• Bulletin of the Korean Chemical Society
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• v.20 no.3
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• pp.285-290
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• 1999

In the present paper, we report a molecular dynamics (MD) simulation study for the structure and dynamics of H+ ions in non-rigid dehydrated H12-A zeolite framework at 298.15 K, using the same method we used in our previous studies of rigid and non-rigid zeolite-A frameworks. It is found that two different structures appear, depending on the choice of the Lennard-Jones parameter (σ) for the H+ ion, as is also observed in the study of rigid dehydrated H12-A zeolite framework, but the ranges of σ are different for the two structures. It is also found that some of the H+ ions exchanged their sites without changing the number of H+ ions at each site. The agreement between experimental and calculated structural parameters for non-rigid dehydrated H12-A zeolite is generally quite good. The calculated IR spectrum by Fourier transform of the total dipole moment auto-correlation function shows two major peaks, one around 2700 cm-1 and the other around 7000 cm-1. The former appears in the calculated IR spectra of non-rigid zeolite-A framework only system and the latter remains unexplained except, perhaps, as an indication of a new formation of a vibrational mode of the framework due to the adsorption of the H+ ions.

• Journal of the Mineralogical Society of Korea
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• v.24 no.4
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• pp.289-300
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• 2011

Atomistic origins of carbon solubility into silicates are essential to understand the effect of carbon on the properties of silicates and evolution of the Earth system through igneous and volcanic processes. Here, we investigate the atomic structure and NMR properties of dissolved carbon in enstatite using Raman spectroscopy and quantum chemical calculations. Raman spectrum for enstatite synthesized with 2.4. wt% of amorphous carbon at 1.5 GPa and $1,400^{\circ}C$ shows vibrational modes of enstatite, but does not show any vibrational modes of $CO_2$ or ${CO_3}^{2-}$. The result indicates low solubility of carbon into enstatite at a given pressure and temperature conditions. Because $^{13}C$ NMR chemical shift is sensitive to local atomic structure around carbon and we calculated $^{13}C$ NMR chemical shielding tensors for C substituted enstatite cluster as well as molecular $CO_2$ using quantum chemical calculations to give insights into $^{13}C$ NMR chemical shifts of carbon in enstatite. The result shows that $^{13}C$ NMR chemical shift of $CO_2$ is 125 ppm, consistent with previous studies. Calculated $^{13}C$ NMR chemical shift of C is ~254 ppm. The current calculation will alllow us to assign potential $^{13}C$ NMR spectra for the enstatite dissolved with carbon and thus may be useful in exploring the atomic environment of carbon.

• Animal Bioscience
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• v.37 no.8
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• pp.1398-1407
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• 2024

Objective: The objective of this study was to determine internal structure spectral profile of by-products from coffee processing that were affected by added-microorganism fermentation duration in relation to truly absorbed feed nutrient supply in ruminant system. Methods: The by-products from coffee processing were fermented using commercial fermentation product, consisting of various microorganisms: for 0 (control), 7, 14, 21, and 28 days. In this study, carbohydrate-related spectral profiles of coffee by-products were correlated with their chemical and nutritional properties (chemical composition, total digestible nutrient, bioenergy values, carbohydrate sub-fractions and predicted degradation and digestion parameters as well as milk value of feed). The vibrational spectra of coffee by-products samples after fermentation for 0 (control), 7, 14, 21, and 28 days were determined using a JASCO FT/IR-4200 spectroscopy coupled with accessory of attenuated total reflectance (ATR). The molecular spectral analyses with univariate approach were conducted with the OMNIC 7.3 software. Results: Molecular spectral analysis parameters in fermented and non-fermented by-products from coffee processing included structural carbohydrate, cellulosic compounds, non-structural carbohydrates, lignin compound, CH-bending, structural carbohydrate peak1, structural carbohydrate peak2, structural carbohydrate peak3, hemicellulosic compound, non-structural carbohydrate peak1, non-structural carbohydrate peak2, non-structural carbohydrate peak3. The study results show that added-microorganism fermentation induced chemical and nutritional changes of coffee by-products including carbohydrate chemical composition profiles, bioenergy value, feed milk value, carbohydrate subfractions, estimated degradable and undegradable fractions in the rumen, and intestinal digested nutrient supply in ruminant system. Conclusion: In conclusion, carbohydrate nutrition value changes by added-microorganism fermentation duration were in an agreement with the change of their spectral profile in the coffee by-products. The studies show that the vibrational ATR-FT/IR spectroscopic technique could be applied as a rapid analytical tool to evaluate fermented by-products and connect with truly digestible carbohydrate supply in ruminant system.

• Journal of Photoscience
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• v.9 no.2
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• pp.106-109
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• 2002

Archaeal rhodopsins possess retinal molecule as their chromophores, and their light-energy and light-signal conversions are triggered by all-trans to 13-cis isomerization of the retinal chromophore. Relaxation through structural changes of protein then leads to functional processes, proton pump in bacteriorhodopsin (bR) and transducer activation in phoborhodopsin (pR). It is known that sensory rhodopsins can pump protons in the absence of their transducers. Thus, there should be common and specific features in their protein structural changes for function. In this paper, our r ecent studies on pR from Natronobacterium pharaonis (ppR) by means of low-temperature Fourier-transform infrared (FTIR) spectroscopy are compared with those of bR. In particular, protein structural changes upon retinal photoisomerization are studied. Comparative investigation of ppR and bR revealed the similar structures of the polyene chain of the chromophore and water-containing hydrogen-bonding network, whereas the structural changes upon photoisomerization were more extended in ppR than in bR. Extended protein structural changes were clearly shown by the assignment of the C=O stretch of Asnl05. FTIR studies of a ppR mutant with the same retinal binding site as in bR revealed that the Schiff base region is important to determine their colors.

• Korean Journal of Materials Research
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• v.29 no.12
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• pp.741-746
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• 2019

New triple tungstate phosphors NaPbLa(WO₄)₃:Yb³⁺/Ho³⁺ (x = Yb³⁺/Ho³⁺ = 7, 8, 9, 10) are successfully fabricated by microwave assisted sol-gel synthesis and their structural and frequency upconversion (UC) characteristics are investigated. The compounds crystallized in the tetragonal space group I4₁/a and the NaPbLa(WO₄)₃ host have unit cell parameters a = 5.3927(1) and c = 11.7961(3) Å, V = 343.05(2) ų, Z = 4. Under excitation at 980 nm, the phosphors have yellowish green emissions, which are derived from the intense ⁵S₂/⁵F₄→⁵I₈ transitions of Ho³⁺ ions in the green spectral range and strong ⁵F₅→⁵I₈ transitions in the red spectral range. The optimal Yb³⁺:Ho³⁺ ratio is revealed to be x = 9, which is attributed to the quenching effect of Ho³⁺ ions, as indicated by the composition dependence. The UC characteristics are evaluated in detail under consideration of the pump power dependence and Commission Internationale de L'Eclairage chromaticity. The spectroscopic features of Raman spectra are discussed in terms of the superposition of Ho³⁺ luminescence and vibrational lines. The possibility of controlling the spectral distribution of UC luminescence by the chemical content of tungstate hosts is demonstrated.

• Journal of the Korean Chemical Society
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• v.48 no.3
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• pp.229-235
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• 2004

For the study of hydrogen bonding phenomenon of high energetic compounds, we have been carried out a theoretical calculations for the nitromethane with the program Gaussian-98. The calculations at levels of restricted BLYP/6-311++G(d,p), B3LYP/6-311++G(d,p) and MP2/6-311++G have been performed to obtain molecular structures, hydrogen bonding effects and vibrational spectra of nitromethane monomer and dimer. The results show nitromethane is favored to make two hydrogen bonds between molecules and the nitromethane dimer is more stable than the monomer about 15.2, 19.4 and 32.6 kJ/mol for the BLYP, B3LYP, and MP2 level calculations, respectively.

• Bulletin of the Korean Chemical Society
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• v.27 no.11
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• pp.1825-1831
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• 2006

The influence of solvent viscosity on conformational dynamics of the heme-pocket, a small vacant site near the binding site of myoglobin (Mb) and hemoglobin (Hb), and playing a functionally important role by serving as a station in ligand binding and escape, was studied by probing time-resolved vibrational spectra of CO photodissociated from MbCO and HbCO in $D_2O$, 75 wt% glycerol/$D_2O$, and trehalose at 283 K. Two absorption bands ($B_1$ and $B_2$) of the sample in viscous solvents, arising from CO in the heme pocket, are very similar to those in $D_2O$. Two bands in Mb and Hb under all three solvents exhibit very similar nonexponential spectral evolution ($B_1$ band; blue shifting and broadening, $B_2$ band; narrowing with a negligible shifting), suggesting that in the present experimental time window of 100 ps, the extents of the spectral shift and narrowing is much influenced neither by the viscosity of solvent nor by the quaternary contact of Hb. Spectral evolution can be described by a biexponential function with a fast universal time constant of 0.52 ps and a slow time constant ranging from 13 to 32 ps. For both proteins in all three solvents majority of spectral evolution occurs with the fast universal time constant. The magnitude of the slow rate in the spectral shift of B1 band decreases with increasing solvent viscosity, indicating that it is influenced by global conformational change which is retarded in viscous solvent, thereby serve as a reporter of global conformational change of heme proteins after deligation.

• Proceedings of the Korean Vacuum Society Conference
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• 2015.08a
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• pp.64-64
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• 2015

Control of plasma processing methodologies can only occur by obtaining a thorough understanding of the physical and chemical properties of plasmas. However, all plasma processes are currently used in the industry with an incomplete understanding of the coupled chemical and physical properties of the plasma involved. Thus, they are often 'non-predictive' and hence it is not possible to alter the manufacturing process without the risk of considerable product loss. Only a more comprehensive understanding of such processes will allow models of such plasmas to be constructed that in turn can be used to design the next generation of plasma reactors. Developing such models and gaining a detailed understanding of the physical and chemical mechanisms within plasma systems is intricately linked to our knowledge of the key interactions within the plasma and thus the status of the database for characterizing electron, ion and photon interactions with those atomic and molecular species within the plasma and knowledge of both the cross-sections and reaction rates for such collisions, both in the gaseous phase and on the surfaces of the plasma reactor. The compilation of databases required for understanding most plasmas remains inadequate. The spectroscopic database required for monitoring both technological and fusion plasmas and thence deriving fundamental quantities such as chemical composition, neutral, electron and ion temperatures is incomplete with several gaps in our knowledge of many molecular spectra, particularly for radicals and excited (vibrational and electronic) species. However, the compilation of fundamental atomic and molecular data required for such plasma databases is rarely a coherent, planned research program, instead it is a parasitic process. The plasma community is a rapacious user of atomic and molecular data but is increasingly faced with a deficit of data necessary to both interpret observations and build models that can be used to develop the next-generation plasma tools that will continue the scientific and technological progress of the late 20th and early 21st century. It is therefore necessary to both compile and curate the A&M data we do have and thence identify missing data needed by the plasma community (and other user communities). Such data may then be acquired using a mixture of benchmarking experiments and theoretical formalisms. However, equally important is the need for the scientific/technological community to recognize the need to support the value of such databases and the underlying fundamental A&M that populates them. This must be conveyed to funders who are currently attracted to more apparent high-profile projects.

• BMB Reports
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• v.38 no.2
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• pp.198-205
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• 2005

Resveratrol (RES) and genistein (GEN) are the dietary natural products known to possess chemopreventive property and also the ability to repair DNA damage induced by mutagens/carcinogens. It is believed that the therapeutic activity of these compounds could be primarily due to their interaction with nucleic acids but detailed reports are not available. We here explore the interaction of these drugs with nucleic acids considering DNA and RNA as a potential therapeutic target. The interaction of RES and GEN has been analysed in buffered solution with DNA [saline sodium citrate (SSC)] and RNA [tris ethylene diammine tetra acetic acid (TE)] using UV-absorption and Fourier transform infrared (FTIR) spectroscopy. The UV analysis revealed lesser binding affinity with nucleic acids at lower concentration of RES (P/D = 5.00 and 10.00), while at higher drug concentration (P/D = 0.75, 1.00 and 2.50) hyperchromic effect with shift in the ${\lambda}_{max}$ is noted for DNA and RNA. A major RES-nucleic acids complexes was observed through base pairs and phosphate backbone groups with K = $35.782\;M^{-1}$ and K = $34.25\;M^{-1}$ for DNA-RES and RNA-RES complexes respectively. At various concentrations of GEN (P/D = 0.25, 0.50, 0.75, 1.00 and 2.50) hyperchromicity with shift in the ${\lambda}_{max}$ from 260 $\rightarrow$ 263 om and 260 $\rightarrow$ 270 nm is observed for DNA-GEN and RNA-GEN complexes respectively. The binding constant (from UV analysis) for GEN-nucleic acids complexes could not be obtained due to GEN absorbance overlap with that of nucleic acids at 260 nm. Nevertheless a detailed analysis with regard to the interaction of these drugs (RES/GEN) with DNA and RNA could feasibly be understood by FTIR spectroscopy. The NH band of free DNA and RNA which appeared at $3550-3100\;cm^{-1}$ and $3650-2700\;cm^{-1}$ shifted to $3450-2950\;cm^{-1}$ and $3550-3000\;cm^{-1}$ in DNA-RES and RNA-RES complexes respectively. Similarly shifts corresponding to $3650-3100\;cm^{-1}$ and $3420-3000\;cm^{-1}$ have been observed in DNA-GEN and RNA-GEN complexes respectively. The observed reduction in NH band of free nucleic acids upon complexation of these drugs is an indication of the involvement of the hydroxyl (OH) and imino (NH) group during the interaction of the drugs and nucleic acids (DNA/RNA) through H-bonded formation. The interaction of RES and GEN with bases appears in the order of G $\geq$ T > C > A and A > C $\geq$ T > G. Further interaction of these natural compounds with DNA and RNA is also supported by changes in the vibrational frequency (shift/intensity) in symmetrical and asymmetrical stretching of aromatic rings of drugs in the complex spectra. No appreciable shift is observed in the DNA and RNA marker bands, indicating that the B-DNA form and A-family conformation of RNA are not altered during their interaction with RES and GEN.

• Journal of the Korean Chemical Society
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• v.17 no.2
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• pp.85-94
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• 1973

The stability constants of the charge-transfer complexes formed between three derivatives of nitrobenzene, i.e., 1,3,5-trinitrobenzene, m-dinitrobenzene, nitrobenzene and eleven organic molecules such as $\alpha-picoline$, pyridine, dimethylsulfoxide, N, N'-dimethylacetamide, tetrahydrofurane, 1, 4-dioxane, diethyl ether, acetonitrile, propylene oxide, epichlorohydrine, and methyl acetate, have been determined by ultraviolet absorption spectroscopy in carbon tetrachloride solution at 25.0$^{\circ}C$. The parameters of the electrostatic effect ($E_D$) and covalent effect ($C_D$) for the eleven organic compounds have been calculated from the modified equation of the double-scale enthalpy,$logK = E_AC_A+E_DC_D$ and also the shift of C=O vibrational frequency in infrared spectra for N,N'-dimethylacetamide have been measured from the solutions of above organic compounds. The empirical equation, ${\Delta}{\nu}_{C=O} = 37.4-5.47E_D+12.1C_D$, related to the parameters and the frequency shift has been derived. It seems that the stabilities of the complexes principally depend on the covalent effect. Especially it is found that $\pi$ orbitals in molecules, in addition to the parameters, play the important role in forming the charge-transfer complexes.