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Poly-liquid behaviors of self-associating fluids and mesoscopic aggregation in liquid solutions
In conflict with standard notions of thermodynamics, mesoscopically sized inclusions (“clusters”) of a solute-rich liquid have been observed in equilibrated solutions of proteins and other molecules. According to a complexation scenario proposed earlier, a steady-state ensemble of finite-sized droplets of a metastable solute-rich liquid can emerge in a solution, if the solute molecules can form transient complexes with each other and/or solute. Here, we solve for the thermodynamics of an explicit model of a self-associating fluid in which particles can form transient dimers. We determine ranges of parameters where two distinct dense liquid phases, dimer-rich and monomer-rich, respectively, can co-exist with each other and the solute-poor phase. We find that within a certain range of the dimer’s binding strength, thermodynamic conditions for mesoscopic clusters to emerge are indeed satisfied. The location and size, respectively, of the corresponding region on the phase diagram are consistent with observation. We predict that the clusters are comprised of a metastable monomer-rich dense liquid, while the bulk solution itself contains substantial amounts of the dimer and exhibits large, pre-critical density fluctuations. Surprisingly, we find that the dense phase commonly observed during the macroscopic liquid–liquid separation should be dimer-rich, another testable prediction. The present findings provide further evidence for the complexation scenario and suggest new experimental ways to test it.
A fast and streamlined method for the measurement of absolute photodetachment and photodissociation cross sections
The absolute photodetachment cross section characterizes the photostability of atomic and molecular anions against photodestruction by neutralization. The measurement of this quantity has been reported only for atomic and simple molecular ions. In 2006, Wester’s group introduced a novel ion-trap-based technique to measure the absolute photodetachment cross section [Trippel et al., Phys. Rev. Lett. 97, 193003 (2006)] of OH−. In the present work, we propose a novel methodology to streamline this technique to reduce the measurement time by several orders of magnitude by combining a single experimental rate measurement with a simulated column density distribution of the trapped ions. We validated our approach by reproducing the cross section reported for OH− at 632.8 nm. Using this technique, we report the first such measurement for a molecule of biological interest, deprotonated indole, at a laser wavelength of 403 nm. The proposed scheme is anticipated to have a significant and transformative impact on the development of a comprehensive database for photodetachment and photodissociation cross sections of molecular ions. Furthermore, these measurements have the potential to drive the development of cutting-edge computational codes for cross section calculations, enabling an unprecedentedly detailed understanding of electron dynamics in large molecules and the light–matter interaction.
Spin-adapted spin-flip-down time-dependent density functional theory
Molecular systems with orbital (near-)degeneracy at the Fermi level tend to adopt a high-spin ground state. In these systems, one often finds low-lying electronic excitations with a lower total spin that can be reached from the ground state by a spin-flip-down excitation. In this work, we present three spin-adapted spin-flip-down time-dependent density functional theory (SFD-TD-DFT) approaches to calculate the excitation energies for these types of electronic transitions. These SFD-TD-DFT methods are based on a restricted open-shell Kohn–Sham (ROKS) formulation within the Tamm–Dancoff approximation (TDA), giving rise to the ROKS-SFD-TDA family of methods. The three methods differ in the kernel, having different two-electron coupling elements in the resulting working equations. In agreement with earlier work, we find that a noncollinear description of the kernel is vital for producing a decent description of these excitations. In terms of obtaining excitations with a definite spin, we present two fully spin-adapted ROKS-SFD-TDA methods that either stem from configuration interaction with single excitations (SF-CIS) or from the already existing equation-of-motion ansatz (SF-TDA). It is shown that the spin-adaptation in SF-CIS and SF-TDA gives rise to artificial double counting of correlation effects by incorporating double excitations. When discarding this double counting, one ends up with an excited state that is partly spin-adapted (only in the open-to-open configurations). This method is called quasi-spin-adapted SF-TDA (Q-SF-TDA) and is shown to be a stable and efficient method that performs similarly to spin-unrestricted SFD-TD-DFT.
A generalized method for refining and selecting random crystal structures using graph theory
Random generation of crystal structures is a key to the success of predicting unknown crystals. In this work, we introduce a general method for refining and selecting random structures that relies on minimal prior information. The method establishes a quotient graph from the random structure using a near-neighbor finding algorithm, which subsequently guides the refinement of the initial structure. To validate this approach, we apply it to nine distinct systems, and the outcomes indicate that it effectively yields a great number of low-energy structures. This technique could be integrated into most structure prediction algorithms to generate more sound initial structures, thereby expediting the search for ground state structures.
A refined atomistic model of functionalized self-assembled monolayers on gold: Assessment of force field parameters
Self-assembled monolayers (SAMs) of alkanethiols on gold surfaces are important for various technological applications, such as electroanalytical sensors, organic electronic devices, and catalysts. However, providing a consistent computational description of the unique structural features of these SAMs, such as adsorption patterns, chain conformations, and superlattice arrangements, is challenging, particularly within a versatile computational framework that can simulate both the structural features of these systems and their irradiation-driven chemical transformations. This study systematically analyzes molecular mechanics force field parameters for bonded and nonbonded (van der Waals and electrostatic) interactions in alkanethiol SAMs with different terminal groups. Using structure optimization and energy decomposition analysis, we assess the impact of force field parameters on key properties, such as the equilibrium tilt angle, ligand packing density, and nanoscale structural organization. Based on this detailed benchmarking, an optimal set of force field parameters has been identified that reproduces the experimentally determined structural and energetic properties of SAMs and ensures their dynamic stability at room temperature. This provides a validated framework for simulating pristine and functionalized alkanethiol-coated substrates under thermal conditions relevant to experimental applications.
An excitation matched local correlation approach to excited state specific perturbation theory
We develop a cubic scaling approach to excited-state-specific second order perturbation theory in which the completeness of a local correlation treatment is carefully matched between the ground and excited states. With this matching, the accuracy of the parent method is maintained even as substantial portions of the correlation energy are neglected. Even when treating a long-range charge transfer excitation, cubic scaling is achieved in systems with as few as ten non-hydrogen atoms. In a test on the influence of an explicit solvent molecule on a long range charge transfer, the approach is qualitatively more accurate than EOM-CCSD and reproduces CC3’s excitation energies and excited state potential energy surface to within about 0.1 eV and 0.5 kcal/mol, respectively.
Memory-induced slow relaxation in the generalized Langevin equation
We investigate the relaxation dynamics of the generalized Langevin equation (GLE) with an exponential memory kernel. Our analysis reveals that the relaxation time to equilibrium scales inversely with the square of the memory decay rate λ, i.e., τrelax ∝ λ−2. To understand the origin of this scaling, we analyze the escape dynamics from a potential well and find that the mean escape time follows the same λ−2 dependence. This indicates that the slow relaxation arises from memory-suppressed fluctuations that delay escape events. To explain these findings, we reformulate the GLE using an auxiliary variable, embedding the non-Markovian dynamics in a higher-dimensional Markovian system. This approach provides a clear physical picture of how memory influences noise, diffusion, and relaxation in non-Markovian systems.
Driven probe particle dynamics in a bubble and pattern forming system
We numerically examine the dynamics of a probe particle driven at a constant force through an assembly of particles with competing long-range repulsion and short-range attraction that forms a bubble or stripe state. In the bubble regime, we identify several distinct types of motion, including an elastic or pinned regime where the probe particle remains inside a bubble and drags all other bubbles with it. There is also a plastic bubble phase where the bubble in which the probe particle is trapped is able to move past the adjacent bubbles. At larger drives, there is a breakthrough regime where the probe particle jumps from bubble to bubble and, in some cases, can induce correlated rotations or plastic rearrangements of the particles within the bubbles. At the highest drives, the probe particle moves sufficiently rapidly that the background particles undergo only small distortions. The distinctive dynamic flow states and the transitions between them are accompanied by signatures in the effective drag on the driven particle, jumps in the velocity–force curves, and changes in the time-dependent velocity fluctuations. We map the dynamic phase diagram for this system for varied interaction lengths, bubble sizes, and densities.
Globally accurate neural network potential energy surface and state-to-state quantum dynamics calculations on Ne(2S) + H2+/D2+ → NeH+/NeD+ + H/D reactions
The proton transfer reactions of the Ne atom with the H2+ molecular ion and its isotope variants have attracted considerable attention due to their importance in plasma physics and the fundamental study of elementary reaction dynamics. To obtain high-precision dynamics results, a globally accurate ground-state NeH2+ potential energy surface (PES) is constructed using the permutation invariant polynomial-neural network method based on 35 035 ab initio points calculated at the UCCSD(T)/AV5Z level. On the new PES, the state-to-state quantum dynamics calculations of the Ne(2S) + H2+/D2+ (v0 = 0, j0 = 0) reactions are performed. The calculated results indicate that the products of the two reactions are generated by the dissociation of short-lived complexes when the collision energy is slightly larger than the reaction thresholds, whereas a direct abstraction process gradually plays the dominant role as the collision energy increases. The newly constructed PES can be used to further accurately study the quantum dynamics of the Ne + H2+ reactive system, including the effects of rovibrational excitations and the spatial alignment of reactant molecules.
Local nonequilibrium thermodynamics of polymer collapse dynamics
Nonequilibrium thermodynamics plays a crucial role in understanding a wide range of physical and chemical processes. While significant advances have been made through frameworks, such as the fluctuation theorem, it remains challenging to define thermodynamic quantities, such as energy, entropy, and free energy, at the local level during nonequilibrium processes. Recently, Jinwoo and Tanaka [Sci. Rep. 5, 7832 (2015)] have proposed a formalism (the JT formalism) that defines local thermodynamic properties via a path ensemble of microstates over time. In this work, we apply the JT formalism to the polymer collapse process as a model nonequilibrium system to observe the collapse dynamics in terms of the end-to-end distance as the mesoscopic variable. Through extensive Langevin dynamics simulations, we quantify conformational free energy, lost information, and nonequilibrium free energy as functions of time and conformation. Our results validate the JT’s work fluctuation theorem, which relates work and local nonequilibrium free energy. This study highlights the utility of the JT formalism in analyzing dynamic thermodynamic behavior in complex soft matter systems.
Uniaxial order parameters associated with surface SFG spectra. I. Distributions with cylindrical symmetry
Order parameters provide a useful qualitative and quantitative description of the distribution of molecules in ordered materials as they are independent of the shape of the orientation distribution. For samples that exhibit uniaxial ordering with no twist preference, extracting ⟨P2⟩ from polarized IR absorption data is common and obtaining ⟨P2⟩ and ⟨P4⟩ from Raman data has also been well-described. However, such an approach is not routine in the analysis of surface sum-frequency generation (SFG) spectra. We first provide a description whereby elements of the second-order susceptibility can be expressed in terms of the order parameters ⟨P1⟩ and ⟨P3⟩. We then illustrate how experimental data would be used to extract those parameters and how a most probable orientation distribution function could be determined by subsequently maximizing the information entropy. Finally, features of this distribution function are explored.
Predicting the shapes of Au55 and Au147: Force fields vs density-functional theory
Gold nanocrystals have been widely used in sensing and medicine, where nanocrystal shape can profoundly influence properties. To describe and predict the structure and properties of Au nanomaterials, first-principles studies are the most accurate. Force fields can provide effective surrogates for first-principles calculations, and in the case of Au, many such force fields exist. To clarify the current state of Au structure prediction using force fields, we used parallel tempering molecular dynamics simulations to explore the temperature-dependent shape distributions of Au147 and Au55 from three different Embedded-Atom Method (EAM) force fields. We used machine learning to classify nanoparticle shapes and observe a wide variation in the temperature-dependent shape distributions among the various force fields, accompanied by a wide range of melting temperatures. We also compared the EAM structures to those from literature studies employing an Artificial Neural Network (ANN), a Gaussian process regression machine-learning force field, density functional tight binding, the Gupta potential, and Density Functional Theory (DFT). We re-optimized the lowest-energy structures from each force field/study using DFT and found that the lowest-energy structures for both Au147 and Au55 are amorphous. These structures were predicted by the ANN and DFT. Most of the 30 structures with minimum energy for each size are either hollow or partially to totally disordered and not icosahedral, as the sizes of these nanocrystals might imply.
Exact lattice summations for Lennard-Jones potentials coupled to a three-body Axilrod–Teller–Muto term applied to cuboidal phase transitions
Three-body interactions have long been conjectured to play a crucial role in the stability of matter. However, rigorous studies have been scarce due to the computational challenge of evaluating small energy differences in high-dimensional lattice sums. This work provides a rigorous analysis of Bain-type cuboidal lattice transformations, which connect the face-centered cubic (fcc), mean-centered cubic (mcc), body-centered cubic (bcc), and axially centered cubic (acc) lattices. Our study incorporates a general (n, m) Lennard-Jones (LJ) two-body potential and a long-range repulsive Axilrod–Teller–Muto (ATM) three-body potential. The two-body lattice sums and their meromorphic continuations are evaluated to full precision using super-exponentially convergent series expansions. Furthermore, we introduce a novel approach to computing three-body lattice sums by converting the multi-dimensional sum into an integral involving products of Epstein zeta functions. This enables us to evaluate three-body lattice sums and their meromorphic continuations to machine precision within minutes on a standard laptop. Using our computational framework, we analyze the stability of cuboidal lattice phases relative to the close-packed fcc structure along a Bain transformation path for varying ATM coupling strengths. We analytically demonstrate that the ATM cohesive energy exhibits an extremum at the bcc phase and show numerically that it corresponds to a minimum for repulsive three-body forces along the Bain path. Our results indicate that strong repulsive three-body interactions can destabilize the fcc phase and render bcc energetically favorable for soft LJ potentials. However, even in this scenario, the bcc phase remains susceptible to further cuboidal distortions. These results suggest that the stability of the bcc phase is, besides vibrational, temperature, and pressure effects, strongly influenced by higher than two-body forces. Because of the wrong short-range behavior of the triple–dipole ATM model, the LJ potential is limited to exponents n > 9 for the repulsive wall, otherwise one observes distortion into a set of linear chains collapsing to the origin.
A quantitative theory and atomistic simulation study on the soft-sphere crystal-melt interfacial properties. II. Interfacial free energies
This study proposes a new method for predicting the crystal-melt interfacial free energy (γ) using the Ginzburg–Landau (GL) model, enhanced by atomistic simulation data for more accurate density wave profiles. The analysis focuses on the soft-sphere system governed by an inverse power potential that stabilizes both BCC and FCC phases. Equilibrium molecular-dynamics simulations are used to obtain density-wave amplitude distributions, which serve as inputs for the GL model to predict γ and its anisotropy. The predicted γ values exhibit strong agreement with prior benchmark simulation experimental studies, particularly for FCC crystal–melt interfaces (CMIs). The GL models for the CMI γ are proved to be both computationally efficient and reasonable, offering quantitative predictions of γ while providing insights into the factors controlling its magnitude and anisotropy. Key improvement is suggested for the variational procedure used in the two-mode CMI free energy functionals, and potential upgrades to the GL model are also proposed to further enhance predictive accuracy.
Vibrational asymmetry across heptad positions in coiled-coil IR spectra: A simulation study of isotope-labeled amide I modes
Isotope-edited infrared (IR) spectroscopy is a powerful tool for probing site-specific structures and dynamics within proteins. However, the interpretation is often complicated by spectral congestion and environmental heterogeneity. In this study, vibrational exciton models combined with molecular dynamics simulations are employed to examine the frequency distributions and IR spectra of isotope-labeled local modes (ILMs) in parallel coiled-coil dimers. Based on the difference spectra obtained by subtracting the unlabeled spectrum from the labeled one, a new method to estimate labeled local-mode frequencies is proposed. The IR peak positions predicted from both the ILMs and specific normal modes systematically deviate from their corresponding average frequencies, primarily owing to asymmetric broadening. This asymmetry, which is characterized by the skewness of the mode density of states, arises from heterogeneous fluctuations in the local environment. Time correlation analysis revealed that solvation-induced dynamics persist on timescales (0.22–3.30 ps) exceeding the vibrational lifetime, causing incomplete motional averaging and pronounced inhomogeneous broadening. These effects result in skewed frequency distributions and contribute to peak localization errors. The application of asymmetric Gaussian fitting models and perturbative corrections improved the accuracy of the ILM frequency estimates, with sub-wavenumber precision achieved when spectral separation was sufficient. The heptad-repeat architecture of coiled coils further introduced register-specific vibrational patterns, emphasizing the role of the local environment. Collectively, the results highlight the critical role of solvation-induced heterogeneity in shaping isotope-edited IR spectra and demonstrate the need to consider both dynamic and statistical spectral asymmetry when performing high-resolution vibrational analysis of proteins.
Memory function for protein diffusion
Standard algorithms to calculate the diffusion constant from computer simulations are based on either the mean-squared displacement or the velocity autocorrelation function of the tagged particle. They register displacements/velocities caused by random forces, but do not address their physical nature. This deficiency is resolved in the force route to the diffusion constant leading to Kirkwood equation for massive diffusive particles (Brownian motion). Approximate Kirkwood equation becomes exact when the force relaxation time is replaced with the memory time. To formulate the force route to the diffusion constant, memory functions were calculated here from molecular dynamics simulations of six charge mutants of the green fluorescent protein and the plastocyanin protein in a wide range of temperatures. The memory time falls between the velocity and force relaxation times, with the Kirkwood equation overestimating diffusion constants of proteins by a factor of ∼4. Diffusion constants from the velocity/displacement route strongly increase with increasing system size. Standard protocols accounting for finite-size effects show serious flaws when applied to protein diffusion by producing system-size corrections far exceeding both the finite-size diffusion constants and their infinite-size extrapolations. Diffusion constants from the force route show much less system-size dependence, and corrected values are mostly independent of the system size.
A multiset matrix product state approach to hierarchical equations of motion and its application to vibrational relaxation on metal surfaces
We develop a multiset matrix product state (MPS) approach based on the time-dependent variational principle to solve the hierarchical equations of motion (HEOM) for the fermionic bath and apply it to inelastic vibrational scattering on metal surfaces. By using a Newns–Anderson model with two nuclear degrees of freedom, we investigate the vibrational energy relaxation of NO scattering on Au(111) and Ag(111) surfaces. Our results show that the extent of vibrational relaxation depends strongly on both incident energy and molecule–surface coupling strength. Vibrational relaxation on the Au(111) surface is enhanced with increasing incident energy due to greater transient electron transfer. The dependence on molecule–surface coupling strength and effective metal bandwidth is more complex. In the case of scattering on the Au(111) surface with low initial vibrational excitation, the landscape of the adiabatic potential energy surface plays an important role. Stronger coupling enhances transient electron transfer and leads to more pronounced vibrational relaxation. However, for high initial vibrational excitation, the extent of transient electron transfer remains similar. Larger coupling strength increases adiabaticity and reduces vibrational relaxation. The vibrational relaxation on the Ag(111) surface is found to be more pronounced than on the Au(111) surface, consistent with experimental observations. Our study provides detailed insights into the nonadiabatic dynamics during molecule–surface scattering and demonstrates the utility of the multiset MPS–HEOM approach for studying such processes.
Bandgap nonlinearity and composition-dependent bowing in <i>α</i>-(AlxGa1−x)2O3 epilayers
Designing functional materials with tailored properties often involves alloying different semiconductors, yet the nonlinear bandgap bowing effect complicates precise bandgap engineering, particularly in ultrawide-bandgap systems, such as Ga2O3 ternary alloys. In this work, we examined the bandgap nonlinearity and composition-dependent bowing in pure-phase α-(AlxGa1−x)2O3 epilayers (0 &lt; x &lt; 0.62) grown via laser molecular beam epitaxy on m-plane sapphire substrates. The variations in the x-ray rocking curve full width at half maximum and surface roughness of epilayers with increasing Al composition x follow the trend predicted by the theoretical formation enthalpy of α-(AlxGa1−x)2O3 alloys. The high crystalline quality of the α-(AlxGa1−x)2O3 epilayers was further confirmed by x-ray diffraction and transmission electron microscopy characterizations. While lattice constants adhered to Vegard’s law, the optical bandgap (5.28–7.22 eV) exhibited nonlinearity, with a bowing factor of 1.33 eV, aligning closely with theoretical predictions. Our findings suggest that the observed optical bandgap nonlinear effect in the α-(AlxGa1−x)2O3 alloy primarily stems from charge exchange, rather than volume deformation or strain relaxation effects, providing a pathway for precise bandgap tuning in Ga2O3 for high-performance power electronics.
Quantum master equations for systems off-diagonally driven by a time-dependent external field
A useful approach to modeling charge transfer (CT) dynamics in complex molecular systems is based on off-diagonal quantum master equations (OD-QMEs), which treat terms that couple different electronic states as a small perturbation. In this paper, we present OD-QMEs for systems with time-dependent electronic coupling terms, which can be accomplished by driving the system with a time-dependent external field. We also present an asymptotic analysis that shows how the dynamics described by the OD-QMEs for a CT system driven by a CW field turns into rate kinetics governed by field-modified Marcus theory rate constants at long times and high temperatures (when Gaussian statistics is assumed). The ability of off-diagonal driving to open up new CT pathways that can compete with non-radiative pathways is demonstrated in the case of the Garg–Onuchic–Ambegaokar CT model driven by a CW field.
Structural evolution and photoluminescence tuning of Bi3+/Sb3+ doped zero-dimensional perovskite [(CH3)3S]2SnCl6 under pressure
The tunable photoluminescence (PL) response of Bi3+/Sb3+ doped zero-dimensional perovskite [(CH3)3S]2SnCl6 via pressure-induced structure evolution is investigated using high-pressure techniques and density-functional theory calculations. In contrast to the rigidification of [SnCl6]2−/[SbCl6]3− octahedra by Sb3+ ions, Bi3+ ions trigger the distortion of the [SnCl6]2−/[BiCl6]3− octahedra at a relatively lower pressure, and even a cubic-to-trigonal phase transition of Bi3+ singly doped [(CH3)3S]2SnCl6 occurs at higher pressures due to its pressure sensitivity, wherein, the organic (CH3)3S+ chains enhance the flexibility of [(CH3)3S]2SnCl6 host structure. For Bi3+/Sb3+ doubly doped [(CH3)3S]2SnCl6, the two metal ion dopants interact with each other, accompanied by synergistic lattice distortion, resulting in novel self-trapped exciton emission behaviors in the host that is distinct from the single-ion doping effects. The pressure-dependent PL performance of Bi3+ and Sb3+ doped [(CH3)3S]2SnCl6 suggests its promising potential in the field of perovskite-based tunable light-emitting devices.