Article
Chemistry, Physical
Deependra Jadoun, Markus Kowalewski
Summary: Conical Intersections (CIs) are common in molecular and biological systems, opening up ultrafast nonradiative decay channels. While photoelectron spectroscopy with femtosecond pulses can resolve the involved electronic states in the energy domain, observing the created electronic coherence in the time domain requires probe pulses with larger bandwidth.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Jie Peng, Xin He, Yao Li, Jianxin Guan, Baihua Wu, Xinmao Li, Zhihao Yu, Jian Liu, Junrong Zheng
Summary: Understanding the mechanisms of aggregation-induced emission (AIE) is crucial for the design of better AIE-gens. Diphenylethylene (DPE) featured molecules, with their propeller structure, are important AIE-gens. Through ultrafast UV/IR spectroscopy and theoretical calculations, three representative DPE-featured AIE-gens, triphenylethylene, cis-stilbene, and trans-stilbene, were investigated. The results suggest that crossing conical intersections (CIs) with flexible structural evolutions in solutions reduces fluorescence, while crossing CIs is restricted in solids, leading to no fast nonradiative decay competing with spontaneous emission.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Issaka Seidu, Simon P. Neville, Ryan J. MacDonell, Michael S. Schuurman
Summary: Time-resolved X-ray absorption spectroscopy is a powerful tool for probing coupled electronic-nuclear dynamics in photo-excited molecules. Using the example of 1,3-butadiene, it has been demonstrated that TRXAS has the potential to resolve competing channels in excited-state non-adiabatic dynamics, offering insight into different electronic structures associated with passage through multiple conical intersections.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Juliana Cuellar-Zuquin, Ana Julieta Pepino, Ignacio Fdez Galvan, Ivan Rivalta, Francesco Aquilante, Marco Garavelli, Roland Lindh, Javier Segarra-Marti
Summary: We characterized the photochemically relevant conical intersections between different DNA/RNA nucleobases using CASSCF algorithms. Our results show that the size of the active space significantly affects the conical intersection topographies, while the basis set size seems to have a minor effect. We ruled out structural changes as a key factor and highlighted the importance of accurately describing the electronic states involved in these intersections.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Daniel Keefer, Jeremy R. Rouxel, Flavia Aleotti, Francesco Segatta, Marco Garavelli, Shaul Mukamel
Summary: Research demonstrates that using a resonant infrared field at conical intersections can enhance coherence features of photoisomerization reactions and bring signals of conical intersections above the detection threshold.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Nanoscience & Nanotechnology
Antonietta De Sio, Ephraim Sommer, Xuan Trung Nguyen, Lynn Gross, Dusko Popovic, Benjamin Tyler Nebgen, Sebastian Fernandez-Alberti, Stefano Pittalis, Carlo Andrea Rozzi, Elisa Molinari, Elena Mena-Osteritz, Peter Baeuerle, Thomas Frauenheim, Sergei Tretiak, Christoph Lienau
Summary: The study reveals the presence of intermolecular conical intersections in molecular aggregates relevant for photovoltaics using ultrafast two-dimensional electronic spectroscopy. The coherent motion of a vibrational wave packet between different states can be observed in a very short timescale.
NATURE NANOTECHNOLOGY
(2021)
Article
Chemistry, Physical
Xiao Liu, Alexander Humeniuk, William J. Glover
Summary: A common strategy for exploring complex systems is to use QM/MM embedding, but popular QM/MM-Pol approaches have issues. This paper presents a solution to these issues with the QM/MM-IEDRF method and demonstrates its effectiveness by studying the conical intersection of photoisomerization.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Materials Science, Multidisciplinary
Luke J. Wirth, Christopher Woodward, Amir A. Farajian
Summary: Advances in first principles methods are used to study the atom-vacancy exchanges near a screw dislocation in fcc Ni, revealing direction-dependent free energy profiles and temperature-dependent correlation effects. The dynamic approach shows intra-cell energy profile asymmetry related to dynamic geometry rearrangements. Despite absolute values of rate constants being similar, the HTST method generally underestimates rates by a factor of 2-5, partially explaining discrepancies between theoretical works and experiments in pipe diffusion diffusivities.
Article
Chemistry, Physical
Max D. J. Waters, Wenpeng Du, Andres Moreno Carrascosa, Brian Stankus, Martina Cacciarini, Peter M. Weber, Theis Solling
Summary: Excited-state chemistry lacks generalized symmetry rules, making it difficult to build up chemical intuition for excited states. Molecular symmetry plays a crucial role in preserving vibrational coherence during electronic state transitions, with even transient symmetrical structures capable of achieving this coherence. This finding adds a new dimension to how symmetry influences electronic transitions and selection rules for excited-state processes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
J. Patrick Zobel, Anna M. Wernbacher, Leticia Gonzalez
Summary: The mechanism of reverse intersystem crossing (rISC) in metal-based TADF emitters is still not clear, as the small singlet/triplet energy gaps necessary for thermal rISC in donor-acceptor systems with charge-transfer excited states have spin-orbit couplings that are too small for effective rISC. In this study, the first nonadiabatic dynamics simulation of rISC process in a carbene-copper(I)-carbazolyl TADF emitter is reported. Efficient rISC on a picosecond time scale is demonstrated, involving an intermediate higher-lying triplet state of metal-to-ligand charge transfer character ((MLCT)-M-3) that enables large spin-orbit couplings with the lowest singlet charge transfer state. The mechanism is completed in the S-1 state where the complex can return to a co-planar coordination geometry with high fluorescence efficiency.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Csaba Fabri, Gabor J. Halasz, Agnes Vibok
Summary: The interaction between a molecule and the quantized electromagnetic field of a nanocavity can create light-induced conical intersections between polaritonic potential energy surfaces. By using time-resolved ultrafast radiative emission of the cavity, we can observe the nuclear wavepacket dynamics and nonadiabatic population transfer between polaritonic surfaces without a probe pulse, providing a clear dynamical fingerprint of light-induced conical intersections.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Shahaf Asban, Daniel Keefer, Vladimir Y. Chernyak, Shaul Mukamel
Summary: Consolidation of ultrafast optics in electron spectroscopies based on free electron energy exchange with matter has matured significantly over the past two decades. Here, we propose a technique for monitoring electronic and nuclear molecular dynamics that is based on self-heterodyne coherent beating of a broadband pulse rather than incoherent population transport by a narrowband pulse.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Solana Di Pino, Yamila A. Peerez A. Sirkin, Uriel N. Morzan, Veronica M. Sanchez, Ali Hassanali, Damian A. Scherlis
Summary: Nanoconfinement effects on water dissociation and reactivity at interfaces, pores, or aerosols remain controversial. Using ab initio simulations, we demonstrate that water dissociation is conserved intact to unexpectedly small length-scales, down to aggregates of only a dozen molecules or pores of widths below 2 nm. This work provides a fundamental description of water dissociation at different scales with implications on reactivity at the air-liquid interface.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Federico Sebastiani, Chun Yu Ma, Sarah Funke, Alexander Baumer, Dominique Decka, Claudius Hoberg, Alexander Esser, Harald Forbert, Gerhard Schwaab, Dominik Marx, Martina Havenith
Summary: This study demonstrates the sensitivity of the N-C-C-O open/close mode at 315 cm(-1) as a label-free probe for the local protonation of the amide group using precise terahertz measurements and molecular dynamics simulations. The approach is shown to be more general, as it can also be applied to other amino acids and allows for direct correlation of titration spectra with pK(a) values, showcasing the potential of terahertz spectroscopy for label-free probing of the charge state of natural amino acids in water.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Stefan Juetten, Thomas Bredow
Summary: The transformation of Ti3O5 from the metastable lambda-phase to the stable beta-phase can be induced by external pressure, irradiation, or electric current. A recent study has revealed a selection rule for the photoinduced phase transition, showing that the transition only occurs when the pump pulse is applied to the ab plane. In this theoretical study, the possible reasons for this phenomenon are investigated, and the relative free energy of different phases under external pressure is calculated using density functional theory (DFT). The phase transition process is further examined by considering the formation and propagation of a beta-phase front in lambda-Ti3O5. The results confirm that phase transitions involving the ab interface are energetically favored, providing a rationalization for the experimental findings. The effect of pressure on the phase transition is attributed to the softening of specific phonon modes.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Biochemistry & Molecular Biology
Giusy Tassone, Marco Paolino, Cecilia Pozzi, Annalisa Reale, Laura Salvini, Gianluca Giorgi, Maurizio Orlandini, Federico Galvagni, Stefano Mangani, Xuchun Yang, Benedetta Carlotti, Fausto Ortica, Loredana Latterini, Massimo Olivucci, Andrea Cappelli
Summary: The use of Morita-Baylis-Hillman adducts allows for facile site-specific, irreversible, and diastereoselective click-functionalization of a lysine residue, producing an unnatural chromophore with an extended pi-system within a lipophilic binding pocket. This approach opens up the possibility of in vitro preparation of a library of synthetic proteins structurally reminiscent of xanthopsin eubacterial photoreceptors, expanding the scope of optogenetic and lab-on-a-molecule tools introduced by rhodopsin mimics.
Article
Chemistry, Multidisciplinary
Xuchun Yang, Madushanka Manathunga, Samer Gozem, Jeremie Leonard, Tadeusz Andruniow, Massimo Olivucci
Summary: This study demonstrates the degeneracy between the reactive excited state and a neighboring state in rhodopsin, which causes the splitting of the rhodopsin population into subpopulations after 15 femtoseconds of light absorption. These subpopulations propagate with different velocities and contribute differently to the quantum efficiency. Furthermore, the study reveals that protein electrostatics modulate this splitting and link amino acid sequence variations to quantum efficiency modulation.
Article
Chemistry, Physical
Laura Pedraza-Gonzalez, Leonardo Barneschi, Michal Marszalek, Daniele Padula, Luca De Vico, Massimo Olivucci
Summary: We propose a computational protocol, implemented through a general Python-based driver, for fast and automated screening of hybrid QM/MM models of rhodopsins as fluorescent probes. The protocol is benchmarked using experimentally measured absorption and emission spectra of different rhodopsin variants. We demonstrate that the protocol can reproduce observed trends in fluorescence and select potentially fluorescent rhodopsins, although it has limitations as a black-box tool. The protocol can also be used for mechanistic investigations of fluorescence enhancement effects associated with S1/S2 states or coupling of S0/S1 wave functions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Abdelaziz Jouaiti, Lavinia Ballerini, Hsiang-Ling Shen, Ronan Viel, Federico Polo, Nathalie Kyritsakas, Stefan Haacke, Yu-Ting Huang, Chin-Wei Lu, Christophe Gourlaouen, Hai-Ching Su, Matteo Mauro
Summary: This study presents two binuclear heteroleptic Cu-I complexes with rigid chelating diphosphines and pi-conjugated 2,5-di(pyridin-2-yl)thiazolo[5,4-d]thiazole ligands. The complexes exhibit a large bathochromic shift of emission, allowing luminescence in the near-infrared (NIR) region. Photophysical and computational investigations confirm the radiative process and structural analysis reveals a unique doubly locked structure. These complexes are successfully used in NIR light-emitting electrochemical cells (LECs) and show potential for white-emitting LECs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Giovanni Li Manni, Ignacio Fdez. Galvan, Ali Alavi, Flavia Aleotti, Francesco Aquilante, Jochen Autschbach, Davide Avagliano, Alberto Baiardi, Jie J. Bao, Stefano Battaglia, Letitia Birnoschi, Alejandro Blanco-Gonzalez, Sergey I. Bokarev, Ria Broer, Roberto Cacciari, Paul B. Calio, Rebecca K. Carlson, Rafael Carvalho Couto, Luis Cerdan, Liviu F. Chibotaru, Nicholas F. Chilton, Jonathan Richard Church, Irene Conti, Sonia Coriani, Juliana Cuellar-Zuquin, Razan E. Daoud, Nike Dattani, Piero Decleva, Coen de Graaf, Mickael G. Delcey, Luca De Vico, Werner Dobrautz, Sijia S. Dong, Rulin Feng, Nicolas Ferre, Michael Filatov (Gulak), Laura Gagliardi, Marco Garavelli, Leticia Gonzalez, Yafu Guan, Meiyuan Guo, Matthew R. Hennefarth, Matthew R. Hermes, Chad E. Hoyer, Miquel Huix-Rotllant, Vishal Kumar Jaiswal, Andy Kaiser, Danil S. Kaliakin, Marjan Khamesian, Daniel S. King, Vladislav Kochetov, Marek Krosnicki, Arpit Arun Kumaar, Ernst D. Larsson, Susi Lehtola, Marie-Bernadette Lepetit, Hans Lischka, Pablo Lopez Rios, Marcus Lundberg, Dongxia Ma, Sebastian Mai, Philipp Marquetand, Isabella C. D. Merritt, Francesco Montorsi, Maximilian Morchen, Artur Nenov, Vu Ha Anh Nguyen, Yoshio Nishimoto, Meagan S. Oakley, Massimo Olivucci, Markus Oppel, Daniele Padula, Riddhish Pandharkar, Quan Manh Phung, Felix Plasser, Gerardo Raggi, Elisa Rebolini, Markus Reiher, Ivan Rivalta, Daniel Roca-Sanjuan, Thies Romig, Arta Anushirwan Safari, Aitor Sanchez-Mansilla, Andrew M. Sand, Igor Schapiro, Thais R. Scott, Javier Segarra-Marti, Francesco Segatta, Dumitru-Claudiu Sergentu, Prachi Sharma, Ron Shepard, Yinan Shu, Jakob K. Staab, Tjerk P. Straatsma, Lasse Kragh Sorensen, Bruno Nunes Cabral Tenorio, Donald G. Truhlar, Liviu Ungur, Morgane Vacher, Valera Veryazov, Torben Arne Voss, Oskar Weser, Dihua Wu, Xuchun Yang, David Yarkony, Chen Zhou, J. Patrick Zobel, Roland Lindh
Summary: This article describes the developments of the open-source OpenMolcas chemistry software environment since spring 2020, focusing on the novel functionalities in the stable branch and interfaces with other packages. These developments cover a wide range of topics in computational chemistry and provide an overview of the chemical phenomena and processes that OpenMolcas can address.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Organic
Yonatan Sukhran, Israel Alshanski, Ofer Filiba, Megan J. Mackintosh, Igor Schapiro, Mattan Hurevich
Summary: Designing and synthesizing orthogonally protected monosaccharide building blocks is important for the controlled preparation of defined oligosaccharides. This study investigates the selective introduction of protecting groups and the unexpected reactivity of a conformationally restricted galactoside. The insights gained from this research offer a new strategy for acylation reactions and can be applied in the synthesis of key monomeric building blocks.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Tzuriel S. Metzger, Harikrishna Batchu, Anil Kumar, Daniil A. Fedotov, Naama Goren, Deb Kumar Bhowmick, Israa Shioukhi, Shira Yochelis, Igor Schapiro, Ron Naaman, Ori Gidron, Yossi Paltiel
Summary: Chirality is a fundamental property in nature, and chiral molecules exist in two forms, each being a mirror image of the other. The chirality of molecules is related to their optical activity, and circular dichroism is often used to determine the chirality of chiral molecules. Recently, the chiral induced spin selectivity (CISS) effect was discovered, showing that electron transfer within chiral molecules depends on the electron's spin. This study found that the CISS properties are similar for the two enantiomers when adsorbed on a metal substrate, while on a nonmetallic surface, the preferred spin depends on the molecule's chirality. The correlation between optical activity and CISS effect suggests a relation to the global polarizability of the molecule.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
R. Bruce Doak, Robert L. Shoeman, Alexander Gorel, Thomas R. M. Barends, Bogdan Marekha, Stefan Haacke, Stanislaw Nizinski, Ilme Schlichting
Summary: A catcher based on a revolving cylindrical collector is introduced, which effectively reduces instabilities in high-viscosity extrusion injection. This simple and cost-effective device enhances the delivery of microcrystals for serial diffraction X-ray crystallography.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2023)
Article
Chemistry, Physical
E. Ikonnikov, M. Paolino, J. C. Garcia-Alvarez, Y. Orozco-Gonzalez, C. Granados, A. Roeder, J. Leonard, M. Olivucci, S. Haacke, O. Kornilov, S. Gozem
Summary: XUV photoelectron spectroscopy (XPS) is a powerful method for investigating the electronic structures of molecules. This study presents experimental aqueous-phase XPS of two organic biomimetic molecular switches, NAIP and p-HDIOP, and theoretical calculations using implicit and explicit solvent models. The results show that the explicit solvent model, ASEC-FEG, gives binding energies in good agreement with the experiment and reveals the contribution of counterions to solvation effects on the switches.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
David Buhrke, Yigal Lahav, Aditya Rao, Jeannette Ruf, Igor Schapiro, Peter Hamm
Summary: In this study, the researchers explored a cyanobacteriochrome called Slr1393-g3, which can switch between red-absorbing and green-absorbing forms. They used advanced IR spectroscopic methods to track the intermediates during the photocycle and discovered a new intermediate with distinct spectroscopic features. Additionally, they measured the vibrational couplings and structural disorder in these intermediate states using stationary and transient 2D IR experiments. Anharmonic QM/MM calculations were also performed to predict the spectra and suggest structural changes of the intermediates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Thibaut Baron, Waad Naim, Mate Kurucz, Ilias Nikolinakos, Baptiste Andrin, Yann Pellegrin, Denis Jacquemin, Stefan Haacke, Frederic Sauvage, Fabrice Odobel
Summary: Fully transparent and colorless dye-sensitized solar cells have attracted much attention, and in this study, a new type of thienyl-PPcy dye was prepared by redshifting the absorption band of diketopyrrolopyrrole chromophores through molecular engineering. The new dyes showed a significant bathochromic shift compared to previous PPcys, leading to a better average visible transmittance of 67%. However, the lower performance of these dyes was attributed to stronger aggregation tendency, slower electron injection rate, and lower driving force, resulting in higher quenching degree by energy transfer towards aggregates.
JOURNAL OF MATERIALS CHEMISTRY A
(2023)
Article
Biophysics
Jonathan R. Church, Jogvan Magnus Haugaard Olsen, Igor Schapiro
Summary: Multiscale simulations have been used to calculate excitation energies in complex systems, with the chromophore treated quantum mechanically and the protein and environment described classically. Electrostatic embedding and polarizable embedding were compared for their effect on excitation energies in two different proteins. Results showed that polarizable embedding produces absorption maxima closer to experimental values and recovers a significant portion of the quantum mechanical improvement in excitation energies. A detailed analysis revealed that aromatic residues have the largest influence on excitation energy.
BIOPHYSICS AND PHYSICOBIOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Yorrick Boeije, Massimo Olivucci
Summary: In the past few decades, conical intersections (CoIns) have evolved from theoretical curiosities to common features in photochemical reactions. They are responsible for the relaxation of electronically excited molecules to their ground state in regions where two electronic states have the same energy. This article reviews the factors controlling CoIn-mediated ultrafast photochemical reactions and highlights the importance of considering the phase matching of multiple molecular modes in the excited state reaction coordinate.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Chemistry, Physical
Giovanni Li Manni, Ignacio Fdez. Galvan, Ali Alavi, Flavia Aleotti, Francesco Aquilante, Jochen Autschbach, Davide Avagliano, Alberto Baiardi, Jie J. Bao, Stefano Battaglia, Letitia Birnoschi, Alejandro Blanco-Gonzalez, Sergey I. Bokarev, Ria Broer, Roberto Cacciari, Paul B. Calio, Rebecca K. Carlson, Rafael Carvalho Couto, Luis Cerdan, Liviu F. Chibotaru, Nicholas F. Chilton, Jonathan Richard Church, Irene Conti, Sonia Coriani, Juliana Cuellar-Zuquin, Razan E. Daoud, Nike Dattani, Piero Decleva, Coen de Graaf, Mickael G. Delcey, Luca De Vico, Werner Dobrautz, Sijia S. Dong, Rulin Feng, Nicolas Ferre, Michael Filatov(Gulak), Laura Gagliardi, Marco Garavelli, Leticia Gonzalez, Yafu Guan, Meiyuan Guo, Matthew R. Hennefarth, Matthew R. Hermes, Chad E. Hoyer, Miquel Huix-Rotllant, Vishal Kumar Jaiswal, Andy Kaiser, Danil S. Kaliakin, Marjan Khamesian, Daniel S. King, Vladislav Kochetov, Marek Krosnicki, Arpit Arun Kumaar, Ernst D. Larsson, Susi Lehtola, Marie-Bernadette Lepetit, Hans Lischka, Pablo Lopez Rios, Marcus Lundberg, Dongxia Ma, Sebastian Mai, Philipp Marquetand, Isabella C. D. Merritt, Francesco Montorsi, Maximilian Morchen, Artur Nenov, Vu Ha Anh Nguyen, Yoshio Nishimoto, Meagan S. Oakley, Massimo Olivucci, Markus Oppel, Daniele Padula, Riddhish Pandharkar, Quan Manh Phung, Felix Plasser, Gerardo Raggi, Elisa Rebolini, Markus Reiher, Ivan Rivalta, Daniel Roca-Sanjuan, Thies Romig, Arta Anushirwan Safari, Aitor Sanchez-Mansilla, Andrew M. Sand, Igor Schapiro, Thais R. Scott, Javier Segarra-Marti, Francesco Segatta, Dumitru-Claudiu Sergentu, Prachi Sharma, Ron Shepard, Yinan Shu, Jakob K. Staab, Tjerk P. Straatsma, Lasse Kragh Sorensen, Bruno Nunes Cabral Tenorio, Donald G. Truhlar, Liviu Ungur, Morgane Vacher, Valera Veryazov, Torben Arne Voss, Oskar Weser, Dihua Wu, Xuchun Yang, David Yarkony, Chen Zhou, J. Patrick Zobel, Roland Lindh
Summary: This article describes the recent developments in the open-source chemistry software environment, OpenMolcas, since spring 2020. It focuses on the new functionalities and interfaces with other packages. The article presents various topics in computational chemistry, including electronic structure theory, electronic spectroscopy simulations, molecular structure optimizations, ab initio molecular dynamics, and other new features. Overall, it highlights the capabilities of OpenMolcas in addressing chemical phenomena and processes, making it an attractive platform for advanced atomistic computer simulations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)