Shell-Isolated Nanoparticle-Enhanced Raman Spectroscopy for Probing Riboflavin on Graphene

Graphene research and technology development requires to reveal adsorption processes and understand how the defects change the physicochemical properties of the graphene-based systems. In this study, shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) and graphene-enhanced Raman spectroscopy (GERS) coupled with density functional theory (DFT) modeling were applied for probing the structure of riboflavin adsorbed on single-layer graphene substrate grown on copper. Intense and detailed vibrational signatures of the adsorbed riboflavin were revealed by SHINERS method. Based on DFT modeling and detected downshift of prominent riboflavin band at 1349 cm⁻¹ comparing with the solution Raman spectrum, π-stacking interaction between the adsorbate and graphene was confirmed. Different spectral patterns from graphene-riboflavin surface were revealed by SHINERS and GERS techniques. Contrary to GERS method, SHINERS spectra revealed not only ring stretching bands but also vibrational features associated with ribityl group of riboflavin and D-band of graphene. Based on DFT modeling it was suggested that activation of D-band took place due to riboflavin induced tilt and distortion of graphene plane. The ability to explore local perturbations by the SHINERS method was highlighted. We demonstrated that SHINERS spectroscopy has a great potential to probe adsorbed molecules at graphene.     

Energy Relaxation and Electron–Phonon Coupling in Laser-Excited Metals

The rate of energy transfer between electrons and phonons is investigated by a first-principles framework for electron temperatures up to Te = 50,000 K while considering the lattice at ground state. Two typical but differently complex metals are investigated: aluminum and copper. In order to reasonably take the electronic excitation effect into account, we adopt finite temperature density functional theory and linear response to determine the electron temperature-dependent Eliashberg function and electron density of states. Of the three branch-dependent electron–phonon coupling strengths, the longitudinal acoustic mode plays a dominant role in the electron–phonon coupling for aluminum for all temperatures considered here, but for copper it only dominates above an electron temperature of Te = 40,000 K. The second moment of the Eliashberg function and the electron phonon coupling constant at room temperature Te=315 K show good agreement with other results. For increasing electron temperatures, we show the limits of the T=0 approximation for the Eliashberg function. Our present work provides a rich perspective on the phonon dynamics and this will help to improve insight into the underlying mechanism of energy flow in ultra-fast laser–metal interaction.     

Gas-Sensing Properties of B/N-Modified SnS2 Monolayer to Greenhouse Gases (NH3, Cl2, and C2H2)

The adsorption capacity of intrinsic SnS₂ to NH₃, Cl₂ and C₂H₂ is very weak. However, non-metallic elements B and N have strong chemical activity, which can significantly improve the conductivity and gas sensitivity of SnS₂. Based on density functional theory, SnS₂ was modified with B and N atoms to analyze its adsorption mechanism and gas sensitivity for NH₃, Cl₂ and C₂H₂ gases. The optimal structure, adsorption energy, state density and frontier molecular orbital theory are analyzed, and the results are in good agreement with the experimental results. The results show that the adsorption of gas molecules is exothermic and spontaneous. Only the adsorption of NH₃ and Cl₂ on B-SnS₂ belongs to chemical adsorption, whereas other gas adsorption systems belong to physical adsorption. Moderate adsorption distance, large adsorption energy, charge transfer and frontier molecular orbital analysis show that gas adsorption leads to the change of the conductivity of the modified SnS₂ system. The adsorption capacity of B-SnS₂ to these gases is Cl₂ > NH₃ > C₂H₂. The adsorption capacity of N-SnS₂ is NH₃ > C₂H₂ > Cl₂. Therefore, according to different conductivity changes, B-SnS₂ and N-SnS₂ materials can be developed for greenhouse gas detection of gas sensors.     

Water Splitting on Multifaceted SrTiO3 Nanocrystals: Calculations of Raman Vibrational Spectrum

Various photocatalysts are being currently studied with the aim of increasing the photocatalytic efficiency of water splitting for production of hydrogen as a fuel and oxygen as a medical gas. A noticeable increase of hydrogen production was found recently experimentally on the anisotropic faces (facets) of strontium titanate (SrTiO₃, STO) nanoparticles. In order to identify optimal sites for water splitting, the first principles calculations of the Raman vibrational spectrum of the bulk and stepped (facet) surface of a thin STO film with adsorbed water derivatives were performed. According to our calculations, the Raman spectrum of a stepped STO surface differs from the bulk spectrum, which agrees with the experimental data. The characteristic vibrational frequencies for the chemisorption of water derivatives on the surface were identified. Moreover, it is also possible to distinguish between differently adsorbed hydrogen atoms of a split water molecule. Our approach helps to select the most efficient (size and shape) perovskite nanoparticles for efficient hydrogen/oxygen photocatalytic production.     

Effect of Boron Doping on the Interlayer Spacing of Graphite

Boron-doped graphite was prepared by the heat treatment of coke using B₄C powder as a graphitization catalyst to investigate the effects of the substitutional boron atoms on the interlayer spacing of graphite. Boron atoms can be successfully incorporated into the lattice of graphite by heat treatment, resulting in a reduction in the interlayer spacing of graphite to a value close to that of ideal graphite (0.3354 nm). With an increase in the catalyst mass ratio, the content of substituted boron in the samples increased significantly, causing a decrease in the interlayer spacing of the boron-doped graphite. Density functional theory calculations suggested that the effects of the substitutional boron atoms on the interlayer spacing of the graphite may be attributed to the transfer of Π electrons between layers, the increase in the electrostatic surface potential of the carbon layer due to the electron-deficient nature of boron atoms, and Poisson contraction along the c-axis.     

Electrochemical behavior of quercetin: Experimental and theoretical studies

Electrochemical oxidation of quercetin, as important biological molecule, has been studied in 0.1 M phosphate buffer solution, using cyclic voltammetry, chronoamperometry, rotating disk electrode voltammetry as well as quantum mechanical calculations. The heterogeneous charge transfer rate constant, k′, transfer coefficient, α, and exchange current density, j₀, for oxidation of quercetin at the glassy carbon electrode are determined as 4.84 × 10^?2 cm s^?1, 0.65 ± 0.01 and (1.17 ± 0.39) × 10^?7 A cm^?2, respectively. The formal potential, E^0′, of quercetin is pH dependent with a slope of ?60.1 mV per unit of pH which is close to the anticipated Nernstian value of ?59 mV for a two electrons and two protons process. The standard formal potential, E⁰, of quercetin was found to be equal with 558 mV versus saturated calomel electrode (SCE). The mechanism of oxidation was deduced from voltammetric data in various pHs and also in different concentrations of quercetin. The diffusion coefficient of quercetin was calculated as 3.18 × 10^?6 cm² s^?1 for the experimental condition, using chronoamperometric results. The results of density functional theory (DFT) calculations for the oxidation of quercetin in aqueous solution, are also presented. The theoretical standard electrode potential of quercetin is obtained to be 568 mV versus SCE, which is in good agreement with the experimental value. The discrepancy between theoretical and experimental values is only 10 mV. The agreement verifies the accuracy of experimental method and the validity of mathematical model.     

Theoretical investigation of a reported antibiotic from the “Miracle Tree” Moringa oleifera

Moringa oleifera, sometimes called the “Miracle Tree,” has received international attention for its potential to improve health in impoverished tropical areas. In addition to high vitamin content in the leaves and pods, the tree contains compounds with antioxidant and antibacterial properties. This study focused on the theoretical investigation of the suggested structure of one antibacterial compound, “pterygospermin,” whose existence was proposed after some studies of the roots of M. oleifera. The structure of pterygospermin was first proposed by a research group working in the 1950s, but later studies have not found evidence of this compound and have instead attributed the antibacterial properties of Moringa to isothiocyanates. In order to investigate the possible existence and properties of pterygospermin, extensive ab initio and DFT calculations were conducted, to determine the most favorable isomer of pterygospermin and examine plausible decomposition pathways. This study concludes that pterygospermin, as proposed, would not be stable enough to exist in ambient conditions.     

Research Article: Computer-Assisted Design of Pro-drugs for Antimalarial Atovaquone

Density Functional Theory (DFT) and ab initio calculation results for the proton transfer reaction in Kirby’s enzyme models 1 - 6 reveal that the reaction rate is largely dependent on the existence of a hydrogen bonding net in the reactants and the corresponding transition states. Further, the distance between the two reacting centers and the angle of the hydrogen bonding formed along the reaction path has profound effects on the rate. Hence, the study on the systems reported herein could provide a good basis for designing antimalarial (atovaquone) pro-drug systems that can be used to release the parent drug in a controlled manner. For example, based on the calculated log EM, the cleavage process for pro-drug 1Pro may be predicted to be about 10¹¹ times faster than that for a pro-drug 4Pro and about 10⁴ times faster than pro-drug 2Pro: rate _1Pro > rate _2Pro > rate _4Pro . Thus, the rate by which the pro-drug releases the antimalarial drug can be determined according to the nature of the linker (Kirby’s enzyme model 1 - 6 ).     

Novel computational study on π-stacking to understand mechanistic interactions of Tryptanthrin analogues with DNA

Based on recently published initial experimental results on the intercalation of a class of broad spectrum antiparasitic compounds, we present a purely theoretical approach for determining if these compounds may preferentially intercalate with guanosine/cytosine (GC)-rich or adenosine/thymidine (TA)-rich regions of DNA. The predictive model presented herein is based upon utilization of density functional theory (DFT) to determine a priori how the best intercalator may energetically and sterically interact with each of the nucleoside base pairs. A potential new method using electrostatic potential maps (EPMs) to visually select the best poses is introduced and compared to the existing brute-force center of mass (COM) approach. The EPM and COM predictions are in agreement with each other, but the EPM method is potentially much more efficient. We report that 4-azatryptantrin, the best intercalator, is predicted to favor π-stacking with GC over that of TA by approximately 2–4?kcal/mol. This represents a significant difference if one takes into account the Boltzmann distribution at physiological temperature. This theoretical method will be utilized to guide future experimental studies on the elucidation of possible mechanism(s) for the action of these antiparasitic compounds at the molecular level.