Article
Chemistry, Physical
Deping Hu, Yu Xie, Jiawei Peng, Zhenggang Lan
Summary: The study implements the symmetrical quasi-classical dynamics method based on the Meyer-Miller mapping Hamiltonian to investigate nonadiabatic dynamics at conical intersections of polyatomic systems, utilizing different approaches for zero-point energy correction of electronic mapping variables. Results show that the gamma-adjusted version of SQC/MM dynamics performs better in certain situations, demonstrating its effectiveness in simulating photoinduced dynamics of polyatomic systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Xiaoyan Wu, Shizheng Wen, Huajing Song, Thomas Frauenheim, Sergei Tretiak, ChiYung Yam, Yu Zhang
Summary: This work presents an efficient nonadiabatic molecular dynamics simulation method based on TDDFTB theory, which accurately describes photophysical and photochemical phenomena and provides a theoretical simulation tool for predicting the properties of complex materials.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Victor M. Freixas, Walter Malone, Xinyang Li, Huajing Song, Hassiel Negrin-Yuvero, Royle Perez-Castillo, Alexander White, Tammie R. Gibson, Dmitry V. Makhov, Dmitrii V. Shalashilin, Yu Zhang, Nikita Fedik, Maksim Kulichenko, Richard Messerly, Luke Nambi Mohanam, Sahar Sharifzadeh, Adolfo Bastida, Shaul Mukamel, Sebastian Fernandez-Alberti, Sergei Tretiak
Summary: We present NEXMD version 2.0, which includes new features andimplements two hybrid quantum-classical dynamics methods. Through a comparison of these three methods in simulating photodynamics, we discuss their strengths and weaknesses. Furthermore, the expanded normal-mode analysis and constraints allow for a deeper understanding of the vibrational motions involved in vibronic dynamics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Tao Liu, Linjiang Chen, Xiaobo Li, Andrew I. I. Cooper
Summary: This study investigates the photocatalytic hydrogen evolution activity of three molecular photocatalysts (1-3) by theoretical investigations. The results reveal that slow exciton recombination, fast relaxation to the lowest-energy excited state, and a shorter charge transfer distance between the photocatalyst and the metal cocatalyst are important factors influencing the photocatalytic activity.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yinan Shu, Donald G. Truhlar
Summary: This paper discusses the tendency of a time-evolved reduced density matrix for a subsystem to assume a statistical ensemble of states rather than a coherent combination of pure-state wave functions. It also explores the decoherence phenomenon in molecular processes involving changes in the electronic state and the coordinates of the nuclei. The paper presents the necessary background for understanding decoherence, including the description of pure states and mixed states using the density matrix, as well as the concepts of pointer states and decoherence time. It further discusses the treatment of decoherence in the coherent switching with decay of mixing algorithm and the trajectory surface hopping method for semiclassical calculations of electronically nonadiabatic processes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Hassiel Negrin-Yuvero, Victor Manuel Freixas, Dianelys Ondarse-Alvarez, Laura Alfonso-Hernandez, German Rojas-Lorenzo, Adolfo Bastida, Sergei Tretiak, Sebastian Fernandez-Alberti
Summary: Photoinduced intramolecular energy transfers in multichromophoric molecules occur through specific motion directions guided by nonadiabatic coupling vectors, forming energy transfer funnels. Vibrational funnels can support persistent coherences between electronic states and reveal minor energy transfer pathways. Nonadiabatic excited-state molecular dynamics simulations with frozen nuclear motions can confirm the role of vibrational funnels in interchromophoric energy transfer. Our work highlights the usefulness of this strategy in identifying and evaluating the impact of vibrational funnels on energy transfer processes and guiding the design of materials with tunable properties and enhanced functionalities. Furthermore, we encourage the application of this methodology to various chemical and biochemical processes, such as reactive scattering and protein conformational changes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Yinan Shu, Donald G. Truhlar
Summary: Decoherence refers to the phenomenon where the density matrix of a subsystem evolves into a statistical ensemble of states instead of a coherent combination of pure-state wave functions. In molecular processes involving changes in electronic states and nuclear coordinates, the interaction between the electronic and nuclear subsystems leads to decoherence of the electronic subsystem. This paper provides background information on decoherence and discusses its treatment in the coherent switching with decay of mixing algorithm and the trajectory surface hopping method for semiclassical calculations of electronically nonadiabatic processes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Hassiel Negrin-Yuvero, Victor M. Freixas, Dianelys Ondarse-Alvarez, Ana E. Ledesma, Sergei Tretiak, Sebastian Fernandez-Alberti
Summary: Progress in the synthesis of new carbon nanorings and nanobelts broadens the library of materials with unique structural and optical properties that can be attractive for further potential applications in host-guest chemistry, nanoelectronics, and photonics. In this study, we investigate the photoexcitation and subsequent energy relaxation and redistribution of a recently synthesized zigzag carbon nanobelt using nonadiabatic excited state molecular dynamics simulations. Our results reveal the excited-state dynamical properties of the zigzag-type nanobelt that differentiate this molecule from other nanobelts, providing insights for further designs tailored for specific nanoelectronic and photonic applications.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Hassiel Negrin-Yuvero, Victor M. Freixas, Dianelys Ondarse-Alvarez, Ana E. Ledesma, Sergei Tretiak, Sebastian Fernandez-Alberti
Summary: The photoexcitation, energy relaxation, and redistribution of a recently synthesized zigzag carbon nanobelt were studied using molecular dynamics simulations. The transition dipole moments and electronic transition density were found to gradually change during the internal conversion process. The electronic relaxation involved long-lived states with large energy gaps and changes in symmetry. These results provide insights into the excited-state properties of the zigzag nanobelt and can inspire the design of tailored nanobelts for specific nanoelectronic and photonic applications.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Pratip Chakraborty, Yusong Liu, Samuel McClung, Thomas Weinacht, Spiridoula Matsika
Summary: Nonadiabatic excited state dynamics play a crucial role in various processes. The combination of theoretical and experimental developments has led to significant progress in this field, providing insights into the photophysical behavior of molecules. This Feature Article utilizes recent work combining time-resolved photoelectron spectroscopy with theoretical non-adiabatic dynamics to highlight important lessons learned. By comparing the nonadiabatic excited state dynamics of three different organic molecules, namely uracil, 1,3-cyclooctadiene, and 1,3-cyclohexadiene, the study aims to elucidate the relationship between structure and dynamics. The comparison emphasizes the influence of rigidity on dynamics and the challenges in accurately capturing dynamics through calculations.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Evaristo Villaseco Arribas, Lea M. Ibele, David Lauvergnat, Neepa T. Maitra, Federica Agostini
Summary: Trajectory-based methods, derived from approximating electron-nuclear correlation terms in the exact factorization approach, successfully capture quantum effects in light-induced molecular processes. The coupling among trajectories in these methods recovers the nonlocal nature of quantum nuclear dynamics, which is overlooked in traditional algorithms. However, some of the approximations introduced in these methods do not conserve the total energy.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Hassiel Negrin-Yuvero, Aliya Mukazhanova, Victor M. Freixas, Sergei Tretiak, Sahar Sharifzadeh, Sebastian Fernandez-Alberti
Summary: Perylene diimide (PDI) is a promising material for organic optoelectronic devices, and its properties have been analyzed in detail using nonadiabatic excited-state molecular dynamics simulations. The study found that the vibronic relaxation of PDI's photoexcitation involves persistent modulations in the spatial localization of electronic and vibrational excitations, driven by strong vibronic couplings. This behavior is independent of the molecule's symmetry, suggesting potential applications in tunable functionalities.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Valeria Bonilla, Victor M. Freixas, Sebastian Fernandez-Alberti, Johan Fabian Galindo
Summary: Organic dendrimers with pi conjugated systems can capture solar energy as a renewable source for human use. This research studied the relationship between the structure and energy transfer mechanism in these molecules through nonadiabatic excited state molecular dynamics (NEXMD). The results showed that the size of the core impacts the inter-branch energy exchange and transient exciton localization/delocalization, affecting the energy relaxation rates.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
T. Barillot, O. Alexander, B. Cooper, T. Driver, D. Garratt, S. Li, A. Al Haddad, A. Sanchez-Gonzalez, M. Agaker, C. Arrell, M. J. Bearpark, N. Berrah, C. Bostedt, J. Bozek, C. Brahms, P. H. Bucksbaum, A. Clark, G. Doumy, R. Feifel, L. J. Frasinski, S. Jarosch, A. S. Johnson, L. Kjellsson, Y. Kumagai, E. W. Larsen, P. Matia-Hernando, M. Robb, J-E Rubensson, M. Ruberti, C. Sathe, R. J. Squibb, A. Tan, J. W. G. Tisch, M. Vacher, D. J. Walke, T. J. A. Wolf, D. Wood, V Zhaunerchyk, P. Walter, T. Osipov, A. Marinelli, T. J. Maxwell, R. Coffee, A. A. Lutman, V Averbukh, K. Ueda, J. P. Cryan, J. P. Marangos, P. Kolorenc
Summary: The study investigated the dynamics of inner valence hole states in isopropanol and successfully detected the transient hole dynamics near the oxygen atom in the molecule. Through an x-ray pump-x-ray probe experiment and an ab initio theoretical treatment, the study made the first tentative observation of dynamics driven by frustrated Auger-Meitner transitions.
Article
Chemistry, Multidisciplinary
Braden M. Weight, Andrew E. Sifain, Brendan J. Gifford, Han Htoon, Sergei Tretiak
Summary: This study investigates the nonradiative relaxation process in single-walled carbon nanotubes (SWCNTs) with covalent surface defects through computational modeling. The results show that the chirality and defect composition of SWCNTs have a significant impact on the population relaxation, and provide insights into the relaxation process between band-edge states and localized excitonic states.
Article
Chemistry, Physical
Rene F. K. Spada, Mauricio P. Franco, Reed Nieman, Adelia J. A. Aquino, Ron Shepard, Felix Plasser, Hans Lischka
Summary: This work discusses the calculation of the spin-density matrix using the graphical unitary group approach. A general equation for the spin-density matrix is derived and the evaluation of this equation using Shavitt loop values is discussed. The spin-density matrix is then calculated for different structures and the physical meaning of spin-density is explained along with the quantification of negative contributions.
Article
Chemistry, Physical
Gabriel Braun, Itamar Borges Jr, Adelia J. A. Aquino, Hans Lischka, Felix Plasser, Silmar A. do Monte, Elizete Ventura, Saikat Mukherjee, Mario Barbatti
Summary: This study simulated the fluorescence of pyrene using two different theoretical approaches and confirmed that the prominent band shoulder observed after a high-energy electronic excitation is due to emission from the second-excited state (S-2). The non-Kasha behavior is a dynamic-equilibrium effect and not caused by a metastable S-2 minimum.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Mario Barbatti, Mattia Bondanza, Rachel Crespo-Otero, Baptiste Demoulin, Pavlo O. Dral, Giovanni Granucci, Fabris Kossoski, Hans Lischka, Benedetta Mennucci, Saikat Mukherjee, Marek Pederzoli, Maurizio Persico, Max Pinheiro, Jiri Pittner, Felix Plasser, Eduarda Sangiogo Gil, Ljiljana Stojanovic
Summary: Newton-X is an open-source computational platform that implements nonadiabatic molecular dynamics based on surface hopping and spectrum simulations. It describes the main features of these methods and highlights the latest developments. These methods are widely used in computational chemistry for photo-physical and photochemical investigations, making them of great importance for understanding molecular dynamics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Mattia Bondanza, Baptiste Demoulin, Filippo Lipparini, Mario Barbatti, Benedetta Mennucci
Summary: This article presents an implementation of trajectory surface-hopping nonadiabatic dynamics for a polarizable embed-ding QM/MM formulation and verifies its feasibility through testing.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Manuel Perez-Escribano, Joanna Jankowska, Giovanni Granucci, Daniel Escudero
Summary: In this article, the radiative surface hopping algorithm is presented, which allows modeling fluorescence within a semi-classical non-adiabatic molecular dynamics framework. The algorithm has been tested for the photodeactivation dynamics of trans-4-dimethylamino-4'-cyanostilbene (DCS). By treating radiative and non-radiative processes equally, the method provides a complete molecular movie of the excited-state deactivation. The proposed approach successfully captures the first fluorescence processes in DCS and reproduces the experimental fluorescence lifetime and quantum yield.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Felix Plasser, Patrick Kimber
Summary: The ability to tune excited-state energies is crucial in molecular design, but considering only the energies of the HOMO and LUMO orbitals is incomplete. In this study, we emphasize the importance of the Coulomb attraction and exchange interaction in contributing to excitation energies and demonstrate how to quantify them through quantum chemistry computations. We provide two paradigmatic examples to explain under which circumstances the lowest excited state may not be accessed via the HOMO/LUMO transition. Overall, this research provides insights into photophysical processes and the challenges in describing them.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Carlotta Pieroni, Filippo Becuzzi, Luigi Creatini, Giovanni Granucci, Maurizio Persico
Summary: We tested different sampling methods of initial conditions in surface hopping simulations, focusing on initial energy distributions and the treatment of zero point energy (ZPE). Using the gas phase photodynamics of azomethane as a test case, we found that most quantum mechanical (QM) and classical Boltzmann (CB) approaches yielded similar results in short time dynamics and decay lifetimes. However, the sampling method significantly affected the rate of ground state dissociation reaction, with QM samplings showing higher rates due to the leaking of ZPE.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Davide Accomasso, Nadia Ben Amor, Maurizio Persico, Giovanni Granucci
Summary: We describe two computational approaches for designing covalently bound dimers for singlet fission. The goal is to maximize the coupling between the singlet excited state and the double triplet state by adjusting the interaction between the chromophore units. In Design I, we search for optimal arrangements of chromophores in a stacked pair geometry and then connect them covalently. In Design II, we consider all viable ways to bind the chromophores covalently and identify the most promising dimers for singlet fission from our tested candidates. These approaches have successfully led to the design of promising dimers with large singlet-triplet couplings and favorable energetics.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY
(2023)
Article
Chemistry, Physical
Troy L. R. Bennett, Adam V. Marsh, James M. Turner, Felix Plasser, Martin Heeney, Florian Gloecklhofer
Summary: Conjugated macrocycles can exhibit concealed antiaromaticity, displaying properties observed in antiaromatic molecules due to their formal macrocyclic 4n pi-electron system. Paracyclophanetetraene (PCT) and its derivatives are prime examples, showing potential applications in battery electrode materials and electronic applications. Two dibrominated PCTs were synthesized and functionalized via Suzuki cross-coupling reactions, with optical, electrochemical, and theoretical studies revealing the tunability of PCT properties by aryl substituents.
MOLECULAR SYSTEMS DESIGN & ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Megan L. Shipton, Fathima A. Jamion, Simon Wheeler, Andrew M. Riley, Felix Plasser, Barry V. L. Potter, Stephen J. Butler
Summary: We report the first molecular probe for the selective and sensitive detection of the most abundant cellular inositol pyrophosphate 5-PP-InsP(5), as well as an efficient new synthesis. Our probe offers a potential screening methodology to identify drug-like compounds that modulate the activity of enzymes of inositol pyrophosphate metabolism.
Article
Chemistry, Multidisciplinary
Mariana T. T. do Casal, Josene M. M. Toldo, Mario Barbatti, Felix Plasser
Summary: Electronic states with partial or complete doubly excited character are important in various areas, but the classification of these states has been controversial. In this study, a physically motivated definition of doubly excited character is proposed, which is based on operator expectation values and density matrices. A classification scheme is also developed to differentiate between three cases. The differences in energy terms and practical computations are discussed, and these three cases are illustrated using different computational methods. The study provides a deeper understanding of doubly excited states and can guide improvements in their computational description.
Article
Materials Science, Biomaterials
Silvio Osella, Giovanni Granucci, Maurizio Persico, Stefan Knippenberg
Summary: This computational study investigates the photoisomerization mechanism of the azobenzene molecule in a DPPC lipid membrane. The trans-to-cis isomerization is shown to be a slow process controlled by a torsional mechanism due to strong environmental interaction, while the cis-to-trans mechanism occurs rapidly in sub-ps time scale and is governed by a pedal-like mechanism involving weaker environmental interactions and a different potential energy surface geometry.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Article
Chemistry, Physical
Bowen Ding, Manik Bhosale, Troy L. R. Bennett, Martin Heeney, Felix Plasser, Birgit Esser, Florian Gloecklhofer
Summary: This study reports the development of an unsubstituted derivative, SqTI-H, of locally aromatic alkyl-N-substituted squarephaneic tetraimide (SqTI) conjugated macrocycles. By removing sidechains, the solubility of SqTI-H is reduced, resulting in improved thermal stability and low solubility. The unsubstituted SqTI-H also exhibits reversible solid state electrochemical reduction to a globally aromatic dianion state. However, further optimization of electrode fabrication procedures is needed to overcome the solubility issues and improve the cycling performance.
FARADAY DISCUSSIONS
(2023)
