Photophysical properties of ruthenium(II) polypyridyl DNA intercalators: effects of the molecular surroundings investigated by theory

Nature of the Ultrafast Interligands Electron Transfers in Dye-Sensitized Solar Cells

Charge-transfer dynamics and interligand electron transfer (ILET) phenomena play a pivotal role in dye-sensitizers, mostly represented by the Ru-based polypyridyl complexes, for TiO₂ and ZnO-based solar cells. Starting from metal-to-ligand charge-transfer (MLCT) excited states, charge dynamics and ILET can influence the overall device efficiency. In this letter, we focus on N3^4- dye ( [Ru(dcbpy)₂(NCS)₂]^4-, dcbpy = 4,4'-dicarboxy-2,2'-bipyridine) to provide a first direct observation with high time resolution (<20 fs) of the ultrafast electron exchange between bpy-like ligands. ILET is observed in water solution after photoexcitation in the ∼400 nm MLCT band, and assessment of its ultrafast time-scale is here given through a real-time electronic dynamics simulation on the basis of state-of-the-art electronic structure methods. Indirect effects of water at finite temperature are also disentangled by investigating the system in a symmetric gas-phase structure. As main result, remarkably, the ILET mechanism appears to be based upon a purely electronic evolution among the dense, experimentally accessible, MLCT excited states manifold at ∼400 nm, which rules out nuclear-electronic couplings and proves further the importance of the dense electronic manifold in improving the efficiency of dye sensitizers in solar cell devices.

KiMoPack: A python Package for Kinetic Modeling of the Chemical Mechanism

Herein, we present KiMoPack, an analysis tool for the kinetic modeling of transient spectroscopic data. KiMoPack enables a state-of-the-art analysis routine including data preprocessing and standard fitting (global analysis), as well as fitting of complex (target) kinetic models, interactive viewing of (fit) results, and multiexperiment analysis via user accessible functions and a graphical user interface (GUI) enhanced interface. To facilitate its use, this paper guides the user through typical operations covering a wide range of analysis tasks, establishes a typical workflow and is bridging the gap between ease of use for less experienced users and introducing the advanced interfaces for experienced users. KiMoPack is open source and provides a comprehensive front-end for preprocessing, fitting and plotting of 2-dimensional data that simplifies the access to a powerful python-based data-processing system and forms the foundation for a well documented, reliable, and reproducible data analysis.

Copper(I) Bis(diimine) Complexes with High Photooxidation Power: Reductive Quenching of the Excited State with a Benzimidazoline Sacrificial Donor

The reductive quenching of photoexcited photosensitizers is a very efficient way to achieve challenging reduction reactions. In this process, the excited photosensitizer is reduced by a sacrificial electron donor. This mechanism is rarely observed with copper(I) bis(diimine) complexes, which are nevertheless acknowledged as very promising photosensitizers. This is due to the fact that they are very poor photooxidants and prove unable to react with common donors once promoted in their excited state. In this article, we evidence the rare reductive quenching cycle with two specially designed copper(I) complexes. These complexes exhibit improved photooxidation power thanks to an optimized coordination sphere made of strongly π-accepting ligands. Reductive quenching of the excited state of the latter complexes with a classical benzimidazoline sacrificial donor is monitored, and reduced complexes are accumulated during prolonged photolysis. Trials to utilize the photogenerated reductive power are presented.

Ruthenium(II) Complexes with (3-Polyamino)phenanthrolines: Synthesis and Application in Sensing of Cu(II) Ions

This work deals with the development of water-soluble optical sensors based on ruthenium(II) tris(diimine) complexes that exhibit high molar absorptivity and are emissive in aqueous media. Palladium-catalyzed arylation of polyamines with 3-bromo-1,10-phenanthroline (Brphen) and [Ru(bpy)2(Brphen)](PF6)2 (bpy = 2,2’-bipyridine) was explored to prepare Ru2+ complexes with 1,10-phenanthrolines (phen) substituted by linear polyamines (PAs) at position 3 of the heterocycle ([Ru(bpy)2(phen⎼PA)](PF6)2). The most convenient synthetic pathway leading to the target molecular probes includes the preparation of phen⎼PA ligands, followed by ruthenium complexation using cis-Ru(bpy)2Cl2. Complexes bearing a polyamine chain directly linked to phenanthroline core are emissive in aqueous media and their quantum yields are comparable to that of parent [Ru(bpy)3](PF6)2. Their structure can be easily adapted for detection of various analytes by modification of amine groups. As an example, we prepared the emissive complex Ru(N2P2phen) which is suitable for the dual channel (spectrophotometry and luminescence (ON–OFF probe)) selective detection of Cu2+ ions at the physiological pH levels with limits of detection (LOD) by spectrophotometry and fluorescence spectroscopy equal to 9 and 6 μM, respectively, that is lower than the action level in drinking water for copper as prescribed by the US Environmental Protection Agency.

Ruthenium(II) complexes with phosphonate-substituted 1,10-phenanthroline ligands: synthesis, characterization and use in organic photocatalysis

Ru(II) complexes with polypyridyl ligands play a central role in the development of photocatalytic organic reactions. This work is aimed at the structural modification of such complexes to increase their...

Direct observation of the solvent organization and nuclear vibrations of [Ru(dcbpy)2(NCS)2]4-, [dcbpy = (4,4'-dicarboxy-2,2'-bipyridine)], via ab initio molecular dynamics

Environmental effects can drastically influence the optical properties and photoreactivity of molecules, particularly in the presence of polar and/or protic solvents. In this work we investigate a negatively charged Ru(II) complex, [Ru(dcbpy)₂(NCS)₂]^4- [dcbpy = (4,4'-dicarboxy-2,2'-bipyridine)], in water solution, since this system belongs to a broader class of transition-metal compounds undergoing upon photo-excitation rapid and complex charge transfer (CT) dynamics, which can be dictated by structural rearrangement and solvent environment. Ab initio molecular dynamics (AIMD) relying on a hybrid quantum/molecular mechanics scheme is used to probe the equilibrium microsolvation around the metal complex in terms of radial distribution functions of the main solvation sites and solvent effects on the overall equilibrium structure. Then, using our AIMD-based generalized normal mode approach, we investigate how the ligand vibrational spectroscopic features are affected by water solvation, also contributing to the interpretation of experimental Infra-Red spectra. Two solvation sites are found for the ligands: the sulfur and the oxygen sites can interact on average with ∼4 and ∼3 water molecules, respectively, where a stronger interaction of the oxygen sites is highlighted. On average an overall dynamic distortion of the C₂ symmetric gas-phase structure was found to be induced by water solvation. Vibrational analysis reproduced experimental values for ligand symmetric and asymmetric stretchings, linking the observed shifts with respect to the gas-phase to a complex solvent distribution around the system. This is the groundwork for future excited-state nuclear and electronic dynamics to monitor non-equilibrium processes of CT excitation in complex environments, such as exciton migration in photovoltaic technologies.

Influence of the Protonation State on the Excited-State Dynamics of Ruthenium(II) Complexes with Imidazole π-Extended Dipyridophenazine Ligands

Ruthenium(II) complexes, like [(tbbpy)₂Ru(dppz)]²⁺ (Ru-dppz; tbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine, dppz = dipyrido-[3,2-a:2',3'-c]phenazine), have emerged as suitable photosensitizers in photoredox catalysis. Since then, there has been ongoing interest in the design of π-extended Ru-dppz systems with red-shifted visible absorption maxima and sufficiently long-lived excited states independent of the solvent or pH value. Herein, we explore the photophysical properties of protonation isomers of the linearly π-extended [(tbbpy)₂Ru(L)]²⁺-type complexes bearing a dppz ligand with directly fused imidazole (im) and methyl-imidazole units (mim) as L. Steady-state UV-vis absorption, resonance Raman, as well as time-resolved emission and transient absorption spectroscopy reveal that Ru-im and Ru-mim show desirable properties for the application in photocatalytic processes, i.e., strong visible absorbance and two long-lived excited states in the ³ILCT and ³MLCT manifold, at pH values between 3 and 12. However, protonation of the (methyl-)imidazole unit at pH ≤ 2 unit causes decreased excited-state lifetimes and an emission switch-off.

Ultrafast excited state dynamics and light-switching of [Ru(phen)2(dppz)]2+ in G-quadruplex DNA

The triplet metal to ligand charge transfer (³MLCT) luminescence of ruthenium (II) polypyridyl complexes offers attractive imaging properties, specifically towards the development of sensitive and structure-specific DNA probes. However, rapidly-deactivating dark state formation may compete with ³MLCT luminescence depending on different DNA structures. In this work, by combining femtosecond and nanosecond pump-probe spectroscopy, the ³MLCT relaxation dynamics of [Ru(phen)₂(dppz)]²⁺ (phen = 1,10-phenanthroline, dppz = dipyridophenazine) in two iconic G-quadruplexes has been scrutinized. The binding modes of stacking of dppz ligand on the terminal G-quartet fully and partially are clearly identified based on the biexponential decay dynamics of the ³MLCT luminescence at 620 nm. Interestingly, the inhibited dark state channel in ds-DNA is open in G-quadruplex, featuring an ultrafast picosecond depopulation process from ³MLCT to a dark state. The dark state formation rates are found to be sensitive to the content of water molecules in local G-quadruplex structures, indicating different patterns of bound water. The unique excited state dynamics of [Ru(phen)₂(dppz)]²⁺ in G-quadruplex is deciphered, providing mechanistic basis for the rational design of photoactive ruthenium metal complexes in biological applications.

Near-IR Charge-Transfer Emission at 77 K and Density Functional Theory Modeling of Ruthenium(II)-Dipyrrinato Chromophores: High Phosphorescence Efficiency of the Emitting State Related to Spin-Orbit Coupling Mediation of Intensity from Numerous Low-Energy Singlet Excited States

Efficient charge-transfer (CT) phosphorescence in the near-IR (NIR) spectral region is reported for four substituted Ru-(R-dipyrrinato) complexes, [Ru(bpy)₂(R-dipy)](PF₆), where bpy is 2,2'-bipyridine and the substituent R is phenyl (ph), 2,4,6-trimethylphenyl, 4-carboxyphenyl (HOOC-ph), or 4-pyridinyl. The experimentally determined phosphorescence efficiency, ι_em(p) = k_RAD(p)/(ν_em(p))³ (where k_RAD(p) and ν_em(p) are the phosphorescence rate constant and the phosphorescence frequency, respectively), of the [Ru(bpy)₂(R-dipy)]⁺ complexes was approximately double that of [Ru(bpy)(Am)₄]²⁺ complexes (Am = ammine ligand) in the NIR region. Density functional theory (DFT) modeling indicated two strikingly different electronic configurations of the triplet emitting state (T_e) in the two types of complexes. The T_e of [Ru(bpy)₂(R-dipy)]⁺ complexes shows a CT-type corresponding to the metal-to-ligand charge transfer (MLCT)-(Ru-(R-dipy)) and the ππ*-(R-dipy) moiety configurations, and the T_e state in the [Ru(bpy)(Am)₄]²⁺ complexes corresponds to an approximately MLCT excited state consisting of mostly MLCT-(Ru-bpy) with a minimal ππ*(bpy) contribution. DFT modeling also indicated that the low-energy singlet excited states in the T_e geometry (S_n(T)) of the [Ru(bpy)₂(ph-dipy)]⁺ complex consist of numerous CT-S_n(T)-type states of the Ru-dipy and Ru-bpy moieties, whereas the [Ru(bpy)(Am)₄]²⁺ ions show quite simple MLCT-S_n(T)-type states of the Ru-bpy moiety. Based on experimental observations, DFT modeling, and the plain spin-orbit coupling (SOC) principle, we conclude that the remarkably high ι_em(p) amplitudes of the [Ru(bpy)₂(R-dipy)]⁺ complexes relative to those of [Ru(bpy)(Am)₄]²⁺ complexes can be attributed to the relatively substantial contribution of intrinsic SOC-mediated intensity stealing from the numerous low-energy CT-type S_n(T) states.

Photophysics of Ruthenium(II) Complexes with Thiazole π-Extended Dipyridophenazine Ligands

Transition-metal-based donor-acceptor systems can produce long-lived excited charge-transfer states by visible-light irradiation. The novel ruthenium(II) polypyridyl type complexes Ru1 and Ru2 based on the dipyridophenazine ligand (L0) directly linked to 4-hydroxythiazoles of different donor strengths were synthesized and photophysically characterized. The excited-state dynamics were investigated by femtosecond-to-nanosecond transient absorption and nanosecond emission spectroscopy complemented by time-dependent density functional theory calculations. These results indicate that photoexcitation in the visible region leads to the population of both metal-to-ligand charge-transfer (¹MLCT) and thiazole (tz)-induced intraligand charge-transfer (¹ILCT) states. Thus, the excited-state dynamics is described by two excited-state branches, namely, the population of (i) a comparably short-lived phenazine-centered ³MLCT state (τ ≈ 150-400 ps) and (ii) a long-lived ³ILCT state (τ ≈ 40-300 ns) with excess charge density localized on the phenazine and tz moieties. Notably, the ruthenium(II) complexes feature long-lived dual emission with lifetimes in the ranges τ_Em,1 ≈ 40-300 ns and τ_Em,2 ≈ 100-200 ns, which are attributed to emission from the ³ILCT and ³MLCT manifolds, respectively.

Iron's Wake: The Performance of Quantum Mechanical-Derived Versus General-Purpose Force Fields Tested on a Luminescent Iron Complex

Recently synthetized iron complexes have achieved long-lived excited states and stabilities which are comparable, or even superior, to their ruthenium analogues, thus representing an eco-friendly and cheaper alternative to those materials based on rare metals. Most of computational tools which could help unravel the origin of this large efficiency rely on ab-initio methods which are not able, however, to capture the nanosecond time scale underlying these photophysical processes and the influence of their realistic environment. Therefore, it exists an urgent need of developing new low-cost, but still accurate enough, computational methodologies capable to deal with the steady-state and transient spectroscopy of transition metal complexes in solution. Following this idea, here we focus on the comparison between general-purpose transferable force-fields (FFs), directly available from existing databases, and specific quantum mechanical derived FFs (QMD-FFs), obtained in this work through the Joyce procedure. We have chosen a recently reported Fe^III complex with nanosecond excited-state lifetime as a representative case. Our molecular dynamics (MD) simulations demonstrated that the QMD-FF nicely reproduces the structure and the dynamics of the complex and its chemical environment within the same precision as higher cost QM methods, whereas general-purpose FFs failed in this purpose. Although in this particular case the chemical environment plays a minor role on the photo physics of this system, these results highlight the potential of QMD-FFs to rationalize photophysical phenomena provided an accurate QM method to derive its parameters is chosen.

Tuning the Luminescent Properties of Ruthenium(II) Amino-1,10-Phenanthroline Complexes by Varying the Position of the Amino Group on the Heterocycle

Eight 1,10-phenanthrolines bearing one or two 2-(1-adamantyloxy)ethylamino substituents attached to different positions of the heterocyclic core were prepared according to S_N Ar or palladium-catalyzed amination reactions. Their reaction with cis-Ru(bpy)₂ Cl₂ (bpy=2,2'-bipyridine) was investigated and Ru(bpy)₂ (L)(PF₆ )₂ (phen=1,10-phenanthroline) (L=amino-substituted 1,10-phenanthroline) complexes were obtained in good yields. The electronic structure and emissive properties of these complexes are strongly dependent on the position of the amino substituent in the heterocycle. Emission bands of the complexes bearing 2- and 4-substituted 1,10-phenanthroline ligands are red-shifted (up to 56 nm) and less intense compared to that of the parent [Ru(phen)(bpy)₂ ](PF₆ )₂ . In contrast, the introduction of the substituent in 3- or 5-position of 1,10-phenanthroline ring induces only small decrease of luminescence and the brightness of the complex with the 3-substituted ligand is comparable to that of the parent complex.

Stabilization of Long-Looped i-Motif DNA by Polypyridyl Ruthenium Complexes

A spectroscopic study of the interactions of Λ- and Δ-[Ru(phen)₂(dppz)]²⁺ with i-motif DNA containing thymine loops of various lengths. In the presence of i-motifs, the luminescence of the Λ enantiomer was enhanced much more than the Δ. Despite this, the effect of each enantiomer on i-motif thermal stability was comparable. The sequences most affected by [Ru(phen)₂(dppz)]²⁺ were those with long thymine loops; this suggests that long-looped i-motifs are attractive targets for potential transition metal complex drugs and should be explored further in drug design.

Targeting G-quadruplexes with Organic Dyes: Chelerythrine-DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy

The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences—representative of different topologies and possessing biological relevance, such as telomeric or regulatory sequences—have been considered. An original multiscale protocol, making use of molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, allowed us to compare the theoretical and experimental circular dichroism spectra of the different DNA topologies, readily providing atomic-level details of the CHE–DNA binding modes. The binding selectivity towards G-quadruplexes is confirmed by both experimental and theoretical determination of the binding free energies. Overall, our mixed computational and experimental approach is able to shed light on the interaction of small molecules with different DNA conformations. In particular, CHE may be seen as the building block of promising drug candidates specifically targeting G-quadruplexes for both antitumoral and antiviral purposes.

Binding properties of two ruthenium(II) polypyridyl complexes [Ru(bpy)2(dppz-Br)]2+ and [Ru(dmb)2(dppz-Br)]2+ with the RNA poly(U)•poly(A)*poly(U) triplex

Two ruthenium(II) polypyridyl complexes containing different ancillary ligands, [Ru(bpy)₂(dppz-Br)]²⁺ (Ru1; bpy = 2,2'-bipyridine dppz-Br = 7-Br-dipyrido[3,2-a,2',3'-c]-phenazine) and [Ru(dmb)₂(dppz-Br)]²⁺ (Ru2; dmb = 4,4'-dimethyl-2,2'-bipyridine), have been synthesized and characterized. Binding properties of Ru1 and Ru2 with the RNA poly(U)•poly(A)*poly(U) triplex have been investigated by UV-Vis spectroscopy, fluorescence spectroscopy, viscosity measurements as well as circular dichroism and thermal denaturation. Spectrophotometric studies together with viscosity measurements suggest that both Ru1 and Ru2 bind with the triplex by intercalation mode, and the melting experiments demonstrate that the two complexes can effectively enhance the triplex stabilization. However, results indicate that Ru1 stabilizes the third-strand and Watson-Crick base-paired duplex of the triplex without obvious selectivity. In contrast, Ru2 prefers to bind with the third strand rather than the Watson-Crick base-paired duplex of the triplex to a some extent under the same conditions used in this study, thereby significantly stabilizing the third strand. The obtained results of this study suggest that slight differences in the ancillary ligands bpy and dmb should be the main factor affecting the binding interactions of the two complexes with the triplex.

Third-strand stabilizing effects of the RNA poly(U)·poly(A)*poly(U) triplex by a ruthenium(II) polypyridine complex and its hexaarginine peptide conjugate

In this work, a Ru(II) complex [Ru(bpy)₂(pip-CO₂H)]²⁺ (Ru1) and its hexaarginine peptide conjugate [Ru(bpy)₂(pic-Arg₆)]⁸⁺ (Ru2) have been synthesized and characterized. The binding of Ru1 and Ru2 with poly(U)•poly(A)*poly(U) triplex has been studied. Results suggest that Ru1 binds in the surface of the minor groove while Ru2 binds to the minor groove of the triplex. Consequently, the triplex stabilization is barely affected by Ru1, while with Ru2 the triplex stabilizing effect is so strong that that dissociation of the triplex shows an overlapping of both melting processes with the melting temperature increased to a maximum of 56.1 °C at the C_Ru2/C_UAU ratio of 0.05, where ΔT_m1 and ΔT_m2 are 19.6 and 10.1 °C, respectively. Furthermore, the effect of Ru2 stabilizing the third strand at such a low binding ratio of 0.05 is more marked than what obsereved for flavone luteolin and [Ru(bpy)₂(mdpz)]²⁺, which are so far the strongest triplex stabilizers in the reported organic small molecules and metal complexes, respectively. Considering the structure natures of Ru2, conceivably except for electrostatic interaction, the forces stabilizing the triplex should also involve hydrophobic interaction and hydrogen bingding. To our knowledge, this work represents a first example of improving the triplex stabilization by a metallopeptide.

Charge-Transfer versus Charge-Separated Triplet Excited States of [ReI (dmp)(CO)3 (His124)(Trp122)]+ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

A computational investigation of the triplet excited states of a rhenium complex electronically coupled with a tryptophan side chain and bound to an azurin protein is presented. In particular, by using high-level molecular modeling, evidence is provided for how the electronic properties of the excited-state manifolds strongly depend on coupling with the environment. Indeed, only upon explicitly taking into account the protein environment can two stable triplet states of metal-to-ligand charge transfer or charge-separated nature be recovered. In addition, it is also demonstrated how the rhenium complex plus tryptophan system in an aqueous environment experiences too much flexibility, which prevents the two chromophores from being electronically coupled. This occurrence disables the formation of a charge-separated state. The successful strategy requires a multiscale approach of combining molecular dynamics and quantum chemistry. In this context, the strategy used to parameterize the force fields for the electronic triplet states of the metal complex is also presented.

Spectro-electrochemical Studies on [Ru(TAP)2(dppz)]2+-Insights into the Mechanism of its Photosensitized Oxidation of Oligonucleotides

[Ru(TAP)₂(dppz)]²⁺ (TAP = 1,4,5,8-tetraazaphenanthrene; dppz = dipyrido[3,2- a:2',3'- c]phenazine) is known to photo-oxidize guanine in DNA. Whether this oxidation proceeds by direct photoelectron transfer or by proton-coupled electron transfer is still unknown. To help distinguish between these mechanisms, spectro-electrochemical experiments have been carried out with [Ru(TAP)₂(dppz)]²⁺ in acetonitrile. The UV-vis and mid-IR spectra obtained for the one-electron reduced product were compared to those obtained by picosecond transient absorption and time-resolved infrared experiments of [Ru(TAP)₂(dppz)]²⁺ bound to guanine-containing DNA. An interesting feature of the singly reduced species is an electronic transition in the near-IR region (with λ_max at 1970 and 2820 nm). Density functional and time-dependent density functional theory simulations of the vibrational and electronic spectra of [Ru(TAP)₂(dppz)]²⁺, the reduced complex [Ru(TAP)₂(dppz)]⁺, and four isomers of [Ru(TAP)(TAPH)(dppz)]²⁺ (a possible product of proton-coupled electron transfer) were performed. Significantly, these predict absorption bands at λ > 1900 nm (attributed to a ligand-to-metal charge-transfer transition) for [Ru(TAP)₂(dppz)]⁺ but not for [Ru(TAP)(TAPH)(dppz)]²⁺. Both the UV-vis and mid-IR difference absorption spectra of the electrochemically generated singly reduced species [Ru(TAP)₂(dppz)]⁺ agree well with the transient absorption and time-resolved infrared spectra previously determined for the transient species formed by photoexcitation of [Ru(TAP)₂(dppz)]²⁺ intercalated in guanine-containing DNA. This suggests that the photochemical process in DNA proceeds by photoelectron transfer and not by a proton-coupled electron transfer process involving formation of [Ru(TAP)(TAPH)(dppz)]²⁺, as is proposed for the reaction with 5'-guanosine monophosphate. Additional infrared spectro-electrochemical measurements and density functional calculations have also been carried out on the free TAP ligand. These show that the TAP radical anion in acetonitrile also exhibits strong broad near-IR electronic absorption (λ_max at 1750 and 2360 nm).

Triplet photosensitization mechanism of thymine by an oxidized nucleobase: from a dimeric model to DNA environment

Nucleic acids are constantly exposed to external agents that can induce chemical and photochemical damage. In spite of the great advances achieved in the last years, some molecular mechanisms of DNA damage are not completely understood yet. A recent experimental report (I. Aparici-Espert et al., ACS Chem. Biol. 2018, 13, 542) proved the ability of 5-formyluracil (ForU), a common oxidatively generated product of thymine, to act as an intrinsic sensitizer of nucleic acids, causing single strand breaks and cyclobutane pyrimidine dimers in plasmid DNA. In the present contribution, we use theoretical methodologies to study the triplet photosensitization mechanism of thymine exerted by ForU in a model dimer and in DNA environment. The photochemical pathways in the former system are described combining the CASPT2 and TD-DFT methods, whereas molecular dynamics simulations and QM/MM calculations are employed for the DNA duplex. It is unambiguously shown that the 1n,π* state localised in ForU mediates the population of the triplet manifold, most likely the 3π,π* state centred in ForU, whereas the 3π,π* state localized in thymine can be populated via triplet-triplet energy transfer given the small energy barrier of <0.23 eV determined for this pathway.

Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules

Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.

Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA

DNA is the target of chemical compounds (drugs, pollutants, photosensitizers, etc.), which bind through non-covalent interactions. Depending on their structure and their chemical properties, DNA binders can associate to the minor or to the major groove of double-stranded DNA. They can also intercalate between two adjacent base pairs, or even replace one or two base pairs within the DNA double helix. The subsequent biological effects are strongly dependent on the architecture of the binding motif. Discriminating between the different binding patterns is of paramount importance to predict and rationalize the effect of a given compound on DNA. The structural characterization of DNA complexes remains, however, cumbersome at the experimental level. In this contribution, we employed all-atom molecular dynamics simulations to determine the standard binding free energy of DNA with netropsin, a well-characterized antiviral and antimicrobial drug, which associates to the minor groove of double-stranded DNA. To overcome the sampling limitations of classical molecular dynamics simulations, which cannot capture the large change in configurational entropy that accompanies binding, we resort to a series of potentials of mean force calculations involving a set of geometrical restraints acting on collective variables.

New Ligand Design Provides Delocalization and Promotes Strong Absorption throughout the Visible Region in a Ru(II) Complex

The new Ru(II)-anthraquinone complex [Ru(bpy)₂(qdpq)](PF₆)₂ (Ru-qdpq; bpy = 2,2'-bipyridine; qdpq = 2,3-di(2-pyridyl)naphtho[2,3-f]quinoxaline-7,12-quinone) possesses a strong ¹MLCT Ru → qdpq absorption with a maximum at 546 nm that tails into the near-IR and is significantly red-shifted relative to that of the related complex [Ru(bpy)₂(qdppz)](PF₆)₂ (Ru-qdppz; qdppz = naphtho[2,3-a]dipyrido[3,2-h:2',3'-f]phenazine-5,18-dione), with λ_max = 450 nm. Ru-qdppz possesses electronically isolated proximal and distal qdppz-based excited states; the former is initially generated and decays to the latter, which repopulates the ground state with τ = 362 ps. In contrast, excitation of Ru-qdpq results in the population of a relatively long-lived (τ = 19 ns) Ru(dπ) → qdpq(π*) ³MLCT excited state where the promoted electron is delocalized throughout the qdpq ligand. Ultrafast spectroscopy, used together with steady-state absorption, electrochemistry, and DFT calculations, indicates that the unique coordination modes of the qdpq and qdppz ligands impart substantially different electronic communication throughout the quinone-containing ligand, affecting the excited state and electron transfer properties of these molecules. These observations create a pathway to synthesize complexes with red-shifted absorptions that possess long-lived, redox-active excited states that are useful for various applications, including solar energy conversion and photochemotherapy.

Guanine Can Direct Binding Specificity of Ru-dipyridophenazine (dppz) Complexes to DNA through Steric Effects

X-ray crystal structures of three Λ-[Ru(L)2 dppz]2+ complexes (dppz=dipyridophenazine; L=1,10-phenanthroline (phen), 2,2'-bipyridine (bpy)) bound to d((5BrC)GGC/GCCG) showed the compounds intercalated at a 5'-CG-3' step. The compounds bind through canted intercalation, with the binding angle determined by the guanine NH2 group, in contrast to symmetrical intercalation previously observed at 5'-TA-3' sites. This result suggests that canted intercalation is preferred at 5'-CG-3' sites even though the site itself is symmetrical, and we hypothesise that symmetrical intercalation in a 5'-CG-3' step could give rise to a longer luminescence lifetime than canted intercalation.

Direct Determination of Metal Complexes' Interaction with DNA by Atomic Telemetry and Multiscale Molecular Dynamics

The lack of molecular mechanistic understanding of the interaction between metal complexes and biomolecules hampers their potential medical use. Herein we present a robust procedure combining resonant X-ray emission spectroscopy and multiscale molecular dynamics simulations, which allows for straightforward elucidation of the precise interaction mechanism at the atomic level. The report unveils an unforeseen hydrolysis process and DNA binding of [Pt{N(p-HC₆F₄)CH₂}₂py₂] (Pt103), which showed potential cytotoxic activity in the past. Pt103 preferentially coordinates to adjacent adenine sites, instead of guanine sites as in cisplatin, because of its hydrogen bond ability. Comparison with previous research on cisplatin suggests that selective binding to guanine or adenine may be achieved by controlling the acidity of the compound.

Monitoring guanine photo-oxidation by enantiomerically resolved Ru(II) dipyridophenazine complexes using inosine-substituted oligonucleotides

The intercalating [Ru(TAP)2(dppz)](2+) complex can photo-oxidise guanine in DNA, although in mixed-sequence DNA it can be difficult to understand the precise mechanism due to uncertainties in where and how the complex is bound. Replacement of guanine with the less oxidisable inosine (I) base can be used to understand the mechanism of electron transfer (ET). Here the ET has been compared for both Λ- and Δ-enantiomers of [Ru(TAP)2(dppz)](2+) in a set of sequences where guanines in the readily oxidisable GG step in {TCGGCGCCGA}2 have been replaced with I. The ET has been monitored using picosecond and nanosecond transient absorption and picosecond time-resolved IR spectroscopy. In both cases inosine replacement leads to a diminished yield, but the trends are strikingly different for Λ- and Δ-complexes.

Direct observation by time-resolved infrared spectroscopy of the bright and the dark excited states of the [Ru(phen)2(dppz)]2+ light-switch compound in solution and when bound to DNA

The [Ru(phen)2(dppz)]2+ complex (1) is non-emissive in water but is highly luminescent in organic solvents or when bound to DNA, making it a useful probe for DNA binding. To date, a complete mechanistic explanation for this "light-switch" effect is still lacking. With this in mind we have undertaken an ultrafast time resolved infrared (TRIR) study of 1 and directly observe marker bands between 1280-1450 cm-1, which characterise both the emissive "bright" and the non-emissive "dark" excited states of the complex, in CD3CN and D2O respectively. These characteristic spectral features are present in the [Ru(dppz)3]2+ solvent light-switch complex but absent in [Ru(phen)3]2+, which is luminescent in both solvents. DFT calculations show that the vibrational modes responsible for these characteristic bands are predominantly localised on the dppz ligand. Moreover, they reveal that certain vibrational modes of the "dark" excited state couple with vibrational modes of two coordinating water molecules, and through these to the bulk solvent, thus providing a new insight into the mechanism of the light-switch effect. We also demonstrate that the marker bands for the "bright" state are observed for both Λ- and Δ-enantiomers of 1 when bound to DNA and that photo-excitation of the complex induces perturbation of the guanine and cytosine carbonyl bands. This perturbation is shown to be stronger for the Λ-enantiomer, demonstrating the different binding site properties of the two enantiomers and the ability of this technique to determine the identity and nature of the binding site of such intercalators.

Interaction of Iron II Complexes with B-DNA. Insights from Molecular Modeling, Spectroscopy, and Cellular Biology

We report the characterization of the interaction between B-DNA and three terpyridin iron II complexes. Relatively long time-scale molecular dynamics (MD) is used in order to characterize the stable interaction modes. By means of molecular modeling and UV-vis spectroscopy, we prove that they may lead to stable interactions with the DNA duplex. Furthermore, the presence of larger π-conjugated moieties also leads to the appearance of intercalation binding mode. Non-covalent stabilizing interactions between the iron complexes and the DNA are also characterized and evidenced by the analysis of the gradient of the electronic density. Finally, the structural deformations induced on the DNA in the different binding modes are also evidenced. The synthesis and chemical characterization of the three complexes is reported, as well as their absorption spectra in presence of DNA duplexes to prove the interaction with DNA. Finally, their effects on human cell cultures have also been evidenced to further enlighten their biological effects.

Understanding DNA under oxidative stress and sensitization: the role of molecular modeling

DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.

Reversal of a Single Base-Pair Step Controls Guanine Photo-Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex

Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo‐oxidation by Λ‐[Ru(TAP)₂(dppz)]²⁺ have been compared in 5′‐{CCGGATCCGG}₂ and 5′‐{CCGGTACCGG}₂ using pico/nanosecond transient visible and time‐resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′‐TA‐3′ versus 5′‐AT‐3′ binding preference predicted by X‐ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides.

Photoaddition of two guanine bases to single Ru-TAP complexes. Computational studies and ultrafast spectroscopies to elucidate the pH dependence of primary processes

The covalent photoadduct (PA) between [Ru(TAP)3](2+) (TAP = 1,4,5,8-tetraazaphenanthrene) and guanosine monophosphate (GMP) opened the way to interesting photobiological applications. In this context, the PA's capability upon illumination to give rise to the addition of a second guanine base is especially interesting. The origins of these intriguing properties are for the first time thoroughly investigated by an experimental and theoretical approach. The PA's spectroscopic and redox data combined with TDDFT results corroborated with resonance Raman data show that the properties of this PA (pKa around 7) depend on the solution pH. Theoretical results indicate that the acid form PA.H(+) when excited should relax to MLCT (metal-to-ligand charge transfer) excited states, in contrast to the basic form PA whose excited state should have LLCT/ILCT (ligand-to-ligand charge transfer/intra ligand charge transfer) characteristics. Ultrafast excitation of PA.H(+) at pH 5.9 produces continuous dynamic processes in a few hundred picoseconds involving coupled proton-electron transfers responsible for luminescence quenching. Long-lived species of a few microseconds capable of reacting with GMP are produced at that pH, in agreement with the formation of covalent addition of a second GMP to PA, as shown by mass spectrometry results. In contrast, at pH 8 (mainly nonprotonated PA), other ultrafast transient species are detected and no GMP biadduct is formed in the presence of GMP. This pH dependence of photoreaction can be rationalized with the different nature of the excited states, thus at pH 8, unreactive LLCT/ILCT states and at pH 5.9 reactive MLCT states.

Photophysics of acetophenone interacting with DNA: why the road to photosensitization is open

Deoxyribonucleic acid photosensitization, i.e. the photoinduced electron- or energy-transfer of chromophores interacting with DNA, is a crucial phenomenon that triggers important DNA lesions such as pyrimidine dimerization, even upon absorption of relatively low-energy radiation. Oxidative lesions may also be produced via the photoinduced production of reactive oxygen species. Aromatic ketones, and acetophenone in particular, are well known for their sensitization effects. In this contribution we model the structural and dynamical properties of the acetophenone/DNA aggregates as well as their spectroscopic and photophysical properties using high-level hybrid quantum mechanics/molecular mechanics methods. We show that the key steps of the photochemistry of acetophenone in gas phase are conserved in the macromolecular environment and thus an ultrafast singlet-triplet conversion of acetophenone is expected prior to the transfer to DNA.