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Publications (10 of 11) Show all publications
Liang, S., Hall, K. W., Laaksonen, A., Zhang, Z. & Kusalik, P. G. (2019). Characterizing key features in the formation of ice and gas hydrate systems. Philosophical Transactions. Series A: Mathematical, physical, and engineering science, 377(2146), Article ID 20180167.
Open this publication in new window or tab >>Characterizing key features in the formation of ice and gas hydrate systems
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2019 (English)In: Philosophical Transactions. Series A: Mathematical, physical, and engineering science, ISSN 1364-503X, E-ISSN 1471-2962, Vol. 377, no 2146, article id 20180167Article, review/survey (Refereed) Published
Abstract [en]

Crystallization in liquids is critical to a range of important processes occurring in physics, chemistry and life sciences. In this article, we review our efforts towards understanding the crystallization mechanisms, where we focus on theoretical modelling and molecular simulations applied to ice and gas hydrate systems. We discuss the order parameters used to characterize molecular ordering processes and how different order parameters offer different perspectives of the underlying mechanisms of crystallization. With extensive simulations of water and gas hydrate systems, we have revealed unexpected defective structures and demonstrated their important roles in crystallization processes. Nucleation of gas hydrates can in most cases be characterized to take place in a two-step mechanism where the nucleation occurs via intermediate metastable precursors, which gradually reorganizes to a stable crystalline phase. We have examined the potential energy landscapes explored by systems during nucleation, and have shown that these landscapes are rugged and funnel-shaped. These insights provide a new framework for understanding nucleation phenomena that has not been addressed in classical nucleation theory. This article is part of the theme issue 'The physics and chemistry of ice: scaffolding across scales, from the viability of life to the formation of planets'.

Place, publisher, year, edition, pages
ROYAL SOC, 2019
Keywords
molecular simulation, nucleation, ice, gas hydrate, crystal growth, crystal defect
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-386369 (URN)10.1098/rsta.2018.0167 (DOI)000466382900005 ()30982452 (PubMedID)
Funder
Wenner-Gren Foundations
Available from: 2019-06-24 Created: 2019-06-24 Last updated: 2019-06-24Bibliographically approved
Dong, Y., Ji, X., Laaksonen, A., Cao, W., An, R., Lu, L. & Lu, X. (2019). Determination of the small amount of proteins interacting with TiO2 nanotubes by AFM-measurement. Biomaterials, 192, 368-376
Open this publication in new window or tab >>Determination of the small amount of proteins interacting with TiO2 nanotubes by AFM-measurement
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2019 (English)In: Biomaterials, ISSN 0142-9612, E-ISSN 1878-5905, Vol. 192, p. 368-376Article in journal (Refereed) Published
Abstract [en]

Detecting the small amounts of proteins interacting effectively with the solid film electrodes surface still remains a challenge. To address this, in this work, a new approach was proposed by the combination of the adhesion forces and the molecular interaction measured with AFM. Cytochrome c (Cyt C) interacting effectively with TiO2 nanotube arrays (TNAs) was chosen as a probe. The amounts of Cyt C molecules interacting effectively on TNAs surface (C-TNA) range from 5.5x10(-12) to 7.0x10(-12) mol/cm(2) (68.2-86.8 ng/cm(2)) and they are comparable with the values obtained by the electrochemistry method in the literature, in evidence of the accuracy of this AFM-based approach. The reliability of the proposed approach was further verified by conducting Surface Enhanced Raman Scattering (SERS) measurements and estimating the enhancement factor (EF). This interaction-based AFM approach can be used to accurately obtain the small amounts of adsorbed substances on the solid film electrodes surface in the applications such as biosensors, biocatalysis, and drug delivery, etc.

Keywords
TiO2 nanotubes, Adsorption amount, AFM, Molecular interaction, Adhesion force, SERS
National Category
Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-377336 (URN)10.1016/j.biomaterials.2018.11.013 (DOI)000456902000030 ()30476718 (PubMedID)
Available from: 2019-02-25 Created: 2019-02-25 Last updated: 2019-02-25Bibliographically approved
Sarman, S., Wang, Y.-L. & Laaksonen, A. (2019). Shear flow simulations of smectic liquid crystals based on the Gay–Berne fluid and the soft sphere string-fluid. Physical Chemistry, Chemical Physics - PCCP, 21(1), 292-305
Open this publication in new window or tab >>Shear flow simulations of smectic liquid crystals based on the Gay–Berne fluid and the soft sphere string-fluid
2019 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 1, p. 292-305Article in journal (Refereed) Published
Abstract [en]

We have studied the shear flow of the smectic A phase of three coarse grained liquid crystal model systems, namely two versions of the Gay-Berne fluid and the soft sphere string-fluid. At low shear rates, the orientation where the smectic layers are parallel to the shear plane and the orientation parallel to the vorticity plane are both stable in all the systems. In one of the Gay-Berne fluids, there is a transition from the orientation parallel to the shear plane to the orientation parallel to the vorticity plane. At higher shear rates, a nonequilibrium nematic phase is obtained in all the systems in the same way as in linear alkanes under shear. If the initial configuration is an equilibrium smectic A phase or a nematic phase with the molecules parallel to the streamlines, the orientation parallel to the shear plane is attained at low shear rates in the Gay-Berne fluids. In order to analyze the stability of the different orientations, the torque acting on the liquid crystal is calculated. It consists of an elastic torque caused by deformations due to the shape of the simulation cell and the periodic boundary conditions and a shear-induced torque. The elastic torque stabilizes both the orientation parallel to the shear plane and the orientation parallel to the vorticity plane because the liquid crystal is deformed if it is turned away from these orientations. The shear-induced torque, on the other hand, always turns the liquid crystal to the orientation parallel to the vorticity plane where the viscosity and the irreversible energy dissipation rate are minimal. Since the latter torque is proportional to the square of the shear rate, rather high shear rates are required for it to overwhelm the elastic torque. However, the elastic torque decreases with the system size so that it is likely that the shear-induced torque will dominate in large systems and that the orientation parallel to the vorticity plane will be attained at low or even zero shear rate.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-374425 (URN)10.1039/c8cp05077e (DOI)000454836700029 ()30520918 (PubMedID)
Funder
Swedish Research Council, 2014-4694Swedish National Infrastructure for Computing (SNIC)
Available from: 2019-01-29 Created: 2019-01-29 Last updated: 2019-01-29Bibliographically approved
Fossépré, M., Leherte, L., Laaksonen, A. & Vercauteren, D. P. (2019). Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Science. In: Biomolecular Simulations in Structure-based Drug Discovery: . Wiley-VCH Verlagsgesellschaft
Open this publication in new window or tab >>Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Science
2019 (English)In: Biomolecular Simulations in Structure-based Drug Discovery, Wiley-VCH Verlagsgesellschaft, 2019Chapter in book (Refereed)
Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2019
National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-396833 (URN)
Available from: 2019-11-11 Created: 2019-11-11 Last updated: 2019-11-11
Shen, G., Laaksonen, A., Lu, X. & Ji, X. (2018). Developing Electrolyte Perturbed-Chain Statistical Associating Fluid Theory Density Functional Theory for CO2 Separation by Confined Ionic Liquids. The Journal of Physical Chemistry C, 122(27), 15464-15473
Open this publication in new window or tab >>Developing Electrolyte Perturbed-Chain Statistical Associating Fluid Theory Density Functional Theory for CO2 Separation by Confined Ionic Liquids
2018 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 27, p. 15464-15473Article in journal (Refereed) Published
Abstract [en]

The electrolyte perturbed-chain statistical associating fluid theory (ePC-SAFT) classical density functional theory (DFT) was developed to describe the behavior of pure ionic liquid (IL) and CO2/IL mixture confined in nanopores, in which a new ionic functional based on the ionic term from ePC-SAFT was proposed for electrostatic free-energy contribution. The developed model was verified by comparing the model prediction with molecular simulation results for ionic fluids, and the agreement shows that the model is reliable in representing the confined behavior of ionic fluids. The developed model was further used to study the behavior of pure IL and CO2/IL mixture in silica nanopores where the IL ions and CO2 were modeled as chains that consisted of spherical segments with the parameters taken from the bulk ePC-SAFT. The results reveal that the nanoconfinement can lead to an increased CO2 solubility, and the solubility increases with increasing pressure. The averaged density of pure IL and solubility of CO2 are strongly dependent on pore sizes and geometries. In addition, the choice of IL ions is very important for the CO2 solubility. Overall, the modeling results for silica-confined systems are consistent with available molecular simulation and experimental results.

National Category
Energy Engineering
Identifiers
urn:nbn:se:uu:diva-362013 (URN)10.1021/acs.jpcc.8b04120 (DOI)000439003600046 ()
Funder
Swedish Research Council
Available from: 2018-10-08 Created: 2018-10-08 Last updated: 2018-10-08Bibliographically approved
Wang, Y.-L., Zhu, Y.-L., Lu, Z.-Y. & Laaksonen, A. (2018). Electrostatic interactions in soft particle systems: mesoscale simulations of ionic liquids. Soft Matter, 14(21), 4252-4267
Open this publication in new window or tab >>Electrostatic interactions in soft particle systems: mesoscale simulations of ionic liquids
2018 (English)In: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 14, no 21, p. 4252-4267Article in journal (Refereed) Published
Abstract [en]

Computer simulations provide a unique insight into the microscopic details, molecular interactions and dynamic behavior responsible for many distinct physicochemical properties of ionic liquids. Due to the sluggish and heterogeneous dynamics and the long-ranged nanostructured nature of ionic liquids, coarse-grained mesa-scale simulations provide an indispensable complement to detailed first-principles calculations and atomistic simulations allowing studies over extended length and time scales with a modest computational cost. Here, we present extensive coarse-grained simulations on a series of ionic liquids of the 1-alkyl-3-methylimidazolium (alkyl = butyl, heptyl-, and decyl-) family with Cl, [BF4], and [PF6] counterions. Liquid densities, microstructures, translational diffusion coefficients, and re-orientational motion of these model ionic liquid systems have been systematically studied over a wide temperature range. The addition of neutral beads in cationic models leads to a transition of liquid morphologies from dispersed apolar beads in a polar framework to that characterized by bi-continuous sponge-like interpenetrating networks in liquid matrices. Translational diffusion coefficients of both cations and anions decrease upon lengthening of the neutral chains in the cationic models and by enlarging molecular sizes of the anionic groups. Similar features are observed in re-orientational motion and time scales of different cationic models within the studied temperature range. The comparison of the liquid properties of the ionic systems with their neutral counterparts indicates that the distinctive microstructures and dynamical quantities of the model ionic liquid systems are intrinsically related to Coulombic interactions. Finally, we compared the computational efficiencies of three linearly scaling O(NlogN) Ewald summation methods, the particle-particle particle-mesh method, the particle-mesh Ewald summation method, and the Ewald summation method based on a non-uniform fast Fourier transform technique, to calculate electrostatic interactions. Coarse-grained simulations were performed using the GALAMOST and the GROMACS packages and hardware efficiently utilizing graphics processing units on a set of extended [1-decyl-3-methylimidazolium][BF4] ionic liquid systems of up to 131072 ion pairs.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-357684 (URN)10.1039/c8sm00387d (DOI)000434244800004 ()29780992 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2018-08-20 Created: 2018-08-20 Last updated: 2018-08-20Bibliographically approved
Engelbrecht, L., Mocci, F., Laaksonen, A. & Koch, K. R. (2018). Pt-195 NMR and Molecular Dynamics Simulation Study of the Solvation of [PtCl6](2-) in Water-Methanol and Water-Dimethoxyethane Binary Mixtures. Inorganic Chemistry, 57(19), 12025-12037
Open this publication in new window or tab >>Pt-195 NMR and Molecular Dynamics Simulation Study of the Solvation of [PtCl6](2-) in Water-Methanol and Water-Dimethoxyethane Binary Mixtures
2018 (English)In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 57, no 19, p. 12025-12037Article in journal (Refereed) Published
Abstract [en]

The experimental Pt-195 NMR chemical shift, delta((195) Pt), of the [PtCl6](2-) anion dissolved in binary mixtures of water and a fully miscible organic solvent is extremely sensitive to the composition of the mixture at room temperature. Significantly nonlinear delta(Pt-195) trends as a function of solvent composition are observed in mixtures of water-methanol, or ethylene glycol, 2methoxyethanol, and 1,2-dimethoxyethane (DME). The extent of the deviation from linearity of the delta((195) Pt) trend depends strongly on the nature of the organic component in these solutions, which broadly suggests preferential solvation of the [PtCl6](2-) anion by the organic molecule. This simplistic interpretation is based on an accepted view pertaining to monovalent cations in similar binary solvent mixtures. To elucidate these phenomena in detail, classical molecular dynamics computer simulations were performed for [PtCl6](2-) in water-methanol and water-DME mixtures using the anionic charge scaling approach to account for the effect of electronic dielectric screening. Our simulations suggest that the simplistic model of preferential solvation of [PtCl6](2-) by the organic component as inferred from nonlinear delta(Pt-195) trends is not entirely accurate, particularly for water-DME mixtures. The delta(Pt-195) trend in these mixtures levels off for high DME mole fractions, which results from apparent preferential location of [PtCl6](2-) anions at the borders of water-rich regions or clusters within these inherently micro-heterogeneous mixtures. By contrast in water-methanol mixtures, apparently less pronounced mixed solvent micro-heterogeneity is found, suggesting the experimental delta(Pt-195) trend is consistent with a more moderate preferential solvation of [PtCl6](2-) anions. This finding underlines the important role of solvent-solvent interactions and micro-heterogeneity in determining the solvation environment of [PtCl6](2-) anions in binary solvent mixtures, probed by highly sensitive Pt-195 NMR. The notion that preferential solvation of [PtCl6](2-) results primarily from competing ion-solvent interactions as generally assumed for monatomic ions, may not be appropriate in general.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
National Category
Inorganic Chemistry
Identifiers
urn:nbn:se:uu:diva-368755 (URN)10.1021/acs.inorgchem.8b01554 (DOI)000446413200021 ()30215514 (PubMedID)
Funder
Swedish Research Council
Available from: 2018-12-10 Created: 2018-12-10 Last updated: 2018-12-10Bibliographically approved
Sarman, S., Wang, Y.-L., Rohlmann, P., Glavatskih, S. & Laaksonen, A. (2018). Rheology of phosphonium ionic liquids: a molecular dynamics and experimental study. Physical Chemistry, Chemical Physics - PCCP, 20(15), 10193-10203
Open this publication in new window or tab >>Rheology of phosphonium ionic liquids: a molecular dynamics and experimental study
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2018 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 15, p. 10193-10203Article in journal (Refereed) Published
Abstract [en]

We have studied the rheological behavior of the ionic liquid trihexyl(tetradecyl)phosphonium bis(mandelato)borate, [P66614][BMB], and compared it with that of another ionic liquid, namely trihexyl(tetradecyl)phosphonium chloride, [P66614][Cl]. The non-halogenated [P66614][BMB] has been selected as it is known to provide enhanced lubrication performance and is, consequently, of technological importance. The ionic liquid [P66614][Cl], despite its relatively simple anion, exhibits viscosities very similar to those of [P66614][BMB], making it an excellent reference fluid for the modeling study. The viscosities of the ionic liquids have been obtained by equilibrium atomistic simulations using the Green–Kubo relation, and by performing nonequilibrium shear flow simulations. The influence of the simulation system size and a reduction of the atomic charges on the viscosities of the ionic liquids are systematically studied. The atomic charges are reduced to mimic the temperature dependent charge transfer and polarization effects. It has been found that scaling the point charges with factors between 0.60 and 0.80 from full ion charges can provide reliable viscosities of [P66614][BMB], consistent with the experimentally measured viscosities within the studied temperature interval from 373 to 463 K. The viscosities of [P66614][Cl] have been obtained with scaling factors between 0.80 and 1.0 reflecting the lower polarizability and charge transfer effects of the chloride anion.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-356100 (URN)10.1039/c7cp08349a (DOI)000430537600052 ()29594283 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, KAW2012.0078Swedish Research Council, 2014-4694
Available from: 2018-07-19 Created: 2018-07-19 Last updated: 2018-07-19Bibliographically approved
Egorov, A. V., Brodskaya, E. N. & Laaksonen, A. (2018). The Effect of Single-Atomic Ions on the Melting of Microscopic Ice Particles According to Molecular Dynamics Data. Colloid Journal of the Russian Academy of Science, 80(5), 484-491
Open this publication in new window or tab >>The Effect of Single-Atomic Ions on the Melting of Microscopic Ice Particles According to Molecular Dynamics Data
2018 (English)In: Colloid Journal of the Russian Academy of Science, ISSN 1061-933X, E-ISSN 1608-3067, Vol. 80, no 5, p. 484-491Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics simulation of microscopic ice particles containing Ca2+, F-, Cl-, Na+, and Li+ ions has been performed in the temperature range of 20-200 K. For all the systems under consideration, phase and structural transformations accompanying their heating have been studied in detail, and the melting points have been determined. The main attention has been focused on the determination of the mechanisms of the effect of ions on the phase state of microcrystals.

National Category
Physical Chemistry Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-365659 (URN)10.1134/S1061933X1805006X (DOI)000444611500004 ()
Funder
Swedish Research Council
Note

Original Russian text published in Kolloidnyi Zhurnal, 2018, Vol. 80, No. 5, pp. 509–517.

Available from: 2018-11-15 Created: 2018-11-15 Last updated: 2018-11-15Bibliographically approved
Ma, C., Laaksonen, A., Liu, C., Lu, X. & Ji, X. (2018). The peculiar effect of water on ionic liquids and deep eutectic solvents. Chemical Society Reviews, 47(23), 8685-8720
Open this publication in new window or tab >>The peculiar effect of water on ionic liquids and deep eutectic solvents
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2018 (English)In: Chemical Society Reviews, ISSN 0306-0012, E-ISSN 1460-4744, Vol. 47, no 23, p. 8685-8720Article, review/survey (Refereed) Published
Abstract [en]

Ionic liquids (ILs) and deep eutectic solvents (DESs) have been suggested as eco-friendly alternatives to organic solvents. A trace amount of water is often unavoidable as impurity, and water is also added on purpose to reduce their problematically high viscosity and lower their high price. Understanding the distinct effects of water on the properties of ILs/DESs is highly important. In this review, we collect published experimental and theoretical results for IL/DES-H2O systems at varied water concentrations and analyze them. Results from mechanistic studies, thermodynamic modelling and advanced experiments are collected and critically discussed. Six commonly studied IL/DES-H2O systems were selected to map experimental observations onto microscopic results obtained in mechanistic studies. A great variety of distinct contours of the excess properties can be observed over the entire compositional range, indicating that the properties of IL/DES-H2O systems are highly unpredictable. Mechanistic studies clearly demonstrate that the added H2O rapidly changes the heterogeneous 3D structures of pure ILs/DESs, leading to very different properties and behaviour. There are similarities between aqueous electrolytes and IL/DES solutions but the bulky and asymmetric organic cations in ILs/DESs do not conform to the standard salt dissolution and hydration concepts. Thermodynamic modelling previously assumes ILs/DESs to be either a neutral ion-pair or completely dissociated ions, neglecting specific ion hydration effects. A new conceptual framework is suggested for thermodynamic modelling of IL/DES-H2O binary systems to enable new technologies for their practical applications.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-372512 (URN)10.1039/c8cs00325d (DOI)000451657800007 ()30298877 (PubMedID)
Funder
Swedish Energy Agency, P40548-1Swedish Research Council, 2016-04023
Available from: 2019-01-08 Created: 2019-01-08 Last updated: 2019-01-08Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-9783-4535

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