Structure of Graphene Grown on Cu(111): X-Ray Standing Wave Measurement and Density Functional Theory Prediction.

We report the quantitative adsorption structure of pristine graphene on Cu(111) determined using the normal incidence x-ray standing wave technique. The experiments constitute an important benchmark reference for the development of density functional theory approximations able to capture long-range dispersion interactions. Electronic structure calculations based on many-body dispersion-inclusive density functional theory are able to accurately predict the absolute measure and variation of adsorption height when the coexistence of multiple moiré superstructures is considered. This provides a structural model consistent with scanning probe microscopy results.

Integrated workflows and interfaces for data-driven semi-empirical electronic structure calculations.

Modern software engineering of electronic structure codes has seen a paradigm shift from monolithic workflows toward object-based modularity. Software objectivity allows for greater flexibility in the application of electronic structure calculations, with particular benefits when integrated with approaches for data-driven analysis. Here, we discuss different approaches to create deep modular interfaces that connect big-data workflows and electronic structure codes and explore the diversity of use cases that they can enable. We present two such interface approaches for the semi-empirical electronic structure package, DFTB+. In one case, DFTB+ is applied as a library and provides data to an external workflow; in another, DFTB+receives data via external bindings and processes the information subsequently within an internal workflow. We provide a general framework to enable data exchange workflows for embedding new machine-learning-based Hamiltonians within DFTB+ or enabling deep integration of DFTB+ in multiscale embedding workflows. These modular interfaces demonstrate opportunities in emergent software and workflows to accelerate scientific discovery by harnessing existing software capabilities.

Efficient implementation and performance analysis of the independent electron surface hopping method for dynamics at metal surfaces.

Independent electron surface hopping (IESH) is a computational algorithm for simulating the mixed quantum-classical molecular dynamics of adsorbate atoms and molecules interacting with metal surfaces. It is capable of modeling the nonadiabatic effects of electron-hole pair excitations on molecular dynamics. Here, we present a transparent, reliable, and efficient implementation of IESH, demonstrating its ability to predict scattering and desorption probabilities across a variety of systems, ranging from model Hamiltonians to full dimensional atomistic systems. We further show how the algorithm can be modified to account for the application of an external bias potential, comparing its accuracy to results obtained using the hierarchical quantum master equation. Our results show that IESH is a practical method for modeling coupled electron-nuclear dynamics at metal surfaces, especially for highly energetic scattering events.

libMBD: A general-purpose package for scalable quantum many-body dispersion calculations.

Many-body dispersion (MBD) is a powerful framework to treat van der Waals (vdW) dispersion interactions in density-functional theory and related atomistic modeling methods. Several independent implementations of MBD with varying degree of functionality exist across a number of electronic structure codes, which both limits the current users of those codes and complicates dissemination of new variants of MBD. Here, we develop and document libMBD, a library implementation of MBD that is functionally complete, efficient, easy to integrate with any electronic structure code, and already integrated in FHI-aims, DFTB+, VASP, Q-Chem, CASTEP, and Quantum ESPRESSO. libMBD is written in modern Fortran with bindings to C and Python, uses MPI/ScaLAPACK for parallelization, and implements MBD for both finite and periodic systems, with analytical gradients with respect to all input parameters. The computational cost has asymptotic cubic scaling with system size, and evaluation of gradients only changes the prefactor of the scaling law, with libMBD exhibiting strong scaling up to 256 processor cores. Other MBD properties beyond energy and gradients can be calculated with libMBD, such as the charge-density polarization, first-order Coulomb correction, the dielectric function, or the order-by-order expansion of the energy in the dipole interaction. Calculations on supramolecular complexes with MBD-corrected electronic structure methods and a meta-review of previous applications of MBD demonstrate the broad applicability of the libMBD package to treat vdW interactions.

Stereodynamics of adiabatic and non-adiabatic energy transfer in a molecule surface encounter.

Molecular energy transfer and reactions at solid surfaces depend on the molecular orientation relative to the surface. While such steric effects have been largely understood in electronically adiabatic processes, the orientation-dependent energy transfer in NO scattering from Au(111) was complicated by electron-mediated nonadiabatic effects, thus lacking a clear interpretation and posing a great challenge for theories. Herein, we investigate the stereodynamics of adiabatic and nonadiabatic energy transfer via molecular dynamics simulations of NO(v = 3) scattering from Au(111) using realistic initial orientation distributions based on accurate neural network fitted adiabatic potential energy surface and electronic friction tensor. Our results reproduce the observed stronger vibrational relaxation for N-first orientation and enhanced rotational rainbow for O-first orientation, and demonstrate how adiabatic anisotropic interactions steer molecules into the more attractive N-first orientation to experience more significant energy transfer. Remaining disagreements with experiment suggest the direction for further developments of nonadiabatic theories for gas-surface scattering.

NQCDynamics.jl: A Julia package for nonadiabatic quantum classical molecular dynamics in the condensed phase.

Accurate and efficient methods to simulate nonadiabatic and quantum nuclear effects in high-dimensional and dissipative systems are crucial for the prediction of chemical dynamics in the condensed phase. To facilitate effective development, code sharing, and uptake of newly developed dynamics methods, it is important that software implementations can be easily accessed and built upon. Using the Julia programming language, we have developed the NQCDynamics.jl package, which provides a framework for established and emerging methods for performing semiclassical and mixed quantum-classical dynamics in the condensed phase. The code provides several interfaces to existing atomistic simulation frameworks, electronic structure codes, and machine learning representations. In addition to the existing methods, the package provides infrastructure for developing and deploying new dynamics methods, which we hope will benefit reproducibility and code sharing in the field of condensed phase quantum dynamics. Herein, we present our code design choices and the specific Julia programming features from which they benefit. We further demonstrate the capabilities of the package on two examples of chemical dynamics in the condensed phase: the population dynamics of the spin-boson model as described by a wide variety of semiclassical and mixed quantum-classical nonadiabatic methods and the reactive scattering of H2 on Ag(111) using the molecular dynamics with electronic friction method. Together, they exemplify the broad scope of the package to study effective model Hamiltonians and realistic atomistic systems.

Topology Effects in Molecular Organic Electronic Materials: Pyrene and Azupyrene*.

Pyrene derivatives play a prominent role in organic electronic devices, including field effect transistors, light emitting diodes, and solar cells. The flexibility in the desired properties has previously been achieved by variation of substituents at the periphery of the pyrene backbone. In contrast, the influence of the topology of the central π-electron system on the relevant properties such as the band gap or the fluorescence behavior has not yet been addressed. In this work, pyrene is compared with its structural isomer azupyrene, which has a π-electron system with non-alternant topology. Using photoelectron spectroscopy, near edge X-ray absorption fine structure spectroscopy, and other methods, it is shown that the electronic band gap of azupyrene is by 0.72 eV smaller than that of pyrene. The difference of the optical band gaps is even larger with 1.09 eV, as determined by ultraviolet-visible absorption spectroscopy. The non-alternant nature of azupyrene is also associated with a more localized charge distribution. Further insight is provided by density functional theory (DFT) calculations of the molecular properties and ab initio coupled cluster calculations of the optical transitions. The concept of aromaticity is used to interpret the major topology-related differences.

First-principles calculations of hybrid inorganic-organic interfaces: from state-of-the-art to best practice.

The computational characterization of inorganic-organic hybrid interfaces is arguably one of the technically most challenging applications of density functional theory. Due to the fundamentally different electronic properties of the inorganic and the organic components of a hybrid interface, the proper choice of the electronic structure method, of the algorithms to solve these methods, and of the parameters that enter these algorithms is highly non-trivial. In fact, computational choices that work well for one of the components often perform poorly for the other. As a consequence, default settings for one materials class are typically inadequate for the hybrid system, which makes calculations employing such settings inefficient and sometimes even prone to erroneous results. To address this issue, we discuss how to choose appropriate atomistic representations for the system under investigation, we highlight the role of the exchange-correlation functional and the van der Waals correction employed in the calculation and we provide tips and tricks how to efficiently converge the self-consistent field cycle and to obtain accurate geometries. We particularly focus on potentially unexpected pitfalls and the errors they incur. As a summary, we provide a list of best practice rules for interface simulations that should especially serve as a useful starting point for less experienced users and newcomers to the field.

Perspective on integrating machine learning into computational chemistry and materials science.

Machine learning (ML) methods are being used in almost every conceivable area of electronic structure theory and molecular simulation. In particular, ML has become firmly established in the construction of high-dimensional interatomic potentials. Not a day goes by without another proof of principle being published on how ML methods can represent and predict quantum mechanical properties-be they observable, such as molecular polarizabilities, or not, such as atomic charges. As ML is becoming pervasive in electronic structure theory and molecular simulation, we provide an overview of how atomistic computational modeling is being transformed by the incorporation of ML approaches. From the perspective of the practitioner in the field, we assess how common workflows to predict structure, dynamics, and spectroscopy are affected by ML. Finally, we discuss how a tighter and lasting integration of ML methods with computational chemistry and materials science can be achieved and what it will mean for research practice, software development, and postgraduate training.

Functional Relevance of the Anaphylatoxin Receptor C3aR for Platelet Function and Arterial Thrombus Formation Marks an Intersection Point Between Innate Immunity and Thrombosis.

BACKGROUND: Platelets have distinct roles in the vascular system in that they are the major mediator of thrombosis, critical for restoration of tissue integrity, and players in vascular inflammatory conditions. In close spatiotemporal proximity, the complement system acts as the first line of defense against invading microorganisms and is a key mediator of inflammation. Whereas the fluid phase cross-talk between the complement and coagulation systems is well appreciated, the understanding of the pathophysiological implications of such interactions is still scant. METHODS: We analyzed coexpression of the anaphylatoxin receptor C3aR with activated glycoprotein IIb/IIIa on platelets of 501 patients with coronary artery disease using flow cytometry; detected C3aR expression in human or murine specimen by polymerase chain reaction, immunofluorescence, Western blotting, or flow cytometry; and examined the importance of platelet C3aR by various in vitro platelet function tests, in vivo bleeding time, and intravital microscopy. The pathophysiological relevance of C3aR was scrutinized with the use of disease models of myocardial infarction and stroke. To approach underlying molecular mechanisms, we identified the platelet small GTPase Rap1b using nanoscale liquid chromatography coupled to tandem mass spectrometry. RESULTS: We found a strong positive correlation of platelet complement C3aR expression with activated glycoprotein IIb/IIIa in patients with coronary artery disease and coexpression of C3aR with glycoprotein IIb/IIIa in thrombi obtained from patients with myocardial infarction. Our results demonstrate that the C3a/C3aR axis on platelets regulates distinct steps of thrombus formation such as platelet adhesion, spreading, and Ca2+ influx. Using C3aR-/- mice or C3-/- mice with reinjection of C3a, we uncovered that the complement activation fragment C3a regulates bleeding time after tail injury and thrombosis. Notably, C3aR-/- mice were less prone to experimental stroke and myocardial infarction. Furthermore, reconstitution of C3aR-/- mice with C3aR+/+ platelets and platelet depletion experiments demonstrated that the observed effects on thrombosis, myocardial infarction, and stroke were specifically caused by platelet C3aR. Mechanistically, C3aR-mediated signaling regulates the activation of Rap1b and thereby bleeding arrest after injury and in vivo thrombus formation. CONCLUSIONS: Overall, our findings uncover a novel function of the anaphylatoxin C3a for platelet function and thrombus formation, highlighting a detrimental role of imbalanced complement activation in cardiovascular diseases.

Hot electron effects during reactive scattering of H2 from Ag(111): assessing the sensitivity to initial conditions, coupling magnitude, and electronic temperature.

Low-lying electronic excitations in metals, so-called hot electrons, efficiently mediate molecule-metal energy transfer and contribute to energy loss during molecular reactions at surfaces. They furthermore play an important role in plasmon-driven chemistry. Electronic friction represents a simple and effective concept to model hot electron-induced energy loss under ambient conditions. Different methods exist that vary in their description of magnitude, coordinate and directional dependence of friction during reactive molecular scattering at metal surfaces. Using molecular dynamics simulations with electronic friction, we systematically study the effect of hot electrons on measurable state-to-state scattering probabilities of molecular hydrogen from a (111) surface of silver. We assess the ability of ab initio electronic friction methods to accurately describe hot electron-mediated energy loss as a function of initial reaction conditions and electronic temperature. We furthermore find that dynamic scattering results and the ensuing energy loss are highly sensitive to the magnitude of electronic friction. Therefore, existing approximate models of electronic friction, which exhibit inherent uncertainties with respect to the magnitude of electronic friction, may not be applicable for a quantitative prediction of plasmon driven hot electron effects in their current state. We outline a development direction to potentially overcome these limitations.

Adhesion, forces and the stability of interfaces.

Weak molecular interactions (WMI) are responsible for processes such as physisorption; they are essential for the structure and stability of interfaces, and for bulk properties of liquids and molecular crystals. The dispersion interaction is one of the four basic interactions types - electrostatics, induction, dispersion and exchange repulsion - of which all WMIs are composed. The fact that each class of basic interactions covers a wide range explains the large variety of WMIs. To some of them, special names are assigned, such as hydrogen bonding or hydrophobic interactions. In chemistry, these WMIs are frequently used as if they were basic interaction types. For a long time, dispersion was largely ignored in chemistry, attractive intermolecular interactions were nearly exclusively attributed to electrostatic interactions. We discuss the importance of dispersion interactions for the stabilization in systems that are traditionally explained in terms of the "special interactions" mentioned above. System stabilization can be explained by using interaction energies, or by attractive forces between the interacting subsystems; in the case of stabilizing WMIs, one frequently speaks of adhesion energies and adhesive forces. We show that the description of system stability using maximum adhesive forces and the description using adhesion energies are not equivalent. The systems discussed are polyaromatic molecules adsorbed to graphene and carbon nanotubes; dimers of alcohols and amines; cellulose crystals; and alcohols adsorbed onto cellulose surfaces.

Erratum: Role of Tensorial Electronic Friction in Energy Transfer at Metal Surfaces [Phys. Rev. Lett. 116, 217601 (2016)].

This corrects the article DOI: 10.1103/PhysRevLett.116.217601.

Mode Specific Electronic Friction in Dissociative Chemisorption on Metal Surfaces: H_{2} on Ag(111).

Electronic friction and the ensuing nonadiabatic energy loss play an important role in chemical reaction dynamics at metal surfaces. Using molecular dynamics with electronic friction evaluated on the fly from density functional theory, we find strong mode dependence and a dominance of nonadiabatic energy loss along the bond stretch coordinate for scattering and dissociative chemisorption of H_{2} on the Ag(111) surface. Exemplary trajectories with varying initial conditions indicate that this mode specificity translates into modulated energy loss during a dissociative chemisorption event. Despite minor nonadiabatic energy loss of about 5%, the directionality of friction forces induces dynamical steering that affects individual reaction outcomes, specifically for low-incidence energies and vibrationally excited molecules. Mode-specific friction induces enhanced loss of rovibrational rather than translational energy and will be most visible in its effect on final energy distributions in molecular scattering experiments.

Interpretation of x-ray absorption spectroscopy in the presence of surface hybridization.

X-ray absorption spectroscopy (XAS) yields direct access to the electronic and geometric structure of hybrid inorganic-organic interfaces formed upon adsorption of complex molecules at metal surfaces. The unambiguous interpretation of corresponding spectra is challenged by the intrinsic geometric flexibility of the adsorbates and the chemical interactions with the interface. Density-functional theory (DFT) calculations of the extended adsorbate-substrate system are an established tool to guide peak assignment in X-ray photoelectron spectroscopy of complex interfaces. We extend this to the simulation and interpretation of XAS data in the context of functional organic molecules on metal surfaces using dispersion-corrected DFT calculations within the transition potential approach. For the prototypical case of 2H-porphine adsorbed on Ag(111) and Cu(111) substrates, we follow the two main effects of the molecule/surface interaction onto the X-ray absorption signatures: (1) the substrate-induced chemical shift of the 1s core levels that dominates in physisorbed systems and (2) the hybridization-induced broadening and loss of distinct resonances that dominate in more chemisorbed systems.

Dynamics of Spatially Confined Bisphenol A Trimers in a Unimolecular Network on Ag(111).

Bisphenol A (BPA) aggregates on Ag(111) shows a polymorphism between two supramolecular motifs leading to formation of distinct networks depending on thermal energy. With rising temperature a dimeric pairing scheme reversibly converts into a trimeric motif, which forms a hexagonal superstructure with complex dynamic characteristics. The trimeric arrangements notably organize spontaneously into a self-assembled one-component array with supramolecular BPA rotors embedded in a two-dimensional stator sublattice. By varying the temperature, the speed of the rotors can be controlled as monitored by direct visualization. A combination of scanning tunneling microscopy and dispersion-corrected density-functional tight-binding (DFTB-vdW(surf)) based molecular modeling reveals the exact atomistic position of each molecule within the assembly as well as the driving force for the formation of the supramolecular rotors.

[Meniscal lesion. A pre-osteoarthritic condition of the knee joint]. / Die Meniskusläsion ­ ein präarthrotischer Zustand des Kniegelenks.

BACKGROUND: A close relationship between meniscal damage and articular cartilage exist. Likewise, (partial) meniscectomy may lead to the development of osteoarthritis (OA). OBJECTIVES: With a special emphasis on therapeutic consequences for orthopaedic surgeons, the structural and functional relationship between meniscal tears/extrusion and cartilage loss, and/or the effect of meniscectomy or meniscal repair on the development of OA, are emphasized. MATERIALS AND METHODS: A selective literature review with implementation of own research findings. RESULTS: The close topographical and functional interplay between the menisci and the tibiofemoral cartilage is the basis for the clinically important relationship between meniscal damage and cartilage degeneration. In particular, due to its close connection to tibiofemoral OA, a degenerative meniscal lesion represents a pre-osteoarthritic condition. Meniscus extrusion is also often associated with tibiofemoral OA. Even large cartilage defects can cause meniscus lesions. Partial meniscectomy is strongly associated with the incidence and risk of progression of OA. Clinical results are particularly problematic after partial resection of the lateral meniscus. Although the use of arthroscopic partial resection for degenerative meniscal lesions has been controversially discussed, no long-term studies are available. A large number of studies emphasize the medium-term value of meniscus reconstruction compared to partial meniscus resection. Combined meniscus and cartilage damage are complex cases, and the value of a simultaneous therapy remains unclear. CONCLUSIONS: Preserving the meniscus is the first step towards cartilage repair. Randomized and controlled studies will provide better information on the long-term outcomes of meniscal resection and repair with regard to OA development.

Role of Tensorial Electronic Friction in Energy Transfer at Metal Surfaces.

An accurate description of nonadiabatic energy relaxation is crucial for modeling atomistic dynamics at metal surfaces. Interfacial energy transfer due to electron-hole pair excitations coupled to motion of molecular adsorbates is often simulated by Langevin molecular dynamics with electronic friction. Here, we present calculations of the full electronic friction tensor by using first order time-dependent perturbation theory at the density functional theory level. We show that the friction tensor is generally anisotropic and nondiagonal, as found for hydrogen atom on Pd(100) and CO on Cu(100) surfaces. This implies that electron-hole pair induced nonadiabatic coupling at metal surfaces leads to friction-induced mode coupling, therefore, opening an additional channel for energy redistribution. We demonstrate the robustness and accuracy of our results by direct comparison to established methods and experimental data.

Thermal and Electronic Fluctuations of Flexible Adsorbed Molecules: Azobenzene on Ag(111).

We investigate the thermal and electronic collective fluctuations that contribute to the finite-temperature adsorption properties of flexible adsorbates on surfaces on the example of the molecular switch azobenzene C_{12}H_{10}N_{2} on the Ag(111) surface. Using first-principles molecular dynamics simulations, we obtain the free energy of adsorption that accurately accounts for entropic contributions, whereas the inclusion of many-body dispersion interactions accounts for the electronic correlations that govern the adsorbate binding. We find the adsorbate properties to be strongly entropy driven, as can be judged by a kinetic molecular desorption prefactor of 10^{24} s^{-1} that largely exceeds previously reported estimates. We relate this effect to sizable fluctuations across structural and electronic observables. A comparison of our calculations to temperature-programed desorption measurements demonstrates that finite-temperature effects play a dominant role for flexible molecules in contact with polarizable surfaces, and that recently developed first-principles methods offer an optimal tool to reveal novel collective behavior in such complex systems.

Spin Manipulation by Creation of Single-Molecule Radical Cations.

All-trans-retinoic acid (ReA), a closed-shell organic molecule comprising only C, H, and O atoms, is investigated on a Au(111) substrate using scanning tunneling microscopy and spectroscopy. In dense arrays single ReA molecules are switched to a number of states, three of which carry a localized spin as evidenced by conductance spectroscopy in high magnetic fields. The spin of a single molecule may be reversibly switched on and off without affecting its neighbors. We suggest that ReA on Au is readily converted to a radical by the abstraction of an electron.