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See detailBinding energies of benzene on coinage metal surfaces: Equal stability on different metals
Maaß, Friedrich; Jiang, Yingda; Liu, Wei et al

in Journal of Chemical Physics (2018), 148

Interfaces between organic molecules and inorganic solids adapt a prominent role in fundamental science, catalysis, molecular sensors, and molecular electronics. The molecular adsorption geometry, which ... [more ▼]

Interfaces between organic molecules and inorganic solids adapt a prominent role in fundamental science, catalysis, molecular sensors, and molecular electronics. The molecular adsorption geometry, which is dictated by the strength of lateral and vertical interactions, determines the electronic structure of the molecule/substrate system. In this study, we investigate the binding properties of benzene on the noble metal surfaces Au(111), Ag(111), and Cu(111), respectively, using temperature-programmed desorption and first-principles calculations that account for non-locality of both electronic exchange and correlation effects. In the monolayer regime, we observed for all three systems a decrease of the binding energy with increasing coverage due to repulsive adsorbate/adsorbate interactions. Although the electronic properties of the noble metal surfaces are rather different, the binding strength of benzene on these surfaces is equal within the experimental error (accuracy of 0.05 eV), in excellent agreement with our calculations. This points toward the existence of a universal trend for the binding energy of aromatic molecules resulting from a subtle balance between Pauli repulsion and many-body van der Waals attraction. [less ▲]

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See detailCatalysis beyond frontier molecular orbitals: Selectivity in partial hydrogenation of multi-unsaturated hydrocarbons on metal catalysts
Liu, Wei; Jiang, Yingda; Dostert, Karl-Heinz et al

in Science Advances (2017), 3

The mechanistic understanding and control over transformations of multi-unsaturated hydrocarbons on transition metal surfaces remains one of the major challenges of hydrogenation catalysis. To reveal the ... [more ▼]

The mechanistic understanding and control over transformations of multi-unsaturated hydrocarbons on transition metal surfaces remains one of the major challenges of hydrogenation catalysis. To reveal the microscopic origins of hydrogenation chemoselectivity, we performed a comprehensive theoretical investigation on the reactivity of two a,b-unsaturated carbonyls—isophorone and acrolein—on seven (111) metal surfaces: Pd, Pt, Rh, Ir, Cu, Ag, and Au. In doing so, we uncover a general mechanism that goes beyond the celebrated frontier molecular orbital theory, rationalizing the C--C bond activation in isophorone and acrolein as a result of significant surface-induced broadening of high-energy inner molecular orbitals. By extending our calculations to hydrogen-precovered surface and higher adsorbate surface coverage, we further confirm the validity of the “inner orbital broadening mechanism” under realistic catalytic conditions. The proposed mechanism is fully supported by our experimental reaction studies for isophorone and acrolein over Pd nanoparticles terminated with (111) facets. Although the position of the frontier molecular orbitals in these molecules, which are commonly considered to be responsible for chemical interactions, suggests preferential hydrogenation of the C--O double bond, experiments show that hydrogenation occurs at the C--C bond on Pd catalysts. The extent of broadening of inner molecular orbitals might be used as a guiding principle to predict the chemoselectivity for a wide class of catalytic reactions at metal surfaces. [less ▲]

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See detailMolecular Seesaw: Intricate Dynamics and Versatile Chemistry of Heteroaromatics on Metal Surfaces
Filimonov, Sergey N.; Liu, Wei; Tkatchenko, Alexandre UL

in The Journal of Physical Chemistry Letters (2017), 8

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See detailTuning the work function of stepped metal surfaces by adsorption of organic molecules
Jiang, Yingda; Li, Jingtai; Su, Guirong et al

in Journal of Physics : Condensed Matter (2017), 29

Understanding the binding mechanisms for aromatic molecules on transition-metal surfaces, especially with defects such as vacancies, steps and kinks, is a major challenge in designing functional ... [more ▼]

Understanding the binding mechanisms for aromatic molecules on transition-metal surfaces, especially with defects such as vacancies, steps and kinks, is a major challenge in designing functional interfaces for organic devices. One important parameter in the performance of organic/inorganic devices is the barrier of charge carrier injection. In the case of a metallic electrode, tuning the electronic interface potential or the work function for electronic level alignment is crucial. Here, we use density-functional theory (DFT) calculations with van der Waals (vdW) interactions treated with both screened pairwise (vdWsurf) and many-body dispersion (MBD) methods, to systematically study the interactions of benzene with a variety of stepped surfaces. Our calculations confirm the physisorptive character of Ag(2 1 1), Ag(5 3 3), Ag(3 2 2), Ag(7 5 5) and Ag(5 4 4) surfaces upon the adsorption of benzene. The MBD effects reduce the adsorption energies by about 0.15 eV per molecule compared to the results from the DFT + vdWsurf method. In addition, we find that the higher the step density, the larger the reduction of the work function upon the adsorption of benzene. We also study the effect of vdW interactions on the electronic structure using a fully selfconsistent implementation of the vdWsurf method in the Kohn–Sham DFT framework. We find that the self-consistent vdWsurf effects increase the work function due to the lowered Fermi level and the increased vacuum level. As a result, the benzene/Ag(2 1 1) system has the lowest work function (3.67 eV) among the five adsorption systems, significantly smaller than the work function of the clean Ag(1 1 1) surface (4.74 eV). Our results provide important insights into the stability and electronic properties of molecules adsorbed on stepped metal surfaces, which could help in designing more appropriate interfaces with low work functions for electron transfer. [less ▲]

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See detailDensity-functional theory with screened van der Waals interactions applied to atomic and molecular adsorbates on close-packed and non-close-packed surfaces
Ruiz, Victor G.; Liu, Wei; Tkatchenko, Alexandre UL

in PHYSICAL REVIEW B (2016), 93(3),

Modeling the adsorption of atoms and molecules on surfaces requires efficient electronic-structure methods that are able to capture both covalent and noncovalent interactions in a reliable manner. In ... [more ▼]

Modeling the adsorption of atoms and molecules on surfaces requires efficient electronic-structure methods that are able to capture both covalent and noncovalent interactions in a reliable manner. In order to tackle this problem, we have developed a method within density-functional theory (DFT) to model screened van der Waals interactions (vdW) for atoms and molecules on surfaces (the so-called DFT+vdW(surf) method). The relatively high accuracy of the DFT+vdW(surf) method in the calculation of both adsorption distances and energies, as well as the high degree of its reliability across a wide range of adsorbates, indicates the importance of the collective electronic effects within the extended substrate for the calculation of the vdW energy tail. We examine in detail the theoretical background of the method and assess its performance for adsorption phenomena including the physisorption of Xe on selected close-packed transition metal surfaces and 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) on Au(111). We also address the performance of DFT+vdW(surf) in the case of non-close-packed surfaces by studying the adsorption of Xe on Cu(110) and the interfaces formed by the adsorption of a PTCDA monolayer on the Ag(111), Ag(100), and Ag(110) surfaces. We conclude by discussing outstanding challenges in the modeling of vdW interactions for studying atomic and molecular adsorbates on inorganic substrates. [less ▲]

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See detailThermal and electronic fluctuations of flexible adsorbed molecules: Azobenzene on Ag(111)
Maurer, Reinhard J.; Liu, Wei; Poltavskyi, Igor UL et al

in Physical Review Letters (2016), 116

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See detailIdentical Binding Energies and Work Functions for Distinct Adsorption Structures: Olympicenes on the Cu(111) Surface
Liu, Wei; Schuler, Bruno; Xu, Yong et al

in The Journal of Physical Chemistry Letters (2016), 7(6), 1022-1027

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See detailAdsorption of isophorone and trimethyl-cyclohexanone on Pd(111): A combination of infrared reflection absorption spectroscopy and density functional theory studies
Dostert, Karl-Heinz; O'Brien, Casey P.; Liu, Wei et al

in Surface Science (2016), 650

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See detailQuantitative Prediction of Molecular Adsorption: Structure and Binding of Benzene on Coinage Metals
Liu, Wei; Maass, Friedrich; Willenbockel, Martin et al

in PHYSICAL REVIEW LETTERS (2015), 115(3),

Interfaces between organic molecules and solid surfaces play a prominent role in heterogeneous catalysis, molecular sensors and switches light-emitting diodes, and photovoltaics. The properties and the ... [more ▼]

Interfaces between organic molecules and solid surfaces play a prominent role in heterogeneous catalysis, molecular sensors and switches light-emitting diodes, and photovoltaics. The properties and the ensuing function of such hybrid interfaces often depend exponentially on molecular adsorption heights and binding strengths, calling for well-established benchmarks of these two quantities. Here we present systematic measurements that enable us to quantify the interaction of benzene with the Ag(111) coinage metal substrate with unprecedented accuracy (0.02 angstrom in the vertical adsorption height and 0.05 eV in the binding strength) by means of normal-incidence x-ray standing waves and temperature-programed desorption techniques. Based on these accurate experimental benchmarks for a prototypical molecule-solid interface, we demonstrate that recently developed first-principles calculations that explicitly account for the nonlocality of electronic exchange and correlation effects are able to determine the structure and stability of benzene on the Ag(111) surface within experimental error bars. Remarkably, such precise experiments and calculations demonstrate that despite different electronic properties of copper, silver, and gold, the binding strength of benzene is equal on the (111) surface of these three coinage metals. Our results suggest the existence of universal binding energy trends for aromatic molecules on surfaces. [less ▲]

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See detailSteps or Terraces? Dynamics of Aromatic Hydrocarbons Adsorbed at Vicinal Metal Surfaces
Camarillo-Cisneros, Javier; Liu, Wei; Tkatchenko, Alexandre UL

in Physical Review Letters (2015), 115(8),

The study of how molecules adsorb, diffuse, interact, and desorb from imperfect surfaces is essential for a complete understanding of elementary surface processes under relevant pressure and temperature ... [more ▼]

The study of how molecules adsorb, diffuse, interact, and desorb from imperfect surfaces is essential for a complete understanding of elementary surface processes under relevant pressure and temperature conditions. Here we use first-principles calculations to study the adsorption of benzene and naphthalene on a vicinal Cu(443) surface with the aim to gain insight into the behavior of aromatic hydrocarbons on realistic surfaces at a finite temperature. Upon strong adsorption at step edges at a low temperature, the molecules then migrate from the step to the (111) terraces, where they can freely diffuse parallel to the step edge. This migration happens at temperatures well below the onset of desorption, suggesting a more complex dynamical picture than previously proposed from temperature-programed desorption studies. The increase of the adsorption strength observed in experiments for Cu(443) when compared to Cu(111) is explained by a stronger long-range van der Waals attraction between the hydrocarbons and the step edges of the Cu(443) surface. Our calculations highlight the need for time-resolved experimental studies to fully understand the dynamics of molecular layers on surfaces. © 2015 American Physical Society. [less ▲]

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See detailInsight into the description of van der Waals forces for benzene adsorption on transition metal (111) surfaces
Tkatchenko, Alexandre UL; Carrasco, Javier; Liu, Wei et al

in Journal of Chemical Physics (2014), 140(8),

Exploring the role of van der Waals (vdW) forces on the adsorption of molecules on extended metal surfaces has become possible in recent years thanks to exciting developments in density functional theory ... [more ▼]

Exploring the role of van der Waals (vdW) forces on the adsorption of molecules on extended metal surfaces has become possible in recent years thanks to exciting developments in density functional theory (DFT). Among these newly developed vdW-inclusive methods, interatomic vdW approaches that account for the nonlocal screening within the bulk [V. G. Ruiz, W. Liu, E. Zojer, M. Scheffler, and A. Tkatchenko, Phys. Rev. Lett. 108, 146103 (2012)] and improved nonlocal functionals [J. Klimes, D. R. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 022201 (2010)] have emerged as promising candidates to account efficiently and accurately for the lack of long-range vdW forces in most popular DFT exchange-correlation functionals. Here we have used these two approaches to compute benzene adsorption on a range of close-packed (111) surfaces upon which it either physisorbs (Cu, Ag, and Au) or chemisorbs (Rh, Pd, Ir, and Pt). We have thoroughly compared the performance between the two classes of vdW-inclusive methods and when available compared the results obtained with experimental data. By examining the computed adsorption energies, equilibrium distances, and binding curves we conclude that both methods allow for an accurate treatment of adsorption at equilibrium adsorbate-substrate distances. To this end, explicit inclusion of electrodynamic screening in the interatomic vdW scheme and optimized exchange functionals in the case of nonlocal vdW density functionals is mandatory. Nevertheless, some discrepancies are found between these two classes of methods at large adsorbate-substrate separations. [less ▲]

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See detailvan der Waals Interactions Determine Selectivity in Catalysis by Metallic Gold
Rodriguez-Reyes, Juan Carlos F.; Siler, Cassandra G. F.; Liu, Wei et al

in JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014), 136(38), 13333-13340

To achieve high selectivity for catalytic reactions between two or more reactants on a heterogeneous catalyst, the relative concentrations of the reactive intermediates on the surface must be optimized ... [more ▼]

To achieve high selectivity for catalytic reactions between two or more reactants on a heterogeneous catalyst, the relative concentrations of the reactive intermediates on the surface must be optimized. If species compete for binding sites, their concentrations depend on their relative binding strengths to the surface. In this article we describe a general framework for predicting the relative stability of organic intermediates involved in oxygen-assisted reactions on metallic gold with broad relevance to catalysis by metals. Combining theory and experiment, we establish that van der Waals interactions between the reactive intermediates and the surface, although weak, determine relative stabilities and thereby dictate the conditions for optimum selectivity. The inclusion of these interactions is essential for predicting these trends. The concepts and methods employed here have broad applicability for determining the stability of intermediates on the surfaces of catalytic metals and specifically demonstrate the critical role of weak interactions in determining reaction selectivity among reactions of complex molecules. [less ▲]

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See detailModeling Adsorption and Reactions of Organic Molecules at Metal Surfaces
Liu, Wei; Tkatchenko, Alexandre UL; Scheffler, Matthias

in ACCOUNTS OF CHEMICAL RESEARCH (2014), 47(11, SI), 3369-3377

CONSPECTUS: The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid ... [more ▼]

CONSPECTUS: The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdW(surf) method that accurately accounts for the collective electronic response effects enables reliable modeling of structure and stability for a broad class of organic molecules adsorbed on metal surfaces. This method was demonstrated to achieve quantitative accuracy for aromatic hydrocarbons (benzene, naphthalene, anthracene, and diindenoperylene), C-60, and sulfur/oxygen-containing molecules (thiophene, NTCDA, and PTCDA) on dose-packed and stepped metal surfaces, leading to an overall accuracy of 0.1 angstrom in adsorption heights and 0.1 eV in binding energies with respect to state-of-the-art experiments. An unexpected finding is that vdW interactions contribute more to the binding of strongly bound molecules on transition-metal surfaces than for molecules physisorbed on coinage metals. The accurate inclusion of vdW interactions also significantly improves tilting angles and adsorption heights for all the studied molecules, and can qualitatively change the potential-energy surface for adsorbed molecules with flexible functional groups. Activation barriers for molecular switches and reaction precursors are modified as well. [less ▲]

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See detailInteraction of Isophorone with Pd(111): A Combination of Infrared Reflection-Absorption Spectroscopy, Near-Edge X-ray Absorption Fine Structure, and Density Functional Theory Studies
Dostert, Karl-Heinz; O'Brien, Casey P.; Riedel, Wiebke et al

in JOURNAL OF PHYSICAL CHEMISTRY C (2014), 118(48), 27833-27842

Atomistic level understanding of interaction of alpha,beta-unsaturated carbonyls with late transition metals is a key prerequisite for rational design of new catalytic materials with the desired ... [more ▼]

Atomistic level understanding of interaction of alpha,beta-unsaturated carbonyls with late transition metals is a key prerequisite for rational design of new catalytic materials with the desired selectivity toward C-C or C-O bond hydrogenation. The interaction of this class of compounds with transition metals was investigated on alpha,beta-unsaturated ketone isophorone on Pd(111) as a prototypical system. In this study, infrared reflectionabsorption spectroscopy (IRAS), near-edge X-ray absorption fine structure (NEXAFS) experiments and density functional theory calculations including van der Waals interactions (DFT+vdW) were combined to obtain detailed information on the binding of isophorone to palladium at different coverages and on the effect of preadsorbed hydrogen on the binding and adsorption geometry. According to these experimental observations and the results of theoretical calculations, isophorone adsorbs on Pd(111) in a flat-lying geometry at low coverages. With increasing coverage, both C-C and C-O bonds of isophorone tilt with respect to the surface plane. The tilting is considerably more pronounced for the C-C bond on the pristine Pd(111) surface, indicating a prominent perturbation and structural distortion of the conjugated p system upon interaction with Pd. Preadsorbed hydrogen leads to higher tilting angles of both p bonds, which points to much weaker interaction of isophorone with hydrogen-precovered Pd and suggests the conservation of the in-plane geometry of the conjugated pi system. The results of the DFT+vdW calculations provide further insights into the perturbation of the molecular structure of isophorone on Pd(111). [less ▲]

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See detailStructure and energetics of benzene adsorbed on transition-metal surfaces: density-functional theory with van der Waals interactions including collective substrate response
Liu, Wei; Ruiz, Victor G.; Zhang, Guo-Xu et al

in NEW JOURNAL OF PHYSICS (2013), 15

The adsorption of benzene on metal surfaces is an important benchmark system for hybrid inorganic/organic interfaces. The reliable determination of the interface geometry and binding energy presents a ... [more ▼]

The adsorption of benzene on metal surfaces is an important benchmark system for hybrid inorganic/organic interfaces. The reliable determination of the interface geometry and binding energy presents a significant challenge for both theory and experiment. Using the Perdew-Burke-Ernzerhof (PBE), PBE+vdW (van der Waals) and the recently developed PBE+vdW(surf) (density-functional theory with vdW interactions that include the collective electronic response of the substrate) methods, we calculated the structures and energetics for benzene on transition-metal surfaces: Cu, Ag, Au, Pd, Pt, Rh and Ir. Our calculations demonstrate that vdW interactions increase the binding energy by more than 0.70 eV for physisorbed systems (Cu, Ag and Au) and by an even larger amount for strongly bound systems (Pd, Pt, Rh and Ir). The collective response of the substrate electrons captured via the vdW(surf) method plays a significant role for most substrates shortening the equilibrium distance by 0.25 angstrom for Cu and decreasing the binding energy by 0.27 eV for Rh. The reliability of our results is assessed by comparison with calculations using the random-phase approximation including renormalized single excitations and the experimental data from temperature-programmed desorption microcalorimetry measurements and low-energy electron diffraction. [less ▲]

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See detailAdsorption Geometry Determination of Single Molecules by Atomic Force Microscopy
Schuler, Bruno; Liu, Wei; Tkatchenko, Alexandre UL et al

in PHYSICAL REVIEW LETTERS (2013), 111(10),

We measured the adsorption geometry of single molecules with intramolecular resolution using noncontact atomic force microscopy with functionalized tips. The lateral adsorption position was determined ... [more ▼]

We measured the adsorption geometry of single molecules with intramolecular resolution using noncontact atomic force microscopy with functionalized tips. The lateral adsorption position was determined with atomic resolution, adsorption height differences with a precision of 3 pm, and tilts of the molecular plane within 0.2 degrees. The method was applied to five pi-conjugated molecules, including three molecules from the olympicene family, adsorbed on Cu(111). For the olympicenes, we found that the substitution of a single atom leads to strong variations of the adsorption height, as predicted by state-of-the-art density-functional theory, including van der Waals interactions with collective substrate response effects. [less ▲]

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See detailA novel immunomodulator, FTY-720 reverses existing cardiac hypertrophy and fibrosis from pressure overload by targeting NFAT (nuclear factor of activated T-cells) signaling and periostin.
Liu, Wei; Zi, Min; Tsui, Hoyee et al

in Circulation. Heart failure (2013), 6(4), 833-44

BACKGROUND: Hypertension or aortic stenosis causes pressure overload, which evokes hypertrophic myocardial growth. Sustained cardiac hypertrophy eventually progresses to heart failure. Growing evidence ... [more ▼]

BACKGROUND: Hypertension or aortic stenosis causes pressure overload, which evokes hypertrophic myocardial growth. Sustained cardiac hypertrophy eventually progresses to heart failure. Growing evidence indicates that restraining hypertrophy could be beneficial; here, we discovered that FTY-720, an immunomodulator for treating multiple sclerosis, can reverse existing cardiac hypertrophy/fibrosis. METHODS AND RESULTS: Male C57/Bl6 mice underwent transverse aortic constriction (TAC) for 1 week followed by FTY-720 treatment for 2 weeks under continuing TAC. Compared with vehicle-treated TAC hearts, FTY-720 significantly reduced ventricular mass, ameliorated fibrosis, and improved cardiac performance. Mechanistic studies led us to discover that FTY-720 appreciably inhibited nuclear factor of activated T-cells (NFAT) activity. Moreover, we found that in primary cardiomyocytes (rat and human) pertussis toxin (Gi-coupled receptor inhibitor) substantially blocked the antihypertrophic effect of FTY-720. This observation was confirmed in a mouse model of pressure overload. Interestingly, gene array analysis of TAC hearts revealed that FTY-720 profoundly decreased gene expression of a group of matricellular proteins, of which periostin was prominent. Analysis of periostin protein expression in TAC-myocardium, as well as in rat and human cardiac fibroblasts, confirmed the array data. Moreover, we found that FTY-720 treatment or knockdown of periostin protein was able to inhibit transforming growth factor-beta responsiveness and decrease collagen expression. CONCLUSIONS: FTY-720 alleviates existing cardiac hypertrophy/fibrosis through mechanisms involving negative regulation of NFAT activity in cardiomyocytes and reduction of periostin expression allowing for a more homeostatic extracellular compartment milieu. Together, FTY-720 or its analogues could be a promising new approach for treating hypertrophic/fibrotic heart disease. [less ▲]

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See detailGuidelines for the use and interpretation of assays for monitoring autophagy.
Klionsky, Daniel J.; Abdalla, Fabio C.; Abeliovich, Hagai et al

in Autophagy (2012), 8(4), 445-544

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field ... [more ▼]

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field. [less ▲]

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See detailToward Low-Temperature Dehydrogenation Catalysis: Isophorone Adsorbed on Pd(111)
Liu, Wei; Savara, Aditya; Ren, Xinguo et al

in Journal of Physical Chemistry Letters (2012), 3(5), 582-586

Adsorbate geometry and reaction dynamics play essential roles in catalytic processes at surfaces. Here we present a theoretical and experimental study for a model functional organic/metal interface ... [more ▼]

Adsorbate geometry and reaction dynamics play essential roles in catalytic processes at surfaces. Here we present a theoretical and experimental study for a model functional organic/metal interface: isophorone (C9H14O) adsorbed on the Pd(111) surface. Density functional theory calculations with the Perdew-Burke-Ernzerhoff (PBE) functional including van der Waals (vdW) interactions, in combination with infrared spectroscopy and temperature-programmed desorption (TPD) experiments reveal the reaction pathway between the weakly chemisorbed reactant (C9H14O) and the strongly chemisorbed product (C9H10O), which occurs by the cleavage of four C-H bonds below 250 K. Analysis of the TPD spectrum is consistent with the relatively small magnitude of the activation barrier derived from PBE+vdW calculations, demonstrating the feasibility of low-temperature dehydrogenation. [less ▲]

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See detailDensity-Functional Theory with Screened van der Waals Interactions for the Modeling of Hybrid Inorganic-Organic Systems
Ruiz, Victor G.; Liu, Wei; Zojer, Egbert et al

in PHYSICAL REVIEW LETTERS (2012), 108(14),

The electronic properties and the function of hybrid inorganic-organic systems (HIOS) are intimately linked to their interface geometry. Here we show that the inclusion of the many-body collective ... [more ▼]

The electronic properties and the function of hybrid inorganic-organic systems (HIOS) are intimately linked to their interface geometry. Here we show that the inclusion of the many-body collective response of the substrate electrons inside the inorganic bulk enables us to reliably predict the HIOS geometries and energies. This is achieved by the combination of dispersion-corrected density-functional theory (the DFT+ van der Waals approach) [Phys. Rev. Lett. 102, 073005 (2009)], with the Lifshitz-Zaremba-Kohn theory for the nonlocal Coulomb screening within the bulk. Our method yields geometries in remarkable agreement (approximate to 0.1 angstrom) with normal incidence x-ray standing wave measurements for the 3, 4, 9, 10-perylene-tetracarboxylic acid dianhydride (C24O6H8, PTCDA) molecule on Cu(111), Ag(111), and Au(111) surfaces. Similarly accurate results are obtained for xenon and benzene adsorbed on metal surfaces. [less ▲]

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