• Journal of the Korean Chemical Society
• /
• v.64 no.6
• /
• pp.350-353
• /
• 2020

The validity of the calculation method based on the local mode in hydrogen-bonded water molecules was investigated by comparing the frequencies of the local and normal modes of OH stretching vibration in water molecules. By calculating a monomer, dimer, and trimer of water molecules using a quantum chemical ab initio theory, we examined how the frequencies of the local and normal modes and the anharmonicity of local modes vary with molecular cluster size. It was shown that, as the number of molecules increases from monomer to trimer, the anharmonicity of OH bonds increases and the difference between local and normal mode frequencies decreases. This confirms that local-mode-based calculations that can easily handle the anharmonicity can be appropriate for the calculation of the OH stretching frequency of water molecules in the condensed phase.

• Genomics & Informatics
• /
• v.20 no.3
• /
• pp.33.1-33.17
• /
• 2022

Nervous necrosis virus (NNV) is a deadly infectious disease that affects several fish species. It has been found that the NNV utilizes grouper heat shock cognate protein 70 (GHSC70) to enter the host cell. Thus, blocking the virus entry by targeting the responsible protein can protect the fishes from disease. The main objective of the study was to evaluate the inhibitory potentiality of 70 compounds of Azadirachta indica (Neem plant) which has been reported to show potential antiviral activity against various pathogens, but activity against the NNV has not yet been reported. The binding affinity of 70 compounds was calculated against the GHSC70 with the docking and molecular dynamics (MD) simulation approaches. Both the docking and MD methods predict 4 (PubChem CID: 14492795, 10134, 5280863, and 11119228) inhibitory compounds that bind strongly with the GHSC70 protein with a binding affinity of -9.7, -9.5, -9.1, and -9.0 kcal/mol, respectively. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the compounds confirmed the drug-likeness properties. As a result of the investigation, it may be inferred that Neem plant compounds may act as significant inhibitors of viral entry into the host cell. More in-vitro testing is needed to establish their effectiveness.

• Molecules and Cells
• /
• v.46 no.8
• /
• pp.513-525
• /
• 2023

Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (GlOCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.

• Journal of Electrochemical Science and Technology
• /
• v.13 no.2
• /
• pp.237-253
• /
• 2022

The methyl 2-(1,3-dithietan -2- ylidene)-3-oxobutanoate (MDYO) and 2-(1,3-dithietan-2-ylidene) cyclohexane -1,3-dione (DYCD) were synthesized and tested at various concentrations as corrosion inhibitors for 316L stainless steel in 1 M HCl using weight loss, electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), surface analysis techniques (SEM / EDX and Raman spectroscopy) and Functional Density Theory (DFT) was also used to calculate quantum parameters. The obtained results indicated that the inhibition efficiency of MDYO and DYCD increases with their concentration, and the highest value of corrosion inhibition efficiency was determined in the range of concentrations investigated (0.01 × 10^-3 - 10^-3 M). Polarization curves (Tafel extrapolation) showed that both compounds act as mixed-type inhibitors in 1M HCl solutions. Electrochemical impedance spectra (Nyquist plots) are characterized by a capacitive loop observed at high frequencies, and another small inductive loop near low frequencies. The thermodynamic data of adsorption of the two compounds on the stainless steel surface and the activation energies were determined and then discussed. Analysis of experimental results shows that MDYO and DYCD inhibitors adsorb to the metal surface according to the Langmuir model and the mechanism of adsorption of both inhibitors involves physisorption. SEM-EDX results confirm the existence of an inhibitor protective film on the stainless steel surface. The results derived from theoretical calculations supported the experimental observation.

• Journal of the Mineralogical Society of Korea
• /
• v.27 no.1
• /
• pp.1-15
• /
• 2014

Probing the electronic structures of crystalline Mg-silicates at high pressure is essential for understanding the various macroscopic properties of mantle materials in Earth's interior. Quantum chemical calculations based on the density functional theory are used to explore the atomic configuration and electronic structures of Earth materials at high pressure. Here, we calculate the partial density of states (PDOS) and O K-edge energy-loss near-edge structure (ELNES) spectra for $MgSiO_3$ perovskite at 25 GPa and 120 GPa using the WIEN2k program based on the full-potential linearized projected augmented wave (FP-LPAW) method. The calculated PDOS and O K-edge ELNES spectra for $MgSiO_3$ Pv show significant pressure-induced changes in their characteristic spectral features and relative peak intensity. These changes in spectral features of $MgSiO_3$ Pv indicate that the pressure-induced changes in local atomic configuration around O atoms such as Si-O, O-O, and Mg-O length can induce the significant changes on the local electronic structures around O atoms. The result also indicates that the significant changes in O K-edge features can results from the topological densification at constant Si coordination number. This study can provide a unique opportunity to understand the atomistic origins of pressure-induced changes in local electronic structures of crystalline and amorphous $MgSiO_3$ at high pressure more systematically.

• Journal of Biomedical Engineering Research
• /
• v.25 no.4
• /
• pp.253-259
• /
• 2004

in this study, we developed a Monte Carlo imaging simulation code written by the visual C$\^$++/ programing language for design optimization of a digital X-ray imaging system. As a digital X-ray imaging system, we considered a Gd$_2$O$_2$S(Tb) scintillator and a photosensor array, and included a 2D parallel grid to simulate general test renditions. The interactions between X-ray beams and the system structure, the behavior of lights generated in the scintillator, and their collection in the photosensor array were simulated by using the Monte Carlo method. The scintillator thickness and the photosensor array pitch were assumed to 66$\mu\textrm{m}$ and 48$\mu\textrm{m}$, respertively, and the pixel format was set to 256 x 256. Using the code, we obtained X-ray images under various simulation conditions, and evaluated their image qualities through the calculations of SNR (signal-to-noise ratio), MTF (modulation transfer function), NPS (noise power spectrum), DQE (detective quantum efficiency). The image simulation code developed in this study can be applied effectively for a variety of digital X-ray imaging systems for their design optimization on various design parameters.

• Korean Journal of Mineralogy and Petrology
• /
• v.33 no.1
• /
• pp.1-10
• /
• 2020

The atomic structures of silicate liquids at high pressure provide insights into the transport properties including thermal conductivities or elemental partitioning behavior between rocks and magmas in Earth's interior. Whereas the local electronic structure around silicon may vary with the arrangement of the nearby oxygens, the detailed nature of such relationship remains to be established. Here, we explored the atomic origin of the pressure-induced changes in the electronic structure around silicon by calculating the partial electronic density of states and L₃-edge X-ray absorption spectra of SiO₂ polymorphs. The result showed that the Si PDOS at the conduction band varies with the crystal structure and local atomic environments. Particularly, d-orbital showed the distinct features at 108 and 130 eV upon the changes in the coordination number of Si. Calculated Si XAS spectra showed features due to the s,d-orbitals at the conduction band and varied similarly with those observed in s,d-orbitals upon changes in the crystal structures. The calculated Si XAS spectrum for α-quartz was analogous to the experimental Si XRS spectrum for SiO₂ glass, implying the overall similarities in the local atomic environments around the Si. The edge energies at the center of gravity of XAS spectra were closely related to the Si-O distance, thus showing the systematic changes upon densification. Current results suggest that the Si L_2,3-edge XRS, sensitive probe of the Si-O distance, would be useful in unveiling the densification mechanism of silicate glasses and melts at high pressure.

• Journal of Astronomy and Space Sciences
• /
• v.36 no.1
• /
• pp.21-33
• /
• 2019

This paper focuses on the interpretation of radiation fluxes from active galactic nuclei. The advantage of positron annihilation spectroscopy over other methods of spectral diagnostics of active galactic nuclei (therefore AGN) is demonstrated. A relationship between regular and random components in both bolometric and spectral composition of fluxes of quanta and particles generated in AGN is found. We consider their diffuse component separately and also detect radiative feedback after the passage of high-velocity cosmic rays and hard quanta through gas-and-dust aggregates surrounding massive black holes in AGN. The motion of relativistic positrons and electrons in such complex systems produces secondary radiation throughout the whole investigated region of active galactic nuclei in form of cylinder with radius R= 400-1000 pc and height H=200-400 pc, thus causing their visible luminescence across all spectral bands. We obtain radiation and electron energy distribution functions depending on the spatial distribution of the investigated bulk of matter in AGN. Radiation luminescence of the non-central part of AGN is a response to the effects of particles and quanta falling from its center created by atoms, molecules and dust of its diffuse component. The cross-sections for the single-photon annihilation of positrons of different energies with atoms in these active galactic nuclei are determined. For the first time we use the data on the change in chemical composition due to spallation reactions induced by high-energy particles. We establish or define more accurately how the energies of the incident positron, emitted ${\gamma}-quantum$ and recoiling nucleus correlate with the atomic number and weight of the target nucleus. For light elements, we provide detailed tables of all indicated parameters. A new criterion is proposed, based on the use of the ratio of the fluxes of ${\gamma}-quanta$ formed in one- and two-photon annihilation of positrons in a diffuse medium. It is concluded that, as is the case in young supernova remnants, the two-photon annihilation tends to occur in solid-state grains as a result of active loss of kinetic energy of positrons due to ionisation down to thermal energy of free electrons. The single-photon annihilation of positrons manifests itself in the gas component of active galactic nuclei. Such annihilation occurs as interaction between positrons and K-shell electrons; hence, it is suitable for identification of the chemical state of substances comprising the gas component of the investigated media. Specific physical media producing high fluxes of positrons are discussed; it allowed a significant reduction in the number of reaction channels generating positrons. We estimate the brightness distribution in the ${\gamma}-ray$ spectra of the gas-and-dust media through which positron fluxes travel with the energy range similar to that recorded by the Payload for Antimatter Matter Exploration and Light-nuclei Astrophysics (PAMELA) research module. Based on the results of our calculations, we analyse the reasons for such a high power of positrons to penetrate through gas-and-dust aggregates. The energy loss of positrons by ionisation is compared to the production of secondary positrons by high-energy cosmic rays in order to determine the depth of their penetration into gas-and-dust aggregations clustered in active galactic nuclei. The relationship between the energy of ${\gamma}-quanta$ emitted upon the single-photon annihilation and the energy of incident electrons is established. The obtained cross sections for positron interactions with bound electrons of the diffuse component of the non-central, peripheral AGN regions allowed us to obtain new spectroscopic characteristics of the atoms involved in single-photon annihilation.