On detour index of cycloparaphenylene and polyphenylene molecular structures

AbstractCycloparaphenylene is a particle that comprises a few benzene rings associated with covalent bonds in the para positions to frame a ring-like structure. Similarly, poly (para-phenylenes) are macromolecules that include benzenoid compounds straightforwardly joined to each other by C–C bonds. Because of their remarkable architectural highlights, these structures have fascinated attention from numerous vantage focuses. Descriptors are among the most fundamental segments of prescient quantitative structure-activity and property relationship (QSAR/QSPR) demonstrating examination. They encode chemical data of particles as quantitative numbers, which are utilized to create a mathematical correlation. The nature of a predictive model relies upon great demonstrating insights, yet additionally on the extraction of compound highlights. To a great extent, Molecular topology has exhibited its adequacy in portraying sub-atomic structures and anticipating their properties. It follows a two-dimensional methodology, just thinking about the interior plan, including molecules. Explicit subsets speak the design of every atom of topological descriptors. When all around picked, these descriptors give a unique method of describing an atomic system that can represent the most significant highlights of the molecular structure. Detour index is one such topological descriptor with much application in chemistry, especially in QSAR/QSPR studies. This article presents an exact analytical expression for the detour index of cycloparaphenylene and poly (para-phenylene).

Download Full-text

Neurotoxicity of Pesticides: The Roadmap for the Cubic Mode of Action

Current Medicinal Chemistry ◽

10.2174/0929867326666190704142354 ◽

2020 ◽

Vol 27 (1) ◽

pp. 54-77 ◽

Cited By ~ 2

Author(s):

Bogdan Bumbăcilă ◽

Mihai V. Putz

Keyword(s):

Biological Activity ◽

Wiener Index ◽

Laboratory Animals ◽

Covalent Bonds ◽

Organophosphate Compounds ◽

Sar Studies ◽

Structure Activity ◽

Cubic Structure

Pesticides are used today on a planetary-wide scale. The rising need for substances with this biological activity due to an increasing consumption of agricultural and animal products and to the development of urban areas makes the chemical industry to constantly investigate new molecules or to improve the physicochemical characteristics, increase the biological activities and improve the toxicity profiles of the already known ones. Molecular databases are increasingly accessible for in vitro and in vivo bioavailability studies. In this context, structure-activity studies, by their in silico - in cerebro methods, are used to precede in vitro and in vivo studies in plants and experimental animals because they can indicate trends by statistical methods or biological activity models expressed as mathematical equations or graphical correlations, so a direction of study can be developed or another can be abandoned, saving financial resources, time and laboratory animals. Following this line of research the present paper reviews the Structure-Activity Relationship (SAR) studies and proposes a correlation between a topological connectivity index and the biological activity or toxicity made as a result of a study performed on 11 molecules of organophosphate compounds, randomly chosen, with a basic structure including a Phosphorus atom double bounded to an Oxygen atom or to a Sulfur one and having three other simple covalent bonds with two alkoxy (-methoxy or -ethoxy) groups and to another functional group different from the alkoxy groups. The molecules were packed on a cubic structure consisting of three adjacent cubes, respecting a principle of topological efficiency, that of occupying a minimal space in that cubic structure, a method that was called the Clef Method. The central topological index selected for correlation was the Wiener index, since it was possible this way to discuss different adjacencies between the nodes in the graphs corresponding to the organophosphate compounds molecules packed on the cubic structure; accordingly, "three dimensional" variants of these connectivity indices could be considered and further used for studying the qualitative-quantitative relationships for the specific molecule-enzyme interaction complexes, including correlation between the Wiener weights (nodal specific contributions to the total Wiener index of the molecular graph) and the biochemical reactivity of some of the atoms. Finally, when passing from SAR to Q(uantitative)-SAR studies, especially by the present advanced method of the cubic molecule (Clef Method) and its good assessment of the (neuro)toxicity of the studied molecules and of their inhibitory effect on the target enzyme - acetylcholinesterase, it can be seen that a predictability of the toxicity and activity of different analogue compounds can be ensured, facilitating the in vivo experiments or improving the usage of pesticides.

Download Full-text

Relation between photochromic properties and molecular structures in salicylideneaniline crystals

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768112010993 ◽

2012 ◽

Vol 68 (3) ◽

pp. 297-304 ◽

Cited By ~ 32

Author(s):

Kohei Johmoto ◽

Takashi Ishida ◽

Akiko Sekine ◽

Hidehiro Uekusa ◽

Yuji Ohashi

Keyword(s):

Dihedral Angle ◽

Steric Hindrance ◽

Molecular Structures ◽

Dihedral Angles ◽

Clear Correlation ◽

X Ray Diffraction ◽

Photochromic Properties ◽

X Ray ◽

Benzene Rings ◽

The Relationship

The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

Download Full-text

Neuraldecipher - Reverse-Engineering ECFP Fingerprints to Their Molecular Structures

10.26434/chemrxiv.12286727 ◽

2020 ◽

Author(s):

Tuan Le ◽

Robin Winter ◽

Frank Noé ◽

Djork-Arné Clevert

Keyword(s):

Molecular Structure ◽

Reverse Engineering ◽

Quantitative Structure Activity Relationship ◽

Molecular Structures ◽

Pharmaceutical Companies ◽

Molecular Fingerprints ◽

Structure Activity ◽

Great Relevance ◽

Validation Set ◽

Private Associations

Protecting molecular structures from disclosure against external parties is of great relevance for industrial and private associations, such as pharmaceutical companies. Within the framework of external collaborations, it is common to exchange datasets by encoding the molecular structures into descriptors. Molecular fingerprints such as the extended-connectivity fingerprints are frequently used for such an exchange, because they typically perform well on quantitative structure-activity relationship tasks. ECFPs are often considered to be non-invertible due to the way they are computed.In this paper, we present a reverse-engineering method to deduce the molecular structure given revealed ECFPs. Our method includes the Neuraldecipher, a neural network model that predicts a compact vector representation of compounds, given ECFPs. We then utilize another pre-trained model to retrieve the molecular structure as SMILES representation. We demonstrate that our method is able to reconstruct molecular structures to some extent, and improves, when ECFPs with larger fingerprint sizes are revealed. For example, given ECFP count vectors of length 4096, we are able to correctly deduce around 60% of molecular structures on a validation set (112K unique samples) with our method.

Download Full-text

Criterion of Mechanical Instability in Inhomogeneous Atomic System

Materials Science Forum ◽

10.4028/www.scientific.net/msf.482.127 ◽

2005 ◽

Vol 482 ◽

pp. 127-130 ◽

Cited By ~ 1

Author(s):

Yoshitaka Umeno ◽

Takayuki Kitamura

Keyword(s):

Mechanical Stability ◽

Atomic System ◽

Instability Criterion ◽

Fundamental Issue ◽

Mechanical Instability ◽

Atomic Systems ◽

Uniform Deformation ◽

Atomic Structures ◽

Homogeneous Structures ◽

Deformation Modes

The mechanical stability of a material is a fundamental issue in strength of atomic systems. Although the criterion of the mechanical stability of homogeneous structures such as perfect crystals have been successfully investigated so far, the criterion has not been able to be precisely evaluated in the cases of non-uniform deformations or bodies of inhomogeneous atomic structures. Now we present an instability criterion of an arbitrary atomic structure based on the energy balance of the whole system. This method gives the mathematically rigorous condition for the onset of an unstable deformation in any inhomogeneous atomic system. Furthermore, the method can be applied to any type of potential field, which means that ab initio evaluations of the mechanical instability of inhomogeneous structure under non-uniform deformation will be possible. The validity of the method is clarified by the application to tension of a cracked body. The onsets of unstable deformations and their deformation modes are precisely evaluated by the method.

Download Full-text

Aminosilanes derived from 1H-benzimidazole-2(3H)-thione

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229615014503 ◽

2015 ◽

Vol 71 (9) ◽

pp. 788-792 ◽

Cited By ~ 1

Author(s):

Juliana Palomo-Molina ◽

Efrén V. García-Báez ◽

Rosalinda Contreras ◽

Kayim Pineda-Urbina ◽

Angel Ramos-Organillo

Keyword(s):

Molecular Structures ◽

Π Interactions ◽

Benzene Rings

Two new molecular structures, namely 1,3-bis(trimethylsilyl)-1H-benzimidazole-2(3H)-thione, C13H22N2SSi2, (2), and 1-trimethylsilyl-1H-benzimidazole-2(3H)-thione, C10H14N2SSi, (3), are reported. Both systems were derived from 1H-benzimidazole-2(3H)-thione. Noncovalent C—H...π interactions between the centroid of the benzmidazole system and the SiMe3groups form helicoidal arrangements in (2). Dimerization of (3) results in the formation ofR22(8) ringsviaN—H...S interactions, along with parallel π–π interactions between imidazole and benzene rings.

Download Full-text

Structure–activity relationship of nanostructured ceria for the catalytic generation of hydroxyl radicals

Nanoscale ◽

10.1039/c8nr09393h ◽

2019 ◽

Vol 11 (10) ◽

pp. 4552-4561 ◽

Cited By ~ 11

Author(s):

Tamra J. Fisher ◽

Yunyun Zhou ◽

Tai-Sing Wu ◽

Meiyu Wang ◽

Yun-Liang Soo ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Hydroxyl Radicals ◽

Structure Activity Relationship ◽

Activity Relationship ◽

Intrinsic Activity ◽

Atomic Structures ◽

Structure Activity ◽

Nanostructured Ceria ◽

Ceria Catalysts ◽

Relationship Of

The morphologies and associated atomic structures of ceria catalysts influence their intrinsic activity towards the catalytic production of hydroxyl radicals from hydrogen peroxide.

Download Full-text

Why Polyphenols have Promiscuous Actions? An Investigation by Chemical Bioinformatics

Natural Product Communications ◽

10.1177/1934578x1601100525 ◽

2016 ◽

Vol 11 (5) ◽

pp. 1934578X1601100

Author(s):

Guang-Yan Tang

Keyword(s):

Redox Potential ◽

Bioinformatics Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Critical Factor ◽

Structural Features ◽

Molecular Structures ◽

Pharmacological Effects ◽

Protein Targets ◽

Structure Activity

Despite their diverse pharmacological effects, polyphenols are poor for use as drugs, which have been traditionally ascribed to their low bioavailability. However, Baell and co-workers recently proposed that the redox potential of polyphenols also plays an important role in this, because redox reactions bring promiscuous actions on various protein targets and thus produce non-specific pharmacological effects. To investigate whether the redox reactivity behaves as a critical factor in polyphenol promiscuity, we performed a chemical bioinformatics analysis on the structure-activity relationships of twenty polyphenols. It was found that the gene expression profiles of human cell lines induced by polyphenols were not correlated with the presence or not of redox moieties in the polyphenols, but significantly correlated with their molecular structures. Therefore, it is concluded that the promiscuous actions of polyphenols are likely to result from their inherent structural features rather than their redox potential.

Download Full-text