6 Computational prediction of toxicity of small organic molecules: state-of-the-art

2020 ◽  
pp. 89-114
Keyword(s):  
Organic Molecules ◽  
State Of The Art ◽  
Computational Prediction ◽  
Small Organic Molecules

Computational prediction of toxicity of small organic molecules: state-of-the-art

2019 ◽  
Vol 4 (10) ◽  
Author(s):  
Janvhi Machhar ◽  
Ansh Mittal ◽  
Surendra Agrawal ◽  
Anil M. Pethe ◽  
Prashant S. Kharkar
Keyword(s):  
Organic Molecules ◽  
State Of The Art ◽  
Computational Prediction ◽  
Quality Data ◽  
End Points ◽  
Small Organic Molecules ◽  
New Chemical Entities ◽  
Other Substances ◽  
Modelling Techniques ◽  
Computational Resources

Abstract The field of computational prediction of various toxicity end-points has evolved over last two decades significantly. Availability of newer modelling techniques, powerful computational resources and good-quality data have made it possible to generate reliable predictions for new chemical entities, impurities, chemicals, natural products and a lot of other substances. The field is still undergoing metamorphosis to take into account molecular complexities underlying toxicity end-points such as teratogenicity, mutagenicity, carcinogenicity, etc. Expansion of the applicability domain of these predictive models into areas other than life sciences, such as environmental and materials sciences have received a great deal of attention from all walks of life, fuelling further development and growth of the field. The present chapter discusses the state-of-the-art computational prediction of toxicity end-points of small organic molecules to balance the trade-off between the molecular complexity and the quality of such predictions, without compromising their immense utility in many fields.

scholarly journals Ferroelectric columnar assemblies from the bowl-to-bowl inversion of aromatic cores

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shunsuke Furukawa ◽  
Jianyun Wu ◽  
Masaya Koyama ◽  
Keisuke Hayashi ◽  
Norihisa Hoshino ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Organic Molecule ◽  
Remanent Polarization ◽  
Organic Molecules ◽  
Materials Science ◽  
State Of The Art ◽  
Condensed Matter ◽  
Small Organic Molecules ◽  
Organic Ferroelectrics ◽  
Potential Use

AbstractOrganic ferroelectrics, in which the constituent molecules retain remanent polarization, represent an important topic in condensed-matter science, and their attractive properties, which include lightness, flexibility, and non-toxicity, are of potential use in state-of-the-art ferroelectric devices. However, the mechanisms for the generation of ferroelectricity in such organic compounds remain limited to a few representative concepts, which has hitherto severely hampered progress in this area. Here, we demonstrate that a bowl-to-bowl inversion of a relatively small organic molecule with a bowl-shaped π-aromatic core generates ferroelectric dipole relaxation. The present results thus reveal an unprecedented concept to produce ferroelectricity in small organic molecules, which can be expected to strongly impact materials science.

CO2-based hydrogen storage: CO2 hydrogenation to formic acid, formaldehyde and methanol

2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Thomas Schaub
Keyword(s):  
Hydrogen Storage ◽  
Formic Acid ◽  
Mobile Applications ◽  
Organic Molecules ◽  
State Of The Art ◽  
Co2 Hydrogenation ◽  
The State ◽  
Reverse Reaction ◽  
Small Organic Molecules ◽  
Hydrogenation Of Co

AbstractThe storage of hydrogen via hydrogenation of CO2to small organic molecules can be attractive for mobile applications. In this article, the state of the art regarding hydrogen storage in Methanol, Formic Acid as well as Formaldehyde and derivates based on CO2hydrogenation is summarized. The reverse reaction, the release of hydrogen from these molecules is also crucial and described in the articles together with possible concepts for the use of hydrogen storage by CO2hydrogenation.

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Leela Dodda ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Organic Molecules ◽  
Force Fields ◽  
Liquid Density ◽  
Small Organic Molecules ◽  
Automated Generation ◽  
Energy Of Hydration ◽  
Novel Method ◽  
Force Field Parameters

<div><div><div><p>Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites. As a proof of concept, we have re-derived a complete set of parameters for 109 small organic molecules, and assessed the accuracy by comparing computed liquid properties with experiment. QUBEKit gives highly competitive results when compared to standard transferable force fields, with mean unsigned errors of 0.024 g/cm3, 0.79 kcal/mol and 1.17 kcal/mol for the liquid density, heat of vaporization and free energy of hydration respectively. This indicates that the derived parameters are suitable for molecular modelling applications, including computer-aided drug design.</p></div></div></div>

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Leela Dodda ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Organic Molecules ◽  
Force Fields ◽  
Liquid Density ◽  
Small Organic Molecules ◽  
Automated Generation ◽  
Energy Of Hydration ◽  
Novel Method ◽  
Force Field Parameters

<div><div><div><p>Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites. As a proof of concept, we have re-derived a complete set of parameters for 109 small organic molecules, and assessed the accuracy by comparing computed liquid properties with experiment. QUBEKit gives highly competitive results when compared to standard transferable force fields, with mean unsigned errors of 0.024 g/cm3, 0.79 kcal/mol and 1.17 kcal/mol for the liquid density, heat of vaporization and free energy of hydration respectively. This indicates that the derived parameters are suitable for molecular modelling applications, including computer-aided drug design.</p></div></div></div>

scholarly journals Interaction Mechanisms between Lithium Polysulfides/Sulfide and Small Organic Molecules

ACS Omega ◽  
2021 ◽  
Vol 6 (7) ◽  
pp. 4995-5000 ◽  
Author(s):  
Jiaxiang Zhang ◽  
Junwen Yang ◽  
Ziyue Liu ◽  
Bin Zheng
Keyword(s):  
Organic Molecules ◽  
Small Organic Molecules ◽  
Interaction Mechanisms

Dual functioning porous catalysts: Robust electro-oxidation of small organic molecules and water electrolysis at bimetallic Ni/Cu foam

2021 ◽  
Author(s):  
Mohamed R. Rizk ◽  
Muhammad G. Gamal ◽  
Amina Mazhar ◽  
Mohamed El-Deab ◽  
Bahgat El-Anadouli
Keyword(s):  
Thin Layer ◽  
Organic Molecules ◽  
Water Electrolysis ◽  
Single Step ◽  
Hydrogen Bubble ◽  
Small Organic Molecules ◽  
Porous Catalysts ◽  
Electro Oxidation ◽  
Bubble Template ◽  
Cu Foam

In this work, we report a single-step preparation of porous Ni-based foams thin layer atop Cu substrate via a facile dynamic hydrogen bubble template technique (DHBT). The prepared porous Ni-based...

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