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Yadav A, Bandyopadhyay P, Coutsias EA, Dill KA. Crustwater: Modeling Hydrophobic Solvation. J Phys Chem B 2022; 126:6052-6062. [PMID: 35926838 PMCID: PMC9393863 DOI: 10.1021/acs.jpcb.2c02695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/13/2022] [Indexed: 11/29/2022]
Abstract
We describe Crustwater, a statistical mechanical model of nonpolar solvation in water. It treats bulk water using the Cage Water model and introduces a crust, i.e., a solvation shell of coordinated partially structured waters. Crustwater is analytical and fast to compute. We compute here solvation vs temperature over the liquid range, and vs pressure and solute size. Its thermal predictions are as accurate as much more costly explicit models such as TIP4P/2005. This modeling gives new insights into the hydrophobic effect: (1) that oil-water insolubility in cold water is due to solute-water (SW) translational entropy and not water-water (WW) orientations, even while hot water is dominated by WW cage breaking, and (2) that a size transition at the Angstrom scale, not the nanometer scale, takes place as previously predicted.
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Affiliation(s)
- Ajeet
Kumar Yadav
- School
of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School
of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Evangelos A. Coutsias
- Department
of Applied Mathematics and Statistics ; Laufer Center for Physical
and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Ken A. Dill
- Laufer
Center for Physical and Quantitative Biology; Department of Physics
and Astronomy ; Department of Chemistry, Stony Brook University, Stony
Brook, New York 11794, United States
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2
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Roterman I, Stapor K, Gądek K, Gubała T, Nowakowski P, Fabian P, Konieczny L. On the Dependence of Prion and Amyloid Structure on the Folding Environment. Int J Mol Sci 2021; 22:ijms222413494. [PMID: 34948291 PMCID: PMC8707753 DOI: 10.3390/ijms222413494] [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: 11/19/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 01/22/2023] Open
Abstract
Currently available analyses of amyloid proteins reveal the necessity of the existence of radical structural changes in amyloid transformation processes. The analysis carried out in this paper based on the model called fuzzy oil drop (FOD) and its modified form (FOD-M) allows quantifying the role of the environment, particularly including the aquatic environment. The starting point and basis for the present presentation is the statement about the presence of two fundamentally different methods of organizing polypeptides into ordered conformations—globular proteins and amyloids. The present study shows the source of the differences between these two paths resulting from the specificity of the external force field coming from the environment, including the aquatic and hydrophobic one. The water environment expressed in the fuzzy oil drop model using the 3D Gauss function directs the folding process towards the construction of a micelle-like system with a hydrophobic core in the central part and the exposure of polarity on the surface. The hydrophobicity distribution of membrane proteins has the opposite characteristic: Exposure of hydrophobicity at the surface of the membrane protein with an often polar center (as in the case of ion channels) is expected. The structure of most proteins is influenced by a more or less modified force field generated by water through the appropriate presence of a non-polar (membrane-like) environment. The determination of the proportion of a factor different from polar water enables the assessment of the protein status by indicating factors favoring the structure it represents.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, 31-034 Kopernika 7, 30-688 Krakow, Poland
- Correspondence:
| | - Katarzyna Stapor
- Department of Applied Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Krzysztof Gądek
- Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland; (K.G.); (T.G.); (P.N.)
| | - Tomasz Gubała
- Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland; (K.G.); (T.G.); (P.N.)
| | - Piotr Nowakowski
- Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland; (K.G.); (T.G.); (P.N.)
| | - Piotr Fabian
- Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Leszek Konieczny
- Department of Medical Biochemistry, Jagiellonian University Medical College, 31-034 Kopernika 7, 31-034 Krakow, Poland;
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Yadav AK, Bandyopadhyay P, Urbic T, Dill KA. Analytical 2-Dimensional Model of Nonpolar and Ionic Solvation in Water. J Phys Chem B 2021; 125:1861-1873. [PMID: 33539097 PMCID: PMC7958497 DOI: 10.1021/acs.jpcb.0c10329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A goal in computational chemistry is computing hydration free energies of nonpolar and charged solutes accurately, but with much greater computational speeds than in today's explicit-water simulations. Here, we take one step in that direction: a simple model of solvating waters that is analytical and thus essentially instantaneous to compute. Each water molecule is a 2-dimensional dipolar hydrogen-bonding disk that interacts around small circular solutes with different nonpolar and charge interactions. The model gives good qualitative agreement with experiments. As a function of the solute radius, it gives the solvation free energy, enthalpy and entropy as a function of temperature for the inert gas series Ne, Ar, Kr, and Xe. For anions and cations, it captures relatively well the trends versus ion radius. This approach should be readily generalizable to three dimensions.
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Affiliation(s)
- Ajeet Kumar Yadav
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000, Ljubljana, Slovenia
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, New York 11794, United States
- Department of Physics and Astronomy, Stony Brook University, New York, New York 11794, United States
- Department of Chemistry, Stony Brook University, New York, New York 11794, United States
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Grabowska J, Kuffel A, Zielkiewicz J. Revealing the Frank-Evans "Iceberg" Structures within the Solvation Layer around Hydrophobic Solutes. J Phys Chem B 2021; 125:1611-1617. [PMID: 33539702 PMCID: PMC7898264 DOI: 10.1021/acs.jpcb.0c09489] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using computer simulations, the structural properties of solvation water of three model hydrophobic molecules, methane and two fullerenes (C60 and C80), were studied. Systems were simulated at temperatures in the range of 250-298 K. By analyzing both the local ordering of the molecules of water in the solvation layers and the structure of hydrogen bond network, it is shown that in the solvation layer of hydrophobic molecules, ordered aggregates consisting of water molecules are formed. Even though it is difficult to define the exact structure of these aggregates, their existence alone is clearly noticeable. Moreover, these aggregates become more pronounced with the decrease of temperature. The existence of the ordered aggregates around the hydrophobic solutes complies with the concept of "icebergs" proposed by Frank and Evans.
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Affiliation(s)
- Joanna Grabowska
- Faculty of Chemistry, Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Anna Kuffel
- Faculty of Chemistry, Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jan Zielkiewicz
- Faculty of Chemistry, Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
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Bogunia M, Makowski M. Influence of Ionic Strength on Hydrophobic Interactions in Water: Dependence on Solute Size and Shape. J Phys Chem B 2020; 124:10326-10336. [PMID: 33147018 PMCID: PMC7681779 DOI: 10.1021/acs.jpcb.0c06399] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Hydrophobicity is a phenomenon of
great importance in biology,
chemistry, and biochemistry. It is defined as the interaction between
nonpolar molecules or groups in water and their low solubility. Hydrophobic
interactions affect many processes in water, for example, complexation,
surfactant aggregation, and coagulation. These interactions play a
pivotal role in the formation and stability of proteins or biological
membranes. In the present study, we assessed the effect of ionic strength,
solute size, and shape on hydrophobic interactions between pairs of
nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene,
ethane, propane, butane, hexane, octane, and decane were simulated
by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P
and TIP4PEW water models were used. Potential of mean force (PMF)
plots of these dimers were determined at four values of ionic strength,
0, 0.04, 0.08, and 0.40 mol/dm3, to observe its impact
on hydrophobic interactions. The characteristic shape of PMFs with
three extrema (contact minimum, solvent-separated minimum, and desolvation
maximum) was observed for most of the compounds for hydrophobic interactions.
Ionic strength affected hydrophobic interactions. We observed a tendency
to deepen contact minima with an increase in ionic strength value
in the case of spherical and spheroidal molecules. Additionally, two-dimensional
distribution functions describing water density and average number
of hydrogen bonds between water molecules were calculated in both
water models for adamantane and hexane. It was observed that the density
of water did not significantly change with the increase in ionic strength,
but the average number of hydrogen bonds changed. The latter tendency
strongly depends on the water model used for simulations.
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Affiliation(s)
- Małgorzata Bogunia
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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Ivanov EV, Kustov AV, Batov DV, Smirnova NL, Pechnikova NL. Thermodynamics of tetramethylurea solutions in ethylene glycol: The evidence of pairwise solvophobic interaction. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Dandekar R, Hassanali AA. Hierarchical lattice models of hydrogen-bond networks in water. Phys Rev E 2018; 97:062113. [PMID: 30011567 DOI: 10.1103/physreve.97.062113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Indexed: 06/08/2023]
Abstract
We develop a graph-based model of the hydrogen-bond network in water, with a view toward quantitatively modeling the molecular-level correlational structure of the network. The networks formed are studied by the constructing the model on two infinite-dimensional lattices. Our models are built bottom up, based on microscopic information coming from atomistic simulations, and we show that the predictions of the model are consistent with known results from ab initio simulations of liquid water. We show that simple entropic models can predict the correlations and clustering of local-coordination defects around tetrahedral waters observed in the atomistic simulations. We also find that orientational correlations between bonds are longer ranged than density correlations, determine the directional correlations within closed loops, and show that the patterns of water wires within these structures are also consistent with previous atomistic simulations. Our models show the existence of density and compressibility anomalies, as seen in the real liquid, and the phase diagram of these models is consistent with the singularity-free scenario previously proposed by Sastry and coworkers [Phys. Rev. E 53, 6144 (1996)1063-651X10.1103/PhysRevE.53.6144].
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Affiliation(s)
- Rahul Dandekar
- Condensed Matter and Statistical Physics Section, International Center for Theoretical Physics, Strada Costiera 11, Trieste, Italy
| | - Ali A Hassanali
- Condensed Matter and Statistical Physics Section, International Center for Theoretical Physics, Strada Costiera 11, Trieste, Italy
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Zhan YY, Kojima T, Koide T, Tachikawa M, Hiraoka S. A Balance between van der Waals and Cation-π Interactions Stabilizes Hydrophobic Assemblies. Chemistry 2018; 24:9130-9135. [DOI: 10.1002/chem.201801376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Yi-Yang Zhan
- Department of Basic Science; Graduate School of Arts and Sciences; The University of Tokyo; 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan
| | - Tatsuo Kojima
- Department of Basic Science; Graduate School of Arts and Sciences; The University of Tokyo; 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan
| | - Takuya Koide
- Quantum Chemistry Division; Graduate School of Science; Yokohama City University; 22-2 Seto Kanazawa-ku Yokohama Kanagawa 236-0027 Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division; Graduate School of Science; Yokohama City University; 22-2 Seto Kanazawa-ku Yokohama Kanagawa 236-0027 Japan
| | - Shuichi Hiraoka
- Department of Basic Science; Graduate School of Arts and Sciences; The University of Tokyo; 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan
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