Accurate molecular polarizabilities with coupled cluster theory and machine learning

The molecular dipole polarizability describes the tendency of a molecule to change its dipole moment in response to an applied electric field. This quantity governs key intra- and intermolecular interactions, such as induction and dispersion; plays a vital role in determining the spectroscopic signatures of molecules; and is an essential ingredient in polarizable force fields. Compared with other ground-state properties, an accurate prediction of the molecular polarizability is considerably more difficult, as this response quantity is quite sensitive to the underlying electronic structure description. In this work, we present highly accurate quantum mechanical calculations of the static dipole polarizability tensors of 7,211 small organic molecules computed using linear response coupled cluster singles and doubles theory (LR-CCSD). Using a symmetry-adapted machine-learning approach, we demonstrate that it is possible to predict the LR-CCSD molecular polarizabilities of these small molecules with an error that is an order of magnitude smaller than that of hybrid density functional theory (DFT) at a negligible computational cost. The resultant model is robust and transferable, yielding molecular polarizabilities for a diverse set of 52 larger molecules (including challenging conjugated systems, carbohydrates, small drugs, amino acids, nucleobases, and hydrocarbon isomers) at an accuracy that exceeds that of hybrid DFT. The atom-centered decomposition implicit in our machine-learning approach offers some insight into the shortcomings of DFT in the prediction of this fundamental quantity of interest.

Ultrafast Photoelectron and Optical Spectroscopies of Photoinduced Processes in Molecular Systems in Solution

Luca Longetti

Investigating molecular excitations with femtosecond time resolution is of pivotal importance to understand the out-of-equilibrium processes taking place in molecular systems upon light absorption. The photochemistry of solvated species is heavily determined by the early steps of the relaxation dynamics. In this thesis, ultrafast electronic spectroscopies are exploited to study relaxation dynamics of photoexcited molecules in solution by probing the transient electronic structure. Vacuum-ultraviolet (VUV) ultrashort monochromatized light pulses (HARMONIUM, 15-100 eV) are exploited for steady-state photoelectron spectroscopy (PES) and time-resolved PES in a pump-probe scheme. This is a powerful tool for investigating electronic structure and ultrafast processes of solvated molecules with high time (50fs) and energy (0.12eV) resolution. PES retrieves binding energies of valence and core electronic states with elemental specificity and without the constraints of selection rules, and is here applied to liquids and solutions by means of a liquid micro-jet. With the aim of extending this technique to a larger class of solutes, we demonstrate the capability to perform studies on volatile liquids such as organic solvents. PES spectra of gas phase and liquid phase aromatic compounds are presented and their valence orbitals are compared and identified. The solvation is discussed and the vertical ionization energies are reported. This retrieves important parameters for electrochemistry and opens new perspectives towards PES studies of molecules in organic solvents. Upon photoexcitation, molecules can undergo several relaxation processes such as nonradiative relaxation processes which include dissociation, internal conversion and intersystem crossing. Energy can also be released to the solvent environment by intermolecular processes such as vibrational energy transfer. All of these phenomena are reflected in a transient electronic configuration. PES can hence probe electronic and structural dynamics along the entire reaction coordinates. The ferric trisoxalate complex represents an ideal coordination compound showing an intriguing cascade of processes upon photoexcitation. We have directly observed the metal photoreduction due to an instantaneous intramolecular charge transfer. We then suggest a branching between photodissociation and a back-electron transfer channels, which completes the picture of the compoundâs photochemistry. This experiment shows PES sensitivity to oxidation state changes, providing an interesting perspective for photoredox reaction studies in solution and for intra- and inter-molecular charge-transfer phenomena. Vibrational wave packets (WP) are interesting observables to map non-adiabatic dynamics, relaxation pathways and coupling to solvent of the excited molecule. We have investigated molecular iodine in ethanol, which we have studied first by optical transient absorption spectroscopy using a white light continuum probe. The electronic absorption spectrum of I2 in ethanol is strongly modified compared to the case of other organic solvents, due to a strong coupling of covalent and ionic states. We have mapped the vibrational WP dynamics, in particular its trajectory and damping along the I-I bond axis. This study is intended to prepare for an ultrafast PES experiment aimed at linking the response of inner shells to the WP launched in the valence states. Preliminary steady-state PES spectra are reported and discussed.

EPFL2020

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.

EPFL2007

Scanning Tunneling Luminescence of Pentacene Nanocrystals

Alexander Kabakchiev

Organic semiconductors are promising materials for future electronic and electroluminescence applications. A detailed understanding of organic layers and nano-sized crystals down to single molecules can address fundamental questions of contacting organic semiconductors at the nanometer limit and obtaining luminescence from them. In this thesis, electroluminescence spectra from pentacene, a policyclic hydrocarbon (acene), are discussed. The luminescence is induced by the current from the tip of a scanning tunneling microscope (STM). Pentacene is an organic semiconductor which gained a lot of attention in technology because of its electronic properties suitable for applications in thin film devices. Moreover, recent fundamental studies employed pentacene as a standard to demonstrate sub-molecular resolution by scanning probe techniques. This work reports the first observation of light emission from nanometer-sized pentacene crystals grown on an ultrathin insulating layer on noble metal surfaces. Different STM-techniques are combined to characterize the individual systems studied with respect to topography, crystal structure, electronic properties and work function changes. The initial step of the project was the implementation of an optical system for light collection from the tunnel-junction of a low-temperature STM. In the set-up, a novel approach based on the use of in situ adjustable lenses has been realized. Three lenses placed in the vicinity of the tip-apex allow light collection into three independent channels which can be used for versatile optical analysis. An important part in the characterization of the organic system was to clarify the interaction between adsorbed molecules and substrates. We investigated individual pentacene molecules on different ultrathin insulator-metal systems. With the STM tip in tunnel contact, the molecules are situated in a double barrier junction formed by the insulating layer on one side and the vacuum gap on the other side. The metal surface and the STM-tip form the electrodes. The electronic properties of pentacene in this configuration have been characterized. Insulator-metal-systems, which provide a good electronic decoupling for pentacene from the metal, have been chosen as substrates for the growth of pentacene nanocrystals. Using the sub-molecular resolution of the STM we resolved the structure of the top-layer of the pentacene nanocrystals and found that the crystal phase agrees with the pentacene bulk structure. Moreover, the comparison of charge injection barriers between individual molecules and nanocrystals of pentacene indicates a significant change of electronic properties after the formation of ordered structure from the individual building blocks. Optical spectroscopy of the emitted light reveals an excitonic emission from the nanocrystals, which is in very good agreement with photoemission spectra of macroscopic crystals. Although a highly localized current-injection by the STM tip is used for excitation, it can be concluded that the source of light emission is delocalized. In contrast to luminescence measurements reported for other organic materials in STM, the excitation is not localized on the individual molecule, into which a charge is injected by the STM-tip. Our study indicates the importance of inter-molecular coupling leading to a high mobility of the excited state which has to be considered in the framework of STM-induced luminescence. A further result is the observation of the Stark shift of pentacene luminescence, that has so far not been measured at large electric fields of the order of 1V/nm. The evaluation of the Stark shift provides information on dipole and polarizability change during the decay of an exciton. The measured large dipole change of the lowest singlet exciton in pentacene indicates a mixing of the Frenkel exciton (FE) with a small contribution of charge-transfer (CT). Finally, we developed a set-up for photon correlation measurements in the STM. The properties of photon statistics is a means which can unambiguously prove that the luminescence is due to a single-photon source, i.e. a light source which emits no more than one photon at a time. A typical example of such a source is the emission from a single molecule. We performed photon correlations measurements of the luminescence from pentacene and C60 nanocrystals. While the excitonic bulk emission of pentacene is not expected to represent a single photon emitter, we also did not observe anticorrelations in the case of C60 indicating the importance of the local environment in the STM-junction, e.g. the short distance to the metal electrodes.

EPFL2010