Contribution to Structural Elucidation： Behaviours of Substructures Partially Defined from 2D NMR

Structural elucidation (automatic determination of the structure of a molecule from its spectra) is frequently hampered by com-binatorial explosion when trying to assemble the identified sub-structures. We devised a new method which can avoid this pit-fall by a systematic examination of allowed t3C chemical shifts ranges for all substructures chemically possible and combined with a progressive pruning thanks to neighbouring relationships appearing from 2D NMR. This method is explained by a de-tailed example.     

Using 2D NMR to determine the degree of branching of complicated hyperbranched polymers

Degree of branching (DB) is a crucial structure parameter of hyperbranched polymers, which can be determined by 1H NMR, quantitative 13C NMR, degradative method, etc. However, for complicated hy-perbranched polymers, intricate structure and severe overlap of spectral signals hinder the determina-tion of DB using traditional methods. In this work, the architecture of complicated hyperbranched polymers has been elucidated with the help of 2D NMR techniques. Using such a method, overlapped NMR signals can be well separated into a two-dimensional space, and additional structural information is also available. Correspondingly, quantitative analysis for complicated systems can be realized. De-termination of DBs for three types of complicated hyperbranched polymers synthesized from step-polymerization, self-condensation vinyl polymerization and self-condensation ring-opening po-lymerization is shown as examples.     

New validation of molecular mass measurements by means of 2D DOSY 1H NMR experiments: Application to surfactants

This study proposes a new correlation equation between surfactant diffusion coefficients and molecular mass using 2D DOSY ¹H NMR experiment. Indeed, DOSY is a suitable NMR technique to discriminate the different components in a mixture. Using Inverse Laplace Transform (ILT), all chemical shifts in the direct dimension are dispersed along the second dimension in relation to the diffusion coefficient. This approach does not make any assumption about the number of exponential components. The empiric equation was determined for anionic and non-ionic surfactants dissolved in dimethylsulfoxide (DMSO). The parameters, K = C_r = 5.18 ± 0.70 and a shape factor α = 0.45 ± 0.02 that is related to the molecular family fractal dimension constant δ_F = 2.21 ± 0.11, have been extracted from the data. The equation validity was checked for simple commercial raw material and a simple mixture composed of three surfactants classically used in detergent formulations. This equation, which describes quite satisfactorily the diffusion phenomenon of surfactants, could be used for deformulation purpose to check commercial products in case of quality control or adulteration assessment.     

Evaluation of double-tuned single-sided planar microcoils for the analysis of small 13C enriched biological samples using 1H-13C 2D heteronuclear correlation NMR spectroscopy

Microcoils provide a cost-effective approach to improve detection limits for mass-limited samples. Single-sided planar microcoils are advantageous in comparison to volume coils, in that the sample can simply be placed on top. However, the considerable drawback is that the RF field that is produced by the coil decreases with distance from the coil surface, which potentially limits more complex multi-pulse NMR pulse sequences. Unfortunately, ¹H NMR alone is not very informative for intact biological samples due to line broadening caused by magnetic susceptibility distortions, and ¹H-¹³C 2D NMR correlations are required to provide the additional spectral dispersion for metabolic assignments in vivo or in situ. To our knowledge, double-tuned single-sided microcoils have not been applied for the 2D ¹H-¹³C analysis of intact ¹³C enriched biological samples. Questions include the following: Can ¹H-¹³C 2D NMR be performed on single-sided planar microcoils? If so, do they still hold sensitivity advantages over conventional 5 mm NMR technology for mass limited samples? Here, 2D ¹H-¹³C HSQC, HMQC, and HETCOR variants were compared and then applied to ¹³C enriched broccoli seeds and Daphnia magna (water fleas). Compared to 5 mm NMR probes, the microcoils showed a sixfold improvement in mass sensitivity (albeit only for a small localized region) and allowed for the identification of metabolites in a single intact D. magna for the first time. Single-sided planar microcoils show practical benefit for ¹H-¹³C NMR of intact biological samples, if localized information within ~0.7 mm of the 1 mm I.D. planar microcoil surface is of specific interest.     

Deciphering composition and connectivity of a natural product with the assistance of MS and 2D NMR

A complementary application of three analytical techniques, viz. multidimensional nuclear magnetic resonance spectroscopy (NMR), mass spectrometry (MS), and single‐crystal X‐ray diffractometry was required to identify and refine two natural products isolated from Millettia versicolor and solvent of crystallization. The two compounds, namely 3‐(2H‐1,3‐benzodioxol‐5‐yl)‐6‐methoxy‐8,8‐dimethyl‐4H ,8H‐pyrano[2,3‐h ]chromen‐4‐one, or durmillone, (I), and (2E )‐1‐(4‐{[(2E )‐3,7‐dimethylocta‐2,6‐dien‐1‐yl]oxy}‐2‐hydroxyphenyl)‐3‐(4‐hydroxyphenyl)prop‐2‐en‐1‐one, (II), could not be separated by routine column chromatography and cocrystallized in a 2:1 ratio with 0.13 molecules of ethanol solvent. Compound (II) and ethanol could not be initially identified by single‐crystal X‐ray analysis due to complex disorder in the aliphatic chain region of (II). Mass spectrometry ensured that (II) represented only one species disordered over several positions in the solid state, rather than several species cohabitating on the same crystallographic site. The atomic identification and connectivity in (II) were established by several 2D (two‐dimensional) NMR techniques, which in turn relied on a knowledge of its exact mass. The derived connectivity was then used in the single‐crystal analysis to model the disorder of the aliphatic chain in (II) over three positions and allowed identification of a partially occupied ethanol solvent molecule that was disordered over an inversion center. The disordered moieties were refined with restraints and constraints.     

An attempted approach to the tricyclic core of haliclonin A:Structural elucidation of the final product by 2D NMR

We describe the design and execution of a novel synthetic route to the tricyclic core of haliclonin A, a tetracyclic marine natural product. The approach features Bachi's thiol-medicated free radical cyclization of alkenyl isocyanide to build the bridged ring system, and ring-closing metathesis (RCM) reaction to form the macrocycle. Execution of the synthetic plan ultimately resulted in a diazatricyclic compound. By means of 2D NMR techniques, the structure of this compound was revealed to an unexpected product 8. Analysis of the synthetic pathways allowed concluding that the unexpected product is a result of an "unexpected" migration of olefinic bond during dioxolanation of the 2-cyclohexenone derivative 7. This investigation also resulted in a concise construction of the functionalized hexahydro-1H-isoindole-1,5 (4H)-dione 12 and the macrocyclic tricyclic ring system 8.     

Quindolinocryptotackieine: the elucidation of a novel indoloquinoline alkaloid structure through the use of computer‐assisted structure elucidation and 2D NMR

Numerous indoloquinoline alkaloid structures have been identified from extracts of the West African plant Cryptolepis sanguinolenta. Recently, through the use of 2D NMR methods and cryogenic NMR probe technology in conjunction with computer‐assisted structure elucidation (CASE) methods, the structures of some chemical degradation products of this family of alkaloids have also been reported. We now report the characterization of a novel indoloquinoline dimeric alkaloid, quindolinocryptotackieine, through the extensive utilization of CASE methods. The NMR data presented here were collected over a decade earlier before the elucidation of the structure was possible, since manual analysis did not present a conclusive structure, whereas CASE produced a series of structures from which the structure could be verified. The original mass spectrometric (MS) data collected for the sample were problematic. Contemporary MS data were instead recollected from remaining small quantities of this alkaloid using modern instrumentation. The re‐collected data gave a usable molecular ion and several key fragment ions that were diagnostically useful. Copyright © 2003 John Wiley & Sons, Ltd.     

Dynamic NMR: A new procedure for the estimation of mixing times in the 2D EXSY experiments. A four-site exchange system studied by 1D and 2D EXSY spectroscopy

A procedure for the estimation of the mixing time between the last two 90° pulses in the classic three-pulse sequence NOESY/EXSY is proposed and tested and some considerations for the treatment of the two-dimensional (2D) ¹H NMR exchange spectra are given. The rate constants are thus obtained with reasonable precision. This procedure was followed to obtain the 2D spectra of the model compound α-[bis(dimethylamino)methylene]-4-nitrophenylacetonitrile, which represents a four-site exchange system. The barriers to restricted rotations found in this compound were also determined from one-dimensional (1D) ¹H NMR spectra, which were processed with the iterative complete lineshape analysis (CLSA) method. The double-fit approach was incorporated in the CLSA method. It is shown that the results from the 2D dynamic NMR spectral studies corroborate those obtained by the CLSA double-fit method.     

One‐step synthesis of 6‐acetamido‐3‐(N‐(2‐(dimethylamino) ethyl) sulfamoyl) naphthalene‐1‐yl 7‐acetamido‐4‐hydroxynaphthalene‐2‐sulfonate and its characterization with 1D and 2D NMR techniques

A one‐step method was reported for the synthesis of 6‐acetamido‐3‐(N‐(2‐(dimethylamino) ethyl) sulfamoyl) naphthalene‐1‐yl 7‐acetamido‐4‐hydroxynaphthalene‐2‐sulfonate by treating 7‐acetamido‐4‐hydroxy‐2‐naphthalenesulfonyl chloride with equal moles of N, N‐dimethylethylenediamine in acetonitrile in the presence of K₂CO₃. The chemical structure of the obtained compounds was characterized by MS, FTIR, ¹H NMR, ¹³C NMR, gCOSY, TOCSY, gHSQC, and gHMBC. The chemical shift differences of ¹H and ¹³C being δ 0.04 and 0.2, respectively, were unambiguously differentiated. Copyright © 2013 John Wiley & Sons, Ltd.     

Study of conformations and hydrogen bonds in the configurational isomers of pyrrole‐2‐carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis

The ¹H, ¹³C and ¹⁵N NMR studies have shown that the E and Z isomers of pyrrole‐2‐carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole‐2‐carbaldehyde oxime is stabilized by the N? H···N and N? H···O intramolecular hydrogen bonds, respectively. The N? H···N hydrogen bond in the E isomer causes the high‐frequency shift of the bridge proton signal by about 1 ppm and increase the ¹J(N, H) coupling by ～3 Hz. The bridge proton shows further deshielding and higher increase of the ¹J(N, H) coupling constant due to the strengthening of the N? H···O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by ～3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of ¹H shielding and ¹J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N? H···N and N? H···O hydrogen bondings to be estimated. The NBO analysis suggests that the N? H···N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N? H bond through the N? H···O hydrogen bond occurs in the Z isomer. Copyright © 2010 John Wiley & Sons, Ltd.     

Low field NMR for quality monitoring of 3D printed surimi from cod by-products: Effects of the pH-shift method compared with conventional washing

Implementation of three-dimensional (3D) food printing and novel analytics can reduce food waste and increase utilization of seafood by-products. Low field nuclear magnetic resonance (LF-NMR) and chemometrics were used to investigate the printability and characteristics of surimi pastes from cod by-products as affected by different processing methods (the pH-shift method vs. conventional washing), addition of salt (0, 1.5, and 3%), length of cold storage (0, 4, and 7 days) until 3D printing, and steam cooking. The analysis revealed two to three water populations in the 3D printed samples. Increasing the salt concentration induced myofibrillar swelling in the conventionally prepared surimi, whereas a more salt-induced gelling effect was observed in the pH-shift processed surimi. Cooking had a decreasing effect on the T₂₁ relaxation time and its corresponding apparent population (A₂₁), corresponding to protein denaturation and water loss during cooking. Increasing the salt concentration to 3% had a protective effect towards water exchange between the A₂₁ and A₂₃ populations in the conventionally washed samples but more subtly in the pH-shift samples. Similar trends in relaxation parameters were observed after 4 and 7 days of storage, although the intermediate population A₂₂ seemed to be most affected by the storage. Overall LF-NMR was an effective quality monitoring tool for the physicochemical changes occurring in the 3D printed surimi. The analysis showed both advantages and disadvantages of the two processing methods. However, it can clearly be concluded that increasing the salt content had a stabilizing effect on the surimi, and printing of fresh raw materials is recommended.     

Reactivity of Waterlogged Archeological Elm Wood with Organosilicon Compounds Applied as Wood Consolidants: 2D 1H–13C Solution-State NMR Studies

Some organosilicon compounds, including alkoxysilanes and siloxanes, proved effective in stabilizing the dimensions of waterlogged archaeological wood during drying, which is essential in the conservation process of ancient artifacts. However, it was difficult to determine a strong correlation between the wood stabilizing effect and the properties of organosilicon compounds, such as molecular weight and size, weight percent gain, and the presence of other potentially reactive groups. Therefore, to better understand the mechanism behind the stabilization effectiveness, the reactivity of organosilicons with wood polymers was studied using a 2D ¹H–¹³C solution-state NMR technique. The results showed an extensive modification of lignin through its demethoxylation and decarbonylation and also the absence of the native cellulose anomeric peak in siloxane-treated wood. The most substantial reactivity between wood polymers and organosilicon was observed with the (3-mercaptopropyl)trimethoxysilane treatment, showing complete removal of lignin side chains, the lowest syringyl/guaiacyl ratio, depolymerization of cellulose and xylan, and reactivity with the C6 primary hydroxyls in cellulose. This may explain the outstanding stabilizing effectiveness of this silane and supports the conclusion that extensive chemical interactions are essential in this process. It also indicates the vital role of a mercapto group in wood stabilization by organosilicons. This 2D NMR technique sheds new light on the chemical mechanisms involved in organosilicon consolidation of wood and reveals what chemical characteristics are essential in developing future conservation treatments.     

Synthetic approaches to 5,7- and 5,8-dimethoxyquinoline. Sonochemical dehalogenation of substituted 2,4-dichloroquinolines. Use of the 2D COLOC spectrum for the NMR assignment of 5,8-dimethoxyquinoline

Summary Sonochemical dehalogenation of 2,4-dichloroquinoline is very facile. However, with 5,7-dimethoxy-2,4-dichloroquinoline the reaction proceeds stepwise to provide the title dimethoxyquinolines which cannot be prepared via theSkraup reaction. The¹³C NMR chemical shift assignments for 5,8-dimethoxyquinoline are presented. These were made by utilising the coupling connectivities from the bridgehead carbons in the 2D COLOC spectrum.

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Synthese von 5,7- und 5,8-Dimethoxychinolin. Sonochemische Dehalogenierung von substituierten 2,4-Dichlorochinolinen. NMR-Spektroskopische Zuordnung von 5,8-Dimethoxychinolin mittels eines COLOC-Experiments

Zusammenfassung 2,4-Dichlorchinoline können sonochemisch leicht dehalogeniert werden. Mit 5,7-Dimethoxy-2,4-dichlorchinolin verläuft die Reaktion in mehreren Schritten zu den Titelverbindungen, die mittelsSkraup-Reaktion nicht hergestellt werden können. Das¹³C-NMR-Spektrum von 5,8-Dimethoxychinolin wurde, ausgehend von den Brückenkopfkohlenstoffatomen, mit Hilfe eines COLOC-Experiments zugeordnet.

     

两个二维层状4-双(咪唑基-1-甲基)-苯钴和镍配位聚合物的合成与表征

以1,4-双(咪唑基-1-甲基)-苯(bix)为配体,间苯二甲酸(IPA)为辅助配体,合成制备了两种新型同构配位聚合物:{[Ni(bix)(IPA)(H_2O)]}_n(1)和{[Co(bix)(IPA)(H_2O)]}_n(2)。单晶结构表明,此两个配合物均形成二维层状空间结构,金属原子均为六配位八面体结构,赤道平面上四个配位原子来自间苯二甲酸和配位水分子,轴向两个配位原子为bix配体的咪唑环上的N原子。金属原子通过配体连接形成四连接的二维4(4).6(2)方格层状结构。     

Spectrometric and 2D NMR Studies on the Complexation of Chlorophenols with Cyclodextrins

The formation and structure of inclusion complexes of - and-cyclodextrins with 2-chlorophenol (2CP), 3-chlorophenol (3CP),4-chlorophenol (4CP), 2,4-dichlorophenol (24DCP), 2,6-dichlorophenol(26DCP) and 3,4-dichlorophenol (34DCP) have been studied by UV-VIS and¹H NMR spectroscopy. Both cyclodextrins were found to form 1:1inclusion complexes. Bindingconstants estimated from titration studies revealed that the stability of the complexes was highly dependent on the structure and polarity of the chlorophenol and on the cyclodextrin used. In general, weaker binding constants were observed for a given chlorophenol with -cyclodextrin than with-cyclodextrin. The weakest binding constants (K_{b < 200} M^-1) were obtained for the ortho-substituted chlorophenols (2CP and 26DCP) and the largest binding constants were obtained between para-chlorophenols (4CP, 24DCP and 34DCP) and-cyclodextrin. 2D-TROESY studies of chlorophenol-cyclodextrincomplexes in D₂O provided insight into the structure of the complexes.     

Combined application of 2D NMR correlation methods and ab initio chemical shift calculations to the structure determination of new heterocyclic compounds

The combined use of 2D NMR correlation methods and ab initio chemical shift calculations is efficient and, in some cases, virtually the only way to determine the structures of new organic compounds. This approach enabled us to establish the structure of the major unusual product of the three-component reaction of imidazo[1,5-a]quinoxalin-4-one, bis(2-chloroethyl)amine hydrochloride, and potassium carbonate in DMF. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2172–2179, December, 2006. Dedicated to Professor A. V. Il’yasov on the occasion of his 70th birthday.     

Preparation of alpha-diazocarbonyl compounds from beta-lapachone derivatives and other 1,2-naphthoquinones: use of the 2D NMR 1H,15N and 1H,13C HMBC techniques in assigning regiochemistry

The assignment of the diazo site in products of the reaction of p-toluenesulfonylhydrazine with beta-lapachone, 3,4-dihydro-2,2-dimethyl-2H-naphtho[1,2-b]pyran-5,6-dione, and other 1,2-naphthoquinones in methanol solution at room temperature has been accomplished using 1H,13C HMBC and 1H,15N HMBC NMR experiments. Only one diazo-naphthalenone product was isolated in yields ranging from 50-100% from each reaction. The site of diazo substitution of beta-lapachone and derivatives is the 1-position, in contrast to substitution at the 2-position in 4-MeO-1,2-naphthoquinone. Steric factors, rather than electronic factors, control the reaction site. Along with 2-diazo-1(2H)-naphthalenone, an additional product isolated from the reaction of p-toluenesulfonylhydrazide with 1,2-naphthoquinone was 2-diazo-4-hydroxy-1(2H)-naphthalenone. Confirmation of the formation of 6-diazo-2,2-dimethyl-2,3,4,6-tetrahydro-2H-benzo[h]cromen-5-one, obtained from beta-lapachone, was achieved using single crystal X-ray diffraction.     

Experimental and theoretical study of the intramolecular C–H···N and C–H···S hydrogen bonding effects in the 1H and 13C NMR spectra of the 2‐(alkylsulfanyl)‐5‐amino‐1‐vinylpyrroles: a particular state of amine nitrogen

In the ¹H NMR spectra of the 1‐vinylpyrroles with amino‐ and alkylsulfanyl groups in 5 and 2 positions, an extraordinarily large difference between resonance positions of the H_A and H_B terminal methylene protons of the vinyl group is discovered. Also, the one‐bond ¹J(C_β,H_B) coupling constant is surprisingly greater than the ¹J(C_β,H_A) coupling constant in pyrroles under investigation, while in all known cases, there was a reverse relationship between these coupling constants. These spectral anomalies are substantiated by quantum chemical calculations. The calculations show that the amine nitrogen lone pair is removed from the conjugation with the π‐system of the pyrrole ring so that it is directed toward the H_B hydrogen. These factors are favorable to the emergence of the intramolecular C–H_B???N hydrogen bonding in the s‐cis(N) conformation. On the other hand, the spatial proximity of the sulfur to the H_B hydrogen provides an opportunity of the intramolecular C–H_B???S hydrogen bonding in the s‐cis(S) conformation. Presence of the hydrogen bond critical points as well as ring critical point for corresponding chelate ring revealed by a quantum theory of atoms in molecules (QTAIM) approach confirms the existence of the weak intramolecular C–H???N and C–H???S hydrogen bonding. Therefore, an unusual high‐frequency shift of the H_B signal and the increase in the ¹J(C_β,H_B) coupling constant can be explained by the effects of hydrogen bonding. Copyright © 2013 John Wiley & Sons, Ltd.