The Journal of Physical Chemistry A最新文献

Transition paths refer to rare events in physics, chemistry, and biology where the molecules cross barriers separating stable molecular conformations. The conventional analysis of the transition path times employs a diffusive and memoryless transition over a smooth potential barrier. However, it is widely acknowledged that the free energy profile between two minima in biomolecular processes is inherently not smooth. In this article, we discuss a theoretical model with a parabolic rough potential barrier and obtain analytical results of the transition path distribution and mean transition path times by incorporating absorbing boundary conditions across the boundaries under the driving of Gaussian white noise. Further, the influence of anomalous dynamics in rough potential driven by a power-law memory kernel is analyzed by deriving a time-dependent scaled diffusion coefficient that coarse-grains the effects of roughness, and the system's dynamics is reduced to a scaled diffusion on a smooth potential. Our theoretical results are tested and validated against numerical simulations. The findings of our study show the influence of the boundary conditions, barrier height, barrier roughness, and memory effect on the transition path time distributions in a rough potential, and the validity of the scaling diffusion coefficient has been discussed.

When trying to reach convergence of quantum chemical calculations toward the complete basis set limit, crystalline solids generally prove to be more challenging than molecules. This is due both to the closer packing of atoms─hence, to linear dependencies─and to the problematic behavior of Ewald techniques used for dealing with the infinite character of Coulomb sums. Thus, a dual basis set approach is even more desirable for periodic systems than for molecules. In such an approach, the self-consistent procedure is implemented in a small basis set, and the effect of the enlargement of the basis set is estimated a posteriori. In this paper, we extend to crystalline solids our previous coupled perturbed dual basis set approach [J. Chem. Theory Comput. 2020, 16, 1, 340-353] in which the basis set enlargement is treated as a perturbation. Among the notable features of this approach are (i) the possibility of obtaining not only a correction to the energy but also to energy bands and electron density; (ii) the absence of a diagonalization step for the full Fock matrix in the large basis set; and (iii) the possibility of extrapolating low order perturbation energy corrections to infinite order. We also present here the first periodic implementation of the dual basis set method of Liang and Head-Gordon [J. Phys. Chem. A 2004, 108, 3206-3210]. The effectiveness of both approaches is, then, compared on a small, but representative, set of solids.

The electrification of chemical processes using plasma generates an increasing demand for sensors, monitoring concentrations of plasma-activated species such as radicals. Radical probes are a low-cost in situ method for spatially resolved quantification of the radical density in a plasma afterglow using the heat from the exothermal recombination of radicals on a catalytic surface. However, distinguishing recombination heating from other heat fluxes in the system is challenging. In this study, we present a heat flux analysis based on probe measurements inside the reactor, with simultaneous IR imaging monitoring of the temperature of the reactor wall. The impact of radiation heat on a single thermocouple as well as the advantage of a dual thermocouple setup (using a catalytic unit together with a reference thermocouple) is shown. We add a heat sink with a monitored temperature to the dual thermocouple setup, allowing the determination of conductive and radiative heat fluxes. The heat sink gives more information on the measurement and reduces ambiguities in the evaluation used by others. The probe was tested by mapping N atom densities throughout the plasma afterglow of our reactor, enabling evaluation of the recombination kinetics of the radicals in the gas phase. Three-body recombination was shown to be the main pathway of recombination, with a recombination rate of k_rec = (2.0 ± 0.9)·10^-44 m⁶/s, which is in line with the known literature findings, demonstrating that the measured species are N radicals and the probe did not influence the plasma or recombination reactions in the afterglow.

I and Br atoms are placed on opposite ends of a n-butyl group, with each allowed to form a halogen bond (XB) with NH₃. DFT calculations show that the intrinsic preference of the nucleophile for the heavier I over Br can be reversed by the proper placement of substituents on the alkyl chain. A similar reversal occurs for NH₂ and OH groups on the alkyl chain, where substituents make the O a better electron donor than N in an XB to an electrophilic ICCH. The highly mobile π-electron cloud of an aromatic ring makes such reversals much more difficult when the pair of competing atoms are placed on, or within, such a ring.

We report the structures, energetics, many-body effects, and vibrational spectra of water clusters stabilizing pairs of halide-anions, X^-(H₂O)_kY^- (k = 2-6, X/Y = F, Cl, Br, I) as well as their stability in the gas phase relative to fragmentation. We find that these metastable cluster structures mimicking the solvent-separated ion pair (SSIP) configurations in aqueous solutions are less stable relative to fragmentation into smaller ionic aqueous clusters containing a single halide anion. The many-body expansion (MBE) at these geometries was found to converge at the 4-body term, which is, however, significant, amounting to >20% of the total binding energy in several instances. The binding motif of these ion pair aqueous clusters starts as networks in which the water molecules form a "bridge" between the two halide-anions. As the cluster grows, these structures become destabilized by a more repulsive 3-body term for distances R(O-O) < 3.45 Å with respect to networks in which water molecules move outside the bridge, solvating the other side of the anion.

π-π interactions decisively shape the supramolecular structure and functionality of π-conjugated molecular semiconductor materials. Despite the customizable molecular building blocks, predicting their supramolecular structure remains a challenge. Traditionally, force field methods have been used due to the complexity of these structures, but advances in computational power have enabled ab initio approaches such as density functional theory (DFT). DFT is particularly suitable for finding energetically favorable structures of dye aggregates, which are determined by a large number of different interactions, but a systematic aggregate search can still be very challenging due to the large number of possible geometries. In this work, we show ways to overcome this challenge. We investigate how finely translational and rotational lattices must be structured to identify all energetic minima of π-stack structures, focusing on porphyrins as a prototype challenge. Our approach involves single-point DFT calculations of systematically varied dimer geometries, identification of local energy minima, hierarchical grouping of geometrically similar structures, and optimization of the energetically favorable representatives of each geometric family. This ab initio method provides a general framework for the systematic prediction of aggregate structures and reveals geometrically diverse and energetically favorable dimers.

Photochemical aging and photooxidation of atmospheric particles play a crucial role in both the chemical and physical processes occurring in the troposphere. In particular, the presence of organic chromophores within atmospheric aerosols can trigger photosensitized oxidation that drives the atmospheric processes in these interfaces. However, the light-induced oxidation of the surface of atmospheric aerosols, especially those enriched with organic components, remains poorly understood. Herein, we present a gravimetric and vibrational spectroscopy study aimed to investigate the photosensitized oxidation of nonanoic acid (NA), a model system of fatty acids within organic aerosols, in the presence of complex organic photosensitizers and molecular proxies. Specifically, this study shows a comparative analysis of the photosensitized reactions of thin films containing nonanoic acid and four different organic photosensitizers, namely marine dissolved organic matter (m-DOM) and humic acids (HA) as environmental photosensitizers, and 4-imidazolecarboxaldehyde (4IC) and 4-benzoylbenzoic acid (4BBA) as molecular proxies. All reactions show predominant photooxidation of nonanoic acid, with important differences in the rate and yield of product formation depending on the photosensitizer. Limited changes were observed in the organic photosensitizer itself. Results show that, among the photosensitizers examined, 4BBA is the most effective in photooxidizing nonanoic acid. Overall, this work underscores the role of chromophores in the photooxidation of organic thin films and the relevance of such reactions on the surface of aerosols in the marine environment.

We adapt our recently developed constraint-based orbital-optimized excited-state method (COOX) for the computation of core excitations. COOX is a constrained density functional theory (cDFT) approach based on excitation amplitudes from linear-response time-dependent DFT (LR-TDDFT), and has been shown to provide accurate excitation energies and excited-state properties for valence excitations within a spin-restricted formalism. To extend COOX to core-excited states, we introduce a spin-unrestricted variant which allows us to obtain orbital-optimized core excitations with a single constraint. Using a triplet purification scheme in combination with the constrained unrestricted Hartree–Fock formalism, scalar-relativistic zero-order regular approximation corrections, and a semiempirical treatment of spin–orbit coupling, COOX is shown to produce highly accurate results for K- and L-edge excitations of second- and third-period atoms with subelectronvolt errors despite being based on LR-TDDFT, for which core excitations pose a well-known challenge. L- and M-edge excitations of heavier atoms up to uranium are also computationally feasible and numerically stable, but may require more advanced treatment of relativistic effects. Furthermore, COOX is shown to perform on par with or better than the popular ΔSCF approach while exhibiting more robust convergence, highlighting it as a promising tool for inexpensive and accurate simulations of X-ray absorption spectra.

The nature of the Ni–S bond is investigated due to its role in the absorption of atmospheric Lewis acid gases such as SO₂ and SO₃ onto Ni surfaces. The vibrational frequency and electronic structure of NiS were predicted using CCSD(T), CASSCF, and internally contracted multireference configuration interaction (icMRCI) + Q. 43 density functional theory (DFT) functionals were benchmarked. CASSCF predicted the ground state of NiS to be the ⁵Δ state arising from the 3d⁸(³F)4s² (³F) and 3d⁹(²D)4s (³D) electronic configurations of Ni. When dynamical correlation effects are included at the icMRCI + Q level, the ground state of Ni–S is predicted to be ³Σ^– consistent with the experiment. The vibrational frequency of Ni–S is calculated to be 519.1 cm^–1 at the icMRCI + Q level, in reasonable agreement with the experimental value of 512.68 cm^–1. CCSD(T) predicts the frequency of Ni–S to be 543.2 cm^–1 when extrapolated to the complete basis set (CBS) limit. The Feller–Peterson–Dixon value based on the CCSD(T)/CBS extrapolation for the bond dissociation energy of NiS is 350.6 kJ/mol, within <4 kJ/mol of experiment. Of the 43 DFT functionals, BP86 and O3LYP predicted the vibrational frequency in closest agreement with the experiment. The applicability of DFT to such acid gas systems was further demonstrated by calculating the energy for displacement of NiO by SO to yield NiS and O₂. This displacement energy was calculated to be within experimental error for ∼50% of the DFT functionals, but large differences were also predicted for some functionals.

The accurate potential energy functions of beryllium monofluoride, BeF, and its anion, BeF^–, have been determined from ab initio calculations using the coupled-cluster approach, up to the CCSDTQP level of approximation, in conjunction with the augmented correlation-consistent core–valence basis sets, aug-cc-pCVnZ, up to septuple-zeta quality. The vibration–rotation energy levels of the two species were predicted to near the “spectroscopic” accuracy. Changes in the electron density distribution upon formation of the Be–F chemical bond are discussed.