30 results on '"Alexander B. Trofimov"'
Search Results
2. XPS and quantum chemical analysis of 4Me-BODIPY derivatives
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Sergey A. Tikhonov, Andrey E. Sidorin, Alexander A. Ksenofontov, Denis Yu. Kosyanov, Ilya S. Samoilov, Anna D. Skitnevskaya, Alexander B. Trofimov, Elena V. Antina, Mikhail B. Berezin, and Vitaliy I. Vovna
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General Physics and Astronomy ,Physical and Theoretical Chemistry - Abstract
This article shows a very satisfactory performance of the DFT Koopmans theorem analogue was demonstrated with respect to the energy intervals between the electronic levels of 4Me-BODIPY derivatives.
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- 2023
3. Two-Sided Impact of Water on the Relaxation of Inner-Valence Vacancies of Biologically Relevant Molecules
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Anna D. Skitnevskaya, Kirill Gokhberg, Alexander B. Trofimov, Emma K. Grigoricheva, Alexander I. Kuleff, and Lorenz S. Cederbaum
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Chemical Physics (physics.chem-ph) ,Physics - Chemical Physics ,FOS: Physical sciences ,General Materials Science ,Physical and Theoretical Chemistry - Abstract
After ionization of an inner-valence electron of molecules, the resulting cation-radicals store substantial internal energy which, if sufficient, can trigger ejection of an additional electron in an Auger decay usually followed by molecule fragmentation. In the environment, intermolecular Coulombic decay (ICD) and electron-transfer mediated decay (ETMD) are also operative, resulting in one or two electrons being ejected from a neighbor, thus preventing the fragmentation of the initially ionized molecule. These relaxation processes are investigated theoretically for prototypical heterocycle-water complexes of imidazole, pyrrole, and pyridine. It is found that the hydrogen-bonding site of the water molecule critically influences the nature and energetics of the electronic states involved, opening or closing certain relaxation processes of the inner-valence ionized system. Our results indicate that the relaxation mechanisms of biologically relevant systems with inner-valence vacancies on their carbon atoms can strongly depend on the presence of the electron-density donating or accepting neighbor, either water or another biomolecule.
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- 2022
4. Positional and Conformational Isomerism in Hydroxybenzoic Acid: A Core-Level Study and Comparison with Phenol and Benzoic Acid
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Elena Yu. Larionova, Robert Richter, Kevin C. Prince, Alexander Hill, Hanan Sa'adeh, David Cameron, Feng Wang, and Alexander B. Trofimov
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Hydroxybenzoic acid ,chemistry.chemical_compound ,Crystallography ,chemistry ,Absorption spectroscopy ,Hydrogen bond ,Structural isomer ,Molecule ,Physical and Theoretical Chemistry ,Absorption (chemistry) ,Conformational isomerism ,Benzoic acid - Abstract
Three positional isomers of hydroxybenzoic acid, as well as phenol and benzoic acid, were studied using core-level photoemission and X-ray absorption spectroscopies, supported by quantum chemical calculations. While 2-hydroxybenzoic (salicylic) acid exists as a single conformer with an internal hydrogen bond, 3- and 4-hydroxybenzoic acids are mixtures of multiple conformers. The effects due to isomerism are clearly seen in the C 1s and O 1s photoelectron spectra, whereas the conformational effects on the binding energies are less pronounced. The O 1s photoelectron spectrum of salicylic acid is significantly different from that of the other two isomers, providing a signature of the hydrogen bond. In contrast, the oxygen K edge X-ray absorption spectra of the three hydroxybenzoic acids show only minor differences. The salicylic acid absorption spectrum at the carbon K edge shows a more resolved vibrational structure than the spectra of the other molecules, which can be explained in part by the existence of a single conformer. Our theoretical study of vibrational excitations in the lowest C 1s absorption bands of salicylic and 4-hydroxybenzoic acids indicates that the observed structure can be assigned to 0-0 lines of various electronic transitions since most of the totally symmetric vibrational modes with sufficiently large frequencies to be resolved are predicted to be inactive. Significant sensitivity of the C 1s excitations in 3-hydroxybenzoic acid to rotational conformerism was predicted but not observed due to spectral crowding.
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- 2021
5. Acetylene-Triggered Reductive Incorporation of Phosphine Chalcogenides into a Quinoline Scaffold: Toward SNHAr Reaction
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Alexandra M. Belogolova, Boris A. Trofimov, Nina K. Gusarova, Anton A. Telezhkin, Kseniya O. Khrapova, Alexander I. Albanov, Nina I. Ivanova, Pavel A. Volkov, and Alexander B. Trofimov
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Scaffold ,chemistry.chemical_compound ,Acetylene ,chemistry ,010405 organic chemistry ,Organic Chemistry ,Polymer chemistry ,Quinoline ,010402 general chemistry ,01 natural sciences ,Phosphine ,0104 chemical sciences - Abstract
Quinolines react with acylacetylenes and secondary phosphine chalcogenides at 20–75 °C to afford N-acylvinyl-2(1)-chalcogenophosphoryldihydroquinolines in good and excellent yields. Unlike the pyri...
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- 2019
6. Hybridogenesis in the water frogs from western russian territory: Intrapopulation variation in genome elimination
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Ikuo Miura, Ivan Sitnikov, V. L. Vershinin, Michihiko Ito, Andrei Lebedinskii, S. D. Vershinina, and Alexander B. Trofimov
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0106 biological sciences ,0301 basic medicine ,Pool frog ,Reproductive Isolation ,lcsh:QH426-470 ,Pelophylax ,Edible frog ,Population ,Serum albumin ,Introgression ,Zoology ,010603 evolutionary biology ,01 natural sciences ,Genome ,Article ,Russia ,03 medical and health sciences ,biology.animal ,Genetics ,Animals ,education ,Genetics (clinical) ,genome introgression ,Pelopylax kl. esculentus ,education.field_of_study ,GENOME INTROGRESSION ,PELOPYLAX KL. ESCULENTUS ,biology ,Cytochrome b ,Reproduction ,Rana esculenta ,Water ,Interspecific competition ,SERUM ALBUMIN ,biology.organism_classification ,Diploidy ,lcsh:Genetics ,030104 developmental biology ,Germ Cells ,CYTOCHROME B ,cytochrome b ,Karyotyping ,Hybridization, Genetic ,Anura - Abstract
Hybridogenesis in an interspecific hybrid frog is a coupling mechanism in the gametogenic cell line that eliminates the genome of one parental species with endoduplication of the remaining genome of the other parental species. It has been intensively investigated in the edible frog Pelophylax kl. esculentus (RL), a natural hybrid between the marsh frog P. ridibundus (RR) and the pool frog P. lessonae (LL). However, the genetic mechanisms involved remain unclear. Here, we investigated the water frogs in the western Russian territory. In three of the four populations, we genetically identified 16 RL frogs living sympatrically with the parental LL species, or with both parental species. In addition, two populations contained genome introgression with another species, P. bedriagae (BB) (a close relative of RR). In the gonads of 13 RL frogs, the L genome was eliminated, producing gametes of R (or R combined with the B genome). In sharp contrast, one RL male eliminated the L or R genome, producing both R and L sperm. We detected a variation in genome elimination within a population. Based on the genetic backgrounds of RL frogs, we hypothesize that the introgression of the B genome resulted in the change in choosing a genome to be eliminated. © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This research was supported by JSPS and Russian Foundation for Basic Research (RFBR) under the Japan–Russia Research Cooperative Program (2018–2019), the Russian Foundation for Basic Research (grant no. 18-54-50013 to V.V.), and the program 211 of the Government of the Russian Federation (agreement no. 02.A03.21.0006). This study was performed within the framework of the state contract with the Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences.
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- 2021
7. Vibronic coupling in the ground and excited states of the pyridine radical cation
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Horst Köppel, Alexander B. Trofimov, E. V. Gromov, A. D. Skitnevskaya, and E. K. Grigoricheva
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Physics ,010304 chemical physics ,General Physics and Astronomy ,Hartree ,010402 general chemistry ,01 natural sciences ,Potential energy ,Molecular physics ,0104 chemical sciences ,Vibronic coupling ,Ab initio quantum chemistry methods ,Excited state ,Ionization ,0103 physical sciences ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Ionization energy ,Ground state - Abstract
Vibronic interactions in the pyridine radical cation ground state, 2A1, and its lowest excited states, 2A2 and 2B1, are studied theoretically. These states originate from the ionization out of the highest occupied orbitals of pyridine, 7a1 (nσ), 1a2 (π), and 2b1 (π), respectively, and give rise to the lowest two photoelectron maxima. According to our previous high-level ab initio calculations [Trofimov et al., J. Chem. Phys. 146, 244307 (2017)], the 2A2 (π−1) excited state is very close in energy to the 2A1 (nσ−1) ground state, which suggests that these states could be vibronically coupled. Our present calculations confirm that this is indeed the case. Moreover, the next higher excited state, 2B1 (π−1), is also involved in the vibronic interaction with the 2A1 (nσ−1) and 2A2 (π−1) states. The three-state vibronic coupling problem was treated within the framework of a linear vibronic coupling model employing parameters derived from the ionization energies of pyridine computed using the linear response coupled-cluster method accounting for single, double, and triple excitations (CC3). The potential energy surfaces of the 2A1 and 2A2 states intersect in the vicinity of the adiabatic minimum of the 2A2 state, while the surfaces of the 2A2 and 2B1 states intersect near the 2B1 state minimum. The spectrum computed using the multi-configuration time-dependent Hartree (MCTDH) method accounting for 24 normal modes is in good qualitative agreement with the experimental spectrum of pyridine obtained using high-resolution He I photoelectron spectroscopy and allows for some assignment of the observed features.
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- 2020
8. Intermediate state representation approach to physical properties of molecular electron-detached states. II. Benchmarking
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Alexander C. Paul, Adrian L. Dempwolff, Andreas Dreuw, Alexandra M. Belogolova, and Alexander B. Trofimov
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Physics ,Density matrix ,010304 chemical physics ,Physics::Instrumentation and Detectors ,General Physics and Astronomy ,Propagator ,Electron ,010402 general chemistry ,01 natural sciences ,Full configuration interaction ,0104 chemical sciences ,Computational physics ,Dipole ,Construction method ,0103 physical sciences ,Molecule ,Intermediate state ,Physical and Theoretical Chemistry - Abstract
The third-order algebraic-diagrammatic construction method for studies of electron detachment processes within the electron propagator framework [IP-ADC(3)] was extended to treat the properties of molecular states with a detached electron using the intermediate state representation (ISR) formalism. The second-order ISR(2) equations for the one-particle (transition) density matrix have been derived and implemented as an extension of the IP-(U)ADC(3) method available in the Q-CHEM program. As a first systematic test of the present IP-(U)ADC(3)/ISR(2) method, the dipole moments of various electronic states of closed- and open-shell molecules have been computed and compared to full configuration interaction (FCI) results. The present study employing FCI benchmarks also provides the first rigorous estimates for the accuracy of electron detachment energies obtained using the IP-ADC(3) method.
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- 2020
9. Experimental evidence for ultrafast intermolecular relaxation processes in hydrated biomolecules
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Alexander Dorn, Kirill Gokhberg, Enliang Wang, Xueguang Ren, Alexander B. Trofimov, and A. D. Skitnevskaya
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Physics ,Proton ,Intermolecular force ,General Physics and Astronomy ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Secondary electrons ,0104 chemical sciences ,Ion ,Ionization ,0103 physical sciences ,Physics::Atomic and Molecular Clusters ,Radiation damage ,Molecule ,010306 general physics ,Electron ionization - Abstract
Cell and gene damage caused by ionizing radiation has been studied for many years. It is accepted that DNA lesions (single- and double-strand breaks, for example) are induced by secondary species such as radicals, ions and the abundant low-energy secondary electrons generated by the primary radiation. Particularly harmful are dense ionization clusters of several ionization processes within a volume typical for the biomolecular system. Here we report the observation of a damage mechanism in the form of a non-local autoionizing process called intermolecular Coulombic decay (ICD). It directly involves DNA constituents or other organic molecules in an aqueous environment. The products are two energetic ions and three reactive secondary electrons that can cause further damage in their vicinity. Hydrogen-bonded complexes that consist of one tetrahydrofuran (THF) molecule—a surrogate of deoxyribose in the DNA backbone—and one water molecule are used as a model system. After electron impact ionization of the water molecule in the inner-valence shell the vacancy is filled by an outer-valence electron. The released energy is transferred across the hydrogen bridge and leads to ionization of the neighbouring THF molecule. This energy transfer from water to THF is faster than the otherwise occurring intermolecular proton transfer. The signature of the ICD reaction is identified in triple-coincidence measurements of both ions and one of the final state electrons. These results could improve the understanding of radiation damage in biological tissue. The authors study intermolecular Coulomb decay that occurs in a sample of THF and water in a reaction microscope employing triple-coincidence measurements of two ions and one electron. They find that ICD is a previously unconsidered effect between water and other organic molecules that are hydrogen-bonded, with ICD outpacing proton transfer.
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- 2018
10. Postnatal LPS Challenge Impacts Escape Learning and Expression of Plasticity Factors Mmp9 and Timp1 in Rats
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Aleksei Umriukhin, Alexander P. Schwarz, Evgeniy Svirin, Niall Mortimer, Klaus-Peter Lesch, O. E. Zubareva, V. M. Klimenko, Andrei Svistunov, Tatyana Strekalova, Alexander B. Trofimov, Promovendi MHN, Psychiatrie & Neuropsychologie, and RS: MHeNs - R3 - Neuroscience
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0301 basic medicine ,Lipopolysaccharides ,Male ,Time Factors ,MATRIX METALLOPROTEINASES ,Lipopolysaccharide (LPS) ,Water maze ,Toxicology ,chemistry.chemical_compound ,0302 clinical medicine ,PRENATAL STRESS ,RatAlexander Trofimov and Tatyana Strekalova equally contributed to this work ,Corticosterone ,Escape Reaction ,SYNAPTIC PLASTICITY ,GLUCOCORTICOID HORMONES ,Prefrontal cortex ,General Neuroscience ,Age Factors ,Brain ,Gene Expression Regulation, Developmental ,Long-term potentiation ,Matrix Metalloproteinase 9 ,Female ,Original Article ,LONG-TERM POTENTIATION ,Psychology ,MMP-9 ,MESSENGER-RNA ,BRAIN-DEVELOPMENT ,medicine.medical_specialty ,Escape response ,Statistics, Nonparametric ,Escape learning ,03 medical and health sciences ,TIMP-1 ,IMMUNOREGULATORY FEEDBACK ,Internal medicine ,Neuroplasticity ,medicine ,Avoidance Learning ,Animals ,RNA, Messenger ,Rats, Wistar ,Maze Learning ,Tissue Inhibitor of Metalloproteinase-1 ,Dentate gyrus ,Rats ,030104 developmental biology ,Endocrinology ,chemistry ,Prenatal stress ,Animals, Newborn ,DENTATE GYRUS ,Immunology ,Exploratory Behavior ,Rat ,030217 neurology & neurosurgery ,NEUROTROPHIC FACTOR - Abstract
Bacterial intoxication associated with inflammatory conditions during development can impair brain functions, in particular evolutionarily novel forms of memory, such as explicit learning. Little is known about the dangers of early-life inflammation on more basic forms of learning, for example, the acquisition of motor escape abilities, which are generally better preserved under pathological conditions. To address this limitation in knowledge, an inflammatory response was elicited in Wistar pups by lipopolysaccharide (LPS) injections (25 μg/kg) on postnatal days P15, P18 and P21. The acquisition of escape behaviour was tested from P77 by active avoidance footshock model and water maze. Open-field behaviour and blood corticosterone levels were also measured. Rat brain tissue was collected from pups 2 h post-injection and from adult rats which either underwent escape training on P77–P81 or remained untrained. mRNA levels of developmental brain plasticity factors MMP-9 and TIMP-1 were investigated in the medial prefrontal cortex and ventral/dorsal hippocampus. LPS-challenged rats displayed moderately deficient escape responses in both memory tests, increased freezing behaviour and, surprisingly, reduced blood cortisol levels. Mmp9 and Timp1, and their ratio to one another, were differentially altered in pups versus adult untrained rats but remained unchanged overall in rats trained in either learning task. Together, our data indicate that systemic pro-inflammatory response during early postnatal development has long-lasting effects, including on the acquisition of motor escape abilities and plasticity factor expression, into adulthood. Our data suggest that altered stress response could possibly mediate these deviations and repeated training might generate positive effects on plasticity under the employed conditions. Electronic supplementary material The online version of this article (doi:10.1007/s12640-017-9720-2) contains supplementary material, which is available to authorized users.
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- 2017
11. 2-Halopyridines in the triple reaction in the P /KOH/DMSO system to form tri(2-pyridyl)phosphine: Experimental and quantum-chemical dissimilarities
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Yurii I. Litvintsev, Natalia A. Belogorlova, Vladimir A. Kuimov, Boris A. Trofimov, Alexandra M. Belogolova, Alexander B. Trofimov, Svetlana F. Malysheva, and Nina K. Gusarova
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Quantum chemical ,010405 organic chemistry ,Chemistry ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,chemistry.chemical_compound ,Nucleophile ,Yield (chemistry) ,Halogen ,Nucleophilic substitution ,Phosphine - Abstract
Experimental and quantum-chemical features of the triple nucleophilic substitution of halogen atoms in 2-chloro- and 2-bromopyridines under the action of P-centered nucleophiles generated in the system Pn/KOH/DMSO to afford tri(2-pyridyl)phosphine in a yield of up to 69% have been compared.
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- 2018
12. Acetylene-Triggered Reductive Incorporation of Phosphine Chalcogenides into a Quinoline Scaffold: Toward S
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Boris A, Trofimov, Pavel A, Volkov, Kseniya O, Khrapova, Anton A, Telezhkin, Nina I, Ivanova, Alexander I, Albanov, Nina K, Gusarova, Alexandra M, Belogolova, and Alexander B, Trofimov
- Abstract
Quinolines react with acylacetylenes and secondary phosphine chalcogenides at 20-75 °C to afford N-acylvinyl-2(1)-chalcogenophosphoryldihydroquinolines in good and excellent yields. Unlike the pyridine-derived similar intermediates, which eliminate E-alkenes to give aromatic chalcogenophosphorylpyridines, thereby completing S
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- 2019
13. Vibronic interaction in trans-dichloroethene studied by vibration- and angle-resolved photoelectron spectroscopy using 19–90 eV photon energy
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David M. P. Holland, John D. Bozek, Ivan Powis, Alexander B. Trofimov, Ayse T. Duran, A. D. Skitnevskaya, E. K. Grigoricheva, and Christophe Nicolas
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Materials science ,010304 chemical physics ,General Physics and Astronomy ,Photon energy ,Conical intersection ,010402 general chemistry ,01 natural sciences ,Potential energy ,Molecular physics ,0104 chemical sciences ,Vibronic coupling ,X-ray photoelectron spectroscopy ,Molecular vibration ,0103 physical sciences ,Potential energy surface ,Physics::Atomic and Molecular Clusters ,Molecular orbital ,Physics::Chemical Physics ,Physical and Theoretical Chemistry - Abstract
Valence photoelectron spectra and photoelectron angular distributions of trans-dichloroethene have been measured with vibrational resolution at photon energies between 19 eV and 90 eV. Calculations of photoelectron anisotropy parameters, β, and harmonic vibrational modes help provide initial insight into the molecular structure. The photon energy range encompasses the expected position of the atomic Cl 3p Cooper minimum. A corresponding dip observed here in the anisotropy of certain photoelectron bands permits the identification and characterization of those molecular orbitals that retain a localized atomic Cl character. The adiabatic approximation holds for the X 2Au state photoelectron band, but vibronic coupling was inferred within the A–B–C and the D–E states by noting various failures of the Franck–Condon model, including vibrationally dependent β-parameters. This is further explored using the linear vibronic coupling model with interaction parameters obtained from ab initio calculations. The A/B photoelectron band is appreciably affected by vibronic coupling, owing to the low-lying conical intersection of the A 2Ag and B 2Bu states. The C 2Bg band is also affected, but to a lesser extent. The adiabatic minima of the D 2Au and E 2Ag states are almost degenerate, and the vibronic interaction between these states is considerable. The potential energy surface of the D 2Au state is predicted to have a double-minimum shape with respect to the au deformations of the molecular structure. The irregular vibrational structure of the resulting single photoelectron band reflects the non-adiabatic nuclear dynamics occurring on the two coupled potential energy surfaces above the energy of their conical intersection.
- Published
- 2021
14. Vibronic coupling in the Pyridine Radical Cation: Nuclear Dynamics Studied Using the Multi-configuration Time-Dependent Hartree method
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E. V. Gromov, Alexander B. Trofimov, A. D. Skitnevskaya, and E. K. Grigoricheva
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Physics ,History ,Vibronic coupling ,chemistry.chemical_compound ,Radical ion ,Nuclear dynamics ,chemistry ,Multi-configuration time-dependent Hartree ,Pyridine ,Molecular physics ,Computer Science Applications ,Education - Abstract
The multi-configuration time-dependent Hartree (MCTDH) method was applied to study nuclear dynamics following transitions to a manifold of vibronically coupled ground 2A1 and excited 2A2 and 2B1 states of the pyridine radical cation (PRC). These states originate from ionization out of the highest occupied orbitals of pyridine, 7a1 (nσ), 1a2 (π), and 2b1 (π), respectively, and give rise to the lowest two photoelectron bands. We focus on various theoretical and computational aspects of the MCTDH method and methodology to calculate the spectrum, taking our study of the vibronically interacting 2A1, 2A2, and 2B1 states of PRC as an example. In particular, the choice of the single-particle functions (SPFs) and schemes to combine vibrational modes are discussed.
- Published
- 2021
15. A complex absorbing potential electron propagator approach to resonance states of metastable anions
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Andreas Dreuw, Adrian L. Dempwolff, Alexander B. Trofimov, and Alexandra M. Belogolova
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Physics ,History ,Metastability ,Propagator ,Electron ,Molecular physics ,Computer Science Applications ,Education - Abstract
An earlier developed electron propagator method for the treatment of electron attachment to molecules within the non-Dyson algebraic-diagrammatic construction framework (EA-ADC) is extended by inclusion of the complex absorbing potential (CAP). The resulting method allows for the investigation of resonance states of metastable anions. Approximation schemes up to third-order perturbation theory for the electron propagator (EA-ADC(3)) are implemented. The CAP operator is treated up to second-order using the intermediate state representation formalism (ISR(2)) and the subspace projection technique. The CAP/EA-ADC(3) method is tested in first applications to the resonances in CO and N2 molecules associated with electron attachment to their low-lying π*-orbitals. The results of the calculations agree well with the available experimental and theoretical data and demonstrate the CAP-augmented EA-ADC modeling can become a useful tool for theoretical studies of metastable electron-attached states.
- Published
- 2021
16. Synthesis and Optical Properties ofmeso-CF3-BODIPY with Acylethynyl Substituents in the 3-Position of the Indacene Core
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Lyubov N. Sobenina, Konstantin B. Petrushenko, Alexander B. Trofimov, A. D. Skitnevskaya, Maxim D. Gotsko, Igor A. Ushakov, Boris A. Trofimov, and Denis N. Tomilin
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Core (optical fiber) ,chemistry.chemical_compound ,Crystallography ,chemistry ,010405 organic chemistry ,Position (vector) ,Organic Chemistry ,BODIPY ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences - Published
- 2016
17. N-Vinyl-2-(trifluoroacetylethynyl)pyrroles and E-2-(1-bromo-2-trifluoroacetylethenyl)pyrroles: Cross-coupling vs. addition during C H-functionalization of pyrroles with bromotrifluoroacetylacetylene in solid Al2O3 medium. H-bonding control
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Alexander B. Trofimov, Denis N. Tomilin, A. V. Afonin, Maxim D. Gotsko, Dmitri Yu. Soshnikov, Igor A. Ushakov, Boris A. Trofimov, Andrey B. Koldobsky, and Lyubov N. Sobenina
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010405 organic chemistry ,Hydrogen bond ,Organic Chemistry ,Substituent ,010402 general chemistry ,Triple bond ,01 natural sciences ,Biochemistry ,Medicinal chemistry ,0104 chemical sciences ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Intramolecular force ,Yield (chemistry) ,Proton NMR ,Environmental Chemistry ,Surface modification ,Coupling (piping) ,Organic chemistry ,Physical and Theoretical Chemistry - Abstract
A topochemical reaction of pyrroles with bromotrifluoroacetylacetylene proceeds in solid Al2O3 at room temperature in two different directions depending on the substituent character at the nitrogen atom. While N-vinylpyrroles undergo the cross-coupling to give N-vinyl-2-(trifluoroacetylethynyl)pyrroles in up to 58% yield, unsubstituted NH-pyrroles add to the triple bond to afford exclusively E-2-(1-bromo-2-trifluoroacetylethenyl)pyrroles in 12–21% yields. It has been shown (1H NMR, quantum-chemical calculations) that the reaction is controlled by the strong intramolecular hydrogen bonding between NH and carbonyl groups.
- Published
- 2016
18. Intermediate state representation approach to physical properties of molecular electron-detached states. I. Theory and implementation
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Alexandra M. Belogolova, Alexander C. Paul, Alexander B. Trofimov, Adrian L. Dempwolff, and Andreas Dreuw
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Density matrix ,Physics ,010304 chemical physics ,Physics::Instrumentation and Detectors ,Computation ,General Physics and Astronomy ,Propagator ,Electron ,010402 general chemistry ,01 natural sciences ,Spectral line ,0104 chemical sciences ,Dipole ,Quantum mechanics ,0103 physical sciences ,Intermediate state ,Physical and Theoretical Chemistry ,Ground state - Abstract
The third-order non-Dyson algebraic-diagrammatic construction approach to the electron propagator [IP-ADC(3)] is extended using the intermediate state representation (ISR) formalism, allowing the wave functions and properties of molecular states with detached electron to be studied. The second-order ISR equations [ISR(2)] for the one-particle (transition) density matrix have been derived and implemented in the Q-CHEM program. The approach is completely general and enables evaluation of arbitrary one-particle operators and interpretation of electron detachment processes in terms of density-based quantities. The IP-ADC(3)/ISR(2) equations were implemented for Ŝz-adapted intermediate states, allowing open-shell molecules to be studied using unrestricted Hartree-Fock references. As a first test for computations of ground state properties, dipole moments of various closed- and open-shell molecules have been computed by means of electron detachment from the corresponding anions. The results are in good agreement with experimental data. The potential of IP-ADC(3)/ISR(2) for the interpretation of photoelectron spectra is demonstrated for the galvinoxyl free radical.
- Published
- 2020
19. Spectroscopic and quantum chemical study of difluoroboron β-diketonate luminophores: Isomeric acetylnaphtholate chelates
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Anatolii G. Mirochnik, A. D. Skitnevskaya, S. A. Tikhonov, Vitaliy I. Vovna, Alexander B. Trofimov, Elena V. Fedorenko, and I. S. Os’mushko
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Chemistry ,Ab initio ,02 engineering and technology ,Electronic structure ,Time-dependent density functional theory ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Analytical Chemistry ,Intersystem crossing ,Physical chemistry ,Density functional theory ,Hypsochromic shift ,0210 nano-technology ,Phosphorescence ,Luminescence ,Instrumentation ,Spectroscopy - Abstract
The electronic structure and optical properties of the isomeric difluoroboron β-diketonates, 2,2-difluoro-4-methylnaphtho-[2,1-e]-1,3,2-dioxaborin (I) and 2,2-difluoro-4-methylnaphtho-[1,2-e]-1,3,2-dioxaborin (II), were studied by means of X-ray photoelectron, absorption and luminescence spectroscopies. The experimental results were interpreted using high-level ab initio quantum chemical computations, including the algebraic-diagrammatic construction method for the polarization propagator of the second and third orders (ADC(2) and ADC(3)), the outer-valence Green's function (OVGF) method, and the time-dependent density functional (TDDFT) approach. The X-ray photoelectron measurements were assigned in the entire energy range using the results of the Kohn-Sham orbital calculations which employed the B3LYP functional. Pronounced hypsochromic shift of crystal-state fluorescence was observed in I upon the lowering of temperature, which can be explained by the deterioration of the conditions for excimers formation. According to our results, remarkable feature of II, absent in I, is its phosphorescence at room temperature. Basing on our calculations, a decay mechanism for the S1 state was proposed, explaining the observed differences in the phosphorescence of I and II.
- Published
- 2018
20. Photoionization dynamics of cis-dichloroethene from investigation of vibrationally resolved photoelectron spectra and angular distributions
- Author
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E. V. Gromov, D.M.P. Holland, Minna Patanen, Ivan Powis, R.C. Menzies, Christophe Nicolas, A. D. Skitnevskaya, Alexander B. Trofimov, Catalin Miron, E. Antonsson, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK., School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK. Code (UMR, EA, ...), Daresbury Laboratory, Laboratory of Quantum Chemistry, Irkutsk State University, Irkutsk State University (ISU), Theoretische Chemie Universität Heidelberg, Universität Heidelberg [Heidelberg] = Heidelberg University, Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Laboratoire Interactions, Dynamiques et Lasers (ex SPAM) (LIDyl), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universität Heidelberg [Heidelberg], and Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[PHYS]Physics [physics] ,Materials science ,Valence (chemistry) ,010304 chemical physics ,Scattering ,Binding energy ,General Physics and Astronomy ,Photoionization ,Photon energy ,010402 general chemistry ,01 natural sciences ,Molecular physics ,Spectral line ,0104 chemical sciences ,Vibronic coupling ,X-ray photoelectron spectroscopy ,0103 physical sciences ,Physics::Atomic and Molecular Clusters ,Physical and Theoretical Chemistry - Abstract
International audience; The influence of vibronic coupling on the outer valence ionic states of cis-dichloroethene has been investigated by recording photoelectron spectra over the excitation range 19–90 eV using plane polarized synchrotron radiation, for two polarization orientations. The photoelectron anisotropy parameters and electronic state branching ratios derived from these spectra have been compared to theoretical predictions obtained with the continuum multiple scattering approach. This comparison shows that the photoionization dynamics of the à 2B2, B̃ 2A1, C̃ 2A2, and D̃ 2B1 states, all of which are formed through the ejection of an electron from a nominally chlorine lone-pair orbital, exhibit distinct evidence of the Cooper minimum associated with the halogen atom. While retaining a high degree of atomic character, these orbital ionizations nevertheless display clear distinctions. Simulations, assuming the validity of the Born-Oppenheimer and the Franck-Condon approximations, of the X̃ 2B1, à 2B2, and D̃ 2B1 state photoelectron bands have allowed some of the vibrational structure observed in the experimental spectra to be assigned. The simulations provide a very satisfactory interpretation for the X̃ 2B1 state band but appear less successful for the à 2B2 and D̃ 2B1 states, with irregularities appearing in both. The B̃ 2A1 and C̃ 2A2 state photoelectron bands exhibit very diffuse and erratic profiles that cannot be reproduced at this level. Photoelectron anisotropy parameters, β, have been evaluated as a function of binding energy across the studied photon energy range. There is a clear step change in the β values of the à 2B2 band at the onset of the perturbed peak intensities, with β evidently adopting the value of the B̃ 2A1 band β. The D̃ 2B1 band β values also display an unexpected vibrational level dependence, contradicting Franck-Condon expectations. These various behaviors are inferred to be a consequence of vibronic coupling in this system
- Published
- 2018
21. Four-Component Polarization Propagator Calculations of Electron Excitations: Spectroscopic Implications of Spin-Orbit Coupling Effects
- Author
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Markus Pernpointner, Lucas Visscher, Alexander B. Trofimov, Theoretical Chemistry, and AIMMS
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Physics ,Valence (chemistry) ,010304 chemical physics ,Four component ,Propagator ,Spin–orbit interaction ,Electron ,010402 general chemistry ,Polarization (waves) ,01 natural sciences ,0104 chemical sciences ,Computer Science Applications ,symbols.namesake ,Quantum electrodynamics ,0103 physical sciences ,symbols ,SDG 7 - Affordable and Clean Energy ,Physical and Theoretical Chemistry ,Hamiltonian (quantum mechanics) ,Excitation - Abstract
A complete implementation of the polarization propagator based on the Dirac-Coulomb Hamiltonian is presented and applied to excitation spectra of various systems. Hereby the effect of spin-orbit coupling on excitation energies and transition moments is investigated in detail. The individual perturbational contributions to the transition moments could now be separately analyzed for the first time and show the relevance of one- and two-particle terms. In some systems different contributions to the transition moments partially cancel each other and do not allow for simple predictions. For the outer valence spectrum of the H2Os(CO)4 complex a detailed final state analysis is performed explaining the sensitivity of the excitation spectrum to spin-orbit effects. Finally, technical issues of handling double group symmetry in the relativistic framework and methodological aspects of our parallel implementation are discussed.
- Published
- 2018
22. A study of the excited electronic states of normal and fully deuterated furan by photoabsorption spectroscopy and high-level ab initio calculations
- Author
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E. V. Gromov, Denis Joyeux, Andreas Dreuw, E. A. Seddon, L. E. Archer, Tatiana Korona, Michael Wormit, N. de Oliveira, Alexander B. Trofimov, and D.M.P. Holland
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Physics ,Valence (chemistry) ,Absorption spectroscopy ,Atomic and Molecular Physics, and Optics ,Spectral line ,symbols.namesake ,Ab initio quantum chemistry methods ,Molecular vibration ,Rydberg formula ,symbols ,Physical and Theoretical Chemistry ,Atomic physics ,Spectroscopy ,Excitation - Abstract
The photoabsorption spectra of C 4 H 4 O and C 4 D 4 O have been measured between ∼5.5 and 17.7 eV using a synchrotron radiation-based Fourier transform spectrometer. In addition to several broad bands due to transitions into valence states, the spectra exhibit numerous sharp bands associated with Rydberg states belonging to series converging onto the X 2 A 2 or the A 2 B 1 state limits. Vertical excitation energies and oscillator strengths have been computed using the second- and third-order algebraic-diagrammic construction polarisation propagator methods (ADC(2) and ADC(3)), and the equation-of-motion coupled-cluster method at the level of singles and doubles model (EOM-CCSD). Adiabatic excitation energies have been estimated using previously computed corrections. The theoretical predictions have allowed assignments to be proposed for the Rydberg series observed in the present single-photon absorption spectra and for some additional series, mainly of A 2 symmetry, reported in previous multiphoton excitation studies. The assignments of some of the Rydberg series converging onto the A 2 B 1 state limit have been revised and, guided by our calculations, the principal series is ascribed to the 2b 1 → n da 2 1 B 2 and 2b 1 → n db 1 1 A 1 transitions. f-type Rydberg series, previously observed only in the multiphoton absorption spectrum of furan, have been observed and assigned. Such f-type series, converging onto either the X 2 A 2 or the A 2 B 1 state thresholds, contribute significantly to the single-photon absorption spectrum. Many of the absorption bands associated with Rydberg states display vibrational progressions which resemble those in the corresponding photoelectron band. It appears that some of the structure associated with the 1a 2 → 3pb 2 1 B 1 and 1a 2 → 3pb 1 1 B 2 transitions involves excitation of non-totally symmetric vibrational modes.
- Published
- 2015
23. 3H-Pyrroles from ketoximes and acetylene: synthesis, stability and quantum-chemical insight
- Author
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Dmitrii Yu. Soshnikov, Elena Yu. Schmidt, Dmitrii A. Shabalin, Marina Yu. Dvorko, Vladimir B. Kobychev, Igor A. Ushakov, Alexander B. Trofimov, Nadezhda I. Protsuk, Al'bina I. Mikhaleva, Boris A. Trofimov, and Nadezhda M. Vitkovskaya
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Quantum chemical ,Reaction conditions ,chemistry.chemical_compound ,Acetylene ,chemistry ,Organic Chemistry ,Drug Discovery ,Superbase ,Organic chemistry ,Oxime ,Biochemistry ,Medicinal chemistry ,Relative stability - Abstract
Rare nonaromatic 3H-pyrroles have been synthesized from ketoximes having only one C–H bond adjacent to the oxime function and acetylene under pressure (10–13 atm) at 70 °C in two-phase superbase media of KOH/DMSO/n-hexane type, the yields ranging 8–36%. The effect of substituents, superbase nature and reaction conditions on yields of the target 3H-pyrroles has been analyzed. Hydroxypyrroline/3H-pyrroles interconversion as well as relative stability of model 3H-pyrroles have been assessed quantum chemically (MP2/6-31++G**//B3LYP/6-31G**).
- Published
- 2015
24. A study of the valence shell electronic structure and photoionisation dynamics of ortho-dichlorobenzene, ortho-bromochlorobenzene and trichlorobenzene
- Author
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I. L. Bodzuk, Alexander B. Trofimov, Anthony W. Potts, Ivan Powis, D.M.P. Holland, D. Yu. Soshnikov, and Leif Karlsson
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Photoionisation cross section ,Chemistry ,medicine ,General Physics and Astronomy ,Synchrotron radiation ,Trichlorobenzene ,Electronic structure ,Physical and Theoretical Chemistry ,Valence electron ,Molecular physics ,Ortho-dichlorobenzene ,medicine.drug - Abstract
The valence shell electronic structure and photoionisation dynamics of ortho-dichlorobenzene, ortho-bromochlorobenzene and trichlorobenzene have been investigated both experimentally and theoretica ...
- Published
- 2015
25. Aluminium oxide-mediated cross-coupling of pyrroles with 1-bromo-2-(trifluoroacetyl)acetylene: a quantum-chemical insight
- Author
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Maxim D. Gotsko, A. V. Afonin, Andrey B. Koldobsky, Alexander B. Trofimov, Lyubov N. Sobenina, Igor A. Ushakov, Dmitri Yu. Soshnikov, Nadezhda M. Vitkovskaya, Boris A. Trofimov, and Denis N. Tomilin
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Quantum chemical ,010405 organic chemistry ,Hydrogen bond ,General Chemistry ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,Coupling (electronics) ,chemistry.chemical_compound ,Acetylene ,chemistry ,Intramolecular force ,Aluminium oxide ,Moiety - Abstract
Cross-coupling of NH-pyrroles with 1-bromo-2-(trifluoroacetyl) acetylene in the Al2O3 medium affords (E)-4-bromo-1,1,1-trifluoro-4-(pyrrol-2-yl)but-3-en-2-ones instead of the expected 2-ethynylated products. Quantum-chemical analysis shows strong intramolecular hydrogen bonding between NH and trifluoroacetyl groups, higher NH acidity and deeper charge transfer to the ethenyl moiety, which determines the reaction pathway.
- Published
- 2016
26. Ionization of pyridine: Interplay of orbital relaxation and electron correlation
- Author
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D.M.P. Holland, L. Karlsson, Alexander B. Trofimov, I.L. Badsyuk, Jochen Schirmer, R.C. Menzies, Anthony W. Potts, E. V. Gromov, and Ivan Powis
- Subjects
010304 chemical physics ,Electronic correlation ,Chemistry ,General Physics and Astronomy ,Photoionization ,010402 general chemistry ,01 natural sciences ,Ionization, Ground states, Basis sets, Photoelectron spectra, Electron densities of states ,0104 chemical sciences ,Atomic orbital ,Ionization ,0103 physical sciences ,Physics::Atomic and Molecular Clusters ,Molecular orbital ,Physical and Theoretical Chemistry ,Atomic physics ,Ionization energy ,Valence electron ,Basis set - Abstract
The valence shell ionization spectrum of pyridine was studied using the third-order algebraic-diagrammatic construction approximation scheme for the one-particle Green’s function and the outer-valence Green’s function method. The results were used to interpret angle resolved photoelectron spectra recorded with synchrotron radiation in the photon energy range of 17–120 eV. The lowest four states of the pyridine radical cation, namely, 2A2 (1a 2 −1 1a2−1 ), 2A1(7a 1 −1 7a1−1), 2B1(2b 1 −1 2b1−1), and 2B2(5b 2 −1 5b2−1), were studied in detail using various high-level electronic structure calculation methods. The vertical ionization energies were established using the equation-of-motion coupled-cluster approach with single, double, and triple excitations (EOM-IP-CCSDT) and the complete basis set extrapolation technique. Further interpretation of the electronic structure results was accomplished using Dyson orbitals, electron density difference plots, and a second-order perturbation theory treatment for the relaxation energy. Strong orbital relaxation and electron correlation effects were shown to accompany ionization of the 7a1 orbital, which formally represents the nonbonding σ-type nitrogen lone-pair (nσ) orbital. The theoretical work establishes the important roles of the π-system (π-π* excitations) in the screening of the nσ-hole and of the relaxation of the molecular orbitals in the formation of the 7a1(nσ)−1 state. Equilibrium geometric parameters were computed using the MP2 (second-order Moller-Plesset perturbation theory) and CCSD methods, and the harmonic vibrational frequencies were obtained at the MP2 level of theory for the lowest three cation states. The results were used to estimate the adiabatic 0-0 ionization energies, which were then compared to the available experimental and theoretical data. Photoelectron anisotropy parameters and photoionization partial cross sections, derived from the experimental spectra, were compared to predictions obtained with the continuum multiple scattering approach.
- Published
- 2017
27. An experimental and theoretical study of the C 1s ionization satellites in CH3I
- Author
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Alexandra M. Belogolova, S A Serebrennikova, D.M.P. Holland, Stephen T. Pratt, Alexander B. Trofimov, and Ruaridh Forbes
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Physics ,010304 chemical physics ,Diabatic ,General Physics and Astronomy ,Photon energy ,010402 general chemistry ,01 natural sciences ,Spectral line ,0104 chemical sciences ,symbols.namesake ,Ionization ,0103 physical sciences ,Rydberg formula ,symbols ,Singlet state ,Physical and Theoretical Chemistry ,Ionization energy ,Atomic physics ,Basis set - Abstract
The C 1s ionization spectrum of CH3I has been studied both experimentally and theoretically. Synchrotron radiation has been employed to record polarization dependent photoelectron spectra at a photon energy of 614 eV. These spectra encompass the main-line due to the C 1s single-hole state and the peaks associated with the shake-up satellites. Vertical ionization energies and relative photoelectron intensities have been computed using the fourth-order algebraic-diagrammatic construction approximation scheme for the one-particle Green's function and the 6-311++G** basis set. The theoretical spectrum derived from these calculations agrees qualitatively with the experimental results, thereby allowing the principal spectral features to be assigned. According to our calculations, two 2A1 shake-up states of the C 1s-1 σCI → σCI * type with singlet and triplet intermediate coupling of the electron spins (S' = 0, 1) play an important role in the spectrum and contribute significantly to the overall intensity. Both of these states are expected to have dissociative diabatic potential energy surfaces with respect to the C-I separation. Whereas the upper of these states perturbs the manifold of Rydberg states, the lower state forms a band which is characterized by a strongly increased width. Our results indicate that the lowest shake-up peak with significant spectral intensity is due to the pair (S' = 0, 1) of 2E (C 1s-1 I 5p → σCI *) states. We predict that these 2E states acquire photoelectron intensity due to spin-orbit interaction. Such interactions play an important role here due to the involvement of the I 5p orbitals.
- Published
- 2019
28. ChemInform Abstract: N-Vinyl-2-(trifluoroacetylethynyl)pyrroles and E-2-(1-Bromo-2-trifluoroacetylethenyl)pyrroles: Cross-Coupling vs. Addition During C-H-Functionalization of Pyrroles with Bromotrifluoroacetylacetylene in Solid Al2O3 Medium. H-Bonding Co
- Author
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Maxim D. Gotsko, Dmitri Yu. Soshnikov, Igor A. Ushakov, Lyubov N. Sobenina, A. V. Afonin, Alexander B. Trofimov, Boris A. Trofimov, Andrey B. Koldobsky, and Denis N. Tomilin
- Subjects
Coupling (electronics) ,Addition reaction ,chemistry.chemical_compound ,chemistry ,Nitrogen atom ,Acetylene ,Hydrogen bond ,Substituent ,Surface modification ,General Medicine ,Medicinal chemistry ,Pyrrole derivatives - Abstract
Depending on the substituent character at the nitrogen atom, pyrroles react acetylene (II) in two different directions.
- Published
- 2016
29. The influence of the bromine atom Cooper minimum on the photoelectron angular distributions and branching ratios of the four outermost bands of bromobenzene
- Author
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Matthias Schneider, Minna Patanen, D.M.P. Holland, Ivan Powis, Andreas Dreuw, D. Yu. Soshnikov, C. Miron, Alexander B. Trofimov, Christophe Nicolas, and E. Antonsson
- Subjects
Atomic orbital ,Scattering ,Chemistry ,Excited state ,Ionization ,Binding energy ,General Physics and Astronomy ,Physical and Theoretical Chemistry ,Atomic physics ,Excitation ,Spectral line ,Ultraviolet photoelectron spectroscopy - Abstract
Angle resolved photoelectron spectra of the X̃(2)B1, Ã(2)A2, B̃(2)B2, and C̃(2)B1 states of bromobenzene have been recorded over the excitation range 20.5-94 eV using linearly polarized synchrotron radiation. The photoelectron anisotropy parameters and electronic branching ratios derived from these spectra have been compared to theoretical predictions obtained with the continuum multiple scattering approach. This comparison shows that ionization from the 8b2 orbital and, to a lesser extent, the 4b1 orbital is influenced by the Cooper minimum associated with the bromine atom. The 8b2 and 4b1 orbitals are nominally bromine lone-pairs, but the latter orbital interacts strongly with the π-orbitals in the benzene ring and this leads to a reduced atomic character. Simulations of the X̃(2)B1, B̃(2)B2, and C̃(2)B1 state photoelectron bands have enabled most of the vibrational structures appearing in the experimental spectra to be assigned. Many of the photoelectron peaks exhibit an asymmetric shape with a tail towards low binding energy. This asymmetry has been examined in the simulations of the vibrationally unexcited peak, due mainly to the adiabatic transition, in the X̃(2)B1 state photoelectron band. The simulations show that the asymmetric profile arises from hot-band transitions. The inclusion of transitions originating from thermally populated levels results in a satisfactory agreement between the experimental and simulated peak shapes.
- Published
- 2015
30. A fresh look at the photoelectron spectrum of bromobenzene: A third-order non-Dyson electron propagator study
- Author
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Christophe Nicolas, Michael Schneider, Michael Wormit, Minna Patanen, Andreas Dreuw, D.M.P. Holland, E. Antonsson, Alexander B. Trofimov, D. Yu. Soshnikov, C. Miron, and Ivan Powis
- Subjects
Photoemission spectroscopy ,Chemistry ,Ionization ,Physics::Atomic and Molecular Clusters ,General Physics and Astronomy ,Molecular orbital ,Photoionization ,Physical and Theoretical Chemistry ,Atomic physics ,Photon energy ,Ionization energy ,Spectral line ,Basis set - Abstract
The valence-shell ionization spectrum of bromobenzene, as a representative halogen substituted aromatic, was studied using the non-Dyson third-order algebraic-diagrammatic construction [nD-ADC(3)] approximation for the electron propagator. This method, also referred to as IP-ADC(3), was implemented as a part of the Q-Chem program and enables large-scale calculations of the ionization spectra, where the computational effort scales as n(5) with respect to the number of molecular orbitals n. The IP-ADC(3) scheme is ideally suited for investigating low-lying ionization transitions, so fresh insight could be gained into the cationic state manifold of bromobenzene. In particular, the present IP-ADC(3) calculations with the cc-pVTZ basis reveal a whole class of low-lying low-intensity two-hole-one-particle (2h-1p) doublet and quartet states, which are relevant to various photoionization processes. The good qualitative agreement between the theoretical spectral profile for the valence-shell ionization transitions generated with the smaller cc-pVDZ basis set and the experimental photoelectron spectrum measured at a photon energy of 80 eV on the PLEIADES beamline at the Soleil synchrotron radiation source allowed all the main features to be assigned. Some theoretical aspects of the ionization energy calculations concerning the use of various approximation schemes and basis sets are discussed.
- Published
- 2015
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