17 results on '"Dana Nachtigallová"'
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2. Structure-directed formation of the dative/covalent bonds in complexes with C70⋯piperidine
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Radek Zbořil, Maximilián Lamanec, Rabindranath Lo, Debashree Manna, Dana Nachtigallová, Weizhou Wang, Aristides Bakandritsos, Martin Dračínský, and Pavel Hobza
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Fullerene ,Spintronics ,010405 organic chemistry ,Chemistry ,Dative case ,Rational design ,General Physics and Astronomy ,010402 general chemistry ,Electrocatalyst ,01 natural sciences ,0104 chemical sciences ,Crystallography ,Molecular dynamics ,chemistry.chemical_compound ,Covalent bond ,Piperidine ,Physical and Theoretical Chemistry - Abstract
The combined experimental-computational study has been performed to investigate the complexes formed between C70 carbon allotrope and piperidine. The results of FT-IR, H-NMR, and C-NMR measurements, together with the calculations based on the DFT approach and molecular dynamics simulations, prove the existence of dative/covalent bonding in C70piperidine complexes. The dative bond forms not only at the region of five- and six-membered rings, observed previously with C60, but also at the region formed of six-membered rings. The structure, i.e., nonplanarity, explains the observed dative bond formation. New findings on the character of interaction of secondary amines with C70 bring new aspects for the rational design of modified fullerenes and their applications in electrocatalysis, spintronics, and energy storage.
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- 2021
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3. Ground state of the Fe(<scp>ii</scp>)-porphyrin model system corresponds to quintet: a DFT and DMRG-based tailored CC study
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Libor Veis, Rabindranath Lo, Dana Nachtigallová, Pavel Hobza, Mikuláš Matoušek, Jiří Pittner, Andrej Antalík, Örs Legeza, and Jakub Lang
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Chemical Physics (physics.chem-ph) ,Physics ,Spin states ,Density matrix renormalization group ,FOS: Physical sciences ,General Physics and Astronomy ,Model system ,Porphyrin ,Molecular physics ,chemistry.chemical_compound ,chemistry ,Physics - Chemical Physics ,Molecule ,Physical and Theoretical Chemistry ,Ground state - Abstract
Fe(II)-porphyrins (FeP) play an important role in many reactions relevant to material science and biological processes, due to their closely lying spin states. However, this small energetic separation also makes it challenging to establish the correct spin state ordering. Although the prevalent opinion is that these systems posses the triplet ground state, the recent experiment on Fe(II)-phthalocyanine under conditions matching those of an isolated molecule points toward the quintet ground state. We present a thorough study of FeP model by means of the density functional theory and density matrix renormalization group based tailored coupled clusters, in which we address all previously discussed correlation effects. We examine the importance of geometrical parameters, the Fe-N distances in particular, and conclude that the system possesses the quintet ground state, which is in our calculations well-separated from the triplet state.
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- 2020
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4. Tuning the UV spectrum of PAHs by means of different N-doping types taking pyrene as paradigmatic example: categorization via valence bond theory and high-level computational approaches
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Hans Lischka, Adelia J. A. Aquino, Michal Otyepka, Dana Nachtigallová, and Xin Shao
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Materials science ,Absorption spectroscopy ,Diradical ,General Physics and Astronomy ,Aromaticity ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Molecular physics ,Spectral line ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Atomic electron transition ,Excited state ,Pyrene ,Valence bond theory ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
Tuning of the electronic spectra of carbon dots by means of inserting heteroatoms into the π-conjugated polycyclic aromatic hydrocarbon (PAH) system is a popular tool to achieve a broad range of absorption and emission frequencies. Especially nitrogen atoms have been used successfully for that purpose. Despite the significant progress achieved with these procedures, the prediction of specific shifts in the UV-vis spectra and the understanding of the electronic transitions is still a challenging task. In this work, high-level quantum chemical methods based on multireference (MR) and single-reference (SR) methods have been used to predict the effect of different nitrogen doping patterns inserted into the prototypical PAH pyrene on its absorption spectrum. Furthermore, a simple classification scheme based on valence bond (VB) theory and the Clar sextet rule in combination with the harmonic oscillator measure of aromaticity (HOMA) index was applied to arrange the different doping structures into groups and rationalize their electronic properties. The results show a wide variety of mostly redshifts in the spectra as compared to the pristine pyrene case. The most interesting doping structures with the largest red shifts leading to absorption energies below one eV could be readily explained by the occurrence of diradical VB structures in combination with Clar sextets. Moreover, analysis of the electronic transitions computed with MR methods showed that several of the low-lying excited states possess double-excitation character, which cannot be realized by the popular SR methods and, thus, are simply absent in the calculated spectra.
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- 2020
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5. Excited states and excitonic interactions in prototypic polycyclic aromatic hydrocarbon dimers as models for graphitic interactions in carbon dots
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Hans Lischka, Adelia J. A. Aquino, Francisco B. C. Machado, Dana Nachtigallová, and Baimei Shi
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Materials science ,Graphene ,Dimer ,General Physics and Astronomy ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Molecular physics ,Coronene ,0104 chemical sciences ,law.invention ,chemistry.chemical_compound ,chemistry ,Quantum dot ,law ,Excited state ,Pyrene ,Emission spectrum ,Physical and Theoretical Chemistry ,0210 nano-technology ,Carbon - Abstract
The study of electronically excited states of stacked polycyclic aromatic hydrocarbons (PAHs) is of great interest due to promising applications of these compounds as luminescent carbon nanomaterials such as graphene quantum dots (GQDs) and carbon dots (CDs). In this study, the excited states and excitonic interactions are described in detail based on four CD model dimer systems of pyrene, coronene, circum-1-pyrene and circum-1-coronene. Two multi-reference methods, DFT/MRCI and SC-NEVPT2, and two single-reference methods, ADC(2) and CAM-B3LYP, have been used for excited state calculations. The DFT/MRCI method has been used as a benchmark method to evaluate the performance of the other ones. All methods produce useful lists of excited states. However, an overestimation of excitation energies and an inverted ordering of states, especially concerning the bright HOMO-LUMO excitation, are observed. In the pyrene-based systems, the first bright state appears among the first four states, whereas the number of dark states is significantly larger for the coronene-based systems. Fluorescence emission properties are addressed by means of geometry optimization in the S1 state. The inter sheet distances for the S1 state decrease in comparison to the corresponding ground-state values. These reductions are largest for the pyrene dimer and decrease significantly for the larger dimers. Several minima have been determined on the S1 energy surface for most of the dimers. The largest variability in emission energies is found for the pyrene dimer, whereas in the other cases a more regular behavior of the emission spectra is observed.
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- 2019
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6. The role of the σ-holes in stability of non-bonded chalcogenide⋯benzene interactions: the ground and excited states
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Dana Nachtigallová, Saltuk M. Eyrilmez, Pavel Hobza, and Robert Sedlak
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010405 organic chemistry ,Chalcogenide ,General Physics and Astronomy ,010402 general chemistry ,01 natural sciences ,Stability (probability) ,Molecular physics ,0104 chemical sciences ,chemistry.chemical_compound ,Monomer ,chemistry ,Excited state ,Physical and Theoretical Chemistry ,Atomic physics ,Ground state ,Benzene ,Conformational isomerism ,Excitation - Abstract
The stability of the T-shaped and stacked complexes of benzene with methanethial (CH2S) and methaneselone (CH2Se) and their difluoro-, dichloro-, dibromo-derivatives is investigated in their ground and first electronic excited states by means of the SCS-ADC2 method. The origin of the stabilization in the ground state is discussed based on the results of calculations performed using the DFT-SAPT method. Calculations show that the stability of the T-shaped conformers increases upon electronic excitation, while it decreases for most of the stacked conformers. Both effects are explained by the changes in the electrostatic potential (ESP) of isolated monomers upon the electronic excitation.
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- 2018
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7. Photodynamic behavior of electronic coupling in a N-methylformamide dimer
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Martina Zámečníková and Dana Nachtigallová
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Field (physics) ,Chemistry ,Dimer ,General Physics and Astronomy ,Surface hopping ,Molecular physics ,chemistry.chemical_compound ,Delocalized electron ,Excited state ,Molecule ,Complete active space ,Physical and Theoretical Chemistry ,Perturbation theory ,Atomic physics - Abstract
The excited state dynamics of a N-methylformamide dimer in complex with water molecules has been studied using the complete active space self-consistent field (CASSCF) and CAS perturbation theory to the second order (CASPT2) methods. The extent of delocalization of the first two excited states resulting from (n → π*) transitions on both monomers was monitored during the time course of on-the-fly surface hopping nonadiabatic dynamics. The results suggest that the excited states prefer delocalization between the two monomers in the complex. The bridging water molecules increase the magnitude of electronic coupling via through-bond interactions.
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- 2015
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8. Structure and energetics of the anisole–Arn (n = 1, 2, 3) complexes: high-resolution resonant two-photon and threshold ionization experiments, and quantum chemical calculations
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Dana Nachtigallová, Maurizio Becucci, Jan Řezáč, Pavel Hobza, Federico Mazzoni, Klaus Müller-Dethlefs, and François Michels
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Chemistry ,Binding energy ,Photodissociation ,General Physics and Astronomy ,Ion ,symbols.namesake ,Excited state ,Ionization ,Field desorption ,Rydberg formula ,symbols ,Physical and Theoretical Chemistry ,Atomic physics ,Ground state - Abstract
We present a concerted experimental and theoretical study of the anisole···Arn 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 anisole···Arn 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'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 "gold standard" 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.
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- 2015
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9. Theoretical study of photoacidity of HCN: the effect of complexation with water
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Vladimír Špirko, Dana Nachtigallová, Eva Muchová, and Pavel Hobza
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Photochemistry ,Hydrogen bond ,Chemistry ,Water ,General Physics and Astronomy ,Hydrogen transfer ,Hydrogen Bonding ,Model system ,Dissociation (chemistry) ,Vibronic coupling ,Models, Chemical ,Chemical physics ,Hydrogen Cyanide ,Excited state ,Quantum Theory ,Physical chemistry ,Molecule ,Computer Simulation ,Protons ,Physical and Theoretical Chemistry ,Ground state - Abstract
The character of the hydrogen bonding and the excited state proton transfer (ESPT) in the model system HCN⋯H2O is investigated. The PES of the two lowest excited states of the H2O⋯HCN complex was calculated using the CASPT2 method. The nonadiabatic coupling of the two states of the (π → π*) and (π → σ*) character is responsible for the excited state proton/hydrogen transfer. Compared to the ground state, the barrier for this process is significantly smaller. An increased number of water molecules in the complex with cyclic hydrogen-bonded network causes a large blue shift of the state of the (π → σ*) character. The question of the dissociation of the complex in its excited state is also addressed.
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- 2006
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10. Localization of Cu+sites and framework Al positions in high-silica zeolites: Combined experimental and theoretical study
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Roman Bulánek, Petr Nachtigall, Dana Nachtigallová, Petr Knotek, and Pavel Čičmanec
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Chemistry ,Stereochemistry ,General Physics and Astronomy ,Physical chemistry ,Physical and Theoretical Chemistry ,High silica ,Spectral line - Abstract
Three types of Cu+ sites are distinguished from the analysis of TPD spectra of CO in high-silica zeolites and the details about the structure and coordination of Cu+ at these sites are obtained from calculations.
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- 2004
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11. Calculations of the site specific stretching frequencies of CO adsorbed on Li+/ZSM-5
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Ota Bludský, Petr Nachtigall, and Dana Nachtigallová
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Bond length ,Adsorption ,Interaction potential ,Chemistry ,Stereochemistry ,General Physics and Astronomy ,Physical chemistry ,Molecule ,Infrared spectroscopy ,Physical and Theoretical Chemistry ,ZSM-5 ,Scaling ,CO binding - Abstract
Interaction of the CO molecule with Li+ within ZSM-5 was investigated by means of the combined quantum mechanics/interaction potential function method. Both, C-on and O-on species were considered. The scaling method based on the linear correlation between CO bond length and stretching frequency has been applied to calculate CO frequencies in CO(OC)–Li+/ZSM-5 adsorption complexes. Three types of C-on adsorption complexes with different r(CO) bond lengths, ν(CO) frequencies, and CO binding energies were identified. The calculated IR spectra of CO adsorbed on the Li+/ZSM-5 system show three distinctive bands at about 2194 cm−1, 2187 cm−1 and 2183 cm−1 for C-on complexes and at about 2116 cm−1, 2114 cm−1 and 2104 cm−1 for O-on complexes, in excellent agreement with experimental data. Calculated adsorption energies and CO stretching frequencies were used for the simulation of the IR spectra at various CO coverages.
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- 2004
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12. Characterization of Ag+ Sites in ZSM-5: A combined quantum mechanics/interatomic potential function study
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Martin Šilhan, Petr Nachtigall, and Dana Nachtigallová
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Extended X-ray absorption fine structure ,Chemistry ,Ab initio quantum chemistry methods ,Quantum mechanics ,Coordination number ,Ab initio ,General Physics and Astronomy ,Molecule ,Interatomic potential ,Interaction energy ,Physical and Theoretical Chemistry ,Ion - Abstract
The interaction of Ag+ ions with the ZSM-5 lattice was studied by means of a combined quantum mechanics/interatomic potential function method. A new Ag(I)–O interaction potential was parametrized based on ab initio data and its quality was tested. The Ag+ ions preferentially occupy the sites on the intersection of the main and zig-zag channels of ZSM-5. Ag–O distances in the range 2.32–2.36 A and coordination to two framework oxygen atoms were found, in good agreement with available EXAFS data. The interaction energies of Ag+ with zeolite (127–132 kcal mol−1 for sites on the channel intersection) are about 20 kcal mol−1 smaller than those found for the Cu+/ZSM-5 system. The calculated vertical excitation energies of the T1←S0 transition show a strong correlation with the coordination number of the Ag+ ions. Since two-coordinated sites on the channel intersection are strongly preferred by the Ag+ ions only a single absorption peak is predicted for the Ag/ZSM-5 system, in agreement with experimental observation.
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- 2001
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13. Coordination of Cu+ and Cu2+ ions in ZSM-5 in the vicinity of two framework Al atoms
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Dana Nachtigallová, Petr Nachtigall, and Joachim Sauer
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Quantitative Biology::Neurons and Cognition ,Stereochemistry ,General Physics and Astronomy ,chemistry.chemical_element ,Interatomic potential ,Electronic structure ,Crystal structure ,Copper ,law.invention ,Crystallography ,chemistry ,law ,Excited state ,Molecule ,Physical and Theoretical Chemistry ,Triplet state ,Electron paramagnetic resonance - Abstract
A combined quantum mechanics/interatomic potential function technique has been used to examine Cu+/Al− sites in the vicinity of H+Al− sites and Cu2+ in the vicinity of two framework Al atoms under dehydrated conditions. The symmetrical coordination of Cu2+ ions to four framework oxygen atoms is the most stable site and Cu2+ is hard to reduce at these sites. In agreement with EPR measurements a square-pyramidal coordination of Cu2+ at these sites is suggested. However, this symmetrical coordination is attained only for specific positions of the framework aluminium pair. Coordination changes upon reduction of divalent to monovalent copper ions and upon excitation of Cu+ ions in the first triplet excited state are also investigated. The coordination of the copper ions does not significantly change during reduction in the dehydrated state. Coordination changes of Cu+ upon excitation in the triplet state and calculated transition energies for Cu+/Al− sites in the vicinity of H+Al− sites are identical to those observed for isolated Cu+/Al− sites.
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- 2001
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14. Coordination and siting of Cu+ ions in ZSM-5: A combined quantum mechanics/interatomic potential function study
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Joachim Sauer, Petr Nachtigall, Dana Nachtigallová, and Marek Sierka
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chemistry ,Quantum mechanics ,Binding energy ,Atom ,General Physics and Astronomy ,chemistry.chemical_element ,Interatomic potential ,Physical and Theoretical Chemistry ,ZSM-5 ,Ring (chemistry) ,Zeolite ,Copper ,Ion - Abstract
Siting and coordination of Cu+ ions in zeolite ZSM-5 have been studied by a combined quantum mechanics/interatomic potential function technique. A new Cu(I)–O interaction potential has been parameterized based on abinitio data which is compatible with abinitio-parametrized shell model potentials for zeolites. Several different sites of Cu+ inside ZSM-5 have been found. The structure of the site and the coordination of the Cu+ ion depend on the T-site where the Si atom is replaced by an Al atom. If Al is at the edge of the main and sinusoidal channels the Cu+ ion prefers to occupy thc open space in the channel intersection and it is coordinated to two oxygen atoms of the AlO4 tetrahedron. The largest binding energy of Cu+ with ZSM-5 was found for Cu+ located inside a six-membered ring on the wall of the sinusoidal channel, where it can coordinate to three or four oxygen atoms of the zeolite framework. The Cu+ sites predicted are in accord with available experimental results.
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- 1999
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15. Reply to the ‘Comment on 'The nature of cationic adsorption sites in alkaline zeolites—single, dual and multiple cation sites'' by O. Cairon, Phys. Chem. Chem. Phys., 2012, 14, DOI: 10.1039/c2cp40963a
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Dana Nachtigallová, Montserrat Rodríguez Delgado, Petr Nachtigall, and Carlos Otero Areán
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Adsorption ,Computational chemistry ,Chemistry ,Cationic polymerization ,General Physics and Astronomy ,Physical and Theoretical Chemistry ,DUAL (cognitive architecture) - Abstract
The preceding comments by O. Cairon, Phys. Chem. Chem. Phys., 2012, 14, DOI: 10.1039/c2cp40963, question several aspects of our perspective article on the nature of cationic adsorption sites in alkaline zeolites (P. Nachtigall, M. R. Delgado, D. Nachtigallova and C. O. Arean, Phys. Chem. Chem. Phys., 2012, 14, 1552). Questioning spans from experimental details, through methodology and to the very concept of dual and multiple cation sites in zeolites. While acknowledging that questioning constitutes an excellent method to foster understanding, we hope that the answers given herein will help to clarify the relevant points under discussion.
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- 2012
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16. Electronic splitting in the excited states of DNA base homodimers and -trimers: an evaluation of short-range and Coulombic interactions
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Pavel Hobza, Dana Nachtigallová, and Hans-Hermann Ritze
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Static Electricity ,General Physics and Astronomy ,Electrons ,Trimer ,Cytosine ,chemistry.chemical_compound ,Static electricity ,Physical and Theoretical Chemistry ,Uracil ,Quantitative Biology::Biomolecules ,Range (particle radiation) ,Adenine ,DNA ,Quantitative Biology::Genomics ,Thymine ,Crystallography ,Models, Chemical ,chemistry ,Excited state ,Nucleic Acid Conformation ,Quantum Theory ,Atomic physics ,Dimerization - Abstract
The nature of the electronic interactions of the stacked nucleic-acid bases (adenine, thymine, cytosine, and uracil) in homodimer and -trimer complexes in their electronically excited states was investigated and analysed in terms of orbital-overlap and Coulombic interactions. The mutual orientations of the adjacent bases were selected so as to correspond to the A- and B-DNA conformations. The extent of the electronic interaction is larger for the former conformation. It is shown that the orbital-overlap interactions at the distance of two bases relevant to the DNA structure do not contribute significantly to the overall electronic coupling. Only the states which are caused by the (pi --pi*) transitions manifest an electronic coupling.
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- 2008
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17. Electronic coupling in the excited electronic state of stacked DNA base homodimers
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Pavel Hobza, Dana Nachtigallová, and Hans-Hermann Ritze
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Physics::Biological Physics ,Quantitative Biology::Biomolecules ,Photochemistry ,Ultraviolet Rays ,Adenine ,General Physics and Astronomy ,Electrons ,Pyrimidine dimer ,DNA ,Electron ,Quantitative Biology::Genomics ,Thymine ,Coupling (electronics) ,Cytosine ,chemistry.chemical_compound ,Crystallography ,chemistry ,Pyrimidine Dimers ,Excited state ,Nucleic acid ,Physical and Theoretical Chemistry ,Dimerization - Abstract
The nature of the electronic coupling of stacked nucleic acid bases adenine (A), thymine (T), and cytosine (C), in A-A, T-T, and C-C complexes in their excited states was investigated; a different character of the electronic coupling for the T-T complex was shown.
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- 2007
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