Subjects -> CHEMISTRY (Total: 928 journals)
    - ANALYTICAL CHEMISTRY (59 journals)
    - CHEMISTRY (661 journals)
    - CRYSTALLOGRAPHY (23 journals)
    - ELECTROCHEMISTRY (28 journals)
    - INORGANIC CHEMISTRY (45 journals)
    - ORGANIC CHEMISTRY (47 journals)
    - PHYSICAL CHEMISTRY (65 journals)

CHEMISTRY (661 journals)            First | 1 2 3 4 | Last

Showing 401 - 600 of 735 Journals sorted alphabetically
Journal of Molecular Liquids     Hybrid Journal   (Followers: 3)
Journal of Molecular Modeling     Hybrid Journal   (Followers: 5)
Journal of Molecular Recognition     Hybrid Journal   (Followers: 2)
Journal of Molecular Spectroscopy     Hybrid Journal   (Followers: 6)
Journal of Molecular Structure     Hybrid Journal   (Followers: 6)
Journal of Nanoparticles     Open Access   (Followers: 4)
Journal of Nanostructure in Chemistry     Open Access   (Followers: 8)
Journal of Organometallic Chemistry     Hybrid Journal   (Followers: 25)
Journal of Photochemistry and Photobiology     Open Access  
Journal of Photochemistry and Photobiology A: Chemistry     Hybrid Journal   (Followers: 3)
Journal of Photochemistry and Photobiology B: Biology     Hybrid Journal   (Followers: 4)
Journal of Photochemistry and Photobiology C: Photochemistry Reviews     Full-text available via subscription   (Followers: 3)
Journal of Polymer & Composites     Full-text available via subscription   (Followers: 17)
Journal of Polymer and Biopolymer Physics Chemistry     Open Access   (Followers: 7)
Journal of Polymer Science Part A: Polymer Chemistry     Hybrid Journal   (Followers: 92)
Journal of Polymers     Open Access   (Followers: 7)
Journal of Porphyrins and Phthalocyanines     Hybrid Journal   (Followers: 1)
Journal of Progressive Research in Chemistry     Open Access  
Journal of Pure and Applied Chemistry Research     Open Access   (Followers: 3)
Journal of Raman Spectroscopy     Hybrid Journal   (Followers: 14)
Journal of Research and Education Chemistry     Open Access   (Followers: 1)
Journal of Research Updates in Polymer Science     Hybrid Journal   (Followers: 2)
Journal of Rubber Research     Hybrid Journal   (Followers: 1)
Journal of Saudi Chemical Society     Open Access  
Journal of Solid State Chemistry     Hybrid Journal   (Followers: 13)
Journal of Solution Chemistry     Hybrid Journal   (Followers: 1)
Journal of Structural Chemistry     Hybrid Journal   (Followers: 1)
Journal of Sulfur Chemistry     Hybrid Journal   (Followers: 1)
Journal of Supercritical Fluids     Hybrid Journal   (Followers: 3)
Journal of Superhard Materials     Hybrid Journal  
Journal of Surface Science and Technology     Hybrid Journal  
Journal of Surfactants and Detergents     Hybrid Journal   (Followers: 3)
Journal of Taibah University for Science     Open Access  
Journal of the American Chemical Society     Hybrid Journal   (Followers: 323)
Journal of the American Society for Mass Spectrometry     Hybrid Journal   (Followers: 32)
Journal of the American Society of Brewing Chemists     Full-text available via subscription   (Followers: 2)
Journal of the Chilean Chemical Society     Open Access   (Followers: 2)
Journal of the Chinese Chemical Society     Hybrid Journal  
Journal of the Indian Chemical Society     Hybrid Journal  
Journal of The Indonesian Society of Integrated Chemistry     Open Access  
Journal of the Iranian Chemical Society     Hybrid Journal   (Followers: 1)
Journal of the Korean Society for Applied Biological Chemistry     Hybrid Journal  
Journal of the Mexican Chemical Society     Open Access   (Followers: 1)
Journal of the Serbian Chemical Society     Open Access  
Journal of the Turkish Chemical Society, Section A : Chemistry     Open Access  
Journal of Theoretical and Computational Chemistry     Hybrid Journal   (Followers: 9)
Jurnal Inovasi Pendidikan Kimia     Open Access  
Jurnal Kimia (Journal of Chemistry)     Open Access  
Jurnal Kimia Riset     Open Access  
Jurnal Pendidikan Kimia     Open Access  
Jurnal Penelitian Sains (JPS)     Open Access  
Karbala International Journal of Modern Science     Open Access  
Kinetics and Catalysis     Hybrid Journal   (Followers: 4)
Konfigurasi : Jurnal Pendidikan Kimia dan Terapan     Open Access  
Korea-Australia Rheology Journal     Hybrid Journal   (Followers: 1)
Langmuir     Hybrid Journal   (Followers: 58)
Lebensmittelchemie     Hybrid Journal   (Followers: 1)
Lipid Insights     Open Access  
Luminescence     Hybrid Journal   (Followers: 2)
Macromolecular Materials & Engineering     Hybrid Journal   (Followers: 5)
Macromolecular Rapid Communications     Hybrid Journal   (Followers: 10)
Macromolecular Research     Hybrid Journal   (Followers: 2)
Macromolecular Symposia     Hybrid Journal   (Followers: 3)
Macromolecular Theory and Simulations     Hybrid Journal   (Followers: 2)
Macromolecules     Hybrid Journal   (Followers: 48)
Magnetic Resonance in Chemistry     Hybrid Journal   (Followers: 8)
Magnetochemistry     Open Access  
Marine Chemistry     Hybrid Journal   (Followers: 6)
Marine Drugs     Open Access   (Followers: 1)
MATEC Web of Conferences     Open Access  
Materials Advances     Open Access   (Followers: 2)
Materials and Devices     Open Access  
Materials Characterization     Hybrid Journal   (Followers: 32)
Materials Chemistry Frontiers     Hybrid Journal   (Followers: 4)
Materials Horizons     Hybrid Journal   (Followers: 6)
Materials Research Bulletin     Hybrid Journal   (Followers: 25)
Materials Science-Poland     Open Access   (Followers: 1)
Materials Sciences and Applications     Open Access   (Followers: 2)
Medicinal Chemistry Research     Hybrid Journal   (Followers: 9)
Mediterranean Journal of Chemistry     Open Access  
Metallography, Microstructure, and Analysis     Hybrid Journal   (Followers: 1)
Micro and Nano Systems Letters     Open Access   (Followers: 6)
Microchimica Acta     Hybrid Journal   (Followers: 2)
Microporous and Mesoporous Materials     Hybrid Journal   (Followers: 9)
Modern Chemistry & Applications     Open Access   (Followers: 1)
Modern Research in Catalysis     Open Access  
Molbank     Open Access  
Molecular Catalysis     Hybrid Journal   (Followers: 6)
Molecules     Open Access   (Followers: 4)
Molecules and Cells     Hybrid Journal   (Followers: 1)
Monatshefte für Chemie - Chemical Monthly     Hybrid Journal   (Followers: 4)
Mongolian Journal of Chemistry     Open Access  
Moscow University Chemistry Bulletin     Hybrid Journal   (Followers: 1)
MRS Bulletin     Full-text available via subscription   (Followers: 4)
Nachrichten aus der Chemie     Hybrid Journal   (Followers: 18)
Nano Convergence     Open Access   (Followers: 1)
Nano Materials Science     Open Access   (Followers: 1)
Nano Reviews & Experiments     Open Access   (Followers: 14)
Nano Select     Open Access  
Nanochemistry Research     Open Access   (Followers: 1)
Nanoscale     Hybrid Journal   (Followers: 18)
Nanoscale Advances     Open Access  
Nanoscale Horizons     Hybrid Journal  
Nanoscale Research Letters     Open Access   (Followers: 8)
Nanoscience and Nanotechnology Letters     Full-text available via subscription   (Followers: 24)
Natural Product Communications     Open Access  
Natural Product Reports     Hybrid Journal   (Followers: 10)
Natural Science     Open Access   (Followers: 8)
Natural Volatiles & Essential Oils     Open Access  
Nature Chemistry     Full-text available via subscription   (Followers: 97)
Nature Protocols     Full-text available via subscription   (Followers: 72)
Nature Reviews Chemistry     Hybrid Journal   (Followers: 17)
New Journal of Chemistry     Hybrid Journal   (Followers: 17)
Nitric Oxide     Hybrid Journal  
Nitrogen     Open Access  
Nukleonika     Open Access  
Open Chemistry Journal     Open Access  
Open Conference Proceedings Journal     Open Access  
Open Journal of Chemistry     Open Access  
Open Journal of Composite Materials     Open Access   (Followers: 22)
Open Journal of Inorganic Non-metallic Materials     Open Access   (Followers: 2)
Open Journal of Medicinal Chemistry     Open Access   (Followers: 4)
Open Journal of Polymer Chemistry     Open Access   (Followers: 12)
Open Journal of Synthesis Theory and Applications     Open Access  
Open Medicinal Chemistry Journal     Open Access  
Orbital - The Electronic Journal of Chemistry     Open Access   (Followers: 1)
Organic & Biomolecular Chemistry     Hybrid Journal   (Followers: 57)
Organometallics     Hybrid Journal   (Followers: 19)
Oxidation of Metals     Hybrid Journal   (Followers: 16)
Passer Journal of Basic and Applied Sciences     Open Access  
Peptide Science     Full-text available via subscription  
Pharmaceuticals     Open Access   (Followers: 4)
Pharmaceutics     Open Access   (Followers: 5)
Phosphorus, Sulfur, and Silicon and the Related Elements     Hybrid Journal   (Followers: 2)
Photochemistry and Photobiology     Hybrid Journal   (Followers: 3)
Physical Science International Journal     Open Access  
Physics and Materials Chemistry     Open Access   (Followers: 1)
Phytochemistry     Hybrid Journal   (Followers: 4)
Phytochemistry Letters     Full-text available via subscription   (Followers: 1)
Plasma     Open Access   (Followers: 3)
Plasma Chemistry and Plasma Processing     Hybrid Journal   (Followers: 3)
Polycyclic Aromatic Compounds     Hybrid Journal  
Polyhedron     Hybrid Journal   (Followers: 4)
Polymer Chemistry     Hybrid Journal   (Followers: 24)
Polymer crystallization     Hybrid Journal  
Polymer Degradation and Stability     Hybrid Journal   (Followers: 23)
Polymer Engineering & Science     Hybrid Journal   (Followers: 14)
Polymer Reviews     Hybrid Journal   (Followers: 32)
Polymer Science Series D     Hybrid Journal   (Followers: 3)
Polymer Testing     Hybrid Journal   (Followers: 193)
Polymer-Plastics Technology and Materials     Hybrid Journal   (Followers: 5)
Polymers     Open Access   (Followers: 21)
Polymers from Renewable Resources     Hybrid Journal  
Proceedings of the Combustion Institute     Full-text available via subscription   (Followers: 8)
Processes     Open Access  
Progress in Lipid Research     Hybrid Journal   (Followers: 3)
Progress in Organic Coatings     Hybrid Journal   (Followers: 7)
Progress in Polymer Science     Full-text available via subscription   (Followers: 36)
Progress in Reaction Kinetics and Mechanism     Open Access  
Progress in Solid State Chemistry     Full-text available via subscription   (Followers: 3)
Progress in Surface Science     Full-text available via subscription   (Followers: 3)
Protein Science     Hybrid Journal   (Followers: 45)
Radiochemistry     Hybrid Journal   (Followers: 1)
Rapid Communications in Mass Spectrometry     Hybrid Journal   (Followers: 33)
Reaction Chemistry & Engineering     Hybrid Journal  
Reaction Kinetics, Mechanisms and Catalysis     Hybrid Journal   (Followers: 3)
Reactions     Open Access  
Reportes Científicos de la FaCEN     Open Access  
Research Journal of Phytochemistry     Open Access   (Followers: 1)
Resources Chemicals and Materials     Full-text available via subscription   (Followers: 2)
Results in Chemistry     Open Access  
Results in Geochemistry     Open Access  
Results in Surfaces and Interfaces     Open Access  
Review Journal of Chemistry     Hybrid Journal   (Followers: 1)
Reviews in Mineralogy and Geochemistry     Hybrid Journal   (Followers: 4)
Revista Boliviana de Química     Open Access  
Revista CENIC. Ciencias Quimicas     Open Access  
Revista Colombiana de Ciencias Químico-Farmacéuticas     Open Access  
Revista Colombiana de Química     Open Access  
Revista Cubana de Química     Open Access  
Revista de Ciencia y Tecnología     Open Access  
Revista de Ciencias     Open Access  
Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales     Open Access  
Revista de la Sociedad Química del Perú     Open Access  
Revista de la Societat Catalana de Química     Open Access  
Revista de Química     Open Access   (Followers: 3)
Revista Debates em Ensino de Química     Open Access  
Revista ION     Open Access  
RSC Advances     Open Access   (Followers: 27)
RSC Chemical Biology     Open Access  
RSC Medicinal Chemistry     Hybrid Journal   (Followers: 6)
Russian Journal of Bioorganic Chemistry     Hybrid Journal   (Followers: 1)
Russian Journal of Coordination Chemistry     Hybrid Journal   (Followers: 1)
Russian Journal of General Chemistry     Hybrid Journal   (Followers: 1)
Russian Journal of Inorganic Chemistry     Hybrid Journal  
Sainstek : Jurnal Sains dan Teknologi     Open Access  
Science China Chemistry     Hybrid Journal   (Followers: 2)
Science Talks     Full-text available via subscription   (Followers: 2)
Sciences & Technologie A : sciences exactes     Open Access  
Scientific Journal of Frontier Chemical Development     Open Access   (Followers: 2)

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Similar Journals
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Journal of Molecular Modeling
Journal Prestige (SJR): 0.36
Citation Impact (citeScore): 1
Number of Followers: 5  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 0948-5023 - ISSN (Online) 1610-2940
Published by Springer-Verlag Homepage  [2469 journals]
  • Molecular dynamics study of the thermal behavior of ammonia refrigerant in
           the presence of copper nanoparticles at different volume ratios and
           initial temperatures

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      Abstract: Generally, the addition of nanoparticles to a fluid significantly increases the thermal conductivity of structures. In the present study, the effect of nanoparticle volume ratio and initial temperature on ammonia/copper nano-refrigerant’s thermal behavior in an external electric field in an aluminum nanochannel was studied by molecular dynamics simulations. To study the thermal behavior of the structures, quantities such as particle phase-changed rates (condensation process), phase change duration, and thermal conductivity were investigated. Results show that with the addition of 5% copper to the base fluid, the rate of the phase-changed particles increases from 53 to 71% during 2.40 ns. Also, increasing the volume ratio of nanoparticles up to 5% leads to an increase in thermal conductivity from 0.76 to 0.86 W/mK. On the other hand, increasing the initial temperature up to 350 K reduces the phase-changed particles’ rate from 53 to 49% during 2.9 ns. The initial temperature increases from 300 to 350 K, and the thermal conductivity decreases from 0.76 to 0.73 W/mK. The results of this simulation are expected to improve the thermal performance of different nano-refrigerants.
      PubDate: 2022-05-19
       
  • Simultaneous catalytic oxidation of elemental mercury and arsine over
           CeO2(111) surface: a density functional theory study

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      Abstract:   Ceria (CeO2)–based materials are potential catalysts for the removal of the Hg0 and AsH3 present in reducing atmospheres. However, theoretical studies investigating the Hg0 and AsH3 removal capacity of ceria remain limited. In this study, the adsorption behavior and mechanistic pathways for the catalytic oxidation of Hg0 and AsH3 on the CeO2(111) surface, including the calculation of optimized adsorption configurations and energies, were investigated using density functional theory calculations. The results suggest that Hg0 and AsH3 are favorably adsorbed on the CeO2(111) surface, whereas CO is not, which is crucial for selective removal when CO is a desirable gas component. Furthermore, AsH3 is adsorbed more favorably than Hg0. In addition, the calculations revealed that the Hg atom is initially adsorbed on the surface and then oxidized by lattice oxygen to form HgO. Concerning AsH3 decomposition, the stepwise dehydrogenation of AsH3 followed by bonding with lattice O atoms to form the As-O bond seems the most plausible. Finally, the adsorbed As-O bond is further forms elemental As and As2O3. Therefore, CeO2 can adsorb and remove Hg0 and AsH3, making it a promising catalyst for the simultaneous catalytic oxidation of Hg0 and AsH3 in strongly reducing off-gas. Graphical abstract
      PubDate: 2022-05-18
       
  • A DFT study on the structure activity relationship of the natural
           xanthotoxin-based pharmaceutical cocrystals

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      Abstract:     In this work, the pharmaceutical cocrystals xanthotoxin-para-aminobenzoic acid (XT-PABA) and xanthotoxin-oxalic acid (XT-OA) were systematically investigated in the gas and water phases by using the quantum chemical approach. The weak intermolecular interactions have been estimated and the O1…H4 (O1…H5) intermolecular hydrogen bond (IHB) with moderate intensity and partial covalent natures was confirmed based on the computed structural parameters, topology analysis, and reduced density gradient (RDG) isosurfaces. The electrophilic and nucleophilic reactivities of different positions associated with intermolecular interactions in XT, PABA, and OA were predicted by plotting the molecular electrostatic potential (MESP) diagrams. The calculated natural bond orbital (NBO) population analysis has quantitatively unveiled the intrinsic reason for the variations in weak intermolecular interactions within XT-PABA and XT-OA cocrystals, from the gas phase to the water phase. Besides, the frontier molecular orbitals (FMOs), Fukui function, and various global reactivity descriptors were computed to measure the chemical reactivity of all the investigated molecular systems. The XT-PABA and XT-OA cocrystals explored in this work could be regarded as valuable exemplar systems to design and synthesize the high-efficiency pharmaceutical cocrystals in the experiment. Graphical abstract
      PubDate: 2022-05-17
       
  • Insights into the value of statistical models, solvent, and relativistic
           effects for investigating Re complexes of
           2-(4′-aminophenyl)benzothiazole: a potential spectroscopic probe

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      Abstract: Cancer affects a major part of the worldwide population, and, to minimize deaths, the diagnosis in the early stages of the disease is fundamental. Thus, to improve diagnosis and treatment new potential spectroscopic probes are crucial. Benzothiazole derivates present antitumor properties and are highly selective and interact strongly with the enzyme phosphoinositide 3-kinase (PI3K), which was associated with cell proliferation and breast cancer cells. In this paper, the rhenium shielding tensors (187Re(σ)) and hydrogen and carbon chemical shifts (1H(δ) and 13C(δ)) of the Re(CO)3(NNO) complex conjugated with 2-(4′-aminophenyl)benzothiazole (ReABT) were evaluated. A statistical HCA model was used to analyze the best DFT protocol to compute σ and δ values and to evaluate the relativistic effects, both in the basis set and Hamiltonian as well as the functionals M06L or PBE0. The best protocol was applied to obtain 187Re(σ) of the ReABT complex in different environments (gas phase, solution, and in the active site of the PI3K enzyme). The results point out that 187Re(σ) values of the ReABT complex change significantly when the complex is docked in the PI3K enzyme.
      PubDate: 2022-05-17
       
  • 2D phosphorus carbide as promising anode materials for Na/K-ion batteries
           from first-principles study

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      Abstract: First-principles calculations based on density functional theory were used to investigate the electrochemical performance of monolayer γ-PC for Na- and K-ion batteries. Molecular dynamics simulations indicate that the monolayer γ-PC have the thermal and dynamic stability. A substantial charge transfer from the Na/K atoms to the γ-PC sheet enhances the electrical conductivity of γ-PC. The results show that the adsorption energies of Na and K are 1.53 eV and 2.04 eV, respectively, which are much higher than Na/K bulk cohesive energy and sufficiently ensure stability and safety. Additionally, the low diffusion barriers on γ-PC monolayer are 0.034 eV for Na and 0.027 eV for K, indicating excellent rate performance. The γ-PC sheet has a high theoretical capacity for both Na (519.9 mAh/g) and K (326.6 mAh/g) ion batteries, which can satisfy the requirement of energy storage devices to anode materials. Our results strongly suggest that 2D γ-PC monolayer is an exceedingly promising anode material for both NIBs and KIBs with high adsorption energies, high capacity, and low diffusion barriers.
      PubDate: 2022-05-16
       
  • Repurposing the natural compounds as potential therapeutic agents for
           COVID-19 based on the molecular docking study of the main protease and the
           receptor-binding domain of spike protein

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      Abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV-2) enters the cell by interacting with the human angiotensin-converting enzyme 2 (ACE2) receptor through the receptor-binding domain (RBD) of spike (S) protein. In the cell, the viral 3-chymotrypsin-like cysteine protease (3CLpro) enzyme is essential for its life cycle and controls coronavirus replication. Therefore, the S-RBD and 3CLpro are hot targets for drug discovery against SARS-CoV-2. This study was to identify repurposing drugs using in silico screening, docking, and molecular dynamics simulation. The study identified bentiamine, folic acid, benfotiamine, and vitamin B12 against the RBD of S protein and bentiamine, folic acid, fursultiamine, and riboflavin to 3CLpro. The strong and stable binding of these safe and cheap vitamins at the important residues (R403, K417, Y449, Y453, N501, and Y505) in the S-protein–ACE2 interface and 3CLpro binding site residues especially active site residues (His 41 and Cys 145), indicating that they could be valuable repurpose drugs for inhibiting SARS-CoV-2 entry into the host and replication.
      PubDate: 2022-05-16
       
  • Magnesium oxide nanotube as a promising material for detection of
           methamphetamine drug: theoretical study

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      Abstract: Owing to the negative impacts of abusing illegal drugs like methamphetamine (MAF), their detection and control are of paramount importance. Therefore, it is very critical to determine MAF in biological samples. The current research study investigated the sensing interaction of inherent and MgO nanotubes (MgONT) toward MAF via density functional theory computations. We determined that the MgONT has a sensing response of 283.31, and it remarkably improves the reactivity toward MAF. The levels of energy for the highest occupied and the lowest unoccupied molecular orbitals have changed to a great extent, thereby reducing bandgap (Eg) values which increased electrical conductivity. Furthermore, a short recovery time (~ 28.65 ms) has been anticipated for MAF desorption from the MgONT exterior. This piece of research showed that MgONT might be a possible electronic sensor and an appropriate choice to deliver MAF in biological samples.
      PubDate: 2022-05-14
       
  • Molecular dynamics simulations of structure and dynamics in aqueous
           solution of neutral and ionized derivatives of poly(F): methyl, n-propyl,
           and isopropyl substitutions

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      Abstract: Chain dimensions, intermolecular structure and hydration of a series of uncharged and cationic poly(vinyl amine) [PVAm] linear polymers having hydrophobic substituent methyl, n-propyl, and isopropyl in the monomer are studied in aqueous solution by molecular dynamics simulations. A conformational transition occurs in the degree of ionization, α, range 0.3 to 0.4. Among the polymers studied, isopropyl substituted PVAm is most hydrophobic and methyl substituted PVAm is the least. The extent of hydrophobicity of the chemical structure is directly correlated to the size of the polymer chain. Conformational dynamics become slower with increase in the degree of charge of the chain and with the size of the substituent side group. The significant hydration of the polymers takes place for 0 ≤ α ≤ 0.5. While the number of H-bonds is not affected significantly by the chemical structure of the chain the relaxation dynamics of polymer-water H-bonds is significantly affected, with the more hydrophobic polymer showing the slowest dynamics. The steric hindrance provided by the hydrophobic substituent groups is responsible for slowing of water orientation dynamics in the vicinity of the polymer. The counter-ion condensation is clearly better and the bound water content is less for the relatively more hydrophobic polymer. The overall behavior of structure and dynamics is in qualitative agreement with that known for other types of polyelectrolytes and solutes in aqueous solution. Graphical abstract
      PubDate: 2022-05-14
       
  • Electronic sensors for alkali and alkaline earth cations based on
           Fullerene-C60 and silicon doped on C60 nanocages: a computational study

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      Abstract: In this research, we have reported the electrical sensitivity of pristine C60 and silicon doped on C60 (SiC59) nanocages as sensors that can be used for detecting the presence of alkali (Li+, Na+, K+) and alkaline earth (Be2+, Mg2+, Ca2+) cations. The computations are carried out at the B3LYP level of theory with a 6-31G(d) basis set. The atoms in molecules (AIM) and natural bond orbital (NBO) analyses are performed to evaluate the intermolecular interactions between cations and nanocages. The physical properties of the selected complexes are also analyzed by the frontier molecular orbital, energy gap, electronegativity, chemical hardness, softness, and other quantities such as work function, number of transferred electron, and dipole moment. The results show that the adsorption process is exothermic and with increasing the charge of cations, the adsorption energies enhance. Our findings also reveal a decrease in the energy gap along with an increase in the electrical conductivity of the respective complexes. Finally, the density of state calculations is presented to confirm the obtained results.
      PubDate: 2022-05-13
       
  • Theoretical insights into effect of surface composition of Pt-Ru
           bimetallic catalysts on CH3OH oxidation: mechanistic considerations

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      Abstract: A deeper mechanistic understanding on CH3OH oxidation on Pt-Ru alloys with different Ru surface compositions is provided by DFT-based theoretical studies in this paper. The present results show that alloying and surface compositions of Ru can change CH3OH oxidation pathway and activity. The optimal surface composition of Ru is speculated to be ca. 50% since the higher Ru surface composition can lead to formation of carbonaceous species that can poison surface. Our present calculated Ru surface composition of ca. 50% exhibits excellent consistency with experimental studies. The origin of enhanced catalytic activity of Pt-Ru alloys is determined. The significantly decreased surface work functions after alloying suggest more electrons are transferred into adsorbates. The calculated lower electrode potentials after alloying imply that lower overpotentials are required for CH3OH oxidation. The excellent consistency with experimental study on decreased onset potentials after alloying further confirms accuracy of our present calculated results. It is hoped that a systematic understanding of the atomic- and molecular-level processes on CH3OH oxidation mechanisms on Pt-Ru alloys will result in the ultimate goal of the explanation of origin of enhanced electrocatalytic activity and design of improved Pt-based alloy electrocatalysts for DMFCs. Graphical
      PubDate: 2022-05-13
       
  • The interaction between H and CH3 of adsorption on the diamond
           (100)-2 × 1 surface based on DFT Calculations

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      Abstract: In this research, the interaction mechanism between H and CH3 of chemisorption on diamond (100)-2 × 1 surface was studied through the density functional theory (DFT) method. The H or CH3 adsorbates were assumed to be directly chemisorbed to the final position on the surface in thermodynamic studies. The adsorption energies of individual H and CH3 chemisorbed on the diamond surface were calculated, respectively. Subsequently, the adsorption energies for another H or CH3 in five different positions adjacent to the initial H or CH3 were calculated and compared. We find the universal law of the most likely chemisorption position. The results revealed that when one carbon atom of the dimer chemisorbed one radical, the other carbon atom of the dimer generated a dangling bond and had more ability to chemisorb other radicals. Therefore, the growth rate is faster along the direction of the carbon dimer than in other directions during the growth of the diamond film. The dimer is exactly towards the [110] direction. As films thicken, diamond tends to grow along the [110] direction. Therefore, it could explain that the [110] texture appears easily in the experiment. And, the results can be used to analyze the detailed process relative to the growth of the diamond film.
      PubDate: 2022-05-12
       
  • DFT exploration of adsorptive performances of borophene to small
           sulfur-containing gases

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      Abstract: Density functional theory (DFT) calculations were applied to study the ability of B36 to adsorb H2S, SO2, SO3, CH3SH, (CH3)2S, and C4H4S gases. Several exchange–correlation including B97D, PBE, B3LYP, M062X, and WB97XD were utilized to evaluate adsorption energies. The initial results showed that boundary boron atoms are the most appropriate interaction sites. The adsorption energies, electron density, electron localized function, and differential charge density plots confirmed the formation of chemical covalent bonds only between SOx and B36. The results of thermochemistry analysis revealed the exothermic nature of the adsorption of sulfur-containing gases on B36; the highest values of ∆H298 were found for SO3/B36 and SO2/B36 systems. The electronic absorption spectra and DOS of B36 did not exhibit significant variations after gases adsorption, while the modeled CD spectra showed a remarkable change in the case of the SOx/B36 system. Accordingly, B36 is not suggested for detecting the studied gases. The effect of imposing mono vacancy defect and external electric field to the adsorption of titled gases on the sorbent showed, while the former did not affect the adsorption energies significantly the later improved the adsorption of gas molecules on the B36 system. The results of the current study could provide deeper molecular insight on the removal of SOx gases by B36 system. Graphical abstract
      PubDate: 2022-05-12
       
  • Virtual screening of PEBP1 inhibitors by combining 2D/3D-QSAR analysis,
           hologram QSAR, homology modeling, molecular docking analysis, and
           molecular dynamic simulations

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      Abstract: Human phosphatidylethanolamine binding protein 1 (hPEBP1) is a novel target affecting many cellular signaling pathways involved in the formation of metastases. It can be used in the treatment of many cases of cancer. For these reasons, pharmaceutical companies use computational approaches, including multi-QSAR (2D, 3D, and hologram QSAR) analysis, homology modeling, molecular docking analysis, and molecular dynamic simulations, to speed up the drug discovery process. In this paper, QSAR modeling was conducted using two quantum chemistry optimization methods (AM1 and DFT levels). As per PLS results, we found that the DFT/B3LYP method presents high predictability according to 2D-QSAR, CoMFA, CoMSIA, and hologram QSAR studies, with Q2 of 0.81, 0.67, 0.79, and 0.67, and external power with R2pred of 0.78, 0.58, 0.66, and 0.56, respectively. This result has been validated by CoMFA/CoMSIA graphics, which suggests that electrostatic fields combined with hydrogen bond donor/acceptor fields are beneficial to the antiproliferative activity. While the hologram QSAR models show the contributions of each fragment in improving the activity. The results from QSAR analyses revealed that ursolic acids with heterocyclic rings could improve the activities. Ramachandran plot validated the modeled PEBP1 protein. Molecular docking and MD simulations revealed that the hydrophobic and hydrogen bond interactions are dominant in the PEBP1’s pocket. These results were used to predict in silico structures of three new compounds with potential anticancer activity. Similar molecular docking stability studies and molecular dynamics simulations were conducted. Graphical abstract
      PubDate: 2022-05-12
       
  • Indole alkaloids as potential candidates against COVID-19: an in silico
           study

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      Abstract: COVID-19 has recently grown to be pandemic all around the world. Therefore, efforts to find effective drugs for the treatment of COVID-19 are needed to improve humans’ life quality and survival. Since the main protease (Mpro) of SARS-CoV-2 plays a crucial role in viral replication and transcription, the inhibition of this enzyme could be a promising and challenging therapeutic target to fight COVID-19. The present study aims to identify alkaloid compounds as new potential inhibitors for SARS-CoV-2 Mpro by the hybrid modeling analyses. The docking-based virtual screening method assessed a collection of alkaloids extracted from over 500 medicinal plants and sponges. In order to validate the docking process, classical molecular dynamic simulations were applied on selected ligands, and the calculation of binding free energy was performed. Based on the proper interactions with the active site of the SARS-CoV-2 Mpro, low binding energy, few side effects, and the availability in the medicinal market, two indole alkaloids were found to be potential lead compounds that may serve as therapeutic options to treat COVID-19. This study paves the way for developing natural alkaloids as stronger potent antiviral agents against the SARS-CoV-2.
      PubDate: 2022-05-11
       
  • Determination of elastic constants of functionalized graphene-based epoxy
           nanocomposites: a molecular modeling and MD simulation study

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      Abstract: Functionalization of graphene is the best way to create a high degree of dispersion and bonding to polymer matrix in order to obtain high performance composites. The effects of carboxyl (−COOH) functionalized graphene (FG) on the mechanical properties of its epoxy-based nanocomposites have been examined by molecular dynamics (MD) simulations. Simulations cells of nanocomposites with varying wt% of FG (1, 2, and 3 wt%) were constructed using Material Studio 6.0. The MD simulation findings of nanocomposites reveal that they have better mechanical properties such as elastic modulus, bulk modulus, shear modulus, and the Poisson’s ratio than pure epoxy. Furthermore, the computational results of nanocomposites have been effectively confirmed with available experimental data. Therefore, the current MD simulation shows a decent computational sign for the existing experimental and simulation outcomes on mechanical properties of FG/epoxy nanocomposites.
      PubDate: 2022-05-11
       
  • Rethinking the MtInhA tertiary and quaternary structure flexibility: a
           molecular dynamics view

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      Abstract: Flexibility and function are related properties in the study of protein dynamics. Flexibility reflects in the conformational potential of proteins and thus in their functionalities. The presence of interactions between protein-ligands and protein-protein complexes, substrates, and environmental changes can alter protein plasticity, acting from the rearrangement of the side chains of amino acids to the folding/unfolding of large structural motifs. To evaluate the effects of the flexibility in protein systems, we defined the enzyme 2-trans-enoyl-ACP (CoA) reductase from Mycobacterium tuberculosis, or MtInhA, as our target system. MtInhA is biologically active as a tetramer in solution; however, computational studies commonly use the monomer justifying the independence of its active sites due to their distances. However, differences in flexibility between tertiary and quaternary structures could present impact on the size of the active site, influencing the drug discovery process. In this study, we investigated the influence of flexibility restrictions in A- and B-loops of the MtInhA in order to suggest a monomeric structure that describes the conformational behavior of the tetrameric system. Overall, we observed that simulations where restrictions were applied to the A- and B-loops present a more similar behavior to the native structure when compared to unrestricted simulations. Therefore, our work presents a monomeric model of MtInhA, which has conformational characteristics of the biologically active structure. Thus, the data obtained in this work can be applied to the MtInhA system for the generation of more reliable flexible models for molecular docking experiments, and also for the performance of longer simulations by molecular dynamics and with a lower computational cost.
      PubDate: 2022-05-10
       
  • Cephalexin degradation initiated by OH radicals: theoretical prediction of
           the mechanisms and the toxicity of byproducts

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      Abstract: In this work, the density functional theory is used to study the local reactivity of cephalexin (CLX) to radical attack and explain the mechanism of the reaction between CLX and hydroxyl radical attack leading to degradation byproducts. The reaction between •OH and CLX is supposed to lead to either an addition of a hydroxyl radical or an abstraction of a hydrogen. The results showed that the affinity of cephalexin for addition reactions increases as it passes from the gas to the aqueous phase and decreases as it passes from the neutral to the ionized form. Thermodynamic data confirmed that OH addition radicals (Radd) are thermodynamically favored over H abstraction radicals (Rabs). The ecotoxicity assessments of CLX and its byproducts are estimated from the acute toxicities toward green algae, Daphnia, and fish. The formation of byproducts is safe for aquatic organisms, and only one byproduct is harmful to Daphnia. Graphical abstract
      PubDate: 2022-05-10
       
  • Integrated virtual screening and molecular dynamics simulation revealed
           promising drug candidates of p53-MDM2 interaction

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      Abstract: In the vast majority of malignancies, the p53 tumor suppressor pathway is compromised. In some cancer cells, high levels of MDM2 polyubiquitinate p53 and mark it for destruction, thereby leading to a corresponding downregulation of the protein. MDM2 interacts with p53 via its hydrophobic pocket, and chemical entities that block the dimerization of the protein–protein complex can restore p53 activity. Thus far, only a few chemical compounds have been reported as potent arsenals against p53-MDM2. The Protein Data Bank has crystallogaphic structures of MDM2 in complex with certain compounds. Herein, we have exploited one of the complexes in the identification of new p53-MDM2 antagonists using a hierarchical virtual screening technique. The initial stage was to compile a targeted library of structurally appropriate compounds related to a known effective inhibitor, Nutlin 2, from the PubChem database. The identified 57 compounds were subjected to virtual screening using molecular docking to discover inhibitors with high binding affinity for MDM2. Consequently, five compounds with higher binding affinity than the standard emerged as the most promising therapeutic candidates. When compared to Nutlin 2, four of the drug candidates (CID_140017825, CID_69844501, CID_22721108, and CID_22720965) demonstrated satisfactory pharmacokinetic and pharmacodynamic profiles. Finally, MD simulation of the dynamic behavior of lead-protein complexes reveals the stability of the complexes after a 100,000 ps simulation period. In particular, when compared to the other three leads, overall computational modeling found CID_140017825 to be the best pharmacological candidate. Following thorough experimental trials, it may emerge as a promising chemical entity for cancer therapy.
      PubDate: 2022-05-10
       
  • Improving 1-propanol force field: a new methodology

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      Abstract: A new force field for 1-propanol, in the united and all atom models, has been obtained by combining two different empirical methodologies. The first was developed by scaling atom charges and Lennard-Jones parameters to fit the dielectric constant, surface tension, and density; this methodology is named three steps systematic parameterization procedure (3SSPP), as reported by Pérez de la Luz et al. (J Chem Theory Comput 14:5949–5958, 2018). The second methodology consists of moving these parameters and together with the bond distance to obtain the liquid-vapor phase diagram of the CO2 molecule as discussed by Harris and Yung (J Phys Chem 99:12021–12024, 1995). The last methodology is used to obtain the self-diffusion coefficient, which was not consider in the 3SSPP. The 3SSPP/bond methodology is the 3SSPP plus the bond distance scaling. With this new methodology, the experimental density, dielectric constant, surface tension, and self-diffusion coefficient at ambient temperature could be achieved. Furthermore, we show the temperature dependence of the aforementioned properties. The static structure factors are in accordance with the experimental spectrum. Solubility is increased to the experimental value for the united atom (UA) model after applying this methodology and for all atom (AA) scheme, the experimental solubility value is maintained. Graphical abstract The reduction in bond distance of the 1-propanol molecule does not modify the structure factor.
      PubDate: 2022-05-07
       
  • Discovery of novel targets and mechanisms of MEK inhibitor Selumetinib for
           LGG treatment based on molecular docking and molecular dynamics simulation
           

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      Abstract: Based on molecular docking and molecular dynamics simulation, to find a new target and mechanism of MEK inhibitor Selumetinib in the treatment of low-grade glioma (LGG), and to provide theoretical guidance for its clinical medication. All possible targets of Selumetinib were fished through the compound target prediction database. New targets of Selumetinib in the treatment of LGG were found and its mechanism was evaluated employing molecular docking, gene difference analysis, molecular dynamics simulation, and protein subcellular localization prediction. A total of 100 Selumetinib targets and 85 LGG-related targets were screened in this study. There were 7 active targets at the intersection of the two. Through protein interaction (PPI), gene enrichment analysis, and gene difference analysis, one effective target of Selumetinib was finally screened, CDK2 mainly existing in the cytoplasm, endoplasmic reticulum, and plasma membrane; the target plays a role in the treatment of LGG by inhibiting the signal pathways of PI3K Akt and participating in biological processes such as peptide amino acid modification, regulation of intracellular signal transduction, and positive regulation of cell metabolism. CDK2 may be a new direction of Selumetinib in the clinical treatment of LGG.
      PubDate: 2022-05-06
       
 
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