Hybrid Docking-Nano-QSPR: An Alternative Approach for Prediction of Chemicals Adsorption on Nanoparticles

NANO ◽  
2016 ◽  
Vol 11 (07) ◽  
pp. 1650078 ◽  
Author(s):  
Afsane Heidari ◽  
Mohammad H. Fatemi
Keyword(s):  
Molecular Docking ◽  
Multiwall Carbon Nanotube ◽  
Quantitative Structure ◽  
Structure Property ◽  
Test Set ◽  
Alternative Approach ◽  
Structure Property Relationship ◽  
Hybrid Docking ◽  
Multiwall Carbon ◽  
Insight Into

In this study, a new hybrid docking-quantitative structure–property relationship (QSPR) methodology was used to model and predict the adsorption coefficients of some small organic compounds on pristine multiwall carbon nanotube (MWCNT). In this method, descriptors are calculated from the reproduced experimental conformations by molecular docking to develop predictive QSPR models. Three MLR models with squared correlation coefficient ([Formula: see text] values of 0.93, 0.94 and 0.95 were selected. The prediction power of models was evaluated on 12-member test set, which was not used during the modeling and led to [Formula: see text] values of 0.88, 0.85 and 0.93. This methodology gives new insight into factors influenced on the adsorption of nanoparticles.

Quantitative Structure- Property Relationship (QSPR) Investigation of Camptothecin Drugs Derivatives

2018 ◽  
Vol 21 (7) ◽  
pp. 533-542 ◽  
Author(s):  
Neda Ahmadinejad ◽  
Fatemeh Shafiei ◽  
Tahereh Momeni Isfahani
Keyword(s):  
Thermodynamic Properties ◽  
Predictive Ability ◽  
Total Sample ◽  
Basis Sets ◽  
Quantitative Structure ◽  
Structure Property ◽  
Quantitative Structure Property Relationship ◽  
Chemical Structures ◽  
Property Relationship ◽  
Structure Property Relationship

Aim and Objective: Quantitative Structure- Property Relationship (QSPR) has been widely developed to derive a correlation between chemical structures of molecules to their known properties. In this study, QSPR models have been developed for modeling and predicting thermodynamic properties of 76 camptothecin derivatives using molecular descriptors. Materials and Methods: Thermodynamic properties of camptothecin such as the thermal energy, entropy and heat capacity were calculated at Hartree–Fock level of theory and 3-21G basis sets by Gaussian 09. Results: The appropriate descriptors for the studied properties are computed and optimized by the genetic algorithms (GA) and multiple linear regressions (MLR) method among the descriptors derived from the Dragon software. Leave-One-Out Cross-Validation (LOOCV) is used to evaluate predictive models by partitioning the total sample into training and test sets. Conclusion: The predictive ability of the models was found to be satisfactory and could be used for predicting thermodynamic properties of camptothecin derivatives.

scholarly journals Architectures and Applications of BODIPY-Based Conjugated Polymers

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 75
Author(s):  
Yiqi Fan ◽  
Jinjin Zhang ◽  
Zhouyi Hong ◽  
Huayu Qiu ◽  
Yang Li ◽  
...  
Keyword(s):  
Conjugated Polymers ◽  
Chemical Doping ◽  
Structure Property ◽  
High Quantum Yield ◽  
Conjugated Materials ◽  
Energy Band Gap ◽  
Photoelectric Properties ◽  
Structure Property Relationship ◽  
Insight Into ◽  
High Absorption

Conjugated polymers generally contain conjugated backbone structures with benzene, heterocycle, double bond, or triple bond, so that they have properties similar to semiconductors and even conductors. Their energy band gap is very small and can be adjusted via chemical doping, allowing for excellent photoelectric properties. To obtain prominent conjugated materials, numerous well-designed polymer backbones have been reported, such as polyphenylenevinylene, polyphenylene acetylene, polycarbazole, and polyfluorene. 4,4′-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)-based conjugated polymers have also been prepared owing to its conjugated structure and intriguing optical properties, including high absorption coefficients, excellent thermal/photochemical stability, and high quantum yield. Most importantly, the properties of BODIPYs can be easily tuned by chemical modification on the dipyrromethene core, which endows the conjugated polymers with multiple functionalities. In this paper, BODIPY-based conjugated polymers are reviewed, focusing on their structures and applications. The forms of BODIPY-based conjugated polymers include linear, coiled, and porous structures, and their structure–property relationship is explored. Also, typical applications in optoelectronic materials, sensors, gas/energy storage, biotherapy, and bioimaging are presented and discussed in detail. Finally, the review provides an insight into the challenges in the development of BODIPY-based conjugated polymers.

scholarly journals RP-HPLC measurement and quantitative structure - property relationship analysis of the n-octanol - water partitioning coefficients of selected metabolites of polybrominated diphenyl ethers

2008 ◽  
Vol 5 (5) ◽  
pp. 332 ◽  
Author(s):  
Yijun Yu ◽  
Weihua Yang ◽  
Zishen Gao ◽  
Michael H. W. Lam ◽  
Xiaohua Liu ◽  
...  
Keyword(s):  
Polybrominated Diphenyl Ethers ◽  
High Performance ◽  
Reversed Phase ◽  
Retention Indices ◽  
Quantitative Structure ◽  
Structure Property ◽  
Rp Hplc ◽  
Structure Property Relationship ◽  
Water Partitioning ◽  
Log Kow

Environmental context. Polybrominated diphenyl ethers (PBDEs) are ubiquitous environmental contaminants and numerous studies have demonstrated a marked increase in the levels of PBDEs in human biological tissues and fluids, especially breast milk. How PBDEs are transported through the environment, taken up by biota, transported across membranes, and metabolised depends strongly on such fundamental properties as lipophilicity (log KOW). However, very little data on log KOW exist for PBDEs. In the present paper, the authors determine PBDE metabolites’ log KOW using reversed-phase high performance liquid chromatography, as recommended by the Organisation for Economic Co-operation and Development and US Environmental Protection Agency, along with quantitative structure–property relationships. Abstract. n-Octanol–water partitioning coefficient (log KOW) values of selected hydroxylated and methoxylated polybrominated diphenyl ether metabolites were measured for the first time by reversed-phase high performance liquid chromatography (RP-HPLC) using a C18 stationary phase with a water/methanol mixture as a mobile phase. The retention parameters, log kw (extrapolated retention indices) and k′ (gradient retention indices) were calibrated to log KOW by a set of calibration standards. For the PBDE metabolites investigated, extrapolated retention indices from isocratic elution seem to be more reliable and their RP-HPLC-derived log KOW values were found to range from 4.63 to 7.67. Some commonly available software, including ClogP, KowWin, AclogP, MlogP, AlogP, MilogP, and XlogP, was used to estimate the log KOW values of the analytes. Significant correlations were obtained between the RP-HPLC-derived log KOW and the software-computed log KOW, with squared correlation coefficients (R2) ranging from 0.793 to 0.922, but the difference between them was also significant. Then a quantitative structure–property relationship model based on topological descriptors was established and showed good reliability and predictive power for the estimation of RP-HPLC-derived log KOW values of PBDE metabolites. It was applied to estimate the log KOW values of some PBDE metabolites that are commercially available or have appeared in the literature. Lastly, factor analysis was carried out using the theoretical linear salvation/free-energy relationships, which indicated the average polarisability (α) and the most negative atomic partial Mulliken charge in the molecule (q–) were the most important parameters affecting their partition between n-octanol and water, supporting the factorisation of log KOW in bulk and electronic terms.

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