HSQC-ADEQUATE: an investigation of data requirements

Utilizing ¹³C‐¹³C connectivity networks for the assembly of carbon skeletons from HSQC‐ADEQUATE spectra was recently reported. HSQC‐ADEQUATE data retain the resonance multiplicity information of the multiplicity‐edited GHSQC spectrum and afford a significant improvement in the signal‐to‐noise (s/n) ratio relative to the 1,1‐ADEQUATE data used in the calculation of the HSQC‐ADEQUATE spectrum by unsymmetrical indirect covariance (UIC) processing methods. The initial investigation into the computation of HSQC‐ADEQUATE correlation plots utilized overnight acquisition of the 1,1‐ADEQUATE data used for the calculation. In this communication, we report the results of an investigation of the reduction in acquisition time for the 1,1‐ADEQUATE data to take advantage of the s/n gain during the UIC processing to afford the final HSQC‐ADEQUATE correlation plot. Data acquisition times for the 1,1‐ADEQUATE spectrum can be reduced to as little as a few hours, while retaining excellent s/n ratios and all responses contained in spectra computed from overnight data acquisitions. Concatenation of multiplicity‐edited GHSQC and 1,1‐ADEQUATE data also allows the interrogation of submilligram samples with 1,1‐ADEQUATE data when using spectrometers equipped with 1.7‐mm Micro CryoProbes ?. Copyright © 2011 John Wiley & Sons, Ltd.     

HSQC-1,n-ADEQUATE: a new approach to long-range 13C-13C correlation by covariance processing

Long-range, two-dimensional heteronuclear shift correlation NMR methods play a pivotal role in the assembly of novel molecular structures. The well-established GHMBC method is a high-sensitivity mainstay technique, affording connectivity information via (n)J(CH) coupling pathways. Unfortunately, there is no simple way of determining the value of n and hence no way of differentiating two-bond from three- and occasionally four-bond correlations. Three-bond correlations, however, generally predominate. Recent work has shown that the unsymmetrical indirect covariance or generalized indirect covariance processing of multiplicity edited GHSQC and 1,1-ADEQUATE spectra provides high-sensitivity access to a (13)C-(13) C connectivity map in the form of an HSQC-1,1-ADEQUATE spectrum. Covariance processing of these data allows the 1,1-ADEQUATE connectivity information to be exploited with the inherent sensitivity of the GHSQC spectrum rather than the intrinsically lower sensitivity of the 1,1-ADEQUATE spectrum itself. Data acquisition times and/or sample size can be substantially reduced when covariance processing is to be employed. In an extension of that work, 1,n-ADEQUATE spectra can likewise be subjected to covariance processing to afford high-sensitivity access to the equivalent of (4)J(CH) GHMBC connectivity information. The method is illustrated using strychnine as a model compound.     

HMBC‐1,1‐ADEQUATE via generalized indirect covariance: a high sensitivity alternative to n,1‐ADEQUATE

1,1‐ADEQUATE and the related long‐range 1,n‐ and n,1‐ADEQUATE variants were developed to provide an unequivocal means of establishing ²J_CH and the equivalent of ⁿJ_CH correlations where n = 3,4. Whereas the 1,1‐ and 1,n‐ADEQUATE experiments have two simultaneous evolution periods that refocus the chemical shift and afford net single quantum evolution for the carbon spins, the n,1‐variant has a single evolution period that leaves the carbon spin to be observed at the double quantum frequency. The n,1‐ADEQUATE experiment begins with an HMBC‐type ⁿJ_CH magnetization transfer, which leads to inherently lower sensitivity than the 1,1‐ and 1,n‐ADEQUATE experiments that begin with a ¹J_CH transfer. These attributes, in tandem, serve to render the n,1‐ADEQUATE experiment less generally applicable and more difficult to interpret than the 1,n‐ADEQUATE experiment, which can in principle afford the same structural information. Unsymmetrical and generalized indirect covariance processing methods can complement and enhance the structural information encoded in combinations of experiments e.g. HSQC‐1,1‐ or ?1,n‐ADEQUATE. Another benefit is that covariance processing methods offer the possibility of mathematically combining a higher sensitivity 2D NMR spectrum with for example 1,1‐ or 1,n‐ADEQUATE to improve access to the information content of lower sensitivity congeners. The covariance spectrum also provides a significant enhancement in the F₁ digital resolution. The combination of HMBC and 1,1‐ADEQUATE spectra is shown here using strychnine as a model compound to derive structural information inherent to an n,1‐ADEQUATE spectrum with higher sensitivity and in a more convenient to interpret single quantum presentation. Copyright © 2012 John Wiley & Sons, Ltd.     

1JCC‐edited HSQC‐1,n‐ADEQUATE: a new paradigm for simultaneous direct and long‐range carbon–carbon correlation

Establishing the carbon skeleton of a molecule greatly facilitates the process of structure elucidation, leaving only heteroatoms to be inserted, heterocyclic rings to be closed, and stereochemical features to be defined. INADEQUATE, and more recently PANACEA, have been the only means of coming close to the goal of totally defining the carbon skeleton of a molecule. Unfortunately, the extremely low sensitivity and prodigious sample requirements of these experiments and the multiple receiver requirement for the latter experiment have severely restricted the usage of these experiments. Proton‐detected ADEQUATE experiments, in contrast, have considerably higher sensitivity and more modest sample requirements. By combining experiments such as 1,1‐ADEQUATE and 1,n‐ADEQUATE with higher sensitivity experiments such as GHSQC through covariance processing, sample requirements can be further reduced with a commensurate improvement in the s/n ratio and F₁ resolution of the covariance processed spectrum. We now wish to report the covariance processing of an inverted ¹J_CC 1,n‐ADEQUATE experiment with a non‐edited GHSQC spectrum to afford a spectrum that can trace the carbon skeleton of a molecule with the exception of correlations between quaternary carbons. Copyright © 2012 John Wiley & Sons, Ltd.     

Analysis and elimination of artifacts in indirect covariance NMR spectra via unsymmetrical processing

Indirect covariance NMR offers an alternative method of extracting spin-spin connectivity information via the conversion of an indirect-detection heteronuclear shift-correlation data matrix to a homonuclear data matrix. Using an IDR (inverted direct response)-HSQC-TOCSY spectrum as a starting point for the indirect covariance processing, a spectrum that can be described as a carbon-carbon COSY experiment is obtained. These data are analogous to the autocorrelated 13C-13C double quantum INADEQUATE experiment except that the indirect covariance NMR spectrum establishes carbon-carbon connectivities only between contiguous protonated carbons. Cyclopentafuranone and the complex polynuclear heteroaromatic naphtho[2',1':5,6]-naphtho[2',1':4,5]thieno[2,3-c]quinoline are used as model compounds. The former is a straightforward example because of its well-resolved proton spectrum, while the latter, which has considerable resonance overlap in its congested proton spectrum, gives rise to two types of artifact responses that must be considered when using the indirect covariance NMR method.     

High‐resolution NMR correlation experiments in a single measurement (HR‐PANACEA)

Three important NMR pulse sequences, INADEQUATE, HSQC and three‐dimensional HMBC have been combined into a single entity called high‐resolution Parallel Acquisition NMR: an All‐in‐one Combination of Experimental Applications (HR‐PANACEA) to provide reliable structural information about a small molecule in a single measurement. This exploits a recent instrumental development that permits simultaneous acquisition of signals from several nuclear species, using multiple receivers. Where high‐precision values of the long‐range heteronuclear splittings are important, selected regions of a large experimental data matrix are extracted and examined with the highest possible resolution. The J‐doubling technique is then applied to derive precise values for these couplings. As proof of principle, the method is applied to the molecule of methyl salicylate, confirming the expected conformation of the C? O? H moiety. Copyright © 2010 John Wiley & Sons, Ltd.     

High resolution‐HMBC (HR‐HMBC), a new method for measuring heteronuclear long‐range coupling constants

A useful pulse sequence for measuring long‐range C? H coupling constants (J_{C? H}) named high resolution‐HMBC (HR‐HMBC) has been developed. In this pulse sequence, the J‐scaling pulse [(nt₁)/2? 180° (H/C) ? (nt₁)/2] is incorporated after the spin evolution period, and then followed by an ¹H 180° pulse to reverse the magnetization of J_{C? H} couplings. As a result, splittings of the cross peaks due to the long‐range J_{C? H} are realigned with separations of nJ_{C? H} along the F₁ dimension, and thus even the small long‐range J_{C? H} values can easily be determined. The efficiency of measuring the long‐range J_{C? H} using the proposed pulse sequences has been demonstrated in application to the complicated natural product, portmicin. Copyright © 2010 John Wiley & Sons, Ltd.     

QQ-HSQC: a quick, quantitative heteronuclear correlation experiment for NMR spectroscopy

Quantitative heteronuclear single quantum coherence (Q-HSQC) is a variant of the HSQC experiment that provides quantitative peak areas. This is accomplished by combining signals acquired using four different INEPT delays. Consequently, the experiment requires four times as many scans as the HSQC experiment to achieve the same resolution in the indirect dimension. We have removed this drawback by modifying the Q-HSQC experiment so that signals corresponding to different INEPT delays are acquired simultaneously from different parts of the sample. This new experiment, which we call Quick, Quantitative HSQC (QQ-HSQC), has the quantitative properties of the Q-HSQC experiment but only requires as many scans as a conventional HSQC experiment.     

Selective COSY‐J‐resolved‐HMBC,a new method for improving sensitivity of cross peaks of methine proton signals attached to a methyl group

Improved pulse sequences for measuring long‐range C‐H coupling constants (ⁿJ_C‐H), named selective COSY‐J‐resolved HMBC‐1 and ?2, have been developed. In the spin systems, such as ‐CH_C‐CH_A(CH₃)‐CH_B‐, a methine proton H_A splits into a multiplet owing to several vicinal couplings with protons, resulting in attenuation of its cross‐peak intensity. Therefore, the measurements of ⁿJ_C‐H with H_A are generally difficult in the J‐resolved HMBC or selective J‐resolved HMBC spectrum. With the aim of accurate measurements of ⁿJ_C‐H in such a spin system, we have developed new pulse sequences, which transfer the magnetization of a methyl group to its adjacent methine proton. The proposed pulse sequences successfully enable to enhance the sensitivity of H_A cross peak in comparison with the selective J‐resolved HMBC pulse sequence. Copyright © 2012 John Wiley & Sons, Ltd.     

Synthesis of 2,4,6,8,9,11-hexaaza[3.3.3]propellanes as a new molecular skeleton for explosives

Azapropellanes are of great interest in many disciplines, including materials science and medicinal chemistry. Various synthetic approaches for azapropellanes have been explored; however, the synthetic study of the polyazapropellane skeleton containing five or more nitrogen atoms is rare. Here, we report a simple yet highly efficient protocol for the synthesis of the hexaaza[3.3.3]propellane skeleton as a building block for high energy materials for the first time. The key reactions include the Boc₂O-assisted cyclization of glycoluril diamine without a column purification step and the first full reduction of all the three carbonyl groups to the methylene groups through a combination of LiAlH₄ and DIBAL-H. All the structures were confirmed by spectroscopic and X-ray analyses.     

A flow process for the multi-step synthesis of the alkaloid natural product oxomaritidine: a new paradigm for molecular assembly

A flow process for the multi-step synthesis of the alkaloid natural product (+/-)-oxomaritidine is described, mediated through the use of microfluidic pumping systems that progress material through various packed columns containing immobilized reagents, catalysts, scavengers or catch and release agents; our route involves the combination of seven separate synthetic steps linked into one continuous sequence utilizing flow chemistry.     

Two-focus fluorescence correlation spectroscopy: a new tool for accurate and absolute diffusion measurements.

We present a new method to measure absolute diffusion coefficients at nanomolar concentrations with high precision. Based on a modified fluorescence correlation spectroscopy (FCS)-setup, this method is improved by introducing an external ruler for measuring the diffusion time by generating two laterally shifted and overlapping laser foci at a fixed and known distance. Data fitting is facilitated by a new two-parameter model to describe the molecule detection function (MDF). We present a recorded MDF and show the excellent agreement with the fitting model. We measure the diffusion coefficient of the red fluorescent dye Atto655 under various conditions and compare these values with a value achieved by gradient pulsed field NMR (GPF NMR). From these measurements we conclude, that the new measurement scheme is robust against optical and photophysical artefacts which are inherent to standard FCS. With two-focus-FCS, the diffusion coefficient of 4.26 x 10(-6) cm2s(-1) for Atto655 in water at 25 degrees C compares well with the GPF NMR value of 4.28 x 10(-6) cm2s(-1).     

Ion mobility–mass spectrometry: a new paradigm for proteomics

Matrix-assisted laser desorption/ionization (MALDI) coupled with ion mobility–mass spectrometry (IM–MS) provides a rapid (μs–ms) means for the two-dimensional (2D) separation of complex biological samples (e.g., peptides, oligonucleotides, glycoconjugates, lipids, etc.), elucidation of solvent-free secondary structural elements (e.g., helices, β-hairpins, random coils, etc.), rapid identification of post-translational modifications (e.g., phosphorylation, glycosylation, etc.) or ligation of small molecules, and simultaneous and comprehensive sequencing information of biopolymers. In IM–MS, protein-identification information is complemented by structural characterization data, which is difficult to obtain using conventional proteomic techniques. New avenues for enhancing the figures of merit (e.g., sensitivity, limits of detection, dynamic range, and analyte selectivity) and optimizing IM–MS experimental parameters are described in the context of deriving new information at the forefront of proteomics research.     

A new NMR approach for structure determination of thermally unstable biflavanones and application to phytochemicals from Garcinia buchananii

Previous activity‐guided phytochemical studies on Garcinia buchananii stem bark, which is traditionally used in Africa to treat various gastrointestinal and metabolic illnesses, revealed xanthones, polyisoprenylated benzophenones, flavanone‐C‐glycosides, biflavonoids, and/or biflavanones as bioactive key molecules. Unequivocal structure elucidation of biflavonoids and biflavanones by means of NMR spectroscopy is often complicated by the hindered rotation of the monomers around the C‐C axis (atropisomerism), resulting in a high spectral complexity. In order to facilitate an unrestricted rotation, NMR spectra are usually recorded at elevated temperatures, commonly over 80 °C, which effects in a single set of resonance signals. However, under these conditions, one of the target compounds of this investigation, (2R,3S,2″R,3″R)‐manniflavanone ( 1 ), undergoes degradation. Therefore, we demonstrated in the present study that the 1,1‐ADEQUATE could be successfully used as a powerful alternative approach to confirm the C‐C connectivities in 1 , avoiding detrimental conditions. However, a moderate increase in temperature up to 50 °C was sufficient to deliver sharp signals in the proton NMR experiment of (2R,3S,2″R,3″R)‐isomanniflavanone ( 2 ) and (2″R,3″R)‐preussianone ( 3 ). In addition, two new compounds could be isolated, namely (2R,3S,2″R,3″R)‐GB‐2 7″‐O‐β‐d ‐glucopyranoside ( 4 ) and (2R,3S,2″R,3″R)‐manniflavanone‐7″‐O‐β‐d ‐glucopyranoside ( 5 ), and whose structures were elucidated by spectroscopic analysis including 1D and 2D NMR and mass spectrometry methods. The absolute configurations were determined by a combination of NMR and electronic circular dichroism (ECD) spectroscopy. The aforementioned compounds exhibited high anti‐oxidative capacity in the H₂O₂ scavenging, hydrophilic Trolox equivalent antioxidant capacity (H‐TEAC) and hydrophilic oxygen radical absorbance capacity (H‐ORAC) assays. Copyright © 2015 John Wiley & Sons, Ltd.     

Basic isoreticular metal–organic framework (IRMOF‐3) porous nanomaterial as a suitable and green catalyst for selective unsymmetrical Hantzsch coupling reaction

A catalytic amount of the basic metal–organic framework (IRMOF‐3) with organic substrates was found to be an efficient, selective and waste‐free green approach for the unsymmetrical Hantzsch coupling reaction. The catalyst can be isolated from the reaction mixture and reused at least four times. Copyright © 2014 John Wiley & Sons, Ltd.     

Heparin-like glycosaminoglycan/amine salt-bridge interactions: a new potential tool for HLGAGs analysis using mass spectrometry

Characterization of glycosaminoglycans poses a challenge for current analytical techniques, as they are highly acidic, polydisperse and heterogeneous compounds. The purpose of this study is the separation and analysis of a partially depolymerized heparin-like glycosaminoglycan by on-line ion-pairing reversed-phase high-performance liquid chromatography/electrospray mass spectrometry. The gas-phase behavior of two synthesized glycosaminoglycans has been investigated. Dibutylamine was found to be the best suited ion-pairing reagents for mass spectrometry analysis. The optimized ion-pairing conditions provide reproducible and easily interpretable electrospray mass spectra in both negative and positive ESI modes. The glycosaminoglycans are detected as a non-covalent complex with amines. In fact, the observed ionic species and their gas-phase dissociation under CID conditions revealed the presence of salt bridge interactions in the gas phase.     

Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances

In modern omics research, it is more rule than exception that multiple data sets are collected in a study pertaining to the same biological organism. In such cases, it is worthwhile to analyze all data tables simultaneously to arrive at global information of the biological system. This is the area of data fusion or multi‐set analysis, which is a lively research topic in chemometrics, bioinformatics, and biostatistics. Most methods of analyzing such complex data focus on group means, treatment effects, or time courses. There is also information present in the covariances among variables within a group, because this relates directly to individual differences, heterogeneity of responses, and changes of regulation in the biological system. We present a framework for analyzing covariance matrices and a new method that fits nicely in this framework. This new method is based on combining covariance prototypes using simultaneous components and is, therefore, coined Covariances Simultaneous Component Analysis (COVSCA). We present the framework and our new method in mathematical terms, thereby explaining the (dis)similarities of the methods. Systems biology models based on differential equations illustrate the type of variation generated in real‐life biological systems and how this type of variation can be modeled within the framework and with COVSCA. The method is subsequently applied to two real‐life data sets from human and plant metabolomics studies showing biologically meaningful results. Copyright © 2015 John Wiley & Sons, Ltd.     

On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

Simulated tempering (ST) is a generalized‐ensemble algorithm that employs trajectories exploring a range of temperatures to effectively sample rugged energy landscapes. When implemented using the molecular dynamics method, ST can require the use of short time steps for ensuring the stability of trajectories at high temperatures. To address this shortcoming, a mass‐scaling ST (MSST) method is presented in which the particle mass is scaled in proportion to the temperature. Mass scaling in the MSST method leads to velocity distributions that are independent of temperature and eliminates the need for velocity scaling after the accepted temperature updates that are required in conventional ST simulations. The homogeneity in time scales with changing temperature improves the stability of simulations and allows for the use of longer time steps at high temperatures. As a result, the MSST is found to be more efficient than the standard ST method, particularly for cases in which a large temperature range is employed. © 2016 Wiley Periodicals, Inc.