Structure Elucidator: a versatile expert system for molecular structure elucidation from 1D and 2D NMR data and molecular fragments

StrucEluc is an expert system that allows the computer-assisted elucidation of chemical structures based on the inputs of a series of spectral data including 1D and 2D NMR and mass spectra. The system has been enabled to allow a chemist to utilize fragments stored in a fragment database as well as user-defined fragments submitted by the chemist in the structure elucidation process. The association of fragments in this way has been shown to dramatically speed up the process of structure generation from 2D NMR data and has helped to minimize or eliminate the need for user intervention thereby further enabling the vision of automated elucidation. The use of fragments has frequently transformed very difficult 2D NMR elucidation challenges into easily solvable tasks. A strategy to utilize molecular fragments has been developed and optimized based on specific challenging examples. This strategy will be described here using real world examples. Experience gained by solving more than 150 structure elucidation problems from a variety of literature sources is also reviewed in this work.     

Synthesis of novel O-alkylbenzochromeno-1,5-benzodiazepinones. Study of the N–H····N and CO····HN hydrogen bonding interactions with 2-aminopyridines

A series of novel 6-(O-alky)lbenzochromeno-1,5-benzodiazepin-2-ones 4a–c was prepared through the condensation between the [1]benzopyrano[4,3-c][1,5]benzodiazepin-7(8H)one 1 and a series of alkylalcohols. Scaffold 4 exhibited interesting hydrogen-bonding interaction with 2-aminopyridine derivatives. The so obtained self-assembled systems 5 were fully characterized by 1D/2D-NMR techniques and mass spectrometry. The hydrogen-bonding interaction was supported by IR and Raman spectroscopy and by ¹H NMR titration experiments, and was confirmed by an X-ray crystal structure analysis.     

Kororamide A,a new tribrominated indole alkaloid from the Australian bryozoan Amathia tortuosa

A new tribrominated indole alkaloid, kororamide A together with the known alkaloid convolutamine F, were isolated through the application of mass directed purification from the bryozoan, Amathia tortuosa collected from northern New South Wales, Australia. The structure of kororamide A was deduced from the analysis of 1D/2D NMR and MS data. Kororamide A exists in solution as a mixture of interconverting cis–trans amide regioisomers in a ratio of 4:5. Bioactivity testing demonstrated that kororamide A was marginally active against chloroquine-sensitive and resistant strains of the malarial parasite Plasmodium falciparum, and was inactive against normal human cell lines.     

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.     

Water cluster calibration reduces mass error in electrospray ionization mass spectrometry of proteins

Herein we report a novel calibration routine for use in positive ion mode electrospray ionization mass spectrometry (ESI-MS). Monoisotopic masses were calculated for a series of water clusters and used as calibration reference files (available at http://www.hbcg.utmb.edu/xray). The water cluster series contains singly charged peaks every 18 Da, which allows calibration curves to be precisely defined over a broad mass-to-charge ratio range. Water clusters, induced by a combination of high flow rate and high cone voltage, were used to accurately calibrate a quadrupole mass spectrometer from 100 to 1900 m/z. Calibration curves thus generated have many more data points and greatly reduced standard deviations compared to those obtained from myoglobin, sodium iodide, cesium iodide, or poly(ethylene glycol) based calibration standards. This calibration routine reduces the error in protein mass measurements by a factor of 3, from ±0.01% to ±0.0035% at the 95% confidence limit. The implications of this increased mass accuracy and wider calibrated mass-to-charge ratio scale for the study of protein sequence, structure, and folding by ESI-MS are discussed.     

Autoxidation of 4-Hydrazinylquinolin-2(1H)-one; Synthesis of Pyridazino[4,3-c:5,6-c′]diquinoline-6,7(5H,8H)-diones

An efficient synthesis of a series of pyridazino[4,3-c:5,6-c′]diquinolines was achieved via the autoxidation of 4-hydrazinylquinolin-2(1H)-ones. IR, NMR (¹H and ¹³C), mass spectral data, and elemental analysis were used to fit and elucidate the structures of the newly synthesized compounds. X-ray structure analysis and theoretical calculations unequivocally proved the formation of the structure. The possible mechanism for the reaction is also discussed.     

Antiprotozoal Activity of Azabicyclo-Nonanes Linked to Tetrazole or Sulfonamide Cores

N-(Aminoalkyl)azabicyclo[3.2.2]nonanes possess antiplasmodial and antitrypanosomal activity. A series with terminal tetrazole or sulfonamido partial structure was prepared. The structures of all new compounds were confirmed by NMR and IR spectroscopy and by mass spectral data. A single crystal structure analysis enabled the distinction between isomers. The antiprotozoal activities were examined in vitro against strains of Plasmodium falciparum and Trypanosoma brucei rhodesiense (STIB 900). The most active sulfonamide and tetrazole derivates showed activities in the submicromolar range.     

Silvaglenamin—a novel dimeric triterpene alkaloid from Aglaia silvestris

An unusual dimeric triterpene structure with two dammarane units linked with an enaminic -NH- group was isolated from the root extract of Aglaia silvestris. The structure was elucidated by 1D and 2D NMR analysis and ESI mass spectrometry.     

Isolation,Structural Analysis and Biological Activity Assays of Biselisabethoxanes A and B: Two Dissymmetric Bis-Diterpenes from the Southwestern Caribbean Sea Gorgonian Coral Pseudopterogorgia elisabethae

Two novel dissymmetric diterpenoids, biselisabethoxanes A and B (1 and 2), were isolated from the hexane extracts of the gorgonian coral Pseudopterogorgia elisabethae. Biselisabethoxane A (1) represents the first example of a marine-derived C₄₀ dimer made of two distinct diterpene fragments, whereas biselisabethoxane B (2) is a fused heterodimer stemming from coupling of two amphilectane-based fragments. The structures of 1 and 2 were elucidated based on 1D and 2D NMR spectral data analysis. The molecular structure of 1 was subsequently confirmed by X-ray crystallographic analysis. When evaluated for their inhibitory effects in a series of well-established biological activity assays the isolated compounds were shown to moderately inhibit the growth of Mycobacterium tuberculosis.     

Antihypertensive Activity of the Alkaloid Aspidocarpine in Normotensive Wistar Rats

The alkaloid Aspidocarpine was isolated from the bark of Aspidosperma desmanthum. Its structure was elucidated by the spectral data of ¹H and ¹³C-NMR (1D and 2D) and high-resolution mass spectrometry (HRESIMS). The antihypertensive activity was investigated by intravenous infusion in Wistar rats. This alkaloid significantly reduced (p < 0.05) the systolic, median, and diastolic blood pressures of rodents, without causing motor incoordination and imbalance in the rotarod test. The results indicate that the alkaloid Aspidocarpine exerts its antihypertensive activity without causing sedation or the impairment of motor functions.     

Ochraceopyronide,a Rare α-Pyrone-C-lyxofuranoside from a Soil-Derived Fungus Aspergillus ochraceopetaliformis

The fungal strain was isolated from a soil sample collected in Giza province, Egypt, and was identified as Aspergillus ochraceopetaliformis based on phenotypic and genotypic data. The ethyl acetate extract of the fungal strain exhibited promising activity levels against several pathogenic test organisms and through a series of ¹H NMR guided chromatographic separations, a new α-pyrone-C-lyxofuranoside (1) along with four known compounds (2–5) were isolated. The planar structure of the new metabolite was elucidated by detailed analysis of its 1D/2D NMR and HRMS/IR/UV spectroscopic data, while the relative configuration of the sugar moiety was determined by a combined study of NOESY and coupling constants data, with the aid of theoretical calculations. The structures of the known compounds—isolated for the first time from A. ochraceopetaliformis—were established by comparison of their spectroscopic data with those in the literature. All isolated fungal metabolites were evaluated for their antibacterial and antifungal activities against six Gram-positive and Gram-negative bacteria as well as against three human pathogenic fungi.     

Isolation and structure determination of a new lasso peptide subterisin from Sphingomonas subterranea

A new lasso peptide named subterisin was isolated from the culture broth of Sphingomonas subterranea NBRC 16086^T. The molecular formula of subterisin was established as C₇₈H₁₂₁O₂₂N₂₁ based on accurate mass analysis. The chemical structure of subterisin was determined by 2D NMR experiments. The presence of macrolactam ring of Gly1–Glu8 was indicated by NOESY experiment and MS/MS analysis. The three-dimensional structure of subterisin in solution was established by calculation based on NMR data. The proposed biosynthetic gene cluster of subterisin was found on the genome of S. subterranea.     

The 'apparent' hydrolysis of alkyl esters during electrospray ionization

Electrospray ionization (ESI) mass spectrometry was employed to obtain both molecular weight confirmation and structural information for a series of novel alkenyldiarylmethane (ADAM) analogs. The mass spectral data were intended for use during the structure elucidation of ester hydrolysis products formed during an in vitro metabolism study of a series of novel ADAM analogs. The data on the precursor molecules show the presence of the molecular ion peak, [M+H](+), as well as a peak consistent with the hydrolysis product of the original ester ([MH-ROH+H(2)O](+)). However, chemical ionization mass spectrometry, elemental analysis and (1)H NMR data indicated the presence of only the intact diester compounds, suggesting that the formation of the hydrolysis product was an instrumental artifact, i.e., in-beam hydrolysis during ESI or a result of longer ion residence times of the ion trap mass analyzer.     

Phase Correction for Absorption Mode Two-Dimensional Mass Spectrometry

Two-dimensional mass spectrometry (2D MS) is a tandem mass spectrometry method that relies on manipulating ion motions to correlate precursor and fragment ion signals. 2D mass spectra are obtained by performing a Fourier transform in both the precursor ion mass-to-charge ratio (m/z) dimension and the fragment ion m/z dimension. The phase of the ion signals evolves linearly in the precursor m/z dimension and quadratically in the fragment m/z dimension. This study demonstrates that phase-corrected absorption mode 2D mass spectrometry improves signal-to-noise ratios by a factor of 2 and resolving power by a factor of 2 in each dimension compared to magnitude mode. Furthermore, phase correction leads to an easier differentiation between ion signals and artefacts, and therefore easier data interpretation.     

Data Processing for 3D Mass Spectrometry Imaging

Data processing for three dimensional mass spectrometry (3D-MS) imaging was investigated, starting with a consideration of the challenges in its practical implementation using a series of sections of a tissue volume. The technical issues related to data reduction, 2D imaging data alignment, 3D visualization, and statistical data analysis were identified. Software solutions for these tasks were developed using functions in MATLAB. Peak detection and peak alignment were applied to reduce the data size, while retaining the mass accuracy. The main morphologic features of tissue sections were extracted using a classification method for data alignment. Data insertion was performed to construct a 3D data set with spectral information that can be used for generating 3D views and for data analysis. The imaging data previously obtained for a mouse brain using desorption electrospray ionization mass spectrometry (DESI-MS) imaging have been used to test and demonstrate the new methodology.     

Dictyotadimer A, a new dissymmetric bis-diterpene from a brown alga of the genus Dictyota

A phytochemical investigation of a Mediterranean brown alga (Dictyota sp.) led to the isolation of a novel C₄₀bis-diterpene, named dictyotadimer A. The chemical structure of this unusual dissymmetric dimer, characterized by a C-C linkage between two different xenicane units, was elucidated by 1D and 2D NMR analyses together with HR-ESI mass spectrometry. The relative configuration of the two diterpenoid components was determined by NOESY NMR correlations and molecular modeling. A plausible biogenetic pathway of dictyotadimer A was also proposed.     

Subcellular and molecular localization of rare earth elements and structural characterization of yttrium bound chlorophyll a in naturally grown fern Dicranopteris dichotoma

A rare earth element (REE) hyperaccumulator, Dicranopteris dichotoma, sampled from an REE mining area in South-Jiangxi region, was chosen for analysis of 15 REEs at subcellular and molecular levels by inductively coupled plasma-mass spectrometry (ICP-MS). The sum of the concentrations of 15 REEs (∑REEs) of D. dichotoma leaf was about 0.1% dry mass. Results indicated that the ∑REEs of different subcellular fractions of D. dichotoma leaf were cell walls>organelles>the ‘soluble’ fraction (i.e., cytosol and vacuoles)>cell membranes. ICP-MS results also showed that REEs existed in chlorophylls and lutein, though REE concentrations in carotene and pheophytin were both lower than the procedural blank levels. The ∑REEs of crude lipopolysaccharide and Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) obtained from D. dichotoma leaf were 1200 and 343 mg/kg, respectively. The extended X-ray absorption fine structure (EXAFS) study of D. dichotoma chlorophyll a indicated that yttrium was bound to the porphyrin ring of chlorophyll a, and one yttrium atom was surrounded by four nitrogen atoms with the average yttrium-nitrogen bond length being 0.236 nm. These data might be useful for understanding of the physiological role of REEs in hyperaccumulator D. dichotoma.     

13-Chloro-3-O-β-d-glucopyranosylsolstitialin from Leontodon palisae: the first genuine chlorinated sesquiterpene lactone glucoside

Apart from a number of known sesquiterpenoids, a novel chlorinated sesquiterpene lactone glucoside--13-chloro-3-O-β-d-glucopyranosylsolstitialin--has been isolated from the Southwestern European plant Leontodon palisae (Asteraceae, tribe Lactuceae). The structure has been established by high resolution mass spectrometry and 1D as well as 2D NMR spectroscopy. The compound represents the first naturally occurring chlorinated sesquiterpene lactone glucoside. The cytotoxicity of the new compound and related ones was evaluated using the MTT assay.     

Katorazone,a new yellow pigment with a 2-azaquinone-phenylhydrazone structure produced by Streptomyces sp. IFM 11299

An unusual alkaloid with a 2-azaquinone-phenylhydrazone structure, katorazone (1), and other metabolites were isolated from the ethyl acetate extract of Streptomyces sp. IFM 11299. The chemical structure of katorazone (1) was elucidated by 1D and 2D NMR analyses together with HR-ESI mass spectrometry. Katorazone (1) showed a synergistic effect in combination with TRAIL and decreased the viability of human gastric adenocarcinoma (AGS) cells.     

Structural analysis of isomeric chondroitin sulfate oligosaccharides using regioselective 6-O-desulfation method and tandem mass spectrometry

A strategy based on a regioselective 6-O-desulfation reaction and negative ion electrospray ionization tandem mass spectrometry (ESI-MS(n)) was developed for the structural delineation of isomeric chondroitin sulfate oligosaccharides. Product ions resulting from the glycosidic cleavage provided information about the number of sulfate groups in each sugar residue. After the regioselective 6-O-desulfation reaction, the number of sulfate groups on each residue was obtained using a tandem mass spectrometry analysis of the reaction product. The sulfation pattern could be obtained based on the product ions of analytes before and after the desulfation reaction. The strategy was demonstrated using a series of tetrasaccharides prepared from shark cartilage chondroitin sulfate D. Among the 12 identified tetrasaccharides, six structures had not been reported before.