On the Potential Role of the (Pseudo-) Jahn-Teller Effect in the Membrane Transport Processes: Enniatin B and Beauvericin.

The molecular structure of mycotoxins enniatin B and beauvericin, which are used as ionophores, was studied using density functional theory in various symmetry groups and singly charged states. We have shown that the charge addition or removal causes significant structural changes. Unlike the neutral C3 molecules, the stability of the charged C1 structures was explained by the Jahn-Teller or Pseudo-Jahn-Teller effect. This finding agrees with the available experimental X-ray structures of their metal complexes where electron density transfer from the metal can be expected. Hence, the membrane permeability of metal sandwich-structure complexes possessing antimicrobial activities is modulated by the conformational changes.

Spectroscopic behavior differences between lumazine and alloxazine in the DMSO-water mixture.

The absorption and emission spectra were investigated for lumazine, alloxazine and their cyanated or fluorinated derivatives, respectively. The spectroscopic properties were modulated by varying water concentration in dimethyl sulfoxide (DMSO). Some intriguing experimental results were found for the samples containing 65 % of water and 35% of DMSO. This finding is consistent with previously published molecular dynamics (MD) simulations confirming the concept of the 'local bulk' model. In this case, a notable decrease in absorption and emission intensities was registered, even larger than the water quenching observed in other cases. The changes in midrange DMSO concentrations could be explained by the formation of local solvents structures as predicted by MD, specifically the formation of DMSO·2H2O dimers. Experimentally, the cyano-substituted lumazine has shown a remarkable sensitivity to DMSO concentration. The spectroscopic measurements were interpreted using the density functional theory where the implicit DMSO solvent model was combined with explicit water molecules. Together with its enhanced water solubility, the cyanated lumazine derivate could be used for non-destructive DMSO detection in vitro for applications such as drug uptake monitoring, since DMSO is often used in pharmaceutical practice.

How Does Pseudo-Jahn-Teller Effect Induce the Photoprotective Potential of Curcumin?

In this paper, the molecular and electronic structure of curcumin is studied. High-symmetric gas-phase tautomers and their deprotonated forms in various symmetry groups are identified. The stability of lower-symmetry structures was explained by using the Pseudo-Jahn-Teller (PJT) effect. This effect leads to stable structures of different symmetries for the neutral enol and keto forms. The presented analysis demonstrated the potential significance of the PJT effect, which may modulate the setting of electronic and vibrational (vibronic) energy levels upon photodynamic processes. The PJT effect may rationalize the photoprotection action and activity of naturally occurring symmetric dyes.

Degradation Mechanisms of 4,7-Dihydroxycoumarin Derivatives in Advanced Oxidation Processes: Experimental and Kinetic DFT Study.

Coumarins represent a broad class of compounds with pronounced pharmacological properties and therapeutic potential. The pursuit of the commercialization of these compounds requires the establishment of controlled and highly efficient degradation processes, such as advanced oxidation processes (AOPs). Application of this methodology necessitates a comprehensive understanding of the degradation mechanisms of these compounds. For this reason, possible reaction routes between HO• and recently synthesized aminophenol 4,7-dihydroxycoumarin derivatives, as model systems, were examined using electron paramagnetic resonance (EPR) spectroscopy and a quantum mechanical approach (a QM-ORSA methodology) based on density functional theory (DFT). The EPR results indicated that all compounds had significantly reduced amounts of HO• radicals present in the reaction system under physiological conditions. The kinetic DFT study showed that all investigated compounds reacted with HO• via HAT/PCET and SPLET mechanisms. The estimated overall rate constants (koverall) correlated with the EPR results satisfactorily. Unlike HO• radicals, the newly formed radicals did not show (or showed negligible) activity towards biomolecule models representing biological targets. Inactivation of the formed radical species through the synergistic action of O2/NOx or the subsequent reaction with HO• was thermodynamically favored. The ecotoxicity assessment of the starting compounds and oxidation products, formed in multistage reactions with O2/NOx and HO•, indicated that the formed products showed lower acute and chronic toxicity effects on aquatic organisms than the starting compounds, which is a prerequisite for the application of AOPs procedures in the degradation of compounds.

Methoxylated flavones with potential therapeutic and photo-protective attributes: Theoretical investigation of substitution effect.

The molecular and electronic structure of parent flavone and 49 (poly)methoxylated flavones (P)MFs were studied theoretically. Selected group of flavonoids consists of compounds naturally occurring in citrus plants or synthetic derivatives of flavone. These compounds exhibit several bioactivities in vitro and in vivo and can protect plants from solar ultraviolet (UV) radiation. Substitution induced structural changes in (P)MFs were correlated with published experimental values of P-glycoprotein inhibition effect. We have demonstrated that the C5-C10 bond length of 1-benzopyran-4-one moiety represents a suitable structural descriptor for this bioactivity. Obtained linear equations for the compounds with substituted and non-substituted C3 position enable the prediction of the potential anti-cancer chemo-preventive effect of the rest of studied (P)MFs. Consequently, potentially more effective substances were suggested. Optical properties of (P)MFs and their relationship with the molecular structure was examined in detail for methanol environment, as well. The multiple linear regression model was applied to assess the correlation between experimental absorption and fluorescence wavelengths with the theoretically predicted ones. The UV photo-protective potential of studied derivatives was estimated from the calculated optical properties.

From phenols to quinones: Thermodynamics of radical scavenging activity of para-substituted phenols.

Radical scavenging activity and subsequent oxidation resulting in quinone products represent one of the important features of phenols occurring in plants and other biological systems. However, corresponding thermochemistry data can be still considered scarce. For phenol and 25 para-substituted phenols, we investigate the thermodynamics of the individual reaction steps, including three subsequent hydrogen atom transfers, as well as hydroxyl HO radical addition, leading to final ortho-quinone formation. The substituent and solvent effect of water on corresponding reactions enthalpies is elucidated. Solvent enhances substituent induced changes in the investigated reaction enthalpies. The reliability of employed computational methods for the thermodynamics of hydrogen atom donating ability of studied phenols and catechols is assessed, too. Obtained linear equations enable estimation of studied reaction enthalpies from Hammett constants of substituents.

Tuning Redox Properties and Self-Assembly of Thienoacene-Extended Tetrathiafulvalenes.

Turning on and off associations between molecules by a reversible change in their redox states is a convenient way of controlling self-assembly and hence for advancing supramolecular chemistry. Here we present systematic studies on a selection of extended tetrathiafulvalenes with thienoacene spacers. By cyclic and differential pulse voltammetry and in situ EPR/UV-Vis-NIR spectroelectrochemistry, in combination with computations, we have elucidated how the number and orientations of thiophene rings in the spacer between the two dithiafulvene rings influence both the donor strength and association properties. The radical cations and their associates were found to cover a remarkable large region of the UV-Vis-NIR spectrum, but the appearance of the absorption spectrum of the radical cations as well as of the unassociated dications also depended strongly on the exact molecular structure.

Thermodynamics of radical scavenging of symmetric carotenoids and their charged species.

For nine symmetric natural carotenoids, a comprehensive thermodynamics study of processes associated with their radical scavenging activity is proposed. We have investigated the hydrogen atom transfer (HAT) from the parent carotenoid, mono-radical species, radical cations and radical anions. Electron transfer and proton transfer reactions were also studied. Terminal units and carbon atoms in their vicinity were identified as thermodynamically favoured reaction sites of the HAT mechanism. Rhodoxanthin, canthaxanthin and astaxanthin, as strong antioxidants, without any pro-oxidative effect, were found to have bond dissociation enthalpies (BDE) higher than 300 kJ mol-1 and the most negative electron affinities. The electron transfer to a carotenoid is exothermic, while other studied reactions are endothermic. In solvent, the electron transfer reactions may be preferred instead of hydrogen atom transfer.

B3LYP Study of 3-hydroxynaphthalene-2-carboxanilide para-derivatives.

A systematic DFT investigation of 3-hydroxy-N-phenylnaphthalene-2-carboxamide and its sixteen para-derivatives is presented. The structural analysis showed that the energetically preferred conformation of all derivatives is practically planar and it is stabilised via intramolecular hydrogen bonds occurring between (C)O...H(3)O atomic pairs. The quantum chemically evaluated partition coefficients logarithms correlate well with Quantitative Structure-Activity Relationship models as well as with experimentally determined isocratic retention factors logarithm. Theoretical gas-phase proton affinities of amido and hydroxyl group together with selected partial atomic charges reflect the terminal phenyl substitution effect. These quantities are linearly dependent on the in vitro activity against the Mycobacterium Kansasii. Obtained linear correlation functions based on quantum chemically evaluated microscopic properties and selected experimental data may serve as the effective tool in modern drug design for the description of substitution effect.

Modeling of the contrast-enhanced perfusion test in liver based on the multi-compartment flow in porous media.

The paper deals with modeling the liver perfusion intended to improve quantitative analysis of the tissue scans provided by the contrast-enhanced computed tomography (CT). For this purpose, we developed a model of dynamic transport of the contrast fluid through the hierarchies of the perfusion trees. Conceptually, computed time-space distributions of the so-called tissue density can be compared with the measured data obtained from CT; such a modeling feedback can be used for model parameter identification. The blood flow is characterized at several scales for which different models are used. Flows in upper hierarchies represented by larger branching vessels are described using simple 1D models based on the Bernoulli equation extended by correction terms to respect the local pressure losses. To describe flows in smaller vessels and in the tissue parenchyma, we propose a 3D continuum model of porous medium defined in terms of hierarchically matched compartments characterized by hydraulic permeabilities. The 1D models corresponding to the portal and hepatic veins are coupled with the 3D model through point sources, or sinks. The contrast fluid saturation is governed by transport equations adapted for the 1D and 3D flow models. The complex perfusion model has been implemented using the finite element and finite volume methods. We report numerical examples computed for anatomically relevant geometries of the liver organ and of the principal vascular trees. The simulated tissue density corresponding to the CT examination output reflects a pathology modeled as a localized permeability deficiency.

Protective role of quercetin against copper(II)-induced oxidative stress: A spectroscopic, theoretical and DNA damage study.

The radical scavenging and metal chelating properties of flavonoids indicate that they may play a protective role in diseases with perturbed metal homeostasis such as Alzheimer's disease. In this work we investigated the effect of the coordination of quercetin to copper(II) in view of the formation of ROS in Cu-catalyzed Fenton reaction. ABTS and DPPH assays confirmed that the copper(II)-quercetin complex exhibits a stronger radical scavenging activity than does quercetin alone. EPR spin trapping experiments have shown that chelation of quercetin to copper significantly suppressed the formation of hydroxyl radicals in the Cu(II)-Fenton reaction. DNA damage experiments revealed a protective effect for quercetin, but only at higher stoichiometric ratios of quercetin relative to copper. DNA protective effect of quercetin against ROS attack was described by two mechanisms. The first mechanism lies in suppressed formation of ROS due to the decreased catalytic action of copper in the Fenton reaction, as a consequence of its chelation and direct scavenging of ROS by free quercetin. Since the Cu-quercetin complex intercalates into DNA, the second mechanism was attributed to a suppressed intercalating ability of the Cu-quercetin complex due to the mildly intercalating free quercetin into DNA, thus creating a protective wall against stronger intercalators.

Polyradical PROXYL/TEMPO-Derived Amides: Synthesis, Physicochemical Studies, DFT Calculations, and Antimicrobial Activity.

A series of polynitroxide amides possessing 2,2,5,5-tetramethyl-1-pyrrolidinyloxy (PROXYL) and/or 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) units connected through various bridges were synthesized and their properties were analyzed. EPR spectroscopy provided detailed insight into their paramagnetic character and related properties. A thorough examination of the EPR spectra of dinitroxides in organic solvents provided valuable information on the intramolecular motions, thermodynamics, and spin-exchange mechanisms. Analysis of low-temperature X- and Q-band EPR spectra of the dissolved dinitroxides provided spin-spin distances that were comparable with the theoretical values obtained by DFT. Cyclic voltammetry investigations revealed (quasi)reversible electrochemical behavior for PROXYL-derived biradicals, whereas significant loss of the reversibility was found for TEMPO-containing bi- and polyradicals. The inhibitory activities of the nitroxides against model bacteria, yeasts, and filamentous fungi were assessed.

Vibronic energy relaxation approach highlighting deactivation pathways in carotenoids.

Energy relaxation between two electronic states of a molecule is mediated by a set of relevant vibrational states. We describe this fundamental process in a fully quantum mechanical framework based on first principles. This approach explains population transfer rates as well as describes the entire transient absorption signal as vibronic transitions between electronic states. By applying this vibronic energy relaxation approach to carotenoids, we show that ß-carotene's transient absorption signal can be understood without invoking the intensely debated S* electronic state. For a carotenoid with longer chain length, we find that vibronic energy relaxation does not suffice to explain all features in the transient absorption spectra, which we relate to an increased ground state structural inhomogeneity. Our modeling approach is generally applicable to photophysical deactivation processes in molecules. As such, it represents a well-founded alternative to data fitting techniques such as global target analysis.

Ab initio X(1)0(+) ground state potential curves of Pb···RG dimers (RG = He, Ne, Ar) including spin-orbit effects. Simulation of diffusion coefficients.

CCSD(T) ground state potential curves of Pb···RG systems (RG = He, Ne and Ar) are presented and the importance of the inclusion of spin-orbit effects is discussed. The closed-shell character of the Pb atom at the two-component relativistic level of relativistic theory leads to shallower potential energy curves compared to scalar relativistic open-shell calculations. The pressure-independent cross-diffusion coefficients pD12 have been simulated using the extrapolated two-component CCSD(T) ground state potential curves. The diffusion coefficients from scattering theory are compared with simulations based on molecular dynamics (MD) using the velocity autocorrelation function (VACF) and the Einstein equation. A correction for the proper assessment of the uncertainty in the VACF is proposed. The acceleration of the MD simulation of Pb in RG diffusion is proposed utilizing the RG in Pb diffusion. The dU[TQ]Z/CCSD(T) potential curve of Pb···He (De = 8.667 cm(-1), re = 4.683 Å) supports only one vibrational level. The anharmonicity of this potential is compared to the potential of He···He which also supports only one vibrational level. The comparison is based on the mean square separations of the vibrational wave function.

Synthesis and optical properties of various thienyl derivatives of pyrene.

A series of various thienyl derivatives of pyrene were synthesized by Stille cross-coupling procedure. Their structures were characterized by (1)H NMR, (13)C NMR and elemental analysis. The spectroscopic characteristics were investigated by UV-vis absorption and fluorescence spectra. Based on quantum chemical calculations, the energy levels of investigated molecules with respect to the pyrene molecule were also discussed.

Combined spectroelectrochemical and theoretical study of electron-rich dendritic 2,5-diaminothiophene derivatives: N,N,N',N'-tetrakis-(4-diphenylamino-phenyl)-thiophene-2,5-diamine.

The in situ spectroelectrochemical and electron spin resonance (ESR) behavior of the recently prepared N,N,N',N'-tetrakis-(4-diphenylamino-phenyl)-thiophene-2,5-diamine 11 is presented. The results are compared to the ones of the parent 2,5-bis-diphenylamino-thiophene 41 as well as to the corresponding high-molar third dendrimer generation 8 containing the same thiophene-2,5-diamine core. The dendritic compound 11 can be reversibly oxidized in three separated steps to yield the corresponding stable monocation 11(•+), dication 11(2+), and tetracation 11(4+). A well resolved ESR spectrum of the corresponding cation radical 11(•+) with dominating splittings from two nitrogen atoms and two hydrogen atoms was observed at the first oxidation peak similar to 41(•+). The shape of the SOMOs orbitals very well correlates with the proposed distribution of the unpaired electron mainly on the thiophene center and neighboring nitrogen atoms. The spin delocalization on the central thiophene moiety in the monocations for all three model compounds 41(•+), 11(•+), and 8(•+) was confirmed. The computed single occupied molecular orbital (SOMO) for trication 11(•3+) is completely different compared to the SOMO of the corresponding monocation 11(•+), and it confirms a largely delocalized unpaired spin density. Dominating diamagnetic product was determined at the third oxidation peak, confirming the formation of a tetracation by a two electron oxidation of ESR silent dication. The positive charge is fully delocalized over the lateral parts of the molecule leading to the high stability of tetracation 11(4+). The estimated theoretical limit energy of the lowest optical transition S0 → S1 is 2.90 eV, and it can be achieved for the 3D dendrimer generation.

Stable radical trianions from reversibly formed sigma-dimers of selenadiazoloquinolones studied by in situ EPR/UV-vis spectroelectrochemistry and quantum chemical calculations.

The redox behavior of the series of 7-substituted 6-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-h]quinolines and 8-substituted 9-oxo-6,9-dihydro[1,2,5]selenadiazolo[3,4-f]quinolines with R(7), R(8) = H, COOC(2)H(5), COOCH(3), COOH, COCH(3), and CN has been studied by in situ EPR and EPR/UV-vis spectroelectrochemistry in dimethylsulfoxide. All selenadiazoloquinolones undergo a one-electron reduction process to form the corresponding radical anions. Their stability strongly depends on substitution at the nitrogen atom of the 4-pyridone ring. The primary generated radical anions from N-ethyl-substituted quinolones are stable, whereas for the quinolones with imino hydrogen, the initial radical anions rapidly dimerize to produce unusually stable sigma-dimer (σ-dimer) dianions. These are reversibly oxidized to the initial compounds at potentials considerably less negative than the original reduction process in the back voltammetric scan. The dimer dianion can be further reduced to the stable paramagnetic dimer radical trianion in the region of the second reversible reduction step. The proposed complex reaction mechanism was confirmed by in situ EPR/UV-vis cyclovoltammetric experiments. The site of the dimerization in the σ-dimer and the mapping of the unpaired spin density both for radical anions and σ-dimer radical trianions with unusual unpaired spin distribution have been assigned by means of density functional theory calculations.

Ultrafast photo-induced charge transfer unveiled by two-dimensional electronic spectroscopy.

The interaction of exciton and charge transfer (CT) states plays a central role in photo-induced CT processes in chemistry, biology, and physics. In this work, we use a combination of two-dimensional electronic spectroscopy (2D-ES), pump-probe measurements, and quantum chemistry to investigate the ultrafast CT dynamics in a lutetium bisphthalocyanine dimer in different oxidation states. It is found that in the anionic form, the combination of strong CT-exciton interaction and electronic asymmetry induced by a counter-ion enables CT between the two macrocycles of the complex on a 30 fs timescale. Following optical excitation, a chain of electron and hole transfer steps gives rise to characteristic cross-peak dynamics in the electronic 2D spectra, and we monitor how the excited state charge density ultimately localizes on the macrocycle closest to the counter-ion within 100 fs. A comparison with the dynamics in the radical species further elucidates how CT states modulate the electronic structure and tune fs-reaction dynamics. Our experiments demonstrate the unique capability of 2D-ES in combination with other methods to decipher ultrafast CT dynamics.

On the electrochemistry and spectroelectrochemistry of small model star-shaped compounds: 1,3,5-triaryl-1-methoxybenzenes and 2,4,6-triaryl-1,3,5-trimethoxybenzenes.

Model structures of 1,3,5-triarylbenzenes with a substituted benzene core linked to thienyl or 3,4-ethylenedioxythienyl (EDOT) terminal groups are studied by electrochemical and in situ ESR/UV/Vis/NIR spectroelectrochemical techniques. Oxidative polymerization of the monomers results in C-C coupling of the thiophene moieties in the 5-position, forming dimeric structures with bithiophene linkers as the first step. Both the doubly charged protonated dimer and the new dimer formed after proton release are studied in detail for 2,4,6-tris[2-(3,4-ethylenedioxythienyl)]-1-methoxybenzene. Quite high stability of the doubly charged σ dimer formed on oxidation with unusual redox behavior at the electrode is observed. Density functional calculations of the molecular structure as well as spectroscopic and electronic properties of charged states in 1,3,5-triarylbenzene derivatives in the monomeric, dimeric, and oligomeric form are presented. The complex spectroelectrochemical response of a thin solid film formed on the electrode surface upon potentiodynamic polymerization indicates the existence of different charge states of oligomeric structures within the solid matrix.

Ab initio calculation of structure and transport properties of He X (X = Zn, Cd, Hg) van der Waals complexes.

The ground state ab initio CCSD(T) potential curves using various basis sets (aug-cc-pVXZ-PP (X = D, T, Q, 5)) is obtained for the dimers of helium with IIb group metals. The effect of the position of the (mid) bond-functions on the interaction energy is discussed. A Symmetry Adapted Perturbation Theory decomposition of the interaction energy is provided and the trends in the dimer stabilizing and destabilizing contributions are depicted. The spline fitted potential curves are applied together with rigorous statistical formulae in order to obtain the transport coefficients (viscosity coefficients, diffusion coefficients) and the second virial coefficient both for pure constituents and mixtures. The obtained theoretical results are compared with available experimental data. Molecular dynamics is used to obtain reliable values of the diffusion coefficients for all the systems under study.