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  • The structure elucidation of the isomeric mixture of 3-[L-threo-2,3,4-tri -hydroxy-1-(phenyl-hydrazono)butyl] quinoxalin-2(1H)-one in dimethyl sulfoxide solution revisited: experimental and theoretical study
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-16
    Mohamed A. El-Atawy, Abdelrahman H. Hegazi, Mohamed Al Khalaf, Adel Amer

    Abstract Based on the analyses of 1D and 2D NMR spectra techniques, such as H–H COSY, HSQC, and HMBC of 3-[L-threo-2,3,4-trihydroxy-1-(phenylhydrazono)butyl]- quinoxalin-2(1H)-one in dimethyl sulfoxide solution, it was concluded that this compound exists as a mixture of two isomeric Z- and E- forms I and II rather than the hydrazine imine and diazeny enamine V tautomers reported earlier. The NMR signals assignment was supported using density functional theory.

    更新日期:2020-01-16
  • A computational study on the potential application of zigzag carbon nanotubes in Mg-ion batteries
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-16
    Saeed Amir Aslanzadeh

    Abstract Although Li-ion batteries are extensively applied for different purposes, they suffer from safety problems, high cost, and short lifetime. Because of low cost, wide availability, and nontoxicity of magnesium, Mg-ion batteries (MIB) might be a good alternative to Li-ion batteries. Here, applying density functional theory calculations, we examined the potential application of zigzag (4,0), (5,0), (6,0), (7,0), and (8,0) carbon nanotubes in the anode of MIBs. We found that by increasing the tube diameter, the Mg2+ adsorption energies are very slightly changed but the Mg adsorption sharply decreased indicating that the adsorption of Mg atom much more depends on the tube diameter and its adsorption energy is the key parameter for generating a cell voltage. We showed that by increasing the curvature of the CNT, the charge transfer is sharply increased upon Mg atom so that in the highest curvature, the interaction becomes ionic in nature with a Jahn-Teller distortion in the CNT structure. However, by increasing the CNT diameter, the cell voltage of MIB increased, from 4.0 V in the (4,0) to 5.3 V in the (8,0) CNT.

    更新日期:2020-01-16
  • Investigation of manganese metal coordination in proteins: a comprehensive PDB analysis and quantum mechanical study
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-14
    Udayalaxmi S., Mohan Rao Gangula, Ravikiran K., Ettaiah P.

    Abstract Manganese (Mn) is an important metal that is crucial in biological cell mechanism and function. However, its binding mechanism is poorly characterized. In the present study, we have carried out a detailed statistical analysis of the Mn-containing proteins through analysis of the metal coordination spheres of the vast number of protein crystal structures present in Protein Data Bank. These results reveal that Mn metal predominantly acquires the coordination number of six and five. In these predominant six and five coordination spheres, Mn metal is majorly stabilized with octahedral and square pyramidal geometries respectively. The water molecules, aspartic acid, and glutamic acid residues bonded frequently with Mn metal ions. These results provided useful insights to characterize the very important Mn-containing subset of the proteome. Quantum mechanical results showed that the complexes with coordination number six are predominantly having high interaction energy, which is in good agreement with statistical analysis.

    更新日期:2020-01-14
  • Exploration of nitroimidazoles as radiosensitizers: application of multilayered feature selection approach in QSAR modeling
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-10
    Priyanka De, Dhananjay Bhattacharyya, Kunal Roy

    Abstract Radiosensitizers are aimed to augment tumor cell killing by radiation while having much less effect on normal tissues. Nitroimidazoles and related analogues are efficient radiation sensitivity enhancers, and they particularly work on hypoxic tumor cells. In the current study, we have developed two partial least squares (PLS) regression-based two-dimensional quantitative structure-activity relationship (2D-QSAR) models using a novel class of 84 nitroimidazole compounds to understand their radiosensitization effectiveness (pC1.6). Feature selection was done by genetic algorithm along with stepwise regression, while model validation was performed using various stringent validation criteria following the strict rules of OECD guidelines of QSAR validation. The variables included in the models were obtained from Dragon (version 7.0) and simplex representation of molecular structures (SiRMS) (version 4.1.2.270) software. The developed models were robust, externally predictive, and useful tools to predict the radiosensitization effectiveness of nitroimidazole compounds. True external prediction was carried out using a group of six nitroimidazole derivatives and the model reliability was checked using the Prediction Reliability Indicator tool (http://dtclab.webs.com/software-tools). Furthermore, the developed models will give an insight for development of new radiosensitizers with enhanced radiation sensitivity.

    更新日期:2020-01-11
  • 4-Oxobenzo[d]1,2,3-triazin-pyridinium-phenylacetamide derivatives as new anti-Alzheimer agents: design, synthesis, in vitro evaluation, molecular modeling, and molecular dynamic study
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-06
    Fahimeh Hosseini, Maryam Mohammadi-Khanaposhtani, Homa Azizian, Ali Ramazani, Maliheh Barazandeh Tehrani, Hamid Nadri, Bagher Larijani, Mahmoud Biglar, Hossein Adibi, Mohammad Mahdavi

    Abstract A new series of 4-oxobenzo[d]1,2,3-triazin-pyridinium-phenylacetamide hybrids 8a–p was designed, synthesized, and screened as the potential cholinesterase inhibitors against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). Obtained anti-cholinesterase activities demonstrated that all the title compounds exhibited excellent inhibition against BuChE and moderate inhibitory activity toward AChE in comparison to standard cholinesterase inhibitor donepezil. For example, compound 8e exhibited about 49-fold higher inhibitory activity than donepezil (IC50 = 3.2 ± 0.3 μM) against BuChE. This compound inhibited BuChE via a mixed-type inhibition mode. This finding demonstrated that compound 8e in addition to catalytic anionic site (CAS) can also interact with the peripheral anionic site (PAS) of BuChE. Molecular modeling and molecular dynamic studies were also performed on synthesized compounds.

    更新日期:2020-01-06
  • Design, synthesis, evaluation, and molecular dynamic simulation of triclosan mimic diphenyl ether derivatives as antitubercular and antibacterial agents
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-06
    Amol B. Khade, Helena I. M. Boshoff, Kriti Arora, K. E. Vandana, Ruchi Verma, G. Gautham Shenoy

    In the present work, we have explored triclosan mimic diphenyl ether derivatives as inhibitors of Mycobacterium tuberculosis enoyl acyl carrier protein reductase (InhA) using a structure-based drug design approach. The virtual library of diphenyl ethers was designed and compounds with acceptable absorption, distribution, metabolism, excretion, and toxicity properties were docked. The compounds with higher dock score (5a-g) than triclosan were synthesized, characterized, and evaluated for in vitro antitubercular activity against Mycobacterium tuberculosis H37Rv. Among the synthesized compounds, compounds 5f and 5c appeared to be the most promising with minimum inhibitory concentration of 18 μM and 36 μM respectively. The molecular dynamics simulation study of the most active compound 5f and triclosan was performed, which correlates with its activity in comparison with triclosan. All the compounds were further evaluated for cytotoxicity studies against Vero, and HepG2 were found to be safe. Furthermore, compound 5f was evaluated for in vitro cytotoxicity against mouse macrophage cell lines (RAW 264.7), and the study indicated its safety in eukaryotes at 50-μM concentration. In addition, compounds 5a-g were also screened for their in vitro antibacterial activity against two gram-positive and two gram-negative bacteria by resazurin-based microtiter dilution assay method. Among the synthesized compounds, 5f and 5b appeared to be promising, against various gram-positive and gram-negative microorganisms, indicating its broad-spectrum potential.

    更新日期:2020-01-06
  • Paradigms and Paradoxes: Additive trends in the absolute entropy of monoxides and homonuclear diatomic molecules
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-03
    Drew Z. Spera, Joel F. Liebman

    Abstract In general, entropy is not additive for the system of a single molecule. We show this by demonstrating that the entropy of a monoxide species, before and after subtracting contributions from electronic degeneracies, is in general not equal to the arithmetic mean of the entropies of the corresponding homonuclear diatomic and O2. This calculation is done with 24 elements for which reliable experimental data could verify both the absolute entropy and ground electronic state.

    更新日期:2020-01-04
  • In silico studies of novel scaffold of thiazolidin-4-one derivatives as anti- Toxoplasma gondii agents by 2D/3D-QSAR, molecular docking, and molecular dynamics simulations
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-03
    Rahman Abdizadeh, Farzin Hadizadeh, Tooba Abdizadeh

    Abstract Toxoplasma gondii is an obligate intracellular protozoa that can infect a wide variety of warm-blooded animals and humans. It was claimed that novel anti-Toxoplasma gondii agents were optimized as potential drug candidates, designed and created as significant agents. In this work, molecular modeling studies, including CoMFA, CoMFA-RF, CoMSIA, and HQSAR were performed on a set of 59 thiazolidin-4-one derivatives as anti-T. gondii agents. The statistical qualities of generating models were justified by internal and external validation, i.e., cross-validated correlation coefficient (q2), non-cross-validated correlation coefficient (\( {r}_{ncv}^2 \)) and predicted correlation coefficient (\( {r}_{pred}^2 \)), respectively. The CoMFA (q2, 0.897;\( \kern0.5em {r}_{ncv}^2 \), 0.933; \( {r}_{pred}^2 \), 0.938), CoMFA-RF (q2, 0.900;\( \kern0.5em {r}_{ncv}^2 \), 0.935; \( {r}_{pred}^2 \), 0.998), CoMSIA (q2, 0.910;\( {r}_{ncv}^2 \), 0.950; \( {r}_{pred}^2 \), 0.998), and HQSAR models (q2, 0.924;\( {r}_{ncv}^2 \), 0.953; \( {r}_{pred}^2 \), 0.995) for training and test set yielded significant statistical results. Therefore, these QSAR models were excellent, robust, and had better predictive capability. Contour maps of the QSAR models were generated and validated by molecular dynamics simulation-assisted molecular docking study. The final QSAR models could be useful for the design and development of novel potent anti-T. gondii agents.

    更新日期:2020-01-04
  • An integrated quantum chemical and experimental approach for exploring the structures and properties of insensitive munitions interacting with ions in bulk water
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-03
    Harley R. McAlexander, Stephen A. Giles, Rebecca A. Crouch, Hannah R. Peel, Stacy Jones, Anthony J. Bednar, Manoj K. Shukla

    Abstract Alternatives to legacy munitions and explosives, materials that feature increased stability against external stimuli without compromising their energetic yields are currently being developed. The environmental interactions of such energetic materials need to be addressed, especially as their use becomes more widespread. In order to explore such compounds with environmental influences in mind, we assess the electronic structure and properties of these insensitive munitions (IMs) compounds in modeled hard water using both theory and experiment. To model the IMs in hard water, we have used density functional theory with the M06-2X functional and the 6-311 + G(d,p) basis set with explicit water molecules to capture features like hydrogen bonding, implicit solvent to incorporate bulk water effects, and select ions that would be present in natural water. We ensured the nature of the potential energy surfaces of optimized geometries through vibrational frequency calculations under the harmonic approximation. Several electronic properties, such as oxidation and reduction potentials and electron affinity and ionization potential, for each system are presented. Additionally, cyclic voltammetry experiments were performed, and obtained results were compared with quantum chemical predictions. The experimental reduction potentials are found to be in good agreement with the predicted results. Overall, the reduction potentials predicted by density functional theory for the IM-ion-water complexes are shifted compared with the corresponding isolated munition such that reduction or oxidation would be more facile in the presence of water and ions.

    更新日期:2020-01-04
  • Kamonolol acetate from Ferula pseudalliacea as AChE inhibitor: in vitro and in silico studies
    Struct. Chem. (IF 1.624) Pub Date : 2020-01-03
    Dara Dastan, Samane Validi, Ahmad Ebadi

    Abstract Alzheimer’s disease is one of the most common causes of dementia. Acetylcholinesterase has been considered as the main therapeutic target in the treatment of Alzheimer’s disease. Natural products are the richest source of lead compounds for the discovery and development of new drugs. In the present contribution, the hierarchical biology–oriented method was applied to discover the active gradients of F. pseudalliacea root as AChE inhibitors. The Kamonolol acetate was extracted and identified from the n-hexane extract of F. pseudalliacea root. The Kamonolol acetate inhibited the AChE with IC50: 63.9 μM. Molecular modeling studies showed that Kamonolol acetate interacted with CAS and PAS of AChE active site. Kinetics in accompany with molecular modeling studies demonstrated that Kamonolol acetate inhibited AChE in the mixed-type model. The results indicated that Kamonolol acetate could be considered as a valuable lead compound in the design of AChE inhibitors.

    更新日期:2020-01-04
  • Phase transition in non-centrosymmetric 2-methyl-5-nitroanilinium dihydrogen phosphate: structural, spectroscopic and optical studies
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-24
    Volodymyr Medviediev, Jan Baran, Jan K. Zaręba, Marek Drozd, Marek Daszkiewicz

    A reversible phase transition in 2-methyl-5-nitroanilinium dihydrogen phosphate, (H2m5na)H2PO4, has been found and characterized. Lattice parameters of (H2m5na)H2PO4 change continuously upon cooling with smooth inflection point at 196 K. The crystal symmetry lowers from orthorhombic, space group Pca21, to monoclinic one, P21. Phase transition to the low-temperature phase features a significant movement of the aromatic ring of H2m5na+ ion assisted by the tilting of a nitro group. Structural modifications of the hydrogen-bonding network in (H2m5na)H2PO4 are identified and described with the use of graph-set descriptors; algebraic equations based on the graph-set descriptors are given. Phase transition was also monitored by temperature-dependent IR spectra, which revealed significant alterations in vibrational characteristics within 1000–950 cm−1 and 830–780 cm−1 spectral ranges. Kurtz-Perry test of (H2m5na)H2PO4 shown that relative SHG efficiency is 0.85 that of KDP at room temperature. Low-temperature phase features over four times weaker SHG than room-temperature one.

    更新日期:2019-12-25
  • Structural features and N-H…O and O-H…O hydrogen-bonded supramolecular frameworks in 2-methylanilinium hydrogen DL-malate hydrate, 4-methoxyanilinium and 4-methylanilinium hydrogen DL-malate salts
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-20
    Jagan Rajamoni, Sivakumar Kandasamy

    Abstract In the crystal structure of 2-methylanilinium hydrogen DL-malate hydrate (I), an additional water molecule is present in asymmetric unit. In the crystal structures of 4-methoxyanilinium hydrogen DL-malate (II) and 4-methylanilinium hydrogen DL-malate (III), the hydrogen malate anions exhibit configurational disorder with major component occupy S-configuration and minor component occupy R-configuration provided both (II) and (III) are prepared from a racemic mixture of DL-malic acid. In crystal structures of compounds (I)–(III), the hydrogen malate anions and anilinium cations from O-H…O and N-H…O hydrogen bonds which exhibit interesting supramolecular frameworks. In compound (I), the N-H…O and O-H…O hydrogen-bonded anionic-cationic framework form two-dimensional hydrophilic and hydrophobic layers in which the lattice water molecules are embedded in hydrophilic layers. However, in crystal structures of (II) and (III), the hydrogen DL-malate anions form two-dimensional anionic substructure through O-H…O hydrogen bond, in which the anilinium cations are anchored through N-H…O hydrogen bonds.

    更新日期:2019-12-20
  • The effect of chitosan adsorption on the stability characteristics of single- and double-walled boron-nitride nanotubes under compressive force using molecular dynamics simulations
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-20
    Shahram Ajori, Amir Ameri, Reza Ansari

    Abstract In this study, the buckling behavior of functionalized single- and double-walled boron-nitride nanotubes (SWBNNTs and DWBNNTs) with a monomer of chitosan using molecular dynamics (MD) simulations is explored. The effect of chemical adsorption of chitosan molecule on the critical buckling force and strain is investigated. The results show that the critical buckling force considerably increases as the chitosan is attached to the side wall of boron-nitride nanotube which is more considerable for larger radii of nanotube. Moreover, increasing the number of walls reduces the sensitivity of boron-nitride nanotube to the functionalization compared with similar SWBNNTs. Further, it is shown that critical buckling of functionalized BNNTs increases by rising the weight percentage of chitosan. Considering the critical strain, it is observed that functionalization reduces the critical strain of functionalized BNNTs which is more pronounced in the case of SWBNNTs with bigger radii. Moreover, the buckling mode shape of functionalized BNNTs is presented.

    更新日期:2019-12-20
  • Fighting cancer with microtubule-stabilizing agents: a computational investigation of the complex between β-tubulin and the microtubule-stabilizing, antitumor marine diterpenoid sarcodictyin A
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-20
    Francesco Pietra

    Abstract The best complex between the marine diterpenoid sarcodictyin A and the protein tubulin is described here from MM-GBSA (molecular mechanics-generalized born surface area) computations of the least effective potential energy of binding. The work started from previous experimental competition experiments, which showed that the sarcodictyins, which are diterpenoids from the stoloniferan coral Sarcodictyon roseum, occupy the same, or overlapping, binding site on tubulin which is taken by paclitaxel (the so-called taxoid binding site). Molecular docking of sarcodictyin A at the taxoid binding site was achieved, with different poses, by using three docking engines and the known coordinates for the experimental complex of non-polymerized α- and β-tubulin with paclitaxel, manually deprived of the latter. These sarcodictyin A-tubulin complexes only served as templates to be subjected, limited to the sarcodictyin A-β-tubulin part, to extensive MD (molecular dynamics) and MM-GBSA simulations with the CHARMM36 force field for the protein and CGenFF force field for the ligand. In contrast, FEP (free energy perturbation) simulations failed to converge with this complex. During MD and MM-GBSA simulations, mutual adaptation of the ligand and receptor was observed. Specifically, stabilization of the complex of lowest effective potential energy of binding, which is submitted here to represent how sarcodictyin A fits into the taxoid binding site of tubulin in nature, resulted from mainly reshaping of the M-loop of β-tubulin, whereby three H-bonds and multiple hydrophobic interactions with sarcodictyin A were established.

    更新日期:2019-12-20
  • Theoretical study on the M-H···π interactions between metal hydrides and inorganic benzene B 3 X 3 H 3 (X = O, S, Se)
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-20
    Pengtao Xie, Meiyan Sun, Xiaoyan Li, Yanli Zeng, Xueying Zhang

    Abstract In this work, we conducted ab initio calculations to evaluate the properties of M-H···π interactions between the metal hydrides MH (M = Li, Na, MgH, CaH, NiH, CuH, ZnH) and inorganic benzenes B3X3H3 (X = O, S, Se). Unlike benzene, inorganic benzene B3X3H3 (X = O, S, Se) supports a large area of positive molecular electrostatic potential above and below the molecule, which acts as a Lewis acid and interacts with the H atom of metal hydride. MP2/6–311++G(d, p) results show that these intermolecular interactions exhibit the characteristics of close shell noncovalent interactions. The electrostatic interaction significantly contributes to stabilizing the complexes. The M-H···π interaction’s strength is associated with the property of group VI atom and metal hydride. X’s atomic number decreasing and the H of MH becoming more negative facilitate stronger interaction. Furthermore, the addition of substituent on the B3O3Y3 (Y = F, Cl, CN, OH, and CH3) significantly impacts the π-hole of inorganic benzene and thus modulates these M-H···π interactions. More elongation and blueshift of the MH bonds upon complexation were found for electron-withdrawing substituents. Analysis of σ and π orbital separation indicates that the π-attractor’s position relative to the B atom in the inorganic benzene changes with different substituents. The M-H···π interaction’s strength is primarily dependent on the π-electron density, not σ-electron density.

    更新日期:2019-12-20
  • Ten years of charge-inverted hydrogen bonds
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-18
    Mirosław Jabłoński

    This article is a review of the current state of knowledge about the so-called charge-inverted hydrogen bond—the type of interaction proposed 10 years ago. Numerous examples of model dimers and molecules in which this type of interaction exists in the inter- and intramolecular forms, respectively, as well as systems actually existing and studied by experimental and theoretical methods will be presented. The results of extensive theoretical research on the physical nature of charge-inverted hydrogen bonds will be thoroughly discussed. Dimers with a recently described hydride-carbene bond, i.e., a particular case of charge-inverted hydrogen bond in which the carbene carbon atom plays the role of an atom with the electron lone-pair vacancy, will also be presented.

    更新日期:2019-12-19
  • N-H…O, C-H… O hydrogen-bonded supramolecular frameworks in 4-fluoroanilinium and dicyclohexylaminium picrate salts
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-17
    Saminathan Kolandaivelu, Jagan Rajamoni, Sivakumar Kandasamy

    The asymmetric unit of compound (I), 4-fluoroanilinium picrate, C6H7NF+.C6H2N3O7− contain one 4-fluoroanilinium cation and one picrate anion whereas in compound (II), dicyclohexylaminium picrate, C12H22N+.C6H2N3O7− the asymmetric unit contains two sets of dicyclohexylaminium cation and picrate anion due to conformational difference between the molecules. In (I), all three nitro groups of the picrate anion are positionally disordered over two sites refined to major and minor components. The molecular ions of (I), interlinked through N–H‧‧‧O and C–H‧‧‧O hydrogen bonds forming two-dimensional supramolecular sheet along (-1 0 1) plane. Whereas in (II), the symmetry-independent molecules labeled as A and B molecule form independent one-dimensional supramolecular tape extending along (1 1 0) and (1 0 0) direction. The supramolecular tapes are interlinked through C–H‧‧‧O interaction to form three-dimensional network in the crystalline solid in (II).

    更新日期:2019-12-18
  • In quest of reversibility of Friedel-Crafts acyl rearrangements in the pyrene series
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-16
    Israel Agranat, Tahani Mala’bi, Yaacov Netanel Oded, Hanna Daniel Kraus

    Friedel-Crafts acyl rearrangements in PPA of diacetylpyrenes (80–120 °C), dibenzoylpyrenes (80–200 °C), and bis(4-flurobenzoyl)pyrenes (80–120 °C) and Scholl reactions in AlCl3/NaCl of dibenzoylpyrenes (140–200 °C) have been studied. The substrates were 1-AcPY, 2-AcPY, 1,3-Ac2PY, 1,6-Ac2PY, 1,8-Ac2PY, 2,7-Ac2PY, 1-BzPY, 1,6-Bz2PY, 1,8-Bz2PY, 1-4FBzPY, 1,6-4FBz2PY, 1,8-4FBz2PY. The mixtures of pyrene, 1-AcPY, 2-AcPY, 1,3-Ac2PY, 1,6-Ac2PY, 1,8-Ac2PY, and 2,7-Ac2PY were separated by HPLC. The following reversible intermolecular isomerizations were established: 1,6-Ac2PY ⇌ 1,8-Ac2PY, 1,6-Bz2PY ⇌ 1,8-Bz2PY, and 1,6-4'FBz2PY ⇌ 1,8-4'FBz2PY, albeit not in high yields. The results substantiate Gore’s 1955 proposition that “The Friedel–Crafts acylation reaction of reactive aromatic hydrocarbons is a reversible process.” The isomerizations reported here differ from the few previously reported completely reversible intramolecular Friedel-Crafts acyl rearrangements. At ≥ 140 °C, in PPA and in AlCl3/NaCl, 1,6-Bz2PY and 1,8-Bz2PY underwent a highly regioselective double Scholl reaction to give pyranthrone (3) and deacylations to 1-BzPy (and pyrene), followed by mono-Scholl reactions to give 8H-dibenzo[def,qr]chrysen-8-one (1), and 11H-indeno[2,1-a]pyren-11-one (2). The formation of 3 and not the expected tribenzo[a,ghi,o]perylene-7,16-dione (4) from 1,8-Bz2PY indicates that 1,8-Bz2PY has first undergone isomerization to 1,6-Bz2PY. The present study confirms the linkage between Friedel-Crafts acyl rearrangements and the Scholl reaction.

    更新日期:2019-12-17
  • The conformational search, the stability, fragment interaction and resistance to acidic attack of epoxyl-polyurethanes in different solvent media
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-14
    Adebayo A. Adeniyi, Cecilia O. Akintayo, Emmanuel T. Akintayo, Jeanet Conradie

    Natural-based polyols are seen by polyurethane industries as an alternative to the petroleum-based polyols because of increasing challenges due to the oil crisis and global warming. In this research, four different derivatives of bio-polyols are examined, which include the precursor Jatropha curcas oil (JC) that was extracted from Jatropha curcas seeds, as well as the derivatives epoxidated-polyol (EJ), hydroxylated epoxy-polyol (JP) and epoxy-polyurethane (JU). The computational studies provide more insight into their experimentally observed properties and can be useful in further customized design of this type of bio-polyols for industrial application. Results show that the JU monomer is more stable in terms of potential energy, level of atomic fluctuation, diffusion, radial distribution function, and with properties indicating the possibility of forming the best crystal solid. Monomer JU is also found to have the best resistance to acidic attack, using the results from the interaction energy, radial distribution function (RDF) and level of diffusion.

    更新日期:2019-12-17
  • A quest for stable 2,2,9,9-tetrahaloplumbacyclonona-3,5,7-trienylidenes at density functional theory
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-14
    Maryam Koohi, Hajieh Bastami

    In contrast to cyclonona-3,5,7-trienylidene (1H) which turns out as a boat-shaped transition state for having a negative force constant, its heavier plumbylenic analogous (2X) where X = H, F, Cl, Br, and I emerge as boat-shaped minima. This unsubstituted carbene has a triplet ground state while exclusive of 2I which initially takes on a triplet multiplicity and eventually transforms to a less stable intramolecular ring opening product; all of the plumbylenes (2H, 2F, 2Cl, and 2Br) have a singlet ground state. Hence, stability anticipated by the singlet (S)–triplet (T) splitting (ΔES-T) decreases by going down in the group 17 column: 2Br > 2Cl > 2F > 2H > 1H > 2I. Also, the HOMO-LUMO gap (ΔEHOMO-LUMO) increases as a result of substituting. From a thermodynamic perspective, our scrutinized 2Br, 2Cl, and 2F are found 1.5–2 times more stable than that of the reported cyclopenta-2,4-dienplumbylene and 2,5-bis(halobora)-cyclopentenplumbylenes analogues, respectively. From a kinetic perspective, these nine-membered plumbylenes are found 20–26 kcal/mol more stable than that of their corresponding five-membered congeners. The NBO analysis on stable singlet 2Br shows that there is a mesomeric interaction between bromine lone-pair electron and the Pb divalent atom of 2Br with bonding (σ) and anti-bonding (σ*) orbitals of carbon–bromine and carbon–lead. The main stabilizing effect appears to be π- and σ-bond hyperconjugation among the iodine heteroatom and divalent center of triplet 2I. This research signifies the thermodynamic and kinetic stabilities of the biggest unsaturated cyclic plumbylenes hoping to prompt the experimental attention toward them.

    更新日期:2019-12-17
  • Design of organic superacids based on triflic and perchloric acid by using DFT-B3LYP calculations
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-12
    Hamid Saeidian

    Comprehensive density functional theory calculations at B3LYP/6-311++G(d, p) level have been undertaken on a new type of organic Brønsted acids based on perchloric and triflic acid in order to design superacids. The deprotonation enthalpy (ΔH acid ) and Gibbs free energy (ΔG acid ) were used to calculate the acidity of the proposed structures. For the acidity comparison, a systematic estimation of aromaticity in the superacids and their anions have been studied using structural (harmonic oscillator model of aromaticity) and magnetic (nucleus-independent chemical shift) criteria. The calculated gas phase ΔH acid for the proposed acids were 319–249 kcal/mol which are less than the most mineral acids. Tautomers of proposed organic acids were also investigated.

    更新日期:2019-12-13
  • The index of ideality of correlation: A statistical yardstick for better QSAR modeling of glucokinase activators
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-11
    Manisha Nimbhal, Kiran Bagri, Parvin Kumar, Ashwani Kumar

    Glucokinase is an enzyme which is responsible for the conversion of glucose to glucose-6-phosphate through ATP-dependent phosphorylation and has a significant role in glycogen synthesis and hepatic glucose production. Allosteric activators of glucokinase could be an attractive approach for the treatment of T2DM (type 2 diabetes mellitus). Recently, an innovative standard “Index of Ideality of Correlation” has been introduced for the estimation of QSAR (quantitative structural activity relationship) model’s potential. In the present work, QSAR models for activators of glucokinase have been developed with target function TF1 and TF2 using index of ideality of correlation (IIC). Along with this, prediction of calibration sets for different QSAR models generated for different splits is also categorized as correct and wrong. Moreover, dispersion in the different runs of same split is also explained. The values of criteria R2 and IIC for best split prepared with target function TF1 are 0.6554 and 0.7912 and that for TF2 are 0.9531 and 0.9758, respectively. The models developed with index of ideality of correlation are better than the models generated without index of ideality of correlation. The IIC could be a better criteria option for predictability of QSAR model for glucokinase activators.

    更新日期:2019-12-11
  • Computational study of [(phenanthroline) 2 Fe II/III –(terephthalate)–Co III/II (phenanthroline) 2 ] 3+ binuclear complex
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-11
    Hossein Shirani, Hassan Sabzyan

    Bistability of the proposed [(phenanthroline)2FeII/III–(terephthalate)–CoIII/II(phenanthroline)2]3+ binuclear complex, arising from intramolecular FeII/III ↔ CoIII/II charge transfer, is investigated based on energetics, geometries, atomic charges, electric polarizabilities, and IR and UV-Vis spectra obtained computationally at (TD)DFT-B3LYP/LANL2DZ level of theory. Two distinct stable states are obtained which have different characteristics, including structures, charge distributions, and spectroscopic properties. Also, the well-defined first-order saddle point obtained between these two states using the QST3 search method, having a 1.182 eV activation (barrier) energy for the FeIICoIII → FeIIICoII reaction, furthermore approves bistability in this complex. This value of activation energy suggests that switching between the two charge distribution states FeII–CoIII and FeIII–CoII in this complex may be induced by electric field and/or infrared radiation, and thus, it can be candidate as an infrared radiation- or electric field-driven molecular two-state switch.

    更新日期:2019-12-11
  • Flat or angular? The impact of the nitrogen atom hybridization on the docking results for arylpiperazine derivatives as an example
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-11
    Katarzyna Rzęsikowska, Mateusz Jabłoński, Justyna Kalinowska-Tłuścik

    Structure-based virtual screening has become a standard approach in modern drug discovery. It involves molecular docking and estimation of the ligand binding likelihood based on the scoring function. Surprisingly, in the search for new pharmaceuticals, one of the bottlenecks can be the ligand’s 3D structure prediction, especially for molecules with amine groups. In our work, the impact of the nitrogen atom hybridization in arylpiperazine derivatives on the results of docking to serotonin receptor type 7 is discussed. Our docking/re-docking studies show that the nitrogen lone pair may be involved in weak ligand–protein interactions. The presented results suggest that assumption of amine group planarity in the arylpiperazine 3D structure prediction may be a misleading factor in computer-aided drug discovery, influencing active conformation prediction. With our paper, we would like to raise awareness that in the case of compounds with amine groups, special care must be taken in the 3D ligand’s structure preparation for molecular docking studies.

    更新日期:2019-12-11
  • Structural and electronic properties of adsorbed nucleobases on pristine and Al-doped coronene in absence and presence of external electric fields: a computational study
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-09
    Tooba Afshari, Mohsen Mohsennia

    The adsorption of nucleobases (NBs) on pristine and aluminum-doped coronene (Al-coronene) has been studied theoretically using density functional theory (DFT) method in the presence/absence of external electric fields (EFs) having different strengths. The changes in geometric and electronic structures upon the adsorption were analyzed in order to reveal the sensitivity of pristine coronene and Al-coronene toward NBs. The results of theoretical calculations at wB97XD/6–31G(d,p) level of theory showed that the molecular adsorption of NBs on Al-coronene under the external EFs can induce significant change in Al-coronene conductivity. On the basis of calculated changes in band gap energy (ΔEg) and adsorption energy (Eads), it was found that electronic properties of Al-coronene, especially in presence of the applied EFs, are very sensitive to the adsorption of NBs. Finally, electronic structures analysis and full characterization of the surface interactions were performed using the quantum theory of atoms in molecules (QTAIM) to elucidate the nature of NB adsorption interaction. As a result, the enhanced electrical properties of NBs/Al-coronene-adsorbed complexes in the presence of the applied external EFs indicated promising perspectives for fabrication of new NBs-sensing devices.

    更新日期:2019-12-09
  • The ability of gold nanoclusters as a new nanocarrier for D-penicillamine anticancer drug: a computational chemistry study
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-06
    H. R. Abd El-Mageed, F. M. Mustafa, Mahmoud K. Abdel-Latif

    In this work, we study the interactions between gold nanocluster (AunNCs, n = 2, 4, and 6) and D-penicillamine (DPA) anticancer drug by different computational methods to study the ability of AunNCs to act as a nanocarrier for DPA for the first time. We calculated the binding energies of all AunNCs-DPA complexes in the gas and water phases by density functional theory. The binding energies calculated by two different functionals, B3LYP and M062X, of the AunNCs-DPA complexes in the solvent phase are lower than those in the gas phase, suggesting that the partially covalent and partially electrostatic bonding stabilizes the complexes. Atoms-in-molecules analysis showed that the intermolecular hydrogen and covalent bonding play an important role in the formation of these complexes. The interactions between AunNCs-DPA complexes and water molecules also were studied by molecular dynamics simulations to summarize the effect of solvent on the binding between AunNCs and DPA. Radial distribution functions and coordination numbers of the interactions between AunNCs-DPA complexes and water are computed and showed that Au6NCs has the strongest interactions with DPA with compared to other complexes. The adsorption and deformation energies of DPA molecules on AuNCs surface has a 6 nm size with different shapes (sphere and box) and are calculated by MC simulations; the adsorption energies for all configurations in sphere and box shapes are negative which revealed that the adsorption of the drug molecule is exothermic and energetically favorable, and this indicated that the adsorption of DPA on the AuNPs surface is spontaneous due to existence of the weak intermolecular interaction. So, the drug molecule can be easily released from AunNPs.

    更新日期:2019-12-06
  • Reaction of HSSS . radical with guanine and formation of 8-thioguanine: a computational study
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-05
    Leyla Mohammadkhani, Majid M. Heravi, Maryam Anafcheh

    Density functional calculations have been applied to study reactions of the HSSS. radical with guanine at the C2, C4, C5, and C8 sites of guanine that yields [GCn-SSSH].n = 2, 4, 5, and 8 adducts. Also, formation of 8-thioguanine from [GC8-SSSH]. adduct has been studied. In all the adducts [GCn-SSSH]., HSSS. radical is placed on the top of the plane of the guanine ring. The results show that there is a possibility of intraresidue S-H…N hydrogen bonding in each [GCn-SSSH]. adduct. Besides, the C8 site of guanine is the most reactive site to add to HSSS. radical with appreciably high rate constant, and the adduct formed at this site would be significantly stable. According to NBO analysis, delocalization energies for all the hydrogen bondings, i.e., E(2) for nN⟶σ*SH interactions, are obtained to be in the range of 1.31–3.46 kcalmo1−1. The biggest E(2) and the largest amount of charge transfer is found for [GC8-SSSH]. adduct, i.e., for the S-H…N7 (Gua) interaction, in which RN…H = 2.588 Å, to be 1.78 kcalmo1−1 and 0.0024e, respectively, well correlated with the prediction of most of its stability among the [GCn-SSSH]. adducts. The ZPE-corrected enthalpy changes for the reactions are obtained to be 0.2–1.4 kcalmo1−1. The reaction enthalpy changes and the barrier energies related to the different sites of guanine are found to be in the order of C8 < C2 < C5 < C4. Starting with the adduct [GC8-SSSH]., 8-thioguanine could be achieved in two steps with two transition states (TS1 and TS2) and an intermediate complex (IM); the overall reaction is exothermic. The first reaction step, the rate-determining step, involves going from the adduct [GC8-SSSH]. to IM via TS1, in which HSS moiety gets dissociated from the HSSS moiety attached to the C8 site of guanine.

    更新日期:2019-12-05
  • The transmission of electronic substituent effects along the polyene chain: evaluation of through-bond and through-space contributions
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-05
    Nina Sadlej-Sosnowska

    Transmission between various parts of molecules determines their reactivity and is important from the perspective of molecular recognition. In a recent paper, the correlation between substituent electronic properties and those of the rest of molecules has been studied using long substituted polyphenylene hydrocarbons. The distance attained between interacting sites (between a substituent and an extreme carbon atom) was 119 Å. The present study was planned to investigate whether similar interactions can be found when the transmitting medium is not a polyphenylene unit, but a polyene one. Some questions had to be answered: How rapidly do interactions between a substituent at one end of a molecule and phenyl ring at the other end decline with the increasing distance between two sites? How would this interaction change upon the removal of some polyene units from inside the molecule and what contribution would the units have to the through-space interactions? What measure characterizes the electronic properties of a substituent attached to the end of a polyenic chain? It was found that the through-space interaction contributions increased as molecules lengthened, but even for the longest molecules, the through-bond mechanism was responsible for about one half of the overall transmission whereas the through-bond transmission dominated for shorter molecules.

    更新日期:2019-12-05
  • Identification of dual site inhibitors of tankyrase through virtual screening of protein-ligand interaction fingerprint (PLIF)–derived pharmacophore models, molecular dynamics, and ADMET studies
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-05
    Manoj G. Damale, Rajesh Patil, Siddique Akber Ansari, Hamad M. Alkahtani, Abdulrahman A. Almehizia, Shahebaaz K. Pathan, Santosh Chhajed, Jaiprakash Sangshetti

    Tankyrases are the group of poly (ADP-ribosyl) polymerases (PARPs) which are the attractive targets in various therapeutic areas such as cancer, antiviral, diabetes, and hormonal imbalance. The selective nature of tankyrase 1 and 2 inhibitors has created solid base to get dual site binders as they bind to induced adenosine binding site and nicotinamide binding site resulting in dual site inhibition. The present work describes the cheminformatics approach to find potential lead molecules as tankyrases dual site inhibitors through pharmacophore model by utilizing protein-ligand interaction fingerprints (PLIF) approach. The constructed pharmacophore model was used in virtually screening of ZINC and Interbioscreen database. Top ten hit molecules of virtual screening were subjected to molecular docking in order gain insights of key interactions at the adenosine and nicotinamide binding sites. The top hits were subjected to molecular dynamics simulation studies to gain deeper insights into probable mechanism of inhibition and stability of the complex. The top hit ZINC12973507 showed all the features required in key interactions at the active site of tankyrases and this hit molecule can be further explored as a potential drug candidate for dual site inhibition of tankyrases.

    更新日期:2019-12-05
  • Theoretical studies of perimidine and its derivatives: structures, energies, and spectra
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-03
    Ibon Alkorta, José Elguero

    Theoretical calculations at the B3LYP/6-311++G(d,p) level plus GIAO calculations for NMR absolute shieldings have been carried out for the parent perimidine and several of its derivatives. These include its anion and cation and the acid-base equilibria and other examples of annular tautomerism, such as the 2-hydroxy (and their radical cations), 2-thiol, 2-amino, and 2-alkyl perimidines, and the functional tautomers, such as the benzologues of perimidone. The protonation of 2-aminoperimidines (cyclic guanidines) and the properties of perimidine carbene (dimerization and addition to carbon dioxide), biperimidine, dihydroperimidine, and spiro bidihydroperimidine were also studied.

    更新日期:2019-12-03
  • Kinetics of the hydrogen abstraction alkane + O 2 → alkyl + HO 2 reaction class: an application of the reaction class transition state theory
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-03
    Maciej Baradyn, Artur Ratkiewicz

    In this work, the kinetics of reaction class of hydrogen abstraction from saturated hydrocarbons by O2 molecules has been studied. The high-pressure reaction rate constants were determined using reaction class transition state theory/structure-activity relationship (RC-TST/SAR) methodology, augmented by linear energy relationship (LER) and/or barrier height grouping (BHG) approximations for evaluation of the reaction barrier heights. The parameters needed have been derived from DFT calculations at M06-2X/aug-cc-pVTZ level for a training set of 23 reactions, involving hydrogen abstraction by O2 molecule at primary, secondary, and tertiary carbon sites. The reference reaction rate constant C2H6 + O2 → C2H5 + HO2 was obtained by extrapolation of the simplest reaction within the title family CH4 + O2 → CH3 + HO2. Kinetic parameters of the later one, calculated from canonical variational transition state theory (CVT), were taken from literature. The influence of low-frequency internal rotations has been investigated in details. The error analysis shows that the average systematic error of RC-TST/SAR-derived rate constants at low temperatures is within 25% compared to the explicit RC-TST results and diminishes at higher temperatures. This suggests that the proposed methodology can be effectively implemented in the automated mechanism generation codes to create the fuel combustion mechanisms.

    更新日期:2019-12-03
  • The association of π–π stacking and hydrogen bonding interactions in substituted Rebek imide with 2,6-di(isobutyramido)pyridine rings: theoretical insight into X-Rebek imide||pyr complexes
    Struct. Chem. (IF 1.624) Pub Date : 2019-12-03
    Sabereh Parvizi Moghadam, Marziyeh Mohammadi, Reza Behjatmanesh-Ardakani

    A host–guest model designed between two hemispheres as Rebek imide receptor and different ligands via triple hydrogen bonding and π−π stacking interactions was surveyed to investigate the substituent effects. The association of Rebek imide with 2,6-di(isobutyramido)pyridine (X-Rebek imide||pyr) in the presence of electron donating/withdrawing substituents was studied (X = (NCH3)2, OCH3, CH3, OH, H, F, Cl, Br and CN, CF3 and NO2, where || and ∙∙∙ denote π–π stacking and hydrogen bonding). It was explained the variation in binding energies, energy decomposition, geometries, NMR properties, and electron density of mentioned complexes and effect of different types of the substituents in studied complexes was identified via computational chemistry at M05-2X/6-311++G** level of theory on π–π stacking and hydrogen bonding interactions.

    更新日期:2019-12-03
  • The conformation of biliverdin in dimethyl sulfoxide: implications for the coordination with copper
    Struct. Chem. (IF 1.624) Pub Date : 2019-05-20
    Milena S. Dimitrijević, Milan Žižić, Mario Piccioli, Jelena Bogdanović Pristov, Ivan Spasojević

    Biliverdin (BV) structure was analyzed by using NMR techniques and unrestricted density function theory simulations to explain the incapacity of BV to build coordination complex(es) with Cu2+ in dimethyl sulfoxide, which was confirmed by UV-Vis, EPR and NMR spectroscopy. NMR showed that N atoms are protonated in all four pyrrole rings. The structure is stabilized by two hydrogen bonds between NH moieties and carbonyl oxygens from opposite terminal pyrrole rings, and by the bending of propionyl chain with carboxyl group out of the plain toward central position of BV. The simulations of deprotonated BV, which builds copper complexes in water and chloroform as described previously, showed a different conformation and organization of hydrogen bonds. Taking into account that deprotonation represents a critical step in coordinate bonds formation, the protonation of an additional N atom may represent a key difference between the interactions of BV with copper in different solvents.

    更新日期:2019-11-06
  • Exploration of H 2 S capture by alkanolamines
    Struct. Chem. (IF 1.624) Pub Date : 2019-06-15
    Xue Song, Yingming Zhang, Chuan Wu, Xia Sheng, Hailiang Zhao

    H2S is a kind of impurity in the alternative energy resource of biogas and landfill gas. Among the removal methods, absorption by alkanolamines is the commonly accepted and widely used ones. This is due to the efficient regeneration. In this study, the absorption mechanism of H2S by two alkanolamines, namely diethanolamine (DEA) and N-methyldiethanolamine (MDEA), was proposed in a different way and analyzed by DFT calculations. The structural, energetic, red shifts and topological analysis of the most stable structures were then investigated. The values of electron densities and Laplacian densities at the bond critical points fall in the range of a hydrogen bond. Two kinds of hydrogen bonds S–H···N and O–H···S formed between H2S and DEA/MDEA are considered to be the driving forces during the absorption process. Thus, it can be known that H2S can act as both a hydrogen bond acceptor and a donor. Besides, the S–H···N hydrogen bond is much stronger than the O–H···S hydrogen bond. According to the change rules of Gibbs energies, the formation of hydrogen bond becomes difficult with increasing temperature and deceasing pressure. The absorption mechanism of H2S captured by alkanolamines via hydrogen bond interaction provides a novel theoretical direction for further study.

    更新日期:2019-11-06
  • A surface-stacking structural model for icosahedral quasicrystals
    Struct. Chem. (IF 1.624) Pub Date : 2019-08-14
    Rima Ajlouni

    An original structural model for the description of icosahedral quasicrystals is proposed. This novel theoretical approach is based on a surface-stacking image of icosahedral quasicrystals and is in concert with the step-terrace morphology observed in many experimental investigations of real icosahedral surfaces. According to this model, the infinite icosahedral structure is constructed by stacking two arrangements of quasi-periodic surfaces along each of the 5-fold axis of the icosahedral symmetry. In this stacking order, the spacings between the layered surfaces are governed by Fibonacci sequence. The proposed model operates within the real physical (Euclidean) space and provides a direct three-dimensional visual representation of the icosahedral superstructure, which can be instrumental for conducting different modes of experimentations, analyses, and fabrication strategies; eliminating a major roadblock for researchers especially outside the fields of crystallography and material science. More importantly, understanding the long-range surface-stacking logic of the icosahedral structure will hopefully provide a deeper understanding of the structure of quasicrystals at an atomic scale and help achieve improved control over material compositions and structure.

    更新日期:2019-11-06
  • Relationship between electronic structures and antiplasmodial activities of xanthone derivatives: a 2D-QSAR approach
    Struct. Chem. (IF 1.624) Pub Date : 2019-05-24
    Gaston A. Kpotin, Affoué Lucie Bédé, Alice Houngue-Kpota, Wilfried Anatovi, Urbain A. Kuevi, Guy S. Atohoun, Jean-Baptiste Mensah, Juan S. Gómez-Jeria, Michael Badawi

    Malaria is an important disease causing many death in several countries of Africa and Asia. In these continents, some plants such as Garcinia cola are used to fight against this disease because they contain xanthone derivatives which present antiplasmodial activity. The present theoretical study aims to establish a relationship between the electronic structure and the antiplasmodial activity of some xanthone derivatives, and more specifically to build a 2D-pharmacophore model in order to predict the biological activity of xanthone derivatives. The calculations are performed within the density functional theory (DFT) using the B3LYP/6-31G(d,p) level of theory. The developed approach quantitative structure-activity relationship (QSAR) follows the Klopman-Peradejordi-Gómez (KPG) methodology. We obtain a statistically significant equation relating the variation of the logarithm of half maximal inhibitory concentration (log(IC50)) with the variation of the numerical values of a set of eight local atomic reactivity descriptors (R = 0.98, R2 = 0.97, adj-R2 = 0.95, F(8.13) = 48.63, p < 0.00000, SD 0.08). The antiplasmodial activity seems to be driven by atomic orbitals and charges. Our 2D-pharmacophore model should be useful to propose new xanthone derivatives with higher antiplasmodial activity.

    更新日期:2019-11-06
  • Structure, stability and reactivity of neutral bimetallic manganese oxide clusters with CO and NO—a DFT study
    Struct. Chem. (IF 1.624) Pub Date : 2019-04-25
    Suresh Sampathkumar, Vijayakumar Subramaniam, Selvarengan Paranthaman

    In this work, the structure, stability and reactivity of neutral bimetallic manganese oxide clusters MnMdO2–4 (Md = Ti, V and Cr) with CO and NO are investigated by means of density functional theory (DFT). The hybrid PBE0 with TZVP basis set is employed to obtain MnMdO2–4 minimum energy structures, reactants, reaction intermediates, transition states and products. Our calculations show that the structural parameters are significantly altered when replacing Mn with Ti, V or Cr. All the clusters considered in this study have higher binding energy per atom, which implies that they are highly stable. Further, these clusters have smaller oxygen dissociation energy than CO2 and NO2. This indicates that the O atom can easily dissociate from these clusters and form CO2 and NO2. Our reactivity study shows that the CO and NO oxidation by MnTiO4 cluster is a favourable reaction. These oxidation reactions are barrierless and thermodynamically and kinetically favourable. Therefore, MnTiO4 can be used as a suitable catalyst for CO and NO oxidation. From this study, it is concluded that the titanium-supported manganese oxide will be a suitable catalyst for the CO and NO oxidation in the condensed phase.

    更新日期:2019-11-06
  • The reaction mechanism study on the decarbonylation of 2-methyl-2-propenal assisted by hydrogen chloride, water, or sulfur acid
    Struct. Chem. (IF 1.624) Pub Date : 2019-05-11
    Benni Du, Weichao Zhang

    The catalytic decarbonylation reaction mechanisms of 2-methyl-2-propenal in the presence of hydrogen chloride (HCl), water (H2O), or sulfuric acid (H2SO4) have been investigated theoretically for the first time. Both concerted and stepwise mechanisms have been considered. Compared with uncatalyzed reaction, the transition state energy is decreased by 90.46, 26.35, or 146.74 kJ/mol when the reaction is carried out with HCl, H2O, or H2SO4 as a catalyst, respectively. Our calculations demonstrate that the presence of HCl can reduce the transition state energy dramatically and make the decarbonylation of 2-methyl-2-propenal to be carried out at much lower temperatures, which is consistent with the experimental result. Moreover, the lowest activation energy assisted by H2SO4 suggests that H2SO4 may have better catalytic ability than that of HCl for the decarbonylation of 2-methyl-2-propenal, and our calculational results may be useful for future experimental studies on the title reaction.

    更新日期:2019-11-06
  • Nitrogen substitution effect on hydrogen adsorption properties of Ti-decorated benzene
    Struct. Chem. (IF 1.624) Pub Date : 2019-04-25
    Priyanka Tavhare, Ajay Chaudhari

    Ab initio calculations are performed to study hydrogen storage properties of Ti-doped benzene and Ti-doped nitrogen-substituted benzene complexes. Two of the carbon atoms in benzene are replaced by two nitrogen atoms. Two nitrogen atoms are substituted either at 1-2, 1-3, or 1-4 positions of a benzene ring and named as BN1-2Ti, BN1-3Ti, and BN1-4Ti, respectively. Maximum four, four, three, and four H2 molecules get adsorbed on C6H6Ti, BN1-2Ti, BN1-3Ti, and BN1-4Ti complexes respectively with respective H2 uptake capacity of 6.02, 5.84, 4.45, and 5.84 wt%. The positive Gibbs free energy corrected H2 adsorption energy values obtained for all these complexes at ambient conditions indicate that the formation of these complexes at room temperature is thermodynamically favorable. Temperature- and pressure-dependent adsorption energy calculations show that the H2 adsorption on all these complexes is feasible over a wide range of temperature and pressure. The gap between the highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbital (LUMO) is found to be greater than 5 eV for all the complexes indicating stability of these complexes. The H2 molecules interact more strongly with Ti-doped nitrogen-substituted benzene than the Ti-doped benzene that results in higher H2 desorption temperature obtained using van 't Hoff equation for the former than the latter. The density of states plots have been used to understand the H2 adsorption mechanism.

    更新日期:2019-11-06
  • Water-induced isomerism of salicylaldehyde and 2-acetylpyridine mono- and bis-(thiocarbohydrazones) improves the antioxidant activity: spectroscopic and DFT study
    Struct. Chem. (IF 1.624) Pub Date : 2019-06-19
    Mohamed H. Assaleh, Aleksandra R. Božić, Snežana Bjelogrlić, Milena Milošević, Milena Simić, Aleksandar D. Marinković, Ilija N. Cvijetić

    Thiocarbohydrazones (TCHs) and structurally related molecules are versatile organic compounds which exert antioxidant, anticancer, and other beneficial health effects. The combination of UV/Vis, NMR spectroscopy, and quantum chemical calculations was used to rationalize the experimentally observed increase in the radical scavenging activity upon the addition of water in DMSO solution of TCHs. Mono- and bis(salicylaldehyde) TCHs (compounds 1 and 2) undergo water-induced E-to-Z isomerization which is followed by disruption of intramolecular hydrogen bond, ground state destabilization, and 11 kcal/mol decrease in the bond dissociation enthalpy (BDE). Electron spin delocalization is more pronounced in Z-isomers of 1 and 2. On the other hand, 2-acetylpyridine TCHs (compounds 3 and 4) undergo thione-to-thiol tautomerism which also decreases the BDE and facilitates the hydrogen atom transfer to 2,2-diphenyl-1-picrylhydrazyl radical (DPPH∙). The appearance of thiolic –SH group as another reactive site toward free radicals improves the antioxidant activity of 3 and 4. The spin density of 3- and 4-thiol radicals is delocalized over the entire thiocarbohydrazide moiety compared to more localized spin of thione radicals. Additional stabilization of thiol radicals corroborates with the increased antioxidant activity. This study provides the new insights on the solution structure of TCHs, and also highlights the importance of solution structure determination when studying the structure-antioxidant relationships of isomerizable compounds.

    更新日期:2019-11-06
  • Structural correlation and computational quantum chemical explorations of two 1,2,3-triazolyl-methoxypyridine derivatives as CYP51 antifungal inhibitors
    Struct. Chem. (IF 1.624) Pub Date : 2019-05-07
    C. Ravikumar, S. Murugavel

    Structural correlation and computational quantum chemical optimization of two 1,2,3-triazolyl-methoxypyridine derivatives fused with a five-membered heterocyclic moiety, furan (I) or thiophene (II), were performed. Compounds I and II belong to the triclinic crystal classification with P-1 space group. The bond lengths and angles of the optimized crystal structures are in good agreement with the XRD experimental data. We confirmed the hydrogen bonding interactions that observed in crystal packing of compounds I and II using Hirshfeld surface and energy framework analysis. The DFT functional non-linear optical and thermochemistry parameters of the title compounds were calculated. The local reactivity domains of compounds I and II were recognized by the Fukui function parameter analysis. In silico molecular docking simulations were carried out to discover the lanosterol 14 α-demethylase (CYP51) enzyme inhibition against target protein (PDB ID: 1EA1). Antifungal activity of the title molecules was predicted by in vitro antifungal studies against three fungal strains using fungal drug fluconazole as a positive control. Compound I exhibited enhanced affinity with receptor 1EA1 and higher inhibition activity with fungal strains compared to compound II.

    更新日期:2019-11-06
  • Biological activity of some ACAT inhibitors in the light of DFT-based quantum descriptors
    Struct. Chem. (IF 1.624) Pub Date : 2019-06-03
    Sutapa Mondal Roy, Bhumika K. Sharma, Debesh R. Roy

    A detailed investigation is performed for a series of 24 aminosulfonyl carbamates as acyl-CoA: cholesterol O-acyltransferase (ACAT) inhibitors. The biological activity of aminosulfonyl carbamates in terms of log (IC50) has been estimated by developing suitable quantum chemical descriptors in the light of density functional theory. In order to understand inhibitor-biosystem interactions and to identify potential descriptors, a model biosystem is considered which comprises five different nucleic acid bases. Accordingly, two global descriptors, viz. electron affinity (EA) and energy transfer during the interaction between inhibitors and biosystems (∆E), and a local descriptor, viz. group atomic charges on sulfonyl moiety (∑QSul), are developed toward understanding bio-activity of aminosulfonyl carbamates. It is noteworthy to achieve that the three-parameter regression model for considered parameters EA, ∆E, and ∑QSul is observed to predict about 90% activities of aminosulfonyl carbamates in terms of log(IC50). The developed regression model is also statistically validated and successfully tested for unknown compounds.

    更新日期:2019-11-06
  • Application of multilayered strategy for variable selection in QSAR modeling of PET and SPECT imaging agents as diagnostic agents for Alzheimer’s disease
    Struct. Chem. (IF 1.624) Pub Date : 2019-06-19
    Priyanka De, Dhananjay Bhattacharyya, Kunal Roy

    Non-invasive imaging of amyloid beta (Aβ) and tau fibrils in the brain may support an early and precise diagnosis of Alzheimer’s disease. Molecular imaging technologies involving radionuclides such as positron emission tomography (PET) and single-photon emission computed tomography (SPECT) against beta amyloid plaques and tau fibrils are among emerging research areas in the field of medicinal chemistry. In the current study, we have developed partial least square (PLS) regression-based two-dimensional quantitative structure-activity relationship (2D-QSAR) models using datasets of 38 PET and 73 SPECT imaging agents targeted against Aβ protein and 31 imaging agents (both PET and SPECT) targeted against tau protein. Following the strict Organization for Economic Co-operation and Development (OECD) guidelines, we have strived to select significant descriptors from the large initial pool of descriptors using multilayered variable selection strategy using the double cross-validation (DCV) method followed by the best subset selection (BSS) method prior to the development of the final PLS models. The developed models showed significant statistical performance and reliability. Molecular docking studies have been performed to understand the molecular interactions between the ligand and receptor, and the results are then correlated with the structural features obtained from the QSAR models. Furthermore, we have also designed some imaging agents based on the information provided by the models developed and some of them are predicted to be similar to or more active than the most active imaging agents present in the original dataset.

    更新日期:2019-11-06
  • Theoretical calculations of a porous coordination polymer formed by isonicotinylhydrazine, 1,4-benzenedicarboxylic and Co 2+ : electronic properties, lithium doping, and H 2 adsorption studies
    Struct. Chem. (IF 1.624) Pub Date : 2019-06-03
    Filipe Barra De Almeida, Heitor Avelino De Abreu, Renata Diniz

    The present work is focused in the theoretical study of a porous coordination polymer formed by isonicotinylhydrazine (INH), 1,4-benzenedicarboxylic (14BDC) acid, and Co2+. This coordination polymer [Co{CP}] was studied by density of states and charge density difference, which allowed determining its electronic properties, transitions of valence to conduction band and its post-synthesis capacity. We have also evaluated the possibility of inserting lithium into the structure and observed that the resulting structure is stable and energetically favorable. Furthermore, taking into account gas adsorption applications, the insertion of a H2 was also conducted in both [Co{CP}] and lithium-doped structure. Our results have showed that the adsorption of hydrogen in Co{CP} is energetically unfavorable, while in the lithium-doped structure, it showed remarkable potential. Overall, we were able to show in this work after thorough calculation that the insertion of lithium ions into the coordination polymer structure is highly beneficial, improving drastically its hydrogen adsorption ability, which opens a wide window of opportunities towards the development of new coordination polymers for gas adsorption.

    更新日期:2019-11-06
  • Exploring the transfer of hydrogen atom from kaempferol-based compounds to hydroxyl radical at ground state using PCM-DFT approach
    Struct. Chem. (IF 1.624) Pub Date : 2019-05-03
    Khajadpai Thipyapong, Nuttawisit Yasarawan

    Thermodynamic and kinetic studies of the hydrogen atom transfer (HAT) from hydroxyl (OH) groups of four kaempferol-based compounds, namely kaempferol, morin, morin-5*-sulfonate and morin-7-O-sulfate to hydroxyl radical (·OH), have been carried out using density functional theory (DFT) methods at the CAM-B3LYP/6–311++G(d,p) level equipped with polarizable continuum model (PCM) of solvation. All HAT reactions in aqueous solution are exothermic and spontaneous. For most compounds, the most preferable OH group for HAT is situated at position C3 (O3-H3) on the pyrone ring. The reaction potential of such a reactive group is found to be highest in morin-7-O-sulfate. The rate constants for the HAT reactions at different OH groups of each compound have been determined based on the transition state theory. The presence of substituents leads to the variation in either the characteristic interactions at the reactive site or the charge distribution on transition-state geometries, hence significantly affecting the kinetics of HAT. The highest rate of HAT is resulted for the OH group at position C4* (O4*-H4*) on the phenyl ring (ring B) of morin-5*-sulfonate because a hydrogen bond between ·OH and the sulfonate group favors the formation of transition state. However, for most compounds under study, the HAT reaction at O3-H3 initiated by ·OH is highly favorable both thermodynamically and kinetically.

    更新日期:2019-11-06
  • Anomeric effect in pyranose-ring derivatives containing carbon, silicon, and germanium as anomeric centers: an ab initio systematic study
    Struct. Chem. (IF 1.624) Pub Date : 2019-05-07
    P. G. Rodríguez Ortega, M. Montejo, M. Sánchez Valera, J. J. López González

    We have performed a systematic conformational analysis focused on the evaluation of the anomeric effect (AE) in a series of pyranose derivatives containing carbon, silicon, and germanium as anomeric centers (c*) using the MP2/aug-cc-pVDZ level of theory together with natural bond orbital (NBO) electronic structure calculations. Although, both endo- and exo-anomeric effects operate within all the systems studied; the conformational preference towards the axial (α) form can be explained in terms of the incidence of the endo-anomeric effect. The magnitude calculated for the AE is considerably higher for compounds containing carbon as c*. On the other hand, the lower magnitude of the hyperconjugative delocalizations towards antibonding exocyclic anomeric orbitals in Si- and Ge-containing compounds can be justified by the availability of energetically accessible vacant d-type orbitals in these atoms. While the conformational preference in the carbon group is purely related to a higher anomeric hyperconjugation in the α conformers, steric and electrostatic factors dictate the conformational α arrangement in the Si- and Ge-containing compounds. Implicit consideration of the solvent (water) produces a notable increase in the population of the β anomers in some of the systems into study. However, the results of NBO energy partition study performed reveal that the merely observation of a change in the α/β ratio for a given system upon solvation should not be taken as an indication of a predominant role of electrostatic effects as the origin for their anomeric preference.

    更新日期:2019-11-06
  • Crystal structures and biological activity of homologated (N)- n -alkylammonium salts of 2-bromo-3-oxido-1,4-naphthoquinone
    Struct. Chem. (IF 1.624) Pub Date : 2019-05-10
    Dinkar Choudhari, Debamitra Chakravarty, Dipali N. Lande, Sana Parveen, Shridhar P. Gejji, Kisan M. Kodam, Sunita Salunke-Gawali

    Homologated (N)-n-alkylammonium salts of 2-bromo-3-oxido-1,4-naphthoquinone (BS-1 to BS-8) have been synthesized and characterized from the single crystal X-ray diffraction experiments combined with density functional theory. The crystal structures revealed diverse noncovalent interactions such as hydrogen bonding, π∙∙∙π, Br∙∙∙π, and others. The measured antifungal activities of the BS-1 to BS-6 against fungal strains Saccharomyces cerevisiae and Candida albicans suggest them to be effective compared to standard drug amphotericin B. Antibacterial activity of BS-1 to BS-6 has been evaluated against Gram-positive and Gram-negative bacteria.

    更新日期:2019-11-06
  • Regulating PdC 3 /PtC 3 ···thiophene interaction by small molecule doping (AgOTf, CuBr, CuI, CuBr 2 , PdCl 2 )
    Struct. Chem. (IF 1.624) Pub Date : 2019-06-15
    Jiao Lv, Ling Wang, Zheng Sun, Qingzhong Li, Xiaoyan Li

    The influences of small molecule doping on PdC3/PtC3···thiophene interaction have been investigated by atoms in molecules (AIM) theory, electron location function (ELF), electron decomposition analysis (EDA), natural bond orbital (NBO) analysis, and molecular formation density difference (MFDD). The results show that PdC3/PtC3···thiophene interactions are of moderate strength and display partial covalent character. Both the strength and the covalent character of PtC3···thiophene interactions are stronger than those of PdC3···thiophene interactions. Small molecules with different valence state metal doping on thiophene ring show different influences on the strength and nature of PdC3/PtC3···thiophene interactions. The bivalent metals enhance both the strength and covalent character of PdC3/PtC3···thiophene interactions. The monovalent metals have little influence on the strength, only enhance the covalent character of PdC3/PtC3···thiophene interactions.

    更新日期:2019-11-06
  • Diarylthiazole and diarylimidazole selective COX-1 inhibitor analysis through pharmacophore modeling, virtual screening, and DFT-based approaches
    Struct. Chem. (IF 1.624) Pub Date : 2019-08-30
    Luminita Crisan, Ana Borota, Alina Bora, Liliana Pacureanu

    The current work is focused on in silico modeling of COX-1 inhibitors with enhanced safety gastric profile. A 5-point pharmacophore model, atom-based 3D quantitative structure-activity relationship (3D-QSAR) and electronic properties were computed for a series of COX-1 inhibitors. The best pharmacophore model AAHRR.10 consisting of two hydrogen bond acceptors, one hydrophobic site, and two rings was developed to derive a predictive, statistically significant 3D-QSAR model at three partial least square factors (R2 = 0.991, SD = 0.059, F = 278.5, Q2 = 0.682, RMSE = 0.325, Pearson’s R = 0.903, Spearman’s rho = 0.872). The AAHRR.10 hypothesis was validated by enrichment studies employing a custom-made validation dataset adopting selective COX-1 inhibitors extracted from ChEMBL and decoys generated via DUD methodology. The global reactivity descriptors, such as HOMO and LUMO energies, the HOMO-LUMO gaps, global hardness, softness, Fukui indices, and electrostatic potential, were carried out using density functional theory (DFT) to confirm the key structural features required to achieve COX-1 selectivity. Well-validated AAHRR.10 hypothesis was further used as 3D query in virtual screening of the DrugBank database to detect novel potential COX-1 inhibitors. Docking algorithm was applied to enhance the pharmacophore prediction and to recommend drugs for repositioning, which can interact selectively with COX-1.

    更新日期:2019-11-06
  • Nitrogen monoxide storage and sensing applications of transition metal–doped boron nitride nanotubes: a DFT investigation
    Struct. Chem. (IF 1.624) Pub Date : 2019-04-25
    Suphawarat Phalinyot, Chanukorn Tabtimsai, Banchob Wanno

    The structural properties, electronic properties, and adsorption abilities for nitrogen monoxide (NO) molecule adsorption on pristine and transition metal (TM = V, Cr, Mn, Nb, Mo, Tc, Ta, W, and Re) doping on B or N site of armchair (5,5) single-walled boron nitride nanotube (BNNT) were investigated using the density functional theory method. The binding energies of TM-doped BNNTs reveal that the Mo atom doping exhibits the strongest binding ability with BNNT. In addition, the NO molecule weakly interacts with the pristine BNNT, whereas it has a strong adsorption ability on TM-doped BNNTs. The increase in the adsorption ability of NO molecule onto the TM-doped BNNTs is due to the geometrical deformation on TM doping site and the charge transfer between TM-doped BNNTs and NO molecule. Moreover, a significant decrease in energy gap of the BNNT after TM doping is expected to be an available strategy for improving its electrical conductivity. These observations suggest that NO adsorption and sensing ability of BNNT could be greatly improved by introducing appropriate TM dopant. Therefore, TM-doped BNNTs may be a useful guidance to be storage and sensing materials for the detection of NO molecule.

    更新日期:2019-11-06
  • Synthesis, crystal structure, spectroscopic investigations, and computational studies of Ni(II) and Pd(II) complexes with asymmetric tetradentate NOON Schiff base ligand
    Struct. Chem. (IF 1.624) Pub Date : 2019-05-14
    Hadi Kargar, Vajiheh Torabi, Alireza Akbari, Reza Behjatmanesh-Ardakani, Atefeh Sahraei, Muhammad Nawaz Tahir

    In the present study, an asymmetric tetradentate NOON Schiff base ligand 2,2′-((4-methyl-1,2-phenylene)bis(nitrilomethylylidene))bis(4-chlorophenol) (H2L) was synthesized by condensation of 4-methylphenylenediamine with 5-chlorosalicylaldehyde. The Ni(II) and Pd(II) Schiff base complexes were synthesized from the reaction of Ni(OAc)2·4H2O and Pd(OAc)2 with the Schiff base ligand (H2L) in methanol and acetonitrile, respectively. The ligand and its complexes were characterized by FT-IR, 1H NMR, UV-Vis spectroscopy, and elemental analyses. Moreover, the crystal structure of the ligand and Pd(II) complex has been determined by single-crystal X-ray crystallography. The single-crystal X-ray analysis of PdL complex demonstrated a four-coordinated complex by two nitrogen atoms and two phenolate groups. In addition, DFT and TD-DFT calculations were done using M06-2X and B3LYP levels of theory along with Def2-TZVP and ATZP basis sets for ligand and its complexes. Theoretical IR and nature of electronic transition in TD-TDFT data were analyzed by frequency and NBO-CMO calculations.

    更新日期:2019-11-06
  • Quantitative structure-activity relationship models for bitter-tasting tripeptides based on integrated descriptors
    Struct. Chem. (IF 1.624) Pub Date : 2019-10-31
    Fangfang Wang, Bo Zhou

    In the present work, three-dimensional quantitative structure-activity relationship (3D-QSAR) models were developed in an attempt to predict the key features of bitter-tasting tripeptides. The 3D-QSAR models were carried out by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods and the corresponding statistical correlation coefficients R2cv for the training set are 0.534 and 0.547, respectively, the predicted correlation coefficients R2pred for the test set are found to be 0.7162 and 0.5792, respectively. The information obtained from the QSAR contour maps enables the interpretation of the structure-activity relationship. In addition, molecular docking was also employed to investigate the interaction between bitter-tasting peptides and related receptor hTAS2R1, results indicate that the Lys76, Pro188 and His243 were significant for binding to the peptides, and some essential features were identified to deduce some interesting structure-activity relationships. The present QSAR models along with information contour maps and molecular docking study may be used for designing and predicting novel bitter-tasting peptides.

    更新日期:2019-11-04
  • Another look at bonds and bonding
    Struct. Chem. (IF 1.624) Pub Date : 2019-10-30
    David Brown

    Because electrostatic flux does not depend on the location of the charges it links, it is independent of the quantum mechanical charge distribution in a molecule. By identifying a chemical bond with the electrostatic flux linking an atom’s core to its valence charge, one can generate a purely classical model of chemical bonding. The resulting bond flux model shows that the chemical bond is a classical, not a quantum, concept. It makes no distinction between covalent and ionic bonds, but provides quantitative insights into chemical structure and properties that complement those of quantum theory.

    更新日期:2019-11-04
  • Dual targeting approach for Mycobacterium tuberculosis drug discovery: insights from DFT calculations and molecular dynamics simulations
    Struct. Chem. (IF 1.624) Pub Date : 2019-10-28
    Murtala A. Ejalonibu, Ahmed A. Elrashedy, Monsurat M. Lawal, Mahmoud E. Soliman, Sphelele C. Sosibo, Hezekiel M. Kumalo, Ndumiso N. Mhlongo

    Drug-resistant tuberculosis (TB) infections are on the rise and anti-tuberculosis drugs that inhibit Mycobacterium tuberculosis (M. tuberculosis) through a new novel mechanism could be an important component of evolving TB therapy. Pantothenate kinase (PanK) and CTP synthetase (PyrG) are both essential for de novo pyrimidine biosynthesis. Given the extensive knowledge base on de novo pyrimidine biosynthesis inhibition of M. tuberculosis growth and survival, these enzymes present an interesting opportunity for anti-mycobacterial drug discovery. A recent experimental study shows that CDD-823953 and GSK-735826A act as dual PanK and PyrG inhibitors, respectively. However, the molecular mechanisms of their selective inhibition remain elusive. Herein, density functional theory (DFT) calculation was applied to unveil the molecular and reactivity properties of two lead compounds targeting these enzymes in a shot. Molecular dynamics simulations were then employed to investigate the inhibitory mechanism as well as selectivity impact of these potential inhibitors for their enzymes. Computational modeling of the ligands and the enzyme–ligand systems reveal that CDD-823953 and GSK-735826A lead compounds can potentially inhibit both PanK and PyrG thereby creating a pathway via the use of double target approach in tuberculosis treatment.

    更新日期:2019-11-04
  • Single-ion magnet behavior of two pentacoordinate Co II complexes with a pincer ligand 2,6-bis(imidazo[1,5-a] pyridin-3-yl)pyridine
    Struct. Chem. (IF 1.624) Pub Date : 2019-10-24
    Yanfeng Cui, Yu Ge, Yahong Li, Jin Tao, Jinlei Yao, Yaping Dong

    Two new air-stable mononuclear pentacoordinate CoII complexes [Co(bpip)(NCS)2] (1) and [Co(bpip)Br2] (2), which are based on a NNN-pincer ligand 2,6-bis(imidazo[1,5-a]pyridin-3-yl)pyridine (abbreviated as bpip), were successfully synthesized and structurally characterized. Although two different halogen and pseudohalogen terminal ligands were employed, single-crystal X-ray crystallographic analyses revealed that the CoII center of 1 and 2 adopts C4v symmetry and displays the similar distorted square-pyramidal geometry. Magnetic studies showed that two compounds exhibit slow magnetic relaxation in the presence of an applied dc field, namely, they display the behavior of single-ion magnets (SIMs). The reported two complexes enrich the chemistry of cobalt(II) single-ion magnets (SIMs) with low coordination numbers and highlight the differences in the magnetic behaviors caused by the different terminal ligands.

    更新日期:2019-11-04
  • Cytotoxicity of doxorubicin conjugated with C 60 fullerene. Structural and in vitro studies
    Struct. Chem. (IF 1.624) Pub Date : 2019-10-22
    Kamila Butowska, Witold Kozak, Magdalena Zdrowowicz, Samanta Makurat, Michał Rychłowski, Aleksandra Hać, Anna Herman-Antosiewicz, Jacek Piosik, Janusz Rak

    Conjugating an anticancer drug of high biological efficacy but large cytotoxicity with a “transporting” molecule of low toxicity constitutes a valuable approach to design safe drug delivery system. In the present study, doxorubicin (DOX) a drug of large cardiotoxicity was chemically conjugated to a C60-fullerene. The synthesized molecule, a fullerene-doxorubicin conjugate (Ful-DOX), was characterized using the 1H NMR and MALDI TOF mass spectrometry. The absorption and fluorescence spectra and dynamic light scattering of the conjugate were recorded in an aqueous solution, while the impact on viability of several cancer cell lines of the free DOX and the conjugate was compared using the SRB and WST-1 assays. A low antiproliferative activity of the conjugate as compared to the free DOX is a consequence of the presence of fullerene moiety in the former, which is also responsible for the conjugate aggregation in an aqueous solution. Unlike free DOX, these aggregates cannot pass through the nuclear membrane (as demonstrated by the confocal microscopy measurements), which makes them marginally cytotoxic.

    更新日期:2019-11-04
  • A new look at the essence of the formation of trigonal planar coordination of the central N and O atoms
    Struct. Chem. (IF 1.624) Pub Date : 2019-10-22
    Rui-ping Huo, Xiang Zhang, Cai-feng Zhang

    In this paper, we argued that the classical explanation to the formation of trigonal planar coordination of the center N and O atoms in N(SiR3)3 and [O(SiR3)3]+ by forming 4-center 2-electron conjugated d-pπ bond was questionable, since it could not correctly predict the configurations of P(SiR3)3 and [S(SiR3)3]+. We found that the trigonal planar configuration of the center N and O atoms was strongly correlated to the greater difference between the electronic negativities of the center atom N/O, and the around Si atoms. We proposed that repulsive interactions among the three positive charged YR3 (Y=Si) moieties resulted in the trigonal planar configuration of the center N and O atoms. This proposal was supported by the predicted trigonal planar configurations of model species [F(BH3)3]− and [O(BH3)3]2−, in which the formation of 4-center 2-electron conjugated d-pπ bond was impossible.

    更新日期:2019-11-04
  • From clusters to crystals: scale chemistry of intermetallics
    Struct. Chem. (IF 1.624) Pub Date : 2019-10-17
    Vladimir Ya. Shevchenko, Inna V. Medrish, Gregory D. Ilyushin, Vladislav A. Blatov

    We review different approaches to description, classification, and understanding of intermetallic structures of any complexity. All these approaches are based on the representation of the intermetallic structure as a periodic graph (net). A special attention is paid to the nanocluster model, which enables one to separate structural units and to describe their assemblage in intermetallics with strict computer algorithms. We demonstrate the abilities of the model with analysis of 12,315 intermetallic structures from the Inorganic Crystal Structure Database.

    更新日期:2019-11-04
  • Synthesis, characterization and biological evaluation of novel 2,2′-((1,2-diphenylethane-1,2-diylidene)bis(azanylylidene))bis(pyridin-3-ol)and metal complexes: molecular docking and in silico ADMET profile
    Struct. Chem. (IF 1.624) Pub Date : 2019-10-16
    S. Syed Ali Fathima, M. Mohamed Sahul Meeran, E. R. Nagarajan

    A novel series of bio vital Schiff base ligand and transition metal complexes was prepared from benzil, 2-amino-3-hydroxy pyridine and metal chlorides. The synthesized compounds were characterized by physicochemical measurements like elemental analysis, magnetic susceptibility, molar conductance and multispectral analysis like Fourier transform, electronic absorption, nuclear magnetic resonance, electron paramagnetic resonance, ESI-mass spectroscopy, XRD and scanning electron microscopy. Based on the spectral results, the synthesized compounds are in crystalline nature and copper complex has square planar geometry. Conversely, cobalt, nickel and zinc complexes have tetrahedral geometry. Furthermore, the biological potential of the synthesized compounds is analysed by DNA binding and cleavage analysis and antimicrobial, anticancer, apoptosis and antioxidant inspections. The DNA binding analysis was performed using UV absorption titration and hydrodynamic experiments, which unveiled that the prepared compounds could be interconnected with calf thymus DNA by the way of intercalative mode. The mode of intercalation is further supported by docking investigations with nucleic acid and Bowman-Birk inhibitor. The DNA cleaving analysis implied that Cu(II) complex has eminent cleaving ability to split up the pUC18 DNA with an oxidising agent. Additionally, the anti-pathogenic screening studies explained that the complexes have antimicrobial skill against selected microbes. The anti-carcinogenic talent of the compounds is scrutinized on human cancer cell lines, which revealed that the prepared compounds possess good anticancer proficiency. During Hoechst staining analysis, the synthesized compounds have undergone the morphological moderations and succeeding cell death. The free radical scavenging investigations display that the metal complexes hold the suited talent to hunt the OH radical effectively. The prediction of in silico ADMET belongings found out that synthesized compounds acquire substantial drug-likeness characters based on Lipinski’s rules.

    更新日期:2019-11-04
  • Small atomic clusters: quantum chemical research of isomeric composition and physical properties
    Struct. Chem. (IF 1.624) Pub Date : 2019-10-14
    Alexander S. Sharipov, Boris I. Loukhovitski

    In this review, we give a brief summary of methodological and computational aspects of determination of structure and different size-dependent properties of small atomic clusters by means of computational quantum chemistry. Particular attention is paid to the accurate calculation of thermodynamic properties of clusters with allowance for the vibrational anharmonicity and contribution of excited electronic states. We describe in detail the problems and consequences related to accounting for the contribution of isomeric forms to the observable physical and thermodynamic characteristics. The physical size-dependent properties discussed in this review are the binding energy, zero-point energy, collision diameter, polarizabilities, ionization potential, electron affinity, specific heat capacity, and reduced Gibbs energy. The major part of the review deals with the methodology for physically sound extrapolating the multitude of size-dependent physical and thermodynamic properties of small clusters toward significantly larger (nanometer- and micrometer-sized) particles.

    更新日期:2019-11-04
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