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Journal articles on the topic 'NMR structure refinement'

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Author: Grafiati

Published: 10 March 2023

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1

Skinner, Simon P., Benjamin T. Goult, Rasmus H. Fogh, Wayne Boucher, Tim J. Stevens, Ernest D. Laue, and Geerten W. Vuister. "Structure calculation, refinement and validation usingCcpNmr Analysis." Acta Crystallographica Section D Biological Crystallography 71, no. 1 (January 1, 2015): 154–61. http://dx.doi.org/10.1107/s1399004714026662.

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CcpNmr Analysisprovides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes howCcpNmr Analysiscan seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral, hydrogen bonds and residual dipolar couplings (RDCs)], exporting these to and subsequently re-importing them from structure-calculation software (such as the programsCYANAorARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements toCcpNmr Analysisdescribed here, this process is now much more intuitive and efficient and less error-prone.

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2

Scarperi, Andrea, Giovanni Barcaro, Aleksandra Pajzderska, Francesca Martini, Elisa Carignani, and Marco Geppi. "Structural Refinement of Carbimazole by NMR Crystallography." Molecules 26, no. 15 (July 29, 2021): 4577. http://dx.doi.org/10.3390/molecules26154577.

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The characterization of the three-dimensional structure of solids is of major importance, especially in the pharmaceutical field. In the present work, NMR crystallography methods are applied with the aim to refine the crystal structure of carbimazole, an active pharmaceutical ingredient used for the treatment of hyperthyroidism and Grave’s disease. Starting from previously reported X-ray diffraction data, two refined structures were obtained by geometry optimization methods. Experimental 1H and 13C isotropic chemical shift measured by the suitable 1H and 13C high-resolution solid state NMR techniques were compared with DFT-GIPAW calculated values, allowing the quality of the obtained structure to be experimentally checked. The refined structure was further validated through the analysis of 1H-1H and 1H-13C 2D NMR correlation experiments. The final structure differs from that previously obtained from X-ray diffraction data mostly for the position of hydrogen atoms.

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3

Ikeya, Teppei, Shiro Ikeda, Takanori Kigawa, Yutaka Ito, and Peter Güntert. "Protein NMR Structure Refinement based on Bayesian Inference." Journal of Physics: Conference Series 699 (March 2016): 012005. http://dx.doi.org/10.1088/1742-6596/699/1/012005.

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4

Laws, David D., Angel C. de Dios, and Eric Oldfield. "NMR chemical shifts and structure refinement in proteins." Journal of Biomolecular NMR 3, no. 5 (September 1993): 607–12. http://dx.doi.org/10.1007/bf00174614.

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5

CUI, FENG, ROBERT JERNIGAN, and ZHIJUN WU. "KNOWLEDGE-BASED VERSUS EXPERIMENTALLY ACQUIRED DISTANCE AND ANGLE CONSTRAINTS FOR NMR STRUCTURE REFINEMENT." Journal of Bioinformatics and Computational Biology 06, no. 02 (April 2008): 283–300. http://dx.doi.org/10.1142/s0219720008003448.

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Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints — NOE, torsion angle, or knowledge-based constraints — or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quality of structural models and whether or not they can be combined with or substituted by the knowledge-based constraints. We have carried out the experiments on a small set of NMR structures. Our preliminary calculations have revealed that the torsion angle constraints contribute substantially to the quality of the structures, but require to be combined with the NOE constraints to be fully effective. The knowledge-based constraints can be functionally as crucial as the torsion angle constraints, although they are statistical constraints after all and are not meant to be able to replace the latter.

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6

Sinelnikova, Anna, and David van der Spoel. "NMR refinement and peptide folding using the GROMACS software." Journal of Biomolecular NMR 75, no. 4-5 (March 28, 2021): 143–49. http://dx.doi.org/10.1007/s10858-021-00363-z.

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AbstractNuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins and nucleic acids. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance restraints, dihedral restraints and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.

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7

Clore, G. M., and A. M. Gronenborn. "New methods of structure refinement for macromolecular structure determination by NMR." Proceedings of the National Academy of Sciences 95, no. 11 (May 26, 1998): 5891–98. http://dx.doi.org/10.1073/pnas.95.11.5891.

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8

Schwieters, Charles D., and G. Marius Clore. "The VMD-XPLOR Visualization Package for NMR Structure Refinement." Journal of Magnetic Resonance 149, no. 2 (April 2001): 239–44. http://dx.doi.org/10.1006/jmre.2001.2300.

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9

Bestaoui, Naima, Xiang Ouyang, Florence Fredoueil, Bruno Bujoli, and Abraham Clearfield. "Structural characterization of Cd3(O3PC2H4CO2)2·2H2O from in-house X-ray powder data and NMR." Acta Crystallographica Section B Structural Science 61, no. 6 (November 14, 2005): 669–74. http://dx.doi.org/10.1107/s0108768105028387.

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The title compound poly[[bis(μ-2-carboxylatoethylphosphonato)cadmium] dihydrate], Cd3(O3PC2H4CO2)2·2H2O, was prepared by a hydrothermal reaction and its crystal structure determined from in-house powder data. The structure was solved in both P21/c and P21 space groups. The refinement converged with Rp = 0.1046, R wp = 0.1378 and Rf = 0.0763 in P21/c. However, the solid-state NMR data could not be explained. The structure was then solved in P21 and the refinement converged with Rp = 0.0750, R wp = 0.1022 and Rf = 0.0409 and satisfied the NMR requirements.

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10

Neuberger, Sven, Sean P. Culver, Hellmut Eckert, Wolfgang G. Zeier, and Jörn Schmedt auf der Günne. "Refinement of the crystal structure of Li4P2S6 using NMR crystallography." Dalton Transactions 47, no. 33 (2018): 11691–95. http://dx.doi.org/10.1039/c8dt02619j.

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11

Bell, A. M. T., and C. M. B. Henderson. "Crystal structures and cation ordering in Cs2MgSi5O12, Rb2MgSi5O12 and Cs2ZnSi5O12 leucites." Acta Crystallographica Section B Structural Science 65, no. 4 (July 16, 2009): 435–44. http://dx.doi.org/10.1107/s0108768109024860.

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The crystal structures of the leucite analogues Cs2MgSi5O12, Cs2ZnSi5O12 and Rb2MgSi5O12 have been determined by synchrotron X-ray powder diffraction using Rietveld refinement in conjunction with 29Si MAS NMR spectroscopy. These leucites are framework structures with distinct tetrahedral sites (T sites) occupied by Si and a divalent cation (either Mg or Zn in these samples); there is also a monovalent extra-framework cation (either Cs or Rb in these samples). The refined crystal structures were based on the Pbca leucite structure of Cs2CdSi5O12, thus a framework with five ordered Si T sites and one ordered Cd T site was used as the starting model for refinement. 29Si MAS NMR shows five distinct Si T sites for Cs2MgSi5O12 and Rb2MgSi5O12, but six Si T sites for Cs2ZnSi5O12. The refined structures for Cs2MgSi5O12 and Rb2MgSi5O12 were determined with complete T-site ordering, but the refined structure for Cs2ZnSi5O12 was determined with partial disorder of Mg and Si over two of the T sites.

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12

Shapiro, Lawrence, Michael Nilges, Magdalena Eriksson, Monika Persson, Irena Valterová, Michel Chanon, Cindy Striley, Johann Weidlein, Ahmad Nasiri, and Yoshito Okada. "NMR Relaxation Matrix Refinement of a DNA Octamer Solution Structure." Acta Chemica Scandinavica 47 (1993): 43–56. http://dx.doi.org/10.3891/acta.chem.scand.47-0043.

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13

Grishaev, Alexander, Jinfa Ying, and Ad Bax. "Pseudo-CSA Restraints for NMR Refinement of Nucleic Acid Structure." Journal of the American Chemical Society 128, no. 31 (August 2006): 10010–11. http://dx.doi.org/10.1021/ja0633058.

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14

Gong, Zhou, Charles D. Schwieters, and Chun Tang. "Conjoined Use of EM and NMR in RNA Structure Refinement." PLOS ONE 10, no. 3 (March 23, 2015): e0120445. http://dx.doi.org/10.1371/journal.pone.0120445.

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15

Carlon, Azzurra, Enrico Ravera, Giacomo Parigi, Garib N. Murshudov, and Claudio Luchinat. "Joint X-ray/NMR structure refinement of multidomain/multisubunit systems." Journal of Biomolecular NMR 73, no. 6-7 (October 11, 2018): 265–78. http://dx.doi.org/10.1007/s10858-018-0212-3.

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16

Lipsitz, Rebecca S., and Nico Tjandra. "Carbonyl CSA Restraints from Solution NMR for Protein Structure Refinement." Journal of the American Chemical Society 123, no. 44 (November 2001): 11065–66. http://dx.doi.org/10.1021/ja016854g.

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17

Kovalevskiy, Oleg, Robert A. Nicholls, Fei Long, Azzurra Carlon, and Garib N. Murshudov. "Overview of refinement procedures withinREFMAC5: utilizing data from different sources." Acta Crystallographica Section D Structural Biology 74, no. 3 (March 1, 2018): 215–27. http://dx.doi.org/10.1107/s2059798318000979.

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Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (Bfactors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented inREFMAC5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures usingREFMAC5 and related tools distributed as part of theCCP4 suite is discussed.

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18

Cheng, Xi. "NMR Observable-Based Structure Refinement of Membrane Proteins in Explicit Membranes." Biophysical Journal 102, no. 3 (January 2012): 399a—400a. http://dx.doi.org/10.1016/j.bpj.2011.11.2182.

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19

Jee, Jun-Goo. "Effects of generalized-Born implicit solvent models in NMR structure refinement." Journal of the Korean Magnetic Resonance Society 17, no. 1 (June 20, 2013): 11–18. http://dx.doi.org/10.6564/jkmrs.2013.17.1.011.

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20

Bertini, Ivano, David A. Case, Lucio Ferella, Andrea Giachetti, and Antonio Rosato. "A Grid-enabled web portal for NMR structure refinement with AMBER." Bioinformatics 27, no. 17 (July 14, 2011): 2384–90. http://dx.doi.org/10.1093/bioinformatics/btr415.

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21

Tjandra, Nico, Motoshi Suzuki, and Shou-Lin Chang. "Refinement of protein structure against non-redundant carbonyl 13C NMR relaxation." Journal of Biomolecular NMR 38, no. 3 (June 7, 2007): 243–53. http://dx.doi.org/10.1007/s10858-007-9165-7.

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22

Brown, Frank K., Judith C. Hempel, and Peter W. Jeffs. "NMR restraint analysis of transforming growth factor α: A key component for NMR structure refinement." Proteins: Structure, Function, and Genetics 13, no. 4 (August 1992): 306–26. http://dx.doi.org/10.1002/prot.340130404.

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23

Pantoja-Uceda, D., M. Bruix, J. Santoro, M. Rico, R. Monsalve, and M. Villalba. "Solution structure of allergenic 2 S albumins." Biochemical Society Transactions 30, no. 6 (November 1, 2002): 919–24. http://dx.doi.org/10.1042/bst0300919.

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The NMR solution structures at different levels of refinement of three different 2 S albumin seed proteins, the recombinant pronapin precursor from Brassica napus, the recombinant RicC3 from Ricinus communis and the methionine-rich protein from sunflower (Helianthus annuus), are described. The resulting common structure consists of a bundle of five α-helices, folded in a right-handed superhelix. The structure is very similar to that of other plant proteins: the hydrophobic protein from soybean, non-specific lipid transfer proteins and amylase/trypsin inhibitors. Analogies and differences in the structures of these families, as well as their possible relationship to allergenicity, are discussed.

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24

Tuel, Alain, Stefano Caldarelli, Anton Meden, Lynne B. McCusker, Christian Baerlocher, Alenka Ristic, Nevenka Rajic, Gregor Mali, and Venceslav Kaucic. "NMR Characterization and Rietveld Refinement of the Structure of Rehydrated AlPO4-34." Journal of Physical Chemistry B 104, no. 24 (June 2000): 5697–705. http://dx.doi.org/10.1021/jp000455a.

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25

Calhoun, Jennifer R., Weixia Liu, Katrin Spiegel, Matteo Dal Peraro, Michael L. Klein, Kathleen G. Valentine, A. Joshua Wand, and William F. DeGrado. "Solution NMR Structure of a Designed Metalloprotein and Complementary Molecular Dynamics Refinement." Structure 16, no. 2 (February 2008): 210–15. http://dx.doi.org/10.1016/j.str.2007.11.011.

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26

Le, Hong-biao, John G. Pearson, Angel C. de Dios, and Eric Oldfield. "Protein Structure Refinement and Prediction via NMR Chemical Shifts and Quantum Chemistry." Journal of the American Chemical Society 117, no. 13 (April 1995): 3800–3807. http://dx.doi.org/10.1021/ja00118a016.

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27

Perilla, Juan R., Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L. Byeon, Angela M. Gronenborn, Tatyana Polenova, and Peijun Zhang. "CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations." Journal of Physical Chemistry B 121, no. 15 (February 22, 2017): 3853–63. http://dx.doi.org/10.1021/acs.jpcb.6b13105.

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28

Jung, Ryu Hyo, Kim Tae-Rae, Ji Sunyoung, and Lee Jinhyuk. "NMR Structure Refinement using Stap and Flat-Bottom Potential Without NOE Data." Biophysical Journal 106, no. 2 (January 2014): 47a—48a. http://dx.doi.org/10.1016/j.bpj.2013.11.343.

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29

Carlon, Azzurra, Enrico Ravera, Giacomo Parigi, Garib N. Murshudov, and Claudio Luchinat. "Correction to: Joint X-ray/NMR structure refinement of multidomain/multisubunit systems." Journal of Biomolecular NMR 73, no. 6-7 (May 8, 2019): 279. http://dx.doi.org/10.1007/s10858-019-00238-4.

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30

Ramelot, Theresa A., Srivatsan Raman, Alexandre P. Kuzin, Rong Xiao, Li-Chung Ma, Thomas B. Acton, John F. Hunt, Gaetano T. Montelione, David Baker, and Michael A. Kennedy. "Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study." Proteins: Structure, Function, and Bioinformatics 75, no. 1 (September 24, 2008): 147–67. http://dx.doi.org/10.1002/prot.22229.

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31

Ryu, Hyojung, GyuTae Lim, Bong Hyun Sung, and Jinhyuk Lee. "NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores." Bioinformatics 32, no. 4 (October 26, 2015): 611–13. http://dx.doi.org/10.1093/bioinformatics/btv595.

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32

Perras, Frédéric A. "Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei." Pure and Applied Chemistry 88, no. 1-2 (February 1, 2016): 95–111. http://dx.doi.org/10.1515/pac-2015-0801.

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AbstractNuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities. Two-dimensional J-resolved-type experiments are then presented for the measurement of dipolar and J coupling, between spin-1/2 and quadrupolar nuclei as well as in pairs of quadrupolar nuclei. Select examples utilizing these techniques for the extraction of structural information are given. Techniques are then described that enable the fine refinement of crystalline structures using solely the electric field gradient tensor, measured using NMR, as a constraint. These approaches enable the solution of crystal structures, from polycrystalline compounds, that are of comparable quality to those solved using single-crystal diffraction.

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33

Borhade, Ashok V., and Sanjay G. Wakchaure. "One-Pot Synthesis, X-Ray Diffraction and MAS NMR Spectroscopic Study of Gallosilicate Nitrate Cancrinite Na8[GaSiO4]6(NO3)4(H2O)6." E-Journal of Chemistry 7, no. 2 (2010): 369–76. http://dx.doi.org/10.1155/2010/608404.

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One-pot synthetic gallosilicate nitrate cancrinite (CAN) framework topology have been synthesized under hydrothermal conditions at 100 °C. The synthesized product was characterized by, X-ray powder diffraction, IR, Raman and29Si,23Na MAS NMR spectroscopy, SEM and thermogravimetry. The crystal structure refinement of pure nitrate cancrinite has been carried out from X-ray data using Rietveld refinement method. Gallosilicate cancrinite Na8[GaSiO4]6(NO3)4(H2O)6crystalline hexagonal with space group P63and a = 12.77981 Å (2), c = 5.20217 Å (1), (Rwp= 0.0696 Rp= 0.0527). The results by MAS NMR spectroscopy confirmed the alternating Si, Ga ordering of the gallosilicate framework for a Si/Ga ratio of 1.0. A distribution of the quadrupolar interaction of the sodium cations caused by the enclatherated water molecules and motional effects can be suggested from the23Na MAS NMR. Thermogravimetric investigation shows the extent of nitrate entrapment, stability within the cancrinite cage and decomposition properties. SEM clearly shows the hexagonal needle shaped crystals of nitrate cancrinite.

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34

IKEYA, Teppei, and Yutaka ITO. "Protein NMR Structure Refinement Based on Bayesian Inference for Dynamical Ordering of Biomacromolecules." Journal of Computer Chemistry, Japan 17, no. 1 (2018): 65–75. http://dx.doi.org/10.2477/jccj.2018-0009.

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35

Kitao, A., Brian Hare, and Gerhard Wagner. "Structure and dynamics of scTCR investigated by a new NMR structural refinement methodology." Seibutsu Butsuri 40, supplement (2000): S26. http://dx.doi.org/10.2142/biophys.40.s26_4.

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36

Tjandra, Nico, John Marquardt, and G. Marius Clore. "Direct Refinement against Proton–Proton Dipolar Couplings in NMR Structure Determination of Macromolecules." Journal of Magnetic Resonance 142, no. 2 (February 2000): 393–96. http://dx.doi.org/10.1006/jmre.1999.1985.

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37

Shimazaki, Manato, Teppei Ikeya, Masaki Mishima, Yutaka Ito, and Peter Guentert. "3P010 Development of a new refinement method for NMR protein structure determination(01A. Protein: Structure,Poster)." Seibutsu Butsuri 53, supplement1-2 (2013): S213. http://dx.doi.org/10.2142/biophys.53.s213_4.

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38

Rinaldelli, Mauro, Enrico Ravera, Vito Calderone, Giacomo Parigi, Garib N. Murshudov, and Claudio Luchinat. "Simultaneous use of solution NMR and X-ray data inREFMAC5 for joint refinement/detection of structural differences." Acta Crystallographica Section D Biological Crystallography 70, no. 4 (March 19, 2014): 958–67. http://dx.doi.org/10.1107/s1399004713034160.

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The programREFMAC5 fromCCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints inREFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

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39

Topolska-Woś, Agnieszka M., Norie Sugitani, John J. Cordoba, Kateryna V. Le Meur, Rémy A. Le Meur, Hyun Suk Kim, Jung-Eun Yeo, et al. "A key interaction with RPA orients XPA in NER complexes." Nucleic Acids Research 48, no. 4 (January 11, 2020): 2173–88. http://dx.doi.org/10.1093/nar/gkz1231.

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Abstract The XPA protein functions together with the single-stranded DNA (ssDNA) binding protein RPA as the central scaffold to ensure proper positioning of repair factors in multi-protein nucleotide excision repair (NER) machinery. We previously determined the structure of a short motif in the disordered XPA N-terminus bound to the RPA32C domain. However, a second contact between the XPA DNA-binding domain (XPA DBD) and the RPA70AB tandem ssDNA-binding domains, which is likely to influence the orientation of XPA and RPA on the damaged DNA substrate, remains poorly characterized. NMR was used to map the binding interfaces of XPA DBD and RPA70AB. Combining NMR and X-ray scattering data with comprehensive docking and refinement revealed how XPA DBD and RPA70AB orient on model NER DNA substrates. The structural model enabled design of XPA mutations that inhibit the interaction with RPA70AB. These mutations decreased activity in cell-based NER assays, demonstrating the functional importance of XPA DBD–RPA70AB interaction. Our results inform ongoing controversy about where XPA is bound within the NER bubble, provide structural insights into the molecular basis for malfunction of disease-associated XPA missense mutations, and contribute to understanding of the structure and mechanical action of the NER machinery.

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40

Birnbaum, George I., Miloš Buděšínský, and Jiří Berànek. "Structure and conformation of 2′,5′-anhydroarabinosylcytosine: X-ray, 1H nmr and 13C nmr analyses." Canadian Journal of Chemistry 65, no. 2 (February 1, 1987): 271–76. http://dx.doi.org/10.1139/v87-044.

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Crystals of 2′,5′-anhydroarabinosylcytosine hemihydrate belong to the monoclinic space group P21. The cell dimensions are a = 9.643(2), b = 10.328(1), c = 10.544(2) Å, β = 94.55(1)°. X-ray intensity data were measured on a diffractometer and the structure was determined by direct methods. Least-squares refinement, which included all nucleoside hydrogen atoms, converged at R = 0.041 for 2298 observed reflections. The asymmetric unit contains two molecules of the nucleoside and one molecule of water. In both nucleoside molecules, the conformation about the glycosyl bond is and, with XCN values of 15.5(3) and 26.3(3)°, respectively. In the bicyclic sugar moiety, the arabinofuranose rings adopt a C(3′)exo/C(2′)endo conformation and are highly puckered (τm = 57°). The solution conformation was studied by 1H and 13C nmr spectroscopy. A difference nOe proton nmr spectrum and 3J(C,H) coupling constants reveal an anti conformation in solution, with torsion angles very similar to those obtained from X-ray analysis. A comparison of observed 3J(H,H) coupling constants with those calculated on the basis of a modified Karplus equation shows significant differences, probably due to the presence of the bicyclic system.

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41

Cao, Guang, Mobae Afeworki, Gordon J. Kennedy, Karl G. Strohmaier, and Douglas L. Dorset. "Structure of an aluminophosphate EMM-8: a multi-technique approach." Acta Crystallographica Section B Structural Science 63, no. 1 (January 15, 2007): 56–62. http://dx.doi.org/10.1107/s0108768106040109.

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The crystal structure of an aluminophosphate, EMM-8 (ExxonMobil Material #8), was determined in its calcined, anhydrous form from synchrotron powder diffraction data using the computer program FOCUS. A linkage of double four-ring (D4R) building units forms a two-dimensional framework with 12-MR and 8-MR channels, and differs from a similar SAPO-40 (AFR) framework only by the relationship between paired D4R units. Rietveld refinement reveals a fit of the model to the observed synchrotron data by R wp = 0.1118, R(F 2) = 0.1769. Local environments of the tetrahedral phosphorus and aluminium sites were established by solid-state NMR, which detects distinct differences between as-synthesized and calcined materials. Distinct, reversible changes in the local symmetry of the P and Al atoms were observed by NMR upon calcination and subsequent hydration. These NMR data provided important constraints on the number of tetrahedral (T) atoms per unit cell and the connectivities of the T atoms. Detailed local structural information obtained by solid-state NMR thereby guided the ultimate determination of the structure of AlPO EMM-8 from the powder data. Comparisons are made to the recently published crystal structure of the fluoride-containing, as-synthesized SSZ-51, indicating that the unit-cell symmetry, axial dimensions and framework structure are preserved after calcination.

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42

Bartsch, Timo, Christopher Benndorf, Hellmut Eckert, Matthias Eul, and Rainer Pöttgen. "La3Cu4P4O2 and La5Cu4P4O4Cl2: synthesis, structure and 31P solid state NMR spectroscopy." Zeitschrift für Naturforschung B 71, no. 2 (February 1, 2016): 149–55. http://dx.doi.org/10.1515/znb-2015-0181.

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AbstractThe phosphide oxides La3Cu4P4O2 and La5Cu4 P4O4Cl2 were synthesized from lanthanum, copper(I) oxide, red phosphorus, and lanthanum(III) chloride through a ceramic technique. Single crystals can be grown in a NaCl/KCl flux. Both structures were refined from single crystal X-ray diffractometer data: I4/mmm, a = 403.89(4), c = 2681.7(3) pm, wR2 = 0.0660, 269 F2 values, 19 variables for La3Cu4P4O2 and a = 407.52(5), c = 4056.8(7) pm, wR2 = 0.0905, 426 F2 values, 27 variables for La5Cu4P4O4Cl2. Refinement of the occupancy parameters revealed full occupancy for the oxygen sites in both compounds. The structures are composed of cationic (La2O2)2+ layers and covalently bonded (Cu4P4)5– polyanionic layers with metallic characteristics, and an additional La3+ between two adjacent (Cu4P4)5– layers. The structure of La5Cu4P4O4Cl2 comprises two additional LaOCl slabs per unit cell. Temperature-dependent magnetic susceptibility studies revealed Pauli paramagnetism. The phosphide substructure of La3Cu4P4O2 was studied by 31P solid state NMR spectroscopy. By using a suitable dipolar re-coupling approach the two distinct resonances belonging to the P24– and the P3– units could be identified.

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Gorelik, Tatiana E., Jacco van de Streek, Andreas F. M. Kilbinger, Gunther Brunklaus, and Ute Kolb. "Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data." Acta Crystallographica Section B Structural Science 68, no. 2 (February 25, 2012): 171–81. http://dx.doi.org/10.1107/s0108768112003138.

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Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal structure of tri-p-benzamide. The same procedure is then applied to solve the previously unknown crystal structure of tetra-p-benzamide. In the crystal structure of tetra-p-benzamide, an unusual hydrogen-bonding scheme is realised; the hydrogen-bonding scheme is, however, in perfect agreement with solid-state NMR data.

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Hnyk, Drahomír, Matthias Hofmann, and Paul von Ragué Schleyer. "4,6-Dicarba-8-thia-arachno-nonaborane(10) Revisited. Theoretical Refinement of Its Structure." Collection of Czechoslovak Chemical Communications 64, no. 6 (1999): 993–1000. http://dx.doi.org/10.1135/cccc19990993.

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The structure of the nine-vertex arachno-thiadicarbaborane C2SB6H10 has been established employing the ab initio/IGLO/NMR method. Theoretical IGLO 11B chemical shifts support C and S atom placements at the 4, 6 and 8 positions, respectively, and unambiguously rule out the 4,6,5-C2SB6H10 structural alternative, suggested earlier on the basis of IR and Raman spectroscopy. Important structural features of the 4,6,8-C2SB6H10 geometry include a small B(7)-S(8)-B(9) angle (MP2(fc)/6-31G*: 97.9°) and long S-B bonds (MP2(fc)/6-31G*: 1.905 and 1.924 Å) compared to B-B bonds spanning the 1.71-1.85 Å range.

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Vila, J. A., J. M. Aramini, P. Rossi, A. Kuzin, M. Su, J. Seetharaman, R. Xiao, L. Tong, G. T. Montelione, and H. A. Scheraga. "Quantum chemical 13C chemical shift calculations for protein NMR structure determination, refinement, and validation." Proceedings of the National Academy of Sciences 105, no. 38 (September 11, 2008): 14389–94. http://dx.doi.org/10.1073/pnas.0807105105.

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Fesik, Stephen W., Giorgio Bolis, Hing L. Sham, and Edward T. Olejniczak. "Structure refinement of a cyclic peptide from two-dimensional NMR data and molecular modeling." Biochemistry 26, no. 7 (April 7, 1987): 1851–59. http://dx.doi.org/10.1021/bi00381a010.

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Tian, Ye, Charles D. Schwieters, Stanley J. Opella, and Francesca M. Marassi. "AssignFit: A program for simultaneous assignment and structure refinement from solid-state NMR spectra." Journal of Magnetic Resonance 214 (January 2012): 42–50. http://dx.doi.org/10.1016/j.jmr.2011.10.002.

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Miah, Habeeba K., Rosalie Cresswell, Dinu Iuga, and Jeremy J. Titman. "1 H CSA parameters by ultrafast MAS NMR: Measurement and applications to structure refinement." Solid State Nuclear Magnetic Resonance 87 (October 2017): 67–72. http://dx.doi.org/10.1016/j.ssnmr.2017.02.002.

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Kim, Seong-Gi, and Brian R. Reid. "Automated NMR structure refinement via NOE peak volumes. Application to a dodecamer DNA duplex." Journal of Magnetic Resonance (1969) 100, no. 2 (November 1992): 382–90. http://dx.doi.org/10.1016/0022-2364(92)90271-8.

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Assfalg, Michael, Lucia Banci, Ivano Bertini, Mireille Bruschi, and Paola Turano. "800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuromonas acetoxidans." European Journal of Biochemistry 256, no. 2 (September 1998): 261–70. http://dx.doi.org/10.1046/j.1432-1327.1998.2560261.x.

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