• Bulletin of the Korean Chemical Society
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• v.25 no.2
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• pp.198-202
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• 2004

Hydrogen bond is an important factor in the structures of carbohydrates. Because of great strength, short range, and strong angular dependence, hydrogen bonding is an important factor stabilizing the structure of carbohydrate. In this study, conformational properties and the hydrogen bonds in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO are investigated through NMR spectroscopy and molecular dynamics simulation. Lowest energy structure in the adiabatic energy map was utilized as an initial structure for the molecular dynamics simulations in DMSO. NOEs, temperature coefficients, SIMPLE NMR data, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O7' and HO3' in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO. In aqueous solution, water molecule makes intermolecular hydrogen bonds with the disaccharides and there was no intramolecular hydrogen bonds in water. Since DMSO molecule is too big to be inserted deep into GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe, DMSO can not make strong intermolecular hydrogen bonding with carbohydrate and increases the ability of O7' in GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe to participate in intramolecular hydrogen bonding. Molecular dynamics simulation in conjunction with NMR experiments proves to be efficient way to investigate the intramolecular hydrogen bonding existed in carbohydrate.

• BMB Reports
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• v.50 no.5
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• pp.269-274
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• 2017

The biological activities of macrophage migration inhibitory factor (MIF) might be mediated through a classical receptor-mediated or non-classical endocytic pathway. JAB1 (C-Jun activation domain-binding protein-1) promotes the degradation of the tumor suppressor, p53, and the cyclin-dependent kinase inhibitor, p27. When MIF and JAB1 are bound to each other in various intracellular sites, MIF inhibits the positive regulatory effects of JAB1 on the activity of AP-1. The intestinal parasite, Anisakis simplex, has an immunomodulatory effect. The molecular mechanism of action of As-MIF and human JAB1 are poorly understood. In this study, As-MIF and hJAB1 were expressed and purified with high solubility. The structure of As-MIF and hJAB1 interaction was modeled by homology modeling based on the structure of Ace-MIF. This study provides evidence indicating that the MIF domain of As-MIF interacts directly with the MPN domain of hJAB1, and four structure-based mutants of As-MIF and hJAB1 disrupt the As-MIF-hJAB1 interaction.

• Korean Chemical Engineering Research
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• v.47 no.6
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• pp.747-754
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• 2009

In this study, adsorption isotherms of o-DCB(ortho-dichlorobenzene) on an activated carbon heated at $1000^{\circ}C$ for 24 hours were obtained by experiment and were predicted by using molecular simulation. The initial molecular structure of the activated carbon was designed on the basis of its molecular formula and functional groups ratio measured experimentally. Then, the molecular structure was optimized using the COMPASS(condensed-phase optimized molecular potentials for atomistic simulation studies) force field. The particle porosity, specific surface area, and particle density obtained from the optimized molecular structure of activated carbon were compared with those experimental data. The errors between experimental data and simulation results of the particle porosity, specific surface area, and particle density were shown as 7.6, 3.8, and 2.8%, respectively. Adsorption isotherms constants of o-DCB are calculated by the GCMC(grand canonical Monte Carlo) method in the optimized molecular structure of activated carbon. The simulation result of the adsorption isotherms showed an error of under 3%, compared to that of experimental data. Adsorption isotherms, adsorption heat and pore diffusivity of 2,3,7,8-TCDD(tetrachlorodibenzo-p-dioxin) was finally obtained in the same molecular structure of the activated carbon as used for o-DCB. Thus, adsorption characteristics of persistent organic pollutants on activated carbon, which are not easy to experimentally evaluate, are predicted by the molecular simulation.

• Animal Bioscience
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• v.36 no.2
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• pp.256-263
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• 2023

Objective: Feed molecular structures can affect its availability to gastrointestinal enzymes which impact its digestibility and absorption. The molecular spectroscopy-attenuated total reflectance Fourier transform infrared vibrational spectroscopy (ATR-FTIR) is an advanced technique that measures the absorbance of chemical functional groups on the infrared region so that we can identify and quantify molecules and functional groups in a feed. The program aimed to reveal the association of intrinsic molecular structure with nutrient supply to animals from canola feedstocks and co-products from bio-oil processing. The objective of this study was to characterize special intrinsic carbohydrate and protein-related molecular structure spectral profiles of feedstock and co-products (meal and pellets) from bio-oil processing from two source origins: Canada (CA) and China (CH). Methods: The samples of feedstock and co-products were obtained from five different companies in each country arranged by the Canola Council of Canada (CCC). The molecular structure spectral features were analyzed using advanced vibrational molecular spectroscopy-ATR-FTIR. The spectral features that accessed included: i) protein-related spectral features (Amide I, Amide II, α-helix, β-sheet, and their spectral intensity ratios), ii) carbohydrate-related spectral features (TC1, TC2, TC3, TC4, CEC, STC1, STC2, STC3, STC4, TC, and their spectral intensity ratios). Results: The results showed that significant differences were observed on all vibrationally spectral features related to total carbohydrates, structural carbohydrates, and cellulosic compounds (p<0.05), except spectral features of TC2 and STC1 (p>0.05) of co-products, where CH meals presented higher peaks of these structures than CA. Similarly, it was for the carbohydrate-related molecular structure of canola seeds where the difference between CA and CH occurred except for STC3 height, CEC and STC areas (p>0.05). The protein-related molecular structures were similar for the canola seeds from both countries. However, CH meals presented higher peaks of amide I, α-helix, and β-sheet heights, α-helix:β-sheet ratio, total amide and amide I areas (p<0.05). Conclusion: The principal component analysis was able to explain over 90% of the variabilities in the carbohydrate and protein structures although it was not able to separate the samples from the two countries, indicating feedstock and coproducts interrelationship between CH and CA.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.797-801
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• 2003

One of the largest challenges for quantum chemistry today is to obtain accurate results for large complex molecular systems, and a variety of approaches have been proposed recently toward this goal. We have developed the ONIOM method, an onion skin-like multi-level method, combining different levels of quantum chemical methods as well as molecular mechanics method. We have been applying the method to many different large systems, including thermochemistry, homogeneous catalysis, stereoselectivity in organic synthesis, solution chemistry, fullerenes and nanochemistry, and biomolecular systems. The method has recently been combined with the polarizable continuum model (ONIOM-PCM), and was also extended for molecular dynamics simulation of solution (ONIOM-XS). In the present article the recent progress in various applications of ONIOM and other electronic structure methods to problems of homogeneous catalyses and nanochemistry is reviewed. Topics include 1. bond energies in large molecular systems, 2. organometallic reactions and homogeneous catalysis, 3. structure, reactivity and bond energies of large organic molecules including fullerenes and nanotubes, and 4. biomolecular structure and enzymatic reaction mechanisms.

• Applied Biological Chemistry
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• v.41 no.8
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• pp.568-571
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• 1998

The conformations of human insulin precursors, proinsulin and preproinsulin, are described in terms of molecular dynamics simulations. Despite the presence of the C-peptide and/or the signal peptide, molecular dynamics calculations utilizing the hydration shell model over a period of 500 ps indicate that the native conformations of the A and B chains are well conserved in both cases. These results further support the NMR spectroscopy results that the C-peptide is relatively disordered and does not influence the overall conformation of the native structure. The robustness of the native structure as demonstrated by experiment and simulation will permit future protein engineering applications, whereby the expression or purification yields can be improved upon sequence modification of the C-peptide and/or the signal peptide.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.417-422
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• 2002

Comparison studies of the Quantitative Structure Activity Relationship (QSAR) methods with new imidazo-quinolinedione derivatives were conducted using Comparative Molecular Field Analysis (CoMFA), Comparative Molecular Similarity Indices Analysis (CoMSIA), and the Hologram Quantitative Structure Activity Relationship (HQSAR). When the CoMFA crossvalidation value, q2, was 0.625, the Pearson correlation coefficient, r2, was 0.973. In CoMSIA, q2 was 0.52 and r2 was 0.979. In the HQSAR, q2 was 0.501 and r2 was 0.924. The best result was obtained using the CoMSIA method according to a comparison of the calculated values with the real in vitro cytotoxic activities against human ovarian cancer cell lines.

• Journal of the Korean Chemical Society
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• v.13 no.1
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• pp.56-61
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• 1969

By the chemical procedure and infra-red spectroscopy, the characteristics of humic acid were studied. The results were as follows: 1. Molecular weight. 5,200. 2. Molecular formula. $C_{240}H_{250}O_{120}N_{1O}$. 3. Rational formula. 4. Confirmation of the accurate structure of humic acid is beyond us nowadays. The structure is speculated that it may be a kind of condensed polymer of many benzene kerns in which above mentioned various functional groups are attached. Also some part of the large quantities of oxygen would be furan type carbonyl and aliphatic ethereal forms.

• Bulletin of the Korean Chemical Society
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• v.16 no.12
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• pp.1153-1162
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• 1995

The conformational details of β-lactose are investigated through molecular dynamics simulations in conjunction with the adiabatic potential energy map. The adiabatic energy map generated in vacuo contains five local minima. The lowest energy structure on the map does not correspond to the structure determined experimentally by NMR and the X-ray crystallography. When aqueous solvent effect is incorporated into the energy map calculation by increasing the dielectric constant, one of the local minima in the vacuum energy map becomes the global minimum in the resultant energy map. The lowest energy structure of the energy map generated in aquo is consistent with the one experimentally determined. Molecular dynamics simulations starting from those fivelocal minima on the vacuum energy map reveal that conformational transitions can take place among various conformations. Molecular dynamics simulations of the lactose and ricin B chain complex system in a stochastic boundary indicate that the most stable conformation in solution phase is bound to the binding site and that there are conformational changes in the exocyclic region of the lactose molecule upon binding.

• Bulletin of the Korean Chemical Society
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• v.22 no.6
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• pp.605-610
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• 2001

The molecular geometries and harmonic vibrational frequencies of dibenzofuran in the ground and lowest triplet state have been calculated using the Hartree-Fock and Becke-3-Lee-Yang-Parr(B3LYP)density functional methods with the 6-31G basis set. Upon the excitation to the lowest triplet state, the molecular structure retains the planar form but distorts from a benzene-like to a quinone-like form in skeleton. Scaled vibrational frequencies for the ground and lowest triplet state obtained from the B3LYP calculation show excellent agreement with the available experimental data. A few vibrational fundamentals for both states are newly assigned based on the B3LYP results.