A Systematic Search for the Adsorption Motif of All Stereoisomers of Propylene Glycol on a Palladium(111) Surface for Fuel Cell Applications.

Small organic molecules have been shown to produce sufficient power densities allowing them to be environmentally friendly renewable fuel sources and an important part of fuel cell research. Affiliated experimental work found propylene glycol, as a source of renewable fuel, produces viable power densities when utilized with an alkaline-acid fuel cell and a Pd(111) catalyst. There is limited theoretical work on propylene glycol's energy reaction pathway. Thus, the first step in understanding how propylene glycol reacts with the Pd(111) slab is understanding its adsorption. In this paper, we present the investigation of adsorption potential energies (APE) of propylene glycol stereoisomers (S)-propane-1,2-diol (1,2PGS), (R)-propane-1,2-diol (1,2PGR), and propane-1,3-diol (1,3PG) on Pd(111). The isomers are systematically scanned through different configurations to analyze the preferred stable orientation and positional motifs. Density functional theory (DFT) is used to optimize the molecular geometries and surface relaxations. The most stable configuration of the 1,2PG stereoisomers resulted in an APE of -0.97 eV. The most stable configuration of the 1,3PG resulted in an APE of -1.19 eV. Both the 1,2PG(S/R) and 1,3PG isomers favor a motif in which at least one hydroxyl oxygen atom interacts with the surface of the Pd(111) catalyst. The 1,2PG carbon backbone prefers to have the center carbon positioned away from the slab, while the 1,3PG prefers to have the center carbon positioned closer to the slab. The most stable 1,3PG differs from other reported 1,3PG and 1,2PG relaxed configurations in that both of the hydroxyl oxygen atoms interact with the Pd(111) surface. These results show more favorable APEs than previously reported calculations. This paper will discuss in detail the differences between the hydroxyl group motifs and their role in affecting adsorption.

Substrate Tumbling in a Chemisorbed Diastereomeric α-Ketoester/1-(1-Naphthyl)ethylamine Complex.

Scanning tunneling microscopy (STM) data for α-ketoester/1-(1-naphthyl)ethylamine complexes on Pt(111) reveal a tumbling motion that couples two neighboring binding states. The interconversion, resulting in prochiral inversion of the α-ketoester, occurs in single complexes without breaking them apart. This is a surprising observation because the overall motion requires rotation of the α-ketoester away from the surface without branching exclusively into diffusion away from the complex or desorption. The multi-step interconversion is rationalized in terms of sequences of bound states that combine transient H-bond interactions with the chiral molecule and weakened adsorption interactions with the metal. The observation of tumbling in single long-lived complexes is of relevance to self-assembly and directed molecular motion on surfaces, to ligand-controlled surface reactions, and most directly to stereocontrol in asymmetric heterogeneous catalysis.

Exciting H2 Molecules for Graphene Functionalization.

Hydrogen functionalization of graphene by exposure to vibrationally excited H2 molecules is investigated by combined scanning tunneling microscopy, high-resolution electron energy loss spectroscopy, X-ray photoelectron spectroscopy measurements, and density functional theory calculations. The measurements reveal that vibrationally excited H2 molecules dissociatively adsorb on graphene on Ir(111) resulting in nanopatterned hydrogen functionalization structures. Calculations demonstrate that the presence of the Ir surface below the graphene lowers the H2 dissociative adsorption barrier and allows for the adsorption reaction at energies well below the dissociation threshold of the H-H bond. The first reacting H2 molecule must contain considerable vibrational energy to overcome the dissociative adsorption barrier. However, this initial adsorption further activates the surface resulting in reduced barriers for dissociative adsorption of subsequent H2 molecules. This enables functionalization by H2 molecules with lower vibrational energy, yielding an avalanche effect for the hydrogenation reaction. These results provide an example of a catalytically active graphene-coated surface and additionally set the stage for a re-interpretation of previous experimental work involving elevated H2 background gas pressures in the presence of hot filaments.

Monitoring interconversion between stereochemical states in single chirality-transfer complexes on a platinum surface.

Elementary steps in enantioselective heterogeneous catalysis take place on the catalyst surface and the targeted synthesis of a desired enantiomer requires the implantation of chiral information at the surface, which can be achieved-for example-by adsorbing chiral molecules. Studies of the structures of complexes formed between adsorbed prochiral reagents and chiral molecules yield information on the forces exerting stereocontrol, but further insight could be gained by studying the dynamics of their interactions. Here, using time-lapsed scanning tunnelling microscopy and density functional theory, we observe coupling between multiple stereochemical states within individual non-covalently bonded chirality-transfer complexes on a metal surface. We identify two modes of transformation between stereochemical states and find that the prochiral reagent can sample several complexation geometries during the lifetime of a complex, switching between states of opposing prochirality in the process. These results provide insight on the contribution of individual stereochemical states to the overall enantioselectivity of reactions occurring on catalyst surfaces.

Structure and Dynamics of Individual Diastereomeric Complexes on Platinum: Surface Studies Related to Heterogeneous Enantioselective Catalysis.

The modification of heterogeneous catalysts through the chemisorption of chiral molecules is a method to create catalytic sites for enantioselective surface reactions. The chiral molecule is called a chiral modifier by analogy to the terms chiral auxiliary or chiral ligand used in homogeneous asymmetric catalysis. While there has been progress in understanding how chirality transfer occurs, the intrinsic difficulties in determining enantioselective reaction mechanisms are compounded by the multisite nature of heterogeneous catalysts and by the challenges facing stereospecific surface analysis. However, molecular descriptions have now emerged that are sufficiently detailed to herald rapid advances in the area. The driving force for the development of heterogeneous enantioselective catalysts stems, at the minimum, from the practical advantages they might offer over their homogeneous counterparts in terms of process scalability and catalyst reusability. The broader rewards from their study lie in the insights gained on factors controlling selectivity in heterogeneous catalysis. Reactions on surfaces to produce a desired enantiomer in high excess are particularly challenging since at room temperature, barrier differences as low as ∼2 kcal/mol between pathways to R and S products are sufficient to yield an enantiomeric ratio (er) of 90:10. Such small energy differences are comparable to weak interadsorbate interaction energies and are much smaller than chemisorption or even most physisorption energies. In this Account, we describe combined experimental and theoretical surface studies of individual diastereomeric complexes formed between chiral modifiers and prochiral reactants on the Pt(111) surface. Our work is inspired by the catalysis literature on the enantioselective hydrogenation of activated ketones on cinchona-modified Pt catalysts. Using scanning tunneling microscopy (STM) measurements and density functional theory (DFT) calculations, we probe the structures and relative abundances of non-covalently bonded complexes formed between three representative prochiral molecules and (R)-(+)-1-(1-naphthyl)ethylamine ((R)-NEA). All three prochiral molecules, 2,2,2-trifluoroacetophenone (TFAP), ketopantolactone (KPL), and methyl 3,3,3-trifluoropyruvate (MTFP), are found to form multiple complexation configurations around the ethylamine group of chemisorbed (R)-NEA. The principal intermolecular interaction is NH···O H-bonding. In each case, submolecularly resolved STM images permit the determination of the prochiral ratio (pr), pro-R to pro-S, proper to specific locations around the ethylamine group. The overall pr observed in experiments on large ensembles of KPL-(R)-NEA complexes is close to the er reported in the literature for the hydrogenation of KPL to pantolactone on (R)-NEA-modified Pt catalysts at 1 bar H2. The results of independent DFT and STM studies are merged to determine the geometries of the most abundant complexation configurations. The structures reveal the hierarchy of chemisorption and sometimes multiple H-bonding interactions operating in complexes. In particular, privileged complexes formed by KPL and MTFP reveal the participation of secondary CH···O interactions in stereocontrol. State-specific STM measurements on individual TFAP-(R)-NEA complexes show that complexation states interconvert through processes including prochiral inversion. The state-specific information on structure, prochirality, dynamics, and energy barriers delivered by the combination of DFT and STM provides insight on how to design better chiral modifiers.

The atomic simulation environment-a Python library for working with atoms.

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Combining Evolutionary Algorithms with Clustering toward Rational Global Structure Optimization at the Atomic Scale.

Predicting structures at the atomic scale is of great importance for understanding the properties of materials. Such predictions are infeasible without efficient global optimization techniques. Many current techniques produce a large amount of idle intermediate data before converging to the global minimum. If this information could be analyzed during optimization, many new possibilities emerge for more rational search algorithms. We combine an evolutionary algorithm (EA) and clustering, a machine-learning technique, to produce a rational algorithm for global structure optimization. Clustering the configuration space of intermediate structures into regions of geometrically similar structures enables the EA to suppress certain regions and favor others. For two test systems, an organic molecule and an oxide surface, the global minimum search proves significantly faster when favoring stable structures in unexplored regions. This clustering-enhanced EA is a step toward adaptive global optimization techniques that can act upon information in accumulated data.

Symmetry-Driven Band Gap Engineering in Hydrogen Functionalized Graphene.

Band gap engineering in hydrogen functionalized graphene is demonstrated by changing the symmetry of the functionalization structures. Small differences in hydrogen adsorbate binding energies on graphene on Ir(111) allow tailoring of highly periodic functionalization structures favoring one distinct region of the moiré supercell. Scanning tunneling microscopy and X-ray photoelectron spectroscopy measurements show that a highly periodic hydrogen functionalized graphene sheet can thus be prepared by controlling the sample temperature (Ts) during hydrogen functionalization. At deposition temperatures of Ts = 645 K and above, hydrogen adsorbs exclusively on the HCP regions of the graphene/Ir(111) moiré structure. This finding is rationalized in terms of a slight preference for hydrogen clusters in the HCP regions over the FCC regions, as found by density functional theory calculations. Angle-resolved photoemission spectroscopy measurements demonstrate that the preferential functionalization of just one region of the moiré supercell results in a band gap opening with very limited associated band broadening. Thus, hydrogenation at elevated sample temperatures provides a pathway to efficient band gap engineering in graphene via the selective functionalization of specific regions of the moiré structure.

An automated nudged elastic band method.

A robust, efficient, dynamic, and automated nudged elastic band (AutoNEB) algorithm to effectively locate transition states is presented. The strength of the algorithm is its ability to use fewer resources than the nudged elastic band (NEB) method by focusing first on converging a rough path before improving upon the resolution around the transition state. To demonstrate its efficiency, it has been benchmarked using a simple diffusion problem and a dehydrogenation reaction. In both cases, the total number of force evaluations used by the AutoNEB method is significantly less than the NEB method. Furthermore, it is shown that for a fast and robust relaxation to the transition state, a climbing image elastic band method where the full spring force, rather than only the component parallel to the local tangent to the path, is preferred especially for pathways through energy landscapes with multiple local minima. The resulting corner cutting does not affect the accuracy of the transition state as long as this is located with the climbing image method. Finally, a number of pitfalls often encountered while locating the true transition state of a reaction are discussed in terms of systematically exploring the multidimensional energy landscape of a given process.

Pyridine adsorption and diffusion on Pt(111) investigated with density functional theory.

The adsorption, diffusion, and dissociation of pyridine, C5H5N, on Pt(111) are investigated with van der Waals-corrected density functional theory. An elaborate search for local minima in the adsorption potential energy landscape reveals that the intact pyridine adsorbs with the aromatic ring parallel to the surface. Piecewise interconnections of the local minima in the energy landscape reveal that the most favourable diffusion path for pyridine has a barrier of 0.53 eV. In the preferred path, the pyridine remains parallel to the surface while performing small single rotational steps with a carbon-carbon double bond hinged above a single Pt atom. The origin of the diffusion pathway is discussed in terms of the C2-Pt π-bond being stronger than the corresponding CN-Pt π-bond. The energy barrier and reaction enthalpy for dehydrogenation of adsorbed pyridine into an adsorbed, upright bound α-pyridyl species are calculated to 0.71 eV and 0.18 eV, respectively (both zero-point energy corrected). The calculations are used to rationalize previous experimental observations from the literature for pyridine on Pt(111).

Depth profiling of polymer films with grazing-incidence small-angle X-ray scattering.

A model-free method of reconstructing depth-specific lateral scattering from incident-angle-resolved grazing-incidence small-angle X-ray scattering (GISAXS) data is proposed. The information on the material which is available through variation of the X-ray penetration depth with incident angle is accessed through reference to the reflected branch of the GISAXS process. Reconstruction of the scattering from lateral density fluctuations is achieved by solving the resulting Fredholm integral equation with minimal a priori information about the experimental system. Results from simulated data generated for hypothetical multilayer polymer systems with constant absorption coefficient are used to verify that the method can be applied to cases with large X-ray penetration depths, as typically seen with polymer materials. Experimental tests on a spin-coated thick film of a blend of diblock copolymers demonstrate that the approach is capable of reconstruction of the scattering from a multilayer structure with the identification of lateral scattering profiles as a function of sample depth.