Article
Chemistry, Multidisciplinary
Gustavo Cardenas, Maximilian F. S. J. Menger, Nicolas Ramos-Berdullas, Pedro A. Sanchez-Murcia
Summary: In this study, we identified the main factors influencing the turn-on/turn-off fluorescence of a Se-modified uracil probe at the ribosomal RNA A-site. The constrained in-plane conformation of the two rings of the fluorophore plays a major role in the turn-on fluorescence emission in the presence of paromomycin, while the electrostatics of the environment has a minor effect. Our computational analysis suggests that in the absence of paromomycin, the probe tends to adopt conformations with a dark S-1 electronic state involving n pi* electronic transition contributions between the selenium atom and the uracil moiety's pi-system.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Spectroscopy
Marcos Mandado, Nicolas Ramos-Berdullas
Summary: Experimental and theoretical studies have shown that 2D hybrid structures formed by boron, nitrogen and carbon atoms possess highly tunable optical responses, motivating a significant amount of research in this area. By controlling the synthesis of these unique structures, it is possible to effectively confine and manipulate the optical responses, allowing for precise tuning and control.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Materials Science, Multidisciplinary
Daniel Garcia-Lojo, David Mendez-Merino, Ignacio Perez-Juste, Angel Acuna, Luis Garcia-Rio, Alfonso Rodriguez-Paton, Isabel Pastoriza-Santos, Jorge Perez-Juste
Summary: This study presents a new solution-based surface-enhanced Raman scattering (SERS) detection method that uses a special surfactant to control the assembly of gold nanoparticles, improving the reliability and reproducibility of the detection. The results show excellent performance in nanomolar drug detection and quantification, with portability. Additionally, using convolutional neural networks allows for accurate classification of different mixture concentrations. Finally, the method was successfully implemented in a millifluidic chip, achieving automation and performance improvement.
ADVANCED MATERIALS TECHNOLOGIES
(2022)
Article
Biochemistry & Molecular Biology
Jesus Sanmartin-Matalobos, Pilar Bermejo-Barrera, Ignacio Perez-Juste, Matilde Fondo, Ana M. Garcia-Deibe, Yeneva Alves-Iglesias
Summary: In this study, the interaction between Cu2+ ions/CuO nanoparticles and the fluorescent Schiff base ligand H3L was investigated using DFT methods and spectroscopic analysis. The results revealed that H3L exhibits similar affinity towards both Cu2+ ions in solution and Cu2+ ions on the surface of CuO nanoparticles. Fluorescence measurements suggested the presence of multiple binding sites for H3L on the CuO nanoparticles. The findings are important for understanding the binding mechanism and developing detection methods for CuO nanoparticles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Organic
Micael Paulino, Ignacio Perez-Juste, Maria Magdalena Cid, Jose P. Da Silva, M. Manuela A. Pereira, Nuno Basilio
Summary: Stimuli-responsive supramolecular receptors are important for self-assembled functional materials. A pH and light-responsive 2-hydroxychalcone-beta-cyclodextrin conjugate was designed and synthesized, and its properties were characterized. The receptor can undergo photochemical reactions under different pH conditions, allowing control over its stability and binding properties using combinations of pH and light stimuli.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Analytical
Jesus Sanmartin-Matalobos, Pilar Bermejo-Barrera, Ignacio Perez-Juste, Matilde Fondo, Ana M. Garcia-Deibe, Yeneva Alves-Iglesias
Summary: We investigated the use of the ligand H3L as a fluorescent chemosensor for detecting CdSe nanoparticles and CdSe-Cys quantum dots in ethanol-water samples. Our results showed that H3L exhibited a significant fluorescence quenching when CdSe NPs and CdSe-Cys QDs were added. We were able to detect CdSe NPs and CdSe-Cys QDs with low limits of detection using H3L, and the fluorescence intensity response of H3L-modified cellulose paper allowed us to easily detect CdSe-Cys QDs using a smartphone color recognizer application.
Article
Chemistry, Medicinal
Alvaro Perez-Barcia, Gustavo Cardenas, Juan J. Nogueira, Marcos Mandado
Summary: In this study, an Energy Decomposition Analysis (EDA) scheme extended to the framework of QM/MM calculations in the context of electrostatic embeddings (QM/MM-EDA) is used to assess the convergence of different interaction energy components for systems interacting with water. The results show that including a bulk solvent environment in the EDA scheme improves the convergence compared to pure QM calculations. The study also reveals that a surprisingly large number of water molecules is necessary for converged values of the electrostatic interaction.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Gustavo Cardenas, Jesus Lucia-Tamudo, Henar Mateo-delaFuente, Vito F. Palmisano, Nuria Anguita-Ortiz, Lorena Ruano, Alvaro Perez-Barcia, Sergio Diaz-Tendero, Marcos Mandado, Juan J. Nogueira
Summary: We introduce a toolkit for preparing QM/MM input files from a collection of molecular geometries. The toolkit is compatible with trajectory and topology files in various formats and can generate QM/MM input files for multiple software programs. It can be used via command line or as a Python application programming interface. The toolkit is applied to different scenarios involving the electronic properties of organic molecules in solvents and complex biological environments, demonstrating its versatility and ability to handle both ground and excited states.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Daniel R. Ramos, Paul G. Furtmueller, Christian Obinger, Angeles Pena-Gallego, Ignacio Perez-Juste, J. Arturo Santaballa
Summary: Electronic structure calculations using DFT were conducted to examine the influence of water molecules and protonation on the heme group of peroxidases in different redox and spin states. The study discusses shared geometries, spectroscopic properties, and thermodynamics of peroxidases. Computed Gibbs free energies suggest that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) center in native ferric peroxidases with a non-bonding water molecule. Protonation of the ferryl oxygen of compound II is found to be necessary and computed Gibbs free energies reveal pK(a) values of approximately 8.5-9.0 for compound II.
Article
Biochemistry & Molecular Biology
Raul Alvarado, Gustavo Cardenas, Juan J. Nogueira, Nicolas Ramos-Berdullas, Marcos Mandado
Summary: This study simulated the permeation of dioxin-like pollutants through lipid membranes using CMD and umbrella sampling. The results showed that TCDD and TCDF reached energy minima at distances of 8 angstrom and 9.5 angstrom from the centre of the membrane, respectively. The interactions between the molecules and the lipid membrane were mainly governed by dispersion forces, independent of the toxicity of the molecules.
Article
Chemistry, Multidisciplinary
Xing Liu, Yanli Du, Shenli Wang, Yu Huang, Yongzhi Tian, Daniel Garcia-Lojo, Ignacio Perez-Juste, Jorge Perez-Juste, Isabel Pastoriza-Santos, Guangchao Zheng
Summary: This article investigates the synthesis of chiral cobalt oxide nanoparticles mediated by histidine and discovers their unique and tunable chiroptical properties. The analysis indicates that the ratio of Co2+/Co3+ and their interactions with the imidazole groups of histidine are behind their chiral properties. Furthermore, the study demonstrates the use of chiral cobalt oxide nanoparticles for the development of sensitive and enantioselective circular dichroism-based sensors.
Article
Chemistry, Analytical
Raul Alvarado, Nicolas Otero, Marcos Mandado, Nicolas Ramos-Berdullas
Summary: The ability of 2D hybrid structures (h-BNCs) formed by boron, nitrogen, and carbon atoms as potential substrates for surface-enhanced Raman spectroscopy (SERS) detection of dioxin-like pollutants is theoretically analyzed. The strong confinement and high tunability of the electromagnetic response of carbon nanostructures within h-BNC sheets make them promising for optical spectroscopies, such as SERS. The analysis of adsorption complexes and Raman spectra shows a high affinity of BNC96 for pollutants, with large enhancement factors observed for both static and pre-resonance Raman spectra.
Article
Chemistry, Inorganic & Nuclear
Carlos Martin-Fernandez, Maxime Ferrer, Ibon Alkorta, M. Merced Montero-Campillo, Jose Elguero, Marcos Mandado
Summary: Multiply charged complexes bound by noncovalent interactions have been studied in organic and main group inorganic systems. In this work, we investigate similar complexes in organometallic systems containing transition metals and provide insights into their existence. Our results reveal that carboxylic acid-containing dimers are more strongly bonded and have higher barriers to dissociation compared to amide ones, and cationic complexes are more stable than anionic ones. Additionally, we report a symmetric proton transfer in the metastable phase.
INORGANIC CHEMISTRY
(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)