Does F4TCNQ Adsorption on Cu(111) Form a 2D-MOF?

The results of a quantitative experimental structural investigation of the adsorption phases formed by 2,3,5,6-tetrafluoro-7,7',8,8'-tetracyanoquinodimethane (F4TCNQ) on Cu(111) are reported. A particular objective was to establish whether Cu adatoms are incorporated into the molecular overlayer. A combination of normal incidence X-ray standing waves, low-energy electron diffraction, scanning tunneling microscopy, and X-ray photoelectron spectroscopy measurements, complemented by dispersion-inclusive density functional theory calculations, demonstrates that F4TCNQ on Cu(111) does cause Cu adatoms to be incorporated into the overlayer to form a two-dimensional metal-organic framework (2D-MOF). This conclusion is shown to be consistent with the behavior of F4TCNQ adsorption on other coinage metal surfaces, despite an earlier report concluding that the adsorption structure on Cu(111) is consistent with the absence of any substrate reconstruction.

Donor-Acceptor Co-Adsorption Ratio Controls the Structure and Electronic Properties of Two-Dimensional Alkali-Organic Networks on Ag(100).

The results are presented of a detailed combined experimental and theoretical investigation of the influence of coadsorbed electron-donating alkali atoms and the prototypical electron acceptor molecule 7,7,8,8-tetracyanoquinodimethane (TCNQ) on the Ag(100) surface. Several coadsorption phases were characterized by scanning tunneling microscopy, low-energy electron diffraction, and soft X-ray photoelectron spectroscopy. Quantitative structural data were obtained using normal-incidence X-ray standing wave (NIXSW) measurements and compared with the results of density functional theory (DFT) calculations using several different methods of dispersion correction. Generally, good agreement between theory and experiment was achieved for the quantitative structures, albeit with the prediction of the alkali atom heights being challenging for some methods. The adsorption structures depend sensitively on the interplay of molecule-metal charge transfer and long-range dispersion forces, which are controlled by the composition ratio between alkali atoms and TCNQ. The large difference in atomic size between K and Cs has negligible effects on stability, whereas increasing the ratio of K/TCNQ from 1:4 to 1:1 leads to a weakening of molecule-metal interaction strength in favor of stronger ionic bonds within the two-dimensional alkali-organic network. A strong dependence of the work function on the alkali donor-TCNQ acceptor coadsorption ratio is predicted.

Quantitative structure determination of adsorbed formate and surface hydroxyls on Fe3O4(001).

Using the chemically specific techniques of normal incidence X-ray standing waves and photoelectron diffraction, we have investigated the dissociative adsorption of formic acid on the Fe3O4(001) surface, specifically probing the local structures of both the adsorbed formate and resulting surface hydroxyl. Using model independent direct methods, we reinforce the observations of a previous surface X-ray diffraction study that the formate molecule adsorbs with both oxygens atop octahedrally coordinated surface Fe cations and that ∼60% of the formate is adsorbed in the so called tet site. We additionally determine, for the first time, that the surface hydroxyl species are found at the so called int site. This confirms previous DFT predictions and reinforces the pivotal role the surface hydroxyl plays in lifting the subsurface cation vacancy termination of the Fe3O4(001) surface.

Stabilisation of tri-valent ions with a vacant coordination site at a corrole-metal interface.

By exploiting an established on-surface metallation strategy, we address the ability of the corrolic macrocycle to stabilise transition metal ions in high-valent (III) oxidation states in metal-supported molecular layers. This approach offers a route to engineer adsorbed metal complexes that cannot be easily fabricated by organic synthesis methods and bear a vacant axial coordination site for catalytic conversions.

Validation of the inverted adsorption structure for free-base tetraphenyl porphyrin on Cu(111).

Utilising normal incidence X-ray standing waves we rigourously scrutinise the "inverted model" as the adsorption structure of free-base tetraphenyl porphyrin on Cu(111). We demonstrate that the iminic N atoms are anchored at near-bridge adsorption sites on the surface displaced laterally by 1.1 ± 0.2 Å in excellent agreement with previously published calculations.

Probing structural changes upon carbon monoxide coordination to single metal adatoms.

In this work, the adsorption height of Ag adatoms on the Fe3O4(001) surface after exposure to CO was determined using normal incidence x-ray standing waves. The Ag adatoms bound to CO (Ag1 CO) are found to be pulled out of the surface to an adsorption height of 1.15 Å ± 0.08 Å, compared to the previously measured height of 0.96 Å ± 0.03 Å for bare Ag adatoms and clusters. Utilizing DFT+vdW+U calculations with the substrate unit cell dimension fixed to the experimental value, the predicted adsorption height for Ag1 CO was 1.16 Å, in remarkably good agreement with the experimental results.

The Structure of VOPc on Cu(111): Does V=O Point Up, or Down, or Both?

The local structure of the nonplanar phthalocyanine, vanadyl phthalocyanine (VOPc), adsorbed on Cu(111) at a coverage of approximately one-half of a saturated molecular layer, has been investigated by a combination of normal-incidence X-ray standing waves (NIXSW), scanned-energy mode photoelectron diffraction (PhD), and density-functional theory (DFT), complemented by scanning tunnelling microscopy (STM). Qualitative assessment of the NIXSW data clearly shows that both "up" and "down" orientations of the molecule (with V=O pointing out of, and into, the surface) must coexist on the surface. O 1s PhD proves to be inconclusive regarding the molecular orientation. DFT calculations, using two different dispersion correction schemes, show good quantitative agreement with the NIXSW structural results for equal co-occupation of the two different molecular orientations and clearly favor the many body dispersion (MBD) method to deal with long-range dispersion forces. The calculated relative adsorption energies of the differently oriented molecules at the lowest coverage show a strong preference for the "up" orientation, but at higher local coverages, this energetic difference decreases, and mixed orientation phases are almost energetically equivalent to pure "up"-oriented phases. DFT-based Tersoff-Hamann simulations of STM topographs for the two orientations cast some light on the extent to which such images provide a reliable guide to molecular orientation.

Local adsorption structure and bonding of porphine on Cu(111) before and after self-metalation.

We have experimentally determined the lateral registry and geometric structure of free-base porphine (2H-P) and copper-metalated porphine (Cu-P) adsorbed on Cu(111), by means of energy-scanned photoelectron diffraction (PhD), and compared the experimental results to density functional theory (DFT) calculations that included van der Waals corrections within the Tkatchenko-Scheffler approach. Both 2H-P and Cu-P adsorb with their center above a surface bridge site. Consistency is obtained between the experimental and DFT-predicted structural models, with a characteristic change in the corrugation of the four N atoms of the molecule's macrocycle following metalation. Interestingly, comparison with previously published data for cobalt porphine adsorbed on the same surface evidences a distinct increase in the average height of the N atoms above the surface through the series 2H-P, Cu-P, and cobalt porphine. Such an increase strikingly anti-correlates the DFT-predicted adsorption strength, with 2H-P having the smallest adsorption height despite the weakest calculated adsorption energy. In addition, our findings suggest that for these macrocyclic compounds, substrate-to-molecule charge transfer and adsorption strength may not be univocally correlated.

Re-evaluating how charge transfer modifies the conformation of adsorbed molecules.

The archetypal electron acceptor molecule, TCNQ, is generally believed to become bent into an inverted bowl shape upon adsorption on the coinage metal surfaces on which it becomes negatively charged. New quantitative experimental structural measurements show that this is not the case for TCNQ on Ag(111). DFT calculations show that the inclusion of dispersion force corrections reduces not only the molecule-substrate layer spacing but also the degree of predicted molecular bonding. However, complete agreement between experimentally-determined and theoretically-predicted structural parameters is only achieved with the inclusion of Ag adatoms into the molecular layer, which is also the energetically favoured configuration. The results highlight the need for both experimental and theoretical quantitative structural methods to reliably understand similar metal-organic interfaces and highlight the need to re-evaluate some previously-investigated systems.

Direct measurement of Ni incorporation into Fe3O4(001).

The normal incidence X-ray standing wave (NIXSW) technique has been used to follow the evolution of the adsorption geometry of Ni adatoms on the Fe3O4(001)-(√2 × âˆš2)R45° surface as a function of temperature. Two primary surface region sites are identified: a bulk-continuation tetrahedral site and a sub-surface octahedral site, the latter site being preferred at higher annealing temperatures. The ease of incorporation is linked to the presence of subsurface cation vacancies in the (√2 × âˆš2)R45° reconstruction and is consistent with the preference for octahedral coordination observed in the spinel compound NiFe2O4.

Probing the interplay between geometric and electronic structure in a two-dimensional K-TCNQ charge transfer network.

Scanning tunnelling microscopy (STM), low energy electron diffraction (LEED), ultraviolet and soft X-ray photoelectron spectroscopy (UPS and SXPS) have been used to characterise the formation of a coadsorption phase of TCNQ and K on Ag(111), while the normal incident X-ray standing waves (NIXSW) technique has been used to obtain quantitative structural information. STM and LEED show that an ordered incommensurate phase is formed in which the K atoms are surrounded by four TCNQ molecules in a 'windmill' motif, characteristic of other metal/TCNQ phases, in which the nominal TCNQ : K stoichiometry is 1 : 1. UPS and SXPS data indicate the TCNQ is in a negatively-charged state. NIXSW results show that the carbon core of the TCNQ is essentially planar at a height above the Ag(111) surface closely similar to that found without coadsorbed K. In the presence of TCNQ the height of the K ions above the surface is significantly larger than on clean Ag(111), and the ions occupy sites above 'holes' in the TCNQ network. NIXSW data also show that the N atoms in the molecules must occupy sites with at least two different heights above the surface, which can be reconciled by a tilt or twist of the TCNQ molecules, broadly similar to the geometry that occurs in bulk TCNQ/K crystals.

Formation of a thermally stable bilayer of coadsorbed intact and deprotonated thymine exploiting the surface corrugation of rutile TiO2(110).

The adsorption of thymine, a pyrimidine based nucleobase, was studied on the (110) termination of rutile titanium dioxide in order to understand the thermal stability and gross structural parameters of the interaction between a strongly polar adsorbate and a highly corrugated transition metal oxide surface. Near-edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron spectroscopy (XPS), temperature programmed XPS and temperature programmed desorption indicated the growth of a room temperature stable bilayer, which could only be removed by annealing to 450 K. The remaining first layer was remarkably robust, surviving annealing up to 550 K before undergoing N-H bond scission. The comparison to XPS of a sub-monolayer exposure of 1-methyluracil shows that the origin of the room temperature stable bilayer is not intermolecular interactions. This discovery, alongside the deprotonation of one of the first layer's pyrimidinic nitrogen atoms at room temperature, suggests that the thymine molecules in the first layer bind to the undercoordinated surface Ti atoms, and the second layer thymine molecules coordinate with the bridging oxygen atoms which protrude above the Ti surface plane on the (110) surface. The NEXAFS results indicate an almost upright orientation of the molecules in both layers, with a 30 ± 10° tilt away from the surface normal.

Toward interfacing organic semiconductors with ferromagnetic transition metal substrates: enhanced stability via carboxylate anchoring.

We demonstrate that chemically well-defined aromatic self-assembled monolayers (SAMs) bonded via a carboxylate head group to surfaces of ferromagnetic (FM = Co, Ni, Fe) transition metals can be prepared at ambient temperature in ultra-high vacuum and are thermally stable up to 350-400 K (depending on the metal). The much superior stability over thiolate-bonded SAMs, which readily decompose above 200 K, and the excellent electronic communication guaranteed by the carboxylate bonding render benzoate/FM-metal interfaces promising candidates for application in spintronics.

An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.

Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward's, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill biologically relevant information from MD trajectories, especially for docking purposes.

wFReDoW: a cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model.

Molecular docking simulations of fully flexible protein receptor (FFR) models are coming of age. In our studies, an FFR model is represented by a series of different conformations derived from a molecular dynamic simulation trajectory of the receptor. For each conformation in the FFR model, a docking simulation is executed and analyzed. An important challenge is to perform virtual screening of millions of ligands using an FFR model in a sequential mode since it can become computationally very demanding. In this paper, we propose a cloud-based web environment, called web Flexible Receptor Docking Workflow (wFReDoW), which reduces the CPU time in the molecular docking simulations of FFR models to small molecules. It is based on the new workflow data pattern called self-adaptive multiple instances (P-SaMIs) and on a middleware built on Amazon EC2 instances. P-SaMI reduces the number of molecular docking simulations while the middleware speeds up the docking experiments using a High Performance Computing (HPC) environment on the cloud. The experimental results show a reduction in the total elapsed time of docking experiments and the quality of the new reduced receptor models produced by discarding the nonpromising conformations from an FFR model ruled by the P-SaMI data pattern.

Face-dependent bond lengths in molecular chemisorption: the formate species on Cu(111) and Cu(110).

Many previous structural studies of molecular adsorbates on metal surfaces indicate that the local coordination and bonding is closely similar to that in organometallic compounds, implying that the metallic substrate has no significant influence. Here we show that such an influence is detectable for one model system, namely, the formate species, HCOO, adsorbed on the atomically rough and smooth (110) and (111) surfaces of Cu, leading to a statistically significant difference (0.09±0.05 Å) in the Cu-O chemisorption bond length. The effect is reproduced in density functional theory calculations.

Uracil on Cu(110): a quantitative structure determination by energy-scanned photoelectron diffraction.

The local adsorption site of the nucleobase uracil on Cu(110) has been determined quantitatively by energy-scanned photoelectron diffraction (PhD). Qualitative inspection of the O 1s and N 1s soft x-ray photoelectron spectra, PhD modulation spectra, and O K-edge near-edge x-ray adsorption fine structure indicate that uracil bonds to the surface through its nitrogen and oxygen constituent atoms, each in near atop sites, with the molecular plane essentially perpendicular to surface and aligned along the close packed [110] azimuth. Multiple scattering simulations of the PhD spectra confirm and refine this geometry. The Cu-N bondlength is 1.96 ± 0.04 Å, while the Cu-O bondlengths of the two inequivalent O atoms are 1.93 ± 0.04 Å and 1.96 ± 0.04 Å, respectively. The molecule is twisted out of the [110]direction by 11 ± 5°.

The structure of furan reaction products on Pd(111).

Previous experimental studies of the interaction of molecular furan, C(4)H(4)O, with Pd(111) have led to the conclusion that partial dissociation leads to two coadsorbed reaction products, CO and a C(3)H(3) species. Using density functional theory (DFT), a range of possible molecular conformation and adsorption sites of the C(3)H(3) species have been explored and the lowest energy structures, and associated C 1s photoelectron core-level binding energy shifts (CLSs), have been determined. Comparison of these CLS values with published experimental measurements allows one possible conformation to be rejected. New simulations of the C 1s scanned-energy mode photoelectron diffraction (PhD) spectra for several of lowest-energy structures found in DFT are compared with the results of an earlier experimental study. The lowest energy structure found in DFT is not consistent with the PhD data, suggesting that energy barriers to achieve the associated conformation cannot be overcome in the dissociation process. Through consideration of the results of both methods, the most probable surface structures are discussed.

Fresh meat and further processing characteristics of ham muscles from finishing pigs fed ractopamine hydrochloride.

Ractopamine hydrochloride (RAC) has consistently led to an advantage in carcass cutting yields of finishing pigs and remains a common feed additive in US finishing pig diets. Less is known about the effect of RAC on further processing characteristics. Some researchers have reported advantages in ultimate pH of the LM in pigs fed RAC. If a greater ultimate pH was also observed in hams, the increased pH could affect further processing characteristics and lead to better protein interaction and improved textural properties. The objective of this experiment was to determine if RAC-fed pigs yielded hams with a greater ultimate pH, and if so, whether or not that advantage improves textural properties and water retention of further processed hams. Two hundred hams from barrows and gilts fed RAC or control diets were selected based on HCW. Hams were fabricated into 5 separate pieces to determine cutting yields, and 6 muscles were evaluated for ultimate pH. Hams were processed to make cured and smoked hams. Ractopamine increased cutting yields of the whole ham (P < 0.0001), inside (P < 0.01), outside (P < 0.01), and knuckle (P < 0.01) when expressed as a percentage of chilled side weight. Ultimate pH of the rectus femoris, vastus lateralis, and semitendinosus were all 0.06 pH units greater (P < 0.05), the biceps femoris was 0.04 pH units greater (P = 0.02), and the semimembranosus and adductor muscles were 0.03 pH units greater in pigs fed 7.4 mg/kg of RAC when compared with control pigs. Cured hams from RAC-fed pigs were heavier at all stages of production. No differences were detected in binding strengths (P = 0.88) or protein fat-free values (P = 0.13) between RAC (9.06 kg and 20.37) and control hams (9.01 kg and 20.13). Ractopamine increased cutting yields, total weight of cured hams, and ultimate muscle pH. Ractopamine can be fed to pigs to achieve the desired growth characteristic advantages and cutting yields without affecting further processed ham characteristics.

Methoxy species on Cu(110): understanding the local structure of a key catalytic reaction intermediate.

Partial oxidation of methanol to formaldehyde over Cu(110) is one of the most studied catalytic reactions in surface science, yet the local site of the reaction intermediate, methoxy, remains unknown. Using a combination of experimental scanned-energy mode photoelectron diffraction, and density functional theory, a consistent structural solution is presented in which all methoxy species occupy twofold coordinated "short-bridge" adsorption sites. The results are consistent with previously-published scanning tunnelling microscopy images and theoretical calculations of the reaction mechanism.