scholarly journals The Inhibitory Effect of Some Natural Bioactive D-Glucopyranoside Derivatives against SARS-CoV-2 Main Protease (Mpro) and Spike Protease (Spro)

2021 ◽  
Vol 16 ◽  
pp. 1-18
Author(s):  
Ajoy Kumer ◽  
Unesco Chakma ◽  
Sarkar Mohammad Abe Kawsar
Keyword(s):  
Active Sites ◽  
Density Functional ◽  
Inhibitory Effect ◽  
Binding Affinities ◽  
Ligand Interaction ◽  
Functional Theory ◽  
Main Protease ◽  
Mean Square Fluctuation ◽  
Chemical Descriptors ◽  
The Stability

Outbreak of coronavirus seems to have exacerbated across the globe, but drugs have not been discovered till now. Due to having the antiviral activity of D-glucopyranoside derivatives, this study was designed to examine as the inhibitor by in sillico study against the main protease (Mpro) and Spike protease (Spro) of SARS-CoV-2. First, these derivatives were optimised by Density Functional Theory (DFT). The observation of this study was monitored by molecular docking tools calculating the binding affinities. Afterwards, the ligand interaction with protein was accounted for selecting the how to bind of active sites of the protein. Next, the root means square deviation (RMSD) and root mean square fluctuation (RMSF) were illustrated for determining the stability of the docked complex. Finally, AMDET properties were calculated as well as the Lipisinki rule. All of the derivates showed a binding affinity more than -6.0 kcal/mol while derivatives 2, 3, and 9 were the best-bonded scoring inhibitor against Mpro and Spro. In addition, the chemical descriptors were more supportive tools as an inhibitor, and the Lipisinki rule was satisfied for maximum molecules as a drug. Besides, D-glucopyranoside derivatives may be predicted that they are non-carcinogenic and low toxic for both aquatic and non-aquatic species.

scholarly journals Assessing the stability of Pd-exchanged sites in zeolites with the aid of a high throughput quantum chemistry workflow

2021 ◽  
Author(s):  
Hassan Aljama ◽  
Martin Head-Gordon ◽  
Alexis Bell
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Active Sites ◽  
Density Functional ◽  
Functional Materials ◽  
No Adsorption ◽  
Functional Theory ◽  
Wide Range ◽  
The Stability ◽  
Shed Light

Abstract Cation exchanged-zeolites are functional materials with a wide range of applications from catalysis to sorbents. They present a challenge for computational studies using density functional theory due to the numerous possible active sites. From Al configuration, to placement of extra framework cation(s), to potentially different oxidation states of the cation, accounting for all these possibilities is not trivial. To make the number of calculations more tractable, most studies focus on a few active sites. We attempt to go beyond these limitations by implementing a workflow for a high throughput screening, designed to systematize the problem and exhaustively search for feasible active sites. We use Pd-exchanged CHA and BEA to illustrate the approach. After conducting thousands of individual calculations, we identify the sites most favorable for the Pd cation and discuss the results in detail. The high throughput screening identifies many energetically favorable sites that are non-trivial. Lastly, we employ these results to examine NO adsorption in Pd-exchanged CHA, which is a promising passive NOx adsorbent (PNA) during the cold start of automobiles. The results shed light on critical active sites for NOx capture that were not previously studied.

scholarly journals Density Functional Theory Analysis of Poly Glycolic Acid with Metal Ions (Na+, K+) Interaction

2019 ◽  
Vol 9 (1S3) ◽  
pp. 366-369
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Density Functional ◽  
Glycolic Acid ◽  
Carbonyl Oxygen ◽  
Chemical Hardness ◽  
Binding Affinities ◽  
Functional Theory ◽  
Fukui Functions ◽  
The Stability

The complexation between Poly glycolic acid (PGA) and alkali metal ions (Na+ , K+ ) have been studied using B3LYP/6-311++G** method. The binding site of metal ion interaction on PGA is carbonyl oxygen. Both metal ions form bidendate complexation with PGA. Further, it can be noted that the PGA with K+ complex is more stable than the PGA with Na+ complex. The binding affinities (ΔH), basicity (ΔG) and the complexation entropies (ΔS) of all the studied systems are calculated. The interaction energy is maximum in PGA-Na+ than the PGA-K + complex. This is due to more charge transfer taking place between PGA and Na. The stability of the complex is studied by the chemical hardness value. The condensed Fukui functions are calculated and are used to predict the favourable reactive site

Theoretical Studies on the Chemical Structure of Carboxymethyl Chitosan

2010 ◽  
Vol 160-162 ◽  
pp. 1822-1827
Author(s):  
Xi Lu ◽  
Juan Qin Xue ◽  
Yu Jie Wang ◽  
Wei Bo Mao ◽  
Ming Wu ◽  
...  
Keyword(s):  
Active Sites ◽  
Density Functional ◽  
Carboxymethyl Chitosan ◽  
Water Soluble ◽  
Functional Theory ◽  
Molecular Orbit ◽  
The Density Functional Theory ◽  
Stability Order ◽  
The Stability ◽  
The One

The density functional theory (DFT) calculations explored the structural optimization and the frequency of N-carboxymethyl chitosan (N-CMCS) and O-carboxymethyl chitosan (O-CMCS). For the isomers, the calculations comparatively were performed. The charge distribution and frontier molecular orbit were analyzed by using the natural bond orbital (NBO) method. The results showed: the two rotational isomers a and b can stably exist, with the stability order a>b; N-carboxymethyl chitosan reaction active sites are concentrated in -OH and -NHCH2COOH, while O-carboxymethyl chitosan reaction active sites are concentrated in -NH2 and -CH2COOH; The water-soluble mechanism of carboxymethyl chitosan was investigated deeply, on the one hand, the presence of carboxymethyl of carboxymethyl chitosan had a tendency to ionize H+, on the other hand the carboxymethyl increased the distance and weakened the hydrogen bonds between molecules, even though Einstein shift H-bond is formed in the carboxymethyl chitosan molecules.

Thermodynamic Stability of Hexagonal and Rhombohedral Bn at Cvd Conditions from Van der Waals Corrected First Principles Calculations

2019 ◽  
Author(s):  
Henrik Pedersen ◽  
Björn Alling ◽  
Hans Högberg ◽  
Annop Ektarawong
Keyword(s):  
Thin Films ◽  
Thermodynamic Stability ◽  
First Principles ◽  
Thermal Equilibrium ◽  
Density Functional ◽  
Van Der Waals ◽  
Chemical Vapor ◽  
First Principles Calculations ◽  
Functional Theory ◽  
The Stability

Thin films of boron nitride (BN), particularly the sp<sup>2</sup>-hybridized polytypes hexagonal BN (h-BN) and rhombohedral BN (r-BN) are interesting for several electronic applications given band gaps in the UV. They are typically deposited close to thermal equilibrium by chemical vapor deposition (CVD) at temperatures and pressures in the regions 1400-1800 K and 1000-10000 Pa, respectively. In this letter, we use van der Waals corrected density functional theory and thermodynamic stability calculations to determine the stability of r-BN and compare it to that of h-BN as well as to cubic BN and wurtzitic BN. We find that r-BN is the stable sp<sup>2</sup>-hybridized phase at CVD conditions, while h-BN is metastable. Thus, our calculations suggest that thin films of h-BN must be deposited far from thermal equilibrium.

Site preference and atomic ordering in the ternary Rh5Ga2As: first-principles calculations

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Nilanjan Roy ◽  
Sucharita Giri ◽  
Harshit ◽  
Partha P. Jana
Keyword(s):  
Total Energy ◽  
First Principles ◽  
Density Functional ◽  
Structure Type ◽  
Site Preference ◽  
X Ray Diffraction ◽  
Atomic Ordering ◽  
Functional Theory ◽  
The Stability ◽  
Bonding Characteristics

Abstract The site preference and atomic ordering of the ternary Rh5Ga2As have been investigated using first-principles density functional theory (DFT). An interesting atomic ordering of two neighboring elements Ga and As reported in the structure of Rh5Ga2As by X-ray diffraction data only is confirmed by first-principles total-energy calculations. The previously reported experimental model with Ga/As ordering is indeed the most stable in the structure of Rh5Ga2As. The calculation detected that there is an obvious trend concerning the influence of the heteroatomic Rh–Ga/As contacts on the calculated total energy. Interestingly, the orderly distribution of As and Ga that is found in the binary GaAs (Zinc-blende structure type), retained to ternary Rh5Ga2As. The density of states (DOS) and Crystal Orbital Hamiltonian Population (COHP) are calculated to enlighten the stability and bonding characteristics in the structure of Rh5Ga2As. The bonding analysis also confirms that Rh–Ga/As short contacts are the major driving force towards the overall stability of the compound.

scholarly journals Study on the adsorption selection of CH$$_4$$ on CuO (110) versus (111) surfaces: a density functional theory study

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Long Lin ◽  
Linwei Yao ◽  
Shaofei Li ◽  
Zhengguang Shi ◽  
Kun Xie ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Adsorption Capacity ◽  
Active Sites ◽  
Density Functional ◽  
Oxygen Vacancies ◽  
Density Functional Theory Calculations ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Strong Adsorption ◽  
Selection Of

AbstractFinding the active sites of suitable metal oxides is a key prerequisite for detecting CH$$_4$$ 4 . The purpose of the paper is to investigate the adsorption of CH$$_4$$ 4 on intrinsic and oxygen-vacancies CuO (111) and (110) surfaces using density functional theory calculations. The results show that CH$$_4$$ 4 has a strong adsorption energy of −0.370 to 0.391 eV at all site on the CuO (110) surface. The adsorption capacity of CH$$_4$$ 4 on CuO (111) surface is weak, ranging from −0.156 to −0.325 eV. In the surface containing oxygen vacancies, the adsorption capacity of CuO surface to CH$$_4$$ 4 is significantly stronger than that of intrinsic CuO surface. The results indicate that CuO (110) has strong adsorption and charge transfer capacity for CH$$_4$$ 4 , which may provide experimental guidance.

scholarly journals The stability and electronic and photocatalytic properties of the ZnWO4 (010) surface determined from first-principles and thermodynamic calculations

RSC Advances ◽  
2021 ◽  
Vol 11 (38) ◽  
pp. 23477-23490
Author(s):  
Yonggang Wu ◽  
Jihua Zhang ◽  
Bingwei Long ◽  
Hong Zhang
Keyword(s):  
Phase Diagram ◽  
Density Functional Theory ◽  
First Principles ◽  
Density Functional ◽  
Thermodynamic Calculations ◽  
Photocatalytic Properties ◽  
Thermodynamic Approach ◽  
Functional Theory ◽  
Stability Phase Diagram ◽  
The Stability

The ZnWO4 (010) surface termination stability is studied using a density functional theory-based thermodynamic approach. The stability phase diagram shows that O-Zn, DL-W, and DL-Zn terminations of ZnWO4 (010) can be stabilized.

scholarly journals Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3631
Author(s):  
Ahmed M. Deghady ◽  
Rageh K. Hussein ◽  
Abdulrahman G. Alhamzani ◽  
Abeer Mera
Keyword(s):  
Density Functional Theory ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Carbonyl Group ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Molecular Docking Study ◽  
Functional Theory

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule’s chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule’s stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol).

A DENSITY FUNCTIONAL STUDY OF THE STRUCTURE OF SILANE COUPLING AGENT 3–AMINOPROPYLTRIETHOXYSILANE

2005 ◽  
Vol 04 (01) ◽  
pp. 117-126
Author(s):  
N. L. MA ◽  
P. WU
Keyword(s):  
Coupling Agent ◽  
Density Functional ◽  
Solution Structure ◽  
Silane Coupling Agent ◽  
Industrial Applications ◽  
Functional Study ◽  
Stable Form ◽  
Functional Theory ◽  
Silane Coupling ◽  
The Stability

Using density functional theory, we predicted the solution structure of the hydrolyzed 3–aminopropyltriethoxysilane (h–APS), which is a silane coupling agent commonly used in many industrial applications. We have located five stable minima on the potential energy surface of h–APS in which four of them are "neutral", and the remaining one is zwitterionic (dipolar) in nature. Our calculations suggested that the stability of the most stable form of h–APS in water (denoted as II_N) arose from strong intramolecular OH ⋯ N hydrogen bond. The least stable form is the zwitterionic form (I_ZW), which is estimated to be over 90 kJ mol -1 less stable than II_N. The factors governing the relative stabilities of different forms are discussed.

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