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The interaction of hydrogen with heteroatoms (B, N)-doped porous graphene: A computational study

CHEMICAL PAPERS 2022年第2期76卷 1009-1017页

作者： Chan, Chen-Wei Wu, Shiuan-Yau Chen, Hsin-Tsung Chung Yuan Christian Univ Dept Chem Taoyuan 32023 Taiwan

Based on first-principles computations, the adsorption ability of hydrogen on heteroatom (B, N)-doped porous graphene has been illustrated. It is found that the adsorption energy (- 0.117 similar to - 0.173 eV) of hydrogen on heteroatom (B, N)-doped porous graphene meets the optimal adsorption energy (- 0.1 similar to - 0.2 eV) on high-performance adsorbent, indicating that the porosity and heteroatom dopant would be the important role for the H-2 adsorption. In addition, the interaction is found to be enhanced by applying positive and negative charges into the system. More important, we demonstrate that the adsorption energy can be dramatically increased to - 0.738 eV on the B-doped porous graphene with one positive charge. The H-2 adsorption/desorption process on the positively charged B-doped porous graphene is spontaneous, reversible, and readily controlled by injecting/removing the additional positive charge. The gravimetric density is predicted to be 10.8 wt % on the positively charged B-doped porous graphene. Graphic abstract Based on density functional theory computations, we investigate the adsorption ability of hydrogen on heteroatom (B, N)-doped porous graphene. Calculation results show that the H-2 adsorption/desorption process on the positively charged B-doped porous graphene is spontaneous and reversible with fast kinetics and readily controlled by the adding/removing the additional positive charge.

关键词： Heteroatom-doped porous graphene Hydrogen adsorption Hydrogen storage capacity computational study

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A computational study on bounding the makespan distribution in stochastic project networks

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ANNALS OF OPERATIONS RESEARCH 2001年第1-4期102卷 49-64页

作者： Ludwig, A Möhring, RH Stork, F Tech Univ Berlin Fak Math & Nat Wissensch 2 Inst Math D-10623 Berlin Germany Lufthansa Syst Berlin GmbH D-10585 Berlin Germany

Due to the practical importance of stochastic project networks (PERT-networks), many methods have been developed over the past decades in order to obtain information about the random project completion time. Of particular interest a-re methods that provide (lower and upper) bounds for its distribution, since these aim at balancing efficiency of calculation with accuracy of the obtained information. We provide a thorough computational evaluation of the most promising of these bounding algorithms with the aim to test their suitability for practical applications both in terms of efficiency and quality. To this end, we have implemented these algorithms and compare their behavior on a basis of nearly 2000 instances with up to 1200 activities of different test-sets. These implementations are based on a suitable numerical representation of distributions which is the basis for excellent computational results. Particularly a distribution-free heuristic based on the Central Limit Theorem provides an excellent tool to evaluate stochastic project networks.

关键词： PERT networks bounding procedures computational study

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Synthesis, Biological Evaluation, and computational study of Novel 1,2,3-Triazole-Tethered Chalcone Derivatives

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RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2024年第9期60卷 1730-1743页

作者： Kawale, R. A. Shaikh, M. H. Akolkar, H. N. Khedkar, V. M. Raut, D. N. Shelke, S. N. Arts Sci & Commerce Coll Mokhada Dept Chem Palghat 401604 Maharashtra India Radhabai Kale Mahila Mahavidyalaya Dept Chem Ahmednagar 414001 Maharashtra India Abasaheb Marathe Arts & New Commerce Sci Coll Raja Dept Chem Ratnagiri 416702 Maharashtra India Vishwakarma Univ Sch Pharm Pune 411048 Maharashtra India Amrutvahini Coll Pharm Sangamner 422605 Maharashtra India RB Narayanrao Borawake Coll Dept Chem Shrirampur 413709 Maharashtra India

In search of novel anti-inflammatory and antioxidant agents with improved potency, a small focused library of 1,2,3-triazole-based chalcone derivatives has been efficiently prepared via the click chemistry approach. All synthesized compounds' Structures were characterized with the help of IR, H-1 NMR, C-13 NMR, and mass spectroscopic techniques. All the synthesized novel derivatives were evaluated for their anti-inflammatory activity. Molecular docking studies against COX-2 gave valuable insights into the mechanistic basis of the demonstrated anti-inflammatory activity. Further, the synthesized compounds were found to have potential antioxidant activity.

关键词： 1,2,3-triazoles molecular docking anti-inflammatory activity antioxidant activity chalcone computational study

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Favipiravir: insight into the crystal structure, Hirshfeld surface analysis and computational study

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JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022年第1期19卷 85-94页

作者： Babashkina, Maria G. Frontera, Antonio Kertman, Alexander, V Saygideger, Yasemin Murugavel, Swaminathan Safin, Damir A. Catholic Univ Louvain Inst Condensed Matter & Nanosci Pl L Pasteur 1 B-1348 Louvain La Neuve Belgium Univ Illes Balears Dept Quim Crta Valldemossa Km 7-5 Palma De Mallorca 07122 Baleares Spain Univ Tyumen Volodarskogo Str 6 Tyumen 625003 Russia Cukurova Univ Inst Nat & Appl Sci Dept Biotechnol Adana Turkey Cukurova Univ Sch Med Dept Pulm Adana Turkey Thanthai Periyar Govt Inst Technol Dept Phys Vellore 632002 Tamil Nadu India Kurgan State Univ Sovetskaya Str 63-4 Kurgan 640020 Russia Ural Fed Univ Innovat Ctr Chem & Pharmaceut Technol Mira Str 19 Ekaterinburg 620002 Russia

In this work we report structural and computational studies of favipiravir, which is now used as a drug for COVID-19 treatment. The molecule is completely flat and stabilized by an intramolecular O-H center dot center dot center dot O hydrogen bond, yielding a six-membered pseudo-aromatic ring. The aromaticity index of this pseudo-aromatic ring was found to be 0.748, while the same indix for the pyrazine ring in favipiravir was found to be 0.954. The crystal packing of favipiravir is mainly constructed through intermolecular N-H center dot center dot center dot O, N-H center dot center dot center dot N and C-H center dot center dot center dot O hydrogen bonds, yielding a 3D supramolecular framework with a zst topology defined by the point symbol of (6(5)center dot 8). The crystal structure of favipiravir is further stabilized by weak C-F center dot center dot center dot F-C intermolecular type II dihalogen interactions, yielding a 1D supramolecular polymeric chain. More than 80% of the total Hirshfeld surface area for favipiravir is occupied by H center dot center dot center dot H/C/N/O/F and C center dot center dot center dot N/O contacts. Energy frameworks have been calculated to additionally analyze the overall crystal packing. It was established that the structure of favipiravir is mainly characterized by the dispersion energy framework followed by the less significant electrostatic energy framework contribution. Finally, by using density functional theory (DFT) calculations and the quantum theory of atoms in molecules, we have assigned the interaction energy of each hydrogen bond, which can be helpful to develop scoring functions to be used in force fields/docking calculations.

关键词： Favipiravir Crystal structure Hirshfeld surface analysis computational study DFT

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A Hartree-Fock, MP2 and DFT computational study of the structures and energies of "b₂ ions derived from deprotonated peptides.: A comparison of method and basis set used on relative product stabilities

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JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 2004年第1-3期675卷 149-162页

作者： Chass, GA Marai, CNJ Setiadi, DH Csizmadia, IG Harrison, AG Univ Toronto Dept Chem Toronto ON M5S 3H6 Canada Global Inst Computat Mol & Mat Sci GIOCOMMS Toronto ON Canada CEA Saclay DSM DRECAM Serv PhotonCNRSURA 2453Lab Francis Perrin F-91191 Gif Sur Yvette France Univ Szeged Dept Med Chem H-6720 Szeged Hungary

A detailed computational study of possible "b(2) ion structures derived by nominal elimination of neutral glycine from deprotonated triglycine along with the structures and energies of the corresponding neutrals has been carried out. These computations of structures and energies have been carried out at the RHF/3-21G, RHF/6-31G(d), B3LYP/6-31G(d), B3LYP/6-31+G(d), MP2(fc)/6-31G(d) and MP2(fc)/6-31+G(d) levels of theory. With the exception of the RHF/3-21G level of theory, all levels gave structures and relative energies of both neutrals and anions, which were in agreement within the expected uncertainty. However, the gas-phase acidities calculated with inclusion of diffuse functions, as in the zero-point coorected B3LYP/6-31+G(d) and MP2/6-31+G(d) levels, were 12-15 kcal mol(-1) lower than those calculated without inclusion of diffuse functions. The inclusion of diffuse functions lowers the absolute energies of both neutrals and anions but has a considerably greater effect on the anions. Nine possible stable structures for "b(2) ions have been identified. Of these, five are of relatively low energy and are candidate structures for the ions formed in the fragmentation of deprotonated peptides. Possible pathways, as suggested by experimental studies, to the various computed anion structures are discussed. (C) 2004 Elsevier B.V. All rights reserved.

关键词： collisional-activation computational study deprotonated peptides

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Synthesis, computational study and cytotoxicity of 4-hydroxycoumarin-derived imines/enamines

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MOLECULAR DIVERSITY 2021年第2期25卷 1011-1024页

作者： Vaseghi, Samaneh Yousefi, Mohammad Shokrzadeh, Mohammad Hossaini, Zinatossadat Hosseini-khah, Zahra Emami, Saeed Islamic Azad Univ Dept Chem Sci & Res Branch Tehran Iran Islamic Azad Univ Dept Chem Yadegar e Imam Khomeini Shahr e Rey Branch Tehran Iran Mazandaran Univ Med Sci Fac Pharm Dept Toxicol & Pharmacol Sari Iran Islamic Azad Univ Dept Chem Qaemshahr Branch Qaemshahr Iran Mazandaran Univ Med Sci Diabet Res Ctr Sari Iran Mazandaran Univ Med Sci Fac Pharm Dept Med Chem & Pharmaceut Sci Res Ctr Sari Iran

In this study, we applied a direct condensation between 3-acetyl-4-hydroxy-2H-chromen-2-one and different amines (anilines and benzyl amines) in order to synthesize some coumarin-based imines/enamines (3a-o) as cytotoxic agents. All the compounds were characterized by means of FT-IR, NMR, mass spectroscopy and elemental analyses. Since the title compounds can exist as different forms including (s-cis)-imine and (s-trans)-imine or (E and Z)-enamines, their conformational and geometrical aspects were investigated computationally by DFT method. The optimized geometry parameters, Delta E, Delta G, Delta H, Mulliken atomic charge, HOMO and LUMO energy, and NBO analysis suggested that these compounds can exist predominantly in (E)-enamine form. All the synthesized compounds (3a-o) were evaluated in vitro for their cytotoxic activities against cancer cell lines (MCF-7 and A549) and normal cell line (BEAS-2B) using the MTT assay. The 4-hydroxybenzyl derivative 3k was found to be the most potent cytotoxic agent with no selectivity, similar to doxorubicin. However, the 4-chlorobenzyl analog 3o could be considered as an equipotent compound respect to doxorubicin with higher selectivity. Graphic abstract

关键词： Anticancer 2H-chromen-2-one Coumarin Schiff bases computational study DFT

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Ambroxol: Insight into the Crystal Structure, Hirshfeld Surface Analysis and computational study

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POLYCYCLIC AROMATIC COMPOUNDS 2023年第3期43卷 2599-2617页

作者： Alkhimova, Larisa E. Sharov, Artem, V Burkhanova, Tatyana M. Babashkina, Maria G. Safin, Damir A. Kurgan State Univ Adv Mat Ind & Biomed Lab Sovetskaya Str 63-4 Kurgan 640020 Russia Univ Tyumen Tyumen Russia Ural Fed Univ Innovat Ctr Chem & Pharmaceut Technol Ekaterinburg Russia Catholic Univ Louvain Inst Condensed Matter & Nanosci Louvain La Neuve Belgium

We report detailed studies of Form II of ambroxol, which crystal packing was examined in detail by a Hirshfeld surface analysis. Molecules in the crystal structure are primarily linked through the N-H center dot center dot center dot N and O-H center dot center dot center dot O hydrogen bonds and C-Br center dot center dot center dot pi interactions. The Hirshfeld molecular surface is characterized by intermolecular contacts H center dot center dot center dot X (X = H, C, N, O, Br) and C/O/Br center dot center dot center dot Br. The overall topology of the energy distributions in the crystal structure of Form II of ambroxol was also established. The structure is mainly characterized by the dispersion interactions. The title compound was further studied by IR and UV-vis spectroscopy. Intermolecular N-H center dot center dot center dot N and O-H center dot center dot center dot O hydrogen bonds dictate the clearly revealed discrepancies between the experimental and calculated IR spectra in the region of 3000-4000 cm(-1). The DFT/B3LYP/6-311++G(d,p) calculations were performed to verify the structure of Form II of ambroxol as well as its electronic and optical properties. Molecular docking was applied to examine the influence of ambroxol on a series of the SARS-CoV-2 proteins. The molecule of ambroxol interacts much more efficiently with a series of studied proteins in comparison to Favipiravir, showing the best binding affinity with RdRp-RNA and nsp14 (N7-MTase).

关键词： Ambroxol crystal structure Hirshfeld surface analysis computational study DFT molecular docking

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Transition states of the gold-catalyzed transannular [4+3] cycloaddition reactions: A computational study

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TETRAHEDRON 2020年第3期76卷 130840-000页

作者： Ma, Ruoyu Gung, Benjamin W. Miami Univ Dept Chem & Biochem Oxford OH 45056 USA

The transition state structures for the gold-catalyzed transannular [4 + 3] cycloaddition reaction are located for two distinct mechanisms at the B3LYP/6-31G(d) level of theory. A direct [4 + 3] cycloaddition pathway is found to be favored over the step-wise cyclopropanation-Cope rearrangement pathway. In the former, partial bonding are apparent between the furan ring and the gold-stabilized allylic carbocation. The gold atom bearing the N-heterocyclic carbene ligand is bonded to the allylic system located near the center carbon. The acetate group, which is attached to C1 of the allylic carbocation, is anti to the gold atom. The C-Au distance in this transition state is 2.06 angstrom. The forming bonds between the furan ring and the allylic carbocation are 1.66 and 2.0 angstrom, respectively, indicating an asynchronous process. The calculated second pathway starts with a gold carbenoid intermediate, which must overcome two higher energy transition states in order to reach the same reaction product. (C) 2019 Elsevier Ltd. All rights reserved.

关键词： Cycloaddition Gold-catalyzed computational study

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Mercuration and Telluration of 2-Fluoro-5-nitroaniline: Synthesis, Antibacterial, and computational study

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RUSSIAN JOURNAL OF GENERAL CHEMISTRY 2020年第4期90卷 703-709页

作者： Al-Asadi, R. H. Mohammed, M. K. Dhaef, H. K. Basrah Univ Coll Educ Pure Sci Dept Chem Basrah 61004 Iraq

New derivatives of organotellurium and organomercury compounds have been synthesized in the reaction of 2-fluoro-5-nitroaniline with mercuric acetate and further with tellurium(IV) tetrabromide. Reaction of (4-amino-5-fluoro-2-nitrophenyl)tellurium(IV) tribromide with 4-hydroxyphenyl mercury(II) chloride gives asymmetrical diaryltellurium(IV) dibromide, whereas reaction of (4-amino-5-fluoro-2-nitrophenyl)mercury(II) chloride with phenol and 4-hydroxy benzaldehyde produces a new aryl mercury(II) chloride that contains the azomethine and azo groups. Reaction of aryl mercury(II) chloride with tellurium(IV) tetrabromide results in aryaltellurium(IV) tribromide furnished by the azomethine and azo groups. Reduction of unsymmetrical diaryltellurium(IV) dibromide and aryltellurium(IV) tribromide by hydrazine hydrate leads to the corresponding asymmetrical diaryltelluride and diarylditelluride. Structures of the new synthesized compounds are supported by FT-IR and(1)H NMR spectra. Anti-bacterial activity of the new products has been tested againstKlebsiella pneumonia Proteus,Escherichia coli,Pseudomonas spp., andStaphylococcus aureus. The compounds are characterized as highly active. The molecular structure level and energies of compounds have been computed through the Density Functional Theory (DFT).

关键词： organotellurium organomercury antibacterial computational study

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Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study

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JOURNAL OF MOLECULAR MODELING 2013年第11期19卷 4669-4680页

作者： Bradac, Ondrej Zimmermann, Tomas Burda, Jaroslav V. Charles Univ Prague Fac Math & Phys Dept Chem Phys & Opt CR-12116 Prague 2 Czech Republic

Hydration reactions of two anticancer Pt(IV) complexes JM149 and JM216 (Satraplatin) were studied computationally together with the hydration of the Pt(II) complex JM118, which is a product of the Satraplatin reduction. Thermodynamic and kinetic parameters of the reactions were determined at the B3LYP/6-311++G(2df.2pd)//B3LYP/6-31 + G(d)) level of theory. The water solution was modeled using the COSMO implicit solvation model, with cavities constructed using Klamt's atomic radii. It was found that hydration of the Pt(IV) complexes is an endergonic/endothermic reaction. It follows the (pseudo)associative mechanism is substantially slower (k a parts per thousand aEuro parts per thousand 10(-11) s(-1)) than the corresponding reaction of Pt(II) analogues ((k a parts per thousand aEuro parts per thousand 10(-5) s(-1)). Such a low value of the reaction constant signifies that the hydration of JM149 and Satraplatin is with high probability a kinetically forbidden reaction. Similarly to JM149 and Satraplatin, the hydration of JM118 is an endothermic/endoergic reaction. On the other hand, the kinetic parameters are similar to those of cisplatin Zimmermann et al. (J Mol Model 17:2385-2393, 2011), allowing the hydration reaction to occur at physiological conditions. These results suggest that in order to become active Satraplatin has to be first reduced to JM118, which may be subsequently hydrated to yield the active species.

关键词： Platinum metallodrugs computational study DFT Thermodynamics Rate constants

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