Accessing the usefulness of atomic adsorption configurations in predicting the adsorption properties of molecules with machine learning.

We present a systematic study into the effect of adding atomic adsorption configurations into the training and validation dataset for a neural network's predictions of the adsorption energies of small molecules on single metal and bimetallic, single crystal surfaces. Specifically, we examine the efficacy of models trained with and without H and X atomic adsorption configurations, where X is C, N, or O, to predict XHn adsorption energies. In addition, we compare our machine learning models to traditional simple scaling relationships. We find that models trained with the atomic adsorption configurations outperform models trained with only molecular adsorption configurations, with as much as a 0.37 eV decrease in the MAE. We find that models trained with the atomic adsorption configurations slightly outperform traditional scaling relationships. In general, these results suggest it may be possible to vastly reduce the number of adsorption configurations one needs for training and validation datasets by supplementing said data with the adsorption configurations of composite atoms or smaller molecular fragments.

Combining Deep Learning Neural Networks with Genetic Algorithms to Map Nanocluster Configuration Spaces with Quantum Accuracy at Low Computational Cost.

The configuration spaces for bimetallic AuPd nanoclusters of various sizes are explored efficiently and analyzed accurately by combining genetic algorithms with neural networks trained on density functional theory. The methodology demonstrated herein provides an optimizable solution to the problem of searching vast configuration spaces with quantum accuracy in a way that is computationally practical. We implement a machine learning algorithm which learns the density functional theory potential with increasing performance while simultaneously generating and relaxing structures within the system's global configuration space unbiasedly. As a result, the algorithm naturally converges onto the system's energy minima while mapping the configuration space as a function of energy. The algorithm's simple design applies not only to nanocluster configurations, as demonstrated, but to bulk, substrate, and adsorption sites as well, and it is designed to scale. To demonstrate its computational efficiency, we work with AuPd nanoclusters of sizes 15, 20, and 25 atoms. Results focus primarily on evaluating the algorithm's performance; however, several physical insights into possible configurations for these nanoclusters naturally emerge as well, such as geometric Au surface segregation and stoichiometric Au minimization as a function of stability.

NEXMD v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations.

We present NEXMD version 2.0, the second release of the NEXMD (Nonadiabatic EXcited-state Molecular Dynamics) software package. Across a variety of new features, NEXMD v2.0 incorporates new implementations of two hybrid quantum-classical dynamics methods, namely, Ehrenfest dynamics (EHR) and the Ab-Initio Multiple Cloning sampling technique for Multiconfigurational Ehrenfest quantum dynamics (MCE-AIMC or simply AIMC), which are alternative options to the previously implemented trajectory surface hopping (TSH) method. To illustrate these methodologies, we outline a direct comparison of these three hybrid quantum-classical dynamics methods as implemented in the same NEXMD framework, discussing their weaknesses and strengths, using the modeled photodynamics of a polyphenylene ethylene dendrimer building block as a representative example. We also describe the expanded normal-mode analysis and constraints for both the ground and excited states, newly implemented in the NEXMD v2.0 framework, which allow for a deeper analysis of the main vibrational motions involved in vibronic dynamics. Overall, NEXMD v2.0 expands the range of applications of NEXMD to a larger variety of multichromophore organic molecules and photophysical processes involving quantum coherences and persistent couplings between electronic excited states and nuclear velocity.

Photoexcitation dynamics in perylene diimide dimers.

We utilize first-principles theory to investigate photo-induced excited-state dynamics of functionalized perylene diimide. This class of materials is highly suitable for solar energy conversion because of the strong optical absorbance, efficient energy transfer, and chemical tunability. We couple time-dependent density functional theory to a recently developed time-resolved non-adiabatic dynamics approach based on a semi-empirical description. By studying the monomer and dimer, we focus on the role stacking plays on the time-scales associated with excited-state non-radiative relaxation from a high excitonic state to the lowest energy exciton. We predict that the time-scale for energy conversion in the dimer is significantly faster than that in the monomer when equivalent excited states are accounted for. Additionally, for the dimer, the decay from the second to the nearly degenerate lowest energy excited-state involves two time-scales: a rapid decay on the order of ∼10 fs followed by a slower decay of ∼100 fs. Analysis of the spatial localization of the electronic transition density during the internal conversion process points out the existence of localized states on individual monomers, indicating that the strength of thermal fluctuations exceeds electronic couplings between the states such that the exciton hops between localized states throughout the simulation.

The Development of an Academic Engagement Intervention for Academically Dismissed Students.

"Reclaim the W" is an academic recovery program at a medium-sized midwestern university that offers undergraduates who have been academically dismissed a chance to reenroll at the institution. In this article we describe the Reclaim the W program and its target population of academically at-risk undergraduates. We then outline the first two phases of the process we used to develop an intervention for students in the Reclaim the W program, which we call Engage to Excel (E2). In the first phase we collected data from focus groups with academically at-risk students and professional staff who serve these students. This qualitative data informed the creation of the E2 intervention for students in the Reclaim the W program. In the second phase we identified key components of the quasi-experimental E2 intervention and outlined the student outcomes that will be evaluated during the intervention. Finally, we highlight research and practice implications of the E2 intervention.

NEXMD Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations.

We present a versatile new code released for open community use, the nonadiabatic excited state molecular dynamics (NEXMD) package. This software aims to simulate nonadiabatic excited state molecular dynamics using several semiempirical Hamiltonian models. To model such dynamics of a molecular system, the NEXMD uses the fewest-switches surface hopping algorithm, where the probability of transition from one state to another depends on the strength of the derivative nonadiabatic coupling. In addition, there are a number of algorithmic improvements such as empirical decoherence corrections and tracking trivial crossings of electronic states. While the primary intent behind the NEXMD was to simulate nonadiabatic molecular dynamics, the code can also perform geometry optimizations, adiabatic excited state dynamics, and single-point calculations all in vacuum or in a simulated solvent. In this report, first, we lay out the basic theoretical framework underlying the code. Then we present the code's structure and workflow. To demonstrate the functionality of NEXMD in detail, we analyze the photoexcited dynamics of a polyphenylene ethynylene dendrimer (PPE, C30H18) in vacuum and in a continuum solvent. Furthermore, the PPE molecule example serves to highlight the utility of the getexcited.py helper script to form a streamlined workflow. This script, provided with the package, can both set up NEXMD calculations and analyze the results, including, but not limited to, collecting populations, generating an average optical spectrum, and restarting unfinished calculations.

Graphics Processing Unit-Accelerated Semiempirical Born Oppenheimer Molecular Dynamics Using PyTorch.

A new open-source high-performance implementation of Born Oppenheimer molecular dynamics based on semiempirical quantum mechanics models using PyTorch called PYSEQM is presented. PYSEQM was designed to provide researchers in computational chemistry with an open-source, efficient, scalable, and stable quantum-based molecular dynamics engine. In particular, PYSEQM enables computation on modern graphics processing unit hardware and, through the use of automatic differentiation, supplies interfaces for model parameterization with machine learning techniques to perform multiobjective training and prediction. The implemented semiempirical quantum mechanical methods (MNDO, AM1, and PM3) are described. Additional algorithms include a recursive Fermi-operator expansion scheme (SP2) and extended Lagrangian Born Oppenheimer molecular dynamics allowing for rapid simulations. Finally, benchmark testing on the nanostar dendrimer and a series of polyethylene molecules provides a baseline of code efficiency, time cost, and scaling and stability of energy conservation, verifying that PYSEQM provides fast and accurate computations.

Triphenylene-Derived Electron Acceptors and Donors on Ag(111): Formation of Intermolecular Charge-Transfer Complexes with Common Unoccupied Molecular States.

Over the past years, ultrathin films consisting of electron donating and accepting molecules have attracted increasing attention due to their potential usage in optoelectronic devices. Key parameters for understanding and tuning their performance are intermolecular and molecule-substrate interactions. Here, the formation of a monolayer thick blend of triphenylene-based organic donor and acceptor molecules from 2,3,6,7,10,11-hexamethoxytriphenylene (HAT) and 1,4,5,8,9,12-hexaazatriphenylenehexacarbonitrile (HATCN), respectively, on a silver (111) surface is reported. Scanning tunneling microscopy and spectroscopy, valence and core level photoelectron spectroscopy, as well as low-energy electron diffraction measurements are used, complemented by density functional theory calculations, to investigate both the electronic and structural properties of the homomolecular as well as the intermixed layers. The donor molecules are weakly interacting with the Ag(111) surface, while the acceptor molecules show a strong interaction with the substrate leading to charge transfer and substantial buckling of the top silver layer and of the adsorbates. Upon mixing acceptor and donor molecules, strong hybridization occurs between the two different molecules leading to the emergence of a common unoccupied molecular orbital located at both the donor and acceptor molecules. The donor acceptor blend studied here is, therefore, a compelling candidate for organic electronics based on self-assembled charge-transfer complexes.

Competing adsorption mechanisms of pyridine on Cu, Ag, Au, and Pt(110) surfaces.

We explore the adsorption of pyridine on Cu, Ag, Au, and Pt(110) surfaces using density functional theory. To account for the van der Waals interaction, we use the optB86b-vdW, optB88-vdW, optPBE-vdW, revPBE-vdW, and rPW86-vdW2 functionals. For comparison, we also run calculations using the generalized gradient approximation-PBE (Perdew-Burke-Ernzerhof) functional. We find the most stable adsorption site to depend on both metal and functional, with two energetically favorable adsorption sites, namely, a vertically oriented site and a flat pyridine site. We calculate that every functional predicts pyridine to lie in the vertical configuration on the coinage metals at a low coverage. On Pt(110), by contrast, we calculate all the functionals-except rPW86-vdW2-to predict pyridine to lie flat at a low coverage. By analyzing these differences for these adsorption configurations, along with various geometric and electronic properties of the adsorbate/substrate system, we access in detail the performance of the 6 functionals we use. We also characterize the nature of the bonding of pyridine on the coinage metals from weak to strong physisorption, depending on the functional used. On Pt(110), we characterize the nature of the bonding of pyridine as ranging from strong physisorption to strong chemisorption depending again on the functional used, illustrating both the importance of the van der Waals interaction to this system and that this system can make a stringent test for computational methods.

Pressure-induced superconductivity in Ba0.5Sr0.5Fe2As2.

High-pressure electrical resistance measurements have been performed on single crystal Ba(0.5)Sr(0.5)Fe(2)As(2) platelets to pressures of 16 GPa and temperatures down to 10 K using designer diamond anvils under quasi-hydrostatic conditions with an insulating steatite pressure medium. The resistance measurements show evidence of pressure-induced superconductivity with an onset transition temperature at ∼31 K and zero resistance at ∼22 K for a pressure of 3.3 GPa. The transition temperature decreases gradually with increasing pressure before completely disappearing for pressures above 12 GPa. The present results provide experimental evidence that a solid solution of two 122-type materials, i.e., Ba(1-x)Sr(x)Fe(2)As(2) (0 < x < 1), can also exhibit superconductivity under high pressure.