China
Africa
Explore chapters and articles related to this topic
Descriptors in Nano-QSAR/QSPR Modeling
Published in Agnieszka Gajewicz, Tomasz Puzyn, Computational Nanotoxicology, 2019
Ewelina Wyrzykowska, Karolina Jagiello, Bakhtiyor Rasulev, Tomasz Puzyn
Descriptors are the quantitative parameters that express the properties of chemical. They aim to provide specific information (structural, intrinsic, or extrinsic properties) of chemicals in simplified form. In QSAR/QSPR modeling, descriptors enable one to determine relationships between chemical structures of analyzed substances with their biological or physicochemical features. However, a perfect descriptor that could be applied in a significant QSAR/QSPR model should display appropriate qualities [46], as follow: A descriptor should correlate with a modeling response.A descriptor should be suitable for a variety of classes of compounds.A descriptor should emphasize even the small structural dissimilarity between compounds.The calculation of a descriptor should be easy and fast.The physical interpretation of a descriptor should be possible and intuitive in relation to the modeling feature.
In Silico Methods for Nanotoxicity Evaluation: Opportunities and Challenges
Published in Vineet Kumar, Nandita Dasgupta, Shivendu Ranjan, Nanotoxicology, 2018
Natalia Sizochenko, Alicja Mikolajczyk, Jerzy Leszczynski, Tomasz Puzyn
To obtain efficient algorithms reliable to estimate the properties of investigated compounds and to identify the structural features responsible for their biological activity (toxicity), molecular descriptors are processed by several methods provided by various computational methods [e.g., molecular topology, molecular mechanics (MM), and quantum mechanics (QM) methods]. Molecular descriptors are based on several different theories, that is, organic chemistry, graph theory, information theory, quantum chemistry, physical chemistry, and so on. As was earlier mentioned, the simplest, zero-dimensional descriptors are derived directly from the formula (e.g., molecular weight, the number of atoms, etc.) (Consonni and Todeschini 2010). 1D descriptors represent bulk properties and structural fragments (Kar et al. 2014; Sizochenko and Leszczynski 2016): these descriptors include properties describing: metal/oxide electronegativity (χ), the charge of the metal cation corresponding to a given oxide (χox), atomic number, valence electron, number of the metal, atomic number, and period of metal nanoparticle (Kar et al. 2014).
Nanotechnology
Published in Vanesa Calvino-Casilda, Antonio José López-Peinado, Rosa María Martín-Aranda, Elena Pérez-Mayoral, Nanocatalysis, 2019
Pablo Fernández-Rodríguez, Jorge Hurtado de Mendoza, José Luis López-Colón, Antonio José López-Peinado, Rosa María Martín-Aranda
Physical and chemical descriptors are experimental or theoretical parameters employed to correlate the structural parameters with the applications through a statistical method. In general, molecular descriptors representing physical and chemical properties of chemicals can be obtained by two ways: theoretical calculations and experimental analysis. Theoretical descriptors are usually obtained from semi-empirical techniques and different theories. The descriptors give information about the structure and composition in correlation which biological activity, and the molecular structures can be described and represented by more than 5000 descriptors.
Estimating the physicochemical properties of antiemetics using degree-based topological descriptors
Published in Molecular Physics, 2023
Zhi-hao Hui, Muhammad Naeem, Abdul Rauf, Adnan Aslam
A topological descriptor is a numerical number assigned to a molecular structure and provides certain information related to the structure. These molecular descriptors have the ability to predict certain physical and chemical properties of the underlying molecular structure. Weiner [9] was the first to propose the idea of a topological descriptor, namely the Weiner index, and showed that this index has a very good correlation with a variety of physical and chemical properties of organic compounds. The first degree-based topological descriptor was proposed by Milan Randić [10] in 1975 to quantitatively characterise the degree of branching. After that, many degree-based topological descriptors were introduced by different researchers. Some of the degree-based topological descriptors that we consider in this work are generalised the Randić index [11, 12], Atom Bond Connectivity index [13], Geometric Arithmetic index [14], sum connectivity index [15], first and second Zagreb indices [16], hyper Zagreb index [17], harmonic index [18], third Zagreb index [19], forgotten index [20], augmented Zagreb index [21], Bablan index [22], and redefined Zagreb indices [23].
A descriptor-based analysis to highlight the mechanistic rationale of mutagenicity
Published in Journal of Environmental Science and Health, Part C, 2021
Domenico Gadaleta, Emilio Benfenati
Quantitative Structure-Activity Relationships (QSARs) are example of in silico approaches that aim at establishing a quantitative relation between an endpoint (e.g. mutagenicity) and the structure of chemicals. The need of representing quantitatively the structural information is resolved with the use of molecular descriptors. A molecular descriptor is a numerical value obtained via particular mathematical treatments encoding several kinds of structural, bio-physical or physico-chemical features of a molecule.12 A set of molecular descriptors calculated for a set of compounds are the independent variables in the mathematical equation that is the QSAR model. Thousands of molecular descriptors have been proposed that are derived from different theories and approaches.12 It is commonly recognized the importance to keep low the number of descriptors used for QSAR model derivation, because a large number of descriptors often leads to chance-correlation13 and returns models that exceed in complexity and are difficult to be interpreted.14
Theoretical and experimental investigation on the electrochemical properties, structural and spectroscopic parameters of 6,7-dihydroxy-9-thia-1,4a-diaza fluoren-2-one (DTDFO)
Published in Journal of Sulfur Chemistry, 2019
Hassan Goodarzi, Alireza Asghari, Davood Nematollahi, Maryam Rajabi
Some reactivity characteristics of a molecule can be described using atomic charges [45,46]. Quantum chemical methods play a pivotal role in calculating these descriptors. Electron populations affect dipole moment, electronic structure, polarization, and other features of a molecule. The NBO charges are displayed in Table 4S. The propensity of nitrogen atom for gaining electrons is obvious from the reduced electron population of the nearby carbon atom. C5, C4, C7, C9, and C11 atoms have high positive charge compared to the other carbon atoms mainly because they are located in close proximity to the electronegative atoms such as nitrogen and oxygen. Accordingly, it is reasonable to expect that the substitution of hydrogen atoms for some electron donor groups in the aromatic ring leads to the increased basicity of the molecule, which rises the electron density of the carbon atoms and their nucleophilic nature.