Article
Chemistry, Physical
Natsumi Orimo, Yo-ichi Yamamoto, Shutaro Karashima, Alexie Boyer, Toshinori Suzuki
Summary: Ultrafast extreme ultraviolet photoelectron spectroscopy was conducted on 6methyluracil (6mUra) and 5-fluorouracil (5FUra) in the gas phase, and on 6mUra and 5fluorouridine in an aqueous environment. In the gas phase, internal conversion (IC) from 1 pi pi* to 1n pi* states occurs in tens of femtoseconds, followed by intersystem crossing to the 3 pi pi* state in several picoseconds. In an aqueous solution, 6mUra undergoes IC almost exclusively to the ground state (S0) in about 100 fs, which is similar to unsubstituted uracil but faster than thymine (5-methyluracil). The different dynamics for C5 and C6 methylation suggest that IC from 1 pi pi* to S0 is facilitated by the out-of-plane (OOP) motion of the C5 substituent. The slow IC for C5-substituted molecules in an aqueous environment is due to the required solvent reorganization for this OOP motion to occur. The slow rate for 5FUrd may be attributed to an increased barrier height caused by C5 fluorination.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Huajing Song, Yeonsig Nam, Daniel Keefer, Marco Garavelli, Shaul Mukamel, Sergei Tretiak
Summary: In this study, nonadiabatic and adiabatic molecular dynamics simulations were used to investigate the transition-state dynamics of photoexcited cyclooctatetraene (COT). The simulations revealed an active excited to ground state relaxation pathway and a double-bond shifting mechanism, with results in good agreement with experimental data. These findings provide valuable insights into the photochemistry of COT and lay a foundation for further research on bond-order inversion and photoswitching processes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Bartlomiej Sadowski, Marzena Kaliszewska, Yevgen M. Poronik, Malgorzata Czichy, Patryk Janasik, Marzena Banasiewicz, Dominik Mierzwa, Wojciech Gadomski, Trevor D. Lohrey, John A. Clark, Mieczyslaw Lapkowski, Boleslaw Kozankiewicz, Valentine Vullev, Andrzej L. Sobolewski, Piotr Piatkowski, Daniel T. Gryko
Summary: Nitroaromatics typically do not fluoresce, but by strategically placing nitro groups farther from the core, researchers have achieved some of the highest fluorescence quantum yields ever recorded for nitroaromatics. This strategy, however, may lead to alternative mechanisms for fluorescence quenching involving transitions to dark n pi* singlet states and aborted photochemistry, highlighting the importance of understanding the excited-state dynamics of such compounds for designing highly fluorescent electron-deficient conjugates.
Article
Multidisciplinary Sciences
Rocio Borrego-Varillas, Artur Nenov, Piotr Kabacinski, Irene Conti, Lucia Ganzer, Aurelio Oriana, Vishal Kumar Jaiswal, Ines Delfino, Oliver Weingart, Cristian Manzoni, Ivan Rivalta, Marco Garavelli, Giulio Cerullo
Summary: Researchers have found that 5-methyluridine has a lifespan an order of magnitude longer than uridine due to solvent reorganization needed for bulky methyl group motion. The photophysical mechanism by which nucleosides dissipate energy after UV light irradiation remains a topic of debate.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Cecilia Vera, Mauro N. Gallucci, Juliana Marioni, Marcelo C. Sosa Morales, Debora M. Martino, Susana Nunez Montoya, Claudio D. Borsarelli
Summary: The antimicrobial photodynamic activity (aPDA) of supramolecular adducts formed between anionic photosensitizer (PS) Rose Bengal (RB2-) and aromatic polycations derived from (p-vinylbenzyl)triethylammonium chloride was evaluated on fungal and bacterial strains. The results showed that the aPDA varied depending on the microorganism, indicating the importance of specific interactions between the cell wall structures and the PSs. The study demonstrated the potential of supramolecular chemistry to obtain targeted aPDA based on the microbe and PS properties.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Julia Westermayr, Michael Gastegger, Dora Voros, Lisa Panzenboeck, Florian Joerg, Leticia Gonzalez, Philipp Marquetand
Summary: This study utilizes a deep neural network-based method to investigate the excited-state dynamics of tyrosine, revealing unconventional dynamics and the potential for photodamage. The findings provide new insights into the photostability and photodamage of biological systems.
Article
Multidisciplinary Sciences
Valeriu Scutelnic, Shota Tsuru, Matyas Papai, Zheyue Yang, Michael Epshtein, Tian Xue, Eric Haugen, Yuki Kobayashi, Anna Krylov, Klaus B. Moller, Sonia Coriani, Stephen R. Leone
Summary: This study reports on the photoinduced dynamics of pyrazine, revealing the participation of an experimentally unobserved optically dark state. The dark state is populated shortly after electronic excitation and plays a key role in the relaxation of pyrazine to the ground state.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Wenhan Guo, Zibin Liang, Yanqun Tang, Kunting Cai, Tianjie Qiu, Yingxiao Wu, Kexin Zhang, Song Gao, Ruqiang Zou
Summary: Transition metal nitrides (TMNs) show promising electrocatalytic performance in the nitrogen reduction reaction, but their deactivation process may involve either structural collapse of the catalyst leading to lattice nitrogen leaching and metal dissolution, or ammonia poisoning caused by the accumulation and strong bonding of ammonia produced on the surface.
JOURNAL OF MATERIALS CHEMISTRY A
(2021)
Article
Chemistry, Multidisciplinary
Demi D. Snabilie, Eva J. Meeus, Roel F. J. Epping, Zhiyuan He, Minghui Zhou, Bas de Bruin
Summary: Transition metal radical-type carbene transfer catalysis is a sustainable and atom-efficient method for C-C bond formation. Understanding off-cycle and deactivation pathways can lead to solutions for avoiding catalyst deactivation and reveal novel reactivity for new applications, stimulating further development of radical-type carbene transfer reactions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Physical
Brandon L. Foley, Blake A. Johnson, Aditya Bhan
Summary: Formaldehyde, formed during methanol-to-hydrocarbon conversion, reacts with organic species causing catalyst deactivation. Olefins may react with formaldehyde in nondeactivating pathways, while aromatics and dienes lead to deactivation. Dienes have a higher propensity for deactivation via formaldehyde-mediated reactions, indicating their critical role in catalyst deactivation in MTH conversion.
Article
Chemistry, Inorganic & Nuclear
Nikita A. Shekhovtsov, Elena B. Nikolaenkova, Sofya N. Vorobyova, Victor F. Plyusnin, Katerina A. Vinogradova, Taisiya S. Sukhikh, Alexsei Ya. Tikhonov, Mark B. Bushuev
Summary: The rational design of ESIPT-capable metal complexes necessitates the spatial separation of an ESIPT site and a metal binding site within the ligand core. Ligands with such sites can bind metal ions without undergoing deprotonation upon coordination. This study presents a new ESIPT-capable ligand, HLb, based on 1-hydroxy-1H-imidazole, and a series of ESIPT-capable zinc(ii) halido complexes, [Zn(HLb)X-2] (X = Cl, Br, I), which show enhanced photoluminescence properties compared to the free HLb ligand.
DALTON TRANSACTIONS
(2023)
Article
Chemistry, Physical
Reza Omidyan, Leila Shahrokh, Abigail L. Whittock, Vasilios G. Stavros
Summary: Different levels of quantum computational models were used to investigate the photophysics and photostability of a mycosporine system, mycosporine glycine (MyG). Molecular mechanics approach and comprehensive studies on electronic excited states were conducted, revealing the transfer of population between different states and ultrafast deactivation mechanisms.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Multidisciplinary Sciences
Anushka Nagpal, Dinesh Dhankhar, Thomas C. Cesario, Runze Li, Jie Chen, Peter M. Rentzepis
Summary: The study investigated the effects of UV irradiation on thymine solutions using various spectroscopic methods, showing that thymine dimer formation and (6-4) photoproduct formation increase with radiation dose. Spectroscopic data revealed the mechanism of thymine dimer formation, which is known to inhibit DNA replication and cause bacterial inactivation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Zhuohao Xie, Peng Li, Haonan Zhan, Liuyan Zhuang, Sijian Tao, Liehua Deng, Jiahao Huang
Summary: An allosterically modulated G-quadruplex-integrated aptamer is designed for efficient and accurate detection of melamine in dairy products. The method is label-free, turn-on, low-cost, and time-efficient, with high specificity and a low detection limit. This approach can be easily manipulated and provides ultra-sensitive detection, making it useful in the field of food safety, biomedical engineering, and clinical diagnosis.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Physical
Aleksei N. Marianov, Alena S. Kochubei, Tanglaw Roman, Oliver J. Conquest, Catherine Stampfl, Yijiao Jiang
Summary: This study investigates the stability mechanism of Co porphyrin-based catalysts during CO2 reduction and identifies the main reasons for gradual activity loss, providing insights into improving catalyst stability.
Article
Chemistry, Physical
Josene M. Toldo, Mariana T. do Casal, Mario Barbatti
Summary: Sinapoyl malate (SM) derivatives have shown promise as a new class of UVA filters, with efficient photoprotective sunscreen properties similar to those observed in plants. Combining experimental and computational results, coumaryl Meldrum (CMe) and sinapoyl Meldrum (SMe) have been identified as outstanding candidates for UVA filters in sunscreen formulations. Excited-state dynamics simulations revealed a two-step logistic decay mechanism, with minor differences between CMe and SMe associated with an additional minimum present only in the latter.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Mario Barbatti
Summary: The microcanonical temperature of an isolated molecule is derived using Boltzmann and Gibbs volume entropies within the quantum harmonic vibrational and equivalent degenerated model approximations. The study examines the effects of entropy functional choice and various approximations. The difference between Boltzmann and Gibbs volume temperatures is negligible for larger molecules but significant for smaller systems, providing an opportunity for experimental exploration. An analytical expression of temperature as a function of vibrational energy is provided, allowing predictions accurate within a 3% margin of error compared to exact harmonic estimation. The microcanonical temperature is discussed and exemplified using polycyclic aromatic hydrocarbon molecules and other molecules of astrophysical interest.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Saikat Mukherjee, Max Pinheiro Jr, Baptiste Demoulin, Mario Barbatti
Summary: This paper explores the challenges and methodologies of nonadiabatic dynamics simulations in computational photochemistry on long timescales (beyond 10 ps), including the computational costs of electronic structure calculations, stability of integration methods, accuracy of nonadiabatic dynamics algorithms, and software optimization. Machine learning is shown to play a crucial role in long timescale dynamics, either as a surrogate for electronic structure calculations or in aiding the parameterization of model Hamiltonians. Conventional methods for integrating classical equations are found to be suitable for extended simulations up to 1 ns, and surface hopping is observed to agree semiquantitatively with wave packet propagation in the weak-coupling regime.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Chemistry, Physical
Saikat Mukherjee, Mario Barbatti
Summary: The problem of zero-point energy leakage in classical trajectory calculations can be prevented by using the LP-ZPE method, which pumps back leaked energy into corresponding vibrational modes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Ritam Mansour, Josene M. Toldo, Mario Barbatti
Summary: Hydrogen bonds can shorten the excited-state lifetime of adenosine, but internal conversion is mainly influenced by electron-driven proton transfer.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Gabriel Braun, Itamar Borges Jr, Adelia J. A. Aquino, Hans Lischka, Felix Plasser, Silmar A. do Monte, Elizete Ventura, Saikat Mukherjee, Mario Barbatti
Summary: This study simulated the fluorescence of pyrene using two different theoretical approaches and confirmed that the prominent band shoulder observed after a high-energy electronic excitation is due to emission from the second-excited state (S-2). The non-Kasha behavior is a dynamic-equilibrium effect and not caused by a metastable S-2 minimum.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Mario Barbatti, Mattia Bondanza, Rachel Crespo-Otero, Baptiste Demoulin, Pavlo O. Dral, Giovanni Granucci, Fabris Kossoski, Hans Lischka, Benedetta Mennucci, Saikat Mukherjee, Marek Pederzoli, Maurizio Persico, Max Pinheiro, Jiri Pittner, Felix Plasser, Eduarda Sangiogo Gil, Ljiljana Stojanovic
Summary: Newton-X is an open-source computational platform that implements nonadiabatic molecular dynamics based on surface hopping and spectrum simulations. It describes the main features of these methods and highlights the latest developments. These methods are widely used in computational chemistry for photo-physical and photochemical investigations, making them of great importance for understanding molecular dynamics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Mattia Bondanza, Baptiste Demoulin, Filippo Lipparini, Mario Barbatti, Benedetta Mennucci
Summary: This article presents an implementation of trajectory surface-hopping nonadiabatic dynamics for a polarizable embed-ding QM/MM formulation and verifies its feasibility through testing.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Multidisciplinary
Temitope T. Abiola, Josene M. Toldo, Mariana T. do Casal, Amandine L. Flourat, Benjamin Rioux, Jack M. Woolley, Daniel Murdock, Florent Allais, Mario Barbatti, Vasilios G. Stavros
Summary: Research suggests that the photoisomerization process of sinapate esters may be more complex than previously thought. By tracking the formation of the isomers in real time, researchers have found that photoinduced internal conversion occurs at multiple points along the potential energy surface.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Saikat Mukherjee, Mario Barbatti
Summary: This article discusses the phenomenon of ultrafast internal conversion that can occur between electronic states without energetically accessible conical intersections. The study uses a simple analytical model to correlate the instantaneous probability to the lifetime.
RESULTS IN CHEMISTRY
(2022)
Article
Chemistry, Physical
Mariana T. do Casal, Josene M. Toldo, Felix Plasser, Mario Barbatti
Summary: By using computational chemistry, this study explains the fluorescence quenching of DPP-thiophene dimer and characterizes its doubly excited state wavefunction. The results show that the low-lying doubly excited state delays fluorescence and allows internal conversion to occur first. The analysis provides core conceptual information on the electronic properties of organic chromophores, offering new ways to control the balance between luminescence and internal conversion.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Daniel W. Polak, Mariana T. do Casal, Josene M. Toldo, Xiantao Hu, Giordano Amoruso, Olivia Pomeranc, Martin Heeney, Mario Barbatti, Michael N. R. Ashfold, Thomas A. A. Oliver
Summary: This study explores the photophysics of three prototypical TDPP molecules using ultrafast transient absorption technique, revealing that their photophysical properties are mainly determined by two excited states with different electronic characters and energy ordering, and the timescales for internal conversion between these states. The study also finds significant variations in the fluorescence quantum yields of TDPP molecules, which are attributed to differences in their electronic structures.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Ritam Mansour, Saikat Mukherjee, Max Pinheiro, Jennifer A. Noble, Christophe Jouvet, Mario Barbatti
Summary: Experimental work shows that the lifetime of the S-3 state of protonated 7-azaindole is about ten times longer than that of protonated 6-azaindole. Simulations reveal that both isomers have different nonradiative decay pathways from S-3 to S-1.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Elizete Ventura, Silmar Andrade do Monte, Mariana T. do Casal, Max Pinheiro, Josene Maria Toldo, Mario Barbatti
Summary: In this work, the ab initio nonadiabatic dynamics of cytosine in different solvents were simulated, and the heating and cooling times were analyzed using an analytical energy-transfer model. The results showed that cytosine heats up in a subpicosecond timescale and cools down fastest in water solvent.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Jessica B. Martins, Carlos E. de Moura, Gildas Goldsztejn, Oksana Travnikova, Renaud Guillemin, Iyas Ismail, Loic Journel, Dimitrios Koulentianos, Mario Barbatti, Alexsandre F. Lago, Denis Ceolin, Maria Luiza M. Rocco, Ralph Puettner, Maria Novella Piancastelli, Marc Simon, Tatiana Marchenko
Summary: In this study, a novel approach using resonant Auger spectroscopy was proposed to indirectly probe conjugation and hyperconjugation in core-excited molecules. The changes in the electronic structure of thiophene and thiazole during resonant sulfur K-shell excitation and Auger decay were found to affect the stabilisation energy from pi-conjugation and hyperconjugation, as manifested in the resonant S KL2,3L2,3 Auger spectra. High-level quantum-mechanical calculations and natural bond orbital analysis were used to interpret the experimental observations, which were further validated through comparisons with the saturated analogue thiolane.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
