Article
Chemistry, Multidisciplinary
Jacob M. Garcia, Scott G. Sayres
Summary: Excited state lifetimes of neutral Cr2On clusters were measured using femtosecond pump-probe spectroscopy. Results show that dynamics of excited states are correlated with changes in the electronic structure of the clusters with increasing oxidation. The study reveals the phenomenon of long-lived response in clusters with significant d-electron character, as well as the gradual transition from semiconductor to metallic behavior at the molecular level.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Ignacio Loaiza, Artur F. Izmaylov, Paul Brumer
Summary: When studying light harvesting processes, it is important to consider that natural processes occur in the presence of incoherent light, leading to a stationary state. While stationary states can be described using the eigenbasis of the molecular Hamiltonian, full diagonalization is often expensive for realistic systems. Three efficient computational approaches have been proposed to obtain the stationary state without requiring system Hamiltonian diagonalization. The connection between incoherent perturbations, decoherence, and Kraus operators has been established.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Review
Chemistry, Multidisciplinary
Christophe Jouvet, Mitsuhiko Miyazaki, Masaaki Fujii
Summary: Excited State Hydrogen Transfer (ESHT) is a new paradigm proposed in the late 20th century, which has become important in understanding excited state dynamics of aromatic molecules and re-defining photoinduced proton-transfer reactions. ESHT is also discussed in relation to photo-protection mechanisms of biomolecules such as DNA.
Article
Chemistry, Multidisciplinary
Chun-Fu Chang, Hikaru Kuramochi, Manish Singh, Rei Abe-Yoshizumi, Tatsuya Tsukuda, Hideki Kandori, Tahei Tahara
Summary: The varied excited-state relaxation dynamics in different microbial rhodopsins mainly originate from the difference in ground-state heterogeneity, specifically the protonation/deprotonation of the PRSB counterion.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Baptiste Demoulin, Margherita Maiuri, Tetyana Berbasova, James H. Geiger, Babak Borhan, Marco Garavelli, Giulio Cerullo, Ivan Rivalta
Summary: The study shows that modifying the electrostatic environment of the chromophore through protein point mutations can affect its excited state properties, allowing control of its photophysics with the same power as chemical modifications of the chromophore. This fine control is essential for the design of bio-mimetic opto-electronic and photonic devices.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Physical
Lingjie Duan, Xiao Zhang, Yu Zhao, Qingtian Meng, Changzhe Zhang
Summary: (ABP)dG is one of the most representative carcinogenic DNA adducts formed by human exposure to 4-ABP, and its ultrasensitive detection is crucial for understanding carcinogenesis mechanisms and mitigating cancer risk.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Crystallography
Darko Vusak, Mia Jurkovic, Neven Smrecki, Biserka Prugovecki
Summary: Seven N-alkylated glycine derivatives were successfully synthesized and characterized using single-crystal X-ray diffraction, infrared spectroscopy, and thermal analysis. These compounds exhibit different structural features and form various molecular networks.
Article
Physics, Multidisciplinary
Angel L. Corps, Armando Relano
Summary: This study discusses a broad class of excited-state quantum phase transitions that lead to two different excited-state quantum phases, where equilibrium expectation values crucially depend on a specific conserved quantity in one phase, while energy is the only relevant thermodynamic magnitude in the other phase. The operator in the first phase acts as a discrete symmetry with two different eigenvalues.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Svetlana Shostak, Woojin Park, Juwon Oh, Jinseok Kim, Seunghoon Lee, Hyeongwoo Nam, Michael Filatov, Dongho Kim, Cheol Ho Choi
Summary: The excited-state aromatization dynamics in the photochemical ring opening of DHA was investigated using nonadiabatic molecular dynamics simulations and the mixed-reference spin-flip (MRSF)-TDDFT method. It was found that the ring opening occurs in the excited state through a series of steps with increasing aromaticity. The competition between Baird and anti-Baird channels suggests that the quantum yield of the photochemical products can be controlled by tipping their balance.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Victor M. Freixas, Alexander J. White, Tammie Nelson, Huajing Song, Dmitry Makhov, Dmitrii Shalashilin, Sebastian Fernandez-Alberti, Sergei Tretiale
Summary: This study compares three popular methods for large chromophores: Ehrenfest, surface hopping, and multiconfigurational Ehrenfest with ab initio multiple cloning (MCE-AIMC). The comparisons reveal method performance for population relaxation and coherent vibronic dynamics. The numerical convergence of MCE-AIMC algorithms is also studied to provide helpful reference data for selecting an optimal methodology for simulating excited-state molecular dynamics.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Victor Manuel Freixas, Sergei Tretiak, Sebastian Fernandez-Alberti
Summary: Progress in organic synthesis allows the exploration of diverse molecules with new structural topologies. The recently synthesized infinitene is a helically twisted figure-eight molecule with unique optoelectronic properties suitable for applications in nanoelectronics and photonics. However, the photophysical properties of infinitene have not been investigated.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Fengzi Ling, Ling Cao, Yanmei Wang, Jie Wei, Zhigao Luo, Zhe Hu, Jiyun Qiu, Dejun Liu, Pengfei Wang, Xinli Song, Song Zhang
Summary: The non-adiabatic relaxation processes and fragmentation dynamics of Rydberg-excited TMMDA were investigated using femtosecond time-resolved photoelectron imaging and time-resolved mass spectroscopy. It was found that excitation at 208 nm led to charge-localized 3p state, followed by rapid internal conversion to charge-delocalized 3s conformers. The 3s conformers exhibited structural evolution on a 1.55 ps timescale and subsequently relaxed to the ground state on a slower timescale of 12.1 ps. Ionization from the 3p state did not result in bond cleavage, while the additional energy acquired from IC allowed for C-N bond breaking, leading to fragment ion formation on the ion surface rather than the Rydberg surface.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Giovanni Batignani, Emanuele Mai, Giuseppe Fumero, Shaul Mukamel, Tullio Scopigno
Summary: This article introduces a nonlinear Raman experiment to access an elusive aspect of the excited-state displacements: their sensed directions relative to the ground-state.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Yiwen Wang, Zehua Chen, Yang Yang
Summary: Modeling and interpreting vibrational spectra are important for studying reaction dynamics. This study presents a new method using excited state constrained minimized energy surfaces (CMESs) to describe vibrational excited state absorptions. Results from various model systems show that this method provides good estimations of transition frequencies for vibrational excited state absorptions, surpassing conventional harmonic approximations using potential energy surfaces.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Jacob M. Garcia, Lauren F. Heald, Ryan E. Shaffer, Scott G. Sayres
Summary: Researchers found that the excited state lifetimes of neutral titanium oxide clusters are correlated with the size and structural rigidity of the clusters, with clusters possessing structural rigidity showing longer excited state lifetimes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
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, Physical
Saruti Sirimatayanant, Tadeusz Andruniow
Summary: This work investigates the impact of increasing electron correlation on two-photon absorption (2PA) strengths for the lowest excited state of a chromophore model. Calculations using different levels of the coupled-cluster method and popular density functional theory (DFT) functionals were performed. The results show that the accuracy of 2PA strengths increases with increasing level of the coupled-cluster method, and certain DFT functionals provide results in good agreement with the reference data, although with a significant error.
JOURNAL OF CHEMICAL PHYSICS
(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, 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, Physical
Matthias Broser, Tadeusz Andruniow, Anastasia Kraskov, Riccardo Palombo, Sagie Katz, Miroslav Kloz, Jakub Dostal, Cesar Bernardo, John T. M. Kennis, Peter Hegeman, Massimo Olivucci, Peter Hildebrandt
Summary: The recently discovered Neorhodopsin (NeoR) exhibits unique optical properties in the near-infrared spectral region, making it attractive for optogenetic applications. This study evaluates the electronic structure of NeoR by resonance Raman spectroscopy and confirms the consistency between the experimental and calculated spectra.
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
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, Inorganic & Nuclear
Swaroop Sasidharanpillai, Jenny S. Cox, Cory C. Pye, Peter R. Tremaine
Summary: Raman spectra analysis of aqueous sodium borate solutions reveals the presence of a new ion, diborate ion, at around 865 cm(-1) at elevated temperatures. The diborate ion is different from previously reported polyborate ions and is most likely [B-2(OH)(7)](-). The study also suggests the existence of unidentified minor equilibrium species.
DALTON TRANSACTIONS
(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)
Article
Chemistry, Physical
Aditya G. G. Rao, Igor Schapiro
Summary: Phytochromes are photoreceptors that undergo photoisomerization upon light illumination, and this study focused on the photoisomerization of chromophore models based on phycocyanobilin. By introducing substitutions into the model, it was found that the isomerization mechanism and preference can be changed.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Ofer Filiba, Veniamin A. Borin, Igor Schapiro
Summary: In this study, the possible involvement of triplet states in the photoisomerization of retinaloids was investigated using the extended multistate (XMS) version of CASPT2. The calculation results of energy positions, spin-orbit coupling matrix elements, etc. revealed differences in the characteristics of different retinaloids during the photoisomerization process.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Jonathan R. Church, Jogvan Magnus Haugaard Olsen, Igor Schapiro
Summary: This study analyzes the absorption spectra and structural changes of jumping spider rhodopsin-1 (JSR1) through hybrid QM/MM simulations, revealing that the distance of a nearby tyrosine residue plays a significant role in predicting the absorption maximum.
