The Journal of Physical Chemistry A最新文献

We have studied the electronic and optical properties of three low-symmetry graphene quantum dots (GQDs), with point-group symmetries C_2v and C_2h. For the calculations of linear optical absorption spectra, we employed both first-principles time-dependent density-functional theory (TDDFT) and the electron-correlated Pariser-Parr-Pople (PPP) model coupled with the configuration-interaction (CI) approach. In the PPP-CI approach, calculations were performed using both screened and standard parameters, along with efficiently incorporating electron correlation effects using multireference singles-doubles CI for both ground and excited states. We assume that the GQDs are saturated by hydrogen atoms at the edges, making them effectively polycyclic aromatic hydrocarbons (PAHs) dibenzo[bc,ef]coronene (also known as benzo(1,14)bisanthene, C₃₀H₁₄) and two isomeric compounds, dinaphtho[8,1,2abc;2',1',8'klm]coronene and dinaphtho[8,1,2abc;2',1',8'jkl]coronene with the chemical formula C₃₆H₁₆. The two isomers have different point group symmetries; therefore, this study will also help us understand the influence of symmetry on the optical properties. A common feature of the absorption spectra of the three GQDs is that the first peak representing the optical gap is of low to moderate intensity, while the intense peaks appear at higher energies. For each GQD, PPP model calculations performed with the screened parameters agree well with the experimental results of the corresponding PAH and also with the TDDFT calculations. To further quantify the influence of electron-correlation effects, we also computed the singlet-triplet gap (spin gap) of the three GQDs, and we found them to be significant.

Polymer mechanochemistry induces chemical reactivity by applying a directed force, which can lead to unexpected reaction mechanisms. Strained cyclic molecules are often used in force-sensitive motifs because of the strong force coupling of ring-opening reactions. In this computational study, the force dependence of the ring-opening reactions of oxirane will be investigated. Density functional theory and multireference methods were used to investigate the electronic character of both symmetry-allowed and symmetry-forbidden reactions. In the latter case, an orbital crossing occurs during the reaction course, forcing the Woodward-Hoffmann-forbidden reaction to proceed via a diradical pathway. The performance of broken-symmetry density functional theory is evaluated and compares well to high-accuracy CASPT2, MRCI, and ic-MRCC computations. Due to the high ring strain, the barrier heights of both ring-opening reactions are steeply reduced by the application of an external force. Furthermore, the use of unsaturated linkers was shown to yield a significant reduction of the barrier heights, explaining previous experimental findings. Finally, we show through analysis of the PES topology how the external force transforms characteristic points such as saddle points and bifurcations, providing insights into force-dependent mechanism changes.

In quantum chemistry, single-reference Coupled Cluster theory, and its refinements introduced by Bartlett, has become a "gold-standard" predictive method for taking into account electronic correlations in molecules. In this article, we introduce a new formalism based on a Coupled Cluster expansion of the wave function that is suited to describe model periodic systems and apply this methodology to the case of hole-doped antiferromagnetic two-dimensional (2D)-square spin-lattices as a proof of concept. More precisely, we focus our study on 1/5 and 1/7 doping ratios and discuss the possible ordering effect due to large hole-hole repulsion. Starting from one of the equivalent single determinants exhibiting a full spin alternation and the most remote location of the holes as a single reference, the method incorporates some corrections to the traditional Coupled Cluster formalism to take into account the nonadditivity of excitation energies to multiply excited determinants. The amplitudes of the excitations, which are possible on the excited determinants but impossible on the reference, are evaluated perturbatively, while their effect is treated as a dressing in the basic equations. The expansion does not show any sign of divergence of the wave operator. Finally, the probabilities of holes moving toward the first- and second-neighboring sites are reported, which confirms the importance of the hole-hole repulsion and offers a picture of how stripes expand around its central line in the "stripe phases" observed in cuprates.

The closed-shell Hückel-London-Pople-McWeeny formalism for ring currents is extended to Aufbau configurations with open shells calculated as configurational averages. The method is applied to the non-Kekulean benzenoid known as the Clar goblet, recently synthesized on the Au(111) surface. Multiplicity of the ground state is a complication: for the Clar goblet, Hund's rule of maximum multiplicity implies a triplet whereas Ovchinnikov's rule implies a singlet. This disagreement has little effect on the predicted ring currents. Ring-current maps are calculated for the 36π dication, 40π dianion, and low-lying states of the 38π neutral, using Hückel-London and Hubbard-London models. All show twin diatropic perimeter currents on separate halves of the molecule. These are compared with ipsocentric pseudo-π and ab initio maps of induced π-current for closed-shell singlet configurations of dianion, dication, and neutral. Configurationally averaged Hückel-London calculations give a good account of the consistent diatropic ring currents in the Clar goblet for the three charge states.

The pK_a's of acids are known to depend on the ionic strength of an electrolyte solution, an effect that qualitatively results from electrostatic interactions of the acid and conjugate base with proximal ions. Here, we explore an intramolecular variation on this theme in which a carboxylic acid group is tethered to a pyridinium cationic charge center with increasingly long alkyl linkages in the series Py⁺-(CH₂)_n-COOH, with n = 1-7. The effective acidities of the carboxylic acid group in the isolated cations are determined by recording the red-shifts in the frequencies of the acid OH stretches upon attachment to D₂ and N₂ molecules, measured by using cryogenic ion spectroscopy. The short chains indeed lead to substantial increases in acidity, with the effect falling off in the range of n = 4-5. The response of the CO stretch on the acid head group is surprisingly strong and, in contrast to the expected red shift of the OH, displays a blue shift as the chain length is reduced. Electronic structure calculations recover these trends and indicate that the proximal cationic charge center acts to draw electron density away from the acid C═O bond. This acts to blue-shift the CO stretch while weakening the C-C bond that attaches the head group to the chain.

One of the most important areas of application for equation-of-motion coupled-cluster (EOM-CC) theory is the prediction, simulation, and analysis of various types of electronic spectra. In this work, the EOM-CC method for ionized states, known as EOM-IP-CC, is applied to the closely lying and coupled pair of states of the ozone cation─X̃²A₁ and òB₂─using highly accurate treatments including up to the full single, double, triple, and quadruple excitations (EOM-IP-CCSDTQ). Combined with a venerable and powerful method for calculating vibronic spectra from the Hamiltonian produced by EOM-IP-CC calculations, the simulations yield a spectrum that is in good agreement with the photoelectron spectrum of ozone. Importantly, the calculations suggest that the adiabatic gap separating these two electronic states is somewhat smaller than currently thought; an assignment of the simulated spectrum together with more precise band positions of the experimental measurements suggests T₀₀ = 1,368 ± 65 cm^-1.

Tuning the polarity of charge carriers is essential for designing molecular logic devices in molecular electronics. In this study, the electrical transport properties of a family of azaindole-anchored single-molecule junctions have been investigated using density functional theory combined with the nonequilibrium Green's function method. The obtained results reveal that dehydrogenation is an effective method for reversing the polarity of charge carriers. The molecular junctions based on the entire azaindole unit are n-type and contain electrons as the principal charge carriers, whereas the dehydrogenated junctions are p-type and contain holes as the main carriers. Furthermore, the azaindole anchors undergo a transition from an electron-rich to an electron-deficient state due to dehydrogenation, which is the original cause of the charge carrier polarity conversion. Dehydrogenated molecular junctions also exhibit the Fermi pinning effect and a sharp highest occupied molecular orbital (HOMO) resonance peak at the Fermi level. In addition, using Pt electrodes instead of Au electrodes is a means of producing a HOMO resonance peak a for azaindole-based molecular junctions. This work demonstrates the enormous potential of utilizing azaindole-anchored molecular junctions for the implementation of molecular logic and multifunctional molecular devices.

Gas-phase reactions of [OsB_x]⁺ (x = 1-4) with methane at ambient temperature have been studied by using quadrupole-ion trap mass spectrometry combined with quantum chemical calculations. The [OsB_x]⁺ (x = 1-4) cluster ions can undergo dehydrogenation reactions with methane. Comprehensive analysis of the [OsB_x]⁺/CH₄ (x = 1-4) system with Os-complexes ([OsC_y]⁺ (y = 1-3) and [OsO_z]⁺ (z = 1-3)) shows that the large polarity of the cluster and the high sum of the pair energies between Os and the ligand in the ETS-NOCV combine to promote the ability of the cluster to activate methane. Cluster polarity may induce heterolytic cleavage of the C-H bond, and the sum of the pair energies of the fragments may reduce the cluster orbital energy to match the methane orbital and improve the cluster stability. The synergistic interplay of these two factors may offer a viable approach for the activation of methane in the condensed phase, which involves modulating the coordination environment of the active sites to enhance the stability and facilitate C-H bond cleavage and the degree of matching with methane orbitals. A nonlinear function is used to extract second-order characteristic features that have a significant impact on the energy difference based on the limited energy difference data of the OsB_mC_nO_lH_k units. A neural network model is next designed to predict the reaction barrier for methane conversion by OsM₄⁺ (M = C, N, O, Al, Si, or P) with high accuracy.

The inherently serial nature and requirement for short integration time steps in the numerical integration of molecular dynamics (MD) calculations place strong limitations on the accessible simulation time scales and statistical uncertainties in sampling slowly relaxing dynamical modes and rare events. Molecular latent space simulators (LSSs) are a data-driven approach to learning a surrogate dynamical model of the molecular system from modest MD training trajectories that can generate synthetic trajectories at a fraction of the computational cost. The training data may comprise single long trajectories or multiple short, discontinuous trajectories collected over, for example, distributed computing resources. Provided the training data provide sufficient sampling of the relevant thermodynamic states and dynamical transitions to robustly learn the underlying microscopic propagator, an LSS furnishes a global model of the dynamics capable of producing temporally and spatially continuous molecular trajectories. Trained LSS models have produced simulation trajectories at up to 6 orders of magnitude lower cost than standard MD to enable dense sampling of molecular phase space and large reduction of the statistical errors in structural, thermodynamic, and kinetic observables. The LSS employs three deep learning architectures to solve three independent learning problems over the training data: (i) an encoding of the high-dimensional MD into a low-dimensional slow latent space using state-free reversible VAMPnets (SRVs), (ii) a propagator of the microscopic dynamics within the low-dimensional latent space using mixture density networks (MDNs), and (iii) a generative decoding of the low-dimensional latent coordinates back to the original high-dimensional molecular configuration space using conditional Wasserstein generative adversarial networks (cWGANs) or denoising diffusion probability models (DDPMs). In this software tutorial, we introduce the mathematical and numerical background and theory of LSS and present example applications of a user-friendly Python package software implementation to alanine dipeptide and a 28-residue beta-beta-alpha (BBA) protein within simple Google Colab notebooks.

We introduce an approach to describe the long-time dynamics of multiatomic molecules by modulating the free energy landscape (FEL) to capture dominant features of the energy-barrier crossing dynamics of the all-atom (AA) system. Notably, we establish that the self-diffusion coefficient of coarse-grained (CG) systems can be accurately delineated by enhancing conservative force fields with high-frequency perturbations. Using theoretical arguments, we show that these perturbations do not alter the lower-order distribution functions, thereby preserving the structure of the AA system after coarse-graining. We demonstrate the utility of this approach using molecular dynamics simulations of simple molecules in bulk with distinct dynamical characteristics with and without time scale separations as well as for inhomogeneous systems where a fluid is confined in a slit-like nanochannel. Additionally, we also apply our approach to more powerful many-body potentials optimized by using machine learning (ML).