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Structure and vibrational spectroscopy of complexes of Al+ and Al2+ with ethane
The binding motifs of clusters of Al+ and Al2+ with ethane, Alx+(C2H6)n (x = 1, 2; n = 1–3), are determined using vibrational photodissociation spectroscopy in the C–H stretching region (2550–3100 cm−1) in conjunction with spectra calculated using density functional theory. The relative energies of candidate structures are determined with the B3LYP-D3 and ωB97X-D density functionals and the 6–311++G(d,p) basis set. Local mode Hamiltonian calculations are better able to reproduce the spectra than scaled harmonic calculations, due to contributions from bending overtones and combination bands. Vibrational photodissociation spectra show a red shift in the stretching frequencies of C–H bonds that are proximate to the cation. This red shift decreases as the number of ethanes increases. For Al+(C2H6)n (n = 1–3), side-on (T-shaped) binding of the metal is preferred to end-on binding, and subsequent ligands bind on the same side of the cation. Similarly, for Al2+(C2H6)n (n = 1–3), T-shaped configurations in which the C–C and Al–Al bonds are approximately perpendicular and the ethane binds side-on to the Al2+ are preferred. In Al2+(C2H6)n (n = 1–3) complexes, intense bands are observed, which are due to overtones and combinations of symmetric deformations in Fermi resonance with the red-shifted C–H stretches.
Modeling electronic absorption spectra with nuclear quantum effects in constrained nuclear–electronic orbital framework
Electronic absorption spectra serve as versatile and powerful tools in experiments. Accurate theoretical simulation of electronic absorption spectra is challenging because multiple factors such as environmental effects and nuclear quantum effects contribute to spectrum lineshapes. This work proposes a protocol to model electronic absorption spectra in the constrained nuclear–electronic orbital framework. Solvent effects, temperature effects, and particularly nuclear quantum effects can be taken into consideration in this unified framework. This protocol is applied to investigate the electronic absorption spectrum of the pyridine molecule in water. Nuclear quantum effects are found to induce a broadening and red shift of the absorption spectrum of pyridine.
Dynamic nuclear polarization mechanisms using TEMPOL and trityl OX063 radicals at 1 T and 77 K
A sensitivity increase of two orders of magnitude in proton (1H) and carbon (13C) spins via dynamic nuclear polarization (DNP) has been accomplished recently using a compact benchtop DNP polarizer operating at 1 T and 77 K. However, the DNP mechanisms at play at such a low magnetic field and high operating temperature are still not fully elucidated. A deeper understanding of the dominant polarization transfer mechanisms between electrons and 1H and 13C spins under these benchtop conditions is, therefore, required if one wants to devise strategies to boost sensitivity further. In this study, we found that DNP is generally dominated by solid effect (two-spin and three-spin) for narrow electron paramagnetic resonance (EPR) line radicals (15 mM trityl OX063) and cross effect for broad EPR line radicals (50 mM TEMPOL). For both radicals, the dominant DNP mechanisms were investigated varying the microwave frequency and measuring the 1H and 13C DNP enhancement factors to obtain 1H and 13C DNP spectra. The impact of varying the microwave power on the 1H DNP buildup times and the 1H nuclear spin relaxation times were important as well to distinguish between solid effect and cross effect DNP. Finally, time-resolved electron saturation simulations under continuous microwave irradiation could replicate the experimental 1H and 13C DNP spectra at 1 T and 77 K for both radicals considering their electron relaxation properties. Only for trityl OX063, the 13C DNP spectra showed additional DNP maxima compared to the simulations. This has been attributed to methyl rotor induced 1H–13C heteronuclear cross relaxation in [1–13C] acetate present at 1 T and 77 K.
Control of optically dark n<i>σ*</i> state mediated photodissociation of thioanisole
The methyl photodissociation of thioanisole molecule has been investigated within the mathematical framework of optimal control theory (OCT) considering a reduced dimensional model of three electronic states (ππ, ππ*, and nσ*) and two vibrational modes (S–CH3 stretching and S–CH3 torsional angle). The model includes two bound states (ground state and the ππ* state) and one repulsive state (nσ* state). The effect of the initial vibrational excitation on the branching ratio of the two dissociation channels is examined. In the presence of optimal pulse, methyl photodissociation predominantly occurs via two successive conical intersections. For further justification of the findings of OCT calculations, the field-free quantum dynamics calculations, where the initial wave packet is vertically excited to the ππ* state, are also examined under different initial conditions. A comparative study of these two types of calculations reveals that in the field-free case, photodissociation occurs via the adiabatic path, whereas it follows the nonadiabatic path in the presence of optimal pulse. Therefore, the branching ratio also changes accordingly with the initial conditions for these two types of dynamical events.
Ionization-induced proton and energy transfer in liquid water
We report computational simulation results addressing the ionization response of liquid water upon valence ionization. The simulations cover ionizations in the whole valence-orbital range of liquid water, i.e., vacancies in 1b1, 3a1, 1b2, and 2a1 orbitals. It is found that ionization in any of these valence orbitals leads to rapid proton-transfer dynamics. The timescale on which the proton transfer occurs depends on which type of orbital is ionized. For ionization in the 2a1 orbitals, the proton transfer takes place in about 22 fs, competing with the intermolecular Coulombic decay mechanism that takes place on a similar timescale. This result is discussed in the context of earlier experimental results (Richter et al., Nat. Commun. 9, 4988) regarding the intermolecular Coulombic decay in water. For ionization in the outer-valence orbitals (1b1, 3a1, 1b2), we see rapid internal conversion via non-adiabatic transitions to the electronic ground state. The proton transfer occurs 46, 70, and 91 fs after the initial ionization from a 1b1, 3a1, and 1b2 orbital, respectively. The initial valence ionization induces strong vibrational excitations in the surrounding water molecules, leading to a considerable increase in the local effective temperature. The created heat diffuses into the liquid environment on a timescale of several hundred femtoseconds. We compare the results using two different embedding schemes, subtractive and electrostatic embedding, and find overall very similar dynamics.
Interaction-induced symmetry breaking in circular quantum dots
This paper investigates interaction-induced symmetry breaking in circular quantum dots. We start by explaining what is known about symmetry breaking in quantum dots, pointing out that the anisotropic “static Wigner molecule” ground states frequently observed in simulations are created by interference effects that occur even in the non-interacting limit. They have nothing in common with the interaction-driven crystallization of the uniform electron gas described by Wigner. This leads us to define the term Wigner molecule more carefully via a finite analog of the spontaneous symmetry breaking that arises in the homogeneous electron gas when the interactions are strong. According to this definition, the charge density patterns characteristic of true interaction-induced Wigner molecules can only be seen if a small symmetry-breaking perturbation is applied to a strongly interacting quantum dot. A simple argument based on separation of variables into center-of-mass and internal coordinates shows that the strength of the perturbation required to produce a finite effect on the density tends to zero in the limit as the strength of the interaction tends to infinity. We confirm computationally that interaction-induced Wigner molecules satisfying this definition exist. The neural-network variational Monte Carlo method used in our simulations proves more accurate than the coupled cluster and diffusion Monte Carlo methods employed in previous benchmark calculations of quantum dots at small to intermediate interaction strengths. For high interaction strengths, our neural-network variational Monte Carlo energies agree very well with existing fixed-node diffusion Monte Carlo benchmarks, proving ∼0.01% better for small values of the total spin projection Sz but ∼0.01% worse for fully spin-polarized systems.
Thermodynamic consistency and fluctuations in mesoscopic stochastic simulations of reactive gas mixtures
It is essential that mesoscopic simulations of reactive systems reproduce the correct statistical distributions at thermodynamic equilibrium. By considering a compressible fluctuating hydrodynamics (FHD) simulation method of ideal gas mixtures undergoing reversible reactions described by the chemical Langevin equations, we show that thermodynamic consistency in reaction rates and the use of instantaneous temperatures for the evaluation of reaction rates is required for fluctuations for the overall system to be correct. We then formulate the required properties of a thermodynamically consistent reaction (TCR) model. As noted in the literature, while reactions are often discussed in terms of forward and reverse rates, these rates should not be modeled independently because they must be compatible with thermodynamic equilibrium for the system. Using a simple TCR model where each chemical species has constant heat capacity, we derive the explicit condition that the forward and reverse reaction rate constants must satisfy in order for the system to be thermodynamically consistent. We perform equilibrium and non-equilibrium simulations of ideal gas mixtures undergoing a reversible dimerization reaction to measure the fluctuational behavior of the system numerically. We confirm that FHD simulations with the TCR model give the correct static structure factor of equilibrium fluctuations. For the statistically steady simulation of a gas mixture between two isothermal walls with different temperatures, we show using the TCR model that the temperature variance agrees with the corresponding thermodynamic-equilibrium temperature variance in the interior of the system, whereas noticeable deviations are present in regions near walls, where chemistry is far from equilibrium.
Modulating vibrational energy redistribution in highly conjugated systems
Elucidating the nature of intramolecular vibrational energy redistribution (IVR) can guide the design of molecular wires. The ability to steer these processes through a mechanistic understanding of IVR is assessed by utilizing two-dimensional infrared (2D IR) spectroscopy. 2D IR spectroscopy allows for the direct investigation of timescales of energy transfer within three aromatic molecular scaffolds: 4′-azido-[1,1′-biphenyl]-4-carbonitrile (PAB), 2′-azido-[1,1′-biphenyl]-4-carbonitrile (OAB), and 4′-(azidomethyl)-[1,1′-biphenyl]-4-carbonitrile (PAMB). Energy transfer pathways between azido (N3)- and cyano (CN)-vibrational reporters uncover the importance of Fermi resonances, anharmonic coupling, and specific structural components in directing energy flow. Among these systems, PAB exhibits the fastest energy transfer (22 ps), facilitated by its co-planar biphenyl structure, enabling strong π–π stacking interactions to optimize vibrational coupling. In contrast, OAB demonstrates a moderate IVR timescale (38 ps) due to an orthogonal molecular plane and steric hindrance, which disrupts coupling pathways. PAMB, with a para-methylene group, introduces a structural bottleneck that significantly impedes energy flow, slowing down the energy transfer to 84 ps. The observed IVR rates align with computational predictions, highlighting intermediate ring modes in PAB as efficient energy transfer bridges, a mechanism that is less pronounced in OAB and PAMB. This study demonstrates that IVR is dictated not only by anharmonic coupling strengths but also by the extended alignment of vibrational modes across molecular planes and their delocalization within aromatic scaffolds. By modulating structural features, such as steric constraints and π–π interactions, we provide a framework for tailoring energy flow in conjugated molecular systems. These findings offer new insights into IVR dynamics for applications in molecular electronics.
Tracking nuclear wave packets in excited-state reactions via quantum mechanics/molecular dynamics simulations
Nuclear wave packets (NWPs) in electronically excited states generated by ultrashort laser pulses can persist through photochemical processes and be detected in the product state. The NWPs that are coupled with the reaction dynamics undergo changes during the process and provide crucial insights into potential energy surfaces and molecular reaction dynamics. We present a computational method to calculate NWPs in the products of ultrafast photochemical processes by projecting nuclear displacements, obtained via Born–Oppenheimer molecular dynamics simulations, onto the normal modes of the reaction product state. Applying this approach to the excited-state intramolecular proton transfer reaction of 10-hydroxybenzo[h]quinoline, we successfully reproduced the experimentally observed NWPs in the reaction product, which were measured by time-resolved fluorescence of the product state with high fidelity. This significant achievement enables the analysis of individual normal mode motions following photoexcitation in chemical and physical processes. By integrating highly time-resolved spectroscopy with computational modeling, this method provides an effective approach to investigate the excited-state potential energy surfaces and the associated nuclear dynamics.
Microsecond-scale observation of phase transition and diffusion in 5CB liquid crystal at the molecular level
Molecular dynamics methods have proven their applicability for the simulation of the structure and properties of liquid crystals. For the reproduction of phase transitions in liquid crystals, many authors have reparameterized the classical force fields. For the first time, we demonstrate that even a general-purpose force field, for example, General AMBER Force Field (GAFF), without modifications is also capable of reproducing an isotropic–nematic transition at 300 K within microsecond-scale simulations. However, the isotropic–nematic transition enthalpy is overestimated, which leads to higher thermodynamic stability of the nematic phase. For the obtained nematic phase, the calculations of self-diffusion are performed during almost 2 μs at different temperatures, which are compared against previous experimental and computational studies. The diffusion coefficients are underestimated compared with the experiment because of stronger molecular interactions. The diffusion anisotropy ratio lies within the experimental observations. Our work justifies the key problems of GAFF in reproducing the properties of the 5CB liquid crystal.
Theoretical study on the core-excited states of the allyl using multi-reference methods with core–valence separation (CVS) approximation
The multi-state n-electron valence second-order perturbation theory with core–valance separation (CVS) approximation (CVS-MS-NEVPT2) and static-dynamic-static multi-state multi-reference second-order perturbation theory with CVS (CVS-SDSPT2) were developed based on the internally contracted multi-reference configuration interaction method with single and double excitations with CVS (CVS-icMRCISD) [Song et al., J. Chem. Phys. 160, 094114 (2024)] due to their high similarity and inheritance in theoretical frameworks and computational implementation. Benchmark calculations demonstrate that these perturbation methods significantly improved computational efficiency while maintaining comparable accuracy to the CVS-icMRCISD method. Moreover, the core-excited states of the allyl system were used as a pilot application for three CVS-multi-reference methods. The CVS-icMRCISD method produced four excited states at 282.10, 285.11, 286.18, and 288.07 eV, accurately reproducing four distinctive peaks (A, B, C, and D) in the experimental x-ray absorption spectra (XAS). Theoretical excitation energies of two core-excited states of the allyl cation (282.64 and 286.88 eV) align with the peaks observed at 282.52 and 286.92 eV in the experimental XAS. However, vibrational analysis of the X–A transition suggests that the α band in the experimental XAS might arise from electronic–vibronic coupling between the antisymmetric stretching of C–H bonds in the -CTH2 group and the core-excited state, leaving the assignment of the α band ambiguous. Overall, the CVS-icMRCISD method achieved excellent agreement with experimental results, with an average deviation of 0.25 eV. While the errors of CVS-SDSPT2 and CVS-MS-NEVPT2 methods were slightly larger, both methods maintained acceptable accuracy, making them suitable for medium-sized molecules by significantly reducing computational costs.
A graph-based statistical model for carbon nanostructures
Energy degeneracy in physical systems may be induced by symmetries of the Hamiltonian, and the resonance of degeneracy states in carbon nanostructures can effectively enhance the stability of the system. Combining the octet rule, we introduce a statistical model to determine the physical properties by lifting the energy degeneracy in carbon nanostructures. This model offers a direct path to accurately ascertain electron density distributions in quantum systems, akin to how charge density is used in density functional theory to deduce system properties. Our methodology diverges from traditional quantum mechanics, focusing instead on this unique statistical model by maximizing bonding entropy to determine the fundamental properties of materials. Applied to carbon nanoclusters and graphynes, our model not only precisely predicts bonding energies and electron density without relying on external parameters but also enhances the prediction of electronic structures through bond occupancy numbers, which act as effective hopping integrals. This innovation offers insights into the structural properties and quantum behavior of electrons across various dimensions.
Impact of carbon dioxide loading on the thermal conductivity of metal organic frameworks
Owing to their unrivaled porosities and high surface areas, metal organic frameworks (MOFs) hold great promise for mitigating the global warming crisis through capturing and storing CO2 gas. However, the exothermic process of CO2 uptake can lead to temperature rises that can severely compromise the efficiency of these materials for such purposes. In this work, we employ reactive molecular dynamics simulations and anharmonic lattice dynamics calculations to investigate the influence of varying levels of CO2 uptake in dictating the heat transfer mechanisms in MOF-5. Compared to the empty framework, we find that the thermal conductivity of the gas loaded framework is highly dependent on the gas diffusivities and temperatures. At low temperatures, where the gases have low diffusivities and are predominantly adsorbed to the pore walls, vibrational scattering from the solid–gas interactions leads to drastically reduced thermal conductivities. At higher temperatures (above ∼200 K), however, we find that the CO2 molecules with increased diffusivities can lead to additional channels of heat conduction for high gas densities. Our spectral analyses show that the addition of gas adsorbates has a negligible influence on the heat carrying acoustic modes of the framework at such relatively higher temperatures. Contrastingly, at lower temperatures, gas infiltration leads to considerable scattering and reduced lifetimes of the acoustic vibrational modes of the framework. These findings provide critical insights into the mechanistic processes dictating heat conduction in guest-infiltrated MOFs and offer a pathway to tailor their thermal properties for advanced applications in gas storage, separation, catalysis, and thermoelectrics.
Spin–orbit interactions, time-reversal symmetry, and spin selection
Spin selective transport is usually associated with spin–orbit interactions. However, these interactions are invariant under time-reversal symmetry, and the Onsager relations and Bardarson’s theorem imply that such interactions cannot yield spin selectivity for transport through a junction between two electronic reservoirs. Here, we review several ways to overcome this restriction, using a Zeeman magnetic field, the Aharonov–Bohm phase, time-dependent electric fields that generate time-dependent spin–orbit interactions, time-dependent transients, more than two terminals, leakage, and more than one level per ion on the junction. Our considerations focus on the transport of noninteracting electrons at low temperatures. A possible connection with the phenomenon of chiral-induced spin selectivity is pointed out in one of the systems considered.
Computational analysis of the spatial distributions of low-energy electrons generated via water photolysis and photoinjection into electrodes in water
Herein, we develop a dynamic Monte Carlo code for simulating physical processes occurring during electron transport and collisions in water. This code explicitly accounts for both collisions and Coulombic interactions when simulating the spatial distributions of low-energy electrons generated via liquid water ionization in two-photon laser excitation experiments. The consideration of the Coulombic field of the parent cation is a critical factor in these calculations. To verify the versatility of dmcc_phys, it is applied to replicate data obtained from contrastive experiments involving the ejection of low-energy electrons through photoinjection into electrodes in water, devoid of parent cations owing to electronic polarization. The calculations successfully reproduce both scenarios, demonstrating that our code, which integrates Monte Carlo and molecular dynamics methods, provides an advantage in simulating electron delocalization and relocalization into the parent cation compared with conventional Monte Carlo track-structure simulations, such as the particle and heavy ion transport code system and Geant4-DNA. Furthermore, we analyze the simulation results by fitting them against a combination of Gaussian and exponential distributions. Our findings indicate that electrons ejected by radiation depositing an energy of 11.9 eV distribute more extensively, resulting in a spur radius of 4 nm—larger than the 3 nm radius predicted using conventional methods. These capabilities enable precise estimation of the initial spur radius, a crucial parameter for predicting the time-dependent yields of hydrated electrons during the chemical stage.
Simulating quantum circuit expectation values by Clifford perturbation theory
The classical simulation of quantum circuits is of central importance for benchmarking near-term quantum devices. The fact that gates belonging to the Clifford group can be simulated efficiently on classical computers has motivated a range of methods that scale exponentially only in the number of non-Clifford gates. Here, we consider the expectation value problem for circuits composed of Clifford gates and non-Clifford Pauli rotations and introduce a heuristic perturbative approach based on the truncation of the exponentially growing sum of Pauli terms in the Heisenberg picture. Numerical results are shown on a quantum approximate optimization algorithm benchmark for the E3LIN2 problem, and we also demonstrate how this method can be used to quantify coherent and incoherent errors of local observables in Clifford circuits. Our results indicate that this systematically improvable perturbative method offers a viable alternative to exact methods for approximating expectation values of large near-Clifford circuits.
A charge calibration strategy for describing the charge transfer during the electrochemical elementary step
Constant potential modeling of electrocatalytic processes remains a significant challenge in the field of computational catalysis, primarily due to the difficulty in simultaneously considering the influence of constant potential conditions, explicit solvent environment, and the double-layer structure. In this work, we propose a charge calibration strategy for electrocatalytic processes. This strategy accounts for charge transfer in systems with explicit solvation and ions during constant-potential free energy modeling. In our strategy, interfacial counter-ions are employed to model the Helmholtz layer and determine the surface charge density, which defines the electrode potential. During the simulation of electrochemical reactions, extra charges are introduced/extracted to/from the system to compensate for electron transfer between the electrode and the reaction species and keep a constant surface charge density along the reaction profile. Our method showcases the impact of potential-dependent solvent reorganization on reaction kinetics and underscores the importance of constant potential kinetics. We anticipate that the strategy presented here will inspire further theoretical and experimental studies for electrochemistry interfaces.
Structural stability of wireframe DNA origami: The role of nanocomponent modifications
Wireframe DNA origami nanostructures hold immense potential for diverse applications in nanotechnology. The design of wireframe DNA origami structures traditionally follows a top–down approach. This study introduces a complementary bottom–up approach to investigate the nano-components constituting these nanostructures and their impact on structural stability. To this end, modifications to edge staple crossovers, poly-T bulges, and staple sequences were examined through coarse-grained molecular dynamics. The results reveal that reducing the number of edge staple crossovers slightly alters the distance between the two double-stranded DNA helices forming the edges but maintains adequate structural stability. The removal of poly-T bulges, however, leads to edge opening under specific thermal conditions, whereas structures containing poly-T bulges remain intact, highlighting their critical role in edge stability. Furthermore, changes to the staple sequences, achieved by repositioning the scaffold nick, showed negligible effects on the overall stability of the wireframe DNA origami structures. The incorporation of a bottom–up approach in designing wireframe DNA origami structures can enable the creation of nanostructures with tailored properties for specific applications. These modifications can be adapted for a variety of wireframe DNA origami structures, broadening their potential uses in nanotechnology.