Unraveling a Cavity-Induced Molecular Polarization Mechanism from Collective Vibrational Strong Coupling.

We demonstrate that collective vibrational strong coupling of molecules in thermal equilibrium can give rise to significant local electronic polarizations in the thermodynamic limit. We do so by first showing that the full nonrelativistic Pauli-Fierz problem of an ensemble of strongly coupled molecules in the dilute-gas limit reduces in the cavity Born-Oppenheimer approximation to a cavity-Hartree equation for the electronic structure. Consequently, each individual molecule experiences a self-consistent coupling to the dipoles of all other molecules, which amount to non-negligible values in the thermodynamic limit (large ensembles). Thus, collective vibrational strong coupling can alter individual molecules strongly for localized "hotspots" within the ensemble. Moreover, the discovered cavity-induced polarization pattern possesses a zero net polarization, which resembles a continuous form of a spin glass (or better polarization glass). Our findings suggest that the thorough understanding of polaritonic chemistry, requires a self-consistent treatment of dressed electronic structure, which can give rise to numerous, so far overlooked, physical mechanisms.

Numerically Exact Solution for a Real Polaritonic System under Vibrational Strong Coupling in Thermodynamic Equilibrium: Loss of Light-Matter Entanglement and Enhanced Fluctuations.

The first numerically exact simulation of a full ab initio molecular quantum system (HD+) under strong ro-vibrational coupling to a quantized optical cavity mode in thermal equilibrium is presented. Theoretical challenges in describing strongly coupled systems of mixed quantum statistics (bosons and Fermions) are discussed and circumvented by the specific choice of our molecular system. Our numerically exact simulations highlight the absence of zero temperature for the strongly coupled matter and light subsystems, due to cavity-induced noncanonical conditions. Furthermore, we explore the temperature dependency of light-matter quantum entanglement, which emerges for the ground state but is quickly lost already in the deep cryogenic regime. This is in contrast to predictions from the Jaynes-Cummings model, which is the standard starting point to model collective strong-coupling chemistry phenomenologically. Moreover, we find that the fluctuations of matter remain modified by the quantum nature of the thermal and vacuum-field fluctuations for significant temperatures, e.g., at ambient conditions. These observations (loss of entanglement and coupling to quantum fluctuations) have implications for the understanding and control of polaritonic chemistry and materials science, since a semiclassical theoretical description of light-matter interaction becomes reasonable, but the typical (classical) canonical equilibrium assumption for the nuclear subsystem remains violated. This opens the door for quantum fluctuation-induced stochastic resonance phenomena under vibrational strong coupling, which have been suggested as a plausible theoretical mechanism to explain the experimentally observed resonance phenomena in the absence of periodic driving that has not yet been fully understood.

Understanding Polaritonic Chemistry from Ab Initio Quantum Electrodynamics.

In this review, we present the theoretical foundations and first-principles frameworks to describe quantum matter within quantum electrodynamics (QED) in the low-energy regime, with a focus on polaritonic chemistry. By starting from fundamental physical and mathematical principles, we first review in great detail ab initio nonrelativistic QED. The resulting Pauli-Fierz quantum field theory serves as a cornerstone for the development of (in principle exact but in practice) approximate computational methods such as quantum-electrodynamical density functional theory, QED coupled cluster, or cavity Born-Oppenheimer molecular dynamics. These methods treat light and matter on equal footing and, at the same time, have the same level of accuracy and reliability as established methods of computational chemistry and electronic structure theory. After an overview of the key ideas behind those ab initio QED methods, we highlight their benefits for understanding photon-induced changes of chemical properties and reactions. Based on results obtained by ab initio QED methods, we identify open theoretical questions and how a so far missing detailed understanding of polaritonic chemistry can be established. We finally give an outlook on future directions within polaritonic chemistry and first-principles QED.

Cavity Born-Oppenheimer Hartree-Fock Ansatz: Light-Matter Properties of Strongly Coupled Molecular Ensembles.

Experimental studies indicate that optical cavities can affect chemical reactions through either vibrational or electronic strong coupling and the quantized cavity modes. However, the current understanding of the interplay between molecules and confined light modes is incomplete. Accurate theoretical models that take into account intermolecular interactions to describe ensembles are therefore essential to understand the mechanisms governing polaritonic chemistry. We present an ab initio Hartree-Fock ansatz in the framework of the cavity Born-Oppenheimer approximation and study molecules strongly interacting with an optical cavity. This ansatz provides a nonperturbative, self-consistent description of strongly coupled molecular ensembles, taking into account the cavity-mediated dipole self-energy contributions. To demonstrate the capability of the cavity Born-Oppenheimer Hartree-Fock ansatz, we study the collective effects in ensembles of strongly coupled diatomic hydrogen fluoride molecules. Our results highlight the importance of the cavity-mediated intermolecular dipole-dipole interactions, which lead to energetic changes of individual molecules in the coupled ensemble.

A perspective on ab initio modeling of polaritonic chemistry: The role of non-equilibrium effects and quantum collectivity.

This Perspective provides a brief introduction into the theoretical complexity of polaritonic chemistry, which emerges from the hybrid nature of strongly coupled light-matter states. To tackle this complexity, the importance of ab initio methods is highlighted. Based on those, novel ideas and research avenues are developed with respect to quantum collectivity, as well as for resonance phenomena immanent in reaction rates under vibrational strong coupling. Indeed, fundamental theoretical questions arise about the mesoscopic scale of quantum-collectively coupled molecules when considering the depolarization shift in the interpretation of experimental data. Furthermore, to rationalize recent findings based on quantum electrodynamical density-functional theory (QEDFT), a simple, but computationally efficient, Langevin framework is proposed based on well-established methods from molecular dynamics. It suggests the emergence of cavity-induced non-equilibrium nuclear dynamics, where thermal (stochastic) resonance phenomena could emerge in the absence of external periodic driving. Overall, we believe that the latest ab initio results indeed suggest a paradigmatic shift for ground-state chemical reactions under vibrational strong coupling from the collective quantum interpretation toward a more local, (semi)-classically and non-equilibrium dominated perspective. Finally, various extensions toward a refined description of cavity-modified chemistry are introduced in the context of QEDFT, and future directions of the field are sketched.

Polaritonic Chemistry: Collective Strong Coupling Implies Strong Local Modification of Chemical Properties.

A fundamental question in the field of polaritonic chemistry is whether collective coupling implies local modifications of chemical properties scaling with the ensemble size. Here we demonstrate from first-principles that an impurity present in a collectively coupled chemical ensemble features such locally scaling modifications. In particular, we find the formation of a novel dark state for a nitrogen dimer chain of variable size, whose local chemical properties are altered considerably at the impurity due to its embedding in the collectively coupled environment. Our simulations unify theoretical predictions from quantum optical models (e.g., collective dark states and bright polaritonic branches) with the single molecule quantum chemical perspective, which relies on the (quantized) redistribution of charges leading to a local hybridization of light and matter. Moreover, our findings suggest that recently developed ab initio methods for strong light-matter coupling are suitable to access these local polaritonic effects and provide a detailed understanding of photon-modified chemistry.

Chemistry in Quantum Cavities: Exact Results, the Impact of Thermal Velocities, and Modified Dissociation.

In recent years tremendous progress in the field of light-matter interactions has unveiled that strong coupling to the modes of an optical cavity can alter chemistry even at room temperature. Despite these impressive advances, many fundamental questions of chemistry in cavities remain unanswered. This is also due to a lack of exact results that can be used to validate and benchmark approximate approaches. In this work we provide such reference calculations from exact diagonalization of the Pauli-Fierz Hamiltonian in the long-wavelength limit with an effective cavity mode. This allows us to investigate the reliability of the ubiquitous Jaynes-Cummings model not only for electronic but also for the case of ro-vibrational transitions. We demonstrate how the commonly ignored thermal velocity of charged molecular systems can influence chemical properties while leaving the spectra invariant. Furthermore, we show the emergence of new bound polaritonic states beyond the dissociation energy limit.

Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm.

Experimental determination of the absolute stereochemistry of chiral molecules has been a fundamental challenge in natural sciences for decades. Vibrational circular dichroism (VCD) spectroscopy represents an attractive alternative to traditional methods like X-ray crystallography due to the use of molecules in solution. The interpretation of measured VCD spectra and thus the assignment of the absolute configuration relies on quantum-mechanical calculations. While such calculations are straightforward for rigid molecules with a single conformation, the need to estimate the correct conformational ensemble and energy landscape to obtain the appropriate theoretical spectra poses significant challenges for flexible molecules. In this work, we present the development of a VCD spectra alignment (VSA) algorithm to compare theoretical and experimental VCD spectra. The algorithm determines which enantiomer is more likely to reproduce the experimental spectrum and thus allows the correct assignment of the absolute stereochemistry. The VSA algorithm is successfully applied to determine the absolute chirality of highly flexible molecules, including commercial drug substances. Furthermore, we show that the computational cost can be reduced by performing the full frequency calculation only for a reduced set of conformers. The presented approach has the potential to allow the determination of the absolute configuration of chiral molecules in a robust and efficient manner.

Fast Nosé-Hoover thermostat: molecular dynamics in quasi-thermodynamic equilibrium.

An extension of the Nosé-Hoover thermostat equation for molecular dynamics (MD) simulation is introduced, which perturbs fast degrees of freedom out of canonical equilibrium, while preserving the average temperature of the system. Based on the generalised Liouville equation, it is shown that the newly introduced fast Nosé-Hoover (FNH) equations give rise to a dynamical system with a well-defined non-equilibrium probability distribution. Corresponding thermostat parameters are identified, which in principle allow to sample arbitrarily close to canonical equilibrium. Results show that the dynamic system properties (e.g. self-diffusion, shear viscosity, dielectric permittivity and rotational relaxation times) are only moderately perturbed for typical FNH setups. However, the non-equilibrium FNH equations modify the occurrence of rare events substantially and thus offer a novel approach for enhanced sampling in MD. In particular, it is shown that the FNH thermostat increased significantly the frequency of the folding and unfolding process of short ß-peptides. The efficiency of the phase-space exploration solely depends on the additionally imposed quasi-equilibrium conditions, i.e. it does not rely on any modification of the potential-energy surface.

Beyond the Rosenfeld Equation: Computation of Vibrational Circular Dichroism Spectra for Anisotropic Solutions.

The difference in absorption of left and right circularly polarized light by chiral molecules can be described by the Rosenfeld equation for isotropic samples. It allows the assignment of the absolute stereochemistry by comparing experimental and computationally derived spectra. Despite the simple form of the Rosenfeld equation, its evaluation in the infrared regime remained challenging, as the contribution from the magnetic dipole operator is zero within the Born-Oppenheimer (BO) approximation. In order to resolve this issue, "beyond BO" theories had to be developed, among which Stephen's magnetic field perturbation (MFP) approach offers a computationally easily accessible form. In this work, optical activity is discussed for cylindrically symmetric solutions, which cannot be described anymore by Rosenfeld's equation due to broken spherical symmetry. Mathematical properties of natural and electric-field induced anisotropies are discussed on the basis of the gauge-independent theoretical framework of Buckingham and Dunn. The issue of achiral noise arising from external field perturbations is considered, and potential remedies are introduced. Natural anisotropic vibrational circular dichroism (VCD) equations are solved numerically by applying the MFP approach within the Hartree-Fock (HF) formalism. Properties of anisotropic VCD spectra are discussed for R-(+)-methyloxirane and (1 S,2 S)-cyclopropane-1,2-dicarbonitrile. In particular, by using a group theoretical argument, a gauge-independent lower bound for the quadrupole contribution of C2-symmetric molecules can be identified, which allows the importance of additional quadrupole terms in anisotropic VCD spectra calculation to be assessed.

Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations.

Reaction-field (RF) methods have been extensively used in molecular dynamics simulations to efficiently compute long-range electrostatic interactions. They assume a continuous dielectric medium outside a certain cutoff, which has shown to be a reasonable approximation in many cases. However, lattice sum or fast multipole methods are nowadays often used instead, which treat long-range interactions explicitly but may introduce different artefacts. In the following work, the major issue of RFs is addressed, i.e., their inability to account for inhomogeneity even in heterogenous environments (e.g., membranes or protein binding pockets). By using a first-order Laplace series expansion of the dielectric permittivity on the cutoff sphere, local anisotropic effects can be described in a simple form. It is shown that the resulting boundary-value problem cannot be solved analytically, but instead a well-behaved approximative anisotropic reaction field (ARF) is introduced, which preserves coordinate invariance and approaches the standard RF solution for homogeneous systems. The comparison of RF to the state-of-the-art particle-particle particle-mesh (P3M) method shows a difference in the orientation of molecules close to the interface between two different dielectrics (water/chloroform). It was found that the ARF leads to a correction of the orientational distribution toward the P3M reference for planar and spherical interfaces.

Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations.

Background: Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts. Methods: The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution. Results: In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces. The presence of the observed artefacts was found to be independent of the interface shape and the thermostatting method used. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs. Conclusion: A SR scheme avoids numerical artefacts and offers an interesting alternative to TR RESPA with respect to performance optimization.

Efficient Round-Trip Time Optimization for Replica-Exchange Enveloping Distribution Sampling (RE-EDS).

Replica-exchange enveloping distribution sampling (RE-EDS) allows the efficient estimation of free-energy differences between multiple end-states from a single molecular dynamics (MD) simulation. In EDS, a reference state is sampled, which can be tuned by two types of parameters, i.e., smoothness parameters(s) and energy offsets, such that all end-states are sufficiently sampled. However, the choice of these parameters is not trivial. Replica exchange (RE) or parallel tempering is a widely applied technique to enhance sampling. By combining EDS with the RE technique, the parameter choice problem could be simplified and the challenge shifted toward an optimal distribution of the replicas in the smoothness-parameter space. The choice of a certain replica distribution can alter the sampling efficiency significantly. In this work, global round-trip time optimization (GRTO) algorithms are tested for the use in RE-EDS simulations. In addition, a local round-trip time optimization (LRTO) algorithm is proposed for systems with slowly adapting environments, where a reliable estimate for the round-trip time is challenging to obtain. The optimization algorithms were applied to RE-EDS simulations of a system of nine small-molecule inhibitors of phenylethanolamine N-methyltransferase (PNMT). The energy offsets were determined using our recently proposed parallel energy-offset (PEOE) estimation scheme. While the multistate GRTO algorithm yielded the best replica distribution for the ligands in water, the multistate LRTO algorithm was found to be the method of choice for the ligands in complex with PNMT. With this, the 36 alchemical free-energy differences between the nine ligands were calculated successfully from a single RE-EDS simulation 10 ns in length. Thus, RE-EDS presents an efficient method for the estimation of relative binding free energies.

Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation.

In molecular dynamics (MD) simulations, free-energy differences are often calculated using free energy perturbation or thermodynamic integration (TI) methods. However, both techniques are only suited to calculate free-energy differences between two end states. Enveloping distribution sampling (EDS) presents an attractive alternative that allows to calculate multiple free-energy differences in a single simulation. In EDS, a reference state is simulated which "envelopes" the end states. The challenge of this methodology is the determination of optimal reference-state parameters to ensure equal sampling of all end states. Currently, the automatic determination of the reference-state parameters for multiple end states is an unsolved issue that limits the application of the methodology. To resolve this, we have generalised the replica-exchange EDS (RE-EDS) approach, introduced by Lee et al. [J. Chem. Theory Comput. 10, 2738 (2014)] for constant-pH MD simulations. By exchanging configurations between replicas with different reference-state parameters, the complexity of the parameter-choice problem can be substantially reduced. A new robust scheme to estimate the reference-state parameters from a short initial RE-EDS simulation with default parameters was developed, which allowed the calculation of 36 free-energy differences between nine small-molecule inhibitors of phenylethanolamine N-methyltransferase from a single simulation. The resulting free-energy differences were in excellent agreement with values obtained previously by TI and two-state EDS simulations.