Physical Chemistry Chemical Physics最新文献

The interactions of carboxylate anions with water and cations are important for a wide variety of systems, both biological and synthetic. To gain insight on properties of the local complexes, we apply density functional theory, to treat the complex electrostatic interactions, and investigate mixtures with varied numbers of carboxylate anions (acetate) and waters binding to monovalent cations, Li⁺, Na⁺ and K⁺. The optimal structure with overall lowest free energy contains two acetates and two waters such that the cation is four-fold coordinated, similar to structures found earlier for pure water or pure carboxylate ligands. More generally, the complexes with two acetates have the lowest free energy. In transitioning from the overall optimal state, exchanging an acetate for water has a lower free energy barrier than exchanging water for an acetate. In most cases, the carboxylates are monodentate and in the first solvation shell. As water is added to the system, hydrogen bonding between waters and carboxylate O atoms further stabilizes monodentate structures. These structures, which have strong electrostatic interactions that involve hydrogen bonds of varying strength, are significantly polarized, with ChelpG partial charges that vary substantially as the bonding geometry varies. Overall, these results emphasize the increasing importance of water as a component of binding sites as the number of ligands increases, thus affecting the preferential solvation of specific metal ions and clarifying Hofmeister effects. Finally, structural analysis correlated with free energy analysis supports the idea that binding to more than the preferred number of carboxylates under architectural constraints are a key to ion transport.

The influence of carotenoid triplet states on the Q_y electronic transitions of chlorophylls has been observed in experiments on light-harvesting complexes over the past three decades, but the interpretation of the resulting spectral feature in the triplet minus singlet (T–S) absorption spectra of photosystems is still debated, as the physical–chemical explanation of this feature has been elusive. Here, we resolve this debate, by explaining the T–S spectra of pigment complexes over the Q_y-band spectral region through a comparative study of chlorophyll–carotenoid model dyads and larger pigment complexes from the main light harvesting complex of higher plants (LHCII). This goal is achieved by combining state-of-the-art time-dependent density functional theory with analysis of the relationship between electronic properties and nuclear structure, and by comparison to the experiment. We find that the special signature in the T–S spectra of both model and natural photosystems is determined by singlet-like triplet excitations that can be described as effective singlet excitations on chlorophylls influenced by a stable electronic triplet on the carotenoid. The comparison with earlier experiments on different light-harvesting complexes confirms our theoretical interpretation of the T–S spectra in the Q_y spectral region. Our results indicate an important role for the chlorophyll–carotenoid electronic coupling, which is also responsible for the fast triplet–triplet energy transfer, suggesting a fast trapping of the triplet into the relaxed carotenoid structure. The gained understanding of the interplay between the electronic and nuclear structures is potentially informative for future studies of the mechanism of photoprotection by carotenoids.

The dimers and trimers formed by imidazole (IM) and F₂TO (T = C, Si, Ge) are studied by ab initio calculations. IM can engage in either a NH⋯O H-bond with F₂TO or a T⋯N tetrel bond (TB) with the π-hole above the T atom. The latter is a true noncovalent TB for T = C but is a much shorter and stronger covalent bond with F₂SiO or F₂GeO. When a second IM is added, the cooperativity emerging from its H-bond with the first IM makes it a stronger nucleophile, leading to two minima with F₂CO. The first structure contains a long noncovalent C⋯O TB and there is a much shorter covalent bond in the other, with a small energy barrier separating them. The same sort of double minimum occurs when the two IM units are situated parallel to one another in a stacked geometry.

Bacterial DNA phosphorothioate (PT) modification provides a specific anchoring site for sulfur-binding proteins (SBDs). Besides, their recognition patterns include phosphate links and bases neighboring the PT-modified site, thereby bringing about genome sequence-dependent properties in PT-related epigenetics. Here, we analyze the contributions of the DNA backbone (phosphates and deoxyribose) and bases bound with two SBD proteins in Streptomyces pristinaespiralis and coelicolor (SBDSco and SBDSpr). The chalcogen–hydrophobic interactions remained constantly at the anchoring site while the adjacent bases formed conditional and distinctive non-covalent interactions. More importantly, SBD/PT–DNA interactions were not limited within the traditional “4-bp core” range from 5′-I to 3′-III but extended to upstream 5′-II and 5′-III bases and even 5′′-I to 5′′-III at the non-PT-modified complementary strand. From the epigenetic viewpoint, bases 3′-II, 5′′-I, and 5′′-III of SBDSpr and 3′-II, 5′′-II, and 5′′-III of SBDSco present remarkable differentiations in the molecular recognitions. From the protein viewpoint, H102 in SBDSpr and R191 in SBDSco contribute significantly while proline residues at the PT-bound site are strictly conserved for the PT-chalcogen bond. The mutual and make-up mutations are proposed to alter the SBD/PT–DNA recognition pattern, besides additional chiral phosphorothioate modifications on phosphates 5′-II, 5′-II, 3′-I, and 3′-II.

The molecular mechanism of a Cu-catalysed coupling reaction was theoretically studied using density functional theory (DFT) and the complete active space self-consistent field method followed by the second-order perturbation theory (CASSCF/CASPT2) to investigate the effects of the strong electron correlation of the Cu centre on the reaction profile. Both DFT and CASSCF/CASPT2 calculations showed that the catalytic cycle proceeds via an oxidative addition (OA) reaction, followed by a reductive elimination (RE) reaction, where OA is the rate-determining step. Although the DFT-calculated activation energies of the OA and RE steps are highly dependent on the choice of functionals, the CASSCF/CASPT2 results are less affected by the choice of DFT-optimised geometries. Therefore, with a careful assessment based on the CASSCF/CASPT2 single-point energy evaluation, an optimal choice of the DFT geometry is of good qualitative use for energetics at the CASPT2 level of theory. Based on the changes in the electron populations of the 3d orbitals during the OA and RE steps, the characteristic features of the DFT-calculated electronic structure were qualitatively consistent with those calculated using the CASSCF method. Further electronic structure analysis by the natural orbital occupancy of the CASSCF wavefunction showed that the ground state is almost single-reference in this system and the strong electron correlation effect of the Cu centre can be dealt with using the MP2 or CCSD method, too. However, the slightly smaller occupation numbers of the 3dπ orbital in the course of reactions suggested that the electron correlation effect of the Cu(III) centre appears through the interaction between the 3dπ orbital and the C–I antibonding σ* orbital in the OA step, and between the 3dπ orbital and the Cu–C antibonding σ* orbital in the RE step.

Understanding the physical origin of materials exhibiting different properties at the mesoscale is of great significance for the design and fabrication of multifunctional quantum devices. In this work, we proposed a simple model without any adjustable parameters to describe the size (D) dependence of Debye temperature Θ_D(D) of metallic nanocrystals. Θ_D(D) drops with the decrease of D, which is verified by relevant experimental and simulation results. In addition, we found that the difference in the size dependence of Θ_D(D) of different metal elements is determined by the ratio of the solid/liquid interface energy γ_sl and surface stress f, and the smaller the D of the nanocrystals, the greater the influence of γ_sl/f on Θ_D(D)/Θ_D.

The understanding of interfacial phenomena between H₂ and geofluids is of great importance for underground H₂ storage, but requires further study. We report the first investigation on the three-phase fluid mixture containing H₂, H₂O, and n-C₁₀H₂₂. Molecular dynamics simulation and PC-SAFT density gradient theory are employed to estimate the interfacial properties under various conditions (temperature ranges from 298 to 373 K and pressure is up to around 100 MPa). Our results demonstrate that interfacial tensions (IFTs) of the H₂–H₂O interface in the H₂ + H₂O + C₁₀H₂₂ three-phase mixture are smaller than IFTs in the H₂ + H₂O two-phase mixture. This decrement of IFT can be attributed to C₁₀H₂₂ adsorption in the interface. Importantly, H₂ accumulates in the H₂O–C₁₀H₂₂ interface in the three-phase systems, which leads to weaker increments of IFT with increasing pressure compared to IFTs in the water + C₁₀H₂₂ two-phase mixture. In addition, the IFTs of the H₂–C₁₀H₂₂ interface are hardly influenced by H₂O due to the limited amount of H₂O dissolved in nonaqueous phases. Nevertheless, positive surface excesses of H₂O are seen in the H₂–C₁₀H₂₂ interfacial region. Furthermore, the values of the spreading coefficient are mostly negative revealing the presence of the three-phase contact for the H₂ + H₂O + C₁₀H₂₂ mixture under studied conditions.

The radiation- and chemically-induced radicals from tributyl phosphate (TBP) have been characterized by EPR spectroscopy and theoretical calculations. The yield of X-ray-generated TBP radicals measured by a PBN spin trap is 0.22 μmol J⁻¹ (2.1 radicals/100 eV) at room temperature (298 K). The EPR spectra obtained by irradiating TBP with an electron beam at 77 K are in close agreement with literature data for samples irradiated with gamma- and X-rays [https://doi.org/10.1007/BF02165504, https://doi.org/10.1016/1359-0197(89)90319-6]. Possible conformers of alkyl-type, TBP-derived radicals were analyzed by Density Functional Theory calculations. The main contribution to the experimental spectrum at 77 K is shown to be made by a conformer of the CH₃˙CHCH₂-radical, which contains all carbon atoms of the butyl group in the same plane. The EPR spectra of TBP radicals induced by the OH radical in aqueous solution were measured for the first time using a continuous flow system. The formation of the alkyl-type TBP radicals CH₃˙CHCH₂-, ˙CH₂CH₂-, and -CH₂˙CHO- in the ratio of 5/4/1 was detected; their spectral assignment was based on quantum chemical calculations with rotational averaging of HFC constants for the corresponding beta- and alpha-protons.

Lithium-ion batteries (LIBs) remain irreplaceable for clean energy storage applications. The intrinsic metallic nature of penta-SiCN ensures its promising application in the electrodes of LIBs. Using first-principles calculations, we evaluate the performance of the intrinsic metallic penta-SiCN monolayer as the anode material for LIBs. Penta-SiCN exhibits a low diffusion energy barrier (0.107 eV) for Li atom migration on Si₁₈C₁₈N₁₈, while the diffusion energy barrier for vacancy migration on Li₁₇Si₁₈C₁₈N₁₈ is only 0.006 eV. Additionally, penta-SiCN possesses a high theoretical capacity of 1485.98 mA h g⁻¹, average open-circuit voltage of 0.97 V, and small volume expansion of 1%. Remarkably, penta-SiCN exhibits robust wettability towards the electrolytes (solvent molecules and metal salts) widely used in commercial LIBs, indicating the excellent compatibility in electrode applications. These intriguing theoretical findings make penta-SiCN a high performance anode material for LIBs.

Using time-dependent density functional theory calculations, we have investigated the generation of hot carriers (HCs) in a system comprising a pyridine molecule and a tetrahedral Au₂₀ plasmonic cluster. Our findings indicate that the decay of the localized surface plasmon resonance (LSPR) induced in the pyridine@Au₂₀ system by a laser pulse facilitates the direct transfer of hot electrons from the occupied states of the Au₂₀ cluster to the unoccupied molecular orbitals of pyridine. Notably, we have identified that the interparticle gap distance between the Au₂₀ cluster and the pyridine molecule plays a critical role in controlling the generation of HCs. By precisely controlling the interaction between the plasmonic cluster and the molecule, we can effectively manipulate the energy distribution of the generated HCs. These insights have the potential to drive advancements in the development of more efficient systems for plasmonic catalysis.