Article
Physics, Multidisciplinary
Xin Shi, Anna-Katharina Pumm, Jonas Isensee, Wenxuan Zhao, Daniel Verschueren, Alejandro Martin-Gonzalez, Ramin Golestanian, Hendrik Dietz, Cees Dekker
Summary: Researchers have demonstrated a self-assembled DNA nanostructure that exhibits flow-driven rotary motion when docked onto a nanopore. These artificial nanoengines operate autonomously under physiological conditions, providing a new approach to constructing energy-transducing motors at nanoscale interfaces.
Article
Chemistry, Multidisciplinary
Monika Schied, Deborah Prezzi, Liu Dongdong, Stefan Kowarik, Peter A. Jacobson, Stefano Corni, James M. Tour, Leonhard Grill
Summary: This study investigates the behavior of molecular motors on solid surfaces. Single motor molecules adsorbed on a Cu(111) surface are excited by voltage pulses from an STM tip, leading to their rotation around a fixed pivot point. The rotation direction of each molecule is found to be enantiomer-specific, determined by its chirality.
Article
Chemistry, Multidisciplinary
Palas Roy, Andy S. Sardjan, Wojciech Danowski, Wesley R. Browne, Ben L. Feringa, Stephen R. Meech
Summary: In this study, a novel push-pull overcrowded alkene motor was synthesized and characterized by steady-state and ultrafast time-resolved electronic spectroscopy. It was found that tuning the charge transfer character in the excited state has a significant effect on the photoisomerization yield, providing new routes for precise control of motor efficiency.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Nanoscience & Nanotechnology
Stefano Corra, Marina Tranfic Bakic, Jessica Groppi, Massimo Baroncini, Serena Silvi, Emanuele Penocchio, Massimiliano Esposito, Alberto Credi
Summary: This study presents a theoretical model and experimental evidence for the operation of an out-of-equilibrium photoactivated artificial molecular pump. The relationship between light energy input and the deviation of the dissipative state from thermodynamic equilibrium in this artificial system is quantitatively analyzed.
NATURE NANOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sofie K. Jensen, Mathias S. Neumann, Rikke Frederiksen, Mathias L. Skavenborg, Mads C. Larsen, Stinne E. Wessel, Jan O. Jeppesen
Summary: Controlling the movement of CBPQT(4+) ring is essential for the full potential utilization of artificial molecular machines. In this study, two isomeric tri-stable [2]rotaxanes incorporating TTF and MPTTF units were synthesized to measure the energy barriers during the movement of CBPQT(4+) ring. By strategically exchanging thiomethyl barriers with thioethyl groups, the movement of CBPQT(4+) ring in the synthesized compounds can be controlled to occur in only one direction. Cyclic voltammetry and H-1 NMR spectroscopy were used to investigate the switching mechanism. The results demonstrate the first successful induction of directional movement of CBPQT(4+) ring in molecular machines using a combination of TTF and MPTTF units with 90% efficiency.
Article
Chemistry, Multidisciplinary
Kuppusamy Kanagaraj, Rui Wang, Ming-Kai Zhao, Pablo Ballester, Julius Rebek Jr, Yang Yu
Summary: A series of alkyl-O-methyl aldoximes with various functional groups were synthesized and showed E-Z isomerization in organic solutions. However, these compounds exhibited high selectivity for the cis-Z isomer when confined in a water-soluble capsule. The affinities for the chalcogen-bonded capsule depended on the guest chain length and functional groups. An E-to-Z isomer selectivity of >99% was achieved with a chain length of 14 heavy atoms, and the isomerization was accelerated by sonication.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Pablo Campomanes, Stefano Vanni
Summary: The role of low-barrier hydrogen bonds (LBHBs) in the enzyme and protein activity has been debated, with computational studies supporting the existence of strong LBHB between pCA and E46 in the photoactive yellow protein (PYP). Additionally, the interaction between pCA and Y42 is described as a typical short ionic H-bond of moderate strength.
Article
Chemistry, Physical
Jing Guo, Ying Xie, Ze-Min Lai, Jiang Weng, Albert S. C. Chan, Gui Lu
Summary: The potential of electron donor-acceptor (EDA) complex photochemistry in visible light-induced photocatalyst-free radical reactions has recently been recognized. However, designing catalytic asymmetric reactions driven by EDA complexes remains challenging. Existing examples are limited to single activation modes with aminocatalysts or phase-transfer catalysts. In this study, chiral bifunctional hydrogen-bonding catalysis is demonstrated to enable the asymmetric reaction of an EDA complex via dual activation modes, resulting in the formation of vicinal tertiary stereocenters at the beta,gamma-positions of pyridines with high yields and good enantio- and diastereoselectivities.
Article
Nanoscience & Nanotechnology
Richard Korytar, Ferdinand Evers
Summary: In this paper, an alternative driving agent for molecular rotors is presented, which works even when angular momentum is conserved. Through quantitative analysis using a classical model, it is shown that in the presence of chirality, the rotor undergoes directed motion as long as the incident current exceeds a threshold value.
BEILSTEIN JOURNAL OF NANOTECHNOLOGY
(2023)
Article
Physics, Fluids & Plasmas
Hirakjyoti Sarma, Ritupan Sarmah, Nilakshi Das
Summary: The dynamics of a harmonically trapped three-dimensional Yukawa ball of charged dust particles immersed in plasma is investigated as a function of external magnetic field and Coulomb coupling parameter using molecular dynamics simulation. It is shown that the trapped dust particles self-organize into nested spherical shells. The particles start rotating in a coherent order as the magnetic field reaches a critical value corresponding to the coupling parameter of the system of dust particles. The magnetically controlled charged dust cluster of finite size undergoes a first-order phase transition from disordered to ordered phase. At sufficiently high coupling and strong magnetic field, the vibrational mode of this finite-sized charged dust cluster freezes, and the system retains only rotational motion.
Article
Chemistry, Medicinal
Prabir Khatua, Madhulika Gupta, Sanjoy Bandyopadhyay
Summary: This study investigates the conformational properties of amyloid beta (Aβ) peptides and the role of solvent (water) in guiding the dynamical environment at their interfaces. Molecular dynamics simulations reveal that the dynamics of water molecules around different segments of Aβ peptides are nonuniform and correlated with the hydrogen bond relaxation time scales. The water molecules around hp1 and hp2 form relatively rigid hydration layers, which are crucial in understanding the early stages of Aβ peptide aggregation.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Yang Zheng, Sven Herbers, Qian Gou, Walther Caminati, Jens-Uwe Grabow
Summary: Besides its typical halogen donor behavior, CF3Cl is shown to reveal a new interaction site with CO2, forming a C-dot-dot-dot-Cl tetrel bond through the Cl equatorial belt. Additionally, a secondary C-dot-dot-dot-O tetrel bond and a F-dot-dot-dot-O halogen bond may also contribute to the relative orientation of the moieties in the complex.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Deng Zhu, Lu Yu, Hui-Yun Luo, Xiao-Song Xue, Zhi-Min Chen
Summary: Selective electrophilic sulfenylation of N-aryl aminoquinone derivatives has been achieved for the first time using a new chiral sulfide catalyst. The reaction produces axially chiral sulfur-containing diarylamine derivatives with moderate to excellent yields and enantioselectivities. Experimental and computational studies confirm the importance of an intramolecular N-H center dot center dot center dot S hydrogen bond and the catalyst rigidity in the reaction.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Construction & Building Technology
Xing Quan Wang, Denvid Lau
Summary: The study shows that chloride environment significantly deteriorates the interfacial adhesion, structure, and mechanical properties of GFRP composites, hindering the formation of hydrogen bonds in the composite material.
ADVANCES IN STRUCTURAL ENGINEERING
(2021)
Article
Chemistry, Analytical
Jayakrishnan Aerathupalathu Janardhanan, Anusha Valaboju, Udesh Dhawan, Tharwat Hassan Mansoure, Ching-Cher Sanders Yan, Chou-Hsun Yang, Bhaskarchand Gautam, Chao-Ping Hsu, Hsiao-hua Yu
Summary: The study revealed that the newly designed chiral sensing platform exhibited stereoselectivity towards biomolecules with higher affinity, especially on nanotubes. The chiral nanotubes showed sensitive chiral recognition of (S)- and (R)-mandelic acid, with in vitro experiments demonstrating increased protein deposition. Molecular dynamics simulations and density functional theory calculations were used to investigate the mechanism underlying the chiral recognition between the chiral sensing platforms and analyte molecules.
Article
Chemistry, Inorganic & Nuclear
Jose Quilez-Alburquerque, Cristina Garcia-Iriepa, Marco Marazzi, Ana B. Descalzo, Guillermo Orellana
Summary: A family of ruthenium(II) complexes containing one 2,2'-biimidazole (bim) ligand and two polypyridyl (NN) ligands were prepared and tested for their photophysical and photochemical properties in the presence of the mycotoxin tenuazonic acid (TeA). The results showed changes in absorption, luminescence intensity, and triplet lifetime of the luminophore due to binding with TeA. Computational analysis using time-dependent density functional theory provided insights into the structure of the adducts and the electronic nature of the absorption bands upon addition of TeA.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Physical
Yuanheng Wang, Stefan Seritan, Dean Lahana, Jason E. Ford, Alessio Valentini, Edward G. Hohenstein, Todd J. Martinez
Summary: INTERACHEM is an interactive molecular dynamics (AI-IMD) visualizer that utilizes virtual reality hardware and graphical processing unit (GPU) acceleration to render quantum chemistry in real time. It allows exploration of electronically excited states and real-time tracking of electronic properties such as molecular orbitals and bond order. This tool aids in the interpretation of excited state chemistry data and makes quantum chemistry more accessible for research and education.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Pharmacology & Pharmacy
Elena Contreras-Garcia, Carmen Lozano, Cristina Garcia-Iriepa, Marco Marazzi, Arthur H. Winter, Carmen Torres, Diego Sampedro
Summary: Controlling the activity of pharmaceutical agents using light has the potential to enhance selectivity, reduce adverse effects, and minimize environmental impact. This study presents photoreleasable quinolones that can be activated by visible/NIR light, protected by BODIPY photocages, and regain antimicrobial activity upon light irradiation. A computational study reveals the importance of explicit solvent molecules in the reaction mechanism and the role of solvent-assisted photodissociation. The light-controlled activity of these compounds has been evaluated on quinolone-susceptible E. coli, demonstrating a significant change in antimicrobial activity.
Article
Chemistry, Multidisciplinary
Beatriz Penin, Nil Sanosa, Diego Sampedro, Ignacio Funes-Ardoiz
Summary: Studying the mechanism of the aza-Piancatelli reaction helps to understand the influence of different substituents on reactivity and guides the design of synthetic routes using this reaction.
Article
Biochemistry & Molecular Biology
Cecilia Hognon, Emmanuelle Bignon, Antonio Monari, Marco Marazzi, Cristina Garcia-Iriepa
Summary: The emergence of SARS-CoV-2 variants, such as the Alpha and Delta variants, has led to increased infectivity. In this study, molecular dynamic simulations and machine learning were used to investigate the changes in molecular interactions caused by these variants, especially in the receptor binding region.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Javier Cerezo, Cristina Garcia-Iriepa, Fabrizio Santoro, Isabelle Navizet, Giacomo Prampolini
Summary: In this study, the absorption spectrum of 5,5-spirocyclopropyl-oxyluciferin (5,5-CprOxyLH) in water was investigated computationally. The results show that non-adiabatic couplings, molecular structure, and interactions with the surrounding environment all play important roles in determining the spectral shape of 5,5-CprOxyLH. The use of quantum dynamics simulations and a mixed quantum classical protocol allows for an accurate description of these effects and provides a good agreement with experimental results.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Nil Sanosa, Diego Ambrosi, Pedro Ruiz-Campos, Diego Sampedro, Ignacio Funes-Ardoiz
Summary: Formation of carbon-carbon bonds through cross-coupling reactions using readily available substrates, like alcohols, is crucial for modern organic chemistry. Recently, direct alkyl alcohol functionalization has been achieved by the use of N-Heterocyclic Carbene (NHC) salts via in situ formation of an alcohol-NHC adduct and its activation by a photoredox catalyst to generate carbon-centered alkyl radicals. Experimental observations show that only electron deficient NHC activators work, but the reasons for this behavior are not well understood. In this study, a DFT computational approach is used to investigate the mechanism of alcohol activation using up to seven NHC salts, providing insights into the influence of their electronic properties on alkyl radical formation. The results reveal that the electron-richness of the NHC salt plays a crucial role in determining the success of the transformation.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Nil Sanosa, Pedro Ruiz-Campos, Diego Ambrosi, Diego Sampedro, Ignacio Funes-Ardoiz
Summary: Photoredox catalysis offers an alternative method for cross-coupling reactions and enables new reactivities. A recent study demonstrated that abundant alcohols and aryl bromides can efficiently promote coupling through the Ir/Ni dual photoredox catalytic cycle, although its mechanism remains unexplored. In this study, we utilized DFT calculations to comprehensively investigate the catalytic cycle and found that nickel catalysts can effectively promote this reactivity. Two different mechanistic scenarios were explored, suggesting that dual catalytic cycles operate simultaneously depending on the concentration of the alkyl radical.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Adam M. Cowden, Raul Losantos, Abigail L. Whittock, Beatriz Penin, Diego Sampedro, Vasilios G. Stavros
Summary: Sunscreens protect our DNA from UV radiation by absorbing or reflecting the rays before they reach the skin. However, concerns regarding the toxicity of current UV filters have led to a focus on natural, microbial-inspired filters. This paper provides new insight into the mechanisms of photoprotection in synthetic analogs of mycosporine-like amino acid-type UV filters, offering potential for the development of more efficient biomimetic DNA photoprotectant materials.
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2023)
Article
Chemistry, Physical
Alejandro Jodra, Cristina Garcia-Iriepa, Luis Manuel Frutos
Summary: The use of mechanical forces at the molecular level to modulate molecular properties has been studied. A new algorithm called LGMF has been developed to determine the optimal mechanical forces for tuning the electronic energy gap and to identify the maximum mechanical response of a molecular system to any mechanical stimulus.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Polymer Science
Christine Elian, Nil Sanosa, Nicolas Bogliotti, Christian Herrero, Diego Sampedro, Davy-Louis Versace
Summary: A novel anthraquinone-based oxime ester system (AQ-Ox) was synthesized and used as a Type I visible-light photoinitiating system. By introducing the anthraquinone moiety to the oxime ester group, high acrylate conversions were achieved under visible-light irradiation, and better photoinitiating properties compared to commonly used Type I photoinitiators were demonstrated. AQ-Ox also enabled the design of 3D objects by 3D photoprinting technology. This is the first example of an anthraquinone-based oxime-ester used as a Type I photoinitiator for FRP at λ > 405 nm and under air.
Article
Chemistry, Multidisciplinary
Alberto Gimenez-Gomez, Benjamin Rollins, Andrew Steele, Helen Holzel, Nicolo Baggi, Kasper Moth-Poulsen, Ignacio Funes-Ardoiz, Diego Sampedro
Summary: Solar energy utilization has gained attention for its abundance and renewability. Developing energy storing compounds that capture and release solar energy on demand is a potential solution. These compounds undergo a photochemical transformation, storing solar energy in high-energy photoisomers. While the photoisomerization of MOlecular Solar Thermal (MOST) systems has been extensively studied, the back-conversion using heterogeneous catalysts is still underexplored. In this study, the performance of 27 catalysts in releasing stored energy in a Norbornadiene/Quadricyclane MOST system is compared using UV-Vis spectroscopy. The findings provide insights for the development of effective catalysts in MOST systems and highlight the importance of further investigation on heterogeneous catalysis.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Beatriz Penin, Nil Sanosa, Diego Sampedro, Ignacio Funes-Ardoiz
Summary: The aza-Piancatelli reaction is a widely used method for synthesizing DASAs, a new class of molecular photoswitches. However, the substitution pattern of the furan core has been limited, and this study investigates the influence of different substituents on the reaction using computational calculations. A simple model is proposed to guide the design of synthetic routes.
