1
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Ogrin P, Urbic T. Thermodynamics perturbation theory for solvation of nonpolar solutes in rose model. Phys Rev E 2023; 108:054135. [PMID: 38115497 DOI: 10.1103/physreve.108.054135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023]
Abstract
A simple model of water, called the rose model, is used in this work. The rose model is a very simple model that can provide insight into the anomalous properties of water. In the rose water model, the molecules are represented as two-dimensional Lennard-Jones disks with potentials for orientation-dependent pairwise interactions mimicking formations of hydrogen bonds. We have recently applied a Wertheim integral equation theory (IET) and a thermodynamic perturbation theory (TPT) to the rose model in bulk. These analytical theories offer the advantage of being computationally less intensive than computer simulations by orders of magnitudes. Here we have applied the TPT to study the transfer of a nonpolar solute into rose water, the so-called hydrophobic effect. Similarly as in our previous work for bulk water, we have found that the theory reproduces the computer simulation results quite well at higher temperatures, while the theories predict the qualitative trends at low temperatures.
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Affiliation(s)
- Peter Ogrin
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
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2
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Ogrin P, Urbic T. Angle-dependent integral equation theory improves results of thermodynamics and structure of rose water model. J Chem Phys 2023; 159:114505. [PMID: 37732557 PMCID: PMC10908565 DOI: 10.1063/5.0159438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023] Open
Abstract
Orientation-dependent integral equation theory (ODIET) was applied to the rose water model. Structural and thermodynamic properties of water modeled with the rose model were calculated using ODIET and compared to results from orientation-averaged integral equation theory (IET) and Monte Carlo simulations. Rose water model is a simple two-dimensional water model where molecules of water are represented as Lennard-Jones disks with explicit hydrogen bonding potential in form of rose functions. Orientational dependency significantly improves IET, as the thermodynamic results obtained using ODIET are significantly more in agreement with results calculated using MC than in the case of the orientationally averaged version. At high temperatures, the agreement between the simulation and theory is quantitative; however, when temperatures lower, a slight deviation between results obtained with different methods appear. ODIET correctly predicts the radial distribution function; moreover, ODIet also enables the calculation of angular distributions. While the angular distributions obtained with ODIET are in qualitative agreement with distributions from MC simulations, the height of the peaks in angular distributions differs between methods. Using results from ODIET, the spatial distribution of water molecules was constructed, which aids in the interpretation of other structural properties. ODIET was also used to calculate fractions of molecules with different number of hydrogen bonds, which is in the agreement with the simulations. Overall, use of ODIET significantly improves the obtained results in comparison to standard IET.
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Affiliation(s)
- Peter Ogrin
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
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3
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Škvára J, Nezbeda I, Urbic T. Supercooled water in two dimensions: Structure and thermodynamics of the Mercedes-Benz model. J Mol Liq 2023; 386:122445. [PMID: 37435361 PMCID: PMC10331298 DOI: 10.1016/j.molliq.2023.122445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
The two-dimensional Mercedes-Benz model of water has been studied by molecular simulations over a wide range of thermodynamic conditions as an attempt to locate the supercooled region where a liquid-liquid separation and, potentially, also other structures may occur. Both the correlation functions and a number of local structure factors have been used to identify different structural arrangements. These include, in addition to the hexatic phase, also the hexagon, pentagon, and quadruplet arrangements. All these structures result from the competition between the hydrogen bonding and Lennard-Jones interactions and their effect at different temperatures and pressures. Based on the obtained results, an attempt is made to sketch a (rather complex) phase diagram of the model.
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Affiliation(s)
- Jiří Škvára
- Institute of Chemical Process Fundamentals, Czech Acad. Sci., 16502 Prague, Czech Republic
- Faculty of Science, J. E. Purkinje University, 40096 Ústí nad Labem, Czech Republic
| | - Ivo Nezbeda
- Faculty of Science, J. E. Purkinje University, 40096 Ústí nad Labem, Czech Republic
| | - Tomaz Urbic
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia
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4
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Abstract
The density, diffusion, and structural anomalies of the simple two-dimensional model of water were determined by Monte Carlo simulations. The rose model was used which is a very simple model for explaining the origin of water properties. Rose water molecules are modelled as two-dimensional Lennard-Jones disks with rose potentials for orientation dependent pairwise interactions mimicking formations of hydrogen bonds. The model can be seen also as a variance of silica-like models. Two parameters of potential in this work were selected in a way that (1) the model exhibits similar properties to Mercedes-Benz (MB) water model; and (2) that the model has real-like properties of water. Beside the known thermodynamic anomaly for the model we also found diffusion and structural anomalies. The orientational order parameters were calculated and maximum encountered for three and six-fold symmetry. For the MB parametrization, the anomalies occur in hierarchy order, which is a slight variation of the hierarchy order in real water. The diffusion anomaly region is the innermost in the hierarchy while for water it is the density anomaly region. In case of real water parametrization the most inner is the structural anomaly.
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Affiliation(s)
- Peter Ogrin
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
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5
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Urbic T. Ben Naim's four-arm model with density anomaly: Theory and computer simulations. Phys Rev E 2023; 108:014136. [PMID: 37583205 DOI: 10.1103/physreve.108.014136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/01/2023] [Indexed: 08/17/2023]
Abstract
Molecular dynamics, Wertheim's integral equation theory (IET), and thermodynamics perturbation theory (TPT) were used to study the thermodynamics and structure of particles interacting through angle-dependent potential. The particles are modeled as two-dimensional Lennard-Jones disks with four hydrogen bonding arms arranged symmetrically. The model was introduced by Ben-Naim and we call it the BN4 model. The BN4 model exhibits density anomaly and other anomalous properties similar to those in water and in the Mercedes-Benz (MB) model. The IET is based on the orientationally averaged version of the Ornstein-Zernike equation and correctly predicts the pair correlation function of the model at high temperatures. Both TPT and IET are in semiquantitative agreement with the simulation values of the molar volume, isothermal compressibility, thermal expansion coefficient, and heat capacity.
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Affiliation(s)
- Tomaz Urbic
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia
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6
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Ogrin P, Urbic T. Simple rose model of water in constant electric field. Phys Rev E 2023; 107:054801. [PMID: 37329104 DOI: 10.1103/physreve.107.054801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/12/2023] [Indexed: 06/18/2023]
Abstract
A simple two-dimensional statistical mechanical water model, called the rose model, was used in this work. We studied how a homogeneous constant electric field affects the properties of water. The rose model is a very simple model that helps explain the anomalous properties of water. Rose water molecules are represented as two-dimensional Lennard-Jones disks with potentials for orientation-dependent pairwise interactions mimicking formations of hydrogen bonds. The original model is modified by addition of charges for interaction with the electric field. We studied what kind of influence the electric field strength has on the model's properties. To determine the structure and thermodynamics of the rose model under the influence of the electric field we used Monte Carlo simulations. Under the influence of a weak electric field the anomalous properties and phase transitions of the water do not change. On the other hand, the strong fields shift the phase transition points as well as the position of the density maximum.
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Affiliation(s)
- Peter Ogrin
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
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7
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Urbic T. The electric field changes the anomalous properties of the Mercedes Benz water model. Phys Chem Chem Phys 2023; 25:4987-4996. [PMID: 36722865 PMCID: PMC9906975 DOI: 10.1039/d2cp05670d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The influence of a homogeneous constant electric field on water properties was assessed. We used a simple two-dimensional statistical mechanical model called the Mercedes-Benz (MB) model of water in the study. The MB water molecules are two-dimensional disks with Gaussian arms that mimic the formation of hydrogen bonds. The model is modified with added charges for interaction with the electric field. The influence of the strength of the electric field on the water's properties was studied using Monte Carlo simulations. The structure and thermodynamics of the water were determined as a function of the strength of the electric field. We observed that the properties and phase transitions of the water in the low strength electric field does not change. In contrast, the high strength electric field shifts boiling and melting points as well as the position of the density maxima. After further increasing the strength of the electric field the density anomaly disappears.
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Affiliation(s)
- Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, SI-1000, Slovenia.
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Ogrin P, Urbic T. Rose water in random porous media: Associative replica Ornstein-Zernike theory study. J Mol Liq 2022; 368:120682. [PMID: 37731589 PMCID: PMC10508880 DOI: 10.1016/j.molliq.2022.120682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The properties of water are vastly affected by its local environment or in other words the system in which water is present. There are many systems in which water is confined in pores of different sizes and shapes. We studied the system in which porous media consisted of quenched Lennard-Jones disks and water modelled as rose water which was allowed to move inside pores. Associative replica Ornstein-Zernike theory was used to calculate the properties of the system. The accuracy of the theory under different conditions was tested against Monte Carlo simulations. The advantage of the theory is that it is magnitudes faster than computer simulations. From pair distribution functions calculated with the theory, the effects of different conditions on the structure of the system was investigated. We also studied how different conditions such as fluid temperature, fluid density, matrix density and matrix particle size affect a fraction of bonded molecules, excess internal energy and isothermal compressibility.
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Affiliation(s)
- Peter Ogrin
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
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Pršlja P, Žibert T, Urbic T. Monte Carlo simulations of simple two dimensional water-alcohol mixtures. J Mol Liq 2022; 368:120692. [PMID: 37731590 PMCID: PMC10508878 DOI: 10.1016/j.molliq.2022.120692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Simple alcohols such as methanol and ethanol, are organic chemicals that can be used to store energy, which can be used as an alternative to fossil fuels. Each alcohol has at least one hydroxyl group attached to a carbon atom of an alkyl group. They can be considered as organic derivatives of water in which one of the hydrogen atoms is replaced by an alkyl group. In this work, we determined the thermodynamic and structural properties of two dimensional water-alcohol mixtures using the Monte Carlo method. We used two-dimensional Mercedes-Benz (MB) model for water and MB based models for lower alcohols. The structural and thermodynamic properties of the mixtures were studied by Monte Carlo simulations in the isothermal-isobaric ensemble. We show that 2D models display similar trends in the density maxima as in real water-alcohol mixtures. With increasing content of alcohols, the temperature of maxima increases and upon further increase starts to decrease and at high concentrations, the density maxima disappears.
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Affiliation(s)
- Paulina Pršlja
- Department of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, 02150 Espoo, Finland
| | - Taja Žibert
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000, Slovenia
| | - Tomaz Urbic
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000, Slovenia
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10
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Computing dissipative particle dynamics interactions to render molecular structure and temperature-dependent properties of simple liquids. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Ogrin P, Urbic T. Liquid-vapour coexistence line and percolation line of rose water model. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Ogrin P, Urbic T, Fennell CJ. Statistical-mechanical liquid theories reproduce anomalous thermodynamic properties of explicit two-dimensional water models. Phys Rev E 2022; 106:034115. [PMID: 36266898 PMCID: PMC10061499 DOI: 10.1103/physreve.106.034115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/12/2022] [Indexed: 11/07/2022]
Abstract
We have developed an analytical theory for a simple model of liquid water. We apply Wertheim's thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids to the rose model, which is among the simplest models of water. The particles interact through rose potentials for orientation dependent pairwise interactions. Modifying both the shape and range of a three-petal rose function, we construct an efficient and dynamical mimic of the two-dimensional (2D) Mercedes-Benz (MB) water model. The particles in 2D MB are 2D Lennard-Jones disks with three hydrogen bonding arms arranged symmetrically, resembling the Mercedes-Benz logo. Both models qualitatively predict both the anomalous properties of pure water and the anomalous solvation thermodynamics of nonpolar molecules. The IET is based on the orientationally averaged version of the Ornstein-Zernike equation. This is one of the main approximations in the present work. IET correctly predicts the pair correlation functions at high temperatures. Both TPT and IET are in semi-quantitative agreement with the Monte Carlo values of the molar volume, isothermal compressibility, thermal expansion coefficient, and heat capacity. A major advantage of these theories is that they require orders of magnitude less computer time than the Monte Carlo simulations.
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Affiliation(s)
- Peter Ogrin
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Christopher J. Fennell
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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Papez P, Urbic T. Simple two-dimensional models of alcohols. Phys Rev E 2022; 105:054608. [PMID: 35706252 PMCID: PMC10040488 DOI: 10.1103/physreve.105.054608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 05/03/2023]
Abstract
Alcohols are organic compounds characterized by one or more hydroxyl groups attached to a carbon atom of an alkyl group. They can be considered as organic derivatives of water in which one of the hydrogen atoms is replaced by an alkyl group. In this work, the Mercedes-Benz model of water is used to design simple two-dimensional (2D) models of lower alcohols. The structural and thermodynamic properties of the constructed simple models are studied by conducting Monte Carlo simulations in the isothermal-isobaric ensemble. We show that 2D models display similar trends in structuring and thermodynamics as in experiments. The present work on the smallest amphiphilc organic solutes provides a simple testing ground to study the competition between polar and non-polar effects within the molecule and physical properties.
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Affiliation(s)
- Petra Papez
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001, Slovenia and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
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14
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Ogrin P, Urbic T. Isothermal-isobaric algorithm to study the effects of rotational degrees of freedom-Benz water model. J Mol Liq 2022; 349:118152. [PMID: 37727581 PMCID: PMC10508877 DOI: 10.1016/j.molliq.2021.118152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed isothermal-isobaric algorithm for non-equilibrium Monte Carlo simulations. As first we have shown that the new method correctly predict density by comparing it to the density determined in canonical Monte Carlo simulations through the virial pressure. The new method was then used to study the effect of translational and rotational degrees of freedom on the structural and thermodynamic properties of the simple Mercedes-Benz water model. By holding one of the temperatures constant and varying the other one, we investigated how the position of the density maxima changes. We have observed that upon increase of rotational temperature the fluid become more Lennard-Jones like and the density maxima disappears.
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Affiliation(s)
- Peter Ogrin
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
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16
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Podjed N, Urbic T. Two-dimensional core-softened model with water like properties: solvation of non-polar solute. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1932876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Nina Podjed
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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17
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Thermodynamic perturbation theory for rotational degrees of freedom. Application to the Mercedes–Benz water model. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Ogrin P, Urbic T. Integral equation study of the effects of rotational degrees of freedom on properties of the Mercedes–Benz water model. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114880] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Urbic T. Two dimensional fluid with one site-site associating point. Monte Carlo, integral equation and thermodynamic perturbation theory study. J Mol Liq 2018; 270:87-96. [PMID: 30546180 DOI: 10.1016/j.molliq.2017.12.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this paper we propose a model for the two dimensional fluid with one site-site associating point. We studied its structural and thermodynamic properties by the Monte Carlo computer simulations, the site-site integral equation theory (RISM), the Wertheim's thermodynamic perturbation theory (TPT) and the Wertheim's integral equation theory (WIET) for associative liquids. The model can have arbitrary position of the associating point from the center of particles. All particles have Lennard-Jones core while interactions between associating points are modeled as Gaussian like potential where the interaction depends only on the distance between sites. The methods were used to study the thermodynamic and structural properties as a function of the position of associating point, temperature and density. The accuracy of the analytic theories were checked by comparing the theoretical results with the corresponding Monte Carlo ones. The theories are quite accurate for cases when the associating point is on the surface and only dimers can be formed. In this case, the theories correctly predict the pair correlation functions of the model, internal energy, ratios of free and bonded particles and chemical potential. This is no longer true when associating point is away from the surface of particles and the higher clusters are formed.
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Affiliation(s)
- Tomaz Urbic
- University of Ljubljana, Department of Chemistry and Chemical Technology, Chair of Physical Chemistry, Večna pot 113, SI-1000 Ljubljana, Slovenia
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20
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Urbic T, Dill KA. Hierarchy of anomalies in the two-dimensional Mercedes-Benz model of water. Phys Rev E 2018; 98:10.1103/physreve.98.032116. [PMID: 32025599 PMCID: PMC7001678 DOI: 10.1103/physreve.98.032116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We investigate by Monte Carlo simulations density, diffusion, and structural anomalies of the simple two-dimensional Mercedes-Benz (MB) model of water, which is a very simple toy model for explaining the origin of water properties. MB water molecules are modeled as two-dimensional Lennard-Jones disks, with three orientation-dependent hydrogen-bonding arms, arranged as in the MB logo. The model is in a way also a variance of silica-like models. Beside the known thermodynamic anomaly for the model we also found diffusion and structural anomalies and map out the cascade of density, structural, pair entropy, and diffusivity anomalies for MB model. The orientational order parameters with three and six-fold symmetry were determined and maximum for each one observed. The anomalies occur in hierarchy order, which is a slight variation of the hierarchy order in real water. The diffusion anomaly region is the innermost in the hierarchy while for water it is the density anomaly region.
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Affiliation(s)
- Tomaz Urbic
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-5252, USA
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21
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Urbic T. Modelling water with simple Mercedes-Benz models. MOLECULAR SIMULATION 2018; 45:279-294. [PMID: 31156291 PMCID: PMC6542362 DOI: 10.1080/08927022.2018.1502430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/14/2018] [Indexed: 10/28/2022]
Abstract
The structures and properties of biomolecules like proteins, nucleic acids, and membranes depend on water. Water is also very important in industry. Overall, water is unusual substance with more than 70 anomalous properties. The understanding of water is advancing significantly due to theoretical and computational modeling. There are different kind of models, models with fine-scale properties and increasing structural detail with increasing computational expense and simple models which focus on global properties of water like thermodynamics, phase diagram and are less computational expensive. Simplified models give a better understanding of water in ways that complement more complex models. Here, we review a simple model, the two dimensional Mercedes-Benz (MB) model of water. We present results by Monte Carlo simulations for anomalies and phase diagram and application of various theoretical methods.
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Affiliation(s)
- Tomaz Urbic
- University of Ljubljana, Faculty of Chemistry and Chemical Technology,
Večna pot 113, SI-1000 Ljubljana, Slovenia
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22
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Abstract
Methanol is the simplest alcohol and possible energy carrier because it is easier to store than hydrogen and burns cleaner than fossil fuels. It is a colorless liquid, completely miscible with water and organic solvents and is very hygroscopic. Here, simple two-dimensional models of methanol, based on Mercedes-Benz (MB) model of water, are examined by Monte Carlo simulations. Methanol particles are modeled as dimers formed by an apolar Lennard-Jones disk, mimicking the methyl group, and a sphere with two hydrogen bonding arms for the hydroxyl group. The used models are the one proposed by Hribar-Lee and Dill (Acta Chimica Slovenica, 53:257, 2006.) with the overlapping discs and a new model with tangentially fused dimers. The comparison was done between the models, in connection to the MB water, as well as with experimental results and with new simulations done for 3D models of methanol. Both 2D models show similar trends in structuring and thermodynamics. The difference is the most pronounced at lower temperatures, where the smaller model exhibits spontaneous crystallization, while the larger model shows metastable states. The 2D structural organization represents well the clustering tendency observed in 3D models, as well as in experiments. The models qualitatively agree with the bulk methanol thermodynamic properties like density and isothermal compressibility, however, heat capacity at the constant pressure shows trend more similar to the water behavior. This work on the smallest amphiphilic organic solute provides a simple testing ground to study the competition between polar and non-polar effects within the molecule and physical properties.
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Affiliation(s)
- Tomislav Primorac
- Faculty of Science, University of Split, Rudjera Boškovića 33, 21000 Split, Croatia
- Fakultät für Maschinenbau, Universität Paderborn, Warburger Str. 100, 33098 Paderborn, Germany
| | - Martina Požar
- Faculty of Science, University of Split, Rudjera Boškovića 33, 21000 Split, Croatia
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600), Université Pierre et Marie Curie, 4 Place Jussieu, F75252, Paris cedex 05, France
| | - Franjo Sokolić
- Faculty of Science, University of Split, Rudjera Boškovića 33, 21000 Split, Croatia
| | - Larisa Zoranić
- Faculty of Science, University of Split, Rudjera Boškovića 33, 21000 Split, Croatia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
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23
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Affiliation(s)
- Tomoaki Yagi
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
- ESICB, Kyoto University, Kyoto 615-8510, Japan
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Torres-Carbajal A, Castañeda-Priego R. Friction and diffusion of a nano-colloidal disk in a two-dimensional solvent with a liquid-liquid transition. Phys Chem Chem Phys 2018; 20:6917-6928. [PMID: 29464245 DOI: 10.1039/c7cp08302e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on the friction and diffusion of a single mobile nano-colloidal disk, whose size and mass are one and two orders of magnitude, respectively, greater than the molecules of the host solvent; all particles are restricted to move in a two-dimensional space. Using molecular dynamics simulations, the variation of the transport coefficients as a function of the thermodynamic state of the supporting fluid, in particular, around those states in the neighbourhood of the liquid-liquid phase coexistence, is investigated. The diffusion coefficient is determined through the fit of the mean-square displacement at long times and with the Green-Kubo relationship for the velocity autocorrelation function, whereas the friction coefficient is computed from the correlation of the fluctuating force. From the determination of the transport properties, the applicability of the Stokes-Einstein relation in two dimensions around the second critical point is discussed.
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Affiliation(s)
- Alexis Torres-Carbajal
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, Mexico.
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Urbic T. Liquid part of the phase diagram and percolation line for two-dimensional Mercedes-Benz water. Phys Rev E 2018; 96:032122. [PMID: 29346988 DOI: 10.1103/physreve.96.032122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Indexed: 11/07/2022]
Abstract
Monte Carlo simulations and Wertheim's thermodynamic perturbation theory (TPT) are used to predict the phase diagram and percolation curve for the simple two-dimensional Mercedes-Benz (MB) model of water. The MB model of water is quite popular for explaining water properties, but the phase diagram has not been reported till now. In the MB model, water molecules are modeled as two-dimensional Lennard-Jones disks, with three orientation-dependent hydrogen-bonding arms, arranged as in the MB logo. The liquid part of the phase space is explored using grand canonical Monte Carlo simulations and two versions of Wertheim's TPT for associative fluids, which have been used before to predict the properties of the simple MB model. We find that the theory reproduces well the physical properties of hot water but is less successful at capturing the more structured hydrogen bonding that occurs in cold water. In addition to reporting the phase diagram and percolation curve of the model, it is shown that the improved TPT predicts the phase diagram rather well, while the standard one predicts a phase transition at lower temperatures. For the percolation line, both versions have problems predicting the correct position of the line at high temperatures.
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Affiliation(s)
- T Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, 1000 Ljubljana, Slovenia
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26
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Gladovic M, Bren U, Urbic T. Thermodynamic properties of water in confined environments: a Monte Carlo study. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1409911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Martin Gladovic
- Laboratory for Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Maribor, Slovenia
- Chair of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Urban Bren
- Laboratory for Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Maribor, Slovenia
- Laboratory of Molecular Modelling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tomaž Urbic
- Chair of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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27
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Urbic T, Najem S, Dias CL. Thermodynamic properties of amyloid fibrils in equilibrium. Biophys Chem 2017; 231:155-160. [PMID: 28318905 PMCID: PMC5589490 DOI: 10.1016/j.bpc.2017.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/01/2017] [Accepted: 03/02/2017] [Indexed: 11/19/2022]
Abstract
In this manuscript we use a two-dimensional coarse-grained model to study how amyloid fibrils grow towards an equilibrium state where they coexist with proteins dissolved in a solution. Free-energies to dissociate proteins from fibrils are estimated from the residual concentration of dissolved proteins. Consistent with experiments, the concentration of proteins in solution affects the growth rate of fibrils but not their equilibrium state. Also, studies of the temperature dependence of the equilibrium state can be used to estimate thermodynamic quantities, e.g., heat capacity and entropy.
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Affiliation(s)
- Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000, Slovenia.
| | - Sara Najem
- National Center for Remote Sensing, National Council for Scientific Research (CNRS), Riad al Soloh, 1107 2260 Beirut, Lebanon
| | - Cristiano L Dias
- New Jersey Institute of Technology, Physics Department, Newark,NJ 07042-1982,United States
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Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšič M, Dill KA. How Water's Properties Are Encoded in Its Molecular Structure and Energies. Chem Rev 2017; 117:12385-12414. [PMID: 28949513 PMCID: PMC5639468 DOI: 10.1021/acs.chemrev.7b00259] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 11/29/2022]
Abstract
How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties.
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Affiliation(s)
- Emiliano Brini
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Christopher J. Fennell
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Marivi Fernandez-Serra
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Barbara Hribar-Lee
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, SI-1000 Ljubljana, Slovenia
| | - Miha Lukšič
- 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, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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29
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Integral equation and thermodynamic perturbation theory for a two-dimensional model of chain-forming fluid. J Mol Liq 2017; 238:129-135. [PMID: 28729752 DOI: 10.1016/j.molliq.2017.04.095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this paper we applied analytical theories for the two dimensional chain-forming fluid. Wertheims thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids were used to study thermodynamical and structural properties of the chain-forming model. The model has polymerizing points at arbitrary position from center of the particles. Calculated analytical results were tested against corresponding results obtained by Monte Carlo computer simulations to check the accuracy of the theories. The theories are accurate for the different positions of patches of the model at all values of the temperature and density studied. The IET's pair correlation functions of the model agree well with computer simulations. Both TPT and IET are in good agreement with the Monte Carlo values of the energy, chemical potential and ratios of free, once and twice bonded particles.
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Urbic T. Integral equation and thermodynamic perturbation theory for a two-dimensional model of dimerising fluid. J Mol Liq 2017; 228:32-37. [PMID: 28529396 DOI: 10.1016/j.molliq.2016.09.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In this paper we applied an analytical theory for the two dimensional dimerising fluid. We applied Wertheims thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids to the dimerising model with arbitrary position of dimerising points from center of the particles. The theory was used to study thermodynamical and structural properties. To check the accuracy of the theories we compared theoretical results with corresponding results obtained by Monte Carlo computer simulations. The theories are accurate for the different positions of patches of the model at all values of the temperature and density studied. IET correctly predicts the pair correlation function of the model. Both TPT and IET are in good agreement with the Monte Carlo values of the energy, pressure, chemical potential, compressibility and ratios of free and bonded particles.
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Affiliation(s)
- Tomaz Urbic
- University of Ljubljana, Department of Chemistry and Chemical Technology, Chair of Physical Chemistry, Večna pot 113, SI-1000 Ljubljana, Slovenia
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31
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Urbic T, Mohoric T. Effects of translational and rotational degrees of freedom on properties of the Mercedes–Benz water model. J Chem Phys 2017. [DOI: 10.1063/1.4977214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- T. Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - T. Mohoric
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
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Urbic T. Properties of the two-dimensional heterogeneous Lennard-Jones dimers: An integral equation study. J Chem Phys 2016; 145:194503. [PMID: 27875894 PMCID: PMC5116027 DOI: 10.1063/1.4967807] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/02/2016] [Indexed: 11/14/2022] Open
Abstract
Structural and thermodynamic properties of a planar heterogeneous soft dumbbell fluid are examined using Monte Carlo simulations and integral equation theory. Lennard-Jones particles of different sizes are the building blocks of the dimers. The site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions and the thermodynamic properties. Obtained results are compared to Monte Carlo simulation data. The critical parameters for selected types of dimers were also estimated and the influence of the Lennard-Jones parameters was studied. We have also tested the correctness of the site-site integral equation theory using different closures.
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Affiliation(s)
- Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Lubljana, Slovenia
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34
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Torres-Carbajal A, Castañeda-Priego R. Characterisation of the thermodynamics, structure and dynamics of a water-like model in 2- and 3-dimensions. Phys Chem Chem Phys 2016; 18:17335-40. [PMID: 27232761 DOI: 10.1039/c6cp01565d] [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
The physical properties of colloidal particles suspended in an aqueous environment are well-understood when the latter is considered to be a continuum and a structureless medium. However, this approach fails to explain complex phenomena, for example, the critical Casimir forces among colloids and the colloidal self-assembly near critical solvents, and the inertial contribution of the solvent molecules on the diffusion of non-spherical Brownian particles. Therefore, the role played by the solvent on the physical properties of colloidal dispersions is of paramount relevance. Recently, there has been an interest in the (non-trivial) diffusion mechanisms of a nano-colloidal particle in a solvent that undergoes a vapour-liquid transition. Nonetheless, the models typically used to incorporate the solvent details do not capture quantitatively the thermodynamic properties of real substances. It is then important to study the Brownian motion of colloids in more realistic models. To reach such goal, one first has to characterise the thermodynamic states and the microscopic features of the solvent. Hence, in this contribution, we have investigated the coexistence densities of a core-softened potential in two- and three-dimensions, whose potential parameters are able to capture some anomalies of water. We show that in the two-dimensional case, the potential model exhibits, besides the normal vapour-liquid coexistence region, additional liquid-liquid coexistence densities. We particularly focus our attention to the structural properties and the dynamical behaviour of the solvent around the liquid-liquid critical point and assess the differences with the three-dimensional case.
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Affiliation(s)
- Alexis Torres-Carbajal
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, México.
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35
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Fennell CJ, Gezelter JD. Computational Free Energy Studies of a New Ice Polymorph Which Exhibits Greater Stability than Ice Ih. J Chem Theory Comput 2015; 1:662-7. [PMID: 26641688 DOI: 10.1021/ct050005s] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The absolute free energies of several ice polymorphs were calculated using thermodynamic integration. These polymorphs are predicted by computer simulations using a variety of common water models to be stable at low pressures. A recently discovered ice polymorph that has as yet only been observed in computer simulations (Ice-i) was determined to be the stable crystalline state for all the water models investigated. Phase diagrams were generated, and phase coexistence lines were determined for all of the known low-pressure ice structures. Additionally, potential truncation was shown to play a role in the resulting shape of the free energy landscape.
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Affiliation(s)
- Christopher J Fennell
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - J Daniel Gezelter
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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36
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Banerjee S, Singh RS, Bagchi B. Orientational order as the origin of the long-range hydrophobic effect. J Chem Phys 2015; 142:134505. [PMID: 25854251 DOI: 10.1063/1.4916744] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The long range attractive force between two hydrophobic surfaces immersed in water is observed to decrease exponentially with their separation-this distance-dependence of effective force is known as the hydrophobic force law (HFL). We explore the microscopic origin of HFL by studying distance-dependent attraction between two parallel rods immersed in 2D Mercedes Benz model of water. This model is found to exhibit a well-defined HFL. Although the phenomenon is conventionally explained by density-dependent theories, we identify orientation, rather than density, as the relevant order parameter. The range of density variation is noticeably shorter than that of orientational heterogeneity. The latter is comparable to the observed distances of hydrophobic force. At large separation, attraction between the rods arises primarily from a destructive interference among the inwardly propagating oppositely oriented heterogeneity generated in water by the two rods. As the rods are brought closer, the interference increases leading to a decrease in heterogeneity and concomitant decrease in free energy of the system, giving rise to the effective attraction. We notice formation of hexagonal ice-like structures at the onset of attractive region which suggests that metastable free energy minimum may play a role in the origin of HFL.
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Affiliation(s)
- Saikat Banerjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Rakesh S Singh
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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37
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Kurtjak M, Urbic T. A simple water model in the presence of inert Lennard-Jones obstacles II: the hydrophobic effect. Mol Phys 2014. [DOI: 10.1080/00268976.2014.973919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Urbic T, Dias CL. Properties of the Lennard-Jones dimeric fluid in two dimensions: an integral equation study. J Chem Phys 2014; 140:094703. [PMID: 24606372 PMCID: PMC3977749 DOI: 10.1063/1.4867289] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 02/19/2014] [Indexed: 12/21/2022] Open
Abstract
The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known.
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Affiliation(s)
- Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
| | - Cristiano L Dias
- Physics Department, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, USA
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39
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Mohorič T, Urbic T, Hribar-Lee B. The application of the integral equation theory to study the hydrophobic interaction. J Chem Phys 2014; 140:024502. [PMID: 24437891 PMCID: PMC3970826 DOI: 10.1063/1.4858398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/10/2013] [Indexed: 11/14/2022] Open
Abstract
The Wertheim's integral equation theory was tested against newly obtained Monte Carlo computer simulations to describe the potential of mean force between two hydrophobic particles. An excellent agreement was obtained between the theoretical and simulation results. Further, the Wertheim's integral equation theory with polymer Percus-Yevick closure qualitatively correctly (with respect to the experimental data) describes the solvation structure under conditions where the simulation results are difficult to obtain with good enough accuracy.
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Affiliation(s)
- Tomaž Mohorič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
| | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
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40
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41
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Mohoric T, Urbic T, Hribar-Lee B. The application of the thermodynamic perturbation theory to study the hydrophobic hydration. J Chem Phys 2013; 139:024101. [PMID: 23862923 DOI: 10.1063/1.4812744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures.
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Affiliation(s)
- Tomaz Mohoric
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
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42
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Cartwright JHE, Piro O, Sánchez PA, Sintes T. Ice polyamorphism in the minimal Mercedes-Benz model of water. J Chem Phys 2012; 137:244503. [PMID: 23277941 DOI: 10.1063/1.4772202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate ice polyamorphism in the context of the two-dimensional Mercedes-Benz model of water. We find a first-order phase transition between a crystalline phase and a high-density amorphous phase. Furthermore, we find a reversible transformation between two amorphous structures of high and low density; however, we find this to be a continuous and not an abrupt transition, as the low-density amorphous phase does not show structural stability. We discuss the origin of this behavior and its implications with regard to the minimal generic modeling of polyamorphism.
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Affiliation(s)
- Julyan H E Cartwright
- Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, E-18071 Granada, Spain.
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43
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Lukšič M, Urbic T, Hribar-Lee B, Dill KA. Simple model of hydrophobic hydration. J Phys Chem B 2012; 116:6177-86. [PMID: 22564051 DOI: 10.1021/jp300743a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water is an unusual liquid in its solvation properties. Here, we model the process of transferring a nonpolar solute into water. Our goal was to capture the physical balance between water's hydrogen bonding and van der Waals interactions in a model that is simple enough to be nearly analytical and not heavily computational. We develop a 2-dimensional Mercedes-Benz-like model of water with which we compute the free energy, enthalpy, entropy, and the heat capacity of transfer as a function of temperature, pressure, and solute size. As validation, we find that this model gives the same trends as Monte Carlo simulations of the underlying 2D model and gives qualitative agreement with experiments. The advantages of this model are that it gives simple insights and that computational time is negligible. It may provide a useful starting point for developing more efficient and more realistic 3D models of aqueous solvation.
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Affiliation(s)
- Miha Lukšič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
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44
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Urbic T, Holovko MF. Mercedes-Benz water molecules near hydrophobic wall: integral equation theories vs Monte Carlo simulations. J Chem Phys 2011; 135:134706. [PMID: 21992334 DOI: 10.1063/1.3644934] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Associative version of Henderson-Abraham-Barker theory is applied for the study of Mercedes-Benz model of water near hydrophobic surface. We calculated density profiles and adsorption coefficients using Percus-Yevick and soft mean spherical associative approximations. The results are compared with Monte Carlo simulation data. It is shown that at higher temperatures both approximations satisfactory reproduce the simulation data. For lower temperatures, soft mean spherical approximation gives good agreement at low and at high densities while in at mid range densities, the prediction is only qualitative. The formation of a depletion layer between water and hydrophobic surface was also demonstrated and studied.
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Affiliation(s)
- T Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana SI-1000, Slovenia.
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45
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Urbic T, Dill KA. A statistical mechanical theory for a two-dimensional model of water. J Chem Phys 2010; 132:224507. [PMID: 20550408 DOI: 10.1063/1.3454193] [Citation(s) in RCA: 28] [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 develop a statistical mechanical model for the thermal and volumetric properties of waterlike fluids. Each water molecule is a two-dimensional disk with three hydrogen-bonding arms. Each water interacts with neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of the Truskett and Dill (TD) treatment of the "Mercedes-Benz" (MB) model. The present model gives better predictions than TD for hydrogen-bond populations in liquid water by distinguishing strong cooperative hydrogen bonds from weaker ones. We explore properties versus temperature T and pressure p. We find that the volumetric and thermal properties follow the same trends with T as real water and are in good general agreement with Monte Carlo simulations of MB water, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds for increasing temperature. The model reproduces that pressure squeezes out water's heat capacity and leads to a negative thermal expansion coefficient at low temperatures. In terms of water structuring, the variance in hydrogen-bonding angles increases with both T and p, while the variance in water density increases with T but decreases with p. Hydrogen bonding is an energy storage mechanism that leads to water's large heat capacity (for its size) and to the fragility in its cagelike structures, which are easily melted by temperature and pressure to a more van der Waals-like liquid state.
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Affiliation(s)
- Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia.
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46
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Bizjak A, Urbic T, Vlachy V, Dill KA. Theory for the three-dimensional Mercedes-Benz model of water. J Chem Phys 2010; 131:194504. [PMID: 19929057 DOI: 10.1063/1.3259970] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the "right answer," we perform isothermal-isobaric Monte Carlo simulations on the 3D MB model for different pressures and temperatures. The purpose of this work is to develop and test Wertheim's Ornstein-Zernike integral equation and thermodynamic perturbation theories. The two analytical approaches are orders of magnitude more efficient than the Monte Carlo simulations. The ultimate goal is to find statistical mechanical theories that can efficiently predict the properties of orientationally complex molecules, such as water. Also, here, the 3D MB model simply serves as a useful workbench for testing such analytical approaches. For hot water, the analytical theories give accurate agreement with the computer simulations. For cold water, the agreement is not as good. Nevertheless, these approaches are qualitatively consistent with energies, volumes, heat capacities, compressibilities, and thermal expansion coefficients versus temperature and pressure. Such analytical approaches offer a promising route to a better understanding of water and also the aqueous solvation.
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Affiliation(s)
- Alan Bizjak
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia
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Zhou S, Solana JR. Progress in the Perturbation Approach in Fluid and Fluid-Related Theories. Chem Rev 2009; 109:2829-58. [DOI: 10.1021/cr900094p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Shiqi Zhou
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083, China, and School of Physics Science and Technology, Central South University, Changsha, Hunan 410083, China
| | - J. R. Solana
- Applied Physics Department, University of Cantabria, 39005 Santander, Spain
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Hlushak SP, Kalyuzhnyi YV. Phase coexistence in the hard-sphere Yukawa chain fluid with chain length polydispersity: Dimer thermodynamic perturbation theory. J Chem Phys 2008; 129:224901. [DOI: 10.1063/1.3028044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Urbic T, Vlachy V, Kalyuzhnyi YV, Dill KA. Theory for the solvation of nonpolar solutes in water. J Chem Phys 2008; 127:174505. [PMID: 17994825 DOI: 10.1063/1.2779329] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We recently developed an angle-dependent Wertheim integral equation theory (IET) of the Mercedes-Benz (MB) model of pure water [Silverstein et al., J. Am. Chem. Soc. 120, 3166 (1998)]. Our approach treats explicitly the coupled orientational constraints within water molecules. The analytical theory offers the advantage of being less computationally expensive than Monte Carlo simulations by two orders of magnitude. Here we apply the angle-dependent IET to studying the hydrophobic effect, the transfer of a nonpolar solute into MB water. We find that the theory reproduces the Monte Carlo results qualitatively for cold water and quantitatively for hot water.
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Affiliation(s)
- T Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia
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Urbic T, Vlachy V, Kalyuzhnyi YV, Dill KA. An improved thermodynamic perturbation theory for Mercedes-Benz water. J Chem Phys 2007; 127:174511. [DOI: 10.1063/1.2784124] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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