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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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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4
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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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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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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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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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8
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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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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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12
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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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13
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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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14
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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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15
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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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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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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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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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19
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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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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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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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22
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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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23
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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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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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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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Mohorič T, Bren U, Vlachy V. Fast rotational motion of water molecules increases ordering of hydrophobes in solutions and may cause hydrophobic chains to collapse. J Chem Phys 2015; 143:244510. [DOI: 10.1063/1.4939085] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tomaž Mohorič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
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30
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Dutta S, Lee Y, Jho YS. Hydration of ions in two-dimensional water. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042152. [PMID: 26565213 DOI: 10.1103/physreve.92.042152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Indexed: 06/05/2023]
Abstract
We present a two-dimensional lattice model of water to study the effects of ion hydration on the properties of water. We map the water molecules as lattice particles consisting of a single oxygen atom at the center of a site and two hydrogen atoms on each side. The internal state of the system, such as the dipole moment at a site, is defined with respect to the location of the hydrogen atoms at the site depending on their role in hydrogen bonds (H bonds) being a donor or an acceptor. We study the influence of the charge and the radius of the ion on the insertion energy and on the H bonds in the first and second hydration layers around the ion and in the bulk. In particular we analyze how the competing interactions of the short-ranged H bonds and the long-ranged electrostatics influence the hydration properties. The role of the ion both as a source of the electrostatic interactions as well as a defect is also discussed. Our model also shows the well-known fact that the polarizability of the water molecules destroys the hydrogen bond network and increases the dipole moment of the molecules near the ion.
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Affiliation(s)
- S Dutta
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, 790-784, Korea
| | - Yongjin Lee
- Department of Physics, Pohang University of Science and Technology and Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, 790-784, Korea
| | - Y S Jho
- Department of Physics, Pohang University of Science and Technology and Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, 790-784, Korea
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31
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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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32
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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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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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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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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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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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38
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Nezbeda I, Jirsák J. Water and aqueous solutions: simple non-speculative model approach. Phys Chem Chem Phys 2011; 13:19689-703. [PMID: 21952227 DOI: 10.1039/c1cp21903k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Different ways of molecular modeling of water are analyzed and their similarities and differences identified. An up-to-date summary of achievements of a general approach to common rigid site-site interaction models of molecular fluids applied to water and aqueous solutions is then presented and discussed. The method is based on considering only a short-range part of a total realistic potential (such as SPC/E or TIPxP) which determines the structure of water (and fluids in general). A simplification of the interactions at short intermolecular separations leads then to simple models, called primitive models. Quite accurate results in an analytic form for the thermodynamic properties of the models are obtained using the thermodynamic perturbation theory. It is shown that the properly constructed primitive models reproduce, qualitatively, anomalies of pure water and basic characteristics of hydrophobic hydration. The concept of an extended excluded volume, based on pseudo-hard bodies, is introduced and exemplified by considering the partial molar volume of apolar solutes. Potential future development towards a theory of water based on the primitive models as a reference with the long-range contributions added as a perturbation is discussed.
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Affiliation(s)
- Ivo Nezbeda
- Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czech Republic.
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39
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Study of heat of micellization and phase separation for Pluronic aqueous solutions by using a high sensitivity differential scanning calorimetry. Colloid Polym Sci 2010. [DOI: 10.1007/s00396-010-2308-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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40
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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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41
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Ababneh AM. The role of polarization interactions in the wrapping/unwrapping of nucleosomal DNA around the histone octamer: Implications to gene regulation. J Theor Biol 2009; 258:229-39. [DOI: 10.1016/j.jtbi.2009.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 02/10/2009] [Accepted: 02/12/2009] [Indexed: 10/21/2022]
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42
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Tsui HW, Hsu YH, Wang JH, Chen LJ. Novel behavior of heat of micellization of pluronics F68 and F88 in aqueous solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:13858-62. [PMID: 19053637 DOI: 10.1021/la803272y] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
It is well understood that the heat of micellization for surfactants is monotonically decreased along with an increase in temperature. However, this behavior for polymeric surfactants has never been carefully examined. In this study, the heat of micellization of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymers (Pluronics F68 and F88) in water as a function of temperature is carefully examined by using a high-sensitivity differential scanning calorimeter (HSDSC). The critical micelle temperature (CMT) decreases along with an increase in the concentration of Pluronic F68 (or F88). The heat of micellization decreases along with an increase in the temperature, as expected, when the CMT is higher than 55 and 42 degrees C for Pluronics F68 and F88, respectively. It is interesting to observe that the heat of micellization increases along with the temperature while the temperature is below 55 and 42 degrees C for Pluronics F68 and F88, respectively. The enthalpy-entropy compensation phenomenon for the micellization of Pluronics F68 and F88 in connection with the hydrophobicity is discussed.
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Affiliation(s)
- Hung-Wei Tsui
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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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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44
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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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45
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Abstract
Whereas heat capacity changes (DeltaCPs) associated with folding transitions are commonplace in the literature of protein folding, they have long been considered a minor energetic contributor in nucleic acid folding. Recent advances in the understanding of nucleic acid folding and improved technology for measuring the energetics of folding transitions have allowed a greater experimental window for measuring these effects. We present in this review a survey of current literature that confronts the issue of DeltaCPs associated with nucleic acid folding transitions. This work helps to gather the molecular insights that can be gleaned from analysis of DeltaCPs and points toward the challenges that will need to be overcome if the energetic contribution of DeltaCP terms are to be put to use in improving free energy calculations for nucleic acid structure prediction.
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Affiliation(s)
- Peter J Mikulecky
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue Bloomington, IN 47401, USA
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Abstract
We study water that is confined within small geometric spaces. We use the Mercedes-Benz (MB) model of water, in NVT and muVT Monte Carlo computer simulations. For MB water molecules between two planes separated by a distance d, we explore the structures, hydrogen bond networks, and thermodynamics as a function of d, temperature T, and water chemical potential mu. We find that squeezing the planes close enough together leads to a vaporization of waters out of the cavity. This vaporization transition has a corresponding peak in the heat capacity of the water. We also find that, in small pores, hydrogen bonding is not isotropic but, rather, it preferentially forms chains along the axis of the cavity. This may be relevant for fast proton transport in pores. Our simulations show oscillations in the forces between the inert plates, due to water structure, even for plate separations of 5-10 water diameters, consistent with experiments by Israelachvili et al. [Nature 1983, 306, 249]. Finally, we find that confinement affects water's heat capacity, consistent with recent experiments of Tombari et al. on Vycor nanopores [J. Chem. Phys. 2005, 122, 104712].
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Affiliation(s)
- T Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, SI-1000 Ljubljana, Slovenia
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Duda Y, Govea-Rueda R, Galicia M, Beltran HI, Zamudio-Rivera LS. Corrosion Inhibitors: Design, Performance, and Computer Simulations. J Phys Chem B 2005; 109:22674-84. [PMID: 16853952 DOI: 10.1021/jp0522765] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of a methodology to predict the performance of a corrosion inhibitor (CI) using specific types of modeled and experimental surfaces and their subsequent estimation is presented. For previously reported imidazoline CIs, the theoretical partition coefficients and molecular volumes were calculated, providing a guide for molecular engineering of new imidazolines. The new CIs, N-[2-(2-alkyl-4,5-dihydroimidazol-1-yl)ethyl]alkylamides and N-[2-(2-alkyloylaminoethylamino)ethyl]alkylamides, were designed, prepared, and their theoretical partition coefficients and molecular volumes calculated. These indexes were correlated between tested and prototype CIs to select the best ones for the corrosion inhibition tests. The inhibition efficiencies were measured through potentiodynamic polarization curves (PPC), linear polarization resistance (LPR), and weight loss measurements (WLM) for SAE-1010 and SAE-1018 steels. The leading molecules were 1-(2-decylaminoethyl)-2-decylimidazoline and 1-(2-dodecylaminoethyl)-2-dodecylimidazoline with WLM efficiencies (steel 1010), of 62.8 and 78.9%, respectively. The efficiencies for the PPC/LPR tests (steel 1018) were 97 and 94%. To understand the mechanism of action of CIs, a simple model is suggested for the growth of self-assembled monolayers of CIs on a crystalline substrate. This model takes into account the amphiphilic nature of the inhibitor molecule on the adsorption process. Despite the simplicity of the model, the Monte Carlo simulations reproduce qualitatively many of the experimentally observed features involved in the formation of monolayers and provide a tentative explanation for the mechanism of corrosion inhibition.
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Affiliation(s)
- Yurko Duda
- Programa de Ingeniería Molecular, Instituto Mexicano del Petróleo, Eje Central L. Cardenas 152, 07730, México, D. F.
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Abstract
Water plays a central role in the structures and properties of biomolecules--proteins, nucleic acids, and membranes--and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global properties-water's thermodynamics, phase diagram, and solvation properties, for example-and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of water-as a pure liquid and as a solvent-derive from the geometric and hydrogen bonding properties of water.
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Affiliation(s)
- Ken A Dill
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-2240, USA.
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Buzano C, De Stefanis E, Pretti M. Hydration of an apolar solute in a two-dimensional waterlike lattice fluid. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 71:051502. [PMID: 16089537 DOI: 10.1103/physreve.71.051502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Indexed: 05/03/2023]
Abstract
In a previous work, we investigated a two-dimensional lattice-fluid model, displaying some waterlike thermodynamic anomalies. The model, defined on a triangular lattice, is now extended to aqueous solutions with apolar species. Water molecules are of the "Mercedes Benz" type, i.e., they possess a D3 (equilateral triangle) symmetry, with three equivalent bonding arms. Bond formation depends both on orientation and local density. The insertion of inert molecules displays typical signatures of hydrophobic hydration: large positive transfer free energy, large negative transfer entropy (at low temperature), strong temperature dependence of the transfer enthalpy and entropy, i.e., large (positive) transfer heat capacity. Model properties are derived by a generalized first order approximation on a triangle cluster.
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Affiliation(s)
- C Buzano
- Istituto Nazionale per la Fisica della Materia (INFM) and Dipartimento di Fisica, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Turin, Italy
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50
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Chen LJ, Sheu YH, Li PJ. Heat Capacity Changes Accompanying Micelle Formation upon Burial of Hydrophobic Tail of Nonionic Surfactants. J Phys Chem B 2004. [DOI: 10.1021/jp045486a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li-Jen Chen
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan 10617, Republic of China
| | - Yih-Heh Sheu
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan 10617, Republic of China
| | - Pei-Juian Li
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan 10617, Republic of China
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