scholarly journals Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model

Author(s):  
Antonio Viayna ◽  
Silvana Pinheiro ◽  
Carles Curutchet ◽  
F. Javier Luque ◽  
William J. Zamora

AbstractWithin the scope of SAMPL7 challenge for predicting physical properties, the Integral Equation Formalism of the Miertus-Scrocco-Tomasi (IEFPCM/MST) continuum solvation model has been used for the blind prediction of n-octanol/water partition coefficients and acidity constants of a set of 22 and 20 sulfonamide-containing compounds, respectively. The log P and pKa were computed using the B3LPYP/6-31G(d) parametrized version of the IEFPCM/MST model. The performance of our method for partition coefficients yielded a root-mean square error of 1.03 (log P units), placing this method among the most accurate theoretical approaches in the comparison with both globally (rank 8th) and physical (rank 2nd) methods. On the other hand, the deviation between predicted and experimental pKa values was 1.32 log units, obtaining the second best-ranked submission. Though this highlights the reliability of the IEFPCM/MST model for predicting the partitioning and the acid dissociation constant of drug-like compounds compound, the results are discussed to identify potential weaknesses and improve the performance of the method.

1998 ◽  
Vol 76 (6) ◽  
pp. 657-661 ◽  
Author(s):  
Yvonne Chiang ◽  
A Jerry Kresge ◽  
Norman P Schepp ◽  
Vladimir V Popik ◽  
Zvi Rappoport ◽  
...  

The acidity constant, pQaE = 8.49, for the stable thioenol, triphenylethenethiol, was determined by spectrophotometric titration, and that, pQaE = 11.37, for its unstable oxygen analog, triphenylethenol, was determined by analysis of its ketonization rate using enol generated flash photolytically from triphenylvinyl bromide. (These acidity constants are concentration quotients applicable at 0.10 M ionic strength in 50 vol.% aqueous methanol.) This appears to be the first determination of the acid strength of a simple thioenol. Triphenylethenethiol was unreactive in dilute acid or base, but in concentrated perchloric acid solutions it was slowly transformed into diphenylacetophenone and 2,3-diphenylbenzo[b]thiophene; the mechanisms of these reactions are believed to involve rapid equilibrium protonation of the enol on the beta -carbon followed by rate-determining capture of the cation so formed, either externally by solvent or internally by one of the beta -phenyl groups of the ion.Key words: enol ketonization, thioenol, flash photolysis, vinyl halide.


2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>


Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 717
Author(s):  
Mariia Nazarkevych ◽  
Natalia Kryvinska ◽  
Yaroslav Voznyi

This article presents a new method of image filtering based on a new kind of image processing transformation, particularly the wavelet-Ateb–Gabor transformation, that is a wider basis for Gabor functions. Ateb functions are symmetric functions. The developed type of filtering makes it possible to perform image transformation and to obtain better biometric image recognition results than traditional filters allow. These results are possible due to the construction of various forms and sizes of the curves of the developed functions. Further, the wavelet transformation of Gabor filtering is investigated, and the time spent by the system on the operation is substantiated. The filtration is based on the images taken from NIST Special Database 302, that is publicly available. The reliability of the proposed method of wavelet-Ateb–Gabor filtering is proved by calculating and comparing the values of peak signal-to-noise ratio (PSNR) and mean square error (MSE) between two biometric images, one of which is filtered by the developed filtration method, and the other by the Gabor filter. The time characteristics of this filtering process are studied as well.


Sensors ◽  
2021 ◽  
Vol 21 (10) ◽  
pp. 3311
Author(s):  
Riccardo Ballarini ◽  
Marco Ghislieri ◽  
Marco Knaflitz ◽  
Valentina Agostini

In motor control studies, the 90% thresholding of variance accounted for (VAF) is the classical way of selecting the number of muscle synergies expressed during a motor task. However, the adoption of an arbitrary cut-off has evident drawbacks. The aim of this work is to describe and validate an algorithm for choosing the optimal number of muscle synergies (ChoOSyn), which can overcome the limitations of VAF-based methods. The proposed algorithm is built considering the following principles: (1) muscle synergies should be highly consistent during the various motor task epochs (i.e., remaining stable in time), (2) muscle synergies should constitute a base with low intra-level similarity (i.e., to obtain information-rich synergies, avoiding redundancy). The algorithm performances were evaluated against traditional approaches (threshold-VAF at 90% and 95%, elbow-VAF and plateau-VAF), using both a simulated dataset and a real dataset of 20 subjects. The performance evaluation was carried out by analyzing muscle synergies extracted from surface electromyographic (sEMG) signals collected during walking tasks lasting 5 min. On the simulated dataset, ChoOSyn showed comparable performances compared to VAF-based methods, while, in the real dataset, it clearly outperformed the other methods, in terms of the fraction of correct classifications, mean error (ME), and root mean square error (RMSE). The proposed approach may be beneficial to standardize the selection of the number of muscle synergies between different research laboratories, independent of arbitrary thresholds.


2021 ◽  
Vol 27 (8) ◽  
Author(s):  
Fernando Marques Carvalho ◽  
Yuri Alves de Oliveira Só ◽  
Alessandra Sofia Kiametis Wernik ◽  
Mônica de Abreu Silva ◽  
Ricardo Gargano

2013 ◽  
Vol 17 (06n07) ◽  
pp. 447-453 ◽  
Author(s):  
Hiroaki Isago ◽  
Harumi Fujita

Dissociation of imino proton(s) in the cavity of the macrocycle of a highly water-soluble, metal-free phthalocyanine ( H 2( H 4 tsppc ); where H 4 tsppc denotes tetrakis{(2′,6′-dimethyl-4′-sulfonic acid)phenoxy}phthalocyaninate) in ethanolic and aqueous solutions has spectrophotometrically been investigated. The spectral changes associated with reaction with NaOH have been found to involve one-proton transfer process in aqueous media while two-protons process in ethanolic media. The acid-dissociation constant of the first imino proton in water (in the presence of Triton X-100) has been determined to be 12.5 ± 0.2 (as pKa) at 25 °C. The doubly deprotonated species in EtOH has been easily converted to its corresponding cobalt(II) derivative by thermal reaction with anhydrous CoCl 2.


2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Elisabeth Gibert-Sotelo ◽  
Isabel Pujol Payet

Abstract The interest in morphology and its interaction with the other grammatical components has increased in the last twenty years, with new approaches coming into stage so as to get more accurate analyses of the processes involved in morphological construal. This special issue is a valuable contribution to this field of study. It gathers a selection of five papers from the Morphology and Syntax workshop (University of Girona, July 2017) which, on the basis of Romance and Latin phenomena, discuss word structure and its decomposition into hierarchies of features. Even though the papers share a compositional view of lexical items, they adopt different formal theoretical approaches to the lexicon-syntax interface, thus showing the benefit of bearing in mind the possibilities that each framework provides. This introductory paper serves as a guide for the readers of this special collection and offers an overview of the topics dealt in each contribution.


1995 ◽  
Vol 74 (6) ◽  
pp. 2665-2684 ◽  
Author(s):  
Y. Kondoh ◽  
Y. Hasegawa ◽  
J. Okuma ◽  
F. Takahashi

1. A computational model accounting for motion detection in the fly was examined by comparing responses in motion-sensitive horizontal system (HS) and centrifugal horizontal (CH) cells in the fly's lobula plate with a computer simulation implemented on a motion detector of the correlation type, the Reichardt detector. First-order (linear) and second-order (quadratic nonlinear) Wiener kernels from intracellularly recorded responses to moving patterns were computed by cross correlating with the time-dependent position of the stimulus, and were used to characterize response to motion in those cells. 2. When the fly was stimulated with moving vertical stripes with a spatial wavelength of 5-40 degrees, the HS and CH cells showed basically a biphasic first-order kernel, having an initial depolarization that was followed by hyperpolarization. The linear model matched well with the actual response, with a mean square error of 27% at best, indicating that the linear component comprises a major part of responses in these cells. The second-order nonlinearity was insignificant. When stimulated at a spatial wavelength of 2.5 degrees, the first-order kernel showed a significant decrease in amplitude, and was initially hyperpolarized; the second-order kernel was, on the other hand, well defined, having two hyperpolarizing valleys on the diagonal with two off-diagonal peaks. 3. The blockage of inhibitory interactions in the visual system by application of 10-4 M picrotoxin, however, evoked a nonlinear response that could be decomposed into the sum of the first-order (linear) and second-order (quadratic nonlinear) terms with a mean square error of 30-50%. The first-order term, comprising 10-20% of the picrotoxin-evoked response, is characterized by a differentiating first-order kernel. It thus codes the velocity of motion. The second-order term, comprising 30-40% of the response, is defined by a second-order kernel with two depolarizing peaks on the diagonal and two off-diagonal hyperpolarizing valleys, suggesting that the nonlinear component represents the power of motion. 4. Responses in the Reichardt detector, consisting of two mirror-image subunits with spatiotemporal low-pass filters followed by a multiplication stage, were computer simulated and then analyzed by the Wiener kernel method. The simulated responses were linearly related to the pattern velocity (with a mean square error of 13% for the linear model) and matched well with the observed responses in the HS and CH cells. After the multiplication stage, the linear component comprised 15-25% and the quadratic nonlinear component comprised 60-70% of the simulated response, which was similar to the picrotoxin-induced response in the HS cells. The quadratic nonlinear components were balanced between the right and left sides, and could be eliminated completely by their contralateral counterpart via a subtraction process. On the other hand, the linear component on one side was the mirror image of that on the other side, as expected from the kernel configurations. 5. These results suggest that responses to motion in the HS and CH cells depend on the multiplication process in which both the velocity and power components of motion are computed, and that a putative subtraction process selectively eliminates the nonlinear components but amplifies the linear component. The nonlinear component is directionally insensitive because of its quadratic non-linearity. Therefore the subtraction process allows the subsequent cells integrating motion (such as the HS cells) to tune the direction of motion more sharply.


2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Mohsen Alipour ◽  
Dumitru Baleanu ◽  
Fereshteh Babaei

We introduce a new combination of Bernstein polynomials (BPs) and Block-Pulse functions (BPFs) on the interval [0, 1]. These functions are suitable for finding an approximate solution of the second kind integral equation. We call this method Hybrid Bernstein Block-Pulse Functions Method (HBBPFM). This method is very simple such that an integral equation is reduced to a system of linear equations. On the other hand, convergence analysis for this method is discussed. The method is computationally very simple and attractive so that numerical examples illustrate the efficiency and accuracy of this method.


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