Design of a Spiropyran-Based Smart Adsorbent with Dual Response: Focusing on Highly Efficient Enrichment of Phosphopeptides

Theoretical Calculations in Separation Science for Analytical Chemistry: Applications and Insights

Separation and enrichment are critical steps in analytical detection, necessitating advanced materials with high selectivity and adsorption capacity for target compounds. In order to improve separation efficiency and selectivity, computational simulation could elucidate interaction mechanisms and analyze potential adsorption/desorption processes, providing a theoretical foundation for the optimization and design of separation materials. Recently, computational simulation has become an indispensable and crucial mean in separation science for analytical chemistry. Using various simulation software, researchers could investigate the structures, properties, and performance of separation materials at multiple levels and scales. In this review, we summarize the applications of computational simulations in the field of separation science, focusing on the separation of polar molecules, geometric isomers, enantiomer compounds, and post-translationally modified peptides. These calculation methods include quantum chemistry, molecular docking, molecular dynamics simulations, high-throughput screening, and machine learning. Finally, we discuss the current challenges and potential breakthroughs in computational simulation, aiming to offer valuable insights for researchers dedicated to computational simulation, material development, and separation applications.

Light-/pH-Regulated Spiropyran Smart-Responsive Hydrophilic Separation Platform for the Identification of Serum Glycopeptides from Hepatocellular Carcinoma Patients

Smart-responsive materials have attracted much attention in the enrichment of post-translational modifications of proteins. In this work, for the first time, we developed a smart enrichment strategy (MNPs-l-DOPA/PEI-SP) based on the change in hydrophilic properties of spiropyran under the regulation of light and pH to realize the controllable enrichment and release of intact glycopeptides. The enrichment mechanism and possible binding mechanism were verified by theoretical calculations. The smart enrichment platform based on MNPs-l-DOPA/PEI-SP was used to screen glycoprotein biomarkers for hepatocellular carcinoma (HCC) to evaluate its cancer diagnostic and monitoring performance. A total of 3,864 intact N-glycopeptides containing 166 N-glycoproteins were successfully identified in serum samples of early-stage HCC patients, while 3,266 intact N-glycopeptides containing 193 glycoproteins were identified in normal control (NC) serum samples. This work not only provides new ideas for the efficient enrichment of intact glycopeptides with smart-responsive material, but also broadens the research possibilities for biomarker discovery in HCC serum liquid biopsies.

Positively Photo-Responsive Adsorption Over Binary Copper Porphyrin Framework and Graphene Film Sorbents

Photo-responsive adsorption has emerged as a vibrant area because it provides a promising route to reduce the energy consumption of the traditional adsorption separation. However, the current methodology to fabricate photo-responsive sorbents is still subject to the photo-deforming molecular units. In this study, a new initiative of photo-dissociated electron-hole pairs is proposed to generate amazing adsorption activity, and prove its feasibility. Employing CuPP [PP = 5,10,15,20-tetrakis(4-carboxyphenyl)porphyrin] framework nanosheets compounded with graphene, binary film (BF) sorbents are successfully fabricated. The paradigmatic BF nanostructure brings about efficiently photo-excited electron-hole pairs with durable enough lifetime to meet the needs of microscopic adsorption equilibrium, which ultimately alters the electron density distribution of adsorption surface, and thus markedly modulates the adsorption activity. Therefore, an amazing photo-enhanced adsorption capability for the index gas CO can be gotten. Once exposed to the visible-light at 420 nm, the CO adsorption capacity (0 °C, 1 bar) is risen from 0.23 mmol g-1 in the darkness to 1.66 mmol g-1, changed by + 622%. This is essentially different from majority of current photo-responsive sorbents based on photo-deforming molecular units, of which adsorption capability is only decreased with photo-induction, and the maximum rate of change reported is just -54%.

Facile synthesis of Fe3+ immobilized magnetic polydopamine-polyethyleneimine composites for phosphopeptide enrichment

As one of the most common post-translational modification of proteins, protein phosphorylation plays a vital role in many physiological processes. The enrichment of phosphopeptides is highly important before the mass spectrometry detection since phosphopeptides are susceptible to interferences from high-abundance non-phosphopeptides. In this study, we designed a novel magnetic composite (Fe3O4@PDA-PEI-Fe3+) for phosphopeptide enrichment with a facile protocol. The developed Fe3O4@PDA-PEI-Fe3+ is a marvelous material with multiple functional groups, and can effectively enrich phosphopeptides through the synergistic effect of three mechanisms, i.e., immobilized metal ion affinity chromatography raised form Fe3+, electrostatic interaction between amine and phosphate groups, and hydrogen bond between the hydrogen atoms of amine groups and oxygen atoms of phosphate groups. Combined with mass spectrometry, the material shows excellent enrichment performance, high sensitivity (0.4 fmol), good selectivity (β-casein:BSA= 1:500, w:w), and stable reusability (at least 5 cycles). In addition, the material was successfully applied to enrich phosphopeptides from skim milk and human saliva samples, implying that it is an ideal adsorbent for the phosphopeptide enrichment in complex biological samples and provides valuable insights into the field of phosphopeptide analysis.

Enrichment of phosphopeptides by arginine-functionalized magnetic chitosan nanoparticles

One of the most crucial and prevalent post-translational modifications is the phosphorylation of proteins. The study and examination of protein phosphorylation hold immense importance in comprehending disease mechanisms and discovering novel biomarkers. However, the inherent low abundance, low ionization efficiency, and coexistence with non phosphopeptides seriously affect the direct analysis of phosphopeptides by mass spectrometry. In order to tackle these problems, it is necessary to carry out selective enrichment of phosphopeptides prior to conducting mass spectrometry analysis. Herein, magnetic chitosan nanoparticles were developed by incorporating arginine, and were then utilized for phosphopeptide enrichment. A tryptic digest of β-casein was chosen as the standard substance. After enrichment, combined with matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS), the detection limit of the method was 0.4 fmol. The synthesized magnetic material demonstrated great potential in the detection of phosphopeptides in complex samples, as proven by its successful application in detecting phosphopeptides in skim milk and human saliva samples.

Photo-Responsive Carbon Capture over Metalloporphyrin-C60 Metal-Organic Frameworks via Charge-Transfer

Great efforts have been devoted to the study of photo-responsive adsorption, but its current methodology largely depends on the well-defined photochromic units and their photo-driven molecular deformation. Here, a methodology to fabricate nondeforming photo-responsive sorbents is successfully exploited. With C60-fullerene doping in metalloporphyrin metal-organic frameworks (PCN-M, M = Fe, Co, or Ni) and intensively interacting with the metalloporphyrin sites, effective charge-transfer can be achieved over the metalloporphyrin-C60 architectures once excited by the light at 350 to 780 nm. The electron density distribution and the resultant adsorption activity are thus changed by excited states, which are also stable enough to meet the timescale of microscopic adsorption equilibrium. The charge-transfer over Co(II)-porphyrin-C60 is proved to be more efficient than the Fe(II)- and Ni(II)-porphyrin-C60 sites, as well as than all the metalloporphyrin sites, so the CO2 adsorption capacity (CAC; at 0 °C and 1 bar) over the C60-doped PCN-Co can be largely improved from 2.05 mmol g-1 in the darkness to 2.69 mmol g-1 with light, increased by 31%, in contrast to photo-irresponsive CAC over all C60-undoped PCN-M sorbents and only the photo-loss CAC over C60.

Effective Enrichment of Phosphopeptides Using Magnetic Polyoxometalate-Based Metal-Organic Frameworks

In this study, magnetic polyoxometalate-based metal-organic frameworks (Fe3O4-POMOFs) were designed and applied to the enrichment of phosphopeptides. Thanks to the abundant metal oxide and metal ion sites, the material had a strong affinity for phosphopeptides. Simultaneously, the high amount of amino and guanidyl groups provided hydrophilicity and positive charge for phosphopeptide capture. By coupling with MS detection, the established platform possessed good reusability, high sensitivity (0.01 fmol), and high selectivity (α-casein/β-casein/bovine serum albumin = 1:1:5000). Furthermore, the method was successfully used for the detection of phosphopeptides in nonfat milk, human serum, saliva, and A549 cell lysate, showing great potential for practical application.

Light, pH, and Temperature Triple-Responsive Magnetic Composites for Highly Efficient Phosphopeptide Enrichment

Smart materials can dynamically and reversibly change their structures and functions in response to external stimuli. In this study, we designed a smart magnetic composite (MNP-pSPA-b-pNIPAm) with a triple response to ultraviolet (UV) light, pH, and temperature. Relying on the response of spiropyranyl acrylate (SPA) and N-isopropylacrylamide (NIPAm) to external stimuli (light, pH, and temperature), MNP-pSPA-b-pNIPAm was used for the controlled capture and release of phosphopeptides. The established phosphopeptide enrichment platform exhibits high sensitivity (detection limit of 0.04 fmol), high selectivity (BSA/β-casein, 1000:1), and good reusability (6 cycles). In addition, the method was also applied to the enrichment of phosphopeptides in real samples (skim milk, human saliva, and serum), demonstrating the feasibility of this method for phosphoproteomic analysis. After enriching from human nonsmall cell lung cancer cell (A549) lysates with MNP-pSPA-b-pNIPAm, 2595 phosphopeptides corresponding to 2281 phosphoproteins were identified. The novel responsive enrichment probe is highly specific for phosphoproteomic analysis and provides an effective method for studying the significance of protein phosphorylation in complex biological samples.

Design of reversibly charge-changeable rhodamine B modified magnetic nanoparticles to enrich phosphopeptides

In the present study, by employing ethylenediaminetetraacetic acid (EDTA), tetraethylene pentaamine (TEPA), and rhodamine B (Rb), we designed and synthesized a magnetic adsorbent (Fe₃O₄@EDTA@TEPA@Rb) on the basis of reversible charge change of Rb and applied to capture phosphopeptides. Rb existing in open planarized zwitterion form when stimulated by acidic loading buffer adsorbs negative phosphopeptides via electrostatic interaction. Under the stimulation of alkalic eluent, ring-closed structure of Rb is formed to elute the enriched phosphopeptides. TEPA containing rich amino groups is used as a crosslinking agent, which is also protonated in acidic loading buffer to bond phosphopeptides. Then phosphopeptides are eluted when TEPA deprotonates in alkalic eluent. Coupled with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) detection, phosphopeptide signals originated from 0.4 fmol/μL β-casein digests were successfully detected. In addition, Fe₃O₄@EDTA@TEPA@Rb can also efficiently enrich phosphopeptides from skimmed milk, human serum and saliva samples (26, 4, 39 phosphopeptides, respectively), opening a new gallery for phosphopeptides-related analysis. In general, the developed adsorbent has the great potential for further application in the near future.

Reversible trans-to-cis photoisomerization and irreversible photocyclization reactions of a Co-coordinated stilbene derivative on chiral di-β-diketonate lanthanide complexes

Six lanthanide complexes constructed from two chiral β-diketonates (d/l-fbc = 3-heptafluorobutyryl-(+)/(-)-camphorate), the stilbene derivative (E)-N',N'-bis(pyridin-2-ylmethyl)-4-styrylbenzoyl hydrazide (L), a trifluoroacetate anion (CF₃CO₂ ^-), and one water molecule, namely [Ln(d/l-fbc)₂(L)(CF₃CO₂)]·H₂O (LnC₅₇H₅₄F₁₇N₄O₈, Ln = La (1, d-fbc), La (2, l-fbc), Sm (3, d-fbc), Eu (4, d-fbc), Eu (5, l-fbc), and Tb (6, d-fbc), were synthesized and characterized by single-crystal X-ray diffraction, ¹H-NMR, elemental analysis, IR and UV-vis spectroscopy, and thermal gravimetric analysis. The photoisomerization reactions of these complexes were systematically studied by means of experimental and theoretical calculations. Crystals of complexes 1, 2, 3, and 4 were obtained and belong to the monoclinic crystal system and the C2 chiral space group. The Λ- and Δ-diastereomers coexist in their crystals and no apparent bisignate couplets are observed in their ECD spectra. Among the complexes, the photocyclization reaction is followed by the trans-to-cis photoisomerization reaction and competes with the trans-to-cis photoisomerization, then the photocyclization reaction continues. The photocyclization reaction is irreversible in this stilbene derivative and is delayed in the lanthanide complexes. These results provide a viable strategy for the design of promising new stilbene-attached dual-functional lanthanide-based optical-switching materials.

Preparation of IgY Oriented Conjugated Fe3O4 MNPs as Immunomagnetic Nanoprobe for Increasing Enrichment Efficiency of Staphylococcus aureus Based on Adjusting the pH of the Solution System

Immunomagnetic separation based on Fe3O4 magnetic nanoparticles (MNPs) has been widely performed in sample pretreatment. The oriented conjugation strategy can achieve a better capture effect than the N-(3-dimethylamlnopropyl)-N'-ethylcarbodiimide hydrochloride (EDC) /N-hydroxysuccinimide (NHS) method. However, immunoglobulin yolk (IgY) cannot be oriented through an SPA strategy like immunoglobulin G (IgG). In this article, an oriented conjugation nanoprobe was prepared for the enrichment of bacteria based on pH adjusting. The main factors affecting the enrichment efficiency were studied, such as the pH of the buffer system, the concentration of IgY, the concentration of nanoprobe, and the enrichment time. Under the optimal conditions, the enrichment efficiency toward target bacteria could reach 92.8%. Combined with PCR, the limit of detection (LOD) was found to be 103 CFU/ml, which was lower than the PCR only. In conclusion, we provided a new protocol for the oriented conjugation of IgY and high sensitivity detection with simple pretreatment.