Article
Chemistry, Physical
Sergio Perez-Conesa, Eric G. Keeler, Dongyu Zhang, Lucie Delemotte, Ann E. McDermott
Summary: The pH-gated prokaryotic channel KcsA has been extensively studied as the first potassium channel with an x-ray structure determined, but questions related to the allosteric coupling between its gates remain open. Solid-state nuclear magnetic resonance (SSNMR) can provide insights into the molecular basis of activation mechanisms by studying the wild-type protein under activating conditions, and simulation techniques such as molecular dynamics (MD) simulations can help determine the activated state captured in SSNMR experiments.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
You Wang, Jorge Ivan Amaro-Estrada, Carlos Torres-Verdin
Summary: In this study, molecular dynamics simulations were used to investigate the NMR and diffusion properties of confined sodium chloride solutions within calcite nanopores. The results demonstrate that the presence of NaCl inhibits water movement, leading to reduced self-diffusion coefficients and relaxation times. However, the effects of NaCl on water mobility are smaller than those caused by pore size and geometry. Moreover, sodium ions have an impact on the trajectory and interactions of water molecules.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2023)
Article
Materials Science, Ceramics
Bhargav Akkinepally, I. Neelakanta Reddy, Tae Jo Ko, Kisoo Yoo, Jaesool Shim
Summary: The performance of NASICON-type LiZr2(PO4)3 solid electrolytes for Li-ion batteries relies on their ion transportation properties. Al doping was found to enhance the ionic conductivity and diffusion in LZP solid electrolytes. Computational and experimental results confirmed the improvement in ion conductivity and diffusion with Al doping, while excessive doping led to a decrease in ionic conductivity due to Li-ion trapping.
CERAMICS INTERNATIONAL
(2022)
Article
Chemistry, Physical
Kalil Bernardino, Mauro C. C. Ribeiro
Summary: Ionic liquids have attracted attention for their unique physical properties and have been explored as lubricants and additives to lubricants. This study uses molecular dynamics simulations to investigate the behavior of a nanoscopic film of an ionic liquid confined between two solid surfaces. The interaction strength between the surfaces and ions is varied, resulting in the formation of a solid-like layer with different structures and stability. Different viscosity definitions, based on microscopic characteristics and forces measured at the solid surfaces, are proposed and show a correlation with the layered structure induced by the surfaces. The viscosities decrease with increasing shear rate due to shear thinning behavior and viscous heating.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Carlos A. Ramos-Guzman, Milorad Andjelkovic, Kirill Zinovjev, J. Javier Ruiz-Pernia, Inaki Tunon
Summary: In this study, the by-residue decomposition of noncovalent interactions and analysis of naturally occurring mutations were used to detect potential mutations in the 3CL protease of SARS-CoV-2 that confer resistance to nirmatrelvir. It was found that the E166V mutation reduces the binding affinity of the protease to nirmatrelvir and increases the activation free energy for the formation of the covalent enzyme-inhibitor complex, resulting in resistance to the treatment with this drug. The conclusions of this study can be useful for predicting the consequences of introducing nirmatrelvir in the virus fitness landscape and designing new inhibitors targeting possible resistance mechanisms.
Article
Chemistry, Physical
Xiaojun Wu, Haizhang Mu, Bihong Li
Summary: In this study, molecular dynamics simulations were used to investigate the microstructure and dynamics of clindamycin confined in nanopores. The results showed layering behavior of clindamycin distribution near the surface of the nanopores, along with strong interactions between carbonyl oxygen and silanol groups on the pore surface. Clindamycin molecules near the surface exhibited higher local diffusion coefficients.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Shu-Shun Hsueh, S. -S. (Steven) Wang, Shu-Han Chen, Chia-Lin Wang, W. (Josephine) Wu, Ta-Hsien Lin
Summary: This study used NMR-solution HGDC structures as starting conformers for molecular dynamics simulations to investigate the unfolding process of HGDC and the early stages of cataractogenesis. The high-resolution details of the conformational dynamics provided insights into the domain swap theories proposed by past studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Polymer Science
Andrey O. Kurbatov, Nikolay K. Balabaev, Kirill A. Litvin, Elena Yu. Kramarenko
Summary: Carbosilane dendrimers are ideal models for studying the effect of a hyperbranched regular structure on molecular response in the absence of specific interactions. This study used atomistic molecular dynamics simulations to investigate the conformational behavior of polybutylcarbosilane dendrimers between impermeable flat surfaces. The results showed that the generation number and branching functionality influenced the number of wall contacts, density distribution, and shape changes of the dendrimers. Additionally, high generation dendrimers had inaccessible inner layers and excess stresses were concentrated in the structural center under high compressions.
Article
Chemistry, Multidisciplinary
Karina Pivnic, J. Pedro de Souza, Alexei A. A. Kornyshev, Michael Urbakh, Martin Z. Z. Bazant
Summary: Water and other polar liquids show nanoscale structuring near charged interfaces, resulting in solvation forces. Molecular dynamics simulations demonstrate strong orientational ordering in nanoconfined polar liquids with different dielectric constants and molecular shapes and sizes. A coarse-grained continuum theory is applied to rationalize the observed structures and establish a simple law for the decay length of interfacial orientations, which depends on molecular size and polarity. These insights are important for understanding solvation forces in various fields.
Article
Polymer Science
Andrey Milchev, Sergei A. Egorov, Kurt Binder
Summary: Lyotropic solutions containing two types of semiflexible macromolecules in spherical confinement were studied through molecular dynamics simulations and density functional theory. In dilute solutions, the main effect of the surfaces is to perturb the random orientation of the end-to-end vectors of the stiff chains. In more concentrated systems, there is an additional observation of a thin layer of wall-attached stiff chains.
Article
Chemistry, Multidisciplinary
Fabio Pietrucci, Mauro Boero, Wanda Andreoni
Summary: Water pollution by heavy metals is a growing concern due to its severe environmental and health impacts. Natural materials, like spent coffee grains or fruit peels, are being explored as potential cheap alternatives for heavy metal removal. Molecular simulations show that hemicellulose may efficiently capture lead ions from water through spontaneous adsorption on specific functional groups.
Article
Biochemistry & Molecular Biology
Loretta Akakpo, Edward Ntim Gasu, Jehoshaphat Oppong Mensah, Lawrence Sheringham Borquaye
Summary: This study used molecular docking and molecular dynamics simulations to explore the inhibitory activity of some natural products against Plasmodium falciparum dihydrofolate reductase (PfDHFR). Two compounds were found to have stable binding and could be considered as potential antifolate agents.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Monica L. Fernandez-Quintero, Eugene F. DeRose, Scott A. Gabel, Geoffrey A. Mueller, Klaus R. Liedl
Summary: In this study, the conformational diversity of an anti-GFP-binding nanobody was characterized using molecular dynamics simulations and experimental data from NMR spectroscopy. The results showed excellent agreement between the distance maps obtained from NMR and MD simulations, as well as similar conformational spaces for simulations with and without time-averaged restraints. The motions observed in the ps-ns timescale, particularly in the CDR3 loop, also showed good agreement between measured and calculated order parameters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Yoshiki Ishii, Nobuyuki Matubayasi, Go Watanabe, Takashi Kato, Hitoshi Washizu
Summary: The molecular simulations on the behavior of water molecules in nanochannels formed by self-assembled ionic liquid crystals reveal that water molecules are confined inside the nanochannels with the formation of hydrogen bonding network, allowing for water transport through the advantages of dissolution and diffusion mechanisms within the ionic nanochannels.
Article
Biochemistry & Molecular Biology
Dorota Kowalska, Joanna Dolzonek, Krzysztof Zamojc, Sergey A. Samsonov, Martyna Maszota-Zieleniak, Joanna Makowska, Piotr Stepnowski, Anna Bialk-Bielinska, Dariusz Wyrzykowski
Summary: Human serum albumin (HSA) plays a crucial role in binding low-molecular-weight compounds and facilitating their distribution in living organisms. This study investigates the impact of counter-ions, such as [B (CN)4]- and [C(CN)3]-, on the affinity of [IM1-12]+ towards HSA. Experimental methods and computational approaches are used to analyze protein-ligand interactions and the thermal stability of resulting complexes. The findings provide valuable insights into the presence of globular proteins and ionogenic compounds in the environment and living organisms.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Materials Science, Ceramics
Alejandra Calvo, Leandro Andrini, Federico J. Williams, Jose M. Ramallo-Lopez, Galo J. A. A. Soler-Illia, Felix G. Requejo
Summary: Mesoporous hybrid materials with inorganic and organic functional groups show potential for advanced applications such as separation, sorption, and catalysis. Studying the structure and variations of these materials under different conditions is crucial for understanding multiscale control and optimizing performance.
JOURNAL OF SOL-GEL SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemical Research Methods
Emilia Silletta, Manuel Velasco, Gustavo A. Monti, Rodolfo H. Acosta
Summary: Diffusion-relaxation correlation experiments in nuclear magnetic resonance are a powerful technique for characterizing fluid dynamics in confined geometries or soft matter. T-1-D acquisition time is always shorter than D-T-2 in single-sided NMR, with this time reduction potentially up to an order of magnitude. The experiments provide analytical calculations and examples in model porous media and dairy products.
JOURNAL OF MAGNETIC RESONANCE
(2022)
Article
Materials Science, Ceramics
Esteban A. Franceschini, Gustavo Gimenez, M. Veronica Lombardo, Andres Zelcer, Galo J. A. A. Soler-Illia
Summary: Interest in core-shell materials with chemically tunable mesoporous surfaces has grown, with aerosol synthesis techniques offering faster production and easier separation of functional materials. A green chemistry method was presented for coating sub-micron colloidal particles with mesoporous metal oxide nanofilms, demonstrating high reproducibility and continuous production capabilities. The obtained nanofilms were characterized by various analytical techniques, showing different pore sizes and film thicknesses depending on the particulate support used.
JOURNAL OF SOL-GEL SCIENCE AND TECHNOLOGY
(2022)
Review
Materials Science, Ceramics
Diego F. Lionello, Juan Ignacio Ramallo, Galo J. A. A. Soler-Illia, Maria Cecilia Fuertes
Summary: The mechanical properties of ordered mesoporous thin films and the experimental techniques used to measure them are discussed in this review. The relationship between hardness (H) and elastic modulus (E) with structural features such as porosity (P) are analyzed for several mesoporous systems. Additionally, tribological and fractomechanical features are assessed.
JOURNAL OF SOL-GEL SCIENCE AND TECHNOLOGY
(2022)
Article
Polymer Science
Estefania Gonzalez Solveyra, David H. Thompson, Igal Szleifer
Summary: Protein adsorption onto nanomaterials is controlled by functionalizing their surface with polymers, and the efficiency depends on design parameters, surface curvature, and solution conditions. A comprehensive study analyzing the effect of these factors was conducted using molecular theory calculations.
Article
Chemistry, Multidisciplinary
M. Jazmin Penelas, Gustavo F. Arenas, Fernando Trabadelo, Galo J. A. A. Soler-Illia, Sergio E. Moya, Paula C. Angelome, Cristina E. Hoppe
Summary: In this study, monodisperse silica-coated gold nanoparticles were synthesized to obtain aqueous colloidal dispersions with an optimal balance between colloidal stability and photothermal activity. The presence of a silica shell not only enhanced the photothermal effect but also controlled the optical properties of the colloidal dispersions, making them highly valuable for biomedical therapies, sensing applications, and other technological applications.
Article
Physics, Applied
Santiago Bussandri, Geronimo Sequeiros, Pablo R. Zangara, Rodolfo H. Acosta, Carlos A. Meriles
Summary: Investigated the dynamics of a system consisting of a spin-1 paramagnetic center and a hyperfine-coupled spin-1/2 nucleus near a level crossing. Theoretical analysis showed efficient nuclear spin polarization under the combined action of thermal fluctuations and a closed-loop feedback protocol. This microwave-free technique benefits from warmer operation temperatures and promises opportunities for high-field dynamic nuclear polarization.
PHYSICAL REVIEW APPLIED
(2022)
Review
Chemistry, Multidisciplinary
Gervasio Zaldivar, Yamila A. Perez Sirkin, Gabriel Debais, Maria Fiora, Leandro L. Missoni, Estefania Gonzalez Solveyra, Mario Tagliazucchi
Summary: The supramolecular organization of soft materials is driven by the balance of weak intermolecular interactions and entropy. The application of molecular theory allows for the study of self-assembly in these materials and provides estimates of stability for different morphologies.
Article
Chemistry, Multidisciplinary
Manuel I. Velasco, Agustin Iborra, Juan M. Giussi, Omar Azzaroni, Rodolfo H. Acosta
Summary: This study explores the use of a benchtop low-field single-sided NMR to determine the species distribution in complex aqueous-organic systems known as Winsor III. The results show that the salinity of the aqueous phase affects the species distribution in the bicontinuous system, and the methodology used provides information at both macroscopic and microscopic levels. Additionally, the study demonstrates the ability of single-sided NMR to determine the phases' dimensions and the species distribution in a polymer-based bicontinuous system.
Article
Physics, Atomic, Molecular & Chemical
Franco A. Milana, Manuel I. Velasco, Gustavo A. Monti, Rodolfo H. Acosta
Summary: Relaxation in nuclear magnetic resonance (NMR) provides microscopic information and can be used to monitor dynamic processes. This study explores the applicability of single-sided NMR for determining the evaporation kinetics of fluid from porous media. The results show that longitudinal relaxation experiments can provide reliable and fast data acquisition for monitoring water evaporation from a model oil-reservoir rock sample.
APPLIED MAGNETIC RESONANCE
(2023)
Editorial Material
Chemistry, Physical
Galo J. A. A. Soler-Illia, Marco Faustini, Luis M. Liz-Marzan
CHEMISTRY OF MATERIALS
(2023)
Review
Chemistry, Multidisciplinary
Maria L. Scala-Benuzzi, Sol N. Fernandez, Gustavo Gimenez, Gabriel Ybarra, Galo J. A. A. Soler-Illia
Summary: Electrochemical sensors are increasingly important in medicine, environmental monitoring, and industrial process control. However, their development faces challenges such as low target compound concentrations and complex analytical matrices. Mesoporous Thin Films (MTFs) have attracted great interest as electrode modifications due to their high surface area, uniform pore distribution, and electrochemical signal modulation possibilities. To fully exploit the advantages of MTFs, reproducible methods for sensitive and selective MTF-modified electrodes need to be developed, and mass and charge transport processes within the film and on the electrode need to be understood.
Article
Chemistry, Multidisciplinary
Sebastian Alberti, Sonja Schmidt, Simone Hageneder, Paula C. Angelome, Galo J. A. A. Soler-lllia, Philipp Vana, Jakub Dostalek, Omar Azzaroni, Wolfgang Knoll
Summary: Nanopores have various applications in biocatalysis, drug delivery, and sensing devices. The interaction between biomacromolecules and surfaces is influenced by nanopore diameter, which is important for their infiltration into porous materials. We present a novel approach for synthesizing large-pore mesoporous silica thin films (MTF) through supramolecular templating and phase separation using block copolymers. The tunability of pore size distribution is achieved through reversible addition-fragmentation chain transfer (RAFT) polymerization.
MATERIALS CHEMISTRY FRONTIERS
(2023)
Article
Materials Science, Multidisciplinary
Roberta Pigliapochi, Daniela Pagliero, Lisandro Buljubasich, Artur Lozovoi, Rodolfo H. Acosta, Pablo R. Zangara, Carlos A. Meriles
Summary: In this study, transitions between hybrid multispin states formed by strongly coupled electronic and nuclear spins in diamond are probed using magnetic field cycling experiments, optical spin pumping, and variable radiofrequency (RF) excitation. Complex nuclear polarization patterns of alternating sign are uncovered, revealing the impact of strongly hyperfine-coupled nuclei on the spin dynamics of the crystal.
