• Bulletin of the Korean Chemical Society
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• 제25권2호
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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.

• 한국자기공명학회논문지
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• 제19권1호
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• pp.29-35
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• 2015

The microscopic dynamics of $CsH_2PO_4$, with two distinct hydrogen bond lengths, are studied by static nuclear magnetic resonance (NMR) and magic angle spinning (MAS) NMR. The proton dynamics of the two crystallographically inequivalent hydrogen sites were discussed in terms of the $^1H$ NMR and $^1H$ MAS NMR spectra. Although the hydrogen bonds have two inequivalent sites, H(1) and H(2), distinct proton dynamics for the two sites were not found. Further, the $^{133}Cs$ spectrum is more or less continuous near $T_{C1}$ (=153 K). Finally, the phase transition mechanism of $T_{C1}$ in $CsH_2PO_4$ is related to the ordering of protons.

• 암석학회지
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• 제10권3호
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• pp.233-245
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• 2001

NMR분광법은 현재 화학에서 빼 놓을 수 없는 아주 중요한 연구방법의 하나지만 또한 지질학의 연구에 있어서도 초전도 자석의 발달과 함께 그 중요성이 부각되고 있다. 지질학에 있어서 NMR의 연구 대상 원소로는 광물의 주 구성 성분이며 여러 가지 구조적 정보를 갖고 있는 $^{29}Si$, $^{27}Al$ 등이 유용하게 사용되며 이들은 각각 다른 여러 정보들을 제공한다. 이 밖에도 $^{23}Na$와 같은 알칼리금속과 더불어 다양한 핵종들이 지질학에서 NMR로 연구되고 있다. NMR을 이용하여 다양한 방면의 연구들이 가능한데 NMR은 XRD, TEM보다도 더욱 작은 미시적인 (분자적 관점에서의) 구조 연구에 사용될 수 있다. 이러한 연구를 통해 Al, Si 질서-무질서, 산소원자와의 배위수, 인근의 다른 양이온의 분포 등을 포함한 구조적 정보를 알 수 있다. 또한 NMR의 또 다른 장점은 정적인 미시 구조뿐만 아니라 분자들의 움직임(dynamics)에 대한 정보도 알 수 있다는 것이다. 이러한 동적인 정보는 기존의 어느 방법으로도 알기 어려웠던 부분이고 NMR을 통하여 분자들의 상호 교환 속도와 활성화 에너지 등에 대한 폭 넓은 이해가 가능할 수 있다. 이 밖에 NMR을 이용하여 비정질 물질에 대한 구조와 더불어 지표면에서 산출되는 유기물에 대한 성분 및 구조도 아주 중요하게 연구될 수 있는 분야이다.

• 한국자기공명학회논문지
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• 제16권2호
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• pp.103-110
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• 2012

Membrane proteins play a essential role in the biological systems and it is not easy to handle a membrane protein for its structural study. Solid-state NMR (ssNMR) can be a good tool to investigate the structures and dynamics of membrane proteins. In ssNMR, Magic Angle Spinning (MAS) and Cross Polarization (CP) can be utilized to reduce the line-broadening, leading to high resolution and sensitivity in the spectrum. ssNMR, if combined with other spectroscopic methods, can provide us a enough knowledge on structures and dynamics of membrane proteins in biological condition.

• 한국자기공명학회논문지
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• 제26권1호
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• pp.17-20
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• 2022

High-pressure (HP) NMR is a versatile tool to investigate diverse features of proteins. This technique has been particularly powerful to elucidate structural dynamics that only populates sufficiently in a pressurized condition. Amyloidogenic proteins, which are prone to aggregate and form amyloid fibrils, often maintains highly dynamic states in its native or aggregation-prone states, and HP NMR contributed much to advance our understandings of the dynamic behaviors of amyloidogenic proteins and the molecular mechanisms of their aggregation. In this mini review, we therefore summarize recent HP NMR studies on amyloid-beta (Aβ), the representative amyloidogenic intrinsically disordered protein (IDP).

• 한국초전도학회:학술대회논문집
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• 한국초전도학회 2006년도 High Temperature Superconductivity Vol.XVI
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• pp.10-10
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• 2006

• 한국초전도학회:학술대회논문집
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• 한국초전도학회 2003년도 High Temperature Superconductivity Vol.XIII
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• pp.20-20
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• 2003

• Bulletin of the Korean Chemical Society
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• 제30권5호
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• pp.1139-1142
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• 2009

Refinement of NMR structures by molecular dynamics (MD) simulations with a solvent model has improved the structural quality. In this study, we applied MD refinement with the generalized Born (GB) implicit solvent model to protein structure determined under membrane-like environments. Despite popularity of the GB model, its applications to the refinement of NMR structures of hydrophobic proteins, in which detergents or organic solvents enclose proteins, are limited, and there is little information on the use of another GB parameter for these cases. We carried out MD refinement of crambin NMR structure in dodecylphosphocholine (DPC) micelles (Ahn et al., J. Am. Chem. Soc. 2006, 128, 4398-4404) with GB/Surface area model and two different surface tension coefficients, one for aquatic and the other for hydrophobic conditions. Our data show that, of two structures by MD refinement with GB model, the one refined with the parameter to consider hydrophobic condition had the better qualities in terms of precision and solvent accessibility.

• 한국자기공명학회논문지
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• 제18권1호
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• pp.24-29
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• 2014

Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stage with experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, we compared the qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fields-ff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13-with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.

• 한국자기공명학회논문지
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• 제23권2호
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• pp.56-60
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• 2019

Study on the structure and dynamics of molecules at the atomic level is of great significance for understanding their function and stability as well as roles for various chemico-physical and biological processes. $^{17}O$ NMR spectroscopy has appeared as an elegant technique for investigating of the physicochemical and structural properties of oxygen-containing compounds such as metal organic frameworks and nanosized oxides. This method has drawn much attention as it provides unique insights into the properties of targets based on atomistic information of local oxygen environments which is otherwise difficult to obtain using other methods. In this mini review, we introduce and discuss the recent study and developments of $^{17}O$ NMR techniques which are tailored for the investigation on the structure and dynamics of water and inorganic materials.