Base pairing patterns of DNA base lesion spiroiminodihydantoin: A DFT study

The DNA base lesion spiroiminodihydantoin (Sp) is produced in biological systems endogenously and can cause mutation and cancer. It is considered to be more mutagenic and deleterious than 8‐oxoguanine and other oxidized guanine products such as guanidinohydantoin (Gh) and imidazolone. In this work, the base pairing patterns of Sp with each of the normal nucleic acid bases of DNA have been investigated thoroughly using the B3LYP, M06‐2X, and wB97X‐D functionals of density functional theory in conjunction with the aug‐cc‐pVDZ basis set. It is found that the magnitudes of interaction energies between the bases and Sp follow the order: Sp‐guanine >> Sp‐cytosine > Sp‐adenine > Sp‐thymine. The strong Sp‐guanine abnormal base pairing may be the main cause of the observed mutagenicity of Sp. © 2013 Wiley Periodicals, Inc.     

Excited state properties,fluorescence energies,and lifetimes of a poly(fluorene‐phenylene), based on TD‐DFT investigation

The structural and electronic properties of fluorene‐phenylene copolymer (FP)_n, n = 1–4 were studied by means of quantum chemical calculations based on density functional theory (DFT) and time dependent density functional theory (TD‐DFT) using B3LYP functional. Geometry optimizations of these oligomers were performed for the ground state and the lowest singlet excited state. It was found that (FP)_n is nonplanar in its ground state while the electronic excitations lead to planarity in its S₁ state. Absorption and fluorescence energies were calculated using TD‐B3LYP/SVP and TD‐B3LYP/SVP+ methods. Vertical excitation energies and fluorescence energies were obtained by extrapolating these values to infinite chain length, resulting in extrapolated values for vertical excitation energy of 2.89 and 2.87 eV, respectively. The S₁ ← S₀ electronic excitation is characterized as a highest occupied molecular orbital to lowest unoccupied molecular orbital transition and is distinguishing in terms of oscillator strength. Fluorescence energies of (FP)_n calculated from TD‐B3LYP/SVP and TD‐B3LYP/SVP+ methods are 2.27 and 2.26 eV, respectively. Radiative lifetimes are predicted to be 0.55 and 0.51 ns for TD‐B3LYP/SVP and TD‐B3LYP/SVP+ calculations, respectively. These fundamental information are valuable data in designing and making of promising materials for LED materials. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Calculation of excited‐state ionization potential for boron‐like sequence

Excited‐state ionization potentials for boron‐like sequence with Z = 5–19 are studied systematically, using the weakest bound electron potential model theory (WBEPM theory) and iso‐spectrum‐level series conception. Nonrelativistic ionization energy is derived from the theory. Relativistic effects are included in the Breit–Pauli approximation. Comparison of the calculated excited‐state ionization potential with available experimental data is carried out for 1s²2s²2p ²P, 1s²2s²3s ²S_1/2, 1 s²2s²3p ²P, 1s²2s²3d ²D_5/2, 1s²2s²4d ²D_5/2, 1s²2s²5d ²D_5/2, and 1s²2s²6d ²D_5/2 series. The present results depart from experimental results by no more than 0.133 eV for all 81 results for which experimental data are available. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Predicting the UV spectrum of polyoxometalates by TD‐DFT

UV absorption spectra of the Lindqvist polyoxometalate [W₆O₁₉]^2? were predicted by relativistic time‐dependent density functional theory with several combinations of density functional and basis set. Hybrid functionals with frozen‐core Slater basis sets were found to provide the best agreement with experiment while keeping reasonable computational demand. The approach was extended to [W₁₀O₃₂]^4? and [PW₁₂O₄₀]^3?, suggesting that it can be applied to the polyoxometalates family. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Absorption and fluorescence emission spectroscopic characters of naphtho‐homologated yy‐DNA bases and effect of methanol solution and base pairing

A comprehensive theoretical study of electronic transitions of naphtho‐homologated base analogs, namely, yy‐T , yy‐C , yy‐A , and yy‐G , was performed. The nature of the low‐lying excited states is discussed, and the results are compared with those from experiment and also with those of y‐bases. Geometrical characteristics of the lowest excited singlet ππ* and nπ* states were explored using the CIS method, and the effects of methanol solution and paring with their complementary natural bases on the relevant absorption and emission spectra of these modified bases were examined. The calculated excitation and emission energies agree well with the measured data, where experimental results are available. In methanol solution, the fluorescence from yy‐A and yy‐G would be expected to occur around 539 and 562 nm, respectively, suggesting that yy‐A is a green‐colored fluorophore, whereas yy‐G is a yellow‐colored fluorophore. The methanol solution was found to red‐shift both the absorption and emission maxima of yy‐A , yy‐T , and yy‐C , but blue‐shift those for yy‐G . Generally, though base pairing has no significant effects on the absorption and fluorescence maxima of yy‐A , yy‐C , and yy‐T , it blue‐shifts those for yy‐G . © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Evaluation of the restricted virtual space approximation in the algebraic‐diagrammatic construction scheme for the polarization propagator to speed‐up excited‐state calculations

The applicability and limitations of the restricted virtual space (RVS) approximation within the algebraic‐diagrammatic construction (ADC) scheme for the polarization propagator up to third order is evaluated. In RVS‐ADC, not only the core but also a substantial amount of energetically high‐lying virtual orbitals is restricted in excitation energy calculations of low‐lying excited electronic states. Using octatetraene, indole, and pyridine as representative examples and different standard basis sets of triple‐zeta quality, RVS‐ADC(2) turns out to be highly useful and to have negligible effects on ππ* excited states. However, for nπ* or πσ* states, the RVS approximation is generally less reliable but better at third‐order than second‐order ADC level. In addition, a unified, basis‐set independent, thus normalized virtual orbital threshold (value) is introduced, making the RVS approximation more controllable and a priori applicable. © 2017 Wiley Periodicals, Inc.     

Photo‐physical Properties of N‐methyl‐3,4‐fulleropyrrolidine and Its Derivatives: A DFT and TD‐DFT Investigation

A series of N‐methyl‐3,4‐fulleropyrrolidine (NMFP) derivatives were designed by selecting different π‐conjugated linkers and electron‐donating groups as D‐π‐A and D‐A systems. The optimised structures and photo‐physical properties of NMFP and its derivatives have been determined using density functional theory (DFT) and time‐dependent density functional theory (TD‐DFT) methods with the B3LYP functional and the 6‐31G basis set. According to the computation analysis, both the π‐conjugated linkers and the electron‐donating groups can influence the electronic and photo‐physical properties of the NMFP derivatives. Our calculated results demonstrated that the electron‐donating groups, with significant electron‐donating ability, had the tendency to increase the highest occupied molecular orbital (HOMO) energy. The π‐conjugated linkers with lower resonance energy decreased the lowest occupied molecular orbital (LUMO) energy and caused a significant decrease in the energy gap (E_g) between the E_HOMO and E_LUMO. A Natural Bond Orbital (NBO) analysis examines the effect of the electron‐donating group, π conjugated linker, and electron‐withdrawing group for these NMFP derivatives. For the NMFP derivatives, a projected density of state (PDOS) analysis demonstrated that the electron density of HOMO and LUMO are concentrated on the electron‐donating group and the π‐conjugated linker, respectively. A TD‐DFT/B3LYP calculation was performed to calculate the electronic absorption spectra of these NMFP derivatives. Both the electron‐donating group and the π‐conjugated linker contribute to the major absorption peaks, which are assigned as HOMO to LUMO transitions and are red‐shifted relative to those of non‐substituted NMFP.     

Contribution of Cytosine‐Containing Cyclobutane Dimers to DNA Damage Produced by Photosensitized Triplet–Triplet Energy Transfer

Mutagenic cyclobutane pyrimidine dimers (CPDs) can be induced in DNA through either direct excitation or photosensitized triplet–triplet energy transfer (TTET). In the latter pathway, thymines are expected to receive the excitation energy from the photosensitizer and react with adjacent pyrimidines. By using state‐of‐the art analytical tools, we provide herein additional information on the formation of cytosine‐containing CPDs. We thus determined the yield of all possible CPDs upon TTET in a series of natural DNAs with various base compositions. We show that the distribution of CPDs cannot be explained only by excitation of individual thymines. We propose that the mechanism for TTET involves at least dinucleotides as the minimal targets. The observation of the formation of cytosine–cytosine CPDs also suggests that additional pathways are involved in this photosensitized reaction.     

DFT and TD‐DFT study of iridium complexes with low‐color‐temperature and low‐efficiency roll‐off properties

A series of heteroleptic cyclometalated Ir (III) complexes with low‐color‐temperature and low‐efficiency roll‐off properties, which cause a fast reduction in efficiency when the drive current increases, for organic light‐emitting devices are investigated theoretically to explore their electronic structures and spectroscopic properties. The geometries, electronic structures, lowest‐lying singlet absorptions and triplet emissions of (ptpy)₂Ir(acac), and the theoretically designed models (ptpy)₂Ir(tpip), (F‐ptpy)₂Ir(acac), (F‐ptpy)₂Ir(tpip), (F₂‐ptpy)₂Ir(acac) and (F₂‐ptpy)₂Ir(tpip), are investigated with density functional theory approaches, where ptpy denotes 4‐phenylthieno [3,2‐c] pyridine, acac denotes acetylacetonate, tpip denotes tetraphenylimido‐diphosphinate, F‐ptpy denotes 4‐(3‐fluorophenyl) thieno [3,2‐c] pyridine, and F₂‐ptpy denotes 4‐(2,4‐difluorophenyl) thieno [3,2‐c] pyridine.     

Investigation of excited‐state properties of fluorene–thiophene oligomers by the SAC‐CI theoretical approach

Excited states of fluorene‐ethylenedioxythiophene (FEDOT) and fluorene‐S,S‐dioxide‐thiophene (FTSO2) monomers and dimers were studied by the symmetry‐adapted cluster (SAC)‐configuration interaction (CI) method. The absorption and emission peaks observed in the experimental spectra were theoretically assigned. The first three excited states of the optimized conformers, and the conformers of several torsional angles, were computed by SAC‐CI/D95(d). Accurate absorption spectra were simulated by taking the thermal average for the conformers of torsional angles from 0° to 90°. The conformers of torsional angles 0°, 15°, and 30° mainly contributed to the absorption spectra. The full width at half‐maximum of the FEDOT absorption band is 0.60 eV (4839 cm^?1), which agrees very well with the experimental value of 0.61 eV (4900 cm^?1). The maximum absorption wavelength is located at 303 nm, which is close to those of the experimental band (327 nm). The calculated absorption spectrum of FTSO2 showed two bands in the range of 225–450 nm. This agrees very well with the available experimental spectrum of a polymer of FTSO2, where two bands are detected. The excited‐state geometries were investigated by CIS/6‐31G(d). These showed a quinoid‐type structure which exhibited a shortening of the inter‐ring distance (0.06 Å for FEDOT and 0.04 Å for FTSO2). The calculated emission energy of FEDOT is 3.43 eV, which agrees very well with the available experimental data (3.46 eV). The fwhm_E is about 0.49 eV (3952 cm^?1), while the experimental fwhm is 0.43 eV (3500 cm^?1). For FTSO2, two bands were also found in the emission spectrum. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Visualisation of inter loop tertiary base pairing and stacking interactions in an unusual slipped loop DNA structure

The conformation of an unusual slipped loop DNA structure exhibited by the sequence d(GAATTCCCGAATTC)₂ is determined using a combination of geometrical and molecular mechanics methods. This sequence is known to form a B-DNA-like duplex with the central non-complementary cytosines extruded into single stranded loop regions. The unusual feature is that the interior guanine does not pair with the cytosine across, instead, it pairs with the cytosine upstream by skipping two cytosines, leading to a slipped loop DNA structure with the loops staggered by two base pairs. The two loops, despite being very small, can fold across minor or major groove symmetrically or asymmetrically disposed, with one of the loop bases partially blocking the major or minor groove. Most interestingly, for certain conformations, the loop bases approach one another at close proximity so as to engage even in base pairing as well as base stacking interactions across the major groove. While such pairing and stacking are common in the tertiary folds of RNA, this is the first time that such an interaction is visualized in a DNA. This observation demonstrates that a W-C pair can readily be accomplished in a typical slipped loop structure postulated for DNA. Such tertiary loop interaction may prevent access to regulatory proteins across the major groove of the duplex DNA, thus providing a structure-function relation for the occurrence of slipped loop structure in DNA. Contribution no. 839 from this department     

DFT/TD‐DFT investigation on Ir(III) complexes with N‐heterocyclic carbene ligands: Geometries,electronic structures,absorption, and phosphorescence properties

Iridium(III) complexes with N‐heterocyclic (NHC) ligands including fac‐Ir(pmb)₃ (1), mer‐Ir(pmb)₃ (2), (pmb)₂Ir(acac) (3), mer‐Ir(pypi)₃ (4), and fac‐Ir(pypi)₃ (5) [pmb = 1‐phenyl‐3H‐benzimidazolin‐2‐ylidene, acac = acetoylacetonate, pypi = 1‐phenyl‐5H‐benzimidazolin‐2‐ylidene; fac = facial, mer = meridional] were investigated theoretically. The geometry structures of 1–5 in the ground and excited state were optimized with restricted and unrestricted DFT (density functional theory) methods, respectively (LANL2DZ for Ir atom and 6‐31G for other atoms). The HOMOs (highest occupied molecular orbitals) of 1–3 are composed of d(Ir) and π(phenyl), while those of 4 and 5 are contributed by d(Ir) and π(carbene). The LUMOs (lowest unoccupied molecular orbitals) of 1, 2, 4, and 5 are localized on carbene, but that of 3 is localized on acac. The calculated lowest‐lying absorptions with TD‐DFT method based on Perdew‐Burke‐Erzenrhof (PBE) functional of 1 (310 nm), 2 (332 nm), and 3 (347 nm) have ML_carbeneCT/IL_{phenyl→carbene}CT (MLCT = metal‐to‐ligand charge transfer; ILCT = intraligand charge transfer) transition characters, whereas those of 4 (385 nm) and 5 (389 nm) are assigned to ML_carbeneCT/IL_{carbene→carbene}CT transitions. The phosphorescences calculated by TD‐DFT method with PBE0 functional of 1 (386 nm) and 2 (388 nm) originate from ³ML_carbeneCT/³IL_{phenyl→carbene}CT excited states, but those of 4 (575 nm) and 5 (578 nm) come from ³ML_carbeneCT/³IL_{carbene→carbene}CT excited states. The calculated results showed that the carbene and phenyl groups act as two independent chromophores in transition processes. Compared with 1 and 2, the absorptions of 4 and 5 are red‐shifted by increasing the effective π‐conjugation groups near the C_carbene atom. We predicated that (pmb)₂Ir(acac) is nonemissive, because the LUMO of 3 is contributed by the nonemissive acac ligand. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

A TD‐DFT study on the cyanide‐chemosensing mechanism of 8‐formyl‐7‐hydroxycoumarin

Proton transfer (PT) and excited‐state PT process are proposed to account for the fluorescent sensing mechanism of a cyanide chemosensor, 8‐formyl‐7‐hydroxycoumarin. The time‐dependent density functional theory method has been applied to investigate the ground and the first singlet excited electronic states of this chemosensor as well as its nucleophilic addition product with cyanide, with a view to monitoring their geometries and spectrophotometrical properties. The present theoretical study indicates that phenol proton of the chemosensor transfers to the formyl group along the intramolecular hydrogen bond in the first singlet excited state. Correspondingly, the nucleophilic addition product undergoes a PT process in the ground state, and shows a similar structure in the first singlet excited state. This could explain the observed strong fluorescence upon the addition of the cyanide anion in the relevant fluorescent sensing mechanism. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011