Theoretical analysis of naproxen reaction with sulfate and hydroxyl radicals in the aqueous phase: Investigating reactive sites and reaction kinetics.

In this study, we have utilized theoretical calculations to predict the reaction active sites of naproxen when reacting with radicals and to further study the thermodynamics and kinetics of the reactions with ·OH and SO4-·. The evidence, derived from the average local ionization energy and electrostatic potential, points to the naphthalene ring as the preferred site of attack, especially for the C2, C6, C9, and C10 sites. The changes in Gibbs free energy and enthalpy of the reactions initiated by ·OH and SO4-· ranged between -19.6 kcal/mol - 26.3 kcal/mol and -22.3 kcal/mol -18.5 kcal/mol, respectively. More in-depth investigation revealed that RA2 pathway for ·OH exhibited the lowest free energy of activation, suggesting this reaction is more inclined to proceed. The second-order rate constant results indicate the ·OH attacking reaction is faster than reactions initiated by SO4·-, yet controlled by diffusion. The consistency between theoretical findings and experimental data underscores the validity of this computational method for our study.

Reductive Elimination from Tetra-Alkyl Cuprates [Me n Cu(CF3)4- n ]- (n = 1 - 4): Beyond Simple Oxidation States.

In recent years, the electronic structures of organocuprates in general and the complex [Cu(CF3)4]- in particular have attracted significant interest. A possible key indicator in this context is the reactivity of these species. Nonetheless, this aspect has received only limited attention. Here, we systematically study the series of tetra-alkyl cuprates [MenCu(CF3)4-n]- and their unimolecular reactivity in the gas phase, which includes concerted formal reductive eliminations as well as radical losses. Through computational studies, we characterize the electronic structures of the complexes and show how these are connected to their reactivity. We find that all [MenCu(CF3)4-n]- ions feature inverted ligand fields and that the distinct reactivity patterns of the individual complexes arise from the interplay of different effects.

A Comparative Study of the Stability, Transport, and Structure-Activity Relationship of Round Scad Derived Peptides with Antineuroinflammatory Ability.

Our previous study identified round scad neuroprotective peptides with different characteristics. However, the intrinsic relationship between their structure and bioactivity, as well as their bioavailability, remains unclear. The aim of this study is to elucidate the bioavailability of these peptides and their structure-activity relationship against neuroinflammation. Results showed that the SR and WCP peptides were resistant to gastrointestinal digestion. Additionally, peptides SR, WCP, and WCPF could transport Caco-2 monolayers as intact peptides. The permeability coefficients (Papp) of SR, WCP, and WCPF in Caco-2 monolayer were (1.53 ± 0.01) × 10-5, (2.12 ± 0.01) × 10-5, and (8.86 ± 0.03) × 10-7 cm/s, respectively. Peptides SR, WCP, and WCPF, as promising inhibitors of JAK2 and STAT3, could attenuate the levels of pro-inflammatory cytokines and regulate the NFκB and JAK2/STAT3 signaling pathway in LPS-treated BV-2 cells. WCPF exerted the highest anti-inflammatory activity. Moreover, bioinformatics, molecular docking, and quantum chemistry studies indicated that the bioactivity of SR was attributed to Arg, whereas those of WCP and WCPF were attributed to Trp. This study supports the application of round-scad peptides and deepens the understanding of the structure-activity relationship of neuroprotective peptides.

Circular dichroism of relativistically-moving chiral molecules.

Understanding the impact of the relativistic motion of a chiral molecule on its optical response is a prime challenge for fundamental science, but it also has a direct practical relevance in our search for extraterrestrial life. To contribute to these significant developments, we describe a multi-scale computational framework that combines quantum chemistry calculations and full-wave optical simulations to predict the chiral optical response from molecules moving at relativistic speeds. Specifically, the effect of a relativistic motion on the transmission circular dichroism (TCD) of three life-essential biomolecules, namely, B-DNA, chlorophyll a, and chlorophyll b, is investigated. Inspired by previous experiments to detect interstellar chiral molecules, we assume that the molecules move between a stationary observer and a light source, and we study the rotationally averaged TCD as a function of the speed of the molecule.We find that the TCD spectrum that contains the signatures of the molecules shifts with increasing speed to shorter wavelengths, with the effects already being visible for moderate velocities.

Symmetric Electron Transfer Coordinates are Intrinsic to Bridged Systems: An ab Initio Treatment of the Creutz-Taube Ion.

A long-standing question in electron transfer research concerns the number and identity of collective nuclear motions that drive electron transfer or localisation. It is well established that these nuclear motions are commonly gathered into a so-called electron transfer coordinate. In this theoretical study, we demonstrate that both anti-symmetric and symmetric vibrational motions are intrinsic to bridged systems, and that both are required to explain the characteristic shape of their intervalence charge transfer bands. Using the properties of a two-state Marcus-Hush model, we identify and quantify these two coordinates as linear combinations of normal modes from ab initio calculations. This quantification gives access to the potential coupling, reorganization energy and curvature of the potential energy surfaces involved in electron transfer, independent of any prior assumptions about the system of interest. We showcase these claims with the Creutz-Taube ion, a prototypical Class III mixed valence complex. We find that the symmetric dimension is responsible for the asymmetric band shape, and trace this back to the offset of the ground and excited state potentials in this dimension. The significance of the symmetric dimension originates from geometry dependent coupling, which in turn is a natural consequence of the well-established superexchange mechanism. The conceptual connection between the symmetric and anti-symmetric motions and the superexchange mechanism appears as a general result for bridged systems.

Reaction mechanism of antioxidant inhibition of hydroxyl radical in coal oxidation.

To solve the problem of unclear targeted inhibition of key free radicals by antioxidants, this paper took the hydroxyl radical with the highest oxidation activity of coal as the inhibition target and selected five antioxidants such as ethylene diamine tetraacetic acid, tea polyphenol, citric acid, vitamin C, and proanthocyanidins. Based on the theory of quantum chemistry, the characteristics and oxidation pathway of antioxidants inhibiting coal oxidation of hydroxyl radical were analyzed. Analyze the influence characteristics of antioxidants on the evolution of free radicals in coal through an electron paramagnetic resonance experiment (ESR). The results showed that the electron density of antioxidants was mainly distributed in the functional groups of carboxyl and hydroxyl, which played a key inhibitory role, and the vicinity of carboxyl and hydroxyl and other functional groups was positive potential, which was the active site of inhibiting hydroxyl radical. The order of inhibitory capacity of the five antioxidants was determined as GTP > PC > EDTA > CA > VC. It is concluded that the energy barrier of hydroxyl radical inhibition by citric acid is much lower than that of EDTA. For the hydrogen extraction reaction, VC inhibited the hydroxyl radical pathway with a higher energy barrier than the other three antioxidants. The mechanism of five antioxidants inhibiting •OH reaction was comprehensively analyzed. It was found that tea polyphenols have more active sites that can react with •OH to quench it, so the inhibition of tea polyphenols should be the most significant. When antioxidants inhibit coal spontaneous combustion, the type, complexity, concentration, and linewidth of free radicals in coal molecules are lower than those in raw coal, with GTP antioxidants having the best inhibitory effect. The research results have important theoretical and practical significance for revealing the mechanism of coal spontaneous combustion inhibition and developing directional coal spontaneous combustion inhibition technology.

Impact of 2-hydroxypropyl-ß-cyclodextrin inclusion complex formation on dopamine receptor-ligand interaction - A case study.

The octanol-water distribution coefficient (logP), used as a measure of lipophilicity, plays a major role in the drug design and discovery processes. While average logP values remain unchanged in approved oral drugs since 1983, current medicinal chemistry trends towards increasingly lipophilic compounds that require adapted analytical workflows and drug delivery systems. Solubility enhancers like cyclodextrins (CDs), especially 2-hydroxypropyl-ß-CD (2-HP-ß-CD), have been studied in vitro and in vivo investigating their ADMET (adsorption, distribution, metabolism, excretion and toxicity)-related properties. However, data is scarce regarding the applicability of CD inclusion complexes (ICs) in vitro compared to pure compounds. In this study, dopamine receptor (DR) ligands were used as a case study, utilizing a combined in silico/in vitro workflow. Media-dependent solubility and IC stoichiometry were investigated using HPLC. NMR was used to observe IC formation-caused chemical shift deviations while in silico approaches utilizing basin hopping global minimization were used to propose putative IC binding modes. A cell-based in vitro homogeneous time-resolved fluorescence (HTRF) assay was used to quantify ligand binding affinity at the DR subtype 2 (D2R). While all ligands showed increased solubility using 2-HP-ß-CD, they differed regarding IC stoichiometry and receptor binding affinity. This case study shows that IC-formation was ligand-dependent and sometimes altering in vitro binding. Therefore, IC complex formation can't be recommended as a general means of improving compound solubility for in vitro studies as they may alter ligand binding.

Thermal oxidation mechanism of palmitic aicd.

The oxidation and degradation of fats lead to a decrease in the nutritional value of food and pose safety concerns. Saturated fatty acids also hold a significant position in the field of lipid oxidation. In this study, the oxidation products of methyl palmitate were investigated by using gas chromatography mass spectrometry (GC-MS). Seven monohydroperoxides and 72 secondary oxidation products were detected. Combined with density functional theory (DFT) calculations, the formation mechanisms of oxidation products can be summarized into four stages. The initial stage involved the formation of monohydroperoxides and alkanes, followed by the subsequent stage involving methyl x-oxo(hydroxy)hexadecanoates. The third stage involved the formation of methyl ketones, carboxylic acids, and aldehydes, while the final stage involved lactones. Meanwhile, methyl ketones were the most abundant oxidation product, approximately 25 times more abundant than aldehydes; the calculated results agreed well with the experimental results. The establishment of a comprehensive thermal oxidation mechanism for palmitic acid provided a new foundation for future lipid oxidation analyses.

Study on the compounding optimization of surfactants and synergistic effects on the wettability of bituminous coal.

To improve the wettability of surfactants on bituminous coal and to explore its wettability and wettability mechanism on bituminous coal, taking the Sandaogou bituminous coal as an example, a single factor experiment was carried out first. Through contact angle and surface tension experiments, three surfactants with good wettability were selected from among the nine surfactants and mixed in equal proportions two by two to determine the optimal compounding method and compounding concentration. The experimental results show that the compounding of nonionic and anionic, nonionic and zwitterionic, anionic and zwitterionic surfactants can have synergistic effects and significantly improve the wettability of bituminous coal. Among them, the 0.5 wt% SDS + 0.5 wt% CAB-50 (R2) compound surfactant had the best wettability on bituminous coal, and the contact angle and surface tension were only 15.24° and 23.62 mN/m, respectively. The surface electrostatic potential values of each material molecule were calculated by Materials Studio software based on the quantum chemistry method, and correlation analysis was carried out with wettability. The results show that the surface electrostatic potentials of CDEA, SDS and CAB-50 were greater than those of water and bituminous coal, and the region of maximum negative electrostatic potential corresponded to oxygen atoms, which are easier to adsorb on bituminous coal and water molecules. Then, through molecular dynamics simulation, the interaction energy and the distribution of contributions along the Z-axis of the water/compound surfactant/bituminous coal system at equilibrium were investigated, and finally, a spray dust reduction test was carried out in the Sandaogou Coal Mine. The results showed that the 0.5 wt% SDS + 0.5 wt% CAB-50 compound solution can be used as a water molecule adsorption carrier, prompting more water molecules to be embedded into coal molecules, increasing the relative concentration of water molecules on the surface of bituminous coal, restricting the diffusion of water molecules, and greatly improving the wettability. After the addition of 0.5 wt% SDS + 0.5 wt% CAB-50 as a spray agent, the concentration of total dust at the driver's position decreased from 65.14 to 9.11 mg/m3, the concentration of exhaled dust decreased from 30.07 to 3.35 mg/m3, and the efficiency of total and exhaled dust reduction compared with that of pure water was 86.01% and 89.35%, respectively.

Vibrational Relaxation of D2O Induced by Collision with He: A Rigid Bender Close Coupling Study.

The vibrational relaxation of the first excited bending state of D2O induced by collision with He is studied at the close coupling level and using the Rigid Bender approximation. A new 4D potential energy surface is calculated and reported for this system. It is then used to determine the low-lying bound states of the D2O-He van der Waals complex and to perform scattering calculations. Collision rates are determined for pure rotational transitions as well as for rovibrational transitions within the first excited bending state. The results are compared with those obtained for the collision of D2O with other noble gases such as Ne and Ar. We also analyse the differences observed with respect to the H2O+He collisions and compare our results with experiment.

In-Electrospray source Hydrogen/Deuterium exchange coupled to multistage fragmentation for the investigation of the protonation and fragmentation pathways of gas phase ions.

Identification of molecules in complex natural matrices relies on matching the fragmentation spectra of ions under investigation and the spectra acquired for the corresponding analytical standards. Currently, there are many databases of experimentally measured tandem mass spectrometry spectra (such as NIST, MzCloud, and Metlin), and considerable progress has been made in the development of software for predicting tandem mass spectrometry fragments in silico using combinatorial, machine learning, and quantum chemistry approaches (such as MetFrag, CFM-ID, and QCxMS). However, the electrospray ionization molecules can be ionized at different sites (protonated or deprotonated), and the fragmentation spectra of such ions are different. Here, we are using the combination of the in-ESI source hydrogen/deuterium exchange reaction and MSn fragmentation for the investigation of the fragmentation pathways for different protomers of organic molecules. It is shown that the distribution of the deuterium in the fragment ions reflects the presence of different protomers. For several molecules, the distribution of deuterium was traced up to the MS5 level of fragmentation revealing many unusual and unexpected effects. For example, we investigated the loss of HF from the ciprofloxacin and norfloxacin ions and observed that for ions protonated at -COOH group, the eliminating hydrogen always comes from -NH group. When ions are protonated at another site, the elimination of hydrogen with a probability of 30% occurs from the -NH group, and with a probability of 70%, it originates from other sites on the molecule. Such effects were not described previously. Quantum chemical simulation was used for the verification of the protonated structures and simulation of the corresponding fragmentation spectra.

New lignans from Phyllanthodendron dunnianum.

A new lignan phyllanins A (1) and a lignan phyllanins B (2) for which the absolute configuration was determined for the first time, along with four known lignans (3-6) were isolated from the branch and leaf extracts of Phyllanthodendron dunnianum. Their planar structures were mainly determined by a combination of 1D and 2D NMR, HRESIMS spectral analyses, and the absolute configurations of the compounds 1 and 2 were established by DFT GIAO 13C NMR and electronic circular dichroism (ECD) calculations. In addition, all these six lignans were firstly tested for the antibacterial activities against MRSA, Staphylococcus aureus, Enterococcus faecalis, Pseudomonas aeruginosa and Escherichia coli. Among these compounds, 2 and 5 showed potential antibacterial activities against MRSA and S. aureus with MIC values of 4 and 8 µg/mL, respectively.

Molecular mechanism of saturated aldehyde oxidation: A DFT insight into volatiles forming from decanal thermal oxidation.

Decanal is one of the main products of lipid oxidation. It has been shown that decanal can oxidize to form volatiles with shorter carbon chains during heating, but the mechanism is still unclear. In this study, volatile compounds formed in the decanal thermal oxidation were verified using thermal-desorption cryo-trapping combined with GC-MS. A total of 32 volatile compounds were identified. The oxidation mechanism of decanal was studied by applying density functional theory. Results revealed that the carbonyl carbon atom was the thermal oxidation site of decanal and two pathways of peroxide oxidation were determined: the ortho­carbon and the meta­carbon oxidation. The ortho­carbon oxidation pathway is superior to the occurrence of the meta­carbon oxidation pathway. The oxidative mechanism of decanal was finally summarized as the peroxide oxidation based on radical attack on the carbonyl carbon, which would provide a theoretical basis for exploring the oxidation mechanism of other saturated aldehydes.

Carbon-based molecular properties efficiently predicted by deep learning-based quantum chemical simulation with large language models.

The prediction of thermodynamic properties of carbon-based molecules based on their geometrical conformation using fluctuation and density functional theories has achieved great success in the field of energy chemistry, while the excessive computational cost provides both opportunities and challenges for the integration of machine learning. In this work, a deep learning-based quantum chemical prediction model was constructed for efficient prediction of thermodynamic properties of carbon-based molecules. We constructed a novel framework - encoding the 3D information into a large language model (LLM), which in turn generates a 2D SMILES string, while embedding a learnable encoding designed to preserve the integrity of the original 3D information, providing better structural information for the model. Additionally, we have designed an equivariant learning module to encompass representations of conformations and feature learning for conformational sampling. This framework aims to predict thermodynamic properties more accurately than learning from 2D topology alone, while providing faster computational speeds than conventional simulations. By combining machine learning and quantum chemistry, we pioneer efficient practical applications in the field of energy chemistry. Our model advances the integration of data-driven and physics-based modeling to unlock novel insights into carbon-based molecules.

Cobalt-Mediated Photochemical C-H Arylation of Pyrroles.

Precious metal complexes remain ubiquitous in photoredox catalysis (PRC) despite concerted efforts to find more earth-abundant catalysts and replacements based on 3d metals in particular. Most otherwise plausible 3d metal complexes are assumed to be unsuitable due to short-lived excited states, which has led researchers to prioritize the pursuit of longer excited-state lifetimes through careful molecular design. However, we report herein that the C-H arylation of pyrroles and related substrates (which are benchmark reactions for assessing the efficacy of photoredox catalysts) can be achieved using a simple and readily accessible octahedral bis(diiminopyridine) cobalt complex, [1-Co](PF6)2. Notably, [1-Co]2+ efficiently functionalizes both chloro- and bromoarene substrates despite the short excited-state lifetime of the key photoexcited intermediate *[1-Co]2+ (8 ps). We present herein the scope of this C-H arylation protocol and provide mechanistic insights derived from detailed spectroscopic and computational studies. These indicate that, despite its transient existence, reduction of *[1-Co]2+ is facilitated via pre-assembly with the NEt3 reductant, highlighting an alternative strategy for the future development of 3d metal-catalyzed PRC.

Striking Borane Planarization in the Thermal Rearrangement (η5-C5H5)Fe(η3-B5H10)→(η5-C5H5)Fe(η5-B5H10).

In 1977 Weiss and Grimes, by means of mass spectrometry and 1H and 11B NMR spectroscopy, proposed two structures (I and II) for the ferraborane (η5-C5H5)Fe(B5H10), isoelectronic with ferrocene. In this work, by means of high-level quantum-chemical computations, we confirm the experimental structures of the two isomers with their corresponding energies, and assign the reported 1H and 11B NMR chemical shifts. A striking result from this study is the planarization (3D→2D) of the B5H10 - ligand - an unknown isolated anion, isoelectronic with aromatic cyclopentadienyl anion C5H5 - - when attached to the (η5-C5H5)Fe+ moiety, thus resulting in a more stable ferraborane isomer II.

Potential new cancer biomarkers revealed by quantum chemistry associated with bioinformatics in the study of selectin polymorphisms.

Understanding the complex mechanisms involved in diseases caused by or related to important genetic variants has led to the development of clinically useful biomarkers. However, the increasing number of described variants makes it difficult to identify variants worthy of investigation, and poses challenges to their validation. We combined publicly available datasets and open source robust bioinformatics tools with molecular quantum chemistry methods to investigate the involvement of selectins, important molecules in the cell adhesion process that play a fundamental role in the cancer metastasis process. We applied this strategy to investigate single nucleotide variants (SNPs) in the intronic and UTR regions and missense SNPs with amino acid changes in the SELL, SELP, SELE, and SELPLG genes. We then focused on thyroid cancer, seeking these SNPs potential to identify biomarkers for susceptibility, diagnosis, prognosis, and therapeutic targets. We demonstrated that SELL gene polymorphisms rs2229569, rs1131498, rs4987360, rs4987301 and rs2205849; SELE gene polymorphisms rs1534904 and rs5368; rs3917777, rs2205894 and rs2205893 of SELP gene; and rs7138370, rs7300972 and rs2228315 variants of SELPLG gene may produce important alterations in the DNA structure and consequent changes in the morphology and function of the corresponding proteins. In conclusion, we developed a strategy that may save valuable time and resources in future investigations, as we were able to provide a solid foundation for the selection of selectin gene variants that may become important biomarkers and deserve further investigation in cancer patients. Large-scale clinical studies in different ethnic populations and laboratory experiments are needed to validate our results.

Structure and Solution Behavior of Rare-Earth-Metal Complexes with Tripodal N-Donor Ligands.

Rare-earth-metal complexes (Ln=Y, La, Ce, Sm and Lu) of tripodal N-donor ligands respecting the CHON principle have been synthetized and characterized. The selectivity of the ligands through the lanthanide cations was investigated and related to their donor strength.

The Effect of Spin Relaxation on Magnetic Compass Sensitivity in ErCry4a.

This study explores the impact of thermal motion on the magnetic compass mechanism in migratory birds, focusing on the radical pair mechanism within cryptochrome photoreceptors. The coherence of radical pairs, crucial for magnetic field inference, is curbed by spin relaxation induced by intra-protein motion. Molecular dynamics simulations, density-functional-theory-based calculations, and spin dynamics calculations were employed, utilizing Bloch-Redfield-Wangsness (BRW) relaxation theory, to investigate compass sensitivity. Previous research hypothesized that European robin's cryptochrome 4a (ErCry4a) optimized intra-protein motion to minimize spin relaxation, enhancing magnetic sensing compared to the plant Arabidopsis thaliana's cryptochrome 1 (AtCry1). Different correlation times of the nuclear hyperfine coupling constants in AtCry1 and ErCry4a were indeed found, leading to distinct radical pair yields in the two species, with ErCry4a showing optimized sensitivity. However, this optimization is likely negligible in realistic spin systems with numerous nuclear spins. Beyond insights in magnetic sensing, the study presents a detailed method employing molecular dynamics simulations to assess spin relaxation effects on chemical reactions with realistically modelled protein motion, relevant for studying radical pair reactions at finite temperature.