Computational Insights into SN 2 and Proton Transfer Reactions of CH3 O- with NH2 Y and CH3 Y

Triazolone-Functionalized Magnetic Nanoparticles for Hemoglobin Purification and Proteomics-Driven Biomarker Discovery in Diabetic Blood

Hemoglobin, particularly glycated hemoglobin, serves as the gold standard for diagnosing diabetes in clinical settings. In this study, a triazolinone derivative, 3-chloromethyl-1,2,4-triazol-5-one (CMTO), was conjugated to polyethylenimide-modified magnetic nanoparticles via an amination reaction, resulting in the formation of a novel composite material, CMTO@Fe3O4-NH2. Molecular simulations revealed that the carbonyl group of CMTO underwent tautomerization to an enol form under neutral pH conditions. The enol form established hydrogen bonds with phenylalanine residues in hemoglobin, while the triazole ring interacted with the hemoglobin β-subunit through π-π interactions. These interactions significantly enhanced the performance of CMTO@Fe3O4-NH2 in the effective separation and purification of hemoglobin. Specifically, 1.0 mg of CMTO@ Fe3O4-NH2 successfully adsorbed hemoglobin from 0.5 mL of a 100 μg mL-1 hemoglobin solution, with an excellent adsorption efficiency of 93.8% in just 45 min. The adsorption process was found to follow the Langmuir model with a theoretical adsorption capacity of 344.83 mg g-1. Furthermore, with a 91.2% elution efficiency, the adsorbed hemoglobin could be efficiently eluted using a 100 mmol L-1 imidazole solution. After five cycles, the material retained 88.1% of its initial adsorption efficiency. Encouraged by its hemoglobin adsorption efficiency, the composite material was applied to selectively separate hemoglobin from human whole blood. Protein sequencing identified 1114 proteins in this process, with 252 differential proteins found between diabetic and healthy individuals. Pathway analysis and protein-protein interaction (PPI) networks identified 12 potential diabetic biomarkers.

Computational Studies of Nucleophilic Substitution at Nitrogen Center: Reactions of NH2Cl with HO-, CH3O- and C2H5O. Chemphyschem 2024;25:e202400365. [PMID: 38923666 DOI: 10.1002/cphc.202400365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The atomic-level mechanisms of the nucleophilic substitution reactions at the nitrogen center (SN2@N) were investigated for the reactions of chloramine (NH2Cl) with the alkoxide ions (RO-, where R=H, CH3, and C2H5) using DFT and MP2 methods. The computed potential energy profiles for the SN2@N pathways involving the back-side attack of the nucleophiles show the typical double-well potential with submerged barriers similar to the SN2 reactions at the carbon center (SN2@C). However, the pre-reaction and post-reaction complexes are, respectively, the N-H⋅⋅⋅O and N-H⋅⋅⋅Cl hydrogen-bonded intermediates, which are different from those generally seen in SN2@C reactions. The SN2@N pathways involving front-side attack of the nucleophiles have high-energy barriers. The potential energy surfaces (PESs) along the proton-transfer pathways were flat. In addition to the proton-transfer and SN2 pathways, we also observed a new path for the methoxide and ethoxide nucleophiles where a hydride-transfer from the nucleophile to chloramine resulted in the products Cl-+R'CHO+NH3, (R'=H, CH3), and was the most exoergic. A comparison of the energetics obtained used different DFT and MP2 methods with that of the benchmark coupled-cluster methods reveals that CAM-B3LYP best describes the PESs.

Mechanistic Insights into the Proton Transfer and Substitution Dynamics of N-Atom Center Reactions: A Study of CH3O- with NH2Cl

Bimolecular substitution reactions involving N as the central atom have continuously improved our understanding of substitution dynamics. This work used chemical dynamics simulations to investigate the dynamics of NH2Cl with N as the central atom and the multiatomic nucleophile CH3O- and compared these results with the F- + NH2Cl reaction. The most noteworthy difference is in the competition between proton transfer (PT) and the SN2 pathways. Our results demonstrate that, for the CH3O- + NH2Cl system, the PT pathway is considerably more favorable than the SN2 pathway. In contrast, no PT pathway was observed for the F- + NH2Cl system at room temperature. This can be attributed to the exothermic reaction of the PT pathway for the CH3O- + NH2Cl reaction and is coupled with a more stable transition state compared to the substitution pathway. Furthermore, the bulky nature of the CH3O- group impedes its participation in SN2 reactions, which enhances both the thermodynamic and the dynamic advantages of the PT reaction. Interestingly, the atomic mechanism reveals that the PT pathway is primarily governed by indirect mechanisms, similar to the SN2 pathway, with trajectories commonly trapped in the entrance channel being a prominent feature. These trajectories are often accompanied by prolonged and frequent proton exchange or proton abstraction processes. This current work provides insights into the dynamics of N-centered PT reactions, which are useful in gaining a comprehensive understanding of the dynamics behavior of similar reactions.

Vibrational mode-specificity in the dynamics of the OH- + CH3I multi-channel reaction

We report a comprehensive characterization of the vibrational mode-specific dynamics of the OH- + CH3I reaction. Quasi-classical trajectory simulations are performed at four different collision energies on our previously-developed full-dimensional high-level ab initio potential energy surface in order to examine the impact of four different normal-mode excitations in the reactants. Considering the 11 possible pathways of OH- + CH3I, pronounced mode-specificity is observed in reactivity: In general, the excitations of the OH- stretching and CH stretching exert the greatest influence on the channels. For the SN2 and proton-abstraction products, the reactant initial attack angle and the product scattering angle distributions do not show major mode-specific features, except for SN2 at higher collision energies, where forward scattering is promoted by the CI stretching and CH stretching excitations. The post-reaction energy flow is also examined for SN2 and proton abstraction, and it is unveiled that the excess vibrational excitation energies rather transfer into the product vibrational energy because the translational and rotational energy distributions of the products do not represent significant mode-specificity. Moreover, in the course of proton abstraction, the surplus vibrational energy in the OH- reactant mostly remains in the H2O product owing to the prevailing dominance of the direct stripping mechanism.