Position Of Bond Research Articles

Evaluating Software Tools for Lipid Identification from Ion Mobility Spectrometry-Mass Spectrometry Lipidomics Data.

The unambiguous identification of lipids is a critical component of lipidomics studies and greatly impacts the interpretation and significance of analyses as well as the ultimate biological understandings derived from measurements. The level of structural detail that is available for lipid identifications is largely determined by the analytical platform being used. Mass spectrometry (MS) coupled with liquid chromatography (LC) is the predominant combination of analytical techniques used for lipidomics studies, and these methods can provide fairly detailed lipid identification. More recently, ion mobility spectrometry (IMS) has begun to see greater adoption in lipidomics studies thanks to the additional dimension of separation that it provides and the added structural information that can support lipid identification. At present, relatively few software tools are available for IMS-MS lipidomics data analysis, which reflects the still limited adoption of IMS as well as the limited software support. This fact is even more pronounced for isomer identifications, such as the determination of double bond positions or integration with MS-based imaging. In this review, we survey the landscape of software tools that are available for the analysis of IMS-MS-based lipidomics data and we evaluate lipid identifications produced by these tools using open-access data sourced from the peer-reviewed lipidomics literature.

Extraction and separation characteristic stilbene compounds from pigeon pea leaves using V-type thymol-based natural deep eutectic solvent systems

In this study, a V-type deep eutectic miniature solvent composed of thymol/coumarin was designed based on the principle of similitude compatibility and π-π conjugate effect for the extraction of stilbene structure compounds from pigeon pea leaves. According to Hansen solubility parameter theory, the optimal DES type and composition molar ratio were screened out. The optimal extraction conditions were thymol/coumarin ratio 2:1, ultrasonic power 200 W, ultrasonic time 20 min, liquid-solid ratio 50:1 (mL/g). According to the hydrophobic DES form hydrogen bond position, we found that add a small amount of ammonia solution can effectively destroy DES hydrogen bonding structure, which reduces the target product solubility in the solvent, combined with macroporous resin adsorption process can be quickly and efficiently recycling target component and separation solvent. Through the rotary evaporator to remove water, HBAs and HBDs are recombined to form DES, which can be directly used for secondary extraction. After three cycles of DES, the rate of recovery of DES was over 80%. Moreover, the FT-IR, UV–vis and NMR were applied to investigate physicochemical properties of DES and extraction mechanism. This study provides a new solvent screening idea for the extraction and separation of natural products, and designs a green and sustainable extraction and separation process of natural products, and provides a new idea for the recycling of hydrophobic DES.

Changes in the structure of polysaccharides under different extraction methods

Changes in the structure of polysaccharides under different extraction methods

Localization of cyclopropyl groups and alkenes within glycerophospholipids using gas-phase ion/ion chemistry.

Shotgun lipid analysis using electrospray ionization tandem mass spectrometry (ESI-MS/MS) is a common approach for the identification and characterization of glycerophohspholipids GPs. ESI-MS/MS, with the aid of collision-induced dissociation (CID), enables the characterization of GP species at the headgroup and fatty acyl sum compositional levels. However, important structural features that are often present, such as carbon-carbon double bond(s) and cyclopropane ring(s), can be difficult to determine. Here, we report the use of gas-phase charge inversion reactions that, in combination with CID, allow for more detailed structural elucidation of GPs. CID of a singly deprotonated GP, [GP - H]- , generates FA anions, [FA - H]- . The fatty acid anions can then react with doubly charged cationic magnesium tris-phenanthroline complex, [Mg(Phen)3 ]2+ , to form charge inverted complex cations of the form [FA - H + MgPhen2 ]+ . CID of the complex generates product ion spectral patterns that allow for the identification of carbon-carbon double bond position(s) as well as the sites of cyclopropyl position(s) in unsaturated lipids. This approach to determining both double bond and cyclopropane positions is demonstrated with GPs for the first time using standards and is applied to lipids extracted from Escherichia coli.

Experimental Determination of an Isolated trans‐Dinitrosyl Manganese(II) Heme Analogue

AbstractThe lack of direct proof in either natural or synthetic systems for trans‐dinitrosyl hemes, a key intermediate in the reactions of heme proteins (e.g. soluble guanylate cyclase (sGC), cytochrome c′ and So H‐NOX) with nitric oxide (NO), has hampered understanding of the exact reaction mechanisms, such as the formation of the five‐coordinate heme complex with NO at the proximal side (5c NOP). Herein, we report the first isolation of a dinitrosyl metalloporphyrin complex, the six‐coordinate, low‐spin {Mn(NO)2}7 species [Mn(TPP)(NO)2] (TPP2−=meso‐tetraphenylporphyrin dianion). The complex shows distinct features, such as an elongated axial bond (1.877(9) vs. 1.641(5) Å), a higher NO stretching bond position (1760 vs. 1735 cm−1) and an isotropic resonance at g = 2.0, in sharp contrast to those of five‐coordinate mononitrosyl analogues. In situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFT) and EPR studies provided deep insight into the reaction processes, demonstrating different responses of porphyrinates to NO.

Experimental Determination of an Isolated trans-Dinitrosyl Manganese(II) Heme Analogue.

The lack of direct proof in either natural or synthetic systems for trans-dinitrosyl hemes, a key intermediate in the reactions of heme proteins (e.g. soluble guanylate cyclase (sGC), cytochrome c' and So H-NOX) with nitric oxide (NO), has hampered understanding of the exact reaction mechanisms, such as the formation of the five-coordinate heme complex with NO at the proximal side (5c NOP ). Herein, we report the first isolation of a dinitrosyl metalloporphyrin complex, the six-coordinate, low-spin {Mn(NO)2 }7 species [Mn(TPP)(NO)2 ] (TPP2- =meso-tetraphenylporphyrin dianion). The complex shows distinct features, such as an elongated axial bond (1.877(9) vs. 1.641(5) Å), a higher NO stretching bond position (1760 vs. 1735 cm-1 ) and an isotropic resonance at g = 2.0, in sharp contrast to those of five-coordinate mononitrosyl analogues. In situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFT) and EPR studies provided deep insight into the reaction processes, demonstrating different responses of porphyrinates to NO.

Chromophore Structure in an Inactive State of a Novel Photosensor Protein Opn5L1: Resonance Raman Evidence for the Formation of a Deprotonated Adduct at the 11th Carbon Atom.

Opsins are photosensitive G protein-coupled receptor proteins and are classified into visual and nonvisual receptors. Opn5L1 is a nonvisual opsin that binds all-trans retinal as a chromophore. A unique feature of Opn5L1 is that the protein exhibits a photocyclic reaction upon photoexcitation. Determining the chromophore structures of intermediates in the photocycle is essential for understanding the functional mechanism of Opn5L1. A previous study revealed that a long-lived intermediate in the photocycle cannot activate the G protein and forms a covalent bond between the retinal chromophore and a nearby cysteine residue. However, the position of this covalent bond in the chromophore remains undetermined. Here, we report a resonance Raman study on isotopically labeled samples in combination with density functional theory calculations and reveal that the 11th carbon atom of the chromophore of the intermediate forms a covalent linkage to the cysteine residue. Furthermore, vibrational assignments based on the isotopic substitutions and density functional theory calculations suggested that the Schiff base of the intermediate is deprotonated. The chromophore structure determined in the present study well explains the mechanism of the photocyclic reaction, which is crucial to the photobiological function of Opn5L1.

Selectivity in Cationic Cyclizations Involving Alkynes: A Computational Study on the Biomimetic Synthesis of Steroids.

Computational studies on the electrophilic cyclization between alkynes and transient carbocations or Lewis-acid-activated epoxides show that the regiochemistry of the reaction depends on the terminal or internal position of the triple bond. Reactants possessing terminal alkynyl groups lead to six-membered rings, whereas internal alkynes yield five-membered rings through 6-endo-dig and 5-exo-dig electrophilic cyclizations, respectively. The regiochemistry of the reaction is not determined by two-electron interactions, but by the minimization of Pauli repulsion. This scenario is preserved in related biomimetic reactions leading to steroid scaffolds. In this latter case, the stereochemistry of the cyclization reaction is oriented towards the formation of equatorial C-C bonds connecting the new six-six- and six-five-membered fused rings.

Role of Cholesterol and its Biosynthetic Precursors on Membrane Organization and Dynamics: A Fluorescence Approach.

Cholesterol is the most representative sterol present in membranes of higher eukaryotes, and is the end product of a long and multistep biosynthetic pathway. Lathosterol and zymosterol are biosynthetic precursors of cholesterol in Kandutsch-Russell and Bloch pathways, respectively. Lathosterol differs with cholesterol merely in the position of the double bond in the sterol ring, whereas zymosterol differs with cholesterol in position and number of double bonds. In this work, we have monitored the effect of cholesterol and its biosynthetic precursors (lathosterol and zymosterol) on membrane organization and dynamics in fluid and gel phase membranes. Toward this goal, we have utilized two fluorescent membrane probes, DPH and its cationic derivative TMA-DPH. Our results using these probes show that cholesterol and its biosynthetic precursors (lathosterol and zymosterol) exhibit similar trend in maintaining membrane organization and dynamics (as reported by fluorescence anisotropy and apparent rotational correlation time), in fluid phase POPC membranes. Notably, although lathosterol and zymosterol show similar trend in maintaining membrane organization and dynamics, the corresponding change for cholesterol is different in gel phase DPPC membranes. These results demonstrate that the position and number of double bonds in sterols is an important determinant in maintaining membrane physical properties. Our results assume significance since accumulation of precursors of cholesterol have been reported to be associated with severe pathological conditions.

Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties.

The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (cis vs. trans), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.

Determination of double bond positions in methyl ketones by gas chromatography-mass spectrometry using dimethyl disulfide derivatives.

Methyl ketones are of interest for the application as biofuels. The fatty acid metabolism of different microbes has been rearranged to achieve a sustainable production of methyl ketones. The biofuel properties and possible further chemical modifications of these methyl ketones are influenced by their chain length, as well as their degree of saturation and the corresponding double bond position. A method based on gas chromatography-electron ionization; mass spectrometry (GC-EI-MS) was used to determine the double bond position of methyl ketones. Derivatization using dimethyl disulfide (DMDS) and an iodine catalyst enabled the activation of the double bonds for selective fragmentation during electron ionization. The cleavage led to key fragments in the Orbitrap high-resolution mass spectrum and allowed the unequivocal localization of the double bond position of the respective monounsaturated methyl ketone. The double bond position of several medium chain length methyl ketones originating from the gram-negative bacterium Pseudomonas taiwanensis (P. taiwanensis) VLB120 was determined. The DMDS derivatives of methyl ketones can yield isobaric fragment ions for different possible double bond positions, which can be distinguished only using high-resolution MS. The double bond position of all methyl ketones deriving from P. taiwanensis VLB120 was the same, counting from the end of the aliphatic chain, and was determined as ω-7. The derivatization of medium chain length monounsaturated methyl ketones with DMDS allowed the determination of the corresponding double bond position via GC-EI-MS. High-resolution MS is needed to differentiate possible double bond positions that yield isobaric fragment ions.

Atomic mean square displacement study of the bond breaking mechanism of energetic materials before explosive initiation.

Understanding and predicting the bond breaking mechanism of energetic materials before explosion initiation is one of the huge challenges in explosion science. By means of the mean square displacement of the atom from the equilibrium position and theoretical bond breaking tensile change of the chemical bond, we establish a new criterion to judge whether the chemical bond is broken. Further, α-RDX is used as the verification object to verify the accuracy of this model. We obtained an initial decomposition temperature of 434-513 K for α-RDX at 0 GPa, and the initial bond breaking type was N-NO2. Finally, based on this model, we discussed in detail the breaking of chemical bonds of solid nitromethane near the detonation pressure. We think that the high temperature and high pressure caused by the shock wave may break all the chemical bonds of nitromethane near the detonation pressure.

Isobaric 6-plex and tosyl dual tagging for the determination of positional isomers and quantitation of monounsaturated fatty acids using rapid UHPLC-MS/MS.

Isobaric labelling of fatty acids is complicated by chromatographic co-elution of double bond isomers. This produces contaminated spectra which can mask important biological changes. Here two derivatization strategies are combined to improve throughput and produce MS2 reporters which change mass depending on double bond position. A 6-plex isobaric tag is attached to the acid group, followed by the tosylation of the double bond using chloramine-T. These two derivatizations allowed for the chromatographic resolution of nearly all investigated isomers using a 3.5 minute ultrafast method. Further isomer differentiation is achieved upon fragmentation as reporter masses scale with the double bond location. This occurs by a dual-fragmentation route which reveals the isobaric labelling and fragments along the double bond of each analyte. These unique fragments allowed for accurate quantitation of co-isolated double bond isomers where traditional isobaric tags would experience ratio distortion. Saturated and monounsaturated fatty acids were characterized by this rapid 6-plex method and produced an average signal RSD of 9.3% and R2 of 0.99. The method was then used to characterize fatty acid dysregulation upon inhibition of stearoyl CoA desaturase with CAY10566.

Top-down mass spectrometry and assigning internal fragments for determining disulfide bond positions in proteins.

Disulfide bonds in proteins have a substantial impact on protein structure, stability, and biological activity. Localizing disulfide bonds is critical for understanding protein folding and higher-order structure. Conventional top-down mass spectrometry (TD-MS), where only terminal fragments are assigned for disulfide-intact proteins, can access disulfide information, but suffers from low fragmentation efficiency, thereby limiting sequence coverage. Here, we show that assigning internal fragments generated from TD-MS enhances the sequence coverage of disulfide-intact proteins by 20-60% by returning information from the interior of the protein sequence, which cannot be obtained by terminal fragments alone. The inclusion of internal fragments can extend the sequence information of disulfide-intact proteins to near complete sequence coverage. Importantly, the enhanced sequence information that arise from the assignment of internal fragments can be used to determine the relative position of disulfide bonds and the exact disulfide connectivity between cysteines. The data presented here demonstrates the benefits of incorporating internal fragment analysis into the TD-MS workflow for analyzing disulfide-intact proteins, which would be valuable for characterizing biotherapeutic proteins such as monoclonal antibodies and antibody-drug conjugates.

Spin-vibronic mechanism at work in a luminescent square-planar cyclometalated tridentate Pt(II) complex: absorption and ultrafast photophysics.

The absorption spectrum of [Pt(dpybMe)Cl] (dpyb = 2,6-di-(2-pyridyl)benzene), representative of luminescent halide-substituted tridentate cyclometalated square planar Pt(II) neutral complexes, has been revisited by means of non-adiabatic wavepacket quantum dynamics. The early photophysics has been investigated on the basis of four singlet and five triplet excited states, namely nineteen "spin-orbit states", coupled with both vibronic and spin-orbit couplings, and includes eighteen normal modes. It is shown that in-plane scissoring and rocking normal modes of the cyclometalated tridentate ligand are responsible for the vibronic structure observed at around 400 nm in the experimental spectrum of the complex. The ultrafast decay of [Pt(dpybMe)Cl], within 1 ps, follows a spin-vibronic mechanism governed by excited state electronic characters, spin-orbit, and active tuning mode interplay. Both spin-orbit coupling and Pt(II) coordination sphere stretching modes and in-plane scissoring/rocking of the cyclometalated ligand activate the ultrafast decay within 20 fs of absorption. At longer time-scales (>100 fs) an asynchronous stretching of the Pt-C and Pt-N bonds activates the depopulation of the upper "reservoir" electronic states to populate the two lowest luminescent T1 and T2 electronic states. The in-plane rocking motion of the ligand controls the T1/T2 population exchange which is equilibrated at about 1 ps. Stabilization of the upper non-radiative metal-centered (MC) states by out-of-plane ligand distortion of low frequency is not competitive with the ultrafast spin-vibronic mechanism discovered here for [Pt(dpybMe)Cl]. Modifying the Pt-C covalent bond position and rigidifying the cyclometalated ligand will have a dramatic influence on the spin-vibronic mechanism and consequently on the luminescence properties of this class of molecules.

Structure of an antennally-expressed carboxylesterase suggests lepidopteran odorant degrading enzymes are broadly tuned.

Insects rely on the detection of chemical cues present in the environment to guide their foraging and reproductive behaviour. As such, insects have evolved a sophisticated chemical processing system in their antennae comprised of several types of olfactory proteins. Of these proteins, odorant degrading enzymes are responsible for metabolising the chemical cues within the antennae, thereby maintaining olfactory system function. Members of the carboxyl/cholinesterase gene family are known to degrade odorant molecules with acetate-ester moieties that function as host recognition cues or sex pheromones, however, their specificity for these compounds remains unclear. Here, we evaluate expression levels of this gene family in the light-brown apple moth, Epiphyas postvittana, via RNAseq and identify putative odorant degrading enzymes. We then solve the apo-structure for EposCCE24 by X-ray crystallography to a resolution of 2.43Å and infer substrate specificity based on structural characteristics of the enzyme's binding pocket. The specificity of EposCCE24 was validated by testing its ability to degrade biologically relevant and non-relevant sex pheromone components and plant volatiles using GC-MS. We found that EposCCE24 is neither capable of discriminating between linear acetate-ester odorant molecules of varying chain length, nor between molecules with varying double bond positions. EposCCE24 efficiently degraded both plant volatiles and sex pheromone components containing acetate-ester functional groups, confirming its role as a broadly-tuned odorant degrading enzyme in the moth olfactory organ.

Establishing carbon-carbon double bond position and configuration in unsaturated fatty acids by gas-phase infrared spectroscopy.

Fatty acids are an abundant class of lipids that are characterised by wide structural variation including isomeric diversity arising from the position and configuration of functional groups. Traditional approaches to fatty acid characterisation have combined chromatography and mass spectrometry for a description of the composition of individual fatty acids while infrared (IR) spectroscopy has provided insights into the functional groups and bond configurations at the bulk level. Here we exploit universal 3-pyridylcarbinol ester derivatization of fatty acids to acquire IR spectra of individual lipids as mass-selected gas-phase ions. Intramolecular interactions between the protonated pyridine moiety and carbon-carbon double bonds present highly sensitive probes for regiochemistry and configuration through promotion of strong and predictable shifts in IR resonances. Gas-phase IR spectra obtained from unsaturated fatty acids are shown to discriminate between isomers and enable the first unambiguous structural assignment of 6Z-octadecenoic acid in human-derived cell lines. Compatibility of 3-pyridylcarbinol ester derivatization with conventional chromatography-mass spectrometry and now gas-phase IR spectroscopy paves the way for comprehensive structure elucidation of fatty acids that is sensitive to regio- and stereochemical variations and with the potential to uncover new pathways in lipid metabolism.

2-(4-Oxo-1,3-thiazolidin-2-ylidene)acetamid as promising scaffold for designing new antifungal compounds

1,3-Thiazolidin-4-one derivatives with a exocyclic C=C double bond in position 2 of the hetero ring have a wide spectrum of biological activity, but their fungicidal activity has not been studied as much as it should be. This paper presents a simple and convenient approach for obtaining potential antifungal agents based on 2-(4-oxo-1,3-thiazolidin-2-ylidene)acetamides. The first examples of evaluating the fungicidal activity of 8 obtained compounds on 8 strains of phytopathogenic fungi are presented. A highly active compound 4e with EC50 of 0.85 and 2.29 µg/mL against A. solani and P. lingam, respectively, was found to be promising for further study.

Comparison of Workflows for Milk Lipid Analysis: Phospholipids.

Milk is a rich source of lipids, with the major components being triglycerides (TAG) and phospholipids (mainly phosphatidylcholine (PC), sphingomyelin (SM), phosphatidylethanolamine (PE), phosphatidylserine (PS) and phosphatidylinositol (PI)). Liquid chromatography-mass spectrometry (LC-MS) is the predominant technique for lipid identification and quantification across all biological samples. While fatty acid (FA) composition of the major lipid classes of milk can be readily determined using tandem MS, elucidating the regio-distribution and double bond position of the FA remains difficult. Various workflows have been reported on the quantification of lipid species in biological samples in the past 20 years, but no standard or consensus methods are currently available for the quantification of milk phospholipids. This study will examine the influence of several common factors in lipid analysis workflow (including lipid extraction protocols, LC stationary phases, mobile phase buffers, gradient elution programmes, mass analyser resolution and isotope correction) on the quantification outcome of bovine milk phospholipids. The pros and cons of the current LC-MS methods as well as the critical problems to be solved will also be discussed.

Computational mass spectrometry accelerates C = C position-resolved untargeted lipidomics using oxygen attachment dissociation

Mass spectrometry-based untargeted lipidomics has revealed the lipidome atlas of living organisms at the molecular species level. Despite the double bond (C = C) position being a crucial factor in biological system, the C = C defined structures have not yet been characterized comprehensively. Here, we present an approach for C = C position-resolved untargeted lipidomics using a combination of oxygen attachment dissociation and computational mass spectrometry to increase the annotation rate. We validated the accuracy of our platform as per the authentic standards of 85 lipids and the biogenic standards of 52 molecules containing polyunsaturated fatty acids (PUFAs) from the cultured cells fed with various fatty acid-enriched media. By analyzing human and mice-derived samples, we characterized 648 unique lipids with the C = C position-resolved level encompassing 24 lipid subclasses defined by LIPIDMAPS. Our platform also illuminated the unique profiles of tissue-specific lipids containing n-3 and/or n-6 very long-chain PUFAs (carbon ge 28 and double bonds ge 4) in the eye, testis, and brain of the mouse.