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Janoš J, Madea D, Mahvidi S, Mujawar T, Švenda J, Suchan J, Slavíček P, Klán P. Conformational Control of the Photodynamics of a Bilirubin Dipyrrinone Subunit: Femtosecond Spectroscopy Combined with Nonadiabatic Simulations. J Phys Chem A 2020; 124:10457-10471. [PMID: 33283519 DOI: 10.1021/acs.jpca.0c08945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The photochemistry of bilirubin has been extensively studied due to its importance in the phototherapy of hyperbilirubinemia. In the present work, we investigated the ultrafast photodynamics of a bilirubin dipyrrinone subunit, vinylneoxanthobilirubic acid methyl ester. The photoisomerization and photocyclization reactions of its (E) and (Z) isomers were studied using femtosecond transient absorption spectroscopy and by multireference electronic structure theory, where the nonadiabatic dynamics was modeled with a Landau-Zener surface hopping technique. The following picture has emerged from the combined theoretical and experimental approach. Upon excitation, dipyrrinone undergoes a very fast vibrational relaxation, followed by an internal conversion on a picosecond time scale. The internal conversion leads either to photoisomerization or regeneration of the starting material. Further relaxation dynamics on the order of tens of picoseconds was observed in the ground state. The nonadiabatic simulations revealed a strong conformational control of the photodynamics. The ultrafast formation of a cyclic photochemical product from a less-populated conformer of the studied subunit was predicted by our calculations. We discuss the relevance of the present finding for the photochemistry of native bilirubin. The work has also pointed to the limits of semiclassical nonadiabatic simulations for simulating longer photochemical processes, probably due to the zero-point leakage issue.
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Affiliation(s)
- Jiří Janoš
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, Czech Republic
| | - Dominik Madea
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Sadegh Mahvidi
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Taufiqueahmed Mujawar
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jakub Švenda
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Suchan
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, Czech Republic
| | - Petr Klán
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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2
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Röder A, Petersen J, Issler K, Fischer I, Mitrić R, Poisson L. Exploring the Excited-State Dynamics of Hydrocarbon Radicals, Biradicals, and Carbenes Using Time-Resolved Photoelectron Spectroscopy and Field-Induced Surface Hopping Simulations. J Phys Chem A 2019; 123:10643-10662. [DOI: 10.1021/acs.jpca.9b06346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anja Röder
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- LIDYL, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Jens Petersen
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Kevin Issler
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ingo Fischer
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Roland Mitrić
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lionel Poisson
- LIDYL, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
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3
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Lindner JO, Sultangaleeva K, Röhr MIS, Mitrić R. metaFALCON: A Program Package for Automatic Sampling of Conical Intersection Seams Using Multistate Metadynamics. J Chem Theory Comput 2019; 15:3450-3460. [PMID: 30995044 DOI: 10.1021/acs.jctc.9b00029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The multistate metadynamics for automatic exploration of conical intersection seams and systematic location of minimum energy crossing points in molecular systems and its implementation into the software package metaFALCON is presented. Based on a locally modified energy gap between two Born-Oppenheimer electronic states as a collective variable, multistate metadynamics trajectories are driven toward an intersection point starting from an arbitrary ground state geometry and are subsequently forced to explore the conical intersection seam landscape. For this purpose, an additional collective variable capable of distinguishing structures within the seam needs to be defined and an additional bias is introduced into the off-diagonal elements of an extended (multistate) electronic Hamiltonian. We demonstrate the performance of the algorithm on the examples of the 1,3-butadiene, benzene, and 9H-adenine molecules, where multiple minimum energy crossing points could be systematically located using the Wiener number or Cremer-Pople parameters as collective variables. Finally, with the example of 9H-adenine, we show that the multistate metadynamics potential can be used to obtain a global picture of a conical intersection seam. Our method can be straightforwardly connected with any ab initio or semiempirical electronic structure theory that provides energies and gradients of the respective electronic states and can serve for systematic elucidation of the role of conical intersections in the photophysics and photochemistry of complex molecular systems, thus complementing nonadiabatic dynamics simulations.
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Affiliation(s)
- Joachim O Lindner
- Institut für Physikalische und Theoretische Chemie , Julius-Maximilians-Universität Würzburg , Emil-Fischer-Str. 42 , 97074 Würzburg , Germany
| | - Karina Sultangaleeva
- Institut für Physikalische und Theoretische Chemie , Julius-Maximilians-Universität Würzburg , Emil-Fischer-Str. 42 , 97074 Würzburg , Germany
| | - Merle I S Röhr
- Institut für Physikalische und Theoretische Chemie , Julius-Maximilians-Universität Würzburg , Emil-Fischer-Str. 42 , 97074 Würzburg , Germany.,Center for Nanosystems Chemistry (CNC) , Julius-Maximilians-Universität Würzburg , Theodor-Boveri-Weg , 97074 Würzburg , Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie , Julius-Maximilians-Universität Würzburg , Emil-Fischer-Str. 42 , 97074 Würzburg , Germany
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4
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Issler K, Röder A, Hirsch F, Poisson L, Fischer I, Mitrić R, Petersen J. Excited state dynamics and time-resolved photoelectron spectroscopy of para-xylylene. Faraday Discuss 2018; 212:83-100. [PMID: 30238117 DOI: 10.1039/c8fd00083b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the excited-state dynamics of para-xylylene using a combination of field-induced surface hopping (FISH) simulations and time-resolved ionisation experiments. Our simulations predict an ultrafast decay of the initially excited bright state (S2/S3) to the S1 state on a sub-100 fs time scale, followed by return to the ground state within ∼1 ps. This is accompanied by a transient change of the biradical character of the molecule, as monitored by calculating natural orbital occupation numbers. Specifically, the initially low biradicality is increased by electronic excitation as well as by vibrational activation. Experimentally, para-xylylene was generated by pyrolysis from [2,2]paracyclophane and excited with 266 nm radiation into the S2/S3 bright state. The subsequent dynamics were followed using ionisation as the probe step, with both mass spectra and photoelectron spectra recorded as a function of pump-probe delay. The observed decay of photoelectron and photoion intensities closely matches the theoretical predictions and is consistent with the sequential mechanism found in the simulations. This mechanism exhibits characteristic signatures in both time-resolved mass and photoelectron spectra, in particular in the appearance of fragment ions that are exclusively generated from the S1 state. This allows for a separation of the S2 and S1 dynamics in the photoelectron and mass spectra. An excellent agreement between the observed and the simulated ion signal is observed.
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Affiliation(s)
- Kevin Issler
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
| | - Anja Röder
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany. and LIDYL, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France.
| | - Florian Hirsch
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
| | - Lionel Poisson
- LIDYL, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France.
| | - Ingo Fischer
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
| | - Roland Mitrić
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
| | - Jens Petersen
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
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Crespo-Otero R, Barbatti M. Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics. Chem Rev 2018; 118:7026-7068. [DOI: 10.1021/acs.chemrev.7b00577] [Citation(s) in RCA: 301] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rachel Crespo-Otero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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Liu J, Thiel W. An efficient implementation of semiempirical quantum-chemical orthogonalization-corrected methods for excited-state dynamics. J Chem Phys 2018; 148:154103. [DOI: 10.1063/1.5022466] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jie Liu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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7
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Tuna D, Lu Y, Koslowski A, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks of Electronically Excited States. J Chem Theory Comput 2016; 12:4400-22. [DOI: 10.1021/acs.jctc.6b00403] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - You Lu
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
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8
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Spörkel L, Thiel W. Adaptive time steps in trajectory surface hopping simulations. J Chem Phys 2016; 144:194108. [DOI: 10.1063/1.4948956] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Lasse Spörkel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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9
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Gerbich T, Schmitt HC, Fischer I, Mitrić R, Petersen J. Dynamics of Isolated 1,8-Naphthalimide and N-Methyl-1,8-naphthalimide: An Experimental and Computational Study. J Phys Chem A 2016; 120:2089-95. [DOI: 10.1021/acs.jpca.6b01226] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thiemo Gerbich
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Hans-Christian Schmitt
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Ingo Fischer
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Roland Mitrić
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Jens Petersen
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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10
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Dral PO, Wu X, Spörkel L, Koslowski A, Weber W, Steiger R, Scholten M, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters. J Chem Theory Comput 2016; 12:1082-96. [PMID: 26771204 PMCID: PMC4785507 DOI: 10.1021/acs.jctc.5b01046] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Semiempirical orthogonalization-corrected
methods (OM1, OM2, and
OM3) go beyond the standard MNDO model by explicitly including additional
interactions into the Fock matrix in an approximate manner (Pauli
repulsion, penetration effects, and core–valence interactions),
which yields systematic improvements both for ground-state and excited-state
properties. In this Article, we describe the underlying theoretical
formalism of the OMx methods and their implementation
in full detail, and we report all relevant OMx parameters
for hydrogen, carbon, nitrogen, oxygen, and fluorine. For a standard
set of mostly organic molecules commonly used in semiempirical method
development, the OMx results are found to be superior
to those from standard MNDO-type methods. Parametrized Grimme-type
dispersion corrections can be added to OM2 and OM3 energies to provide
a realistic treatment of noncovalent interaction energies, as demonstrated
for the complexes in the S22 and S66×8 test sets.
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Affiliation(s)
- Pavlo O Dral
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Lasse Spörkel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Weber
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rainer Steiger
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Mirjam Scholten
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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11
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Nikiforov A, Gamez JA, Thiel W, Huix-Rotllant M, Filatov M. Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules. J Chem Phys 2015; 141:124122. [PMID: 25273427 DOI: 10.1063/1.4896372] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Quantum-chemical computational methods are benchmarked for their ability to describe conical intersections in a series of organic molecules and models of biological chromophores. Reference results for the geometries, relative energies, and branching planes of conical intersections are obtained using ab initio multireference configuration interaction with single and double excitations (MRCISD). They are compared with the results from more approximate methods, namely, the state-interaction state-averaged restricted ensemble-referenced Kohn-Sham method, spin-flip time-dependent density functional theory, and a semiempirical MRCISD approach using an orthogonalization-corrected model. It is demonstrated that these approximate methods reproduce the ab initio reference data very well, with root-mean-square deviations in the optimized geometries of the order of 0.1 Å or less and with reasonable agreement in the computed relative energies. A detailed analysis of the branching plane vectors shows that all currently applied methods yield similar nuclear displacements for escaping the strong non-adiabatic coupling region near the conical intersections. Our comparisons support the use of the tested quantum-chemical methods for modeling the photochemistry of large organic and biological systems.
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Affiliation(s)
- Alexander Nikiforov
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Jose A Gamez
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Miquel Huix-Rotllant
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Michael Filatov
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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12
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Girod M, Sanader Z, Vojkovic M, Antoine R, MacAleese L, Lemoine J, Bonacic-Koutecky V, Dugourd P. UV photodissociation of proline-containing peptide ions: insights from molecular dynamics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:432-43. [PMID: 25503080 DOI: 10.1007/s13361-014-1038-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/27/2014] [Accepted: 10/27/2014] [Indexed: 05/16/2023]
Abstract
UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S(2) and S(3), lie close to 213 nm. Non-adiabatic MD simulation starting from S(2) and S(3) shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.
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13
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Gerbich T, Schmitt HC, Fischer I, Petersen J, Albert J, Mitrić R. Time-Resolved Study of 1,8-Naphthalic Anhydride and 1,4,5,8-Naphthalene-tetracarboxylic Dianhydride. J Phys Chem A 2015; 119:6006-16. [DOI: 10.1021/jp511843q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thiemo Gerbich
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Hans-Christian Schmitt
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Ingo Fischer
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Jens Petersen
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Julian Albert
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Roland Mitrić
- Institute of Physical and
Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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14
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An overview of nonadiabatic dynamics simulations methods, with focus on the direct approach versus the fitting of potential energy surfaces. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1526-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Thiel W. Semiempirical quantum–chemical methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1161] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Walter Thiel
- Max‐Planck‐Institut für KohlenforschungMülheimGermany
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16
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Röhr MIS, Petersen J, Wohlgemuth M, Bonačić-Koutecký V, Mitrić R. Nonlinear Absorption Dynamics Using Field-Induced Surface Hopping: Zinc Porphyrin in Water. Chemphyschem 2013; 14:1377-86. [DOI: 10.1002/cphc.201300053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/13/2013] [Indexed: 11/11/2022]
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17
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Barbatti M, Lan Z, Crespo-Otero R, Szymczak JJ, Lischka H, Thiel W. Critical appraisal of excited state nonadiabatic dynamics simulations of 9H-adenine. J Chem Phys 2012; 137:22A503. [DOI: 10.1063/1.4731649] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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18
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Gadaczek I, Krause K, Hintze KJ, Bredow T. Analytical Gradients for the MSINDO-sCIS and MSINDO-UCIS Method: Theory, Implementation, Benchmarks, and Examples. J Chem Theory Comput 2012; 8:986-96. [DOI: 10.1021/ct200867n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Immanuel Gadaczek
- Mulliken
Center for Theoretical Chemistry, Institut
für Physikalische und Theoretische Chemie, Universität
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Katharina Krause
- Mulliken
Center for Theoretical Chemistry, Institut
für Physikalische und Theoretische Chemie, Universität
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Kim Julia Hintze
- Mulliken
Center for Theoretical Chemistry, Institut
für Physikalische und Theoretische Chemie, Universität
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Thomas Bredow
- Mulliken
Center for Theoretical Chemistry, Institut
für Physikalische und Theoretische Chemie, Universität
Bonn, Beringstr. 4, 53115 Bonn, Germany
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Petersen J, Wohlgemuth M, Sellner B, Bonačić-Koutecký V, Lischka H, Mitrić R. Laser pulse trains for controlling excited state dynamics of adenine in water. Phys Chem Chem Phys 2012; 14:4687-94. [DOI: 10.1039/c2cp24002e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Gadaczek I, Krause K, Hintze KJ, Bredow T. MSINDO-sCIS: A New Method for the Calculation of Excited States of Large Molecules. J Chem Theory Comput 2011; 7:3675-85. [DOI: 10.1021/ct200595b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Immanuel Gadaczek
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Katharina Krause
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Kim Julia Hintze
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Thomas Bredow
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstr. 12, 53115 Bonn, Germany
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21
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Wohlgemuth M, Bonačić-Koutecký V, Mitrić R. Time-dependent density functional theory excited state nonadiabatic dynamics combined with quantum mechanical/molecular mechanical approach: Photodynamics of indole in water. J Chem Phys 2011; 135:054105. [DOI: 10.1063/1.3622563] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lan Z, Lu Y, Fabiano E, Thiel W. QM/MM Nonadiabatic Decay Dynamics of 9H-Adenine in Aqueous Solution. Chemphyschem 2011; 12:1989-98. [DOI: 10.1002/cphc.201001054] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 04/08/2011] [Indexed: 11/09/2022]
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Fekete ZA, Hoffmann EA, Körtvélyesi T, Penke B. Harmonic vibrational frequency scaling factors for the new NDDO Hamiltonians: RM1 and PM6. Mol Phys 2010. [DOI: 10.1080/00268970701598089] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Petersen J, Mitrić R, Bonacić-Koutecký V, Wolf JP, Roslund J, Rabitz H. How shaped light discriminates nearly identical biochromophores. PHYSICAL REVIEW LETTERS 2010; 105:073003. [PMID: 20868039 DOI: 10.1103/physrevlett.105.073003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Indexed: 05/29/2023]
Abstract
We present a general mechanism for successful discrimination of spectroscopically indistinguishable biochromophores by shaped light. For this purpose we use nonadiabatic dynamics in excited electronic states in the frame of the field-induced surface hopping method driven by the experimentally shaped laser fields. Our findings show that optimal laser fields drive low-frequency vibrational modes localized in the side chains of two biochromophores, thus selecting the parts of their potential energy surfaces characterized by different transition dipole moments leading to different ionization probabilities. The presented mechanism leads to selective fluorescence depletion which serves as a discrimination signal. Our findings offer a promising perspective for using optimally shaped laser pulses in bioanalytical applications by increasing the selectivity beyond the current capability.
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Affiliation(s)
- Jens Petersen
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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Lei Y, Suo B, Dou Y, Wang Y, Wen Z. New implementations of MRCI in semiempirical frameworks. J Comput Chem 2010; 31:1752-8. [DOI: 10.1002/jcc.21464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Comparison of algorithms for conical intersection optimisation using semiempirical methods. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0331-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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