Kinetic and molecular orbital studies on the rate of oxidation of monosubstituted phenols and anilines by horseradish peroxidase compound II

The second-order rate constant (k4) for the oxidation of a series of aromatic donor molecules (monosubstituted phenols and anilines) by horseradish peroxidase (HRP) compound II was examined with a stopped-flow apparatus. The electronic states of these substrates were calculated by an ab initio molecular orbital method. It was found that in both phenols and anilines log k4 values correlate well with the highest occupied molecular orbital (HOMO) energy level and the lowest unoccupied molecular orbital (LUMO) energy level, but not with the net charge or frontier electron density on atoms of these molecules. The HOMO and LUMO energy levels of phenols and anilines further showed linear relationships with Hammett's sigma values with negative slopes. Similar results were obtained in the oxidation of substrates by HRP compound I, except that the rate of reaction was much higher than in the case of HRP compound II. In addition, the rates of oxidation of phenols by compound I or II were found to be about 1000 times higher than those of anilines with similar HOMO energy levels. On the basis of these results, the mechanism of electron transfer from the substrate to the heme iron of HRP compound II is discussed.     

Evaluation of the energetic position of the lowest excited singlet state of beta-carotene by NEXAFS and photoemission spectroscopy.

In carotenoids the lowest energetic optical transition belonging to the pi-electron system is forbidden by symmetry, therefore the energetic position of the S(1) (2(1)A(g)) level can hardly be assessed by optical spectroscopy. We introduce a novel experimental approach: For molecules with pi-electron systems the transition C1s-->2p(pi*) from inner-atomic to the lowest unoccupied molecular orbital (LUMO) appears in X-ray absorption near edge spectra (NEXAFS) as an intense, sharp peak a few eV below the carbon K-edge. Whereas the peak position reflects the energy of the first excited singlet state in relation to the ionization potential of the molecule, intensity and width of the transition depend on hybridization and bonding partners of the selected atom. Complementary information can be obtained from ultraviolet photoelectron spectroscopy (UPS): At the low binding energy site of the spectrum a peak related to the highest occupied molecular orbital (HOMO) appears. We have measured NEXAFS and UPS of beta-carotene. Based on these measurements and quantum chemical calculations the HOMO and LUMO energies can be derived.     

Ab initio electronic structure of the progestogen norethisterone and its 5 alpha-derivatives

The steroid 17 alpha-ethynyl-19-nor-4-androsten-17 beta-ol, 3-one (Norethisterone; NET) and its 5 alpha-dihydro (5 alpha-NET), 3 alpha- and 3 beta-tetrahydro derivatives (3 alpha,5 alpha- and 3 beta,5 alpha-NET), were comparatively studied by the ab initio quantum mechanics theory. Additionally, 5 alpha-androstan-3 beta,17 beta-diol (ADIOL) was also studied. The Hartree-Fock method and the 6-31G(*) basis set were used to obtain the lowest energy conformation, geometries, electronic structure and physicochemical properties of the steroids. The results showed bond distances and valence angles similar among all steroids, but some differences in dihedral angles in the A-B-ring system were observed. The electronic structure analysis showed that NET has both frontier orbitals that is, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) located at the C4-C5 pi-bond. In A-ring reduced derivatives, the HOMO was found at the 17 beta-OH and ethynyl groups. In the case of 5 alpha-NET, the LUMO was confined to the A-ring and its C3 carbonyl group while the two NET tetrahydro-reduced derivatives showed the LUMO at the 17 beta-OH and ethynyl groups. The energy changes of the rotational barrier of the 17 beta-OH group suggest that its movement is somewhat restricted by the 17 alpha-ethynyl group. Interestingly both groups at C17 form a single electrostatic potential with high electronic density. On the other side, the 19-nor condition increases the A-ring mobility. However, the 3 beta-OH group of 3 beta,5 alpha-NET may rotate without significant energy differences as compared to the same group in ADIOL. The electronic structure of NET and its A-ring reduced derivatives explains in some extent their interaction with androgen and progesterone receptors as well as their selectivity for the estrogen alpha-receptor.     

Kinetic and molecular orbital studies on the rate of oxidation of monosubstituted phenols and anilines by lactoperoxidase compound II in comparison with the case of horseradish peroxidase

The second-order rate constant (k4) for the oxidation of monosubstituted phenols and anilines by lactoperoxidase compound II was examined by Chance's method [B. Chance, Arch. Biochem. Biophys. 71 (1957), 130–136]. When the electronic states of these substrates were calculated by an ab initio molecular orbital method, it was found that the log k4 value correlates well with the highest occupied molecular orbital (HOMO) energy level but not with the net charge or frontier electron density. These results are essentially similar to those reported previously in the case of horseradish peroxidase [J. Sakurada, R. Sekiguchi, K. Sato, and T. Hosoya, Biochemistry 29 (1990), 4093–4098], showing some dissimilar features which are considered to reflect the structural difference between the two enzymes.Abbreviations HOMO highest occupied molecular orbital - HRP horseradish peroxidase - LPO lactoperoxidase (EC 1.11.1.7) - LUMO lowest unoccupied molecular orbital     

Functionalized pyrene‐based AIEgens: synthesis,photophysical characterization and density functional theory studies

Three new pyrene‐based derivatives P1 , P2 and P3 with a substituted pyrazole were designed, synthesized and characterized using standard spectroscopic techniques. Ultraviolet–visible (UV–vis) spectroscopic studies for P1–P3 uncovered a finite bathochromic shift of the molecules in solvents of varying polarity. Photoluminescence (PL) studies revealed the significant fluorescence emission of all molecules in higher polar solvents such as MeOH and dimethylformamide (DMF). Fluorescence quantum yield studies demonstrated the importance of P3 possessing cyanofunctionality for imparting higher emission with a quantum yield of 0.36%. Ratiometric studies performed in a tetrahydrofuran (THF)/H₂O mixture indicated fluorescence enhancement with increasing overall percentage of water, confirming the aggregation‐induced emission effect. Cyclic voltammetry study of molecules P1–P3 revealed an irreversible oxidation peak and the band gaps were calculated to be 2.26 eV for P1 and 2.31 eV for P2 and P3 respectively. Density functional theory (DFT) studies performed on molecules P1–P3 validate the structure correlation of the molecules. Theoretically estimated highest occupied molecular orbital ( HOMO), lowest unoccupied molecular orbital (LUMO) and bandgap correlated well with the experimental values. Furthermore, time‐dependent (TD)DFT showed that the major contribution for the electronic transitions occurring in the system was governed by HOMO‐1 and LUMO+1 orbitals.     

π‐Extended Narrow‐Bandgap Diketopyrrolopyrrole‐Based Oligomers for Solution‐Processed Inverted Organic Solar Cells

A series of narrow‐bandgap π‐conjugated oligomers based on diketopyrrolopyrrole chromophoric units coupled with benzodithiophene, indacenodithiophene, thiophene, and isoindigo cores are designed and synthesized for application as donor materials in solution‐processed small‐molecule organic solar cells. The impacts of these different central cores on the optoelectronic and morphological properties, carrier mobility, and photovoltaic performance are investigated. These π‐extended oligomers possess broad and intense optical absorption covering the range from 550 to 750 nm, narrow optical bandgaps of 1.52–1.69 eV, and relatively low‐lying highest occupied molecular orbital (HOMO) energy levels ranging from ?5.24 to ?5.46 eV in their thin films. A high power conversion efficiency of 5.9% under simulated AM 1.5G illumination is achieved for inverted organic solar cells based on a small‐molecule bulk‐heterojunction system consisting of a benzodithiophene‐diketopyrrolopyrrole‐containing oligomer as a donor and [6,6]‐phenyl‐C₇₁‐butyric acid methyl ester (PC₇₁BM) as an acceptor. Transmission electron microscopy and energy‐dispersive X‐ray spectroscopy reveal that interpenetrating and interconnected donor/acceptor domains with pronounced mesoscopic phase segregation are formed within the photoactive binary blends, which is ideal for efficient exciton dissociation and charge transport in the bulk‐heterojunction devices.     

Tuning electronic structure and photophysical properties of [Ir(ppy)2(py)2]+ by substituents binding in pyridyl ligand: a computational study

Iridium (III) 2-phenylpyridine (ppy) complexes with two suitable monodentate L ligands [Ir(ppy)(2)(L)(2)](+) (ppy = 2-phenylpyridine, py = pyridine, L = 4-pyCN 1, 4-pyCHO 2, 4-pyCl 3, py 4, 4-pyNH(2) 5) were studied by density functional theory (DFT) and time-dependent DFT methods. The influences of ligands L on the electronic structure and photophysical properties were investigated in detail. The compositions and energy levels of the lowest unoccupied molecular orbital (LUMO) are changed more significantly than those of the highest occupied molecular (HOMO) by tuning L ligands. With the electronegativity decrease of L ligands 4-pyCN > 4-pyCHO > 4-pyCl > py > 4-pyNH(2), the LUMO distributing changes from py to ppy, and the absorptions have an obvious red shift. The calculated results showed that the transition character of the absorption and emission can be changed by adjusting the electronegativity of the L ligands. In addition, no solvent effect was observed in the absorptions and emissions.     

On the influence of point defects on the structural and electronic properties of graphene-like sheets: a molecular simulation study

The influence of vacancies and substitutional defects on the structural and electronic properties of graphene, graphene oxide, hexagonal boron nitride, and boron nitride oxide two-dimensional molecular models was studied using density functional theory (DFT) at the level of local density approximation (LDA). Bond length, dipole moment, HOMO–LUMO energy gap, and binding energy were calculated for each system with and without point defects. The results obtained indicate that the formation of a point defect does not necessary lead to structural instability; nevertheless, surface distortions and reconstruction processes were observed, mainly when a vacancy-type defect is generated. For graphene, it was found that incorporation of a point defect results in a semiconductor–semimetal transition and also increases notably its polar character. As with graphene, the formation of a point defect in a hexagonal boron nitride sheet reduces its energy gap, although its influence on the resulting dipole moment is not as dramatic as in graphene. The influence of point defects on the structural and electronic properties of graphene oxide and boron nitride oxide sheets were found to be mediated by the chemisorbed species.     

Donor-enhanced bridge effect on the electronic properties of triphenylamine based dyes: density functional theory investigations

The geometries have been optimized by using density functional theory. The highest occupied molecular orbitals are delocalized on triphenylamine moiety while lowest unoccupied molecular orbital are localized on anchoring group. Intramolecular charge transfer has been observed from highest occupied molecular orbitals to lowest unoccupied molecular orbital. By replacing the vinyl hydrogens with methoxy as well as one benzene ring as bridge leads to a raised energy gap while extending the bridge decreases the energy gap compared to parent molecule. The HOMO energies bump up by extending the bridge. The LUMO energies of all the investigated dyes are above the conduction band of TiO(2) and HOMOs are below the redox couple except 3c. The distortion between anchoring group and triphenylamine can hamper the recombination reaction.     

Electronic structure study using density functional theory in organic dendrimers

The electronic and structural properties of pyrrolic ring derivatives were studied using density functional theory (DFT) in terms of their application as organic semiconductor materials in photovoltaic devices. The B3LYP hybrid functional in combination with Pople type 6-31G(d) basis set with a polarization function was used in order to determine the optimized geometries and the electronic properties of the ground state, while transition energies and excited state properties were obtained from time-dependent (TD)-DFT with B3LYP/6-31G(d) calculation. The investigation of pyrrolic derivatives formed by the arrangement of several monomeric units revealed that three-dimensional (3D) conjugated architectures in which the combination of a triphenylamine (TPA) core with π-conjugated rings attached to the core, present the best geometric and electronic characteristics for use as an organic semiconductor material. The highest occupied molecular orbital (HOMO) − lowest unoccupied molecular orbital (LUMO) energy gap was decreased in 3D-structures that extend the absorption spectrum toward longer wavelengths, revealing a feasible intramolecular charge transfer process in these systems. All calculations in this work were performed using the Gaussian 03 W software package.     

Hyperfine structure of the photoexcited triplet state 3P680 in plant PS II reaction centres as determined by pulse ENDOR spectroscopy

The triplet states in plant photosystem II (PS II), 3P680, and from chlorophyll a, 3Chl a, in organic solution have been investigated using pulse ENDOR combined with repetitive laser excitation at cryogenic temperature with the aim to obtain their hyperfine (hf) structure. The large zero field splitting (ZFS) tensor of 3P680 enabled orientation selection via the electron spin resonance (EPR) field setting along the ZFS tensor axes. ENDOR spectra have been obtained for the first time also for the in-plane X- and Y-orientations of the ZFS tensor. This allowed a full determination of the hf-tensors of the three methine protons and one methyl group of 3P680. Based on the orientations of the axes of these hf-tensors, a unique orientation of the axes of the ZFS tensor of 3P680 in the Chl a molecular frame was obtained. These data serve as a structural basis for determining the orientation of 3P680 in the PS II protein complex by EPR on single crystals (see M. Kammel et al. in this issue). The data obtained represent the first complete set of the larger hf-tensors of the triplet state 3P680. They reflect the spin density distribution both in the highest occupied (HOMO) and lowest unoccupied (LUMO) orbitals. The data clearly confirm that 3P680 is a monomeric Chl a species at low temperature (T=10 K) used, as has been proposed earlier based on D- and E-values obtained from EPR and optically detected magnetic resonance (ODMR) studies. Comparison with the hf data for the cation and anion radicals of Chl a indicates a redistribution of spin densities in particular for the LUMO orbital of the triplet states. The electron spin distribution in the LUMO orbital is of special interest since it harbours the excited electron in the excited P680 singlet state, from which light-induced electron transfer proceeds. Observed shifts of hf couplings from individual nuclei of 3P680 as compared with 3Chl a in organic solution are of special interest, since they indicate specific protein interactions, e.g. hydrogen bonding, which might be used in future studies for assigning 3P680 to a particular chlorophyll molecule in PS II.     

Density functional studies of the substituent effect on absorption and emission properties of 1, 8-naphthalimide derivatives

Using TD-PBE1PBE/6-31G* and TD-B3LYP/6-31G* approaches, we calculated the absorption and emission spectra of 1,8-naphthalmide derivatives in gas-phase. The geometric structures optimized by HF/6-31G* and B3LYP/6-31G* models and the absorption and emission maxima were in good agreement with existed experimental measurements. It was also found that the lowest singlet states corresponded mainly to the electronic transition from the highest occupied orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO). Intramolecular charge transfer occurred between substituents and naphthalimic rings. Study also showed that most compounds with low absorption excitation energies had low vertical ionization potentials. Finally, the delocalization electronic energies between substituents and naphthalimic rings of isomers were investigated to obtain further sight into their stability.     

Adsorption of tetracyanoquinodimethane and tetrathiafulvalene on aluminium (100) surface – a first principle study of structural and electronic properties

Possible adsorption configurations and electronic properties, such as charge analysis, density of states, work function and Schottky barrier height of tetracyanoquinodimethane (TCNQ) and tetrathiafulvalene (TTF) on Aluminium (100) surface is studied by using density functional theory methods with local density approximation (LDA), generalised gradient approximation (GGA), PBE and PBE-D2 methods. TCNQ is strongly adsorbed on Al(100) with adsorption energy of ?3.66?eV. The charge is transferred from Al(100) to TCNQ and charge transfer occurs mainly through cyano group of TCNQ. Adsorption on Al(100) surface leads to downshift in energy difference between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of TCNQ by 2.5?eV as result of hybridisation of p orbital of carbon and nitrogen atoms of TCNQ and p orbital of surface Al atoms. Compared to TCNQ adsorption, TTF adsorption on Al(100) surface is having less adsorption energy and type of interaction is physisorption. The charge transfer from TTF to Al(100) surface leads to decrease in work function of Al by 0.24?eV. The n-type Schottky barrier height of TCNQ/Al(100) and p-type Schottky barrier height of TTF/Al(100) is 0.68eV and 1.97?eV, respectively showing that TCNQ and Al(100) are suitable for organic photovoltaic and electrochemical applications.     

An experimental and theoretical approach to 5alpha-cholestan-6-spiro-1',2',4'-triazolidine-3'-one

The 5alpha-cholestan-6-one semicarbazone (1) on reaction with hydrogen peroxide at 0 degrees C affords selectively 5alpha-cholestan-6-spiro-1',2',4'-triazolidine-3'-one. (2) The structural assignment of the product was confirmed on the basis of its elemental, analytical and spectral analysis. The Hartree-Fock method using 6-31G* basis set was employed in order to explore the reaction mechanism. The results of the computational study show that the reaction proceeds through two radical intermediates formation. The different characteristics involved during the reaction were explained, firstly, the lower energy conformation of each molecule using total energy, hardness and dipole moment, and secondly, the explanation of the free radical mechanism, using frontier molecular orbital (FMO) theory, encoded electrostatic potential, spin electronic density and atomic charges. The localization of highest occupied molecular orbital (HOMO) or alpha-HOMO, lowest unoccupied molecular orbital (LUMO) or alpha-LUMO and the flow of atomic charges are in good agreement to support the present mechanism of the reaction. Stability and feasibility of all the optimized structures were supported by their respective fundamental frequencies and energy minima.     

Quantum chemical study in the direction to design efficient donor-bridge-acceptor triphenylamine sensitizers with improved electron injection

The ground state geometries have been computed by using density functional theory. The excitation energies for dye sensitizers were performed by using time dependant density functional theory. The polarizable continuum model (PCM) has been used for evaluating bulk solvent effects at all stages. The calculations have been carried out in methanol according to the experimental set up. The long-range-corrected functional (PCM-TD-LC-BLYP) underestimate the absorption spectrum of parent molecule while PCM-TDBHandHLYP is in good agreement with the experimental data. The highest occupied molecular orbital (HOMO) is delocalized on TPA moiety while lowest unoccupied molecular orbital (LUMO) is localized on anchoring group, conjugated chain and the benzene ring near to the anchoring group. The LUMO energies of all the investigated dyes are above the conduction band of TiO(2), HOMOs are below the redox couple and HOMO-LUMO energy gaps of studied dyes are smaller compared to TC4. The 1 and 3 are 7 and 12?nm blue shifted while 2 and 4 are 25 and 22?nm red shifted, respectively compared to TC4. The trend of electron injection (ΔG(inject)), relative electron injection (ΔG (r) (inject) ()), and electronic coupling constant (|VRP|) has been observed as 3?>?1?>?4?>?2?>?TC4. The improved ΔG(inject), |VRP| and light harvesting efficiency (LHE) of new designed sensitizers revealed that these materials would be excellent sensitizers. The broken coplanarity between the benzene near anchoring group having LUMO and the last benzene attached to TPA unit in 1-4 consequently would hamper the recombination reaction.     

Docking and DFT Studies to explore the Topoisomerase II ATP Pocket employing 3-Substituted 2,6-Piperazindiones for drug design

Topoisomerases (Topos) are very important protein targets for drug design in cancer treatment. Human Topo type IIα (hTopo IIα) has been widely studied experimentally and theoretically. Here, we performed protein rigid/flexible side-chain docking to study a set of thirty-nine 3-substituted-2,6-piperazindiones (labelled 1a, (R)-[(2–20)a] and (S)-[(2–20)b]) derived from α-amino acids. To explain the ligand–protein complexes at the electronic level [using the highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO) energies], density functional theory calculations were carried out. Finally, to show adenosine triphosphate (ATP) binding-site constituents, the Q-SiteFinder program was used. The docking results showed that all of the test compounds bind to the ATP-binding site on hTopo IIα. Recognition is mediated by the formation of several hydrogen bond acceptors or donators. This site was the largest (631 Å³) according to the Q-SiteFinder program. When using the protein rigid docking protocol, compound 13a derived from (R)-Lys showed the highest affinity. However, when a flexible side-chain docking protocol was used, the compound with the highest affinity was 16a, derived from (R)-Trp. Frontier molecular orbital studies showed that the HOMO of the ligand interacts with the LUMO located at side-chain residues from the protein-binding site. The HOMO of the binding site interacts with the LUMO of the ligand. We conclude that some ligand properties including the hindrance effect, hydrogen bonds, π–π interactions and stereogenic centres are important for the ligand to be recognised by the ATP-binding site of hTopo IIα.     

DFT calculation of the electronic properties of fluorene-1,3,4-thiadiazole oligomers

Thiadiazole derivatives have been widely employed in the areas of pharmaceutical, agricultural, industrial, and polymer chemistry. The electronic and molecular structures of thiadiazoles are of interest because they have an equal number of valence electrons and similar molecular structures to thiophenes, which are currently used in the construction of organic solar cells due to their relatively high hole mobilities and good light-harvesting properties. For this reason, the electronic properties of fluorene-1,3,4-thiadiazole oligomers warrant investigation. In the present work, the structure of fluorene-1,3,4-thiadiazole with one thiadiazole unit in the structure was analyzed. This molecule was then expanded until there were 10 thiadiazole units in the structure. The band gap, HOMO and LUMO distributions, and absorption spectrum were analyzed for each molecule. All calculations were performed by applying the B3LYP/6-31G(d) chemical model in the Gaussian 03W and GaussView software packages. The electronic properties were observed to significantly enhance as the number of monomeric units increased, which also caused the gap energy to decrease from 3.51 eV in the oligomer with just one thiadiazole ring to 2.33 eV in the oligomer with 10 units. The HOMO and LUMO regions were well defined and separated for oligomers with at least 5 monomer units of thiadiazole.