| 1. |
- Nørby, Morten Steen
(författare)
-
Extending the capabilities of polarizable embedding through damped linear response theory
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- One of the greater challenges of modern quantum chemistry is to meet the growing demands of a detailed description of macro molecules, such as proteins and RNA/DNA. The size of such systems make it an almost impossible task to, from first principle calculations, obtain any detailed information regarding electronic structure. This thesis is focused on development of new computational tools for investigation of electronic transitions within large molecular systems. Central to this is the polarizable embedding (PE) model. For many of these systems electronic transitions are localized to one or a few active sites which in turn will be described by accurate quantum chemical methods. The remaining part of the system, defining the environment, is then treated at a lower level using a classical electrostatic approach. The environment is further incorporated into the Hamiltonian describing the quantum region in an effective manner.The work presented in this thesis covers extensions to the PE model both in the quantum region and in the environmental description. The former, starts by combining the PE model with a damped linear response formalism. This coupling enables the study of electronic processes near resonance and in any frequency range desirable thus covering all from core hole transitions to valence transitions. Another important aspect of this work is the coupling of PE to a polarizable continuum model which allows for inclusion of bulk solvent effects in an effective manner. In addition to these extensions we have further considered alternative ways of acquiring parameters used in the construction of the embedding potential. This is essential for accurate embedding calculations as the embedding potential enters directly in the wave function optimization.
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| 2. |
- Ahmadzadeh, Karan, 1991-
(författare)
-
Efficient Calculation of Nonlinear Spectroscopic Properties within the Time-Dependent Density Functional Theory Approximation
- 2023
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis introduces a novel computational scheme tailored for efficient calculations of nonlinear spectroscopic observables. First, a derivation and implementation of an algorithm designed to harness the linearity of the Fock matrix construction in calculating two-photon absorption cross-sections within the self-consistent field approximation is presented. Subsequently, this computational scheme is extended to the density functional theory approximation for functionals belonging to the generalized gradient approximation. Lastly the derivation and implementation of the nonlinear exchange-correlation kernel for functionals belonging to the meta generalized gradient approximation are presented for the first time.Collectively, the advancements presented in this thesis contribute new methodologies and insights to the computational realm of nonlinear spectroscopic calculations, offering the potential for large-scale theoretical spectroscopy calculations at the level of density functional theory.
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| 3. |
- Brand, Manuel
(författare)
-
Implementation of complex polarization propagator theory for linear response properties of large molecular systems
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Since its beginning, the remarkable development from the first commercially available computers toward exascale supercomputers just within the span of a lifetime has been closely intertwined with the perpetual quest for the utilization of the arising computing power for the avail of theoretical chemistry. With the aim of further pushing the limits of computationally accessible molecular system sizes, this thesis includes the presentation of programming efforts, which brought forth two quantum chemical software codes, as well as a range of ab initio studies on carbon-based systems, enabled by the former.The VeloxChem and Gator programs, developed for spectroscopy simulations at the level of density-functional theory (DFT) and correlated wave function methods, respectively, employ a hybrid message passing interface (MPI)/open multiprocessing (OpenMP) parallelization scheme embedded in a modular program structure written in a Python/C++ layered fashion for the execution in contemporary high-performance computing (HPC) environments. Included numerical solvers for the evaluation of real and complex linear response functions in combination with the parallel construction of auxiliary Fock matrices enable the efficient calculation of one-photon absorption or electronic circular dichroism (CD) spectra in the ultraviolet/visible (UV/vis) or X-ray spectral region, as well as van der Waals C6 dispersion coefficients.Employing the VeloxChem program in two comprehensive investigations, the C6 dispersion coefficients of carbon fullerenes up to a system size of C540 and the CD spectra of carbohelicenes ranging from CH[5] to CH[30] have been calculated at the DFT level of theory. The revealed non-additive scaling with respect to the number of carbon atoms of N2.2 in the former and nontrivial CD band progressions, arguably linked to the number of overlapping layers in the helical conjugated systems, in the latter rectify the current conception in their respective fields.In a benchmark for the Gator program on a series of guanine oligomers, the full UV/vis spectrum for a tetrad was calculated at the level of a second-order algebraic-diagrammatic construction (ADC(2)) scheme in just under 15 hours by efficient employment of 32,768 central processing unit (CPU) cores.Exceeding the limit of 10,000 and 1,000 contracted basis functions for a treatment with the DFT and ADC(2) methods, respectively, these practical examples demonstrate the capability of VeloxChem and Gator to harness vast computational resources made available by contemporary and future HPC systems and thereby routinely address scopes of system sizes that were previously out of reach.
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| 4. |
- Falklöf, Olle
(författare)
-
Computational Studies of Photobiological Keto-Enol Reactions and Chromophores
- 2015
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis presents computational chemistry studies of keto-enol reactions and chromophores of photobiological signicance.The rst part of the thesis is concerned with two protein-bound chromophores that, depending on the chemical conditions, can exist in a number of dierent ketonic and enolic forms. The rst chromophore is astaxanthin, which occurs in the protein complex responsible for the deep-blue color of lobster carapace. By investigating how dierent forms of astaxanthin absorb UV-vis radiation of dierent wavelengths, a model is presented that explains the origin of the dramatic color change from deep-blue to red upon cooking of live lobsters.The second chromophore is the oxyluciferin light emitter of fireflies, which is formed in the catalytic center of the enzyme firefly luciferase. To date, there is no consensus regarding which of the possible ketonic and enolic forms is the key contributor to the light emission. In the thesis, the intrinsic tendency of oxyluciferin to prefer one particular form over other possible forms is established through calculation of keto-enol and acid-base excited-state equilibrium constants in aqueous solution.The second part of the thesis is concerned with two families of biological photoreceptors: the blue-light-absorbing LOV-domain proteins and the red-light-absorbing phytochromes. Based on the ambient light environment, these proteins regulate physiological and developmental processes by switching between inactive and active conformations. In both families, the conversion of the inactive into the active conformation is triggered by a chemical reaction of the respective chromophore.The LOV-domain proteins bind a LOV-domain proteins bidn in flavin chromophore and regulate processes such as chloroplast relocation and phototropism in plants. An important step in the activation of these photoreceptors is a singlet-triplet transition between two electronically excited states of the flavin chromophore. In the thesis, this transition is used as a prototype example for illustrating, for the rst time, the ability of rst-principles methods to calculate rate constants of inter-excited state phosphorescence events.Phytochromes, in turn, bind bilin chromophores and are active in the regulation of processes like seed germination and flowering time in plants. Following two systematic studies identifying the best way to model the UV-vis absorption and fluorescence spectra of these photoreceptors, it is demonstrated that steric interactions between the chromophore and the apoprotein play a decisive role for how phytochromes are activated by light.
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| 5. |
- Fransson, Thomas, 1986-
(författare)
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X-ray spectroscopies through damped linear response theory
- 2016
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In order to reach a fundamental understanding of interactions between electromagnetic radiation and molecular materials, experimental measurements need to be supplemented with theoretical models and simulations. With the use of this combination, it is possible to characterize materials in terms of, e.g., chemical composition and molecular structure, as well as achieve time-resolution in studies of chemical reactions. This doctoral thesis focuses on the development and evaluation of theoretical methods with which, amongst others, X-ray absorption and X-ray emission spectroscopies can be interpreted and predicted. In X-ray absorption spectroscopy the photon energy is tuned such that core electrons are targeted and excited to either bound or continuum states, and X-ray emission spectroscopy measures the subsequent decay from such an excited state. These core excitations/de-excitations exhibit strong relaxation effects, making theoretical considerations of the processes particularly challenging. While the removal of a valence electron leaves the remaining electrons relatively unaffected, removing core electrons has a substantial effect on the other electrons due to the significant change in the screening of the nucleus. Additionally, the core-excited states are embedded in a manifold of valence-excited states that needs to be considered by some computationally feasible method. In this thesis, a damped formalism of linear response theory, which is a perturbative manner of considering the interactions of (weak) external or internal fields with molecular systems, has been utilized to investigate mainly the X-ray absorption spectra of small- to medium-sized molecular systems.Amongst the standard quantum chemical methods available, coupled cluster is perhaps the most accurate, with a well-defined, hierarchical manner of approaching the correct electronic wave function. Combined with response theory, it provides a reliable theoretical method in which relaxation effects are addressed by means of an accurate treatment of electron correlation. The first part of this thesis deals with the development and evaluation of such an approach, and it is shown that the relaxation effects can be addressed by the inclusion of double excitations in the coupled cluster manifold. However, these calculations are computationally very demanding, and in order to treat larger systems the performance of the coupled cluster approach has been compared to that of the less demanding method of time-density dependent functional theory (TDDFT). Both methods have been used to investigate the X-ray absorption spectrum of water, which has been extensively debated in the scientific community following a relatively recent hypothesis concerning the underlying structure of liquid water. Water exhibits a great number of anomalous properties that stand out from those of most compounds, and the importance of reaching a fundamental understanding of this substance cannot be overstated. It has been demonstrated that TDDFT yields excellent results for liquid water, opening up possibilities of investigating the correlation between spectral features and local structures.Furthermore, recent developments in damped linear response TDDFT in the four-component relativistic regime have enabled the inclusion of spin-orbit coupling in damped linear response calculations, making black-box calculations of absorption spectra in a relativistic setting practical. With this approach, it is possible to address the spin-orbit splitting in L2,3-edge X-ray absorption spectra, and the performance of such a method has been demonstrated for a set of small molecules. Excellent agreement with experiment is obtained in terms of relative features, but an anomalous error in absolute energy has been observed for silane derivatives featuring fluorine-substitutions. This is likely a result of the strong influence of the very electronegative fluorine atoms on the electron density of the core-excited atom.Finally, the treatment of non-resonant X-ray emission spectroscopy using damped linear response theory is discussed. The expansion needed for the development of a simple method by which this spectroscopy can be treated using damped linear response theory at the TDDFT level of theory has been identified, and proof of principle calculations at the time-dependent Hartree-Fock level of theory are presented.
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| 6. |
- Gustafsson, Camilla
(författare)
-
Modeling environment effects on spectroscopic properties of biomarkers and catalytic mechanisms in enzymes
- 2020
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Arguably, humans are in need of both better diagnostic tools to prevent pro- gression of diseases as well as greener catalysts for synthesis of chemicals.Neurodegenerative diseases affecting neurons in the brain leads to demen- tias, where Alzheimer’s disease (AD) is the most prevalent. It is estimated that about 50 million people worldwide suffer from AD, a number that has more than doubled during the last 30 years. Currently, there is no cure for AD, but in order to slow the progression of symptoms it is crucial to develop biomarkers for early detection and initiation of clinical interventions.With theoretical tools it is possible to better understand the optical prop- erties of fluorescent biomarkers, and thus contribute to steering the design of biomarkers for distinguishing different types of disease-associated proteins. Lu- minescent conjugated oligothiophenes (LCO) is a class of molecules that binds to aggregates of misfolded amyloid-β proteins, facilitating in vivo-detection of the pathological hallmarks of AD. By performing molecular dynamics (MD) simulations and subsequent response theory calculations of a LCO, it could be concluded that the differences in the spectroscopic fingerprints for the bound and free biomarker were predominantly due to conformational changes of the conjugated π-system in the molecular backbone. The introduction of differ- ent central units with donor properties yield donor-acceptor-donor electronic systems that increase the range of spectroscopic detection of LCO biomark- ers, without reducing the selectivity towards amyloid-β. It was also revealed that in order to capture more of the two-photon absorption (TPA) signal it would be optimal to design biomarkers with the dominant TPA signal at longer wavelenghts.The second part of this work is centered around computational enzyme design, and how single point mutations can alter the flow of water in the active site. The altered flow of water likely impacts the catalysis in the active site of the enzymes. The enzymes considered in this work belongs to two different enzyme classes, and catalyse different kinds of reactions. Squalene hopene cyclase (SHC) is a monotopic membrane enzyme that catalyses the cyclization of squalene to hopene, and ω-transaminase catalyses the transfer of an amino and keto group between an amino acid and a keto acid. Enzyme variants of both SHC and ω-transaminase, where single-point mutations have been introduced, display different experimentally observed properties compared to their corresponding wild-types (WT). By performing MD simulations, the flow of water in the active sites of both enzymes could be tracked. Distinct differences in the flow of water in the WT and enzyme variants could be detected. These changes are proposed to influence the catalysis, and help to explain the experimentally observed differences in the protein variants.
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| 7. |
- Jakobsson, Mattias, 1981-
(författare)
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Monte Carlo Studies of Charge Transport Below the Mobility Edge
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Charge transport below the mobility edge, where the charge carriers are hopping between localized electronic states, is the dominant charge transport mechanism in a wide range of disordered materials. This type of incoherent charge transport is fundamentally different from the coherent charge transport in ordered crystalline materials. With the advent of organic electronics, where small organic molecules or polymers replace traditional inorganic semiconductors, the interest for this type of hopping charge transport has increased greatly. The work documented in this thesis has been dedicated to the understanding of this charge transport below the mobility edge.While analytical solutions exist for the transport coefficients in several simplified models of hopping charge transport, no analytical solutions yet exist that can describe these coefficients in most real systems. Due to this, Monte Carlo simulations, sometimes described as ideal experiments performed by computers, have been extensively used in this work.A particularly interesting organic system is deoxyribonucleic acid (DNA). Besides its overwhelming biological importance, DNA’s recognition and self-assembly properties have made it an interesting candidate as a molecular wire in the field of molecular electronics. In this work, it is shown that incoherent hopping and the Nobel prize-awarded Marcus theory can be used to describe the results of experimental studies on DNA. Furthermore, using this experimentally verified model, predictions of the bottlenecks in DNA conduction are made.The second part of this work concerns charge transport in conjugated polymers, the flagship of organic materials with respect to processability. It is shown that polaronic effects, accounted for by Marcus theory but not by the more commonly used Miller-Abrahams theory, can be very important for the charge transport process. A significant step is also taken in the modeling of the off-diagonal disorder in organic systems. By taking the geometry of the system from large-scale molecular dynamics simulations and calculating the electronic transfer integrals using Mulliken theory, the off-diagonal disorder is for the first time modeled directly from theory without the need for an assumed parametric random distribution.
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| 8. |
- Sjöqvist, Jonas, 1985-
(författare)
-
Luminescence properties of flexible conjugated dyes
- 2012
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this licentiate thesis the luminescence properties of two flexible conjugated dyes have been studied. The first, Pt1, is a platinum(II) acetylide chromophore used in optical power limiting materials. The second is a set of optical probes known as luminescent conjugated oligothiophenes (LCOs), which are used to detect and characterize the protein structures associated with amyloid diseases such as Alzheimer’s disease.MM3 and CHARMM force field parameters have been derived for the Pt1 chromophore and LCOs, respectively, based on potential energy surface references calculated at the density functional theory (DFT)/B3LYP level of theory. The parameters have been used to perform room temperature molecular dynamics simulations of the chromophores in solvent, where tetrahydrofuran was used for Pt1 and water for the LCOs. Conformationally averaged absorption spectra were obtained, based on response theory calculations at the time-dependent DFT(TDDFT)/CAM-B3LYP level of theory for a selection of structures from the simulations. For one of the LCOs, p-HTAA, force field parameters were also created describing the dominant first excited state, based on TDDFT/B3LYP reference potential energy surfaces. These were used for molecular dynamics simulations of the chromophore in the excited state, allowing the creation of an emission spectrum. A theoretically obtained Stokes shift of 112 nm could be computed based on the absorption and emission spectra, which is in good agreement with the experimental value of 124 nm.In addition, a quantum mechanics/molecular mechanics study of the effects of solvation on the absorption properties of the p-HTAA chromophore in water has been conducted, resulting in two models for including these effects in the averaged spectra. The first includes explicit water molecules in the form of point charges and polarizable dipole moments, and results in an absorption wavelength that is blueshifted by 2 nm from a high quality reference calculation. The second model involves the complete removal of the solvent as well as the ionic groups of the chromophore. The resulting absorption wavelength is blueshifted by an additional 4 nm as compared to the first model, but requires only one fifth of the computational resources.
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| 9. |
- Todarwal, Yogesh
(författare)
-
Accurate Force Fields for Spectroscopic Studies of Protein–Ligand Interactions and Self-Assembly Structures
- 2024
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The computational prediction of complex molecular behaviors is an essen- tial component of modern chemistry, as it provides a faster and more cost- effective way to explore molecular interactions that may be difficult or even impossible to study experimentally. Molecular dynamics (MD) simulations of- ten serve as a valuable tool for such predictions; however, their accuracy is inherently dependent on the force field (FF) parameters employed. While the general amber force field (GAFF) is designed to provide reasonable results for a broad array of small molecules, it often requires further refinement when using it for a specific small organic molecule. Especially for ligands of the oligothiophene class, the dihedral potential representing the rotatable bond between the two thiophene rings (of the SCCS type) is inadequately described. An objective of this dissertation is to refine FF parameters for producing meaningful MD trajectories that capture key molecular interactions, binding modes, and thermodynamic properties, and subsequent accurate calculations of spectroscopic properties. The refined FF parameters were first tested by comparing the dihedral potential derived from the FF method to the density functional theory (DFT) based dihedral potential. They were then validated by assessing the relative energies of conformers optimized using both FF and DFT methods, and by comparing the transition wavelengths calculated based on geometries optimized with both FF and DFT approaches. Importantly, the errors in dihedral potential were kept below 1 kcal/mol, and the discrepancies in transition energies were less than 0.1 eV for molecular transitions around 5 eV. This FF parametrization methodology was used in research studies focus- ing on two classes of supramolecular systems: host-guest chemistry related to neurodegenerative diseases, and self-assembly systems for material development. Specifically, we examine host-guest interactions involving proteins such as amyloid-beta, tau, and transthyretin (TTR), which are associated with neu- rodegenerative diseases. Various fluorescent ligands are used for the detection of these proteins in pathological samples. Our results for these protein–ligand systems propose strong binding sites and modes, and include estimations of binding energies for different ligands interacting with the targeted proteins. Additionally, comparative studies among the ligands have been conducted. Interestingly, no fluorescence was observed when low binding energy ligands interacted with amyloid fibrils. In the case of bTVBT4 binding to tau associated with Alzheimer’s disease (AD), a unique binding site was identified. This site was not accessible in the tau fold found in Pick’s disease (PiD), thus explaining the specificity of bTVBT4 for AD-related tau. For self-assembly systems, our findings encompass spectral profiles altered by tyrosine substitutions in oligothiophenes, a stable self-assembly model formed by chiral sulfonimidamides that explains the involved interactions, and comparisons of experimental circular dichroism (CD) profiles to assign isomers of [4]cyclonaphthodithiophene diimides to specific spectral profiles. We also investigated the solvent effects on the spectroscopic properties of symmetric and asymmetric azaoxahelicenes. In conclusion, the methodological development of FF parameters provides a robust framework for accurately modeling the behavior of complex supramolecular systems. The improvements in the dihedral potential align closely with DFT-based calculations, thereby elevating the predictive power of MD simulations for both binding modes and subsequent spectroscopic properties. The research has direct applications in the detection of neurodegenerative diseases at an early stage by designing fluorescent ligands that specifically bind to targeted proteins. It also contributes to the creation of advanced materials with finely-tuned properties. Furthermore, the methodology employed can serve as a blueprint for future studies aiming to refine computational models for other classes of molecules.
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| 10. |
- De Oliveira, Danilo Hirabae, et al.
(författare)
-
Silk Assembly against Hydrophobic Surfaces?Modeling and Imaging of Formation of Nanofibrils
- 2023
-
Ingår i: ACS Applied Bio Materials. - : AMER CHEMICAL SOC. - 2576-6422. ; 6:3, s. 1011-1018
-
Tidskriftsartikel (refereegranskat)abstract
- A detailed insight about the molecular organization behind spider silk assembly is valuable for the decoding of the unique properties of silk. The recombinant partial spider silk protein 4RepCT contains four poly-alanine/glycine-rich repeats followed by an amphiphilic C-terminal domain and has shown the capacity to self-assemble into fibrils on hydrophobic surfaces. We herein use molecular dynamic simulations to address the structure of 4RepCT and its different parts on hydrophobic versus hydrophilic surfaces. When 4RepCT is placed in a wing arrangement model and periodically repeated on a hydrophobic surface, fi-sheet structures of the poly-alanine repeats are preserved, while the CT part is settled on top, presenting a fibril with a height of similar to 7 nm and a width of similar to 11 nm. Both atomic force microscopy and cryo-electron microscopy imaging support this model as a possible fibril formation on hydrophobic surfaces. These results contribute to the understanding of silk assembly and alignment mechanism onto hydrophobic surfaces.
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| 11. |
- Fahleson, Tobias
(författare)
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Development and characterization of damped cubic response functions with application to two-photon absorption
- 2015
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Molecular response to electromagnetic fields - static or optical - within a framework of perturbation theory diverges close to resonance with molecular transitionen energies, and need work-around solutions for real-valued response functions. This licentiate thesis deals with nonlinear response, with focus being on cubic polarizaibilities, and outlines the underlying mathematics for exact-state and approximatestate, complex-valued response functions applicable to quantum chemical computation. Such a complex-valued response theory is commonly known as dampedresponse theory, for which the response functions consists of a real and an imaginary component, each of them representing various spectroscopies in nature. In addition to the mathematics, the formulas have been implemented in the quantum chemical package DALTON, and several tests determining the integrity of the implementation has been conducted.The fourth and final major part of the thesis is concerned with applied nonlinear response theory, including not only cubic response functions, but also quadratic and linear response functions, some of which are of the more exotic character. Three spectroscopies have been investigated for small and medium-sized organic molecules and the neon atom: two-photon absorption (TPA), Jones birefringence (JB), and magnetic circular dichroism (MCD).The TPA part is a simple demonstration of capability of the damped cubic response code, for which neon is the example system. Perfect agreement is shown for the Ehrenfest approach and an independent implementation based on the quasienergy formalism.JB is an optical eect in which induced refractive anisotropy, by means of external electric and magnetic static elds, results in ellipticity of linearly polarized light beams. This part mainly discuss implications from a paper which the current author took part in. The paper ultimately attempts to indentify the general observable strength of the effect, and coincidentaly pin-point some particular system suitable for experiments. Among other finds, JB is found to be correlated to the electric dipole moment, and for monosubstituted benzenes, the para-Hammett constant.Finally, MCD is discussed based on three papers in which the present author is included. The elegant MCD solution to broad absorption peaks, for which it is desired to distinguish individual states, is demonstrated on adenine and three additional purine derivatives. A drawn out debate regarding relative stability of certain low-lying states could be settled by this method. Furthermore, appropriate description of solvation environment in conjunction with the exchange-correlation functionals B3LYP and CAM-B3LYP is investigated on purine and pyrimidine derivatives. CAM-B3LYP is found to be superior in terms of general prole shapes, while results regarding solvation model are rather inconclusive, although the results suggests some level of solvation model is appropriate, such as a polarizable continuum model or explicit solvation molecules.
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| 12. |
- Henriksson, Johan, 1979-
(författare)
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Molecular Quadratic Response Properties with Inclusion of Relativity
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis concerns quadratic response properties and their application to properties in Jablonski diagrams such as resonant two-photon absorption and excited state absorption. Our main interest lies in optical power limiting applications, and in this context, molecules containing heavy metal atoms prove superior. Therefore, we are interested in how relativity affects these properties, and in order to assess this, a four-component relativistic framework is adopted.To properly address the molecular properties of interest, both relativistic effects and electron correlation need to be accounted for. These two properties are not additive, and, therefore, correlation needs to be incorporated into the four-component framework. We present the implementation of quadratic response properties at the four-component density functional level of theory. For second-harmonic generation, we have, with numerical examples, demonstrated that correlation and relativity are indeed not additive and that the inclusion of noncollinear magnetization is of little importance. We report that both electron correlation as well as relativity strongly affect results for second-harmonic generation. For example, relativity alone reduces the µβ-response signal by 62% and 75% for meta- and ortho-bromobenzene, respectively, and enhances the same response by 17% and 21% for meta- and ortho-iodobenzene, respectively.In the four-component framework, we present the implementations of single and double residues of the quadratic response function, which allows for the evaluation of resonant two-photon absorption cross sections and excited state properties. Using these tools, we discuss different levels of approximation to the relativistic Hamiltonian and we demonstrate that for two-photon absorption, a proper treatment of relativistic effects qualitatively alters the spectrum. For example, already for an element as light as neon, significant differences are seen between the relativistic and nonrelativistic spectra as triplet transitions acquire substantial absorption cross sections in the former case.Finally, quantum mechanics in conjunction with electrodynamics is applied to determine clamping levels in macroscopic samples. The microscopic properties of the optically active chromophores are determined by response theory, and then, electrodynamics is used to describe the interactions between the chromophores and incident laser pulses. Using this approach a series of molecules have been investigated and their performances have been compared and ranked in order to find novel materials for optical power limiting applications.
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| 13. |
- Jiemchooroj, Auayporn, 1978-
(författare)
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Long-range intermolecular dispersion forces and circular dichroism spectra from first-principles calculations
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This work presents first-principles calculations of long-range intermolecular dispersion energies between two atoms or molecules and of electronic circular dichroism spectra of chiral molecules. The former is expressed in terms of the C6 dipole-dipole dispersion coefficients Δε, and the latter is given in terms of the extinction coefficient. In a series of publications, the complex linear polarization propagator method has been shown to be a powerful tool to provide accurate ab initio and first-principles density functional theory results. This was the case not only for the C6 dispersion coefficients but also for the electronic circular dichroism at an arbitrary wavelength ranging from the optical to the X-ray regions of the spectrum. The selected samples for the investigation of dispersion interactions in the electronic ground state are the noble gases, n-alkanes, polyacenes, azabenzenes, alkali-metal clusters, and C60. It is found that the values of C6 for the sodium-cluster-to-fullerene interactions are well within the error bars of the experiment. The proposed method can also be used to determine dispersion energies for species in their respective excited electronic states. The C6 dispersion coefficients for the first π → π* excited state of the azabenzene molecules have been obtained with the adopted method in the multiconfiguration self-consistent field approximation. The dispersion energy of the π → π* excited state is smaller than that of the ground state. It is found that the characteristic frequencies ω1 defined in the London approximation of n-alkanes vary in a narrow range which makes it possible to construct a simple structure-to-property relationship based on the number of π-bonds for the dispersion interaction in these saturated compounds. However, this simple approach is not applicable to the interactions of the π-conjugated systems since, depending on the systems, their characteristic frequencies ω1 can vary greatly. In addition, an accomplishment of calculations of the electronic circular dichroism spectra in the near-edge X-ray absorption has been demonstrated.
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| 14. |
- Norman, Patrick, 1968-
(författare)
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Nonlinear Optical Properties of Fullerenes, Oligomers, and Solutions
- 1998
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This work presents development and applications of modern tools in ab initio quantum chemistry for obtaining linear and nonlinear response properties of molecules in the gas phase and in solution. The external perturbing fields are primarily electric in nature with frequencies in the optical region.The framework for this achievement is denoted response theory, a formulation of time-dependent perturbation theory, which has been extended to include fourth-order properties fully analytically for self-consistent field (SCF) and multi-configurational SCF (MCSCF) reference states. This extension refers both to the vacuum theory as well as to a self-consistent reaction field model for properties in solution.Applications are presented, displaying both the possibilities and limitations of the theory. Highly electron correlated MCSCF reference states are used for small molecules both in the gas phase and in solution to obtain accurate values of ground and excited state polarizabilities $\alpha$, and ground state hyperpolarizabilities $\beta$ and $\gamma$. Excited state properties are addressed without explicit optimization of the state in question but instead by computing a double residue of the cubic response function. We have in some cases considered both the electronic and the vibrational contributions to these properties. Another direction that has been pursued is to, at the random phase approximation (RPA) level, extend the range of applications for large-scale systems by means of direct atomic orbital driven routines in a parallel scheme. In this context, we address structure-to-property relations for two-dimensional hydrocarbon oligomers, and electron-delocalization of fullerenes. With small we mean molecules with up to 15 atoms and with large-scale we mean molecules with up to 150 atoms.
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| 15. |
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| 16. |
- Proietti, Giampiero, et al.
(författare)
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Ultralight aerogels via supramolecular polymerization of a new chiral perfluoropyridine-based sulfonimidamide organogelator
- 2024
-
Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 16:15, s. 7603-7611
-
Tidskriftsartikel (refereegranskat)abstract
- Chiral and enantiopure perfluorinated sulfonimidamides act as low-molecular weight gelators at low critical gelation concentration (<1 mg mL-1) via supramolecular polymerization in nonpolar organic solvents and more heterogenic mixtures, such as biodiesel and oil. Freeze-drying of the organogel leads to ultralight aerogel with extremely low density (1 mg mL-1). The gelation is driven by hydrogen bonding resulting in a helical molecular ordering and unique fibre assemblies as confirmed by scanning electron microscopy, CD spectroscopy, and computational modeling of the supramolecular structure.
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| 17. |
- Sjöqvist, Jonas, 1985-
(författare)
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Light interactions in flexible conjugated dyes
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis methodological developments have been made for the description of flexible conjugated dyes in room temperature spectrum calculations.The methods in question target increased accuracy and efficiency by combining classical molecular dynamics (MD) simulations with time-dependent response theory spectrum calculations. For absorption and fluorescence spectroscopies a form of conformational averaging is used, where the final spectrum is obtained as an average of spectra calculated for geometries extracted from ground and excited state MD simulations. For infrared and Raman spectroscopies averaged spectra are calculated based on individual spectra, obtained for zero-temperature optimized molecular structures, weighted by conformational statistics from MD trajectories. Statistics for structural properties are also used in both cases to gain additional information about the systems, allowing more efficient utilization of computational resources. As it is essential that the molecular mechanics description of the system is highly accurate for methods of this nature to be effective, high quality force field parameters have been derived, describing the molecules of interest in either the MM3 or CHARMM force fields.These methods have been employed in the study of three systems. The first is a platinum(II) actylide chromophore used in optical power limiting materials, for which a ultraviolet/visible absorption spectrum has been calculated. The second is a family of molecular probes called luminescent conjugated oligothiophenes, used to detect and characterize amyloid proteins, for which both absorption and fluorescence spectra have been calculated. Finally, infrared and Raman spectra have been calculated for a group of branched oligothiophenes used in organic solar cells.In addition, solvation effects have been studied for conjugated poly\-eletrolytes in water, resulting in the development of two solvation models suitable for this class of molecules. The first uses a quantum meachanics/molecular mechanics (QM/MM) description, in which the solute mole\-cule is described using accurate quantum mechanical methods while the surrounding water molecules are described using point charges and polarizable point dipoles. The second discards the water entirely and removes the ionic groups of the solute. The QM/MM model provides highly accurate results while the cut-down model gives results of slightly lower quality but at a much reduced computational cost.Finally, a study of protein-dye interactions has been performed, with the goal of explaining changes in the luminescence properties of the LCO chromophores when in the presence of amyloid proteins. Results were less than conclusive.
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| 18. |
- Vinbladh, Jimmy
(författare)
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Two photon above threshold ionization in a relativistic framework : Attosecond delays in high Z elements
- 2018
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Recent advances in experimental physics opens up for improved time resolution on measurements of ionizing processes in atoms caused by an EM-field. There exist non-relativistic models that describe photo-ionization events involving two photons, for various atoms, where relativistic effects, e.g. spin-orbit interactions, are small. The ambition of this thesis project was to develop a computational software that includes relativistic effects by starting from the Dirac equation. Investigation of the photo-ionization events are done by calculating the two-photon matrix elements, taking into account essential many body effects using Random Phase Approximation with Exchange (RPAE) for the atomic response to the interaction with the first photon. During the development of the software it was discovered that the choice of dipole operator, length or velocity, had a large influence on the results when including the second photon, and it is concluded that the more straightforward calculations are done with the dipole operator in length gauge. The examined results demonstrate a program that works as desired; it agrees well with the non-relativistic calculations for the lighter elements and provides data for more detailed analysis of heavier elements.
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