molecular descriptors
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2022 ◽  
Vol 66 ◽  
pp. 102090
Author(s):  
Adrià Fernández-Torras ◽  
Arnau Comajuncosa-Creus ◽  
Miquel Duran-Frigola ◽  
Patrick Aloy

Nanomaterials ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 217
Author(s):  
Giulia Mancardi ◽  
Matteo Alberghini ◽  
Neus Aguilera-Porta ◽  
Monica Calatayud ◽  
Pietro Asinari ◽  
...  

Titanium dioxide nanoparticles have risen concerns about their possible toxicity and the European Food Safety Authority recently banned the use of TiO2 nano-additive in food products. Following the intent of relating nanomaterials atomic structure with their toxicity without having to conduct large-scale experiments on living organisms, we investigate the aggregation of titanium dioxide nanoparticles using a multi-scale technique: starting from ab initio Density Functional Theory to get an accurate determination of the energetics and electronic structure, we switch to classical Molecular Dynamics simulations to calculate the Potential of Mean Force for the connection of two identical nanoparticles in water; the fitting of the latter by a set of mathematical equations is the key for the upscale. Lastly, we perform Brownian Dynamics simulations where each nanoparticle is a spherical bead. This coarsening strategy allows studying the aggregation of a few thousand nanoparticles. Applying this novel procedure, we find three new molecular descriptors, namely, the aggregation free energy and two numerical parameters used to correct the observed deviation from the aggregation kinetics described by the Smoluchowski theory. Ultimately, molecular descriptors can be fed into QSAR models to predict the toxicity of a material knowing its physicochemical properties, enabling safe design strategies.


Marine Drugs ◽  
2022 ◽  
Vol 20 (1) ◽  
pp. 58
Author(s):  
José X. Soares ◽  
Daniela R. P. Loureiro ◽  
Ana Laura Dias ◽  
Salete Reis ◽  
Madalena M. M. Pinto ◽  
...  

The marine environment is an important source of specialized metabolites with valuable biological activities. Xanthones are a relevant chemical class of specialized metabolites found in this environment due to their structural variety and their biological activities. In this work, a comprehensive literature review of marine xanthones reported up to now was performed. A large number of bioactive xanthone derivatives (169) were identified, and their structures, biological activities, and natural sources were described. To characterize the chemical space occupied by marine-derived xanthones, molecular descriptors were calculated. For the analysis of the molecular descriptors, the xanthone derivatives were grouped into five structural categories (simple, prenylated, O-heterocyclic, complex, and hydroxanthones) and six biological activities (antitumor, antibacterial, antidiabetic, antifungal, antiviral, and miscellaneous). Moreover, the natural product-likeness and the drug-likeness of marine xanthones were also assessed. Marine xanthone derivatives are rewarding bioactive compounds and constitute a promising starting point for the design of other novel bioactive molecules.


2022 ◽  
Vol 2022 ◽  
pp. 1-15
Author(s):  
Zeeshan Saleem Mufti ◽  
Rukhshanda Anjum ◽  
Ayesha Abbas ◽  
Shahbaz Ali ◽  
Muhammad Afzal ◽  
...  

Topological indices are such numbers or set of numbers that describe topology of structures. Nearly 400 topological indices are calculated so far. The prognostication of physical, chemical, and biological attributes of organic compounds is an important and still unsolved problem of computational chemistry. Topological index is the tool to predict the physicochemical properties such as boiling point, melting point, density, viscosity, and polarity of organic compounds. In this study, some degree-based molecular descriptors of hydrocarbon structure are calculated.


Author(s):  
Shehani T. Wetthasinghe ◽  
Chunyan Li ◽  
Huina Lin ◽  
Tianyu Zhu ◽  
Chuanbing Tang ◽  
...  

Separations ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 7
Author(s):  
Isabella Bolognino ◽  
Antonio Carrieri ◽  
Rosa Purgatorio ◽  
Marco Catto ◽  
Rocco Caliandro ◽  
...  

The enantiomeric separation of 15 racemic 4-aryl-3,4-dihydropyrimidin-2(1H)-one (DHP) alkoxycarbonyl esters, some of which proved to be highly active as A2B adenosine receptor antagonists, was carried out by HPLC on ChirobioticTM TAG, a chiral stationary phase (CSP) bearing teicoplanin aglycone (TAG) as the chiral selector. The racemic compounds were separated under polar organic (PO) conditions. Preliminarily, the same selectands were investigated on three different Pirkle-type CSPs in normal-phase (NP) conditions. A baseline separation was successfully obtained on TAG-based CSPs for the majority of compounds, some of which achieved high enantioselectivity ratios (α > 2) in contrast with the smaller α values (1–1.5) and the lack of baseline resolution observed with the Pirkle-type CSPs. In particular, the racemic tetrazole-fused DHP ester derivatives, namely compounds 8 and 9, were separated on TAG-based HPLC columns with noteworthy α values (8.8 and 6.0, respectively), demonstrating the potential of the method for preparative purposes. A competition experiment, carried out with a racemic analyte (6) by adding N-acetyl-d-alanine (NADA) to the mobile phase, suggested that H-bonding interactions involved in the recognition of the natural dipeptide ligand d-Ala-d-Ala into the TAG cleft should be critical for enantioselective recognition of 4-aryl DHPs by TAG. The X-ray crystal structure of TAG was elucidated at a 0.77 Å resolution, whereas the calculation of molecular descriptors of size, polar, and H-bond interactions, were complemented with molecular docking and molecular dynamics calculations, shedding light on repulsive (steric effects) and attractive (H-bond—polar and apolar) interactions between 4-aryl DHP selectands and TAG chiral selectors.


2021 ◽  
Author(s):  
Loukas Kollias ◽  
Roger Rousseau ◽  
Vassiliki-Alexandra Glezakou ◽  
Matteo Salvalaglio

Molecular modeling is ordinarily employed to understand the synthesis of complex materials. In this work, we investigate the collective assembly of building units that have been experimentally observed to initiate Metal-Organic Framework (MOF) nucleation. MOFs exhibit attractive characteristics such as remarkable surface area and diverse porosities, however, a mechanistic understanding of their synthesis and scale-up remains underexplored due to the complicated nature of the building block interactions. Here, we tackle this problem with large-scale molecular dynamics simulations under a variety of synthesis conditions and mixture compositions. We observe that the connectivity of building units, as well as their level of crystalline order and fractal dimension, largely vary depending on the synthesis conditions. However, these properties naturally emerge when interpreting the self-assembly process of MOF nuclei as the time-evolution of an undirected graph. The results show that solution-induced conformational complexity and ionic concentration have a dramatic effect on the morphology of clusters emerging during assembly, such diversity is captured by key features of the graph representation. Principal Component Analysis (PCA) on graph properties successfully deconvolutes MOF self-assembly to be characterized by a small number of molecular descriptors, such as average coordination number between half-secondary building units (half-SBUs) and fractal dimension, which can be followed by time-resolved spectroscopy. We conclude that graph theory can be used to understand complex processes such as MOF nucleation by providing molecular descriptors accessible by both simulation and experiment.


Author(s):  
Giulia Mancardi ◽  
Matteo Alberghini ◽  
Neus Aguilera-Porta ◽  
Monica Calatayud ◽  
Pietro Asinari ◽  
...  

Titanium dioxide nanoparticles have risen concerns about their possible toxicity and the European Food Safety Authority recently banned the use of TiO2 nano-additive in food products. Following the intent of relating nanomaterials atomic structure with their toxicity without having to conduct large scale experiments on living organisms, we investigate the aggregation of titanium dioxide nanoparticles using a multi-scale technique: starting from ab initio Density Functional Theory to get an accurate determination of the energetics and electronic structure, we switch to classical Molecular Dynamics simulations to calculate the Potential of Mean Force for the connection of two identical nanoparticles in water; the fitting of the latter by a set of mathematical equations is the key for the upscale. Lastly, we perform Brownian Dynamics simulations where each nanoparticle is a spherical bead. This coarsening strategy allows studying the aggregation of a few thousand nanoparticles. Applying this novel procedure, we find three new molecular descriptors, namely, the aggregation free energy and two numerical parameters used to correct the observed deviation from the aggregation kinetic described by the Smoluchowski theory. Molecular descriptors can be fed into QSAR models to predict the toxicity of a material knowing its physicochemical properties, without having to conduct large scale experiments on living organisms.


Author(s):  
Jia-bao Liu ◽  
Ting Zhang

Cyclooctane is mainly used in the synthesis of cyclooctanone, cyclooctanol, caprolactam and octanoic acid. At the same time, it can also be used as an intermediate in organic synthesis and a chemical reagent. By discussing the resistance distance between any two points of cyclooctane derivative Tn(C8), some invariants about resistance distance are obtained, such as Kirchhoff index, multiplicative degree-Kirchhoff index, and additive degree-Kirchhoff index. Topological index can help scholars better understand some physical and chemical properties of compounds, and we obtain the closed expressions of valency-based topological indices for Tn(C8), such as ABC index, GA index, etc.


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