Poly –N = N– linked 1,5-dihydro-1,5-diazocine,the two-dimensional polymer with Dirac insulator properties: ab initio study

A new material – the monolayered, π-conjugated, poly dinitrogen-linked 1,5-dihydro-1,5-diazocine – is proposed. Density functional theory calculations reveal that the material is a two-dimensional Dirac insulator with a direct band gap. The generalised gradient approximation (GGA) and the local density approximation (LDA) give band gaps of E _gap ^GGA = 0.045 eV and E _gap ^LDA = 0.035 eV. Anisotropy of the Dirac cones results in variation of Fermi velocities of the charge carriers: [0.85–5.30] × 10⁶ m/s (GGA) and [0.86–5.38] × 10⁶ m/s (LDA). Corresponding effective masses are ～10³ lower than that of a free electron. G₀W₀ calculations confirm the topology of density functional theory band structure and show band gap of E _gap = 0.121 eV. Cohesive energies are estimated at E _c ^GGA = 5.30 eV/atom and E _c ^LDA = 6.15 eV/atom. Thus, the results provide the first evidence for the existence of Dirac insulators among organic polymers.     

Crystal and electronic structures and high-pressure behavior of AgSO<Subscript>4</Subscript>, a unique narrow band gap antiferromagnetic semiconductor: LDA(+U) picture

We demonstrate that DFT calculations performed with the local density approximation (LDA) allow for significantly better reproduction of lattice constants, the unit cell volume and the density of Ag(II)SO₄ than those done with generalized gradient approximation (GGA). The LDA+U scheme, which accounts for electronic correlation effects, enables the accurate prediction of the magnetic superexchange constant of this strongly correlated material and its band gap at the Fermi level. The character of the band gap places the compound on the borderline between a Mott insulator and a charge transfer insulator. The size of the band gap (0.82 eV) indicates that AgSO₄ is a ferrimagnetic semiconductor, and possibly an attractive material for spintronics. A bulk modulus of 27.0 GPa and a compressibility of 0.037 GPa^–1 were determined for AgSO₄ from the third-order Birch–Murnaghan isothermal equation of state up to 20 GPa. Several polymorphic types compete with the ambient pressure P-1 phase as the external pressure is increased. The P-1 phase is predicted to resist pressure-induced metallization up to at least 20 GPa.     

Oesophagostomum dentatum: effect of glutathione S-transferase (GST) inhibitors on GST activity and larval development

Sulphobromophthalein (SBP) inhibits isolated glutathione S-transferase of the porcine nodule worm Oesophagostomum dentatum (Od-GST) and reduces larval development in vitro. In this study possible inhibitory effects of various inhibitors were evaluated in an enzymatic (CDNB) assay with isolated Od-GST and in a larval development assay (LDA). Reversibility was tested in the LDA by removing the inhibitor from culture halfway through the cultivation period. SBP, indomethacin and ethacrynic acid inhibited both enzyme activity and larval development in a dose-dependent and reversible manner. HQL-79 also reduced larval development but had only a minor effect on the isolated enzyme. The phospholipase A₂ inhibitors dexamethasone and hydrocortisone had no major effect. High thermal stability of Od-GST was demonstrated with increasing activity between 4 and 50 °C. Differences between Od-GST and GST of other organisms indicate structural and possibly functional peculiarities and highlight the potential of such enzymes as targets of intervention.     

Structure and electronic absorption spectra of nematogenic alkoxycinnamic acids - a comparative study based on semiempirical and DFT methods

Structure of nematogenic p-n-Alkoxy cinnamic acids (nOCAC) with various alkyl chain carbon atoms (n = 2, 4, 6, 8) has been optimized using density functional B3LYP with 6-31+G (d) basis set using crystallographic geometry as input. Using the optimized geometry, electronic structure of the molecules has been evaluated using the semiempirical methods and DFT calculations. Molecular charge distribution and phase stability of these systems have been analyzed based on Mulliken and L?wdin population analysis. The electronic absorption spectra of nOCAC molecules have been simulated by employing DFT method, semiempirical CNDO/S and INDO/S parameterizations. Two types of calculations have been performed for model systems containing single and double molecules of nOCAC. UV-Visible spectra have been calculated for all single molecules. The UV stability of the molecules has been discussed in light of the electronic transition oscillator strength (f). The dimer complexes of higher homologues (n = 6, 8) have also been reported to enable the comparison between single and double molecules.     

Experimental and Calculated CPL Spectra and Related Spectroscopic Data of Camphor and Other Simple Chiral Bicyclic Ketones

UV, circular dichroism (CD), fluorescence and circularly polarized luminescence (CPL) spectra were recorded for a set of four related [2.2.1] bicyclic compounds ((1S,4S)‐and (1R,4R)‐1,7,7‐trimethylbicyclo[2.2.1]heptan‐2‐one, namely (1S)‐ and (1R)‐camphor ( 1 ), (1S,4R)‐4,7,7‐trimethylbicyclo[2.2.1]hept‐5‐en‐2‐one, (1S)‐dehydro‐epicamphor ( 2 ), (1S,4S)‐1,7,7‐trimethylbicyclo[2.2.1]heptane‐2,5‐dione, (1S)‐5‐oxocamphor ( 3 ), (1S,4R)‐ and (1R,4S)‐1,7,7‐trimethylbicyclo[2.2.1]heptane‐2,3‐dione, (1S)‐ and (1R)‐camphorquinone ( 4 )) and a set of three related [2.2.2] bicyclic compounds (1S,4S)‐bicyclo[2.2.2]octan‐2,5‐dione (saturated diketone ( 5 )), (1R,4R)‐bicyclo[2.2.2]oct‐7‐en‐2,5‐dione (unsaturated diketone ( 6 )), ((1S,4S)‐bicyclo[2.2.2]oct‐7‐en‐5(S)‐ol‐2‐one (which we refer to as unsaturated hydroxy‐ketone ( 7 )). For the latter three compounds also mid‐IR vibrational circular dichroism (VCD) spectra were recorded and are presented. Time‐Dependent Density Functional (TD‐DFT) calculations provide a satisfactory interpretation of both absorption and emission chiroptical spectra and permit insight into ground and excited state electronic properties. We discuss the applicability of the octant rule or of other approximated models to rationalize the observed sign of the CPL. Chirality 25:589–599, 2013. © 2013 Wiley Periodicals, Inc.     

Electronic transitions and heterogeneity of the bacteriophytochrome Pr absorption band: An angle balanced polarization resolved femtosecond VIS pump–IR probe study

Photoisomerization of biliverdin (BV) chromophore triggers the photoresponse in native Agp1 bacteriophytochrome. We discuss heterogeneity in phytochrome Pr form to account for the shape of the absorption profile. We investigated different regions of the absorption profile by angle balanced polarization resolved femtosecond VIS pump–IR probe spectroscopy. We studied the Pr form of Agp1 with its natural chromophore and with a sterically locked 18Et-BV (locked Agp1). We followed the dynamics and orientations of the carbonyl stretching vibrations of ring D and ring A in their ground and electronically excited states. Photoisomerization of ring D is reflected by strong signals of the ring D carbonyl vibration. In contrast, orientational data on ring A show no rotation of ring A upon photoexcitation. Orientational data allow excluding a ZZZasa geometry and corroborates a nontwisted ZZZssa geometry of the chromophore. We found no proof for heterogeneity but identified a new, to our knowledge, electronic transition in the absorption profile at 644 nm (S₀→S₂). Excitation of the S₀→S₂ transition will introduce a more complex photodynamics compared with S₀→S₁ transition. Our approach provides fundamental information on disentanglement of absorption profiles, identification of chromophore structures, and determination of molecular groups involved in the photoisomerization process of photoreceptors.     

Chromophoric dissolved organic matter (CDOM) absorption characteristics in relation to fluorescence in Lake Taihu,China, a large shallow subtropical lake

Absorption measurements from chromophoric dissolved organic matter (CDOM) and their relationships with dissolved organic carbon (DOC) and fluorescence were studied in Lake Taihu, a large, shallow, subtropical lake in China. Absorption spectra of lake water samples were measured from 240 nm to 800 nm. Highest values of a(λ), DOC and F _n (355) occurred near the river inflow to Meiliang Bay and decreased towards the central lake basin. A significant spatial difference was found between Meiliang Bay and the central lake basin in absorption coefficient, DOC-specific absorption coefficient, exponential slope coefficient, DOC concentration and fluorescence value. The spatial distribution of CDOM suggested that a major part of CDOM in the lake was from river input. CDOM absorption coefficients were correlated with DOC over the wavelength range 280–500 nm, and a(355) was also correlated with F _n (355), which showed that CDOM absorption could be inferred from DOC and fluorescence measurement. The coefficient of variation between a(λ) and DOC concentration decreased with increase in wavelength from 240 nm to 800 nm. Furthermore, a significant negative linear relationship was recorded between S value and CDOM absorption coefficient, as well as DOC-specific absorption coefficient. S value and DOC-specific absorption coefficient were used as a proxy for CDOM composition and source. Accurate CDOM absorption measurements are very useful in explaining UV attenuation and in developing, validating remote sensing model of water quality in Lake Taihu.     

Pressure-induced phase transition in wurtzite ZnTe: an ab initio study

A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in wurtzite ZnTe. A first-order phase transition from the wurtzite structure to a Cmcm structure was successfully observed in a constant-pressure molecular dynamics simulation. This phase transformation was also analyzed using enthalpy calculations. We also investigated the stability of wurtzite (WZ) and zinc-blende (ZB) phases from energy–volume calculations, and found that both structures show quite similar equations of state and transform into a Cmcm structure at 16 GPa using enthalpy calculations, in agreement with experimental observations. The transition phase, lattice parameters and bulk properties we obtained are comparable with experimental and theoretical data.     

Spectroscopic Studies on Nicotine and Nornicotine in the UV Region

The UV absorption and electronic circular dichroism (ECD) spectra of (R)‐ and (S)‐nicotine and (S)‐nornicotine in aqueous solution were measured to a significantly lower wavelength range than previously reported, allowing the identification of four previously unobserved electronic transitions. The ECD spectra of the two enantiomers of nicotine were equal in magnitude and opposite in sign, while the UV absorption spectra were coincidental. In line with previous observations, (S)‐nicotine exhibited a negative cotton effect centered on 263 nm with vibronic structure (π–π₁* transition) and a broad, positive ECD signal at around 240 nm associated with the n–π₁* transition. As expected this band disappeared when the pyridyl aromatic moiety was protonated. Four further electronic transitions are reported between 215 and 180 nm; it is proposed the negative maxima around 206 nm is either an n–σ* transition or a charge transfer band resulting from the movement of charge from the pyrrolidyl N lone pair to the pyridyl π* orbital. The pyridyl π–π₂* transition may be contained within the negative ECD signal envelope at around 200 nm. Another negative maximum at 188 nm is thought to be the pyridyl π–π₃* transition, while the lowest wavelength end‐absorption and positive ECD may be associated with the π–π₄* transition. The UV absorption spectra of (S)‐nornicotine was similar to that of (S)‐nicotine in the range 280–220 nm and acidification of the aqueous solution enhanced the absorption. The ECD signals of (S)‐nornicotine were considerably less intense compared to (S)‐nicotine and declined further on acidification; in the far UV region the ECD spectra diverge considerably. Chirality 25:288–293, 2013. © 2013 Wiley Periodicals, Inc.     

Electronic transitions and heterogeneity of the bacteriophytochrome Pr?absorption band: An angle balanced polarization resolved femtosecond VIS pump–IR probe study

Photoisomerization of biliverdin (BV) chromophore triggers the photoresponse in native Agp1 bacteriophytochrome. We discuss heterogeneity in phytochrome Pr form to account for the shape of the absorption profile. We investigated different regions of the absorption profile by angle balanced polarization resolved femtosecond VIS pump–IR probe spectroscopy. We studied the Pr form of Agp1 with its natural chromophore and with a sterically locked 18Et-BV (locked Agp1). We followed the dynamics and orientations of the carbonyl stretching vibrations of ring D and ring A in their ground and electronically excited states. Photoisomerization of ring D is reflected by strong signals of the ring D carbonyl vibration. In contrast, orientational data on ring A show no rotation of ring A upon photoexcitation. Orientational data allow excluding a ZZZasa geometry and corroborates a nontwisted ZZZssa geometry of the chromophore. We found no proof for heterogeneity but identified a new, to our knowledge, electronic transition in the absorption profile at 644 nm (S₀→S₂). Excitation of the S₀→S₂ transition will introduce a more complex photodynamics compared with S₀→S₁ transition. Our approach provides fundamental information on disentanglement of absorption profiles, identification of chromophore structures, and determination of molecular groups involved in the photoisomerization process of photoreceptors.     

Geometric and electronic structures of new endohedral fullerenes: Eu@C72

The geometric and electronic structures of rare earth metallofullerenes Eu@C₇₂ were investigated using density functional theory (DFT) within a generalized gradient approximation (GGA). The geometric optimization revealed that the most favorable endohedral site for Eu is off-center along the C₂ axis on the σ_v plane pointing to the (5, 5) bond at the fusion of two pentagons. Calculations for electronic structures show that two 6s electrons in Eu transfer to the lowest-unoccupied-molecular orbitals of C₇₂ while 4f electrons remain in Eu.     

Transmission vs. Diffuse Transmission in Circular Dichroism: What to Choose for Probing Solid‐State Samples?

Recent advances in equipment enabled the collection of solid‐state electronic circular dichroism (ECD) spectra using the commercially available integrating sphere attachment for a regular ECD spectrometer. This accessory was designed to reduce negative factors occurring in solid‐state ECD measurements, and is, thereby, very useful for recording diffuse transmittance CD (DTCD) spectra using the pellet technique. In the present article, the operating principle of the integrating sphere and utility of the DTCD method in recording solid‐state ECD spectra is demonstrated. Based on illustrative examples, i.e., 10‐camphorsulfonic acid ammonium, cholest‐4‐en‐3‐one, (3R,4R,5S)‐oseltamivir, and (S)‐linezolid, ECD solid‐state measurements were performed by means of both transmission and diffusion methods and later compared. Selection of these compounds as models for comparative studies was made in view of their different chromophoric systems and the profound importance in the pharmaceutical industry. During the course of this work the benefits and limitations of the use of integrating sphere are presented. The final conclusion is that more relevant solid‐state spectra can be obtained by means of the DTCD method. Chirality 27:441–448, 2015. © 2015 Wiley Periodicals, Inc.     

Enantiomeric 4‐Acylamino‐6‐alkyloxy‐2 Alkylthiopyrimidines As Potential A3 Adenosine Receptor Antagonists: HPLC Chiral Resolution and Absolute Configuration Assignment by a Full Set of Chiroptical Spectroscopy

The chiral separation of enantiomeric couples of three potential A₃ adenosine receptor antagonists: (R/S)‐N‐(6‐(1‐phenylethoxy)‐2‐(propylthio)pyrimidin‐4‐yl)acetamide ( 1 ), (R/S)‐N‐(2‐(1‐phenylethylthio)‐6‐propoxypyrimidin‐4‐yl)acetamide ( 2 ), and (R/S)‐N‐(2‐(benzylthio)‐6‐sec‐butoxypyrimidin‐4‐yl)acetamide ( 3 ) was achieved by high‐performance liquid chromatography (HPLC). Three types of chiroptical spectroscopies, namely, optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD), were applied to enantiomeric compounds. Through comparison with Density Functional Theory (DFT) calculations, encompassing extensive conformational analysis, full assignment of the absolute configuration (AC) for the three sets of compounds was obtained. Chirality 28:434–440, 2016. © 2016 Wiley Periodicals, Inc.     

Synthesis of a Base-Protected xylo-LNA Adenine Nucleoside

Abstract

Synthesis of (1S,3R,4R,7R)-7-hydroxy-1-hydroxymethyl-3-(6-N-benzoyl-adenin-9-yl)-2,5-dioxabicyclo[2.2.1]heptane (2), a base-protected xylo-LNA adenine nucleoside, has been accomplished using a convergent synthetic strategy starting from 1,2-di-O-acetylfuranose 3.     

Multispectroscopic studies of the interaction of folic acid with glycated human serum albumin

Abstract

The interaction between glycated human serum albumin (gHSA) and folic acid (FA) was investigated by various spectroscopic techniques, such as fluorescence, circular dichroism, UV–vis absorption spectroscopy and electrophoretic light scattering technique. These methods characterize the binding properties of an albumin–folic acid system. The binding constants values (K_a) at 300 and 310 K are about 10⁴ M^?1. The standard enthalpy change (ΔH) and the standard entropy change (ΔS) were calculated to be ～?20?kJ mol^?1 and ～16 J mol^?1 K^?1, respectively, which indicate characteristic electrostatic interactions between gHSA and folic acid. The CD studies showed that there are no significant conformational changes in the secondary structure of the protein. Moreover, the zeta potential measurements proved that under physiological conditions the gHSA–folic acid complex shows instability. No significant changes in the secondary structure of the protein and reversible drug binding are the desirable effect from pharmacological point of view.

Communicated by Ramaswamy H. Sarma     

Racemization of the aqua-{N-salicylidene-(S)-alaninato}copper(II) by reaction with potassium cyanate

Copper(II) N-salicylidene-(S)-alaninate trihydrate reacting as the S-enantiomeric parent compound with KOCN in hot diluted methanol yielded by slow crystallisation from the cooled reaction mixture (in the course of 1 day) the racemic product K[Cu{sal-(RS)-ala}(NCO)]. The parameters of the axial type EPR spectrum in X-band region and the LF band position in the electronic spectrum are typical of an axially distorted square pyramidal coordination of the Cu(II) atom in this complex. The spectral properties of the complex cuprate prepared and its basal crystallographic data are consistent with those of the earlier studied¹⁵ K₂[Cu₂{sal-(RS)-ala}₂(μ-NCO)₂] synthetized by using [Cu{sal-(RS)-ala}(H₂O)].H₂O as the racemic parent complex in the reaction mixture with KOCN.     

A novel cadmium(II) complex of bipyridine derivative: synthesis,X-ray crystal structure,DNA-binding and antibacterial activities

Abstract

A mononuclear cadmium(II) complex of formula [Cd(5,5′-dmbipy)₂(OAc)₂]·2H₂O (5,5′-dmbipy = 5,5′-dimethyl-2,2′-bipyridine and OAc?=?acetato ligand) has been synthesized and characterized by FT-IR, UV–Vis, ¹H-NMR, elemental analysis and single-crystal X-ray structure analysis. The molecular structure of the complex shows a distorted tetragonal antiprism CdN₄O₄ coordination geometry around the cadmium atom, resulting in coordination by four nitrogen atoms from two 5,5′-dmbipy ligands and four oxygen atoms from two acetate anions. The interaction of this complex to FS-DNA (fish sperm DNA) has also been studied by electronic absorption, fluorescence and gel electrophoresis techniques. Binding constant (K_b), Stern–Volmer constant (K_sv), number of binding sites (n) and bimolecular quenching rate constant (k_q) have been calculated from these spectroscopic data. These results have revealed that the metal complex can bind effectively to FS-DNA via groove binding. The calculated thermodynamic parameters (ΔH°, ΔS° and ΔG°) show that hydrogen bonding and van der Waals forces have an important function in the Cd(II) complex–DNA interaction. The antibacterial effects of the synthesized cadmium complex have also been examined in vitro against standard bacterial strains: one Gram-positive (Staphylococcus aureus, ATCC 25923) and one Gram-negative (Escherichia coli, ATCC 25922) bacteria, using disk diffusion and macro-dilution broth methods. The obtained results show that the Cd(II) complex exhibits a marked antibacterial activity which is significantly better than those observed for its free ligand and metal salt for both Gram-positive and Gram-negative bacteria. However, this metal complex is a more potent antibacterial agent against the Gram-positive than that of the Gram-negative bacteria.

Communicated by Ramaswamy H. Sarma     

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.     

Inhibition of lysine-specific demethylase 1 by the acyclic diterpenoid geranylgeranoic acid and its derivatives

Lysine-specific demethylase 1 (LSD1) is upregulated in many cancers, especially neuroblastoma. We set out to explore whether geranylgeranoic acid (GGA) inhibits LSD1 activity by using recombinant human LSD1. GGA inhibited LSD1 activity with IC₅₀ similar to that of the clinically used drug tranylcypromine. In human neuroblastoma SH-SY5Y cells, GGA induced NTRK2 gene expression alongside upregulation of histone H3 with dimethylated lysine-4 in the regulatory regions of the NTRK2 gene. Dihydrogenation of GGA reinforced the LSD1-inhibitory effect in a position-dependent manner. The inhibitory effects of dihydro-derivatives of GGA on recombinant LSD1 strongly correlated with the induction of NTRK2 gene expression in SH-SY5Y cells. These data demonstrate for the first time the efficient LSD1-inhibitor activity of GGA and its derivatives, providing a novel prospect of preventing cancer onset by using GGA to regulate epigenetic modification.     

Synthesis and characterization of homochiral polymeric S-malato molybdate(VI): toward the potentially stereospecific formation and absolute configuration of iron-molybdenum cofactor in nitrogenase

Reaction of sodium or potassium molybdate and excess malic acid in a wide range of pH values (pH 4.0–7.0) resulted in the isolation of two cis-dioxo-bis(malato)-Mo(VI) complexes, viz. Na₃[MoO₂H(S-mal)₂] and K₃[MoO₂H(S-mal)₂]·H₂O (H₃mal=malic acid). The sodium complex is also characterized by an X-ray structure analysis, showing that the mononuclear Mo units are linked together via very strong symmetric CO₂···H··· O₂C-hydrogen bond [2.432(5) Å], forming a polymeric chain. The molybdenum atoms are quasi-octahedrally coordinated by two cis-oxo groups and two bidentate malate ligands via its alkoxy and α-carboxyl groups, while the β-carboxylic and carboxylate groups remain uncomplexed, as the coordination of vicinal carboxylate and alkoxide of homocitrate in FeMo cofactor of nitrogenase. The absolute configuration of the metal center in this S-malato complex is assigned as Λ and the homochirality within the chain is established as a homochiral form ···Λ_S–Λ_S–Λ_S–Λ_S···. It is proposed that the chiral configuration of the metal center in wild-type FeMo-co biosynthesis might be induced by the early coordination of the chiral R-homocitric acid, while a mixture of raceme might be obtained in the biosynthesis of NifV⁻ FeMo-cofactor. The absolute configuration of wild-type FeMo-cofactor is assigned as Δ_R.