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Permethylation as a strategy for high-molecular-weight polysaccharide structure analysis by nuclear magnetic resonance—Case study of Xylella fastidiosa extracellular polysaccharide 核磁共振分析高分子量多糖结构的过甲基化策略——以苛化木藻胞外多糖为例。
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-11-20 DOI: 10.1002/mrc.5413
Ikenna E. Ndukwe, Ian Black, Claudia A. Castro, Jiri Vlach, Christian Heiss, Caroline Roper, Parastoo Azadi

Current practices for structural analysis of extremely large-molecular-weight polysaccharides via solution-state nuclear magnetic resonance (NMR) spectroscopy incorporate partial depolymerization protocols that enable polysaccharide solubilization in suitable solvents. Non-specific depolymerization techniques utilized for glycosidic bond cleavage, such as chemical degradation or ultrasonication, potentially generate structural fragments that can complicate complete and accurate characterization of polysaccharide structures. Utilization of appropriate enzymes for polysaccharide degradation, on the other hand, requires prior structural knowledge and optimal enzyme activity conditions that are not available to an analyst working with novel or unknown compounds. Herein, we describe an application of a permethylation strategy that allows the complete dissolution of intact polysaccharides for NMR structural characterization. This approach is utilized for NMR analysis of Xylella fastidiosa extracellular polysaccharide (EPS), which is essential for the virulence of the plant pathogen that affects multiple commercial crops and is responsible for multibillion dollar losses each year.

目前通过溶液态核磁共振(NMR)波谱法对特大分子量多糖进行结构分析的实践包括部分解聚方案,使多糖在合适的溶剂中溶解。用于糖苷键裂解的非特异性解聚技术,如化学降解或超声,可能会产生结构片段,使多糖结构的完整和准确表征复杂化。另一方面,利用适当的酶进行多糖降解,需要事先的结构知识和最佳的酶活性条件,这对于研究新的或未知化合物的分析人员来说是不可用的。在这里,我们描述了一个应用过甲基化策略,允许完整的多糖的核磁共振结构表征完全溶解。该方法被用于对苛化木藻胞外多糖(EPS)的NMR分析,EPS对影响多种经济作物的植物病原体的毒力至关重要,每年造成数十亿美元的损失。
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引用次数: 0
Theoretical studies on the local structure and spin Hamiltonian parameters for Cu2+ ions in LiTaO3 crystal LiTaO3晶体中Cu2+离子的局部结构和自旋哈密顿参数的理论研究。
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-11-17 DOI: 10.1002/mrc.5414
Yun Chen, Lu Tang, Houdao Cai, Meiyun Zhang, Xunjie Wang, Cuidi Feng, Wenbo Xiao, Huaming Zhang

The local structure and spin Hamiltonian parameters (SHPs) g factors (gx, gy, gz) and the hyperfine structure constants (Ax, Ay, Az) for Cu2+ doped in the LiTaO3 crystal are theoretically investigated by the perturbation formulas for a 3d9 ion under rhombically elongated octahedral based on the cluster approach. The impurity Cu2+ was assumed to occupy the host trigonally-distorted octahedral Li+ site and experience the Jahn–Teller (JT) distortion from the host trigonal octahedral [TaO6]10− to the impurity rhombically elongated octahedral [CuO6]10−. Based on the calculations, the impurity-ligand bond lengths parallel and perpendicular to the C2-axis are found to be R||(≈ 2.305 Å) and R (≈ 2.112 Å) for the studied [CuO6]10− cluster, with the planar bond angle θ (≈ 78.2°). Meanwhile, the ground-state wave function for Cu2+ center in LiTaO3 was also obtained. The calculated SHPs based on the above local lattice distortions agree well with the experimental data, and the results are discussed.

利用基于簇法的3d9离子在正交八面体下的微扰公式,从理论上研究了掺杂Cu2+在LiTaO3晶体中的局部结构、自旋哈密顿参数(SHPs)、g因子(gx、gy、gz)和超精细结构常数(Ax、Ay、Az)。假设杂质Cu2+占据了主体三角畸变八面体Li+的位置,并经历了从主体三角八面体[TaO6]10-到杂质菱形拉长八面体[CuO6]10-的Jahn-Teller (JT)畸变。根据计算,研究的[CuO6]10-簇平行和垂直于C2轴的杂质-配体键长为R||(≈2.305 Å)和R⊥(≈2.112 Å),平面键角为θ(≈78.2°)。同时,得到了LiTaO3中Cu2+中心的基态波函数。基于上述局域晶格畸变计算的SHPs与实验数据吻合较好,并对结果进行了讨论。
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引用次数: 0
Solid-state 35/37Cl NMR detection of chlorine atoms directly bound to paramagnetic cobalt(II) ions in powder samples 粉末样品中直接与顺磁性钴(II)离子结合的氯原子的固态35/37Cl NMR检测。
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-11-11 DOI: 10.1002/mrc.5407
Lukas Bauder, Gang Wu

We report high-quality solid-state 35/37Cl NMR spectra for chlorine atoms directly bonded to paramagnetic cobalt(II) ions (high spin S = 3/2) in powered samples of CoCl2, CoCl2·2H2O, CoCl2·6H2O, and CoCl2(terpy) (terpy = 2,2′:6′,2″-terpyridine). Because solid-state 35/37Cl NMR spectra for paramagnetic cobalt(II) compounds often cover an extremely wide spectral range, they were recorded in this work in the form of variable-offset cumulative spectra. Solid-state 35/37Cl NMR measurements were performed at three magnetic fields (11.7, 14.1, and 16.5 T) and analysis of data yielded information about 35/37Cl quadrupole coupling and hyperfine coupling tensors in these paramagnetic cobalt(II) compounds. Experimental 35/37Cl NMR tensors were found to be in reasonable agreement with quantum chemical calculations based on a periodic DFT method implemented in BAND.

我们报道了与顺磁性钴(II)离子直接键合的氯原子的高质量固态35/37Cl NMR光谱(高自旋S = 3/2)在CoCl2、CoCl2·2H2O、CoCl3·6H2O和CoCl2(萜品)(萜品 = 2,2':6',2〃-联吡啶)。由于顺磁性钴(II)化合物的固态35/37Cl NMR光谱通常覆盖非常宽的光谱范围,因此在本工作中以可变偏移累积光谱的形式记录了它们。在三个磁场(11.7、14.1和16.5T)下进行固态35/37Cl NMR测量,数据分析产生了关于这些顺磁性钴(II)化合物中35/37Cl四极耦合和超精细耦合张量的信息。实验35/37Cl NMR张量与基于在BAND中实现的周期DFT方法的量子化学计算结果合理一致。
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引用次数: 0
Can simple ‘molecular’ corrections outperform projector augmented-wave density functional theory in the prediction of 35Cl electric field gradient tensor parameters for chlorine-containing crystalline systems? 在预测含氯晶体体系的35cl电场梯度张量参数时,简单的“分子”校正是否优于投影增强波密度泛函理论?
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-11-11 DOI: 10.1002/mrc.5408
Cory M. Widdifield, Fatemeh Zakeri

Many-body expansion (MBE) fragment approaches have been applied to accurately compute nuclear magnetic resonance (NMR) parameters in crystalline systems. Recent examples demonstrate that electric field gradient (EFG) tensor parameters can be accurately calculated for 14N and 17O. A key additional development is the simple molecular correction (SMC) approach, which uses two one-body fragment (i.e., isolated molecule) calculations to adjust NMR parameter values established using ‘benchmark’ projector augmented-wave (PAW) density functional theory (DFT) values. Here, we apply a SMC using the hybrid PBE0 exchange-correlation (XC) functional to see if this can improve the accuracy of calculated 35Cl EFG tensor parameters. We selected eight organic and two inorganic crystal structures and considered 15 chlorine sites. We find that this SMC improves the accuracy of computed values for both the 35Cl quadrupolar coupling constant (CQ) and the asymmetry parameter (ηQ) by approximately 30% compared with benchmark PAW DFT values. We also assessed a SMC that offers local improvements not only in terms of the quality of the XC functional but simultaneously in the quality of the description of relativistic effects via the inclusion of spin–orbit effects. As the inorganic systems considered contain heavy atoms bonded to the chlorine atoms, we find further improvements in the accuracy of calculated 35Cl EFG tensor parameters when both a hybrid functional and spin–orbit effects are included in the SMC. On the contrary, for chlorine-containing organics, the inclusion of spin–orbit relativistic effects using a SMC does not improve the accuracy of computed 35Cl EFG tensor parameters.

多体展开(MBE)碎片法已被应用于晶体体系核磁共振参数的精确计算。最近的例子表明,电场梯度(EFG)张量参数可以精确地计算14 N和17 o。一个关键的附加发展是简单分子校正(SMC)方法,它使用两个单体片段(即孤立分子)计算来调整使用“基准”投影增强波(PAW)密度函数理论(DFT)值建立的核磁共振参数值。在这里,我们使用混合PBE0交换相关(XC)函数应用SMC,看看这是否可以提高计算35 Cl EFG张量参数的准确性。我们选择了8种有机晶体结构和2种无机晶体结构,并考虑了15个氯位。我们发现,该SMC将35 Cl四极耦合常数(CQ)和不对称参数(η Q $$ {eta}_{mathrm{Q}} $$)的计算值的精度提高了约30% compared with benchmark PAW DFT values. We also assessed a SMC that offers local improvements not only in terms of the quality of the XC functional but simultaneously in the quality of the description of relativistic effects via the inclusion of spin-orbit effects. As the inorganic systems considered contain heavy atoms bonded to the chlorine atoms, we find further improvements in the accuracy of calculated 35 Cl EFG tensor parameters when both a hybrid functional and spin-orbit effects are included in the SMC. On the contrary, for chlorine-containing organics, the inclusion of spin-orbit relativistic effects using a SMC does not improve the accuracy of computed 35 Cl EFG tensor parameters.
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引用次数: 0
6aH-Benzo[α]fluorene: NMR evidence of the unexpected product of the reaction of butyryl chloride with 1,2-diphenylacetylene 6aH-苯并[α]芴:丁酰氯与1,2-二苯基乙炔反应意外产物的NMR证据。
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-11-08 DOI: 10.1002/mrc.5406
Sergey V. Zinchenko, Valentina A. Kobelevskaya, Alexander V. Popov

The reaction of butyryl chloride with ethynylbenzene in the presence of AlCl3 afforded a mixture of the Z/E-isomers of 1-chloro-2-phenylhex-1-en-3-one. 1,2-Diphenylethyne under these conditions gave a novel polycarbocycle core, 6aH-benzo[a]fluorene. The chemical structure of 11-chloro-5,6-diphenyl-6a-propyl-6aH-benzo[a]fluorene was established by means of IE-MS, 1H, 13C NMR, COSY, HSQC, HMBC, and 2D INADEQUATE technique.

丁酰氯与乙炔苯在AlCl3存在下的反应得到1-氯-2-苯基己-1-烯-3-酮的Z/E异构体的混合物。1,2-二苯基乙炔在这些条件下得到了新的聚碳环核6aH-苯并[a]芴。利用IE-MS、1H、13C NMR、COSY、HSQC、HMBC和2D INADEQUATE等方法,建立了11-氯-5,6-二苯基-6a-丙基-6aH-苯并[a]芴的化学结构。
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引用次数: 0
The effect of tube quality on externally calibrated quantitative nuclear magnetic resonance analysis: How bad can it be? 试管质量对外部校准的定量核磁共振分析的影响:有多糟糕?
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-11-05 DOI: 10.1002/mrc.5404
Jessica L. Ochoa, Stephan Germann, Breanna Conklin, Kenji Kurita, David J. Russell, Cassie Yang, José G. Napolitano

Externally calibrated quantitative nuclear magnetic resonance (NMR) approaches offer practical means to simultaneously evaluate chemical identity and content without the addition of calibrants to the test sample. Despite continuous advances in external calibration over the last few decades, adoption of these approaches has been slower than expected. Variations in NMR tube geometry are a commonly overlooked factor that can have a substantial effect on externally calibrated quantitation methods. In this report, we investigate the extent to which tube-to-tube volume variability can affect quantitative NMR outcomes. The results highlight the importance of considering tube quality during the development stages of externally calibrated quantitative methods. In addition, we propose a simple, yet effective volume correction strategy using the residual protonated solvent signal that, based on experiments with mixed NMR tubes of varying quality, alleviates the effect of tube-to-tube variability.

外部校准的定量核磁共振(NMR)方法提供了在不向试样中添加校准物的情况下同时评估化学特性和含量的实用方法。尽管在过去几十年中,外部校准不断取得进展,但这些方法的采用速度比预期的要慢。NMR管几何结构的变化是一个经常被忽视的因素,它可能对外部校准的定量方法产生实质性影响。在本报告中,我们研究了管与管之间的体积变化对定量NMR结果的影响程度。研究结果强调了在外部校准定量方法的开发阶段考虑试管质量的重要性。此外,我们提出了一种使用残余质子化溶剂信号的简单而有效的体积校正策略,该策略基于不同质量的混合NMR管的实验,减轻了管间可变性的影响。
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引用次数: 0
Challenges and opportunities in elucidating the structures of biofilm exopolysaccharides: A case study of the Pseudomonas aeruginosa exopolysaccharide called Pel 阐明生物膜胞外多糖结构的挑战和机遇:一个名为Pel的铜绿假单胞菌胞外多糖类的案例研究。
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-11-02 DOI: 10.1002/mrc.5405
Kristen Amyx-Sherer, Courtney Reichhardt

Biofilm formation protects bacteria from antibiotic treatment and host immune responses, making biofilm infections difficult to treat. Within biofilms, bacterial cells are entangled in a self-produced extracellular matrix that typically includes exopolysaccharides. Molecular-level descriptions of biofilm matrix components, especially exopolysaccharides, have been challenging to attain due to their complex nature and lack of solubility and crystallinity. Solid-state nuclear magnetic resonance (NMR) has emerged as a key tool to determine the structure of biofilm matrix exopolysaccharides without degradative sample preparation. In this review, we discuss challenges of studying biofilm matrix exopolysaccharides and opportunities to develop solid-state NMR approaches to study these generally intractable materials. We specifically highlight investigations of the exopolysaccharide called Pel made by the opportunistic pathogen, Pseudomonas aeruginosa. We provide a roadmap for determining exopolysaccharide structure and discuss future opportunities to study such systems using solid-state NMR. The strategies discussed for elucidating biofilm exopolysaccharide structure should be broadly applicable to studying the structures of other glycans.

生物膜的形成保护细菌免受抗生素治疗和宿主免疫反应的影响,使生物膜感染难以治疗。在生物膜中,细菌细胞被自身产生的细胞外基质缠住,该基质通常包括胞外多糖。生物膜基质成分,特别是胞外多糖,由于其复杂的性质以及缺乏溶解性和结晶性,很难获得分子水平的描述。固态核磁共振(NMR)已成为在没有降解样品制备的情况下确定生物膜基质胞外多糖结构的关键工具。在这篇综述中,我们讨论了研究生物膜基质胞外多糖的挑战,以及开发固态NMR方法来研究这些通常难以处理的材料的机会。我们特别强调了对机会病原体铜绿假单胞菌产生的称为Pel的胞外多糖的研究。我们提供了确定胞外多糖结构的路线图,并讨论了使用固态NMR研究此类系统的未来机会。所讨论的阐明生物膜胞外多糖结构的策略应广泛适用于研究其他聚糖的结构。
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引用次数: 0
Simulation of oriented NMR spectra: Combining molecular dynamics and chemical shift tensor calculations 定向NMR光谱的模拟:结合分子动力学和化学位移张量计算。
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-10-26 DOI: 10.1002/mrc.5403
Ulrich Sternberg, Raiker Witter

Solid state NMR is widely used to study the orientation and other structural features of proteins and peptides in lipid bilayers. Using data obtained by PISEMA (Polarization Inversion Spin Exchange at Magic Angle) experiments, periodic spectral patterns arise from well-aligned α-helical molecules. Significant problems in the interpretation of PISEMA spectra may arise for systems that do not form perfectly defined secondary structures, like α-helices, or the signal pattern is disturbed by molecular motion. Here, we present a new method that combines molecular dynamics simulation with tensorial orientational constraints (MDOC) and chemical shift tensor calculations for the simulation and interpretation of PISEMA-like spectra. The calculations include the spectra arising from non α-helical molecules and molecules with non-uniform intrinsic mobility. In a first step, dipolar or quadrupolar interaction tensors drive molecular rotations and reorientations to obtain the proper mean values as observed in corresponding NMR experiments. In a second step, the coordinate snapshots of the MDOC simulations are geometry optimized with the isotropic 15N chemical shifts as constraints using Bond Polarization Theory (BPT) to provide reliable 15N CS tensor data. The averaged dipolar 1H-15N couplings and the δzz tensor components can then be combined to simulate PISEMA patterns. We apply this method to the ß-helical peptide gramicidin A (gA) and demonstrate that this method enables the assignment of most PISEMA resonances. In addition, MDOC simulations provide local order parameters for the calculated sites. These local order parameters reveal large differences in backbone mobility between L- and D-amino acids of gA.

固态NMR被广泛用于研究脂质双层中蛋白质和肽的取向和其他结构特征。利用PISEMA(魔角极化反转自旋交换)实验获得的数据,周期性光谱模式由排列良好的α-螺旋分子产生。对于没有形成完美定义的二级结构(如α-螺旋)的系统,或者信号模式受到分子运动干扰的系统,在解释PISEMA光谱时可能会出现重大问题。在这里,我们提出了一种新的方法,将分子动力学模拟与张量取向约束(MDOC)和化学位移张量计算相结合,用于模拟和解释类PISEMA光谱。计算包括非α-螺旋分子和具有非均匀本征迁移率的分子产生的光谱。在第一步中,偶极或四极相互作用张量驱动分子旋转和重定向,以获得在相应NMR实验中观察到的适当平均值。在第二步中,使用键极化理论(BPT)以各向同性15N化学位移作为约束对MDOC模拟的坐标快照进行几何优化,以提供可靠的15N CS张量数据。然后可以将平均偶极1H-15N耦合和δzz张量分量组合起来模拟PISEMA模式。我们将该方法应用于ß-螺旋肽gramicidin A(gA),并证明该方法能够分配大多数PISEMA共振。此外,MDOC模拟为计算的站点提供了局部阶数参数。这些局部序参数揭示了gA的L-和D-氨基酸之间主链迁移率的巨大差异。
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引用次数: 0
Molecular precursors to produce para-hydrogen enhanced metabolites at any field 在任何领域产生对氢增强代谢产物的分子前体。
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-10-11 DOI: 10.1002/mrc.5402
Anil P. Jagtap, Salvatore Mamone, Stefan Glöggler

Enhancing magnetic resonance signal via hyperpolarization techniques enables the real-time detection of metabolic transformations even in vivo. The use of para-hydrogen to enhance 13C-enriched metabolites has opened a rapid pathway for the production of hyperpolarized metabolites, which usually requires specialized equipment. Metabolite precursors that can be hyperpolarized and converted into metabolites at any given field would open up opportunities for many labs to make use of this technology because already existing hardware could be used. We report here on the complete synthesis and hyperpolarization of suitable precursor molecules of the side-arm hydrogenation approach. The better accessibility to such side-arms promises that the para-hydrogen approach can be implemented in every lab with existing two channel NMR spectrometers for 1H and 13C independent of the magnetic field.

通过超极化技术增强磁共振信号,即使在体内也能实时检测代谢转化。使用对氢来增强13种富含C的代谢物为产生超极化代谢物开辟了一条快速途径,这通常需要专门的设备。可以在任何特定领域超极化并转化为代谢物的代谢物前体将为许多实验室利用这项技术开辟机会,因为可以使用现有的硬件。我们在这里报道了侧臂氢化方法的合适前体分子的完全合成和超极化。这种侧臂的更好可达性保证了对氢方法可以在每个实验室中实施,现有的1H和13C的双通道NMR光谱仪独立于磁场。
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引用次数: 0
Low-field, not low quality: 1D simplification, selective detection, and heteronuclear 2D experiments for improving low-field NMR spectroscopy of environmental and biological samples 低场,而不是低质量:1D简化、选择性检测和异核2D实验,用于改进环境和生物样品的低场NMR光谱。
IF 2 3区 化学 Q2 Chemistry Pub Date : 2023-10-09 DOI: 10.1002/mrc.5401
Katelyn Downey, Wolfgang Bermel, Ronald Soong, Daniel H. Lysak, Kiera Ronda, Katrina Steiner, Peter M. Costa, William W. Wolff, Venita Decker, Falko Busse, Benjamin Goerling, Agnes Haber, Myrna J. Simpson, Andre J. Simpson

Understanding environmental change is challenging and requires molecular-level tools to explain the physicochemical phenomena behind complex processes. Nuclear magnetic resonance (NMR) spectroscopy is a key tool that provides information on both molecular structures and interactions but is underutilized in environmental research because standard “high-field” NMR is financially and physically inaccessible for many and can be overwhelming to those outside of disciplines that routinely use NMR. “Low-field” NMR is an accessible alternative but has reduced sensitivity and increased spectral overlap, which is especially problematic for natural, heterogeneous samples. Therefore, the goal of this study is to investigate and apply innovative experiments that could minimize these challenges and improve low-field NMR analysis of environmental and biological samples. Spectral simplification (JRES, PSYCHE, singlet-only, multiple quantum filters), selective detection (GEMSTONE, DREAMTIME), and heteronuclear (reverse and CH3/CH2/CH-only HSQCs) NMR experiments are tested on samples of increasing complexity (amino acids, spruce resin, and intact water fleas) at-high field (500 MHz) and at low-field (80 MHz). A novel experiment called Doubly Selective HSQC is also introduced, wherein 1H signals are selectively detected based on the 1H and 13C chemical shifts of 1H–13C J-coupled pairs. The most promising approaches identified are the selective techniques (namely for monitoring), and the reverse and CH3-only HSQCs. Findings ultimately demonstrate that low-field NMR holds great potential for biological and environmental research. The multitude of NMR experiments available makes NMR tailorable to nearly any research need, and low-field NMR is therefore anticipated to become a valuable and widely used analytical tool moving forward.

理解环境变化具有挑战性,需要分子水平的工具来解释复杂过程背后的物理化学现象。核磁共振(NMR)光谱是一种提供分子结构和相互作用信息的关键工具,但在环境研究中没有得到充分利用,因为标准的“高场”NMR在经济和物理上对许多人来说都是不可获得的,并且对那些常规使用NMR的学科之外的人来说可能是压倒性的。“低场”NMR是一种可供选择的方法,但灵敏度降低,光谱重叠增加,这对天然、异质样品来说尤其有问题。因此,本研究的目标是研究和应用创新实验,以最大限度地减少这些挑战,并改进环境和生物样品的低场NMR分析。在高场(500 MHz)和低场(80 MHz)。还介绍了一种称为双选择性HSQC的新实验,其中基于1H-13C J耦合对的1H和13C化学位移选择性地检测1H信号。确定的最有前景的方法是选择性技术(即监测),以及反向和仅CH3的HSQC。研究结果最终表明,低场核磁共振在生物和环境研究中具有巨大的潜力。大量的核磁共振实验使核磁共振几乎可以满足任何研究需求,因此低场核磁共振有望成为一种有价值且广泛使用的分析工具。
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引用次数: 0
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Magnetic Resonance in Chemistry
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