@article{Flamme2017, author = {Flamme, Benjamin and {Rodriguez Garcia}, Gonzalo and Weil, Marcel and Haddad, Mansour and Phansavath, Phannarath and Ratovelomanana-Vidal, Virginie and Chagnes, Alexandre}, journal = {Green Chemistry}, number = {8}, pages = {1828--1849}, title = {{Guidelines to design organic electrolytes for lithium-ion batteries: Environmental impact, physicochemical and electrochemical properties}}, volume = {19}, year = {2017}, abstract = {Electrolytes for lithium-ion batteries (LiBs) have been put aside for too long because a few new solvents have been designed to match electrolyte specifications. Conversely, significant attention has been paid to synthesize new electrode materials and especially positive electrodes. Particularly, most of the studies dedicated to the investigation of electrolytes for LiBs have been focused on mixing different molecules. Currently, the development of high-voltage materials for LiBs stimulates the synthesis of new solvents and new salts that are more stable against oxidation. Despite the challenges, only a few teams are active in this field in developing a rational approach combining physicochemistry, electrochemistry and modelling from the molecular to the macromolecular levels. After assembling a critical collection of physicochemical and electrochemical data from the literature, this study highlights the main trends between the chemical structure of the organic dipolar aprotic solvents and their physicochemical and electrochemical properties to provide a guide for chemists to design new electrolytes for LiBs. This guide also includes indicators to take into account the environmental impact of solvent production by including a life cycle assessment of eight different solvents.}, doiurl = {10.1039/c7gc00252a}, issn = {14639270}, } @article{Xu2023, author = {Xu, Jijian and others}, journal = {Nature}, pages = {694}, publisher = {Springer US}, title = {{Electrolyte design for Li-ion batteries under extreme operating conditions}}, volume = {614}, year = {2023}, abstract = {The ideal electrolyte for the widely used LiNi0.8Mn0.1Co0.1O2 (NMC811)||graphite lithium-ion batteries is expected to have the capability of supporting higher voltages (≥4.5 volts), fast charging (≤15 minutes), charging/discharging over a wide temperature range (±60 degrees Celsius) without lithium plating, and non-flammability1–4. No existing electrolyte simultaneously meets all these requirements and electrolyte design is hindered by the absence of an effective guiding principle that addresses the relationships between battery performance, solvation structure and solid-electrolyte-interphase chemistry5. Here we report and validate an electrolyte design strategy based on a group of soft solvents that strikes a balance between weak Li+–solvent interactions, sufficient salt dissociation and desired electrochemistry to fulfil all the aforementioned requirements. Remarkably, the 4.5-volt NMC811||graphite coin cells with areal capacities of more than 2.5 milliampere hours per square centimetre retain 75 per cent (54 per cent) of their room-temperature capacity when these cells are charged and discharged at −50 degrees Celsius (−60 degrees Celsius) at a C rate of 0.1C, and the NMC811||graphite pouch cells with lean electrolyte (2.5 grams per ampere hour) achieve stable cycling with an average Coulombic efficiency of more than 99.9 per cent at −30 degrees Celsius. The comprehensive analysis further reveals an impedance matching between the NMC811 cathode and the graphite anode owing to the formation of similar lithium-fluoride-rich interphases, thus effectively avoiding lithium plating at low temperatures. This electrolyte design principle can be extended to other alkali-metal-ion batteries operating under extreme conditions.}, doiurl = {10.1038/s41586-022-05627-8}, issn = {14764687}, } @article{gao2022, author = {{Zhiyi Gao, Zongjing Lu, Yining Zhang, Jing Xia, Xuejing Zhang, Chao Sun, Yijun Yang, Yong Xu, Ke Wang, Xi Wang}, Jiannian Yao}, journal = {Chemical Engineering Science}, pages = {117633}, title = {{Regulating interfacial desolvation via a weakly coordinating solvent molecule enhances Li-ion storage at subzero temperatures}}, volume = {254}, year = {2022}, } @article{Zhang2015, author = {Zhang, Yong and Otani, Akihito and Maginn, Edward J.}, journal = {Journal of Chemical Theory and Computation}, number = {8}, pages = {3537--3546}, title = {{Reliable Viscosity Calculation from Equilibrium Molecular Dynamics Simulations: A Time Decomposition Method}}, volume = {11}, year = {2015}, abstract = {Equilibrium molecular dynamics is often used in conjunction with a Green?Kubo integral of the pressure tensor autocorrelation function to compute the shear viscosity of fluids. This approach is computationally expensive and is subject to a large amount of variability because the plateau region of the Green?Kubo integral is difficult to identify unambiguously. Here, we propose a time decomposition approach for computing the shear viscosity using the Green?Kubo formalism. Instead of one long trajectory, multiple independent trajectories are run and the Green?Kubo relation is applied to each trajectory. The averaged running integral as a function of time is fit to a double-exponential function with a weighting function derived from the standard deviation of the running integrals. Such a weighting function minimizes the uncertainty of the estimated shear viscosity and provides an objective means of estimating the viscosity. While the formal Green?Kubo integral requires an integration to infinite time, we suggest an integration cutoff time tcut, which can be determined by the relative values of the running integral and the corresponding standard deviation. This approach for computing the shear viscosity can be easily automated and used in computational screening studies where human judgment and intervention in the data analysis are impractical. The method has been applied to the calculation of the shear viscosity of a relatively low-viscosity liquid, ethanol, and relatively high-viscosity ionic liquid, 1-n-butyl-3-methylimidazolium bis(trifluoromethane-sulfonyl)imide ([BMIM][Tf2N]), over a range of temperatures. These test cases show that the method is robust and yields reproducible and reliable shear viscosity values. Equilibrium molecular dynamics is often used in conjunction with a Green?Kubo integral of the pressure tensor autocorrelation function to compute the shear viscosity of fluids. This approach is computationally expensive and is subject to a large amount of variability because the plateau region of the Green?Kubo integral is difficult to identify unambiguously. Here, we propose a time decomposition approach for computing the shear viscosity using the Green?Kubo formalism. Instead of one long trajectory, multiple independent trajectories are run and the Green?Kubo relation is applied to each trajectory. The averaged running integral as a function of time is fit to a double-exponential function with a weighting function derived from the standard deviation of the running integrals. Such a weighting function minimizes the uncertainty of the estimated shear viscosity and provides an objective means of estimating the viscosity. While the formal Green?Kubo integral requires an integration to infinite time, we suggest an integration cutoff time tcut, which can be determined by the relative values of the running integral and the corresponding standard deviation. This approach for computing the shear viscosity can be easily automated and used in computational screening studies where human judgment and intervention in the data analysis are impractical. The method has been applied to the calculation of the shear viscosity of a relatively low-viscosity liquid, ethanol, and relatively high-viscosity ionic liquid, 1-n-butyl-3-methylimidazolium bis(trifluoromethane-sulfonyl)imide ([BMIM][Tf2N]), over a range of temperatures. These test cases show that the method is robust and yields reproducible and reliable shear viscosity values.}, doiurl = {10.1021/acs.jctc.5b00351}, isbn = {1549-9618}, issn = {15499626}, } @article{Deshchenya2022, author = {Deshchenya, V. I. and Kondratyuk, N. D. and Lankin, A. V. and Norman, G. E.}, journal = {Journal of Molecular Liquids}, pages = {120456}, publisher = {Elsevier B.V.}, title = {{Molecular dynamics study of sucrose aqueous solutions: From solution structure to transport coefficients}}, volume = {367}, year = {2022}, abstract = {In this work, we study the applicability of the equilibrium molecular dynamics methods for the prediction of solution structure, equation of state and transport properties of sucrose aqueous solution for various concentrations and temperatures. The OPLS-AA force field with 1.14*CM1A charge corrections is used to describe the interactions in the model. We analyze the prediction power of the model against the experimental data and simulation results, obtained previously in CHARMM, OPLS-AA, GLYCAM06 and their modifications. The glycosidic linkage conformations of sucrose in solution are found. Their independence from the sugar concentration and the appearance of the conformation region at temperatures from 283 K to 308 K are observed. Sucrose solution densities are calculated for different sugar concentrations and temperatures. The obtained viscosities and sucrose diffusion coefficients match the experimental data at low sucrose concentrations, and diverge within 41% from the experiment as the concentration increases. The change of boundary condition in Stokes–Einstein formula is observed with an increase of the sucrose concentration above 40%.}, doiurl = {10.1016/j.molliq.2022.120456}, issn = {01677322}, url = {https://doi.org/10.1016/j.molliq.2022.120456}, } @article{Jamali2018b, author = {Jamali, Seyed Hossein and Hartkamp, Remco and Bardas, Christos and S{\"{o}}hl, Jakob and Vlugt, Thijs J. H. and Moultos, Othonas A.}, journal = {J. Chem. Theory Comput.}, number = {11}, pages = {5959--5968}, title = {{Shear Viscosity Computed from the Finite-Size Effects of Self-Diffusivity in Equilibrium Molecular Dynamics}}, volume = {14}, year = {2018}, doiurl = {10.1021/acs.jctc.8b00625}, issn = {1549-9618}, url = {http://pubs.acs.org/doi/10.1021/acs.jctc.8b00625}, } @article{Kondratyuk2020, author = {Kondratyuk, N. D. and Orekhov, M. A.}, journal = {Journal of Physics: Conference Series}, number = {1}, title = {{Shear viscosity of n-pentane from diffusivity based molecular dynamics methods}}, volume = {1556}, year = {2020}, abstract = {The molecular dynamics methods for calculation of shear viscosity based on liquid diffusivity are tested against the classical Green-Kubo relation for n-pentane at 330 K and 0.601 g/cm3. The D-based method is shown to be as accurate as calculation of viscosity from the Green-Kubo formalism for pentane liquid. Stokes-Einstein relation is also in agreement with simulation results. However, it has much bigger uncertainty. The results of the simulation are in agreement with experimental data.}, doiurl = {10.1088/1742-6596/1556/1/012048}, issn = {17426596}, } @article{Hwang1994, author = {Hwang, M. J. and Stockfisch, T. P. and Hagler, A. T.}, journal = {Journal of the American Chemical Society}, number = {6}, pages = {2515--2525}, title = {{Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules}}, volume = {116}, year = {1994}, abstract = {A second generation Class II force field is derived for the alkyl group and alkane molecules. The Class II functional form is presented and force constants are given. The criteria that define this second generation force field are the following: (1) it accounts for the properties of both isolated small molecules, condensed phases, and macromolecular systems and (2) the functional form is characterized by being anharmonic, with quartic stretching and quartic angle bending, and includes a variety of important intramolecular coupling interactions. It is also characterized by a soft repulsion, either 9th power or exponential, rather than the more usual 12th power repulsion. The force Held is derived by scaling an analytical representation derived from a fit to a quantum mechanical energy surface. Only seven parameters were needed in this scaling to reproduce 150 experimental observables. The resulting Class II force field is shown to fit the structural, energetic, and dynamic properties of the alkane molecules comprising the training set well. These molecules include small acyclic alkanes, strained molecules such as isobutane, and small rings including cyclopropane and cyclobutane. Thus the properties of highly strained molecules including small rings are accounted for with one set of transferable parameters. The results are compared with those obtained from Class I diagonal quadratic force fields commonly used in simulations of biological systems and the Class II functional form is shown to reproduce trends unattainable by the simpler forms where anharmonicity and coupling interactions are not accounted for. Most dramatic is its ability to fit the small ring compounds, cyclopropane and cyclobutane, with the same tfansferable energy functions that account for larger rings and acyclic molecules. This is the first energy surface able to achieve this range of applicability, a degree of transferability hypothesized in the literature to be unachievable. Finally, and perhaps most importantly it is pointed out that the methodology presented here provides a paradigm for the straightforward derivation of force fields for arbitrary molecules of interest even where experimental data is sparse or missing. The force field can be derived based on the techniques described here as long as the quantum mechanical calculation can be carried out. The resulting quantum force field, at that point, could either be used on its own or scaled to provide a pragmatic and reasonably accurate force field. {\textcopyright} 1994, American Chemical Society. All rights reserved.}, doiurl = {10.1021/ja00085a036}, issn = {15205126}, } @article{ML_kolya2023, author = {Kondratyuk, N and Ryltsev, R and Ankudinov, V and Chtchelkatchev, N}, journal = {J Mol Liq}, pages = {121751}, title = {{First-principles calculations of the viscosity in multicomponent metallic melts: Al-Cu-Ni as a test case}}, volume = {380}, year = {2023}, } @article{Dajnowicz2022, author = {Dajnowicz, Steven and Agarwal, Garvit and Stevenson, James M. and Jacobson, Leif D. and Ramezanghorbani, Farhad and Leswing, Karl and Friesner, Richard A. and Halls, Mathew D. and Abel, Robert}, journal = {Journal of Physical Chemistry B}, number = {33}, pages = {6271--6280}, title = {{High-Dimensional Neural Network Potential for Liquid Electrolyte Simulations}}, volume = {126}, year = {2022}, abstract = {Liquid electrolytes are one of the most important components of Li-ion batteries, which are a critical technology of the modern world. However, we still lack the computational tools required to accurately calculate key properties of these materials (viscosity and ionic diffusivity) from first principles necessary to support improved designs. In this work, we report a machine learning-based force field for liquid electrolyte simulations, which bridges the gap between the accuracy of range-separated hybrid density functional theory and the efficiency of classical force fields. Predictions of material properties made with this force field are quantitatively accurate compared to experimental data. Our model uses the QRNN deep neural network architecture, which includes both long-range interactions and global charge equilibration. The training data set is composed solely of non-periodic density functional theory (DFT), allowing the practical use of an accurate theory (here, $\omega$B97X-D3BJ/def2-TZVPD), which would be prohibitively expensive for generating large data sets with periodic DFT. In this report, we focus on seven common carbonates and LiPF6, but this methodology has very few assumptions and can be readily applied to any liquid electrolyte system. This provides a promising path forward for large-scale atomistic modeling of many important battery chemistries.}, doiurl = {10.1021/acs.jpcb.2c03746}, issn = {15205207}, } @article{Jacobson2022, author = {Jacobson, Leif D. and Stevenson, James M. and Ramezanghorbani, Farhad and Ghoreishi, Delaram and Leswing, Karl and Harder, Edward D. and Abel, Robert}, journal = {Journal of Chemical Theory and Computation}, number = {4}, pages = {2354--2366}, title = {{Transferable Neural Network Potential Energy Surfaces for Closed-Shell Organic Molecules: Extension to Ions}}, volume = {18}, year = {2022}, abstract = {Transferable high dimensional neural network potentials (HDNNPs) have shown great promise as an avenue to increase the accuracy and domain of applicability of existing atomistic force fields for organic systems relevant to life science. We have previously reported such a potential (Schr{\"{o}}dinger-ANI) that has broad coverage of druglike molecules. We extend that work here to cover ionic and zwitterionic druglike molecules expected to be relevant to drug discovery research activities. We report a novel HDNNP architecture, which we call QRNN, that predicts atomic charges and uses these charges as descriptors in an energy model that delivers conformational energies within chemical accuracy when measured against the reference theory it is trained to. Further, we find that delta learning based on a semiempirical level of theory approximately halves the errors. We test the models on torsion energy profiles, relative conformational energies, geometric parameters, and relative tautomer errors.}, doiurl = {10.1021/acs.jctc.1c00821}, issn = {15499626}, } @article{Kondratyuk2021, author = {Kondratyuk, Nikolay D. and Pisarev, Vasily V.}, journal = {Fluid Phase Equilibria}, pages = {113100}, publisher = {Elsevier B.V.}, title = {{Predicting shear viscosity of 1,1-diphenylethane at high pressures by molecular dynamics methods}}, volume = {544-545}, year = {2021}, abstract = {In this paper, we use the molecular dynamics methods to predict the pressure-viscosity dependencies of model lubricant 1,1-diphenylethane up to 800 MPa along three isotherms: 37.8 °C, 60 °C and 98.9 °C. The precise COMPASS class II force field is used to determine atomic interactions in the model. The Green-Kubo method is used to calculate the shear viscosities. The time decomposition method is applied for accurate calculation of the Green-Kubo integral limit. For the pressures below 340 MPa, the results match the available experimental data. The faster-than-exponential behavior of the pressure-viscosity dependence is observed for all the temperatures which agrees with the experimental data from Scott Bair.}, doiurl = {10.1016/j.fluid.2021.113100}, issn = {03783812}, url = {https://doi.org/10.1016/j.fluid.2021.113100}, } @article{Jorgensen1996, author = {Jorgensen, William L. and Maxwell, David S. and Tirado-Rives, Julian}, journal = {Journal of the American Chemical Society}, number = {45}, pages = {11225--11236}, title = {{Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids}}, volume = {118}, year = {1996}, abstract = {The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were determined by fitting to rotational energy profiles obtained from ab initio molecular orbital calculations at the RHF/6-31G*//RHF/6-31G* level for more than 50 organic molecules and ions. The quality of the fits was high with average errors for conformational energies of less than 0.2 kcal/mol. The force-field results for molecular structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodynamic and structural properties for 34 pure organic liquids including alkanes, alkenes, alcohols, ethers, acetals, thiols, sulfides, disulfides, aldehydes, ketones, and amides. Average errors in comparison with experimental data are 2% for heats of vaporization and densities. The Monte Carlo simulations included sampling all internal and intermolecular degrees of freedom. It is found that such non-polar and monofunctional systems do not show significant condensed-phase effects on internal energies in going from the gas phase to the pure liquids.}, doiurl = {10.1021/ja9621760}, issn = {00027863}, } @article{Dodda2017, author = {Dodda, Leela S. and {De Vaca}, Israel Cabeza and Tirado-Rives, Julian and Jorgensen, William L.}, journal = {Nucleic Acids Research}, number = {W1}, pages = {W331--W336}, title = {{LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands}}, volume = {45}, year = {2017}, abstract = {The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14∗CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements.}, doiurl = {10.1093/nar/gkx312}, issn = {13624962}, } @article{Malde2011, author = {Malde, Alpeshkumar K and Zuo, Le and Breeze, Matthew and Stroet, Martin and Poger, David and Nair, Pramod C and Oostenbrink, Chris and Mark, Alan E}, journal = {J. Chem. Theory Comput.}, number = {12}, pages = {4026--4037}, title = {{An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0}}, volume = {7}, year = {2011}, abstract = {The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb) is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement. The ATB has three primary functions: (1) to act as a repository for molecules that have been parametrized as part of the GROMOS family of force fields, (2) to act as a repository for pre-equilibrated systems for use as starting configurations in molecular dynamics simulations (solvent mixtures, lipid systems pre-equilibrated to adopt a specific phase, etc.), and (3) to generate force field descriptions of novel molecules compatible with the GROMOS family of force fields in a variety of formats (GROMOS, GROMACS, and CNS). Force field descriptions of novel molecules are derived using a multistep process in which results from quantum mechanical (QM) calculations are combined with a knowledge-based approach to ensure compatibility (as far as possible) with a specific parameter set of the GROMOS force field. The ATB has several unique features: (1) It requires that the user stipulate the protonation and tautomeric states of the molecule. (2) The symmetry of the molecule is analyzed to ensure that equivalent atoms are assigned identical parameters. (3) Charge groups are assigned automatically. (4) Where the assignment of a given parameter is ambiguous, a range of possible alternatives is provided. The ATB also provides several validation tools to assist the user to assess the degree to which the topology generated may be appropriate for a given task. In addition to detailing the steps involved in generating a force field topology compatible with a specific GROMOS parameter set (GROMOS 53A6), the challenges involved in the automatic generation of force field parameters for atomic simulations in general are discussed.}, } @article{dioxane2021, author = {Bakulin, I and Kondratyuk, N and Lankin, A and Norman, G}, journal = {J. Chem. Phys.}, pages = {154501}, title = {{Properties of aqueous 1,4-dioxane solution via molecular dynamics}}, volume = {155}, year = {2021}, } @article{LAMMPS_Plimpton1995, author = {Plimpton, Steve}, journal = {J. Comput. Phys.}, pages = {1}, title = {{Fast Parallel Algorithms for Short-Range Molecular Dynamics}}, volume = {117}, year = {1995}, abstract = {Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.}, annote = {lammps}, doiurl = {10.1006/jcph.1995.1039}, isbn = {0021-9991}, issn = {00219991}, url = {http://www.sciencedirect.com/science/article/pii/ S002199918571039X}, } @article{Yeh2004, author = {Yeh, In-Chul and {and Gerhard Hummer}}, journal = {J. Phys. Chem. B}, number = {40}, pages = {15873}, title = {{System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions}}, volume = {108}, year = {2004}, doiurl = {10.1021/jp0477147}, url = {http://dx.doi.org/10.1021/jp0477147}, } @article{Moultos2016, author = {Moultos, Othonas A. and Zhang, Yong and Tsimpanogiannis, Ioannis N. and Economou, Ioannis G. and Maginn, Edward J.}, journal = {J. Chem. Phys.}, number = {7}, pages = {074109}, title = {{System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO2, n -alkanes, and poly(ethylene glycol) dimethyl ethers}}, volume = {145}, year = {2016}, abstract = {{\textcopyright} 2016 Author(s).Molecular dynamics simulations were carried out to study the self-diffusion coefficients of CO2, methane, propane, n-hexane, n-hexadecane, and various poly(ethylene glycol) dimethyl ethers (glymes in short, CH3O-(CH2CH2O)n-CH3 with n = 1, 2, 3, and 4, labeled as G1, G2, G3, and G4, respectively) at different conditions. Various system sizes were examined. The widely used Yeh and Hummer [J. Phys. Chem. B 108, 15873 (2004)] correction for the prediction of diffusion coefficient at the thermodynamic limit was applied and shown to be accurate in all cases compared to extrapolated values at infinite system size. The magnitude of correction, in all cases examined, is significant, with the smallest systems examined giving for some cases a self-diffusion coefficient approximately 15% lower than the infinite system-size extrapolated value. The results suggest that finite size corrections to computed self-diffusivities must be used in order to obtain accurate results.}, doiurl = {10.1063/1.4960776}, issn = {00219606}, url = {http://dx.doi.org/10.1063/1.4960776}, } @article{Orekhov2021, author = {Orekhov, M. A.}, journal = {Journal of Molecular Liquids}, pages = {114554}, title = {{Improving molecular dynamics calculation of diffusivity in liquids with theoretical models}}, volume = {322}, year = {2021}, abstract = {An effect of the collective motions on the variance of diffusivity in liquids is considered. It is shown theoretically and with simulation that collective fluctuations increase statistical uncertainty of diffusivity in liquids. On this basis we develop approach that combines molecular dynamics and theoretical models to calculate diffusion coefficient in liquids. We decompose diffusivity into a low scale molecular part and a large scale hydrodynamic part. The low scale term is calculated with the molecular dynamics. It is performed using a small simulation box with less than 100 particles. Local molecular motions appear in such simulations while collective hydrodynamical fluctuations are absent. The large scale hydrodynamics is included with a theoretical model. Thus, molecular dynamics term includes only molecular processes such as rearrangements of molecules, and hydrodynamical term includes collective processes. This approach provides lower statistical uncertainty compared with simulations of large systems. The improvement in statistical accuracy is shown theoretically and confirmed with simulations. It is connected to the relation between diffusivity due to local molecular processes and diffusivity due to hydrodynamics. To illustrate the application of this approach, we compute the self-diffusion coefficient in Lennard-Jones liquid and liquid water, diffusivity of divalent ions in aqueous solutions.}, doiurl = {10.1016/j.molliq.2020.114554}, issn = {01677322}, } @article{Smith1993, author = {Smith, Paul E and van Gunsteren, Wilfred F}, journal = {Chemical Physics Letters}, number = {4}, pages = {315--318}, title = {{The viscosity of SPC and SPC/E water at 277 and 300 K}}, volume = {215}, year = {1993}, abstract = {The shear viscosity of the SPC and SPC/E water models at 277 and 300 K has been determined using equilibrium molecular dynamics. Good agreement with experiment was obtained for the SPC/E model at both temperatures. The viscosity of the SPC model was lower than the experimental value at both temperatures and displayed only a small temperature dependence. The effect of using a reaction field treatment for the long-range electrostatic interaction was also investigated and found to be negligible. {\textcopyright} 1993.}, doiurl = {10.1016/0009-2614(93)85720-9}, isbn = {0009-2614}, issn = {00092614}, } @article{Gonzalez2010, author = {Gonz{\'{a}}lez, Miguel Angel and Abascal, Jo{\'{s}} L.F.}, journal = {J. Chem. Phys.}, number = {9}, pages = {096101}, title = {{The shear viscosity of rigid water models}}, volume = {132}, year = {2010}, abstract = {In this work, the shear viscosity at ambient conditions of several water models (SPC/E, TIP4P, TIP5P, and TIP4P/2005) is evaluated using the Green-Kubo formalism. The performance of TIP4P/2005 is excellent, that of SPC/E and TIP5P is more or less acceptable, whereas TIP4P and especially TIP3P give a poor agreement with experiment. Further calculations have been carried out for TIP4P/2005 to provide a wider assessment of its performance. In accordance with experimental data, TIP4P/2005 predicts a minimum in the shear viscosity for the 273 K isotherm, a shift in the minimum toward lower pressures at 298 K, and its disappearance at 373 K.}, doiurl = {10.1063/1.3330544}, isbn = {1089-7690 (Electronic)\r0021-9606 (Linking)}, issn = {00219606}, } @book{LB_vics, author = {Landolt, Hans and Bornstein, Richard}, booktitle = {NBER Working Papers}, pages = {89}, publisher = {Springer}, title = {{Landolt-B{\"{o}}rnstein Numerical Data and Functional Relationships in Science and Technology}}, year = {2013}, isbn = {978-3-540-56050-0}, url = {http://www.nber.org/papers/w16019}, }