Modeling the conformational preference, spectroscopic properties, UV light harvesting efficiency, biological receptor inhibitory ability and other physico-chemical properties of five imidazole derivatives using quantum mechanical and molecular mechanics tools

2020 ◽  
Vol 310 ◽  
pp. 112871 ◽  
Author(s):  
Jamelah S. Al-Otaibi ◽  
Aljawhara H. Almuqrin ◽  
Y. Sheena Mary ◽  
Renjith Thomas
2020 ◽  
Author(s):  
Hussein Hassan-Harrirou ◽  
Ce Zhang ◽  
Thomas Lemmin

ABSTRACTThe worldwide increase and proliferation of drug resistant microbes, coupled with the lag in new drug development represents a major threat to human health. In order to reduce the time and cost for exploring the chemical search space, drug discovery increasingly relies on computational biology approaches. One key step in these approaches is the need for the rapid and accurate prediction of the binding affinity for potential leads.Here, we present RosENet (Rosetta Energy Neural Network), a three-dimensional (3D) Convolutional Neural Network (CNN), which combines voxelized molecular mechanics energies and molecular descriptors for predicting the absolute binding affinity of protein – ligand complexes. By leveraging the physico-chemical properties captured by the molecular force field, our model achieved a Root Mean Square Error (RMSE) of 1.26 on the PDBBind v2016 core set. We also explored some limitations and the robustness of the PDBBind dataset and our approach, on nearly 500 structures, including structures determined by Nuclear Magnetic Resonance and virtual screening experiments. Our study demonstrated that molecular mechanics energies can be voxelized and used to help improve the predictive power of the CNNs. In the future, our framework can be extended to features extracted from other biophysical and biochemical models, such as molecular dynamics simulations.Availabilityhttps://github.com/DS3Lab/RosENet


2017 ◽  
Vol 71 (3) ◽  
pp. 259-269 ◽  
Author(s):  
Marija Vasic ◽  
Marjan Randjelovic ◽  
Jelena Mitrovic ◽  
Nikola Stojkovic ◽  
Branko Matovic ◽  
...  

Titania based catalyst and TiO2 doped with zirconia were prepared by modified sol?gel method. The synthesized catalysts samples were characterized by BET, XRD, SEM and FTIR techniques. Photocatalytic activity was tested in the reaction of crystal violet (CV) dye decolorization/decomposition under UV light irradiation. The effect of several operational parameters, such as catalyst dosage, initial dye concentrations, duration of UV irradiation treatment and number of reaction cycles were also considered. The obtained results indicated faster dye decolorization with the increase of the catalyst amount and a decrease of initial CV concentrations. An influence of doping with zirconia on the physico-chemical properties of bare titania was studied. The doping procedure had affected photocatalytic properties of the final catalytic material, and had improved photocatalytic performances of doped catalyst on crystal violet decolorization/degradation in comparison to bare titania.


2020 ◽  
Vol 979 ◽  
pp. 169-174 ◽  
Author(s):  
C. Karthikeyan ◽  
M. Thamima ◽  
S. Karuppuchamy

The nanostructured photocatalysts are the most promising materials for the degradation of toxic dyes. Particularly, CaTiO3 has been used in several applications including catalytic, optical, biological and electronic. In this present study, perovskite structured CaTiO3 nanomaterials have been synthesized by microwave irradiation method. The physico-chemical properties of the prepared CaTiO3 nanomaterials were studied by various advanced characterization techniques. The XRD patterns confirm the presence of perovskite structure of the prepared nanomaterials. FT-IR analysis confirms the presence of Ca-Ti-O vibrational bonds. Micro Raman study display the existence of O-Ca-Ti-O with B1g mode of vibrations. Morphological studies revealed the presence of truncated nanospheres. The dye degradation property of prepared CaTiO3 was investigated by Malachite green (MG) by UV-light.


2021 ◽  
Author(s):  
Alex van der Ham ◽  
Thomas Hansen ◽  
Hermen S. Overkleeft ◽  
Trevor A. Hamlin ◽  
Dmitri V. Filippov ◽  
...  

The targeted application of multiple helicenes in photo-optical applications requires their rational design. Toward this goal, we report on the synthesis of pyrene-based triple helicene 1 and investigate the positional effect of extension of the π-conjugated system on the photo-chemical and chiro-optical properties of triple helicenes. The conformational and aggregatory behavior of 1 were studied both experimentally using VT NMR spectroscopy and computationally using high-level DFT computations. Although π-extension was observed to have a marked effect on the spectroscopic properties of triple helicenes, comparison with other known π-extended helicenes reveals that the position at which π-extension is introduced is only of nominal importance. Our results thus suggest that the presence of a particular helicene motif is dominant in dictating the physico-chemical properties of triple helicenes.


2013 ◽  
Vol 13 (6) ◽  
pp. 1425-1436 ◽  
Author(s):  
D. Vries ◽  
B. A. Wols ◽  
P. de Voogt

The efficiency of water treatment systems in removing emerging (chemical) substances is often unknown. Consequently, the prediction of the removal of contaminants in the treatment and supply chain of drinking water is of great interest. By collecting and processing existing chemical properties of contaminants, QSARs (quantitative structure-activity relationships) for typical removal parameters can be constructed. Depending on the definition of the predicted endpoint, QSARs are (1) embedded in a process model suite, where they serve to predict a model parameter and the total, hybrid model predicts a removal rate or (2) used to directly predict, e.g., the removal rate, or a rejection coefficient for membrane systems. The different types of resulting prediction models, ranging from mechanistic (causal) to empirical (data-based), allow for hypothesis testing of current physico-chemical mechanisms and interactions between the contaminant, the type of water and the materials or energy (e.g. UV light) of the removal barrier. Two case studies illustrate this viewpoint and also pinpoint that, firstly, QSAR development, validation and residual analysis stress the linkage between the QSAR endpoints and process model predictions, and secondly, they lay bare the need to share data, algorithms and models.


1985 ◽  
Vol 50 ◽  
Author(s):  
N. Paxéus ◽  
B. Allard ◽  
U. Olofsson ◽  
M. Bengtsson

AbstractThe humic materials isolated from ground waters of a borehole in Fjällveden (Sweden) were characterized by elemental and functional group analyses. Spectroscopic properties, molecular weight distributions as well as acid-base properties of the fulvic and humic fractions were also studied. The ground water humic substances were found to be quite similar in many respects (but not identical) to the Swedish surface water humics concentrated from the Gτ(b, A)öta River but appeared to be quite different from the American ground water humics from Biscayne Florida Aquifer or Laramie Fox-Hills in Colorado. The physico-chemical properties of the isolated humic materials are discussed.


2021 ◽  
Author(s):  
Alex van der Ham ◽  
Thomas Hansen ◽  
Hermen S. Overkleeft ◽  
Dmitri V. Filippov ◽  
Grégory F. Schneider ◽  
...  

The physico-chemical properties of chiral propeller-shaped PAHs (propellerenes) are strongly dependent on their conformational behavior. A sound, physical model to understand why propellerenes exhibit a conformation preference for either a C2 or D3 conformation that moves beyond a phenomenological explanation is needed. We have therefore performed a computational study to rationalize the conformational preference of propellerenes. Using an activation strain analysis approach, we find that the conformational preference of propellerenes is ultimately determined by the flexibility of the wings. When wings are relatively flexible, as is the case for ortho-substituted propellerenes, a favorable contraction of the radial bonds connecting the core and the propellerene wings is possible, and the more distorted C2 conformation will be preferred. The more rigid wings of benzenoid propellerenes, on the other hand, cannot deform sufficiently, and will therefore always adopt a D3 conformation. Our approach represents a unique method to pinpoint the conformational preferences of propellerenes, and, in principle, any sterically congested molecule.


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