Vibrational Degrees Of Freedom Research Articles

Large Orbital Moment and Dynamical Jahn-Teller Effect of AlCl-Phthalocyanine on Cu(100).

Submonolayer amounts of chloroaluminum-phthalocyanine on Cu(100) were studied with scanning tunneling spectroscopy. The molecule can be prepared in a fourfold symmetric state whose conductance spectrum exhibits a zero-bias feature similar to a Kondo resonance. In magnetic fields, however, this resonance splits far more than expected from the spin of a single electron. Density functional theory calculations reveal a charge transfer of 1.3 electrons to the degenerate lowest unoccupied molecular orbitals. These orbitals are mixed by the orbital momentum operator L[over ^]_{z} with a large matrix element corresponding to m_{L}≈2.7. Dehydrogenation of a ligand lifts the degerenracy of the lowest unoccupied molecular orbital, reduces the splitting in magnetic fields, and induces a polarity dependence of the spectra. Using model calculations of the spin, orbital, and vibrational degrees of freedom we show that a dynamical Jahn-Teller effect reproduces the main experimental observations.

First-Principles Modeling of the Absorption Spectrum of Crystal Violet in Solution: The Importance of Environmentally Driven Symmetry Breaking.

Theoretical spectroscopy plays a crucial role in understanding the properties of the materials and molecules. One of the most promising methods for computing optical spectra of chromophores embedded in complex environments from the first principles is the cumulant approach, where both (generally anharmonic) vibrational degrees of freedom and environmental interactions are explicitly accounted for. In this work, we verify the capabilities of the cumulant approach in describing the effect of complex environmental interactions on linear absorption spectra by studying Crystal Violet (CV) in different solvents. The experimental absorption spectrum of CV strongly depends on the nature of the solvent, indicating strong coupling to the condensed-phase environment. We demonstrate that these changes in absorption line shape are driven by an increased splitting between absorption bands of two low-lying excited states that is caused by a breaking of the D3 symmetry of the molecule and that in polar solvents, this symmetry breaking is mainly driven by electrostatic interactions with the condensed-phase environment rather than distortion of the structure of the molecule, in contrast with conclusions reached in a number of previous studies. Our results reveal the importance of explicitly including a counterion in the calculations in nonpolar solvents due to electrostatic interactions between CV and the ion. In polar solvents, these interactions are strongly reduced due to solvent screening effects, thus minimizing the symmetry breaking. Computed spectra in methanol are found to be in reasonable agreement with the experiment, demonstrating the strengths of the outlined approach in modeling strong environmental interactions.

Spectral Signatures of Vibronic Coupling in Trapped Cold Ionic Rydberg Systems.

Atoms and ions confined with electric and optical fields form the basis of many current quantum simulation and computing platforms. When excited to high-lying Rydberg states, long-ranged dipole interactions emerge which strongly couple the electronic and vibrational degrees of freedom through state-dependent forces. This vibronic coupling and the ensuing hybridization of internal and external degrees of freedom manifest through clear signatures in the many-body spectrum. We illustrate this by considering the case of two trapped Rydberg ions, for which the interaction between the relative vibrations and Rydberg states realizes a quantum Rabi model. We proceed to demonstrate that the aforementioned hybridization can be probed by radio frequency spectroscopy and discuss observable spectral signatures at finite temperatures and for larger ion crystals.

MesoHOPS: Size-invariant scaling calculations of multi-excitation open quantum systems.

The photoexcitation dynamics of molecular materials on the 10-100nm length scale depend on complex interactions between electronic and vibrational degrees of freedom, rendering exact calculations difficult or intractable. The adaptive Hierarchy of Pure States (adHOPS) is a formally exact method that leverages the locality imposed by interactions between thermal environments and electronic excitations to achieve size-invariant scaling calculations for single-excitation processes in systems described by a Frenkel-Holstein Hamiltonian. Here, we extend adHOPS to account for arbitrary couplings between thermal environments and vertical excitation energies, enabling formally exact, size-invariant calculations that involve multiple excitations or states with shared thermal environments. In addition, we introduce a low-temperature correction and an effective integration of the noise to reduce the computational expense of including ultrafast vibrational relaxation in Hierarchy of Pure States (HOPS) simulations. We present these advances in the latest version of the open-source MesoHOPS library and use MesoHOPS to characterize charge separation at a one-dimensional organic heterojunction when both the electron and hole are mobile.

Basis Electronic Activity of Molecular Systems. A Theory of Bond Reactivity.

In this paper, we present a new finding, the basis electronic activity (BEA) of molecular systems; it corresponds to the significant, although nonreactive, vibrationally induced electronic activity that takes place in any molecular system. Although the molecule's BEA is composed of an equal number of local contributions as the vibrational degrees of freedom, our results indicate that only stretching modes contribute to it. To account for this electronic activity, a new descriptor, the bond electronic flux (BEF), is introduced. The BEF combined with the force constant of the potential well hosting the electronic activity gives rise to the effective bond reactivity index (EBR), which turns out to be the first density functional theory-based descriptor that simultaneously accounts for structural and electronic effects. Besides quantifying the bond reactivity, EBR provides a basis to compare the reactivities of bonds inserted in different chemical environments and paves the way for the exertion of selective control to enhance or inhibit their reactivities. The new concepts formulated in this paper and the associated computational tools are illustrated with characterization of the BEA of a set of representative molecules. In all cases, the BEFs follow the same linear pattern, whose slopes indicate the intensity of the electronic activity and quantify the reactivity of chemical bonds.

Electronic Moment Tensor Potentials include both electronic and vibrational degrees of freedom

We present the electronic moment tensor potentials (eMTPs), a class of machine-learning interatomic models and a generalization of the classical MTPs, reproducing both the electronic and vibrational degrees of freedom, up to the accuracy of ab initio calculations. Following the original polynomial interpolation idea of the MTPs, the eMTPs are defined as polynomials of vibrational and electronic degrees of freedom, corrected to have a finite interatomic cutoff. Practically, an eMTP is constructed from the classical MTPs fitted to a training set, whose energies and forces are calculated with electronic temperatures corresponding to the Chebyshev nodes on a given temperature interval. The eMTP energy is hence a Chebyshev interpolation of the classical MTPs. Using the eMTP, one can obtain the temperature-dependent vibrational free energy including anharmonicity coming from phonon interactions, the electronic free energy coming from electron interactions, and the coupling of atomic vibrations and electronic excitations. Each of the contributions can be accessed individually using the proposed formalism. The performance of eMTPs is demonstrated for two refractory systems which have a significant electronic, vibrational and coupling contribution up to the melting point—unary Nb, and a disordered TaVCrW high-entropy alloy. Highly accurate thermodynamic and kinetic quantities can now be obtained just by using eMTPs, without any further ab initio calculations. The proposed construction to include the electronic degree of freedom can also be applied to other machine-learning models.

Connecting dielectric response to dominant vibrations and tolerance factors in pyrochlore oxides

Dielectric screening originating from electronic and vibrational degrees of freedom is a fundamental material’s property. This property is crucial for materials used as high K-gate dielectric with metal gates in field-effect transistors in integrated circuits. Therefore, we atomically explore phonons responsible for dielectric screening in rare-earth pyrochlores zirconate oxides, RE2Zr2O6O’ (RE = Pr, Nd, Sm, Eu, and Gd), and suggest pathways for engineering the dielectric response for better dielectric insulators. The predicted crystal structures are close to the ideal pyrochlore structure but show a tendency towards the fluorite structure along the family (which alters dielectric screening). A significant contribution towards the dielectric screening originates from the infrared-active vibration (F1u named as m2) near 125 cm−1, which is mainly due to O’-RE-O’ bend. The vibration near 200 cm−1 also has notable contribution but shows a gradual decrease along the family. A relation between tolerance factors (t1 and t2) of pyrochlores and dielectric response is developed for the first time. Specifically, a linear relation of t2 with dominating vibration (m2) contributing to the dielectric constant paves the way to engineer the dielectric screening by a simple calculation of the tolerance factor in pyrochlore zirconates.

Solving Vibronic Dynamics in Electron Continuum.

We present a general two-dimensional model of conical intersection between metastable states that are vibronically coupled not only directly but also indirectly through a virtual electron in the autodetachment continuum. This model is used as a test ground for the design and comparison of iterative solvers for resonance dynamics in low-energy electron-molecule collisions. Two Krylov-subspace methods with various preconditioning schemes are compared. To demonstrate the applicability of the proposed methods on even larger models, we also test the performance of one of the methods on a recent model of vibrational excitation of CO2 by electron impact based on three vibronically coupled discrete states in continuum (Renner-Teller doublet of shape resonances coupled to a sigma virtual state) including four vibrational degrees of freedom. Two-dimensional electron energy-loss spectra resulting from electron-molecule scattering within the models are briefly discussed.

Cavity-Mediated Molecular Entanglement and Generation of Non-classical States of Light.

The generation and control of entanglement in a quantum mechanical system are critical elements of nearly all quantum applications. Molecular systems are promising candidates, with numerous degrees of freedom able to be targeted. However, knowledge of intersystem entanglement mechanisms in such systems is limited. In this work, we demonstrate the generation of entanglement between vibrational degrees of freedom in molecules via strong coupling to a cavity mode driven by a weak coherent field. In a bimolecular system, we show that entanglement can be generated not only between the cavity and molecular system but also between molecules. This process also results in the generation of nonclassical states of light, providing potential pathways for harnessing entanglement in molecular systems.

Vibronic effects on the quantum tunnelling of magnetisation in Kramers single-molecule magnets

Single-molecule magnets are among the most promising platforms for achieving molecular-scale data storage and processing. Their magnetisation dynamics are determined by the interplay between electronic and vibrational degrees of freedom, which can couple coherently, leading to complex vibronic dynamics. Building on an ab initio description of the electronic and vibrational Hamiltonians, we formulate a non-perturbative vibronic model of the low-energy magnetic degrees of freedom in monometallic single-molecule magnets. Describing their low-temperature magnetism in terms of magnetic polarons, we are able to quantify the vibronic contribution to the quantum tunnelling of the magnetisation, a process that is commonly assumed to be independent of spin-phonon coupling. We find that the formation of magnetic polarons lowers the tunnelling probability in both amorphous and crystalline systems by stabilising the low-lying spin states. This work, thus, shows that spin-phonon coupling subtly influences magnetic relaxation in single-molecule magnets even at extremely low temperatures where no vibrational excitations are present.

Understanding and fine tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine.

Liquid-liquid phase separation (LLPS) plays a pivotal role in the organization and functionality of living cells. It is imperative to understand the underlying driving forces behind LLPS and to control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool to investigate systems comprising oligolysine and adenosine triphosphate (ATP) under conditions of various ionic concentrations and oligolysine lengths. Consistent with experimental observations, our CG simulations captured the formation of LLPS upon the addition of ATP and tendency of dissociating under high ionic concentration. The electrostatic interaction between oligolysine and ATP is of great importance in forming LLPS. An in-depth analysis on the structural properties of LLPS was conducted, where the oligolysine structure remained unchanged with increased ionic concentration and the addition of ATP led to a more pronounced curvature, aligning with the observed enhancement of α-helical secondary structure in experiments. In terms of the dynamic properties, the introduction of ATP led to a significant reduction in translational and vibrational degrees of freedom but not rotational degrees of freedom. Through keeping the total number of charged residues constant and varying their entropic effects, we constructed two systems of similar biochemical significance and further validated the entropy effects on the LLPS formation. These findings provide a deeper understanding of LLPS formation and shed lights on the development of novel bioreactor and primitive artificial cells for synthesizing key chemicals for certain diseases.

Resonance Enhancement of Vibrational Polariton Chemistry Obtained from the Mixed Quantum-Classical Dynamics Simulations.

We applied a variety of mixed quantum-classical (MQC) approaches to simulate the VSC-influenced reaction rate constant. All of these MQC simulations treat the key vibrational levels associated with the reaction coordinate in the quantum subsystem (as quantum states), whereas all other degrees of freedom (DOFs) are treated inside the classical subsystem. We find that, as long as we have the quantum state descriptions for the vibrational DOFs, one can correctly describe the VSC resonance condition when the cavity frequency matches the bond vibrational frequency. This correct resonance behavior can be obtained regardless of the detailed MQC methods that one uses. The results suggest that the MQC approaches can generate semiquantitative agreement with the exact results for rate constant changes when changing the cavity frequency, the light-matter coupling strength, or the cavity lifetime. The finding of this work suggests that one can use computationally economic MQC approaches to explore the collective coupling scenario when many molecules are collectively coupled to many cavity modes in the future.

Cavity-Modified Chemiluminescent Reaction of Dioxetane.

Chemiluminescence is a thermally activated chemical process that emits a photon of light by forming a fraction of products in the electronic excited state. A well-known example of this spectacular phenomenon is the emission of light in the firefly beetle, where the formation of a four-membered cyclic peroxide compound and subsequent dissociation produce a light-emitting product. The smallest cyclic peroxide, dioxetane, also exhibits chemiluminescence but with a low quantum yield as compared to that of firefly dioxetane. Employing the strong light-matter coupling has recently been found to be an alternative strategy to modify the chemical reactivity. In the presence of an optical cavity, the molecular degrees of freedom greatly mix with the cavity mode to form hybrid cavity-matter states called polaritons. These newly generated hybrid light-matter states manipulate the potential energy surfaces and significantly change the reaction dynamics. Here, we theoretically investigate the effects of a strong light-matter interaction on the chemiluminescent reaction of dioxetane using the extended Jaynes-Cummings model. The cavity couplings corresponding to the electronic and vibrational degrees of freedom have been included in the interaction Hamiltonian. We explore how the cavity alters the ground- and excited-state path energy barriers and reaction rates. Our results demonstrate that the formation of excited-state products in the dioxetane decomposition process can be either accelerated or suppressed, depending on the molecular orientation with respect to the cavity polarization.

Transition Temperature for Spin-Crossover Materials with the Mean Value Ensemble Hubbard-U Correction.

Calculation of transition temperatures T1/2 for thermally driven spin-crossover in condensed phases is challenging, even with sophisticated state-of-the-art density functional approximations. The first issue is the accuracy of the adiabatic crossover energy difference ΔEHL between the low- and high-spin states of the bistable metal-organic complexes. The other is the proper inclusion of entropic contributions to the Gibbs free energy from the electronic and vibrational degrees of freedom. We discuss the effects of treatments of both contributions upon the calculation of thermochemical properties for a set of 20 spin-crossover materials using a Hubbard-U correction obtained from a reference ensemble spin-state. The U values obtained from a simplest bimolecular representation may overcorrect, somewhat, the ΔEHL values, hence giving somewhat excessive reduction of the T1/2 results with respect to their U = 0 values in the crystalline phase. We discuss the origins of the discrepancies by analyzing different sources of uncertainties. By use of a first-coordination-sphere approximation and the assumption that vibrational contributions from the outermost atoms in a metal-organic complex are similar in both low- and high-spin states, we achieve T1/2 results with the low-cost, widely used PBE generalized gradient density functional approximation comparable to those from the more costly, more sophisticated r2SCAN meta-generalized gradient approximation. The procedure is promising for use in high-throughput materials screening, because it combines rather low computational effort requirements with freedom from user manipulation of parameters.

Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism.

Proteins are natural polymers that play an essential role in both living organisms and biotechnological applications. During certain bioprocessing steps, they can be exposed to significant mechanical stress induced by, for example, shear flow or sonication, resulting in reduced therapeutic efficacy, aggregation, or even a loss of activity. For this reason, there is a need to understand and determine the susceptibility of the protein activity to the experienced mechanical stress. To acquire this knowledge, it is necessary to study the rotational dynamics of the protein. Commonly, the rotational dynamics of soft molecules is interpreted based on a theoretical analysis performed in an inertial laboratory frame. However, the obtained angular velocity mixes pure rotations and vibrations with angular momentum, consequently lacking a clear dynamical interpretation. On the other hand, the use of the noninertial internal Eckart frame allows the determination of pure angular velocity as it minimizes the coupling between the rotational and vibrational degrees of freedom. In the present work, by conducting open-boundary molecular dynamics simulations and exploiting the Eckart frame formalism, we study the rotational dynamics of a small protein under the shear flow of various strengths. Our results show that the angular velocity increases nonlinearly with increasing shear rate. Furthermore, the protein gains vibrational angular momentum at higher shear rates, which is reflected in the higher angular velocity computed by employing the Eckart frame formalism and confirmed by analysis of the contributions to the total kinetic energy of the biomolecule.

Multi-degree-of-freedom kinetic model and its applications in simulation of three-dimensional nonequilibrium flows

A multi-degree-of-freedom (MDOF) kinetic model is developed to simulate three-dimensional nonequilibrium flows. By modifying collision term of Boltzmann model equation, a multi-scale molecular collision mechanism with translational, rotational and vibrational degrees of freedom is indicated by three coupled relaxation processes. Molecular vibration is modeled by harmonic oscillator. As a result, the degree of freedom of vibration may be directly related to temperature. Internal energy of various degrees of freedom are computed based on the equipartition theorem, and equilibrium distribution functions for each relaxation step are calculated. The present MDOF kinetic model is beneficial for assessing multi-scale evolutions of internal energy and molecular inelastic collisions. Several three-dimensional flow cases, including lid-driven cavity flow and hypersonic flows around a blunt cone at varying angles of attack, are simulated using the current MDOF technique. All numerical results were consistent with the reference data. It was shown that the proposed MDOF kinetic model well explains the vibration–rotation-translation energy exchange of polyatomic molecules in high-temperature gas, and that the current computational technique is a useful engineering tool for nonequilibrium aerodynamic research.

Performance of two complementary machine-learned potentials in modelling chemically complex systems

Chemically complex multicomponent alloys possess exceptional properties derived from an inexhaustible compositional space. The complexity however makes interatomic potential development challenging. We explore two complementary machine-learned potentials—the moment tensor potential (MTP) and the Gaussian moment neural network (GM-NN)—in simultaneously describing configurational and vibrational degrees of freedom in the Ta-V-Cr-W alloy family. Both models are equally accurate with excellent performance evaluated against density-functional-theory. They achieve root-mean-square-errors (RMSEs) in energies of less than a few meV/atom across 0 K ordered and high-temperature disordered configurations included in the training. Even for compositions not in training, relative energy RMSEs at high temperatures are within a few meV/atom. High-temperature molecular dynamics forces have similarly small RMSEs of about 0.15 eV/Å for the disordered quaternary included in, and ternaries not part of training. MTPs achieve faster convergence with training size; GM-NNs are faster in execution. Active learning is partially beneficial and should be complemented with conventional human-based training set generation.

Spin-vibronic coherence drives singlet-triplet conversion.

Design-specific control over the transitions between excited electronic states with different spin multiplicities is of the utmost importance in molecular and materials chemistry1-3. Previous studies have indicated that the combination of spin-orbit and vibronic effects, collectively termed the spin-vibronic effect, can accelerate quantum-mechanically forbidden transitions at non-adiabatic crossings4,5. However, it has been difficult to identify precise experimental manifestations of the spin-vibronic mechanism. Here we present coherence spectroscopy experiments that reveal the interplay between the spin, electronic and vibrational degrees of freedom that drive efficient singlet-triplet conversion in four structurally related dinuclear Pt(II) metal-metal-to-ligand charge-transfer (MMLCT) complexes. Photoexcitation activates the formation of a Pt-Pt bond, launching a stretching vibrational wavepacket. The molecular-structure-dependent decoherence and recoherence dynamics of this wavepacket resolve the spin-vibronic mechanism. We find that vectorial motion along the Pt-Pt stretching coordinates tunes the singlet and intermediate-state energy gap irreversibly towards the conical intersection and subsequently drives formation of the lowest stable triplet state in a ratcheting fashion. This work demonstrates the viability of using vibronic coherences as probes6-9 to clarify the interplay among spin, electronic and nuclear dynamics in spin-conversion processes, and this could inspire new modular designs to tailor the properties of excited states.

High-temperature reactivity of vanadium oxide clusters in methane activation: Vibrational degrees of freedom matter.

Understanding the properties of small particles working under high-temperature conditions at the atomistic scale is imperative for exact control of related processes, but it is quite challenging to achieve experimentally. Herein, benefitting from state-of-the-art mass spectrometry and by using our newly designed high-temperature reactor, the activity of atomically precise particles of negatively charged vanadium oxide clusters toward hydrogen atom abstraction (HAA) from methane, the most stable alkane molecule, has been measured at elevated temperatures up to 873K. We discovered the positive correlation between the reaction rate and cluster size that larger clusters possessing greater vibrational degrees of freedom can carry more vibrational energies to enhance the HAA reactivity at high temperature, in contrast with the electronic and geometric issues that control the activity at room temperature. This finding opens up a new dimension, vibrational degrees of freedom, for the simulation or design of particle reactions under high-temperature conditions.

Current-induced forces in nanosystems: A hierarchical equations of motion approach

An approach to calculating current-induced forces in charge transport through nanosystems is introduced. Starting from the fully quantum mechanical hierarchical equations of motion formalism, a timescale separation between electronic and vibrational degrees of freedom is used to derive a classical Langevin equation of motion for the vibrational dynamics as influenced by current-induced forces, such as the electronic friction. The resulting form of the friction is shown to be equivalent to previously derived expressions. The numerical exactness of the hierarchical equations of motion approach, however, allows the investigation of transport scenarios with strong intrasystem and system-environment interactions. As a demonstration, the electronic friction of three example systems is calculated and analyzed: a single electronic level coupled to one classical vibrational mode, an Anderson impurity model coupled to one classical vibrational mode, and a single electronic level coupled to both a classical and quantum vibrational mode.