Journal of Chemical Physics最新文献

Polymorphism has been observed in viral capsid assembly, demonstrating the ability of identical protein dimers to adopt multiple geometries under the same solution conditions. A well-studied example is the hepatitis B virus (HBV), which forms two stable capsid morphologies both in vivo and in vitro. These capsids differ in diameter, containing either 90 or 120 protein dimers. Experiments have shown that their relative prevalence depends on the ionic conditions of the solution during assembly. We developed a model that incorporates salt effects by altering the intermolecular binding free energy between capsid proteins, thereby shifting the relative thermodynamic stability of the two morphologies. This model reproduces experimental results on the prevalence ratios of the large and small HBV capsids. We also constructed a kinetic model that captures the time-dependent ratio of the two morphologies under subcritical capsid concentrations, consistent with experimental data.

The interaction of molecular water with the GaP(110) surface has been studied under ultrahigh vacuum conditions with a combination of x-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), and temperature-programmed desorption (TPD) methods. An adlayer of water at 1 ML coverage (referenced to the number of undercoordinated Ga surface atoms) desorbs from the GaP(110) surface over the temperature range of 250-370 K in TPD experiments. This water monolayer exhibited a c(2 × 2) surface structure, observed with both LEED and STM, consisting of alternating OH and H2O surface-bound species, as determined by XPS data. However, at water coverages below 1 ML, the surface concentrations of OH species were higher than that of molecular H2O, and in the 0-0.75 ML surface coverage range, the (OH:H2O) ratio was constant at 2:1. We also observed another stable surface adlayer at 4/3 ML water coverage that exhibited quasi-ordering with a c(3 × 2) LEED pattern. TPD spectra showed that this extra 1/3 ML desorbed near 210 K before the onset of the desorption of the 1 ML coverage.

Heterogeneous catalysts have long been considered rigid structures hosting localized active sites, but growing evidence from both experiments and simulations is revealing a more dynamic picture in which the entire catalyst evolves under reaction conditions. In this study, we explore such behavior in Li14Cr2N8O, a lithium chromium nitride oxide recently proposed as a candidate for ammonia decomposition. Using machine learning-accelerated molecular dynamics, combined with in situ x-ray diffraction and catalytic activity measurements, we show that the pristine material undergoes significant structural transformation upon exposure to ammonia at elevated temperature. Surface disorder, lithium mobility, and the progressive formation of amides and imides give rise to a reactive interface, where chromium centers mediate key redox processes. These interfacial fluctuations create the conditions necessary for key steps in ammonia decomposition, including N-N coupling, hydride formation, and hydrogen release. Our findings highlight the importance of a global, dynamic view of heterogeneous catalysts under operando conditions, where activity arises not from predefined sites but from the evolving nature of the catalyst.

Accurate and efficient simulation of vibrational Raman spectra for systems with strong anharmonicity and nuclear quantum effects remains challenging. Herein, we apply the recently developed constrained nuclear-electronic orbital (CNEO) framework to simulate Raman spectra. We implement analytic static polarizabilities within CNEO density functional theory (CNEO-DFT) and compute Raman spectra using both CNEO harmonic analysis and CNEO molecular dynamics (CNEO-MD). In the harmonic analysis approach, vibrational frequencies are obtained by diagonalizing the mass-weighted CNEO Hessian, and Raman intensities are derived from the projected derivatives of the polarizability with respect to normal-mode coordinates. In CNEO-MD, both frequency and intensity information are extracted from the Fourier transform of the projected polarizability time-derivative autocorrelation function. Applications to formic acid and the mixed water dimer/trimer system show that, compared to conventional DFT, CNEO-DFT achieves substantially improved accuracy, particularly for modes with significant hydrogen motion. Overall, the CNEO framework provides an accurate and efficient approach for simulating vibrational Raman spectra and is especially promising for systems in which hydrogen motion plays a critical role.

The dynamic structure factor (DSF) is a central quantity for interpreting a vast array of inelastic scattering experiments in chemistry and materials science, but its accurate simulation poses a considerable challenge for classical computational methods. In this work, we present a quantum algorithm and an end-to-end simulation framework to compute the DSF, providing a general approach for simulating momentum-resolved spectroscopies. We apply this approach to the simulation of electron energy loss spectroscopy (EELS) in the core-level electronic excitation regime, a spectroscopic technique offering sub-nanometer spatial resolution and capable of resolving element-specific information, crucial for analyzing battery materials. We derive a quantum algorithm for computing the DSF for EELS by evaluating the off-diagonal terms of the time-domain Green's function, enabling the simulation of momentum-resolved spectroscopies. To showcase the algorithm, we study the oxygen K-edge EELS spectrum of lithium manganese oxide (Li2MnO3), a prototypical cathode material for investigating the mechanisms of oxygen redox in battery materials. For a representative model of an oxygen-centered cluster of Li2MnO3 with an active space of 18 active orbitals, the algorithm requires a circuit depth of 3.25 × 108 T gates, 100 logical qubits, and roughly 104 shots.

Water contained within biological membranes plays a critical role in maintaining the separation between intracellular and extracellular environments and facilitating biochemical processes. Variations in membrane composition and temperature lead to phase state changes in lipid membranes, which in turn influence the structure and dynamics of the associated interfacial water. In this study, molecular dynamics simulations were performed on membranes composed of dipalmitoylphosphatidylcholine (DPPC) or palmitoyl sphingomyelin mixed with cholesterol (Chol). To elucidate the effects of Chol on interfacial water, we examined the orientation and hydrogen-bonding behavior of water molecules spanning from the membrane interior to the interface. As the Chol concentration increased, a transient slowdown in water dynamics was observed in the ripple phase at 303 K. Conversely, at higher Chol concentrations, water dynamics were accelerated relative to pure lipid membranes across all temperatures studied. In particular, at a Chol concentration of 50%, the hydrogen bond lifetime in DPPC membranes decreased to ∼0.5-0.7 times that of pure lipid membranes. This nonmonotonic behavior is attributed to the combined effects of membrane packing induced by Chol and reduced density of lipid molecules in the hydrophilic region, offering key insights for modulating the dynamical properties of interfacial water.

The Nonequilibrium Fermi's Golden Rule (NE-FGR) provides a convenient theoretical framework for calculating the charge transfer (CT) rate between a photoexcited bright donor electronic state and a dark acceptor electronic state when the nuclear degrees of freedom start out in a nonequilibrium initial state. In this paper, we show that NE-FGR rates can be significantly modified by placing the molecular system inside an electromagnetic microcavity, even when the coupling with the cavity modes is weak. In this case, cavity-modified NE-FGR rates can also be estimated from the same inputs needed for calculating the cavity-free NE-FGR rates, thereby bypassing the need for an explicit simulation of the molecular system inside the cavity. We also introduce an approximate limit of the cavity-modified NE-FGR, which we denote cavity-modified instantaneous Marcus theory, since it is based on the same assumptions underlying Marcus theory. The utility of the proposed framework for calculating cavity-modified NE-FGR rates is demonstrated by applications to photo-induced CT in the carotenoid-porphyrin-C60 molecular triad dissolved in liquid tetrahydrofuran and the Garg-Onuchic-Ambegaokar model for a CT reaction in the condensed phase.

Here, we present a detailed workflow for clustering and enhanced sampling of biomolecular conformations using the ShapeGMM methodology. This approach fits a probabilistic model of biomolecular conformations rooted in the idea that the free energy can be expressed in terms of local fluctuations in atomic positions around metastable states. We demonstrate using a single model system how to generate and fit equilibrium molecular dynamics simulation data. We then demonstrate how to use the resulting model to generate a reaction coordinate between two states, how to sample along that coordinate using metadynamics using our size-and-shape PLUMED module, and how to cluster those biased conformations to obtain a refined equilibrium ShapeGMM model.

We devise an ideal three-dimensional octagonal quasicrystal that is based upon the two-dimensional Ammann-Beenker tiling and that is potentially suitable for realization with patchy particles. Based on an analysis of its local environments, we design a binary system of five- and eight-patch particles that in simulations assembles into a three-dimensional octagonal quasicrystal. The local structure is subtly different from the original ideal quasicrystal possessing a narrower coordination-number distribution; in fact, the eight-patch particles are not needed and a one-component system of the five-patch particles assembles into an essentially identical octagonal quasicrystal. We also consider a one-component system of the eight-patch particles; this assembles into a cluster with a number of crystalline domains, which, because of the coherent boundaries between the crystallites, has approximate eightfold order. We envisage that these systems could be realized using DNA origami or protein design.

An efficient implementation for the relativistic exact two-component core-valence-separated equation-of-motion coupled-cluster singles and doubles (X2C-CVS-EOM-CCSD) method is reported. The explicit exclusion of pure valence excitations in the EOM-CCSD excited-state eigenvalue equations significantly improves the efficiency for calculations of core-excited states. Benchmark relativistic CVS-EOM-CC calculations with systematic inclusion of relativistic, correlation, and basis-set effects are shown to provide highly accurate results for core ionized and excited states involving heavy atoms.