Hole transfer in DNA and photosensitized DNA damage: importance of adenine oxidation

Photosensitized DNA damage reactions were investigated for two well-known DNA-damaging photosensitizers (Sens), naphthalimide (NI) and napthaldiimide (NDI), which have similar photophysical properties but differ in their redox properties. NI and NDI derivatives (NIN, NDIN), which have cationic side chains and electrostatically binding to DNA due to favorable electrostatic interactions between the negatively charged phosphate groups of DNA and cationic groups, and NIP and NDIP, which possess phosphate groups and do not bind to DNA, were synthesized. NIN and NDIN can oxidize A and G via their singlet excited state, and NDIP oxidizes A and G via its triplet excited state, whereas NIP oxidizes only G. A combination of laser flash photolysis kinetic studies and quantitative HPLC analyses of photosensitized DNA damage was performed for several DNA sequences in the presence of Sens. NIN, NDIN, and NDIP, which oxidizes A, caused significant DNA damage upon photoirradiation, and DNA damage yield increased with the length of the consecutive A stretch. In contrast, NIP, which oxidizes only G, caused only moderate damage to DNA and showed no preference for the consecutive A sequences. These results clearly demonstrate the importance of A-oxidation, especially in consecutive A sequences, which triggers the rapid hole transfer between A's.     

Consecutive adenine sequences are potential targets in photosensitized DNA damage

Based on direct spectroscopic measurements of hole transfer in DNA and quantification of the yield of DNA oxidative damage, consecutive adenine sequences were found to be a good launching site for photosensitizers to inject a hole in DNA, where the following rapid hole transfer between adenines causes a long-lived charge-separated state leading to DNA oxidative damage. According to the results, the essential requisites for an efficient and/or harmful photosensitizer are determined as follows: to be able to oxidize adenine to trigger hole transfer between adenines, and react rapidly with molecular oxygen following its reduction, avoiding charge recombination and making the reaction irreversible. These results will greatly help us to classify photosensitizers harmful to human health, and to design an improved photosensitizer for biochemical applications.     

Syntheses and crystal structures of new aurate salts of adenine or guanine nucleobases

Two new gold(III) complexes with adenine or guanine nitrogenous bases as counter‐cations were synthesized. These are 6‐amino‐7H‐purine‐1,9‐diium tetrachloridogold(III) chloride monohydrate, (C₅H₇N₅)[AuCl₄]Cl·H₂O, 1 , and 2‐amino‐6‐oxo‐6,7‐dihydro‐1H‐purin‐9‐ium tetrachloridogold(III) hemihydrate, (C₅H₆N₅O)[AuCl₄]·0.5H₂O, 2 . Their crystal structures were studied using single‐crystal X‐ray diffraction and FT–IR spectroscopic techniques. The arrangement of species in the studied crystal structures implies π‐stacking interactions, as well as concomitant C—H…π interactions, hydrogen bonds and other types of noncovalent interactions, which were studied qualitatively and quantitatively using the method of molecular Voronoi–Dirichlet polyhedra. The variation of the nitrogenous base from adenine to guanine results in evident differences in the packing of the species in the crystals of 1 and 2 . The splitting and shifting of bands in the FT–IR spectra of the title compounds reveals several features representative of noncovalent interactions in their crystal structures.     

Satellite Hole Investigation of the Vibrational Modes of 9-Aminoacridine upon Binding to DNA

The spectral features of satellite holes are used to investigate 9-aminoacridine-DNA interactions. The hole depths of the outer ring vibronic modes are reduced more than that of the inner ring vibronic modes, implying that inner ring motion is less perturbed than outer ring motion. As a result, the mode coupling between the inner ring and outer ring is reduced upon binding to DNA. However, similar hole frequency and width of the satellite hole corresponding to the NH₂ mode upon binding to DNA imply that the amino group of 9-aminoacridine sits outside the DNA.     

On the bonding of first-row transition metal cations to guanine and adenine nucleobases

The binding of first-row transition metal monocations (Sc+-Cu+) to N7 of guanine and N7 or N3 of adenine nucleobases has been analyzed using the hybrid B3LYP density functional theory (DFT) method. The nature of the bonding is mainly electrostatic, the electronic ground state being mainly determined by metal-ligand repulsion. M+-guanine binding energies are 18-27 kcal/mol larger than those of M+-adenine, the difference decreasing along the row. Decomposition analysis shows that differences between guanine and adenine mainly arise from Pauli repulsion and the deformation terms, which are larger for adenine. Metal cation affinity values at this level of calculation are in very good agreement with experimental data obtained by Rodgers et al. (J. Am. Chem. Soc. 2002, 124, 2678) for adenine nucleobases.     

Electronic excitation energy transfer between nucleobases of natural DNA

Transfer of the electronic excitation energy in calf thymus DNA is studied by time-resolved fluorescence spectroscopy. The fluorescence anisotropy, after an initial decay starting on the femtosecond time scale, dwindles down to ca. 0.1. The in-plane depolarized fluorescence decays are described by a stretched exponential law. Our observations are consistent with one-dimensional transfer mediated by charge-transfer excited states.     

MS-CASPT2 calculation of excess electron transfer in stacked DNA nucleobases

Calculations using the complete active space self-consistent field (CASSCF) and complete active space second-order perturbation (CASPT2) methods, and the multistate formulation of CASPT2 (MS-CASPT2), are performed for the ground and excited states of radical anions consisting of two pi-stacked nucleobases. The electronic couplings for excess electron transfer (EET) in the pi-stacks are estimated by using the generalized Mulliken-Hush approach. We compare results obtained within the different methods with data derived using Koopmans' theorem approximation at the Hartree-Fock level. The results suggest that although the one-electron scheme cannot be applied to calculate electron affinities of nucleobases, it provides reasonable estimates for EET energies. The electronic couplings calculated with KTA lie between the CASPT2 and the MS-CASPT2 based values in almost all cases.     

Vibrational frequencies and structural determination of tetrafluoroformaldazine

The normal mode frequencies and corresponding vibrational assignments of tetrafluoroformaldazine (F(2)CNNCF(2)) are examined theoretically using the Gaussian98 set of quantum chemistry codes. Each of the vibrational modes was assigned to one of nine types of motion predicted by a group theoretical analysis (C-F stretch, C[triple bond]N stretch, N-N stretch, C=C-N bend, CF(2) wag, CF(2) rock CF(2) scissors, CF(2) twist, and C=N-N=C torsion) utilizing the C(2h) symmetry of the molecule. Uniform scaling factors was derived for each type of motion. Predicted infrared and Raman intensities are reported.     

Vibrational frequencies and structural determination of disilylcarbodiimide

The vibrational frequencies and corresponding normal mode assignments of disilylcarbodiimide are examined theoretically using the GAUSSIAN98 set of quantum chemistry codes. MP2 and DFT (B3LYP) calculations predict a non-linear structure with C₂ symmetry. All normal modes were successfully assigned to one of eight types of motion (NCN asymmetric stretch, NCN symmetric stretch, Si–H stretch, Si–N stretch, H–Si–H bend, SiH₃ wag, SiH₃ twist, and Si–NN–Si torsion) utilizing the C₂ symmetry of the molecule. Uniform scaling factors were derived for each type of motion. Predicted infrared and Raman intensities are reported. Calculated normal mode frequencies for disilylcarbodiimide-d₆ are also reported.     

Vibrational frequencies and structural determinations of tetraisocyanatosilane

The normal mode frequencies and corresponding vibrational assignments of Si(NCO)(4) are examined theoretically using the GAUSSIAN 98 set of quantum chemistry codes. Each of the vibrational modes was assigned to one of six types of motion predicted by a group theoretical analysis (Si-N stretch, N-C-O symmetric stretch, N-C-O asymmetric stretch, N-C-O bend, Si-N-C bend, and N-Si-N bend) utilizing the T(d) symmetry of the molecule. Uniform scaling factors were derived for each type of motion. Predicted infrared and Raman intensities are reported.     

Vibrational frequencies and structural determinations of tetrachlorobutatriene

The normal mode frequencies and corresponding vibrational assignments of tetrachlorobutatriene in D2h symmetry are examined theoretically using the Gaussian 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of the six types of motion (C=C stretch, CCl2 scissors, CCl2 twist, CCl2 wag, CCl2 rock, and C=C=C bend) predicted by a group theoretical analysis. By comparing the vibrational frequencies with IR and Raman spectra available in the literature, a set of scaling factors is derived.     

Vibrational frequencies and structural determination of triethynylmethylgermane

The normal mode frequencies and corresponding vibrational assignments of triethynylmethylgermane are examined theoretically using the Gaussian98 set of quantum chemistry codes. Each of the vibrational modes was assigned to one of nine types of motion predicted by a group theoretical analysis Ge-C stretch, C[triple bond]C stretch, C-H stretch, C[triple bond]C-H bend, Ge-C[triple bond]C bend, C-Ge-C bend, H-C-H bend, CH3 wag, and CH3 twist) utilizing the C3v symmetry of the molecule. Uniform scaling factors were derived for each type of motion. Predicted infrared and Raman intensities are reported.     

Vibrational frequencies and structural determination of adamantane

The normal mode frequencies and corresponding vibrational assignments of adamantane in Td symmetry are examined theoretically using the Gaussian 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of eight types of motion predicted by a group theoretical analysis. The vibrational modes of the deuterated form of adamantane were also calculated and compared against experimental data.     

Vibrational frequencies and structural determination of tetraethynylstannane

The normal mode frequencies and corresponding vibrational assignments of Sn(CCH)₄ are examined theoretically using the 98 set of quantum chemistry codes. Each of the vibrational modes was assigned to one of six types of motion predicted by a group theoretical analysis (Sn–C stretch, CC stretch, C–H stretch, CC–H bend, Sn–CC bend, and C–Sn–C bend) utilizing the T_d symmetry of the molecule. A set of uniform scaling factors were derived for each type of motion. Predicted infrared and Raman intensities are reported.     

Vibrational frequencies and structural determination of tetraazidogermane

The vibrational frequencies and corresponding normal mode assignments of tetraazidogermane are examined theoretically using the Gaussian98 set of quantum chemistry codes. All normal modes were successfully assigned to one of seven types of motion predicted by a group theoretical analysis (N-N-N asymmetric stretch, N-N-N symmetric stretch, Ge-N stretch, N-N-N bend, Ge-N-N bend, N-Ge-N bend, and N-Ge-N-N torsion) utilizing the S(4) symmetry of the molecule. The molecular orbitals of Ge(N(3))(4) are examined.     

Vibrational frequencies and structural determinations of hexamethylenetetraamine

The normal mode frequencies and corresponding vibrational assignments of hexamethylenetetraamine (HMTA) in Td symmetry are examined theoretically using the Gaussian 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of eight types of motion predicted by a group theoretical analysis. The vibrational modes of the deuterated form of HMTA (HMTA d-12) were also calculated and compared against experimental data. The normal mode vibrational frequencies were shifted to lower frequencies as on deuteration as expected. However, in some cases the dominant motion type changed on deuteration leading to an apparent 'blue shift' of some of the N-C stretching modes. It is possible that the observed frequency shifts are the result of a Fermi resonance condition.     

Vibrational frequencies and structural determination of dicyanodifluorosulfur

The normal mode frequencies and corresponding vibrational assignments of dicyanodifluorosulfur are examined theoretically using the Gaussian03 set of quantum chemistry codes. Each of the vibrational modes was assigned to one of six types of motion predicted by a group theoretical analysis (CN stretch, SC stretch, SF stretch, FSC bend, SCN bend, and CSC bend) utilizing the C(2v) symmetry of the molecule. A set of uniform scaling factors was derived for each type of motion. Predicted infrared and Raman intensities are reported.     

Vibrational frequencies and structural determination of trichloroboroxine

The normal mode frequencies and corresponding vibrational assignments of trichloroboroxine (B3O3Cl3) in D3h symmetry are examined theoretically using the Gaussian 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of five types of motion (B-Cl stretch, B-O stretch, B-Cl bend, O-B-O bend, and B(OOCl) umbrella motion) predicted by a group theoretical analysis. By comparing the vibrational frequencies with IR and Raman spectra available in the literature, a set of scaling factors is derived. Molecular orbitals and bonding are examined.     

Vibrational frequencies and structural determination of phosphirane

The normal mode frequencies and corresponding vibrational assignments of phosphirane in are examined theoretically using the GAUSSIAN 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of nine types of motion (C–C stretch, P–C stretch C–H stretch, P–H stretch, CH₂ scissors, CH₂ wag, CH₂ rock, CH₂ twist, and P–H wag) predicted by a group theoretical analysis. Comparing the vibrational frequencies with IR and Raman spectra available in the literature, a set of scaling factors are derived. Predicted infrared and Raman intensities are reported.     

Vibrational frequencies and structural determinations of urazole

The vibrational frequencies and corresponding normal mode assignments of urazole are examined theoretically using the Gaussian98 set of quantum chemistry codes. All normal modes were successfully assigned to one of eight types of motion (N--H stretch, C=O stretch, C--N stretch, N--N stretch, N--H bend, C=O bend, N--C--N bend, ring torsion) utilizing the C2 symmetry of the molecule. The molecular orbitals of urazole are examined. The simultaneous double inversion of the amine groups in urazole is also examined.