Local Chemical Activity Research Articles

Synthesis, single crystal X-ray, Hirshfeld surface analysis and DFT calculation based NBO, HOMO-LUMO, MEP, ECT and molecular docking analysis of N'-[(2,6-dichlorophenyl)methylidene]-2-{[3-(trifluoromethyl)phenyl]amino}benzohydrazide

A new Schiff base compound of N'-[(2,6-dichlorophenyl)methylidene]-2-{[3-(trifluoromethyl)phenyl]amino}benzohydrazide was synthesized and characterized through various spectroscopic techniques, including infrared, 1H NMR, 13C NMR spectroscopy and X–ray diffraction. Experimental results collected by XRD were compared with theoretical results obtained from Density functional theory method. Hirshfeld surface analysis was used to obtain three dimension molecular surface and two dimension fingerprint plots to illustrate the intermolecular bonding. Theoretical calculations provide valuable insights into both global and local chemical activity, as well as the properties of molecules and chemicals, including their nucleophilic and electrophilic nature. The DFT method at B3LYP/6–311++G (d,p) basis set was employed to study the optimized structure and geometric parameters, as well as to explore the frontier molecular orbitals, global reactive parameters, Mullikan population analaysis, Natural bond orbital and molecular electrostatic potential characteristics which cannot be obtained by experimental methods. Additionally, electrophilicity based charge transfer study was carried out with DNA bases to determine the direction of charge transfer. Finally, an investigation was carried out using molecular docking analysis to examine the binding energies of the title compound with PDB ID: 2QDJ protein target. The analysis yielded significant insights into the possible interactions, offering valuable findings in the process.

Microfluidic Bi-Layer Platform to Study Functional Interaction between Co-Cultured Neural Networks with Unidirectional Synaptic Connectivity

The complex synaptic connectivity architecture of neuronal networks underlies cognition and brain function. However, studying the spiking activity propagation and processing in heterogeneous networks in vivo poses significant challenges. In this study, we present a novel two-layer PDMS chip that facilitates the culturing and examination of the functional interaction of two interconnected neural networks. We utilized cultures of hippocampal neurons grown in a two-chamber microfluidic chip combined with a microelectrode array. The asymmetric configuration of the microchannels between the chambers ensured the growth of axons predominantly in one direction from the Source chamber to the Target chamber, forming two neuronal networks with unidirectional synaptic connectivity. We showed that the local application of tetrodotoxin (TTX) to the Source network did not alter the spiking rate in the Target network. The results indicate that stable network activity in the Target network was maintained for at least 1–3 h after TTX application, demonstrating the feasibility of local chemical activity modulation and the influence of electrical activity from one network on the other. Additionally, suppression of synaptic activity in the Source network by the application of CPP and CNQX reorganized spatio-temporal characteristics of spontaneous and stimulus-evoked spiking activity in the Target network. The proposed methodology and results provide a more in-depth examination of the network-level functional interaction between neural circuits with heterogeneous synaptic connectivity.

Spectroscopic, molecular structure, electronic, Hirshfeld surface, molecular docking, and thermodynamic investigations of trans-4-hydroxy-L-proline by DFT method

In present study, title compound Trans-4-Hydroxy-L-Proline is investigated theoretically and experimentally by FT-IR, NMR and UV–Vis spectra. The theoretical optimized geometrical parameters, vibrational analysis were performed by Density Functional Theory (DFT) with the B3LYP method at 6-311++G(d,p) basis set. Hirshfeld surface analysis has been performed and studied the nature of intermolecular interactions within the crystal structure via 3D and 2D surfaces, and demonstrated the H-bonding with close contacts in crystal via dnorm surface. Local chemical activity was studied via molecular electrostatic potential (MEP) and analyzed the reactive areas of the titled molecule, and local chemical reactivity was studied by population analysis and Fukui function analysis. FMOs investigation given various chemical activity parameters like- chemical hardness, chemical softness and electrophilicity index. NLO has been performed and analyzed the hyperpolarizability value and polarity of molecule. Natural Bond Orbital (NBO) analysis was carried out, reporting the hybridization of atoms that form bonds. The charge transfer of title molecule have been examined by TD-DFT method. The compound was docked with (A) 1TKZ, (B) 4WKE, (C) 5KK7, (D) 5OSC, (E) 6B6G, (F) 6HSN, and (G) 6YW0 Protein receptors to find the best ligand–protein interactions, the best and lowest binding energy obtained was −5.4 Kcal/mol. Drug likeness was also performed on titled molecule and its different derivatives for the confirmation of drug-like character of titled molecule.

Novel methoxyquinoline derivative: Synthesis, characterization, crystal structure, Hirshfeld surface, thermodynamic properties, and quantum chemical calculation of 3,6,8-trimethoxyquinoline

In this study, we describe the synthesis and structural characterization of novel 3,6,8-trimethoxyquinoline (2) by X-ray, FT-IR, NMR analysis, and its computational investigations. The molecular geometry of title coumpound was also optimized by using density functional theory (DFT/B3LYP) and Hartree–Fock (HF) methods with the 6-311 G(d,p) basis set, and geometric parameters were compared with the experimental data. Theoretical calculations are a good way for obtaining comprehensive information about global and local chemical activity, and chemical and molecular properties that reveal the nucleophilic and electrophilic nature. Molecular electrostatic potential (MEP) distribution, thermodynamic parameters, frontier molecular orbitals (FMOs), Fukui functions, and net charge analysis of (2) were also investigated. Also, the interactions between the molecule with DNA bases such as guanine, adenine, thymine, and cytosine were investigated by using the electrophilicity-based charge transfer (ECT) method and charge transfer (ΔN) for investigating the charge transfer, electrophilic, and nucleophilic nature.

Çinko(II)–Sulfatiyazol-Dietilentriamin Kompleksinin Hesaplamalı Kimya Yöntemi ile Spektroskopik Özelliklerinin İncelenmesi: Moleküler Modelleme Çalışması

ışını kırınım deneyi ve spektroskopik özellikleri incelenen yapının kuramsal hesaplamaları DFT, B3LYP ve LanL2DZ baz seti kullanılarak hesaplanmıştır. Optimize yapının ve X-ışını kırınımı sonucunda elde dilen deneysel yapının geometrik parametreleri oldukça uyumludur. Sulfatiyazol ligantı ise DFT/B3LYP/6-311G baz seti kullanılarak hesaplanmıştır. Kompleksin en kararlı hali elde edildikten sonra HOMO ve LUMO enerjilerinden lokal ve global kimyasal aktiviteleri belirlenmiştir. Moleküller arası etkileşimlerin % katkısı, parmak izi tayini ve toplam yüzey haritaları Hirshfeld yüzey analizi yöntemi ile incelenmiştir. Öncü moleküler orbitaller olan HOMO ve LUMO enerjileri kullanılarak hesaplanan sertlik ve yumuşaklık parametreleri ile global kimyasal aktiviteleri belirlenmiştir ve Mulliken popülasyon analizi ve moleküler elektrostatik potansiyel ile lokal kimyasal aktivite verileri elde edilmiştir. Böylece yapının elektrofilik ve nükleofilik indeksi belirlenmektedir. Ayrıca daha önce Öztürk tarafından sentezlenen Zn-stz komleksin teorik IR değerleri deneysel sonuçları ile karşılaştırılmıştır.

X–ray diffraction, Hirshfeld surface, local and global chemical activity studies of a Bis{(E)-2,4-di-tert-butyl-6-((3-iodo-4-methylphenylimino)methyl)phenolato-N,O-}copper(II) complex

Cu(II) complex of (BINO)Cu, (E)-2,4-di-tert-butyl-6-((3-iodo-4-methylphenylimino)methyl)phenol, has been synthesized and characterized by FT-IR, UV–Vis and X–ray diffraction techniques. The (BINO)Cu complex crystallizes in the triclinic space group P-1 with a = 14.0545 (5) Å, b = 18.5744 (8) Å, c = 20.0541 (7) Å, α = 93.317 (3)°, β = 109.053 (3)°, ɣ = 95.229 (3)°, Z = 4 and Z’ = 2, the asymmetric unit contains 2 molecules. X–ray diffraction technique results showed that title complex is in a distorted square environment with τ=0.0436. Also, Hirshfeld surface (HS) analysis is carried out to understand the molecular interactions (fingerprint plots) and molecular surface contours. The close contacts of H⋯H/H⋯H (61.9%) and Cl⋯H/H⋯Cl (15.8%) shows a largest portion of total HS. Optimization of the title molecule was studied using B3LYP and M05–2X functionals in DFT method at the LANL2DZ basis set. Theoretical calculations is a good way for obtaining detailed information about local and global chemical activity, molecular and chemical properties which are reveal the electrophilic and nucleophilic nature. According to local chemical activity results (MEP, Fukui function and net charge analyses), the optimized structure shows more electrophilic nature than nucleophilic one. Optimized structure is a soft molecule (η=1.689 eV for spin α and η = 1.131eV for spin β and s = 0.296 eV-1 for spin α and s = 0.442 eV-1 for spin β) so it shows very high chemical reactivity, low kinetic stability and displays higher intramolecular charge transfer. The stability of the molecule arising from hyperconjugative interactions, charge delocalization was analyzed by using natural bond orbital analysis (NBO).

Atomic-Scale Charge Distribution Mapping of Single Substitutional p- and n-Type Dopants in Graphene

Tuning the chemical properties of graphene by controlled doping is a widely investigated strategy. The effect of substitutional single dopant on graphene local reactivity is much less explored. To improve understanding of the role of p- and n-type dopants in graphene’s local chemical activity and quantification of its interaction with single molecules we report an atomic-scale investigation of single boron (B) and nitrogen (N) dopants in graphene and their interaction with a CO molecule by means of atomic force microscopy (AFM), Kelvin probe force microscopy (KPFM) experiments and theoretical calculations. We report an atomic-scale investigation of single boron (B) and nitrogen (N) dopants in graphene and their interaction with a CO molecule by means of atomic force microscopy (AFM), Kelvin probe force microscopy (KPFM) experiments and theoretical calculations. We infer that N/B doping significantly increases/lowers the chemical interaction of graphene with individual CO molecule as a result of weak elect...

Thermostatics of Concentration Polarization and the Possible Effects of Surface Ad-Ions in SOFC Composite Cathodes

In situations common to high-temperature SOFC (Solid-Oxide Fuel Cell) operation at steady-state, the dependence of the activity of oxide ions on the oxygen partial pressure (p_O2) becomes relatively unimportant for p_O2>0.15 bar. Nevertheless, one might question what would be the indirect effect (if any) of surface ad-ions on the evaluation of concentration polarization due to changes on the oxygen partial pressure near to the grain boundary between electronic, ionic, and gas phases. From thermostatics considerations and macroscale-continuum phenomenological equations it is shown that the definition of concentration polarization, as commonly found in the literature, may contain a series of limitations and, among these limitations, it is discussed the relative importance of oxygen surface ad-ions on the formation of concentration cells,when it is compared to the concentration gradients of “bulk” gas species in the porous channels of SOFC cathodes. This theoretical discussion about the influence of contact chemistry near the TPB (three-phase boundary) region indicates that concentration polarization could in fact either increase or decrease, depending on whether the chemical activity of oxide ions is affected by the local chemical activity of O2 near the gas/solid interface. In order to verify this, one needs to know how the differences of interfacial potential step and chemical activity relate to changes in the contact chemistry and space charge zone near this interface. Particularly, the evaluation of the potential step between the electronic conductor and the ion adsorbed layer requires the prescription of certain phenomenological parameters. In the present study, one of these parameters is the density of “active” surface sites near the TPB region, which represents just a fraction of the total surface site density available over the entire electrode phase. It is a fraction because only those sites sufficiently close to the TPB “hot spot” are considered “active” for the adsorption of charged species, which are then subsequently able to undergo electrochemical reduction at the TPB. So to calculate this density of “active” surface sites and thus the corresponding electrostatic potential step, a phenomenological governing equation for oxygen ad-ions on the electrode surface is proposed (i.e., in terms of surface coverage of ad-ions) to account for electrocatalytic and interfacial transport processes (i.e., competing surface diffusion and adsorption processes near the TPB “hot spot”) within a composite porous cathode.

Nanofabrication of the gold scanning probe for the STM-SECM coupling system with nanoscale spatial resolution

Scanning probe is the key issue for the electrochemical scanning probe techniques (EC-SPM) such as EC-scanning tunnel microscopy (STM), EC-atomic force microscopy (AFM) and scanning electrochemical microscopy (SECM), especially the insulative encapsulation of the nanoelectrode probe for both positioning and electrochemical feedbacks. To solve this problem, we develop a novel fabrication method of the gold nanoelectrodes: firstly, a micropipette with nanomter-sized orifice was prepared as the template by a laser puller; secondly, the inside wall of micropipette apex was blocked by compact and conic Au nano-piece through electroless plating; thirdly, the Au nano-piece was grown by bipolar electroplating and connected with a silver wire as a current collector. The fabricated Au nanoelectrode has very good voltammetric responses for the electrodic processes of both mass transfer and adsorption. The advantage lies in that it is well encapsulated by a thin glass sealing layer with a RG value lowered to 1.3, which makes it qualified in the SECM-STM coupling mode. On one hand, it can serve as STM tip for positioning which ensures the high spatial resolution; on the other hand, it is a high-quality nanoelectrode to explore the local chemical activity of the substrate. The nanofabrication method may promote the SPM techniques to obtain simultaneously the physical and chemical images with nanoscale spatial resolution, which opens a new approach to tip chemistry in electrochemical nanocatalysis and tip-enhanced spectroscopy.

A model of chemical etching of olivine in the vicinity of the trajectory of a swift heavy ion

Searching of superheavy elements, the charge spectra of heavy nuclei in Galactic Cosmic Rays was investigated within the OLYMPIA experiment using the database of etched ion tracks in meteorite olivine. Etching results in the formation of hollow syringe-like channels with diameters of 1–10μm along the trajectories of these swift heavy ions (SHI). According to the activated complex theory, the local chemical activity is determined by an increase of the specific Gibbs energy of the lattice stimulated by structure transformations, long-range elastic fields, and interatomic bonds breaking generated in the vicinity of the ion trajectory. To determine the dependencies of the Gibbs free energy increase in SHI tracks in olivine on the mass, energy and charge of a projectile, we apply a multiscale model of excitation and relaxation of materials in the vicinity of the SHI trajectory (SHI tracks). Effect of spreading of fast electrons from the ion trajectory causing neutralization of metallic atoms resulting in an increase of the chemical activity of olivine at long distances from the ion trajectory (up to 5μm) is estimated and discussed.

Monolayer Graphene and h-BN on Metal Substrates as Versatile Templates for Metallic Nanoclusters

A well-ordered and active support would be very valuable for tailoring nanoclusters and molecular self-assembly to achieve size-dependent chemical properties. Graphene and h-BN nanomesh on metal surfaces have been recently considered as successful candidates to this end by displaying periodic corrugated topography. However, the fundamental link between the topographic buckling and the growth modes of transition-metal (TM) or organic superstructures remains elusive. By investigating by means of extensive DFT calculations, the structure of monolayer graphene (MLG) on Rh(111) and Ru(0001) and h-BN on a Ru(0001) surface and comparing the local chemical activity, we show that these supports provide different template functionalities ranging from zero-dimensional clusters to a two-dimensional network for adsorbates. For a wide range of TMs, we find that the TM–MLG interaction controls the morphology of TM clusters on MLG/Ru, which qualifies as a versatile template for tuning metallic growth.

A new AC-SECM mode: On the way to high-resolution local impedance measurements in SECM

Scanning electrochemical microscopy (SECM) is frequently employed to detect local chemical activity of inhomogeneous samples. Here, a modified AC-SECM mode is proposed for detecting perturbations of concentration gradients of a redox couple and electric fields imposed by the local electrochemical activity of the sample while simultaneously recording the overall impedance of the sample. The method is based on an alternating current-perturbation of the sample while recording the local alternate potential of the positioned SECM tip. The low frequency part is predominantly determined by the spatial changes in the electrochemical activity of the sample. The proposed method is intrinsically not limited by the tip size and is hence able to substantially increase the resolution of local impedance measurements.

Chemical activity induces dynamical force with global structure in a reaction-diffusion-convection system

We found a rotating global structure induced by the dynamical force of local chemical activity in a thin solution layer of excitable Belousov-Zhabotinsky reaction coupled with diffusion. The surface flow and deformation associated with chemical spiral waves (wavelength about 1 mm) represents a global unidirectional structure and a global tilt in the entire Petri dish (100 mm in diameter), respectively. For these observations, we scanned the condition of hierarchal pattern selection. From this result, the bromomalonic acid has an important role to induce the rotating global structure. An interaction between a reaction-diffusion process and a surface-tension-driven effect leads to such hierarchal pattern with different scales.

Visualization of local electrochemical activity and local nickel ion release on laser-welded NiTi/steel joints using combined alternating current mode and stripping mode SECM

Smoothly polished cross-sections of laser-fabricated welds between NiTi shape memory alloy and stainless steel (SS) microwires of approximately the same diameter and, for comparison, between identical stainless steel or NiTi wires have been subjected to local chemical activity and nickel release measurements using scanning electrochemical microscopy (SECM). In the alternating current mode (AC-SECM), the measurements detected clear differences in the local interfacial chemical activity of the passivated weld and the base metals only for the heterogeneous joints of the type NiTi-SS. In this case the local electrochemical acvtivity was lower above the weld material. Subjecting cross-sections of NiTi-SS to stripping mode SECM (SM-SECM), higher Ni(2+) concentrations were measured above the regions of the parental NiTi wire, which correlates well with the results from AC-SECM imaging which showed this region as being less passivated. An energy-dispersive elemental analysis of the specimen in a scanning electron microscope revealed the coexistence of Ti and Cr in the weld mass. Possibly, a joint action of these two metals in terms of protective oxide formation is better for passivation of the weld region than the individual action of one or the other element for passivating the original wires. Better passivation of course led to decreased electrochemical activity of the weld surface. Apparently, AC- and SM-mode SECM imaging were sufficiently sensitive to detect and visualize the impact of the changed surface passivation upon laser welding.

Monoamine oxidase, an intracellular probe of oxygen pressure in isolated cardiac myocytes.

The activity of monamine oxidase, an enzyme located almost exclusively at the outer mitochondrial membrane, toward the substrate phenylethylamine is used to report the oxygen pressure at the outer mitochondrial membrane of intact cardiac myocytes isolated from hearts of adult rats. The rate of substrate oxidation, under the conditions used, follows the Michaelis-Menten relation, and accordingly can be used as a measure of the local chemical activity of dissolved oxygen. The oxygen pressure at the outer mitochondrial membrane of myocytes, at rest and after 2- to 3-fold stimulation of respiratory oxygen consumption, differs from the extracellular oxygen pressure by at most 2 torr. This implies that most of the large, about 20 torr, difference in oxygen pressure between capillary lumen and mitochondria of the working heart must be extracellular. At physiologically relevant concentrations of the substrates phenylethylamine and norepinephrine, monoamine oxidase activity is relatively insensitive to extracellular oxygen pressure in the range 155 to 8 torr, suggesting a limited role for regulation of biogenic amine oxidation by oxygen availability.

On Diffusion Flames in Turbulent Shear Flows: Modeling Reactant Consumption in a Circular Fuel Jet

The turbulent portion of the circular fuel jet is analyzed for isobaric subsonic flow under fast direct one-step irreversible reaction between unpremixed fuel and oxidant. Mean spatial profiles for the dependent variables are found numerically from the governing nonlinear partial differential equations, based upon an explicit eddy diffusion and upon a mean rate of reactant consumption proportional to the product of the mean mass fraction of fuel, the mean mass fraction of oxidant, and the appropriate local characterization of the mean rate of strain. Experimental results are employed to evaluate the pertinent constants in the theoretical formulation of the model. I. Introduction T HE structure of the turbulent diffusion flame in the circular fuel-jet geometry is studied theoretically. As such, this represents an extension of the work by Bush, Feldman, and Fendell on the structure of turbulent diffusion flames in the planar fuel-jet1 and in the planar mixing-layer2 geometries. In this present paper, as in these previous papers, the emphasis is on the solution of a model formulation of the boundary-value problem for a turbulent diffusion flame in a flow geometry of practical interest, when the model is based upon the premise that the consumption of reactants and the generation of product(s) and chemical exothermicity are controlled by unsteady, inviscid, inertial, large-scale mixing. In this model, in time-average, for a direct one-step irreversible bimolecular chemical reaction, the mean rate of reactant consumption is taken to be related to the product of the mean mass fraction of oxidant, the mean mass fraction of fuel, and the magnitude of the principal mean strain rate (for the parabolic formulation appropriate for the thin shear layers of interest here). It is argued (as in Refs. 1 and 2) that, in general, the magnitude of the principal mean strain rate furnishes a characteristic frequency for the mean rate of local chemical activity in a turbulent diffusion flame in which macroscopic mixing is rate-controll ing. This explicit local algebraic (as opposed to field-type differential) expression adopted for the mean rate of chemical reaction is compatible with the adoption of an explicit local algebraic (eddy viscosity) expression for the mean rate of diffusive transport. The present model was first studied in detail for the planar mixing layer formed by two parallel streams.2 However, whereas the fully developed mixing layer is tractable for analysts, it is not tractable for experimentalists and, therefore, some empirical constants in the theory remained unassigned for lack of data. Experimentalists38 have treated the fuel jet exhausting into an oxidant-conta ining ambient, and, under the assumption that values for empirical factors may be transferable between geometries, solutions were