Assignment of the natural abundance carbon-13 spectrum of proteins using carbon-13-proton detected heteronuclear multiple-bond correlation NMR spectroscopy: structural information and stereospecific assignments from two- and three-bond carbon-hydrogen coupling constants

ABSTRACT Various pulse techniques of NMR spectroscopy were applied to CR to assign some small signals in 13C and 1H NMR spectra for the rubber. First, the rubber was subjected to distortionless enhancement by polarization transfer and attached proton test. The small signals in the 13C NMR spectrum were assigned to secondary, tertiary, and quaternary carbons. Second, correlations between 13C and 1H were investigated by heteronuclear multiple quantum correlation, heteronuclear two bond correlation, and heteronuclear multiple bond correlation measurements to assign the small signals in the 13C NMR spectrum in detail. By using the resulting correlations between 13C and 1H, the small unassigned signals in 1H NMR spectrum were assigned to methylene and methine protons of the rubber.

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Some Applications of Ultrahigh Resolution 15N NMR Spectroscopy

Zeitschrift für Naturforschung B ◽

10.1515/znb-1998-0403 ◽

1998 ◽

Vol 53 (4) ◽

pp. 411-415 ◽

Cited By ~ 9

Author(s):

Bernd Wrackmeyer ◽

Ēriks Kupče

Keyword(s):

Nmr Spectroscopy ◽

Nmr Spectra ◽

Chemical Shifts ◽

Absolute Magnitude ◽

Natural Abundance ◽

Coupling Constants ◽

15N Nmr ◽

Ultrahigh Resolution ◽

Tert Butyl ◽

15N Nmr Spectroscopy

Abstract Ultrahigh resolution 15N NMR spectra were measured for two nitroalkanes (MeNO2 la, tBuNO2 1c), two isocyanates (tBuNCO 2c, Me3SiNCO 2d), four isothiocyanates (MeNCS 3a, EtNCS 3b, tBuNCS 3c, Me3SiNCS 3d), one carbodiimide (Me3SiNCNSiMe3 4d), one keteneimine [Me3SiNCC(SiMe3)2 5d], two sulphinyl imides (tBuNSO 6c, Me3SiNSO 6d), and N-tert-butyl-pyrrole 7c, in order to determine coupling constants J(15N ,I3C) and isotope induced chemical shifts 1∆12/13C (15N) at the natural abundance of the isotopes. The values 1∆12/13C (15N) can be separated into two groups, one dealing with NC single and another one with NC double bonds. In each group (with few exceptions), the values 1∆12/13C (15N) become more negative with a decrease in the absolute magnitude of l1J(l5N ,13C)l. The corresponding values 1∆14/15N (13C) show a sim ilar behaviour. However, N-substituted pyrroles appear to be exceptional in this respect.

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Molecular Conformations of Di-, Tri-, and Tetra-α-(2→8)-Linked Sialic Acid from NMR Spectroscopy and MD Simulations

International Journal of Molecular Sciences ◽

10.3390/ijms21010030 ◽

2019 ◽

Vol 21 (1) ◽

pp. 30

Author(s):

Aysegül Turupcu ◽

Markus Blaukopf ◽

Paul Kosma ◽

Chris Oostenbrink

Keyword(s):

Sialic Acid ◽

Nmr Spectroscopy ◽

Structural Information ◽

Sampling Technique ◽

Md Simulations ◽

Coupling Constants ◽

Enhanced Sampling ◽

Molecular Conformations ◽

J Coupling ◽

Dynamics Simulations

By using molecular dynamics simulations with an efficient enhanced sampling technique and in combination with nuclear magnetic resonance (NMR) spectroscopy quantitative structural information on α -2,8-linked sialic acids is presented. We used a bottom-up approach to obtain a set of larger ensembles for tetra- and deca-sialic acid from model dimer and trimer systems that are in agreement with the available J-coupling constants and nuclear Overhauser effects. The molecular dynamic (MD) simulations with enhanced sampling are used to validate the force field used in this study for its further use. This empowered us to couple NMR observables in the MD framework via J-coupling and distance restraining simulations to obtain conformations that are supported by experimental data. We used these conformations in thermodynamic integration and one-step perturbation simulations to calculate the free-energy of suggested helical conformations. This study brings most of the available NMR experiments together and supplies information to resolve the conflict on the structures of poly- α -2,8-linked sialic acid.

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Gradient-Enhanced Inverse-Detected NMR Techniquesfor Determination of 1H-15N Coupling Constants in 2,2-Dimethylpenta-3,4-dienal Derivatives

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19971747 ◽

1997 ◽

Vol 62 (11) ◽

pp. 1747-1753 ◽

Cited By ~ 5

Author(s):

Radek Marek

Keyword(s):

Double Bond ◽

Chemical Shifts ◽

Multiple Bond ◽

Coupling Constants ◽

Single Quantum ◽

Nmr Techniques ◽

Phase Sensitive ◽

Heteronuclear Coupling

Determination of 15N chemical shifts and heteronuclear coupling constants of substituted 2,2-dimethylpenta-3,4-dienal hydrazones is presented. The chemical shifts were determined by gradient-enhanced inverse-detected NMR techniques and 1H-15N coupling constants were extracted from phase-sensitive gradient-enhanced single-quantum multiple bond correlation experiments. Stereospecific behaviour of the coupling constants 2J(1H,15N) and 1J(1H,13C) has been used to determine the configuration on a C=N double bond. The above-mentioned compounds exist predominantly as E isomers in deuteriochloroform.

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The Application of NMR Spectroscopy and Chemometrics in Authentication of Spices

Molecules ◽

10.3390/molecules26020382 ◽

2021 ◽

Vol 26 (2) ◽

pp. 382

Author(s):

Barbara Pacholczyk-Sienicka ◽

Grzegorz Ciepielowski ◽

Łukasz Albrecht

Keyword(s):

Quality Assurance ◽

Nmr Spectroscopy ◽

Sample Preparation ◽

Bioactive Compounds ◽

Analytical Methods ◽

Structural Information ◽

Chemometric Analysis ◽

Spectroscopic Methods ◽

Regular Consumption ◽

No Sample Preparation

Spices and herbs are among the most commonly adulterated food types. This is because spices are widely used to process food. Spices not only enhance the flavor and taste of food, but they are also sources of numerous bioactive compounds that are significantly beneficial for health. The healing effects of spices are connected with their antimicrobial, anti-inflammatory and carminative properties. However, regular consumption of adulterated spices may cause fatal damage to our system because adulterants in most cases are unhealthy. For that reason, the appropriate analytical methods are necessary for quality assurance and to ensure the authenticity of spices. Spectroscopic methods are gaining interest as they are fast, require little or no sample preparation, and provide rich structural information. This review provides an overview of the application of NMR spectroscopy combined with chemometric analysis to determine the quality and adulteration of spices.

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High-quality oligo-RNA synthesis using the new 2′-O-TEM protecting group by selectively quenching the addition of p-tolyl vinyl sulphone to exocyclic amino functions

Canadian Journal of Chemistry ◽

10.1139/v07-025 ◽

2007 ◽

Vol 85 (4) ◽

pp. 293-301 ◽

Cited By ~ 11

Author(s):

Chuanzheng Zhou ◽

Wimal Pathmasiri ◽

Dmytro Honcharenko ◽

Subhrangsu Chatterjee ◽

Jharna Barman ◽

...

Keyword(s):

Michael Addition ◽

Chemical Biology ◽

Rna Synthesis ◽

Spectroscopic Analysis ◽

Multiple Bond ◽

Protecting Group ◽

High Quality ◽

Heteronuclear Multiple Bond Correlation ◽

Michael Adducts

During the F–-promoted deprotection of the oligo–RNA, synthesized using our 2′-O-(4-tolylsulfonyl)ethoxymethyl (2′-O-TEM) group [Org. Biomol. Chem. 5, 333 (2007)], p-tolyl vinyl sulphone (TVS) is formed as a by-product. The TVS formed has been shown to react with the exocyclic amino functions of adenosine (A), guanosine (G), and cytidine (C) of the fully deprotected oligo–RNA to give undesirable adducts, which are then purified by HPLC and unambiguously characterized by 1H, 13C Heteronuclear Multiple Bond Correlation (HMBC) NMR and mass spectroscopic analysis. The relative nucleophilic reactivities of the nucleobases toward TVS have been found to be the following: N6–A > N4–C > N2–G > > N3–U. This reactivity of TVS toward RNA nucleobases to give various Michael adducts could, however, be suppressed by using various amines as scavengers. Among all these amines, morpholine and piperidine are the most efficient scavenger for TVS, which gave highly pure oligo–RNA even in the crude form and can be used directly in RNA chemical biology studies.Key words: RNA synthesis, RNA alkylation, p-tolyl vinyl sulphone, Michael addition.

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Natural abundance 13C-NMR spectroscopy for the quantitative determination of fecal fat

Clinical Biochemistry ◽

10.1016/s0009-9120(03)00075-4 ◽

2003 ◽

Vol 36 (7) ◽

pp. 505-510 ◽

Cited By ~ 1

Author(s):

P Kunz ◽

B Künnecke ◽

I Kunz ◽

H Lengsfeld ◽

M von Kienlin

Keyword(s):

Nmr Spectroscopy ◽

Quantitative Determination ◽

13C Nmr ◽

13C Nmr Spectroscopy ◽

Natural Abundance ◽

Fecal Fat

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Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling – the beginning of a wonderful friendship

Biological Chemistry ◽

10.1515/hsz-2021-0119 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Georg Künze ◽

Daniel Huster ◽

Sergey A. Samsonov

Keyword(s):

Nmr Spectroscopy ◽

Structural Information ◽

Md Simulations ◽

Specific Protein ◽

Regulatory Proteins ◽

Structural Constraints ◽

Modeling Tools ◽

Nuclear Overhauser ◽

Nmr Methods ◽

High Flexibility

Abstract The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.

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