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.     

Intrinsic mutagenicity of polycyclic aromatic hydrocarbons: A quantitative structure activity study based upon molecular shape analysis

The mutagenic potencies of 30 polycyclic aromatic hydrocarbons, (PAHs) were quantitatively related to the physicochemical properties of the parent structures. The goal of the work was to identify how much information regarding overall mutagenicity of PAHs reside in the unmetabolized structures. Quantitative structure activity relationships (QSARs) were established between measured mutagenic potency and two molecular properties: (1) ΔE, the difference in energy between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO), and, (2) molecular shape, as measured by common overlap steric volumes between pairs of PAHs. Mutagenic potency can be predicted with an average error of about ±11% for these 30 PAHs. It appears that the physicochemical properties of a parent PAH dictate much of the mutagenic behavior ultimately realized through metabolic activation. Consequently, QSARs developed for the parent PAHs might serve as reliable empirical guides in ranking mutagenic potency.     

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.     

Molecular orbital theory on cellulolytic reactivity between pNP-cellooligosccharides and beta-glucosidase from Cellulomonas uda CS1-1

A beta-glucosidase with the molecular mass of 160,000 Da was purified to homogeneity from cell extract of a cellulolytic bacterium, Cellulomonas uda CS1-1. The kinetic parameters (Km and Vmax) of the enzyme were determined with pNP-cellooligosccharides (DP 1-5) and cellobiose. The molecular orbital theoretical studies on the cellulolytic reactivity between the pNP-cellooligosaccharides as substrate (S) molecules and the purified beta-glucosidase (E) were conducted by applying the frontier molecular orbital (FMO) interaction theory. The results of the FMO interaction between E and S molecules verified that the first stage of the reaction was induced by exocyclic cleavage, which occurred in an electrophilic reaction based on a strong charge-controlled reaction between the highest occupied molecular orbital (HOMO) energy of the S molecule and the lowest occupied molecular orbital (LUMO) energy of the hydronium ion (H3O+), more than endocyclic cleavage, whereas a nucleophilic substitution reaction was induced by an orbital-controlled reaction between the LUMO energy of the oxonium ion (SH+) protonated to the S molecule and the HOMO energy of the H2O2 molecule. A hypothetic reaction route was proposed with the experimental results in which the enzymatic acid-catalyst hydrolysis reaction of E and S molecules would be progressed via SN1 and SN2 reactions. In addition, the quantitative structure-activity relationships (QSARs) between these kinetic parameters showed that Km has a significant correlation with hydrophobicity (logP), and specific activity has with dipole moment, respectively.     

Comparing the spectroscopic and electrochemical properties of ruthenium and osmium complexes of the tridentate polyazine ligands 2,2′:6′,2″-terpyridine and 2,3,5,6-tetrakis(2-pyridyl)pyrazine

A number of osmium and ruthenium complexes of the tridentate ligands 2,2′:6′,2″-terpyridine (tpy) and 2,3,5,6-tetrakis(2-pyridyl)pyrazine (tpp) have been prepared and characterized by our laboratory. All these complexes possess metal based oxidations and ligand based reductions localized on each polyazine ligand. Polymetallic complexes bridged by the tpp ligand exhibit two sequential tpp based reductions prior to the reduction of other polyazine ligands in these complexes. The spectroscopy of these complexes is dominated by ligand based π-π^* transitions in the ultraviolet and MLCT (metal-to-ligand charge transfer) bands terminating on each polyzine ligand in the visible. For the complexes reported herein the lowest lying optical transitionis a M → BL CT band. For most of the complexes reported, occupation of this excited state gives rise to an observable emission at room temperature. For ruthenium complexes of these tridentate ligands, the presence of a low-lying LF state shortens the excited state lifetimes of these chromophores. This gives rise to ruthenium complexes that display shorter excited state lifetimes than the analogous osmium based systems. Incorporation of tpp based chromophores into polymetallic frameworks leads to the production of bimetallic species with long-lived excited states, 100 ns at room temperature. This makes these chromophores good candidates for the development of stereochemically defined supramolecular complexes. It is possible to measure an electrochemical HOMO-LUMO energy gap and a correlation between this electrochemically measured energy gap and the spectroscopic energy associated with this HOMO→LUMO transition are reported herein (HOMO== highest occupied molecular orbital, LUMO = lowest unoccupied molecular orbital).     

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.     

Theoretical evaluation of inhibition performance of purine corrosion inhibitors

Inhibition mechanism of three purine compounds, adenine (A), 2-amino-6-thiol-9H-purine (B) and 2,6-dithiol-9H-purine (C), was investigated by quantum chemical calculation and molecular dynamic simulation. The molecular reactivity was studied by quantum chemical calculation, and the distribution of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), the energy gap between HOMO and LUMO and the Fukui index were proposed to describe the active sites of molecules, and the inferred inhibition efficiency followed the order of A < B < C. Furthermore, the adsorption behaviour of these three purine molecules on a metal surface was investigated via molecular dynamics simulation. The analysis of adsorption configuration indicated that these three purine molecules adsorbed parallely onto the metal surface, and the inferred inhibition efficiency from interaction energy also followed the order of A < B < C. These inferred inhibition efficiency from theoretical calculation was in good accordance with experimental results. This accordance indicated that our proposed theoretical method might be a feasible approach to assess the inhibition performance of inhibitors. Moreover, our research was helpful to filter the aimed inhibitor and design of the new inhibitor.     

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.     

Suppression of Recombination Losses in Polymer:Nonfullerene Acceptor Organic Solar Cells due to Aggregation Dependence of Acceptor Electron Affinity

Here, it is investigated whether an energetic cascade between mixed and pure regions assists in suppressing recombination losses in non‐fullerene acceptor (NFA)‐based organic solar cells. The impact of polymer‐NFA blend composition upon morphology, energetics, charge carrier recombination kinetics, and photocurrent properties are studied. By changing film composition, morphological structures are varied from consisting of highly intermixed polymer‐NFA phases to consisting of both intermixed and pure phase. Cyclic voltammetry is employed to investigate the impact of blend morphology upon NFA lowest unoccupied molecular orbital (LUMO) level energetics. Transient absorption spectroscopy reveals the importance of an energetic cascade between mixed and pure phases in the electron–hole dynamics in order to well separate spatially localized electron–hole pairs. Raman spectroscopy is used to investigate the origin of energetic shift of NFA LUMO levels. It appears that the increase in NFA electron affinity in pure phases relative to mixed phases is correlated with a transition from a relatively planar backbone structure of NFA in pure, aggregated phases, to a more twisted structure in molecularly mixed phases. The studies focus on addressing whether aggregation‐dependent acceptor LUMO level energetics are a general design requirement for both fullerene and NFAs, and quantifying the magnitude, origin, and impact of such energetic shifts upon device performance.     

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.     

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.     

Study on the regioselectivity and mechanism of the aromatic hydroxylation of monofluoroanilines.

The in vitro and in vivo metabolism of monofluoroanilines was investigated. Special attention was focused on the regioselectivity of the aromatic hydroxylation by cytochromes P-450 and the mechanism by which this reaction might proceed. The results clearly demonstrate that the in vitro and in vivo regioselectivity of the aromatic hydroxylation by cytochromes P-450 is dependent on the fluoro-substituent pattern of the aromatic aniline-ring. Results from experiments with liver microsomes from differently pretreated rats demonstrate that the observed regioselectivity for the aromatic hydroxylation is not predominantly determined by the active site of the cytochromes P-450. To investigate the underlying reason for the observed regioselectivity, semi-empirical molecular orbital calculations were performed. Outcomes of these calculations show that neither the frontier orbital densities of the LUMO/LUMO + 1 (lowest unoccupied molecular orbital) of the monofluoroanilines nor the spin-densities in their NH. radicals can explain the observed regioselectivities. The frontier orbital densities of the HOMO/HOMO - 1 (highest occupied molecular orbital) of the monofluoroanilines however, qualitatively correlate with the regioselectivity of the aromatic hydroxylation. Based on these results it is concluded that the cytochrome P-450 dependent aromatic hydroxylation of monofluoroanilines does not proceed by hydrogen or electron abstraction from the aniline substrate to give an aniline-NH. radical. The results rather suggest that cytochrome P-450 catalyzed aromatic hydroxylation of monofluoroanilines proceeds by an electrophilic attack of the (FeO)3+ species of cytochrome P-450 on a specific carbon atom of the aromatic aniline-ring.     

Identification of Potential Carbonic Anhydrase Inhibitors for Glaucoma Treatment Through an In-Silico Approach

Glaucoma is a neurodegenerative disease and second leading cause of blindness in western world. The disease is characterized by an elevated intraocular pressure. Carbonic anhydrase plays a major role by forming aqueous humor and its inhibition can reduce intraocular pressure by partially suppressing the secretion of aqueous humor. Thus in this study, we proposed to identify the potential novel compounds targeting the carbonic anhydrase. The diversity set-II molecules library consisting of 1880 compounds from National Cancer Institute were virtually screened (molecular docking) against human carbonic anhydrase protein. For the obtained best compounds, the nature of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), which determine nucleophilic and electrophilic activity, were calculated by using density functional theory (DFT). The in silico screening suggested 5 best compounds that are effective in comparison to the dorzolamide, a widely used carbonic anhydrase inhibitor for glaucoma treatment. Of the five compounds, 4-nitro-7-[(1-oxidopyridin-1-ium-2-yl) thio] benzofurazan (ZINC01757986) exhibited the better binding affinity (??9.2 cal/mol) in comparison to dorzolamide (??7.2 kcal/mol). The DFT studies on novel identified compound, ZINC01757986 exhibited less HOMO–LUMO energy gap, low hardness and more softness (0.2305 eV, 0.1152 eV and 8.6805 eV) when compared to dorzalamide (0.9536 eV, 0.4768 eV and 2.0973 eV). These studies emphasize that ZINC01757986 can be used as potential carbonic anhydrase inhibitor and lead compounds for the development of an effective anti-glaucoma drug. The results emphasize that these compounds could be potential lead molecules for further structure-based discovery of antiglaucoma drugs.

     

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.     

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     

A theoretical model of the catalytic mechanism of the Delta5-3-ketosteroid isomerase reaction

The present paper describes a theoretical approach to the catalytic reaction mechanism involved in the conversion of 5-androstene-3,17-dione to 4-androstene-3,17-dione. The model incorporates the side chains of the residues tyrosine (Tyr(14)), aspartate (Asp(38)) and aspartic acid (Asp(99)) of the enzyme Delta(5)-3-ketosteroid isomerase (KSI; EC 5.3.3.1). The reaction involves two steps: first, Asp(38) acts as a base, abstracting the 4beta-H atom (proton) from C-4 of the steroid to form a dienolate as the intermediate; next, the intermediate is reketonized by proton transfer to the 6beta-position. Each step goes through its own transition state. Functional groups of the Tyr(14) and Asp(99) side chains act as hydrogen bond donors to the O1 atom of the steroid, providing stability along the reaction coordinate. Calculations were assessed at high level Hartree-Fock theory, using the 6-31G(*) basis set and the most important physicochemical properties involved in each step of the reaction, such as total energy, hardness, and dipole moment. Likewise, to explain the mechanism of reaction, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), atomic orbital contributions to frontier orbitals formation, encoded electrostatic potentials, and atomic charges were used. Energy minima and transition state geometries were confirmed by vibrational frequency analysis. The mechanism described herein accounts for all of the properties, as well as the flow of atomic charges, explaining both catalytic mechanism and proficiency of KSI.     

Synthesis and luminescence properties of pyrazolone derivatives and their terbium complexes

Seven novel pyrazolone derivatives were synthesized and characterized by ¹H NMR and ¹³C NMR spectra, mass spectra, infrared spectra and elemental analysis. Their terbium complexes were prepared and characterized by elemental analysis, EDTA titrimetric analysis, UV/vis spectra, infrared spectra and molar conductivity, as well as thermal analysis. The fluorescence properties and fluorescence quantum yields of the complexes were investigated at room temperature. The results indicated that pyrazolone derivatives had good energy‐transfer efficiency for the terbium ion. All the terbium complexes emitted green fluorescence characteristic of terbium ions, possessed strong fluorescence intensity, and showed relatively high fluorescence quantum yields. Cyclic voltammograms of the terbium complexes were studied and the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) energy levels of these complexes were estimated. Copyright © 2014 John Wiley & Sons, Ltd.     

Understanding the Reduced Efficiencies of Organic Solar Cells Employing Fullerene Multiadducts as Acceptors

The use of fullerenes with two or more adducts as acceptors has been recently shown to enhance the performance of bulk‐heterojunction solar cells using poly(3‐hexylthiophene) (P3HT) as the donor. The enhancement is caused by a substantial increase in the open‐circuit voltage due to a rise in the fullerene lowest unoccupied molecular orbital (LUMO) level when going from monoadducts to multiadducts. While the increase in the open‐circuit voltage is obtained with many different polymers, most polymers other than P3HT show a substantially reduced photocurrent when blended with fullerene multiadducts like bis‐PCBM (bis adduct of Phenyl‐C₆₁‐butyric acid methyl ester) or the indene C₆₀ bis‐adduct ICBA. Here we investigate the reasons for this decrease in photocurrent. We find that it can be attributed partly to a loss in charge generation efficiency that may be related to the LUMO‐LUMO and HOMO‐HOMO (highest occupied molecular orbital) offsets at the donor‐acceptor heterojunction, and partly to reduced charge carrier collection efficiencies. We show that the P3HT exhibits efficient collection due to high hole and electron mobilities with mono‐ and multiadduct fullerenes. In contrast the less crystalline polymer Poly[[9‐(1‐octylnonyl)‐9H‐carbazole‐2,7‐diyl]‐2,5‐thiophenediyl‐2,1,3‐benzothiadiazole‐4,7‐diyl‐2,5‐thiophenediyl (PCDTBT) shows inefficient charge carrier collection, assigned to low hole mobility in the polymer and low electron mobility when blended with multiadduct fullerenes.