1
|
Zima V, Gladwish O, Marek A, Tureček F. Nucleoside Cation Radicals: Generation, Radical-Induced Hydrogen Atom Migrations, and Ribose Ring Cleavage in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1594-1608. [PMID: 38842116 DOI: 10.1021/jasms.4c00198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Nucleoside ions that were furnished on ribose with a 2'-O-acetyl radical group were generated in the gas phase by multistep collision-induced dissociation of precursor ions tagged with radical initiator groups, and their chemistry was investigated in the gas phase. 2'-O-Acetyladenosine cation radicals were found to undergo hydrogen transfer to the acetoxyl radical from the ribose ring positions that were elucidated using specific deuterium labeling of 1'-H, 2'-H, and 4'-H and in the N-H and O-H exchangeable positions, favoring 4'-H transfer. Ion structures and transition-state energies were calculated by a combination of Born-Oppenheimer molecular dynamics and density functional theory and used to obtain unimolecular rate constants for competitive hydrogen transfer and loss of the acetoxyl radical. Migrations to the acetoxyl radical of ribose hydrogens 1'-H, 2'-H, 3'-H, and 4'-H were all exothermic, but product formation was kinetically controlled. Both Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations indicated preferential migration of 4'-H in a qualitative agreement with the deuterium labeling results. The hydrogen migrations displayed substantial isotope effects that along with quantum tunneling affected the relative rate constants and reaction branching ratios. UV-vis action spectroscopy indicated that the cation radicals from 2'-O-acetyladenosine consisted of a mixture of isomers. Radical-driven dissociations were also observed for protonated guanosine, cytosine, and thymidine conjugates. However, for those nucleoside ions and cation radicals, the dissociations were dominated by the loss of the nucleobase or formation of protonated nucleobase ions.
Collapse
Affiliation(s)
- Václav Zima
- Department of Chemistry, University of Washington, 351700 Bagley Hall, Seattle, Washington 98195-1700, United States
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Owen Gladwish
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, United States
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, 351700 Bagley Hall, Seattle, Washington 98195-1700, United States
| |
Collapse
|
2
|
Miao X, Diemer K, Mitrić R. A CASSCF/MRCI trajectory surface hopping simulation of the photochemical dynamics and the gas phase ultrafast electron diffraction patterns of cyclobutanone. J Chem Phys 2024; 160:124309. [PMID: 38526800 DOI: 10.1063/5.0197768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
We present the simulation of the photochemical dynamics of cyclobutanone induced by the excitation of the 3 s Rydberg state. For this purpose, we apply the complete active space self-consistent field method together with the spin-orbit multireference configuration interaction singles treatment, combined with the trajectory surface hopping for the inclusion of nonadiabatic effects. The simulations were performed in the spin-adiabatic representation, including nine electronic states derived from three singlet and two triplet spin-diabatic states. Our simulations reproduce the two previously observed primary dissociation channels: the C2 pathway yielding C2H4 + CH2CO and the C3 pathway producing c-C3H6 + CO. In addition, two secondary products, CH2 + CO from the C2 pathway and C3H6 from the C3 pathway, both of them previously reported, are also observed in our simulation. We determine the ratio of the C3:C2 products to be about 2.8. Our findings show that most of the trajectories reach their electronic ground state within 200 fs, with dissociation events finished after 300 fs. We also identify the minimum energy conical intersections that are responsible for the relaxation and provide an analysis of the photochemical reaction mechanism based on multidimensional scaling. Furthermore, we demonstrate a minimal impact of triplet states on the photodissociation mechanism within the observed timescale. In order to provide a direct link to experiments, we simulate the gas phase ultrafast electron diffraction patterns and connect their features to the underlying structural dynamics.
Collapse
Affiliation(s)
- Xincheng Miao
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany
| | - Kira Diemer
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany
| |
Collapse
|
3
|
Zima V, Marek A, Tureček F. Competitive Radical Migrations and Ribose Ring Cleavage in Adenosine and 2'-Deoxyadenosine Cation Radicals. J Phys Chem A 2024; 128:1109-1123. [PMID: 38316031 DOI: 10.1021/acs.jpca.3c07906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
We report a combined experimental and computational study of adenosine cation radicals that were protonated at adenine and furnished with a radical handle in the form of an acetoxyl radical, •CH2COO, that was attached to ribose 5'-O. Radicals were generated by collision-induced dissociation (CID) and characterized by tandem mass spectrometry and UV-vis photodissociation action spectroscopy. The acetoxyl radical was used to probe the kinetics of intramolecular hydrogen transfer from the ribose ring positions that were specifically labeled with deuterium at C1', C2', C3', C4', C5', and in the exchangeable hydroxyl groups. Hydrogen transfer was found to chiefly involve 3'-H with minor contributions by 5'-H and 2'-H, while 4'-H was nonreactive. The hydrogen transfer rates were affected by deuterium isotope effects. Hydrogen transfer triggered ribose ring cleavage by consecutive dissociations of the C4'-O and C1'-C2' bonds, resulting in expulsion of a C6H9O4 radical and forming a 9-formyladenine ion. Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations of unimolecular constants were carried out using the effective CCSD(T)/6-311++G(3d,2p) and M06-2X/aug-cc-pVTZ potential energy surfaces for major isomerizations and dissociations. The kinetic analysis showed that hydrogen transfer to the acetoxyl radical was the rate-determining step, whereas the following ring-opening reactions in ribose radicals were fast. Using DFT-computed energies, a comparison was made between the thermochemistry of radical reactions in adenosine and 2'-deoxyadenosine cation radicals. The 2'-deoxyribose ring showed lower TS energies for both the rate-determining 3'-H transfer and ring cleavage reactions.
Collapse
Affiliation(s)
- Václav Zima
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| |
Collapse
|
4
|
Wan J, Nytka M, Qian H, Vu K, Lemr K, Tureček F. Nitrile Imines as Peptide and Oligonucleotide Photo-Cross-Linkers in Gas-Phase Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:344-356. [PMID: 38252626 DOI: 10.1021/jasms.3c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Nitrile imines produced by photodissociation of 2,5-diaryltetrazoles undergo cross-linking reactions with amide groups in peptide-tetrazole (tet-peptide) conjugates and a tet-peptide-dinucleotide complex. Tetrazole photodissociation in gas-phase ions is efficient, achieving ca. 50% conversion with 2 laser pulses at 250 nm. The formation of cross-links was detected by CID-MS3 that showed structure-significant dissociations by loss of side-chain groups and internal peptide segments. The structure and composition of cross-linking products were established by a combination of UV-vis action spectroscopy and cyclic ion mobility mass spectrometry (c-IMS). The experimental absorption bands were found to match the bands calculated for vibronic absorption spectra of nitrile imines and cross-linked hydrazone isomers. The calculated collision cross sections (CCSth) for these ions were related to the matching experimental CCSexp from multipass c-IMS measurements. Loss of N2 from tet-peptide conjugates was calculated to be a mildly endothermic reaction with ΔH0 = 80 kJ mol-1 in the gas phase. The excess energy in the photolytically formed nitrile imine is thought to drive endothermic proton transfer, followed by exothermic cyclization to a sterically accessible peptide amide group. The exothermic nitrile imine reaction with peptide amides is promoted by proton transfer and may involve an initial [3 + 2] cycloaddition followed by cleavage of the oxadiazole intermediate. Nucleophilic groups, such as cysteine thiol, did not compete with the amide cyclization. Nitrile imine cross-linking to 2'-deoxycytidylguanosine was found to be >80% efficient and highly specific in targeting guanine. The further potential for exploring nitrile-imine cross-linking for biomolecular structure analysis is discussed.
Collapse
Affiliation(s)
- Jiahao Wan
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Marianna Nytka
- Department of Analytical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, Olomouc 779 00, Czech Republic
| | - Haocheng Qian
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Kim Vu
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Karel Lemr
- Department of Analytical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, Olomouc 779 00, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| |
Collapse
|
5
|
Zima V, Vlk M, Wan J, Cvačka J, Tureček F. Tracking Isomerizations of High-Energy Adenine Cation Radicals by UV-Vis Action Spectroscopy and Cyclic Ion Mobility Mass Spectrometry. J Phys Chem A 2023. [PMID: 37433135 DOI: 10.1021/acs.jpca.3c03179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
We report experimental and computational studies of protonated adenine C-8 σ-radicals that are presumed yet elusive reactive intermediates of oxidative damage to nucleic acids. The radicals were generated in the gas phase by the collision-induced dissociation of C-8-Br and C-8-I bonds in protonated 8-bromo- and 8-iodoadenine as well as by 8-bromo- and 8-iodo-9-methyladenine. Protonation by electrospray of 8-bromo- and 8-iodoadenine was shown by cyclic-ion mobility mass spectrometry (c-IMS) to form the N-1-H, N-9-H and N-3-H, N-7-H protomers in 85:15 and 81:19 ratios, respectively, in accordance with the equilibrium populations of these protomers in water-solvated ions that were calculated by density functional theory (DFT). Protonation of 8-halogenated 9-methyladenines yielded single N-1-H protomers, which was consistent with their thermodynamic stability. The radicals produced from the 8-bromo and 8-iodo adenine cations were characterized by UV-vis photodissociation action spectroscopy (UVPD) and c-IMS. UVPD revealed the formation of C-8 σ-radicals along with N-3-H, N-7-H-adenine π-radicals that arose as secondary products by hydrogen atom migrations. The isomers were identified by matching their action spectra against the calculated vibronic absorption spectra. Deuterium isotope effects were found to slow the isomerization and increase the population of C-8 σ-radicals. The adenine cation radicals were separated by c-IMS and identified by their collision cross sections, which were measured relative to the canonical N-9-H adenine cation radical that was cogenerated in situ as an internal standard. Ab initio CCSD(T)/CBS calculations of isomer energies showed that the adenine C-8 σ-radicals were local energy minima with relative energies at 76-79 kJ mol-1 above that of the canonical adenine cation radical. Rice-Ramsperger-Kassel-Marcus calculations of unimolecular rate constants for hydrogen and deuterium migrations resulting in exergonic isomerizations showed kinetic shifts of 10-17 kJ mol-1, stabilizing the C-8 σ-radicals. C-8 σ-radicals derived from N-1-protonated 9-methyladenine were also thermodynamically unstable and readily isomerized upon formation.
Collapse
Affiliation(s)
- Václav Zima
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Mikuláš Vlk
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Jiahao Wan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| |
Collapse
|
6
|
Gelin MF, Chen L, Domcke W. Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals. Chem Rev 2022; 122:17339-17396. [PMID: 36278801 DOI: 10.1021/acs.chemrev.2c00329] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Femtosecond nonlinear spectroscopy is the main tool for the time-resolved detection of photophysical and photochemical processes. Since most systems of chemical interest are rather complex, theoretical support is indispensable for the extraction of the intrinsic system dynamics from the detected spectroscopic responses. There exist two alternative theoretical formalisms for the calculation of spectroscopic signals, the nonlinear response-function (NRF) approach and the spectroscopic equation-of-motion (EOM) approach. In the NRF formalism, the system-field interaction is assumed to be sufficiently weak and is treated in lowest-order perturbation theory for each laser pulse interacting with the sample. The conceptual alternative to the NRF method is the extraction of the spectroscopic signals from the solutions of quantum mechanical, semiclassical, or quasiclassical EOMs which govern the time evolution of the material system interacting with the radiation field of the laser pulses. The NRF formalism and its applications to a broad range of material systems and spectroscopic signals have been comprehensively reviewed in the literature. This article provides a detailed review of the suite of EOM methods, including applications to 4-wave-mixing and N-wave-mixing signals detected with weak or strong fields. Under certain circumstances, the spectroscopic EOM methods may be more efficient than the NRF method for the computation of various nonlinear spectroscopic signals.
Collapse
Affiliation(s)
- Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Lipeng Chen
- Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching,Germany
| |
Collapse
|
7
|
Zima V, Liu Y, Tureček F. Radical Cascade Dissociation Pathways to Unusual Nucleobase Cation Radicals. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1038-1047. [PMID: 35536606 DOI: 10.1021/jasms.2c00098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We report unusual dissociations of protonated RNA nucleosides tagged with radical initiator groups at ribose 5'-O and furnished with a 2',3'-O-isopropylidene protecting group. The ions undergo collision-induced radical cascade dissociations starting at the radical initiator that break down the dioxolane ring and trigger the formation of nucleobase cations and cation radicals. The adenine cation radical that was formed by radical cascade dissociations was identified by MS5 UV-vis photodissociation action spectroscopy to be a higher-energy N-3-H tautomer of the canonical ionized nucleobase. The guanine cation radical was formed by radical cascade dissociations as the N-7-H tautomer. In contrast to adenosine and guanosine, radical cascade dissociations of the tagged ribocytidine ion produced protonated cytosine, whereas tagged ribothymidine showed yet different dissociations resulting in predominant thymine loss. Reaction mechanisms were suggested for the cascade dissociations that were based on Born-Oppenheimer molecular dynamics and density functional theory calculations that were used to map the relevant parts of the potential energy surfaces for adenosine, guanosine, and cytidine radical ions. The reported radical cascade dissociations represent a new, nonredox approach to nucleobase and nucleoside cation radicals that has the potential of being expanded to the generation of various oligonucleotide cation radicals.
Collapse
Affiliation(s)
- Václav Zima
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 981195-1700, United States
| | - Yue Liu
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 981195-1700, United States
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 981195-1700, United States
| |
Collapse
|
8
|
Xu C, Lin K, Hu D, Gu FL, Gelin MF, Lan Z. Ultrafast Internal Conversion Dynamics through the on-the-Fly Simulation of Transient Absorption Pump-Probe Spectra with Different Electronic Structure Methods. J Phys Chem Lett 2022; 13:661-668. [PMID: 35023755 DOI: 10.1021/acs.jpclett.1c03373] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An on-the-fly surface-hopping simulation protocol is developed for the evaluation of transient absorption (TA) pump-probe (PP) signals of molecular systems exhibiting internal conversion to the electronic ground state. We study the nonadiabatic dynamics of azomethane and the associating TA PP spectra at three levels of the electronic-structure theory, OM2/MRCI, SA-CASSCF, and XMS-CASPT2. The impact of these methods on the population dynamics and time-resolved TA PP signals is substantially different. This difference is attributed to the strong non-Condon effects that must be taken into account for the proper understanding and interpretation of time-resolved TA PP signals of nonadiabatic polyatomic systems. This shows that the combination of the dynamical and spectral simulations definitely provides more accurate and detailed information on the microscopic mechanisms of photophysical and photochemical processes. Hence the simulation of time-resolved spectroscopic signals provides another important dimension to examine the accuracy of quantum chemistry methods.
Collapse
Affiliation(s)
- Chao Xu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Kunni Lin
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Deping Hu
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou, 510006, P. R. China
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou, 310018, P. R. China
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou, 510006, P. R. China
| |
Collapse
|
9
|
Miyazaki M, Kamiya T, Wohlgemuth M, Chatterjee K, Mitrić R, Dopfer O, Fujii M. Real-time observation of photoionization-induced water migration dynamics in 4-methylformanilide-water by picosecond time-resolved infrared spectroscopy and ab initio molecular dynamics simulations. Phys Chem Chem Phys 2021; 24:73-85. [PMID: 34633007 DOI: 10.1039/d1cp03327a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A novel time-resolved pump-probe spectroscopic approach that enables to keep high resolution in both the time and energy domain, nanosecond excitation-picosecond ionization-picosecond infrared probe (ns-ps-ps TRIR) spectroscopy, has been applied to the trans-4-methylformanilide-water (4MetFA-W) cluster. Water migration dynamics from the CO to the NH binding site in a peptide linkage triggered by photoionization of 4MetFA-W is directly monitored by the ps time evolution of IR spectra, and the presence of an intermediate state is revealed. The time evolution is analyzed by rate equations based on a four-state model of the migration dynamics. Time constants for the initial to the intermediate and hot product and to the final product are obtained. The acceleration of the dynamics by methyl substitution and the strong contribution of intracluster vibrational energy redistribution in the termination of the solvation dynamics is suggested. This picture is well confirmed by the ab initio on-the-fly molecular dynamics simulations. Vibrational assignments of 4MetFA and 4MetFA-W in the neutral (S0 and S1) and ionic (D0) electronic states measured by ns IR dip and electron-impact IR photodissociation spectroscopy are also discussed prior to the results of time-resolved spectroscopy.
Collapse
Affiliation(s)
- Mitsuhiko Miyazaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan. .,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Tairiku Kamiya
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Matthias Wohlgemuth
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany.
| | - Kuntal Chatterjee
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany.
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany. .,World Research Hub Initiatives, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-15, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan.,World Research Hub Initiatives, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-15, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
| |
Collapse
|
10
|
Hu D, Peng J, Chen L, Gelin MF, Lan Z. Spectral Fingerprint of Excited-State Energy Transfer in Dendrimers through Polarization-Sensitive Transient-Absorption Pump-Probe Signals: On-the-Fly Nonadiabatic Dynamics Simulations. J Phys Chem Lett 2021; 12:9710-9719. [PMID: 34590858 DOI: 10.1021/acs.jpclett.1c02640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The time-resolved polarization-sensitive transient-absorption (TA) pump-probe (PP) spectra are simulated using on-the-fly surface-hopping nonadiabatic dynamics and the doorway-window representation of nonlinear spectroscopy. A dendrimer model system composed of two linear phenylene ethynylene units (2-ring and 3-ring) is taken as an example. The ground-state bleach (GSB), stimulated emission (SE), and excited-state absorption (ESA) contributions as well as the total TA PP signals are obtained and carefully analyzed. It is shown that intramolecular excited-state energy transfer from the 2-ring unit to the 3-ring unit can be conveniently identified by employing pump and probe pulses with different polarizations. Our results demonstrate that time-resolved polarization-sensitive TA PP signals provide a powerful tool for the elucidation of excited-state energy-transfer pathways, notably in molecular systems possessing several optically bright nonadiabatically coupled electronic states with different orientations of transition dipole moments.
Collapse
Affiliation(s)
- Deping Hu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Jiawei Peng
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Lipeng Chen
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Zhenggang Lan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| |
Collapse
|
11
|
Hoche J, Flock M, Miao X, Philipp LN, Wenzel M, Fischer I, Mitric R. Excimer formation dynamics in the isolated tetracene dimer. Chem Sci 2021; 12:11965-11975. [PMID: 34667562 PMCID: PMC8457379 DOI: 10.1039/d1sc03214c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/01/2021] [Indexed: 12/20/2022] Open
Abstract
The understanding of excimer formation and its interplay with the singlet-correlated triplet pair state 1(TT) is of high significance for the development of efficient organic electronics. Here, we study the photoinduced dynamics of the tetracene dimer in the gas phase by time-resolved photoionisation and photoion imaging experiments as well as nonadiabatic dynamics simulations in order to obtain mechanistic insight into the excimer formation dynamics. The experiments are performed using a picosecond laser system for excitation into the S2 state and reveal a biexponential time dependence. The time constants, obtained as a function of excess energy, lie in the range between ≈10 ps and 100 ps and are assigned to the relaxation of the excimer on the S1 surface and to its deactivation to the ground state. Simulations of the quantum-classical photodynamics are carried out in the frame of the semi-empirical CISD and TD-lc-DFTB methods. Both theoretical approaches reveal a dominating relaxation pathway that is characterised by the formation of a perfectly stacked excimer. TD-lc-DFTB simulations have also uncovered a second relaxation channel into a less stable dimer conformation in the S1 state. Both methods have consistently shown that the electronic and geometric relaxation to the excimer state is completed in less than 10 ps. The inclusion of doubly excited states in the CISD dynamics and their diabatisation further allowed to observe a transient population of the 1(TT) state, which, however, gets depopulated on a timescale of 8 ps, leading finally to the trapping in the excimer minimum. The understanding of excimer formation and its interplay with the singlet-correlated triplet pair state 1(TT) is of high significance for the development of efficient organic electronics.![]()
Collapse
Affiliation(s)
- Joscha Hoche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Marco Flock
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Xincheng Miao
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Luca Nils Philipp
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Michael Wenzel
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Ingo Fischer
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Roland Mitric
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| |
Collapse
|
12
|
Piteša T, Sapunar M, Ponzi A, Gelin MF, Došlić N, Domcke W, Decleva P. Combined Surface-Hopping, Dyson Orbital, and B-Spline Approach for the Computation of Time-Resolved Photoelectron Spectroscopy Signals: The Internal Conversion in Pyrazine. J Chem Theory Comput 2021; 17:5098-5109. [PMID: 34269561 DOI: 10.1021/acs.jctc.1c00396] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A computational protocol for simulating time-resolved photoelectron signals of medium-sized molecules is presented. The procedure is based on a trajectory surface-hopping description of the excited-state dynamics and a combined Dyson orbital and multicenter B-spline approach for the computation of cross sections and asymmetry parameters. The accuracy of the procedure has been illustrated for the case of ultrafast internal conversion of gas-phase pyrazine excited to the 1B2u(ππ*) state. The simulated spectra and the asymmetry map are compared to the experimental data, and a very good agreement was obtained without applying any energy-dependent rescaling or broadening. An interesting side result of this work is the finding that the signature of the 1Au(nπ*) state is indistinguishable from that of the 1B3u(nπ*) state in the time-resolved photoelectron spectrum. By locating four symmetrically equivalent minima on the lowest-excited (S1) adiabatic potential energy surface of pyrazine, we revealed the strong vibronic coupling of the 1Au(nπ*) and 1B3u(nπ*) states near the S1 ← S0 band origin.
Collapse
Affiliation(s)
- Tomislav Piteša
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Marin Sapunar
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Aurora Ponzi
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Piero Decleva
- Dipartimento di Scienze Chimiche, Università di Trieste, I-34127 Trieste, Italy
| |
Collapse
|
13
|
Liu Y, Ma C, Leonen CJA, Chatterjee C, Nováková G, Marek A, Tureček F. Tackling a Curious Case: Generation of Charge-Tagged Guanosine Radicals by Gas-Phase Electron Transfer and Their Characterization by UV-vis Photodissociation Action Spectroscopy and Theory. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:772-785. [PMID: 33567214 PMCID: PMC8579407 DOI: 10.1021/jasms.0c00459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We report the generation of gas-phase riboguanosine radicals that were tagged at ribose with a fixed-charge 6-(trimethylammonium)hexane-1-aminocarbonyl group. The radical generation relied on electron transfer from fluoranthene anion to noncovalent dibenzocrown-ether dication complexes which formed nucleoside cation radicals upon one-electron reduction and crown-ether ligand loss. The cation radicals were characterized by collision-induced dissociation (CID), photodissociation (UVPD), and UV-vis action spectroscopy. Identification of charge-tagged guanosine radicals was challenging because of spontaneous dissociations by loss of a hydrogen atom and guanine that occurred upon storing the ions in the ion trap without further excitation. The loss of H proceeded from an exchangeable position on N-7 in guanine that was established by deuterium labeling and was the lowest energy dissociation of the guanosine radicals according to transition-state energy calculations. Rate constant measurements revealed an inverse isotope effect on the loss of either hydrogen or deuterium with rate constants kH = 0.25-0.26 s-1 and kD = 0.39-0.54 s-1. We used time-dependent density functional theory calculations, including thermal vibronic effects, to predict the absorption spectra of several protomeric radical isomers. The calculated spectra of low-energy N-7-H guanine-radical tautomers closely matched the action spectra. Transition-state-theory calculations of the rate constants for the loss of H-7 and guanine agreed with the experimental rate constants for a narrow range of ion effective temperatures. Our calculations suggest that the observed inverse isotope effect does not arise from the isotope-dependent differences in the transition-state energies. Instead, it may be caused by the dynamics of post-transition-state complexes preceding the product separation.
Collapse
Affiliation(s)
- Yue Liu
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Congcong Ma
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Calvin J A Leonen
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Champak Chatterjee
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | | |
Collapse
|
14
|
Huang SR, Tureček F. Cation Radicals of Hachimoji Nucleobases P and Z: Generation in the Gas Phase and Characterization by UV-Vis Photodissociation Action Spectroscopy and Theory. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:373-386. [PMID: 33206519 DOI: 10.1021/jasms.0c00381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report the generation of gas-phase cation radicals of unusual nucleobases 5-aza-7-deazaguanine (P) and 6-amino-5-nitro-(1H)pyrid-2-one (Z) that have been used as building blocks of base-expanded (hachimoji) DNA. The cation radicals were generated by collision-induced intramolecular electron transfer and dissociation of ternary copper-terpyridine complexes. The cation radicals were characterized by deuterium labeling and tandem mass spectrometry including MS3 collision-induced dissociation, UV-vis photodissociation, and action spectroscopy. Vibronic absorption UV-vis spectra were calculated by time-dependent density functional theory (TD-DFT) and compared with the action spectra to unequivocally assign the most closely matching structures for the gas-phase cation radicals. Ab initio calculations up to the coupled clusters-complete basis set (CCSD(T)/CBS) level of theory were used to rank by energy the P and Z neutral molecules and cation-radical isomers and provided transition-state and dissociation energies. The 5-aza-7-deazaguanine cation radicals were determined to have the canonical N-1-H, 6-oxo structure (P1+•) that was the global energy minimum within this group of isomers. The Z cation radicals were found to have the 1H-pyrid-2-one structure (Z1+•). The formation of P1+• and Z1+• was shown to be controlled by the solution thermodynamics of the Cu-terpyridine complexes and the kinetics of their dissociations. We also report and compare CCSD(T)/CBS-calculated adiabatic recombination energies of cation radicals for the entire hachimoji set of eight nucleobases, P+• (7.92 eV), Z+• (8.51 eV), S+• (8.51 eV), B+• (7.76 eV), T+• (8.98 eV), C+• (8.62 eV), A+• (8.32 eV), and G+• (7.97 eV), to assess the thermodynamics of base-to-base electron transfer following random ionization.
Collapse
Affiliation(s)
- Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| |
Collapse
|
15
|
Huang SR, Nováková G, Marek A, Tureček F. The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2′-Deoxyadenosine. J Phys Chem A 2020; 125:338-348. [DOI: 10.1021/acs.jpca.0c10293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| |
Collapse
|
16
|
Titov E, Humeniuk A, Mitrić R. Comparison of moving and fixed basis sets for nonadiabatic quantum dynamics at conical intersections. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
17
|
Zobel JP, Nogueira JJ, González L. Finite-temperature Wigner phase-space sampling and temperature effects on the excited-state dynamics of 2-nitronaphthalene. Phys Chem Chem Phys 2019; 21:13906-13915. [DOI: 10.1039/c8cp03273d] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The concept of finite temperature Wigner phase-space sampling allowing the population of vibrationally excited states is introduced and employed to study temperature effects on the absorption spectrum of 2-nitronaphtalene (2NN) and its relaxation dynamics.
Collapse
Affiliation(s)
- J. Patrick Zobel
- Institute of Theoretical Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - Juan J. Nogueira
- Institute of Theoretical Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - Leticia González
- Institute of Theoretical Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| |
Collapse
|
18
|
Shahi A, McCaslin L, Albeck Y, Continetti RE, Gerber RB, Strasser D. Double Photodetachment of F -·H 2O: Experimental and Theoretical Studies of [F·H 2O] . J Phys Chem Lett 2018; 9:6808-6813. [PMID: 30433784 DOI: 10.1021/acs.jpclett.8b02562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Double photodetachment of the cluster F-·H2O in a strong laser field is explored in a combined experimental-theoretical study. Products are observed experimentally by coincidence photofragment imaging following double ionization by intense laser pulses. Theoretically, equation of motion coupled cluster calculations (EOM-CC), suitable for modeling strong correlation effects in the electronic wave function, shed light on the Franck-Condon region, and ab initio molecular dynamics simulations also performed using EOM-CC methods reveal the fragmentation dynamics in time on the lowest-lying singlet and triplet states of [F·H2O]+. The simulations show the formation of H2O+ + F, which is the predominant experimentally observed product channel. Suggestions are proposed for the formation mechanisms of the minor products, for example, the very interesting H2F+, which involves significant geometrical rearrangement. Analysis of the results suggests interesting future directions for the exploration of photodetachment of anionic clusters in an intense laser field.
Collapse
Affiliation(s)
- Abhishek Shahi
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Laura McCaslin
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Yishai Albeck
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Robert E Continetti
- Department of Chemistry and Biochemistry , University of California San Diego , La Jolla , California 92093-0340 , United States
| | - R Benny Gerber
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
- Department of Chemistry , University of California , Irvine , California 92697 , United States
| | - Daniel Strasser
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| |
Collapse
|
19
|
Zobel JP, Heindl M, Nogueira JJ, González L. Vibrational Sampling and Solvent Effects on the Electronic Structure of the Absorption Spectrum of 2-Nitronaphthalene. J Chem Theory Comput 2018; 14:3205-3217. [PMID: 29694042 DOI: 10.1021/acs.jctc.8b00198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The influence of vibrational motion on electronic excited state properties is investigated for the organic chromophore 2-nitronaphtalene in methanol. Specifically, the performance of two vibrational sampling techniques - Wigner sampling and sampling from an ab initio molecular dynamics trajectory- is assessed, in combination with implicit and explicit solvent models. The effects of the different sampling/solvent combinations on the energy and electronic character of the absorption bands are analyzed in terms of charge transfer and exciton size, computed from the electronic transition density. The absorption spectra obtained using sampling techniques and its underlying properties are compared to those of the electronic excited states calculated at the Franck-Condon equilibrium geometry. It is found that the absorption bands of the vibrational ensembles are red-shifted compared to the Franck-Condon bright states, and this red-shift scales with the displacement from the equilibrium geometry. Such displacements are found larger and better described when using ensembles from the harmonic Wigner distribution than snapshots from the molecular dynamics trajectory. Particularly relevant is the torsional motion of the nitro group that quenches the charge transfer character of some of the absorption bands. This motion, however, is better described in the molecular dynamics trajectory. Thus, none of the vibrational sampling approaches can satisfactorily capture all important aspects of the nuclear motion. The inclusion of solvent also red-shifts the absorption bands with respect to the gas phase. This red-shift scales with the charge-transfer character of the bands and is found larger for the implicit than for the explicit solvent model. The advantages and drawbacks of the different sampling and solvent models are discussed to guide future research on the calculation of UV-vis spectra of nitroaromatic compounds.
Collapse
Affiliation(s)
- J Patrick Zobel
- Institute of Theoretical Chemistry, Faculty of Chemistry , University of Vienna , Währinger Straße 17 , A-1090 Vienna , Austria
| | - Moritz Heindl
- Institute of Theoretical Chemistry, Faculty of Chemistry , University of Vienna , Währinger Straße 17 , A-1090 Vienna , Austria
| | - Juan J Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry , University of Vienna , Währinger Straße 17 , A-1090 Vienna , Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry , University of Vienna , Währinger Straße 17 , A-1090 Vienna , Austria
| |
Collapse
|
20
|
Jena P, Sun Q. Super Atomic Clusters: Design Rules and Potential for Building Blocks of Materials. Chem Rev 2018; 118:5755-5870. [DOI: 10.1021/acs.chemrev.7b00524] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Puru Jena
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284-2000, United States
| | - Qiang Sun
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284-2000, United States
| |
Collapse
|
21
|
Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
| |
Collapse
|
22
|
Fedunov RG, Plotnikova AV, Ivanov AI, Vauthey E. Simulations of the Ultrafast Transient Absorption Dynamics of a Donor–Acceptor Biaryl in Solution. J Phys Chem A 2017; 121:471-481. [DOI: 10.1021/acs.jpca.6b11581] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roman G. Fedunov
- Volgograd State University, University
Avenue 100, Volgograd 400062, Russia
| | | | - Anatoly I. Ivanov
- Volgograd State University, University
Avenue 100, Volgograd 400062, Russia
| | - Eric Vauthey
- Department
of Physical Chemistry, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| |
Collapse
|
23
|
Wohlgemuth M, Miyazaki M, Tsukada K, Weiler M, Dopfer O, Fujii M, Mitrić R. Deciphering environment effects in peptide bond solvation dynamics by experiment and theory. Phys Chem Chem Phys 2017; 19:22564-22572. [DOI: 10.1039/c7cp03992a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Probing solvation dynamics at the molecular level: different water migration pathways around a peptide bond.
Collapse
Affiliation(s)
- Matthias Wohlgemuth
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
| | - Mitsuhiko Miyazaki
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Kohei Tsukada
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Martin Weiler
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
| |
Collapse
|
24
|
Du L, Lan Z. An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications. J Chem Theory Comput 2016; 11:1360-74. [PMID: 26574348 DOI: 10.1021/ct501106d] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).
Collapse
Affiliation(s)
- Likai Du
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101 Shandong, People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China.,The Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101 Shandong, People's Republic of China
| | - Zhenggang Lan
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101 Shandong, People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China.,The Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101 Shandong, People's Republic of China
| |
Collapse
|
25
|
Albert J, Kaiser D, Engel V. Communication: Adiabatic and non-adiabatic electron-nuclear motion: Quantum and classical dynamics. J Chem Phys 2016; 144:171103. [DOI: 10.1063/1.4948777] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Julian Albert
- Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Emil-Fischer-Str. 42, Campus Nord, 97074 Würzburg, Germany
| | - Dustin Kaiser
- Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Emil-Fischer-Str. 42, Campus Nord, 97074 Würzburg, Germany
| | - Volker Engel
- Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Emil-Fischer-Str. 42, Campus Nord, 97074 Würzburg, Germany
| |
Collapse
|
26
|
Dopfer O, Fujii M. Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level. Chem Rev 2016; 116:5432-63. [DOI: 10.1021/acs.chemrev.5b00610] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Otto Dopfer
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Masaaki Fujii
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| |
Collapse
|
27
|
Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 332] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
Collapse
Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
| |
Collapse
|
28
|
Fedunov RG, Plotnikova AV, Ionkin VN, Ivanov AI. Dynamics of ground state absorption spectra in donor-acceptor pairs with ultrafast charge recombination. J Phys Chem A 2015; 119:1964-72. [PMID: 25686470 DOI: 10.1021/acs.jpca.5b00725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A theoretical approach to simulation of the transient spectra in molecular systems with ultrafast photoinduced nonradiative electronic transitions is developed. The evolution of the excited and ground state populations as well as the nonradiative transitions between them are calculated in the framework of the stochastic multichannel point-transition model involving the reorganization of the medium and the intramolecular high frequency vibrational modes. Simulations of transient spectra of donor-acceptor pairs excited in the charge-transfer band that are accompanied by ultrafast charge recombination into the ground state demonstrate a possibility of positive band appearance in the transient absorption spectrum caused by those systems in the ground state, which returned there from the excited state. The region of the parameters of the donor-acceptor systems where a positive ground state absorption signal can be observed is discussed. A qualitative comparison of the simulated transient spectra with the experimental data on betaine-30 is presented.
Collapse
Affiliation(s)
- Roman G Fedunov
- Volgograd State University , University Avenue 100, Volgograd 400062, Russia
| | | | | | | |
Collapse
|
29
|
Wohlgemuth M, Miyazaki M, Weiler M, Sakai M, Dopfer O, Fujii M, Mitrić R. Aufklärung der Solvatationsdynamik eines einzelnen Wassermoleküls durch Infrarotspektroskopie: Theorie und Experiment. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
30
|
Wohlgemuth M, Miyazaki M, Weiler M, Sakai M, Dopfer O, Fujii M, Mitrić R. Solvation Dynamics of a Single Water Molecule Probed by Infrared Spectra-Theory Meets Experiment. Angew Chem Int Ed Engl 2014; 53:14601-4. [DOI: 10.1002/anie.201409047] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Indexed: 11/09/2022]
|
31
|
Plasser F, Crespo-Otero R, Pederzoli M, Pittner J, Lischka H, Barbatti M. Surface Hopping Dynamics with Correlated Single-Reference Methods: 9H-Adenine as a Case Study. J Chem Theory Comput 2014; 10:1395-405. [PMID: 26580359 DOI: 10.1021/ct4011079] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface hopping dynamics methods using the coupled cluster to approximated second order (CC2), the algebraic diagrammatic construction scheme to second order (ADC(2)), and the time-dependent density functional theory (TDDFT) were developed and implemented into the program system Newton-X. These procedures are especially well-suited to simulate nonadiabatic processes involving various excited states of the same multiplicity and the dynamics in the first excited state toward an energetic minimum or up to the region where a crossing with the ground state is found. 9H-adenine in the gas phase was selected as the test case. The results showed that dynamics with ADC(2) is very stable, whereas CC2 dynamics fails within 100 fs, because of numerical instabilities present in the case of quasi-degenerate excited states. ADC(2) dynamics correctly predicts the ultrafast character of the deactivation process. It predicts that C2-puckered conical intersections should be the preferential pathway for internal conversion for low-energy excitation. C6-puckered conical intersection also contributes appreciably to internal conversion, becoming as important as C2-puckered for high-energy excitations. In any case, H-elimination plays only a minor role. TDDFT based on a long-range corrected functional fails to predict the ultrafast deactivation. In the comparison with several other methods previously used for dynamics simulations of adenine, ADC(2) has the best performance, providing the most consistent results so far.
Collapse
Affiliation(s)
- Felix Plasser
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls-University , Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Rachel Crespo-Otero
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Marek Pederzoli
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Jiri Pittner
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Hans Lischka
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States.,Institute for Theoretical Chemistry, University of Vienna , Währingerstr. 17, A-1090 Vienna, Austria
| | - Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
32
|
Krčmář J, Gelin MF, Domcke W. Calculation of third-order signals via driven Schrödinger equations: General results and application to electronic 2D photon echo spectroscopy. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
33
|
Arasaki Y, Takatsuka K. Pulse-Train Photoelectron Spectroscopy of Electronic and Nuclear Dynamics in Molecules. Chemphyschem 2013; 14:1387-96. [DOI: 10.1002/cphc.201201094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/06/2013] [Indexed: 11/06/2022]
|
34
|
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
|
35
|
Schmidt BE, Gause O, Hagemann F, Li S, Unrau W, Wöste L, Siebert T. Optimal white light control of the negative to neutral to positive charge transition (NeNePo) in the electronic manifold of the silver trimer. J Phys Chem A 2012; 116:11459-66. [PMID: 22954161 DOI: 10.1021/jp307197w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Control over the electronic state of the Ag(3) cluster is approached via a progression of ultrafast photoinduced transitions within the full electronic manifold of the negative to the neutral and finally the cationic state of the system. High-bandwidth supercontinuum laser pulses ranging from 500 to 950 nm are employed for addressing the wide range of electronic resonance conditions associated with the ladder climbing process of a tandem photoelectron detachment and a resonance enhanced multiphoton ionization (REMPI). With the control of the phase over the full spectral envelope of the supercontinuum in a pulse shaper arrangement, pulse forms are generated with the aim of synchronizing ultrashort subpulse sequences to the characteristic dynamics of the system during charge reversal. Pulse forms ranging over several hundred femtoseconds in total duration and subpulse structures down to 15 fs duration with a variable spectral composition can be obtained for this purpose. A free optimization based on a closed-loop genetic algorithm is employed for ordering the subpulse sequences to match the structural evolution of the system. The effective control attainable in this scenario is evaluated in view of maintaining a defined sequence of electronic transitions within the complex dynamic response of the system during the photoexcitation. Further emphasis is made on analyzing the degree of control attainable in the nonlinear regime of multiphoton excitation at supercontinuum bandwidths.
Collapse
Affiliation(s)
- B E Schmidt
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | | | | | | | | | | |
Collapse
|
36
|
von den Hoff P, Thallmair S, Kowalewski M, Siemering R, de Vivie-Riedle R. Optimal control theory--closing the gap between theory and experiment. Phys Chem Chem Phys 2012; 14:14460-85. [PMID: 23019574 DOI: 10.1039/c2cp41838j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Optimal control theory and optimal control experiments are state-of-the-art tools to control quantum systems. Both methods have been demonstrated successfully for numerous applications in molecular physics, chemistry and biology. Modulated light pulses could be realized, driving these various control processes. Next to the control efficiency, a key issue is the understanding of the control mechanism. An obvious way is to seek support from theory. However, the underlying search strategies in theory and experiment towards the optimal laser field differ. While the optimal control theory operates in the time domain, optimal control experiments optimize the laser fields in the frequency domain. This also implies that both search procedures experience a different bias and follow different pathways on the search landscape. In this perspective we review our recent developments in optimal control theory and their applications. Especially, we focus on approaches, which close the gap between theory and experiment. To this extent we followed two ways. One uses sophisticated optimization algorithms, which enhance the capabilities of optimal control experiments. The other is to extend and modify the optimal control theory formalism in order to mimic the experimental conditions.
Collapse
Affiliation(s)
- Philipp von den Hoff
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | | | | | | | | |
Collapse
|
37
|
Wu R, Zhang J, Li C, Long G, Tarn T. Control problems in quantum systems. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-012-5193-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
38
|
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]
|
39
|
Klaumünzer B, Kröner D, Lischka H, Saalfrank P. Non-adiabatic excited state dynamics of riboflavin after photoexcitation. Phys Chem Chem Phys 2012; 14:8693-702. [DOI: 10.1039/c2cp40978j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
40
|
Yonehara T, Hanasaki K, Takatsuka K. Fundamental Approaches to Nonadiabaticity: Toward a Chemical Theory beyond the Born–Oppenheimer Paradigm. Chem Rev 2011; 112:499-542. [DOI: 10.1021/cr200096s] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takehiro Yonehara
- Department of Basic Sciences, Graduate School of Arts and Sciences, The University of Tokyo Komaba, 153-8902 Tokyo, Japan
| | - Kota Hanasaki
- Department of Basic Sciences, Graduate School of Arts and Sciences, The University of Tokyo Komaba, 153-8902 Tokyo, Japan
| | - Kazuo Takatsuka
- Department of Basic Sciences, Graduate School of Arts and Sciences, The University of Tokyo Komaba, 153-8902 Tokyo, Japan
| |
Collapse
|
41
|
Schäfer-Bung B, Hartmann C, Schmidt B, Schütte C. Dimension reduction by balanced truncation: Application to light-induced control of open quantum systems. J Chem Phys 2011; 135:014112. [DOI: 10.1063/1.3605243] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
|
42
|
Mitrić R, Petersen J, Wohlgemuth M, Werner U, Bonačić-Koutecký V. Field-induced surface hopping method for probing transition state nonadiabatic dynamics of Ag3. Phys Chem Chem Phys 2011; 13:8690-6. [PMID: 21483897 DOI: 10.1039/c0cp02935a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We present the simulation of time-resolved photoelectron spectra of Ag(3) involving excitation from the linear transition state, where nonadiabatic relaxation takes place in a complex manifold of electronic states. Thus, we address ultrafast processes reachable by negative ion-to neutral-to positive ion (NeNePo) spectroscopy starting from the linear Ag anionic species. For this purpose we use our newly developed field-induced surface hopping method (FISH) augmented for the description of photoionization processes. Furthermore we employ our method for nonadiabatic molecular dynamics "on the fly" in the framework of time-dependent density functional theory generalized for open shell systems. Our presented approach is generally applicable for the prediction of time-resolved photoelectron spectra and their analysis in systems with complex electronic structure as well as many nuclear degrees freedom. This theoretical development should serve to stimulate new ultrafast experiments.
Collapse
Affiliation(s)
- Roland Mitrić
- Freie Universität Berlin, Fachbereich Physik, Arnimallee 14, D-14195 Berlin, Germany.
| | | | | | | | | |
Collapse
|
43
|
Fuji T, Suzuki YI, Horio T, Suzuki T, Mitrić R, Werner U, Bonačić-Koutecký V. Ultrafast photodynamics of furan. J Chem Phys 2011; 133:234303. [PMID: 21186867 DOI: 10.1063/1.3518441] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ultrafast photodynamics of furan has been studied by time-resolved photoelectron imaging (TRPEI) spectroscopy with an unprecedented time resolution of 22 fs. The simulation of the time-dependent photoelectron kinetic energy distribution (PKED) has been performed with ab initio nonadiabatic dynamics "on the fly" in the frame of time-dependent density functional theory. Based on the agreement between experimental and theoretical time-dependent photoelectron signal intensity as well as on PKED, precise time scales of ultrafast internal conversion from S(2) over S(1) to the ground state S(0) of furan have been revealed for the first time. Upon initial excitation of the S(2) state which has π-π* character, a nonadiabatic transition to the S(1) state occurs within 10 fs. Subsequent dynamics invokes the excitation of the C-O stretching and C-O-C out of plane vibrations which lead to the internal conversion to the ground state after 60 fs. Thus, we demonstrate that the TRPEI combined with high level nonadiabatic dynamics calculations provide fundamental insight into ultrafast photodynamics of chemically and biologically relevant chromophores.
Collapse
Affiliation(s)
- Takao Fuji
- Chemical Dynamics Laboratory, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama, 351-0198, Japan
| | | | | | | | | | | | | |
Collapse
|
44
|
Gelin MF, Egorova D, Domcke W. Optical N-wave-mixing spectroscopy with strong and temporally well-separated pulses: the doorway-window representation. J Phys Chem B 2011; 115:5648-58. [PMID: 21425818 DOI: 10.1021/jp112055h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have extended the doorway-window representation of optical pump-probe spectroscopy with weak pulses toward N-wave-mixing spectroscopy with temporally well-separated pulses of arbitrary strength. The expressions for the signals in the strong-pulse doorway-window representation are derived in the framework of the nonperturbative theory of N-wave-mixing spectroscopy. The strong-pulse doorway-window representation is complementary to the equation-of-motion phase-matching approach. The latter fully accounts for pulse-overlap effects in signals induced by weak pulses but is computationally more expensive. The performance of the doorway-window approximation for temporally well-separated strong pulses is illustrated for an electronic two-level system with an underdamped Condon-active vibrational mode.
Collapse
Affiliation(s)
- Maxim F Gelin
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | | | | |
Collapse
|
45
|
Schneider J, Wollenhaupt M, Winzenburg A, Bayer T, Köhler J, Faust R, Baumert T. Efficient and robust strong-field control of population transfer in sensitizer dyes with designed femtosecond laser pulses. Phys Chem Chem Phys 2011; 13:8733-46. [DOI: 10.1039/c0cp02723e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
46
|
Wollenhaupt M, Baumert T. Ultrafast laser control of electron dynamics in atoms, molecules and solids. Faraday Discuss 2011; 153:9-26; discussion 73-91. [DOI: 10.1039/c1fd00109d] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
47
|
Mitrić R, Petersen J, Wohlgemuth M, Werner U, Bonačić-Koutecký V, Wöste L, Jortner J. Time-Resolved Femtosecond Photoelectron Spectroscopy by Field-Induced Surface Hopping. J Phys Chem A 2010; 115:3755-65. [DOI: 10.1021/jp106355n] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roland Mitrić
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany,
| | - Jens Petersen
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Matthias Wohlgemuth
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Ute Werner
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Vlasta Bonačić-Koutecký
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
- Interdisciplinary Center for Advanced Science and Technology, University of Split, Meštrovićevo Šetalište bb., HR-21000 Split, Croatia
| | - Ludger Wöste
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany,
| | - Joshua Jortner
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
48
|
Vazdar M, Eckert-Maksić M, Barbatti M, Lischka H. Excited-state non-adiabatic dynamics simulations of pyrrole. Mol Phys 2010. [DOI: 10.1080/00268970802665639] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
49
|
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.
Collapse
Affiliation(s)
- Jens Petersen
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | | | | | | | | | | |
Collapse
|
50
|
Kondorskiy A, Nanbu S, Teranishi Y, Nakamura H. Control of Chemical Dynamics by Lasers: Theoretical Considerations. J Phys Chem A 2010; 114:6171-87. [DOI: 10.1021/jp911579h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexey Kondorskiy
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8585, Japan
| | - Shinkoh Nanbu
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8585, Japan
| | - Yoshiaki Teranishi
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8585, Japan
| | - Hiroki Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8585, Japan
| |
Collapse
|