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Article ; Online: FP-ADMET

Vishwesh Venkatraman

Journal of Cheminformatics, Vol 13, Iss 1, Pp 1-

a compendium of fingerprint-based ADMET prediction models

2021 Volume 12

Abstract: Abstract Motivation The absorption, distribution, metabolism, excretion, and toxicity (ADMET) of drugs plays a key role in determining which among the potential candidates are to be prioritized. In silico approaches based on machine learning methods are ... ...

Abstract	Abstract Motivation The absorption, distribution, metabolism, excretion, and toxicity (ADMET) of drugs plays a key role in determining which among the potential candidates are to be prioritized. In silico approaches based on machine learning methods are becoming increasing popular, but are nonetheless limited by the availability of data. With a view to making both data and models available to the scientific community, we have developed FPADMET which is a repository of molecular fingerprint-based predictive models for ADMET properties. Summary In this article, we have examined the efficacy of fingerprint-based machine learning models for a large number of ADMET-related properties. The predictive ability of a set of 20 different binary fingerprints (based on substructure keys, atom pairs, local path environments, as well as custom fingerprints such as all-shortest paths) for over 50 ADMET and ADMET-related endpoints have been evaluated as part of the study. We find that for a majority of the properties, fingerprint-based random forest models yield comparable or better performance compared with traditional 2D/3D molecular descriptors. Availability The models are made available as part of open access software that can be downloaded from https://gitlab.com/vishsoft/fpadmet .
Keywords	ADMET ; Machine learning ; Molecular fingerprints ; Information technology ; T58.5-58.64 ; Chemistry ; QD1-999
Subject code	006
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An Open Access Data Set Highlighting Aggregation of Dyes on Metal Oxides

Vishwesh Venkatraman / Lethesh Kallidanthiyil Chellappan

Data, Vol 5, Iss 45, p

2020 Volume 45

Abstract: The adsorption of a dye to a metal oxide surface such as TiO 2 , NiO and ZnO leads to deprotonation and often undesirable aggregation of dye molecules, which in turn impacts the photophysical properties of the dye. While controlled aggregation is useful ... ...

Abstract	The adsorption of a dye to a metal oxide surface such as TiO 2 , NiO and ZnO leads to deprotonation and often undesirable aggregation of dye molecules, which in turn impacts the photophysical properties of the dye. While controlled aggregation is useful for some applications, it can result in lower performance for dye-sensitized solar cells. To understand this phenomenon better, we have conducted an extensive search of the literature and identified over 4000 records of absorption spectra in solution and after adsorption onto metal oxide. The total data set comprises over 3500 unique compounds, with observed absorption maxima in solution and after adsorption on the semiconductor electrode. This data may serve to provide further insight into the structure-property relationships governing dye-aggregation behaviour.
Keywords	dye sensitized solar cell ; aggregation ; database ; absorption ; solvent polarity ; Bibliography. Library science. Information resources ; Z
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Prediction of Absorption Spectrum Shifts in Dyes Adsorbed on Titania

Vishwesh Venkatraman / Amsalu Efrem Yemene / John de Mello

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 13

Abstract: Abstract Dye adsorption on metal-oxide films often results in small to substantial absorption shifts relative to the solution phase, with undesirable consequences for the performance of dye-sensitized solar cells and optical sensors. While density ... ...

Abstract	Abstract Dye adsorption on metal-oxide films often results in small to substantial absorption shifts relative to the solution phase, with undesirable consequences for the performance of dye-sensitized solar cells and optical sensors. While density functional theory is frequently used to model such behaviour, it is too time-consuming for rapid assessment. In this paper, we explore the use of supervised machine learning to predict whether dye adsorption on titania is likely to induce a change in its absorption characteristics. The physicochemical features of each dye were encoded as a numeric vector whose elements are the counts of molecular fragments and topological indices. Various classification models were subsequently trained to predict the type of absorption shift i.e. blue, red or unchanged (\|Δλ\| ≤ 10 nm). The models were able to predict the nature of the shift with a good likelihood (~80%) of success when applied to unseen data.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Ionic Liquid Property Explorer

Vishwesh Venkatraman / Sigvart Evjen / Kallidanthiyil Chellappan Lethesh

Data, Vol 4, Iss 2, p

An Extensive Library of Task-Specific Solvents

2019 Volume 88

Abstract: Ionic liquids have a broad spectrum of applications ranging from gas separation to sensors and pharmaceuticals. Rational selection of the constituent ions is key to achieving tailor-made materials with functional properties. To facilitate the discovery ... ...

Abstract	Ionic liquids have a broad spectrum of applications ranging from gas separation to sensors and pharmaceuticals. Rational selection of the constituent ions is key to achieving tailor-made materials with functional properties. To facilitate the discovery of new ionic liquids for sustainable applications, we have created a virtual library of over 8 million synthetically feasible ionic liquids. Each structure has been evaluated for their-task suitability using data-driven statistical models calculated for 12 highly relevant properties: melting point, thermal decomposition, glass transition, heat capacity, viscosity, density, cytotoxicity, CO <math display="inline"> <semantics> <msub> <mrow></mrow> <mn>2</mn> </msub> </semantics> </math> solubility, surface tension, and electrical and thermal conductivity. For comparison, values of six properties computed using quantum chemistry based equilibrium thermodynamics COSMO-RS methods are also provided. We believe the data set will be useful for future efforts directed towards targeted synthesis and optimization.
Keywords	ionic liquids ; machine learning ; database ; properties ; combinatorial screening ; Bibliography. Library science. Information resources ; Z
Subject code	660
Language	English
Publishing date	2019-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Synthesis of Novel 3,6-Dithienyl Diketopyrrolopyrrole Dyes by Direct C‒H Arylation

Amsalu Efrem Yemene / Vishwesh Venkatraman / David Moe Almenningen / Bård Helge Hoff / Odd Reidar Gautun

Molecules, Vol 25, Iss 2349, p

2020 Volume 2349

Abstract: Direct C‒H arylation coupling is potentially a more economical and sustainable process than conventional cross-coupling. However, this method has found limited application in the synthesis of organic dyes for dye‒sensitized solar cells. Although direct C‒ ...

Abstract	Direct C‒H arylation coupling is potentially a more economical and sustainable process than conventional cross-coupling. However, this method has found limited application in the synthesis of organic dyes for dye‒sensitized solar cells. Although direct C‒H arylation is not an universal solution to any cross-coupling reactions, it efficiently complements conventional sp 2 ‒sp 2 bond formation and can provide shorter and more efficient routes to diketopyrrolopyrrole dyes. Here, we have applied palladium catalyzed direct C‒H arylation in the synthesis of five new 3,6-dithienyl diketopyrrolopyrrole dyes. All prepared sensitizers display broad absorption from 350 nm up to 800 nm with high molar extinction coefficients. The dye‒sensitized solar cells based on these dyes exhibit a power conversion efficiency in the range of 2.9 to 3.4%.
Keywords	direct C‒H arylation ; dye‒sensitized solar cells ; diketopyrrolopyrrole ; phenothiazine ; triarylamine ; dye ; Organic chemistry ; QD241-441
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The dye-sensitized solar cell database

Vishwesh Venkatraman / Rajesh Raju / Solon P. Oikonomopoulos / Bjørn K. Alsberg

Journal of Cheminformatics, Vol 10, Iss 1, Pp 1-

2018 Volume 9

Abstract: Abstract Background Dye-sensitized solar cells (DSSCs) have garnered a lot of attention in recent years. The solar energy to power conversion efficiency of a DSSC is influenced by various components of the cell such as the dye, electrolyte, electrodes ... ...

Abstract	Abstract Background Dye-sensitized solar cells (DSSCs) have garnered a lot of attention in recent years. The solar energy to power conversion efficiency of a DSSC is influenced by various components of the cell such as the dye, electrolyte, electrodes and additives among others leading to varying experimental configurations. A large number of metal-based and metal-free dye sensitizers have now been reported and tools using such data to indicate new directions for design and development are on the rise. Description DSSCDB, the first of its kind dye-sensitized solar cell database, aims to provide users with up-to-date information from publications on the molecular structures of the dyes, experimental details and reported measurements (efficiencies and spectral properties) and thereby facilitate a comprehensive and critical evaluation of the data. Currently, the DSSCDB contains over 4000 experimental observations spanning multiple dye classes such as triphenylamines, carbazoles, coumarins, phenothiazines, ruthenium and porphyrins. Conclusion The DSSCDB offers a web-based, comprehensive source of property data for dye sensitized solar cells. Access to the database is available through the following URL: www.dyedb.com.
Keywords	Dye sensitized solar cells ; Database ; Information technology ; T58.5-58.64 ; Chemistry ; QD1-999
Subject code	670
Language	English
Publishing date	2018-04-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Hydroxyl Functionalized Pyridinium Ionic Liquids

Kallidanthiyil Chellappan Lethesh / Sigvart Evjen / Jaganathan Joshua Raj / Denis C. D. Roux / Vishwesh Venkatraman / Kaushik Jayasayee / Anne Fiksdahl

Frontiers in Chemistry, Vol

Experimental and Theoretical Study on Physicochemical and Electrochemical Properties

2019 Volume 7

Abstract: Structurally modified hydroxyl functionalized pyridinium ionic liquids (ILs), liquid at room temperature, were synthesized and characterized. Alkylated N-(2-hydroxyethyl)-pyridinium ILs were prepared from alkylpyridines via corresponding bromide salts by ...

Abstract	Structurally modified hydroxyl functionalized pyridinium ionic liquids (ILs), liquid at room temperature, were synthesized and characterized. Alkylated N-(2-hydroxyethyl)-pyridinium ILs were prepared from alkylpyridines via corresponding bromide salts by N-alkylation (65–93%) and final anion exchange (75–96%). Pyridinium-alkylation strongly influenced the IL physicochemical and electrochemical properties. Experimental values for the ILs physicochemical properties (density, viscosity, conductivity, and thermal decomposition temperature), were in good agreement with corresponding predicted values obtained by theoretical calculations. The pyridinium ILs have electrochemical window of 3.0–5.4 V and were thermally stable up to 405°C. The IL viscosity and density were measured over a wide temperature range (25–80°C). Pyridine alkyl-substitution strongly affected the partial positive charge on the nitrogen atom of the pyridinium cations, as shown by charge distribution calculations. On-going studies on Mg complexes of the new ILs demonstrate promising properties for high current density electrodeposition of magnesium.
Keywords	charge distribution ; conductivity ; COSMO-RS ; electrodeposition ; ionic liquid ; Chemistry ; QD1-999
Language	English
Publishing date	2019-09-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Phthalate metabolites in harbor porpoises (Phocoena phocoena) from Norwegian coastal waters

May Britt Rian / Kristine Vike-Jonas / Susana Villa Gonzalez / Tomasz Maciej Ciesielski / Vishwesh Venkatraman / Ulf Lindstrøm / Bjørn Munro Jenssen / Alexandros G. Asimakopoulos

Environment International, Vol 137, Iss , Pp - (2020)

2020

Abstract: The exposure of marine mammals to phthalates has received considerable attention due to the ubiquitous occurrence of these pollutants in the marine environment and their potential adverse health effects. The occurrence of phthalate metabolites is well ... ...

Abstract	The exposure of marine mammals to phthalates has received considerable attention due to the ubiquitous occurrence of these pollutants in the marine environment and their potential adverse health effects. The occurrence of phthalate metabolites is well established in human populations, but data is scarce for marine mammals. In this study, concentrations of 17 phthalate metabolites were determined in liver samples collected from one hundred (n = 100) by-caught harbor porpoises (Phocoena phocoena) along the coast of Norway. Overall, thirteen phthalate metabolites were detected in the samples. Monoethyl phthalate (mEP), mono-iso-butyl phthalate (mIBP), mono-n-butyl phthalate (mBP) and phthalic acid (PA) were the most abundant metabolites, accounting for detection rates ≥ 85%. The highest median concentrations were found for mIBP (30.6 ng/g wet weight [w.w.]) and mBP (25.2 ng/g w.w.) followed by PA (7.75 ng/g w.w.) and mEP (5.67 ng/g w.w.). The sum of the median phthalate metabolites concentrations that were found in the majority of samples (detection rates > 50%) indicated that concentrations were lower for porpoises collected along the coastal area of Bodø (Nordland), Lebesby (Finnmark) and Varangerfjord (as compared to other coastal areas); these areas are among the least populated coastal areas but also the most distant (>700 km) from offshore active oil and gas fields. The monomethyl phthalate metabolite (mMP) was detected in 69% of the samples, and to our knowledge, alongside with PA, this is the first report of their occurrence in marine mammals. PA, as the non-specific marker of phthalate exposures, showed a statistically significant negative association with the body mass and length of the harbor porpoises. Among the phthalate metabolites, statistically significant positive associations were found between mBP and mIBP, mMP and mEP, PA and mEP, mIBP and mono(2-ethyl-5-oxohexyl) phthalate (mEOHP), mIBP and mono(2-ethyl-5-hydroxyhexyl) phthalate (mEHHP), mBP and mEHHP, mono-n-nonyl phthalate (mNP) and PA, ...
Keywords	Environmental sciences ; GE1-350
Subject code	333
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Benzotriazoles, benzothiazoles and trace elements in an urban road setting in Trondheim, Norway: Re-visiting the chemical markers of traffic pollution

Asheim, Johannes / Kristine Vike-Jonas / Susana V. Gonzalez / Syverin Lierhagen / Vishwesh Venkatraman / Inga-Loise S. Veivåg / Brynhild Snilsberg / Trond P. Flaten / Alexandros G. Asimakopoulos

Science of the total environment. 2019 Feb. 01, v. 649

2019

Abstract: Road traffic emissions are known to contribute heavily to the pollution in urban environments. The aim of this study was to establish specific traffic pollution markers in an urban road setting based on the occurrence profiles of benzotriazoles, ... ...

Abstract	Road traffic emissions are known to contribute heavily to the pollution in urban environments. The aim of this study was to establish specific traffic pollution markers in an urban road setting based on the occurrence profiles of benzotriazoles, benzothiazoles and trace elements in road dust and relevant matrices, including airborne particulate matter and core asphalt. Benzotriazoles and benzothiazoles are high-production volume chemicals that are used as complexing and anticorrosive agents for metals, act as vulcanizing accelerators for rubber materials, and possess anti-freezing/anti-icing properties. In this study, six benzothiazoles (benzothiazole, 2‑morpholin‑4‑yl‑benzothiazole, 2‑hydroxy‑benzothiazole, 2‑thio‑benzothiazole, 2‑methylthio‑benzothiazole, and 2‑amino‑benzothiazole), seven benzotriazoles (1H‑benzotriazole, 1‑hydroxy‑benzotriazole, 5‑chloro‑1H‑benzotriazole, tolyltriazole, xylyltriazole, benzotriazole‑5‑carboxyl acid, and 5‑amino‑1H‑benzotriazole), and 66 trace elements were determined in road dust samples from a sub-arctic urban road setting in Norway, and seasonal occurrence profiles were assessed between the studded and the non-studded tire season. The road dust was collected as suspended particulate matter in an aqueous phase with the introduced dust sampler in Scandinavia, the Wet Dust Sampler. The concentrations of the sum of seven benzotriazoles (Σ(7)BTRs) and six benzothiazoles (Σ(6)BTHs) in road dust ranged from 191 to 3054 ng/L and 93.4 to 1903 ng/L, respectively. To the best of our knowledge, 1H‑benzotriazole and tolyltriazole are reported for the first time as suitable markers of metal corrosion in vehicles. From the benzothiazole class, 2‑thio‑benzothiazole was found to be a suitable marker of tire rubber particles, while its methylated derivative, 2‑methylthio‑benzothiazole, was found to be a marker of chemical leaching. In addition, different types of new unused tires (summer, studded, and non-studded) were analyzed to assess their benzothiazoles and benzotriazoles content. Based on the concentrations found for benzotriazoles and benzothiazoles in airborne particulate matter, human exposure doses were calculated, and the estimated daily intake doses were found on the order of picograms per day.
Keywords	average daily intake ; bitumen ; corrosion ; dust ; emissions ; humans ; leaching ; metals ; methylation ; particulates ; pollution ; rubber ; summer ; tires ; trace elements ; traffic ; triazoles ; urban areas ; Norway ; Scandinavia
Language	English
Dates of publication	2019-0201
Size	p. 703-711.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2018.08.299
Database	NAL-Catalogue (AGRICOLA)

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