Molecular Systems Research Articles

Strong coupling in molecular systems: a simple predictor employing routine optical measurements

Abstract We provide a simple method that enables readily acquired experimental data to be used to predict whether or not a candidate molecular material may exhibit strong coupling. Specifically, we explore the relationship between the hybrid molecular/photonic (polaritonic) states and the bulk optical response of the molecular material. For a given material, this approach enables a prediction of the maximum extent of strong coupling (vacuum Rabi splitting), irrespective of the nature of the confined light field. We provide formulae for the upper limit of the splitting in terms of the molar absorption coefficient, the attenuation coefficient, the extinction coefficient (imaginary part of the refractive index) and the absorbance. To illustrate this approach, we provide a number of examples, and we also discuss some of the limitations of our approach.

Noncovalent Catalyst-cum-Inhibitor Directed Supramolecular Pathway Selection and Asymmetry Amplification by Aggregate Cross-Nucleation.

The key to any controlled supramolecular polymerization (CSP) process lies in controlling the nucleation step, which is typically achieved by sequestering monomers in a kinetically trapped state. However, kinetic traps that are shallow cannot prevent spontaneous nucleation, thus limiting the applicability of the CSP in such systems. We use a molecular additive to overcome this limitation by modifying the energy landscape of a competitive self-assembly process and increasing the kinetic stability of an otherwise short-lived trap state. The additive achieves this by simultaneously catalyzing OFF-pathway nucleation and inhibiting ON-pathway aggregation. In the process, it guides the molecular assembly exclusively toward the OFF-pathway aggregate analogue. The mechanisms of OFF-pathway catalysis and ON-pathway inhibition are elucidated. By specifically targeting the nucleation step, it was possible to achieve pathway selection at an extremely low additive-to-monomer ratio of 1:100. The generality of our approach is also demonstrated for other related molecular systems. Finally, removing the additive triggers the cross-nucleation of the ON-pathway aggregate on the surface of a less stable, OFF-pathway aggregate analogue. The resultant supramolecular polymer not only exhibits a more uniform morphology but more importantly, a marked improvement in the structural order that leads to an amplification of chiral asymmetry and a high absorption dissymmetry factor (gAbs) of ∼0.05.

A potential building block for spintronic devices: Theoretical description of electronic transport and magnetoresistance of catechol under an external magnetic field stimulus

Understanding the electronic transport properties of low-dimensional devices has increased dramatically in recent decades, especially for those with a promising future for application in nanotechnology. Among these nanoscopic systems are molecular systems, particularly organic molecules such as catechol, representing the small piece of a potential conductor assembled through larger biomolecules and inserted between two or more metal contacts. In this work, we present a theoretical description of the electronic transport of catechol, based on its π-conjugated aromatic system, under an external magnetic field stimulus, which is transverse to the alignment of the molecule. Thus, we analyze catechol’s spintronic properties through the magnetoresistance generated by this field. We model the molecule using a tight-binding Hamiltonian and Green’s functions; the transmission probability is calculated by means of the Fisher-Lee relation, and the characteristic current–voltage, spin polarization, and magnetoresistance curves based on Landauer’s approach for two linking models of catechol to the metallic contacts. The results suggest a strong dependence on the spin direction of the charge carriers and the Zeeman energy (Ez) on the Fermi level, generating a switch-like mechanism going from conducting to semiconducting material. This behavior opens a potential application of these catechol-based systems in future spintronic devices.

Unveiling the interaction mechanisms of cold atmospheric plasma and amino acids by machine learning

AbstractPlasma medicine has attracted tremendous interest in a variety of medical conditions, ranging from wound healing to antimicrobial applications, even in cancer treatment, through the interactions of cold atmospheric plasma (CAP) and various biological tissues directly or indirectly. The underlying mechanisms of CAP treatment are still poorly understood although the oxidative effects of CAP with amino acids, peptides, and proteins have been explored experimentally. In this study, machine learning (ML) technology is introduced to efficiently unveil the interaction mechanisms of amino acids and reactive oxygen species (ROS) in seconds based on the data obtained from the reactive molecular dynamics (MD) simulations, which are performed to probe the interaction of five types of amino acids with various ROS on the timescale of hundreds of picoseconds but with the huge computational load of several days. The oxidative reactions typically start with H‐abstraction, and the details of the breaking and formation of chemical bonds are revealed; the modification types, such as nitrosylation, hydroxylation, and carbonylation, can be observed. The dose effects of ROS are also investigated by varying the number of ROS in the simulation box, indicating agreement with the experimental observation. To overcome the limits of timescales and the size of molecular systems in reactive MD simulations, a deep neural network (DNN) with five hidden layers is constructed according to the reaction data and employed to predict the type of oxidative modification and the probability of occurrence only in seconds as the dose of ROS varies. The well‐trained DNN can effectively and accurately predict the oxidative processes and productions, which greatly improves the computational efficiency by almost ten orders of magnitude compared with the reactive MD simulation. This study shows the great potential of ML technology to efficiently unveil the underpinning mechanisms in plasma medicine based on the data from reactive MD simulations or experimental measurements.

Extracting accurate light–matter couplings from disordered polaritons

Abstract The vacuum Rabi splitting (VRS) in molecular polaritons stands as a fundamental measure of collective light–matter coupling. Despite its significance, the impact of molecular disorder on VRS is not fully understood yet. This study delves into the complexities of VRS amidst various distributions and degrees of disorder. Our analysis provides precise analytical expressions for linear absorption, transmission, and reflection spectra, along with a “sum” rule, offering a straightforward protocol for extracting accurate collective light–matter coupling values from experimental data. Importantly, our study cautions against directly translating large VRS to the onset of ultrastrong coupling regime. Furthermore, for rectangular disorder, we witness the emergence of narrow side bands alongside a broad central peak, indicating an extended coherence lifetime even in the presence of substantial disorder. These findings not only enhance our understanding of VRS in disordered molecular systems but also open avenues for achieving prolonged coherence lifetimes between the cavity and molecules via the interplay of collective coupling and disorder.

Template Synthesis of Disilacycloalkanes Utilizing the Reactivity of a Siloxane Bond.

The investigation of large and flexible macrocyclic compounds has garnered significant attention due to their functions as host molecules and linkers. Although the synthetic yields of such compounds, achieved by linking two molecular fragments, are often hindered by the flexibility of the molecular skeleton, one of the effective solutions is template synthesis for the macrocycles. In this study, a novel template synthesis for disilacycloalkanes by leveraging the reactivity of a siloxane bond was investigated. The yields obtained through the template methods surpassed those of the nontemplate approach, and the introduction of substituents to the silicon atoms was also accomplished with success. All of the resulting disilacycloalkanes crystallized exceptionally well, enabling their structural determination through X-ray crystallography. Notably, the stability of these structures was elucidated by analyzing dispersion forces between alkyl chains, using density functional theory (DFT) calculations. This template synthesis method demonstrates its efficacy in synthesizing molecular systems that encompass two functional moieties linked with macroalkanes.

Photodriven electron-transfer dynamics in a series of heteroleptic Cu(I)-anthraquinone dyads.

Solar fuels catalysis is a promising route to efficiently harvesting, storing, and utilizing abundant solar energy. To achieve this promise, however, molecular systems must be designed with sustainable components that can balance numerous photophysical and chemical processes. To that end, we report on the structural and photophysical characterization of a series of Cu(I)-anthraquinone-based electron donor-acceptor dyads. The dyads utilized a heteroleptic Cu(I) bis-diimine architecture with a copper(I) bis-phenanthroline chromophore donor and anthraquinone electron acceptor. We characterized the structures of the complexes using x-ray crystallography and density functional theory calculations and the photophysical properties via resonance Raman and optical transient absorption spectroscopy. The calculations and resonance Raman spectroscopy revealed that excitation of the Cu(I) metal-to-ligand charge-transfer (MLCT) transition transfers the electron to a delocalized ligand orbital. The optical transient absorption spectroscopy demonstrated that each dyad formed the oxidized copper-reduced anthraquinone charge-separated state. Unlike most Cu(I) bis-phenanthroline complexes where increasingly bulky substituents on the phenanthroline ligands lead to longer MLCT excited-state lifetimes, here, we observe a decrease in the long-lived charge-separated state lifetime with increasing steric bulk. The charge-separated state lifetimes were best explained in the context of electron-transfer theory rather than with the energy gap law, which is typical for MLCT excited states, despite the complete conjugation between the phenanthroline and anthraquinone moieties.

Scalable Approach to Molecular Motor-Polymer Conjugates for Light-Driven Artificial Muscles.

The integration of molecular machines and motors into materials represents a promising avenue for creating dynamic and functional molecular systems, with potential applications in soft robotics or reconfigurable biomaterials. However, the development of truly scalable and controllable approaches for incorporating molecular motors into polymeric matrices has remained a challenge. Here, we show that light-driven molecular motors with sensitive photo-isomerizable double bonds can be converted into initiators for Cu-mediated controlled/living radical polymerization enabling the synthesis of star-shaped motor-polymer conjugates. This approach enables scalability, precise control over molecular structure, block copolymer structures, and high end group fidelity. Moreover, we demonstrate that these materials can be crosslinked to form gels with quasi-ideal network topology, exhibiting light-triggered contraction. We investigate the influence of arm length and polymer structure, and develop the first molecular dynamics simulation framework to gain deeper insights into the contraction processes. Leveraging this scalable methodology, we showcase the creation of bilayer soft robotic devices and cargo-lifting artificial muscles, highlighting the versatility and potential applications of this advanced polymer chemistry approach. We anticipate that our integrated experimental and simulation framework will accelerate scalable approaches for active polymer materials based on molecular machines, opening up new horizons in materials science and bioscience. This article is protected by copyright. All rights reserved.

Semiclassical Truncated-Wigner-Approximation Theory of Molecular Vibration-Polariton Dynamics in Optical Cavities.

It has been experimentally demonstrated that molecular-vibration polaritons formed by strong coupling of a molecular vibration to an infrared cavity mode can significantly modify the physical properties and chemical reactivities of various molecular systems. However, a complete theoretical understanding of the underlying mechanisms of the modifications remains elusive due to the complexity of the hybrid system, especially the collective nature of polaritonic states in systems containing many molecules. We develop here the semiclassical theory of molecular vibration-polariton dynamics based on the truncated Wigner approximation (TWA) that is tractable in large molecular systems and simultaneously captures the quantum character of photons in the optical cavity. The theory is then applied to investigate the nuclear quantum dynamics of a system of identical diatomic molecules having the ground-state Morse potential and being strongly coupled to an infrared cavity mode in the ultrastrong coupling regime. The validity of TWA is examined by comparing it with the full quantum dynamics of a single-molecule system for two different initial states in the dipole and Coulomb gauges. For the initial tensor-product ground state in the dipole gauge, which corresponds to a light-matter entangled state in the Coulomb gauge, the collective and resonance effects of molecular vibration-polariton formation on the nuclear dynamics are observed in a system of many molecules.

Theoretical investigation on action mechanism and mollifying efficacy of propellant stabilizers.

This project performed quantum chemical computation, through kinetic and thermodynamic analyses to compare relative reactivity, reaction rate, and equilibrium composition from the possible pathways in connection with stabilizer-nitrodioxide reactions to determine the stability of the materials for practical application. Corresponding achievements have promoted the use of N-methyl-p-nitroaniline (MNA) and dinitrophenyl malonamide series (M3, M4, and M5) stabilizers as high priorities for selection. The Gaussian 09 program (G09) (Frisch et al 2009) and density functional theory (DFT) calculations with the B3LYP/6-31G(d,p) function were performed to obtain related geometric and thermodynamic energy data for the molecular systems in this study. The synchronous transit-guided quasi-Newton method (STQN) (Peng and Schlegel Isr J Chem 33:49, 1993) was applied through the QST3 procedure to identify single imaginary frequency-valued transition-state species. The related reaction rate constant (k) and pre-exponential factor (A) were obtained, based on transition state theory (Su 2008), using Eqs. 11 and 12.

Unraveling the Dynamic Molecular Motions of a Twin‐Cavity Cage with Slow Configurational but Rapid Conformational Interconversions

Featuring diverse structural motions/changes, dynamic molecular systems hold promise for executing complex tasks. However, their structural complexity presents formidable challenge in elucidating their kinetics, especially when multiple structural motions are intercorrelated. We herein introduce a twin‐cavity cage that features interconvertible C3‐ and C1‐configurations, each configuration exhibiting interchangeable P‐ and M‐conformations. This molecule is therefore composed of four interconnected chiral species (P)‐C3, (M)‐C3, (P)‐C1, (M)‐C1. We showcase an effective methodology to decouple these sophisticated structural changes into two kinetically distinct pathways. Utilizing time‐dependent 1H NMR spectroscopy at various temperatures, which disregards the transition between mirror‐image conformations, we first determine the rate constant (kc) for C3‐ to C1‐configuration interconversion; while time‐dependent circular dichroism spectroscopy at different temperatures quantifies the observed rate constant (kobs) of ensemble of all structural changes. As kobs >> kc, it allows us to decouple the overall molecular motions into a slow configurational transformation and rapid conformational interconversions, the latter further dissected into two independent conformational interchanges, namely (P)‐C3 ⇄ (M)‐C3 and (P)‐C1 ⇄ (M)‐C1. This work therefore sheds light on comprehensive kinetic study of complex molecular dynamics, offering valuable insights for the rational design of smart dynamic materials for applications of sensing, separation, catalysis, molecular machinery, etc.

Unraveling the Dynamic Molecular Motions of a Twin-Cavity Cage with Slow Configurational but Rapid Conformational Interconversions.

Featuring diverse structural motions/changes, dynamic molecular systems hold promise for executing complex tasks. However, their structural complexity presents formidable challenge in elucidating their kinetics, especially when multiple structural motions are intercorrelated. We herein introduce a twin-cavity cage that features interconvertible C3- and C1-configurations, each configuration exhibiting interchangeable P- and M-conformations. This molecule is therefore composed of four interconnected chiral species (P)-C3, (M)-C3, (P)-C1, (M)-C1. We showcase an effective methodology to decouple these sophisticated structural changes into two kinetically distinct pathways. Utilizing time-dependent 1H NMR spectroscopy at various temperatures, which disregards the transition between mirror-image conformations, we first determine the rate constant (kc) for C3- to C1-configuration interconversion; while time-dependent circular dichroism spectroscopy at different temperatures quantifies the observed rate constant (kobs) of ensemble of all structural changes. As kobs >> kc, it allows us to decouple the overall molecular motions into a slow configurational transformation and rapid conformational interconversions, the latter further dissected into two independent conformational interchanges, namely (P)-C3 ⇄ (M)-C3 and (P)-C1 ⇄ (M)-C1. This work therefore sheds light on comprehensive kinetic study of complex molecular dynamics, offering valuable insights for the rational design of smart dynamic materials for applications of sensing, separation, catalysis, molecular machinery, etc.

Generalized Born-Huang expansion under macroscopic quantum electrodynamics framework.

Born-Huang expansion is the cornerstone for studying potential energy surfaces and non-adiabatic couplings (NACs) in molecular systems. However, the traditional approach is insufficient to describe the molecular system, which strongly interacts with quantum light. Inspired by the work by Schäfer et al., we develop the generalized Born-Huang expansion theory within a macroscopic quantum electrodynamics (QED) framework. The theory we present allows us to describe electromagnetic vacuum fluctuations in dielectric media and incorporate the effects of dressed photons (or polaritons) into NACs. With the help of the generalized Born-Huang expansion, we clearly classify electronic nuclear NACs, polaritonic nuclear NACs, and polaritonic electronic NACs. Furthermore, to demonstrate the advantage of the macroscopic QED framework, we estimate polaritonic electronic NACs without any free parameter, such as the effective mode volume, and demonstrate the distance dependence of the polaritonic electronic NACs in a silver planar system. In addition, we take a hydrogen atom in free space as an example and derive spontaneous emission rates from photonic electronic NACs (polaritonic electronic NACs are reduced to photonic electronic NACs). We believe that this work not only provides an avenue for the theoretical exploration of NACs in a nucleus-electron-polariton coupled system but also offers a more comprehensive understanding for molecules coupled with quantum light.

Qubit Count Reduction by Orthogonally Constrained Orbital Optimization for Variational Quantum Excited-State Solvers.

We propose a state-averaged orbital optimization scheme for improving the accuracy of excited states of the electronic structure Hamiltonian for use on near-term quantum computers. Instead of parameterizing the orbital rotation operator in the conventional fashion as an exponential of an antihermitian matrix, we parameterize the orbital rotation as a general partial unitary matrix. Whereas conventional orbital optimization methods minimize the state-averaged energy using successive Newton steps of the second-order Taylor expansion of the energy, the method presented here optimizes the state-averaged energy using an orthogonally constrained gradient projection method that does not require any expansion approximations. Through extensive benchmarking of the method on various small molecular systems, we find that the method is capable of producing more accurate results than fixed basis FCI while simultaneously using fewer qubits. In particular, we show that for H2, the method is capable of matching the accuracy of FCI in the cc-pVTZ basis (56 qubits) while only using 14 qubits.

Advances in the Homogeneously Catalyzed Hydrogen Production from Biomass Derived Feedstocks: a Review.

Biomass‐derived feedstocks for hydrogen production are crucial as an alternative to fossil fuel especially in those areas where green electricity and clean water are scarce. In this framework the transformation of simple (formic acid, alcohols) and more complex (polyalcohols, sugars and cellulose) bio‐derivatives in pure hydrogen is recognized as a promising approach. Parallel to great effort in heterogeneous catalysis, milder molecular systems represent a more selective eye for alternative solutions and mechanistic insights. In the present review the introduction summarizes the challenges in the catalytic utilization of biomass‐derived feedstocks, followed by the advances in homogeneously catalyzed hydrogen production from different substrates which will cover formic acid, with oustanding efficiency with noble metals and promising results with earth abundant ones and alcohols and polyalcohols, with particular emphasis to the development of heterogenized systems, ligand assisted catalysts and bi‐catalytic synergistic solutions which allow to avoid base and to promote catalyst stability and recyclability. In the last part, description of hydrogen production from more complex substrates, such as sugars and cellulose, will show the role of molecular complexes in main and side reactions. Critical comments on the reported advances are provided along the whole discussion.

Classical and quantum light-induced non-adiabaticity in molecular systems

The exchange of energy between electronic and nuclear motion is the origin of non-adiabaticity and plays an important role in many molecular phenomena and processes. Conical intersections (CIs) of different electronic potential energy surfaces lead to the most singular non-adiabaticity and have been intensely investigated. The coupling of light and matter induces conical intersections, which are termed light-induced conical intersections (LICIs). There are two kinds of LICIs, those induced by classical (laser) light and those by quantum light like that provided by a cavity. The present work reviews the subject of LICIs, discussing the achievements made so far. Particular attention is paid to comparing classical and quantum LICIs, their similarities and differences and their relationship to naturally occurring CIs. In contrast to natural CIs, the properties of which are dictated by nature, the properties of their light-induced counterparts are controllable by choosing the frequency and intensity (or coupling to the cavity) of the external light source. This opens the door to inducing and manipulating various kinds of non-adiabatic effects. Several examples of diatomic and polyatomic molecules are presented covering both dynamics and spectroscopy. The computational methods employed are discussed as well. To our opinion, the young field of LICIs and their impact shows much future potential.

A Scanning Tunneling Microscopy Study of the Photoisomerization of Diazocine.

Azobenzenes are fascinating molecular machines that can reversibly transform between two isomeric forms by an external stimulus. Diazocine, a type of bridged azobenzene, has been shown to possess enhanced photoexcitation properties. Due to the distortion caused by the ethyl bridge in the E-isomer, the Z-form becomes the thermodynamically stable configuration. Despite a comprehensive understanding of its photophysical properties, there is still much to learn about the behavior of diazocine on a metal surface. Here we show the operando photoswitching of diazocine molecules deposited directly on a Au(111) surface using scanning tunneling microscopy. Molecules were shown to aggregate into disordered islands with edge sites being susceptible to photon-induced movement. A few molecules were shown to undergo directional movement under UV irradiation with the motion reversed under blue light exposure. These findings contribute new insight into the activity of single and ensemble molecular systems toward purposefully guided motion.

Direct Observation of Polaritonic Chemistry by Nuclear Magnetic Resonance Spectroscopy

Polaritonic chemistry is emerging as a powerful approach to modifying the properties and reactivity of molecules and materials. However, probing how the electronics and dynamics of molecular systems change under strong coupling has been challenging due to the narrow range of spectroscopic techniques that can be applied in situ. Here we develop microfluidic optical cavities for vibrational strong coupling (VSC) that are compatible with nuclear magnetic resonance (NMR) spectroscopy using standard liquid NMR tubes. VSC is shown to influence the equilibrium between two conformations of a molecular balance sensitive to London dispersion forces, revealing an apparent change in the equilibrium constant under VSC. In all compounds studied, VSC does not induce detectable changes in chemical shifts, J‐couplings, or spin‐lattice relaxation times. This unexpected finding indicates that VSC does not substantially affect molecular electron density distributions, and in turn has profound implications for the possible mechanisms at play in polaritonic chemistry under VSC and suggests that the emergence of collective behavior is critical.

Direct Observation of Polaritonic Chemistry by Nuclear Magnetic Resonance Spectroscopy.

Polaritonic chemistry is emerging as a powerful approach to modifying the properties and reactivity of molecules and materials. However, probing how the electronics and dynamics of molecular systems change under strong coupling has been challenging due to the narrow range of spectroscopic techniques that can be applied in situ. Here we develop microfluidic optical cavities for vibrational strong coupling (VSC) that are compatible with nuclear magnetic resonance (NMR) spectroscopy using standard liquid NMR tubes. VSC is shown to influence the equilibrium between two conformations of a molecular balance sensitive to London dispersion forces, revealing an apparent change in the equilibrium constant under VSC. In all compounds studied, VSC does not induce detectable changes in chemical shifts, J-couplings, or spin-lattice relaxation times. This unexpected finding indicates that VSC does not substantially affect molecular electron density distributions, and in turn has profound implications for the possible mechanisms at play in polaritonic chemistry under VSC and suggests that the emergence of collective behavior is critical.

Metalloid-Organic Intermolecular Complexes with Charge State-Controlled Conformations.

Shape alterations of molecular systems, induced by their (electric) charging/discharging, could facilitate useful electronic and/or mechanical functions in molecular-scale devices and machines. The present study reports structures, stabilities, charge distributions, and IR spectra for a group of complexes of a main-group metalloid (boron) atom with hydrocarbon molecules. The considered systems include the smallest species demonstrating the basic principle of operation, as well as their size-extended analogues, generalizing it to larger counterparts based on such units. The system geometries vary considerably between neutral and ionic counterparts and exhibit two-three typical conformations related to twisting by up to about 90 degrees. The predicted structures correlate with specific infrared spectra, which can enable their experimental identification and transformation tracking. The above-mentioned characteristics suggest the potential utility of such systems for intermolecular switches, with the possible spectral monitoring of their functioning.