Effect of electric field on the microcosmic properties of cation compound containing 2,2,6,6-tetramethyl-1-piperidinyloxy and imidazole unit.

A theoretical study of the electric-field effect on the electronic structures and related properties of the cation compound containing 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and imidazole unit has been carried out, using the density functional theory (DFT) at the (U) B3LYP/6-31+G(d,p) level. The changes and regularities of geometric and electronic properties of the researched compound under electric field were revealed in detail. The results show the following: (1) Electric field has a very important effect on the orbital energy, dipole moment, natural population, and structure of the cation compound.

Exploration of the binding mode between (-)-zampanolide and tubulin using docking and molecular dynamics simulation.

The binding mode of (-)-zampanolide (ZMP) to tubulin was investigated using docking, molecular dynamics (MD) simulation, and binding free-energy calculations. The docking studies validated the experimental results indicating that the paclitaxel site is the binding site for (-)-ZMP. The 18 ns MD simulation shows the docking mode has changed a lot, whereas it offers more reliable binding data.

Docking and molecular dynamics studies of the binding between Peloruside A and tubulin.

The molecular docking, MD simulation and binding free energy calculation were performed to explore the probable binding modes between PLA and tubulin. Through docking study, three possible binding sites for PLA were speculated as follows: the taxane site, the alternative site and a new site in α-tubulin. Then, 12.

Theoretical studies on DNA-photocleavage efficiencies of Ru(II) polypyridyl complexes.

Theoretical studies on the DNA-photocleavage efficiencies of Ru(II) polypyridyl complexes 1-4 have been carried out using density functional theory (DFT). First, an evaluation of the computational accuracy of the redox potentials for [Ru(bpy)(3)](2+) in the ground state and the excited state was tested by different computational methods. Secondly, the redox potentials of complexes 1-4 in the excited state were accurately computed.

Theoretical studies on DNA-photocleavage efficiencies and mechanisms of Ru(II) polypyridyl complexes.

Theoretical studies on the DNA-photocleavage efficiencies and mechanisms of Ru(II) complexes [Ru(bpy)(2)(L)](2+) (bpy = 2,2'-bipyridine; L: dppz = dipyrido[3,2-a:2',3'-c]phenazine; mitatp = 5-methoxy-isatino[1,2-b]-1,4,8,9-tetraazatriphenylene; nitatp = 5-nitro-isatino [1,2-b]-1,4,8,9-tetraazatriphenylene) 1-3 were carried out using density functional theory (DFT). First, the accuracies of redox potentials computed for [Ru(bpy)(3)](2+) in the ground state and the excited state by different computational methods were tested, and then the redox potentials of complexes 1-3 in their excited states were computed accurately. Secondly, the trend in the DNA-photocleavage efficiencies (ϕ) of complexes 1-3 [i.

Theoretical studies of QSAR and molecular design on a novel series of ethynyl-3-quinolinecarbonitriles as SRC inhibitors.

A theoretical study on the two-dimensional, three-dimensional quantitative structure-activity relationships and docking analysis of a novel series of ethynyl-3-quinolinecarbonitriles acting as Src inhibitors has been carried out. To correlate the c-Src kinase-inhibition activity of these compounds with the two-dimensional and three-dimensional structural properties for 39 known compounds, some excellent quantitative structure-activity relationships models with satisfying internal and external predictive abilities were established. A combined method of the density functional theory, molecular mechanics and statistics as well as the comparative molecular field analysis was applied to develop two-dimensional- and three-dimensional-quantitative structure-activity relationship models.

Theoretical studies on the related properties of Co(III) polypyridyl complexes interacting with DNA.

Theoretical studies on the related properties of Co(III) polypyridyl complexes [Co(phen)(2)L](3+) (L: dppz = dipyrido[3,2-a:2',3'-c]phenazine; phen = 1,10-phenanthroline; dione = 1,10-phenanthroline-5,6-diketone) 1-3 interacting with DNA, including the DNA-binding, DNA-photocleavage and spectral properties, have been carried out. First, the full geometry-optimizations of these three complexes in their ground states were carried out in aqueous solution. The optimized structures of these three complexes were docked into DNA-base-pairs using the Dock6.

Theoretical studies on pyrimidine substituent derivatives as dual inhibitors of AP-1 and NF-kappaB.

Theoretical studies on the three-dimensional (3D) quantitative structure-activity relationship (QSAR) and mechanisms of action of a series of pyrimidine substituent derivatives as dual inhibitors of AP-1 and NF-kappaB were carried out using comparative molecular field analysis (CoMFA) and docking methods. The established 3D-QSAR model exhibits a satisfying statistical quality and prediction ability. Docking results show somewhat lower average values of the flexible and rigid energy scores in the chosen binding sites.

Binding conformations and QSAR of CA-4 analogs as tubulin inhibitors.

A theoretical study on the binding conformations and the quantitative structure-activity relationship (QSAR) of combretastatin A4 (CA-4) analogs as inhibitors toward tubulin has been carried out using docking analysis and comparative molecular field analysis (CoMFA). The appropriate binding orientations and conformations of these compounds interacting with tubulin were revealed by the docking study; and a 3D-QSAR model showing significant statistical quality and satisfactory predictive ability was established, in which the correlation coefficient (R(2)) and cross-validation coefficient (q(2)) were 0.955 and 0.

[Luminescence dynamics analysis on ruthenium polypyridyl complexes bonding to DNA].

Time-resolved spectra of six kinds of ruthenium polypyridyl complexes [Ru(L)2 (R)]2+ (L = bpy, phen, bpy = 2,2'-bipyridine, phen = 1,10-phenanthroline, R = 7-CH3-dppz, 7-F-dppz, dpbpd(NH2)2) bonding to calf thymus DNA in aqueous solution were compared and analyzed by using the three energy level kinetic model. And the effects of the substituent groups on the interaction ways for the ruthenium complexes bonding to DNA were discussed. The result shows that first, the six complexes all show two binding modes on bonding to DNA, i.

Binding orientations, QSAR, and molecular design of thiophene derivative inhibitors.

A theoretical study on binding orientations and quantitative structure-activity relationship of thiophene derivatives as inhibitors towards tubulin has been carried out by using the docking analysis and the comparative molecular field analysis. The appropriate binding orientations and conformations of these compounds interacting with tubulin were revealed by docking study; and a 3D-quantitative structure-activity relationship model showing significant statistical quality and satisfying predictive ability was established, in which the correlation coefficient (R(2)) and cross-validation coefficient (q(2)) are 0.949 and 0.

A theoretical study on the hydrolysis process of two Keppler-type antitumor complexes [TzH][trans-RuCl4(Tz)2] and [2-NH2TzH][trans-RuCl4(2-NH2Tz)2].

The hydrolysis processes of two Keppler-type antitumor ruthenium(III) complexes of [TzH][trans-RuCl4(Tz)2] (TzICR) and [2-NH2TzH][trans-RuCl4(2-NH2Tz)2] ((2-NH2)TzICR) have been investigated by using density functional theory (DFT) method, and the solvent effect was also considered and calculated by conductor-like polarizable calculation model (CPCM). The structural characteristics and the detailed energy profiles for the hydrolysis processes of title complexes have been obtained. The analysis of thermodynamic and kinetic characteristics of hydrolysis reaction suggests the following: For the 1st hydrolysis step, the complex TzICR has a lower hydrolysis rate than the reported drug [ImH][trans-RuCl4Im2](ICR, Im=imidazole).

CoMFA and docking studies of 2-phenylindole derivatives with anticancer activity.

Three-dimensional (3D) quantitative structure-activity relationship (QSAR) and docking studies of 43 tubulin inhibitors, 2-phenylindole derivatives with anticancer activity against human breast cancer cell line MDA-MB 231, have been carried out. The established 3D-QSAR model from the comparative molecular field analysis (CoMFA) in training set shows not only significant statistical quality, but also satisfying predictive ability, with high correlation coefficient value (R(2)=0.910) and cross-validation coefficient value (q(2)=0.

Electronic structures, DNA-binding and spectral properties of Co(III) complexes [Co(bpy)2(L)]3+ (L=pip, odhip, hnoip).

Studies on the electronic structures and trend in DNA-binding affinities of a series of Co(III) complexes have been carried out, using the density functional theory (DFT) at the B3LYP/LanL2DZ level. The optimized geometric structures of these Co(III) complexes in aqueous solution are more close to experimental data than those in vacuo. The electronic structures of these Co(III) complexes were analyzed on the basis of their geometric structures optimized in aqueous solution, and the trend in the DNA-binding constants (K(b)) was reasonably explained.

Binding to DNA purine base and structure-activity relationship of a series of structurally related Ru(II) antitumor complexes: a theoretical study.

The thermodynamics of the binding of a series of structurally related Ru(II) antitumor complexes, that is, alpha-[Ru(azpy)2Cl2] 1, beta-[Ru(azpy)2Cl2] 2, alpha-[Ru(azpy)(bpy)Cl2] 3, and cis-[Ru(bpy)2Cl2] 4 to DNA purine bases (gunine, adenine at N7 site) has been studied by using the DFT method. The binding of imine form of 9-methyladenine (9-MeAde) to the Ru(II) moiety in a didentate fashion via its N6 and N7 atoms was also considered. The geometrical structures of the DNA model base adducts were obtained at the B3LYP/(LanL2DZ + 6-31G(d)) level in vacuo.

Experimental and DFT studies on DNA binding and photocleavage of two cationic porphyrins. Effects of the introduction of a carboxyphenyl into pyridinium porphyrin.

The DNA-binding affinities and DNA photocleavage abilities of cationic porphyrin, 5-(4-carboxyphenyl)-10,15,20-tris(4-methylpyridiniumyl)porphyrin (CTMPyP), and its reference compound meso-tetrakis(N-methyl-4-pyridiniumyl)porphyrin (H2TMPyP) have been investigated. The DNA-binding behaviors of the two compounds in NaH2PO4 buffer were compared systematically by using absorption, fluorescence and circular dichroism (CD) spectra, thermal denaturation as well as viscosity measurements. The experimental results show that CTMPyP binds to DNA in an outside binding mode, while H2TMPyP in an intercalative mode.

Tricationic pyridium porphyrins appending different peripheral substituents: experimental and DFT studies on their interactions with DNA.

Four tricationic pyridium porphyrins appending hydroxyphenyl, methoxyphenyl, propionoxyphenyl or carboxyphenyl group at meso-20-position of porphyrin core have been synthesized and their abilities to bind and cleave DNA have been investigated. Using a combination of absorption, fluorescence, circular dichroism (CD) spectra, thermal DNA denaturation as well as viscosity measurements, their binding modes and intrinsic binding constants (K(b)) to calf DNA (CT DNA) were comparatively studied and also compared with those of 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin (TMPyP). The results suggest that the K(b) values of these porphyrins are greatly influenced by the number of positive charges and steric hindrance.

Two new sesquiterpenoids from the soft coral Sinularia polydactyla (Ehreberg).

Two new sesquiterpenoids, polydactins A (1) and B (2) and a known sesquiterpene, 10alpha-hydroxycadin-4-en-15-al (3), were isolated from the soft coral Sinularia polydactyla (Ehreberg). Their structures were determined mainly by spectroscopic methods. Polydactin A (1) showed moderate cytotoxic activities against human oral epidermoid carcinoma cell lines (KB) and human breast carcinoma (MCF) tumour cell lines (in vitro).

DNA binding and photocleavage properties of a novel cationic porphyrin-anthraquinone hybrid.

A novel cationic porphyrin-anthraquinone (Por-AQ) hybrid has been synthesized and characterized. Using the combination of absorption titration, fluorescence spectra, circular dichroism (CD) as well as viscosity measurements, the binding properties of the hybrid to calf thymus (CT) DNA have been investigated compared with its parent porphyrin. The experimental results show that at low [Por]/[DNA] ratios, the parent porphyrin binds to DNA in an intercalative mode while the hybrid binds in a combined mode of outside binding (for porphyrin moiety) and partial intercalation (for anthraquinone).

A combined computational and experimental study on DNA-photocleavage of Ru(II) polypyridyl complexes [Ru(bpy)2(L)]2+ (L = pip, o-mopip and p-mopip).

A combined computational and experimental study on DNA-photocleavage by Ru(II) polypyridyl complexes [Ru(bpy)2(L)]2+ 1-3 (bpy = 2,2-bipyridine; L: pip = 2-phenylimidazo[4,5-f]1,10-phenanthroline, o-mopip = 2-(2-methoxyphenyl)imidazo[4,5-f]1,10-phenanthroline and p-mopip = 2-(4-methoxyphenyl)imidazo[4,5-f]1,10-phenanthroline) has been carried out. The DNA-photocleavage behavior of these complexes was comparably measured by the gel electrophoresis experiments. The experimental results show that they can induce considerable DNA-photocleavage, and have different DNA-photocleavage efficiencies (phi) following the order phi (1) < phi (2) < phi (3).

QSAR, action mechanism and molecular design of flavone and isoflavone derivatives with cytotoxicity against HeLa.

The quantitative structure-activity relationship (QSAR) of 32 flavone and isoflavone derivatives with cytotoxicity expressed as pGC50, which is defined as the negative value of the logarithm of necessary molar concentration of this series of compounds to cause 50% growth inhibition against the human cervical epithelioid carcinoma cell line (HeLa), has been studied by using the density functional theory (DFT), molecular mechanics (MM2) and statistical methods. In order to obtain QSAR model with high predictive ability, the original dataset was randomly divided into a training set comprising 26 compounds and a test set comprising the rest 6 compounds. An optimal model for the training set with significant statistical quality (RA2=0.

Synthesis, characterization, DNA-binding and spectral properties of complexes [Ru(L)4(dppz)]2+ (L=Im and MeIm).

Two new Ru(II) complexes [Ru(L)(4)(dppz)](2+) (L=imidazole (Im), 1-methylimidazole (MeIm); dppz=dipyrido[3,2-a:2',3'-c]phenazine), have been synthesized and characterized in detail by elemental analysis, (1)H NMR, Electrospray ionization mass spectrometry (ESI-MS) and UV-visible (UV-Vis) spectroscopic techniques. The interaction of these complexes with calf thymus DNA (CT-DNA) has been explored by using electronic absorption titration, competitive binding experiment, circular dichroism (CD), thermal denaturation and viscosity measurements. The experimental results show that: both the two complexes can bind to DNA in an intercalation mode; the DNA-binding affinity of complex [Ru(Im)(4)(dppz)](2+)1 (K(b)=2.

Anion-selective interaction and colorimeter by an optical metalloreceptor based on ruthenium(II) 2,2'-biimidazole: hydrogen bonding and proton transfer.

A new anion sensor [Ru(bpy)2(H2biim)](PF6)2 (1) (bpy = 2,2'-bipyridine and H2biim = 2,2'-biimidazole) has been developed, in which the Ru(II)-bpy moiety acts as a chromophore and the H2biim ligand as an anion receptor via hydrogen bonding. A systematic investigation shows that 1 is an eligible sensor for various anions. It donates protons for hydrogen bonding to Cl-, Br-, I-, NO3-, HSO4-, H2PO4-, and OAc- anions and further actualizes monoproton transfer to the OAc- anion, changing color from yellow to orange brown.

Theoretical studies on the excited states, DNA photocleavage, and spectral properties of complex [Ru(phen)(2)(6-OH-dppz)](2+).

The structures and related properties of the complex [Ru(phen)2(6-OH-dppz)]2+ (phen = 1,10-phenanthroline; dppz = dipyrido [3,2-a:2',3'-c]phenazine) in the ground state (S0), the first singlet excited state (S1), and the first triplet excited state (T1) have been studied using density functional theory (DFT), time-dependent (TD) DFT, Hartree-Fock (HF), and configuration interaction singles (CIS) methods. Three electronic absorption-spectral bands (1MLCT, 1LL, and 1LL) lying in the range of 250-550 nm in vacuo and in aqueous solution were theoretically calculated, simulated, and assigned with TDDFT method. In particular, the theoretical results show the following: (1) The positive charges of central Ru atom in the excited states (S1 and T1) are greatly increased relative to those in the ground state (S0), and thus the Ru atom in the excited states can be regarded as Ru(III).

Density functional theory/time-dependent DFT studies on the structures, trend in DNA-binding affinities, and spectral properties of complexes [Ru(bpy)2(p-R-pip)]2+ (R = -OH, -CH3, -H, -NO2).

Studies on the electronic structures and trend in DNA-binding affinities of a series of Ru(II) complexes [Ru(bpy)2(p-R-pip)]2+ (bpy = 2,2-bipyridine; pip = 2-phenylimidazo[4,5-f] [1,10]-phenanthroline; R = -OH, -CH3, -H, -NO2) 1-4 have been carried out, using the density functional theory (DFT) at the B3LYP/LanL2DZ level. The electronic absorption spectra of these complexes were also investigated using time-dependent DFT (TDDFT) at the B3LYP//LanL2DZ/6-31G level. The computational results show that the substituents on the parent ligand (pip) have a significant effect on the electronic structures of the complexes, in particular, on the energies of the lowest unoccupied molecular orbital (LUMO) and near some unoccupied molecular orbitals (LUMO+x, x = 1-4).