Journal of Chemical Physics最新文献

As a precursor to various reactive nitrogen species formed in biological systems, nitric oxide (•NO) participates in numerous processes, including enhancing DNA radiosensitivity in ionizing radiation-based radiotherapy. Forming guanine radical cations is another common DNA lesion resulting from ionization and oxidation damage. As such, the interaction of •NO with guanine radical cations (G•+) may contribute to the radiosensitization of •NO. An intriguing aspect of this process is the participation of multiple spin configurations in the reaction, including open-shell singlet 1,OS[G•+(↑)⋯(↓)•NO], closed-shell singlet 1,CS[G(↑↓)⋯NO+], and triplet 3[G•+(↑)⋯(↑)•NO]. In this study, the reactions of •NO with both unsubstituted guanine radical cations (in the 9HG•+ conformation) and 9-methylguanine radical cations (9MG•+, a guanosine-mimicking model compound) were investigated in the absence and presence of monohydration of radical cations. Kinetic-energy dependent reaction product ions and cross sections were measured using an electrospray ionization guided-ion beam tandem mass spectrometer. The reaction mechanisms, kinetics, and dynamics were comprehended by interpreting the reaction potential energy surface using spin-projected density functional theory, coupled cluster theory, and multiconfiguration complete active space second-order perturbation theory, followed by RRKM kinetics modeling. The combined experimental and computational findings revealed closed-shell singlet 1,CS[7-NO-9MG]+ as the major, exothermic product and triplet 3[8-NO-9MG]+ as the minor, endothermic product. Singlet biradical products were not detected due to high reaction endothermicities, activation barriers, and inherent instability.

The microstructure plays a crucial role in the manufacturing and application of polyacrylonitrile fibers, which serve as precursors for carbon fibers. Synchrotron radiation small angle x-ray scattering (SR-SAXS) is a non-destructive and precise technique for analyzing fiber structures. This study employed one-dimensional SR-SAXS mapping to extract key structural parameters such as periodicity, lamellae thickness, and the extent of amorphous regions, as well as the directional orientation in γ-irradiated, pre-oxidized polyacrylonitrile fibers. The analysis revealed a three-layered structure comprising a surface skin, a transitional layer, and a central core. Notably, the lamellar thickness exhibits a "U"-shaped distribution, while the long-period structures, amorphous regions, and orientational properties demonstrate a "wave-like" pattern. Within this structure, the skin exhibits a higher level of orientation, with the orientation decreasing progressively from the skin toward the core layer. The structure of the layered crystal was further corroborated by the morphological analysis. In addition, molecular simulations were performed to propose the mechanisms underlying the formation of this layered structure. This comprehensive investigation using SR-SAXS and one-dimensional mapping provides detailed insights into the microstructural and morphological characteristics of polyacrylonitrile fibers, which can inform future advancements in material processing and refinement techniques for the production of advanced fibers.

The interfacial local field is of critical importance in data analysis to deduce intrinsic surface responses from optical measurements of interfaces of condensed media but has not yet been well interrogated. We present here a simple approach to find local fields approximately at various interfaces of isotropic or nearly isotropic media. We divide a medium into atomic planes or molecular layers. It is found that the dipolar field contribution to the local field in a plane or layer from induced dipoles residing in planes beyond the nearest neighbor planes or layers is negligible; in many cases, the contribution is dominated by in-plane dipoles and the local field has a simple expression very much like that for an isotropic bulk. This finding allows us to calculate approximate local field variation at various interfaces. With the interfacial local field known, intrinsic surface response coefficients can be extracted from the optically measured surface responses.

Nonlinear response theory is employed to derive a closure to the polymer reference interaction site model equation. The closure applies to a liquid of neutral polymers at melt densities. It can be considered a molecular generalization of the mean spherical approximation (MSA) closure of Lebowitz and Percus to the atomic Ornstein-Zernike (OZ) equation and is similar in some aspects to the reference "molecular" MSA (R-MMSA) closure of Schweizer and Yethiraj to PRISM. For a model binary blend of freely-jointed chains, the new closure predicts an unmixing critical temperature, Tc, via the susceptibility route that scales linearly with molecular weight, N, in agreement with Flory theory. Predictions for Tc of the new closure differ greatest from those of the R-MMSA at intermediate N, the latter being about 40% higher than the former there, but at large N, both theories give about the same values. For an isotopic blend of polyethylene, the new and R-MMSA closures predict a Tc about 25% higher than the experimental value, which is only moderately less accurate than the prediction of atomic OZ-MSA theory for Tc of methane. In this way, the derivation and its consequences help to identify the ingredients in a theory needed to properly model the equilibrium properties of a polymeric liquid at both short and long lengthscales.

Calculating molecular properties using quantum devices can be performed through the quantum linear response (qLR) or, equivalently, the quantum equation of motion (qEOM) formulations. Different parameterizations of qLR and qEOM are available, namely naïve, projected, self-consistent, and state-transfer. In the naïve and projected parameterizations, the metric is not the identity, and we show that it depends on redundant orbital rotations. This dependency may lead to divergences in the excitation energies for certain choices of the redundant orbital rotation parameters in an idealized noiseless setting. Furthermore, this leads to a significant variance when calculations include statistical noise from finite quantum sampling.

We introduce a Python package based on matrix product states (MPS) to simulate both the time-dependent Schrödinger equation (TDSE) and the hierarchical equations of motion (HEOM). The wave function in the TDSE or the reduced density operator/auxiliary density operators in the HEOM are represented using MPS. A matrix product operator (MPO) is then constructed to represent the Hamiltonian in the TDSE or the generalized Liouvillian in the HEOM. The fourth-order Runge-Kutta method and the time-dependent variational principle are used to propagate the MPS. Several examples, including the nonadiabatic interconversion dynamics of the pyrazine molecule, excitation energy transfer dynamics in molecular aggregates and photosynthetic light-harvesting complexes, the spin-boson model, a laser driven two-state model, the Holstein model, and charge transport in the Anderson impurity model, are presented to demonstrate the capability of the package.

Investigating molecular excitation induced by collisions requires the prior determination of accurate analytical potential energy surfaces for the colliding partners. For carbon-chain molecules, such as cyanopolyynes, this has been a longstanding challenge, resulting in the absence of rate coefficients for HC5N, HC7N, HC9N, and others, induced by collisions with He. To overcome this bottleneck, we introduce a new approach: the Radial Angular Network with Gradual Expansion (RANGE). This method jointly connects the construction of ab initio interaction potentials with the determination of their analytical forms. We use the HC3N-He molecular complex as a reference to assess the reliability of our method, given that its analytical potential has been derived using various methods. Additionally, we apply the RANGE approach to construct the analytical representation of the interaction potential for HC5N-He and HC7N-He. The analysis of the analytical potentials reveals three systematic trends: (i) the anisotropy increases with the length of the carbon chain, (ii) the number of local minima correlates with the number of carbon atoms, and (iii) the shallowest local minimum is consistently located at ∼30 cm-1 below the dissociation limit of the complex. Using the time-independent quantum mechanical close-coupling formalism, we briefly estimate the propensity rules governing the excitation of HC3N, HC5N, and HC7N induced by collisions with He. Consequently, the three collisional systems exhibit the same propensity rule, favoring Δj = 2 transitions.

Multi-criteria optimization is used for developing molecular models for ethylene carbonate (EC) and propylene carbonate (PC), organic solvents commonly used in Li-ion batteries. The molecular geometry and partial charges of the solvents are obtained from quantum mechanical calculations. Using a novel optimization strategy that combines systematic variations of the Lennard-Jones parameters with a reduced units approach, the models are fitted to experimental data on the liquid density, vapor pressure, relative permittivity, and self-diffusion coefficient. Since no experimental data for the self-diffusion coefficient of pure EC were available in the literature, they are measured in this work using a gradient-based nuclear magnetic resonance technique. For all pure component properties, excellent agreement between experiment and simulation is obtained. Moreover, the predictive capabilities of the new solvent models are assessed by comparison to experimental data for the liquid density and relative permittivity of mixtures of EC and PC. In addition, molecular models for the anions PF6-, BF4-, and ClO4- in solutions of their lithium electrolytes in PC are developed using experimental data on the solution densities. Finally, the self-diffusion coefficients of LiPF6 in PC and in aqueous solution are predicted and compared, showing that diffusion is much slower in the organic solution due to the formation of larger solvent shells around the ions. Furthermore, an analysis of the radial distribution functions in these solutions suggests that the ions have much less impact on the structure of the solvent PC than on water.

The nitrile (C≡N) stretching vibration is widely used as a site-specific environmental probe of proteins and, as such, many computational studies have been used to investigate the factors that affect its frequency (νCN). These studies, most of which were carried out in the ground electronic state of the molecule of interest, revealed that the formation of a normal or linear hydrogen bond (H-bond) with the nitrile group results in a blueshift in its νCN. Recently, however, several experimental studies showed that for certain aromatic nitriles, solvent relaxations in their excited electronic state(s) induce a redshift (blueshift) in νCN in protic (aprotic) solvents, suggesting that the effect of hydrogen-bonding (H-bonding) interactions on νCN may depend on the electronic state of the molecule. To test this possibility, herein we combine molecular dynamics simulations and quantum mechanical calculations to assess the effect of H-bonding interactions on the νCN of 5-cyanoindole (5-CNI) in its different electronic states. We find that its C≡N group can form either one H-bond (single-H-bond) or two H-bonds (d-H-bonds) with the solvent molecules and that in the ground electronic state, a single-H-bond can lead νCN to shift either to a higher or lower frequency, depending on its angle, which is consistent with previous studies, whereas the d-H-bonds cause νCN to redshift. However, in its lowest-lying excited electronic state (i.e., S1), which has the characteristics of a charge-transfer state, all H-bonds induce a redshift in νCN, with the d-H-bonds being most effective in this regard.

The ring-opening reaction of aromatic molecules is a significant and critical process for the construction of carbon-based and related functional materials with desired structures and properties. However, direct observation and control of such a process at a molecular level remains a challenge. Here, we employed the octahedral voids in endohedral metallofullerene (EMF) crystals as nanoreactors to accommodate aromatic m-xylene molecules and regulate the ring-opening reaction of guest m-xylene by applying a high pressure. We found that the ring-opening reaction of m-xylenes strongly depends on the degree of charge transfer between m-xylene and EMF, which can be tuned by varying the electronegativity of the carbon cages with different endohedral metals. A positive relationship between the electronegativity of fullerenes and the reactivity of m-xylene was revealed. This work demonstrates the potential of tuning the ring-opening reaction of aromatic molecules by charge transfer and manipulates the reaction at a molecule level, providing new insights into the synthesis of carbon materials and fullerene derivatives.