摘要 :
The MM2 method has been modified using a three-center charge model aimed at determining stacking geometries. The stacking interactions for the benzene dimer, porphine dimer, and bis( 4,5-diazafluoren-9-one thiosemicarbazonato)pall...
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The MM2 method has been modified using a three-center charge model aimed at determining stacking geometries. The stacking interactions for the benzene dimer, porphine dimer, and bis( 4,5-diazafluoren-9-one thiosemicarbazonato)palladium(II) have been assessed with both the three-center charge model and the conventional single-center charge model using the MM2 method. The modified MM2 method always gave better results than the conventional method, and the obtained structures by the former method are in good~greement with the proposed structures from those theoretical and experimental results. The possible advantages of using the three-center charge model for complex systems are also discussed.
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In the crystal structure of the bis(acetone-1-naphthoylhydrazinato)copper(II) complex there are interactions of neigh-bouring molecules via naphthyl groups; the naphthyl group of one molecule interacts with the copper centre and C...
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In the crystal structure of the bis(acetone-1-naphthoylhydrazinato)copper(II) complex there are interactions of neigh-bouring molecules via naphthyl groups; the naphthyl group of one molecule interacts with the copper centre and CH_3 group of another molecule. The geometry of the crystal structure and disposition of charges in the naphthyl and chelate rings indicate that there are stacking interactions between the aromatic ring and, not only the copper atom, but also the whole chelate ring.
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A series of semi-rigid N-phenylsuccinimides I (11Xy), N-arylmethylsuccinimides II (18Xy), and N,N0-(1,4- arylenebis(methylene))disuccinimides III (19XyX) walled by quinoxaline (QX), dimethylquinoxaline (diMQX), or benzoquinoxaline...
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A series of semi-rigid N-phenylsuccinimides I (11Xy), N-arylmethylsuccinimides II (18Xy), and N,N0-(1,4- arylenebis(methylene))disuccinimides III (19XyX) walled by quinoxaline (QX), dimethylquinoxaline (diMQX), or benzoquinoxaline (BQX) ring were synthesized. Intramolecular pep interactions in solution were detected by NMR and fluorescence spectroscopy, in terms of reciprocal anisotropic shielding and exciplex formation, respectively. The X-ray crystallographic analysis revealed the preferential conformations in solid state, which were compatible with the results of conformational studies by NMR and fluorescence spectroscopy. The results collectively indicated that 18Xy and 19XyX are driven by intramolecular π-π interactions in the mode of p-stacking (face-to-face) or T-shaped (edge-to-face) configuration to preferentially adopt the folded- and the double folded-conformation, respectively, where the spaced aromatic rings are oriented syn to each other in close proximity.
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The interaction between different cations and certain aromatic dimers (benzene, naphthalene, anthracene) and heteroaromatic dimers (pyridine, pyrazine, sym-triazine and sym-tetrazine) has been investigated employing the MP2 level ...
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The interaction between different cations and certain aromatic dimers (benzene, naphthalene, anthracene) and heteroaromatic dimers (pyridine, pyrazine, sym-triazine and sym-tetrazine) has been investigated employing the MP2 level of theory with the 6-31G** and 6-311++G** basis sets. The trend in the stabilization energy for aromatic dimers is found to be: (anthracene)2-cation(naphthalene)2-cation(benzene)2-cation. In all three cases, the cation remains sandwiched between the rings. In the case of the heteroaromatic systems, on the other hand, the cation prefers to interact with the nitrogen atom of the ring. These results can be rationalized by molecular electrostatic potential maps for the systems under consideration. In addition, these results are in conformity with the available cation aromatic database.
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Two new non-innocent ligands, H2LOPh and H2LSPh, were synthesized. Both ligands reacted with 0.5 equiv. of CuCl2 center dot 2H(2)O to provide the corresponding mononuclear diradical-containing Cu-II complexes[Cu(L-OPh(SQ))(2)](1) ...
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Two new non-innocent ligands, H2LOPh and H2LSPh, were synthesized. Both ligands reacted with 0.5 equiv. of CuCl2 center dot 2H(2)O to provide the corresponding mononuclear diradical-containing Cu-II complexes[Cu(L-OPh(SQ))(2)](1) and[Cu(L-SPh(SQ))(2)] (2). Both complexes were characterized by single-crystal X-ray diffraction measurements. Molecular structure analyses indicated that, in complex 1, the two -OPh groups of two [L-OPh(SQ)](-) ligands are situated trans to each other, while in complex 2, the two - SPh groups of two [L-SPh(SQ)](-) ligands were found to maintain a cis relationship. In complex 1, Cu-C-Ph interactions as well as two pi-pi interactions were observed between -OPh-group-containing C-6 phenyl rings and the radical-containing coordinated chelate rings. In complex 2, Cu-CPh interactions were ab-sent, although intramolecular pi-pi interactions within one of the two coordinating ligands were present. The pi-pi interactions were between the C-6 phenyl ring of an -SPh group and the 3,5-di-tert-butyl-amidophenolate unit. Variable-temperature magnetic susceptibility measurements indicated that both complexes acquire an S = 1/2 ground state. X-band EPR measurements confirmed that the unpaired electron is on the CuII center in both complexes. This implies that the expected Cu-II-S secondary interactions in complex 2 are suppressed by the dominating pi-pi stacking interactions, and the ground-state electronic configuration was found to be (up arrow up arrow down arrow) instead of the expected (up arrow down arrow up arrow).
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A parametrization of the Generalized Molecular Interaction Potential with polarization (GMIPp) for the study of aromatic stacking is presented. Parametrization is limited to the van der Waals parameters defining the dispersion-rep...
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A parametrization of the Generalized Molecular Interaction Potential with polarization (GMIPp) for the study of aromatic stacking is presented. Parametrization is limited to the van der Waals parameters defining the dispersion-repulsion interactions between the quantum and classical molecules, while electrostatic and polarization contributions are computed at the quantum mechanical level using a perturbational approach. The new parametrized GMIPp has been used to study different stacking interactions between nucleic acid bases.
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The title compound, C13H8IN3O5, crystallizes with Z' = 2 in the space group P2(1)/n. The two independent molecules, which are both almost planar, are conformational isomers. The molecules are linked into complex sheets by a combin...
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The title compound, C13H8IN3O5, crystallizes with Z' = 2 in the space group P2(1)/n. The two independent molecules, which are both almost planar, are conformational isomers. The molecules are linked into complex sheets by a combination of five independent C-H center dot center dot center dot O hydrogen bonds and an almost linear two-centre iodo-nitro interaction.
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Analysis of crystal structure data deposited in the Cambridge Structural Database (CSD) has shown that aromatic rings tend to stack with square planar transition metal complexes when they contain chelate rings. In these interactio...
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Analysis of crystal structure data deposited in the Cambridge Structural Database (CSD) has shown that aromatic rings tend to stack with square planar transition metal complexes when they contain chelate rings. In these interactions, the orientation between chelate and aryl ring is a parallel-displaced orientation, like stacking interactions between aromatic molecules. In fused systems containing chelate and aryl rings, the aryl rings prefer to stack with the chelate rather than with other aryl rings. Quantum chemical calculations show that chelate-aryl stacking is stronger than aryl-aryl stacking. Interaction energies of six-membered chelates of the acetylacetonato type with benzene exceed -6 kcal/mol (CCSD(T)/CBS), more that twice as strong as that for two benzene molecules. Further analysis of the CSD has shown that chelate rings, both isolated and fused stack with other chelate rings. These chelate-chelate stacking interactions can have both face-to-face and parallel-displaced geometries, unlike the stacking interactions between aromatic molecules, for which face-to-face geometry is not typical. Chelate-chelate stacking is stronger than aryl-aryl stacking and stronger even than chelate-aryl stacking. Stacking energies between six-membered chelates of acetylacetonato type exceed -9 kcal/mol, while those between five-membered dithiolene chelates are even stronger. Calculated interaction energies and analysis of supramolecular structures have shown that chelate-chelate and chelate-aryl stacking must be considered in understanding the packing and organization of supramolecular systems and crystal engineering. (C) 2017 Elsevier B.V. All rights reserved.
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A series of 10-[(4-halo-2,6-diisopropylphenyl)imino]- phenanthren-9-ones and derivatives of the phenanthrene-9,10- dione ligand have been synthesised and structurally characterised to explore two types of noncovalent interactions,...
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A series of 10-[(4-halo-2,6-diisopropylphenyl)imino]- phenanthren-9-ones and derivatives of the phenanthrene-9,10- dione ligand have been synthesised and structurally characterised to explore two types of noncovalent interactions, namely the influence of the steric bulk upon the resulting C-H···π and π-stacking interactions and halogen bonding. Selected noncovalent interactions have additionally been analysed by DFT and AIM techniques. No halogen bonding has been observed in these systems, but X lone pair···π, C-H···O=C and C-H···π interactions are the prevalent ones in the halogenated systems. Removal of the steric bulk in N-(2,4,6-trimethylphenyl)-9,10- iminophenanthrenequinone affords different noncovalent interactions, but the C-H···O=C hydrogen bonds are observed. Surprisingly, in N-(2,6-dimethylphenyl)-9,10-iminophenanthrenequinone and N-(phenyl)-9,10-iminophenanthrenequinone these C-H···O=C hydrogen bonds are not observed. However, they are observed in the related 2,6-di-tert-butylphenanthrene-9,10- dione. The π-interactions in dimers extracted from the crystal structures have been analysed by DFT and AIM. Spectroscopic investigations are also presented and these show only small perturbations to the O=C-C=N fragment.
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In this study, we propose that three consecutive cationic p-methylstilbazoles tethered on D-threoninols (Z residues) at 5′ termini act as a unique "glue" connecting DNA duplexes by their interstrand cluster formation. Interstrand...
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In this study, we propose that three consecutive cationic p-methylstilbazoles tethered on D-threoninols (Z residues) at 5′ termini act as a unique "glue" connecting DNA duplexes by their interstrand cluster formation. Interstrand clustering of p-methylstilbazoles (ZZZ triplets) induces narrowing and hypsochromic shift of bands at 350nm, which can be assigned to the absorption of p-methylstilbazole. However, single-stranded DNA conjugates involving a ZZZ triplet at the 5′ terminus of 8-mer native nucleotides is found not to induce such large spectral changes, which implies that the intrinsic self-assembling property of ZZZ triplets is weak. Interestingly, when this conjugate is hybridized with a complementary 8-mer native oligonucleotide, a remarkable spectral change is observed, indicating the dimerization of a duplex through the interstrand clustering of ZZZ triplets. Dimerization of the duplex is also evidenced by cold-spray ionization mass spectrometry. This interstrand clustering is observed only when a ZZZ triplet is tethered to a 5′ rather than 3′ terminus. Furthermore, the stability of the interstrand cluster increases by increasing the number of nucleobases of the DNA portion, and when mismatched base pairs are incorporated or when a base next to the Z residue is deleted, the stability substantially drops. When we apply the ZZZ triplet to the formation of a nanowire using two complementary DNA conjugates, each of which has a ZZZ triplet at the 5′ termini as overhang, we demonstrate the successful formation of a nanowire by native PAGE analysis. Since native sticky ends that have three nucleotides do not serve as "glue", ZZZ triplets with their unique glue-like properties are prime candidates for constructing DNA-based nanoarchitectures. Stick together! A unique "glue" of cationic p-methylstilbazoles tethered on D-threoninols connects DNA duplexes by intermolecular clustering. When the "glue" is attached to both termini of a DNA duplex, a nanowire is formed (see graphic). Thus, the "glue" can be utilized for constructing DNA-based nanoarchitectures.
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