Semiempirical ZINDO Method Research Articles

Respiratory complex II acting as a homeostatic regulatory sensor.

The succinate-ubiquinone oxidoreductase (SQR) complex connects two of the cell's most vital energy-producing metabolic processes: the tricarboxylic acid cycle and the electron transport chain. Hence, the SQR complex is essential in cell metabolism, and its malfunction leads to the progression of multiple metabolic disorders and other diseases, such as cancer. In the current study, we calculated the electron tunneling (ET) pathways between the different redox systems in the SQR complex, including the SQR ligands and the distant heme b redox center, using the broken-symmetry semi-empirical ZINDO method. Interestingly, we discovered a water channel running from the mitochondrial matrix, filling the space between Fe3S4 and heme b redox centers. To investigate the physiological function of the water channel, we performed extensive molecular dynamics (MD) simulations of the membrane-embedded SQR complex in small and large water boxes, representing regular (MDA) and extended (MDB) volume states, respectively. We found that under regular volume conditions (MDA), the ET reaction is conducted through both the iron-sulfur cluster chain (i.e., pathway A) and through heme b (i.e., pathway B). Hence, the SQR complex encompasses an internal interferometer similar to the Mach-Zender interferometer, such that the tunneling electron experiences a self-interference effect through pathways A and B, enhancing the SQR complex's overall ET thermodynamics and favoring the forward ET direction of oxidizing succinate to fumarate and reducing ubiquinone to ubiquinol. On the other hand, we found that under extended volume conditions (MDB), the internal water channel of the SQR complex "senses" the expansion in the mitochondrial volume, pushing the heme b and Fe4S3 redox centers apart and hence lowering the SQR equilibrium constant to almost unity. Therefore, the SQR complex could be driven to work in the reverse direction, catalyzing the production of ubiquinone molecules essential for the physiological function of respiratory complexes I and III and restoring the inner-mitochondrial membrane potential, which leads to restoring the function of the H-K anti-porter, pumping K+ outward from the matrix and restoring the regular mitochondrial volume.

Vacuum UV Polarization Spectroscopy of p-Terphenyl.

p-Terphenyl is used as a component in a variety of optical devices. In this investigation, the electronic transitions of p-terphenyl are investigated by synchrotron radiation linear dichroism (SRLD) spectroscopy in the range 30000-58000 cm-1 (330-170 nm) on molecular samples aligned in stretched polyethylene, thereby extending the region investigated by polarization spectroscopy into the vacuum UV. The resulting partial absorbance curves reveal that the vacuum UV band system with a maximum at 55000 cm-1 (180 nm) is predominantly short axis-polarized. This result is of interest in the optical applications of p-terphenyl, for example as a wavelength shifter. The observed polarization spectra are compared with the results of quantum chemical model calculations. Convoluted versions of the transitions predicted with the semiempirical ZINDO method and with the long-range-corrected time-dependent density functional theory (TD-DFT) procedures TD-CAM-B3LYP, TD-LC-ωPBE, and TD-ωB97XD are in similar qualitative agreement with the observed partial absorbance curves throughout the investigated spectral regions, while TD-B3LYP fails to predict qualitatively the spectrum of p-terphenyl in the region above 40000 cm-1 (250 nm).

Absolute Configuration Assignment of Chiral Resorcin[4]arenes from ECD Spectra.

Racemates of five chiral resorcin[4]arenes, four tetra-O-substituted and one hepta-O-substituted, have been resolved by enantioselective HPLC, and their ECD spectra have been recorded online by stopped-flow measurements. The absolute configuration has been assigned by comparison of the experimental ECD spectra with DFT and semiempirical calculations. For the four tetra-O-substituted resorcin[4]arenes, the ECD exciton couplet at longer wavelength depends on the chirality induced in the arene scaffold by the substituents rather than on the precise nature of the substituents themselves. Accordingly, the exciton chirality model with excitons localized on the arene scaffold, here generalized to Cn symmetry, accurately describes the relationship between stereochemistry and chiroptical properties for this couplet, while its application at shorter wavelengths is unsafe. For the significantly larger hepta-O-substituted system the assignment particularly benefits from the use of the semiempirical ZINDO method.

An Initio Theoretical Study for the Electronic Spectra of β-Thioxoketones

Problem statement: β-thioxoketones exist as equilibrium mixtures of the tautomeric enol and enethiol forms which interconvert very rapidly by intramolecular chelate proton transfer. Accordingly their electronic spectra in the u.v.-visible region exhibit absorption bands arising from transitions within the electronic systems involved in these tautomers. Approach: The structures of several β-thioxoketones were geometrically optimized using B3LYP/cc-pVTZ, B3LYP/6-311++G (2d,p), PM2/6-311++G(2d,p) and B3LYPl6-311G(d,p) and their electronic spectra were theoretically calculated. TD-DFT, EOM-CCSD, CIS and semi empirical ZINDO methods were used to calculate the electronic spectra. Results: The spectrum of the enolic form of thiomalonaldehyde is characterized by three absorption bands at 460, 305 and 223 nm due to H→L, H-1→L and both H→L+1 and H→L+2 transitions. The first band is attributed to n→π* transition within the C = S group while the others are due to transitions with the O-C = C-C = S conjugated system. Both TD-DFT and ZINDO methods were able to predict the electronic spectra of the molecules studied that are in very good agreement with the observed spectra. The observed spectra were agreed to large degree with calculated spectra of the enolic tautomer of the studied compounds. Conclusion: The observed spectra were agreed to large degree with calculated spectra of the enolic tautomer of the studied compounds.

DFT and TD DFT study of isomeric linear benzodifuranones, benzodipyrrolinones and their homologues

Ground state energy and geometry of till unknown 24 mutually isomeric and π-isoelectronic linear polyacenes with two furanone or pyrrolinone rings as the end groups were investigated by density functional theory (DFT). Their 16 symmetrical diphenyl derivatives, among which two were synthesized, were studied, too. Vertical excitation energies were computed by time dependent (TD) DFT and semiempirical ZINDO methods. No tendency to perimeter carbon–carbon bond unification was found, the central hydrocarbon moiety is of quinodimethane character. Both methods predict the similar energies of the lowest allowed spectral transition and its dependence on a size of a conjugated system, but strikingly differ in a prediction of the energies of symmetry forbidden transitions. The comparison with experimental room and low temperature absorption spectra favours the TD DFT results to the ZINDO ones.

A density functional theory study on photophysical properties of red light-emitting materials: Meso-substituted porphyrins

The density functional theory (DFT) has been applied to investigate the photophysical properties of meso-substituted porphyrins: 5,15-difluorenylporphyrin (DFP), 5,10,15,20-tetrafluorenylporphyrin (TFP), Zn-5,10,15,20-tetrafluorenylporphyrin (FPZ) and Zn-5,10,15,20-tetrafluorenoneporphyrin (OPZ). The geometry structures, frontier molecular orbitals, ionization potential (IP), electron affinity (EA) and reorganization energy ( λ) together with the absorption and emission wavelengths of these compounds were investigated. Theoretical calculations indicated that the introduction of meso-substitutions brought about significant effect on the photophysical properties. The TFP molecule has lowest hole injection energy barrier of all the studied compounds, and OPZ owns lowest electron injection energy barrier of them. The equilibrium of the hole and electron transport of FPZ is better than those of porphyrin (FBP), DPZ, TFP, and OPZ. The electron reorganization energies ( λ electron) of FBP, DFP, TFP, FPZ and OPZ are 0.22 eV, 0.20 eV, 0.23 eV, 0.26 eV and 0.13 eV, respectively, which are smaller than tris(8-hydroxyquinolinato) aluminum(III), thus these molecules are potential electron transport materials. Their visible absorption wavelengths are calculated by TD-B3LYP and semi-empirical ZINDO methods, and these results agree with corresponding experimental values. The fluorescence spectra of these complexes predicted by TD-HF method exhibit more consistent results with experimental data than by TD-B3LYP method.

Inherent Chirality Dominates the Visible/Near-Ultraviolet CD Spectrum of Rhodopsin

The visible (alpha) and near-UV (beta) CD bands of rhodopsin have been studied extensively, but their source(s) have never been definitively established. Do they result from the intrinsic chirality of the polyene chromophore of the protonated Schiff base of retinal (retPSB) or from the coupling of the transitions of this chromophore with those of protein groups? We have calculated the contributions of these two mechanisms to the CD of rhodopsin. The intrinsic CD of the retPSB chromophore was calculated using time-dependent density functional theory (TDDFT) and, for comparison, the semiempirical ZINDO method. First-order perturbation theory was used to calculate the effects of coupling of the retPSB transitions with the pi pi* transitions of the aromatic chromophores and the pi pi* and n pi* transitions of the peptide groups in rhodopsin. Calculations were performed for eight structures based upon the two molecules in the asymmetric unit of four crystal structures. The most reliable results were obtained from TDDFT calculations on the structure of Okada et al. (J. Mol. Biol. 2004, 342, 571), PDB 1U19. Averaging over the two molecules in the asymmetric unit, the intrinsic rotational strengths are 0.62 +/- 0.00 DBM (Debye-Bohr magneton) and 0.90 +/- 0.03 DBM for the alpha- and beta-bands, respectively. The contributions from coupling with protein groups are, respectively, -0.32 +/- 0.05 and -0.01 +/- 0.03 DBM. Our results show that the visible/near-UV CD bands of rhodopsin are determined by the intrinsic chirality of the retPSB chromophore and that the contributions of coupling with the protein are significantly smaller for the alpha-band and negligible for the beta-band.

Theoretical investigation on the one- and two-photon absorption properties of a series of porphyrazines with annulated 1,2,5-thiadiazole and 1,4-dimethyloxybenzene moieties

On the basis of equilibrium geometries optimized by B3LYP/6-31G(d) method, the one-photon absorption properties of a series of substituted porphyrazines have been investigated theoretically using time-dependent density functional theory and the semiempirical ZINDO method, respectively. The comparisons with the available experimental data confirmed that the reliability of the ZINDO method in predicting the electronic absorption properties. According to the one-photon absorption properties obtained from the ZINDO method, two-photon absorption properties of molecules have been studied, using ZINDO and sum-over-states methods. The results have showed that the molecule with symmetrically substituted with electron donors exhibits the maximum two-photon absorption cross-section (up to 5276.8 GM) in all the studied molecules. The molecular centrosymmetry has a positive effect on the enhancement of the two-photon absorption cross-section. For the molecules with multi two-photon absorption peaks, the cross-section in the region from 750 to 860 nm is enhanced by one order of magnitude compared with that in the region from 1050 to 1200 nm.

Theoretical investigation of stokes shift of 3,4-diaryl-substituted maleimide fluorophores

According to the experimental data, a new type of fluorophores based on 3,4-diaryl substituted maleimide compounds was found to exhibit moderate to large Stokes shift. This large Stokes shift is assumed to be the consequence of a substantial change of the geometric structure from the ground state (S 0) to the first excited state (S 1). In this study, the hypothesis is examined by the computational methods. The semiempirical AM1 and the density functional computational methods were used to generate the ground and the excited state structures of maleimide and its derivatives. The absorption and emission energies of maleimide derivatives were obtained by the semiempirical ZINDO method. The calculated Stokes shift ( Δ E ) is related to the difference between the absorption and emission energies. The theoretical calculations confirmed that the magnitude of the Stokes shift is parallel to a change of the molecular structure from non-planar in the S 0 ground state to more planar in the S 1 excited state. The calculated absorption and emission energies and related Stokes shift agree well with the experimental results.

Estimation of Electron Spectra Transitions of Free-Based Porphin and Mg-Porphin Using Various Quantum Chemical Approaches

For optimized molecules of free-base porphin and magnesium-porphin (at Hartree-Fock level and 6-31G* basis set) excitation spectra were determined using several ab initio methods: CIS, RPA, CASSCF, and TDDFT. Obtained values were compared with semiempirical ZINDO method, other calculations found recently in literature and experimental data. It was demonstrated that for qualitatively correct spectra description the AO basis must include both the polarization and diffuse functions. The later play an important role in formation of Rydberg MOs. Estimated energies of the spectra transitions using the CIS method remain relatively far from the measured values. RPA method can be already considered as a quantitatively accurate method when sufficiently large basis set is used. For CASSCF approach, it was shown that even the lowest energy transitions are insufficiently described in CAS formalism and much larger active space or inclusion of more inactive orbitals in correlation treatment would be necessary for obtaining sufficient accuracy. It can be stated that without sufficiently large correlation contributions, the determined spectra are not able to reach quantitative agreement with experimental data. From the methods treated in this study, only TDDFT can be considered as a useful tool for spectra prediction, at least for calculations of lower excited states. It is relatively fast and feasible for calculation of middle-size molecules. ZINDO approximation is also relatively successful for such large systems. Acceptable predictions of experimentally observed energy transitions in the range of Q and B bands were obtained. Until higher (UV) part of spectra is examined where the excitations to Rydberg orbital will happen, it can be considered as a good candidate for electron spectra calculations.

Theoretical studies on the one- and two-photon absorption of tetrabenzoporphyrins and phthalocyanines

The one-photon absorption (OPA) properties of tetrabenzoporphyrins (TBPs) and phthalocyanines (Pcs) were studied using the semiempirical ZINDO method and time-dependent density functional theory (TDDFT), respectively. The compared results confirmed that the semiempirical ZINDO method was reasonably reliable when calculating the OPA of tetrabenzoporphyrins and phthalocyanines. On the basis of the OPA properties obtained from the ZINDO method, two-photon absorption (TPA) properties of two series of molecules were investigated, using ZINDO and sum-over-states (SOS) methods. The results showed that the TPA cross-sections of all molecules were in the range of 220.6 × 10–50 – 345.9 × 10–50 cm4·s·photon–1, which were in the same order of magnitude as the values reported in the literature. The relatively larger δ(ω) value for Pcs with respect to that for corresponding TBPs originates from larger intramolecular charge transfer, which can be characterized by the difference of dipole moment between S0 and S1 and the transition dipole moment between S1 and S5.Key words: two-photon absorption, ZINDO, sum-over-states, tetrabenzoporphyrin, phthalocyanines.

Theoretical study of the nonlinear optical properties of C 74 and Ca@C 74

Using density functional theory and the semiempirical ZINDO method, we have investigated the equilibrium geometries, electronic spectra, and the second and third hyperpolarizabilities of C 74 and the metallofullerene Ca@C 74. Theory predicts that Ca@C 74 has greater stability than C 74 and that the UV–Vis spectrum of Ca@C 74 shifts to the blue. Both species possess relatively large β μ values and thus are promising as nonlinear optical materials.

Ab initio computation of the UV resonance Raman intensity pattern of aqueous imidazole

AbstractThe UV resonance Raman (RR) spectrum of aqueous imidazole was modeled by evaluating the gradients of the resonant π→π* excited state, using various levels of theory. To take account of H‐bonding effects, two water molecules were included in the model, one accepting an H‐bond from and the other donating an H‐bond to imidazole. The ground‐state geometry and force field of the ImH·2H2O complex was computed via SQM‐DFT theory, with the B3LYP functional, yielding good agreement with experimental vibrational wavenumbers for the in‐plane imidazole modes. Evaluation of excited‐state gradients with the semiempirical ZINDO method, which has previously been applied successfully to metalloporphyrin RR spectra, failed to reproduce the imidazole UVRR spectrum. However, the ab initio CIS method gave fairly good results. Agreement with the experimental intensity pattern improved when minimal STO‐3G or 3–21G* basis sets were upgraded to 6–31G*, but further refinement, to 6–31G**, did not alter the pattern, and addition of diffuse functions actually degraded the spectral quality. Likewise, more elaborate levels of ab initio theory, TDDFT and CASSCF(4,4), gave poorer agreement with experiment then CIS. Thus optimum modeling of the UVRR spectrum was achieved with the popular CIS/6–31G* methodology. Application of the Kramers–Kronig transform frequency correction to the ωk2 approximation (‘short‐time limit’) altered the intensity distribution only slightly. Copyright © 2001 John Wiley & Sons, Ltd.

Extended rodlike polyaromatic receptors with bent tridentate units complexed to lanthanide metal ions.

A synthetic strategy is developed to attach semirigid lipophilic sidearms to the 6-positions of bent aromatic tridentate 2,6-bis(benzimidazol-2-yl)pyridine cores to produce U-shaped ligands, L6,7. Differential scanning calorimetry (DSC) reveals that entropic contributions severely affect the isotropization processes of these flexible receptors, but no mesomorphism is detected. The attachment of oxygen linkers to the 5- or 6-positions of the benzimidazole sidearms lowers the ligand-centered 1 pi pi* and 3 pi pi* excited states, and the semiempirical ZINDO method assigns this effect to a destabilization of the HOMO orbitals resulting from pi-interactions. Reactions of L6 with Ln(NO3)3.xH2O provide the rodlike 1:1 complexes [Ln(L6)(NO3)3] (Ln = La-Lu), which are stable in the solid state but partially dissociate in acetonitrile. The crystal structure of [Lu(L6)(NO3)3].CH3CN (18a, LuC63H84N9O13, monoclinic, P2(1)/n, Z = 4) reveals an I-shaped arrangement of the ligand strand arising from the meridional complexation of the bent tridentate unit to nine-coordinate Lu(III). The replacement of nitrate anions with trifluoroacetate anions gives the centrosymmetric dimer [Lu(L6)(CF3CO2)3]2 (23, Lu2C134H162N10O20F18, triclinic, P1, Z = 1), in which the symmetry-related Lu atoms are connected by two bridging carboxylates, leading to an H-shaped dimetallic edifice. These complexes [Ln(L6)(NO3)3] and [Ln(L6)(CF3CO2)3]2 fulfill the geometrical criteria required by precursors of calamitic metallomesogens, but no mesomorphism can be detected, while photophysical studies indicate that the low energies of ligand-centered 3 pi pi* excited states drastically limit the luminescence of Eu(III) complexes. The relationships between structural and electronic properties resulting from 5- or 6-substitutions of the benzimidazole rings and the effects of these substitutions on photophysical and thermal properties are discussed.