Article
Chemistry, Multidisciplinary
Thomas Quenzel, Daniel Timmer, Moritz Gittinger, Jennifer Zablocki, Fulu Zheng, Manuela Schiek, Arne Lutzen, Thomas Frauenheim, Sergei Tretiak, Martin Silies, Jin-Hui Zhong, Antonietta De Sio, Christoph Lienau
Summary: Increasing the exciton coherence length of squaraine aggregates by preparing them on a metallic substrate rather than a dielectric substrate can improve the transport properties and optical response of molecular nanostructures. The reduced disorder and enhanced exciton-plasmon coupling effects observed on a gold film demonstrate the potential for improving coherent transport properties of molecular aggregates and tailoring their collective optical response for quantum optical applications.
Article
Chemistry, Multidisciplinary
Chalmers Chau, Fabio Marcuccio, Dimitrios Soulias, Martin Andrew Edwards, Andrew Tuplin, Sheena E. Radford, Eric Hewitt, Paolo Actis
Summary: This study presents a polymer-electrolyte solid-state nanopore system for analyzing biomolecular conformation under physiological conditions. By using specific salts, the system's performance is enhanced, allowing for the analysis of Chikungunya virus RNA conformation.
Article
Chemistry, Physical
Qizhou Chen, Yan Ho Kwok, Weijun Zhou, Guanhua Chen, Shaul Mukamel
Summary: A new time-domain simulation protocol for two-dimensional electronic spectra with photocurrent detection is presented in this study. Time-dependent density functional theory is applied to evaluate the photocurrent response, and a non-perturbative phase-matching approach is implemented to extract the fourth-order photocurrent signal. The simulations reveal resonant interactions between transition dipoles and incident pulses, and the identification of different sample-electrode couplings based on peaks/valleys in photocurrent spectra. Additionally, the qualitative reproduction of experimental spectra of a PbS quantum dot photocell shows stimulated electron dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Lukas Graf, Martin Knupfer, Qingqing Wang, Mats Fahlman, Xianjie Liu
Summary: Two-dimensional, high-quality perylene single crystals were successfully grown using a space-confined strategy method. The films exhibited alpha form crystallization, which was confirmed through various techniques. The optical absorption measurements showed strong anisotropy and excellent agreement with literature data, while the field-effect transistor's anisotropic mobility data demonstrated high crystalline order. Momentum-dependent studies using electron energy-loss spectroscopy revealed negative dispersion of the first exciton along the crystal b direction, with an exciton bandwidth of 72 meV. The observed behavior is believed to be a result of charge-transfer exciton coupling between perylene dimers in the unit cell.
Article
Biochemistry & Molecular Biology
Mashari Alangari, Busra Demir, Caglanaz Akin Gultakti, Ersin Emre Oren, Joshua Hihath
Summary: DNA has unique electronic properties that are sensitive to its sequence and structure, making it an attractive material for electronic DNA biosensors. This study investigates the origin of multiple conductance peaks in single-molecule break-junction measurements on DNA and demonstrates that these peaks come from different DNA conformations, such as double-stranded B-form DNA and G-quadruplex structures. By using various techniques and controls, the study shows that specific conductance values correspond to specific DNA conformations and that the occurrence of these conductance peaks can be controlled by the local environment.
Article
Crystallography
Anuradha R. Pallipurath, Jonathan M. Skelton, Andrew Britton, Elizabeth A. Willneff, Sven L. M. Schroeder
Summary: This study investigates the conformational behavior of the drug molecule lovastatin in crystallographically disordered solid and at crystal surfaces using computational modeling and spectroscopy. The results indicate that bulk disorder is driven by cooperative motion of specific groups in a crystallographic direction, while a second conformation may be present at the crystal surface.
Article
Chemistry, Multidisciplinary
Yao Fu, Zhengzhong Kang, Weicheng Cao, Jinglin Yin, Yaoquan Tu, Jianhua Li, Hanxi Guan, Yiran Wang, Qi Wang, Xueqian Kong
Summary: Understanding drug-carrier interactions in metal-organic frameworks (MOFs) is crucial for designing drug-delivery systems. This study found that defects in MOFs play a key role in loading pharmaceuticals with phosphate or phosphonate groups, enhancing capacity due to Coulombic attraction. Solid-state NMR spectroscopy and molecular simulations were used to elucidate the mechanisms of drug-carrier interactions at defects.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Medicinal
Yoseph Atilaw, Vasanthanathan Poongavanam, Caroline Svensson Nilsson, Duy Nguyen, Anja Giese, Daniel Meibom, Mate Erdelyi, Jan Kihlberg
Summary: PROTACs induce intracellular degradation of target proteins through a bifunctional structure. Structural insights into a VHL-based PROTAC revealed elongated and polar conformations in solutions, suggesting the importance of molecular chameleonicity for cell permeability.
ACS MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Christopher A. Ryan, Md Motiar Rahman, Vipin Kumar, Eriks Rozners
Summary: RNA folding is influenced by the presence of bulges consisting of unpaired nucleotides, which play a significant role in stabilizing various interactions involving RNA. This study demonstrates that triplex-forming peptide nucleic acids (PNAs) have a high affinity for single-purine-nucleotide bulges in double-helical RNA. The formation of the RNA-PNA triplex alters the equilibrium between looped out and stacked-in conformations, potentially providing a valuable tool for studying RNA structure-function relationships and developing therapeutic strategies targeting disease-related RNAs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Spectroscopy
Yukihiro Ozaki, Yusuke Morisawa, Ichiro Tanabe, Krzysztof B. Bec
Summary: Far-ultraviolet (FUV) spectroscopy in the condensed phase has attracted significant interest as a new electronic spectroscopy. The introduction of the ATR technique to the FUV region has opened up new avenues for studying electronic structures of molecules in liquids and solids, showing great promise for various applications.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Biochemistry & Molecular Biology
Asem Alenaizan, Joshua L. Barnett, Nicholas Hud, C. David Sherrill, Anton S. Petrov
Summary: The helical structures of DNA and RNA were revealed through experimental data, and the modeling programs were guided by known structures. Alternative backbone Xeno nucleic acids (XNAs) with different properties can be computationally modeled to search for plausible analogs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
P. Bryan Changala, Nadav Genossar-Dan, Ella Brudner, Tomer Gur, Joshua H. Baraban, Michael C. McCarthy
Summary: The unique optical cycling efficiency of alkaline earth metal-ligand molecules has led to significant advancements in polyatomic laser cooling and trapping. Rotational spectroscopy provides insights into the molecular properties underlying optical cycling, which is crucial for expanding the chemical diversity and scope of these platforms in quantum science. A comprehensive study of alkaline earth metal acetylides has been conducted, revealing their structure, electronic properties, and hyperfine structure, providing valuable information for precision measurement and quantum control of complex polyatomic molecules.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Spectroscopy
Yugao Xu, Tingting Yang, Tao Lu, Gang Feng
Summary: The conformational equilibria of cyclohexyl isothiocyanate and its complex with water were investigated by microwave spectroscopy and theoretical calculations. The rotational spectra of the two conformers of the bare cyclohexyl isothiocyanate, a-trans and e-trans, were measured and analyzed, as well as their isotopologues. For the binary complex with water, the rotational spectra of the monohydrates of both a-trans and e-trans were measured, and water isotopologues were also observed. The noncovalent bonding features of the monohydrates were examined using natural bond orbital analysis and symmetry-adapted perturbation theory analysis.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Materials Science, Multidisciplinary
Ivan Amelio
Summary: Multidimensional spectroscopy is a popular tool for studying electronic transitions and many-body dynamics in correlated materials. In this study, we use a proposed protocol to extract two-dimensional polaron spectra in a Fermi superfluid with an impurity. Our results show that multidimensional spectroscopy does not provide much additional information, especially in the absence of incoherent processes. Although our calculation is based on ultracold gases, we discuss the implications for exciton polarons in two-dimensional materials.
Review
Biochemistry & Molecular Biology
Tom Miclot, Aurane Froux, Luisa D'Anna, Emmanuelle Bignon, Stephanie Grandemange, Giampaolo Barone, Antonio Monari, Alessio Terenzi
Summary: In this review, the important studies on the interactions between G4s and peptides are examined, and the strengths and limitations of current analytic approaches are highlighted. It is found that the combined use of high-level molecular simulation techniques and experimental spectroscopy is the best way to design specifically tuned and selective peptides, thus controlling important biological functions.
Article
Electrochemistry
Mattia Belotti, Mohsen M. T. El-Tahawy, Nadim Darwish, Marco Garavelli, Simone Ciampi
Summary: This study explores the current response, light intensity, and spectral signatures of the cathodic electrochemiluminescence (ECL) in room temperature ionic liquids (RTILs). It demonstrates the viability of using electrode reactions to generate light emitters in RTILs and discovers that the ECL signal can persist for a certain duration after the removal of the external cathodic pulse due to the stabilization of superoxide.
Article
Chemistry, Analytical
Mattia Belotti, Mohsen M. T. El-Tahawy, Marco Garavelli, Michelle L. Coote, K. Swaminathan Iyer, Simone Ciampi
Summary: The study develops a direct, spatiotemporally resolved optical tracking method to detect and resolve convective disturbances in electrochemical reactivity. It is found that parasitic gas evolving reactions lead to overestimates of macroscopic diffusion coefficients by 10 times. A hypothesis is proposed linking large barriers to inner-sphere redox reactions to the formation of cation-rich overscreening and crowding double layer structures in imidazolium-based ionic liquids.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Abed Mohamadzade, Artur Nenov, Marco Garavelli, Irene Conti, Susanne Ullrich
Summary: Sulfur-substituted nucleobases are efficient in photoinduced intersystem crossing (ISC), making them versatile for various applications. However, a comprehensive understanding of wavelength-dependent changes in IC and ISC events is still lacking.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Giacomo Fanciullo, Silvia Orlandi, Andrey S. Klymchenko, Luca Muccioli, Ivan Rivalta
Summary: The aggregation of charged dyes in a solution, such as Rhodamine B (RB), is affected by the type of counterion, which determines the self-assembled structure and optical properties. Hydrophobic and bulky fluorinated tetraphenylborate counterions, like F5TPB, can enhance RB aggregation and form nanoparticles, affecting the fluorescence quantum yield (FQY) depending on the degree of fluorination. A classical force field (FF) based on the generalized Amber parameters was developed to model the self-assembling process of RB/F5TPB systems, consistent with experimental evidence. The simulations demonstrated the formation of nanoparticles in the RB/F5TPB system and only RB dimeric species in the presence of iodide counterions. This research provides atomistic details on the role of F5TPB counterions as spacers and represents progress towards reliable modeling of dye aggregation in RB-based materials.
Article
Multidisciplinary Sciences
Federica Maschietto, Uriel N. Morzan, Florentina Tofoleanu, Aria Gheeraert, Apala Chaudhuri, Gregory W. Kyro, Peter Nekrasov, Bernard Brooks, J. Patrick Loria, Ivan Rivalta, Victor S. Batista
Summary: Through molecular dynamics simulations and nuclear magnetic resonance spectroscopy, the authors investigate the effect of temperature on allostery in imidazole glycerol phosphate synthase (IGPS). They find that an increase in temperature triggers local amino acid dynamics, providing insights into the mechanism of allosteric regulation. This study offers an atomistic understanding of temperature-dependent allostery and its potential for controlling enzyme function.
NATURE COMMUNICATIONS
(2023)
Correction
Multidisciplinary Sciences
Federica Maschietto, Uriel N. Morzan, Florentina Tofoleanu, Aria Gheeraert, Apala Chaudhuri, Gregory W. Kyro, Peter Nekrasov, Bernard Brooks, J. Patrick Loria, Ivan Rivalta, Victor S. Batista
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Francesca Liuzzi, Alessia Ventimiglia, Alessandro Allegri, Elena Rodriguez-Aguado, Juan Antonio Cecilia, Ivan Rivalta, Nikolaos Dimitratos, Stefania Albonetti
Summary: Different series of Au on carbon catalysts were prepared via sol-immobilization using different polymers as gold nanoparticle stabilizers, which were investigated for their effects on catalyst properties and catalytic activity in the HMF oxidation reaction. Results showed that PVA led to the formation of smaller and more active nanoparticles, while PEG affected gold exposure and reduced catalyst activity due to steric effects. PVP-based catalysts had bigger and more covered Au nanoparticles. Computational studies provided insights into NP-polymer interactions and catalytic activities.
Article
Chemistry, Physical
Juliana Cuellar-Zuquin, Ana Julieta Pepino, Ignacio Fdez Galvan, Ivan Rivalta, Francesco Aquilante, Marco Garavelli, Roland Lindh, Javier Segarra-Marti
Summary: We characterized the photochemically relevant conical intersections between different DNA/RNA nucleobases using CASSCF algorithms. Our results show that the size of the active space significantly affects the conical intersection topographies, while the basis set size seems to have a minor effect. We ruled out structural changes as a key factor and highlighted the importance of accurately describing the electronic states involved in these intersections.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Aria Gheeraert, Claire Lesieur, Victor S. Batista, Laurent Vuillon, Ivan Rivalta
Summary: Describing protein dynamical networks through amino acid contacts is a powerful way to analyze complex biomolecular systems. The connected component analysis (CCA) approach allows for fast and robust analysis of dynamical perturbation contact networks (DPCNs) and outperforms clustering methods in capturing the propagation of allosteric signals within protein graphs. CCA reduces the DPCN size and provides connected components that effectively describe the allosteric propagation of signals in different conditions and for different enzymes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Henar Mateo-delaFuente, Davide Avagliano, Marco Garavelli, Juan J. Nogueira
Summary: The absorption and emission spectra of luciferine/luciferase were calculated using molecular dynamics simulations, hybrid quantum mechanics/molecular mechanics calculations, and transition density analysis. The presence of the enzyme hampers the torsional motion of the chromophore, reducing the intramolecular charge transfer nature of the absorbing and emitting state. However, a polar environment around the oxygen atom enhances the charge transfer character of the emitting state.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Optics
Swati Gangwar, Rajeev Dwivedi, V. K. Jaiswal, Ranjana Mehrotra, Shibu Saha, Parag Sharma
Summary: Traditionally, interference patterns are important for determining the orbital angular momentum (OAM) of a vortex beam. However, we demonstrate that they are also crucial for identifying and mitigating lateral misalignment in optical set-ups using the Radial Shearing Self-Interferometric (RSSI) technique. The splitting of interference patterns can help identify minute misalignments in the optical set-up, and an algorithm for automating the mitigation process has been proposed. This technique could lead to self-aligning optical set-ups.
JOURNAL OF MODERN OPTICS
(2023)
Article
Chemistry, Multidisciplinary
Eleonora Monti, Alessia Ventimiglia, Luke Forster, Elena Rodriguez-Aguado, Juan Antonio Cecilia, Francesca Ospitali, Tommaso Tabanelli, Stefania Albonetti, Fabrizio Cavani, Ivan Rivalta, Carmine D'Agostino, Nikolaos Dimitratos
Summary: Supported Au colloidal nanoparticles were synthesized with the presence of stabilizing polymers, including PVA, PVP and PEG. The polymer to Au weight ratio was varied to control the particle size and distribution of the nanoparticles, resulting in mean diameters ranging from 3 to 8 nm. The synthesized Au catalysts were evaluated for the oxidation of glucose to glucaric acid, with the highest yield (22%) achieved using Au-PVA catalysts. Deactivation of the Au catalysts was observed and further investigation was conducted to determine the reasons.
Article
Chemistry, Multidisciplinary
Yeonsig Nam, Huajing Song, Victor M. Freixas, Daniel Keefer, Sebastian Fernandez-Alberti, Jin Yong Lee, Marco Garavelli, Sergei Tretiak, Shaul Mukamel
Summary: Understanding conical intersection (CI) dynamics and subsequent conformational changes is crucial for exploring and controlling photo-reactions in aromatic molecules. In this study, we simulate the photoinduced S-3 to S-1 non-adiabatic dynamics of cyclooctatetraene (COT) and find good agreement with experimental relaxation times. We also investigate the potential of TRUECARS and TRXD to directly probe CI passages in COT, showing that these signals can sensitively monitor key chemical features and resolve ultrafast changes in aromaticity and geometries during the dynamics.
Article
Chemistry, Physical
Aria Gheeraert, Claire Lesieur, Victor S. Batista, Laurent Vuillon, Ivan Rivalta
Summary: This paper proposes a connected component analysis (CCA) approach for analyzing protein dynamical perturbation contact networks (DPCNs). The study demonstrates that CCA outperforms clustering methods in capturing allosteric signal propagation in protein graphs, and reduces the size of DPCNs while providing connected components that describe the propagation of the signal from the effector to the active sites of the protein.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
