Anela Ivanova

Synthesis, magnetic properties and theoretical calculations of novel nitronyl nitroxide and imino nitroxide diradicals grafted on terpyridine moiety

Abstract The synthetic route based on Stille coupling between tributyltinpyridyl derivatives and bromo substituted mono- and dipyridyl-carbaldehyde is used for the synthesis of 5,5″-diformyl-2,2′:6′,2″-terpyridine ( 8 ). A sequence of Ullman coupling with 2,3-bis(hydroxylamino)-2,3-dimethylbutane followed by oxidation under phase transfer conditions affords either 5,5″-Bis(1-oxyl-3-oxo-4,4,5,5-tetramethylimidazolidin-2-yl)2,2′:6′,2″-terpyridine ( 10 ) (diNN-Terpy) or the related 5,5″-Bis(1-oxyl-4,4,5,5-tetramethylimidazolidin-2-yl)2,2′:6′,2″-terpyridine ( 11 ) (diIN-Terpy), where both biradicals display clear intramolecular ferromagnetic interaction between the single spin units as evidenced by ESR spectroscopy. Quantum chemical calculations (ROHF/AM1) are performed showing the triplet ground-state for both 10 and 11 radicals.

Fully Doped Oligomers of Emeraldine Salt: Polaronic versus Bipolaronic Configuration

Calculations for model oligomers of the emeraldine salt with UBLYP/6-31G*/PCM are performed. The models differ in number of monomers, in the position of the counterions (Cl(-)), and in multiplicity. The molecular features affected most prominently by the protonation, namely, structure, energetics, and electron and spin density partitioning are analyzed. The results show unequivocally that the studied molecular characteristics are essentially size independent. The octamer profiles of all parameters are repeated in the dodecamer and the hexadecamer. The bipolaronic forms are energetically more favorable than the polaronic ones within the chosen protocol. The electronic structure in the intermediate multiplicities differs from the bipolaronic and polaronic periodicity. The geometrical changes and electron density redistribution upon increase of multiplicity illustrate the pathway of intramolecular bipolaron-polaron conversion. The orbital analysis rationalizes the observed behavior of the oligomers.

Effect of solvent polarization on the reorganization energy of electron transfer from molecular dynamics simulations

The solvent contribution lambda(s) to the reorganization energy of electron transfer can be estimated from averages of the potential energy gaps between neutral-pair and ion-pair states over an ensemble of structures generated from molecular dynamics simulations. Invoking a Marcus-type two-sphere model for charge separation and recombination in an aqueous environment, we explored the effect of a polarizable force field and noted a strong reduction of lambda(s) (by approximately 45%) compared to the corresponding value obtained with a standard nonpolarizable force field. Both types of force fields yield lambda(s) values that in agreement with the Marcus theory, vary strictly linearly with the inverse of the donor-acceptor distance; the corresponding slopes translate into appropriate effective optical dielectric constants, epsilon(infinity) approximately 1.0+/-0.2 for a nonpolarizable and epsilon(infinity) approximately 1.7+/-0.4 for a polarizable force field. The reduction in the solvent reorganization energy due to a polarizable force field translates into a scaling factor that is essentially independent of the donor-acceptor distance. The corresponding effective optical dielectric constant, epsilon(infinity) approximately 1.80, is in excellent agreement with experiment for water.

Is 2D graphite an ultimate large hydrocarbon?: III. Structure and energy spectra of large polybenzenoid hydrocarbons with different edge structures☆

Abstract The structure and energy spectra of very large polybenzenoid alternant hydrocarbons (with up to N ∼10 3 C-atoms) with different edge structures and defects were investigated theoretically. In all the cases, the calculated values of the energy gap width tend monotonically to a value different from zero when the electron correlation is taken into account. Typical surface (Tamm) states, namely non-bonding MOs, appear in the cases of non-Kekule, open-shell hydrocarbons featuring point defects with a definite topology. The electrons occupying the non-bonding MOs are ferromagnetically coupled. These hydrocarbons are in fact polyradicals with a substantial value of the specific π-electron energy, which determines their relative stability.

Solvent Reorganization Energies in A-DNA, B-DNA, and Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations with a Polarizable Force Field

We estimate solvent reorganization energies lambda(s) of electron transfer (ET) in DNA stacks between positively charged guanine (acceptor) and neutral guanine (donor), as well as in rhodamine 6G (R6G)-DNA complexes between R6G (acceptor) and neutral guanine (donor) from molecular dynamics simulations that used a polarizable force field in combination with a polarizable water model. We compare results from the polarizable scheme with those from a common nonpolarizable analogue. We also discuss the influence of charge sets, separate contributions of solute and solvent electronic polarizations, and partial contributions of different molecular groups to changes of lambda(s) due to electronic polarization. Independent of donor-acceptor distances, solvent reorganization energies of ET processes in DNA duplexes from a polarizable force field are about 30% smaller than the corresponding results from a nonpolarizable force field. The effective optical dielectric constant epsilon(infinity) = 1.5, extracted from pertinent scaling factors, is also independent of the donor-acceptor separation over a wide range of distances, from 3.4 to 50.0 A. Reorganization energies calculated with the polarizable force field agree satisfactorily with experimental data for DNA duplexes. Comparison of results for A-DNA and B-DNA forms as well as for the conformational alignment of the dye relative to the duplex in R6G-DNA complexes demonstrates that the conformation of a duplex hardly affects lambda(s). Among these DNA-related systems, the effective parameter epsilon(infinity) is remarkably constant over a broad range of donor-acceptor distances.

Understanding the Fluorescence of TADF Light-Emitting Dyes

In order to afford in a controlled fashion fine-tuning of the color and the intensity of the emitted light of potential fluorophores for organic light-emitting diodes (OLED), directed molecular design based on a donor-spacer-acceptor model is undertaken. One way of increasing emission efficiency is triplet harvesting. This can be achieved by thermally activated delayed fluorescence (TADF) when triplet and singlet excited states are quasi degenerate. Molecular building units are selected and bound in a specific pattern to allow for increase in emission performance, also due to TADF. Using time-dependent density functional theory, the relevant singlet-singlet and triplet-singlet energy gaps corresponding to absorption or emission transitions of the compounds are computed to simulate the electroluminescent spectrum. The results are analyzed in depth and relations between some spectral and structural properties are proposed. The best suited molecules are delineated as potential OLED building blocks. Guidelines for systematic improvement of the molecular characteristics are outlined.

Molecular dynamics approach to water structure of HII mesophase of monoolein

The goal of the present work is to study theoretically the structure of water inside the water cylinder of the inverse hexagonal mesophase (H(II)) of glyceryl monooleate (monoolein, GMO), using the method of molecular dynamics. To simplify the computational model, a fixed structure of the GMO tube is maintained. The non-standard cylindrical geometry of the system required the development and application of a novel method for obtaining the starting distribution of water molecules. A predictor-corrector schema is employed for generation of the initial density of water. Molecular dynamics calculations are performed at constant volume and temperature (NVT ensemble) with 1D periodic boundary conditions applied. During the simulations the lipid structure is kept fixed, while the dynamics of water is unrestrained. Distribution of hydrogen bonds and density as well as radial distribution of water molecules across the water cylinder show the presence of water structure deep in the cylinder (about 6 Å below the GMO heads). The obtained results may help understanding the role of water structure in the processes of insertion of external molecules inside the GMO∕water system. The present work has a semi-quantitative character and it should be considered as the initial stage of more comprehensive future theoretical studies.

Structural aspects of lipid monolayers: computer simulation analyses.

Extensive molecular dynamics simulations at room temperature were carried out for model films of two dissimilar lipids (DPPC and dicaprin) at the air/water interface. To study the peculiarities of the organization patterns at different average areas per molecule, surface concentrations corresponding to five almost equally spaced points along the isotherms of the two surfactants were considered. A variable of prime interest was the density distribution in a direction normal to the interface of the monolayer components: interfacial water and surfactant on one hand and the separate moieties of the lipids on the other hand. The packing pattern and cluster size dispersion were studied by means of Voronoi tessellation and radial distribution functions. Speculations regarding structural changes upon phase-state changes during film compression were made. Individual characteristics for surfactant heads and tails as well as for interfacial water were outlined and related to the available experimental data. An analysis of the diffusion coefficients revealed the limiting factors for lipid lateral and normal diffusion. Structural arguments in support of changes in monolayer dielectric properties with the area per molecule were provided.

Molecular Structure and Pronounced Conformational Flexibility of Doxorubicin in Free and Conjugated State within a Drug–Peptide Compound

The search for targeted drug delivery systems requires the design of drug-carrier complexes, which could both reach the malignant cells and preserve the therapeutic substance activity. A promising strategy aimed at enhancing the uptake and reducing the systemic toxicity is to bind covalently the drug to a cell-penetrating peptide. To understand the structure-activity relationship in such preparations, the chemotherapeutic drug doxorubicin was investigated by unrestrained molecular dynamics simulations, supported by NMR, which yielded its molecular geometry in aqueous environment. Furthermore, the structure and dynamics of a conjugate of the drug with a cell-penetrating peptide was obtained from molecular dynamics simulations in aqueous solution. The geometries of the unbound compounds were characterized at different temperatures, as well as the extent to which they change after covalent binding and whether/how they influence each other in the drug-peptide conjugate. The main structural fragments that affect the conformational ensemble of every molecule were found. The results show that the transitions between different substructures of the three compounds require a modest amount of energy. At increased temperature, either more conformations become populated as a result of the thermal fluctuations or the relative shares of the various conformers equalize at the nanosecond scale. These frequent structural interconversions suggest expressed conformational freedom of the molecules. Conjugation into the drug-peptide compound partially immobilizes the molecules of the parent compounds. Nevertheless, flexibility still exists, as well as an effective intra- and intermolecular hydrogen bonding that stabilizes the structures. We observe compact packing of the drug within the peptide that is also based on stacking interactions. All this outlines the drug-peptide conjugate as a prospective building block of a more complex drug-carrier system.

Structure and Properties of New Classes of Coupled Polymethine Dyes

Abstract The structure and the energy spectra of new classes of coupled polymethines ( CP ) (coupled cyanines, merocyanines and oxonoles) were investigated theoretically. The CP s may be considered as being composed of two identical or two different streptopolymethine fragments or as derivatives of poly(peri-naphthylene)s. All CP s display low-energy 1 S o → 1 S 1 transitions with a high transition probability. The transition energies are comparable with those of the streptopolymethine substructures. The similarity of the energy spectra of streptopolymethines and CP s is determined by the symmetry of the frontier MOs of the streptopolymethine fragments and the CP s.