Predicting Octanol/Water Partition Coefficients of Alcohol Ethoxylate Surfactants Using a Combination of Molecular Dynamics and the Conductor-like Screening Model for Realistic Solvents

Quantum chemical calculation of the vapor pressure of volatile and semi volatile organic compounds

The vapor pressure is a specific and temperature-dependent parameter that describes the volatility of a substance and thus its driving force for evaporation or sublimation into the gas phase. Depending on the magnitude of the vapor pressure, there are different methods for experimental determination. However, these are usually associated with a corresponding amount of effort and become less accurate as the vapor pressure decreases. For purposes of vapor pressure prediction, algorithms were developed that are usually based on quantitative structure-activity relationships (QSAR). The quantum mechanical (QM) approach followed here applies an alternative, much less empirical strategy, where the change in Gibbs free energy for the transition from the condensed to the gas phase is obtained from conformer ensembles computed for each phase separately. The results of this automatic, so-called CRENSO workflow are compared with experimentally determined vapor pressures for a large set of environmentally relevant compounds. In addition, comparisons are made with the single structure-based COSMO-RS QM approach, linear-free-energy relationships (LFER) as well as results from the SPARC program. We show that our CRENSO workflow is superior to conventional prediction models and provides reliable vapor pressures for liquids and sub-cooled liquids over a wide pressure range.

Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

The partitioning of compounds between aqueous and other phases is important for predicting toxicity. Although thousands of octanol-water partition coefficients have been measured, these represent only a small fraction of the anthropogenic compounds present in the environment. The octanol phase is often taken to be a mimic of the inner parts of phospholipid membranes. However, the core of such membranes is typically more hydrophobic than octanol, and other partition coefficients with other compounds may give complementary information. Although a number of (cheap) empirical methods exist to compute octanol-water (log k _OW) and hexadecane-water (log k _HW) partition coefficients, it would be interesting to know whether physics-based models can predict these crucial values more accurately. Here, we have computed log k _OW and log k _HW for 133 compounds from seven different pollutant categories as well as a control group using the solvation model based on electronic density (SMD) protocol based on Hartree-Fock (HF) or density functional theory (DFT) and the COSMO-RS method. For comparison, XlogP3 (log k _OW) values were retrieved from the PubChem database, and KowWin log k _OW values were determined as well. For 24 of these compounds, log k _OW was computed using potential of mean force (PMF) calculations based on classical molecular dynamics simulations. A comparison of the accuracy of the methods shows that COSMO-RS, KowWin, and XlogP3 all have a root-mean-square deviation (rmsd) from the experimental data of ≈0.4 log units, whereas the SMD protocol has an rmsd of 1.0 log units using HF and 0.9 using DFT. PMF calculations yield the poorest accuracy (rmsd = 1.1 log units). Thirty-six out of 133 calculations are for compounds without known log k _OW, and for these, we provide what we consider a robust prediction, in the sense that there are few outliers, by averaging over the methods. The results supplied may be instrumental when developing new methods in computational ecotoxicity. The log k _HW values are found to be strongly correlated to log k _OW for most compounds.

Predicting Octanol-Water Partition Coefficients: Are Quantum Mechanical Implicit Solvent Models Better than Empirical Fragment-Based Methods?

In this work, we examined the performance of contemporary quantum mechanical implicit solvent models (SMD, SM8, SM12, and ADF-COSMO-RS) and empirical fragment-based methods for predicting octanol-water partition coefficients (log P_ow). Two test sets were chosen: the first is composed of 34 organic molecules from a recent study by Mobley J. Chem. Theory Comput , 2016 , 12 , 4015 - 4024 , and the second set is based on a collection of 55 fluorinated alkanols and carbohydrates from Linclau Angew. Chem., Int. Ed. , 2016 , 55 , 674 - 678 . Our analysis indicates that the errors in the solvation free energies of implicit models are reasonably systematic in both solvents such that there is substantial cancellation of errors in the calculation of transfer free energies. Overall, implicit solvent models performed very well across the two test sets with mean absolute errors (MAEs) of about 0.6 log unit and are superior to explicit solvent simulations (GAFF and GAFF-DC). Interestingly, the best performers were empirical fragment-based methods, including ALOGP and miLOGP with significantly lower MAEs (0.2 to 0.4 log unit). The ALOGP method was further tested against the recent SAMPL6 log P_ow challenge consisting of 11 drug-like molecules where it obtained an MAE of 0.32 log unit compared to the best-performing COSMOtherm model (0.31 log unit).

New Properties of a Bioinspired Pyridine Benzimidazole Compound as a Novel Differential Staining Agent for Endoplasmic Reticulum and Golgi Apparatus in Fluorescence Live Cell Imaging

In this study, we explored new properties of the bioinspired pyridine benzimidazole compound B2 (2,4-di-tert-butyl-6-(3H-imidazo[4,5-c]pyridine-2-yl)phenol) regarding its potential use as a differential biomarker. For that, we performed 1D ¹HNMR (TOCSY), UV-Vis absorption spectra in different organic solvents, voltammetry profile (including a scan-rate study), and TD-DFT calculations that including NBO analyses, to provide valuable information about B2 structure and luminescence. In our study, we found that the B2 structure is highly stable, where the presence of an intramolecular hydrogen bond (IHB) seems to have a crucial role in the stability of luminescence, and its emission can be assigned as fluorescence. In fact, we found that the relatively large Stokes Shift observed for B2 (around 175 nm) may be attributed to the stability of the B2 geometry and the strength of its IHB. On the other hand, we determined that B2 is biocompatible by cytotoxicity experiments in HeLa cells, an epithelial cell line. Furthermore, in cellular assays we found that B2 could be internalized by passive diffusion in absence of artificial permeabilization at short incubation times (15 min to 30 min). Fluorescence microscopy studies confirmed that B2 accumulates in the endoplasmic reticulum (ER) and Golgi apparatus, two organelles involved in the secretory pathway. Finally, we determined that B2 exhibited no noticeable blinking or bleaching after 1 h of continuous exposure. Thus, B2 provides a biocompatible, rapid, simple, and efficient way to fluorescently label particular organelles, producing similar results to that obtained with other well-established but more complex methods.

Two New Fluorinated Phenol Derivatives Pyridine Schiff Bases: Synthesis, Spectral, Theoretical Characterization, Inclusion in Epichlorohydrin-β-Cyclodextrin Polymer, and Antifungal Effect

It has been reported that the structure of the Schiff bases is fundamental for their function in biomedical applications. Pyridine Schiff bases are characterized by the presence of a pyridine and a phenolic ring, connected by an azomethine group. In this case, the nitrogen present in the pyridine is responsible for antifungal effects, where the phenolic ring may be also participating in this bioactivity. In this study, we synthesized two new pyridine Schiff Bases: (E)-2-[(3-Amino-pyridin-4-ylimino)-methyl]-4,6-difluoro-phenol (F1) and (E)- 2-[(3-Amino-pyridin-4-ylimino)-methyl]-6-fluoro-phenol (F2), which only differ in the fluorine substitutions in the phenolic ring. We fully characterized both F1 and F2 by FTIR, UV-vis, ¹H; ¹³C; ¹⁹F-NMR, DEPT, HHCOSY, TOCSY, and cyclic voltammetry, as well as by computational studies (DFT), and NBO analysis. In addition, we assessed the antifungal activity of both F1 (two fluorine substitution at positions 4 and 6 in the phenolic ring) and F2 (one fluorine substitution at position 6 in the phenolic ring) against yeasts. We found that only F1 exerted a clear antifungal activity, showing that, for these kind of Schiff bases, the phenolic ring substitutions can modulate biological properties. In addition, we included F1 and F2 into in epichlorohydrin-β-cyclodextrin polymer (βCD), where the Schiff bases remained inside the βCD as determined by the k_i, TGA, DSC, and S_BET. We found that the inclusion in βCD improved the solubility in aqueous media and the antifungal activity of both F1 and F2, revealing antimicrobial effects normally hidden by the presence of common solvents (e.g., DMSO) with some cellular inhibitory activity. The study of structural prerequisites for antimicrobial activity, and the inclusion in polymers to improve solubility, is important for the design of new drugs.