Review
Chemistry, Multidisciplinary
Amel Abdou-Mohamed, Clara Aupic, Corentin Fournet, Jean-Luc Parrain, Gaelle Chouraqui, Olivier Chuzel
Summary: Four-coordinate organoboron derivatives have interesting properties in chemistry, physics, biology, electronics, and optics. The synthesis of smart functional materials based on chiral organoboron compounds is in high demand, making the exploration of stereoselective synthesis of boron-stereogenic organo-derivatives desirable. However, the stereoselective construction of organoboron compounds stereogenic at boron has been less studied due to configurational stability concerns. Nowadays, configurationally stable compounds have been highlighted, showing the potential for stereoselective building of the four-coordinate boron center and encouraging future endeavors and developments in the field.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Chemistry, Applied
Jiawei You, Shuai Zhang, Qiuying Li, Weijie Zhang, Huili Ma, Jianquan Hou, Engui Zhao, Zikai He
Summary: This article presents two new azobenzene derivatives with photoisomerization properties and solid-state fluorescence. The study reveals that these derivatives exhibit unusual fluorescence in the solid state, with TPE-Azo-2OH showing even stronger fluorescence due to the suppression of photoisomerization by intramolecular hydrogen bonds. Additionally, these azobenzene derivatives undergo fluorescence transformation from red to green upon reduction. These new derivatives with AIE attributes and stimuli-responsiveness are expected to provide a new platform for developing photo-responsive luminescent materials.
Article
Chemistry, Physical
Mengqi Wang, Yanan Shi, Yurong Guo, Yibing Chen, Chenyang Zhao, Yi Zhou, Yongze Xiao, Ye Wang, Song Zhang, Bing Jin, Zibo Wu, Guangjiu Zhao
Summary: This study proposes natural molecules chlorogenic acid (CA) and isochlorogenic acid A (ICAA) as potential sunscreens for the first time, revealing their non-radiative energy relaxation mechanisms and photoisomerization channels. The dual conjugated system improves energy absorption efficiency, providing insights for designing novel sunscreen compounds.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Mathematics, Applied
Yibo Xia, Serhiy Yanchuk, Yichuan Cao, Qinsheng Bi, Juergen Kurths
Summary: This study investigates the slow-fast dynamics of a system with a double-Hopf bifurcation and a slowly varying parameter. The model consists of coupled Bonhoffer-van der Pol oscillators excited by a periodic slow-varying AC source. Two cases are considered where the slowly varying parameter passes by or crosses the double-Hopf bifurcation. Due to multistability, two bursting solutions are observed in each case: single-mode bursting and two-mode bursting. The mechanism of coexistence of these bursting solutions is explained using the slowly changing phase portraits of the fast subsystem. The robustness of the observed effect near the double-Hopf bifurcation is also demonstrated.
Article
Physics, Multidisciplinary
Xiangrong Wang, Alejandro Tejedor, Yi Wang, Yamir Moreno
Summary: The study found that directionality in multilayer networks can fundamentally change the behavior of diffusive dynamics, leading to non-monotonic diffusion. In certain multilayer network configurations, directionality can induce a superdiffusion regime for intermediate values of interlayer coupling.
NEW JOURNAL OF PHYSICS
(2021)
Review
Chemistry, Organic
Yong-Liang Liu, Xiao-Ping Wang, Jie Wei, Ya Li
Summary: 3,3-Disubstituted oxindoles with a stereogenic 3-fluorinated carbon center are important structural motifs in bioactive molecules. The functionalization of 3-fluorooxindoles is a powerful method for synthesizing 3-fully substituted 3-fluorooxindoles, with many papers published on this topic in the past decade. Asymmetric catalytic methods have been developed for the enantioselective synthesis of these valuable compounds.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Article
Chemistry, Physical
Aljaz Godec, Dmitrii E. Makarov
Summary: In this paper, we discuss the practical challenges of using stochastic thermodynamics to determine the directionality of molecular machines from experimental single-molecule trajectories. Due to the limitations of spatiotemporal resolution in these experiments and the inability to detect both forward and backward transitions between the same states, distinguishing the forward and backward directions of ATP-consuming periodic molecular machines becomes a nontrivial task. By extending the commonly used Markov-state model to analyze single-molecule transition-path measurements, we show how irreversibility can be hidden in these measurements but can be revealed when non-Markov effects in low-dimensional single-molecule trajectories are considered.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Liangzhi Pang, Zhan Huang, Qilin Sun, Gen Li, Jiaojiao Liu, Baoli Li, Congyue Ma, Jiaxu Guo, Chuanzhi Yao, Jie Yu, Qiankun Li
Summary: Chiral monodentate biaryl phosphines (MOPs) have been extensively studied as chiral ligands. The authors demonstrate a diverse synthesis method for structurally diverse MOPs containing both phosphorus and axial chirality. They employ a distinct strategy for diversity-oriented synthesis, enabled by the enantioselective cleavage of C-P bond, to create chiral Pd-II intermediates that can be transformed into enantioenriched MOPs with high diastereo- and enantioselectivities. These chiral MOPs show excellent catalytic properties in the asymmetric [3 + 2] annulation reaction, leading to the formation of chiral functionalized bicyclic imide.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Fei Jin, Jinpeng Xin, Runnan Guan, Xiao-Ming Xie, Muqing Chen, Qianyan Zhang, Alexey A. Popov, Su-Yuan Xie, Shangfeng Yang
Summary: A novel trimetallic carbide clusterfullerene based on dysprosium was synthesized for the first time, exhibiting an unusual three-center single-electron metal-metal bond in its encapsulated cluster. This electronic structure differs from that of the similar scandium-based clusterfullerene, showing no metal-metal bonding and a different charge distribution.
Article
Chemistry, Multidisciplinary
Kallol Mukherjee, Nicolas Grimblat, Somratan Sau, Koushik Ghosh, Majji Shankar, Vincent Gandon, Akhila K. Sahoo
Summary: A direct Pd(ii)-catalyzed kinetic resolution of heteroaryl-enabled sulfoximines through an ortho-C-H alkenylation/arylation of arenes has been developed, providing access to a wide range of enantiomerically enriched unreacted aryl-pyridyl-sulfoximine precursors and C(aryl)-H alkenylation/arylation products in good yields with high enantioselectivity. The coordination of the directing group, ligand effect, geometry constraints, and the transient six-membered concerted-metalation-deprotonation species dictate the stereoselectivity, which is validated by DFT studies.
Article
Multidisciplinary Sciences
Himanshu Pandey, Emanuel Reithmann, Alina Goldstein-Levitin, Jawdat Al-Bassam, Erwin Frey, Larisa Gheber
Summary: The study reveals clustering-induced directionality switching of the bidirectional kinesin-5 Cin8, where the motor protein is able to change direction under the influence of opposing forces. By developing a model, researchers successfully predicted and explained this mechanism, which can account for the reversal of direction in bidirectional motor proteins under different experimental conditions.
Article
Mathematics, Applied
Cong Liu, Zhi-Xi Wu, Chong-Yang Wang, Han-Xin Yang, Jian-Yue Guan
Summary: The study shows that astrocytes can listen to the talk between neurons, give advice, and contribute to heterogeneous couplings. The research focuses on the regulation function of astrocytes and explores the role of heterogeneous couplings among neuron-astrocyte components in signal response.
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
Chemistry, Physical
Jindrich Fanfrlik, Jiri Brynda, Michael Kugler, Martin Lepsik, Klara Pospisilova, Josef Holub, Drahomir Hnyk, Jan Nekvinda, Bohumir Gruner, Pavlina Rezacova
Summary: This paper provides the first example of B-H...pi hydrogen bonding in a protein-ligand complex through high-resolution X-ray crystallography and quantum-chemical calculations. The study demonstrates that the B-H...pi interaction is stabilized by dispersion, followed by electrostatics. It also shows that the similar C-H...pi interaction is twice as strong, with a slightly smaller contribution of dispersion and a slightly higher contribution of electrostatics. Such insights will facilitate the rational design of future protein ligands, controlling these types of non-covalent interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Dzung Nguyen, Dinar Abdullin, Caspar A. Heubach, Toni Pfaffeneder, Andreas Nguyen, Andreas Heine, Klaus Reuter, Francois Diederich, Olav Schiemann, Gerhard Klebe
Summary: Mechanistic insights into protein-ligand interactions can provide chemical tools for modulating protein function. The type of ligand can affect the equilibrium between functional and twisted dimers in the homodimeric enzyme TGT. The experiments suggest a dissociation-association mechanism for the formation of the twisted dimer upon ligand binding.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
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.
Review
Chemistry, Multidisciplinary
Laura Pedraza-Gonzalez, Leonardo Barneschi, Daniele Padula, Luca De Vico, Massimo Olivucci
Summary: Rhodopsins, such as photoactive proteins, have become a popular target in optogenetics research. Computational methods, like the Automatic Rhodopsin Modeling (ARM) protocol, provide the necessary tools for analyzing experimental results and driving the design of new systems.
TOPICS IN CURRENT CHEMISTRY
(2022)
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
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
Alejandro Jodra, Cristina Garcia-Iriepa, Luis Manuel Frutos
Summary: The use of mechanical forces at the molecular level to modulate molecular properties has been studied. A new algorithm called LGMF has been developed to determine the optimal mechanical forces for tuning the electronic energy gap and to identify the maximum mechanical response of a molecular system to any mechanical stimulus.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(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
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)
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)