| 1. |
- Linares, Mathieu, et al.
(författare)
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Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra
- 2019
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 21:7, s. 3637-3643
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Tidskriftsartikel (refereegranskat)abstract
- DNA binding modes of the stereoisomeric rotamers of two dithenylethene derivatives (DTE1 and DTE2) representing candidate molecular photoswitches of great promise for photopharmacology and nanotechnology have been identified and characterized in terms of their binding energies and electronic circular dichroism (CD) responses. In the open form, two binding modes are identified namely minor-groove binding of the lowest-energy conformer with an anti-parallel arrangement of methyl groups and major-groove double-intercalation of the P-enantiomers of an intermediate-state rotamer. Only the latter binding mode is found to be enantiomerically selective and expected to have an overall negative linear dichroism (LD) as observed in the experiment for DTE1 (Angew. Chem., Int. Ed., 2013, 52, 4393). In the closed form, the most favorable binding mode is found to be minor groove binding. Also this binding mode is found to be enantiomerically selective and for DTE1, it is the M-enantiomer that binds the strongest, showing a positive theoretical signature CD band in the long wavelength region with origin in pyridinium ligands. The theoretical CD spectrum is found to be in good agreement with the experimental one, which provides an indirect evidence for a correct identification of the binding mode in the closed form.
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| 2. |
- da Cruz, Vinicius Vaz, et al.
(författare)
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Nuclear dynamics in resonant inelastic X-ray scattering and X-ray absorption of methanol
- 2019
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 150:23
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Tidskriftsartikel (refereegranskat)abstract
- We report on a combined theoretical and experimental study of core-excitation spectra of gas and liquid phase methanol as obtained with the use of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS). The electronic transitions are studied with computational methods that include strict and extended second-order algebraic diagrammatic construction [ADC(2) and ADC(2)-x], restricted active space second-order perturbation theory, and time-dependent density functional theory-providing a complete assignment of the near oxygen K-edge XAS. We show that multimode nuclear dynamics is of crucial importance for explaining the available experimental XAS and RIXS spectra. The multimode nuclear motion was considered in a recently developed "mixed representation" where dissociative states and highly excited vibrational modes are accurately treated with a time-dependent wave packet technique, while the remaining active vibrational modes are described using Franck-Condon amplitudes. Particular attention is paid to the polarization dependence of RIXS and the effects of the isotopic substitution on the RIXS profile in the case of dissociative core-excited states. Our approach predicts the splitting of the 2a RIXS peak to be due to an interplay between molecular and pseudo-atomic features arising in the course of transitions between dissociative core- and valence-excited states. The dynamical nature of the splitting of the 2a peak in RIXS of liquid methanol near pre-edge core excitation is shown. The theoretical results are in good agreement with our liquid phase measurements and gas phase experimental data available from the literature. (C) 2019 Author(s).
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| 3. |
- Falklöf, Olle, et al.
(författare)
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Inter-Excited-State Phosphorescence in the Four-Component Relativistic Kohn-Sham Approximation : A Case Study on Lumiflavin
- 2015
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 119:49, s. 11911-11921
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Tidskriftsartikel (refereegranskat)abstract
- Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states can be supplemented by the ability to also describe inter-excited-state phosphorescence. Specifically, by performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL∗) singlet state of lumiflavin to the 3(πHπL∗), 3(nN2πL∗), and 3(πH-1πL∗) triplet states, and subsequently, we compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically 2 to 5 orders of magnitude smaller than the nonradiative ones.
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| 4. |
- Ahmadzadeh, Karan, et al.
(författare)
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Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation
- 2024
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 15:4, s. 969-974
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Tidskriftsartikel (refereegranskat)abstract
- In this Letter, we present a pioneering analysis of the density functional approximations (DFAs) beyond the generalized gradient approximation (GGA) for predicting two-photon absorption (2PA) strengths of a set of push-pull π-conjugated molecules. In more detail, we have employed a variety of meta-generalized gradient approximation (meta-GGA) functionals, including SCAN, MN15, and M06-2X, to assess their accuracy in describing the 2PA properties of a chosen set of 48 organic molecules. Analytic quadratic response theory is employed for these functionals, and their performance is compared against the previously studied DFAs and reference data obtained at the coupled-cluster CC2 level combined with the resolution-of-identity approximation (RI-CC2). A detailed analysis of the meta-GGA functional performance is provided, demonstrating that they improve upon their predecessors in capturing the key electronic features of the π-conjugated two-photon absorbers. In particular, the Minnesota functional MN15 shows very promising results as it delivers pleasingly accurate chemical rankings for two-photon transition strengths and excited-state dipole moments.
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| 5. |
- Olsen, Jogvan Magnus Haugaard, et al.
(författare)
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Dalton Project : A Python platform for molecular- and electronic-structure simulations of complex systems
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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Tidskriftsartikel (refereegranskat)abstract
- The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.
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| 6. |
- Rodrigues, Gabriel Libânio Silva, et al.
(författare)
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Simulations of x-ray absorption spectra for CO desorbing from Ru(0001) with transition-potential and time-dependent density functional theory approaches
- 2022
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Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- The desorption of a carbon monoxide molecule from a Ru(0001) surface was studied by means of X-ray Absorption Spectra (XAS) computed with Transition Potential (TP-DFT) and Time Dependent (TD-DFT) DFT methods. By unraveling the evolution of the CO electronic structure upon desorption, we observed that at 2.3 & ANGS; from the surface, the CO molecule has already predominantly gas-phase character. While C 1s XAS is quite insensitive to changes in the C-O bond length, the O 1s excitation is very sensitive with the pi* coming down in energy upon CO bond stretching, which competes with the increase in orbital energy due to the repulsive interaction with the metallic surface. We show in a systematic way that the TP-DFT method can describe the XAS rather well at the endpoints (chemisorbed and gas phase) but is affected by artificial charge transfer and/or incorrect spin treatment in the transition region in cases like CO, where there are low-lying pi* orbitals and large exchange interactions between the core 1s and valence-acceptor pi* orbitals. As an alternative, we demonstrate by comparing with experimental data that a linear response approach using TD-DFT employing common exchange-correlation functionals and finite-size clusters can yield a good description of the spectral evolution of the 1s & RARR; pi* transition with correct spin and gas-to-chemisorbed chemical shifts in good agreement with experiment.
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| 7. |
- 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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| 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. |
- Sjöqvist, Jonas, 1985-, et al.
(författare)
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A combined MD/QM and experimental exploration of conformational richness in branched oligothiophenes
- 2014
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 16:45, s. 24841-24852
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Tidskriftsartikel (refereegranskat)abstract
- Infrared (IR) absorption and vibrational Raman spectra of a family of branched oligothiophenes have been determined experimentally as well as theoretically. The molecular spectra have been compared to those of the linear analogues, with identification made of spectral features due to structural properties that are valued in organic solar cell applications. The theoretical spectra have been obtained through a newly developed method in which individual conformer spectra, calculated at the time-dependent DFT level in this work, are weighted by statistics extracted from classical molecular dynamics trajectories. The agreement with experiment for the resulting averaged spectra is at least as good as, and often better than, what is observed for Boltzmann-weighted spectra. As the weights are available before the costly step of spectrum calculation, the method has the additional advantage of enabling efficient approximations. For simulating the molecular dynamics of the studied α,β-linked thiophenes and 2-methylthiophenes, high quality parameters have been derived for the CHARMM force field. Furthermore, the temperature dependence of the IR and Raman spectra have been investigated, both experimentally and theoretically.
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| 10. |
- Sjöqvist, Jonas, 1985-, et al.
(författare)
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Toward a molecular understanding of the detection of amyloid proteins with flexible conjugated oligothiophenes
- 2014
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 118:42, s. 9820-9827
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Tidskriftsartikel (refereegranskat)abstract
- Molecular and electronic structures and optical absorption properties of oligothiophenes used for spectral assignment of amyloid deposits have been investigated for a family of probes known as luminescent conjugated oligothiophenes (LCOs). Theoretical absorption spectra have been determined using conformational averaging, combining classical molecular dynamics (MD) simulations with quantum mechanical/molecular mechanics (QM/MM) time-dependent density functional theory (TD-DFT) spectrum calculations. Theoretical absorption spectra are in excellent agreement with experiments, showing average errors below 5 nm for absorption maxima. To couple observed properties to molecular structures, a measure of planarity is defined, revealing a strong correlation between the transition wavelength of the first and dominating electronically excited state and dihedral rotations. It is shown that from this correlation, predictions can be made of the absorption properties of probes based only on information from MD trajectories. We show experimentally that red shifts observed in the excitation maxima of LCOs when bound to amyloid protein aggregates are also evident in absorption spectra. We predict that these red shifts are due to conformational restriction of the LCO in a protein binding pocket, causing a planarization of the conjugated backbone. On the basis of our studies of planarity, it is shown that such shifts are both possible and realistic.
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