Evaluating Charge Equilibration Methods To Generate Electrostatic Fields in Nanoporous Materials

Charge equilibration (Qeq) methods can estimate the electrostatic potential of molecules and periodic frameworks by assigning point charges to each atom, using only a small fraction of the resources needed to compute density functional (DFT)-derived charges. This makes possible, for example, the computational screening of thousands of microporous structures to assess their performance for the adsorption of polar molecules. Recently, different variants of the original Qeq scheme were proposed to improve the quality of the computed point charges. One focus of this research was to improve the gas adsorption predictions in metal-organic frameworks (MOFs), for which many different structures are available. In this work, we review the evolution of the method from the original Qeq scheme, understanding the role of the different modifications on the final output. We evaluated the result of combining different protocols and set of parameters, by comparing the Qeq charges with high quality DFT-derived DDEC charges for 2338 MOF structures. We focused on the systematic errors that are attributable to specific atom types to quantify the final precision that one can expect from Qeq methods in the context of gas adsorption where the electrostatic potential plays a significant role, namely, CO2 and H2S adsorption. In conclusion, both the type of algorithm and the input parameters have a large impact on the resulting charges, and we draw some guidelines to help the user to choose the proper combination of the two for obtaining a meaningful set of charges. We show that, considering this set of MOFs, the accuracy of the original Qeq scheme is often still comparable with the most recent variants, even if it clearly fails in the presence of certain atom types, such as alkali metals.

Design of Surface-Supported Bio-inspired Networks for CO2 and O2 Activation at Room Temperature

Daniel Eduardo Hurtado Salinas

The structure of a biological system defines its function. Therefore, nature has developed sophisticated systems that catalyze chemical reactions that are vital for life on earth. For instance, the photosynthesis is a biological process that is partially regulated by the metallo-enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase), whose function is to catalyze the capture and transfer of CO2 into organic molecules. This carboxylation reaction occurs at the active site, where a magnesium ion (Mg2+) is bound to organic molecules with carboxylate (COO-) and amine (NH2) functional groups. In the last decades, supramolecular chemistry has proven to be a valid approach to replicate the structural characteristics of these natural metal-organic systems. Metal atoms and organic molecules are used as building blocks to form two-dimensional (2D) metal-organic networks (MONs) on metal surfaces, through a self-assembly process that occurs spontaneously. In these systems the molecules bind to the metal centers and control their oxidation states that, as found in metallo-enzymes, is crucial to perform a catalytic task. Therefore, these supramolecular assemblies show promising features to be explored for heterogeneous catalysis. The main objective of this thesis is to reverse the structure-function equation, that is: instead of finding specific functions of well-known 2D structures for future applications, 2D structures are designed to reproduce the specific functions of well-known bio-systems. Thus, inspired in the structure of the active site of RuBisCO, 2D Mg-based supramolecular assemblies are rationally designed on Cu(100) or Mg(0001) surfaces at room temperature (RT) as a platform for CO2 adsorption. This work is the first study of self-assembly of alkaline earth metal atoms (Mg) with organic molecules ((1,4-benzenedicarboxylic acid (TPA) and 2,4,6-tris(4-aminophenyl)-1,3,5-triazine (TAPT)) on metal surfaces. The first part of this thesis investigates the self-assembly of TAPT molecules. Scanning Tunneling Microscopy (STM) and High Resolution X-ray Photoemission Spectroscopy (HR-XPS) demonstrate that the molecules typically semi-deprotonate to form MONs with the adatoms from the host substrates. The exposure of these structures to CO2 results in the carboxylation of the amino groups. The second part proves that the COOH moieties of TPA molecules fully-deprotonate to form homo-molecular structures. The incorporation of Mg adatoms result in ionic MONs, which reproduce the carboxylate environment of the active site of RuBiSCO. STM, XPS and Density Functional Theory (DFT) analyze the structural changes, the chemical reactions and charge transfer during either the CO2 or O2 adsorption on the Mg2+ centers. The last part focusses on the co-deposition of both molecules to form 2D metallic-hetero-molecular networks with Mg2+ centers. The role of the Mg2+ centers as active sites for molecular adsorption and model systems for gas storage is studied. STM reveals that CO2 partially modifies the network towards a configuration that resembles the active site of RuBisCO. The formation of 3D structures to enhance CO2 adsorption is also evaluated.

EPFL2018

Stereoselectivity and electrostatics in charge-transfer Mn- and Cs-TCNQ(4) networks on Ag(100)

Nasiba Abdurakhmanova, Andrea Floris, Klaus Kern, Sebastian Stepanow, Tzu-Chun Tseng

Controlling supramolecular self-assembly is a fundamental step towards molecular nanofabrication, which involves a formidable reverse engineering problem. It is known that a variety of structures are efficiently obtained by assembling appropriate organic molecules and transition metal atoms on well-defined substrates. Here we show that alkali atoms bring in new functionalities compared with transition metal atoms because of the interplay of local chemical bonding and long-range forces. Using atomic-resolution microscopy and theoretical modelling, we investigate the assembly of alkali (Cs) and transition metals (Mn) co-adsorbed with 7,7,8,8-tetracyanoquinodimethane (TCNQ) molecules, forming chiral superstructures on Ag(100). Whereas Mn-TCNQ(4) domains are achiral, Cs-TCNQ(4) forms chiral islands. The specific behaviour is traced back to the different nature of the Cs- and Mn-TCNQ bonding, opening a novel route for the chiral design of supramolecular architectures. Moreover, alkali atoms provide a means to modify the adlayer electrostatic properties, which is important for the design of metal-organic interfaces.

Nature Publishing Group2012

Single-molecule-level characterization of supramolecular systems at surfaces

Dietmar Payer

This thesis deals with the self-organization of individual building blocks, specifically organic molecules and metal atoms, into supramolecular structures on metal surfaces under ultra high vacuum conditions (UHV). Self-organization of supramolecular systems is a promising candidate for a bottom-up approach in the fabrication of complex structures with specific properties. This process is steered by interactions between functional groups of the individual building blocks and is of apparent interest to gain a detailed understanding of the influence and the behavior of these functional groups enabling intermolecular binding. In the first part of the thesis, we investigate hydrogen bonded structures on metal surfaces. Of especial interest is the possibility of the formation of ionic hydrogen bonds, a special class of hydrogen bond which connects a charged donor (acceptor) and a neutral acceptor (donor) and is important in biological systems. By combined Scanning Tunneling Microscopy (STM), X-ray Photoelectron Spectroscopy (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) measurement we show the deprotonation of carboxylic functions in the molecules, forming carboxylate groups involved in intermolecular binding. With our complementary experimental and theoretical examinations we clearly show that the carboxylate groups are indeed still charged although adsorbed onto a conducting metal surface and that the observed structures can be computationally reproduced by using these charges in classical molecular dynamic calculations. Our investigations clearly reveal that all requirements for the formation of ionic hydrogen bonds in these samples at metal surfaces under solvent free conditions are fulfilled. In the second part, the confinement of surface state electrons in self-assembled hydrogen-bonded structures is investigated. The examined structure contains two-dimensional cavities, with different inner diameters in the periodic arrangement and in domain boundaries. Inside the cavities we detect a spatially localized modification in the local density of states (LDOS) of the Ag(111) surface state electrons. The energy of the peak correlates with the cavity area as predicted by a simple "particle in a box" model. This clearly shows that the surface state electrons form a confined state inside the cavities. Furthermore we examine self-assembled periodic structures as templates for binding single macrocyclic molecules. The macrocyclic molecules can be deposited by sublimation, as STM-topographs with submolecular resolution reflect the shape of the intact molecules and reveal a coverage dependent aggregation behavior. We show that it is possible to fabricate a structure in which at most one macrocyclic molecule per pore can be found in a defined binding position. In the last part of the thesis we investigate the influence of individual metal atoms on the chemical activity and the self-assembly process of molecules on metal surfaces. First, we demonstrate the high chemical reactivity of these metal atoms. In our experiments we address the chemical reactivity of static active sites, like kinks and step edges, and of dynamic active sites, like the metal atoms, separately. Doing this we show that a non-negligible amount of the chemical reactivity of a metal surface is due to this dynamic adatom gas. Furthermore the influence of metal atoms on the structure formation of organic molecules is investigated. We show that two-dimensional structures based on a complex formation between metal centers and ligands can be formed and that the coordination number is independent of the substrate symmetry. Furthermore, we show the possibility that on metal surfaces one can prepare three-fold coordinated Fe-centers, a coordination number which is rarely seen in three dimensional chemistry. In the last part we study catenanes, which consist of two interlocked macrocyclic molecules. Main interest is on the confirmation of a structural change of the catenanes adsorbed on a metal substrate. For our experiments we use the fact that the catenanes are designed to "trap" a Cu-atom by complex formation. As this reaction is associated with a structural change and a change in intermolecular interaction, we can verify a reaction of catenanes adsorbed onto a surface with Cu adatoms and therefore a structural alteration by simply imaging the formed structures. Our measurements show the possibility of depositing large molecules like catenanes by sublimation and of their potential for use as molecular machines adsorbed onto metal surfaces.