Analysis of 5-hydroxyisoflavones by surface-enhanced Raman spectroscopy : genistein and methoxy derivatives

A series of 5-hydroxy-isoflavones—genistein, biochanin A, prunetin, and 4′,7-dimethoxygenistein—have been studied by surface-enhanced Raman spectroscopy (SERS). Citrate reduced silver colloids were employed as a standard technique to measure SER spectra over a range of pH and concentrations. Density functional theory calculations were used to assist in determining the mode of interaction of isoflavones with the silver nanoparticles. It is revealed that biochanin A and prunetin interact with the silver nanoparticles upon deprotonation of the 7- and the 4′-OH groups, respectively, to show SERS activity. Correlations of their spectra with SERS of genistein strongly support the presence of multiple interaction modes involving both of the OH groups in genistein, in a similar manner to daidzein. Surprisingly, however, under these conditions, the 5-OH group was found to be noninteractive as revealed by attempts to measure SERS of 4′,7-dimethoxygenistein. This was attributed partly to the low solubility and, more importantly, to the influence of steric hindrance, caused by the position of the pendant phenyl ring, which prevented interaction with the Ag colloid surface. These results complement recent work on daidzein and formononetin and provide further insight into understanding the SER spectra of isoflavones.

Surface-enhanced raman scattering spectroscopy of resveratrol

We report here, for the first time, the surface-enhanced Raman scattering (SERS) spectra of resveratrol using KNO₃-aggregated citrate-reduced silver (Ag) colloids. The technique provided a substantial spectral enhancement and therefore good quality spectra of resveratrol at parts per million (ppm) concentrations. The detection limit was found to be <1 μM, equivalent to <0.2 ppm. The SERS profile additionally closely resembled its normal solid-state Raman spectrum with some changes in relative intensity. These intensity changes, together with a precise band assignment aided by density functional theory calculations at the B3LYP/6–31G(d) level, allowed the determination of the structural orientation of the adsorbed resveratrol on the surface of the metal nanoparticles. In particular, the SERS spectra obtained at different resveratrol concentrations exhibited concentration-dependent features, suggesting an influence of surface coverage on the orientation of the adsorbed molecules. At a high concentration, an adoption of close-to-upright orientation of resveratrol adsorbed on the metal surface through the p-OH phenyl ring is favoured. The binding structure is, however, altered at lower surface coverage when the concentration decreases to a tilted orientation with the trans-olefin C=C bond aligning closer to parallel to the surface of the Ag nanoparticles.

Electronic structure of the azide group in 3′-Azido-3′- deoxythymidine (AZT) compared to small azide compounds

Theoretical calculations for some structural and electronic properties of the azide moiety in the nucleoside reverse transcriptase (RT) inhibitor 3′-azido-3′- deoxythymidine (AZT) are reported. These properties, which include geometrical properties in three dimensional space, Hirshfeld charges, electrostatic potential (MEP), vibrational frequencies, and core and valence ionization spectra, are employed to study how the azide group is affected by the presence of a larger fragment. For this purpose, two small but important organic azides, hydrazoic acid and methyl azide, are also considered. The general features of trans Cs configuration for RNNN fragments[1] is distorted in the large AZT bio-molecule. Hirshfeld charge analysis shows charges are reallocated more evenly on azide when the donor group R is not a single atom. Infrared and photoelectron spectra reveal different aspects of the compounds. In conclusion, the electronic structural properties of the compounds depend on the specific property, the local structure and chemical environment of a species.

Mesityltellurenyl cations stabilized by triphenylpnictogens [MesTe(EPh₃)] + (E = P, As, Sb)

The homoleptic 1:1 Lewis pair (LP) complex [MesTe(TeMes₂)]O₃SCF₃ (1) featuring the cation [MesTe(TeMes₂)]+ (1a) was obtained by the reaction of Mes₂Te with HO₃SCF₃. The reaction of 1 with Ph₃E (E = P, As, Sb, Bi) proceeded with substitution of Mes₂Te and provided the heteroleptic 1:1 LP complexes [MesTe(EPh₃)]O₃SCF₃ (2, E = P; 3, E = As) and [MesTe(SbPh₃)][Ph₂Sb(O₃SCF₃)₂] (4) featuring the cations [MesTe(EPh₃)]+ (2a, E = P; 3a, E = As; 4a, E = Sb) and the anion [Ph₂Sb(O₃SCF₃)₂]− (4b). In the reaction with Ph₃Bi, the crude product contained the cation [MesTe(BiPh₃)]+ (5a) and the anion [Ph₂Bi(O₃SCF₃)₂]− (5b); however, the heteroleptic 1:1 LP complex [MesTe(BiPh₃)][Ph₂Bi(O₃SCF₃)₂] (5) could not be isolated because of its limited stability. Instead, fractional crystallization furnished a large amount of Ph₂BiO₃SCF₃ (6), which was also obtained by the reaction of Ph₃Bi with HO₃SCF₃. The formation of the anions 4b and 5b involves a phenyl group migration from Ph₃E (E = Sb, Bi) to the MesTe+ cation and afforded MesTePh as the byproduct, which was identified in the mother liquor. The heteroleptic 1:1 LP complexes 2–4 were also obtained by the one-pot reaction of Mes₂Te, Ph₃E (E = P, As, Sb) and HO₃SCF₃. Compounds 1–4 and 6 were investigated by single-crystal X-ray diffraction. The molecular structures of 1a–4a were used for density functional theory calculations at the B3PW91/TZ level of theory and studied using natural bond order (NBO) analyses as well as real-space bonding descriptors derived from an atoms-in-molecules (AIM) analysis of the theoretically obtained electron density. Additionally, the electron localizability indicator (ELI-D) and the delocalization index are derived from the corresponding pair density.

Hydrogen evolution by a metal-free electrocatalyst

Electrocatalytic reduction of water to molecular hydrogen via the hydrogen evolution reaction may provide a sustainable energy supply for the future, but its commercial application is hampered by the use of precious platinum catalysts. All alternatives to platinum thus far are based on nonprecious metals, and, to our knowledge, there is no report about a catalyst for electrocatalytic hydrogen evolution beyond metals. Here we couple graphitic-carbon nitride with nitrogen-doped graphene to produce a metal-free hybrid catalyst, which shows an unexpected hydrogen evolution reaction activity with comparable overpotential and Tafel slope to some of well-developed metallic catalysts. Experimental observations in combination with density functional theory calculations reveal that its unusual electrocatalytic properties originate from an intrinsic chemical and electronic coupling that synergistically promotes the proton adsorption and reduction kinetics.

Ultra-wideline 14N solid-state NMR as a method for differentiating polymorphs: glycine as a case study

Nitrogen-14 solid-state NMR (SSNMR) is utilized to differentiate three polymorphic forms and a hydrochloride (HCl) salt of the amino acid glycine. Frequency-swept Wideband, Uniform Rate, Smooth Truncated (WURST) pulses were used in conjunction with Carr-Purcell Meiboom-Gill refocusing, in the form of the WURST-CPMG pulse sequence, for all spectral acquisitions. The ¹⁴N quadrupolar interaction is shown to be very sensitive to variations in the local electric field gradients (EFGs) about the ¹⁴N nucleus; hence, differentiation of the samples is accomplished through determination of the quadrupolar parameters CQ and ηQ, which are obtained from analytical simulations of the ¹⁴N SSNMR powder patterns of stationary samples (i.e., static NMR spectra). Additionally, differentiation of the polymorphs is also possible via the measurement of ¹⁴N effective transverse relaxation time constants, T^eff2(¹⁴N). Plane-wave density functional theory (DFT) calculations, which exploit the periodicity of crystal lattices, are utilized to confirm the experimentally determined quadrupolar parameters as well as to determine the orientation of the ¹⁴N EFG tensors in the molecular frames. Several signal-enhancement techniques are also discussed to help improve the sensitivity of the ¹⁴N SSNMR acquisition method, including the use of selective deuteration, the application of the BRoadband Adiabatic INversion Cross-Polarization (BRAIN-CP) technique, and the use of variable-temperature (VT) experiments. Finally, we examine several cases where ¹⁴N VT experiments employing Carr-Purcell-Meiboom-Gill (CPMG) refocusing are used to approximate the rotational energy barriers for RNH3⁺ groups.

Modelagem molecular na caracterização eletrônica de oligopeptídeos e na descrição quântica da interação fármaco-receptor

In this dissertation, the theoretical principles governing the molecular modeling were applied for electronic characterization of oligopeptide α3 and its variants (5Q, 7Q)-α3, as well as in the quantum description of the interaction of the aminoglycoside hygromycin B and the 30S subunit of bacterial ribosome. In the first study, the linear and neutral dipeptides which make up the mentioned oligopeptides were modeled and then optimized for a structure of lower potential energy and appropriate dihedral angles. In this case, three subsequent geometric optimization processes, based on classical Newtonian theory, the semi-empirical and density functional theory (DFT), explore the energy landscape of each dipeptide during the search of ideal minimum energy structures. Finally, great conformers were described about its electrostatic potential, ionization energy (amino acids), and frontier molecular orbitals and hopping term. From the hopping terms described in this study, it was possible in subsequent studies to characterize the charge transport propertie of these peptides models. It envisioned a new biosensor technology capable of diagnosing amyloid diseases, related to an accumulation of misshapen proteins, based on the conductivity displayed by proteins of the patient. In a second step of this dissertation, a study carried out by quantum molecular modeling of the interaction energy of an antibiotic ribosomal aminoglicosídico on your receiver. It is known that the hygromycin B (hygB) is an aminoglycoside antibiotic that affects ribosomal translocation by direct interaction with the small subunit of the bacterial ribosome (30S), specifically with nucleotides in helix 44 of the 16S ribosomal RNA (16S rRNA). Due to strong electrostatic character of this connection, it was proposed an energetic investigation of the binding mechanism of this complex using different values of dielectric constants (ε = 0, 4, 10, 20 and 40), which have been widely used to study the electrostatic properties of biomolecules. For this, increasing radii centered on the hygB centroid were measured from the 30S-hygB crystal structure (1HNZ.pdb), and only the individual interaction energy of each enclosed nucleotide was determined for quantum calculations using molecular fractionation with conjugate caps (MFCC) strategy. It was noticed that the dielectric constants underestimated the energies of individual interactions, allowing the convergence state is achieved quickly. But only for ε = 40, the total binding energy of drug-receptor interaction is stabilized at r = 18A, which provided an appropriate binding pocket because it encompassed the main residues that interact more strongly with the hygB - C1403, C1404, G1405, A1493, G1494, U1495, U1498 and C1496. Thus, the dielectric constant ≈ 40 is ideal for the treatment of systems with many electrical charges. By comparing the individual binding energies of 16S rRNA nucleotides with the experimental tests that determine the minimum inhibitory concentration (MIC) of hygB, it is believed that those residues with high binding values generated bacterial resistance to the drug when mutated. With the same reasoning, since those with low interaction energy do not influence effectively the affinity of the hygB in its binding site, there is no loss of effectiveness if they were replaced.

Estudo in silico da interação da albumina de soro humano com o ibuprofeno

Currently, computational methods have been increasingly used to aid in the characterization of molecular biological systems, especially when they relevant to human health. Ibuprofen is a nonsteroidal antiinflammatory or broadband use in the clinic. Once in the bloodstream, most of ibuprofen is linked to human serum albumin, the major protein of blood plasma, decreasing its bioavailability and requiring larger doses to produce its antiinflamatory action. This study aimes to characterize, through the interaction energy, how is the binding of ibuprofen to albumin and to establish what are the main amino acids and molecular interactions involved in the process. For this purpouse, it was conducted an in silico study, by using quantum mechanical calculations based on Density Functional Theory (DFT), with Generalized Gradient approximation (GGA) to describe the effects of exchange and correlation. The interaction energy of each amino acid belonging to the binding site to the ligand was calculated the using the method of molecular fragmentation with conjugated caps (MFCC). Besides energy, we calculated the distances, types of molecular interactions and atomic groups involved. The theoretical models used were satisfactory and show a more accurate description when the dielectric constant ε = 40 was used. The findings corroborate the literature in which the Sudlow site I (I-FA3) is the primary binding site and the site I-FA6 as secondary site. However, it differs in identifying the most important amino acids, which by interaction energy, in order of decreasing energy, are: Arg410, Lys414, Ser 489, Leu453 and Tyr411 to the I-Site FA3 and Leu481, Ser480, Lys351, Val482 and Arg209 to the site I-FA6. The quantification of interaction energy and description of the most important amino acids opens new avenues for studies aiming at manipulating the structure of ibuprofen, in order to decrease its interaction with albumin, and consequently increase its distribution

Molecular and morphological characterization of bis benzimidazo perylene films and surface-enhanced phenomena

Thin solid films of bis benzimidazo perylene (AzoPTCD) were fabricated using physical vapor deposition (PVD) technique. Thermal stability and integrity of the AzoPTCD PVD films during the fabrication (similar to 400 degrees C at 10(-6) Torr) were monitored by Raman scattering. Complementary thermogravimetric results showed that thermal degradation of AzoPTCD occurs at 675 degrees C. The growth of the PVD films was established through UV-vis absorption spectroscopy, and the surface morphology was surveyed by atomic force microscopy (AFM) as a function of the mass thickness. The AzoPTCD molecular organization in these PVD films was determined using the selection rules of infrared absorption spectroscopy (transmission and reflection-absorption modes). Despite the molecular packing, X-ray diffraction revealed that the PVD films are amorphous. Theoretical calculations (density functional theory, B3LYP) were used to assign the vibrational modes in the infrared and Raman spectra. Metallic nanostructures, able to sustain localized surface plasmons (LSP) were used to achieve surface-enhanced resonance Raman scattering (SERRS) and surface-enhanced fluorescence (SEF).

Cálculos AB initio de propriedades estruturais, eletrônicas e ópticas de colmpostos CaXo3 (X=Si, Ge, Sn)

In this work we present a study of structural, electronic and optical properties, at ambient conditions, of CaSiO3, CaGeO3 and CaSnO3 crystals, all of them a member of Ca-perovskite class. To each one, we have performed density functional theory ab initio calculations within LDA and GGA approximations of the structural parameters, geometry optimization, unit cell volume, density, angles and interatomic length, band structure, carriers effective masses, total and partial density of states, dielectric function, refractive index, optical absorption, reflectivity, optical conductivity and loss function. A result comparative procedure was done between LDA and GGA calculations, a exception to CaSiO3 where only LDA calculation was performed, due high computational cost that its low symmetry crystalline structure imposed. The Ca-perovskite bibliography have shown the absence of electronic structure calculations about this materials, justifying the present work

Sistemas Nanoestruturados: Heteroestruturas Quasi-Periódicas de Nitretos e Cálculos Ab initio em Polimorfos CaCO3

The physical properties and the excitations spectrum in oxides and semiconductors materials are presented in this work, whose the first part presents a study on the confinement of optical phonons in artificial systems based on III-V nitrides, grown in periodic and quasiperiodic forms. The second part of this work describes the Ab initio calculations which were carried out to obtain the optoeletronic properties of Calcium Oxide (CaO) and Calcium Carbonate (CaCO3) crystals. For periodic and quasi-periodic superlattices, we present some dynamical properties related to confined optical phonons (bulk and surface), obtained through simple theories, such as the dielectric continuous model, and using techniques such as the transfer-matrix method. The localization character of confined optical phonon modes, the magnitude of the bands in the spectrum and the power laws of these structures are presented as functions of the generation number of sequence. The ab initio calculations have been carried out using the CASTEP software (Cambridge Total Sequential Energy Package), and they were based on ultrasoft-like pseudopotentials and Density Functional Theory (DFT). Two di®erent geometry optimizations have been e®ectuated for CaO crystals and CaCO3 polymorphs, according to LDA (local density approximation) and GGA (generalized gradient approximation) approaches, determining several properties, e. g. lattice parameters, bond length, electrons density, energy band structures, electrons density of states, e®ective masses and optical properties, such as dielectric constant, absorption, re°ectivity, conductivity and refractive index. Those results were employed to investigate the confinement of excitons in spherical Si@CaCO3 and CaCO3@SiO2 quantum dots and in calcium carbonate nanoparticles, and were also employed in investigations of the photoluminescence spectra of CaCO3 crystal

Structural and Electronic Effects of Incorporating Mn in TiO2 Films Grown by Sputtering: Anatase versus Rutile

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Optical Behavior of Conjugated Pt-Containing Polymetallaynes Exposed to Gamma-Ray Radiation Doses

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evaluation of Bulk and Surfaces Absorption Edge Energy of Sol-Gel-Dip-Coating SnO2 Thin Films

The absorption edge and the bandgap transition of sol-gel-dip-coating SnO2 thin films, deposited on quartz substrates, are evaluated from optical absorption data and temperature dependent photoconductivity spectra. Structural properties of these films help the interpretation of bandgap transition nature, since the obtained nanosized dimensions of crystallites are determinant on dominant growth direction and, thus, absorption energy. Electronic properties of the bulk and (110) and (101) surfaces are also presented, calculated by means of density functional theory applied to periodic calculations at B3LYP hybrid functional level. Experimentally obtained absorption edge is compared to the calculated energy band diagrams of bulk and (110) and (101) surfaces. The overall calculated electronic properties in conjunction with structural and electro-optical experimental data suggest that the nature of the bandgap transition is related to a combined effect of bulk and (101) surface, which presents direct bandgap transition.