Ion mobility studies and density functional theory calculations were used to study the structures of [Zn/diethylenetriamine/Hexose/Cl]+ complexes in an effort to probe differences in the three-dimensional conformations. This information allows us to gain insight into the structure of these complexes before collisional activation, which is the first step in understanding the stereoselective dissociations observed under collisionally activated conditions. The collision cross sections obtained from the ion mobility measurements showed that the mannose structure is more compact than the galactose and glucose complexes, respectively. Using density functional theory, candidate structures for each of the experimentally observed complexes were generated. Two criteria were used to determine the most likely structures of these complexes before activation: (1) The allowed relative energies of the molecules (between 0-90 kJ/mol) and (2) collision cross section agreement (within 2%) between the theoretically determined structures and the experimentally determined cross section. It was found that the identity of the monosaccharide made a difference in the overall conformation of the metal-ligand-monosaccharide complex. For glucose and galactose, metal coordination to O(6) was found to be favorable, with the monosaccharide occupying the 4C1 chair conformation, while for mannose, O(2) metal coordination was found with the monosaccharide in a B3,0 conformation. Coordination numbers varied between four and six for the Zn(II) metal centers. Given these results, it appears that the stereochemistry of the monosaccharide influences the conformation and metal coordination sites of the Zn(II)/monosaccharide/dien complex. These differences may influence the dissociation products observed under collisionally activated conditions.
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http://dx.doi.org/10.1016/S1044-0305(01)00362-2 | DOI Listing |
Biopolymers
March 2025
Centro de Investigación en Química Aplicada, Saltillo, Coahuila, Mexico.
Exploring new ecological and simultaneous processes to modify wood fibers (WF) by-products is a required pathway toward circular economy and sustainability. Thus, plasma-activated water (PAW) and ultrasound (U) were employed as alternative methods to modify WF in a continuous process. Such treatments promoted the etching and cavities on the WF surface that destabilized the hydrogen bonds of the hemicellulose and lignin molecules, increasing the cellulose fraction.
View Article and Find Full Text PDFNat Protoc
January 2025
Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
Deep and accurate proteome analysis is crucial for understanding cellular processes and disease mechanisms; however, it is challenging to implement in routine settings. In this protocol, we combine a robust chromatographic platform with a high-performance mass spectrometric setup to enable routine yet in-depth proteome coverage for a broad community. This entails tip-based sample preparation and pre-formed gradients (Evosep One) combined with a trapped ion mobility time-of-flight mass spectrometer (timsTOF, Bruker).
View Article and Find Full Text PDFNat Protoc
January 2025
Advanced Research Support Center, Ehime University, Ehime, Japan.
Top-down analysis of intact proteins and middle-down analysis of proteins subjected to limited digestion require efficient detection of traces of proteoforms in samples, necessitating the reduction of sample complexity by thorough pre-fractionation of the proteome components in the sample. SDS-PAGE is a simple and inexpensive high-resolution protein-separation technique widely used in biochemical and molecular biology experiments. Although its effectiveness for sample preparation in bottom-up proteomics has been proven, establishing a method for highly efficient recovery of intact proteins from the gel matrix has long been a challenge for its implementation in top-down and middle-down proteomics.
View Article and Find Full Text PDFAdv Clin Chem
January 2025
Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, United States. Electronic address:
Advancements in clinical chemistry have major implications in terms of public health, prompting many clinicians to seek out chemical information to aid in diagnoses and treatments. While mass spectrometry (MS) and hyphenated-MS techniques such as LC-MS or tandem MS/MS have long been the analytical methods of choice for many clinical applications, these methods routinely demonstrate difficulty in differentiating between isomeric forms in complex matrices. Consequently, ion mobility spectrometry (IM), which differentiates molecules on the basis of size, shape, and charge, has demonstrated unique advantages in the broad application of stand-alone IM and hyphenated IM instruments towards clinical challenges.
View Article and Find Full Text PDFJ Hazard Mater
December 2024
College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; Key Laboratory of Plant Nutrition and the Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, China. Electronic address:
The interactions between microplastic-derived dissolved organic matter (MPs-DOM) and heavy metals (Cu, Pb, and Cd) regulate the complex environmental transport behavior of pollutants in terrestrial and aquatic environments. In this study, fluorescence excited emission matrix spectroscopy combined with parallel factor analysis (EEM-PARAFAC) and electrospray ionization coupled Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) were employed to investigate the complexation mechanism of MPs-DOM with heavy metals, as well as the effects of different environmental occurrences of MPs-DOM on the transport behaviors of heavy metals in saturated porous medium. The findings demonstrated that MPs-DOM, particularly humic-like substances containing aromatic structures and various oxygen functional groups, could form stable complexes with heavy metals.
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