Article
Chemistry, Physical
Daniel R. Nascimento, Elisa Biasin, Benjamin Poulter, Munira Khalil, Dimosthenis Sokaras, Niranjan Govind
Summary: The method utilizes TDDFT theory to calculate the light-matter couplings between different excited state manifolds in 4d transition metal systems, for solving RIXS and other two-photon spectroscopy problems. By avoiding the need to solve expensive TDDFT quadratic-response equations, the method can capture experimental features and enable the assignment of experimental peaks.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Physics, Multidisciplinary
Norimasa Sasabe, Motoi Kimata, Tetsuya Nakamura
Summary: In this study, XMCD signal was observed from compensated two-dimensional triangle AFM structures on a Kagome lattice, based on the different absorption coefficients of the three sublattices and the sign of the spin chirality. This XMCD signal is only present when the spin chirality is negative, reflecting the unique charge density anisotropies and directions of spin and orbital magnetic moments in the system.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Blazej Gierczyk, Michal F. Rode, Gotard Burdzinski
Summary: In this study, the photochromic reaction of 3-(2-methoxyphenyl)-3-phenyl-3H-benzo[f]chromene (2) was investigated using both experimental and theoretical approaches. Experimental results demonstrated that irradiation at 365 nm can generate colored transoid-cis isomers with varying lifetimes. The theoretical interpretation can potentially guide the design of new photochromic systems with optimized photofunctionality.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Joseph E. Lawrence, Jindrich Dusek, Jeremy O. Richardson
Summary: We introduce a method for calculating perturbative corrections to tunneling splittings in ring-polymer instanton approximation (RPI+PC) by computing higher-order terms in the asymptotic expansion. The method goes beyond standard instanton theory by including additional anharmonic effects through information on the third and fourth derivatives of the potential along the tunneling path. We demonstrate the applicability of RPI+PC by computing tunneling splitting in malonaldehyde and a deuterated derivative, and achieve more accurate results than previous methods.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Maria Fedyaeva, Sergey Lepeshkin, Artem R. Oganov
Summary: With the use of ab initio evolutionary algorithm USPEX, we were able to predict the structures of sulfur molecules S-n (n = 2 - 21). Our findings show that sulfur molecules with n >= 5 have stable closed helical ring structures, which aligns with experimental data and previous calculations. By examining second-order energy difference (Delta E-2), fragmentation energy (E-frag), and HOMO-LUMO gaps, we evaluated the stability of these molecules. The S-8 molecule exhibited the highest Delta E-2 value and forms the most commonly found allotropic form of sulfur, while S-12 and S-6 also showed strong positive Delta E-2 values.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Dorothea Golze, Markus Hirvensalo, Patricia Hernandez-Leon, Anja Aarva, Jarkko Etula, Toma Susi, Patrick Rinke, Tomi Laurila, Miguel A. Caro
Summary: We present a quantitatively accurate machine-learning model that can predict core-electron binding energies and obtain X-ray photoelectron spectroscopy spectra. The model combines density functional theory with GW and utilizes kernel ridge regression for machine learning predictions. We applied this new approach to disordered materials and small molecules containing carbon, hydrogen, and oxygen, achieving qualitative and quantitative agreement with experimental results, resolving spectral features within 0.1 eV of reference experimental spectra. The method only requires users to provide a structural model for the material under study to obtain XPS predictions within seconds. Our new tool is freely available online through the XPS Prediction Server.
CHEMISTRY OF MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Cheng Giuseppe Chen, Massimiliano Aschi, Marco D'Abramo, Andrea Amadei
Summary: In this paper, we presented a simplified approach to incorporate a large number of vibronic transitions into calculations, and demonstrated its accuracy and efficiency through reproducing absorption and emission spectra of aqueous indole.
Article
Astronomy & Astrophysics
Sergio V. M. C. B. Xavier, Carolina L. Benone, Luiz C. S. Leite, Luis C. B. Crispino
Summary: In this study, we investigate the scattering behavior of axially incident massless scalar waves by the Kerr-Sen black hole, a charged and rotating black hole solution from heterotic string theory. We calculate the scattering cross section using the partial wave approach for arbitrary incident wavelengths, and compare our results with those of the Kerr-Newman black hole, the general relativistic version of a charged and rotating black hole. Our numerical results demonstrate that these compact objects exhibit similar scattering properties.
Article
Chemistry, Physical
Bogdan R. Borodin, Fedor A. Benimetskiy, Valery Yu. Davydov, Ilya A. Eliseyev, Alexander N. Smirnov, Dmitry A. Pidgayko, Sergey I. Lepeshov, Andrey A. Bogdanov, Prokhor A. Alekseev
Summary: This article proposes a nano-fabrication method to create microcavities from indirect TMD multilayer flakes, which enables pronounced resonant photoluminescence enhancement due to cavity modes. High refractive index materials are used for efficient light trapping and the creation of high-Q resonators. Experimental results demonstrate the promising prospects of this approach in the field of nanophotonics.
NANOSCALE HORIZONS
(2023)
Article
Chemistry, Multidisciplinary
Zhilin Li, Qiaoqiao Li, Mengyan Cao, Zhihui Rao, Xinyu Shi, Liujiang Zhou, Xiujian Zhao, Xiao Gong
Summary: In this study, Sb3+-doped Cs2ZrCl6 crystals with excellent optical properties and stability were successfully synthesized. The crystals exhibited blue and orange-red emissions under 254 nm and 365 nm light, respectively, attributed to the presence of [ZrCl6]2- and [SbCl6]3- octahedra. The Cs2ZrCl6:xSb(3+) crystals with a PLQY of up to 52.5% showed potential for white light-emitting diode (WLED) fabrication.
Article
Multidisciplinary Sciences
Kenji Tamasaku, Munetaka Taguchi, Ichiro Inoue, Taito Osaka, Yuichi Inubushi, Makina Yabashi, Tetsuya Ishikawa
Summary: X-ray fluorescence spectroscopy is employed to analyze a two-dimensional fluorescence spectrum of copper metal, revealing two-hole satellite features resulting from atomic transitions. The use of nonlinear resonant inelastic X-ray scattering (RIXS) allows for better understanding of the complex electronic structure and the resolution of overlapping spectral features. The results obtained in this study demonstrate that RIXS can open doors for further exploration in the nonlinear regime of fluorescence spectroscopy.
NATURE COMMUNICATIONS
(2023)
Article
Materials Science, Ceramics
Osama Bagi Aljewaw, Muhammad Khalis Abdul Karim, Halimah Mohamed Kamari, Mohd Hafiz Mohd Zaid, Ali Aqeel Salim, Mohammad Hasan Abu Mhareb
Summary: The study evaluated the influence of different Nd2O3 doping contents on the physical and optical properties of glasses, showing that Nd2O3 content affects properties such as density, ion concentration, and refractive indices. Analysis of FTIR spectra and emission spectra revealed the presence of structural units in the glasses and electronic transition characteristics of Nd3+, respectively. The proposed glass system demonstrated high sensitivity to changes in Nd2O3 contents.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2022)
Article
Chemistry, Multidisciplinary
Hanen Souissi, Tahani A. Alrebdi
Summary: In this study, the transition dipole moments of the 13 (1)sigma(+) states of the (SrK)(+) molecular ion were investigated using the ab initio method based on the pseudo-potential approach. The radiative lifetimes for all vibrational levels of A and C-1 sigma(+) were calculated using these transition dipole moment curves. The inclusion of bound-free emissions probabilities and the breakdown of the approximate evaluation revealed significant changes in the lifetimes of highly excited vibrational levels.
APPLIED SCIENCES-BASEL
(2022)
Article
Chemistry, Physical
Pamela H. W. Svensson, Lucas Schwob, Oscar Granaes, Isaak Unger, Olle Bjoerneholm, Nicusor Timneanu, Rebecka Lindblad, Anna-Lydia Vieli, Vicente Zamudio-Bayer, Martin Timm, Konstantin Hirsch, Carl Caleman, Marta Berholts
Summary: The present study investigates the photofragmentation behavior of iodine-enhanced nitroimidazole-based radiosensitizer model compounds in their protonated form using near-edge X-ray absorption mass spectrometry and quantum mechanical calculations. The experimental results are explained using theoretical simulations based on density functional theory, providing important insights into the properties of these compounds.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Computer Science, Information Systems
Takashi Kusaka, Takayuki Tanaka
Summary: In modern computers, signal processing is optimized with compilers and high-speed floating-point units, reducing the need for programmers to be involved in the process. However, the residual correction method can produce accurate approximations with minimal computation cycles, which is particularly useful for low-power microcontroller units.
Article
Biochemistry & Molecular Biology
Haritha Asha, Petr Stadlbauer, Lara Martinez-Fernandez, Pavel Banas, Jiri Sponer, Roberto Improta, Luciana Esposito
Summary: The study investigates the structural behavior of a quadruplex helix sequence in human telomeres when one of the G bases is ionized to G(center dot+). It is found that the position of G(center dot+) influences structural rearrangements, electrostatic repulsion, and solvent exposure, providing new insights into guanine reactions. The research suggests structural determinants of reactivity and implications for understanding reactivity in other G-quadruplex topologies.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Physical
Paloma Lizondo-Aranda, Lara Martinez-Fernandez, Miguel A. Miranda, Roberto Improta, Thomas Gustavsson, Virginie Lhiaubet-Vallet
Summary: Joint femtosecond fluorescence upconversion experiments and theoretical calculations provide unprecedented characterization and understanding of the mutagenic etheno adduct εdC excited state relaxation. The fluorescence behavior of εdC is modified compared to dC, with increased lifetime and quantum yield. Quantum mechanical calculations reveal the involvement of a conical intersection in the nonradiative decay pathway, which explains the unique fluorescence properties of εdC and εdCH(+).
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Review
Chemistry, Multidisciplinary
Lara Martinez Fernandez, Fabrizio Santoro, Roberto Improta
Summary: This Account discusses the chemical physical effects of the interaction between light and multichromophoric assemblies (MCAs), aiming to control these processes based on our experience with nucleic acids. The article highlights the photophysics and photochemistry of DNA and its components, emphasizing the effects of nucleobases, reaction paths involving multiple bases, and factors such as backbone flexibility and solvent effect. The integration of complementary approaches, both computational and experimental, is stressed for a comprehensive understanding of the complex phenomena triggered by light absorption in MCAs.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Chemistry, Physical
Maximiliane Horz, Hafiz M. A. Masood, Hendrik Brunst, Javier Cerezo, David Picconi, Hannah Vormann, Madhava Shyam Niraghatam, Luuk J. G. W. van Wilderen, Jens Bredenbeck, Fabrizio Santoro, Irene Burghardt
Summary: In this study, we investigate the two-photon-induced vibronic transitions in polyatomic molecules using the VIbrationally Promoted Electronic Resonance experiment. Theoretical and experimental methods are employed to compute the vibronic spectra and analyze the intensity distribution in the two-photon experiment. The results demonstrate the importance of interference between Franck-Condon and Herzberg-Teller effects in this process.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Javier Cerezo, Fabrizio Santoro
Summary: We introduce FCclasses3, a code for vibronic simulations of electronic spectra and nonradiative rates. The code includes several new features such as the implementation of vertical and adiabatic harmonic models, vibrational analysis in curvilinear coordinates, extension to various electronic spectroscopies, and time-dependent approaches.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(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, Medicinal
Haritha Asha, James A. Green, Luciana Esposito, Fabrizio Santoro, Roberto Improta
Summary: This study uses the FrDEx model to simulate the ECD spectra of guanine-rich DNA sequences in quadruple helices with different topologies. The parameters of the FrDEx Hamiltonian are obtained from TD-DFT calculations with the M052X functional. The FrDEx spectra are in good agreement with the TD-DFT ones and show improvement compared to a standard excitonic Hamiltonian. The inclusion of the inner K+ cation in the calculation affects the ECD spectra.
Article
Chemistry, Physical
Francesco Segatta, Daniel Aranda Ruiz, Flavia Aleotti, Martha Yaghoubi, Shaul Mukamel, Marco Garavelli, Fabrizio Santoro, Artur Nenov
Summary: This paper presents an accurate and efficient approach for calculating the linear and nonlinear optical spectroscopy of a closed quantum system. The method includes the effect of ultrafast nonadiabatic dynamics by numerically propagating the nuclear wave packet. The expressions for the evaluation of response functions are recast in a general form and validated using the multiconfiguration time-dependent Hartree method. The application to pyrene reveals the remarkable influence of ultrafast nonadiabatic dynamics on spectral line shapes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Qiushuang Xu, Yanli Liu, Meishan Wang, Javier Cerezo, Roberto Improta, Fabrizio Santoro
Summary: In this study, the vibrational Resonance Raman (vRR) spectra of cytosine in water were computationally investigated using potential energy surfaces (PES) calculated by time-dependent density functional theory (TD-DFT) and CAM-B3LYP and PBE0 functionals. The close-lying and coupled electronic states of cytosine posed a challenge for the commonly used approach to compute vRR spectra. Two recently developed time-dependent approaches, based on either quantum dynamical numerical propagations or analytical correlation functions, were adopted to compute the vRR spectra. The inclusion of specific solute-solvent interactions remarkably improved the agreement with experiments by altering the composition of the normal modes.
Article
Biochemistry & Molecular Biology
Javier Cerezo, Sheng Gao, Nicola Armaroli, Francesca Ingrosso, Giacomo Prampolini, Fabrizio Santoro, Barbara Ventura, Mariachiara Pastore
Summary: We conducted a joint experimental and theoretical study on the steady-state spectroscopy and time-resolved emission of the coumarin C153 dye in methanol. The lowest energy excited state of this molecule exhibits an intramolecular charge transfer, which results in significant shifts in the time-resolved emission spectra due to the methanol reorganization dynamics. By applying a novel computational protocol that combines the Ad-MD|gVH approach with nonequilibrium molecular dynamics simulations, we achieved accurate predictions of the transient emission spectral shapes, including both vibronic and solvent effects. The overall agreement between the calculated spectra and the experimental results demonstrates the effectiveness of our approach, although some deviations were found at low energies and in the sub-ps timescale due to fast solvent dynamics and experimental time resolution limitations.
Article
Biochemistry & Molecular Biology
Roberto Improta
Summary: I-motifs are non-canonical DNA structures composed of intercalated hemiprotonated (CH.C)+ pairs. This study characterizes the photoactivated behavior of the (CH.C)+ core of I-motifs using time-dependent DFT calculations, providing a comprehensive understanding of their absorption, emission, and possible photochemical reactions. The results reproduced and assigned the spectral signatures of I-motifs, including infrared, absorption, fluorescence, and circular dichroism spectra, and proposed potential photoproducts through a photodimerization reaction with strong C?CH+ charge transfer character.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Lara Martinez-Fernandez, Roberto Improta
Summary: In this study, the effect of pH reduction on the excited state processes of cytidine and a cytidine/cytidine pair in solution was investigated. Time-dependent density functional theory and CASSCF/CASPT2 calculations were used, along with a mixed discrete/continuum model to account for solvent effects. The results revealed the influence of N3 protonation on the steady-state infrared and absorption spectra of protonated cytidine, and predicted the presence of a non-radiative deactivation route for its spectroscopic state.
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2023)