• 한국안광학회지
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• 제2권1호
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• pp.17-24
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• 1997

Gauss 함수와 Lorentz 함수의 convolution인 Voight 함수를 혼합 알칼리 유리, 전이금속 산화물을 첨가시킨 유리 등의 MAS-NMR 스펙트럼의 시뮬레이션에 적용시켜 보았다. Gauss와 Lorentz의 convolution은 적분할 수 없으므로 어떤 형태를 갖는 Voight 함수는 없다. 그래서 컴퓨터를 이용한 개념적(원시적) 적분 방법으로 각 진동수에 대하여 Voight 함수 값을 얻었고, 그것은 MAS-NMR 스펙트럼과 매우 잘 일치하였다. 이 과정에서 MAS-NMR lineshape의 변화(Gauss에서 Lorentz lineshape으로의 변화 또는 그 반대)를 알 수 있다. 그러므로 다음과 같은 경우는 주의해야 할 것으로 생각된다. 유리의 구조, 전도 기구 또는 혼합 알칼리 효과 등을 연구하기 위해 NMR 스펙트럼을 컴퓨터 시뮬레이션 할 때 NMR 스펙트럼의 lineshape을 Gauss 함수 꼴로 가정해서 수행하는 경우가 대부분인데 이때 주의해야 할 것이다. 왜냐하면, NMR 스펙트럼 선 모양이 실제로는 Voight 함수 형태로 나타날 수 있기 때문이다.

• 지구물리와물리탐사
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• 제16권2호
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• pp.97-105
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• 2013

자기공명검층은 수소와 자기장의 상호작용을 측정, 분석하는 물리검층 방법으로 이는 저류층 평가를 위한 중요한 물리검층 방법 중 하나이다. 측정된 감쇠 신호 즉, 이완은 측정지역 내 수소의 밀도에 대한 정보와 유체의 종류에 따른 감쇠속도에 대한 정보를 포함하고 있으며, 이를 바탕으로 공극률, 투과도와 습윤도 등을 예측할 수 있다. 1950년대 초반 랜덤워크로 자기공명의 이완감쇠를 시뮬레이션한 것을 시작으로 자기공명반응에 대한 연구가 급격히 발전되었다. 이 논문에서는 자기공명 시뮬레이션의 연구 동향을 먼저 살펴 보고, 자기공명반응인 이완을 발생시키는 이완메커니즘에 대해 간단히 알아본다. 이에 기초하여 자기공명검층에서 주로 측정하는 횡축이완곡선을 자기장구배를 고려하는 경우와 고려하지 않는 시뮬레이션 방법에 대해 비교분석하고 자기장구배가 이완메커니즘 및 횡축이완곡선에 미치는 영향에 대해 분석한다.

• 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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• 제10권1호
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• pp.1-37
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• 2006

General expressions for solid state NMR lines are described for transitions under static, magic angle spinning, and variable angle spinning conditions in the case where the principal axis system for the anisotropic chemical shift tensor is noncoincident with that of the quadrupole coupling tensor. It is demonstrated that solid state NMR powder pattern simulation program VMAS based on the conventional grid point method of integrating over the Euler angle space is fast enough in comparison with the POWDER simulation package and Gauss-point method.

• 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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• 제19권1호
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• pp.1-10
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• 2015

Refinements with atomistic molecular dynamics (MD) simulation have contributed to improving the qualities of NMR structures. In most cases, the calculations with atomistic MD simulation for NMR structures employ generalized-Born implicit solvent model (GBIS) to take into accounts solvation effects. Developments in algorithms and computational capacities have ameliorated GBIS to approximate solvation effects that explicit solvents bring about. However, the quantitative comparison of NMR structures in the latest GBIS and explicit solvents is lacking. In this study, we report the direct comparison of NMR structures that atomistic MD simulation coupled with GBIS and water molecules refined. Two model proteins, GB1 and ubiquitin, were recalculated with experimental distance and torsion angle restraints, under a series of simulated annealing time steps. Whereas the root mean square deviations of the resulting structures were apparently similar, AMBER energies, the most favored regions in Ramachandran plot, and MolProbity clash scores witnessed that GBIS-refined structures had the better geometries. The outperformance by GBIS was distinct in the structure calculations with sparse experimental restraints. We show that the superiority stemmed, at least in parts, from the inclusion of all the pairs of non-bonded interactions. The shorter computational times with GBIS than those for explicit solvents makes GBIS a powerful method for improving structural qualities particularly under the conditions that experimental restraints are insufficient. We also propose a method to separate the native-like folds from non-violating diverged structures.

• 한국자기공명학회논문지
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• 제10권1호
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• pp.46-58
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• 2006

With a simple pulse sequence ($\pi/2$-{gradient, duration T}-acquisition) in solution NMR, detected signal has slowly grown up to percents of the equilibrium magnetization. The source of this unusual resurrection of dephased magnetization after a crushed gradient is cross-correlated effects of radiation damping and the distant dipolar field, which has been demonstrated by a numerical simulation and theoretical analysis.

• 한국자기공명학회논문지
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• 제9권1호
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• pp.67-73
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• 2005

$^{27}AI$ triple quantum magic angle spinning (3QMAS) NMR spectra of several mordenite (MOR) sample were simulated with the point charge model method and compared with experimental 3QMAS spectra. Signal positions from different tetrahedral (T) sites in 3QMAS spectra are mainly governed by local structures of T sites such as T-O-T angles and T-O bond lengths. When preparation methods, cations in addition to Si/Al rations vary, the local structures of T sites in MOR change enough to alter signal patterns in 3QMAS of MOR. This inhibits to study the of Al distribution variation over 4 different T sites in mordenite during process such as dealumination by 3QMAS spectra.

• 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.

• 한국초전도ㆍ저온공학회논문지
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• 제18권3호
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• pp.21-24
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• 2016

Recently, production technique and property of the High-Temperature Superconductor (HTS) tape have been improved. Thus, the study on applying an HTS magnet to the high magnetic field application is rapidly increased. A Nuclear Magnetic Resonance (NMR) spectrometer requires high magnitude and homogeneous of central magnetic field. However, the HTS magnet has fabrication errors because shape of HTS is tape and HTS magnet is manufactured by winding HTS tape to the bobbin. The fabrication errors are winding error, bobbin diameter error, spacer thickness error and so on. The winding error occurs when HTS tape is departed from the arranged position on the bobbin. The bobbin diameter and spacer thickness error occur since the diameter of bobbin and spacer are inaccurate. These errors lead magnitude and homogeneity of central magnetic field to be different from its ideal design. The purpose of this paper is to investigate the effect of winding error, bobbin diameter error and spacer thickness error on the central field and field homogeneity of HTS magnet using the virtual NMR signals in MATLAB simulation.