Article
Chemistry, Organic
Souvik Ghosh, Christoph Eschen, Nadi Eleya, Anne Staubitz
Summary: This article presents the synthesis and functionalization of 12-membered azobenzene macrocycles (AzMs) to obtain meta- and para-aryl substituted AzMs. The substituents significantly impact the thermal stability of the less-stable Z isomers.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Organic
Souvik Ghosh, Christoph Eschen, Nadi Eleya, Anne Staubitz
Summary: This study presents the synthesis and versatile functionalization of 12-membered azobenzene macrocycles (AzMs). By introducing different substituents at different positions in the periphery, the thermal half-lives of the less-stable Z isomers can be significantly influenced. Meta-substitution leads to slower thermal relaxation compared to para-substitution, and electron-withdrawing groups result in slower relaxation than electron-donating groups.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Materials Science, Multidisciplinary
Qingbin Yang, Jing Ge, Mengmeng Qin, Hui Wang, Xiaoyu Yang, Xinlei Zhou, Bo Zhang, Yiyu Feng, Wei Feng
Summary: This study investigated the characteristics of three asymmetric alkoxy-substituted azobenzene molecules in terms of crystallization and isomerization. It was found that by optimizing molecular structures and interactions, phase-change azobenzene derivatives can be designed for ideal energy storage systems at different temperatures.
SCIENCE CHINA-MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Seonghyeon Park, Dongwon Kim, Doheon Kim, Dongwook Kim, Ok-Sang Jung
Summary: The cyclic manipulation of peanut cage isomers has been achieved through anion exchange and unusual cage isomerism.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Inorganic & Nuclear
Piotr Cecot, Anna Walczak, Grzegorz Markiewicz, Artur R. Stefankiewicz
Summary: By incorporating a photoresponsive azobenzene linker into a doubly chelating bis(diimine)-type ligand, complexation with transition metal ions yielded structurally distinct metallosupramolecular architectures. These complexes exhibit reversible interconversions in solution by varying the M : L ratio, or turning into a dynamic library of mononuclear species upon addition of a competing monoamine. Despite the reversible photoactivity of the azo bond in the unbound ligand, the complexes are photochemically inert due to the inherent topology resulting from coordinate bond formation restrictions.
INORGANIC CHEMISTRY FRONTIERS
(2021)
Article
Biochemistry & Molecular Biology
Javeed Ahmad Sheikh, Himanshu Sekhar Jena, Sanjit Konar
Summary: Two structurally dissimilar 3d-4f cages were isolated under similar reaction conditions, with Co3Gd4 exhibiting a significant magnetocaloric effect and Co3Dy3 showing single molecule magnet behavior. The incorporation of a μ3-carbonate anion seems to be the main factor for the structural diversity between the two complexes.
Article
Chemistry, Multidisciplinary
Kang-Kai Liu, Zong-Jie Guan, Mengting Ke, Yu Fang
Summary: Researchers reported a series of porous coordination cage (PCC) flexible supercapacitors with tunable three-dimensional (3D) cavities and redox centers. These supercapacitors exhibited excellent capacitor performances, including a superior molecular capacitance of 2510 F mmol-1, high areal capacitances of 250 mF cm-2, and unique cycle stability. The electrochemical behavior of PCCs was found to be influenced by the size, type, and open-close state of the cavities. These findings provide crucial theoretical support for designing powerful electrode materials for flexible energy storage devices.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Massimo Delle Piane, Luca Pesce, Matteo Cioni, Giovanni M. Pavan
Summary: Spatial confinement is widely used in nature to control chemical reactions, and supramolecular metal-organic cages have attracted increasing interest for their ability to control and accelerate reactions under confinement. However, the complex nature of these systems makes it difficult to understand the factors controlling reactivity in dynamic regimes. This study focuses on a coordination cage that can enhance the hydrolysis of amide guests by favoring their mechanical twisting under confinement. A multiscale simulation approach is used to reconstruct the reactivity in these host-guest systems, and the results are in good agreement with experimental trends. This study provides a flexible computational framework for understanding and controlling reactions in reactive host-guest systems.
Article
Engineering, Environmental
Marcel Jonathan Hidajat, Gwang-Nam Yun, Dong Won Hwang
Summary: This study aimed to develop a sustainable and renewable production process for linear a-olefins (LAOs) through the dehydration of alcohols. Lanthanum (La)-incorporated ?-Alumina (Al2O3) was selected as the catalyst, with a loading of up to 10 wt%. The addition of La modified the properties of Al2O3, including its acidity and basicity. The prepared catalysts were then used to dehydrate 1-octanol, resulting in the selective production of 1-octene due to the suppression of isomerization activity by lanthanum oxide (La2O3) species anchored on Al2O3, which caused a significant decrease in the number of strong acid sites of Al2O3. The effects of temperature and La loading on the dehydration and isomerization rates were also investigated.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Multidisciplinary Sciences
Anna S. Kamenik, Isha Singh, Parnian Lak, Trent E. Balius, Klaus R. Liedl, Brian K. Shoichet
Summary: Protein flexibility poses a major challenge in library docking, and energy penalties from molecular dynamics simulations were used to test flexible receptor docking in this study. Incorporating penalty terms was crucial for balanced sampling of molecules in docking results.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Inorganic & Nuclear
Bo Dong, Yanling Yu, Zdenek Slanina, Feng Wang, Yongfu Lian, Filip Uhlik, Lai Feng
Summary: The study isolated two isomers of Ho2C94 and confirmed that the internal carbide cluster displays variable configurations with very small distortion energy in a relatively large fullerene cage. The research showed that the nanoscale compression effect is almost negligible in the broad geometrical range of the internal carbide cluster within the fullerene cage.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Physical
Jing Sun, Oriol Vendrell
Summary: This letter investigates the observed modification of thermal chemical rates in Fabry-Perot cavities and explains the mechanism behind the reduction in transmission coefficient and rate due to friction caused by cavity-reactor coupling. The authors evaluate the transmission coefficient and identify conditions for rate acceleration using an ab initio potential energy surface for the cis-trans isomerization of HONO.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Courtney Ngai, Hoi-Ting Wu, Bryce Camara, Christopher G. Williams, Leonard J. Mueller, Ryan R. Julian, Richard J. Hooley
Summary: A self-assembled cage structure was synthesized by controlling the self-assembly of internal amines. Despite carrying a positive charge, the structure can extract protons from water in solution. The internal amines have lower basicity compared to their counterparts in free solution. This moderation is a hallmark of enzymatic catalysis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Anssi Peuronen, Anni I. I. Taponen, Elina Kalenius, Ari Lehtonen, Manu Lahtinen
Summary: In this study, a coordination cage assembled from Cu3I4- clusters and tripodal cationic N-donor ligands was synthesized and its structure was determined. The cage selectively binds iodide anions in specific regions through ionic interactions, which enables the selective binding of bromomethanes as secondary guest species. This selective binding was confirmed by single-crystal X-ray diffraction.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Inorganic & Nuclear
Valentinos Mouarrawis, Eduard O. Bobylev, Bas de Bruin, Joost N. H. Reek
Summary: In this study, three novel cubic cages were synthesized to encapsulate a catalytically active cobalt(II) meso-tetra(4-pyridyl)porphyrin guest. The different exo-functionalization of the newly developed caged catalysts led to variations in the polarity of the peripheral environment surrounding the cage, affecting the local concentration of substrates and ultimately influencing the substrate availability for catalysis. The resulting increased local substrate concentrations resulted in higher catalytic activities of the respective caged catalysts in metalloradical catalyzed cyclopropanation reactions.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Chiara Lionello, Claudio Perego, Andrea Gardin, Rafal Klajn, Giovanni M. Pavan
Summary: The self-assembly of nanoparticles driven by small molecules or ions can produce colloidal superlattices with properties resembling those of metals or semiconductors. In this study, molecular simulations show that a behavior evocative of semiconductors can emerge in a colloidal superlattice. By focusing on gold nanoparticles self-assembling into FCC crystals via mediation by citrate counterions, it is shown that the diverse behavior of ions in different superlattice domains allows the opening of conductive ionic gates under applied electric fields. Crossing the band gap at a supramolecular level requires sufficient electrostatic stimulus to break intermolecular interactions and enable ion diffusion.
Review
Chemistry, Multidisciplinary
Tarak Karmakar, Aaron R. Finney, Matteo Salvalaglio, A. Ozgur Yazaydin, Claudio Perego
Summary: Concentration-driven processes in solution are fundamental chemical processes that are crucial for various applications. Molecular dynamics plays a vital role in understanding these processes, but the computational costs limit the scale of simulation systems, making it difficult to study such phenomena effectively. A novel simulation technique called constant chemical potential molecular dynamics (C mu MD) has been proposed to address this challenge.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Chemistry, Physical
Matteo Cioni, Daniela Polino, Daniele Rapetti, Luca Pesce, Massimo Delle Piane, Giovanni M. Pavan
Summary: Metals can undergo dynamic reconfigurations even below the melting temperature, which is important for understanding their surface properties. This study uses deep-potential molecular dynamics simulations to analyze the complex dynamics of different copper surfaces near the Huttig temperature. The use of high-dimensional structural descriptors and unsupervised machine learning allows the identification and tracking of atomic environments in these surfaces. The findings reveal the statistical identity of metal surfaces and their dynamic interconversions networks.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Giovanni M. Pavan, Annalisa Cardellini, Martina Crippa, Chiara Lionello, Syed Pavel Afrose, Dibyendu Das
Summary: We propose a machine-learning approach to reconstruct the structural and dynamic complexity of mono- and bicomponent surfactant micelles using high-dimensional data. By clustering smooth overlap of atomic position (SOAP) data, we can identify the dominant local molecular environments in multicomponent surfactant micelles and trace their dynamics. Tested on micelles of various sizes and chemical compositions, this approach successfully recognizes molecular motifs and correlates them to their constitutive surfactant species in an unbiased and unsupervised manner.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Weichao Xue, Luca Pesce, Adinarayana Bellamkonda, Tanya K. Ronson, Kai Wu, Dawei Zhang, Nicolas Vanthuyne, Thierry Brotin, Alexandre Martinez, Giovanni M. Pavan, Jonathan R. Nitschke
Summary: This article reports on a tetrahedral FeII4L4 cage formed by the coordination of triangular chiral, face-capping ligands to iron(II). This cage exists as two diastereomers in solution, which differ in the stereochemistry of their metal vertices but share the same point chirality of the ligand. Guest binding subtly perturbs the equilibrium between these cage diastereomers, and atomistic well-tempered metadynamics simulations provide insight into the interplay between stereochemistry and fit. Understanding the stereochemical impact on guest binding enables the design of a straightforward process for the resolution of enantiomers.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Hugh P. Ryan, Zachary S. Fishman, Jacob T. Pawlik, Angela Grommet, Malgorzata Musial, Felix Rizzuto, James C. Booth, Christian J. Long, Kathleen Schwarz, Nathan D. Orloff, Jonathan R. Nitschke, Angela C. Stelson
Summary: The environment around a host-guest complex is determined by intermolecular interactions and plays a crucial role in their solubility and reaction rates. However, these interactions are difficult to detect with standard analytical techniques. In this study, we used microwave microfluidic measurements and principal component analysis to quantify the hydration and ion pairing of a coordination cage. The results showed that introducing guest molecules into the solution displaced the bound counterions and the solvent solubility of the guest had the greatest impact on the solvent and ion-pairing dynamics surrounding the host.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Antara Reja, Sumit Pal, Kishalay Mahato, Baishakhi Saha, Massimo Delle Piane, Giovanni M. Pavan, Dibyendu Das
Summary: Researchers reported a light-responsive reaction system where the binding sites for C-C bond manipulation were regulated by a photosensitive molecular cofactor. This system achieved a more efficient catalytic state under nonequilibrium conditions with the energy of the light source. Additionally, the binding of a molecular catalyst enhanced activity and facilitated the in situ generation of a light-sensitive cofactor.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Martina Crippa, Annalisa Cardellini, Cristina Caruso, Giovanni M. Pavan
Summary: We propose a descriptor called Local Environments and Neighbors Shuffling (LENS) that controls the behavior of complex systems by identifying dynamic domains and detecting local fluctuations. LENS characterizes the global dynamics of molecular systems, including phase transitions, phases coexistence, and local fluctuations, by tracking the changes in the surrounding of each molecular unit based on neighbor individuals over time. Statistical analysis of LENS time series data from molecular dynamics trajectories enables efficient tracking of dynamic domains and local fluctuations. LENS is robust, versatile, and applicable to various systems, as long as trajectory information on the relative motion of interacting units is available.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Luigi Leanza, Claudio Perego, Luca Pesce, Matteo Salvalaglio, Max von Delius, Giovanni M. Pavan
Summary: Mechanically-interlocked molecules (MIMs) are the basis of artificial molecular machines and have various potential applications. The dynamics of MIMs at sub-molecular resolution and on relevant timescales is challenging to study experimentally and computationally. In this study, molecular dynamics and metadynamics simulations are used to investigate the thermodynamics and kinetics of different types of MIMs.
Article
Chemistry, Multidisciplinary
Ignacio Insua, Annalisa Cardellini, Sandra Diaz, Julian Bergueiro, Riccardo Capelli, Giovanni M. Pavan, Javier Montenegro
Summary: This study investigates the sequential assembly mechanism of new monolayer architectures of cyclic peptide nanotubes. The results demonstrate the potential of cyclic peptide scaffolds for the rational design of supramolecular polymerization processes and hierarchical self-assembly.
Article
Computer Science, Artificial Intelligence
Martina Crippa, Annalisa Cardellini, Matteo Cioni, Gabor Csanyi, Giovanni M. Pavan
Summary: In complex molecular systems, it is important to understand the relationships between local structural environments and dynamic events in order to explain macroscopic behavior. By combining advanced structural and dynamical descriptors, it is possible to improve the analysis and extract useful microscopic-level relationships.
MACHINE LEARNING-SCIENCE AND TECHNOLOGY
(2023)