Article
Chemistry, Physical
Marketa Paloncyova, Martin Srejber, Petra Cechova, Petra Kuhrova, Filip Zaoral, Michal Otyepka
Summary: RNA-based therapies have shown promise in various applications. Encapsulation of RNA into lipid nanoparticles allows for safe and targeted delivery. Simulations of pH-sensitive RNA-carrying nanoparticles reveal their self-assembly process and internal structure, providing insights into their composition and potential interactions for improving RNA-based medicine.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Michal Langer, Lukas Zdrazil, Miroslav Medved, Michal Otyepka
Summary: The establishment of structure-photoluminescence (PL) relationships in carbon dots (CDs) is still a challenge. The core, surface, and molecular states are the main sources of PL, but their interaction and effects on each other are not well understood. By performing TD-DFT calculations, researchers found that different structural arrangements support the communication between PL centers. This study provides insights for designing CDs with desired surface/core characteristics.
Article
Chemistry, Medicinal
Zhengyue Zhang, Jiri Sponer, Giovanni Bussi, Vojtech Mlynsky, Petr Sulc, Chad R. Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Summary: HJ is a crucial DNA structure involved in DNA repair, recombination, and DNA nanotechnology. Molecular dynamics simulations revealed complex conformational transitions of HJs, including previously unconsidered half-closed intermediates. This study provides detailed insights into the rearrangement process of HJs and opens up possibilities for more accurate computational studies of biological processes and nanomaterials involving HJs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Petra Kuhrova, Vojtech Mlynsky, Michal Otyepka, Jiri Sponer, Pavel Banas
Summary: RNA molecules play a key role in biochemical processes and interact closely with ions and water molecules. Double-stranded RNA is important for RNA folding and the design of RNA-based nanostructures. This study used molecular dynamics simulations to investigate the effects of ion concentrations and solvation box size on A-RNA structure.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Aby Cheruvathoor Poulose, Miroslav Medved, Vasudeva Rao Bakuru, Akashdeep Sharma, Deepika Singh, Suresh Babu Kalidindi, Hugo Bares, Michal Otyepka, Kolleboyina Jayaramulu, Aristides Bakandritsos, Radek Zboril
Summary: This study presents a reusable graphene catalyst that can convert glycerol, produced from biomass fermentation, to high-value chemicals at room temperature without solvents. The catalyst shows excellent activity and selectivity for glycerol conversion to solketal, and it can also convert oils to biodiesel.
NATURE COMMUNICATIONS
(2023)
Article
Nanoscience & Nanotechnology
Akshay Kumar K. Padinjareveetil, Juan V. Perales-Rondon, Dagmar Zaoralova, Michal Otyepka, Osamah Alduhaish, Martin Pumera
Summary: Electrochemical reduction of nitrate into ammonia is a promising solution to address the challenges of growing global energy demand. Metal-organic framework (MOF)-based catalysts are being investigated for their enhanced structural and compositional integrity, making them effective in catalytic reduction reactions.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Sujit Deshmukh, Kalyan Ghosh, Martin Pykal, Michal Otyepka, Martin Pumera
Summary: Microsupercapacitors with mechanical flexibility offer potential applications in portable biomonitoring devices. Researchers have developed high-energy-density micro-SCs integrated with a force sensing device using picosecond pulsed laser technology, and demonstrated their effectiveness in monitoring human body's radial artery pulses.
Article
Biochemistry & Molecular Biology
Remi Coulon, Barbora Papouskova, Elmira Mohammadi, Michal Otyepka, Sreekar Wunnava, Jiri Sponer, Judit E. Sponer
Summary: 3',5'-Cyclic nucleotides play a fundamental role in modern biochemical processes and may have played a central role in the origin of early terrestrial life. A formamide-based systems chemistry could explain their availability on early Earth, as demonstrated by the formation of 3',5'-cyclic nucleotides in liquid formamide environments at elevated temperatures.
Article
Chemistry, Medicinal
Petr Stadlbauer, Vojtech Mlynsky, Miroslav Krepl, Jiri Sponer
Summary: In this study, steered molecular dynamics simulations were performed to investigate the unfolding mechanism of human telomeric GQs. The results showed that the direction of force, pulling velocity, and pulling force all affected the unfolding process. Additionally, it was found that a GQ could continue to unfold after a force drop. Furthermore, the study revealed that different unfolding intermediates could have similar chain end-to-end distances, suggesting limitations in structural interpretations of single-molecule spectroscopic data.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Rabindranath Lo, Martin Pykal, Andreas Schneemann, Radek Zboril, Roland A. Fischer, Kolleboyina Jayaramulu, Michal Otyepka
Summary: Covalent hybrids of graphene and metal-organic frameworks (MOFs) have great potential in various technologies, especially catalysis and energy applications, due to their combination of conductivity and porosity. The formation of an amide bond between carboxylate-functionalized graphene acid (GA) and amine-functionalized UiO-66-NH2 MOF is an efficient strategy for creating such hybrids. This study used density functional theory (DFT) calculations to elucidate the mechanism of amide bond formation between GA and UiO-66-NH2, highlighting the crucial role of zirconium within UiO-66 as a catalyst. Insight into the binding interactions between graphene derivatives and MOFs can lead to tailored synthesis strategies for these nanocomposite materials.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Dehui Qiu, Mingpan Cheng, Petr Stadlbauer, Jielin Chen, Michal Langer, Xiaobo Zhang, Qiang Gao, Huangxian Ju, Jiri Sponer, Jean-Louis Mergny, David Monchaud, Jun Zhou
Summary: The active sites of natural and artificial enzymes play a crucial role in their catalytic performance. This study focuses on G-quadruplex (GQ)/hemin DNAzymes and investigates how their active sites can be controlled and manipulated. Experimental and molecular dynamics simulation results reveal that the topology of the GQ and the flanking nucleotides influence the activation of hemin, providing valuable insights into the biocatalytic activity of GQs.
Article
Materials Science, Multidisciplinary
Rehan Anwar, Jan Navratil, Rajani K. Vijayaraghavan, Patrick J. McNally, Michal Otyepka, Piotr Blonski, M. Veronica Sofianos
Summary: The development of long-term renewable energy storage systems is crucial for a sustainable energy future. In this study, the use of CaZrO3 nanoadditives with tailored oxygen vacancies was investigated to improve the cycling performance of Limestone for long-term renewable energy storage. The sample mixed with 20% CaZrO3 nanoadditives showed the best performance, with enhanced ionic conductivity and the highest energy density values.
MATERIALS ADVANCES
(2023)
Article
Chemistry, Multidisciplinary
Yang Qiuyue, Emily P. Nguyen, David Panacek, Veronika Sedajova, Vitezslav Hruby, Giulio Rosati, de Carvalho Castro Silva Cecilia, Aristides Bakandritsos, Michal Otyepka, Arben Merkoci
Summary: Heavy metal pollutants are highly toxic and pose great concern in environmental monitoring. Electrochemical detection, hindered by mutual interferences of heavy metal ions, is a main technique with limited sensitivity to Cd2+ ions. This study introduces a metal-free and sustainable nanomaterial, cysteamine covalently functionalized graphene (GSH), which significantly enhances the sensitivity of screen-printed carbon electrode (SPCE) to Cd2+ ions while maintaining sensitivity to other heavy metals. The enhancement is attributed to the grafted thiols on the GSH sheets with strong affinity to Cd2+ ions, based on Pearson's principle. The GSH-modified SPCE also exhibits high reusability and outperforms existing SPCEs modified by non-covalently functionalized graphene derivatives. The GSH-SPCE is successfully validated in tap water.
Article
Chemistry, Physical
Vojtech Mlynsky, Petra Kuhrova, Petr Stadlbauer, Miroslav Krepl, Michal Otyepka, Pavel Banas, Jiri Sponer
Summary: Molecular dynamics simulations are commonly used to study RNA molecules. By adjusting the nonbonded parameters, the widely used AMBER OL3 ff in RNA simulations can be improved. The modified simulations show better agreement with experimental results.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(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)