Theoretical evidence of photo-induced charge transfer from DNA to intercalated ruthenium (II) organometallic complexes

Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action

Phenanthriplatin (PtPPH) is a monovalent platinum(II)-based complex with a large cytotoxicity against cancer cells. Although the aqua-activated drug has been assumed to be the precursor for DNA damage, it is still under debate whether the way in which that metallodrug attacks to DNA is dominated by a direct binding to a guanine base or rather by an intercalated intermediate product. Aiming to capture the mechanism of action of PtPPH, the present contribution used theoretical tools to systematically assess the sequence of all possible mechanisms on drug activation and reactivity, for example, hydrolysis, intercalation, and covalent damage to DNA. Ab initio quantum mechanical (QM) methods, hybrid QM/QM′ schemes, and independent gradient model approaches are implemented in an unbiased protocol. The performed simulations show that the cascade of reactions is articulated in three well-defined stages: (i) an early and fast intercalation of the complex between the DNA bases, (ii) a subsequent hydrolysis reaction that leads to the aqua-activated form, and (iii) a final formation of the covalent bond between PtPPH and DNA at a guanine site. The permanent damage to DNA is consequently driven by that latter bond to DNA but with a simultaneous π–π intercalation of the phenanthridine into nucleobases. The impact of the DNA sequence and the lateral backbone was also discussed to provide a more complete picture of the forces that anchor the drug into the double helix.

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.

2,3-(Dibenzimidazol-2-yl)quinoxalines: Unexpected Dynamical Effect on Steady-State Electronic Absorption Spectra

We report on the electronic absorption spectra, conformational behavior, and intra- and intermolecular hydrogen bonds of 2,3-(dibenzimidazol-2-yl)-quinoxaline (DBIQ). The experimentally found strong solvent dependence of the absorption spectra of DBIQ solutions cannot be assigned to electronic excitations of the equilibrium ground-state DBIQ structure. Extended consideration including the nonequilibrium structures within the framework of ab initio molecular dynamics (MD) revealed the importance of torsion molecular motions not covered by the static case. The strong impact of solute-solvent hydrogen bonding on stabilization of these nonequilibrium structures and on conformational composition of DBIQ was demonstrated. A presence of twisted nonplanar geometries along the whole MD trajectory was shown to drastically influence not only energies but also characters of electronic excitations, resulting in a change of local π-π* character in a solution of 1,2-dichloroethane to charge-transfer character in polar dimethylsulfoxide.

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.

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.

Transition matrices and orbitals from reduced density matrix theory

In this contribution, we report two different methodologies for characterizing the electronic structure reorganization occurring when a chromophore undergoes an electronic transition. For the first method, we start by setting the theoretical background necessary to the reinterpretation through simple tensor analysis of (i) the transition density matrix and (ii) the natural transition orbitals in the scope of reduced density matrix theory. This novel interpretation is made more clear thanks to a short compendium of the one-particle reduced density matrix theory in a Fock space. The formalism is further applied to two different classes of excited states calculation methods, both requiring a single-determinant reference, that express an excited state as a hole-particle mono-excited configurations expansion, to which particle-hole correlation is coupled (time-dependent Hartree-Fock/time-dependent density functional theory) or not (configuration interaction single/Tamm-Dancoff approximation). For the second methodology presented in this paper, we introduce a novel and complementary concept related to electronic transitions with the canonical transition density matrix and the canonical transition orbitals. Their expression actually reflects the electronic cloud polarisation in the orbital space with a decomposition based on the actual contribution of one-particle excitations from occupied canonical orbitals to virtual ones. This approach validates our novel interpretation of the transition density matrix elements in terms of the Euclidean norm of elementary transition vectors in a linear tensor space. A proper use of these new concepts leads to the conclusion that despite the different principles underlying their construction, they provide two equivalent excited states topological analyses. This connexion is evidenced through simple illustrations of (in)organic dyes electronic transitions analysis.

Dehalogenation of persistent halogenated organic compounds: A review of computational studies and quantitative structure-property relationships

Dehalogenation is one of the highly important degradation reactions for halogenated organic compounds (HOCs) in the environment, which is also being developed as a potential type of the remediation technologies. In combination with the experimental results, intensive efforts have recently been devoted to the development of efficient theoretical methodologies (e.g. multi-scale simulation) to investigate the mechanisms for dehalogenation of HOCs. This review summarizes the structural characteristics of neutral molecules, anionic species and excited states of HOCs as well as their adsorption behavior on the surface of graphene and the Fe cluster. It discusses the key physiochemical properties (e.g. frontier orbital energies and thermodynamic properties) calculated at various levels of theory (e.g. semiempirical, ab initio, density functional theory (DFT) and the periodic DFT) as well as their connections to the reactivity and reaction pathway for the dehalogenation. This paper also reviews the advances in the linear and nonlinear quantitative structure-property relationship models for the dehalogenation kinetics of HOCs and in the mathematical modeling of the dehalogenation processes. Furthermore, prospects of further expansion and exploration of the current research fields are described in this article.

Dye chemistry with time-dependent density functional theory

In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.

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.

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

The environmental effects on the structural and photophysical properties of [Ru(L)2 (dppz)](2+) complexes (L=bpy=2,2'-bipyridine, phen=1,10-phenanthroline, tap=1,4,5,8-tetraazaphenanthrene; dppz=dipyrido[3,3-a:2',3'-c]phenazine), used as DNA intercalators, have been studied by means of DFT, time-dependent DFT, and quantum mechanics/molecular mechanics calculations. The electronic characteristics of the low-lying triplet excited states in water, acetonitrile, and DNA have been investigated to decipher the influence of the environment on the luminescent behavior of this class of molecules. The lowest triplet intra-ligand (IL) excited state calculated at λ≈800 nm for the three complexes and localized on the dppz ligand is not very sensitive to the environment and is available for electron transfer from a guanine nucleobase. Whereas the lowest triplet metal-to-ligand charge-transfer ((3)MLCT) states remain localized on the ancillary ligand (tap) in [Ru(tap)2 (dppz)](2+), regardless of the environment, their character is drastically modified in the other complexes [Ru(phen)2 (dppz)](2+) and [Ru(bpy)2 (dppz)](2+) upon going from acetonitrile (MLCTdppz/phen or MLCTdppz/bpy) to water (MLCTdppz) and DNA (MLCTphen and MLCTbpy). The change in the character of the low-lying (3) MLCT states accompanying nuclear relaxation in the excited state controls the emissive properties of the complexes in water, acetonitrile, and DNA. The light-switching effect has been rationalized on the basis of environment-induced control of the electronic density distributed in the lowest triplet excited states.