The Journal of Physical Chemistry A最新文献

The Independent Gradient Model (IGM) reveals interaction signatures by analyzing the electron density (ED) gradient. In this report it is used to analyze the variations of the electronic structure of a molecular system undergoing, along a series of highly sampled Intrinsic Reaction Coordinates (IRC), a concerted reductive elimination reaction staging a doublet ground state metallacyclic [Cp*{C,N}Co^IV(X{Y})]⁺ (X{Y} = 1 electron ligand, {Y} = assisting atom) prereactive complex (RC). The IGM interfragment Δg^inter score and the degree of interaction (DOI(Co)) of the cobalt center reveal meaningful electronic changes occurring during the reaction, which inform of the active interactions of the ligands with the metal: the Cp* ligand intervenes in the reductive-elimination reaction as an ED reservoir supplementing the Co center. The sourcing of atomic contributions of peripheral atoms to the changes of DOI(Co) at valleys and peaks of DOI reveals, in a nonintuitive way, the role of cobalt's ligands when the system passes through remarkable transient structures. The peaks of DOI either precede or follow the transition state (TS) and are similar to σ-complex structures, suggesting, counterintuitively, that significant electronic changes do not occur at the TS.

Development of antioxidant-type anti-inflammatory inhibitors is essential to mitigate free radical-mediated inflammatory damage, where natural flavonoids with multiple bioactivities are promising candidate compounds. By employing density functional theory/time-dependent density functional theory, molecular docking, and molecular dynamics simulations, the association between excited-state intramolecular/intermolecular proton transfer (ESIntraPT/ESInterPT) mechanisms and antioxidant/anti-inflammatory activity of 6-methoxyflavonol (6-MF) is elucidated. To simulate the ESIntraPT/ESInterPT process, three conditions are set: gas phase, water phase (implicit solvent), and an explicit water molecule. Based on Hirshfeld surface and potential energy curves, the results suggest that excited-state 6-MF in the water phase tends to occur in the ESInterPT process rather than the ESIntraPT process. Density-of-state combined with frontier molecular orbitals demonstrates that antioxidant activity is enhanced during the ESIntraPT process. Molecular docking reveals that keto-form 6-MF has lower binding energy to cyclooxygenase-2 (COX-2) and forms interactions with critical amino acid residues such as TYR385, indicating its anti-inflammatory activity. 50-ns molecular dynamics simulation further confirms the stability of the enol-/keto-6-MF-COX-2 complex.

Heterotopic mechanically interlocked molecules contain different binding sites within their structure, allowing them to recognize specific ion pairs (cations and anions) with a high affinity. The employment of heteroditopic receptors offers advantages over monotopic analogues, in general, being composed of both cation and anion binding sites. The present study elucidates the electronic structure-based recognition of anions and cations of a heteroditopic [2]catenane, IO. Spherical cations and anions have been employed. The structure of IO was modified by replacing its original oxygen atoms of the crown-ether moiety by sulfur atoms and σ-hole donor iodines by -Te-CH₃ groups leading to the modified [2]catenanes IS and TeO, respectively. Energy decomposition analysis (EDA) and natural orbital for chemical valence reveals that the cations exhibit the strongest interaction with the binding pockets of all structures, with Cu⁺, Li⁺, and Ni²⁺ presenting the most stabilizing values, $\Delta E_{\mathrm{IO}}^{tot}$ = -198.2, -175.1, and -653.4 kcal·mol^-1, and $\Delta E_{\mathrm{IS}}^{tot}$= -226.4, -154.0, -702.5 kcal·mol^-1, respectively. In contrast, anion recognition presented to be significantly lower, being purely dependent on the strength of the σ-hole donors and the size of the applied anion, with Cl^- exhibiting the most stable interaction, where $\Delta E_{\mathrm{IO}}^{tot}$ = -109.9 kcal·mol^-1. It was also found that the anion recognition for this particular molecule does not affect the cation recognition, significantly. The EDA results confirm that changing from a harder (O) to a softer (S) interactive environment will have considerable impact on cation recognition, thereby demonstrating the pivotal role, following the size match rule.

Elucidating reaction mechanisms in complex solvation environments presents a significant challenge in computational chemistry. This study establishes a robust computational protocol that combines density functional tight-binding molecular dynamics (DFTB-MD) simulations with high-level quantum chemical calculations to investigate the reactions of water-reactive molecules (SiH₂Cl₂, PCl₃, and SOCl₂) under realistic solvation conditions. The protocol addresses limitations of conventional approaches by incorporating explicit solvation with numerous water molecules surrounding reactants, enabling the identification of frequently occurring reaction pathways through DFTB-MD simulations. Subsequently, density functional theory and domain-based local pair natural orbital coupled cluster singles and doubles with perturbative triples calculations provide quantitative evaluations of energetic values. Validation using SiH₄, a Cl-free analogue, demonstrates the protocol's ability to distinguish reactivity differences. The results reveal that Cl atoms bonded to central atoms (Si, P, and S) act as effective electron acceptors, facilitating electron transfer from H atoms of coordinated H₂O molecules and significantly enhancing the reactivity. For PCl₃, phosphorous acid (H₃PO₃) formation in both isomeric forms (P(OH)₃ and HPO(OH)₂) is observed, while for SOCl₂, sequential SO₂ formation followed by H₂SO₃ production is captured, demonstrating excellent agreement with experimental behavior. All reactions are spontaneous and strongly exothermic, producing hydrochloric acid. Rate constants calculated using transition-state theory and compared with diffusion-controlled limits or experimental data confirm that our solvation model accurately reflects bulk-liquid-phase conditions. The established computational protocol successfully reproduces experimental observations by accurately reflecting realistic reaction conditions, demonstrating its potential for broader application to complex chemical reactions in diverse solvent environments, with significant practical implications.

Benzene is an organic compound that exhibits uniqueness due to its aromaticity. The uniqueness of benzene results in the ubiquity of its derivatives, for example, Trp-Cage and a self-healing polymer. The reaction regarding of the aryl functional group tends to be difficult to occur because of the high energy requirement in the dearomatization process. In the presence of a photocatalyst, aryl migration is possible under relatively mild conditions. In this research, the mechanism of aryl transfer reaction from oxygen toward nitrogen of 2-phenoxyethane-1-amine to 2-(phenylamino)ethane-1-ol has been studied. The previously proposed mechanism is elucidated by using the density-functional theory (DFT) method. The proposed mechanism was partially refuted, and a new alternative is necessary regarding the proton transfer migration step. One of the alternative pathways is that the proton transfer is catalyzed by the reactant as described in the present work.

Chlorophyll pigments and derivatives were studied under isolated conditions and at low temperatures in their anionic deprotonated form. Neutral and deprotonated chlorophyll pigments are isoelectronic, which likens their electronic properties, as is confirmed by electronic structure calculations. The study of these anionic pigments is directed toward understanding the electronic structure of their neutral counterparts involved in photosynthetic processes. In this goal, we measured the photodetachment thresholds that characterize the deprotonated anions unequivocally. Four systems have been studied: pheophytin a, its simpler ester equivalents methyl pheophorbide and metalated zinc methyl pheophorbide, and pheophorbide. By a combination of direct laser one photon detachment measurements and quantum chemical calculations, we could characterize the localization of the charge on these deprotonated anions. Two major sites have been found, one on the carboxylate group of pheophorbide and the other on the carbon atom in the α position of the peripheral methyl ester of the chlorophyll cycle. The experimental electron binding energies to these sites ∼2.7 eV and ∼3.1 eV agree with quantum chemistry calculations and correspond to macrocycle and carboxylate attachment, respectively. In addition, the HOMOs are similar for neutral and both anionic deprotonated pigments, allowing for the comparison of the spectroscopic properties of both species and using anionic deprotonated pigments as models for their neutral counterparts.

This study computationally investigates the open and locked conformations of substituted 1,3,2-dioxaborol-2-yl-2-oxoacetate (DOBOA) derivatives. The results reveal that the locked conformations, stabilized by B···O triel bonding interactions, are consistently more stable than the corresponding open forms. Systematic substitution with electron-withdrawing groups on the dioxaborolane ring and/or electron-donating groups on the oxoacetate moiety further enhances the strength of the B···O interaction, thereby increasing the stability of the locked conformation. Geometric, energetic, and topological analyses of the electron density reveal that these interactions can be categorized into two regimes: noncovalent and dative. Complementary orbital analysis confirms that this B···O interaction arises due to the O(lp)→B(p-orbital) charge transfer. These findings highlight the role of B···O triel bonding as a conformational locking mechanism, offering a new strategy for rational conformational control in molecular design and functional materials.

In this work, we explore the use of constrained density functional theory for the calculation of the charge transfer parameters of 2,1,3-benzothiadiazole (BTZ), a promising redoxmer, in acetonitrile (MeCN) solvent. The BTZ molecule has been studied as an anolyte in redox flow batteries, where charge transfer is a crucial process. It is highly desirable to simulate ab initio charge-transfer parameters, given their accuracy in predicting electron-transfer rates and structure-activity relationships. This work explores the state of the art in charge-transfer simulation for this process. Constrained density functional theory (DFT) calculations are used to predict charge-transfer free energies and electronic couplings, which are crucial for evaluating charge transfer within the Marcus theory. Based on the simulations, we find that electronic coupling fluctuates rapidly with time and also depends on the difference between the donor and acceptor state energies (reaction gap energy). Based on our evaluation of Marcus theory, BTZ has a predicted self-exchange reaction rate constant on the order of 0.5 M^-1 s^-1 at 1 M concentration in MeCN. Our work demonstrates the utility of constrained DFT for providing physical insight into a charge-transfer process, while also highlighting current limitations in computational and algorithmic capacity in achieving desirable system sizes and levels of ergodicity in molecular dynamics simulations. A significant conclusion of this work is that time-dependent sampling of electronic coupling as a function of the reaction gap energy, as described herein, is essential for future predictions of charge and electron transfer.

The study of amorphous carbon structures of different sizes and extensions is relevant to many research areas, including electrode processes (e.g., intercalation), astrochemistry, catalysis, and sensors. While the structure of amorphous carbon structures has been investigated thoroughly in the past, a systematic analysis of their properties upon doping with functional groups is far less extensive. This aspect is particularly important for carbon nanodots (CNDs), a photoluminescent species of carbon-based nanoparticles whose optical properties arise from the interplay between core electronic structure, surface states, heteroatom doping, and molecular fluorophores. Despite extensive experimental work, an atomistic rationalization of their optical properties is still not available. In this study, we adopt a bottom-up computational approach using amorphous pure carbon clusters (C₁₀-C₆₀) and nitrogen-substituted ones (C₉N-C₅₉N) as models for the unsaturated and partially doped domains of CND cores. Structural isomers were generated along with computed UV/vis spectra to rationalize the property changes upon nitrogen substitution.

Naphthalene-to-azulene isoelectronic structural reconstruction in perylene (P), perylenediimide (PDI), and its chalcogenides (X-PDI, X = O, S, Se), similar to the Stone-Wales defect in graphene, may significantly alter the intrinsic electronic structure and thus poses scientific curiosity about how and to what extent their structure-function relationships change with such reconstruction. Structural, electronic, and photophysical properties for the reconstructed analogues of P (rP) and X-PDI (X-rPDI) are studied for the first time, adopting polarization-consistent optimally tuned range-separated hybrid (OT-RSH) in toluene. All X-rPDIs, including rP are found to be planar and dynamically stable, with thermodynamic formation energies comparable to those of their pristine congeners, indicating synthetic feasibility. The complex interplay of chalcogens and reconstruction produces an increased electronic gap in S/Se-rPDI compared to their respective PDI analogues, which, in competition with varied exciton binding energy in X-rPDIs produce red- and blue-shifted lowest excited singlet (S₁) and triplet (T₁ > 1.0 eV), respectively. Optically forbidden S₁ in rP and all X-rPDIs, with closely lying optically bright S_n suggests fluorescence turn-off. Similar ππ^* excitonic characters and lesser chalcogen contributions yield relatively smaller intersystem crossing (ISC) rates for X-rPDIs than X-PDIs. The rate increases down the chalcogen group for both X-rPDIs and X-PDIs due to gradually increased heavy-atom effects. Interestingly, reconstruction lowers the excited singlet-triplet gap and generates nonzero spin-orbit coupling, yielding ∼4 orders higher ISC rates in rP and O-rPDI compared to their pristine analogues. Further, while S-rPDI shows ∼6 orders smaller rate than S-PDI, both Se-rPDI and Se-PDI display remarkably high ISC rates (∼10¹²-10¹³ s^-1). Importantly, Se-rPDI with moderately high energy T₁ and a considerably large ISC rate, could serve as a better triplet photosensitizer than Se-PDI. These insights into the reconstruction-tailored structure-function relationships will help to design new azulene-based functional organic molecules.