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54 results for “Solvation”
Supporting dataset for the publication "The Crucial Role of Solvation Forces in the Steric Stabilization of Nanoplatelets"
<p>Here, we provide an example of our umbrella sampling simulations (35.6 nm²×1.5 nm, 4 ligand beads, 250k solvent molecules), the input and output data of our WHAM calculations, free energy curves, and simulation data from the comparison of the MARTINI force field to the TraPPE-UA force field. Additional, we provide a modified file of the HOOBAS molecular builder. This file includes the "platelet" class we use to create nonoplatelets in our simulations.</p> <p> </p> <p> </p>
Raw Data to "Performance of the COSMO solvation model for photoacidity and basicity in water"
<p>This data is a supplement to the publication entitled "Performance of the COSMO solvation model for photoacidity and basicity in water" in the the Journal of Computational Chemistry A (DOI: 10.1002/jcc.27173).<br> It contains:</p> <p>Additional information on the file structure is given in the README file.</p>
Supporting data for:"An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations."
<p>PLUMED_NEST_REPO.zip contains the plumed.dat file and the template PDB used to perform the metainference MD simulations of Gelsolin and UP1-RNA, with and without the Solvation Layer Contribution.</p> <p>TRAJECTORIES.zip contains the Gelsolin and UP1-RNA trajectories and additional data generated with GROMACS. In details:</p> <p>-Gelsolin. Production Molecular Dynamics Parameter file (production.mdp), a topology file (topol.top), and 3 folders: TPRs (with 10 TPR files -one for each replica-), TRJ_SLC_OFF (with data from simulations without Solvation Layer Contribution), and TRJ_SLC_ON (with data from simulations with Solvation Layer Contribution). The last two contain an index file, a trajectory obtained from the concatenation of the 10 replicas (concat.xtc), and a template PDB file.</p> <p>-UP1-RNA. TPR file (md.tpr) and 2 folders: TRJ_SLC_OFF (with data from simulations without solvent correction), and TRJ_SLC_ON (with data from simulations with solvent correction). Each folder contains an index file, a template PDB file and a trajectory file (trj.xtc)</p> <p> </p>
Input files for binding energy calculations in "Coupling finite and boundary element methods to solve the Poisson--Boltzmann equation for electrostatics in molecular solvation"
<p>Input files (meshes, pqr, cavities) for binding energy calculations in the manuscript "Coupling finite and boundary element methods to solve the Poisson--Boltzmann equation for electrostatics in molecular solvation" (preprint at https://arxiv.org/abs/2305.11886). This data set of molecular structures was originally proposed by Harris, R.C., Boschtisch, A.H., and Fenley, M.O., JCTC 9 (8) (2013) (<a href="https://doi.org/10.1021/ct300765w">https://doi.org/10.1021/ct300765w</a>). Scripts to generate results are available in https://github.com/MichalBosy/FEM_BEM_coupling/.</p>
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
<p>A dye-sensitized solar cell was solvated by RTILs; using optimized empirical potentials, a molecular dynamics simulation was applied to compute vibrational properties. The obtained vibrational spectra were compared with experiment and ab initio molecular dynamics; various empirical potential spectra show how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction.</p>
Underlying data for "Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field"
<p>This dataset provides the parameters and results generated for the study "Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field"</p> <p>Contents of dataset:<br /> PARAMETERS.tar.gz<br /> A gzipped and tar'd directory with the parameters of all solutes sorted by solvent for AMOEBA and GAFF force field. This parameters directory is distributed to 4 different subdirectories: a)chloroform (21 solutes) b)toluene (21 solutes) c)dmso (6 solutes) d)acetonitrile (6 solutes). Each solvent includes two set of parameters for each solute (AMOEBA and GAFF).</p> <p>RESULTS.tar.gz<br /> A gzipped and tar'd directory with the solvation free energy results of all solutes in kcal/mol, with AMOEBA and GAFF force fields, for each solvent, in text format. A single set of conditions for a single solute is one row in the text files. The first column represents the experimental data, the remaining columns (2, 3 and 4) correspond to the three repeat simulations.</p>
Datasets for: Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy
<p>The datasets and supplementary materials for the manuscript "Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy". <strong>Citations should refer directly to the manuscript (refer to the DOI </strong><a href="https://doi.org/10.1021/acs.jcim.1c01103">10.1021/acs.jcim.1c01103</a><strong>)</strong>.</p> <p>The preprint version of of the manuscript is also available at: <a href="https://doi.org/10.33774/chemrxiv-2021-djd3d-v2">10.33774/chemrxiv-2021-djd3d-v2</a></p> <p> </p> <p>Regarding "<strong>Solvation_data-1.0.0.zip</strong>":</p> <p>The datasets include the curated data for: (1) Abraham solute parameters, (2) solvation free energy, (3) solvation enthalpy, (4) gas-water partition coefficient (logKw), (5) water-1-octanol partition coefficient (logPow). The fitted Abraham and Mintz solvent parameters are also included.</p> <p>Detailed information can be found in the "README.txt" file of the zip file.</p> <p> </p> <p>Regarding "<strong>ML_model_files.zip</strong>":</p> <p>This contains the machine learning model files for SoluteML and DirectML. For the instruction on how to use it, please refer to the <em>chemprop_solvation</em> git repository (<a href="https://github.com/fhvermei/chemprop_solvation">https://github.com/fhvermei/chemprop_solvation</a>)</p> <p> </p>
Non-fluorinated electrolytes with micelle-like solvation for ultrahigh energy density lithium metal batteries
<p>Electrolyte engineering plays a critical role in enabling lithium (Li) metal batteries. However, the simultaneous realization of anion-rich solvation structure and high ionic conductivity of electrolytes via solvation structure design remains challenging. Here, we report a low-cost, non-fluorinated electrolyte with a micelle-like solvation structure by introducing amphiphilic n-butyl methyl ether (MNBE) into lithium bis(fluorosulfonyl)imide (LiFSI)/1,2-dimethoxyethane (DME) for stable Li metal batteries. MNBE can effectively promote Li+-FSI- coordination through steric crowding. Meanwhile, the inert alkyl chains of MNBE can mitigate the reaction between electrolyte and Li metal due to their lithiophobicity. Specifically, the micelle-like, non-fluorinated electrolyte exhibits an ionic conductivity as high as 12.55 mS cm-1 and its anion-rich solvation structure promotes the formation of LiF-rich solid-electrolyte-interphase. We constructed a 7.3 Ah Li||NMC811 pouch cell employing this electrolyte under harsh conditions, exhibiting ultrahigh specific energy of 503.7 Wh kg-1 with impressive cycling stability of 84.1% capacity retention after 100 cycles. </p>
Data for "A Surface-Promoted Redox Reaction Occurs Spontaneously on Solvating Inorganic Aerosol Surfaces"
<p>Dataset for "A Surface-Promoted Redox Reaction Occurs Spontaneously on Solvating Inorganic Aerosol Surfaces"</p>
DFT data for "The Role of Ion Solvation in Lithium Mediated Nitrogen Reduction"
<p>Density Functional Theory data used in the paper "The Role of Ion Solvation in Lithium Mediated Nitrogen Reduction".</p>
DOX_BDW: Incorporating Solvation and Desolvation Effects of Cavity Water into Nonfitting Protein–Ligand Binding Affinity Prediction
<p><strong>structures.zip:</strong> including the coordinates of all optimized proteinligand complex structure obtained by DOX_BDW calculation. (compressed PDB file). These pdb files could also be used as input for the binding energy calculation,as illustrated in SI section 8. </p> <p><strong>mdinput.zip:</strong> Including the input files,parameter files, topology files needed to run MD simulation for water mapping, as illustrated in SI section 8. Note that all of the parameter files and topology files would be automatically generated using the RUNMD program we uploaded with the example file. </p> <p><strong>example.zip:</strong> The programs and input files needed to run an example, as illustrated in SI section 9. And all the output files except MD trajectories are in there,too.</p>
Parameters for the solvated KcsA-LAB-TEA, when the LAB-TEA is placed inside the channel cavity without K+-ion
<p>Parameters for the solvated KcsA-LAB-TEA. These KcsA-LAB-TEA systems were solvated by truncated octahedron TIP3PBOX, using the leap program in AMBER20. The LAB-TEA is placed inside the channel cavity. The simulation is performed without K<sup>+</sup>-ion.</p>
Parameters for the solvated KcsA-K+-LAB-TEA, when both LAB-TEA and K+-ion placed inside the channel cavity
<p>Parameters for the solvated KcsA-K<sup>+</sup>-LAB-TEA. These KcsA-K<sup>+</sup>-LAB-TEA systems were solvated by truncated octahedron TIP3PBOX, using the leap program in AMBER20. Both LAB-TEA and K<sup>+</sup>-ion are placed inside the channel cavity.</p>
Endo_TS1_G16_PCM_chloroform_def2tzvpp_v_02_solvated_1
Gaussian 16 (C01) calculation
Endo_TS1_G16_PCM_chloroform_def2tzvpp_v_02_reactant_solvated_1
Gaussian 16 (C01) calculation
Endo_TS1_G16_PCM_chloroform_def2tzvpp_v_02_solvated_2
Gaussian 16 (C01) calculation
Endo_TS1_G16_PCM_chloroform_def2tzvpp_v_02_reactant_solvated_2
Gaussian 16 (C01) calculation
Endo_TS1_G16_PCM_chloroform_def2tzvpp_v_03_reactant_solvated
Gaussian 16 (C01) calculation
Endo_TS1_G16_PCM_chloroform_def2tzvpp_v_01_solvated
Gaussian 16 (C01) calculation
Fig. 3 in The phenolic profile extracted from the desiccation-tolerant medicinal shrub Myrothamnus flabellifolia using Natural Deep Eutectic Solvents varies according to the solvation conditions
Fig. 3. Heatmap and dendrogram based on Euclidean distance and Ward's clustering algorithm. FSG = fructose–sucrose–glucose; Glu_ChCl = glucose–choline chloride; Pro_Mal = proline–malic acid; Su_Ca = sucrose–citric acid.
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