Papers by Dana Nachtigallová
Physical Chemistry Chemical Physics, 2022
Functionalization is used to restrict the torsional, excited-state proton transfer and cyclizatio... more Functionalization is used to restrict the torsional, excited-state proton transfer and cyclization modes in UV-excited tetraphenylethylenes.
Journal of Physical Chemistry Letters, Sep 3, 2019
Emission spectra of paradigmatic single-sheet polycyclic aromatic hydrocarbons (PAHs), pyrene, ci... more Emission spectra of paradigmatic single-sheet polycyclic aromatic hydrocarbons (PAHs), pyrene, circum-1-pyrene, coronene, circum-1-coronene and circum-2-coronene and Stokes shifts were computed and compared with previously calculated comparable data for relaxed excimer structures using the SOS-ADC(2), TD-B3LYP and TD-CAM-B3LYP methods with multireference DFT/MRCI data as benchmark. Vertical emission transitions and Stokes shifts were extrapolated to infinite PAH size. Comparison of Stokes shifts computed from theoretical monomer and dimer data confirm assumptions that relaxed excimers are responsible for the unusually large Stokes shifts in carbon dots observed in experimental investigations.
Journal of the American Chemical Society, Aug 14, 2012
Ab initio surface hopping dynamics calculations were performed to study the photophysical behavio... more Ab initio surface hopping dynamics calculations were performed to study the photophysical behavior of cytosine and guanine embedded in DNA using a quantum mechanical/ molecular mechanics (QM/MM) approach. It was found that the decay rates of photo excited cytosine and guanine were affected in a completely different way by the hydrogen bonding to the DNA environment. In case of cytosine, the geometrical restrictions exerted by the hydrogen bonds did not influence the relaxation time of cytosine significantly due to the generally small cytosine ring puckering required to access the crossing region between excited and ground state. On the contrary, the presence of hydrogen bonds significantly altered the photodynamics of guanine. The analysis of the dynamics indicates that the major contribution to the lifetime changes comes from the interstrand hydrogen bonds. These bonds considerably restricted the out-of-plane motions of the NH 2 group of guanine which are necessary for the ultrafast decay to the ground state. As a result, only a negligible amount of trajectories decayed into the ground state for guanine embedded in DNA within the simulation time of 0.5 ps, while for comparison, the isolated guanine relaxed to the ground state with a lifetime of about 0.22 ps. These examples show that, in addition to phenomena related to electronic interactions between nucleobases, there also exist relatively simple mechanisms in DNA by which the lifetime of a nucleobase is significantly enhanced as compared to the gas phase.
WORLD SCIENTIFIC eBooks, Oct 1, 1997
Photochemical and Photobiological Sciences, Aug 1, 2013
The behavior of monomers and dimers of methylated xanthine derivatives in their excited states is... more The behavior of monomers and dimers of methylated xanthine derivatives in their excited states is investigated by means of the ADC(2), CASSCF, and CASPT2 methods. The results of the calculations of stationary points in the ground and excited states, minima on the S 0 /S 1 crossing seams and the relaxation pathways are used to provide the interpretation of experimental observations of the monomer xanthine derivatives. The effect of dimerization on the excited state properties is studied for various relative orientations of the monomers in the dimer complexes in comparison with the relevant monomer species. A significant stabilization in the excited state minima of dimers is observed. These can act as trapping sites. Various types of conical intersections, with both localized and delocalized characters of wavefunctions, have been found, mainly energetically above the lowest bright excited state in the FC region. In addition, structures with the bonds formed between the two monomers were also found on the crossing seams. The possibility of ultrafast relaxation via these conical intersections is discussed. † Electronic supplementary information (ESI) available. See
Journal of Computational Chemistry, 1991
Interaction of a rigid fragment of B-DNA (polyanionic as well as screened by Na+ cations) with th... more Interaction of a rigid fragment of B-DNA (polyanionic as well as screened by Na+ cations) with the flexible tripeptide Lys-Ala-Ala (in both L and D configurations) were investigated with the aid of an empirical potential. The potential consists of intramolecular (MM2 potential) and intermolecular (pair potential described in reference 1) parts; hence total energy is formed by intra-and intermolecular components. The results demonstrate that intramolecular relaxation of the peptide results in a considerable decrease in total energy. While energies of DNA complexes with L-Lys-L-Ala-L-Ala were comparable to those with D-Lys-D-Ala-D-Ala the respective geometries exhibit considerable differences.
Physical Chemistry Chemical Physics, 2015
We present a concerted experimental and theoretical study of the anisoleArn complexes with n = 1-... more We present a concerted experimental and theoretical study of the anisoleArn complexes with n = 1-3. Experimentally, anisole was seeded into a pulsed supersonic argon jet producing a molecular beam. Resonant two-photon, two-colour ionisation (R2PI) spectra of anisoleArn complexes with n = 1-3 were obtained. Also, the photodissociation of the (1 : 1) cluster was probed synchronously by - Zero Electron Kinetic Energy Photoelectron Spectroscopy (ZEKE) - and - Mass Resolved Threshold Ionization (MATI) - measuring electrons and ions obtained from pulsed field ionization of high-n Rydberg states upon two-colour laser excitation. The experimental results are compared to quantum chemical calculations at the DFT-D3 (B-LYP/def2-QZVP level with Grimme&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s D3 dispersion correction) level. Structure and energetics due to microsolvation effects by the direct interaction of the argon atoms with the π-system were evaluated. The experimental binding energy of the 1 : 1 cluster is finally compared to computational results; in the S0 ground state the theoretical value based on the &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;gold standard&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; CCSD(T)/CBS calculations lies within the error bars of the observed value. In the excited state the agreement between theory and experiment is not so spectacular but relative values of observed dissociation energies (D0) in the ground and excited states and of calculated ones agree well.
Studies in Surface Science and Catalysis, 2005
ABSTRACT The question of site-spec if, city of IR spectra of adsorbed CO molecule on metal ion ex... more ABSTRACT The question of site-spec if, city of IR spectra of adsorbed CO molecule on metal ion exchanged zeolites was addressed. The vibrational dynamics of CO adsorbed oil Cu+, Li+, and Na+ sites in FER was investigated by the combination of experimental and theoretical methods allowing the Calculations of CO frequencies with &quot;near spectroscopic accuracy&quot;. The details of experimental spectra in the CO stretching region are assigned based oil the calculations. The effects contributing to the overall CO stretching are discussed. The general rules for site-specificity of vibrational dynamics of adsorbed probe molecules are suggested.
ACS Nano, Jul 20, 2020
Functionalization of surfaces with derivatives of Buckminsterfullerene fragment molecules seems a... more Functionalization of surfaces with derivatives of Buckminsterfullerene fragment molecules seems a promising approach towards bottom up fabrication of carbon nanotube modified electrode surfaces. The modification of a Cu(100) surface with molecules of the buckybowl pentaindenocorannulene has been studied by means of scanning tunneling microscopy, carbon monoxide-modified non-contact atomic force microscopy, time-of-flight secondary mass spectrometry and quantum chemical calculations. Two different adsorbate modes are identified, in which the majority is oriented such that the bowl cavity points away from the surface and the convex side is partially immersed into a fouratom vacancy in the Cu(100) surface. A minority is oriented such that the convex side points away from the surface with the five benzo tabs oriented basically parallel to the surface. Thermal annealing leads to hydrogenation and planarization of the molecules in two steps under specific CC bond cleavage. The benzo tabs of the convex side up species serve as hydrogen source. The final product has an open shell electron structure that is quenched on the surface.
Physical Chemistry Chemical Physics, 2015
Please note that technical editing may introduce minor changes to the text and/or graphics, which... more Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal's standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains.
Physical Chemistry Chemical Physics, 2006
The keto-enol tautomerization of 7-methyl-guanine and 9-methyl-guanine in the excited state was i... more The keto-enol tautomerization of 7-methyl-guanine and 9-methyl-guanine in the excited state was investigated using the time-dependent DFT (TDDFT) method. For both species, the potential energy surfaces of the ground state and two lowest singlet excited states (due to pi--&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;pi* and n--&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;pi* transitions) have been investigated and their features discussed in terms of consequences on the excited state dynamics. The findings suggest that, for both species, the state due to the n--&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;pi* transition, suspected to be an intermediate in the excited state deactivation, exhibits two minima with the second minimum characterized by an elongated N1-H distance. This structure, intermediate between enol and keto tautomers, might play a role in the excited state relaxation. The existence of this second well, however, is observed in both 7- and 9-methyl-guanine, which suggests that it cannot account alone for the different photophysical behavior of these species.
Journal of Physical Chemistry B, Apr 4, 2001
The interaction of the Cu+ ion in the lowest 3d10 singlet and 3d9s1 triplet states with the ferri... more The interaction of the Cu+ ion in the lowest 3d10 singlet and 3d9s1 triplet states with the ferrierite matrix is studied computationally by means of a combined quantum mechanics/interatomic potential function technique. The excitation and emission energies found for the Cu/ferrierite and Cu/ZSM-5 systems are very similar. The 540 and 480 nm peaks in the photoluminescence emission spectra are assigned to the Cu+ ion located on the channel intersection and on the walls of the main or perpendicular channels, respectively. The structure and coordination of individual binding sites of Cu+ in ferrierite are very similar to those found in ZSM-5. Contrary to ZSM-5, the sites on the wall of the main and perpendicular channels of ferrierite are more stable than the sites located on the channel intersection. Therefore, the population of the sites on the channel intersection will be lower in ferrierite than in ZSM-5. It is suggested that the differences in populations of sites on the channel intersection found for ZS...
Chemical Reviews, Jul 24, 2018
Obtaining an understanding of the properties of electronically excited states is a challenging ta... more Obtaining an understanding of the properties of electronically excited states is a challenging task that becomes increasingly important for numerous applications in Chemistry, Molecular Physics, Molecular Biology, and Materials Science. A substantial impact is exerted by the fascinating progress in time-resolved spectroscopy, which leads to a strongly growing demand for theoretical methods to describe the characteristic features of excited states accurately. Whereas for electronic ground state problems of stable molecules the quantum chemical methodology is now so well developed that informed non-experts can use it efficiently, the situation is entirely different concerning the investigation of excited states. This review is devoted to a specific class of approaches, usually denoted as multireference (MR) methods, the generality of which is needed for solving many spectroscopic or photodynamical problems. However, the understanding and proper application of these MR methods is often found to be difficult due to their complexity and their computational cost. The purpose of this review is to provide an overview of the most important facts about the different theoretical approaches available and to present by means of a collection of characteristic examples useful information, which can guide the reader in performing their own applications.
De Gruyter eBooks, Apr 6, 2021
Chemical Physics Letters, Feb 1, 1999
An analytical force field for the study of water photolysis and the cage effect in argon environm... more An analytical force field for the study of water photolysis and the cage effect in argon environment is constructed. A set of more than 200 ab initio CASPT2 points mapping important regions on the first exited potential energy surface of the H OAr cluster is fitted to a physically justified empirical model and the quality of the fit is discussed.
Journal of Physical Chemistry C, Nov 13, 2015
The metal–organic framework CAU-10-NO2 [Al(OH)BDC-NO2] (CAU stands for Christian-Albrechts-Univer... more The metal–organic framework CAU-10-NO2 [Al(OH)BDC-NO2] (CAU stands for Christian-Albrechts-University; H2BDC-NO2 is 5-nitroisophthalic acid) was observed to exhibit unexpected photochemical reactivity. Upon irradiation of the MOF with UV light with a wavelength of 365 nm (or with sunlight), guest molecules inside the pore system of the MOF can be oxidized and stable radicals are formed from the organic linker molecules. The reactivity toward different alcohols was studied by UV/vis spectroscopy and EPR spectroscopy. The amount of generated radicals depends on the size of the solvent molecules; however, as an exception, methanol shows a much lower reactivity than ethanol. DFT calculations were carried out to gain insights into these photochemical reactions. The results indicate that the nitro group is reduced to form a nitroso moiety. This was confirmed by means of NMR spectroscopy. The exact nature of the radical could not be revealed, but the results indicate that it could be a further reduced anionic ni...
Journal of Physical Chemistry C, Jun 3, 2020
The explanation of the origin of the fluorescence properties of carbon dots (CDs) represents an i... more The explanation of the origin of the fluorescence properties of carbon dots (CDs) represents an important task because of the great interest in the promising capabilities of these nanomaterials. 5-oxo-1,2,3,5-tetrahydroimidazo-[1,2-α]-pyridine-7-carboxylic acid (IPCA), a molecular fluorophore, which is being created during the synthesis of CDs from citric acid and ethylenediamin, has been identified as an origin for the fluorescence of CDs. Using a combination of computational methods, we analyzed the UV absorption and fluorescence properties of the IPCA monomer and stacked IPCA dimers as basic models for the fluorescent centers in CDs. Density functional theory (DFT) for the ground state and time-dependent DFT calculations for excited states have been performed for the gas phase and for aqueous solution using a polarized continuum model. Classical molecular dynamics (MD) simulation of the dimer in the ground state have been carried out as well to investigate spontaneous association processes of IPCA and to analyze the ground state dynamics. Due to the complex charge distribution of the monomer and various possibilities of forming hydrogen bonds, in total seven dimer structures have been identified at DFT level as ground-state minima with similar energies. Stabilities have been confirmed by domain-based local pair natural orbital (DLPNO) coupled cluster with singles and doubles and perturbative triples CCSD(T) calculations. The MD simulations confirm this picture showing rotational flexibility processes of the two monomers with respect to each other. The lowest excited states have been characterized in terms of their orbital excitations and excitonic splitting. These calculations demonstrate the dominance of monomer ππ* transitions for the explanation of the observed UV spectra. Optimization of the dimer did not lead to well defined single structures, but show the picture of either intersection pathways to S 1 /S 0 crossings which would quench fluorescence or to stacked dimers with red-shifted fluorescence in comparison to the UV absorption. In gas phase, both types of processes have been observed whereas in solution only the stacked structures were found without any nonadiabatic radiationless deactivation processes. …
Journal of Physical Chemistry B, Feb 15, 2003
Journal of Physical Chemistry A, Oct 20, 2022
Journal of Physical Chemistry A, Jan 26, 2017
We generate a molecular beam of ice nanoparticles (H 2 O) N ,N ≈ 130-220, which pick up several i... more We generate a molecular beam of ice nanoparticles (H 2 O) N ,N ≈ 130-220, which pick up several individual gas phase uracil (U) or 5-bromouracil (BrU) molecules. The mass spectra of the doped nanoparticles prove that the uracil and bromouracil molecules coagulate to clusters on the ice nanoparticles. Calculations of U and BrU monomers and dimers on the ice nanoparticles provide theoretical support for the cluster formation. The (U) m H + and (BrU) m H + intensity dependencies on m extracted from the mass spectra suggest a smaller tendency of BrU to coagulate compared to U, which is substantiated by a lower mobility of bromouracil on the ice surface. The hydrated U m •(H 2 O) n H + series are also reported and discussed. Based on comparison with the previous experiments, we suggest that the observed propensity for aggregation on ice nanoparticles is a more general trend for biomolecules forming strong hydrogen bonds. This, together with their mobility, leads to their coagulation on ice nanoparticles which is an important aspect for astrochemistry.
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Papers by Dana Nachtigallová