Single-walled carbon nanotubes binding to human telomeric i-motif DNA under molecular-crowding conditions: More water molecules released

The natural occurrence of the human telomeric G-quadruplex or i-motif in vivo has not been demonstrated and the biological effects of the induction of these structures need to be clarified. Intracellular environments are highly crowded with various biomolecules and in vitro studies under molecular-crowding conditions will provide important information on how biomolecules behave in cells. Here we report that cell-mimic crowding can increase i-motif stability at acid pH and cause dehydration.

Magnetic Coupling between Copper(II) Ions Mediated by Hydrogen-Bonded (Neutral) Water Molecules

A new hydrogen-bonded dinuclear copper(II) coordination compound has been synthesized from the Schiff-base ligand 6-(pyridine-2-ylhydrazonomethyl)phenol (Hphp). The molecular structure of [Cu-2(php)(2)(H2O2)(2)(ClO4)](ClO4)- (H2O) (1), determined by single-crystal X-ray diffraction, reveals the presence of two copper(II) centers held together by means of two strong hydrogen bonds, with O center dot O contacts of only 2.60-2.68 angstrom. Temperature-dependent magnetic susceptibility measurements down to 3 K show that the two metal ions are antiferromagnetically coupled (J = -19.8(2) cm(-1)). This exchange is most likely through two hydrogen-bonding pathways, where a coordinated water on the first Cu, donates a H bond to the O atoms of the coordinated php at the other Cu. This strong O center dot H (water) bonding interaction has been clearly evidenced by theoretical calculations. In the relatively few related cases from the literature, this exchange path, mediated by a (neutral) coordinated water molecule, was not recognized.

Hydration of drug-DNA complexes: Greater water uptake for adriamycin compared to daunomycin

Water is an integral part of DNA, and the conserved water molecules at the binding sites can modulate drug binding to DNA or protein. We report here that anthracycline antitumor antibiotics, adriamycin (AM) and daunomycin (DM), binding to DNA is accompanied by different hydration changes, with AM binding resulting in the uptake of about twice as many water molecules as DM. These results indicate that water is playing an important role in drug binding to DNA.

A zinc/p-sulfonatocalix[4]arene/phenanthroline supramolecular compound with novel (H2O)(10) water clusters

A supramolecular complex Zn-2[Cl2H8N2](2)[C28H2OS4O16][H2O](17.7) (1), has been synthesized under hydrothermal conditions, and characterized by IR spectroscopy, TG and DTA analysis, and single crystal X-ray diffraction. Unprecedented (H2O)(10) water clusters consisting of cyclic pentamer (H2O)(5) and five dangling water molecules were observed in the lattice.

Assembly of 'discrete' (H2O)(16) water clusters within a supramolecular compound of calixarene

A 'discrete' (H2O)(16) cluster, featuring four basic cyclic nine-membered rings and a twelve-membered ring, illustrates a new mode of supramolecular association of water molecules.

Two new Cu-II coordination polymers: Studies of topological networks and water clusters

Two new Cull coordination polymers, namely [Cu-2(BDC)(2)(L)(4)(H2O)(2)]center dot 14H(2)O (1) and [Cu-1.5(BTC)(L)(1.5)(H2O)(0.5)]center dot 2H(2)O (2), where L = 1,1'-(1,4-butanediyl)bis(imidazole), BDC = 1,4-benzene dicarboxylate, and BTC = 1,3,5-benzenetricarboxylate, have been synthesized at room temperature. Complex 1 exhibits an unusual, square-planar, four-connected 2D (2)(6)4 net, which has been predicated by Wells. Interestingly, three types of water clusters, namely (H2O)(6), (H2O)(8), and (H2O)(10), are observed in the hydrogen-bonded layers constructed by the BDC ligands and water molecules. The BTC anion in compound 2 is coordinated to the Cu" cation as tetradentate ligand to form a (6(6))(2)(4(2)6(4)8(4))(2)(6(4)810) net containing three kinds of nonequivalent points, Thermogravimetric analyses (TGA) and IR spectra for 1 and 2 are also discussed in detail.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

Hybrid Qm/Mm Simulation Of The Hydration Phenomena Of Dipalmitoylphosphatidylcholine Headgroup

The polar headgroup of dipalmitoylphosphatidylcholine (DPPC) molecule both in gas phase and aqueous Solution is investigated by the hybrid quantum mechanical/molecular mechanical (QM/MM) method, in which the polar head of DPPC molecule and the bound water molecules are treated with density functional theory (DFT), while the apolar hydrocarbon chain of DPPC molecule is treated with MM method. It is demonstrated that the hybrid QM/MM method is both accurate and efficient to describe the conformations of DPPC headgroup. Folded structures of headgroup are found in gas phase calculations. In this work, both monohydration and polyhydration phenomena are investigated. In monohydration, different water association sites are studied. Both the hydration energy and the quantum properties of DPPC and water molecules are calculated at the DFT level of theory after geometry optimization. The binding force of monohydration is estimated by using the scan method. In polyhydration, more extended conformations are found and hydration energies in different polyhydration styles are estimated. (C) 2008 Elsevier Inc. All rights reserved.

用分子动力学模拟甲烷水合物热激法分解

用分子动力学模拟方法研究甲烷水合物热激法分解，系统地研究注入340 K液态水的结构Ⅰ型甲烷水合物的分解机理.模拟显示水合物表层水分子与高温液态水分子接触获得热能，分子运动激烈，摆脱水分子间的氢键束缚，笼状结构被破坏.甲烷分子获得热能从笼中挣脱，向外体系扩散.热能通过分子碰撞从外层传递给内层水分子，水合物逐层分解.对比注入277K液态水体系模拟结果，得出热激法促进水合物分解.

Molecular Dynamics Simulation of Methane Hydrate Dissociation Process in the Presence of Thermodynamic Inhibitor

The dissociation of methane hydrate in the presence of ethylene glycol (11.45 mol.L-1) at 277.0 K was studied using canonical ensemble (NVT) molecular dynamics simulations. Results show that hydrate dissociation starts from the surface layer of the solid hydrate and then gradually expands to the internal layer. Thus, the solid structure gradually shrinks until it disappears. A distortion of the hydrate lattice structure occurs first and then the hydrate evolves from a fractured frame to a fractional fragment. Finally, water molecules in the hydrate construction exist in the liquid state. The inner dissociating layer is, additionally, coated by a liquid film formed from outer dissociated water molecules outside. This film inhibits the mass transfer performance of the inner molecules during the hydrate dissociation process.

NADPH oxidase-mediated generation of reactive oxygen species: A new mechanism for X-ray-induced HeLa cell death

Oxidative damage is an important mechanism in X-ray-induced cell death. Radiolysis of water molecules is a source of reactive oxygen species (ROS) that contribute to X-ray-induced cell death. In this study, we showed by ROS detection and a cell survival assay that NADPH oxidase has a very important role in X-ray-induced cell death. Under X-ray irradiation, the upregulation of the expression of NADPH oxidase membrane Subunit gp91(phox) was dose-dependent. Meanwhile, the cytoplasmic subunit p47(phox) was translocated to the cell membrane and localized with p22(phox) and gp91(phox) to form reactive NADPH oxidase. Our data Suggest, for the first time, that NADPH oxidase-mediated generation of ROS is an important contributor to X-ray-induced cell death. This suggests a new target for combined gene transfer and radiotherapy.

Synthesis, Spectroscopic Properties, and Stabilities of Ternary Europium Complex in SBA-15 and Periodic Mesoporous Organosilica: A Comparative Study

Ternary europium complex Eu(tta)(3)phen was covalently bonded with the general mesoporous. material SBA-15 and SBA-15-type of periodic mesoporous organosilica (PMO) material via impregnation of Eu(tta)(3)center dot 2H(2)O into phen-S15 and phen-PMO, respectively, through a ligand exchange reaction. The parent materials of phen-S15 and phen-PMO were synthesized by co-condensation of tetraethylorthosilicate (TEOS) or 1,2-bis(triethoxysilyl)ethane (BTESE) and the functionalized chelate ligand 5-(N,N-bis(3-triethoxysilyl)propyl)ureyl-1,10-phenanthroline (phen-Si) in the presence of Pluronic P123 surfactant as template, which were confirmed by SEM, XRD, FTIR, Si-29 CP-MAS NMR, and N-2 adsorption measurements.

Metal-organic frameworks based on the pyridine-2,3-dicarboxylate and a flexible bispyridyl ligand: syntheses, structures, and photoluminescence

Three new metal-organic coordination polymers, [Cu(2,3-pydc)(bpp)]center dot 2.5H(2)O (1), [Zn(2,3-pydc)(bpp)]center dot 2.5H(2)O (2) and [Cd(2,3-pydc)(bpp)(H2O)]center dot 3H(2)O (3) (2,3-pydcH(2) = pyridine-2,3-dicarboxylic acid, bpp 1,3-bis(4-pyridyl)propane), have been synthesized at room temvperature. All complexes have metal ions serving as 4-connected nodes but represent two quite different structural motifs. Complexes 1 and 2 are isomorphous, both of which feature 2D -> 3D parallel interpenetration. Each two-dimensional (2D) layer with (4, 4) topology is interlocked by two nearest neighbours, one above and one below, thus leading to an unusual 3D motif. Complex 3 has a non-interpenetrating 3D CdSO4 framework with cavities occupied by uncoordinated water molecules.