Article
Chemistry, Physical
Leila Shahrokh, Reza Omidyan, Gholamhassan Azimi
Summary: The study utilizes ab initio and surface-hopping nonadiabatic dynamics simulation methods to investigate relaxation mechanisms in protonated thymine (TH+) and cytosine (CH+). Multiple conical intersections were located between (1)pi pi* and S-0 states for each system, with particular focus on the barrier-free out-of-plane deformation governing relaxation from the (1)pi pi* state to the ground state. The ring puckering coordinate from the C-6 position of the heterocycle ring was found to play a prominent role in the deactivation mechanism of the considered systems, supported by excited-state nonadiabatic dynamics simulations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Leila Shahrokh, Reza Omidyan, Gholamhassan Azimi
Summary: The non-radiative relaxation mechanism of protonated adenine was investigated using quantum chemical computational methods and dynamics simulations. It was found that the out-of-plane deformation of the six-member ring plays a significant role in the deactivation of the excited state to the ground state, which is important for the photostability of protonated DNA/RNA bases.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Yanjiao Wang, Ge Han, Xiuying Jiang, Tairan Yuwen, Yi Xue
Summary: NH groups in proteins or nucleic acids are challenging for chemical shift prediction. A lookup table linking base pair triplets to experimental chemical shifts can predict imino chemical shifts of RNAs accurately, even for non-canonical motifs. Combining this prediction with NMR relaxation dispersion experiments helps verify the presence of excited states in RNA motifs.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Ruth Chau-Ting Chan, Chris Tsz-Leung Chan, Chensheng Ma, Kang-Yi Gu, Han-Xin Xie, Allen Ka-Wa Wong, Qing-Wu Xiong, Ming-Liang Wang, Wai-Ming Kwok
Summary: This study investigates the excited state dynamics of protonated Adenosine (AdoH(+)) using ultrafast time-resolved fluorescence spectroscopy and theoretical calculation, revealing different conformers leading to distinct excited states and decay dynamics. Protonation and solvent environment play a crucial role in dramatically altering the excited states of Ado, providing valuable insights for understanding the nonradiative dynamics of both monomeric bases and oligomeric or polymeric DNAs.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Keisuke Hirata, Ken-Ichi Kasai, Koki Yoshizawa, Gilles Gregoire, Shun-Ichi Ishiuchi, Masaaki Fujii
Summary: This study investigates protonated dopamine water clusters using electronic and vibrational spectroscopy in a cryogenic ion trap. The spectroscopic results are compared and assigned with quantum chemistry calculations performed in different states. The researchers observe a significant hydration effect when dopamine is solvated by three water molecules. The study also reveals conformer selectivity in the 1-3 complex, where the occurrence of an excited state proton transfer reaction depends on the hydrogen bond network formed between dopamine and water molecules.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Ivana Stankovic, Sonja Zrilic, Branislav Milovanovic, Ana Stanojevic, Milena Petkovic, Mihajlo Etinski
Summary: Stabilizing G-quadruplexes with small molecules can control oncogenes' overexpression in cancer cells, but the success depends on ligand-quadruplex selectivity. In this study, TPyP4 was found to have stronger selectivity towards the overhang of the c-MYC promoter G-quadruplex compared to other ligands. The binding affinity of TPyP4 for intercalation was higher than for end-stacking, and metalation of TPyP4 with an octahedral cation might further stabilize intercalation.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Wataru Aiba, Takamitsu Amai, Mitsuyoshi Ueda, Kouichi Kuroda
Summary: This study successfully increased the efficiency of precise genome editing by creating a donor DNA/guide RNA hybrid duplex. Compared to editing with separately introduced gRNA and donor DNA, the HDR-mediated editing efficiency using this hybrid duplex technique was improved by 1.8-fold.
Article
Chemistry, Organic
Xin Ma, Erlu Feng, Hanning Jiang, Victoria M. Boulos, Jinshan Gao, John J. Nash, Hilkka Kenttamaa
Summary: The gaseous 2,6-didehydropyridinium cation and its derivatives undergo proton transfer reactions from their lowest-energy excited triplet states, potentially due to unfavorable molecular orbital interactions in their singlet ground states. These cations have smaller singlet-triplet splittings compared to other analogues, likely due to reduced orbital overlap caused by the presence of a nitrogen atom. Both singlet and triplet states are believed to be generated upon formation of biradicals, with triplet states leading to faster proton transfer rates unless heavy atoms are present in the biradicals.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Physical
Massimo Olivucci, Thierry Tran, Graham A. Worth, Michael A. Robb
Summary: The study examines the nuclear dynamics during the photoisomerization reaction, focusing on double bond inversion. The molecule exhibits characteristics similar to a conical intersection during the process of double bond inversion, even when the states are nondegenerate.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Analytical
Zai-Ming Qiu, Fei Liu, Zhi-Wu Yu, Xin-Yu Li
Summary: In this study, the protonation properties of hypoxanthine (I) and DNA bases were investigated using the MP2 method. The stability of protonated base pairs in DNA was found to decrease in the order of (I:A + H) + > (I:C + H) + > (I:G + H) + > (I + H:T) + based on CID results and calculated structures.
CHINESE JOURNAL OF ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Shi-Jie Hou, Yi-Fan Yang, Zhong-hua Cui, Lorenz S. Cederbaum
Summary: Anions play an important role in chemistry, but their excited states are generally unstable. This study focused on two promising prototype candidates, Li@C-12 and Li@C-20 anions, and found stable doubly-excited states in addition to stable singly-excited states. The discovery provides insights into designing anions with stable valence singly- and doubly-excited states, and potential applications are mentioned.
Article
Chemistry, Inorganic & Nuclear
Z. -M. Qiu, X. -P. Zhang
Summary: This study utilized density functional theory to investigate the protonation properties of xanthine, adenine, cytosine, guanine, and thymine, revealing the relative stability of protonated base pairs in the order of X:AH(+) > X:CH+ > X:GH(+) > XH+:T. The occurrence of a specific structure between xanthine and adenine may lead to a transition from G:C to T:A.
JOURNAL OF STRUCTURAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Ge Han, Yi Xue
Summary: This study developed a method to design excited states of RNA and verified their existence through experiments. Additionally, a mechanism of multi-step sequential transition was revealed, expanding the scope of RNA rational design and improving predictions of RNA secondary structure.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Rocio Borrego-Varillas, Artur Nenov, Piotr Kabacinski, Irene Conti, Lucia Ganzer, Aurelio Oriana, Vishal Kumar Jaiswal, Ines Delfino, Oliver Weingart, Cristian Manzoni, Ivan Rivalta, Marco Garavelli, Giulio Cerullo
Summary: Researchers have found that 5-methyluridine has a lifespan an order of magnitude longer than uridine due to solvent reorganization needed for bulky methyl group motion. The photophysical mechanism by which nucleosides dissipate energy after UV light irradiation remains a topic of debate.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Keisuke Hirata, Ken-ichi Kasai, Gilles Gregoire, Shun-ichi Ishiuchi, Masaaki Fujii
Summary: UV and IR spectra of protonated dopamine and its hydrated clusters were measured, showing different spectral features. Structure and excited state lifetime were determined through calculations, suggesting that water insertion inhibits excited state proton transfer.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Lucinda E. Mulko, Maximiliano Rossa, Juan P. Aranguren-Abrate, Gustavo A. Pino
APPLIED SURFACE SCIENCE
(2019)
Article
Chemistry, Physical
Martin I. Taccone, Andres F. Cruz-Ortiz, Jordan Dezalaly, Satchin Soorkia, Michel Broquier, Gilles Gregoire, Cristian G. Sanchez, Gustavo A. Pino
JOURNAL OF PHYSICAL CHEMISTRY A
(2019)
Article
Chemistry, Physical
Rafael A. Jara-Toro, Javier A. Barrera, Juan P. Aranguren-Abrate, Raul A. Taccone, Gustavo A. Pino
JOURNAL OF PHYSICAL CHEMISTRY A
(2020)
Article
Chemistry, Physical
Lucinda E. Mulko, Emma A. Cuello, Cesar A. Barbero, Gustavo A. Pino, Maria Molina, Maximiliano Rossa
APPLIED SURFACE SCIENCE
(2020)
Article
Chemistry, Physical
Andres F. Cruz-Ortiz, Martin I. Taccone, Philippe Maitre, Maximiliano Rossa, Gustavo A. Pino
Article
Chemistry, Physical
Walter E. Olmedo, Liliana B. Jimenez, Andres F. Cruz-Ortiz, Philippe Maitre, Gustavo A. Pino, Maximiliano Rossa
Summary: This study presents the first structural characterization of protonated cyameluric acid ([CA + H](+)) in the gas phase, revealing that the available O positions on neutral CA are energetically favored protonation sites. Ab initio computations predict different reduced isomer populations of [CA + H](+) in solution and gas phases, indicating the occurrence of isomer interconversion reactions during their transfer into the gas phase.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Optics
Andres F. Cruz-Ortiz, Rafael A. Jara-Toro, Matias Berdakin, Estelle Loire, Gustavo A. Pino
Summary: The silver-mediated cytosine-guanine [CGAg](+) pair was characterized by mass-resolved IRMPD spectroscopy and electronic structure calculations at the DFT level. Two isomers of the [CGAg](+) complex were identified based on the mass-resolved IRMPD spectra recorded on the mass of each fragment. The yields of each fragment are strongly dependent on the isomer of the precursor ion due to the fragmentation energy of the different channels.
EUROPEAN PHYSICAL JOURNAL D
(2021)
Article
Chemistry, Physical
Andres F. Cruz-Ortiz, Franco L. Molina, Philippe Maitre, Gustavo A. Pino
Summary: This paper presents IRMPD spectra of ionic complexes between guanine and silver, showing the presence of two isomers containing different keto-amino tautomers. Experimental results in aqueous solution are in agreement with calculated results, indicating coexistence of specific tautomers. Other tautomers' presence depends on the theoretical method for solvent effects.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Environmental Sciences
Maria de los A. Garavagno, Federico J. Hernandez, Rafael A. Jara-Toro, Genesys Mahecha, Javier A. Barrera, Raul A. Taccone, Gustavo A. Pino
Summary: The degradation process of cyclobutanol by hydroxyl radical under atmospheric conditions was studied, and the reaction mechanism and rate coefficient were determined using experimental and theoretical methods. The identification of reaction products in clean and NOx-contaminated atmospheres was performed, and the atmospheric implications were discussed.
ATMOSPHERIC ENVIRONMENT
(2022)
Article
Chemistry, Physical
Andres F. Cruz-Ortiz, Rafael A. Jara-Toro, Juan P. Aranguren, Debora Scuderi, Gustavo A. Pino
Summary: The collision-induced dissociation of the protonated cytosine-guanine pair was studied using MS3 coupled to infrared multiple photon dissociation spectroscopy. The structure of the CH+ and GH(+) ionic fragments was determined, and electronic structure calculations were used for rationalization. Several tautomers of each fragment were identified, including two unexpected ones. These results emphasize the importance of tautomerization in DNA base pairs assisted by proton or hydrogen transfer.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Franco L. Molina, Rafael A. Jara-Toro, Jennifer A. Noble, Claude Dedonder-Lardeux, Christophe Jouvet, Gustavo A. Pino
Summary: The photodetachment and stability of R-Mandelate, the deprotonated form of R-Mandelic acid, were investigated. It was found that R-Mandelate has the possibility to form an intramolecular ionic hydrogen-bond, and the stability of the resulting radicals is dependent on the position of the proton.
Article
Chemistry, Physical
Franco Molina, Jordan Dezalay, Satchin Soorkia, Michel Broquier, Majdi Hochlaf, Gustavo Ariel Pino, Gilles Gregoire
Summary: By photodissociating cold cytosine-silver complexes, isomer-selected radical cations of DNA bases have been successfully generated, leading to unambiguous structural assignment of cytosine and providing important data for studying the stability of DNA strands.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Martin Taccone, Ricardo A. Fernandez, Franco L. Molina, Ignacio Gustin, Cristian G. Sanchez, Sergio A. Dassie, Gustavo A. Pino
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
Jennifer Anna Noble, Juan P. Aranguren-Abate, Claude Dedonder, Christophe Jouvet, Gustavo A. Pino
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2019)
Article
Chemistry, Physical
Gustavo A. Pino, Rafael A. Jara-Toro, Juan P. Aranguren-Abrate, Claude Dedonder-Lardeux, Christophe Jouvet
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2019)
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)
