Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM.

We present a series of new implementations that we recently introduced in COBRAMM, the open-source academic software developed in our group. The goal of these implementations is to offer an automatized workflow and interface to simulate time-resolved transient absorption (TA) spectra of medium-to-big chromophore embedded in a complex environment. Therefore, the excited states absorption and the stimulated emission are simulated along nonadiabatic dynamics performed with trajectory surface hopping. The possibility of treating systems from medium to big size is given by the use of time-dependent density functional theory (TD-DFT) and the presence of the environment is taken into account employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. The full implementation includes a series of auxiliary scripts to properly setup the QM/MM system, the calculation of the wavefunction overlap along the dynamics for the propagation, the evaluation of the transition dipole moment at linear response TD-DFT level, and scripts to setup, run and analyze the TA from an ensemble of trajectories. Altogether, we believe that our implementation will open the door to the easily simulate the time-resolved TA of systems so far computationally inaccessible.

Spectral Tuning and Photoisomerization Efficiency in Push-Pull Azobenzenes: Designing Principles.

This work demonstrates how push-pull substitution can induce spectral tuning toward the visible range and improve the photoisomerization efficiency of azobenzene-based photoswitches, making them good candidates for technological and biological applications. The red-shifted bright ππ* state (S2) behaves like the lower and more productive dark nπ* (S1) state because less potential energy along the planar bending mode is available to reach higher energy unproductive nπ*/S0 crossing regions, which are responsible for the lower quantum yield of the parent compound. The stabilization of the bright ππ* state and the consequent increase in isomerization efficiency may be regulated via the strength of push-pull substituents. Finally, the torsional mechanism is recognized here as the unique productive route because structures with bending values attributable to the inversion mechanism were never detected, out of the 280 ππ* time-dependent density functional theory (RASPT2-validated) dynamics simulations.

First-principles description of intra-chain exciton migration in an oligo(para-phenylene vinylene) chain. I. Generalized Frenkel-Holstein Hamiltonian.

A generalized Frenkel-Holstein Hamiltonian is constructed to describe exciton migration in oligo(para-phenylene vinylene) chains, based on excited state electronic structure data for an oligomer comprising 20 monomer units (OPV-20). Time-dependent density functional theory calculations using the ωB97XD hybrid functional are employed in conjunction with a transition density analysis to study the low-lying singlet excitations and demonstrate that these can be characterized to a good approximation as a Frenkel exciton manifold. Based on these findings, we employ the analytic mapping procedure of Binder et al. [J. Chem. Phys. 141, 014101 (2014)] to translate one-dimensional (1D) and two-dimensional (2D) potential energy surface (PES) scans to a fully anharmonic, generalized Frenkel-Holstein (FH) Hamiltonian. A 1D PES scan is carried out for intra-ring quinoid distortion modes, while 2D PES scans are performed for the anharmonically coupled inter-monomer torsional and vinylene bridge bond length alternation modes. The kinetic energy is constructed in curvilinear coordinates by an exact numerical procedure, using the TNUM Fortran code. As a result, a fully molecular-based, generalized FH Hamiltonian is obtained, which is subsequently employed for quantum exciton dynamics simulations, as shown in Paper II [R. Binder and I. Burghardt, J. Chem. Phys. 152, 204120 (2020)].

Tailoring Spectral and Photochemical Properties of Bioinspired Retinal Mimics by in Silico Engineering.

Controlling the spectral tunability and isomerization activity is currently one of the hot topics in the design of photoreversible molecular switches for application in optoelectronic devices. The present work demonstrates how to manipulate the absorption of the retinal protonated Schiff base (rPSB) chromophore over the entire visible range by targeted functionalization of the retinal backbone. Moreover, a correlation between the vertical excitation energy and the profile of the potential energy surface of the bright excited state responsible for the photoreactivity of rPSB is established. This correlation was exploited to rank the functionalized rPSBs into different classes with characteristic photoisomerization activity. Eventually, the synergic effects of functionalization and of external electric fields in the range of a few MV cm-1 were applied to achieve reversable and regioselective control of the photoisomerization propensity of selected rPBS derivatives.

To bend or not to bend, the dilemma of multiple bonds.

Beyond the second row of the periodic table, the nature of the multiple bonds between the elements of the main groups remains yet elusive, and "non-classical" bonding schemes are often invoked for their description. Here, focusing on group 14, we have performed an accurate modeling of the Si-Si and C-C double bonds, including electron correlation effects. We have shown that Si[double bond, length as m-dash]Si bonds are "classical" and closely resemble C[double bond, length as m-dash]C ones, being similarly subjected to a sort of tug of war in which the σ bond favors distortion and the π bond opposes it. The essential difference between Si and C boils down to the sizes of their valence shells, which determine the π-bending stiffness. In carbon, such a stiffness is large because, upon bending, the atomic s orbitals interfere destructively with the p ones. In silicon, the s shell is smaller than the p one, the bending stiffness is reduced and the π bonds typically succumb, distort, and weaken. Electron correlation plays a major role in this context, since π bonds are far from their molecular orbital limit. Hence, we have further shown that upon weakening the effective repulsion between π electrons one may remove any structural instability, strengthen the π bonds and turn Si into a closer relative of C than it used to be.

Full quantum dynamical investigation of the Eley-Rideal reaction forming H2 on a movable graphitic substrate at T = 0 K.

The dynamics of the Eley-Rideal abstraction reaction of hydrogen atoms on a movable graphitic surface is investigated for the first time in a numerically exact fully quantum setting. A system-bath strategy was applied where the two recombining H atoms and a substrate C atom form a relevant subsystem, while the rest of the lattice takes the form of an independent oscillator bath. High-dimensional wavepacket simulations were performed in the collision energy range 0.2-1.0 eV with the help of the multi-layer multi-configuration time-dependent Hartree method, focusing on the collinear reaction on a zero-temperature surface. Results show that the dynamics is close to a sudden limit in which the reaction is much faster than the substrate motion. Unpuckering of the surface is fast (some tens of fs) but starts only after the formation of H2 is completed, thereby determining a considerable substrate heating (∼0.8 eV per reactive event). Energy partitioning in the product molecule favors translational over vibrational energy, and H2 molecules are vibrationally hot (∼1.5 eV) though to a lesser extent than previously predicted.

Multi-configurational Ehrenfest simulations of ultrafast nonadiabatic dynamics in a charge-transfer complex.

Multi-configurational Ehrenfest (MCE) approaches, which are intended to remedy the lack of correlations in the standard mean-field Ehrenfest method, have been proposed as coherent-state based ansätze for quantum propagation [D. V. Shalashilin, J. Chem. Phys. 130, 244101 (2009)] and also as the classical limit of the variational Gaussian-based multiconfiguration time dependent Hartree (G-MCTDH) method [S. Römer and I. Burghardt, Mol. Phys. 111, 3618 (2013)]. In the present paper, we establish the formal connection between these schemes and assess the performance of MCE for a coherent-state representation of the classical-limit subsystem. As a representative model system, we address the ultrafast, coherent charge transfer dynamics in an oligothiophene-fullerene donor-acceptor complex described by a two-state linear vibronic coupling model. MCE calculations are compared with reference calculations performed with the MCTDH method, for 10-40 vibrational modes. Beyond a dimensionality of 10 modes, it is shown that the correct representation of electronic coherence depends crucially on the sampling of initially unoccupied Gaussians.

Quantum dynamical investigation of the isotope effect in H2 formation on graphite at cold collision energies.

The Eley-Rideal abstraction of hydrogen atoms on graphitic surfaces at cold collision energies was investigated using a time-dependent wave packet method within the rigid-flat surface approximation, with a focus on hydrogen-deuterium isotopic substitutions. It is found that the marked isotope effect of collinear collisions disappears when the full dimensionality of the problem is taken into account, thereby suggesting that abstraction is less direct than commonly believed and proceeds through glancing rather than head-on collisions. In contrast, a clear isotope effect is observed for "hot-atom" formation, which appears to be strongly favored for heavy projectiles because of their higher density of physisorbed states. Overall, the dynamics is essentially classical and reasonably well described by quasi-classical trajectory methods at all but the lowest energies (≲10 meV). A comparison of the results obtained in the (substrate) adiabatic and diabatic limits suggests that the reaction is only marginally affected by the lattice dynamics, but highlights the importance of including energy dissipation processes in order to accurately describe the internal excitation of the product molecules.

Hydrogen on silicene: like or unlike graphene?

Hydrogenation of free-standing silicene, the two-dimensional allotrope of silicon, is investigated in detail using first-principles methods and compared with the adsorption of H atoms on graphene. Similarly to graphene, chemisorption of a single H atom on silicene induces the formation of a semilocalized state around the adatom, a sharp peak in the density of states at the Fermi level which acts as a strong resonant scatterer for charge carriers. This state hosts an unpaired electron, the itinerant electron of the resonating valence bond picture which primarily resides on the "majority" sublattice and biases the reactivity towards specific lattice positions. Contrary to graphene, sticking of hydrogen atoms is barrierless, on both the pristine and the hydrogenated surface. As a consequence, hydrogen adsorption on silicene is expected to proceed randomly under typical laboratory conditions, and preferential binding to form balanced dimers (or clusters) only occurs when thermodynamic equilibrium conditions prevail. The absence of clustering can be experimentally confirmed using scanning tunneling microscopy techniques since simulated imaging shows that the investigated structures provide distinguishable features that should allow their easy identification, if present on the surface. Overall, our findings can be rationalized by the fact that in silicene π bonds are weaker and the lattice is softer than in graphene and suggest that in silicene adatoms may severely limit carrier mobility.

Methane dissociation on Pt(111): Searching for a specific reaction parameter density functional.

The theoretical description of methane dissociating on metal surfaces is a current frontier in the field of gas-surface dynamics. Dynamical models that aim at achieving a highly accurate description of this reaction rely on potential energy surfaces based on density functional theory calculations at the generalized gradient approximation. We focus here on the effect that the exchange-correlation functional has on the reactivity of methane on a metal surface, using CHD3 + Pt(111) as a test case. We present new ab initio molecular dynamics calculations performed with various density functionals, looking also at functionals that account for the van der Waals (vdW) interaction. While searching for a semi-empirical specific reaction parameter density functional for this system, we find that the use of a weighted average of the PBE and the RPBE exchange functionals together with a vdW-corrected correlation functional leads to an improved agreement with quantum state-resolved experimental data for the sticking probability, compared to previous PBE calculations. With this semi-empirical density functional, we have also investigated the surface temperature dependence of the methane dissociation reaction and the influence of the rotational alignment on the reactivity, and compared our results with experiments.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling.

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.

Quantum dynamics of hydrogen atoms on graphene. II. Sticking.

Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (∼0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

Adiabatic potential energy surfaces for the low-energy collisional dynamics of C(+)((2)P) ions with H2 molecules.

The low-energy electronic states of the CH2(+) molecular ion are investigated with multireference configuration interaction calculations based on complete active space self-consistent field reference wave functions using a large C(6s5p4d3f)/H(8s6p3d1f) basis set. The focus is on the three lowest-lying states describing formation and destruction of the astrophysically relevant methylidine cation CH(+). Both processes are discussed in light of the topology of the relevant potential energy surfaces and their intersections.

From sniffer dogs to emerging sniffer devices for airport security: an opportunity to rethink privacy implications?

Dogs are known for their incredible ability to detect odours, extracting them from a "complex" environment and recognising them. This makes sniffer dogs precious assets in a broad variety of security applications. However, their use is subject to some intrinsic restrictions. Dogs can only be trained to a limited set of applications, get tired after a relatively short period, and thus require a high turnover. This has sparked a drive over the past decade to develop artificial sniffer devices-generally known as "chemical sniffers" or "electronic noses"-able to complement and possibly replace dogs for some security applications. Such devices have been already deployed, or are intended to be deployed, at borders, airports and other critical installation security checkpoints. Similarly to dogs, they are adopted for detecting residual traces that indicate either the presence of, or recent contact with, substances like drugs and explosives. It goes without saying that, as with sniffer dogs, the use of artificial sniffer devices raises many sensitive issues. Adopting an ethical and legal perspective, the present paper discusses the privacy and data protection implications of the possible deployment of a hand-held body scanning sniffer for screening passengers at EU airport security checkpoints.

Societal and ethical implications of anti-spoofing technologies in biometrics.

Biometric identification is thought to be less vulnerable to fraud and forgery than are traditional forms of identification. However biometric identification is not without vulnerabilities. In a 'spoofing attack' an artificial replica of an individual's biometric trait is used to induce a system to falsely infer that individual's presence. Techniques such as liveness-detection and multi-modality, as well as the development of new and emerging modalities, are intended to secure biometric identification systems against such threats. Unlike biometrics in general, the societal and ethical issues raised by spoofing and anti-spoofing techniques have not received much attention. This paper examines these issues.

Thermal lattice expansion effect on reactive scattering of H2 from Cu(111) at T(s) = 925 K.

Surface phonons and surface temperature may have important effects on reactions of molecules at surfaces, and at present much remains unknown about these effects. A question addressed here, which has received little attention so far, is how reaction at elevated temperature is affected by thermal lattice expansion. To answer this question for the benchmark reaction of H2 and D2 with Cu(111), we have performed quantum and quasi-classical dynamics calculations. The specific reaction parameter (SRP) approach to density functional theory (DFT) has been used to compute the required six-dimensional potential energy surfaces (PES). Computed reaction probabilities and rotational quadrupole alignment parameters have been compared for surface temperatures Ts = 0 and 925 K. Surface thermal expansion of the lattice leads to a considerable decrease of reaction barrier heights and thereby to increased reaction probabilities as well as decreased rotational quadrupole alignment parameter values in associative desorption.

RAGE engagement by SARS-CoV-2 enables monocyte infection and underlies COVID-19 severity.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fueled the COVID-19 pandemic with its enduring medical and socioeconomic challenges because of subsequent waves and long-term consequences of great concern. Here, we chart the molecular basis of COVID-19 pathogenesis by analyzing patients' immune responses at single-cell resolution across disease course and severity. This approach confirms cell subpopulation-specific dysregulation in COVID-19 across disease course and severity and identifies a severity-associated activation of the receptor for advanced glycation endproducts (RAGE) pathway in monocytes. In vitro THP1-based experiments indicate that monocytes bind the SARS-CoV-2 S1-receptor binding domain (RBD) via RAGE, pointing to RAGE-Spike interaction enabling monocyte infection. Thus, our results demonstrate that RAGE is a functional receptor of SARS-CoV-2 contributing to COVID-19 severity.

Hydrogen dissociation on Cu(111): the influence of lattice motion. Part I.

We have studied the effect of lattice displacement on the interaction of H(2) with the Cu(111) surface using the Specific Reaction Parameter (SRP) approach to Density Functional Theory (DFT). We have systematically investigated how the motion of the surface atoms affects some features of the Potential Energy Surface (PES), such as the dissociation barrier height and the barrier geometry corresponding to some representative reaction pathways, and the anisotropy of the potential at these geometries. This analysis has allowed us to identify the surface degrees of freedom that are likely to be most relevant for H(2) dissociation. In particular, we have found that the lattice coordinate displacements that have the largest effect on the H(2)/Cu(111) DFT-SRP barrier heights and locations concern the motion of the 1st layer and 2nd layer Cu atoms in the Z direction, and motion of the 1st layer atoms in the directions parallel to the surface. Whereas the first degree of freedom mostly affects the barrier geometry, the second and third motions can lower or raise the barrier height. The latter effect cannot be described with the usual surface oscillator dynamical models employed in the past to include surface motion, and its dynamical influence on the dissociative adsorption needs to be further investigated.

Surface models and reaction barrier in Eley-Rideal formation of H2 on graphitic surfaces.

The exothermic, collinearly-dominated Eley-Rideal hydrogen formation on graphite is studied with electronic structure and quantum dynamical means. In particular, the focus is on the importance of the model used to describe the graphitic substrate, in light of the marked discrepancies present in available literature results. To this end, the collinear reaction is considered and the potential energy surface is computed for a number of different graphitic surface models using Density Functional Theory (DFT) for different dynamical regimes. Quantum dynamics is performed with wavepacket techniques down to the cold collision energies relevant for the chemistry of the interstellar medium. Results show that the reactivity at moderate-to-high collision energies sensitively depends on the shape of the PES in the entrance channel, which in turn is related to the adopted surface model. At low energies we rule out the presence of any barrier to reaction, thereby highlighting the importance of quantum reflection in limiting the reaction efficiency.