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Improving the accuracy of GIPAW chemical shielding calculations with cluster and fragment corrections 通过簇和片段校正提高GIPAW化学屏蔽计算的准确性
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-12-01 DOI: 10.1016/j.ssnmr.2022.101832
Joshua D. Hartman , James K. Harper
<div><p><span>Ab initio methods<span> for predicting NMR parameters in the solid state are an essential tool for assigning experimental spectra and play an increasingly important role in structural characterizations. Recently, a molecular correction (MC) technique has been developed which combines the strengths<span> of plane-wave methods (GIPAW) with single molecule calculations employing Gaussian basis sets. The GIPAW + MC method relies on a periodic calculation performed at a lower level of theory to model the crystalline environment. The GIPAW result is then corrected using a single molecule calculation performed at a higher level of theory. The success of the GIPAW + MC method in predicting a range of NMR parameters is a result of the highly local character of the tensors underlying the NMR observable. However, in applications involving strong intermolecular interactions we find that expanding the region treated at the higher level of theory more accurately captures local many-body contributions to the </span></span></span><span><math><mmultiscripts><mrow><mi>N</mi></mrow><none></none><none></none><mprescripts></mprescripts><none></none><mrow><mn>15</mn></mrow></mmultiscripts></math></span> NMR chemical shielding (CS) tensor. We propose alternative corrections to GIPAW which capture interactions between adjacent molecules at a higher level of theory using either fragment or cluster-based calculations. Benchmark calculations performed on <span><math><mmultiscripts><mrow><mi>N</mi></mrow><none></none><none></none><mprescripts></mprescripts><none></none><mrow><mn>15</mn></mrow></mmultiscripts></math></span> and <span><math><mmultiscripts><mrow><mi>C</mi></mrow><none></none><none></none><mprescripts></mprescripts><none></none><mrow><mn>13</mn></mrow></mmultiscripts></math></span> data sets show that these advanced GIPAW-corrected calculations improve the accuracy of chemical shielding tensor predictions relative to existing methods. Specifically, cluster-based <span><math><mmultiscripts><mrow><mi>N</mi></mrow><none></none><none></none><mprescripts></mprescripts><none></none><mrow><mn>15</mn></mrow></mmultiscripts></math></span> corrections show a 24% and 17% reduction in RMS error relative to GIPAW and GIPAW + MC calculations, respectively. Comparing the benchmark data sets using multiple computational models demonstrates that <span><math><mmultiscripts><mrow><mi>N</mi></mrow><none></none><none></none><mprescripts></mprescripts><none></none><mrow><mn>15</mn></mrow></mmultiscripts></math></span> CS tensor calculations are significantly more sensitive to intermolecular interactions relative to <span><math><mmultiscripts><mrow><mi>C</mi></mrow><none></none><none></none><mprescripts></mprescripts><none></none><mrow><mn>13</mn></mrow></mmultiscripts></math></span><span>. However, fragment and cluster-based corrections that include direct hydrogen bond<span> partners are sufficient for optimizing the accuracy of GIPAW-corrected methods. Finally, GIPAW
从头算方法预测固体核磁共振参数是分配实验光谱的重要工具,在结构表征中发挥着越来越重要的作用。近年来,一种将平面波方法(GIPAW)的优点与采用高斯基集的单分子计算相结合的分子校正技术得到了发展。GIPAW + MC方法依赖于在较低理论水平上进行的周期性计算来模拟晶体环境。然后使用在更高的理论水平上执行的单分子计算对GIPAW结果进行校正。GIPAW + MC方法在预测核磁共振参数范围方面的成功是核磁共振观测值下张量的高度局域性的结果。然而,在涉及强分子间相互作用的应用中,我们发现在更高的理论水平上扩展区域更准确地捕获局部多体对N15核磁共振化学屏蔽(CS)张量的贡献。我们提出了对GIPAW的替代修正,它使用片段或基于簇的计算在更高的理论水平上捕获相邻分子之间的相互作用。在N15和C13数据集上进行的基准计算表明,相对于现有方法,这些先进的gipaw校正计算提高了化学屏蔽张量预测的准确性。具体来说,与GIPAW和GIPAW + MC计算相比,基于聚类的N15修正分别显示了24%和17%的均数误差降低。使用多种计算模型比较基准数据集表明,相对于C13, N15 CS张量计算对分子间相互作用明显更敏感。然而,包括直接氢键伙伴在内的基于片段和簇的校正足以优化gipaw校正方法的准确性。最后,将gipaw校正方法应用于非对称单元中含有两个鸟苷分子的二水合物鸟苷的核磁共振谱分配。
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引用次数: 3
19F fast MAS (60–111 kHz) dipolar and scalar based correlation spectroscopy of organic molecules and pharmaceutical formulations 有机分子和药物制剂的19F快速MAS (60-111 kHz)偶极和标量相关光谱
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-12-01 DOI: 10.1016/j.ssnmr.2022.101831
Gal Porat-Dahlerbruch , Jochem Struppe , Caitlin M. Quinn , Angela M. Gronenborn , Tatyana Polenova

19F magic angle spinning (MAS) NMR spectroscopy is a powerful tool for characterization of fluorinated solids. The recent development of 19F MAS NMR probes, operating at spinning frequencies of 60–111 kHz, enabled analysis of systems spanning from organic molecules to pharmaceutical formulations to biological assemblies, with unprecedented resolution. Herein, we systematically evaluate the benefits of high MAS frequencies (60–111 kHz) for 1D and 2D 19F-detected experiments in two pharmaceuticals, the antimalarial drug mefloquine and a formulation of the cholesterol-lowering drug atorvastatin calcium. We demonstrate that 1H decoupling is essential and that scalar-based, heteronuclear single quantum coherence (HSQC) and heteronuclear multiple quantum coherence (HMQC) correlation experiments become feasible and efficient at the MAS frequency of 100 kHz. This study opens doors for the applications of high frequency 19F MAS NMR to a wide range of problems in chemistry and biology.

19F魔角旋转(MAS)核磁共振波谱是表征氟化固体的有力工具。最近开发的19fmas NMR探针,在60-111 kHz的旋转频率下工作,能够以前所未有的分辨率分析从有机分子到药物配方到生物组件的系统。在此,我们系统地评估了高MAS频率(60-111 kHz)在两种药物(抗疟疾药物甲氟喹和降胆固醇药物阿托伐他汀钙制剂)的1D和2D 19f检测实验中的益处。我们证明了1H解耦是必不可少的,并且在100 kHz的MAS频率下,基于标量的异核单量子相干(HSQC)和异核多量子相干(HMQC)相关实验变得可行和有效。该研究为高频19fmas NMR在化学和生物学领域的广泛应用打开了大门。
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引用次数: 1
Improved resolution for spin-3/2 isotopes in solids via the indirect NMR detection of triple-quantum coherences using the T-HMQC sequence 利用T-HMQC序列间接核磁共振检测三量子相干提高固体中自旋3/2同位素的分辨率
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-12-01 DOI: 10.1016/j.ssnmr.2022.101835
Racha Bayzou , Julien Trébosc , Ivan Hung , Zhehong Gan , Andrew Rankin , Olivier Lafon , Jean-Paul Amoureux

The indirect NMR detection of quadrupolar nuclei in solids under magic-angle spinning (MAS) is possible with the through-space HMQC (heteronuclear multiple-quantum coherence) scheme incorporating the TRAPDOR (transfer of population in double-resonance) dipolar recoupling. This sequence, called T-HMQC, exhibits limited t1-noise. In this contribution, with the help of numerical simulations of spin dynamics, we show that most of the time, the fastest coherence transfer in the T-HMQC scheme is achieved when TRAPDOR recoupling employs the highest radiofrequency (rf) field compatible with the probe specifications. We also demonstrate how the indirect detection of the triple-quantum (3Q) coherences of spin-3/2 quadrupolar nuclei in solids improves the spectral resolution for these isotopes. The sequence is then called T-HMQC3. We demonstrate the gain in resolution provided by this sequence for the indirect proton detection of 35Cl nuclei in l-histidine∙HCl and l-cysteine∙HCl, as well as that of 23Na isotope in NaH2PO4. These experiments indicate that the gain in resolution depends on the relative values of the chemical and quadrupolar-induced shifts (QIS) for the different spin-3/2 species. In the case of NaH2PO4, we show that the transfer efficiency of the T-HMQC3 sequence employing an rf-field of 80 kHz with a MAS frequency of 62.5 kHz reaches 75% of that of the t1-noise eliminated (TONE) dipolar-mediated HMQC (D-HMQC) scheme.

利用结合TRAPDOR(双共振居群转移)偶极重偶联的跨空间HMQC(异核多量子相干)方案,可以在魔角自旋(MAS)下对固体中的四极核进行间接核磁共振检测。这个序列被称为T-HMQC,表现出有限的t1噪声。在这项贡献中,借助自旋动力学的数值模拟,我们表明,在大多数情况下,当TRAPDOR重新耦合采用与探头规格兼容的最高射频(rf)场时,T-HMQC方案中最快的相干转移是实现的。我们还演示了间接检测固体中自旋3/2四极核的三量子(3Q)相干如何提高这些同位素的光谱分辨率。这个序列被称为T-HMQC3。我们展示了该序列为l-组氨酸∙HCl和l-半胱氨酸∙HCl中35Cl核的间接质子检测以及NaH2PO4中23Na同位素的分辨率提供的增益。这些实验表明,分辨率增益取决于不同自旋为3/2的物质的化学和四极诱导位移(QIS)的相对值。在NaH2PO4的情况下,我们表明,采用80 kHz的rfid场和62.5 kHz的MAS频率的T-HMQC3序列的传输效率达到了t1噪声消除(TONE)偶极体介导HMQC (D-HMQC)方案的75%。
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引用次数: 0
A case study on the influence of hydrophilicity on the signal enhancement by dynamic nuclear polarization 亲水性对动态核极化信号增强影响的实例研究
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-12-01 DOI: 10.1016/j.ssnmr.2022.101829
Sonja C. Döller , Torsten Gutmann , Markus Hoffmann , Gerd Buntkowsky

In this work, the behavior of four different commercially available polarizing agents is investigated employing the non-ionic model surfactant 1-octanol as analyte. A relative method for the comparison of the proportion of the direct and indirect polarization transfer pathways is established, allowing a direct comparison of the polarization efficacy for different radicals and different parts of the 1-octanol molecule despite differences in radical concentration or sample amount. With this approach, it could be demonstrated that the hydrophilicity is a key factor in the way polarization is transferred from the polarizing agent to the analyte. These findings are confirmed by the determination of buildup times Tb, illustrating that the choice of polarizing agent plays an essential role in ensuring an optimal polarization transfer and therefore the maximum amount of enhancement possible for DNP enhanced NMR measurements.

在这项工作中,研究了四种不同的市售极化剂的行为,采用非离子模型表面活性剂1-辛醇作为分析物。建立了一种比较直接和间接极化转移途径比例的相对方法,可以直接比较不同自由基和1-辛醇分子不同部位的极化效率,而不管自由基浓度或样品量的不同。通过这种方法,可以证明亲水性是极化从极化剂转移到分析物的关键因素。这些发现通过累积时间Tb的测定得到了证实,说明极化剂的选择在确保最佳极化转移和DNP增强核磁共振测量的最大增强量方面起着至关重要的作用。
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引用次数: 1
Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions 固体核磁共振方法表征生物偶联和蛋白质-材料相互作用
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-12-01 DOI: 10.1016/j.ssnmr.2022.101828
Linda Cerofolini , Giacomo Parigi , Enrico Ravera , Marco Fragai , Claudio Luchinat

Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.

在过去的二十年里,随着新的硬件和样品制备方法的发展,蛋白质固态核磁共振已经发生了巨大的变化。这项技术现在已经成熟,可以用于复杂的应用,其中可以计算生物偶联,蛋白质化学和功能生物材料。本文综述了蛋白质固态核磁共振在这方面的研究进展。
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引用次数: 0
Narrowing down the conformational space with solid-state NMR in crystal structure prediction of linezolid cocrystals 利用固体核磁共振缩小利奈唑胺共晶的构象空间
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-10-01 DOI: 10.1016/j.ssnmr.2022.101813
Mehrnaz Khalaji, Piotr Paluch, Marek J. Potrzebowski, Marta K. Dudek

Many solids crystallize as microcrystalline powders, thus precluding the application of single crystal X-Ray diffraction in structural elucidation. In such cases, a joint use of high-resolution solid-state NMR and crystal structure prediction (CSP) calculations can be successful. However, for molecules showing significant conformational freedom, the CSP-NMR protocol can meet serious obstacles, including ambiguities in NMR signal assignment and too wide conformational search space to be covered by computational methods in reasonable time. Here, we demonstrate a possible way of avoiding these obstacles and making as much use of the two methods as possible in difficult circumstances. In a simple case, our experiments led to crystal structure elucidation of a cocrystal of linezolid (LIN), a wide-range antibiotic, with 2,3-dihydroxybenzoic acid, while a significantly more challenging case of a cocrystal of LIN with 2,4-dihydroxybenzoic acid led to the identification of the most probable conformations of LIN inside the crystal. Having four rotatable bonds, some of which can assume many discreet values, LIN molecule poses a challenge in establishing its conformation in a solid phase. In our work, a set of 27 conformations were used in CSP calculations to yield model crystal structures to be examined against experimental solid-state NMR data, leading to a reliable identification of the most probable molecular arrangements.

许多固体结晶为微晶粉末,因此阻碍了单晶x射线衍射在结构解析中的应用。在这种情况下,联合使用高分辨率固态核磁共振和晶体结构预测(CSP)计算可以取得成功。然而,对于具有显著构象自由度的分子,CSP-NMR协议可能会遇到严重的障碍,包括核磁共振信号分配的模糊性以及计算方法在合理的时间内无法覆盖太宽的构象搜索空间。在这里,我们展示了一种避免这些障碍的可能方法,并在困难的情况下尽可能多地使用这两种方法。在一个简单的案例中,我们的实验导致了宽范围抗生素利奈唑胺(LIN)与2,3-二羟基苯甲酸共晶的晶体结构的阐明,而一个更具挑战性的案例是LIN与2,4-二羟基苯甲酸共晶导致了LIN在晶体内最可能的构象的鉴定。LIN分子有四个可旋转的键,其中一些键可以假设许多离散值,这对确定其在固相中的构象提出了挑战。在我们的工作中,在CSP计算中使用了一组27种构象来产生模型晶体结构,以对照实验固态核磁共振数据进行检查,从而可靠地识别出最可能的分子排列。
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引用次数: 3
Solid-state NMR studies of metal ion and solvent influences upon the flexible metal-organic framework DUT-8 金属离子和溶剂对柔性金属-有机骨架DUT-8影响的固态核磁共振研究
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-08-01 DOI: 10.1016/j.ssnmr.2022.101809
Marcus Rauche , Sebastian Ehrling , Leila Abylgazina , Christopher Bachetzky , Irena Senkovska , Stefan Kaskel , Eike Brunner

Within the present contribution, we describe solid-state NMR spectroscopic studies of the paddle wheel unit in the prototypic flexible MOF compound DUT-8(M) (M = Ni, Co, Zn). The 13C NMR chemical shift of these carboxylates shows a remarkable behavior. The pure 2,6-H2ndc linker carboxylates as well as DUT-8(Zn) exhibit a13C chemical shift of only about 170 ppm. In contrast, much higher values are observed for DUT-8(Ni) and especially DUT-8(Co). In the open pore state, the shift strongly depends on the solvent polarity in these two latter cases. The present contribution elucidates the reason for this solvent influence. It is concluded that the solvent mainly modifies the isotropic Fermi contact coupling constant for the excited high-spin states in DUT-8(Ni) and DUT-8(Co).

在目前的贡献中,我们描述了原型柔性MOF化合物DUT-8(M) (M = Ni, Co, Zn)中桨轮单元的固态核磁共振光谱研究。这些羧酸盐的13C核磁共振化学位移表现出显著的行为。纯2,6- h2ndc连接剂羧酸盐和DUT-8(Zn)的13c化学位移仅为170 ppm左右。相比之下,DUT-8(Ni),特别是DUT-8(Co)的值要高得多。在开孔状态下,后两种情况下的位移强烈依赖于溶剂极性。目前的贡献阐明了溶剂影响的原因。结果表明,溶剂主要改变DUT-8(Ni)和DUT-8(Co)中激发高自旋态的各向同性费米接触耦合常数。
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引用次数: 2
Combining heteronuclear correlation NMR with spin-diffusion to detect relayed Cl–H–H and N–H–H proximities in molecular solids 结合异核相关核磁共振和自旋扩散检测分子固体中Cl-H-H和N-H-H - h邻近值
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-08-01 DOI: 10.1016/j.ssnmr.2022.101808
Parth Raval , Julien Trébosc , Tomasz Pawlak , Yusuke Nishiyama , Steven P. Brown , G.N. Manjunatha Reddy

Analysis of short-to-intermediate range intermolecular interactions offers a great way of characterizing the solid-state organization of small molecules and materials. This can be achieved by two-dimensional (2D) homo- and heteronuclear correlation NMR spectroscopy, for example, by carrying out experiments at high magnetic fields in conjunction with fast magic-angle spinning (MAS) techniques. But, detecting 2D peaks for heteronuclear dipolar coupled spin pairs separated by greater than 3 Å is not always straightforward, particularly when low-gamma quadrupolar nuclei are involved. Here, we present a 2D correlation NMR experiment that combines the advantages of heteronuclear-multiple quantum coherence (HMQC) and proton-based spin-diffusion (SD) pulse sequences using radio-frequency-driven-recouping (RFDR) to probe inter and intramolecular 1H-X (X = 14N, 35Cl) interactions. This experiment can be used to acquire 2D 1H{X}-HMQC filtered 1H–1H correlation as well as 2D 1H-X HMQC spectra. Powder forms of dopamine·HCl and l-histidine·HCl·H2O are characterized at high fields (21.1 T and 18.8 T) with fast MAS (60 kHz) using the 2D HMQC-SD-RFDR approach. Solid-state NMR results are complemented with NMR crystallography analyses using the gauge-including projector augmented wave (GIPAW) approach. For histidine·HCl·H2O, 2D peaks associated with 14N–1H–1H and 35Cl–1H–1H distances of up to 4.4 and 3.9 Å have been detected. This is further corroborated by the observation of 2D peaks corresponding to 14N–1H–1H and 35Cl–1H–1H distances of up to 4.2 and 3.7 Å in dopamine·HCl, indicating the suitability of the HMQC-SD-RFDR experiments for detecting medium-range proximities in molecular solids.

分析分子间的中短程相互作用为表征小分子和材料的固态组织提供了一种很好的方法。这可以通过二维(2D)同核和异核相关核磁共振波谱来实现,例如,通过在高磁场下与快速魔角旋转(MAS)技术相结合进行实验。但是,检测距离大于3 Å的异核偶极耦合自旋对的二维峰并不总是直截了当地,特别是当涉及低伽马四极核时。在这里,我们提出了一个二维相关核磁共振实验,结合了异核-多量子相干(HMQC)和基于质子的自旋扩散(SD)脉冲序列的优势,利用射频驱动补偿(RFDR)来探测分子间和分子内的1H-X (X = 14N, 35Cl)相互作用。本实验可获得经1H{X}-HMQC滤波后的二维1H- 1H相关光谱和二维1H-X HMQC光谱。采用二维HMQC-SD-RFDR方法,在高场(21.1 T和18.8 T)和快速MAS (60 kHz)下,对粉末形式的多巴胺·HCl和l-组氨酸·HCl·H2O进行了表征。固态核磁共振结果补充了核磁共振晶体学分析,使用包括投影仪增强波(GIPAW)方法。对于组氨酸·HCl·H2O,已检测到与14n - 1h和35cl - 1h距离达4.4和3.9 Å的2D峰。通过观察多巴胺·HCl中14n - 1h和35cl - 1h距离分别为4.2和3.7 Å的2D峰进一步证实了这一点,表明HMQC-SD-RFDR实验适用于检测分子固体中的中程距离。
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引用次数: 1
19F Solid-state NMR characterization of pharmaceutical solids 19F药物固体的固体核磁共振表征
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-08-01 DOI: 10.1016/j.ssnmr.2022.101796
Yong Du , Yongchao Su

Solid-state NMR has been increasingly recognized as a high-resolution and versatile spectroscopic tool to characterize drug substances and products. However, the analysis of pharmaceutical materials is often carried out at natural isotopic abundance and a relatively low drug loading in multi-component systems and therefore suffers from challenges of low sensitivity. The fact that fluorinated therapeutics are well represented in pipeline drugs and commercial products offers an excellent opportunity to utilize fluorine as a molecular probe for pharmaceutical analysis. We aim to review recent advancements of 19F magic angle spinning NMR methods in modern drug research and development. Applications to polymorph screening at the micromolar level, structural elucidation, and investigation of molecular interactions at the Ångström to submicron resolution in drug delivery, stability, and quality will be discussed.

固体核磁共振作为一种高分辨率和多用途的光谱工具,已越来越多地被认为是表征原料药和产品的工具。然而,药物材料的分析通常是在天然同位素丰度和多组分系统中相对较低的药物负荷下进行的,因此受到低灵敏度的挑战。氟化疗法在管道药物和商业产品中很有代表性,这一事实为利用氟作为分子探针进行药物分析提供了极好的机会。本文综述了19F魔角自旋核磁共振方法在现代药物研究和开发中的最新进展。将讨论在微摩尔水平上的多晶筛选、结构解析以及在Ångström到亚微米分辨率下分子相互作用在药物传递、稳定性和质量方面的应用。
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引用次数: 7
t1-noise elimination by continuous chemical shift anisotropy refocusing t1-连续化学位移各向异性重聚焦噪声消除
IF 3.2 3区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2022-08-01 DOI: 10.1016/j.ssnmr.2022.101807
Frédéric A. Perras , Tian Wei Goh , Wenyu Huang

Due to their high gyromagnetic ratio, there is considerable interest in measuring distances and correlations involving protons, but such measurements are compounded by the simultaneous recoupling of chemical shift anisotropy (CSA). This secondary recoupling adds additional modulations to the signal intensities that ultimately lead to t1-noise and signal decay. Recently, Venkatesh et al. demonstrated that the addition of CSA refocusing periods during 1H-X dipolar recoupling led to sequences with far higher stability and performance. Herein, we describe a related effort and develop a symmetry-based recoupling sequence that continually refocuses the 1H CSA. This sequence shows superior performance to the regular and t1-noise eliminated D-HMQC sequences in the case of spin-1/2 nuclei and comparable performance to the later for half-integer quadrupoles.

由于它们的高回旋磁比,人们对测量涉及质子的距离和相关性有相当大的兴趣,但这种测量由于化学位移各向异性(CSA)的同时重新耦合而复杂化。这种二次重耦增加了信号强度的额外调制,最终导致t1噪声和信号衰减。最近,Venkatesh等人证明,在1H-X偶极重耦期间增加CSA重聚焦周期可以使序列具有更高的稳定性和性能。在这里,我们描述了一个相关的努力,并开发了一个基于对称的重偶联序列,不断地重新聚焦1H CSA。该序列在自旋为1/2核的情况下表现出优于常规和t1噪声消除的D-HMQC序列的性能,并且在半整数四极子的情况下表现出与后者相当的性能。
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引用次数: 3
期刊
Solid state nuclear magnetic resonance
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