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Azizi K, Laio A, Hassanali A. Solvation thermodynamics from cavity shapes of amino acids. PNAS NEXUS 2023; 2:pgad239. [PMID: 37545648 PMCID: PMC10400782 DOI: 10.1093/pnasnexus/pgad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.
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Affiliation(s)
- Khatereh Azizi
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Alessandro Laio
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- SISSA, Via Bonomea 265, I-34136 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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A subtle interplay between hydrophilic and hydrophobic hydration governs butanol (de)mixing in water. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Schönfeldová T, Dupertuis N, Chen Y, Ansari N, Poli E, Wilkins DM, Hassanali A, Roke S. Charge Gradients around Dendritic Voids Cause Nanoscale Inhomogeneities in Liquid Water. J Phys Chem Lett 2022; 13:7462-7468. [PMID: 35930807 DOI: 10.1021/acs.jpclett.2c01872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Water is the matrix of life and serves as a solvent for numerous physical and chemical processes. The origins of the nature of inhomogeneities that exist in liquid water and the time scales over which they occur remains an open question. Here, we report femtosecond elastic second harmonic scattering (fs-ESHS) of liquid water in comparison to an isotropic liquid (CCl4) and show that water is indeed a nonuniform liquid. The coherent fs-ESHS intensity was interpreted, using molecular dynamics simulations, as arising from charge density fluctuations with enhanced nanoscale polarizabilities around transient voids having an average lifetime of 300 fs. Although voids were also present in CCl4, they were not characterized by hydrogen bond defects and did not show strong polarizability fluctuations, leading to fs-ESHS of an isotropic liquid. The voids increased in number at higher temperatures above room temperature, in agreement with the fs-ESHS results.
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Affiliation(s)
- Tereza Schönfeldová
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nathan Dupertuis
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Yixing Chen
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Narjes Ansari
- Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Emiliano Poli
- Condensed Matter and Statistical Physics (CMSP), The Abdus Salam International Center For Theoretical Physics, 34151 Trieste, Italy
| | - David M Wilkins
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, United Kingdom
| | - Ali Hassanali
- Condensed Matter and Statistical Physics (CMSP), The Abdus Salam International Center For Theoretical Physics, 34151 Trieste, Italy
| | - Sylvie Roke
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Sun Q, Fu Y, Wang W. Temperature effects on hydrophobic interactions: Implications for protein unfolding. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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