Chemphyschem最新文献

Accurate and efficient prediction of high energy ligand conformations is important in structure-based drug discovery for the exclusion of unrealistic structures in docking-based virtual screening and de novo design approaches. In this work, we constructed a database of 140 solution conformers from 20 druglike molecules of varying size and chemical complexity, with energetics evaluated at the DLPNO-CCSD(T)/complete basis set (CBS) level. We then assessed a selection of machine learning potentials and semiempirical quantum mechanical models for their ability to predict conformational energetics. The GFN2-xTB tight binding density functional method correlates with reference conformer energies, yielding a Kendall's τ of 0.63 and mean absolute error of 2.2 kcal/mol. As putative internal energy filters for screening, we find that the GFN2-xTB, ANI-2x and MACE-OFF23(L) models perform well in identifying low energy conformer geometries, with sensitivities of 95 %, 89 % and 95 % respectively, but display a reduced ability to exclude high energy conformers, with respective specificities of 80 %, 61 % and 63 %. The GFN2-xTB method therefore exhibited the best overall performance and appears currently the most suitable of the three methods to act as an internal energy filter for integration into drug discovery workflows. Enrichment of high energy conformers in the training of machine learning potentials could improve their performance as conformational filters.

The phenomena of bond alternation and bond equalisation in conjugated hydrocarbons are studied using dynamic orbital forces (DOF) which provide an index of intrinsic CC binding, with its sigma and pi components. Some linear polyenes, polyynes and cumulenes have been analysed. Dealing with linear polyenes and polyynes, it is shown that sigma bonds can be considered as weak "inverted" ones in formally multiple bonds and strong "superdirect" ones in formally single ones. This alternance in sigma bonding partly compensates and, in some cases, overcome the alternance in pi binding. Moreover, it was shown from a panel of seven aromatic annulenes and allyl compounds that the bond equalization is favoured by sigma bonding. It can be unfavoured or favoured by the pi binding according to the system and the nature of its deformation into a bond alternant structure.

Polyoligomeric silsesquioxane (POSS) tailored with trifluoromethanesulfonylimide-lithium and solvated in tetraglyme (G4) is a potential electrolyte for Li-ion batteries. Using classical MD simulations, at different G4/POSS(-LiNSO2CF3)8 molar ratios, the interactions of Li+ ions with the oxygen atoms of G4 and, oxygen/nitrogen sites of the pendant tails, the behavior of POSS(--NSO2CF3)8 anion, and the mobility of species are investigated. The RDFs showed that there exist competing interactions of the O(G4), O(POSS), and N(POSS) sites with Li+ ions. The lifetime analysis indicated that Li+---O(POSS) and Li+--- N(POSS) interactions are longer-lived compared to Li+---O(G4). The morphology changes of the POSS tails upon interaction with Li+ ions were analyzed using rotational lifetimes, coiling, and end-to-end distances. The ion-speciation analysis indicated the presence of solvent-separated ion pairs (SSIPs), contact ion pairs (CIPs), and higher-order ion clusters, with SSIPs being the more dominant species at 32/1. The self-diffusion coefficients for the 32/1 system, which showed the least cation-anion interaction, followed the trend: [[EQUATION]] > [[EQUATION]] > [[EQUATION]] > [[EQUATION]]. The computed cationic transference number (t+) using the [[EQUATION]] is consistent with NMR experimental data. The t+ (and the trends with temperature) computed using the [[EQUATION]] and ionic conductivities are in good agreement.

Spherical nucleic acids (SNAs), with their densely packed nucleic acid shells and programmable functionalities, have become indispensable in nanomedicine and biosensing. Developed synthesis methods, including salt aging, pH modulation, freeze-thaw cycling, n-butanol dehydration, evaporation drying, and microwave heating, have enabled foundational advances but are constrained by slow kinetics, compromised structural uniformity and especially harsh reaction conditions, making them unsuitable for in situ tracking of biological events. This concept article introduces acoustic levitation synthesis as a groundbreaking alternative, uniquely addressing these limitations through a rapid, green, and highly controllable process. By leveraging non-contact acoustic radiation forces, this method enables the synthesis of ultrahigh-density SNAs within minutes under ambient conditions, eliminating the need for toxic reagents or energy-intensive steps. The resulting SNAs exhibit superior homogeneity and stability compared to conventional approaches. We critically evaluate the conceptual novelty and limitations of this technique. Potential applications in surface-enhanced Raman spectroscopy (SERS) and targeted therapeutics are highlighted, positioning acoustic levitation as a transformative tool for next-generation nanobiotechnology.

The adsorption of CO2 in MOF-808, NU-1000 and a series of rare-earth CU-10 analogues has been studied with first principles DFT and classical Monte-Carlo methods. DFT calculations describe the interaction of CO2 with the different metal-organic frameworks (MOFs) as physisorption, but where we can distinguish several adsorption sites in the vicinity of the metal nodes. Beyond the identification of adsorption sites, the MOFs were synthesized, activated, and characterized to evaluate their experimental N2 and CO2 adsorption capacity. Classical Grand Canonical Monte-Carlo (GCMC) simulations for the adsorption of CO2 are in very good agreement with DFT results for identifying the most favored adsorption sites in the MOFs. In contrast, a rather mixed agreement between GCMC simulations and experimental results is found for the estimation of adsorption capacity {of several MOFs studied toward N2 and CO2.

Supported catalytically active liquid metal solutions (SCALMS) are materials composed of a liquid metal alloy deposited on a porous support. Due to the dynamic properties of the liquid metal alloy, these systems are suggested to form single atom sites, resulting in unique catalytic properties. Ga-Ni SCALMS were successfully applied to ethylene oligomerization, yielding catalysts that were stable up to 120 h time on stream. A workflow based on synchrotron-based X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) as well as density function theory (DFT) and ab initio molecular dynamics (AIMD) simulations was applied to investigate the nature of the active species in these materials. The combination of XPS with DFT calculations indeed indicates the presence of isolated single Ni atoms on the liquid metal surface, while TEM measurements show high dynamics in the liquid metal with intermetallic phase dissolution and transformation. Furthermore, DFT/AIMD methods allowed for rationalizing the role of hydrogen pretreatment in enriching the Ni atom at the surface of the liquid metal alloy.

Using first-principles structure search calculations, we investigated the phase stability of sodium-nitrogen (Na-N) compounds under high pressure. Our study reveals that increasing pressure promotes the formation of Na-rich nitrides, leading to the prediction of three previously unreported stoichiometries: Na₂N, Na₅N, and Na₈N. Notably, the electride Na₅N undergoes a pressure-induced structural transition from a P6/mmm to a P6₃/mmc phase. This transformation is characterized by spatial reorientation and redistribution of interstitial anionic electrons (IAEs). In the P6₃/mmc phase, IAEs adopt a zero-dimensional, triangular-like configuration, whereas in the low-pressure P6/mmm phase, they form an interconnected, graphene-like network. With increasing pressure, P6₃/mmc phase undergoes a transition from metallic to semiconducting behavior due to the increased interaction between sodium and IAEs. Additionally, C2/m Na₈N, featuring triangular- and ship-like IAEs, is predicted to exhibit superconductivity. Our findings provide new insights into the behavior and stability of Na-rich nitrides under high-pressure conditions.

Halogens are usually involved in numerous anticancer drugs and play an important role in anticancer activity. Taking the IMeAuCl, a potent anticancer drug as an example, the substituent effect of superhalogens X@B₁₂N₁₂ (X=F, Cl, and Br) on the structures, electronic properties, and chemical reactivity with biomolecular targets of this metallodrug has been investigated. Substituting X@B₁₂N₁₂ for the Cl atom of IMeAuCl results in polar covalent bonds between Au and N atoms in the resulting Au-X (X=F, Cl, and Br) derivatives. The introduction of superhalogens enhances the polarity and solubility of Au-X, which enables them to directly react with biological target molecules without undergoing hydrolysis. In particular, it is found that the higher electron affinity (EA) of X@B₁₂N₁₂ results in the lower energy barrier of the reaction between Au-X and target molecules, which maybe benefit its high biological activity. With regard to this, another complex Au-BF₄ with better anticancer activity has been also designed by replacing the Cl atom of IMeAuCl with BF₄, a well-known superhalogen with higher EA value than X@B₁₂N₁₂. Thus, this study provides a new strategy to improve the antitumor activity of halogen-containing drugs from a theoretical point of view.

Lithium-oxygen batteries have gained prominence in recent years due to their potential advantages over conventional lithium-ion batteries, including higher energy density, cost-effectiveness and environmental sustainability. To fully exploit these advantages, it is essential to understand the interplay between porous carbon electrode materials and electrolytes in these devices. This study presents a nuclear magnetic resonance investigation of the confined LiTFSI (lithium bis(trifluoromethanesulfonyl)imide) - TEGDME (tetraethylene glycol dimethyl ether) electrolyte within carbonaceous materials with different pore sizes.  Three carbon materials (microporous, mesoporous, and hierarchical) were synthesized from the same precursor to ensure equivalent surface chemistry, which was verified by X-ray photoelectron spectroscopy. The dynamics and distribution of solvent and Li ions in the different pores were studied by 1H and 7Li, 1D and 2D exchange, NMR spectroscopy. It was found that the accessibility of Li+ within the pores of the carbonaceous material depends not only on their size but also on their size distribution. The knowledge gained from this study can contribute to the design of the appropriate pore size distribution, which could optimize the electrolyte utilization and consequently increase the energy density of lithium-oxygen batteries.

We performed an ab initio molecular dynamics study with a nitrogen atom in the 1/2 spin state, which corresponds to an excited electronic state, in contrast to the ground state with 3/2 spin state. This N atom was encapsulated with an H₂ molecule in a C70 fullerene, as a "nanoflask" for experimentation. This approach was initially proposed by Morinaka and colleagues (Angew. Chem. Int. Ed. 2017, 56, 6488-6491), where they demonstrated, using spectroscopy, that the N(⁴S) atom, does not react with the H₂ molecule. By analyzing the trajectory from Car-Parrinello molecular dynamics simulations and performing Density Functional Theory, Quantum Theory of Atoms in Molecules, Reduced Density Gradient and Interaction Region Indicator calculations, we successfully reproduced the experiment observations, examining the interaction between the N atom and the H₂ molecule encapsulated within the fullerene C₇₀.