In silico study on the mechanism of formation of hydrazine and nitrogen in the reactions of excess hydroxylamine with 2,4-dinitrophenyl diethyl phosphate

2015 ◽  
Vol 39 (5) ◽  
pp. 3558-3563 ◽  
Author(s):  
Nellore Bhanu Chandar ◽  
Bishwajit Ganguly
Keyword(s):  
Quantum Chemical Calculations ◽  
In Silico ◽  
Quantum Chemical ◽  
Mechanism Of Formation ◽  
Nitrogen Gas ◽  
In Silico Study ◽  
Diethyl Phosphate

Decomposition study of 2,4-dinitrophenyl diethyl phosphate to hydrazine and nitrogen gas with excess of hydroxylamine using quantum chemical calculations.

Stereoisomers of oseltamivir – synthesis, in silico prediction and biological evaluation

2017 ◽  
Vol 15 (8) ◽  
pp. 1828-1841 ◽  
Author(s):  
Viktória Hajzer ◽  
Roman Fišera ◽  
Attila Latika ◽  
Július Durmis ◽  
Jakub Kollár ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
In Silico ◽  
Quantum Chemical ◽  
Biological Evaluation ◽  
In Silico Prediction ◽  
Antiviral Activities

Three diastereoisomers of oseltamivir were synthesized, their properties predicted by quantum-chemical calculations and their antiviral activities evaluated.

scholarly journals Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2

2021 ◽  
pp. 66-67
Author(s):  
P.V. Artyushenko ◽  
◽  
V.A. Mironov ◽  
D.I. Morozov ◽  
I.A. Shchugoreva ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Molecular Dynamic ◽  
Quantum Chemical Calculations ◽  
In Silico ◽  
Quantum Chemical ◽  
Computational Approach ◽  
Receptor Binding Domain ◽  
Dynamic Simulations ◽  
X Ray ◽  
X Ray Scattering

The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifi cations in order to increase the binding with the RBD. Th us, a new aptamer Apt25 was designed. Th e procedure of 1) aptamer structure modeling/modifi cation, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed several times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. Th e proposed computational approach to selection and refi nement of aptamers is universal and can be used for wide range of molecular ligands and targets

scholarly journals Interacting Cubane Assisted Bi-Cytidine with COVID-19 Main Protease: In Silico Study

2021 ◽  
Vol 11 (6) ◽  
pp. 13962-13967
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
In Silico ◽  
Quantum Chemical ◽  
Imaginary Frequency ◽  
Docking Simulations ◽  
Patients With Cancer ◽  
Main Protease ◽  
In Silico Study ◽  
Quantum Chemical Computations

In silico approach, the quantum chemical computations and molecular docking simulations have been used to investigate the formation of cubane assisted cytidine (B-Cyt) derivative for examining its interactions with the COVID-19 main protease. The obtained results indicated that the new B-Cyt derivative could be stabilized without any imaginary frequency. Its orbital orbital-based electronic properties indicated that the structure could have a better interaction with the target than the singular Cyt ligand. The docking process results approved the trend, in which the value of binding energy was very much favorable regarding the singular models, and the number of interaction amino acids was increased. The idea of forming a Cyt derivative with efficient activity against COVID-19 main protease was approved here, which is very much important for protecting the patients with cancer or HIV against the COVID-19 pandemic.

scholarly journals An In Silico Study of the Antioxidant Ability for Two Caffeine Analogs Using Molecular Docking and Quantum Chemical Methods

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2801 ◽  
Author(s):  
Josivan Costa ◽  
Ryan Ramos ◽  
Karina Costa ◽  
Davi Brasil ◽  
Carlos Silva ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Molecular Docking ◽  
In Silico ◽  
Quantum Chemical ◽  
Structural Changes ◽  
Redox Homeostasis ◽  
Antioxidant Ability ◽  
Antioxidant Agents ◽  
In Silico Study ◽  
Ligand Interactions

The antioxidant activity of molecules constitutes an important factor for the regulation of redox homeostasis and reduction of the oxidative stress. Cells affected by oxidative stress can undergo genetic alteration, causing structural changes and promoting the onset of chronic diseases, such as cancer. We have performed an in silico study to evaluate the antioxidant potential of two molecules of the zinc database: ZINC08706191 (Z91) and ZINC08992920 (Z20). Molecular docking, quantum chemical calculations (HF/6-31G**) and Pearson’s correlation have been performed. Molecular docking results of Z91 and Z20 showed both the lower binding affinity (BA) and inhibition constant (Ki) values for the receptor-ligand interactions in the three tested enzymes (cytochrome P450—CP450, myeloperoxidase—MP and NADPH oxidase—NO) than the control molecules (5-fluorouracil—FLU, melatonin—MEL and dextromethorphan—DEX, for each receptor respectively). Molecular descriptors were correlated with Ki and strong correlations were observed for the CP450, MP and NO receptors. These and other results attest the significant antioxidant ability of Z91 and Z20, that may be indicated for further analyses in relation to the control of oxidative stress and as possible antioxidant agents to be used in the pharmaceutical industry.

Discovery of a Difluoroglycine Synthesis Method through Quantum Chemical Calculations

2020 ◽  
Author(s):  
Tsuyoshi Mita ◽  
Yu Harabuchi ◽  
Satoshi Maeda
Keyword(s):  
Quantum Chemical Calculations ◽  
Experimental Verification ◽  
Quantum Chemical ◽  
Synthesis Method ◽  
Target Product ◽  
Systematic Exploration ◽  
Hands On ◽  
Retrosynthetic Analysis ◽  
Synthetic Routes ◽  
Verification Process

The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced ‘quantum chemistry aided retrosynthetic analysis’ (QCaRA), which uses quantum chemical calculations to search systematically for decomposition paths of the target product and propose a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the seemingly most promising path led to the discovery of a synthesis method for the difluoroglycine derivative. The extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes.

Discovery of a Difluoroglycine Synthesis Method through Quantum Chemical Calculations

2020 ◽  
Author(s):  
Tsuyoshi Mita ◽  
Yu Harabuchi ◽  
Satoshi Maeda
Keyword(s):  
Quantum Chemical Calculations ◽  
Experimental Verification ◽  
Quantum Chemical ◽  
Synthesis Method ◽  
Target Product ◽  
Systematic Exploration ◽  
Hands On ◽  
Retrosynthetic Analysis ◽  
Synthetic Routes ◽  
Verification Process

The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced ‘quantum chemistry aided retrosynthetic analysis’ (QCaRA), which uses quantum chemical calculations to search systematically for decomposition paths of the target product and propose a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the seemingly most promising path led to the discovery of a synthesis method for the difluoroglycine derivative. The extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes.

The Nature of Chemisorbed CO2 in Zeolite A

2019 ◽  
Author(s):  
Przemyslaw Rzepka ◽  
Zoltán Bacsik ◽  
Andrew J. Pell ◽  
Niklas Hedin ◽  
Aleksander Jaworski
Keyword(s):  
Solid State ◽  
Ir Spectroscopy ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Surface Coverage ◽  
Gas Mixtures ◽  
Mas Nmr ◽  
Significant Fraction ◽  
Zeolite A

Formation of CO<sub>3</sub><sup>2-</sup> and HCO<sub>3</sub><sup>-</sup> species without participation of the framework oxygen atoms upon chemisorption of CO<sub>2</sub> in zeolite |Na<sub>12</sub>|-A is revealed. The transfer of O and H atoms is very likely to have proceeded via the involvement of residual H<sub>2</sub>O or acid groups. A combined study by solid-state <sup>13</sup>C MAS NMR, quantum chemical calculations, and <i>in situ</i> IR spectroscopy showed that the chemisorption mainly occurred by the formation of HCO<sub>3</sub><sup>-</sup>. However, at a low surface coverage of physisorbed and acidic CO<sub>2</sub>, a significant fraction of the HCO<sub>3</sub><sup>-</sup> was deprotonated and transformed into CO<sub>3</sub><sup>2-</sup>. We expect that similar chemisorption of CO<sub>2</sub> would occur for low-silica zeolites and other basic silicates of interest for the capture of CO<sub>2</sub> from gas mixtures.

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