Ab initio investigation on the structures and spectra of the firefly luciferin

The ground state (S0) geometry of the firefly luciferin (LH2) was optimized by both DFT B3LYP and CASSCF methods. The vertical excitation energies (Tv) of three low-lying states (S1, S2, and S3) were calculated by TD-DFT B3LYP//CASSCF method. The S1 geometry was optimized by CASSCF method. Its Tv and the transition energy (Te) were calculated by MS-CASPT2//CASSCF method. Both the TD-DFT and MS-CASPT2 calculated S1 state Tv values agree with the experimental one. The IPEA shift greatly affects the MS-CASPT2 calculated Tv values. Some important excited states of LH2 and oxyluciferin (oxyLH2) are charge-transfer states and have more than one dominant configuration, so for deeply researching the firefly bioluminescence, the multireference calculations are desired.     

Photoexcitation of dinucleoside radical cations: a time-dependent density functional study

The excited states of dinucleoside phosphates (dGpdG, dApdA, dApdT, TpdA, and dGpdT) in their cationic radical states were studied with time-dependent density functional theory (TD-DFT). The ground-state geometries of all the dinucleoside phosphate cation radicals considered, in their base stacked conformation, were optimized with the B3LYP/6-31G(d) method. Further, to take into account the effect of the aqueous environment surrounding the dinucleoside phosphates, the polarized continuum model (PCM) was considered and the excitation energies were computed by using the TD-B3LYP/6-31G(d) method. From this study, we find that the first transition in all the dinucleoside molecules involves hole transfer from base to base. dG*+pdG and dApdA*+ were found to have substantially lower first transition energies than others with two different DNA bases. Higher energy transitions involve base to sugar as well as base to base hole transfer. The calculated TD-B3LYP/6-31G(d) transition energies are in good agreement with previous calculations with CASSCF/CAS-PT2 level of theory. This TD-DFT work supports the experimental findings that sugar radicals formed upon photoexcitation of G*+ in gamma-irradiated DNA and suggests an explanation for the wavelength dependence found.     

Electronic states of o-nitrobenzaldehyde: a combined experimental and theoretical study

The experimental UV/vis absorption spectrum of ortho-nitrobenzaldehyde (o-NBA) has been assigned by means of MS-CASPT2/CASSCF, TD-DFT, and RI-CC2 theoretical computations. Additional information on the nature of the absorbing bands was obtained by comparing the o-NBA spectrum with that of related compounds, as, e.g., nitrobenzene and benzaldehyde. For wavelengths larger than approximately 280 nm, the absorption spectrum of o-NBA is dominated by a series of weak n pi* absorptions from the NO2 and CHO groups. These weak transitions are followed in energy by a more intense band, peaking at 250 nm and arising from charge transfer pi pi* excitations involving mainly benzene and nitro orbitals. Finally, the most intense band centered at 220 nm has its origin in the overlap of two different absorptions: the first one localized in the NO2 substituent and the second one arising from a charge transfer excitation involving the NO2 and the CHO fragments, respectively.     

Theoretical study of the singlet electronically excited states of N4

Vertical excitation energies for the lowest eleven singlet states of T_d N₄ were calculated using the TD-DFT method with the B3LYP functional, and at the EOM-CCSD level of theory. The vertical excitation energies for the five lowest-lying excited states were also obtained using the state-averaged CASSCF, CASPT2, CASPT3, and MRCI + Q methods. Our results show that the five lowest-lying states are of valence character. EOM-CCSD/d-aug-cc-pVTZ calculations predict that there are two weakly allowed optical transitions of T₂ symmetry at 10.44 and 10.82 eV. The transition to the third T₂ state, which is predicted to be at 10.89 eV, has an oscillator strength about one order of magnitude higher.     

Performance of time-dependent density functional and Green functions methods for calculations of excitation energies in radicals and for Rydberg electronic states

Time-dependent density functional (TD-DFT) and perturbation theory-based outer valence Green functions (OVGF) methods have been tested for calculations of excitation energies for a set of radicals, molecules, and model clusters simulating points defects in silica. The results show that the TD-DFT approach may give unreliable results not only for diffuse Rydberg states, but also for electronic states involving transitions between MOs localized in two remote from each other spatial regions, for example, for charge-transfer excitations. For the. O-SiX(3) clusters, where X is a single-valence group, TD-DFT predicts reasonable excitation energies but incorrect sequence of electronic transitions. For a number of cases where TD-DFT is shown to be unreliable, the OVGF approach can provide better estimates of excitation energies, but this method also is not expected to perform universally well. The OVGF performance is demonstrated to be satisfactory for excitations with predominantly single-determinant wave functions where the deviations of the calculated energies from experiment should not exceed 0.1-0.3 eV. However, for more complicated transitions involving multiple bonds or for excited states with multireference wave functions the OVGF approach is less reliable and error in the computed energies can reach 0.5-1 eV.     

UV-vis spectra of <Emphasis Type="Italic">p</Emphasis>-benzoquinone anion radical in solution by a TD-DFT/PCM approach

Excited electronic states of the anion radical of para-benzoquinone were studied by time dependent density functional theory (TD-DFT) including bulk solvent effects by the polarizable continuum model (PCM). The computed vertical excitation energies for the first four low-lying doublet states are in good agreement with previous post-Hartree–Fock computations. Geometry optimization of excited states and inclusion of solvent effects lead to a remarkable agreement between computed adiabatic transition energies and experimental band maxima. Together with their specific interest, the results point out the reliability of TD-DFT/PCM approach for valence excitations and the need to take geometry relaxation and solvent effects into the proper account for a meaningful comparison between computed and experimental absorption spectra.     

The role of Ag(I) ions in the electronic spectroscopy of adenine–cytosine mispairs: A MS-CASPT2 theoretical study

Adenine–cytosine (AC) mispairs have been theoretically studied with MS-CASPT2//CASSCF methods in the presence and absence of Ag ions. The electronically excited states of the most stable AC mispair in the reverse-Wobble (RW) conformation have been compared with those of different Ag(I)–AC complexes, including (i) metalated RW conformations, and (ii) the most stable structures in gas phase which contain the Ag ion bridging A and C. The spectra of these complexes are characterized by charge-transfer (CT) and strong locally excited (LE) states. The metal-to-metal, metal-to-ligand, and Rydberg transitions are very weak in comparison to the nucleobase transitions. Attending to the LE and CT states, and except for the shifts induced by the presence of the Ag, the electronic spectrum of metalated AC mispairs resembles the one of the RW, showing two intense LE bands around 4.5 and 5.5 eV, corresponding to transitions within the adenine and cytosine π-system, respectively. Additionally TD-DFT results obtained with the B3LYP functional are compared with MS-CASPT2//CASSCF calculations. The results clearly evidence the weakness of TD-DFT to describe long range exchange interactions leading to strongly underestimated CT states.     

Electronic excitations of hypervalent configurations in amorphous selenium: Quantum-chemical modeling

The first excited states of the clusters modeling fragments of a continuous random network and the most stable local defects in solid selenium have been calculated by different ab initio methods (TD-DFT, EOM CCSD, CASSCF). A split-valence double-zeta basis set augmented with polarization and diffuse functions has been used. The effect of the cluster size and structure on the energies of transitions is considered, and the tendencies of geometric relaxation of excited states for the most typical structures are assessed.     

Ab initio investigation on the structures and spectra of the firefly luciferin

The ground state (S₀) geometry of the firefly luciferin (LH2) was optimized by both DFT B3LYP and CASSCF methods. The vertical excitation energies (T _v) of three low-lying states (S₁, S₂, and S₃) were calculated by TD-DFT B3LYP//CASSCF method. The S₁ geometry was optimized by CASSCF method. Its T _v and the transition energy (T _e) were calculated by MS-CASPT2//CASSCF method. Both the TD-DFT and MS-CASPT2 calculated S₁ state T _v values agree with the experimental one. The IPEA shift greatly affects the MS-CASPT2 calculated T _v values. Some important excited states of LH2 and oxyluciferin (oxyLH2) are charge-transfer states and have more than one dominant configuration, so for deeply researching the firefly bioluminescence, the multireference calculations are desired. Supported by the National Natural Science Foundation of China (Grant No. 20673012) and the Major State Basic Research Development Programs (Grant No. 2004CB719903)     

An ab initio simulation of the UV/Visible spectra of substituted chalcones

The electronic absorption spectra of 29 phenyl-ring substituted chalcones have been investigated with the time-dependent density functional theory (TD-DFT) and polarizable continuum TD-DFT (PCM-TD-DFT). It turns out that the hybrid PBE1PBE functional with the 6-31G basis set provide reliable λ_max when the solvent effects are included in the model. Comparisons with experimental values lead to a mean absolute error of 12 nm (0.136 eV). Moreover, the observed substituent effects are reproduced by calculation qualitatively. The λ_max of substituted chalcone in phenyl ring A is less sensitive to substitution than that in ring B. The linear correlation of Hammett’s substituent constants (σ_P) with LUMO energies is better with respect to HOMO energies. The calculation reveals that the maximum absorption band mainly results from the π→π* transition from HOMO to LUMO. The analysis of the electron density plots of frontier molecular orbitals show that most transitions should be of valence excitation nature.      

Theoretical study of singlet and triplet excitation energies in oligothiophenes

We have analyzed singlet and triplet excitation energies in oligothiophenes (up to five rings) using time-dependent density-functional theory (TD-DFT) with different exchange-correlation functionals and compared them with results from the approximate coupled-cluster singles and doubles model (CC2) and experimental data. The excitation energies have been calculated in geometries obtained by TD-DFT optimization of the lowest excited singlet state and in the ground-state geometries of the neutral and anionic systems. TD-DFT methods underestimate photoluminescence energies but the energy difference between singlet and triplet states shows trends with the chain-length similar to CC2. We find that the second triplet excited state is below the first singlet excited state for long oligomers in contrast with the previous assignment of Rentsch et al. (Phys.Chem. Chem. Phys. 1999, 1, 1707). Their photodetachment photoelectron spectroscopy measurements are better described by considering higher triplet excited states.     

Time-dependent density functional theory as a tool for isomer assignments of hydrogen-bonded solute.solvent clusters

Can isomer structures of hydrogen-bonded solute x solvent clusters be assigned by correlating gas-phase experimental S0 <--> S1 transitions with vertical or adiabatic excitation energies calculated by time-dependent density functional theory (TD-DFT)? We study this question for 7-hydroxyquinoline (7HQ), for which an experimental database of 19 complexes and clusters is available. The main advantage of the adiabatic TD-B3LYP S0 <--> S1 excitations is the small absolute error compared to experiment, while for the calculated vertical excitations, the average offset is +1810 cm(-1). However, the empirically adjusted vertical excitations correlate more closely with the experimental transition energies, with a standard deviation of sigma = 72 cm(-1). For the analogous correlation with calculated adiabatic TD-DFT excitations, the standard deviation is sigma = 157 cm(-1). The vertical and adiabatic TD-DFT correlation methods are applied for the identification of isomers of the 7-hydroxyquinoline.(MeOH) n , n = 1-3 clusters [Matsumoto, Y.; Ebata, T.; Mikami, N. J. Phys. Chem. B 2002, 106, 5591]. These confirm that the vertical TD-DFT/experimental correlation yields more effective isomer assignments.     

间位取代卟啉及其锌卟啉的电子吸收光谱

取代的卟啉类衍生物在气敏传感器方面具有广泛的应用前景.本文采用了密度泛函理论(DFT)和含时密度泛函理论(TD-DFT)研究了四种不同取代基的卟啉衍生物(meso位四硝基苯基/四氨基苯基卟啉(NO2PP,NH2PP)及其相应的锌金属卟啉衍生物(NO2ZnPP,NH2ZnPP))的紫外和近紫外光谱特征.利用两种不同的交换相关泛函(广义梯度近似泛函(PBE)和杂化密度泛函(B3LYP))优化了上述四种物质的结构,并应用TD-DFT计算了相应的电子激发能量和振动强度.结果表明,取代卟啉的吸收光谱与大量的电子跃迁有关;与B3LYP泛函预测的光谱相比,PBE泛函所得B带以及Q带的波长位置与实验值更为接近.另外,计算所得硝基取代基卟啉的B带相对于氨基取代基卟啉的B带发生了红移,这与实验现象也保持一致.由于卟啉衍生物的三重激发态在电子转移中有很重要的应用,因此在PBE/6-31G(d)水平上计算了四种物质的最低三重激发态能量,分别为1.426、1.469、1.608和1.581eV.     

Density functional calculations on electronic circular dichroism spectra of chiral transition metal complexes

Time-dependent density functional theory (TD-DFT) has for the first time been applied to the computation of circular dichroism (CD) spectra of transition metal complexes, and a detailed comparison with experimental spectra has been made. Absorption spectra are also reported. Various Co(III) complexes as well as [Rh(en)(3)](3+) are studied in this work. The resulting simulated CD spectra are generally in good agreement with experimental spectra after corrections for systematic errors in a few of the lowest excitation energies are applied. This allows for an interpretation and assignment of the spectra for the whole experimentally accessible energy range (UV/vis). Solvent effects on the excitations are estimated via inclusion of a continuum solvent model. This significantly improves the computed excitation energies for charge-transfer bands for complexes of charge +3, but has only a small effect on those for neutral or singly charged complexes. The energies of the weak d-to-d transitions of the Co complexes are systematically overestimated due to deficiencies of the density functionals. These errors are much smaller for the 4d metal complex. Taking these systematic errors and the effect of a solvent into consideration, TD-DFT computations are demonstrated to be a reliable tool in order to assist with the assignment and interpretation of CD spectra of chiral transition metal complexes.     

Theoretical and experimental study of the vertical excitation energies in the ionic and tautomeric forms of 4-aminomethylpyridine

4-Aminomethylpyridine (4-PAM) has been widely used as a model compound to elucidate the mechanisms of biological and biomedical action of the amino derivatives of vitamin B₆. By virtue of the presence of two ionizable groups (viz. a pyridine nitrogen and an amino function) in its structure, 4-PAM in solution occurs as various ionic and tautomeric forms in equilibrium. In this work, we optimized the geometries of such forms and found the protonation status of the ionizable groups in 4-PAM to affect the molecular geometry and frontier orbitals. In addition, we determined the experimental electronic excitation energies for each molecular species of 4-PAM from deconvoluted UV–vis spectra. The results thus obtained were compared with their theoretical counterparts as determined from TD-DFT calculations. Based on the outcome, the theoretical methodology used affords correct simulation of electronic excitation energies. The theoretical and experimental results showed that the deprotonation of the pyridine nitrogen has no effect on the energy of the first electronic transition, however it affects its intensity. Additionally, the deprotonation of both pyridine nitrogen and methylamino group increases the number of bands, by increasing the n–π^* transitions.     

Photophysical properties of fluorescent imaging biological probes of nucleic acids: SAC-CI and TD-DFT Study

Recently, exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probe, which shows strong emission in the near-infrared region via hybridization to the target DNA and/or RNA strand, has been developed. In this work, photophysical properties of the chromophores of these probes and the fluorescent mechanism have been investigated by the SAC-CI and TD-DFT calculations. Three fluorescent cyanine chromophores whose excitation is challenging for TD-DFT methods, have been examined regarding the photo-absorption and emission spectra. The SAC-CI method well reproduces the experimental values with respect to transition energies, while the quantitative prediction by TD-DFT calculations is difficult for these chromophores. Some stable structures of H-aggregate system were computationally located and two of the configurations were examined for the photo-absorption. The present results support for the assumption based on experimental measurement in which strong fluorescence is due to the monomer unit in nearly planar structure and its suppression of probes is to the H-aggregates of two exciton units. Stokes shifts of these three chromophores were qualitatively reproduced by the theoretical calculations, while the energy splitting due to H-aggregate in the hybridized probe was slightly overestimated. © 2018 Wiley Periodicals, Inc.     

Theoretical study of structure, vibrational frequencies, and electronic spectra of dibenzofuran and its polychlorinated derivatives

Minimum structures and harmonic vibrational frequencies of dibenzofuran (DF), 2,3,7,8-tetrachlorodibenzofuran (TCDF), and octachlorodibenzofuran (OCDF) were calculated using the multiconfigurational complete active space self-consistent field (CASSCF) and density functional theory (DFT) methods. The electronic transitions in these compounds were studied via the single-state multireference second-order perturbation theory (CASPT2) based on the CASSCF(14,13) references, as well as the time-dependent DFT (TD-B3P86) employing the cc-pVDZ (CASSCF/CASPT2) and 6-31G(d,p) (TD-B3P86) basis sets. The B3P86 geometry and harmonic vibrational frequencies of ground state DF agree very well with the experimental data, and the CASSCF/CASPT2 excitation energies and oscillator strengths are accurate enough to provide a reliable assignment of the absorption bands in the 200-300 nm region. The close agreements with experiment for the parent DF give the present theoretical approaches a valuable credit in predicting the properties of the environmentally toxic polychlorinated congeners, which is all the more important considering the difficulties and hazards in obtaining the experimental data.     

Influence of the halogen ligand on the near-UV-visible spectrum of [Ru(X)(Me)(CO)2(alpha-diimine)] (X = Cl, I; alpha-diimine = Me-DAB, iPr-DAB; DAB = 1,4-diaza-1,3-butadiene): an ab initio and TD-DFT analysis

The near-UV-vis electronic spectroscopy of [Ru(X)(Me)(CO)(2)(iPr-DAB)] (X = Cl or I; iPr-DAB = N,N'-di-isopropyl-1,4-diaza-1,3-butadiene) is investigated through CASSCF/CASPT2 and TD-DFT calculations on the model complexes [Ru(X)(Me)(CO)(2)(Me-DAB)] (X = Cl or I). Convergence of the calculated transition energies for the low-lying metal-to-ligand charge-transfer (MLCT), X-to-ligand charge-transfer (XLCT, X halide ligand), or sigma-bond-to-ligand charge-transfer (SBLCT) to experimental values is analyzed for both methods. On the basis of these accurate calculations, it is shown that whereas the lowest singlet state can be assigned to a nearly pure XLCT state in [Ru(I)(Me)(CO)(2)(Me-DAB)], its character is mainly MLCT in [Ru(Cl)(Me)(CO)(2)(Me-DAB)]. These results are in agreement with time-resolved emission/IR and resonance Raman experimental data. The experimental UV-vis bands are well reproduced by the CASSCF/CASPT2 calculations. The TD-DFT transition energies to the long-range charge transfer states are dramatically affected by the nature of the functional, with lowering leading to meaningless values in the case of nonhybrid functionals. Both methods reproduce well the red shift of the absorption bands on going from the chloride to the iodide complex as well as the shift of the strongly absorbing higher MLCT transition from the visible to the UV domain of energy.     

Time-dependent density functional theory calculations of the photoabsorption of fluorinated alkanes

Time-dependent density functional theory (TD-DFT) calculations of the transition energies and oscillator strengths of fluorinated alkanes have been performed. The TD-DFT method with the non-local B3LYP potential yields transition energies for the methanes, which are smaller by about 10% as compared to the experimental values. An empirical linear correlation was found between the calculated and experimental transition energies both at the B3LYP/DZ+Ryd(C, F) and B3LYP/cc-pVTZ+Ryd(C, F, H) levels for a total of 19 transitions of the fluorinated methanes with linear correlation coefficients of 0.987 for the former and 0.988 for the latter. This empirical correlation for fluorinated methane molecules is found to agree well with the previously obtained empirical correlations between calculated and experimental values for non-fluorinated molecules. The results show that a single empirical-correlation relationship can be used for both non-fluorinated and fluorinated molecules to predict transition energies. This linear relationship is then used to predict the photoabsorption spectra of ethane, propane, butane, and partially and fully fluorinated derivatives. A key result of these calculations is the dominance of Rydberg transitions in the spectral region of interest.