| 1. |
- Brumboiu, Iulia E., 1987-, et al.
(författare)
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Photooxidation of PC60BM : new insights from spectroscopy
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:42, s. 25753-25766
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Tidskriftsartikel (refereegranskat)abstract
- This joint experimental-theoretical spectroscopy study of the fullerene derivative PC60BM ([6,6]-phenyl-C60-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 π* 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 C60 cage. This comparison confirms that photooxidation of PC60BM disrupts the conjugation of the fullerene cage by a transition from sp2 to sp3-hybridized carbon and causes the formation of several oxidation products, earlier proposed for C60. 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 O2 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.
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| 2. |
- Brumboiu, Iulia E., 1987-, et al.
(författare)
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Analytical gradients for core-excited states in the algebraic diagrammatic construction (ADC) framework
- 2021
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 155:4
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Tidskriftsartikel (refereegranskat)abstract
- Expressions for analytical molecular gradients of core-excited states have been derived and implemented for the hierarchy of algebraic diagrammatic construction (ADC) methods up to extended second-order within the core-valence separation (CVS) approximation. We illustrate the use of CVS-ADC gradients by determining relaxed core-excited state potential energy surfaces and optimized geometries for water, formic acid, and benzene. For water, our results show that in the dissociative lowest core-excited state, a linear configuration is preferred. For formic acid, we find that the O K-edge lowest core-excited state is non-planar, a fact that is not captured by the equivalent core approximation where the core-excited atom with its hole is replaced by the "Z + 1" neighboring atom in the periodic table. For benzene, the core-excited state gradients are presented along the Jahn-Teller distorted geometry of the 1s -> pi* excited state. Our development may pave a new path to studying the dynamics of molecules in their core-excited states.
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| 3. |
- Fransson, Thomas, et al.
(författare)
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Computational Chemistry from Laptop to HPC : A notebook exploration of quantum chemistry
- 2022. - 1
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- Quantum chemistry is a powerful tool. It is now possible to model complex chemical processes even on a laptop getting insights into matter at its fundamental scale.But quantum chemistry is also very complex. Answering a chemical question requires selecting parameters among a wide variety of choices. Choosing a model system, an electronic structure method, a basis set, a set of properties, and a wide array of parameters which can affect the results in small but sometimes meaningful way… It can be a very daunting task, even for veterans of the field.Similarly, for those who wish to get a deeper understanding of a method, going through the pages of equation often riddled with inconsistent notations and formulations is very challenging. And at the end, the link between the equation and the computer implementation found in existing softwares can be vague at best.We believe that a core issue is that humans are not good at learning in abstract terms. We can get very far with a lecture or a textbook, but we will never build as much intuition about how a clock work as by simply breaking one apart and rebuilding it from scratch.This is exactly the aim of this page, allowing a hands-on approach to computational chemistry. Together we will dismantle the black box that a computational chemistry code often seems to be, go through all the cogs and gears, and build back together some of the main computational methods of modern computational chemistry. We will do this by presenting the underlying equations, all expressed with consistent notations, as well as by suggesting a simple python implementation, to really display in action how the theory is implemented into a practical tool. Additionally, we will put these methods in context by showing how they can be used to address concrete chemical questions, discussing the strengths and weaknesses of each method and how to best use them to solve practical problems.
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| 4. |
- Fransson, Thomas, et al.
(författare)
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XABOOM : An X-ray Absorption Benchmark of Organic Molecules Based on Carbon, Nitrogen, and Oxygen 1s -> π* Transitions
- 2021
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 17:3, s. 1618-1637
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Tidskriftsartikel (refereegranskat)abstract
- The performance of several standard and popular approaches for calculating X-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges of 40 primarily organic molecules up to the size of guanine has been evaluated, focusing on the low-energy and intense 1s -> pi* transitions. Using results obtained with CVS-ADC(2)-x and fc-CVS-EOM-CCSD as benchmark references, we investigate the performance of CC2, ADC(2), ADC(3/2), and commonly adopted density functional theory (DFT)-based approaches. Here, focus is on precision rather than on accuracy of transition energies and intensities-in other words, we target relative energies and intensities and the spread thereof, rather than absolute values. The use of exchange-correlation functionals tailored for time-dependent DFT calculations of core excitations leads to error spreads similar to those seen for more standard functionals, despite yielding superior absolute energies. Long-range corrected functionals are shown to perform particularly well compared to our reference data, showing error spreads in energy and intensity of 0.2-0.3 eV and similar to 10%, respectively, as compared to 0.3-0.6 eV and similar to 20% for a typical pure hybrid. In comparing intensities, state mixing can complicate matters, and techniques to avoid this issue are discussed. Furthermore, the influence of basis sets in high-level ab initio calculations is investigated, showing that reasonably accurate results are obtained with the use of 6-311++G**. We name this benchmark suite as XABOOM (X-ray absorption benchmark of organic molecules) and provide molecular structures and ground-state self-consistent field energies and spectroscopic data. We believe that it provides a good assessment of electronic structure theory methods for calculating X-ray absorption spectra and will become useful for future developments in this field.
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| 5. |
- Rehn, D. R., et al.
(författare)
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Gator : A Python-driven program for spectroscopy simulations using correlated wave functions
- 2021
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Ingår i: WIREs Computational Molecular Science. - : John Wiley and Sons Inc. - 1759-0876 .- 1759-0884. ; 11:6
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Tidskriftsartikel (refereegranskat)abstract
- The Gator program has been developed for computational spectroscopy and calculations of molecular properties using real and complex propagators at the correlated level of wave function theory. Currently, the focus lies on methods based on the algebraic diagrammatic construction (ADC) scheme up to the third order of perturbation theory. An auxiliary Fock matrix-driven implementation of the second-order ADC method for excitation energies has been realized with an underlying hybrid MPI/OpenMP parallelization scheme suitable for execution in high-performance computing cluster environments. With a modular and object-oriented program structure written in a Python/C++ layered fashion, Gator additionally enables time-efficient prototyping of novel scientific approaches, as well as interactive notebook-driven training of students in quantum chemistry. This article is categorized under: Computer and Information Science > Computer Algorithms and Programming Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry.
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| 6. |
- Savchenko, Viktoriia, et al.
(författare)
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Hydrogen bond effects in multimode nuclear dynamics of acetic acid observed via resonant x-ray scattering
- 2021
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 154:21
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Tidskriftsartikel (refereegranskat)abstract
- A theoretical and experimental study of the gas phase and liquid acetic acid based on resonant inelastic x-ray scattering (RIXS) spectroscopy is presented. We combine and compare different levels of theory for an isolated molecule for a comprehensive analysis, including electronic and vibrational degrees of freedom. The excitation energy scan over the oxygen K-edge absorption reveals nuclear dynamic effects in the core-excited and final electronic states. The theoretical simulations for the monomer and two different forms of the dimer are compared against high-resolution experimental data for pure liquid acetic acid. We show that the theoretical model based on a dimer describes the hydrogen bond formation in the liquid phase well and that this bond formation sufficiently alters the RIXS spectra, allowing us to trace these effects directly from the experiment. Multimode vibrational dynamics is accounted for in our simulations by using a hybrid time-dependent stationary approach for the quantum nuclear wave packet simulations, showing the important role it plays in RIXS.
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| 7. |
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| 8. |
- Savchenko, Viktoriia, et al.
(författare)
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Vibrational resonant inelastic X-ray scattering in liquid acetic acid : a ruler for molecular chain lengths
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Quenching of vibrational excitations in resonant inelastic X-ray scattering (RIXS) spectra of liquid acetic acid is observed. At the oxygen core resonance associated with localized excitations at the O-H bond, the spectra lack the typical progression of vibrational excitations observed in RIXS spectra of comparable systems. We interpret this phenomenon as due to strong rehybridization of the unoccupied molecular orbitals as a result of hydrogen bonding, which however cannot be observed in x-ray absorption but only by means of RIXS. This allows us to address the molecular structure of the liquid, and to determine a lower limit for the average molecular chain length.
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| 9. |
- Zhang, Teng, 1988-, et al.
(författare)
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Electronic Structure Study of Free and Adsorbed m-MTDATA
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The starburst p-conjugated molecule based on triphenylamine (TPA) building block, 4,4',4" -Tris(N-3-methylphenyl-N-phenyl-amino)triphenylamine (m-MTDATA), is widely used in optoelectronic devices due to its electron-donating properties. The electronic structure of m-MTDATA was investigated in the gas-phase and when deposited in thin films on a Au(111) surface by means of PhotoElectron Spectroscopy (PES) and Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy. Density Functional Theory (DFT) calculations were compared to the experimental gas-phase results, providing a comprehensive description of the molecular electronic structure. Moreover, the results were compared with previous TPA measurements, shedding light on the electronic structure modification due to the increased molecular complexity. Similar to TPA, but more complex, the binding energy of the C 1s photoelectron line of m-MTDATA results from the balance of two counter-acting effects: (1) the electronegativity of the N atoms and (2) the delocalization of lone-pair electrons of the nitrogen. Compared to TPA, the outermost valence PE spectrum of m-MTDATA shows a 3-peak feature with N 2pz character and a lowering of the binding energy of the HOMO. When adsorbed on Au(111), the changes observed in PES and NEXAFS spectra with respect to the free molecules, can be explained by a significant modification of m-MTDATA molecular and electronic structure, due to the molecule-substrate interaction.
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| 10. |
- Zhang, Teng, 1988-, et al.
(författare)
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Lone-Pair Delocalization Effects within Electron Donor Molecules: The Case of Triphenylamine and Its Thiophene-Analog
- 2018
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 122:31, s. 17706-17717
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Tidskriftsartikel (refereegranskat)abstract
- Triphenylamine (TPA) and its thiophene-analog, N,N-diphenyl-2-thiophenamine (DPTA), are both well-known as electron-donating molecules implemented in optoelectronic devices such as organic solar cells and LEDs. Comprehensive valence and core level photoelectron spectroscopy, as well as near edge X-ray absorption spectroscopy (NEXAFS), measurements have been performed on gas phase TPA and DPTA. The experimental results have been compared to density functional theory calculations, providing a detailed description of the molecular electronic structure. Specifically, the C 1s photoelectron lines of both TPA and DPTA were resolved in the different C atom contributions and their binding energies explained as the result of two counter-acting effects: (1) the electronegativity of the nitrogen atom (and sulfur atom in DPTA) and (2) the the N (and S in DPTA) lone-pair electrons. In addition, the C K-edge NEXAFS spectrum of DPTA reveals that the lowest unoccupied molecular orbital (LUMO) energy position is affected differently if the core hole site is on the phenyl compared to the thiophene ring. The electron-donating properties of these two molecules are largely explained by the significant contribution of the N lone-pair electrons (p(z)) to the highest occupied molecular orbital. The contribution to the LUMO and to the empty density of states of the sulfur of the thiophene ring in DPTA explains the better performance of donor-pi-acceptor molecules containing this moiety and implemented in photoenergy conversion devices.
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