from the neat liquid to diluted aqueous solutions. Our main findings indicate that in the diluted regime the water rearrangement can trigger the motion of FA solute molecules, which are forced to reorient at the same rate as water. This highlights an exceptional behavior of FA, which perfectly substitutes water within its network. Besides other fundamental implications connected with the relevance of FA, its water-like behavior provides rare experimental evidence of a solute whose dynamics is completely slaved to the solvent.
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Affiliation(s)
- S Perticaroli
- Shull Wollan Center, a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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13
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Perticaroli S, Mostofian B, Ehlers G, Neuefeind JC, Diallo SO, Stanley CB, Daemen L, Egami T, Katsaras J, Cheng X, Nickels JD. Structural relaxation, viscosity, and network connectivity in a hydrogen bonding liquid. Phys Chem Chem Phys 2017; 19:25859-25869. [DOI: 10.1039/c7cp04013j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The structure and dynamics of the model H-bonding liquid,n-methylacetamide (NMA) have been studied, revealing the connection between the timescale of H-bond network reorganization and viscosity.
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14
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Perticaroli S, Ehlers G, Stanley CB, Mamontov E, O'Neill H, Zhang Q, Cheng X, Myles DAA, Katsaras J, Nickels JD. Description of Hydration Water in Protein (Green Fluorescent Protein) Solution. J Am Chem Soc 2016; 139:1098-1105. [PMID: 27783480 DOI: 10.1021/jacs.6b08845] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structurally and dynamically perturbed hydration shells that surround proteins and biomolecules have a substantial influence upon their function and stability. This makes the extent and degree of water perturbation of practical interest for general biological study and industrial formulation. We present an experimental description of the dynamical perturbation of hydration water around green fluorescent protein in solution. Less than two shells (∼5.5 Å) were perturbed, with dynamics a factor of 2-10 times slower than bulk water, depending on their distance from the protein surface and the probe length of the measurement. This dependence on probe length demonstrates that hydration water undergoes subdiffusive motions (τ ∝ q-2.5 for the first hydration shell, τ ∝ q-2.3 for perturbed water in the second shell), an important difference with neat water, which demonstrates diffusive behavior (τ ∝ q-2). These results help clarify the seemingly conflicting range of values reported for hydration water retardation as a logical consequence of the different length scales probed by the analytical techniques used.
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Affiliation(s)
- Stefania Perticaroli
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Georg Ehlers
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Christopher B Stanley
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Eugene Mamontov
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Hugh O'Neill
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Qiu Zhang
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Xiaolin Cheng
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Dean A A Myles
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - John Katsaras
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jonathan D Nickels
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
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15
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Comez L, Paolantoni M, Sassi P, Corezzi S, Morresi A, Fioretto D. Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water. SOFT MATTER 2016; 12:5501-5514. [PMID: 27280176 DOI: 10.1039/c5sm03119b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
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16
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Comez L, Paolantoni M, Corezzi S, Lupi L, Sassi P, Morresi A, Fioretto D. Aqueous solvation of amphiphilic molecules by extended depolarized light scattering: the case of trimethylamine-N-oxide. Phys Chem Chem Phys 2016; 18:8881-9. [PMID: 26958663 DOI: 10.1039/c5cp04357c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrophilic and hydrophobic interactions strongly affect the solvation dynamics of biomolecules. To understand their role, small model systems are generally employed to simplify the investigations. In this study the amphiphile trimethylamine N-oxide (TMAO) is chosen as an exemplar, and studied by means of extended frequency range depolarized light scattering (EDLS) experiments as a function of solute concentration. This technique proves to be a suitable tool for investigating different aspects of aqueous solvation, being able at the same time to provide information about relaxation processes and vibrational modes of solvent and solute. In the case study of TMAO, we find that the relaxation dynamics of hydration water is moderately retarded compared to the bulk, and the perturbation induced by the solute on surrounding water is confined to the first hydration shell. The results highlight the hydrophobic character of TMAO in its interaction with water. The number of molecules taking part in the solvation process decreases as the solute concentration increases, following a trend consistent with the hydration water-sharing model, and suggesting that aggregation between solute molecules is negligible. Finally, the analysis of the resonant modes in the THz region and the comparison with the corresponding results obtained for the isosteric molecule tert-butyl alcohol (TBA) allow us to provide new insights into the different solvating properties of these two biologically relevant molecules.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy. and Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - M Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - S Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - L Lupi
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | - P Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - A Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - D Fioretto
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
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17
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Rossi B, Venuti V, Mele A, Punta C, Melone L, D'Amico F, Gessini A, Crupi V, Majolino D, Trotta F, Masciovecchio C. Vibrational signatures of the water behaviour upon confinement in nanoporous hydrogels. Phys Chem Chem Phys 2016; 18:12252-9. [DOI: 10.1039/c5cp07936e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibrational spectroscopy is used to investigate how the hydrogen-bond dynamics of water is influenced by nano-confinement and hydrophobic/hydrophilic solvation effects.
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Affiliation(s)
- B. Rossi
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
- Department of Physics University of Trento and INSTM Local Unit
- Trento
| | - V. Venuti
- Department of Physics and Earth Sciences
- University of Messina
- 98166 Messina
- Italy
| | - A. Mele
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM local unit
- Milano
- Italy
| | - C. Punta
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM local unit
- Milano
- Italy
| | - L. Melone
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM local unit
- Milano
- Italy
| | - F. D'Amico
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
| | - A. Gessini
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
| | - V. Crupi
- Department of Physics University of Trento and INSTM Local Unit
- Trento
- Italy
| | - D. Majolino
- Department of Physics University of Trento and INSTM Local Unit
- Trento
- Italy
| | - F. Trotta
- Department of Chemistry
- University of Torino
- 10125 Torino
- Italy
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18
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Martin DR, Matyushov DV. Hydration shells of proteins probed by depolarized light scattering and dielectric spectroscopy: orientational structure is significant, positional structure is not. J Chem Phys 2015; 141:22D501. [PMID: 25494772 DOI: 10.1063/1.4895544] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water interfacing hydrated proteins carry properties distinct from those of the bulk and is often described as a separate entity, a "biological water." We address here the question of which dynamical and structural properties of hydration water deserve this distinction. The study focuses on different aspects of the density and orientational fluctuations of hydration water and the ability to separate them experimentally by combining depolarized light scattering with dielectric spectroscopy. We show that the dynamics of the density fluctuations of the hydration shells reflect the coupled dynamics of the solute and solvent and do not require a special distinction as "biological water." The orientations of shell water molecules carry dramatically different physics and do require a separation into a sub-ensemble. Depending on the property considered, the perturbation of water's orientational structure induced by the protein propagates 3-5 hydration shells into the bulk at normal temperature.
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Affiliation(s)
- Daniel R Martin
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA
| | - Dmitry V Matyushov
- Department of Physics and Department of Chemistry and Biochemistry, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA
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19
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Sagawa N, Shikata T. Dangling OH Vibrations of Water Molecules in Aqueous Solutions of Aprotic Polar Compounds Observed in the Near-Infrared Regime. J Phys Chem B 2015; 119:8087-95. [DOI: 10.1021/acs.jpcb.5b02886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naoya Sagawa
- Division of Natural Resources
and Eco-materials, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Toshiyuki Shikata
- Division of Natural Resources
and Eco-materials, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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20
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Comez L, Perticaroli S, Paolantoni M, Sassi P, Corezzi S, Morresi A, Fioretto D. Concentration dependence of hydration water in a model peptide. Phys Chem Chem Phys 2015; 16:12433-40. [PMID: 24829171 DOI: 10.1039/c4cp00840e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular dynamics of aqueous solutions of a model amphiphilic peptide is studied as a function of concentration by broad-band light scattering experiments. Similarly to protein aqueous solutions, a considerable retardation, of about a factor 6-8, of hydration water dynamics with respect to bulk water is found, showing a slight dependence on solute concentration. Conversely, the average number of water molecules perturbed by the presence of peptide, i.e. the hydration number, appears to be strongly modified by adding solute. Its behaviour, decreasing upon increasing concentration, can be interpreted considering the random close-to-contact condition experienced by solute particles. Overall, the present findings support the view of a "long range" effect of peptides on the surrounding water, extending beyond the first two hydration shells.
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Affiliation(s)
- Lucia Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy.
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21
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Rossi B, Venuti V, D'Amico F, Gessini A, Castiglione F, Mele A, Punta C, Melone L, Crupi V, Majolino D, Trotta F, Masciovecchio C. Water and polymer dynamics in a model polysaccharide hydrogel: the role of hydrophobic/hydrophilic balance. Phys Chem Chem Phys 2015; 17:963-71. [DOI: 10.1039/c4cp04045g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The role of hydrophobicity/hydrophilicity balance in the gelation phenomena in water-swollen polymers is explored in a model polysaccharide hydrogel.
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22
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Abstract
Water is crucial to the structure and function of biological membranes. In fact, the membrane's basic structural unit, i.e. the lipid bilayer, is self-assembled and stabilized by the so-called hydrophobic effect, whereby lipid molecules unable to hydrogen bond with water aggregate in order to prevent their hydrophobic portions from being exposed to water. However, this is just the beginning of the lipid-bilayer-water relationship. This mutual interaction defines vesicle stability in solution, controls small molecule permeation, and defines the spacing between lamella in multi-lamellar systems, to name a few examples. This chapter will describe the structural and dynamical properties central to these, and other water- lipid bilayer interactions.
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Affiliation(s)
- Jonathan D Nickels
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - John Katsaras
- Biology & Soft Matter and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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23
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Perticaroli S, Russo D, Paolantoni M, Gonzalez MA, Sassi P, Nickels JD, Ehlers G, Comez L, Pellegrini E, Fioretto D, Morresi A. Painting biological low-frequency vibrational modes from small peptides to proteins. Phys Chem Chem Phys 2015; 17:11423-31. [DOI: 10.1039/c4cp05388e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We use experiments and simulation to investigate the validity of different model systems used to study the low-frequency vibrations of proteins.
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Affiliation(s)
- S. Perticaroli
- Joint Institute for Neutron Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Chemical and Materials Sciences Division
| | - D. Russo
- CNR-IOM
- Italy c/o Institut Laue Langevin
- France
- Institut Lumière Matière
- Université de Lyon 1
| | - M. Paolantoni
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
| | | | - P. Sassi
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
| | - J. D. Nickels
- Joint Institute for Neutron Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Department of Chemistry
| | - G. Ehlers
- Quantum Condensed Matter Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - L. Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia
- Università di Perugia
- I-06123 Perugia
- Italy
- Dipartimento di Fisica e Geologia
| | | | - D. Fioretto
- Dipartimento di Fisica e Geologia
- Università di Perugia
- I-06123 Perugia
- Italy
- Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN)
| | - A. Morresi
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
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24
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Comez L, Paolantoni M, Lupi L, Sassi P, Corezzi S, Morresi A, Fioretto D. Hydrophobic Hydration in Water–tert-Butyl Alcohol Solutions by Extended Depolarized Light Scattering. J Phys Chem B 2014; 119:9236-43. [DOI: 10.1021/jp509854a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Comez
- IOM-CNR
c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Dipartimento
di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - M. Paolantoni
- Dipartimento
di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - L. Lupi
- Department
of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - P. Sassi
- Dipartimento
di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - S. Corezzi
- Dipartimento
di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - A. Morresi
- Dipartimento
di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - D. Fioretto
- Dipartimento
di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Centro
di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
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25
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Palombo F, Heisler IA, Hribar-Lee B, Meech SR. Tuning the Hydrophobic Interaction: Ultrafast Optical Kerr Effect Study of Aqueous Ionene Solutions. J Phys Chem B 2014; 119:8900-8. [DOI: 10.1021/jp506701a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Francesca Palombo
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
- School
of Physics, University of Exeter, Stocker Road, Exeter EX4 4QL, U.K
| | - Ismael A. Heisler
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Barbara Hribar-Lee
- Faculty
of Chemistry and Chemical Technology, University of Ljubljana, Askerceva
5, 1000 Ljubljana, Slovenia
| | - Stephen R. Meech
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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26
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Corezzi S, Sassi P, Paolantoni M, Comez L, Morresi A, Fioretto D. Hydration and rotational diffusion of levoglucosan in aqueous solutions. J Chem Phys 2014; 140:184505. [DOI: 10.1063/1.4873575] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Conti Nibali V, D'Angelo G, Paciaroni A, Tobias DJ, Tarek M. On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water. J Phys Chem Lett 2014; 5:1181-1186. [PMID: 26274468 DOI: 10.1021/jz500023e] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Picosecond time scale dynamics of hydrated proteins has been connected with the onset of biological activity as it coincides with solvent-solute hydrogen bond rearrangements and amino acid rotational relaxation time scales. The presence and fluctuations of protein hydration water (PHW) largely influence protein motions that are believed to be slaved to those of the solvent, yet to date, how protein and hydration water dynamics are coupled remains unclear. Here, we provide a significant advance in characterizing this coupling; we present the first full study of both the longitudinal and transverse coherent collective motions in a protein-solvent system. The data show unexpectedly the presence in the water dynamics of collective modes belonging to the protein. The properties of these modes, in particular, their propagation velocities and amplitudes, indicate a strengthening of the interactions and a higher rigidity of the network of solvent molecules close to the protein surface. Accordingly, the present study presents the most compelling and clear evidence of a very strong dynamical coupling between a protein and its hydration water, previously suggested by studies using various experimental techniques.
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Affiliation(s)
| | - Giovanna D'Angelo
- †Dipartimento di Fisica, Università degli Studi di Messina, Messina, Italy
| | | | - Douglas J Tobias
- ¶Department of Chemistry, University of California, Irvine, California 92697-2025 United States
| | - Mounir Tarek
- §CNRS, UMR Structure et Réactivité des Systèmes Moléculaires Complexes, University of Lorraine, Nancy, France
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28
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Martin DR, Fioretto D, Matyushov DV. Depolarized light scattering and dielectric response of a peptide dissolved in water. J Chem Phys 2014; 140:035101. [DOI: 10.1063/1.4861965] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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29
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Cerveny S, Swenson J. Dynamics of supercooled water in a biological model system of the amino acid l-lysine. Phys Chem Chem Phys 2014; 16:22382-90. [DOI: 10.1039/c4cp02487g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lysine solutions establish a new relaxation behaviour of supercooled interfacial water.
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Affiliation(s)
- Silvina Cerveny
- Centro de Física de Materiales-Material Physics Centre (MPC)
- CSIC-Universidad del País Vasco (UPV/EHU)
- San Sebastian, Spain
- Donostia International Physics Center
- San Sebastián, Spain
| | - Jan Swenson
- Department of Applied Physics
- Chalmers University of Technology
- SE-412 96 Göteborg, Sweden
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30
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Palombo F, Sassi P, Paolantoni M, Barontini C, Morresi A, Giorgini MG. Complex Dynamical Aspects of Organic Electrolyte Solutions. J Phys Chem B 2013; 118:215-25. [DOI: 10.1021/jp4066604] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Francesca Palombo
- School of Physics, University of Exeter , EX4 4QF Exeter, United Kingdom
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31
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Sassi P, Perticaroli S, Comez L, Giugliarelli A, Paolantoni M, Fioretto D, Morresi A. Volume properties and spectroscopy: A terahertz Raman investigation of hen egg white lysozyme. J Chem Phys 2013; 139:225101. [DOI: 10.1063/1.4838355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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32
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D’Amico F, Bencivenga F, Camisasca G, Gessini A, Principi E, Cucini R, Masciovecchio C. Thermodynamic hydration shell behavior of glycine. J Chem Phys 2013; 139:015101. [DOI: 10.1063/1.4812283] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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33
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Solvent Sharing Models for Non-Interacting Solute Molecules: The Case of Glucose and Trehalose Water Solutions. FOOD BIOPHYS 2013. [DOI: 10.1007/s11483-013-9306-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Perticaroli S, Nakanishi M, Pashkovski E, Sokolov AP. Dynamics of Hydration Water in Sugars and Peptides Solutions. J Phys Chem B 2013; 117:7729-36. [DOI: 10.1021/jp403665w] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefania Perticaroli
- Chemical and Materials Sciences Division at Oak Ridge National Laboratory,
Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996,
United States
| | - Masahiro Nakanishi
- Chemical and Materials Sciences Division at Oak Ridge National Laboratory,
Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996,
United States
| | - Eugene Pashkovski
- Unilever R&D Trumbull, 40 Merritt Boulevard, Trumbull, Connecticut 06611, United States
| | - Alexei P. Sokolov
- Chemical and Materials Sciences Division at Oak Ridge National Laboratory,
Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996,
United States
- Joint Institute
for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
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35
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Comez L, Lupi L, Morresi A, Paolantoni M, Sassi P, Fioretto D. More Is Different: Experimental Results on the Effect of Biomolecules on the Dynamics of Hydration Water. J Phys Chem Lett 2013; 4:1188-1192. [PMID: 26282040 DOI: 10.1021/jz400360v] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biological interfaces characterized by a complex mixture of hydrophobic, hydrophilic, or charged moieties interfere with the cooperative rearrangement of the hydrogen-bond network of water. In the present study, this solute-induced dynamical perturbation is investigated by extended frequency range depolarized light scattering experiments on an aqueous solution of a variety of systems of different nature and complexity such as small hydrophobic and hydrophilic molecules, amino acids, dipeptides, and proteins. Our results suggest that a reductionist approach is not adequate to describe the rearrangement of hydration water because a significant increase of the dynamical retardation and extension of the perturbation occurs when increasing the chemical complexity of the solute.
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Affiliation(s)
- Lucia Comez
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Laura Lupi
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Assunta Morresi
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Marco Paolantoni
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Paola Sassi
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Daniele Fioretto
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
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Boopathi S, Kolandaivel P. Molecular dynamics simulations and density functional theory studies of NALMA and NAGMA dipeptides. J Biomol Struct Dyn 2013; 31:158-73. [DOI: 10.1080/07391102.2012.698380] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Comez L, Lupi L, Paolantoni M, Picchiò F, Fioretto D. Hydration properties of small hydrophobic molecules by Brillouin light scattering. J Chem Phys 2013; 137:114509. [PMID: 22998273 DOI: 10.1063/1.4752732] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the relaxation of water molecules next to hydrophobic solutes with different functional groups by Brillouin light scattering. Evidence is given for (i) water activation energy in trimethylamine-N-oxide, proline and t-butyl alcohol diluted solutions which is comparable to that of neat water, almost independent from solute mole fraction and (ii) moderate slowdown of relaxation time of proximal water compared to the bulk, which is consistent with excluded volume models. Assuming that the main contribution to viscosity comes from bulk and hydration water, a rationale is given of the phenomenological Arrhenius' laws for the viscosity of diluted aqueous solutions.
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Affiliation(s)
- L Comez
- IOM-CNR, c/o Dipartimento di Fisica, Università di Perugia, I-06123, Perugia, Italy
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Heyden M, Tobias DJ, Matyushov DV. Terahertz absorption of dilute aqueous solutions. J Chem Phys 2012; 137:235103. [DOI: 10.1063/1.4772000] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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39
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Lupi L, Comez L, Paolantoni M, Perticaroli S, Sassi P, Morresi A, Ladanyi BM, Fioretto D. Hydration and Aggregation in Mono- and Disaccharide Aqueous Solutions by Gigahertz-to-Terahertz Light Scattering and Molecular Dynamics Simulations. J Phys Chem B 2012. [DOI: 10.1021/jp3079869] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Lupi
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123,
Perugia, Italy
| | - M. Paolantoni
- Dipartimento
di Chimica, Università di Perugia, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - S. Perticaroli
- Dipartimento
di Chimica, Università di Perugia, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - P. Sassi
- Dipartimento
di Chimica, Università di Perugia, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - A. Morresi
- Dipartimento
di Chimica, Università di Perugia, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - B. M. Ladanyi
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872,
United States
| | - D. Fioretto
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Centro di
Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università of Perugia, via Elce di Sotto 8,
06123 Perugia, Italy
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40
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Lupi L, Comez L, Paolantoni M, Fioretto D, Ladanyi BM. Dynamics of Biological Water: Insights from Molecular Modeling of Light Scattering in Aqueous Trehalose Solutions. J Phys Chem B 2012; 116:7499-508. [DOI: 10.1021/jp301988f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Laura Lupi
- Dipartimento di
Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Lucia Comez
- Dipartimento di
Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli,
I-06123, Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Università di Perugia, via Elce di Sotto, I-06123
Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di
Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Branka M. Ladanyi
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872,
United States
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