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Kulschewski T, Pleiss J. A molecular dynamics study of liquid aliphatic alcohols: simulation of density and self-diffusion coefficient using a modified OPLS force field. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.769680] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Phan A, Cole DR, Striolo A. Liquid Ethanol Simulated on Crystalline Alpha Alumina. J Phys Chem B 2013; 117:3829-40. [DOI: 10.1021/jp312238d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Anh Phan
- School of Chemical, Biological,
and Materials Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - David R. Cole
- School of Earth Sciences, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Alberto Striolo
- School of Chemical, Biological,
and Materials Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States
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Ponomarev SY, Kaminski GA. Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone. J Chem Theory Comput 2011; 7:1415-1427. [PMID: 21743799 DOI: 10.1021/ct1007197] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06Å). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins.
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Affiliation(s)
- Sergei Y Ponomarev
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609
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Zhong Y, Patel S. Nonadditive empirical force fields for short-chain linear alcohols: methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models. J Phys Chem B 2010; 114:11076-92. [PMID: 20687517 PMCID: PMC2928884 DOI: 10.1021/jp101597r] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Building upon the nonadditive electrostatic force field for alcohols based on the CHARMM charge equilibration (CHEQ) formalism, we introduce atom-pair specific solute-solvent Lennard-Jones (LJ) parameters for alcohol-water interaction force fields targeting improved agreement with experimental hydration free energies of a series of small molecule linear alcohols as well as ab initio water-alcohol geometries and energetics. We consider short-chain, linear alcohols from methanol to butanol as they are canonical small-molecule organic model compounds to represent the hydroxyl chemical functionality for parametrizing biomolecular force fields for proteins. We discuss molecular dynamics simulations of dilute aqueous solutions of methanol and ethanol in TIP4P-FQ water, with particular discussion of solution densities, structure defined in radial distribution functions, electrostatic properties (dipole moment distributions), hydrogen bonding patterns of water, as well as a Kirkwood-Buff (KB) integral analysis. Calculation of the latter provides an assessment of how well classical force fields parametrized to at least semiquantitatively match experimental hydration free energies capture the microscopic structures of dilute alcohol solutions; the latter translate into macroscopic thermodynamic properties through the application of KB analysis. We find that the CHEQ alcohol force fields of this work semiquantitatively match experimental KB integrals for methanol and ethanol mole fractions of 0.1 and 0.2. The force field combination qualitatively captures the concentration dependence of the alcohol-alcohol and water-water KB integrals, but due to inadequacies in the representation of the microscopic structures in such systems (which cannot be parametrized in any systematic fashion), a priori quantitative description of alcohol-water KB integrals remains elusive.
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Affiliation(s)
- Yang Zhong
- Department of Chemistry and Biochemistry, 238 Brown Lab, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, 238 Brown Lab, University of Delaware, Newark, Delaware 19716, USA
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Guevara-Carrion G, Nieto-Draghi C, Vrabec J, Hasse H. Prediction of Transport Properties by Molecular Simulation: Methanol and Ethanol and Their Mixture. J Phys Chem B 2008; 112:16664-74. [DOI: 10.1021/jp805584d] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gabriela Guevara-Carrion
- Laboratory for Engineering Thermodynamics, University Kaiserslautern, 67663 Kaiserslautern, Germany, IFP, 1-4 Avenue de Bois Préau, 92852 Rueil-Malmaison Cedex, France, and Institute of Thermodynamics and Thermal Process Engineering, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Carlos Nieto-Draghi
- Laboratory for Engineering Thermodynamics, University Kaiserslautern, 67663 Kaiserslautern, Germany, IFP, 1-4 Avenue de Bois Préau, 92852 Rueil-Malmaison Cedex, France, and Institute of Thermodynamics and Thermal Process Engineering, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Jadran Vrabec
- Laboratory for Engineering Thermodynamics, University Kaiserslautern, 67663 Kaiserslautern, Germany, IFP, 1-4 Avenue de Bois Préau, 92852 Rueil-Malmaison Cedex, France, and Institute of Thermodynamics and Thermal Process Engineering, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Hans Hasse
- Laboratory for Engineering Thermodynamics, University Kaiserslautern, 67663 Kaiserslautern, Germany, IFP, 1-4 Avenue de Bois Préau, 92852 Rueil-Malmaison Cedex, France, and Institute of Thermodynamics and Thermal Process Engineering, Universität Stuttgart, 70550 Stuttgart, Germany
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Wang S, Cann NM. A molecular dynamics study of chirality transfer: The impact of a chiral solute on an achiral solvent. J Chem Phys 2008; 129:054507. [PMID: 18698914 DOI: 10.1063/1.2958911] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A solvation shell may adapt to the presence of a chiral solute by becoming chiral. The extent of this chirality transfer and its dependence on the solute and solvent characteristics are explored in this article. Molecular dynamics simulations of solvated chiral analytes form the basis of the analysis. The chirality induced in the solvent is assessed based on a series of related chirality indexes originally proposed by Osipov [M. A. Osipov et al., Mol. Phys. 84, 1193 (1995)]. Two solvents are considered: Ethanol and benzyl alcohol. Ethanol provides insight into chirality transfer when the solvent interacts with the solute primarily by a hydrogen bond. Several ethanol models have been considered starting with a nonpolarizable model, progressing to a fluctuating charge model, and finally, to a fully polarizable model. This progression provides some insights into the importance of solvent polarizability in the transfer of chirality. Benzyl alcohol, by virtue of the aromatic ring, increases the number of potential solvent-solute interactions. Thus, with these two solvents, the issue of compatibility between the solvent and solute is also considered. The solvation of three chiral solutes is examined: Styrene oxide, acenaphthenol, and n-(1-(4-bromophenyl)ethyl)pivalamide (PAMD). All three solutes have the possibility of hydrogen bonding with the solvent, the last two may also form ring-ring interactions, and the last also has multiple hydrogen bonding sites. For PAMD, the impact of conformational averaging is examined by comparing the chirality transfer about rigid and flexible solutes.
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Affiliation(s)
- Shihao Wang
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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Abstract
A polarizable, flexible model for ethanol is obtained based on an extensive series of B3LYP/6-311++G(d,p) calculations and molecular dynamics simulations. The ethanol model includes electric-field dependence in both the atomic charges and the intramolecular degrees of freedom. Field-dependent intramolecular potentials have been attempted only once previously, for OH and HH stretches in water [P. Cicu et al., J. Chem. Phys. 112, 8267 (2000)]. The torsional potential involving the hydrogen-bonding hydrogen in ethanol is found to be particularly field sensitive. The methodology for developing field-dependent potentials can be readily generalized to other molecules and is discussed in detail. Molecular dynamics simulations of bulk ethanol are performed and the results are assessed based on comparisons with the self-diffusion coefficient [N. Karger et al., J. Chem. Phys. 93, 3437 (1990)], dielectric constant [J. T. Kindt and C. A. Schmuttenmaer, J. Phys. Chem. 100, 10373 (1996)], enthalpy of vaporization [R. C. Wilhoit and B. J. Zwolinski, J. Phys. Chem. Ref. Data, Suppl. 2, 2 (1973)], and experimental interatomic distributions [C. J. Benmore and Y. L. Loh, J. Chem. Phys. 112, 5877 (2000)]. The simultaneous variation of the atomic charges and the intramolecular potentials requires modified equations of motion and a multiple time step algorithm has been implemented to solve these equations. The article concludes with a discussion of the bulk structure and properties with an emphasis on the hydrogen bonding network.
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Affiliation(s)
- Shihao Wang
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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Durov VA, Tereshin OG. Modeling of Supramolecular Ordering and Physicochemical Properties in Cyclohexane−Ethanol Mixtures. J Phys Chem B 2006; 110:8441-50. [PMID: 16623530 DOI: 10.1021/jp056541y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The quasichemical model of the nonideal associated solution (QCNAS) was used to analyze the excess thermodynamic functions and permittivity of cyclohexane-ethanol mixtures in the entire range of compositions and in a wide temperature range. A new model of supramolecular organization was substantiated, taking into account chain and cyclic aggregation of alcohol with the formation of chain aggregates of arbitrary size, which describes a set of physicochemical properties of this mixture with complicated behavior of both thermodynamic and dielectric properties. Equilibrium constants and thermodynamic parameters of H bonding having cooperative character and integral and differential characteristics of aggregation and the structural parameters of aggregates were determined. It was established that the role of nonpolar cyclic structures increases as alcohol concentration decreases. The model describes the permittivity of solutions in the entire range of compositions and reproduces a minimum of the dipolar correlation factor in the range of dilute alcohol solutions. The new data obtained on the supramolecular ordering characterized by the long-range molecular correlations due to H bonding are discussed in detail.
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Affiliation(s)
- Vladimir A Durov
- Faculty of Chemistry, Moscow State University, Vorobyevy Gory, Moscow, 119992, Russia.
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Madurga S, Vilaseca E. Solvent Effect on the Conformational Equilibrium of 1,2-Dichloroethane in Water. The Role of Solute Polarization. J Phys Chem A 2004. [DOI: 10.1021/jp0491358] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergio Madurga
- Departament de Química Física i Centre Especial de Recerca en Química Teòrica, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, 08028-Barcelona, Catalunya, Spain
| | - Eudald Vilaseca
- Departament de Química Física i Centre Especial de Recerca en Química Teòrica, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, 08028-Barcelona, Catalunya, Spain
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Wensink EJW, Hoffmann AC, van Maaren PJ, van der Spoel D. Dynamic properties of water/alcohol mixtures studied by computer simulation. J Chem Phys 2003. [DOI: 10.1063/1.1607918] [Citation(s) in RCA: 235] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kaminski GA, Friesner RA, Zhou R. A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. J Comput Chem 2003; 24:267-76. [PMID: 12548718 DOI: 10.1002/jcc.10170] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present an approximation, which allows reduction of computational resources needed to explicitly incorporate electrostatic polarization into molecular simulations utilizing empirical force fields. The proposed method is employed to compute three-body energies of molecular complexes with dipolar electrostatic probes, gas-phase dimerization energies, and pure liquid properties for five systems that are important in biophysical and organic simulations-water, methanol, methylamine, methanethiol, and acetamide. In all the cases, the three-body energies agreed with high level ab initio data within 0.07 kcal/mol, dimerization energies-within 0.43 kcal/mol (except for the special case of the CH(3)SH), and computed heats of vaporization and densities differed from the experimental results by less than 2%. Moreover, because the presented method allows a significant reduction in computational cost, we were able to carry out the liquid-state calculations with Monte Carlo technique. Comparison with the full-scale point dipole method showed that the computational time was reduced by 3.5 to more than 20 times, depending on the system in hand and on the desired level of the full-scale model accuracy, while the difference in energetic results between the full-scale and the presented approximate model was not great in the most cases. Comparison with the nonpolarizable OPLS-AA force field for all the substances involved and with the polarizable POL3 and q90 models for water and methanol, respectively, demonstrates that the presented technique allows reduction of computational cost with no sacrifice of accuracy. We hope that the proposed method will be of benefit to research employing molecular modeling technique in the biophysical and physical organic chemistry areas.
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Affiliation(s)
- George A Kaminski
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA.
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Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YX, Murphy RB, Zhou R, Halgren TA. Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J Comput Chem 2002; 23:1515-31. [PMID: 12395421 PMCID: PMC3963406 DOI: 10.1002/jcc.10125] [Citation(s) in RCA: 244] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.
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Affiliation(s)
- George A Kaminski
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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Paolantoni M, Ladanyi BM. Polarizability anisotropy relaxation in liquid ethanol: A molecular dynamics study. J Chem Phys 2002. [DOI: 10.1063/1.1494775] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Jedlovszky P, Mezei M, Vallauri R. Comparison of polarizable and nonpolarizable models of hydrogen fluoride in liquid and supercritical states: A Monte Carlo simulation study. J Chem Phys 2001. [DOI: 10.1063/1.1413973] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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16
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Llanta E, Ando K, Rey R. Fluctuating Charge Study of Polarization Effects in Chlorinated Organic Liquids. J Phys Chem B 2001. [DOI: 10.1021/jp010390r] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Estanis Llanta
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
| | - Koji Ando
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Rossend Rey
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
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Chen B, Potoff JJ, Siepmann JI. Monte Carlo Calculations for Alcohols and Their Mixtures with Alkanes. Transferable Potentials for Phase Equilibria. 5. United-Atom Description of Primary, Secondary, and Tertiary Alcohols. J Phys Chem B 2001. [DOI: 10.1021/jp003882x] [Citation(s) in RCA: 637] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Jedlovszky P. The local structure of various hydrogen bonded liquids: Voronoi polyhedra analysis of water, methanol, and HF. J Chem Phys 2000. [DOI: 10.1063/1.1319617] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Saiz L, Guàrdia E, Padró JÀ. Dielectric properties of liquid ethanol. A computer simulation study. J Chem Phys 2000. [DOI: 10.1063/1.1305883] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gonzalez MA, Enciso E, Bermejo FJ, Jimenez-Ruiz M, Bee M. Molecular approach to the interpretation of the dielectric relaxation spectrum of a molecular glass former. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 2000; 61:3884-95. [PMID: 11088169 DOI: 10.1103/physreve.61.3884] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/1999] [Indexed: 11/07/2022]
Abstract
The frequency-dependent dielectric function of ethanol at temperatures within the normal liquid range is evaluated by means of computer molecular dynamics simulations and compared with recent experimental data. The calculated spectra show a similar structure to those reported from experimental measurements and the temperature dependence of its most prominent bands also follows the experimental estimates. An attempt is also made to assign the most intense bands to specific molecular reorientations.
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Affiliation(s)
- MA Gonzalez
- Institut Laue Langevin, Boiinsertion markte Postale 156, F-38042 Grenoble Cedex 9, France
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