Hristina R. Zhekova

Applications of Time Dependent and Time Independent Density Functional Theory to the First π to π* Transition in Cyanine Dyes.

The first π → π* transition in a number of cyanine dyes was studied using both time dependent and time independent density functional methods using a coupled cluster (CC2) method as the benchmark scheme. On the basis of 10 different functionals, it was concluded that adiabatic time dependent density functional theory (ATDDFT) almost independently of the functional gives rise to a singlet-triplet separation that is too large by up to 1 eV, leading to too high singlet energies and too low triplet energies. This trend is even clearer when the Tamm-Dancoff (TD) approximation is introduced and can in ATDDFT/TD be traced back to the representation of the singlet-triplet separation by a HF-type exchange integral between π and π*. The time independent DFT methods (ΔSCF and RSCF-CV-DFT) afford triplet energies that are functional independent and close to those obtained by ATDDFT. However, both the singlet energies and the singlet-triplet separations increases with the fraction α of HF exchange. This trend can readily be explained in terms of the modest magnitude of a KS-exchange integral between π and π* in comparison to the much larger HF-exchange integral. It was shown that a fraction α of 0.5 affords good estimates of both the singlet energies and the singlet-triplet separations in comparison to several ab initio benchmarks.

Magnetic Circular Dichroism of Phthalocyanine (M = Mg, Zn) and Tetraazaporphyrin (M = Mg, Zn, Ni) Metal Complexes. A Computational Study Based on Time-Dependent Density Functional Theory

We present here simulated magnetic circular dichroism (MCD) spectra of MTAP (M=Mg, Ni, Zn) and MPc (M=Mg, Zn) where TAP=tetraazaporphyrin and Pc=phthalocyanine. The study is based on magnetically perturbed time-dependent density functional theory (MP-TDDFT) and a newly implemented method for the calculation of A and B terms from the theory of MCD. It follows from our investigation that the MCD spectrum for the MTAP and MPc systems in the Q-band region consists of a single positive A term augmented by a positive B term, in agreement with experiment where available. The Q band can be fully characterized in terms of the 2a1u-->2eg one-electron excitation. For the aza systems MgTAP and ZnTAP, the simulated MCD spectra in the Soret region are dominated by the two one-electron excitations 2a2u-->2eg and 1a2u-->2eg and has the appearance of a positive A term (with values between 1.33-1.55, depending on the MTAP system) made asymmetric by a negative B term, in good agreement with experiment. We find, in agreement with all available experimental findings on MPc (M=Mg, Zn) type systems, that the MCD spectra in the Soret region are dominated by two transitions with positive A/ D-term values and two negative B/ D-term values. The major contribution to the two transitions comes from the 2a2u-->2eg and 1a2u-->2eg one-electron excitations. It appears that the ratio of A/ B for the term parameters is underestimated by theory.

Calculation of exchange coupling constants in triply-bridged dinuclear Cu(II) compounds based on spin-flip constricted variational density functional theory.

The performance of the second-order spin-flip constricted variational density functional theory (SF-CV(2)-DFT) for the calculation of the exchange coupling constant (J) is assessed by application to a series of triply bridged Cu(II) dinuclear complexes. A comparison of the J values based on SF-CV(2)-DFT with those obtained by the broken symmetry (BS) DFT method and experiment is provided. It is demonstrated that our methodology constitutes a viable alternative to the BS-DFT method. The strong dependence of the calculated exchange coupling constants on the applied functionals is demonstrated. Both SF-CV(2)-DFT and BS-DFT affords the best agreement with experiment for hybrid functionals.

Calculation of the exchange coupling constants of copper binuclear systems based on spin-flip constricted variational density functional theory

We have recently developed a methodology for the calculation of exchange coupling constants J in weakly interacting polynuclear metal clusters. The method is based on unrestricted and restricted second order spin-flip constricted variational density functional theory (SF-CV(2)-DFT) and is here applied to eight binuclear copper systems. Comparison of the SF-CV(2)-DFT results with experiment and with results obtained from other DFT and wave function based methods has been made. Restricted SF-CV(2)-DFT with the BH&HLYP functional yields consistently J values in excellent agreement with experiment. The results acquired from this scheme are comparable in quality to those obtained by accurate multi-reference wave function methodologies such as difference dedicated configuration interaction and the complete active space with second-order perturbation theory.

A magnetic and electronic circular dichroism study of azurin, plastocyanin, cucumber basic protein, and nitrite reductase based on time-dependent density functional theory calculations.

The excitation, circular dichroism, magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) spectra of small models of four blue copper proteins are simulated on the TDDFT/BP86 level. X-Ray diffraction geometries are used for the modeling of the blue copper sites in azurin, plastocyanin, cucumber basic protein, and nitrite reductase. Comparison with experimental data reveals that the calculations reproduce most of the qualitative trends of the observed experimental spectra with some discrepancies in the orbital decompositions and the values of the excitation energies, the g( parallel) components of the g tensor, and the components of the A tensor. These discrepancies are discussed relative to deficiencies in the time-dependent density functional theory (TDDFT) methodology, as opposed to previous studies which address them as a result of insufficient model size or poor performance of the BP86 functional. In addition, attempts are made to elucidate the correlation between the MCD and EPR signals.

First principle simulation of the temperature dependent magnetic circular dichroism of a trinuclear copper complex in the presence of zero field splitting.

We present a test of a recently developed density functional theory (DFT) based methodology for the calculation of magnetic circular dichroism (MCD) spectra in the presence of zero-field splitting (ZFS). The absorption and MCD spectra of the trinuclear copper complex μ(3)O ([Cu(3)(L)(μ(3)-O)](4+)), which models the native intermediate produced in the catalytic cycle of the multicopper oxidases, have been simulated from first principle within the framework of adiabatic time dependent density functional theory. The effects of the ZFS of the quartet (4)A(2) ground state on the theoretical MCD spectrum of μ(3)O have been analyzed. The simulated spectra are consistent with the experimental ones. The theoretical assignments of the MCD spectra are based on direct simulation as well as a detailed analysis of the molecular orbitals in μ(3)O. Some of the assignments differ from those given in previous studies. The ZFS effects in the presence of a strong external magnetic field (7 T) prove negligible. The change of the sign of the ZFS changes systematically the intensity of the MCD bands of the z-polarized excitations. The effect of the ZFS on the x,y-polarized excitations is not uniform.

Homology Modelling of Sodium Iodide Symporter

FlgL, respectively. FliJ is a general chaperone that assists and regulates the export process. FlhA and FlhB constitute the export gate and determines the hierarchy of the export process. Despite detailed understanding of the morphology of flagellum, flagella export process is poorly understood. We have determined the solution structure of FliT in its apo form along with its complex with FliD, FliI, and FliJ. Solution structure of FliT differs from its crystal structure and explains the regulatory role of FliT. FliT stays in an auto-inhibitory form in the absence of substrates to avoid any unwanted interaction with export gate. Substrate binding activates FliT-substrate complex to bind to the export gate. This targeting mechanism of FliT is appeared to be shared among all export chaperones, FlgN and FliS. We further characterized the interactions among export chaperones and showed that strict binding sequence among chaperones determines chaperone recycling process and regulate subsequent export events.