Time-Resolved Resonance Raman Study of the Exciplex Formed between Excited Cu−Porphyrin and DNA

Excited-State Dynamics Leading Either to Triplet Formation or Coordinative Expansion following Photolysis of Cu(II)-Porphyrins: A DFT, TD-DFT, Luminescence and Femtosecond Time-Resolved Absorbance Study

The photophysical properties of Cu(II) complexes with 5,10,15,20-meso-tetrakis(phenyl)porphyrin and 5,10,15,20-meso-tetrakis(N-methylpyridium-4-yl)porphyrin are examined via the luminescence and femtosecond time-resolved absorbance methods, respectively. These studies are supported by DFT and TD-DFT calculations, which highlight the important role played by ligand-to-metal charge-transfer states in directing the system toward either intersystem crossing to the triplet hypersurface or coordinative expansion to a five-coordinate quasi-stable intermediate. The latter processes occur when the porphyrin is photolyzed in the presence of suitably located Lewis bases. Femtosecond time-resolved absorbance measurements of Cu(II)-5,10,15,20-meso-tetrakis(N-methylpyridium-4-yl)porphyrin confirm that the coordinative expansion in water occurs in approximately 700 fs, while crossing to the triplet hypersurface takes approximately 140 fs in the same solvent. These processes are mutually exclusive, although both can occur simultaneously depending on the environment of the porphyrin. The ratio of the two processes depends on the relative orientation of the Lewis base with respect to the copper atom at the time of excitation. As a consequence, copper porphyrins such as these are excellent probes in the environment of the porphyrin and can be used to identify the location of the porphyrin when interacting with DNA fragments.

The structural features of poly(dG-dC).poly(dG-dC) at complexation with some porphyrins

The binding peculiarities of the water-soluble meso-tetra-(4N-hydroxyethylpyridyl) porphyrin (H₂TOEtPyP4) and its Cu- and Co-derivatives (CuTOEtPyP4 and CoTOEtPyP4) with synthetic double-stranded alternating polynucleotide poly(dG-dC).poly(dG-dC) were investigated by UV/Vis absorption and circular dichroism (CD) methods. It was shown that the porphyrins with planar structure such as H₂TOEtPyP4 and CuTOEtPyP4 interact with poly(dG-dC).poly(dG-dC) via intercalation at low relative concentrations (r = [porphyrin]/[polynucleotide]), while at high r - via intercalation and external binding modes. In the case of no planar porphyrin CoTOEtPyP4 complexation occurs only by external binding mode. The binding constant K_b and the exclusion parameter n calculated for H₂TOEtPyP4, CuTOEtPyP4 and CoTOEtPyP4 porphyrins with poly(dG-dC).poly(dG-dC) complexes was 1.50 x10⁷, M^-1 (n = 1.76); 9.29 x10⁷, M^-1 (n = 1.18); and 0.28 x10⁷, M^-1 (n = 2.65) correspondingly. The values of binding parameters for each porphyrin-poly(dG-dC).poly(dG-dC) complexes demonstrated good agreement with the proposed binding models. Communicated by Ramaswamy H. Sarma.

Excited-state structural dynamics of nickel complexes probed by optical and X-ray transient absorption spectroscopies: insights and implications

Excited states of nickel complexes undergo a variety of photochemical processes, such as charge transfer, ligation/deligation, and redox reactions, relevant to solar energy conversion and photocatalysis. The efficiencies of the aforementioned processes are closely coupled to the molecular structures in the ground and excited states. The conventional optical transient absorption spectroscopy has revealed important excited-state pathways and kinetics, but information regarding the metal center, in particular transient structural and electronic properties, remains limited. These deficiencies are addressed by X-ray transient absorption (XTA) spectroscopy, a detailed probe of 3d orbital occupancy, oxidation state and coordination geometry. The examples of excited-state structural dynamics of nickel porphyrin and nickel phthalocyanine have been described from our previous studies with highlights on the unique structural information obtained by XTA spectroscopy. We close by surveying prospective applications of XTA spectroscopy to active areas of Ni-based photocatalysis based on the knowledge gained from our previous studies.

Development of viscometric methods for studying the interaction of various porphyrins with DNA. Part IV: Meso-tetra-(4N-allylpyridyl) porphyrin and its Cu-, Co- and Zn-containing derivatives

The influence of water soluble cationic meso-tetra-(4N-allylpyridyl) porphyrin (H2TAlPyP4) and its metal complexes with Cu, Co and Zn on hydrodynamic and spectral behavior of DNA solutions has been studied by viscometry, CD and UV-vis spectroscopy methods. The results were compared with the results of previously conducted similar studies on meso-tetra-(3N-allylpyridyl) porphyrin (H2TAllPyP3). It has been shown that the change in position of peripheral radicals on the pyridylic ring has absolutely no effect on the rules of interaction of investigated porphyrins with DNA in the case of outside binders CoTAllPyP4 and ZnTAllPyP4. Planar porphyrin H2TAllPyP4 interacts with DNA predominantly by the intercalation mode at low relative concentrations of [Formula: see text] ([Formula: see text] [Porphyrin]/[DNA]) and by external binding mode at high values of [Formula: see text]. CuTAllPyP4 shows unusual behavior by interacting with DNA via a non-classical (partial) intercalation binding mode. It was shown that H[Formula: see text]TAllPyP3 and its metal complexes bind to DNA much more intensely than H2TAllPyP4 and its metal complexes.

Development of viscometric methods for studying the interaction of various porphyrins with DNA. Part I: meso-tetra-(4N-hydroxyethylpyridyl) porphyrin and its Ni-, Cu-, Co- and Zn- containing derivatives

The influence of water soluble cationic meso-tetra(4N-hydroxyethyl)pyridyl porphyrin ( H 2 THOEtPyP 4) and it's metal complexes with Ni ( II ), Cu ( II ), Co ( II ) and Zn ( II ) on hydrodynamic and spectral behavior of DNA solutions has been studied by viscometry and UV-vis absorption methods. It was shown that the presence of planar porphyrins, such as H 2 THOEtPyP 4, NiTHOEtPyP 4 and CuTHOEtPyP 4 leads to an increase in viscosity at relatively small concentrations, and then decreases to stable values. Such behavior corresponds to intercalation of these porphyrins in DNA structure, which results in a decrease of helical twist and lengthening of the DNA molecule. In the case of porphyrins with axial ligands, such as ZnTHOEtPyP 4 and CoTHOEtPyP 4, the relative viscosity decreases, which is explained by self-stacking of these porphyrins on DNA surface. Calculation and interpretation of binding parameters (Kb and n) demonstrated good agreement of viscometric and spectrophotometric measurements.

Photoinduced reduction of manganese(III) meso-tetrakis(1-methylpyridinium-4-yl)porphyrin at AT and GC base pairs

The photoreduction of water-soluble cationic manganese(III) meso-tetrakis(1-methylpyridium-4-yl)porphyrin (Mn(III)(TMPyP)(4+)) bound to a synthetic polynucleotide, either poly[d(A-T)2] or poly[d(G-C)2], was examined by conventional absorption and circular dichroism (CD) spectroscopy, transient absorption, and transient Raman spectroscopy. Upon binding, Mn(III)(TMPyP)(4+) produced a positive CD signal for both polynucleotides, suggesting external binding. In the poly[d(A-T)2]-Mn(III)(TMPyP)(4+) adduct case, an interaction between the bound porphyrin was suggested. The transient absorption spectral features of Mn(III)(TMPyP)(4+) in the presence of poly[d(A-T)2] and poly[d(G-C)2] were similar to those of the photoreduced products, Mn(II)(TMPyP)(4+), whereas Mn(III)(TMPyP)(4+) in the absence of polynucleotides retained its oxidation state. This indicated that both poly[d(A-T)2] and poly[d(G-C)2] act as electron donors, resulting in photo-oxidized G and A bases. The transient Raman bands (ν2 and ν4) that were assigned to porphyrin macrocycles exhibited a large downshift of ~25 cm(-1), indicating the photoreduction of Mn(III) to Mn(II) porphyrins when bound to both polynucleotides. The transient Raman bands for pyridine were enhanced significantly, suggesting that the rotation of peripheral groups for binding with polynucleotides is the major change in the geometry expected in the photoreduction process. These photoinduced changes do not appear to be affected by the binding mode of porphyrin.

Elucidation of the binding properties of a photosensitizer to salmon sperm DNA and its photobleaching processes by spectroscopic methods

Methylene blue (MB) is a tricyclic heteroaromatic photosensitizer with a promising application in the photodynamic therapy (PDT) for anticancer treatment. The binding properties of MB to salmon sperm DNA have been investigated by the measurements of absorption spectra, quenching experiments and the photobleaching processes. Remarkable hypochromic and bathochromic effects of MB in the presence of increasing amounts of DNA have been observed in the absorption spectra. The quenching of MB by the DNA bases obeys the Stern-Volmer equation and ferrocyanide quenching of MB in the absence and presence of DNA is also measured as extended experiments. Results from the above spectral measurements are all consistent with the intercalative binding mode of MB to DNA with the K b value of 5.6 × 10(3) M(-1). The photobleaching processes of MB and its DNA complex have also been studied, which indicate that the photobleaching of MB and its DNA complex proceed with different mechanisms and the reactive oxygen species are responsible for the self-sensitized photooxidation of MB.

Primary photoprocesses in cationic 5,10,15,20-meso-tetrakis(4-N-methylpyridiniumyl)porphyrin and its transition metal complexes bound with nucleic acids

Photophysical properties of meso-tetrakis(4-N-methylpyridiniumyl)porphyrin ( TMpyP 4) and its metallocomplexes M (II) TMpy P4 ( M = Zn , Cu , Ni , Co ) bound to natural DNA and synthetic poly-, oligo- and mononucleotides are considered with a primary emphasis placed upon intermolecular interaction of the photoexcited porphyrins with the nearest environment. Quenching of the fluorescent S 1 (but not triplet T 1) state due to guanine to porphyrin electron transfer is observed for TMpyP 4 intercalated between GC base pairs of the double-strand helixes, whereas in the case of TMpyP 4 complexed with guanosine monophosphate (GMP) both S 1 and T 1 states of the porphyrin are quenched. Furthermore, a dependence of the efficiency of TMpyP 4 triplet state quenching by the dissolved molecular oxygen from air on the porphyrin localization enables one to readily distinguish porphyrin groove binding mode from intercalation. Excited states of the TMpyP 4 complexes with transition metals, in spite of their very short lifetimes, also interact with nucleic acid components by means of an axial ligand binding/release to/from the metal. A possible structure of the five-coordinate excited complex (“exciplex”) formed in case of CuTMpyP 4 groove binding to some single- and double-strand polynucleotides is discussed.

Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. III. The nu(4) and nu(7) modes of nonplanar nickel porphyrin models

The time scales and pathways of vibrational energy relaxation (VER) of the nu(4) and nu(7) modes of three nickel porphyrin models, nickel porphine (NiP), nickel protoporphyrin IX (Ni-heme), and nickel octaethylporphyrin (NiOEP), were studied using a non-Markovian time-dependent perturbation theory at the B3LYP/6-31G(d) level. When NiP is calculated with D(4h) symmetry, it has the planar structure and the same VER properties as ferrous iron porphine (FeP). The porphine cores of both Ni-heme and NiOEP were distorted from a planar geometry, assuming a nonplanar structure, similar to that of the heme structure in cytochrome c. The VER time scales of Ni-heme are found to be similar to those predicted for a planar iron heme, but the derived pathways have distinctly different features. In particular, the strong coupling between the nu(7) mode and the overtone of the approximately 350 cm(-1) gamma(7) mode, observed for planar porphyrins, is absent in both nonplanar nickel porphyrins. Direct energy exchange between the nu(4) and nu(7) modes is not observed in NiOEP, but is found to play an essential role in the VER of the nu(4) mode in Ni-heme. The Ni-heme isopropionate groups are involved in the dominant VER pathways of both the nu(4) and nu(7) modes of Ni-heme. However, in contrast with VER pathways derived in planar iron heme, the isopropionate groups are not observed to play an essential role relative to other side chains in spatially directing the vibrational energy flow.

Ultrafast heme dynamics in ferrous versus ferric cytochrome c studied by time-resolved resonance Raman and transient absorption spectroscopy

Cytochrome c (Cyt c) is a heme protein involved in electron transfer and also in apoptosis. Its heme iron is bisaxially ligated to histidine and methionine side chains and both ferric and ferrous redox states are physiologically relevant, as well as a ligand exchange between internal residue and external diatomic molecule. The photodissociation of internal axial ligand was observed for several ferrous heme proteins including Cyt c, but no time-resolved studies have been reported on ferric Cyt c. To investigate how the oxidation state of the heme influences the primary photoprocesses, we performed a comprehensive comparative study on horse heart Cyt c by subpicosecond time-resolved resonance Raman and femtosecond transient absorption spectroscopy. We found that in ferric Cyt c, in contrast to ferrous Cyt c, the photodissociation of an internal ligand does not take place, and relaxation dynamics is dominated by vibrational cooling in the ground electronic state of the heme. The intermolecular vibrational energy transfer was found to proceed in a single phase with a temperature decay of approximately 7 ps in both ferric and ferrous Cyt c. For ferrous Cyt c, the instantaneous photodissociation of the methionine side chain from the heme iron is the dominant event, and its rebinding proceeds in two phases, with time constants of approximately 5 and approximately 16 ps. A mechanism of this process is discussed, and the difference in photoinduced coordination behavior between ferric and ferrous Cyt c is explained by an involvement of the excited electronic state coupled with conformational relaxation of the heme.

DNA binding studies of a new dicationic porphyrin. Insights into interligand interactions

Cationic porphyrins have an affinity for DNA and potential for applications in the fields of photodynamic therapy and cellular imaging. This report describes a new dicationic porphyrin, 5,15-dimethyl-10,20-di(N-methylpyridinium-4-yl)porphyrin, abbreviated H2tMe2D4. Although tetrasubstituted, H2tMe2D4 presents modest steric requirements and forms in reasonable yield by a "2+2" synthetic method. Accordingly, studies of the zinc(II)- and copper(II)-containing derivatives, Zn(tMe2D4) and Cu(tMe2D4), have also been possible. Methods used to characterize DNA-binding motifs include absorption, emission, linear, and circular dichroism spectroscopies, as well as viscometry. An unusually detailed picture of porphyrin uptake emerges. As the ratio of DNA to porphyrin increases during a typical titration, H2tMe2D4 or Cu(tMe2D4) initially aggregates on the host and then shifts to intercalative binding at close quarters before finally dispersing into non-interacting intercalation sites of the host. Emission studies of the copper(II) porphyrin have been very valuable. The existence of a measurable signal is diagnostic of intercalative binding, and the saturation behavior establishes that internalization typically monopolizes approximately three base pairs. In the moderate loading regime, emission data are most telling because dipole-dipole interactions between near-neighbor porphyrins tend to confuse other spectroscopic assays. The third ligand, Zn(tMe2D4), behaves differently in that the uptake is a strictly cooperative process. The mode of binding also varies with the base content of the DNA host. When the DNA is rich in A=T base pairs, the porphyrin remains five-coordinate and binds externally; however, Zn(tMe2D4) loses its axial ligand and binds by intercalation if the host contains only G[triple bond]C base pairs.

Subpicosecond oxygen trapping in the heme pocket of the oxygen sensor FixL observed by time-resolved resonance Raman spectroscopy

Dissociation of oxygen from the heme domain of the bacterial oxygen sensor protein FixL constitutes the first step in hypoxia-induced signaling. In the present study, the photodissociation of the heme-O2 bond was used to synchronize this event, and time-resolved resonance Raman (TR(3)) spectroscopy with subpicosecond time resolution was implemented to characterize the heme configuration of the primary photoproduct. TR(3) measurements on heme-oxycomplexes are highly challenging and have not yet been reported. Whereas in all other known six-coordinated heme protein complexes with diatomic ligands, including the oxymyoglobin reported here, heme iron out-of-plane motion (doming) occurs faster than 1 ps after iron-ligand bond breaking; surprisingly, no sizeable doming is observed in the oxycomplex of the Bradyrhizobium japonicum FixL sensor domain (FixLH). This assessment is deduced from the absence of the iron-histidine band around 217 cm(-1) as early as 0.5 ps. We suggest that efficient ultrafast oxygen rebinding to the heme occurs on the femtosecond time scale, thus hindering heme doming. Comparing WT oxy-FixLH, mutant proteins FixLH-R220H and FixLH-R220Q, the respective carbonmonoxy-complexes, and oxymyoglobin, we show that a hydrogen bond of the terminal oxygen atom with the residue in position 220 is responsible for the observed behavior; in WT FixL this residue is arginine, crucially implicated in signal transmission. We propose that the rigid O2 configuration imposed by this residue, in combination with the hydrophobic and constrained properties of the distal cavity, keep dissociated oxygen in place. These results uncover the origin of the "oxygen cage" properties of this oxygen sensor protein.

Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin

The time scale and mechanism of vibrational energy relaxation of the heme moiety in myoglobin was studied using molecular dynamics simulation. Five different solvent models, including normal water, heavy water, normal glycerol, deuterated glycerol and a nonpolar solvent, and two forms of the heme, one native and one lacking acidic side chains, were studied. Structural alteration of the protein was observed in native myoglobin glycerol solution and native myoglobin water solution. The single-exponential decay of the excess kinetic energy of the heme following ligand photolysis was observed in all systems studied. The relaxation rate depends on the solvent used. However, this dependence cannot be explained using bulk transport properties of the solvent including macroscopic thermal diffusion. The rate and mechanism of heme cooling depends upon the detailed microscopic interaction between the heme and solvent. Three intermolecular energy transfer mechanisms were considered: (i) energy transfer mediated by hydrogen bonds, (ii) direct vibration-vibration energy transfer via resonant interaction, and (iii) energy transfer via vibration-translation or vibration-rotation interaction, or in other words, thermal collision. The hydrogen bond interaction and vibration-vibration interaction between the heme and solvent molecules dominates the energy transfer in native myoglobin aqueous solution and native myoglobin glycerol solutions. For modified myoglobin, the vibration-vibration interaction is also effective in glycerol solution, different from aqueous solution. Thermal collisions form the dominant energy transfer pathway for modified myoglobin in water solution, and for both native myoglobin and modified myoglobin in a nonpolar environment. For native myoglobin in a nonpolar solvent solution, hydrogen bonds between heme isopropionate side chains and nearby protein residues, absent in the modified myoglobin nonpolar solvent solution, are key interactions influencing the relaxation pathways.

The DNA-Porphyrin Interactions Studied by Vibrational and Electronic Circular Dichroism Spectroscopy

The interactions of three different porphyrins, without axial ligands - 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Cu(II) tetrachloride (Cu(II)TMPyP), with axial ligands - 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Fe(III) pentachloride (Fe(III)TMPyP), and with bulky meso substituents - 5,10,15,20-tetrakis(N,N,N-trimethylanilinium-4-yl)-porphyrin tetrachloride (TMAP), with calf thymus DNA were studied by combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopy, and by IR and UV-VIS absorption spectroscopy. It has been shown that Cu(II)TMPyP prefers the intercalative binding mode with DNA in the GC-rich regions and the intercalative sites are saturated at the c(DNA)/c(Cu(II)TMPyP) ratio ~3:1, where c(DNA) and c(Cu(II)TMPyP) are total molar concentrations of nucleic acid in base pairs and porphyrin, respectively. Fe(III)TMPyP does not intercalate between the GC base pairs but binds to DNA in the minor groove. At higher c(DNA)/c(TMAP) ratios, TMAP interacts with DNA in the minor groove, but at lower ratios in the major groove and by the external binding mode accompanied by self-stacking of porphyrins along the phosphate backbone. VCD spectroscopy reliably discriminates the binding modes and specifies the conformational changes of the DNA matrices. It has been also shown that VCD spectroscopy is an effective tool for the conformational studies of DNA-porphyrin complexes. New spectroscopic "markers" in VCD spectra have been found for the specific DNA-porphyrin interactions.

Photodissociation of heme distal methionine in ferrous cytochrome C revealed by subpicosecond time-resolved resonance Raman spectroscopy

Cytochrome c (cyt c) is an electron-transfer heme protein that also binds nitric oxide (NO). In resting cyt c, two endogenous ligands of the heme iron are histidine-18 (His) and methionine-80 (Met) side chains, and NO binding requires the cleavage of one of the axial bonds. Previous femtosecond transient absorption studies suggested the photolysis of either Fe-His or Fe-Met bonds. We aimed at unequivocally identifying the internal side chain that is photodissociated in ferrous cyt c and at monitoring heme structural dynamics, by means of time-resolved resonance Raman (TR3) spectroscopy with approximately 0.6 ps time resolution. The Fe-His stretching mode at 216 cm-1 has been observed in photoproduct TR3 spectra for the first time for a c-type heme. The same transient mode was observed for a model ferrous cyt c N-fragment (residues 1-56) ligated with two His in the resting state. Our TR3 data reveal that upon ferrous cyt c photoexcitation, (i) distal Met side chain is instantly released, producing a five-coordinated domed heme structure, (ii) proximal His side chain, coupled to the heme, exhibits distortion due to strain exerted by the protein, and (iii) alteration in heme-cysteine coupling takes place along with the relaxation of the protein-induced deformations of the heme macrocycle.

Structural features of two distinct molecular complexes of copper(II) cationic porphyrin and deoxyribonucleotides

The associations of the water-soluble cationic copper(II)-5,10,15,20-meso-tetrakis(4-N-methylpyridyl) porphyrin (CuP) with d(pT)9 oligothymidylate and its building blocks deoxythymidine (dT) and deoxythymidine 5'-monophosphate (dTMP) were investigated by spectrophotometric titration [absorption, nanosecond transient resonance Raman (ns-RR) and picosecond time-resolved resonance Raman (ps-TR3) spectroscopies] to elucidate the structural requirements for the CuP exciplex formation in molecular complexes with unchained mononucleotides. In the d(pT)9 a factor analysis and global fit of the CuP absorption spectra revealed the formation of a single spectral species attributable to a 1 : 1 CuP. d(pT)9 complex throughout a wide range of d(pT)9/CuP ratios (0-10). Using ps-TR3 spectroscopy, the CuP. d(pT)9 complex was shown to be fully responsible for exciplex formation. In contrast, CuP mixed with dTMP ([dTMP]/[CuP] < 3000) yielded two spectroscopically distinct types of molecular complexes with 1 : 1 (CuP. dTMP) and 1 : 2 (CuP. (dTMP)2) (or even higher for [dTMP]/[CuP] > 3000) stoichiometry, the latter being spectroscopically identical to the CuP. d(pT)9 and providing a microenvironment favorable for exciplex formation to the same extent as the oligothymidylate. On the other hand, the 1 : 1 CuP. dTMP complex (prevailing for [dTMP]/[CuP] < 100) yielded no exciplex features. Similar behavior was observed for the CuP complexed with dT. To explain the difference in the ability of the CuP. dTMP and CuP. (dTMP)2 species to form the exciplex, two types of molecular complexes were suggested and discussed, differing in the orientation of the thymine planes with respect to the porphyrin macrocycle.