Binding of piano‐stool Ru(II) complexes to DNA; QM/MM study

Ru(II) “piano‐stool” complexes belong to group of biologically active metallocomplexes with promising anticancer activity. In this study, we investigate the reaction mechanism of [(η⁶‐benzene)Ru(II)(en)(H₂O)]²⁺ (en = ethylenediamine) complex binding to DNA by hybrid QM/MM computational techniques. The reaction when the Ru(II) complex is coordinated on N7‐guanine from major groove is explored. Two reaction pathways, direct binding to N7 position and two‐step mechanism passing through O6 position, are considered. It was found that the reaction is exothermic and the direct binding process is preferred kinetically. In analogy to cisplatin, we also explored the possibility of intrastrand cross‐link formation where the Ru(II) complex makes a bridge between two adjacent guanines. Two different pathways were found, leading to a final structure with released benzene ligand. This process is exothermic; however, one pathway is blocked by relatively high initial activation barrier. Geometries, energies, and electronic properties analyzed by atoms in molecules and natural population analysis methods are discussed. © 2012 Wiley Periodicals, Inc.     

Solvation structure of coronene-transition metal complex: a RISM-SCF study

Coronene (C(24)H(12)) is a flat polyaromatic hydrocarbon consisting of seven peri-fused benzene rings and attracts lots of attention as a fragment of graphene. Using a hybrid method of quantum chemistry and statistical mechanics called RISM-SCF, which is an alternative to QM/MM, the electronic structure and solvation structure of a coronene-transition metal complex were computed in a self-consistent manner. The binding of a ruthenium complex ([C(5)H(5)Ru](+)) was extensively studied, especially the changing of the solvation structure.     

Cellular Uptake of a Polypyridyl Ruthenium Complex Revealed Using a Fluorescent Rhodamine‐modified Ruthenium Complex

A fluorescent polypyridyl ruthenium complex was successfully prepared using an amide bond linkage to link two rhodamine moieties through bipyridine groups. Although photo‐induced electron transfer (PET) quenched the fluorescent intensity, the quantum yield of the rhodamine‐modified Ru(II) complex was 0.17 in water, sufficient for observing the fluorophore behaviour in biological systems. The rhodaminemodified Ru(II) complex was found to inhibit the bacterial growth of E. coli. In vitro fluorescence images of human hepatoma cells (SK‐Hep1) showed that a fluorescent polypyridyl ruthenium complex not only supported the above observation but also preferably accumulated in the cytoplasmic region inside the cell. These observations suggest that in addition to strong Ru–DNA interactions, Ru‐protein interactions in the cytoplasmic regions are strong and are therefore important to the development of metallopharmaceuticals.     

Synthesis and Characterization of a Ruthenium(II) Complex for Photovoltaic Cells

We have designed and synthesized a new ruthenium complex, [(5‐amino‐1,10‐phenanthroline)bis(4,4′‐dicarboxylic acid‐2,2′‐bipyridine)]ruthenium(II) by introducing two types of ligands, 5‐amino‐1,10‐phenanthroline and 4,4′‐dicarboxylic acid‐2,2′‐bipyridine. We investigated the electronic, spectroscopic, electrochemical, and photovoltaic properties of the Ru(II) complex. The short‐circuit current density and overall solar‐to‐electric energy conversion efficiency of photovoltaic cells made with this Ru(II) complex were found to be 8.9 mA/cm² and 2.1%, respectively. A series of analogous Ru(II) complexes have also been synthesized and investigated to compare the effects of functional groups on various ligands. HOMO‐LUMO energies and molecular orbital surfaces have been investigated using semiempirical quantum chemical methods.     

Covalent Interaction of Ru(terpy)(tmephen)Cl+ with DNA: A Potential Ruthenium‐Based Anticancer Drug

The use of ruthenium complexes in antitumor therapy was launched two decades ago. In view of their low toxicity and good selectivity for solid tumor metastasis, ruthenium complexes have great potential as alternative drugs to cisplatin in cancer chemotherapy. A series of monochloro ruthenium complexes, Ru(terpy) (NN)Cl⁺ (NN, bidentate nitrogen ligand), containing different electron‐donating groups were prepared. The reactivity towards the formation of Ru‐DNA adduct were revealed by gel mobility shift assay. Their DNA binding sites of Ru(terpy)(tmephen)Cl⁺ were located predominantly at the purine residues i.e., guanine and adenine, by terminating DNA elongation in vitro using PCR and primer extension techniques. Surprisingly, the ability of Ru(terpy)(tmephen)Cl⁺ to inhibit cell growth was found to be approximately two times better than that of a known cross‐linking agent, Ru(bpy)₂Cl₂. Therefore, the increase in liability of the chloro ligand was demonstrated to improve the reactivity of these ruthenium complexes towards the covalent bond formation in Ru‐DNA adducts and result also in a significant inhibition of cell growth. Based on our results, these ruthenium complexes modified with electron‐rich groups provide new consideration in the tune of ruthenium‐based drugs in cancer chemotherapy.     

Photocontrolled DNA binding of a receptor-targeted organometallic ruthenium(II) complex

A photoactivated ruthenium(II) arene complex has been conjugated to two receptor-binding peptides, a dicarba analogue of octreotide and the Arg-Gly-Asp (RGD) tripeptide. These peptides can act as "tumor-targeting devices" since their receptors are overexpressed on the membranes of tumor cells. Both ruthenium-peptide conjugates are stable in aqueous solution in the dark, but upon irradiation with visible light, the pyridyl-derivatized peptides were selectively photodissociated from the ruthenium complex, as inferred by UV-vis and NMR spectroscopy. Importantly, the reactive aqua species generated from the conjugates, [(η(6)-p-cym)Ru(bpm)(H(2)O)](2+), reacted with the model DNA nucleobase 9-ethylguanine as well as with guanines of two DNA sequences, (5')dCATGGCT and (5')dAGCCATG. Interestingly, when irradiation was performed in the presence of the oligonucleotides, a new ruthenium adduct involving both guanines was formed as a consequence of the photodriven loss of p-cymene from the two monofunctional adducts. The release of the arene ligand and the formation of a ruthenated product with a multidentate binding mode might have important implications for the biological activity of such photoactivated ruthenium(II) arene complexes. Finally, photoreactions with the peptide-oligonucleotide hybrid, Phac-His-Gly-Met-linker-p(5')dCATGGCT, also led to arene release and to guanine adducts, including a GG chelate. The lack of interaction with the peptide fragment confirms the preference of such organometallic ruthenium(II) complexes for guanine over other potential biological ligands, such as histidine or methionine amino acids.     

Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach

Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H(2)O)(6)(2+/3+) and Ru(H(2)O)(6)(2+/3+). The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.     

Interactions of the “piano‐stool” [ruthenium(II) (η6‐arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study

Piano stool ruthenium complexes of the composition [Ru(II)(η⁶‐arene)(en)Cl]^+/2+ (en = ethylenediamine) represent an emerging class of cisplatin‐analogue anticancer drug candidates. In this study, we use computational quantum chemistry to characterize the structure, stability and reactivity of these compounds. All these structures were optimized at DFT(B3LYP)/6‐31G(d) level and their single point properties were determined by the MP2/6‐31++G(2df,2pd) method. Thermodynamic parameters and rate constants were determined for the aquation process, as a replacement of the initial chloro ligand by water and subsequent exchange reaction of aqua ligand by nucleobases. The computations were carried out at several levels of DFT and ab initio theories (B3LYP, MP2 and CCSD) utilizing a range of bases sets (from 6‐31G(d) to aug‐cc‐pVQZ). Excellent agreement with experimental results for aquation process was obtained at the CCSD level and reasonable match was achieved also with the B3LYP/6‐31++G(2df,2pd) method. This level was used also for nucleobase‐water exchange reaction where a smaller rate constant for guanine exchange was found in comparison with adenine. Although adenine follows a simple replacement mechanism, guanine complex passes by a two‐step mechanism. At first, Ru‐O6(G) adduct is formed, which is transformed through a chelate TS2 to the Ru‐N7(G) final complex. In case of guanine, the exchange reaction is more favorable thermodynamically (releasing in total by about 8 kcal/mol) but according to our results, the rate constant for guanine substitution is slightly smaller than the analogous constant in adenine case when reaction course from local minimum is considered. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

钌(II)多吡啶配合物光断裂DNA的实验研究

研究了一系列钌(II)多吡啶配合物对pBR 322 DNA 的光断裂作用, 并与光谱法和粘度法的研究结果进行了对比. 实验结果表明, 钌(II)多吡啶配合物光断裂DNA的能力不仅与配合物与DNA相互作用的结合模式和结合强度有关, 还与配合物自身的电子结构有关; 钌(II)多吡啶配合物对DNA的光断裂存在立体选择性; 其断裂机理是激发态的配合物与溶液中的氧分子发生能量转移生成单线态氧活性氧化物种, 将鸟嘌呤碱基氧化而导致DNA断裂. 本研究对于遗传工程中的化学核酸酶以及以DNA为靶标的药物设计有重要的意义.     

Luminescence properties of a di-ruthenium(II) complex with an intramolecular hydrogen bond modulated by DNA and copper(II) ion

Modulation of the luminescence properties of a di-ruthenium(II) complex [(bpy)₂Ru(BL)Ru(bpy)₂]⁴⁺ (bpy = 2,2′-bipyridine, BL = 2-hydroxyl-5-methyl-1,3-bis([1,10]phenanthroline-[5,6-d]imidazol-2-yl)benzene) by DNA and/or Cu²⁺ ion has been investigated. It is found that the ruthenium(II) complex can coordinate to the Cu²⁺ ion in both the absence and presence of DNA. Binding to DNA is through electrostatic interactions and the intramolecular hydrogen bond in the complex is located outside of the DNA. The binding constant is 1.6 × 10⁴ M⁻¹. Moreover, it is demonstrated that DNA has the ability to enhance the luminescence intensities of both the di-ruthenium(II) complex and the tri-metallic system generated by chelating with Cu²⁺. Conversely, Cu²⁺ ion can quench the luminescence of both the free ruthenium(II) complex and the DNA-bound ruthenium(II) complex.     

New QM/MM implementation of the DFTB3 method in the gromacs package

The approximate density‐functional tight‐binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free‐energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) electron‐induced repair of a DNA lesion. Also discussed is the further development of the framework, regarding mostly the options for parallelization. © 2015 Wiley Periodicals, Inc.     

Ultrasensitive and Signal‐on Electrochemiluminescence Aptasensor Using the Multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin Complexes

An ultrasensitive and signal‐on electrochemiluminescence (ECL) aptasensor to detect target protein (thrombin or lysozyme) was developed using the host‐guest recognition between a metallocyclodextrin complex and single‐stranded DNA (ss‐DNA). The aptasensor uses both the photoactive properties of the metallocyclodextrins named multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin complexes and their specific recognition with ss‐DNA, which amplified the ECL signal without luminophore labeling. After investigating the ECL performance of different multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin (multi‐Ru‐β‐CD) complexes, tris‐tris(bipyridine)‐ruthenium(II)‐β‐cyclodextrin (tris(bpyRu)‐β‐CD) was selected as a suitable host molecule to construct an atasensor. First, double‐stranded DNA (ds‐DNA) formed by hybridization of the aptamer and its target DNA was attached to a glassy carbon electrode via coupling interaction, which showed low ECL intensity with 2‐(dibutylamino) ethanol (DBAE) as coreactant, because of the weak recognition between ds‐DNA and tris(bpyRu)‐β‐CD. Upon addition of the corresponding protein, the ECL intensity increased when target ss‐DNA was released because of the higher stability of the aptamer‐protein complex than the aptamer‐DNA one. A linear relationship was observed in the range of 0.01 pmol/L to 100 pmol/L between ECL intensity and the logarithm of thrombin concentrations with a limited detection of 8.5 fmol/L (S/N=3). Meanwhile, the measured concentration of lysozyme was from 0.05 pmol/L to 500 pmol/L and the detection limit was 33 fmol/L (S/N=3). The investigations of proteins in human serum samples were also performed to demonstrate the validity of detection in real clinical samples. The simplicity, high sensitivity and specificity of this aptasensor show great promise for practical applications in protein monitoring and disease diagnosis.     

Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level

In this article, the convergence of quantum mechanical (QM) free‐energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa‐acid deep‐cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158–224 atoms). We use single‐step exponential averaging (ssEA) and the non‐Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi‐empirical PM6‐DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free‐energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Contributions of pauli repulsions to the energetics and physical properties computed in QM/MM methods

Conventional combined quantum mechanical/molecular mechanical (QM/MM) methods lack explicit treatment of Pauli repulsions between the quantum‐mechanical and molecular‐mechanical subsystems. Instead, classical Lennard‐Jones (LJ) potentials between QM and MM nuclei are used to model electronic Pauli repulsion and long‐range London dispersion, despite the fact that the latter two are inherently of quantum nature. Use of the simple LJ potential in QM/MM methods can reproduce minimal geometries and energies of many molecular clusters reasonably well, as compared to full QM calculations. However, we show here that the LJ potential cannot correctly describe subtle details of the electron density of the QM subsystem because of the neglect of Pauli repulsions between the QM and MM subsystems. The inaccurate electron density subsequently affects the calculation of electronic and magnetic properties of the QM subsystem. To explicitly consider Pauli interactions with QM/MM methods, we propose a method to use empirical effective potentials on the MM atoms. The test case of the binding energy and magnetic properties of a water dimer shows promising results for the general application of effective potentials to mimic Pauli repulsions in QM/MM calculations. © 2013 Wiley Periodicals, Inc.     

Charge separation in a ruthenium-quencher conjugate bound to DNA

A novel tris heteroleptic dipyridophenazine complex of ruthenium(II), [{Ru(phen)(dppz)(bpy'-his)}{Ru(NH3)5}]5+, containing a covalently tethered ruthenium pentammine quencher coordinated through a bridging histidine has been synthesized and characterized spectroscopically and biochemically in a DNA environment and in organic solvent. Steady-state and time-resolved luminescence measurements indicate that the tethered Ru complex is quenched relative to the parent complexes [Ru(phen)(dppz)(bpy')]2+ and [Ru(phen)(dppz)(bpy'-his)]2+ in DNA and acetonitrile, consistent with intramolecular photoinduced electron transfer. Intercalated into guanine-containing DNA, [{Ru(phen)(dppz)(bpy'-his)}{Ru(NH3)5}]5+, upon excitation and intramolecular quenching, is capable of injecting charge into the duplex based upon the EPR detection of guanine radicals. DNA-mediated charge transport is also indicated using a kinetically fast cyclopropylamine-substituted base as an electron hole trap. Guanine damage is not observed, however, in measurements using the guanine radical as the kinetically slower hole trap, indicating that back electron-transfer reactions are competitive with guanine oxidation. Moreover, transient absorption measurements reveal a novel photophysical reaction pathway for [{Ru(phen)(dppz)(bpy'-his)}{Ru(NH3)5}]5+ in the presence of DNA that is competitive with the intramolecular flash-quench process. These results illustrate the remarkably rich redox chemistry that can occur within a bimolecular ruthenium complex intercalated in duplex DNA.     

Asymmetric Mixed‐Valence Complexes that Consist of Cyclometalated Ruthenium and Ferrocene: Synthesis,Characterization, and Electronic‐Coupling Studies

Three bis‐tridentate ferrocene‐containing cyclometalated ruthenium complexes, [(Fcdpb)Ru(tpy)]⁺ ( 1 ⁺), [(Fctpy)Ru(dpb)]⁺ ( 2 ⁺), and [(Fcdpb)Ru(Fctpy)]⁺ ( 3 ⁺), have been prepared and characterized, where Fcdpb is the 2‐deprotonated form of 1,3‐di(2‐pyridyl)‐5‐ferrocenylbenzene, tpy is 2,2′:6′,2“‐terpyridine, dpb is the 2‐deprotonated form of 1,3‐di(2‐pyridyl)benzene, and Fctpy is 4′‐ferrocenyl‐2,2′:6′,2”‐terpyridine. Single crystals of compounds 2 ⁺ and 3 ⁺ have been studied by X‐ray analysis. Complexes 1 ⁺ and 2 ⁺ displayed two anodic redox waves, whilst three well‐separated redox couples were observed for compound 3 ⁺. A combined experimental and computational study suggested that the ferrocene unit on the Fcdpb moiety in compounds 1 ⁺ and 3 ⁺ was oxidized first. In contrast, the order of the oxidation of ruthenium and ferrocene in complex 2 ⁺ was reversed. Metal‐to‐metal‐charge‐transfer transitions (MM′CT) have been observed for the singly oxidized states 1 ²⁺, 2 ²⁺, and 3 ²⁺ in the near‐infrared region. Hush analysis showed that the metal–metal electronic couplings in compounds 1 ²⁺ and 3 ²⁺ were much stronger than those in compound 2 ²⁺.     

Two‐Photon Chemistry in Ruthenium 2,2′‐Bipyridyl‐Functionalized Single‐Wall Carbon Nanotubes

Ruthenium polypyridyl complexes are widely used as light harvesters in dye‐sensitized solar cells. Since one of the potential applications of single‐wall carbon nanotubes (SWCNTs) and their derived materials is their use as active components in organic and hybrid solar cells, the study of the photochemistry of SWCNTs with tethered ruthenium polypyridyl complexes is important. A water‐soluble ruthenium tris(bipyridyl) complex linked through peptidic bonds to SWCNTs (Ru‐SWCNTs) was prepared by radical addition of thiol‐terminated SWCNT to a terminal C?C double bond of a bipyridyl ligand of the ruthenium tris(bipyridyl) complex. The resulting macromolecular Ru‐SWCNT (≈500 nm, 15.6 % ruthenium complex content) was water‐soluble and was characterized by using TEM, thermogravimetric analysis, chemical analysis, and optical spectroscopy. The emission of Ru‐SWCNT is 1.6 times weaker than that of a mixture of [Ru(bpy)₃]²⁺ and SWCNT of similar concentration. Time‐resolved absorption optical spectroscopy allows the detection of the [Ru(bpy)₃]²⁺‐excited triplet and [Ru(bpy)₃]⁺. The laser flash studies reveal that Ru‐SWCNT exhibits an unprecedented two‐photon process that is enabled by the semiconducting properties of the SWCNT. Thus, the effect of the excitation wavelength and laser power on the transient spectra indicate that upon excitation of two [Ru(bpy)₃]²⁺ complexes of Ru‐SWCNT, a disproportionation process occurs leading to delayed formation of [Ru(bpy)₃]⁺ and the performance of the SWCNT as a semiconductor. This two‐photon delayed [Ru(bpy)₃]⁺ generation is not observed in the photolysis of [Ru(bpy)₃]³⁺; SWCNT acts as an electron wire or electron relay in the disproportionation of two [Ru(bpy)₃]²⁺ triplets in a process that illustrates that the SWCNT plays a key role in the process. We propose a mechanism for this two‐photon disproportionation compatible with i) the need for high laser flux, ii) the long lifetime of the [Ru(bpy)₃]²⁺ triplets, iii) the semiconducting properties of the SWNT, and iv) the energy of the HOMO/LUMO levels involved.     

Preparation of Organometallic Ruthenium–Arene–Diaminotriazine Complexes as Binding Agents to DNA

The reactions of two diaminotriazine ligands 2,4‐diamino‐6‐(2‐pyridyl)‐1,3,5‐triazine (2‐pydaT) and 6‐phenyl‐2,4‐diamino‐1,3,5‐triazine (PhdaT) with ruthenium–arene precursors led to a new family of ruthenium(II) compounds that were spectroscopically characterized. Four of the complexes were cationic, with the general formula [(η⁶‐arene)Ru(κ²‐N,N‐2‐pydaT)Cl]X (X=BF₄, TsO; arene=p‐cymene: 1.BF4 , 1.TsO arene=benzene: 2.BF4 , 2.TsO ). The neutral cyclometalated complex [(η⁶‐p‐cymene)Ru(κ²‐C,N‐PhdaT*)Cl] ( 3 ) was also isolated. The structures of complexes 2.BF4 and 3.H2O were determined by X‐ray diffraction. Complex 1.BF4 underwent a partial reversible‐aquation process in water. UV/Vis and NMR spectroscopic measurements showed that the reaction was hindered by the addition of NaCl and was pH‐controlled in acidic solution. At pH 7.0 (sodium cacodylate) Ru–Cl complex 1.BF4 was the only species present in solution, even at low ionic strength. However, in alkaline medium (KOH), complex 1.BF4 underwent basic hydrolysis to afford a Ru–OH complex ( 5 ). Fluorimetric studies revealed that the interaction of complex 1.BF4 with DNA was not straightforward; instead, its main features were closely linked to ionic strength and to the [DNA]/complex ratio. The bifunctional complex 1.BF4 was capable of interacting concurrently through both its p‐cymene and 2‐pydaT groups. Cytotoxicity and genotoxicity studies showed that, contrary to the expected behavior, the complex species was biologically inactive; the formation of a Ru–OH complex could be responsible for such behavior.