Article
Chemistry, Physical
Anne P. Rasmussen, Elisabeth Gruber, Ricky Teiwes, Mordechai Sheves, Lars H. Andersen
Summary: This study investigates the effects of steric constraints on the spectroscopy and isomerization dynamics of retinal derivatives in comparison to protonated Schiff-base retinal. The results show significant alterations in both spectroscopy and isomerization speed due to steric constraints.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Review
Chemistry, Multidisciplinary
Saumik Sen, Rajiv K. Kar, Veniamin A. Borin, Igor Schapiro
Summary: The photoisomerization of retinal is a crucial primary event in the rhodopsin protein family, highly optimized in the protein for ultrafast, selective, and efficient reactions. Space saving mechanisms based on the rotation of multiple double bonds have been proposed to elucidate the highly complex process inside the protein.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Biology
Shoun Taguchi, Satomi Niwa, Hoang-Anh Dao, Yoshihiro Tanaka, Ryota Takeda, Shuya Fukai, Kazuya Hasegawa, Kazuki Takeda
Summary: Crystal structures and quantum mechanical calculations are used to investigate the interaction and conformation of the retinal chromophore in the K intermediate of bacteriorhodopsin. The results provide insights into light-driven proton pumping in bacteriorhodopsin. The accurate X-ray crystallographic analysis reveals an S-shaped conformation of the polyene chain of 13-cis retinal in the K structure.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Physical
Rodrigo A. Vargas-Hernandez, Chern Chuang, Paul Brumer
Summary: This passage discusses the use of multi-objective optimization to find the best model for multiple target observables, as well as the approximation of predicted errors using Gaussian process models to reduce computational costs.
JOURNAL OF CHEMICAL PHYSICS
(2021)
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
Electrochemistry
Mattia Belotti, Mohsen M. T. El-Tahawy, Nadim Darwish, Marco Garavelli, Simone Ciampi
Summary: This study explores the current response, light intensity, and spectral signatures of the cathodic electrochemiluminescence (ECL) in room temperature ionic liquids (RTILs). It demonstrates the viability of using electrode reactions to generate light emitters in RTILs and discovers that the ECL signal can persist for a certain duration after the removal of the external cathodic pulse due to the stabilization of superoxide.
Article
Chemistry, Analytical
Mattia Belotti, Mohsen M. T. El-Tahawy, Marco Garavelli, Michelle L. Coote, K. Swaminathan Iyer, Simone Ciampi
Summary: The study develops a direct, spatiotemporally resolved optical tracking method to detect and resolve convective disturbances in electrochemical reactivity. It is found that parasitic gas evolving reactions lead to overestimates of macroscopic diffusion coefficients by 10 times. A hypothesis is proposed linking large barriers to inner-sphere redox reactions to the formation of cation-rich overscreening and crowding double layer structures in imidazolium-based ionic liquids.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Francesco Segatta, Daniel Aranda Ruiz, Flavia Aleotti, Martha Yaghoubi, Shaul Mukamel, Marco Garavelli, Fabrizio Santoro, Artur Nenov
Summary: This paper presents an accurate and efficient approach for calculating the linear and nonlinear optical spectroscopy of a closed quantum system. The method includes the effect of ultrafast nonadiabatic dynamics by numerically propagating the nuclear wave packet. The expressions for the evaluation of response functions are recast in a general form and validated using the multiconfiguration time-dependent Hartree method. The application to pyrene reveals the remarkable influence of ultrafast nonadiabatic dynamics on spectral line shapes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Abed Mohamadzade, Artur Nenov, Marco Garavelli, Irene Conti, Susanne Ullrich
Summary: Sulfur-substituted nucleobases are efficient in photoinduced intersystem crossing (ISC), making them versatile for various applications. However, a comprehensive understanding of wavelength-dependent changes in IC and ISC events is still lacking.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Giacomo Fanciullo, Silvia Orlandi, Andrey S. Klymchenko, Luca Muccioli, Ivan Rivalta
Summary: The aggregation of charged dyes in a solution, such as Rhodamine B (RB), is affected by the type of counterion, which determines the self-assembled structure and optical properties. Hydrophobic and bulky fluorinated tetraphenylborate counterions, like F5TPB, can enhance RB aggregation and form nanoparticles, affecting the fluorescence quantum yield (FQY) depending on the degree of fluorination. A classical force field (FF) based on the generalized Amber parameters was developed to model the self-assembling process of RB/F5TPB systems, consistent with experimental evidence. The simulations demonstrated the formation of nanoparticles in the RB/F5TPB system and only RB dimeric species in the presence of iodide counterions. This research provides atomistic details on the role of F5TPB counterions as spacers and represents progress towards reliable modeling of dye aggregation in RB-based materials.
Article
Multidisciplinary Sciences
Federica Maschietto, Uriel N. Morzan, Florentina Tofoleanu, Aria Gheeraert, Apala Chaudhuri, Gregory W. Kyro, Peter Nekrasov, Bernard Brooks, J. Patrick Loria, Ivan Rivalta, Victor S. Batista
Summary: Through molecular dynamics simulations and nuclear magnetic resonance spectroscopy, the authors investigate the effect of temperature on allostery in imidazole glycerol phosphate synthase (IGPS). They find that an increase in temperature triggers local amino acid dynamics, providing insights into the mechanism of allosteric regulation. This study offers an atomistic understanding of temperature-dependent allostery and its potential for controlling enzyme function.
NATURE COMMUNICATIONS
(2023)
Correction
Multidisciplinary Sciences
Federica Maschietto, Uriel N. Morzan, Florentina Tofoleanu, Aria Gheeraert, Apala Chaudhuri, Gregory W. Kyro, Peter Nekrasov, Bernard Brooks, J. Patrick Loria, Ivan Rivalta, Victor S. Batista
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Francesca Liuzzi, Alessia Ventimiglia, Alessandro Allegri, Elena Rodriguez-Aguado, Juan Antonio Cecilia, Ivan Rivalta, Nikolaos Dimitratos, Stefania Albonetti
Summary: Different series of Au on carbon catalysts were prepared via sol-immobilization using different polymers as gold nanoparticle stabilizers, which were investigated for their effects on catalyst properties and catalytic activity in the HMF oxidation reaction. Results showed that PVA led to the formation of smaller and more active nanoparticles, while PEG affected gold exposure and reduced catalyst activity due to steric effects. PVP-based catalysts had bigger and more covered Au nanoparticles. Computational studies provided insights into NP-polymer interactions and catalytic activities.
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, Physical
Aria Gheeraert, Claire Lesieur, Victor S. Batista, Laurent Vuillon, Ivan Rivalta
Summary: Describing protein dynamical networks through amino acid contacts is a powerful way to analyze complex biomolecular systems. The connected component analysis (CCA) approach allows for fast and robust analysis of dynamical perturbation contact networks (DPCNs) and outperforms clustering methods in capturing the propagation of allosteric signals within protein graphs. CCA reduces the DPCN size and provides connected components that effectively describe the allosteric propagation of signals in different conditions and for different enzymes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Henar Mateo-delaFuente, Davide Avagliano, Marco Garavelli, Juan J. Nogueira
Summary: The absorption and emission spectra of luciferine/luciferase were calculated using molecular dynamics simulations, hybrid quantum mechanics/molecular mechanics calculations, and transition density analysis. The presence of the enzyme hampers the torsional motion of the chromophore, reducing the intramolecular charge transfer nature of the absorbing and emitting state. However, a polar environment around the oxygen atom enhances the charge transfer character of the emitting state.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Eleonora Monti, Alessia Ventimiglia, Luke Forster, Elena Rodriguez-Aguado, Juan Antonio Cecilia, Francesca Ospitali, Tommaso Tabanelli, Stefania Albonetti, Fabrizio Cavani, Ivan Rivalta, Carmine D'Agostino, Nikolaos Dimitratos
Summary: Supported Au colloidal nanoparticles were synthesized with the presence of stabilizing polymers, including PVA, PVP and PEG. The polymer to Au weight ratio was varied to control the particle size and distribution of the nanoparticles, resulting in mean diameters ranging from 3 to 8 nm. The synthesized Au catalysts were evaluated for the oxidation of glucose to glucaric acid, with the highest yield (22%) achieved using Au-PVA catalysts. Deactivation of the Au catalysts was observed and further investigation was conducted to determine the reasons.
Article
Chemistry, Multidisciplinary
Yeonsig Nam, Huajing Song, Victor M. Freixas, Daniel Keefer, Sebastian Fernandez-Alberti, Jin Yong Lee, Marco Garavelli, Sergei Tretiak, Shaul Mukamel
Summary: Understanding conical intersection (CI) dynamics and subsequent conformational changes is crucial for exploring and controlling photo-reactions in aromatic molecules. In this study, we simulate the photoinduced S-3 to S-1 non-adiabatic dynamics of cyclooctatetraene (COT) and find good agreement with experimental relaxation times. We also investigate the potential of TRUECARS and TRXD to directly probe CI passages in COT, showing that these signals can sensitively monitor key chemical features and resolve ultrafast changes in aromaticity and geometries during the dynamics.
Article
Chemistry, Physical
Aria Gheeraert, Claire Lesieur, Victor S. Batista, Laurent Vuillon, Ivan Rivalta
Summary: This paper proposes a connected component analysis (CCA) approach for analyzing protein dynamical perturbation contact networks (DPCNs). The study demonstrates that CCA outperforms clustering methods in capturing allosteric signal propagation in protein graphs, and reduces the size of DPCNs while providing connected components that describe the propagation of the signal from the effector to the active sites of the protein.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Sergey Yu. Ketkov, Sheng-Yuan Tzeng, Elena A. Rychagova, Anton N. Lukoyanov, Wen-Bih Tzeng
Summary: Metallocenes, including methylcobaltocene, play important roles in various fields of chemistry. The ionization energy and vibrational structure of (Cp ')(Cp)Co can be influenced by introducing methyl substituents. The mass-analyzed threshold ionization spectrum and DFT calculations provide accurate information about the properties and transformations of (Cp ')(Cp)Co.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Review
Chemistry, Physical
Qifeng Mu, Jian Hu
Summary: Polymer mechanochemistry has experienced a renaissance due to the rapid development of mechanophores and principles governing mechanochemical transduction or material strengthening. It has not only provided fundamental guidelines for converting mechanical energy into chemical output, but also found applications in engineering and smart devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Da Hye Yang, Francesco Ricci, Fredrik L. Nordstrom, Na Li
Summary: Through systematic evaluation of the oiling-out behavior of procaine, we identified both stable and metastable liquid-liquid phase separation, and established phase diagrams to assist in rational selection of crystallization strategies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Vikki Anand Varma, Simmie Jaglan, Mohd Yasir Khan, Sujin B. Babu
Summary: Designing engineering structures like nanocages, shells, and containers through self-assembly of colloids is a challenging problem. This work proposes a simple model for the subunit, which leads to the formation of monodispersed spherical cages or containers. The model with only one control parameter can be used to design cages with the desired radius.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Hainan Jiang, Yaolong He, Xiaolin Li, Zhiyao Jin, Huijie Yu, Dawei Li
Summary: The cycling lifespan and coulombic efficiency of lithium-ion batteries are crucial for high C-rate applications. The Li-ion concentration plays a crucial role in determining the mechanical integrity and structural stability of electrodes. This study focuses on graphite as the working electrode and establishes an experimental system to investigate the mechanical properties of composite graphite electrode at different C-rates. Considering the effect of Li-ion concentration in stress analysis is found to be significant.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Zhiye Wang, Yunchuan Li, Mingjun Sun
Summary: This study investigates the influence of intramolecular pi-pi interactions on the electronic transport capabilities of molecules. By designing and analyzing three pi-conjugated molecules, the researchers observe that different pi-conjugated structures have varying effects on electron transport. The findings provide a theoretical foundation for designing single-molecule electronic devices with multiple electron channels based on intramolecular pi-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Yuandong Xu, Haoyang Feng, Chaoyang Dong, Yuqing Yang, Meng Zhou, Yajun Wei, Hui Guo, Yaqing Wei, Jishan Su, Yingying Ben, Xia Zhang
Summary: Hollow MoS2 cubes and spheres were successfully synthesized using a one-step hydrothermal method with the hard template method. The hollow MoS2 cubes exhibited higher specific capacitance and energy density compared to the hollow MoS2 spheres. The symmetrical supercapacitors assembled with these hollow structures showed good performance and high capacity retention after multiple cycles. These findings suggest that controlling the pore structure and surface characteristics of MoS2 is crucial for enhancing its electrochemical properties.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Ainhoa Oliden-Sanchez, Rebeca Sola-Llano, Joaquin Perez-Pariente, Luis Gomez-Hortiguela, Virginia Martinez-Martinez
Summary: The combination of photoactive molecules and inorganic structures is important for the development of advanced materials in optics. In this study, bulky dyes were successfully encapsulated in a zeolitic framework, resulting in emission throughout the visible spectrum.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Miaomiao Zhang, Cunyuan Pei, Qiqi Xiang, Lintao Liu, Zhongxu Dai, Huijuan Ma, Shibing Ni
Summary: The design of a solid electrolyte interphase (SEI) plays a crucial role in improving the electrochemical performance of anode materials. In this study, lithium difluoro(oxalate)borate (LiDFOB) is used as an electrolyte additive to form a protective SEI film on Li3VO4 (LVO) anodes. The addition of LiDFOB results in a dense, uniform, stable, and LiF-richer SEI, which enhances the Li-ion storage kinetics. The generated SEI also prevents further decomposition of the electrolyte and maintains the morphology of LVO anodes during charge/discharge processes. This work demonstrates the effectiveness of LiDFOB as a multi-functional additive for LiPF6 electrolytes and provides insights into SEI construction for high-performance LVO anodes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
B. V. Andryushechkin, T. V. Pavlova, V. M. Shevlyuga
Summary: The atomic structure of the Ag(111)-p(4 x 4)-O phase was reexamined and two phases with the same periodicity were discovered. It was demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
S. L. Romo-Avila, D. Marquez-Ruiz, R. A. Guirado-Lopez
Summary: In this study, we used density functional theory (DFT) calculations to investigate the interaction between model graphene oxide (GO) nanostructures and chlorine monoxide ClO. We aimed to understand the role of this highly oxidizing species in breaking C-C bonds and forming significant holes on GO sheets. Our results showed that C-C bonds in a single graphene oxide sheet can be broken through a simple mechanism involving the dissociation of two chemically attached ClO molecules. The formation of carbonyl groups and holes on the GO surface was also observed. This study provides important insights into the degradation of carbon nanotubes and the stability of GO during the myeloperoxidase (MPO) catalytic cycle.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Alberto Garcia-Fernandez, Birgit Kammlander, Stefania Riva, Hakan Rensmo, Ute B. Cappel
Summary: In this study, the X-ray stability of five different lead halide perovskite compositions (MAPbI3, MAPbCl3, MAPbBr3, FAPbBr3, CsPbBr3) was investigated using photoelectron spectroscopy. Different degradation mechanisms and resistance to X-ray were observed depending on the crystal composition. Overall, perovskite compositions based on the MA+ cation were found to be less stable than those based on FA+ or Cs+. Metallic lead formation was most easily observed in the chloride perovskite, followed by bromide, and very little in MAPbI3. Multiple degradation processes were identified for the bromide compositions, including ion migration, formation of volatile and solid products, as well as metallic lead. CsBr was formed as a solid degradation product on the surface of CsPbBr3.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Timofei Rostilov, Vadim Ziborov, Alexander Dolgoborodov, Mikhail Kuskov
Summary: The shock-loading behavior of nanomaterials is investigated in this study. It is found that shock compaction waves exhibit a distinct two-step structure, with the formation of faster precursor waves that travel ahead of the main compaction waves. The complexity of the shock Hugoniot curve of the tested nanomaterial is described, and the effect of initial porosity on the compressed states is demonstrated.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Sergey S. Nikitin, Alexander D. Koryakov, Elizaveta A. Antipinskaya, Alexey A. Markov, Mikhail V. Patrakeev
Summary: The stability of La1/3Sr2/3Fe1-xMnxO3-delta, a perovskite-type oxide, under reducing conditions is dependent on the manganese content. Increasing the manganese content leads to a decrease in stability. The behavior of iron and manganese in the oxide shows distinct differences, which can be attributed to the difference in the enthalpy of oxidation reactions. Additionally, the change in the La/Sr ratio affects the concentration of iron and manganese ions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Mosayeb Naseri, Shirin Amirian, Mehrdad Faraji, Mohammad Abdur Rashid, Maicon Pierre Lourenco, Venkataraman Thangadurai, D. R. Salahub
Summary: Inspired by the successful transfer of freestanding ultrathin films of SrTiO3 and BiFeO3, this study assessed the structural stability and investigated the electronic, optical, and thermoelectric properties of a group of two-dimensional perovskite-type materials called perovskenes. The findings revealed that these materials are wide bandgap semiconductors with potential application in UV shielding. Moreover, they exhibit better electrical and thermal conductivity at high temperatures, enabling efficient power generation in thermoelectric devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)