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1.
Masoud Darvish Ganji Mahnaz Nashtahosseini Saeed Yeganegi Mahyar Rezvani 《Journal of molecular modeling》2013,19(4):1929-1936
The interaction between oxazepam and C60 fullerene was explored using first-principles vdW-DF calculations. It was found that oxazepam binds weakly to the fullerene cage via its carbonyl group. The binding of oxazepam to C60 is affected drastically by nonlocal dispersion interactions, while vdW forces affect the corresponding geometries only a little. Furthermore, aqueous solution affects the geometries of the oxazepam approaching to fullerene slightly, while oxazepam binds slightly farther away from the nanocage. The results presented provide evidence for the applicability of the vdW-DF method and serve as a practical benchmark for the investigation of host–guest interactions in biological systems. Figure
ab initio vdW-DF study on the possibility of formation of oxazepam/C60 complex at aqueous solution 相似文献
2.
Hoi Lym Kwon Jae-Ho Kim Dong Hee Na Dae Heung Byeun Ying Wu Si Wouk Kim Eon Seon Jin Hoon Cho 《Biotechnology and Bioprocess Engineering》2013,18(5):932-941
A series of naphthoquinone-benzothiazole conjugates were synthesized as algicides, and their efficacies against harmful algal blooming species, such as Chattonella marina, Heterosigma akashiwo and Cochlodinium polykrikoides, were examined. The introduction of substituted benzothiazole at the C2 position of 1,4-naphthoquinone (compounds 1–9) resulted in higher algicidal activity against C. polykrikoides than the C6 conjugates (compounds 10–20). On the other hand, of the C6 conjugates, compounds 11 and 12 exhibited better algicidal activity against H. akashiwo, C. marina, and C. polykrikoides than the C2 conjugates. Further structure-activity analysis indicated that a replacement of the methoxy groups with hydroxyl groups (compounds 21–26) decreased the algicidal activity significantly. Among the various synthetic naphthoquinonebezothiazole conjugates tested, compound 12 was found to affect the most significant decrease in the level of C. polykrikoides growth, with an IC50 of 0.19 μM. Compound 11 was found to be the most potent inhibitor against H. akashiwo and C. polykrikoides, with IC50 values of 0.32 and 0.12 μM, respectively. Overall, these results highlight a possible method for controlling and inhibiting red tide forming algae using NQ derivatives. 相似文献
3.
Qi Liang Lu Wen Jun Song Jun Wei Meng Jian Guo Wan 《Journal of molecular modeling》2013,19(3):1205-1209
The possibility of a new endohedral fullerene with a trapped aluminum carbide cluster, Al4C @C80-I h , was theoretical investigated. The geometries and electronic properties of it were investigated using density functional theory methods. The Al4C unit formally transfers six electrons to the C80 cage which induces stabilization of Al4C@C80. A favorable binding energy, relatively large HOMO-LUMO gap, electron affinities and ionization potentials suggested the Al4C@C80 is rather stable. The analysis of vertical ionization potential and vertical electron affinity indicate Al4C@C80 is a good electron acceptor. Figure
An endohedral fullerene with a trapped aluminum carbide cluster, Al4C @C80-I h , was investigated using density functional theory. A favorable binding energy, relatively large HOMO-LUMO gap, electron affinities and ionization potentials suggested it is rather stable 相似文献
4.
The interaction between lanthanum atom (La) and C74 (D 3h) was investigated by all-electron relativistic density function theory (DFT). With the aid of the representative patch of C74 (D 3h), we studied the interaction between C74 (D 3h) and La and obtained the interaction potential. Optimized structures show that there are three equivalent stable isomers, with La located about 1.7 Å off center. There is one transition state between every two stable isomers. According to the minimum energy pathway, the possible movement trajectory of La atoms in the C74 (D 3h) cage was explored. The calculated energy barrier for La atoms moving from the stable isomer to the transition state is 18.4 kcal mol?1. In addition, the dynamic NMR spectra of La@C74 according to the trajectory was calculated. Figure
Optimized structure of La@C74, the ring trajectory of La in C74, and the dynamic 13C NMR spectrum as investigated by all-electron relativistic density function theory 相似文献
5.
Qing-guo Wei Wen-jing Shi Fu-de Ren Yong Wang Jun Ren 《Journal of molecular modeling》2013,19(1):453-463
The changes of bond dissociation energy (BDE) in the C–NO2 bond and nitro group charge upon the formation of the molecule-cation interaction between Na+ and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO2 bond was enhanced in comparison with that in the isolated nitrotriazole molecule upon the formation of molecule-cation interaction. The increment of the C–NO2 bond dissociation energy (ΔBDE) correlated well with the molecule-cation interaction energy. Electron density shifts analysis showed that the electron density shifted toward the C-NO2 bond upon complex formation, leading to the strengthened C-NO2 bond and the possibly reduced explosive sensitivity. Figure
C1-N2 bond turns strong upon molecule-cation interaction formation, leading to a possibly reduced explosive sensitivity. 相似文献
6.
Lecoq L Bougault C Kern T Hugonnet JE Veckerlé C Pessey O Arthur M Simorre JP 《Biomolecular NMR assignments》2012,6(2):205-208
The d,d-transpeptidase activity of Penicillin Binding Proteins (PBPs) is essential to maintain cell wall integrity. PBPs catalyze the final step of the peptidoglycan synthesis by forming 4 → 3 cross-links between two peptide stems. Recently, a novel β-lactam resistance mechanism involving l,d-transpeptidases has been identified in Enterococcus faecium and Mycobacterium tuberculosis. In this resistance pathway, the classical 4 → 3 cross-links are replaced by 3 → 3 cross-links, whose formation are catalyzed by the l,d-transpeptidases. To date, only one class of the entire β-lactam family, the carbapenems, is able to inhibit the l,d-transpeptidase activity. Nevertheless, the specificity of this inactivation is still not understood. Hence, the study of this new transpeptidase family is of considerable interest in order to understand the mechanism of the l,d-transpeptidases inhibition by carbapenems. In this context, we present herein the backbone and side-chain 1H, 15N and 13C NMR assignment of the l,d-transpeptidase from Bacillus subtilis (LdtBs) in the apo and in the acylated form with a carbapenem, the imipenem. 相似文献
7.
Density functional theory calculations were performed to examine the effect of a C vacancy on the physisorption of H2 onto Ti-functionalized C60 fullerene when H2 is oriented along the x-, y-, and z-axes of the fullerene. The effect of the C vacancy on the physisorption modes of H2 was investigated as a function of H2 binding energy within the energy window (?0.2 to ?0.6 eV) targeted by the Department of Energy (DOE), and as functions of a variety of other physicochemical properties. The results indicate that the preferential orientations of H2 in the defect-free (i.e., no C vacancy) C60TiH2 complex are along the x- and y-axes of C60 (with adsorption energies of ?0.23 and ?0.21 eV, respectively), making these orientations the most suitable ones for hydrogen storage, in contrast to the results obtained for defect-containing fullerenes. The defect-containing (i.e., containing a C vacancy) C59TiH2 complex do not exhibit adsorption energies within the targeted energy range. Charge transfer occurs from Ti 3d to C 2p of the fullerene. The binding of H2 is dominated by the pairwise support–metal interaction energy E(i)Cn...Ti, and the role of the fullerene is not restricted to supporting the metal. The C vacancy enhances the adsorption energy of Ti, in contrast to that of H2. A significant reduction in the energy gap of the pristine C60 fullerene is observed when TiH2 is adsorbed by it. While the C n fullerene readily participates in nucleophilic processes, the adjacent TiH2 fragment is available for electrophilic processes. Figure
The effect of a C vacancy on the interaction of H2 with Ti-functionalized C60 fullerene. H2 preferentially orients itself along the x- and y-axes of C60, yielding adsorption energies in the energy window targeted by the DOE. The C vacancy enhances the adsorption energy of Ti, in contrast to that of H2. The role of fullerene is not restricted to supporting the metal. The physicochemical properties investigated in the present work characterize the H2 interaction 相似文献
8.
The reaction mechanisms involved in the scavenging of hydroxyl (OH·), methoxy (OCH3 ·), and nitrogen dioxide (NO2 ·) radicals by ellagic acid and its monomethyl and dimethyl derivatives were investigated using the transition state theory and density functional theory. The calculated Gibbs barrier energies associated with the abstraction of hydrogen from the hydroxyl groups of ellagic acid and its monomethyl and dimethyl derivatives by an OH· radical in aqueous media were all found to be negative. When NO2 · was the radical involved in hydrogen abstraction, the Gibbs barrier energies were much larger than those calculated when the OH· radical was involved. When OCH3 · was the hydrogen-abstracting radical, the Gibbs barrier energies lay between those obtained with OH· and NO2 · radicals. Therefore, the scavenging efficiencies of ellagic acid and its monomethyl and dimethyl derivatives towards the three radicals decrease in the order OH· >> OCH3 · > NO2 ·. Our calculated rate constants are broadly in agreement with those obtained experimentally for hydrogen abstraction reactions of ellagic acid with OH· and NO2· radicals. Figure
Reactant complex (RC), transition state (TS), and product complex (PC) for hydrogen abstraction from ellagic acid by an OH· radical 相似文献
9.
10.
Maciej Roman Agnieszka Kaczor Malgorzata Baranska 《Journal of molecular modeling》2010,16(10):1549-1557
The structural and thermodynamic properties of an anthraquinone derivative were studied by means of quantum-chemical calculations. Conformational analysis using ab initio and density functional theory methods revealed 14 low-energy conformers. In order to discuss similarities and differences in entropy of the conformers, the rotational and vibrational contributions to entropy were correlated with changes in conformer structure. The component of the moment of inertia perpendicular to the molecular plane gives significant input to ΔS rot , whereas the largest contributions to the ΔS vib have vibrations associated with the τ S1C20 coordinate. Figure
Optimized B3LYP/6-311++G(d,p) geometry of 1-[(2-mercaptoethyl)amino]-9,10-anthraquinone (MEAA) and vibrational contributions to entropy (ΔSvib, in J mol?1?K?1) relative to the most stable conformer 相似文献
11.
Electronic structure, 1H NMR and infrared spectra of diquat (6,7-dihydrodipyrido[1,2-b:1′,2′-e] pyrazine-5,8-diium or DQ2+) encapsulated by cucurbit[n]uril (n?=?7,8) hosts are obtained using the density functional theory. Theoretical calculations have shown that both CB[7] or CB[8] host possesses strong affinity toward DQ2+ compared to its reduced cation or neutral species. Calculated 1H NMR spectra reveal that Hα protons on bi-pyridinium rings of DQ2+@CB[8] complex are de-shielded owing to C=O?H interactions. On the other hand aromatic (Hβ and Hδ) of DQ2+ within the CB[8] cavity exhibit significant shielding. The complexation of CB[8] with DQ2+ splits the carbonyl stretching vibration (1788 cm?1) into two distinct vibrations which correspond to 1765 cm?1 arising from hydrogen bonded carbonyls and the 1792 cm?1 band from non-interacting ones. Further, the CN stretching vibration in DQ2+ exhibits a frequency blue-shift of 6 cm?1 on its encapsulation within the CB[8] cavity. The direction of frequency shift has been explained on the basis of natural bond orbital analyses. Figure
Diquat-cucurbituril complexes 相似文献
12.
Jian-Ying Li Li-Min Liu Bo Jin Hua Liang Hai-Jun Yu Hong-Chang Zhang Shi-Jin Chu Ru-Fang Peng 《Journal of molecular modeling》2013,19(4):1705-1710
The applications of endohedral non-metallic fullerenes are limited by their low production rate. Recently, an explosive method developed in our group shows promise to prepare He@C60 at fairly high yield, but the mechanism of He inserting into C60 cage at explosive conditions was not clear. Here, ab initio molecular dynamics analysis has been used to simulate the collision between C60 molecules at high-temperature and high-pressure induced by explosion. The results show that defects formed on the fullerene cage by collidsion can effectively decrease the reaction barrier for the insertion of He into C60, and the self-healing capability of the defects was also observed. Figure
Simulation of He@C60 formation by explosive method. Ab initio molecular dynamics has been used to simulate collision of C60. Defects caused by fullerenes reaction in explosion are shown by theory. The defects decrease the reaction barrier for He inserting into C60 cage. The method provides a promising technique to synthesized He@C60 相似文献
13.
Dimerization of 2-naphthalenecarbonitrile (2-NpCN) mediated by cucurbit[8]uril (CB[8]) has been investigated employing the density functional theory. Different structures of 2-NpCN dimers were generated by combining monomers in anti-head-to-head (A), anti-head-to-tail (B) and syn-head-to-tail (C) fashion. All these dimeric structures possess rigid cube-like architecture. On confinement within the CB[8] dimer A turns out to be the lowest energy structure. Calculated 1H NMR spectra revealed that the 2-NpCN dimer exhibits large shielding for aromatic protons consistent with the experiment. The protons attached to cubane moiety on the other hand, led to down-field signals. Dimerization mediated with CB[8] cavitand is further accompanied by the frequency up-shift (blue shift) of methylene stretching vibration in its infrared spectra. Figure
2-naphthalenecarbonitrile 相似文献
14.
Rafik Karaman Ghadeer Dokmak Maryam Bader Hussein Hallak Mustafa Khamis Laura Scrano Sabino Aurelio Bufo 《Journal of molecular modeling》2013,19(1):439-452
Density functional theory (DFT) calculations at B3LYP/6-31 G (d,p) and B3LYP/6-311?+?G(d,p) levels for the substituted pyridine-catalyzed isomerization of monomethyl maleate revealed that isomerization proceeds via four steps, with the rate-limiting step being proton transfer from the substituted pyridinium ion to the C=C double bond in INT1. In addition, it was found that the isomerization rate (maleate to fumarate) is solvent dependent. Polar solvents, such as water, tend to accelerate the isomerization rate, whereas apolar solvents, such as chloroform, act to slow down the reaction. A linear correlation was obtained between the isomerization activation energy and the dielectric constant of the solvent. Furthermore, linearity was achieved when the activation energy was plotted against the pK a value of the catalyst. Substituted-pyridine derivatives with high pK a values were able to catalyze isomerization more efficiently than those with low pK a values. The calculated relative rates for prodrugs 1–6 were: 1 (406.7), 2 (7.6?×?106), 3 (1.0), 4 (20.7), 5 (13.5) and 6 (2.2?×?103). This result indicates that isomerizations of prodrugs 1 and 3–5 are expected to be slow and that of prodrugs 2 and 6 are expected to be relatively fast. Hence, prodrugs 2 and 3–5 have the potential to be utilized as prodrugs for the slow release of monomethylfumarate in the treatment of psoriasis and multiple sclerosis. Figure
Substituted pyridine-catalyzed isomerization of monomethylmaleate (prodrug, cis-isomer) to monomethylfumerate (parental drug, trans-isomer) 相似文献
15.
Veysel T. Yilmaz Elif Gocmen Ceyda Icsel Murat Cengiz Sunde Y. Susluer Orhan Buyukgungor 《Journal of biological inorganic chemistry》2014,19(1):29-44
A series of new silver(I) saccharinate (sac) complexes, [Ag2(sac)2(μ-dppm)H2O]·H2O (1), {[Ag2(μ-sac)2(μ-dppe)]·3H2O·CH2Cl2} n (2), [Ag2(μ-sac)2(μ-dppp)] n (3), and [Ag(sac)(μ-dppb)] n (4) [dppm is 1,1-bis(diphenylphosphino)methane, dppe is 1,2-bis(diphenylphosphino)ethane, dppp is 1,3-bis(diphenylphosphino)propane, and dppb is 1,4-bis(diphenylphosphino)butane], have been synthesized and characterized by C, H, N elemental analysis, IR spectroscopy, 1H NMR, 13C NMR, and 31P NMR spectroscopy, electrospray ionization mass spectrometry, and thermogravimetry–differential thermal analysis. Single-crystal X-ray studies show that the diphosphanes act as bridging ligands to yield a dinuclear complex (1) and one-dimensional coordination polymers (2 and 4), whereas the sac ligand adopts a μ2-N/O bridging mode in 2, and is N-coordinated in 1 and 4. The interaction of the silver(I) complexes with fish sperm DNA was investigated using UV–vis spectroscopy, fluorescence spectroscopy, and agarose gel electrophoresis. The binding studies indicate that the silver(I) complexes can interact with fish sperm DNA through intercalation, and complexes 1 and 3 have the highest binding affinity. The gel electrophoresis assay further confirms the binding of the complexes with the pBR322 plasmid DNA. The minimum inhibitory concentrations of the complexes indicate that complex 1 exhibits very high antibacterial activity against standard bacterial strains of Escherichia coli, Salmonella typhimurium, and Staphylococcus aureus, being much higher than those of AgNO3, silver sulfadiazine, ciprofloxacin, and gentamicin. Moreover, complexes 1–3 exhibit very high cytotoxic activity against A549 and MCF-7 cancer cell lines, compared with AgNO3 and cisplatin. The bacterial and cell growth inhibitions of the silver(I) complexes are closely related to their DNA binding affinities. 相似文献
16.
17.
Masoud Darvish Ganji Maryam Mohseni Anahita Bakhshandeh 《Journal of molecular modeling》2013,19(3):1059-1067
We have investigated the interaction between open-ended zig-zag single-walled carbon nanotube (SWCNT) and a few benzene derivatives using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such sp 2-like materials are typically investigated using conventional DFT methods, which significantly underestimate non-local dispersion forces (vdW interactions), therefore affecting interactions between respected molecules. Here, we considered the vdW forces for the interacting molecules that originate from the interacting π electrons of the two systems. The ?0.54 eV adsorption energy reveals that the interaction of benzene with the side wall of the SWCNT is typical of the strong physisorption and comparable with the experimental value for benzene adsorption onto the graphene sheet. It was found that aromatics are physisorbed on the sidewall of perfect SWCNTs, as well as at the edge site of the defective nanotube. Analysis of the electronic structures shows that no orbital hybridization between aromatics and nanotubes occurs in the adsorption process. The results are relevant in order to identify the potential applications of noncovalent functionalized systems. Figure
First-principles van der Waals density functional (vdW-DF) calculations show that aromatics are physisorbed on the side wall of perfect single-walled carbon nanotubes (SWCNTs) as well as at the edge site of defective nanotubes 相似文献
18.
Bienvenu Glinma Sika D. S. Kpoviessi Fernand A. Gbaguidi Coco N. Kapanda Joanne Bero Joëlle Quetin-Leclercq Mansourou Moudachirou Jacques Poupaert Georges C. Accrombessi Emma W. Gachomo Lamine Baba-Moussa Simeon O. Kotchoni 《Molecular biology reports》2014,41(3):1617-1622
Thiosemicarbazones have become one of the promising compounds as new clinical candidates due to their wide spectrum of pharmaceutical activities. The wide range of their biological activities depends generally on their related aldehyde or ketone groups. Here, we report the pharmacological activities of some thiosemicarbazones synthesized in this work. Benzophenone and derivatives were used with N(4)-phenyl-3-thiosemicarbazide to synthesize corresponding five thiosemicarbazones (1–5). Their structures were characterized by spectrometrical methods analysis IR, NMR 1H & 13C and MS. The compounds were then screened in vitro for their antiparasitic activity and toxicity on Trypanosoma brucei brucei and Artemia salina Leach respectively. The selectivity index of each compound was also determined. Four thiosemicarbazones such as 4, 2, 3 and 1 reveal interesting trypanocidal activities with their half inhibitory concentration (IC50) equal to 2.76, 2.83, 3.86 and 8.48 μM respectively, while compound 5 (IC50 = 12.16 μM) showed a moderate anti-trypanosomal activity on parasite. In toxicity test, except compound 1, which showed a half lethal concentration LC50 >281 μM, the others exerted toxic effect on larvae with LC50 of 5.56, 13.62, 14.55 and 42.50 μM respectively for thiosemicarbazones 4, 5, 3 and 2. In agreement to their selectivity index, which is greater than 1 (SI >1), these compounds clearly displayed significant selective pharmaceutical activities on the parasite tested. The thiosemicarbazones 2–5 that displayed significant anti-trypanosomal and cytoxicity activities are suggested to have anti-neoplastic and anti-cancer activities. 相似文献
19.
Shanshan Tang Binbin Tang Dadong Liang Guang Chen Ruifa Jin 《Journal of molecular modeling》2013,19(9):3875-3881
A series of oligo(thienylenevinylene) derivatives with 1,4-dihydropyrrolo[3,2-b]pyrrole as core has been investigated at the PBE0/6-31G(d) and the TD-PBE0/6-31+G(d,p) levels to design materials with high performances such as broad absorption spectra and higher balance transfer property. The results show that position and amount of arm affect the electronic density contours of frontier molecular orbitals significantly. The molecule with four arms owns the narrowest energy gap and the largest maximum absorption wavelength, and the molecule with two arms in positions a and c has the broadest absorption region among the designed molecules. Calculated reorganization energies of the designed molecules indicate that the molecules with two arms can be good potential ambipolar transport materials under proper operating conditions.
1,4-dihydropyrrolo[3,2-b]pyrrole-cored branched molecules 相似文献