Beyond generative models: superfast traversal,optimization, novelty,exploration and discovery (STONED) algorithm for molecules using SELFIES

Inverse design allows the generation of molecules with desirable physical quantities using property optimization. Deep generative models have recently been applied to tackle inverse design, as they possess the ability to optimize molecular properties directly through structure modification using gradients. While the ability to carry out direct property optimizations is promising, the use of generative deep learning models to solve practical problems requires large amounts of data and is very time-consuming. In this work, we propose STONED – a simple and efficient algorithm to perform interpolation and exploration in the chemical space, comparable to deep generative models. STONED bypasses the need for large amounts of data and training times by using string modifications in the SELFIES molecular representation. First, we achieve non-trivial performance on typical benchmarks for generative models without any training. Additionally, we demonstrate applications in high-throughput virtual screening for the design of drugs, photovoltaics, and the construction of chemical paths, allowing for both property and structure-based interpolation in the chemical space. Overall, we anticipate our results to be a stepping stone for developing more sophisticated inverse design models and benchmarking tools, ultimately helping generative models achieve wider adoption.

Interpolation and exploration within the chemical space for inverse design.     

Particle and surface characterization of a natural illite and study of its copper retention

Illite clays are known to have a strong affinity for metallic pollutants in the environment and can be applied as low-cost adsorbents for industrial waste treatment. A crucial factor in the development of such applications, however, is the understanding of the chemical, mineralogical, and colloidal properties of these clays. It is also important to understand the mechanisms involved in the surface adsorption of metals by these adsorbants. In order to study the retention of transition metals on illite clays, we have applied surface characterization techniques such as FPIA, SEM-EDX, XRD, N2 (77 K) adsorption, and FTIR. In addition to these experimental techniques, we have also employed a theoretical model that accounts for the chemistry of transition metal ions, and considers the global retention process to be the sum of several single retention processes. This model adequately fits the experimental data and allows for the speciation of metal retention on illite surfaces. Between pH values of 2.53 and 3.01 the only adsorption processes are the electrostatic sorption of [Cu(H2O)6]2+, and the surface complexation of [Cu(H2O)6]2+ and [Cu(OH)(H2O)5]+ ions. Surface complexation of [Cu(OH)(H2O)5]+ ions increases with pH, overcoming [Cu(H2O)6]2+ retention, and thus contributing to the surface precipitation of Cu(OH)2.     

Dual Nucleophilic Substitution Reactions of O,O‐Diethyl 2,4‐dinitrophenyl Phosphate and Thionophosphate Triesters

The reactions of the title compounds with phenoxides, secondary alicyclic (SA) amines, and pyridines, in 44 wt% ethanol–water, at 25°C and an ionic strength of 0.2 M, were subjected to kinetic and product studies. From analytical techniques (HPLC and NMR), two pathways were detected (nucleophilic attack at the phosphoryl center and at the C‐1 aromatic carbon) for the reactions of all the nucleophiles with the phosphate ( 2 ) and for the pyridinolysis of the thionophosphate ( 1 ). Only aromatic nucleophilic substitution was found for the reactions of 1 with phenoxides and SA amines. For the dual reactions, the nucleophilic rate constants (k_N) were separated in two terms: $k_{\rm N}^{\rm P}$ and $k_{\rm N}^{{\rm Ar}}$, which are the rate constants for the corresponding electrophilic centers. The absence of a break in the Brønsted‐type plots for the attack at P is consistent with concerted mechanisms. The Brønsted slopes, β_Ar 0.32–0.71, for the attack at the aromatic C‐1, are in agreement with stepwise mechanisms where formation of a Meisenheimer complex is the rate‐determining step. © 2013 Wiley Periodicals, Inc. Int J Chem Kinet 45: 202–211, 2013     

A Simple Method for Producing Pure (+) trans-1,2-Epoxylimonene

In this paper we report a simple methodology for obtaining (+) trans - 1,2 - epoxylimonene (1b) in high purity (>99% HRGC) and reasonable quantity. The mixture of 1a and 1b in CH₂Cl₂ is stirred with 1M NaHSO₃ in water. Under these conditions 1a is completely destroyed, while 1b is only partially destroyed.     

Narrow band quantitative and multivariate electroencephalogram analysis of peri-adolescent period

ABSTRACT: BACKGROUND: The peri-adolescent period is a crucial developmental moment of transition from childhood to emergent adulthood. The present report analyses the differences in Power Spectrum (PS) of the Electroencephalogram (EEG) between late childhood (24 children between 8 and 13 years old) and young adulthood (24 young adults between 18 and 23 years old). RESULTS: The narrow band analysis of the Electroencephalogram was computed in the frequency range of 0--20 Hz. The analysis of mean and variance suggested that six frequency ranges presented a different rate of maturation at these ages, namely: low delta, delta-theta, low alpha, high alpha, low beta and high beta. For most of these bands the maturation seems to occur later in anterior sites than posterior sites. Correlational analysis showed a lower pattern of correlation between different frequencies in children than in young adults, suggesting a certain asynchrony in the maturation of different rhythms. The topographical analysis revealed similar topographies of the different rhythms in children and young adults. Principal Component Analysis (PCA) demonstrated the same internal structure for the Electroencephalogram of both age groups. Principal Component Analysis allowed to separate four subcomponents in the alpha range. All these subcomponents peaked at a lower frequency in children than in young adults. CONCLUSIONS: The present approaches complement and solve some of the incertitudes when the classical brain broad rhythm analysis is applied. Children have a higher absolute power than young adults for frequency ranges between 0-20 Hz, the correlation of Power Spectrum (PS) with age and the variance age comparison showed that there are six ranges of frequencies that can distinguish the level of EEG maturation in children and adults. The establishment of maturational order of different frequencies and its possible maturational interdependence would require a complete series including all the different ages.     

Study of benznidazole–cyclodextrin inclusion complexes, cytotoxicity and trypanocidal activity

The current chemotherapy for Chagas disease is still based on benznidazole, which has low solubility, but complexation with cyclodextrins provides a way of increasing the solubility. The objective of this work was to characterize the inclusion complexes formed between benznidazole (BNZ) and randomly 2-methyled-β-cyclodextrin (RM-β-CD) in aqueous solution and study cytotoxicity and trypanocidal. BNZ:RM-β-CD solution complex systems were prepared and characterized using the phase solubility diagram, nuclear magnetic resonance and a photostability assays, also to investigate the in vitro trypanocidal activity with epimastigote forms of Trypanossoma cruzi and the study of cytotoxicity against mammal cells. The phase-solubility diagram displayed an A _L-type feature, providing evidence of the formation of soluble inclusion complexes. The continuous variation method showed the existence of a complex with 1:1 stoichiometry. Toxicity assays demonstrated that inclusion complexes were able to reduce the toxic effects caused by benznidazole alone and that this did not interfere with the trypanocidal activity of the benznidazole. The use of inclusion complexes benznidazole:cyclodextrin is thus a promising alternative for the development of a safe and stable liquid formulation and a new option for the treatment of Chagas disease.     

Malva sylvestris L. extract suppresses desferrioxamine‐induced PGE2 and PGD2 release in differentiated U937 cells: the development and validation of an LC‐MS/MS method for prostaglandin quantification

Malva sylvestris is a species used worldwide as an alternative to anti‐inflammatory therapies; however, its mechanism of action remains unknown. In this paper, the anti‐inflammatory effects of M. sylvestris alcoholic extracts were evaluated by measuring the pro‐inflammatory mediators PGE₂ and PGD₂ in desferrioxamine‐stimulated phorbol 12‐myristate 13‐acetate‐differentiated U937 cells. An HPLC‐DAD fingerprint of the M. sylvestris extract was performed and caffeic acid, ferulic acid and scopoletin were identified and quantified. An HPLC‐MS/MS method was developed and validated to separate and measure the prostaglandins. The lower limits of detection (~0.5 ng/mL for PGE₂ and PGD₂) and quantification (1.0 ng/mL for PGE₂ and PGD₂) indicated that the method is highly sensitive. The calibration curves showed excellent coefficients of correlation (r > 0.99) over the range of 1.0–500.0 ng/mL, and at different levels, the accuracy ranged from 96.4 to 106.4% with an RSD < 10.0% for the precision study. This method was successfully applied using U937‐d cells. A significant dose‐dependent reduction of PGE₂ and PGD₂ levels occurred using 10 µg/mL (10.74 ± 2.86 and 9.60 ± 6.89%) and 50 µg/mL of extract (48.37 ± 3.24 and 53.06 ± 6.15%), suggesting that the anti‐inflammatory mechanisms evoked by M. sylvestris may be related to modulation of these mediators. Copyright © 2014 John Wiley & Sons, Ltd.     

Analysis of high resolution electron spin resonance spectra

Previous interpretations of the electron spin resonance spectrum of Wurster's Blue cation are shown to be incorrect. In particular the nitrogen hyperfine splitting constant previously quoted as 0·28 gauss is, in fact, 7·0 gauss. A complete analysis of the spectrum is described.     

Whiteness process of tile ceramics: using a synthetic flow as a modifier agent of color firing

Synthetic flow is proposed as a modifier agent of color firing in tile ceramic mass during the sinterization process, turning the red color firing into whiteness. Therefore, the ⁵⁷Fe Mössbauer spectroscopy was used to understand how the interaction of the iron element in the mechanism of color firing mass occurs in this system. The results suggest that the change of color firing can be alternatively due to two main factors: (i) diluting the hematite content in the sample because of the use of synthetic flow and (ii) part of the hematite is converted in other uncolored crystal structures, which makes the final color firing lighter.