Article
Biology
Yuta Nakajima, Laura Pedraza-Gonzalez, Leonardo Barneschi, Keiichi Inoue, Massimo Olivucci, Hideki Kandori
Summary: Mutations of amino acid at position 219 of the sodium pump rhodopsin, KR2, play a crucial role in color tuning of the retinal chromophore, with the exception of P219R. The red-shifting variations are mainly induced by electrostatic interactions of the G/P switch, while the blue-shifted P219R variant involves both electrostatic and steric changes accompanied by protonation state and hydrogen bond networks modifications. The complexity of the results highlights the difficulty in predicting the operation of the switch without considering atomistic details and environmental consequences of the side chain replacement.
COMMUNICATIONS BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Keisuke Ichijo, Sayuri Kimura, Tsukasa Yoshida, Ryohei Yamakado, Shuji Okada
Summary: In this study, cyanine cations with various counter anions were prepared as examples of ionic materials constructed using charged pi-conjugated systems. The optical properties and packing structures of these ion pairs were investigated through UV/vis absorption, fluorescence spectroscopy, and single-crystal X-ray analysis. It was found that the location and delocalization of the anions relative to the cations, as well as the stack formation of cyanine cations, depend on the size and structure of the anions.
Article
Chemistry, Multidisciplinary
Woojae Kim, Shinya Tahara, Hikaru Kuramochi, Satoshi Takeuchi, Taeyeon Kim, Tahei Tahara, Dongho Kim
Summary: This study investigates the interplay between exciton delocalization and bond length alternation along the conjugation coordinate in archetypical conjugated oligothiophenes with different chain lengths, using femto-second stimulated Raman spectroscopy. The results provide a more general picture of exciton delocalization in the context of molecular structures for conjugated materials, showcasing the complexity of the interaction between exciton delocalization and bond length alternation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Davide Romanin, Lorenzo Monacelli, Raffaello Bianco, Ion Errea, Francesco Mauri, Matteo Calandra
Summary: The study examines the phase transition of carbon chains, showing the significant role of quantum anharmonicity and predicting an insulator-to-metal transition at high temperatures within polyyne phases in insulating nanotubes with a large dielectric constant.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Chikashi Ota, Akifumi Matsumoto, Tsubasa Hidaka, Keita Sugihara, Takahiro Teramoto, Yutaka Nagasawa
Summary: Femtosecond time-resolved transient absorption spectroscopy was conducted on a nonfluorescent solvatochromic dye, phenol blue, revealing ultrafast non-radiative decay and spectral evolution in the ground state; the experiment also identified low-frequency coherent wavepacket oscillations that modulated the ground-state bleach.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Svitlana V. Shishkina, Alexander A. Ishchenko, Andrii V. Kulinich
Summary: This study presents an X-ray crystallographic characterization of a tetramethine merocyanine compound based on benzimidazole and thiobarbituric acid, revealing negative solvatochromism in organic solvents. The crystal structure features three non-equivalent dye molecules and one water molecule, forming specific π-stacked columns. The findings suggest that a single hydrogen bond has less impact on the electronic structure of merocyanine compounds in the crystal compared to pi-stacking and other multiple close-range interactions.
STRUCTURAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Svitlana Shishkina, Viktoriya V. Dyakonenko, Alexander A. Ishchenko, Andrii Kulinich
Summary: The concept of the ideal polymethine state is crucial in the theory of color of pi-conjugated organic compounds. Through an X-ray crystallographic study of a vinylogous series of merocyanines, it is found that achieving the ideal polymethine state in the crystal can be done through a careful choice of the donor-acceptor properties of the end-groups. The length of the polymethine chain has minimal impact on the electronic symmetry of these dyes in the solid state.
STRUCTURAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Girishma Grover, John D. Tovar, Miklos Kertesz
Summary: Quinonoid ground state polymers are rare, and this study aims to expand the portfolio of such systems. The diradical character is a useful parameter to classify polymer ground states. The diradical character of quinonoid systems is correlated with the size, interring C-C distance, and singlet-triplet energy gaps.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Review
Chemistry, Applied
Heinz Mustroph
Summary: Polymethine dyes are a class of compounds with a conjugated chain, characterized by terminal electron accepting and donating groups. They have unique structure-absorption relationships. Over the years, the general definition has been divided into sub-classes, but some aspects have been misunderstood or overlooked.
Article
Chemistry, Multidisciplinary
Shuguo An, Aiyou Hao, Pengyao Xing
Summary: In this work, the [N center dot center dot center dot I center dot center dot center dot N]+ halogen bond was utilized to drive the formation of supramolecular helical polymers, showing tunable supramolecular chirality. Multiple protocols in regulating helicity were provided by ion exchange and solvent environments.
Article
Chemistry, Multidisciplinary
Jieyu Yang, Fenghua Xu, Wenli Zhao, Luqiong Liu, Baicheng Weng
Summary: This study proposes a simple method to improve the performance of Co3O4 by incorporating large-sized single atoms, which enhances its interaction and charge transfer with absorbents for more efficient oxygen evolution reaction. Additionally, a solar water-splitting device constructed using this method achieves a high solar-to-hydrogen conversion efficiency.
Article
Nanoscience & Nanotechnology
AbhayRam Balakrishnan, Rahul Suresh, S. Vijayakumar
Summary: The structural and conducting properties of amine terminated polyynes were studied, showing improved conductance and reduced transport barrier. The amine termination also led to a reduction in bond length alternation and a transfer of negative charge.
PHYSICA E-LOW-DIMENSIONAL SYSTEMS & NANOSTRUCTURES
(2022)
Article
Chemistry, Physical
Jun Wang, Bo Durbeej
Summary: A study on the impact of thermal motion on the excitation energies of astaxanthin found that thermal fluctuations can cause a significant shift in the excitation energy. It is concluded that thermal motion can have a large effect on the excitation energies of conjugated systems, even for molecules with distinct potential-energy minima.
Article
Materials Science, Multidisciplinary
V. A. Stoica, D. Puggioni, J. Zhang, R. Singla, G. L. Dakovski, G. Coslovich, M. H. Seaberg, M. Kareev, S. Middey, P. Kissin, R. D. Averitt, J. Chakhalian, H. Wen, J. M. Rondinelli, J. W. Freeland
Summary: This study used ultrashort X-ray pulses to investigate the structural and magnetic dynamics of the nickelate model NdNiO3 under photoexcitation. The experiments revealed the ultrafast quenching of magnetic order and the delayed collapse of the insulating phase during the photoinduced insulator-to-metal transition. It was found that both the magnetic and structural degrees of freedom contribute to driving the transition.
Article
Chemistry, Multidisciplinary
Lei Zhang, Chao Xu, Wenguang Hu
Summary: In this study, a molecular approach is used to improve the optoelectronic performance of halide perovskite materials. Data mining is employed to find suitable organic molecules for adsorption onto the materials, and their interactions and impacts on properties are thoroughly investigated through first-principles calculations.
STRUCTURAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Dmitrii M. M. Nikolaev, Vladimir N. N. Mironov, Andrey A. A. Shtyrov, Iaroslav D. D. Kvashnin, Andrey S. S. Mereshchenko, Andrey V. V. Vasin, Maxim M. S. Panov, Mikhail N. N. Ryazantsev
Summary: Membrane potential is a fundamental property of cells, and changes in membrane potential are involved in various important biological processes. Recording membrane potential changes using organic dyes or genetically-encoded voltage indicators with voltage-dependent fluorescence is a common strategy. However, to investigate long-term processes, the measured signal needs to be corrected to exclude the contribution from voltage-independent factors. This review focuses on techniques that enable such measurements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Medicinal
Daniel Sethio, Vasanthanathan Poongavanam, Ruisheng Xiong, Mohit Tyagi, Duc Duy Vo, Roland Lindh, Jan Kihlberg
Summary: Conformational analysis is crucial for the design of bioactive molecules, and it becomes even more challenging for macrocycles due to their unique characteristics. In this study, we simulated the conformations of five designed macrocycles and verified the results against experimental measurements. Our simulations accurately predicted the intramolecular interactions and revealed a solvent-induced conformational switch of the macrocyclic ring. This provides a foundation for the rational design of molecular chameleons that can adapt to different environments.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Simone Bonfrate, Nicolas Ferre, Miquel Huix-Rotllant
Summary: Hybrid quantum mechanics/molecular mechanics (QM/MM) models are effective for studying biological macromolecules. However, they are often too time-consuming for general application to biological systems in solution. In this study, a simple and efficient electrostatic embedding QM/MM model in periodic boundary conditions (PBC) is proposed, which successfully reproduces the experimental absorption maximum in a model for Arabidopsis thaliana cryptochrome 1 with approximately 93,000 atoms.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Aleksandra A. Vidyakina, Andrey A. Shtyrov, Mikhail N. Ryazantsev, Alexander F. Khlebnikov, Ilya E. Kolesnikov, Vladimir V. Sharoyko, Dar'ya Spiridonova, Irina A. Balova, Stefan Braese, Natalia A. Danilkina
Summary: Fluorescent isocoumarin-fused cycloalkynes have been developed, which react in SPAAC and give fluorescent triazoles regardless of the azide nature. The introduction of a pi-acceptor group at the C6 position of the isocoumarin ring converts the non-fluorescent cycloalkyne/triazole pair to its fluorescent counterpart. The design of the fluorescent cycloalkyne/triazole pairs is based on theoretical studies of the deactivation mechanism and electron density redistribution.
CHEMISTRY-A EUROPEAN JOURNAL
(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
Viktor G. Nosov, Anna A. Betina, Tatyana S. Bulatova, Polina B. Guseva, Ilya E. Kolesnikov, Sergey N. Orlov, Maxim S. Panov, Mikhail N. Ryazantsev, Nikita A. Bogachev, Mikhail Yu Skripkin, Andrey S. Mereshchenko
Summary: Luminescent NaYF4:Sm3+ nano- and microcrystalline materials co-doped with La3+, Gd3+, and Lu3+ ions were synthesized using the hydrothermal method. The synthesis process involved the use of rare earth chlorides as precursors and citric acid as a stabilizing agent. The synthesized materials exhibited a beta-NaYF4 crystalline phase, except for those with high La3+ content which formed LaF3. Particle size was significantly affected by the type and content of doping REE. Excitation at 400 nm resulted in distinct emission peaks in the visible spectrum due to transitions of the Sm3+ ion. Increasing the Sm(III) content led to concentration quenching, with an optimum concentration of 2%. Co-doping with non-luminescent La3+, Gd3+, and Lu3+ ions increased the emission intensity, explained by the viewpoint of Sm3+ local symmetry.
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
Gustavo Cardenas, Vincent Ledentu, Miquel Huix-Rotllant, Massimo Olivucci, Nicolas Ferre
Summary: The ARM+MEM protocol incorporates all relevant protonation microstates to provide a more accurate modeling of rhodopsins' absorption spectrum. By simulation on a toy model and Anabaenasensory rhodopsin, it is confirmed that considering multiple microstates improves the description of the absorption spectrum.
JOURNAL OF PHYSICAL CHEMISTRY A
(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
Leonardo Barneschi, Danil Kaliakin, Miquel Huix-Rotllant, Nicolas Ferre, Michael Filatov(Gulak), Massimo Olivucci
Summary: This study compares the performance of different electronic structure methods and implementation of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method. The results show that REKS method behaves differently in some systems compared to other methods, which can be attributed to the effect of the employed density functional approximation.
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 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)
