The Journal of Physical Chemistry A最新文献

We have formulated a Riemannian framework for describing the geometry of collective variable (CV) spaces in molecular simulations and demonstrate its applicability through both toy model potentials and a biomolecular example. This formalism addresses significant theoretical challenges arising from the inherent nonlinearity of CV transformations, ensuring critical quantities such as the potential of mean force (PMF), minimum free energy path (MFEP), and rate constant remain invariant under coordinate transformations. Our framework identifies and addresses the noninvariance issues of conventional PMF definitions, clearly illustrating their limitations through simple illustrative examples. To overcome these issues, we introduce invariant definitions of PMF and MFEP using Riemannian geometry. Moreover, we propose a generalized Riemannian diffusion model applicable to diffusive dynamics within CV spaces, allowing rigorous estimation of kinetic properties. Through this model, we derive practical numerical methods for determining the PMF, diffusion constant, metric tensor, and transition rates from unbiased simulations conducted along identified transition pathways. By integrating Bayesian approaches with the Riemannian framework, our method provides a statistically robust technique for accurately calculating free energy landscapes and transition kinetics, thereby enhancing the reliability and interpretability of biomolecular simulations.

Herein we report on the impact of C3′- and C4′-substitution on the photophysics of the heptamethine cyanine dye (Cy7) using electron-withdrawing (−CN) and donating (−OMe) groups. Frontier orbital analysis predicts that C3′-substitution mainly perturbs the HOMO, while C4′-substitution mainly perturbs the LUMO. Position- and substituent-dependent derivatization should thus enable tuning of the HOMO–LUMO gap, and consequently lead to selective red- or blue-shifting of the S₁ ← S₀ absorption band. Even though absorption spectra shift accordingly, fluorescence lifetimes deviate from simple energy-gap law predictions. However, within each substituent class, the more red-absorbing dye shows the shorter lifetime. Solvatochromic studies on the parent Cy7 dye further show that its fluorescence lifetime is independent of viscosity and is instead quenched by OH-containing solvents via an energy transfer mechanism. Transient absorption measurements covering fs to μs time scales further point to neither significant excited-state isomerization nor triplet formation. Cyclic voltammetry experiments show increasingly reversible reductions for C4′-substituted derivatives, likely due to the suppression of radical–radical dimerization pathways. Overall, these findings provide detailed insight into how solvent effects and regio-specific substitution modulate the photophysics and electrochemistry of Cy7, aiding in the rational design of near-infrared fluorophores.

Hydrogen bonds are fundamental interactions that govern molecular aggregation. Although the O–H···O hydrogen bond is dominant in simple hydroxylic dimers, how this dominance is perturbed by substituents remains a key question. This study investigates the 2-butyn alcohol dimer using pulsed-jet Fourier transform microwave spectroscopy and theoretical calculations to quantitatively assess the impact of an alkynyl substituent on the dominant O–H···O hydrogen bond. The observed isomer is stabilized by a primary −H···O hydrogen bond and secondary O–H···π and C–H···π interactions. Quantum theory of atoms in molecules analysis revealed that the −H···O hydrogen bond energy contributes merely 55.0% to the total dimerization energy─the lowest value observed among a series of hydroxylic dimers, including water, alcohols, and phenols. This systematic comparative analysis reveals that introducing substituents, particularly those with π-systems or elongated alkyl chains, consistently reduces the energetic contribution ratio of the O–H···O hydrogen bond. The 2-butyn alcohol dimer, with its significantly weakened relative energy contribution ratio of the dominant hydrogen bond, approaches a threshold where the dominance of the O–H···O hydrogen bond could be challenged, providing a crucial perspective for understanding hierarchical molecular self-assembly.

The conformational space of N,N-diethyl-2-hydroxyacetamide (DEHyA) was elucidated through an integrated experimental-computational approach combining matrix isolation infrared spectroscopy and density functional theory (DFT) calculations. Quantum chemical analysis revealed 15 distinct conformers, with the CC(g^±g^±) form constituting the global minimum and the closely related CC(g^±g^∓) geometry lying slightly higher in energy. Infrared spectral evidence for these conformers was obtained from the O–H, C=O, and C–O stretching regions in N₂ and Ar matrices at cryogenic temperatures. Both low-energy structures are primarily stabilized by intramolecular hydrogen bonding, further modulated by hyperconjugative and weak tetrel interactions. The relative energetic and electronic contributions of these effects were quantified through Non-Covalent Interaction (NCI), Electrostatic Potential (ESP) mapping, Intrinsic Bond Strength Index (IBSI), and Natural Bond Orbital (NBO) analyses. These results establish hydrogen bonding as the principal stabilizing force, complemented by secondary hyperconjugative and tetrel effects. Targeted orbital deletion studies further demonstrated that charge-transfer electron delocalization governs the conformational preference, underscoring the cooperative nature of noncovalent interactions in defining the structural stability of DEHyA. A comprehensive comparison with the higher homologue, N,N-dioctyl-2-hydroxyacetamide (DOHyA), was undertaken to elucidate whether conformational modulation arises solely from intrinsic electronic factors or is additionally influenced by steric encumbrance imposed by bulky alkyl substituents.

We present elastic and electronically inelastic cross sections for the scattering of low-energy electrons by pyrimidine. The calculations employed the Schwinger multichannel method for impact energies up to 50 eV. The cross sections were computed within the minimal orbital basis for single configuration interactions (MOB-SCI) strategy, considering from 1 to 295 open channels. Our results are compared with theoretical and experimental data available in the literature. Although we found good agreement in the elastic scattering, there are discrepancies between the inelastic cross sections, which are discussed in light of the multichannel coupling. We also estimated the total cross section by summing the elastic, electronically inelastic, and total ionization cross sections, where the latter was obtained using the binary-encounter-Bethe model.

Two-dimensional (2D) topological half-metals (THMs) hold great potential for developing low-dissipation spintronics. Based on the structural derivation strategy inspired by experimentally synthesized quasi-2D kagome metals, we propose a promising 2D intrinsic ferromagnetic THM, the Fe₃SSe₄ monolayer, by first-principles calculations. Specifically, the stable Fe₃SSe₄ monolayer exhibits a robust ferromagnetic ground state with a Curie temperature of 210 K. It exhibits a sizable magnetic anisotropy energy of 3.72 meV per unit cell, significantly higher than that of several reported high-performance magnetic recording materials. Most strikingly, the calculated band structure reveals that the Fe₃SSe₄ system demonstrates coexisting half-metallicity and quantum anomalous Hall effect, characterized by a Chern number of C = 1. Furthermore, the Weyl cone is located very close to the Fermi level and is classified as type-I along the corresponding k path. The maximum Fermi velocity of 5.75 × 10⁵ m/s is higher than those of the 2D THMs reported to date. Our work would open up new opportunities for the design of other THMs.

In our recent work (D’haese, L. C. G.; et al., Spectrochim. Acta, Part A 2024, 306, 123484), we have studied the cryptophane-111 system and observed a peculiar behavior on the relative energies of its conformers, induced by the addition of empirical dispersion corrections to our original method, B3LYP. Then, we have decided to deeply investigate the addition of different corrections to B3LYP, namely, the empirical dispersion corrections and the long-range corrections. We have observed systematic behaviors while increasing the amount of constant Hartree–Fock (HF) exchange, increasing the final amount of HF exchange, and increasing the coefficient ω. However, some changes have opposite effects on the conformations and normal modes. Thanks to these observations, we have identified two specific regions where the increase of the HF exchange has different impacts, namely, the short-range interatomic distance and the long-range interatomic distance. Concerning the normal modes, we have noticed interesting results while adding the empirical dispersion corrections, even though they lead to poor Boltzmann weights.

The photophysical properties of six disubstituted 2-(2′-hydroxyphenyl)-benzothiazole (HBT) derivatives (diHBT1–6) are systematically investigated using density functional theory (DFT) and TD-DFT with the CAM-B3LYP/TZVP and B3LYP/TZVP levels and RI-CC2/def2-TZVP level. Ground- and excited-state geometries, vertical excitation and emission energies, frontier molecular orbitals, hole–electron distributions, and potential energy curves along the excited-state intramolecular proton transfer (ESIPT) coordinate are analyzed to elucidate the interplay between substituent positioning, intramolecular charge transfer (CT), and excited-state intramolecular proton transfer (ESIPT) behavior. We reveal a previously unrecognized structure–property relationship: emission wavelength and ESIPT barrier are inversely tunable through substituent topology. Specifically, meta-electron-withdrawing group(meta-EWG)/para-electron-donating group(para-EDG) configurations (diHBT3 and diHBT6) maximize CT character, yielding the longest emission wavelengths, while simultaneously elevating the forward ESIPT barrier to >4.5 kcal/mol. In contrast, ortho-EWG/para-EDG isomers (diHBT2 and diHBT5) preserve locally excited (LE) character and exhibit ultralow ESIPT barriers (<0.7 kcal/mol) at the cost of blue-shifted emission. This decoupling of spectral tuning from proton transfer energy landscape, governed by the spatial alignment of donor and acceptor moieties, establishes a generalizable design paradigm for HBT-based fluorophores. Our findings provide a rigorous theoretical framework for rationally engineering emission color and ESIPT behavior independently, enabling precise optimization of fluorescent probes for bioimaging and optoelectronic applications.

Trifluoroacetic acid (TFA), the most atmospherically abundant perfluorocarbocylic acid, is a molecule of increasing environmental and biological significance. In this paper, we examine TFA’s role in new particle formation (NPF), a critical yet lesser-understood step in cloud formation in which aerosols that act as cloud condensation nuclei are formed. We used conformational sampling to find low-energy structures for TFA-nH₂O (n = 1–8) clusters and determined accurate DLPNO–CCSD(T)/haug-cc-pV5Z//ωB97X-D/6–31++G** enthalpies at 0 K and Gibbs free energies at 216.65, 273.15, and 298.15 K. Then, atmospheric concentrations were determined at relevant atmospheric temperatures. Rotational constants for the lowest energy n = 1–3 structures corroborate existing microwave spectroscopic data, validating our methodology. Additionally, spectroscopic properties for n = 4–8 structures were identified for comparison with future experimental findings. All lowest energy structures were found to have neutral, rather than ion-pair monomers. Near Earth's surface, we predict significant concentrations of n = 1–2 clusters (2.06 × 10⁵ molecules cm^–3 and 1.13 × 10⁴, respectively); however, the absence of larger clusters indicates that TFA likely serves a negligible role in NPF.

Resonant two-color two-photon excitation of p-xylene with a total energy of 8.33 eV, below its adiabatic ionization energy of 8.45 eV, in the p-xylene•••trimethylamine (PX•••TMA) cluster results in ionization of TMA due to the outer-valence Intermolecular Coulombic Decay (ICD) mechanism. The dynamics of the PX•••TMA cluster cation, created due to the ICD process, results in fragmentation of the cluster with the appearance of the TMA cation, whose translational energy was measured using the velocity-mapped imaging method. The Born–Oppenheimer molecular dynamics (BOMD) simulations establish that the translational energy distribution profile of the TMA cation originates primarily from the {Ar}C–H•••N hydrogen-bonded structure in the neutral ground electronic state of the PX•••TMA cluster. It is also demonstrated that the translational energy distribution profile of the fragment cation, following ICD, can be exploited to differentiate the structures of the binary complexes.