5′,8-Cyclopurine-2′-deoxynucleosides: Molecular structure and charge distribution – DFT study in gaseous and aqueous phase

Oxidatively generated damage to DNA frequently appears in the human genome as an effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents. Due to these facts, it has been decided to present the structural propriety and charge distribution of 5′,8-cyclo-2′-deoxyadenosine/guanosine (cdA, cdG) in their 5′R and 5′S diastereomeric forms. For all points of quantum mechanics studies presented, the density functional theory (DFT) with B3LYP parameters on 6-311++G** basis set level was used. The 2-deoxyribose moiety of cyclopurines has adopted the ₀T¹ conformation in their cationic, neutral and anionic forms. The natural population analysis (NPA) of charge distribution between purine/2-deoxyribose moieties exhibited positive/positive value for cations, positive/negative for neutral molecules. NPA data for anionic forms showed negative/negative values in gas (exclude (5′S)cdG) and positive/negative in water. The dipole moments of 5′,8-cyclopurine-2′-deoxynucleosides were found as follows: 7.83(5′R)cdG, 6.86(5′S)cdG, 3.99(5′R)cdA, 1.99(5′S)cdA in the gaseous phase, 11.29(5′R)cdG, 9.99(5′S)cdG, 6.44(5′R)cdA, 4.14(5′S)cdA in the aqueous phase.     

Synthesis and characterization of novel α- or β-tetra[6,7-dihexyloxy-3-(4-oxyphenyl)coumarin]-substituted metal-free and metallo phthalocyanines

The synthesis of novel phthalonitriles substituted at 3- or 4-position with 6,7-dihexyloxy-3-(4-oxyphenyl)coumarin were performed. The metal-free and metallo phthalocyanines (MPcs) (M = Zn, Co, Cu) were prepared by cyclotetramerization of 6,7-dihexyloxy-3-[p-(2′,3′-dicyanophenoxy)phenyl]coumarin or 6,7-dihexyloxy-3-[p-(3′,4′-dicyanophenoxy)phenyl]coumarin. The newly prepared compounds, phthalonitriles and Pcs, have been characterized by elemental analysis, ¹H NMR, ¹³C NMR, MALDI-TOF, IR, UV–Vis and fluorescence spectral data. The electronic spectra exhibit bands of coumarin identity along with characteristic Q and B bands of the Pc core. The IR-spectra of all Pcs showed three characteristic intense bands at 1709–1700 cm⁻¹ for lactone carbonyl, two bands at 1489–1604 cm⁻¹ for conjugated olefinic system.     

Stationary and time-resolved spectra of 2,2′:5′,2″-terthiophene

By analyzing the stationary absorption spectrum of 2,2′:5′,2″-terthiophene in dichloromethane at room temperature, the zero–zero S₁←S₀ transition energy is determined. Time-resolved fluorescence measurements show that the S₁→S₀ radiative relaxation in various solvents decays exponentially with a common time constant of 170±10 ps. The fluorescence anisotropy of 2,2′:5′,2″-terthiophene in dichloromethane is also studied and the transient dichroism is interpreted in terms of the revolution of a hydrodynamic prolate ellipsoid with the emission dipole aligned parallel to the long molecular axis.     

A polarographic study of the iron-2-hydroxymethyl-6-(2′-hydroxymethyl-5′-hydroxy-4′-pyrone-6′)-pyranyl-3,2[b]pyran-4,8-dione complex

A polarographic study has been carried out on the colored product formed in the interaction of iron(III) with 2-hydroxymethyl-6-(2′-hydroxymethyl-5′-hydroxy-4′-pyrone-6′)-pyranyl-3,2[b]pyran-4,8-dione. Measurements using the differential pulse method show that iron(III) exhibits a coordination number of 2 and a reproducible formation constant that varies somewhat depending upon the supporting electrolyte employed.     

Fluorescence properties of (R)- and (S)-[1,1′-binaphthalene]-2,2′-diols solutions and their complexes with cyclodextrins in aqueous medium

Steady-state and time-resolved fluorescence techniques were used to study (R)- and (S)-[1,1′-binaphthalene]-2,2′-diol (1,1′-binaphthol or BINOL) dilute solutions of different polarity solvents, as well as their inclusion complexes with α- and βcyclodextrins (CDs) in water. BINOLs in dilute water solutions exhibited a surprisingly high fluorescence anisotropy that was explained as being due to the formation of fairly large order π–π stacking aggregates in aqueous polar media. Stoichiometries, formation constants and the changes of enthalpy and entropy upon inclusion were also obtained by measuring the variation of the fluorescence intensity with [CD] and temperature. Results agree with the formation of 1:1 stoichiometry complexes, but the association constants are rather low and very similar for both enantiomers. Molecular mechanic calculations in the presence of water were employed to study the formation of BINOL complexes with both α- and βCDs. For the most stable structures of any of the complexes only a small portion of the guests, in agreement with thermodynamics parameters and quenching experiments, penetrates inside the CD cavities. Driving forces for 1:1 inclusion processes may be dominated by non-bonded van der Waals host:guest interactions. The low guest:host binding constants and poor enantioselectivity of α- and βCDs for BINOLS may be a consequence of the BINOL aggregation in water.     

Reaction and relaxation of vibrationally excited molecules: a classical trajectory study of Br + HCl(υ′) and Br + DCl(υ′) collisions

a quasiclassical trajectory study has been carried out to investigate the dynamics of collisions between Br + HCl (1 υ′ 4) and Br + DCl (υ′ = 2,3). For HCl (υ′ 2) and DCl (υ′ = 3), the endoergic reaction producing Cl + HBr occurs readily, and at approximately the same rate as vibrational deactivation in non-reactive collisions. For HCl(υ′ = 2) and DCl(υ′ = 3), where the initial vibrational energies are similar to |ΔE₀ for the reaction, the rates of both reactive and inelastic processes are quite strongly temperature dependent but the ratio of reactive to inelastic encounters is not a strong function of T. Comparison of the calculated results for Br + HCl(υ′ = 1) with experimentally determined rates strongly suggests that, at least at low temperatures, removal of HCl(υ′ = 1) by Br atoms occurs predominantly via electronically non-adiabatic vibrational relaxation.     

Electrochemical, spectroelectrochemical and theoretical studies on the reduction and deprotonation of the photovoltaic sensitizer [(H3-tctpy)Ru(NCS)3] (H3-tctpy=2,2′:6′,2′′-terpyridine-4,4′,4′′-tricarboxylic acid)

The electrochemical reduction of the black dye photosensitizer [(H₃-tctpy)Ru^II(NCS)₃]⁻ (H₃-tctpy=2,2′:6′,2′′-terpyridine-4,4′,4′′-tricarboxylic acid) used in photovoltaic cells has been found to be a complex process when studied in dimethylformamide. At low temperatures, fast scan rates and at a glassy carbon electrode, the chemically reversible ligand based one-electron reduction process [(H₃-tctpy)Ru(NCS)₃]⁻+e⁻[(H₃-tctpy√⁻)Ru(NCS)₃]²⁻ is detected. This process has a reversible half-wave potential (E^r_1/2) of −1585±20 mV versus Fc/Fc⁺ at 25°C. Under other conditions, a deprotonation reaction occurs upon reduction, which produces [(H_3−x-tctpy^x−)Ru(NCS)₃]^(1+x)− and hydrogen gas. Mechanistic pathways giving rise to the final products are discussed. The E^r_1/2-value for the ligand based reductions of the deprotonated complex is 0.70 V more negative than for [(H₃-tctpy)Ru(NCS)₃]⁻. Consequently, data obtained from molecular orbital calculations are consistent with the reaction [(H₃-tctpy)Ru(NCS)₃]⁻+e⁻→[(H₂-tctpy⁻)Ru(NCS)₃]²⁻+1/2H₂ yielding the monodeprotonated complex as the major product obtained after electrochemical reduction of [(H₃-tctpy)Ru(NCS)₃]⁻. The E^r_1/2-values for the metal based Ru^II/III process differ by 0.30 V when data obtained for the protonated and deprotonated forms of the black dye are compared. Electronic spectra obtained during the course of experiments in an optically transparent thin layer electrolysis configuration are consistent with the overall reaction scheme proposed on the basis of voltammetric measurements and molecular orbital calculations. Reduction studies on the free ligand, H₃-tcpy, are consistent with results obtained with [(H₃-tctpy)Ru(NCS)₃]⁻.     

A divergent synthesis of - and -carbocyclic 4′-fluoro-2′,3′-dideoxynucleosides as potential antiviral agents

- and -Carbocyclic 4′-fluoro-2′,3′-dideoxynucleosides have been synthesized from 2, which can be conveniently prepared from 1,2:5,6-di-O-isopropylidene- -mannitol 1 in eight steps. Ruthenium-catalyzed ring-closing metathesis has been employed in the synthesis of -nucleosides, whereas the -series have been obtained through an intramolecular nucleophilic substitution reaction. The Mitsunobu condensation was used as a general tool for the synthesis of both purine and pyrimidine nucleosides.     

TICT state formation in the 4′-dimethylaminoacetophenone–α-cyclodexdtrin inclusion complex

Fluorescence properties of excited 4′-dimethylaminoacetophenone (DMAAP) complexed with α-cyclodextrin (CD) were studied. The complex exhibited dual fluorescence in neutral aqueous solutions and no TICT fluorescence was observed in alkaline solutions. The dependence of TICT emission intensity on pH and α-CD concentration suggested that a 1:2 DMAAP–α-CD complex, which was formed by the association of the 1:1 complex and α-CD, was responsible for the TICT fluorescence.     

Resonance-enhanced Raman scattering by aggregated 2,2′-cyanine on colloidal silver

The Raman scattering spectrum of 2,2′-cyanine on colloidal silver metal particles is discussed. Preliminary assignments of some of the vibrational Raman bands to the motions of specific chromophoric units are presented and multiplet character of some bands is discussed. Enhanced Raman scattering of 2,2′-cyanine occurs when the laser radiation is tuned to the J-aggregate absorption feature at 575 nm. The enhancement in Raman intensity is the result of a diminution of fluorescence intensity, as well as a quantitative increase in Raman scattering intensity, and is distinct from other types of enhancement phenomena (e.g., resonance Raman of monomeric solution dye, and surface-enhanced Raman scattering (SERS)). The resonance Raman enhancement, due to excitation at the frequency corresponding to the J-aggregate absorption, is found to be 2 × 10⁺³.     

Infrared spectroscopy of isolated nucleotides. 1. The cyclic 3′,5′-adenosine monophosphate anion

The intracellular second messenger deprotonated adenosine 3′,5′-cyclic monophosphate anion (cAMP-H)⁻, generated as gaseous species by electrospray ionization (ESI) and stored in a Paul ion-trap mass spectrometer, has been investigated by mass-resolved infrared multiple photon dissociation (IRMPD) spectroscopy in the 900–1800 cm⁻¹ fingerprint wavenumber range, exploiting the powerful and continuously tunable radiation from a free electron laser (FEL) at the Centre Laser Infrarouge d’Orsay (CLIO). The IRMPD features are interpreted by comparison with the IR spectra obtained by quantum chemical calculations for different low-lying conformers, allowing an assignment for the observed IRMPD bands. It is to be noted that the calculated IR spectra for the most stable conformers look all rather similar and do not allow an unambiguous structural assignment, based exclusively on the IRMPD spectrum. However, the positions and intensities of the IRMPD features of isolated (cAMP-H)⁻ ions are consistent with a species deprotonated at the phosphate group and compatible with the main equilibrium structures lying within 18 kJ mol⁻¹ from the lowest lying conformation, the anti-chair form with a C3′-endo sugar twist.     

Resonance Raman spectra of metalloporphyrins. On the methine-bridge vibrations of ferric octaethylporphyrins and its α′, β′, γ′, and δ′ deutero derivatives

Raman spectra of Fe³⁺ and Pd²⁺ octaethylporphyrin (OEP) and their α′, β′, γ′, and δ′ deutero derivatives were measured with the 5145, 4880 and 4765 Å lines of an Ar ion laser. Raman bands due to methine-bridge stretching vibrations were assigned and their vibrational amplitudes were calculated from the observed frequency shifts on deuterium substitution of methine-bridge hydrogens. These vibrations correspond to the spin-state sensitive Raman bands of heme proteins. On the basis of symmetry considerations and the observed polarizations, vibrational assignments of other Raman bands were made.     

Charge-transfer host complex with channel-like cavity using disubstituted-1,1′-bi-2-naphthol and benzylviologen

A novel charge-transfer (CT) host system is developed using CT complexes composed of rac-3,3′-dihydroxy-1,1′-bi-2-naphthol and 1,1′-dibenzyl-4,4′-bipyridinium dichloride. This CT host complex has a 1D channel-like cavity in which guest (MeOH and EtOH) molecules can be discharged and adsorbed. The color and DRS of the CT crystals change according to the presence of guest molecules in the host complex.     

Hydrothermal synthesis, crystal structures, and properties of Co and Ni supramolecular complexes with 2,4,6-trimethyl benzoate and 4,4′-bipyridyl

Two new coordination complexes, viz. [Co(tmb)₂(4,4′-bpy)₂(H₂O)₂](Htmb)₂ (1) and {[Ni(tmb)₂(μ-4,4′-bpy)₂(H₂O)₂](4,4′-bpy)}_n (2), have been hydrothermally synthesized by reaction of the corresponding metal acetate with 2,4,6-trimethylbenzoic acid (Htmb) and 4,4′-bipyridyl (4,4′-bpy). X-ray single-crystal diffraction suggests that complex 1 represents a discrete mononuclear species in which the central metal ion is coordinated by the terminal carboxylate moiety and the 4,4′-bipyridyl ligand. The crystal structure of complex 2 reveals a 1D chain coordination polymer in which the Ni(II) ions are connected by the bridging 4,4′-bipyridyl ligands. In both cases, the coordination arrays are further extended via hydrogen bonding interactions to generate 3D supramolecular networks. Complexes 1 and 2 have also been characterized by spectroscopic (IR and UV/Vis), thermal (TGA) and magnetic susceptibility measurements. In addition, both complexes exhibit antimicrobial activity.     

Synthesis and Characterization of Novel Phthalimide‐pyrano[3,2‐c]chromene and Phthalimide‐pyrano‐2‐one Hybrids

Coumarin skelton holds substantial promise for further exploration because of its immense pharmacological potential. In this pursuit, a series of phthalimide‐chromen and phthalimide‐pyran‐2‐one hybrids were synthesized in efficient yields via one‐pot multicomponent reaction of aldehyde linked to phthalimide moiety, 4‐hydroxy coumarin/4‐hydroxy‐6‐methyl‐2H‐pyran‐2‐one, and malanonitrile by Knoevenagel reaction at room temperature in the presence of DABCO as catalyst. The compounds were characterized by ¹H NMR and ¹³C NMR, MS, and FTIR. All the compounds consisting of phthalimide‐chromen/pyrano‐2‐one moieties tethered by spacers of varying lengths were evaluated for their biological activity in Ellman's assay. Most of the compounds feebly inhibited Acetylcholinesterase Enzyme and were inactive toward Butyrylcholinesterase Enzyme.     

High solubility and optical transparency of novel polyimides containing 3,3′,5,5′-tetramethyl pendant groups and 4-tert-butyltoluene moiety

A series of novel polyimides (3a–d) were prepared from 3,3′,5,5′-tetramethyl-4,4′-diaminodiphenyl-4”-tert-butyltoluene (1) with four aromatic dianhydrides via a one-step high-temperature polycondensation procedure. The obtained polyimides showed excellent solubility, with the dissolvability at a concentration of 10 wt% in most amide polar solvents and chlorinated solvents. Their films were nearly colorless and exhibited high optical transparency, with the UV cutoff wavelength in the range of 322–350 nm and the wavelength of 80% transparency in the range of 395–414 nm. They also showed low dielectric constant (2.72–2.91 at 1 MHz) and low water absorptions (0.37–0.62%). Moreover, these polyimides possessed high glass transition temperatures (T_g) (above 321 °C) and good thermal stability with 10% weight loss temperatures in the range of 526–547 °C in nitrogen atmosphere. In comparison with the analogous polyimides non-containing 3,3′,5,5′ -tetramethyl pendant groups, the resultant polyimides 3a–d showed better solubility, higher optical transparency and lower dielectric constant.     

Approaches to wired terpyridine: Bithienyl alkynyl derivatives of 2,2′:6′,2″-terpyridine and their ruthenium(II) complexes

Two approaches to the formation of ruthenium(II) complexes containing ligands with conjugated 2,2′:6′,2″-terpyridine (tpy), alkynyl and bithienyl units have been investigated. Bromination of 4′-(2,2′-bithien-5′-yl)-2,2′:6′,2″-terpyridine leads to 4′-(5-bromo-2,2’-bithien-5′-yl)-2,2′:6′,2″-terpyridine (1), the single crystal structure of which has been determined. The complexes [Ru(1)₂][PF₆]₂ and [Ru(tpy)(1)][PF₆]₂ have been prepared and characterized. Sonogashira coupling of the bromo-substituent with (TIPS)CCH did not prove to be an efficient method of preparing the corresponding complexes with pendant alkynyl units. The reaction of 4′-ethynyl-2,2′:6’,2″-terpyridine with 5-bromo-2,2′-bithiophene under Sonogashira conditions yielded ligand 2, and the heteroleptic ruthenium(II) complex [Ru(2)(tpy)][PF₆]₂ has been prepared and characterized.     

Theoretical studies on the structural and optical properties of a series of Os(II) diimine complexes [Os(NN)(CO)2I2] (NN = 2,2′-bipyridine(bpy), 4,4′-di-tert-butyl-2,2′-bipyridine(dbubpy), 4,4′-dichlorine-2,2′-bipyridine(dclbpy))

The ground- and excited-state structures for a series of Os(II) diimine complexes [Os(NN)(CO)₂I₂] (NN = 2,2′-bipyridine (bpy) (1), 4,4′-di-tert-butyl-2,2′-bipyridine (dbubpy) (2), and 4,4′-dichlorine-2,2′-bipyridine (dclbpy) (3)) were optimized by the MP2 and CIS methods, respectively. The spectroscopic properties in dichloromethane solution were predicted at the time-dependent density functional theory (TD-DFT, B3LYP) level associated with the PCM solvent effect model. It was shown that the lowest-energy absorptions at 488, 469 and 539 nm for 1–3, respectively, were attributed to the admixture of the [d_xy (Os) → π^*(bpy)] (metal-to-ligand charge transfer, MLCT) and [p(I) → π^*(bpy)] (interligand charge transfer, LLCT) transitions; their lowest-energy phosphorescent emissions at 610, 537 and 687 nm also have the ³MLCT/³LLCT transition characters. These results agree well with the experimental reports. The present investigation revealed that the variation of the substituents from H → t-Bu → Cl on the bipyridine ligand changes the emission energies by altering the energy level of HOMO and LUMO but does not change the transition natures.     

High-performance liquid chromatographic separation of enantiomers of 1,1′-binaphthyl-substituted α-aminoisobutyric acid

The direct and indirect stereochemical resolution of the enantiomers of free and N-protected (R,S)-2′,1′:1,2;1″,2″:3,4-dinaphthcyclohepta-1,3-diene-6-amino-6-carboxylic acid (Bin) was achieved by high-performance liquid chromatographic methods. The direct separation was carried out on a β-cyclodextrin-based chiral stationary phase, ChiraDex, and the indirect resolution by applying pre-column derivatization with 2,3,4,6-tetra-O-acetyl-β-

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-glucopyranosyl isothiocyanate.