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The eChem project features an e-book published as a web page (10.30746/978-91-988114-0-7), collecting a repository of Jupyter notebooks developed for the dual purpose of explaining and exploring the theory underlying computational chemistry in a highly interactive manner as well as providing a tutorial-based presentation of the complex workflows needed to simulate embedded molecular systems of real biochemical and/or technical interest. For students ranging from beginners to advanced users, the eChem book is well suited for self-directed learning, but workshops led by experienced instructors and targeting student bodies with specific needs and interests can readily be formed from its components. This has been done by using eChem as the base for a workshop directed toward graduate students learning the theory and practices of quantum chemistry, resulting in very positive assessment of the interactive nature of this framework. The members of the eChem team are engaged in both education and research, and as a mirroring activity, we develop the open-source software upon which this e-book is predominantly based. The overarching vision and goal of our work is to provide a science- and education-enabling software platform for quantum molecular modeling on contemporary and future high-performance computing systems, and to document the resulting development and workflows in the eChem book., QC 20230705

We performed a spectroscopic study on the m-MTDATA (donor) and PPT (acceptor) molecular vertical heterostructure. The electronic properties of the donor/acceptor interface have been comprehensively characterized by synchrotron radiation-based photoelectron spectroscopy and near-edge x-ray absorption fine structure. The spectroscopic results reveal the existence of new hybridization states in the original molecular energy gap, likely attributed to the interaction between the donor and the acceptor molecules at the interface. Such hybridized states can have a significant impact on the charge transport in organic electronic devices based on donor-acceptor molecules and can explain the increased efficiency of device using such molecules.

The starburst pi-conjugated molecule based on triphenylamine (TPA) building blocks, 4,4',4 ''-tris(N-3-ethylphenyl-N-phenylamino)triphenylamine (C57H48N4, m-MTDATA), is widely used in optoelectronic devices due to its electron-donating properties. The electronic structure of m-MTDATA adsorbed on an Au(111) surface was investigated by means of photoelectron spectroscopy (PES) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The results were further compared to gas-hase measurements and DFT calculations. Our results clearly indicate a significant molecule-substrate interaction that induces considerable modifications on the electronic structure of the adsorbate compared to the isolated molecule. The energy level alignment analysis shows that the HOMO-LUMO gap is filled by new interface states.

In this article, we analyze the electronic structure modifications of triphenylamine (TPA), a well-known electron donor molecule widely used in photovoltaics and optoelectronics, upon deposition on Au(111) at a monolayer coverage. A detailed study was carried out by synchrotron radiation-based photoelectron spectroscopy, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, scanning tunneling microscopy (STM), and ab initio calculations. We detect a new feature in the pre-edge energy region of the N K-edge NEXAFS spectrum that extends over 3 eV, which we assign to transitions involving new electronic states. According to our calculations, upon adsorption, a number of new unoccupied electronic states fill the energy region between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the free TPA molecule and give rise to the new feature the pre-edge region of the NEXAFS spectrum. This finding highlights the occurrence of a considerable modification of the electronic structure of TPA. The appearance of new states in the HOMO-LUMO gap of TPA when adsorbed on Au(111) has crucial implications for the design of molecular nanoelectronic devices based on similar donor systems.

This joint experimental-theoretical spectroscopy study of the fullerene derivative PC60BM ([6,6]-phenyl-C-60-butyric acid methyl ester) aims to improve the understanding of the effect of photooxidation on its electronic structure. We have studied spin-coated thin films of PC60BM by X-ray Photoelectron Spectroscopy (XPS), Near-edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy, and Fourier Transform Infrared Spectroscopy (FTIR), before and after intentional exposure to simulated sunlight in air for different lengths of time. The pi* resonance in the C1s NEXAFS spectrum was found to be a very sensitive probe for the early changes to the fullerene cage, while FTIR spectra, in combination with O1s NEXAFS spectra, enabled the identification of the oxidation products. The changes observed in the spectra obtained by these complementary methods were compared with the corresponding Density Functional Theory (DFT) calculated single-molecule spectra of a large set of in silico generated oxidation products of PC60BM where oxygen atoms were attached to the C-60 cage. This comparison confirms that photooxidation of PC60BM disrupts the conjugation of the fullerene cage by a transition from sp(2) to sp(3)-hybridized carbon and causes the formation of several oxidation products, earlier proposed for C-60. The agreement between experimental and calculated IR spectra suggests moreover the presence of dicarbonyl and anhydride structures on the fullerene cage, in combination with cage opening at the adsorption site. By including PC60BM with physisorbed O-2 molecules on the cage in our theoretical description in order to model oxygen diffused through the film, the experimental O1s XPS and O1s NEXAFS spectra could be reproduced.

The bottom-up synthesis and preliminary characterizations of a new biphenylene-based 2D framework are presented. This new low-dimensional carbon allotrope potentially completes the many hypothesized carbon networks based on biphenylene.

It is established that density functional theory (DFT) + U is a better choice compared to DFT for describing the correlated electron metal center in organometallics. The value of the Hubbard U parameter may be determined from linear response, either by considering the response of the metal site alone or by additionally considering the response of other sites in the compound. We analyze here in detail the influence of ligand shells of increasing size on the U parameter calculated from the linear response for five transition metal phthalocyanines. We show that the calculated multiple-site U is larger than the single-site U by as much as 1 eV and the ligand atoms that are mainly responsible for this difference are the isoindole nitrogen atoms directly bonded to the central metal atom. This suggests that a different U value may be required for computations of chemisorbed molecules compared to physisorbed and gas-phase cases.

There exists an extensive literature on the electronic structure of transition-metal phthalocyanines (TMPcs), either as single molecules or adsorbed on surfaces, where explicit intra-atomic Coulomb interactions of the strongly correlated orbitals are included in the form of a Hubbard U term. The choice of U is, to a large extent, based solely on previous values reported in the literature for similar systems. Here, we provide a systematic analysis of the influence of electron correlation on the electronic structure and magnetism of several TMPcs (MnPc, FePc, CoPc, NiPc, and CuPc). By comparing calculated results to valence-band photoelectron spectroscopy measurements, and by determining the Hubbard term from linear response, we show that the choice of U is not as straightforward and can be different for each different TMPc. This, in turn, highlights the importance of individually estimating the value of U for each system before performing any further analysis and shows how this value can influence the final results.

Two of the main technological challenges of the century are the production of clean energy, on the one hand, and the development of new materials for electronic and spintronic applications that could increase the speed and the storage capacity of regular electronic devices, on the other hand. Organic materials, including fullerenes, organic polymers and organic molecules with metal centres are promising candidates for low-cost, flexible and clean technologies that can address these challenges. A thorough description of the electronic properties of such materials is, therefore, crucial. The interaction of electromagnetic radiation with the molecule can provide the needed insight into the electronic and vibrational levels and on possible chemical interactions. In order to explain and interpret experimentally measured spectra, a good theoretical description of the particular spectroscopy is necessary. Within density functional theory (DFT), the current thesis discusses the theoretical tools used to describe the spectroscopic properties of molecules with emphasis on two classes of organic materials for photovoltaics, molecular electronics and spintronics. Specifically, the stability of the fullerene derivative PC60BM is investigated in connection with its use as an electron acceptor in organic solar cells and the valence band electronic structure of several transition metal phthalocyanines is studied for their possible application in electronics and spintronics. The spectroscopies discussed in the current work are: the photoelectron spectroscopy of the valence band, X-ray photoelectron spectroscopy of the core levels, near-edge X-ray absorption fine structure, Infrared and Raman vibrational spectroscopies

Fullerenes have been a main focus of scientific research since their discovery due to the interesting possible applications in various fields like organic photovoltaics (OPVs). In particular, the derivative [6,6]-phenyl-C-60-butyric acid methyl ester (PCBM) is currently one of the most popular choices due to its higher solubility in organic solvents compared to unsubstituted C-60. One of the central issues in the field of OPVs is device stability, since modules undergo deterioration (losses in efficiency, open circuit voltage, and short circuit current) during operation. In the case of fullerenes, several possibilities have been proposed, including dimerization, oxidation, and impurity related deterioration. We have studied by means of density functional theory the possibility of oxygen adsorption on the C-60 molecular moiety of PCBM. The aim is to provide guidelines for near edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectroscopy (XPS) measurements which can probe the presence of atomic or molecular oxygen on the fullerene cage. By analysing several configurations of PCBM with one or more adsorbed oxygen atoms, we show that a joint core level XPS and O1s NEXAFS investigation could be effectively used not only to confirm oxygen adsorption but also to pinpoint the bonding configuration and the nature of the adsorbate.

To shed light on the metal 3d electronic structure of manganese phthalocyanine, so far controversial, we performed photoelectron measurements both in the gas phase and as thin film. With the purpose of explaining the experimental results, three different electronic configurations close in energy to one another were studied by means of density functional theory. The comparison between the calculated valence band density of states and the measured spectra revealed that in the gas phase the molecules exhibit a mixed electronic configuration, while in the thin film, manganese phthalocyanine finds itself in the theoretically computed ground state, namely, the b2g1eg3a1g1b1g0 electronic configuration.

In the quest towards more durable solution-processed solar cells, the stability of the active layer materials under operation conditions is important. While lifetimes of several years have been demonstrated for encapsulated organic solar cells, it is generally known that degradation events can be accounted for by air components (O2 and/or water vapour) leaking into the cell through a non-ideal sealing. Here we present a fundamental study of intentional photo-degradation of the electron-acceptor PC60BM ([6,6]-phenyl-C61-butyric acid methyl ester) in air, with the purpose of improving the understanding of the electronic effects of fullerene photo-oxidation. We have studied spincoated thin films of PC60BM by X-ray Photoelectron Spectroscopy, Near-edge X-ray Absorption Fine Structure spectroscopy, and Fourier Transform Infrared Spectroscopy, before and after exposing them to simulated sunlight in air. The changes observed in the spectra obtained by these complementary methods were compared with calculated spectra of a large set of possible oxidation products of PC60BM where oxygen atoms have been attached to the C60 cage. The best fit with experimental IR spectra of photodegraded PC60BM films was obtained for a linear combination of calculated spectra for two degradation products, a dicarbonyl and an anhydride, both with open cages with 58 carbon atoms, and the pristine PC60BM molecule. From this comparison, we conclude that the conjugation of the fullerene cage is disturbed by the formation of several carbonyl-based derivatives on the C60 cage, accompanied by a transition from sp2 to sp3-hybridized carbon. The π* resonance in the C1s NEXAFS spectrum was found to be a very sensitive probe for small changes to the fullerene cage, and FT-IR was needed in combination with O1s NEXAFS, to identify the oxidation products., Manuscript