A solution to the 1D NMR alignment problem using an extended generalized fuzzy Hough transform and mode support

This paper approaches the problem of intersample peak correspondence in the context of later applying statistical data analysis techniques to 1D ¹H-nuclear magnetic resonance (NMR) data. Any data analysis methodology will fail to produce meaningful results if the analyzed data table is not synchronized, i.e., each analyzed variable frequency (Hz) does not originate from the same chemical source throughout the entire dataset. This is typically the case when dealing with NMR data from biological samples. In this paper, we present a new state of the art for solving this problem using the generalized fuzzy Hough transform (GFHT). This paper describes significant improvements since the method was introduced for NMR datasets of plasma in Csenki et al. (Anal Bioanal Chem 389:875-885, 15) and is now capable of synchronizing peaks from more complex datasets such as urine as well as plasma data. We present a novel way of globally modeling peak shifts using principal component analysis, a new algorithm for calculating the transform and an effective peak detection algorithm. The algorithm is applied to two real metabonomic ¹H-NMR datasets and the properties of the method are compared to bucketing. We implicitly prove that GFHT establishes the objectively true correspondence. Desirable features of the GFHT are: (1) intersample peak correspondence even if peaks change order on the frequency axis and (2) the method is symmetric with respect to the samples. Figure From chaos to order: heatmaps of a H-NMR spectral segment prior and post sorting on one peak position. Post sorting sample order reveals that peak positions exhibits distinctive patterns which are modeled by the GFHT to establish correspondence. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Characterization and analysis of mycobacteria and Gram-negative bacteria and co-culture mixtures by Raman microspectroscopy, FTIR, and atomic force microscopy

The molecular composition of mycobacteria and Gram-negative bacteria cell walls is structurally different. In this work, Raman microspectroscopy was applied to discriminate mycobacteria and Gram-negative bacteria by assessing specific characteristic spectral features. Analysis of Raman spectra indicated that mycobacteria and Gram-negative bacteria exhibit different spectral patterns under our experimental conditions due to their different biochemical components. Fourier transform infrared (FTIR) spectroscopy, as a supplementary vibrational spectroscopy, was also applied to analyze the biochemical composition of the representative bacterial strains. As for co-cultured bacterial mixtures, the distribution of individual cell types was obtained by quantitative analysis of Raman and FTIR spectral images and the spectral contribution from each cell type was distinguished by direct classical least squares analysis. Coupled atomic force microscopy (AFM) and Raman microspectroscopy realized simultaneous measurements of topography and spectral images for the same sampled surface. This work demonstrated the feasibility of utilizing a combined Raman microspectroscopy, FTIR, and AFM techniques to effectively characterize spectroscopic fingerprints from bacterial Gram types and mixtures.

Preparation, spectral and biological investigation of formaldehyde-based ligand containing piperazine moiety and its various polymer metal complexes

A novel tetradentate salicylic acid-formaldehyde ligand containing piperazine moiety (SFP) was synthesized by condensation of salicylic acid, formaldehyde and piperazine in presence of base catalyst, which was subjected for the preparation of coordination polymers with metal ions like manganese(II), cobalt(II), copper(II), nickel(II) and zinc(II). All the synthesized polymeric compounds were characterized by elemental analysis, IR, (1)H NMR and electronic spectral studies. The thermal stability was determined by thermogravimetric analysis and thermal data revealed that all the polymer metal complexes show good thermal stability than their parent ligand. Electronic spectral data and magnetic moment values revealed that polymer metal complexes of Mn(II), Co(II) and Ni(II) show an octahedral geometry while Cu(II) and Zn(II) show distorted octahedral and tetrahedral geometry respectively. The antimicrobial screening of the ligand and coordination polymers was done by using Agar well diffusion method against various bacteria and fungi. It was evident from the data that antibacterial and antifungal activity increased on chelation and all the polymer metal complexes show excellent antimicrobial activity than their parent ligand.     

Evaluation of biological activities of some Schiff bases and metal complexes

Several Schiff bases were synthesised from sulphonamide and resacetophenone. The characterisation was done by CHN analysis, IR and NMR spectral data. These Schiff bases were evaluated for their antimicrobial activity against both Gram-positive and Gram-negative bacteria as well as fungi. The antibacterial activity was studied against B. megaterium, E. coli, B. subtilis, P. fluorescens and antifungal activity against A. awamori. In addition, copper, nickel, cobalt, and iron complexes of two Schiff bases were also synthesised. Their structural characterisation was performed using CHN analysis and IR spectral data and their antibacterial and antifungal activities were also evaluated. The comparison of antimicrobial activities of the ligands and complexes shows that the presence of metal causes more inhibition i.e., more activity. Out of the four metals studied, cobalt and iron were found to have more antimicrobial activity.     

Topological data analysis: A promising big data exploration tool in biology,analytical chemistry and physical chemistry

An important feature of experimental science is that data of various kinds is being produced at an unprecedented rate. This is mainly due to the development of new instrumental concepts and experimental methodologies. It is also clear that the nature of acquired data is significantly different. Indeed in every areas of science, data take the form of always bigger tables, where all but a few of the columns (i.e. variables) turn out to be irrelevant to the questions of interest, and further that we do not necessary know which coordinates are the interesting ones. Big data in our lab of biology, analytical chemistry or physical chemistry is a future that might be closer than any of us suppose. It is in this sense that new tools have to be developed in order to explore and valorize such data sets. Topological data analysis (TDA) is one of these. It was developed recently by topologists who discovered that topological concept could be useful for data analysis. The main objective of this paper is to answer the question why topology is well suited for the analysis of big data set in many areas and even more efficient than conventional data analysis methods. Raman analysis of single bacteria should be providing a good opportunity to demonstrate the potential of TDA for the exploration of various spectroscopic data sets considering different experimental conditions (with high noise level, with/without spectral preprocessing, with wavelength shift, with different spectral resolution, with missing data).     

Many-electron effects in the x-ray emission spectra and the one-particle green's function. Correspondence theorem

Within the framework of reasonable approximation the intensity of spectral bands in the X-ray emission spectrum was shown to be proportional to the imaginary part of the one-particle Green's function. From this ensues a statement about a correspondence between the distribution of the intensity in the X-ray emission and photoelectron spectra — correspondence theorem.     

The application of multivariate techniques to data from spanish glass-making objects from the Roman Era

Three multivariate techniques (principal components analysis, correspondence factor analysis and spectral map analsis) are applied to x-ray fluorescence data from glass-making objects from the 5th century AD found in Tarragona (Tarraco in the Roman Empire). The information obtained by displaying th eobjects and variables in each reduced factor space is compared. The presence of redundant information is shown. The visualization of groups of objects and of the relationship between objects and variables allows the formulation of hypotheses concerning the origin of the samples and the presence of local glassworks.     

Microbial metabolism of loganin by intestinal bacteria and identification of new metabolites in rat

Loganin is an important constituent of the traditional Chinese medicine Fructus Corni, with several bioactivities. Microbial metabolism of loganin by intestinal bacteria was investigated. Two metabolites (log-1 and log-2) were isolated from anaerobic culture and their structures were identified by means of their ESI-MS, (1)H-NMR, (13)C-NMR and 2D-NMR spectral data. Log-1 was an aglycone of loganin and log-2 was proved to be a new compound. In vivo metabolites of loganin were detected in rat urine, bile and feces after oral administration of loganin and the structures were proved to be identical with that of the microbial metabolites log-1 and log-2 by HPLC-PDA analysis and comparison with the reference standards. Therefore we can prepare metabolites by anaerobic culture with intestinal bacteria.     

Synthesis and Antimicrobial Activity of 1,3,4‐Oxadiazole‐2(3H)‐thione and Azidomethanone Derivatives Based on Quinoline‐4‐carbohydrazide Derivatives

A new series compounds of quinoline derivatives were synthesized by reaction of 3‐(carboxymethyl)‐2‐arylquinoline‐4‐carboxylic acids 1a , 1b , 1c with different nucleophiles. The structures of the new compounds were elucidated on the basis of FTIR, ¹H‐NMR, ¹³C‐NMR spectral data, GC/MS, and chemical analysis. Investigation of antimicrobial activity of all new compounds was evaluated using a broth dilution technique in terms of minimal inhibitory concentration count against four pathogenic bacteria and two pathogenic fungi. Most of the new compounds were significantly active against bacteria and fungi.     

Complete assignments of (1)H and (13)C NMR spectral data of nine surfactin isomers

A new surfactin isomer (1) was isolated from a mangrove bacteria strain 'Bacillus sp'. Its structure was identified, and full assignments of (1)H and (13)C NMR spectral data were achieved for the first time by a combination of mass spectrometry and 1D and 2D NMR experiments including DEPT, (1)H-(1)H COSY, HSQC, HMBC, TOCSY, ROESY, and HSQC-TOCSY. The NMR spectral data of eight known analogs (2-9) are also reported.     

A structural mode-coupling approach to 15N NMR relaxation in proteins.

The two-body Slowly Relaxing Local Structure (SRLS) model was applied to (15)N NMR spin relaxation in proteins and compared with the commonly used original and extended model-free (MF) approaches. In MF, the dynamic modes are assumed to be decoupled, local ordering at the N-H sites is represented by generalized order parameters, and internal motions are described by effective correlation times. SRLS accounts for dynamical coupling between the global diffusion of the protein and the internal motion of the N-H bond vector. The local ordering associated with the coupling potential and the internal N-H diffusion are tensors with orientations that may be tilted relative to the global diffusion and magnetic frames. SRLS generates spectral density functions that differ from the MF formulas. The MF spectral densities can be regarded as limiting cases of the SRLS spectral density. SRLS-based model-fitting and model-selection schemes similar to the currently used MF-based ones were devised, and a correspondence between analogous SRLS and model-free parameters was established. It was found that experimental NMR data are sensitive to the presence of mixed modes. Our results showed that MF can significantly overestimate order parameters and underestimate local motion correlation times in proteins. The extent of these digressions in the derived microdynamic parameters is estimated in the various parameter ranges, and correlated with the time scale separation between local and global motions. The SRLS-based analysis was tested extensively on (15)N relaxation data from several isotropically tumbling proteins. The results of SRLS-based fitting are illustrated with RNase H from E. coli, a protein extensively studied previously with MF.     

Desorption electrospray ionization mass spectrometry of intact bacteria

Desorption electrospray ionization (DESI) mass spectrometry (MS) was used to differentiate seven bacteria species on the basis of their measured DESI-mass spectral profile. Both gram-positive and gram-negative bacteria were tested and included Escherichia coli, Staphyloccocus aureus, Enterococcus sp., Bordetella bronchiseptica, Bacillus thuringiensis, Bacillus subtilis and Salmonella typhimurium. Distinct DESI-mass spectra, in the mass range of 50-500 u, were obtained from whole bacteria in either positive or negative ion modes in less than 2 mins analysis time. Positive ion DESI-mass spectral fingerprints were compared using principal components analysis (PCA) to investigate reproducibility for the intraday and the day-to-day measurements and the method selectivity to differentiate the bacteria studied. Detailed study of variances in the assay revealed that a large contribution to the DESI-mass spectral fingerprint variation was the growth media preparation procedure. Specifically, experiments conducted with the growth media prepared using the same batch yielded highly reproducible DESI-mass spectra, both in intraday and in day-to-day analyses (i.e. one batch of growth media used over a 3-day period versus a new batch every day over the same 3-day period). Conclusions are drawn from our findings in terms of strategies for rapid biodetection with DESI-MS.     

Non-invasive identification of chemical compounds by energy dispersive X-ray fluorescence spectrometry, combined with chemometric methods of data evaluation

Chemicals from customers’ returns have to be analyzed before they can be reused as raw materials in production. A procedure for non-invasive qualitative analysis of compounds in a closed container based on energy dispersive X-ray fluorescence (EDXRF) spectrometry is described. EDXRF was chosen as method for non-invasive analysis of chemicals through PE bottle walls without opening the bottle. This analysis aims for a quick proof of correspondence between the declaration of a reagent on the label of the bottle and its content. This analytical result cannot be achieved by a mere evaluation of characteristic element lines in EDXRF-spectra in combination with the method of matrix correction or the method of mean atomic number. These methods take into account only a small part of the total information available in an X-ray spectrum. It is shown here that valuable additional information is extractable from the spectral ranges of the Compton-scattering and Rayleigh-scattering areas by the use of methods of multivariate data analysis, especially by principle component analysis (PCA). Regularized discriminant analysis (RDA) was employed to establish a classification scheme for unknown samples.     

Non-invasive identification of chemical compounds by energy dispersive X-ray fluorescence spectrometry, combined with chemometric methods of data evaluation

Chemicals from customers' returns have to be analyzed before they can be reused as raw materials in production. A procedure for non-invasive qualitative analysis of compounds in a closed container based on energy dispersive X-ray fluorescence (EDXRF) spectrometry is described. EDXRF was chosen as method for noninvasive analysis of chemicals through PE bottle walls without opening the bottle. This analysis aims for a quick proof of correspondence between the declaration of a reagent on the label of the bottle and its content. This analytical result cannot be achieved by a mere evaluation of characteristic element lines in EDXRF-spectra in combination with the method of matrix correction or the method of mean atomic number. These methods take into account only a small part of the total information available in an X-ray spectrum. It is shown here that valuable additional information is extractable from the spectral ranges of the Compton-scattering and Rayleigh-scattering areas by the use of methods of multivariate data analysis, especially by principle component analysis (PCA). Regularized discriminant analysis (RDA) was employed to establish a classification scheme for unknown samples.     

Organotin(IV) complexes of 4-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)benzoic acid: Synthesis, spectral characterization and biological applications

4-(2,5-Dioxo-2,5-dihydro-1H-pyrrol-1-yl)benzoic acid and its complexes with methyl-, n-butyl-, phenyl-, benzyl- and octyl-tin have been synthesized and characterized by elemental analysis and spectral studies. The geometry around the tin atom has been deduced from both solid and solution studies. These complexes were also tested against different bacteria and fungi to determine their toxicity. LD50 data was also calculated using the Brine Shrimp method.     

Quantum chemical interpretation of redox properties of ruthenium complexes with vinyl and TCNX type non-innocent ligands

This review provides an overview of density functional theory (DFT) calculations in a consequence with spectroelectrochemical measurements on mononuclear and symmetrically or unsymmetrically bridged di- and tetranuclear ruthenium complexes of vinyl and TCNX ligands. The DFT approach is used for the calculations of molecular structures, vibrational frequencies, electronic and electron paramagnetic resonance (EPR) spectral data. DFT calculations enable us to identity the primary redox site and the electron and spin-density distribution between the individual components for the individual redox congeners. The DFT technique reproduces the spectral properties of the presented complexes and their radical ions. The generally close correspondence between experimental and quantum chemical results demonstrate that modern DFT is a powerful tool to address issues like ligand non-innocence and electron and spin delocalization in systems containing both redox-active metal ions and redox-active ligands.     

Two diketopiperazine cyclo(pro-phe) isomers from marine bacteria <Emphasis Type="Italic">Bacillus subtilis</Emphasis> sp. 13-2

Two bioactive diketopiperazines, cyclo(S-Pro-S-Phe) and cyclo(R-Pro-S-Phe), against Bacillus subtilis (terrestrial), Staphylococcus aureus, and Escherichia coli DH5a were isolated from marine surface sediment bacteria Bacillus subtilis sp.13-2. To our knowledge, this was the first time that cyclo(S-Pro-S-Phe) and cyclo(R-Pro-S-Phe) were isolated from Bacillus subtilis, and the first time that cyclo(R-Pro-S-Phe) was isolated from a natural source. These two compounds were established on the basis of ESI-MS spectral data, as well as NMR 1D and 2D (COSY, HMQC, and HMBC) spectral data.     

Towards a fast, high specific and reliable discrimination of bacteria on strain level by means of SERS in a microfluidic device

The interest in a fast, high specific and reliable detection method for bacteria identification is increasing. We will show that the application of vibrational spectroscopy is feasible for the validation of bacteria in microfluidic devices. For this purpose, reproducible and specific spectral pattern as well as the establishment of large databases are essential for statistical analysis. Therefore, short recording times are beneficial concerning the time aspect of fast identification. We will demonstrate that the requirements can be fulfilled by measuring ultrasonic busted bacteria by means of microfluidic lab-on-a-chip based SERS. With the applied sample preparation, high specificity and reproducibility of the spectra are achieved. Taking advantage of the SERS enhancement, the spectral recording time is reduced to 1 s and a database of 11,200 spectra is established for a model system E. coli including nine different strains. The validation of the bacteria on strain level is achieved accomplishing SVM accuracies of 92%. Within this contribution the potential of our approach of bacterial identification for future application is discussed, focusing on the time-benefit and the combination with other microfluidic applications.     

Synthesis of Some Series of 1,3‐Thiazolidin‐4‐ones and Indoles Incorporating Furoxan Moiety Starting with Anethole Isolated from Star Anise Oil

Some series of 1,3‐thiazolidin‐4‐ones and indoles incorporating furoxan moiety were synthesized from anethole, a main component of star anise oil. The structure of these compounds and the intermediates was examined by elemental and spectral data. Ten compounds were screened against some bacteria and fungi.