Review
Chemistry, Physical
Tim J. Zuehlsdorff, Sapana V. Shedge, Shao-Yu Lu, Hanbo Hong, Vincent P. Aguirre, Liang Shi, Christine M. Isborn
Summary: Including both environmental and vibronic effects is crucial for accurate simulation of optical spectra. Two approaches are outlined in the study, one based on static snapshots of chromophore-environment configurations and the other on dynamic excitation energies for time-correlated snapshots. Both approaches show significant potential for advancing accurate optical spectroscopy simulations of complex condensed phase systems.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 72
(2021)
Article
Biochemistry & Molecular Biology
Shuxian Li, Yan Zhao, Yuechun Jiao, Jianming Zhao, Changyong Li, Suotang Jia
Summary: In this study, the vibrational features of 2-fluorobenzonitrile and 3-fluorobenzonitrile in their excited and cationic ground states were investigated using two-color resonance two photon ionization and mass analyzed threshold ionization spectroscopy. The stable structures and vibrational frequencies in different states were calculated using density functional theory, and the theoretical results were in good agreement with the experimental data. The findings of this research provide valuable insights into the physicochemical properties of fluorinated organic compounds.
Article
Chemistry, Physical
Theo Cavignac, Stephane Jobic, Camille Latouche
Summary: In this study, a methodology based on constrained density functional theory and vibrational mode computations is presented to simulate and interpret the luminescence spectra of periodic solids. By combining electronic and vibrational contributions, an overall vibrationally resolved emission spectrum is accurately reproduced for Ti-doped BaZrO3, allowing for an unambiguous assignment of the observed luminescence to a Ti3+ + O- -> Ti4+ + O2- charge transfer.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Rami Gherib, Scott N. Genin, Ilya G. Ryabinkin
Summary: This paper discusses two difficulties associated with the computations of thermal vibrational correlation functions, one being the lack of a well-behaved expression valid at both high temperature and T→0K limits, and the other being the multivaluedness of the vibrational correlation function. The author resolves the first difficulty by jointly considering the partition function and the propagator in the harmonic approximation, and proposes a phase tracking procedure to ensure continuity of the correlation function and recover the correct spectra. The findings are supported by simulating the UV-vis absorption spectra of pentacene at 4K and benzene at 298K, both showing good agreement with experimental results.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Michael H. Palmer, Marcello Coreno, Monica de Simone, Cesare Grazioli, Nykola C. Jones, Soren Vronning Hoffmann, R. Alan Aitken
Summary: A new synchrotron-based photoionization spectrum of 6,6-dimethylfulvene reveals significant vibrational fine structure (VFS) that was successfully analyzed using Franck-Condon (FC) methods. The order of ionic states in the range of 7 to 19 eV was determined through symmetry adapted cluster configuration interaction and density functional methods, particularly employing the long-range corrected version of the Becke three-parameter hybrid functional (B3LYP) with the Coulomb-attenuating method (CAM-B3LYP). Both methods provide reliable theoretical values for calculated vertical and adiabatic ionization energies. The FC profile for the lowest ionization energy (IE1, X(2)A(2)) exhibits extensive VFS, while the second ionization energy (A(2)B(1)) shows truncated structure due to overlap with IE1.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Samer Gozem, Anna I. Krylov
Summary: A molecule's spectrum serves as a unique fingerprint encoding information about its structure and electronic properties, acting as a molecular ID. Quantum chemistry calculations play a crucial role in interpreting spectra, but modeling the spectra often requires additional steps considering electronic and nuclear degrees of freedom and experimental specifics. The ezSpectra suite, comprising ezFCF and ezDyson, offers tools for calculating Franck-Condon factors and absolute cross-sections for various processes.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Chemistry, Physical
Christian Henrichs, Malte Reineke, Marie-Luise Hebestreit, Michael Schmitt
Summary: The changes in the structure of 4-cyanoindole upon electronic excitation were determined through a combined Franck-Condon method and rotational constants fitting. These geometry changes were fitted to simultaneously reproduce the intensities of 72 lines in the fluorescence emission spectra, obtained through excitation of six different vibronic bands in the first excited singlet state, along with the three rotational constants obtained from rotationally resolved electronic spectra.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Multidisciplinary
Omer Faruk Bicer, Rana Lomlu, Fatmagul Katmer, Sefik Suzer
Summary: In this study, the vibrational fine structure observed in the He-IUV photoelectron spectra of H-2 and N-2 molecules was examined and compared with calculations of Franck-Condon factors (FCFs). It was found that the FCFs of vibrational excited molecules may deviate from those of the ground states. It is suggested to construct the vibrational wave functions numerically using programs such as Excel, Origin, or Python to verify the normalization and orthogonality of the wave functions.
JOURNAL OF CHEMICAL EDUCATION
(2023)
Article
Chemistry, Physical
Sapana V. Shedge, Tim J. Zuehlsdorff, Ajay Khanna, Stacey Conley, Christine M. Isborn
Summary: This research focuses on simulating the linear and nonlinear spectra of chromophores in condensed phase systems, combining various methods to overcome challenges in capturing vibronic transitions and specific chromophore-environment interactions. Three approaches of different computational costs are presented for simulating linear spectra, with two analogous approaches for nonlinear spectra. Results include simulated absorption spectra and two-dimensional electronic spectra for the Nile red chromophore in different solvent environments.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Boutheina Ben Abdelaziz, Nazir Mustapha, Idriss M. Bedja, Osamah Aldaghri, Hajo Idriss, Moez Ibrahem, Khalid H. Ibnaouf
Summary: This study examines the impact of zinc oxide nanoparticles (ZnO NPs) on the spectrum features of MDMO-PPV. Different techniques were used to assess the characteristics of MDMO-PPV and doped ZnO NP samples. The addition of ZnO NPs resulted in significant changes in the UV-Vis and PL spectra, including shifts in absorption bands and improvements in spectral profiles.
Article
Spectroscopy
Qin Yang, Marco Fuse, Julien Bloino, Vincenzo Barone
Summary: Chiroptical spectra are effective techniques for studying the electronic states of chiral systems, but their interpretation requires accurate computational models that consider stereo-electronic and vibrational effects. This contribution focuses on the latest developments in computational methods rooted in density functional theory for describing stereo-electronic effects in organometallic systems. Additionally, chiral iridium complexes are highlighted as a suitable case study for investigating bright phosphorescence and tuning properties for applications such as OLEDs and biomarkers.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Chemistry, Physical
Christian Henrichs, Marie-Luise Hebestreit, Daniel Krugler, Michael Schmitt
Summary: The geometry changes of two rotamers of 1,3-dimethoxybenzene were determined by fitting line intensities in fluorescence emission spectra and the changes of rotational constants upon electronic excitation. These changes were compared to results of CC2 calculations and found to be in agreement with excitation to an L-1(b)-state for the C-2v symmetric B-conformer.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Physical
Daniel Aranda, Francisco Garcia-Gonzalez, Francisco Jose Avila Ferrer, Isabel Lopez-Tocon, Juan Soto, Juan Carlos Otero
Summary: This study presents a computational model for electrochemical surface-enhanced Raman scattering (EC-SERS) and validates its applicability through experiments. The results demonstrate the importance of explicitly considering the surface charges in EC-SERS models, and highlight the ability of EC-SERS to study excited-state coupling by manipulating the electrode potential.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Ali Abou Taka, Shao-Yu Lu, Duncan Gowland, Tim J. Zuehlsdorff, Hector H. Corzo, Aurora Pribram-Jones, Liang Shi, Hrant P. Hratchian, Christine M. Isborn
Summary: The simulation of optical spectra is essential but traditional methods may lead to state mixings and inaccurate description. In this study, an alternative method using self-consistent field and maximum overlap model is proposed, which produces spectra more aligned with vertical gradient and molecular dynamics. The study warns against using excited-state adiabatic Hessian in simulation and showcases three alternatives.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Sung Man Park, Yu Ran Lee, Chan Ho Kwon
Summary: This study investigates the conformational structures and dynamics of Pivaldehyde using IR-resonant VUV-MATI mass spectroscopy. The results show that the global minima of Pivaldehyde exist only in the eclipsed conformation in both the neutral and cationic states. The correspondence between the measured vibrational spectra and the S-0 state gauche conformer is revealed. Additionally, analysis confirms that most peaks in the VUV-MATI spectrum are attributed to the ionic transitions between the neutral gauche and cationic eclipsed conformers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Jaya Mehara, Adarsh Koovakattil Surendran, Teun van Wieringen, Deeksha Setia, Cina Foroutan-Nejad, Michal Straka, Lubomir Rulisek, Jana Roithova
Summary: Gold(II) complexes are not commonly used in catalyzing chemical transformations due to their easy oxidation or reduction to more stable gold(III) or gold(I) complexes. In this study, we investigated the thermodynamics, stability, and spectral properties of [Au-II(L)(X)](+) complexes (L=ligand, X=halogen) in the gas phase. It was found that bidentate and tridentate ligands with nitrogen donor atoms are the best choices for stabilizing gaseous [Au-II(L)(X)](+) complexes. Quantum chemical calculations revealed that the molecular and electronic structures, as well as the spectroscopic properties, of the investigated gold(II) complexes are similar to those of stable copper(II) complexes.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Biochemical Research Methods
Guilherme L. Tripodi, Jana Roithova
Summary: This study investigates the application of ArIO as an oxidant for FeII species, revealing its oxidation mechanism and reaction properties, providing theoretical guidance for the design and synthesis of related reactions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Physical
Juraj Jasik, Stanislav Valtera, Mykhailo Vaidulych, Muntaseer Bunian, Yu Lei, Avik Halder, Hana Tarabkova, Martin Jindra, Ladislav Kavan, Otakar Frank, Stephan Bartling, Stefan Vajda
Summary: The effects of composition and support on the catalytic activity and selectivity in the oxidative dehydrogenation of cyclohexene were investigated. The study found that ultra-nanocrystalline diamond supported clusters were highly active and mainly produced benzene, while some mixed clusters produced cyclohexadiene. TiO2-supported tetramers solely produced benzene without any combustion to CO2. The selectivity of zirconia-supported mixed CuPd clusters and monometallic Cu cluster differed significantly, with the former producing significant fractions of cyclohexadiene.
FARADAY DISCUSSIONS
(2023)
Article
Chemistry, Inorganic & Nuclear
Rob Bakker, Abhinav Bairagi, Monica Rodriguez, Guilherme L. Tripodi, Aleksandr Y. Pereverzev, Jana Roithova
Summary: Cobalt(III)peroxo complexes were studied to investigate the effect of hydrogen bonding on the O2 binding energy and the O-O bond activation. The results showed that hydrogen bonding stabilized the cobalt(III)peroxo core by 10-20 kJ mol-1. The introduction of the first amino group had the largest stabilization effect, while additional amino groups did not significantly change the results. The amino group could transfer a hydrogen atom to the peroxo ligands, leading to O-O bond cleavage with thermodynamic favorability but entropic disfavorability.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Yujeong Lee, Guilherme L. Tripodi, Donghyun Jeong, Sunggi Lee, Jana Roithova, Jaeheung Cho
Summary: A high-valent manganese(IV)-hydroxo complex was synthesized and characterized in this study. It was found that this complex can activate C-H bonds of aliphatic and aromatic compounds under mild conditions. Detailed kinetic studies revealed that the activation of C-H bonds occurs via rate-determining hydrogen atom abstraction and electron-transfer pathway.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Organic
Marek Martinek, Lucie Ludvikova, Maria Srankova, Rafael Navratil, Lucie Muchova, Jiri Huzlik, Libor Vitek, Petr Klan, Peter Sebej
Summary: Fluorescein, eosin Y, and rose bengal, commonly used dyes in clinical medicine, have been found to release carbon monoxide (CO) and low-mass secondary photoproducts when extensively irradiated with visible light in aqueous solutions. This photochemistry should be taken into consideration in their applications and they could also be used as visible-light activatable CO-releasing molecules with biological implications.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Chemistry, Physical
Monica Rodriguez, Aleksandr Y. Pereverzev, Jana Roithova
Summary: A novel octahedral non-heme iron-acyl-nitrenoid complex was presented, and its reactivity was studied using a flow chemistry setup with online mass spectrometry detection. It was found that the iron-acyl-nitrenoid complex can activate C-H bonds via hydrogen-atom transfer and form new N-S bonds in the reaction with thiophenol. However, the reaction with hydrocarbons results in the activation of C-H bonds without a subsequent rebound process.
Article
Chemistry, Multidisciplinary
Erik Andris, Michal Straka, Jan Vrana, Ales Ruliska, Jana Roithova, Lubomir Rulisek
Summary: Gold(I) centers can form moderately strong (Au...H) hydrogen bonds with tertiary ammonium groups, but similar hydrogen bonding interactions with isoelectronic silver(I) or copper(I) centers are unknown. The replacement of Cl with Br or I in 3AuCl(+) had only a small effect on the Au...H bond strength. Experimental and computational results showed that the Ag...H and Cu...H interactions were only marginal in the complexes studied, while a Cl...H hydrogen bond was formed. However, when less flexible ligands were used, the presence of Ag...H and Cu...H hydrogen bonds with similar strength to the Au...H bond in 3AuCl(+) was predicted.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Jaya Mehara, Jana Roithova
Summary: Copper(II) complexes with N-oxyl reagents like TEMPO can selectively oxidize alcohols to aldehydes or ketones. Intermediate copper complexes were theoretically studied but never experimentally detected. This study presents an analysis of frozen intermediates containing alcohols lacking α-hydrogen atoms, preventing oxidation.
ISRAEL JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Physical
Aleksandr Y. Pereverzev, Corentin Rossi, Jana Roithova
Summary: The search for chemical structures responsible for diffuse interstellar bands remains a major challenge in astrochemistry, requiring experimental verification of structures obtained under laboratory conditions. In this study, we demonstrate the isomerization of the doubly charged polyaromatic hydrocarbon phenanthrene obtained through electron ionization. Our results show that the phenanthrene dication has a broad visible spectrum, making it unsuitable for diffuse interstellar band search. We also observe the isomerization of phenanthrene dication during the ionization process, leading to the detection of another C14H102+ isomer.
Article
Chemistry, Physical
Sreekanta Debnath, Alexander Schaefer, Karolina A. Haupa, Dmitry Strelnikov, Jana Roithova, Juraj Jasik, Sergei Lebedkin, Manfred M. Kappes
Summary: Helium tagging photodissociation action spectroscopy and laser-induced fluorescence spectroscopy in neon matrix were used to study the photophysics of electrosprayed rhodamine B cation at low temperatures. The experiments were conducted using He-TAG apparatus for helium tagging and Depo-II machine for LIF measurements. The resulting electronic spectra provide benchmarks for theoretical description of this organic dye.
Article
Chemistry, Physical
Shashikant A. Kadam, Stefania Sandoval, Zdenek Bastl, Karolina Simkovicova, Libor Kvitek, Juraj Jasik, Joanna Elzbieta Olszowka, Stanislav Valtera, Mykhailo Vaidulych, Jaroslava Moravkova, Petr Sazama, David Kubicka, Arnaud Travert, Jeroen A. van Bokhoven, Alessandro Fortunelli, Armin Kleibert, Martin Kalbac, Stefan Vajda
Summary: In this study, the cyclohexane oxidative dehydrogenation (ODH) catalyzed by cobalt ferrite nanoparticles supported on reduced graphene oxide (RGO) was investigated. The active sites responsible for full and partial dehydrogenation were identified using advanced spectroscopic techniques and kinetic analysis. The study revealed the cooperativity between different sites and the role of the support in controlling the abundance of undesired active sites.
Article
Chemistry, Multidisciplinary
Kananat Naksomboon, Enrique Gomez-Bengoa, Jaya Mehara, Jana Roithova, Edwin Otten, M. Angeles Fernandez-Ibanez
Summary: Pd-catalyzed C-H functionalization reactions of non-directed substrates have emerged as a promising alternative to the use of directing groups. A new type of S,O-ligand has been found to be highly efficient in promoting Pd-catalyzed C-H olefination reactions of non-directed arenes, although its role in the process was unclear. Through various mechanistic tools, it was discovered that C-H activation is the rate-determining step and the S,O-ligand triggers the formation of more reactive Pd cationic species, explaining the observed acceleration of the reaction. These findings provide important insights into the role of the S,O-ligand in promoting Pd-catalyzed C-H functionalization reactions.
Article
Chemistry, Multidisciplinary
Pieter J. Gilissen, Quentin Duez, Guilherme L. Tripodi, Magda M. J. Dekker, Jiangkun Ouyang, Kais Dhbaibi, Nicolas Vanthuyne, Jeanne Crassous, Jana Roithova, Johannes A. A. W. Elemans, Roeland J. M. Nolte
Summary: The kinetic enantio-recognition of chiral viologen guests by planar-chiral porphyrin cage compounds is determined by the planar chirality of the host and influenced by its size, but not the chirality of its substituents.
CHEMICAL COMMUNICATIONS
(2023)
