Numerical analysis of electroosmotic flow in dense regular and random arrays of impermeable, nonconducting spheres

We present a numerical scheme for analyzing steady-state isothermal electroosmotic flow (EOF) in three-dimensional random porous media, involving solution of the coupled Poisson, Nernst-Planck, and Navier-Stokes equations. While traditional finite-difference methods were used to resolve the Poisson-Nernst-Planck problem, the (electro)hydrodynamics has been addressed with high efficiency using the lattice-Boltzmann method. The developed model allows simulation of electrokinetic transport under most general conditions, including arbitrary value and distribution of electrokinetic potential at the solid-liquid interface, electrolyte composition, and pore space morphology. The approach provides quantitative information on a spatial distribution of simulated velocities. This feature was utilized to characterize EOF fields in regular and random, confined and bulk packings of hard (i.e., impermeable, nonconducting) spheres. Important aspects of pore space morphology (sphere size distribution), surface heterogeneity (mismatch in electrokinetic potentials at confining wall and sphere surface), and fluid phase properties (electrical double layer thickness) were investigated with respect to their influence on the EOF dynamics over microscopic and macroscopic spatial domains. Most important is the observation of a generally nonuniform pore-level EOF velocity profile in the sphere packings (even in the thin double layer limit) which is caused by pore space morphology and which is in contrast to the pluglike velocity distribution in a single, straight capillary under the same conditions.     

Generation of Mixed Anhydrides via Oxidative Fragmentation of Tertiary Cyclopropanols with Phenyliodine(III) Dicarboxylates

Oxidative fragmentation of tertiary cyclopropanols with phenyliodine(III) dicarboxylates in aprotic solvents (dichloromethane, chloroform, toluene) produces mixed anhydrides. The fragmentation reaction is especially facile with phenyliodine(III) reagents bearing electron-withdrawing carboxylate ligands (trifluoroacetyl, 2,4,6-trichlorobenzoyl, 3-nitrobenzoyl), and affords 95−98% yields of the corresponding mixed anhydride products. The latter can be straightforwardly applied for the acylation of various nitrogen, oxygen and sulfur-centered nucleophiles (primary and secondary amines, hydroxylamines, primary alcohols, phenols, thiols). Intramolecular acylation yielding macrocyclic lactones can also be performed. The developed transformation has bolstered the synthetic utility of cyclopropanols as pluripotent intermediates in diversity-oriented synthesis of bioactive natural products and their synthetic congeners. For example, it was successfully applied for the last-stage modification of a cyclic peptide to produce a precursor of a known histone deacetylase inhibitor.     

Protein–ligand docking using FFT based sampling: D3R case study

Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein–protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein–peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein–ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein–ligand interaction landscape, which will be explored in further applications.     

An Abnormal N‐Heterocyclic Carbene–Carbon Dioxide Adduct from Imidazolium Acetate Ionic Liquids: The Importance of Basicity

In the reaction of 1‐ethyl‐3‐methylimidazolium acetate [C₂C₁Im][OAc] ionic liquid with carbon dioxide at 125 °C and 10 MPa, not only the known N‐heterocyclic carbene (NHC)–CO₂ adduct I , but also isomeric aNHC‐CO₂ adducts II and III were obtained. The abnormal NHC‐CO₂ adducts are stabilized by the presence of the polarizing basic acetate anion, according to static DFT calculations and ab initio molecular dynamics studies. A further possible reaction pathway is facilitated by the high basicity of the system, deprotonating the initially formed NHC‐CO₂ adduct I , which can then be converted in the presence of the excess of CO₂ to the more stable 2‐deprotonated anionic abnormal NHC–CO₂ adduct via the anionic imidazolium‐2,4‐dicarboxylate according to DFT calculations on model compounds. This suggests a generalizable pathway to abnormal NHC complex formation.     

Extremely Low Vapor-Pressure Data as Access to PC-SAFT Parameter Estimation for Ionic Liquids and Modeling of Precursor Solubility in Ionic Liquids

Precursor solubility is a crucial factor in industrial applications, dominating the outcome of reactions and purification steps. The outcome and success of thermodynamic modelling of this industrially important property with equations of states, such as Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT), vastly depends on the quality of the pure-component parameters. The pure-component parameters for low-volatile compounds such as ionic liquids (ILs) have been commonly estimated using mixture properties, e. g. the osmotic pressure of aqueous solutions. This leads to parameters that depend on the solvent, and transferability to other mixtures often causes poor modeling results. Mixture-independent experimental properties would be a more suitable basis for the parameter estimation offering a way to universal parameter sets. Model parameters for ILs are available in the literature [10.1016/j.fluid.2012.05.029], but they were estimated using pure-IL density data. The present work focuses on a step towards a more universal estimation strategy that includes new experimental vapor-pressure data of the pure IL. ILs exhibit an almost negligible vapor pressure in magnitude of usually 10⁻⁵ Pa even at elevated temperatures. In this work, such vapor-pressure data of a series of 1-ethyl-3-methyl-imidazolium-based [C₂mim]-ILs with various IL-anions (e. g. tetrafluoroborate [BF₄]⁻, hexafluorophosphate [PF₆]⁻, bis(trifluoromethylsulfonyl)imide [NTf₂]⁻) were experimentally determined and subsequently used for PC-SAFT parameter estimation. The so-determined parameters were used to predict experimental molecular precursor solubility in ILs and infinitely diluted activity coefficients of various solvents in ILs. The parameters were further compared to modeling results using classical parametrization methods (use of liquid-density data only for the molecular PC-SAFT and the ion-based electrolyte PC-SAFT). As a result, the modeled precursor solubilities using the new approach are much more precise than using the classical parametrization methods, and required binary parameters were found to be much smaller (if needed). In sum, including the pure-component vapor-pressure data of ILs opens the door towards parameter estimation that is not biased by mixture data. This procedure might be suitable also for polymers and for all kind of ionic species but needs extension to ion-specific parametrization in the long term.     

Inhomogeneous Diophantine approximation on curves and Hausdorff dimension

The goal of this paper is to develop a coherent theory for inhomogeneous Diophantine approximation on curves in Rn akin to the well established homogeneous theory. More specifically, the measure theoretic results obtained generalize the fundamental homogeneous theorems of R.C. Baker (1978) [2], Dodson, Dickinson (2000) [18] and Beresnevich, Bernik, Kleinbock, Margulis (2002) [8]. In the case of planar curves, the complete Hausdorff dimension theory is developed.     

Estimation of Lattice Enthalpies of Ionic Liquids Supported by Hirshfeld Analysis

New measurements of vaporization enthalpies for 15 1:1 ionic liquids are performed by using a quartz‐crystal microbalance. Collection and analysis of 33 available crystal structures of organic salts, which comprise 13 different cations and 12 anions, is performed. Their dissociation lattice enthalpies are calculated by a combination of experimental and quantum chemical quantities and are divided into the relaxation and Coulomb components to give an insight into elusive short‐range interaction enthalpies. An empirical equation is developed, based on interaction‐specific Hirshfeld surfaces and solvation enthalpies, which enables the estimation of the lattice enthalpy by using only the crystal‐structure data.     

Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes

The time scale for ordering of the polypeptide backbone relative to the side chains is a critical issue in protein folding. The interplay between ordering of the backbone and ordering of the side chains is particularly important for the formation of β-sheet structures, as the polypeptide chain searches for the native stabilizing cross-strand interactions. We have studied these issues in the N-terminal domain of protein L9 (NTL9), a model protein with mixed α/β structure. We have developed a general approach for introducing site-specific IR probes for the side chains (azide) and backbone ((13)C═(18)O) using recombinant protein expression. Temperature-jump time-resolved IR spectroscopy combined with site-specific labeling enables independent measurement of the respective backbone and side-chain dynamics with single residue resolution. We have found that side-chain ordering in a key region of the β-sheet structure occurs on a slower time scale than ordering of the backbone during the folding of NTL9, likely as a result of the transient formation of non-native side-chain interactions.