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Emsley L. Spiers Memorial Lecture: NMR crystallography. Faraday Discuss 2024. [PMID: 39405130 PMCID: PMC11477664 DOI: 10.1039/d4fd00151f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 09/03/2024] [Indexed: 10/19/2024]
Abstract
Chemical function is directly related to the spatial arrangement of atoms. Consequently, the determination of atomic-level three-dimensional structures has transformed molecular and materials science over the past 60 years. In this context, solid-state NMR has emerged to become the method of choice for atomic-level characterization of complex materials in powder form. In the following we present an overview of current methods for chemical shift driven NMR crystallography, illustrated with applications to complex materials.
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Affiliation(s)
- Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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2
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Rehman Z, Franks WT, Nguyen B, Schmidt HF, Scrivens G, Brown SP. Discovering the Solid-State Secrets of Lorlatinib by NMR Crystallography: To Hydrogen Bond or not to Hydrogen Bond. J Pharm Sci 2023; 112:1915-1928. [PMID: 36868358 DOI: 10.1016/j.xphs.2023.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023]
Abstract
Lorlatinib is an active pharmaceutical ingredient (API) used in the treatment of lung cancer. Here, an NMR crystallography analysis is presented whereby the single-crystal X-ray diffraction structure (CSD: 2205098) determination is complemented by multinuclear (1H, 13C, 14/15N, 19F) magic-angle spinning (MAS) solid-state NMR and gauge-including projector augmented wave (GIPAW) calculation of NMR chemical shifts. Lorlatinib crystallises in the P21 space group, with two distinct molecules in the asymmetric unit cell, Z' = 2. Three of the four NH2 hydrogen atoms form intermolecular hydrogen bonds, N30-H…N15 between the two distinct molecules and N30-H…O2 between two equivalent molecules. This is reflected in one of the NH21H chemical shifts being significantly lower, 4.0 ppm compared to 7.0 ppm. Two-dimensional 1H-13C, 14N-1H and 1H (double-quantum, DQ)-1H (single-quantum, SQ) MAS NMR spectra are presented. The 1H resonances are assigned and specific HH proximities corresponding to the observed DQ peaks are identified. The resolution enhancement at a 1H Larmor frequency of 1 GHz as compared to 500 or 600 MHz is demonstrated.
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Affiliation(s)
- Zainab Rehman
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | | | | | | | - Steven P Brown
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK.
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Tatman BP, Modha H, Brown SP. Comparison of methods for 14N- 1H recoupling in 14N- 1H HMQC MAS NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107459. [PMID: 37148711 DOI: 10.1016/j.jmr.2023.107459] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/08/2023] [Accepted: 04/19/2023] [Indexed: 05/08/2023]
Abstract
1H-detected 14N heteronuclear multiple-quantum coherence (HMQC) magic-angle-spinning (MAS) NMR experiments performed at fast magic-angle spinning (≥50 kHz) are finding increasing application, e.g., to pharmaceuticals. Of importance to the efficacy of these techniques is the recoupling technique applied to reintroduce the 1H-14N dipolar coupling. In this paper, we compare, by experiment and 2-spin density matrix simulations, two classes of recoupling scheme: first, those based on n = 2 rotary resonance, namely R3 and spin-polarisation inversion SPI-R3, and the symmetry based SR412 method and, second, the TRAPDOR method. Both classes require optimisation depending on the magnitude of the quadrupolar interaction, and thus there is a compromise choice for samples with more than one nitrogen site, as is the case for the studied dipeptide β-AspAla that contains two nitrogen sites with a small and large quadrupolar coupling constant. Considering this, we observe better sensitivity for the TRAPDOR method, though noting the marked sensitivity of TRAPDOR to the 14N transmitter offset, with both SPI-R3 and SR412 giving similar recoupling performance.
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Affiliation(s)
- Ben P Tatman
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Haritosh Modha
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
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Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.
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Affiliation(s)
- Yusuke Nishiyama
- JEOL Ltd., Akishima, Tokyo196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa230-0045, Japan
| | - Guangjin Hou
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian116023, China
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad500 046, India
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan41809-1055, United States
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5
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Synthesis, characterization, and biological activities of new conjugates of Guanosine grafted on polyvinyl alcohol, carbohydrate chitosan, and cellulose. Polym Bull (Berl) 2022. [DOI: 10.1007/s00289-022-04363-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractGuanosine (GU) is a purine nucleoside that has different biological applications. This study aimed to synthesize, characterize, and enhance the biological activities of GU through its covalently grafting on polyvinyl alcohol (PVA), chitosan (CS), and cellulose (CL). In this regard, the conjugation was constructed by different linkers such as chloroacetyl chloride, 2-bromopropionyl bromide, and epichlorohydrin (EPCH). The resulted novel conjugates were characterized by FT-IR, 1H-NMR, GPC, and TGA techniques. FT-IR spectra revealed the main characteristic groups, O–H, N–H, C=O and C=N of GU moieties. Furthermore, 1H-NMR spectra showed the aromatic C–H, O–H, and N–H protons of the grafted GU moieties. Two decomposition stages of grated polymers with high thermal stability are illustrated by TGA. GU showed no antifungal activity against Aspergillus fumigatus and Candida albicans. However, its conjugates: P-1A, P-1B, P-2A, P-2B, P-3A, and P-3B displayed significant antifungal effect with inhibitory zones in the range 8–11 mm. As compared to GU group, most of GU-polymer conjugates showed significant in vivo antitumor activity against EAC-bearing mice via the reduction in total tumor volume. In summary, these conjugates are biologically active macromolecules and may act as candidate carrier systems for other applications such as drug delivery.
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Mathew R, Sergeyev IV, Aussenac F, Gkoura L, Rosay M, Baias M. Complete resonance assignment of a pharmaceutical drug at natural isotopic abundance from DNP-Enhanced solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 119:101794. [PMID: 35462269 DOI: 10.1016/j.ssnmr.2022.101794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Solid-state dynamic nuclear polarization enhanced magic angle spinning (DNP-MAS) NMR measurements coupled with density functional theory (DFT) calculations enable the full resonance assignment of a complex pharmaceutical drug molecule without the need for isotopic enrichment. DNP dramatically enhances the NMR signals, thereby making possible previously intractable two-dimensional correlation NMR spectra at natural abundance. Using inputs from DFT calculations, herein we describe a significant improvement to the structure elucidation process for complex organic molecules. Further, we demonstrate that a series of two-dimensional correlation experiments, including 15N-13C TEDOR, 13C-13C INADEQUATE/SARCOSY, 19F-13C HETCOR, and 1H-13C HETCOR, can be obtained at natural isotopic abundance within reasonable experiment times, thus enabling a complete resonance assignment of sitagliptin, a pharmaceutical used for the treatment of type 2 diabetes.
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Affiliation(s)
- Renny Mathew
- Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Ivan V Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, USA
| | - Fabien Aussenac
- Bruker France, 34 rue de l'industrie, 67166, Wissembourg, France.
| | - Lydia Gkoura
- Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates.
| | - Melanie Rosay
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, USA
| | - Maria Baias
- Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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R Luginbuhl B, Raval P, Pawlak T, Du Z, Wang T, Kupgan G, Schopp N, Chae S, Yoon S, Yi A, Jung Kim H, Coropceanu V, Brédas JL, Nguyen TQ, Reddy GNM. Resolving Atomic-Scale Interactions in Nonfullerene Acceptor Organic Solar Cells with Solid-State NMR Spectroscopy, Crystallographic Modelling, and Molecular Dynamics Simulations. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2105943. [PMID: 34818688 DOI: 10.1002/adma.202105943] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Fused-ring core nonfullerene acceptors (NFAs), designated "Y-series," have enabled high-performance organic solar cells (OSCs) achieving over 18% power conversion efficiency (PCE). Since the introduction of these NFAs, much effort has been expended to understand the reasons for their exceptional performance. While several studies have identified key optoelectronic properties that govern high PCEs, little is known about the molecular level origins of large variations in performance, spanning from 5% to 18% PCE, for example, in the case of PM6:Y6 OSCs. Here, a combined solid-state NMR, crystallography, and molecular modeling approach to elucidate the atomic-scale interactions in Y6 crystals, thin films, and PM6:Y6 bulk heterojunction (BHJ) blends is introduced. It is shown that the Y6 morphologies in BHJ blends are not governed by the morphology in neat films or single crystals. Notably, PM6:Y6 blends processed from different solvents self-assemble into different structures and morphologies, whereby the relative orientations of the sidechains and end groups of the Y6 molecules to their fused-ring cores play a crucial role in determining the resulting morphology and overall performance of the solar cells. The molecular-level understanding of BHJs enabled by this approach will guide the engineering of next-generation NFAs for stable and efficient OSCs.
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Affiliation(s)
- Benjamin R Luginbuhl
- Center for Polymers & Organic Solids, Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Parth Raval
- University of Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181, Unité de Catalyse et Chimie du Solide, Lille, F-59000, France
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Zhifang Du
- Center for Polymers & Organic Solids, Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Tonghui Wang
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721-0088, USA
| | - Grit Kupgan
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721-0088, USA
| | - Nora Schopp
- Center for Polymers & Organic Solids, Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Sangmin Chae
- Center for Polymers & Organic Solids, Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Sangcheol Yoon
- Center for Polymers & Organic Solids, Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Ahra Yi
- Department of Organic Material Science and Engineering, School of Chemical Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Hyo Jung Kim
- Department of Organic Material Science and Engineering, School of Chemical Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Veaceslav Coropceanu
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721-0088, USA
| | - Jean-Luc Brédas
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721-0088, USA
| | - Thuc-Quyen Nguyen
- Center for Polymers & Organic Solids, Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - G N Manjunatha Reddy
- University of Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181, Unité de Catalyse et Chimie du Solide, Lille, F-59000, France
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8
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Zeng P, Zhang WD. A strategy for integrating transition metal-complex cocatalyst onto g-C3N4 to enable efficient photocatalytic hydrogen evolution. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Iuga D, Corlett EK, Brown SP. 35 Cl- 1 H Heteronuclear correlation magic-angle spinning nuclear magnetic resonance experiments for probing pharmaceutical salts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:1089-1100. [PMID: 34196042 DOI: 10.1002/mrc.5188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Heteronuclear multiple-quantum coherence (HMQC) pulse sequences for establishing heteronuclear correlation in solid-state nuclear magnetic resonance (NMR) between 35 Cl and 1 H nuclei in chloride salts under fast (60 kHz) magic-angle spinning (MAS) and at high magnetic field (a 1 H Larmor frequency of 850 MHz) are investigated. Specifically, recoupling of the 35 Cl-1 H dipolar interaction using rotary resonance recoupling with phase inversion every rotor period or the symmetry-based SR42 1 pulse sequences are compared. In our implementation of the population transfer (PT) dipolar (D) HMQC experiment, the satellite transitions of the 35 Cl nuclei are saturated with an off-resonance WURST sweep, at a low nutation frequency, over the second spinning sideband, whereby the WURST pulse must be of the same duration as the recoupling time. Numerical simulations of the 35 Cl-1 H MAS D-HMQC experiment performed separately for each crystallite orientation in a powder provide insight into the orientation dependence of changes in the second-order quadrupolar-broadened 35 Cl MAS NMR lineshape under the application of dipolar recoupling. Two-dimensional 35 Cl-1 H PT-D-HMQC MAS NMR spectra are presented for the amino acids glycine·HCl and l-tyrosine·HCl and the pharmaceuticals cimetidine·HCl, amitriptyline·HCl and lidocaine·HCl·H2 O. Experimentally observed 35 Cl lineshapes are compared with those simulated for 35 Cl chemical shift and quadrupolar parameters as calculated using the gauge-including projector-augmented wave (GIPAW) method: the calculated quadrupolar product (PQ ) values exceed those measured experimentally by a factor of between 1.3 and 1.9.
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Affiliation(s)
- Dinu Iuga
- Department of Physics, University of Warwick, Coventry, UK
| | | | - Steven P Brown
- Department of Physics, University of Warwick, Coventry, UK
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Samanta S, Raval P, Manjunatha Reddy GN, Chaudhuri D. Cooperative Self-Assembly Driven by Multiple Noncovalent Interactions: Investigating Molecular Origin and Reassessing Characterization. ACS CENTRAL SCIENCE 2021; 7:1391-1399. [PMID: 34471682 PMCID: PMC8393228 DOI: 10.1021/acscentsci.1c00604] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Indexed: 05/20/2023]
Abstract
Cooperative interactions play a pivotal role in programmable supramolecular assembly. Emerging from a complex interplay of multiple noncovalent interactions, achieving cooperativity has largely relied on empirical knowledge. Its development as a rational design tool in molecular self-assembly requires a detailed characterization of the underlying interactions, which has hitherto been a challenge for assemblies that lack long-range order. We employ extensive one- and two-dimensional magic-angle-spinning (MAS) solid-state NMR spectroscopy to elucidate key structure-directing interactions in cooperatively bound aggregates of a perylene bisimide (PBI) chromophore. Analysis of 1H-13C cross-polarization heteronuclear correlation (CP-HETCOR) and 1H-1H double-quantum single-quantum (DQ-SQ) correlation spectra allow the identification of through-space 1H···13C and 1H···1H proximities in the assembled state and reveals the nature of molecular organization in the solid aggregates. Emergence of cooperativity from the synergistic interaction between a stronger π-stacking and a weaker interstack hydrogen-bonding is elucidated. Finally, using a combination of optical absorption, circular dichroism, and high-resolution MAS NMR spectroscopy based titration experiments, we investigate the anomalous solvent-induced disassembly of aggregates. Our results highlight the disparity between two well-established approaches of characterizing cooperativity, using thermal and good solvent-induced disassembly. The anomaly is explained by elucidating the difference between two disassembly pathways.
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Affiliation(s)
- Samaresh Samanta
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Parth Raval
- Univ.
Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181, Unité
de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - G. N. Manjunatha Reddy
- Univ.
Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181, Unité
de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Debangshu Chaudhuri
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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12
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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Wu B, Liu Y, Chen F, Li J, Yu Y, Zhou Y, Li L, Xiao J, Ma Y. Investigation on the formation mechanism of twinned crystals of hypoxanthine-doped beta-phase anhydrous guanine microplatelets. CrystEngComm 2021. [DOI: 10.1039/d1ce00148e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Herein, hypoxanthine-doped β phase anhydrous guanine (I-doped β-AG) twinned crystals with varying hypoxanthine contents were obtained in formamide. The occlusion of hypoxanthine in β-AG might be a key factor for formation of twinned β-AG crystals.
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Affiliation(s)
- Bianbian Wu
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Yanan Liu
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Fenghua Chen
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Jiangfeng Li
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Yue Yu
- College of Chemistry
- Peking University
- Beijing
- China
| | - Yinglin Zhou
- College of Chemistry
- Peking University
- Beijing
- China
| | - Ling Li
- Department of Mechanical Engineering
- Virginia Polytechnic Institute and State University
- Blacksburg
- 24061 USA
| | - Jie Xiao
- Department of Highly Sensitive X-ray Spectroscopy
- Helmholtz-Zentrum Berlin für Materialien und Energie
- Berlin
- Germany
| | - Yurong Ma
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
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14
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Grosu IG, Filip X, Miclăuș MO, Filip C. Hydrogen-Mediated Noncovalent Interactions in Solids: What Can NMR Crystallography Tell About? Molecules 2020; 25:E3757. [PMID: 32824749 PMCID: PMC7463941 DOI: 10.3390/molecules25163757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/15/2020] [Accepted: 08/16/2020] [Indexed: 12/18/2022] Open
Abstract
Hydrogen atoms play a crucial role in the aggregation of organic (bio)molecules through diverse number of noncovalent interactions that they mediate, such as electrostatic in proton transfer systems, hydrogen bonding, and CH-π interactions, to mention only the most prominent. To identify and adequately describe such low-energy interactions, increasingly sensitive methods have been developed over time, among which quantum chemical computations have witnessed impressive advances in recent years. For reaching the present state-of-the-art, computations had to rely on a pool of relevant experimental data, needed at least for validation, if not also for other purposes. In the case of molecular crystals, the best illustration for the synergy between computations and experiment is given by the so-called NMR crystallography approach. Originally designed to increase the confidence level in crystal structure determination of organic compounds from powders, NMR crystallography is able now to offer also a wealth of information regarding the noncovalent interactions that drive molecules to pack in a given crystalline pattern or another. This is particularly true for the noncovalent interactions which depend on the exact location of labile hydrogen atoms in the system: in such cases, NMR crystallography represents a valuable characterization tool, in some cases complementing even the standard single-crystal X-ray diffraction technique. A concise introduction in the field is made in this mini-review, which is aimed at providing a comprehensive picture with respect to the current accuracy level reached by NMR crystallography in the characterization of hydrogen-mediated noncovalent interactions in organic solids. Different types of practical applications are illustrated with the example of molecular crystals studied by our research group, but references to other representative developments reported in the literature are also made. By summarizing the major concepts and methodological progresses, the present work is also intended to be a guide to the practical potential of this relatively recent analytical tool for the scientists working in areas where crystal engineering represents the main approach for rational design of novel materials.
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Affiliation(s)
| | | | | | - Claudiu Filip
- National Institute for R&D of Isotopic and Molecular Technologies, 400293 Cluj, Romania; (I.G.G.); (X.F.); (M.O.M.)
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15
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Hodgkinson P. NMR crystallography of molecular organics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:10-53. [PMID: 32883448 DOI: 10.1016/j.pnmrs.2020.03.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/25/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.
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Affiliation(s)
- Paul Hodgkinson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, UK.
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16
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Self‐Assembly of DNA and RNA Building Blocks Explored by Nitrogen‐14 NMR Crystallography: Structure and Dynamics. Chemphyschem 2020; 21:1044-1051. [DOI: 10.1002/cphc.201901214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/18/2020] [Indexed: 12/20/2022]
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17
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Bai J, Sun X, Wang H, Li C, Qiao R. Guanosine-Based Self-Assembly as an Enantioselective Catalyst Scaffold. J Org Chem 2020; 85:2010-2018. [PMID: 31935325 DOI: 10.1021/acs.joc.9b02718] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A self-assembled G-quadruplex formed by guanosine and borate as the chiral scaffold was used to catalyze the asymmetric Friedel-Crafts reaction in water. Catalysis, depending on the self-assembly of guanosine and borate into a fibrillar structure in the presence of Cu2+ ions, can be modulated by the assembly concentration, temperature, and amount of Cu2+ ions. Detailed spectral experiments proved that the guanosine-based assembly in solution was responsible for the enantioselective catalysis, rather than small-molecule species. Some of the similar G-quartet assemblies were unable to promote the asymmetric reaction, implying unique properties of the current system, including excellent lifetime stability and supramolecular chiral structures. This work provided the first example of the self-assembled G-quadruplex achieving enantioselective catalysis and some perspective to better understand the design of nucleoside-based self-assemblies for an enantioselective reaction. In view of guanosine as a building block, these findings may be applied to discuss the prebiotic chiral catalyst preceded ribozymes.
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Affiliation(s)
- Jiakun Bai
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , No. 15, Beisanhuan East Road , Beijing 100029 , China
| | - Xiaolin Sun
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , No. 15, Beisanhuan East Road , Beijing 100029 , China
| | - Haisheng Wang
- Harbin Pharmaceutical Group Holding Co., Ltd. , Harbin 150018 , China
| | - Chao Li
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , No. 15, Beisanhuan East Road , Beijing 100029 , China
| | - Renzhong Qiao
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , No. 15, Beisanhuan East Road , Beijing 100029 , China
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Haimovich A, Goldbourt A. How does the mood stabilizer lithium bind ATP, the energy currency of the cell: Insights from solid-state NMR. Biochim Biophys Acta Gen Subj 2019; 1864:129456. [PMID: 31678143 DOI: 10.1016/j.bbagen.2019.129456] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/07/2019] [Accepted: 10/24/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Lithium, in the form of a salt, is a mood stabilizer and a leading drug for the treatment of bipolar disorder. It has a very narrow therapeutic range and a variety of side effects. Lithium can replace magnesium and other cations in enzymes and small molecules, among them ATP, thereby affecting and inhibiting many biochemical pathways. The form of binding of lithium ions to ATP is not known. METHODS Here we extract the binding environment of lithium in solid ATP using a multi-nuclear multi-dimensional solid-state NMR approach. RESULTS We determine that the coordination sphere of lithium includes, at a distance of 3.0(±0.4) Å, three phosphates; the two phosphates closest to the ribose ring from one ATP molecule, and the middle phosphate from another ATP molecule. A water molecule most probably completes the fourth coordination. Despite the use of excess lithium in the preparations, sodium ions still remain bound to the sample, at distances of 4.3-5.5 Å from Li, and coordinate the first phosphate and two terminal phosphates. CONCLUSIONS Solid-state NMR enables to unravel the exact coordination of lithium in ATP showing binding to three phosphates from two molecules, none of which are the terminal gamma phosphate. GENERAL SIGNIFICANCE The methods we use are applicable to study lithium bound to a variety of ATP-bound enzymes, or to other cellular targets of lithium, consequently suggesting a molecular basis for its mode of action.
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Affiliation(s)
- A Haimovich
- School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - A Goldbourt
- School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.
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Chen M, Lin W, Hong L, Ji N, Zhao H. The Development and Lifetime Stability Improvement of Guanosine-Based Supramolecular Hydrogels through Optimized Structure. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6258248. [PMID: 31312660 PMCID: PMC6595390 DOI: 10.1155/2019/6258248] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/12/2019] [Accepted: 04/24/2019] [Indexed: 02/05/2023]
Abstract
Guanosine is an important building block for supramolecular gels owing to the unique self-assembly property that results from the unique hydrogen bond acceptors and donor groups. Guanosine-derived supramolecular hydrogels have promise in the fields of drug delivery, targeted release, tissue engineering applications, etc. However, the property of poor longevity and the need for excess cations hinder the widespread applications of guanosine hydrogels. Although guanosine-derived supramolecular hydrogels have been reviewed previously by Dash et al., the structural framework of this review is different, as the modification of guanosine is described at the molecular level. In this review, we summarize the development and lifetime stability improvement of guanosine-based supramolecular hydrogels through optimized structure and elaborate on three aspects: sugar modification, base modification, and binary gels. Additionally, we introduce the concept and recent research progress of self-healing gels, providing inspiration for the development of guanosine-derived supramolecular hydrogels with longer lifespans, unique physicochemical properties, and biological activities.
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Affiliation(s)
- Miao Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Weimin Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Le Hong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ning Ji
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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20
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Lu X, Skomski D, Thompson KC, McNevin MJ, Xu W, Su Y. Three-Dimensional NMR Spectroscopy of Fluorinated Pharmaceutical Solids under Ultrafast Magic Angle Spinning. Anal Chem 2019; 91:6217-6224. [DOI: 10.1021/acs.analchem.9b00884] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xingyu Lu
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Daniel Skomski
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Karen C. Thompson
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Michael J. McNevin
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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21
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Giovine R, Trébosc J, Pourpoint F, Lafon O, Amoureux JP. Magnetization transfer from protons to quadrupolar nuclei in solid-state NMR using PRESTO or dipolar-mediated refocused INEPT methods. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 299:109-123. [PMID: 30594000 DOI: 10.1016/j.jmr.2018.12.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/11/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
In solid-state NMR spectroscopy, the through-space transfer of magnetization from protons to quadrupolar nuclei is employed to probe proximities between those isotopes. Furthermore, such transfer, in conjunction with Dynamic Nuclear Polarization (DNP), can enhance the NMR sensitivity of quadrupolar nuclei, as it allows the transfer of DNP-enhanced 1H polarization to surrounding nuclei. We compare here the performances of two approaches to achieve such transfer: PRESTO (Phase-shifted Recoupling Effects a Smooth Transfer of Order), which is currently the method of choice to achieve the magnetization transfer from protons to quadrupolar nuclei and which has been shown to supersede Cross-Polarization under Magic-Angle Spinning (MAS) for quadrupolar nuclei and D-RINEPT (Dipolar-mediated Refocused Insensitive Nuclei Enhanced by Polarization Transfer) using symmetry-based SR412 recoupling, which has already been employed to transfer the magnetization in the reverse way from half-integer quadrupolar spin to protons. We also test the PRESTO sequence with R1676 recoupling using 270090180 composite π-pulses as inversion elements. This recoupling scheme, which has previously been proposed to reintroduce 1H Chemical Shift Anisotropy (CSA) at high MAS frequencies with high robustness to rf-field inhomogeneity, has not so far been employed to reintroduce dipolar couplings with protons. These various techniques to transfer magnetization from protons to quadrupolar nuclei are analyzed using (i) an average Hamiltonian theory, (ii) numerical simulations of spin dynamics, and (iii) experimental 1H → 27Al and 1H → 17O transfers in as-synthesized AlPO4-14 and 17O-labelled fumed silica, respectively. The experiments and simulations are done at two magnetic fields (9.4 and 18.8 T) and several spinning speeds (15, 18-24 and 60 kHz). This analysis indicates that owing to its γ-encoded character, PRESTO yields the highest transfer efficiency at low magnetic fields and MAS frequencies, whereas owing to its higher robustness to rf-field inhomogeneity and chemical shifts, D-RINEPT is more sensitive at high fields and MAS frequencies, notably for protons exhibiting large offset or CSA, such as those involved in hydrogen bonds.
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Affiliation(s)
- Raynald Giovine
- Univ. Lille, CNRS-8181, UCCS: Unit of Catalysis and Chemistry of Solids, F-59000 Lille, France
| | - Julien Trébosc
- Univ. Lille, CNRS-8181, UCCS: Unit of Catalysis and Chemistry of Solids, F-59000 Lille, France
| | - Frédérique Pourpoint
- Univ. Lille, CNRS-8181, UCCS: Unit of Catalysis and Chemistry of Solids, F-59000 Lille, France
| | - Olivier Lafon
- Univ. Lille, CNRS-8181, UCCS: Unit of Catalysis and Chemistry of Solids, F-59000 Lille, France; IUF, Institut Universitaire de France, 1 rue Descartes, 75231 Paris, France.
| | - Jean-Paul Amoureux
- Univ. Lille, CNRS-8181, UCCS: Unit of Catalysis and Chemistry of Solids, F-59000 Lille, France; Bruker France, 34 rue de l'Industrie, F-67166 Wissembourg, France.
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22
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Chen F, Wu B, Elad N, Gal A, Liu Y, Ma Y, Qi L. Controlled crystallization of anhydrous guanine β nano-platelets via an amorphous precursor. CrystEngComm 2019. [DOI: 10.1039/c9ce00245f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We realized a pure phase of anhydrous guanine (AG) β form for the first time via a transformation from hydrated amorphous guanine phase (HAmG). The specified transformation was probably due to the similar short-range order between AG β and HAmG.
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Affiliation(s)
- Fenghua Chen
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- College of Chemistry
- Peking University
- Beijing 100871
| | - Bianbian Wu
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Nadav Elad
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 760001
- Israel
| | - Assaf Gal
- Department of Plant and Environmental Sciences
- Weizmann Institute of Science
- Rehovot 760001
- Israel
| | - Yanan Liu
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Yurong Ma
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Limin Qi
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- College of Chemistry
- Peking University
- Beijing 100871
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23
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24
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Choi CH, Lin L, Gim S, Lee S, Kim H, Wang X, Choi W. Polymeric Carbon Nitride with Localized Aluminum Coordination Sites as a Durable and Efficient Photocatalyst for Visible Light Utilization. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03512] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Chi Hun Choi
- Department of Chemical Engineering/Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Lihua Lin
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350002, People’s Republic of China
| | - Suji Gim
- Graduate School of Energy, Environment, Water, and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Shinbi Lee
- Department of Chemical Engineering/Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyungjun Kim
- Graduate School of Energy, Environment, Water, and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Xinchen Wang
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350002, People’s Republic of China
| | - Wonyong Choi
- Department of Chemical Engineering/Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
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25
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Advanced solid-state NMR methods for characterising structure and self-assembly in supramolecular chemistry, polymers and hydrogels. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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26
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Venâncio T, Oliveira LM, Ellena J, Boechat N, Brown SP. Probing intermolecular interactions in a diethylcarbamazine citrate salt by fast MAS 1H solid-state NMR spectroscopy and GIPAW calculations. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:73-79. [PMID: 28342733 DOI: 10.1016/j.ssnmr.2017.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 06/06/2023]
Abstract
Fast magic-angle spinning (MAS) NMR is used to probe intermolecular interactions in a diethylcarbamazine salt, that is widely used as a treatment against adult worms of Wuchereria bancrofti which cause a common disease in tropical countries named filariasis. Specifically, a dihydrogen citrate salt that has improved thermal stability and solubility as compared to the free form is studied. One-dimensional 1H, 13C and 15N and two-dimensional 1H-13C and 14N-1H heteronuclear correlation NMR experiments under moderate and fast MAS together with GIPAW (CASTEP) calculations enable the assignment of the 1H, 13C and 14N/15N resonances. A two-dimensional 1H-1H double-quantum (DQ) -single-quantum (SQ) MAS spectrum recorded with BaBa recoupling at 60kHz MAS identifies specific proton-proton proximities associated with citrate-citrate and citrate-diethylcarbamazine intermolecular interactions.
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Affiliation(s)
- Tiago Venâncio
- Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luis, km 235, São Carlos, SP 13565-905, Brazil; Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
| | - Lyege Magalhaes Oliveira
- Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luis, km 235, São Carlos, SP 13565-905, Brazil
| | - Javier Ellena
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador são-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Nubia Boechat
- Fundação Oswaldo Cruz - FioCruz, Instituto de Tecnologia em Fármacos-FarManguinhos, Rua Sizenando Nabuco 100, Rio de Janeiro, RJ 21041-250, Brazil
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
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27
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Hughes CE, Reddy GNM, Masiero S, Brown SP, Williams PA, Harris KDM. Determination of a complex crystal structure in the absence of single crystals: analysis of powder X-ray diffraction data, guided by solid-state NMR and periodic DFT calculations, reveals a new 2'-deoxyguanosine structural motif. Chem Sci 2017; 8:3971-3979. [PMID: 28553539 PMCID: PMC5433513 DOI: 10.1039/c7sc00587c] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/15/2017] [Indexed: 12/20/2022] Open
Abstract
Derivatives of guanine exhibit diverse supramolecular chemistry, with a variety of distinct hydrogen-bonding motifs reported in the solid state, including ribbons and quartets, which resemble the G-quadruplex found in nucleic acids with sequences rich in guanine. Reflecting this diversity, the solid-state structural properties of 3',5'-bis-O-decanoyl-2'-deoxyguanosine, reported in this paper, reveal a hydrogen-bonded guanine ribbon motif that has not been observed previously for 2'-deoxyguanosine derivatives. In this case, structure determination was carried out directly from powder XRD data, representing one of the most challenging organic molecular structures (a 90-atom molecule) that has been solved to date by this technique. While specific challenges were encountered in the structure determination process, a successful outcome was achieved by augmenting the powder XRD analysis with information derived from solid-state NMR data and with dispersion-corrected periodic DFT calculations for structure optimization. The synergy of experimental and computational methodologies demonstrated in the present work is likely to be an essential feature of strategies to further expand the application of powder XRD as a technique for structure determination of organic molecular materials of even greater complexity in the future.
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Affiliation(s)
- Colan E Hughes
- School of Chemistry , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | | | - Stefano Masiero
- Dipartimento di Chimica "G. Ciamician" , Alma Mater Studiorum - Università di Bologna , via San Giacomo , 11-40126 Bologna , Italy
| | - Steven P Brown
- Department of Physics , University of Warwick , Coventry , CV4 7AL , UK
| | - P Andrew Williams
- School of Chemistry , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - Kenneth D M Harris
- School of Chemistry , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
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28
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Reddy GNM, Huqi A, Iuga D, Sakurai S, Marsh A, Davis JT, Masiero S, Brown SP. Co-existence of Distinct Supramolecular Assemblies in Solution and in the Solid State. Chemistry 2016; 23:2315-2322. [PMID: 27897351 PMCID: PMC5396329 DOI: 10.1002/chem.201604832] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 11/24/2022]
Abstract
The formation of distinct supramolecular assemblies, including a metastable species, is revealed for a lipophilic guanosine (G) derivative in solution and in the solid state. Structurally different G‐quartet‐based assemblies are formed in chloroform depending on the nature of the cation, anion and the salt concentration, as characterized by circular dichroism and time course diffusion‐ordered NMR spectroscopy data. Intriguingly, even the presence of potassium ions that stabilize G‐quartets in chloroform was insufficient to exclusively retain such assemblies in the solid state, leading to the formation of mixed quartet and ribbon‐like assemblies as revealed by fast magic‐angle spinning (MAS) NMR spectroscopy. Distinct N−H⋅⋅⋅N and N−H⋅⋅⋅O intermolecular hydrogen bonding interactions drive quartet and ribbon‐like self‐assembly resulting in markedly different 2D 1H solid‐state NMR spectra, thus facilitating a direct identification of mixed assemblies. A dissolution NMR experiment confirmed that the quartet and ribbon interconversion is reversible–further demonstrating the changes that occur in the self‐assembly process of a lipophilic nucleoside upon a solid‐state to solution‐state transition and vice versa. A systematic study for complexation with different cations (K+, Sr2+) and anions (picrate, ethanoate and iodide) emphasizes that the existence of a stable solution or solid‐state structure may not reflect the stability of the same supramolecular entity in another phase.
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Affiliation(s)
- G N Manjunatha Reddy
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
| | - Aida Huqi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy
| | - Dinu Iuga
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
| | - Satoshi Sakurai
- JEOL (UK), Silver Court, Watchmead, Welwyn Garden City, AL7 1LT, UK
| | - Andrew Marsh
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
| | - Jeffery T Davis
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Stefano Masiero
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy
| | - Steven P Brown
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
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29
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Yuan Y, Shu J, Kolman K, Kiersnowski A, Bubeck C, Zhang J, Hansen MR. Multiple Chain Packing and Phase Composition in Regioregular Poly(3-butylthiophene) Films. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01828] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yuan Yuan
- Key Laboratory of Rubber-Plastics, Ministry of Education/Shandong Provincial Key Laboratory of Rubber-plastics, Qingdao University of Science & Technology, Qingdao 266042, China
- Max Planck Institute
for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
| | - Jie Shu
- Max Planck Institute
for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
- Analysis and Testing Center, Suzhou University, Renai Road 199, 215123 Suzhou, China
| | - Krzysztof Kolman
- Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
- Division of Applied Chemistry, Department of Chemistry and Chemical
Engineering, Chalmers University of Technology, SE 412 96 Gothenburg, Sweden
| | - Adam Kiersnowski
- Max Planck Institute
for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
- Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Christoph Bubeck
- Max Planck Institute
for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
| | - Jianming Zhang
- Key Laboratory of Rubber-Plastics, Ministry of Education/Shandong Provincial Key Laboratory of Rubber-plastics, Qingdao University of Science & Technology, Qingdao 266042, China
- Max Planck Institute
for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
| | - Michael Ryan Hansen
- Max Planck Institute
for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
- Institute of Physical Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
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30
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Reddy GNM, Malon M, Marsh A, Nishiyama Y, Brown SP. Fast Magic-Angle Spinning Three-Dimensional NMR Experiment for Simultaneously Probing H—H and N—H Proximities in Solids. Anal Chem 2016; 88:11412-11419. [DOI: 10.1021/acs.analchem.6b01869] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | - Michal Malon
- JEOL RESONANCE Inc., Musashino, Akishima,
Tokyo 196-8558, Japan
- RIKEN CLST-JEOL Collaboration Centre, Yokohama, Kanagawa 230-0045, Japan
| | | | - Yusuke Nishiyama
- JEOL RESONANCE Inc., Musashino, Akishima,
Tokyo 196-8558, Japan
- RIKEN CLST-JEOL Collaboration Centre, Yokohama, Kanagawa 230-0045, Japan
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31
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Peters GM, Davis JT. Supramolecular gels made from nucleobase, nucleoside and nucleotide analogs. Chem Soc Rev 2016; 45:3188-206. [PMID: 27146863 DOI: 10.1039/c6cs00183a] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Supramolecular or molecular gels are attractive for various applications, including diagnostics, tissue scaffolding and targeted drug release. Gelators derived from natural products are of particular interest for biomedical purposes, as they are generally biocompatible and stimuli-responsive. The building blocks of nucleic acids (i.e. nucleobases, nucleosides, and nucleotides) are desirable candidates for supramolecular gelation as they readily engage in reversible, noncovalent interactions. In this review, we describe a number of organo- and hydrogels formed through the assembly of nucleosides, nucleotides, and their derivatives. While natural nucleosides and nucleotides generally require derivatization to induce gelation, guanosine and its corresponding nucleotides are well known gelators. This unique gelating ability is due to propensity of the guanine nucleobase to self-associate into stable higher-order assemblies, such as G-ribbons, G4-quartets, and G-quadruplexes.
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Affiliation(s)
- Gretchen Marie Peters
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, Stop A5300, Austin, Texas 78712-1224, USA.
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32
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Fenniri H, Tikhomirov GA, Brouwer DH, Bouatra S, El Bakkari M, Yan Z, Cho JY, Yamazaki T. High Field Solid-State NMR Spectroscopy Investigation of 15N-Labeled Rosette Nanotubes: Hydrogen Bond Network and Channel-Bound Water. J Am Chem Soc 2016; 138:6115-8. [DOI: 10.1021/jacs.6b02420] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hicham Fenniri
- 313 Snell
Engineering Center, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | | | - Darren H. Brouwer
- Department of Chemistry, Redeemer University College, 777 Garner Road East, Ancaster, Ontario L9K 1J4, Canada
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Pinon A, Rossini AJ, Widdifield CM, Gajan D, Emsley L. Polymorphs of Theophylline Characterized by DNP Enhanced Solid-State NMR. Mol Pharm 2015; 12:4146-53. [PMID: 26393368 PMCID: PMC4699642 DOI: 10.1021/acs.molpharmaceut.5b00610] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/15/2015] [Accepted: 09/22/2015] [Indexed: 11/29/2022]
Abstract
We show how dynamic nuclear polarization (DNP) enhanced solid-state NMR spectroscopy can be used to characterize polymorphs and solvates of organic solids. We applied DNP to three polymorphs and one hydrated form of the asthma drug molecule theophylline. For some forms of theophylline, sample grinding and impregnation with the radical-containing solution, which are necessary to prepare the samples for DNP, were found to induce polymorphic transitions or desolvation between some forms. We present protocols for sample preparation for solid-state magic-angle spinning (MAS) DNP experiments that avoid the polymorphic phase transitions in theophylline. These protocols include cryogrinding, grinding under inert atmosphere, and the appropriate choice of the impregnating liquid. By applying these procedures, we subsequently demonstrate that two-dimensional correlation experiments, such as (1)H-(13)C and (1)H-(15)N HETCOR or (13)C-(13)C INADEQUATE, can be obtained at natural isotopic abundance in reasonable times, thus enabling more advanced structural characterization of polymorphs.
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Affiliation(s)
- Arthur
C. Pinon
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
| | - Aaron J. Rossini
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
| | - Cory M. Widdifield
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
| | - David Gajan
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
| | - Lyndon Emsley
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Institut
de Sciences Analytiques (CNRS/ENS de Lyon/UCB-Lyon 1), Centre de RMN
à Très Hauts Champs, Université
de Lyon, 69100 Villeurbanne, France
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Robertson AJ, Pandey MK, Marsh A, Nishiyama Y, Brown SP. The use of a selective saturation pulse to suppress t1 noise in two-dimensional (1)H fast magic angle spinning solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 260:89-97. [PMID: 26432398 DOI: 10.1016/j.jmr.2015.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/01/2015] [Accepted: 09/07/2015] [Indexed: 06/05/2023]
Abstract
A selective saturation pulse at fast magic angle spinning (MAS) frequencies (60+kHz) suppresses t1 noise in the indirect dimension of two-dimensional (1)H MAS NMR spectra. The method is applied to a synthetic nucleoside with an intense methyl (1)H signal due to triisopropylsilyl (TIPS) protecting groups. Enhanced performance in terms of suppressing the methyl signal while minimising the loss of signal intensity of nearby resonances of interest relies on reducing spin diffusion--this is quantified by comparing two-dimensional (1)H NOESY-like spin diffusion spectra recorded at 30-70 kHz MAS. For a saturation pulse centred at the methyl resonance, the effect of changing the nutation frequency at different MAS frequencies as well as the effect of changing the pulse duration is investigated. By applying a pulse of duration 30 ms and nutation frequency 725 Hz at 70 kHz MAS, a good compromise of significant suppression of the methyl resonance combined with the signal intensity of resonances greater than 5 ppm away from the methyl resonance being largely unaffected is achieved. The effectiveness of using a selective saturation pulse is demonstrated for both homonuclear (1)H-(1)H double quantum (DQ)/single quantum (SQ) MAS and (14)N-(1)H heteronuclear multiple quantum coherence (HMQC) two-dimensional solid-state NMR experiments.
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Affiliation(s)
- Aiden J Robertson
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom; Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Manoj Kumar Pandey
- RIKEN CLST-JEOL Collaboration Centre, Yokohama, Kanagawa 230-0045, Japan
| | - Andrew Marsh
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Centre, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom.
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Märker K, Pingret M, Mouesca JM, Gasparutto D, Hediger S, De Paëpe G. A New Tool for NMR Crystallography: Complete 13C/15N Assignment of Organic Molecules at Natural Isotopic Abundance Using DNP-Enhanced Solid-State NMR. J Am Chem Soc 2015; 137:13796-9. [DOI: 10.1021/jacs.5b09964] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katharina Märker
- Univ. Grenoble Alpes, INAC, F-38000 Grenoble, France
- CEA, INAC, F-38000 Grenoble, France
| | - Morgane Pingret
- Univ. Grenoble Alpes, INAC, F-38000 Grenoble, France
- CEA, INAC, F-38000 Grenoble, France
| | - Jean-Marie Mouesca
- Univ. Grenoble Alpes, INAC, F-38000 Grenoble, France
- CEA, INAC, F-38000 Grenoble, France
| | - Didier Gasparutto
- Univ. Grenoble Alpes, INAC, F-38000 Grenoble, France
- CEA, INAC, F-38000 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, INAC, F-38000 Grenoble, France
- CEA, INAC, F-38000 Grenoble, France
- CNRS, SCIB, F-38000 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, INAC, F-38000 Grenoble, France
- CEA, INAC, F-38000 Grenoble, France
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36
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Peters GM, Skala LP, Plank TN, Oh H, Manjunatha Reddy GN, Marsh A, Brown SP, Raghavan SR, Davis JT. G4-Quartet·M+ Borate Hydrogels. J Am Chem Soc 2015; 137:5819-27. [DOI: 10.1021/jacs.5b02753] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Gretchen Marie Peters
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Luke P. Skala
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Taylor N. Plank
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Hyuntaek Oh
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - G. N. Manjunatha Reddy
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Andrew Marsh
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Steven P. Brown
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Srinivasa R. Raghavan
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Jeffery T. Davis
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
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37
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Reddy GNM, Cook DS, Iuga D, Walton RI, Marsh A, Brown SP. An NMR crystallography study of the hemihydrate of 2', 3'-O-isopropylidineguanosine. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 65:41-48. [PMID: 25686689 DOI: 10.1016/j.ssnmr.2015.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 01/05/2015] [Accepted: 01/08/2015] [Indexed: 06/04/2023]
Abstract
An NMR crystallography study of the hemihydrate of 2', 3'-O-isopropylidineguanosine (Gace) is presented, together with powder X-ray diffraction and thermogravimetric analysis. (1)H double-quantum and (14)N-(1)H HMQC spectra recorded at 850MHz and 75kHz MAS (using a JEOL 1mm probe) are presented together with a (1)H-(13)C refocused INEPT spectrum recorded at 500MHz and 12.5kHz MAS using eDUMBO-122(1)H homonuclear decoupling. NMR chemical shieldings are calculated using the GIPAW (gauge-including projector augmented wave) method; good two-dimensional agreement between calculation and experiment is observed for (13)C and (1)H chemical shifts for directly bonded CH and CH3 peaks. There are two Gace molecules in the asymmetric unit cell: differences in specific (1)H chemical shifts are rationalised in terms of the strength of CH-π and intermolecular hydrogen bonding interactions.
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Affiliation(s)
| | - Daniel S Cook
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Dinu Iuga
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Richard I Walton
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Andrew Marsh
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
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38
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Garcia M, Kempe K, Haddleton DM, Khan A, Marsh A. Templated polymerizations on solid supports mediated by complementary nucleoside interactions. Polym Chem 2015. [DOI: 10.1039/c4py01783h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The preparation of immobilized poly(methacryloyl nucleosides) and their abilities for template polymerizations is discussed.
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Affiliation(s)
| | | | | | - Afzal Khan
- Department of Chemistry
- University of Warwick
- Coventry
- UK
| | - Andrew Marsh
- Department of Chemistry
- University of Warwick
- Coventry
- UK
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39
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Abstract
Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry
- Prague
- Czech Republic
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40
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Wang L, Kong H, Zhang C, Sun Q, Cai L, Tan Q, Besenbacher F, Xu W. Formation of a G-quartet-Fe complex and modulation of electronic and magnetic properties of the Fe center. ACS NANO 2014; 8:11799-11805. [PMID: 25347538 DOI: 10.1021/nn5054156] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Although the G-quartet structure has been extensively investigated due to its biological importance, the formation mechanism, in particular, the necessity of metal centers, of an isolated G-quartet on solid surfaces remains ambiguous. Here, by using scanning tunneling microscopy under well-controlled ultra-high-vacuum conditions and density functional theory calculations we have been able to clarify that besides the intraquartet hydrogen bonding a metal center is mandatory for the formation of an isolated G-quartet. Furthermore, by subtly perturbing the local coordination bonding schemes within the formed G-quartet complex via local nanoscale scanning tunneling microscopy manipulations, we succeed in modulating the d orbitals and the accompanying magnetic properties of the metal center. Our results demonstrate the feasibility of forming an isolated G-quartet complex on a solid surface and that the strategy of modulating electronic and magnetic properties of the metal center can be extended to other related systems such as molecular spintronics.
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Affiliation(s)
- Likun Wang
- Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials and College of Materials Science and Engineering, Tongji University , Caoan Road 4800, Shanghai 201804, People's Republic of China
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41
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Shen M, Trébosc J, Lafon O, Pourpoint F, Hu B, Chen Q, Amoureux JP. Improving the resolution in proton-detected through-space heteronuclear multiple quantum correlation NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 245:38-49. [PMID: 24929867 DOI: 10.1016/j.jmr.2014.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/02/2014] [Accepted: 05/05/2014] [Indexed: 06/03/2023]
Abstract
Connectivities and proximities between protons and low-gamma nuclei can be probed in solid-state NMR spectroscopy using two-dimensional (2D) proton-detected heteronuclear correlation, through Heteronuclear Multiple Quantum Correlation (HMQC) pulse sequence. The indirect detection via protons dramatically enhances the sensitivity. However, the spectra are often broadened along the indirect F1 dimension by the decay of heteronuclear multiple-quantum coherences under the strong (1)H-(1)H dipolar couplings. This work presents a systematic comparison of the performances of various decoupling schemes during the indirect t1 evolution period of dipolar-mediated HMQC (D-HMQC) experiment. We demonstrate that (1)H-(1)H dipolar decoupling sequences during t1, such as symmetry-based schemes, phase-modulated Lee-Goldburg (PMLG) and Decoupling Using Mind-Boggling Optimization (DUMBO), provide better resolution than continuous wave (1)H irradiation. We also report that high resolution requires the preservation of (1)H isotropic chemical shifts during the decoupling sequences. When observing indirectly broad spectra presenting numerous spinning sidebands, the D-HMQC sequence must be fully rotor-synchronized owing to the rotor-synchronized indirect sampling and dipolar recoupling sequence employed. In this case, we propose a solution to reduce artefact sidebands caused by the modulation of window delays before and after the decoupling application during the t1 period. Moreover, we show that (1)H-(1)H dipolar decoupling sequence using Smooth Amplitude Modulation (SAM) minimizes the t1-noise. The performances of the various decoupling schemes are assessed via numerical simulations and compared to 2D (1)H-{(13)C} D-HMQC experiments on [U-(13)C]-L-histidine⋅HCl⋅H2O at various magnetic fields and Magic Angle spinning (MAS) frequencies. Great resolution and sensitivity enhancements resulting from decoupling during t1 period enable the detection of heteronuclear correlation between aliphatic protons and ammonium (14)N sites in L-histidine⋅HCl⋅H2O.
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Affiliation(s)
- Ming Shen
- Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China; UCCS, University Lille North of France, Villeneuve d'Ascq 59652, France
| | - J Trébosc
- UCCS, University Lille North of France, Villeneuve d'Ascq 59652, France
| | - O Lafon
- UCCS, University Lille North of France, Villeneuve d'Ascq 59652, France
| | - F Pourpoint
- UCCS, University Lille North of France, Villeneuve d'Ascq 59652, France
| | - Bingwen Hu
- Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Qun Chen
- Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - J-P Amoureux
- Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China; UCCS, University Lille North of France, Villeneuve d'Ascq 59652, France.
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42
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Wu N, Lan J, Yan L, You J. A sensitive colorimetric and fluorescent sensor based on imidazolium-functionalized squaraines for the detection of GTP and alkaline phosphatase in aqueous solution. Chem Commun (Camb) 2014; 50:4438-41. [PMID: 24643794 DOI: 10.1039/c4cc00752b] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Imidazolium-functionalized squaraine ImSQ8 is synthesized as a sensitive colorimetric and fluorescent chemosensor for GTP in aqueous solution. The detection limit of GTP reaches 5.4 ppb. Its applications in the live-cell imaging and enzyme activity assay have also been demonstrated.
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Affiliation(s)
- Ningjie Wu
- Key Laboratory of Green Chemistry, Technology of Ministry of Education, College of Chemistry, State Key Laboratory of Biotherapy, West China Medical School, Sichuan University, 29 Wangjiang Road, Chengdu 610064, PR China.
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Althaus SM, Mao K, Stringer JA, Kobayashi T, Pruski M. Indirectly detected heteronuclear correlation solid-state NMR spectroscopy of naturally abundant 15N nuclei. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2014; 57-58:17-21. [PMID: 24287060 DOI: 10.1016/j.ssnmr.2013.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/22/2013] [Accepted: 11/01/2013] [Indexed: 06/02/2023]
Abstract
Two-dimensional indirectly detected through-space and through-bond (1)H{(15)N} solid-state NMR experiments utilizing fast magic angle spinning (MAS) and homonuclear multipulse (1)H decoupling are evaluated. Remarkable efficiency of polarization transfer can be achieved at a MAS rate of 40 kHz by both cross-polarization and INEPT, which makes these methods applicable for routine characterizations of natural abundance solids. The first measurement of 2D (1)H{(15)N} HETCOR spectrum of natural abundance surface species is also reported.
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Affiliation(s)
- Stacey M Althaus
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA; Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA
| | - Kanmi Mao
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA; Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA
| | - John A Stringer
- Agilent Technologies, 900 South Taft, Loveland, CO 80537, USA
| | - Takeshi Kobayashi
- Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA
| | - Marek Pruski
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA; Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA.
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44
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Halse ME, Schlagnitweit J, Emsley L. High-Resolution1H Solid-State NMR Spectroscopy Using Windowed LG4 Homonuclear Dipolar Decoupling. Isr J Chem 2014. [DOI: 10.1002/ijch.201300101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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45
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Baias M, Dumez JN, Svensson PH, Schantz S, Day GM, Emsley L. De novo determination of the crystal structure of a large drug molecule by crystal structure prediction-based powder NMR crystallography. J Am Chem Soc 2013; 135:17501-7. [PMID: 24168679 DOI: 10.1021/ja4088874] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of form 4 of the drug 4-[4-(2-adamantylcarbamoyl)-5-tert-butyl-pyrazol-1-yl]benzoic acid is determined using a protocol for NMR powder crystallography at natural isotopic abundance combining solid-state (1)H NMR spectroscopy, crystal structure prediction, and density functional theory chemical shift calculations. This is the first example of NMR crystal structure determination for a molecular compound of previously unknown structure, and at 422 g/mol this is the largest compound to which this method has been applied so far.
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Affiliation(s)
- Maria Baias
- Centre de RMN à Très Hauts Champs, CNRS/ENS-Lyon/UCB Lyon 1, Université de Lyon , 5 rue de la Doua, 69100 Villeurbanne, France
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Lu X, Trébosc J, Lafon O, Carnevale D, Ulzega S, Bodenhausen G, Amoureux JP. Broadband excitation in solid-state NMR using interleaved DANTE pulse trains with N pulses per rotor period. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 236:105-116. [PMID: 24095842 DOI: 10.1016/j.jmr.2013.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/06/2013] [Accepted: 09/08/2013] [Indexed: 06/02/2023]
Abstract
We analyze the direct excitation of wide one-dimensional spectra of nuclei with spin I=1/2 or 1 in rotating solids submitted to pulse trains in the manner of Delays Alternating with Nutations for Tailored Excitation (DANTE), either with one short rotor-synchronized pulse of duration τp in each of K rotor periods (D1(K)) or with N interleaved equally spaced pulses τp in each rotor period, globally also extending over K rotor periods (D(N)(K)). The excitation profile of D(N)(K) scheme is a comb of rf-spikelets with Nν(R)=N/T(R) spacing from the carrier frequency, and a width of each spikelet inversely proportional to the length, KT(R), of D(N)(K) scheme. Since the individual pulse lengths, τp, are typically of a few hundreds of ns, D(N)(K) scheme can readily excite spinning sidebands families covering several MHz, provided the rf carrier frequency is close enough to the resonance frequency of one the spinning sidebands. If the difference of isotropic chemical shifts between distinct chemical sites is less than about 1.35/(KT(R)), D(N)(K) scheme can excite the spinning sidebands families of several sites. For nuclei with I=1/2, if the homogeneous and inhomogeneous decays of coherences during the DANTE sequence are neglected, the K pulses of a D1(K) train have a linearly cumulative effect, so that the total nutation angle is θ(tot)=K2πν1τp, where ν1 is the rf-field amplitude. This allows obtaining nearly ideal 90° pulses for excitation or 180° rotations for inversion and refocusing across wide MAS spectra comprising many spinning sidebands. If one uses interleaved DANTE trains D(N)(K) with N>1, only spinning sidebands separated by intervals of Nν(R) with respect to the carrier frequency are observed as if the effective spinning speed was Nν(R). The other sidebands have vanishing intensities because of the cancellation of the N contributions with opposite signs. However, the intensities of the remaining sidebands obey the same rules as in spectra obtained with νR. With increasing N, the intensities of the non-vanishing sidebands increase, but the total intensity integrated over all sidebands decreases. Furthermore, the NK pulses in a D(N)(K) train do not have a simple cumulative effect and the optimal cumulated flip angle for optimal excitation, θ(tot)(opt)=NK2πν1τp, exceeds 90°. Such D(N)(K) pulse trains allow achieving efficient broadband excitation, but they are not recommended for broadband inversion or refocusing as they cannot provide proper 180° rotations. Since D(N)(K) pulse trains with N>1 are shorter than basic D1(K) sequences, they are useful for broadband excitation in samples with rapid homogeneous or inhomogeneous decay. For nuclei with I=1 (e.g., for (14)N), the response to basic D1(K) pulse train is moreover affected by inhomogeneous decay due to 2nd-order quadrupole interactions, since these are not of rank 2 and therefore cannot be eliminated by spinning about the magic angle. For large quadrupole interactions, the signal decay produced by second-order quadrupole interaction can be minimized by (i) reducing the length of D(N)(K) pulse trains using N>1, (ii) fast spinning, (iii) large rf-field, and (iv) using high magnetic fields to reduce the 2nd-order quadrupole interaction.
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Affiliation(s)
- Xingyu Lu
- Unit of Catalysis and Chemistry of Solids (UCCS), UMR 8181 CNRS, Lille North of France University, 59652 Villeneuve d'Ascq, France
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47
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Tsai ZTY, Chu WY, Cheng JH, Tsai HK. Associations between intronic non-B DNA structures and exon skipping. Nucleic Acids Res 2013; 42:739-47. [PMID: 24153112 PMCID: PMC3902930 DOI: 10.1093/nar/gkt939] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Non-B DNA structures are abundant in the genome and are often associated with critical biological processes, including gene regulation, chromosome rearrangement and genome stabilization. In particular, G-quadruplex (G4) may affect alternative splicing based on its ability to impede the activity of RNA polymerase II. However, the specific role of non-B DNA structures in splicing regulation still awaits investigation. Here, we provide a genome-wide and cross-species investigation of the associations between five non-B DNA structures and exon skipping. Our results indicate a statistically significant correlation of each examined non-B DNA structures with exon skipping in both human and mouse. We further show that the contributions of non-B DNA structures to exon skipping are influenced by the occurring region. These correlations and contributions are also significantly different in human and mouse. Finally, we detailed the effects of G4 by showing that occurring on the template strand and the length of G-run, which is highly related to the stability of a G4 structure, are significantly correlated with exon skipping activity. We thus show that, in addition to the well-known effects of RNA and protein structure, the relative positional arrangement of intronic non-B DNA structures may also impact exon skipping.
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Affiliation(s)
- Zing Tsung-Yeh Tsai
- Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan, Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan and Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 112, Taiwan
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48
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Novotná J, Goncharova I, Urbanová M. Guanosine assemblies: newly used matrices for chiroptical studies on biliverdin. Supramol Chem 2013. [DOI: 10.1080/10610278.2013.814774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jana Novotná
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
| | - Iryna Goncharova
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
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49
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Dudenko DV, Williams PA, Hughes CE, Antzutkin ON, Velaga S, Brown SP, Harris KDM. Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2013; 117:12258-12265. [PMID: 24386493 PMCID: PMC3876745 DOI: 10.1021/jp4041106] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Indexed: 05/25/2023]
Abstract
We report a strategy for structure determination of organic materials in which complete solid-state nuclear magnetic resonance (NMR) spectral data is utilized within the context of structure determination from powder X-ray diffraction (XRD) data. Following determination of the crystal structure from powder XRD data, first-principles density functional theory-based techniques within the GIPAW approach are exploited to calculate the solid-state NMR data for the structure, followed by careful scrutiny of the agreement with experimental solid-state NMR data. The successful application of this approach is demonstrated by structure determination of the 1:1 cocrystal of indomethacin and nicotinamide. The 1H and 13C chemical shifts calculated for the crystal structure determined from the powder XRD data are in excellent agreement with those measured experimentally, notably including the two-dimensional correlation of 1H and 13C chemical shifts for directly bonded 13C-1H moieties. The key feature of this combined approach is that the quality of the structure determined is assessed both against experimental powder XRD data and against experimental solid-state NMR data, thus providing a very robust validation of the veracity of the structure.
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Affiliation(s)
- Dmytro V. Dudenko
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, Wales,
U.K
- Department of Physics, University of Warwick, Coventry CV4 7AL, England, U.K
| | - P. Andrew Williams
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, Wales,
U.K
| | - Colan E. Hughes
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, Wales,
U.K
| | - Oleg N. Antzutkin
- Department of Physics, University of Warwick, Coventry CV4 7AL, England, U.K
- Chemistry of Interfaces, Luleå University of Technology, Luleå
S-97187, Sweden
| | - Sitaram
P. Velaga
- Department
of Health Science, Luleå University of Technology, Luleå S-97187, Sweden
| | - Steven P. Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, England, U.K
| | - Kenneth D. M. Harris
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, Wales,
U.K
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50
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Kuttatheyil AV, Lässig D, Lincke J, Kobalz M, Baias M, König K, Hofmann J, Krautscheid H, Pickard CJ, Haase J, Bertmer M. Synthesis, Crystal Structure, and Solid-State NMR Investigations of Heteronuclear Zn/Co Coordination Networks — A Comparative Study. Inorg Chem 2013; 52:4431-42. [DOI: 10.1021/ic302643w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | - Daniel Lässig
- Universität Leipzig, Fakultät für Chemie und Mineralogie,
Johannisallee 29, D-04103, Germany
| | - Jörg Lincke
- Universität Leipzig, Fakultät für Chemie und Mineralogie,
Johannisallee 29, D-04103, Germany
| | - Merten Kobalz
- Universität Leipzig, Fakultät für Chemie und Mineralogie,
Johannisallee 29, D-04103, Germany
| | - Maria Baias
- Universitè de Lyon, Centre de RMN
à très hauts champs, CNRS/ENS Lyon/UCBL, 5 Rue de la
Doua, 69100 Villeurbanne, France
| | - Katja König
- Institut für Nichtklassische Chemie e. V., Permoserstr.15, D-04318, Germany
| | - Jörg Hofmann
- Institut für Nichtklassische Chemie e. V., Permoserstr.15, D-04318, Germany
| | - Harald Krautscheid
- Universität Leipzig, Fakultät für Chemie und Mineralogie,
Johannisallee 29, D-04103, Germany
| | - Chris J. Pickard
- Department of Physics & Astronomy, University College London, Gower Street, London, United Kingdom
| | - Jürgen Haase
- Universität Leipzig, Fakultät
für Physik und Geowissenschaften, Linnéstr. 5, D-04103,
Germany
| | - Marko Bertmer
- Universität Leipzig, Fakultät
für Physik und Geowissenschaften, Linnéstr. 5, D-04103,
Germany
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