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Capone M, Romanelli M, Castaldo D, Parolin G, Bello A, Gil G, Vanzan M. A Vision for the Future of Multiscale Modeling. ACS PHYSICAL CHEMISTRY AU 2024; 4:202-225. [PMID: 38800726 PMCID: PMC11117712 DOI: 10.1021/acsphyschemau.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 05/29/2024]
Abstract
The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first principles. Indeed, countless biological, catalytic and photophysical processes require ab initio treatments to be properly described, but the breadth of length and time scales involved makes it practically unfeasible. A way to address these issues is to couple theories and algorithms working at different scales by dividing the system into domains treated at different levels of approximation, ranging from quantum mechanics to classical molecular dynamics, even including continuum electrodynamics. This approach is known as multiscale modeling and its use over the past 60 years has led to remarkable results. Considering the rapid advances in theory, algorithm design, and computing power, we believe multiscale modeling will massively grow into a dominant research methodology in the forthcoming years. Hereby we describe the main approaches developed within its realm, highlighting their achievements and current drawbacks, eventually proposing a plausible direction for future developments considering also the emergence of new computational techniques such as machine learning and quantum computing. We then discuss how advanced multiscale modeling methods could be exploited to address critical scientific challenges, focusing on the simulation of complex light-harvesting processes, such as natural photosynthesis. While doing so, we suggest a cutting-edge computational paradigm consisting in performing simultaneous multiscale calculations on a system allowing the various domains, treated with appropriate accuracy, to move and extend while they properly interact with each other. Although this vision is very ambitious, we believe the quick development of computer science will lead to both massive improvements and widespread use of these techniques, resulting in enormous progresses in physical chemistry and, eventually, in our society.
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Affiliation(s)
- Matteo Capone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, L’Aquila 67010, Italy
| | - Marco Romanelli
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Davide Castaldo
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Giovanni Parolin
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Alessandro Bello
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Gabriel Gil
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Instituto
de Cibernética, Matemática y Física (ICIMAF), La Habana 10400, Cuba
| | - Mirko Vanzan
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, University of Milano, Milano 20133, Italy
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2
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Sarangi R, Nanda KD, Krylov AI. Two- and one-photon absorption spectra of aqueous thiocyanate anion highlight the role of symmetry in the condensed phase. J Comput Chem 2024; 45:878-885. [PMID: 38156823 DOI: 10.1002/jcc.27282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 01/03/2024]
Abstract
We present the two-photon absorption (2PA) spectrum of aqueous thiocyanate calculated using high-level quantum-chemistry methods. The 2PA spectrum is compared to the one-photon absorption (1PA) spectrum computed using the same computational protocol. Although the two spectra probe the same set of electronic states, the intensity patterns are different, leading to an apparent red-shift of the 2PA spectrum relative to the 1PA spectrum. The presented analysis explains the intensity patterns and attributes the differences between the 1PA and 2PA spectra to the native symmetry of isolated SCN - , which influences the spectra in the low-symmetry solvated environment. The native symmetry also manifests itself in variations of the polarization ratio (e.g., parallel vs. perpendicular cross sections) across the spectrum. The presented results highlight the potential of 2PA spectroscopy and high-level quantum-chemistry methods in studies of condensed-phase phenomena.
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Affiliation(s)
- Ronit Sarangi
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Kaushik D Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
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3
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Haggag O, Baer R, Ruhman S, Krylov AI. Revisiting the benzene excimer using [2,2] paracyclophane model system: Experiment and theory. J Chem Phys 2024; 160:124111. [PMID: 38530011 DOI: 10.1063/5.0196641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
We report high-level calculations of the excited states of [2,2]-paracyclophane (PCP), which was recently investigated experimentally by ultrafast pump-probe experiments on oriented single crystals [Haggag et al., ChemPhotoChem 6 e202200181 (2022)]. PCP, in which the orientation of the two benzene rings and their range of motion are constrained, serves as a model for studying benzene excimer formation. The character of the excimer state and the state responsible for the brightest transition are similar to those of the benzene dimer. The constrained structure of PCP allows one to focus on the most important degree of freedom, the inter-ring distance. The calculations explain the main features of the transient absorption spectral evolution. This brightest transition of the excimer is polarized along the inter-fragment axis. The absorption of the light polarized in the plane of the rings reveals the presence of other absorbing states of Rydberg character, with much weaker intensities. We also report new transient absorption data obtained by a broadband 8 fs pump, which time-resolve strong modulations of the excimer absorption. The combination of theory and experiment provides a detailed picture of the evolution of the electronic structure of the PCP excimer in the course of a single molecular vibration.
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Affiliation(s)
- Omer Haggag
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 9190401, Israel
| | - Roi Baer
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 9190401, Israel
| | - Sanford Ruhman
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 9190401, Israel
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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4
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Palmisano VF, Agnorelli C, Fagiolini A, Erritzoe D, Nutt D, Faraji S, Nogueira JJ. Membrane Permeation of Psychedelic Tryptamines by Dynamic Simulations. Biochemistry 2024. [PMID: 38324395 PMCID: PMC10882957 DOI: 10.1021/acs.biochem.3c00598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Renewed scientific interest in psychedelic compounds represents one of the most promising avenues for addressing the current burden of mental health disorders. Classic psychedelics are a group of compounds that exhibit structural similarities to the naturally occurring neurotransmitter serotonin (5-HT). Acting on the 5-HT type 2A receptors (HT2ARs), psychedelics induce enduring neurophysiological changes that parallel their therapeutic psychological and behavioral effects. Recent preclinical evidence suggests that the ability of psychedelics to exert their action is determined by their ability to permeate the neuronal membrane to target a pool of intracellular 5-HT2ARs. In this computational study, we employ classical molecular dynamics simulations and umbrella sampling techniques to investigate the permeation behavior of 12 selected tryptamines and to characterize the interactions that drive the process. We aim at elucidating the impact of N-alkylation, indole ring substitution and positional modifications, and protonation on their membrane permeability. Dimethylation of the primary amine group and the introduction of a methoxy group at position 5 exhibited an increase in permeability. Moreover, there is a significant influence of positional substitutions on the indole groups, and the protonation of the molecules substantially increases the energy barrier at the center of the bilayer, making the compounds highly impermeable. All the information extracted from the trends predicted by the simulations can be applied in future drug design projects to develop psychedelics with enhanced activity.
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Affiliation(s)
- Vito F Palmisano
- Department of Chemistry, Universidad Autonoma de Madrid, Madrid 28049, Spain
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Claudio Agnorelli
- Center for Psychedelic Research, Division of Psychiatry, Department of Brain Science, Imperial College of London, London SW7 2BX, U.K
- Unit of Psychiatry, Department of Molecular Medicine, University of Siena, Siena 53100, Italy
| | - Andrea Fagiolini
- Unit of Psychiatry, Department of Molecular Medicine, University of Siena, Siena 53100, Italy
| | - David Erritzoe
- Center for Psychedelic Research, Division of Psychiatry, Department of Brain Science, Imperial College of London, London SW7 2BX, U.K
| | - David Nutt
- Center for Psychedelic Research, Division of Psychiatry, Department of Brain Science, Imperial College of London, London SW7 2BX, U.K
| | - Shirin Faraji
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autonoma de Madrid, Madrid 28049, Spain
- IADCHEM, Institute for Advanced Research in Chemistry, Universidad Autonoma de Madrid, Madrid 28049, Spain
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5
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Kähler S, Cebreiro-Gallardo A, Pokhilko P, Casanova D, Krylov AI. State-Interaction Approach for Evaluating g-Tensors within EOM-CC and RAS-CI Frameworks: Theory and Benchmarks. J Phys Chem A 2023; 127:8459-8472. [PMID: 37774315 DOI: 10.1021/acs.jpca.3c04134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Among various techniques designed for studying open-shell species, electron paramagnetic resonance (EPR) spectroscopy plays an important role. The key quantity measured by EPR is the g-tensor, describing the coupling between an external magnetic field and molecular electronic spin. One theoretical framework for quantum chemistry calculations of g-tensors is based on response theory, which involves substantial developments that are specific to the underlying electronic structure models. A simplified and easier-to-implement approach is based on the state-interaction scheme, in which perturbation is included by considering a small number of states. We describe and benchmark the state-interaction approach using equation-of-motion coupled-cluster and restricted-active-space configuration interaction wave functions. The analysis confirms that this approach can deliver accurate results and highlights caveats of applying it, such as a choice of the reference state, convergence with respect to the number of states used in calculations, etc. The analysis also contributes toward a better understanding of challenges in calculations of higher-order properties using approximate wave functions.
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Affiliation(s)
- Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - David Casanova
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Euskadi, Spain
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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6
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Huang SQ, Wang LL, Pan QQ, Zhao ZW, Gao Y, Su ZM. A Theoretical Study on the Underlying Factors of the Difference in Performance of Organic Solar Cells Based on ITIC and Its Isomers. Molecules 2023; 28:6968. [PMID: 37836811 PMCID: PMC10574239 DOI: 10.3390/molecules28196968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/19/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Recently, non-fullerene-based organic solar cells (OSCs) have made great breakthroughs, and small structural differences can have dramatic impacts on the power conversion efficiency (PCE). We take ITIC and its isomers as examples to study their effects on the performance of OSCs. ITIC and NFBDT only differed in the side chain position, and they were used as models with the same donor molecule, PBDB-T, to investigate the main reasons for the difference in their performance in terms of theoretical methods. In this work, a detailed comparative analysis of the electronic structure, absorption spectra, open circuit voltage and interfacial parameters of the ITIC and NFBDT systems was performed mainly by combining the density functional theory/time-dependent density functional theory and molecular dynamics simulations. The results showed that the lowest excited state of the ITIC molecule possessed a larger ∆q and more hybrid FE/CT states, and PBDB-T/ITIC had more charge separation paths as well as a larger kCS and smaller kCR. The reason for the performance difference between PBDB-T/ITIC and PBDB-T/NFBDT was elucidated, suggesting that ITIC is a superior acceptor based on a slight modulation of the side chain and providing a guiding direction for the design of superior-performing small molecule acceptor materials.
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Affiliation(s)
- Si-Qi Huang
- College of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China;
| | - Li-Li Wang
- Jilin Provincial Key Laboratory of Straw–Based Functional Materials, Institute for Interdisciplinary Biomass Functional Materials Studies, Jilin Engineering Normal University, Changchun 130052, China;
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Jilin Provincial Science and Technology Innovation Center of Optical Materials and Chemistry, Jilin Provincial International Joint Research Center of Photo-Functional Materials and Chemistry, Changchun 130022, China; (Q.-Q.P.); (Z.-M.S.)
| | - Qing-Qing Pan
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Jilin Provincial Science and Technology Innovation Center of Optical Materials and Chemistry, Jilin Provincial International Joint Research Center of Photo-Functional Materials and Chemistry, Changchun 130022, China; (Q.-Q.P.); (Z.-M.S.)
| | - Zhi-Wen Zhao
- College of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China;
| | - Ying Gao
- Jilin Provincial Key Laboratory of Straw–Based Functional Materials, Institute for Interdisciplinary Biomass Functional Materials Studies, Jilin Engineering Normal University, Changchun 130052, China;
| | - Zhong-Min Su
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Jilin Provincial Science and Technology Innovation Center of Optical Materials and Chemistry, Jilin Provincial International Joint Research Center of Photo-Functional Materials and Chemistry, Changchun 130022, China; (Q.-Q.P.); (Z.-M.S.)
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
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7
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Jayadev NK, Skomorowski W, Krylov AI. Molecular-Orbital Framework of Two-Electron Processes: Application to Auger and Intermolecular Coulomb Decay. J Phys Chem Lett 2023; 14:8612-8619. [PMID: 37728255 DOI: 10.1021/acs.jpclett.3c01966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
States with core- or inner-shell vacancies, which are commonly created by absorption of high-energy photons, can decay by a two-electron process in which one electron fills the core hole and the second one is ejected. These processes accompany many X-ray spectroscopies. Depending on the nature of the initial core- or inner-shell-hole state and the decay valence-hole state, these processes are called Auger decay, intermolecular Coulomb decay, or electron-transfer-mediated decay. To connect many-body wave functions of the initial and final states with the molecular orbital picture of the decay, we introduce the concept of natural Auger orbitals (NAOs). NAOs are obtained by a two-step singular value decomposition of the two-body Dyson orbitals, reduced quantities that enter the expression of the decay rate in the Feshbach-Fano treatment. NAOs afford chemical insight and interpretation of the high-level ab initio calculations of Auger decay and related two-electron relaxation processes.
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Affiliation(s)
- Nayanthara K Jayadev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Wojciech Skomorowski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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8
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Grigorenko BL, Polyakov IV, Khrenova MG, Giudetti G, Faraji S, Krylov AI, Nemukhin AV. Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms. J Am Chem Soc 2023; 145:13204-13214. [PMID: 37294056 DOI: 10.1021/jacs.3c02229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work. They were derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of reacting with the catalytic cysteine residue in the MPro active site. The reaction mechanisms of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) simulations. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro. From the chemical perspective, the reactions of these four molecules with MPro follow three distinct mechanisms. The reactions are initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir (which has a reactive nitrile group) leads to the formation of a covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. Our results contribute to the ongoing search for efficient inhibitors of the SARS-CoV-2 enzymes.
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Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia
| | - Goran Giudetti
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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9
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Arslan E, Haslak ZP, Monard G, Dogan I, Aviyente V. Quantum Mechanical Prediction of Dissociation Constants for Thiazol-2-imine Derivatives. J Chem Inf Model 2023; 63:2992-3004. [PMID: 37126823 PMCID: PMC10207282 DOI: 10.1021/acs.jcim.2c01468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Indexed: 05/03/2023]
Abstract
As weak acids or bases, in solution, drug molecules are in either their ionized or nonionized states. A high degree of ionization is essential for good water solubility of a drug molecule and is required for drug-receptor interactions, whereas the nonionized form improves a drug's lipophilicity, allowing the ligand to cross the cell membrane. The penetration of a drug ligand through cell membranes is mainly governed by the pKa of the drug molecule and the membrane environment. In this study, with the aim of predicting the acetonitrile pKa's (pKa(MeCN)) of eight drug-like thiazol-2-imine derivatives, we propose a very accurate and computationally affordable protocol by using several quantum mechanical approaches. Benchmark studies were conducted on a set of training molecules, which were selected from the literature with known pKa(water) and pKa(MeCN). Highly well-correlated pKa values were obtained when the calculations were performed with the isodesmic method at the M062X/6-31G** level of theory in conjunction with SMD solvation model for nitrogen-containing heterocycles. Finally, experimentally unknown pKa(MeCN) values of eight thiazol-2-imine structures, which were previously synthesized by some of us, are proposed.
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Affiliation(s)
- Evrim Arslan
- Department
of Chemistry, Bogazici University, Bebek, 34342 Istanbul, Turkey
| | - Zeynep Pinar Haslak
- Department
of Chemistry, Bogazici University, Bebek, 34342 Istanbul, Turkey
- Université
de Reims Champagne-Ardenne, 51687 Reims, France
| | - Gérald Monard
- Université
de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Ilknur Dogan
- Department
of Chemistry, Bogazici University, Bebek, 34342 Istanbul, Turkey
| | - Viktorya Aviyente
- Department
of Chemistry, Bogazici University, Bebek, 34342 Istanbul, Turkey
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10
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Foreman MM, Alessio M, Krylov AI, Weber JM. Influence of Transition Metal Electron Configuration on the Structure of Metal-EDTA Complexes. J Phys Chem A 2023; 127:2258-2264. [PMID: 36877889 DOI: 10.1021/acs.jpca.2c07996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The vibrational spectra of cold complexes of ethylenediaminetetraacetic acid (EDTA) with transition metal dications in vacuo show how the electronic structure of the metal provides a geometric template for interaction with the functional groups of the binding pocket. The OCO stretching modes of the carboxylate groups of EDTA serve as structural probes, informing on the spin state of the ion as well as the coordination number in the complex. The results highlight the flexibility of EDTA in accepting a large range of metal cations in its binding site.
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Affiliation(s)
- Madison M Foreman
- JILA and Department of Chemistry, University of Colorado at Boulder, UCB 440, Boulder, Colorado 80309, United States
| | - Maristella Alessio
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado at Boulder, UCB 440, Boulder, Colorado 80309, United States
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11
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Jayadev NK, Ferino-Pérez A, Matz F, Krylov AI, Jagau TC. The Auger spectrum of benzene. J Chem Phys 2023; 158:064109. [PMID: 36792526 DOI: 10.1063/5.0138674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We present an ab initio computational study of the Auger electron spectrum of benzene. Auger electron spectroscopy exploits the Auger-Meitner effect, and although it is established as an analytic technique, the theoretical modeling of molecular Auger spectra from first principles remains challenging. Here, we use coupled-cluster theory and equation-of-motion coupled-cluster theory combined with two approaches to describe the decaying nature of core-ionized states: (i) Feshbach-Fano resonance theory and (ii) the method of complex basis functions. The spectra computed with these two approaches are in excellent agreement with each other and also agree well with experimental Auger spectra of benzene. The Auger spectrum of benzene features two well-resolved peaks at Auger electron energies above 260 eV, which correspond to final states with two electrons removed from the 1e1g and 3e2g highest occupied molecular orbitals. At lower Auger electron energies, the spectrum is less well resolved, and the peaks comprise multiple final states of the benzene dication. In line with theoretical considerations, singlet decay channels contribute more to the total Auger intensity than the corresponding triplet decay channels.
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Affiliation(s)
- Nayanthara K Jayadev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Florian Matz
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Thomas-C Jagau
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
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12
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Tikhonov SA, Sidorin AE, Ksenofontov AA, Kosyanov DY, Samoilov IS, Skitnevskaya AD, Trofimov AB, Antina EV, Berezin MB, Vovna VI. XPS and quantum chemical analysis of 4Me-BODIPY derivatives. Phys Chem Chem Phys 2023; 25:5211-5225. [PMID: 36723097 DOI: 10.1039/d2cp04541a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The results of a X-ray photoelectron spectroscopy (XPS) and steady-state absorption spectroscopy study of the electronic structure, and cationic and excited states of a series of 1,3,5,7-tetramethyl-substituted BODIPYs (4Me,2R-BODIPYs) are presented. The experimental data were interpreted using high-level ab initio quantum chemical computations, including the algebraic diagrammatic construction method for the polarization propagator of the second order (ADC(2)), the outer-valence Green's function (OVGF) method, the density functional (DFT) approach, and the time-dependent DFT (TD-DFT) approach. Substitution effects on the XPS and absorption spectra were determined for 2,6-positions of 4Me,2R-BODIPY pyrrole nuclei (R = H, Br, Bu, benzyl). A very satisfactory performance of the DFT Koopmans theorem analogue was demonstrated with respect to the energy intervals between the electronic levels of 4Me,2R-BODIPY above 13 eV (BHHLYP functional) and the values of the HOMO-LUMO energy gap (ωB97X functional).
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Affiliation(s)
- Sergey A Tikhonov
- Kamchatka Branch of the Geophysical Survey of the Russian Academy of Sciences, Piip blvd. 9, 683023 Petropavlovsk-Kamchatsky, Russian Federation.
| | - Andrey E Sidorin
- Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russian Federation
| | - Alexander A Ksenofontov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Str. 1, 153045 Ivanovo, Russian Federation
| | - Denis Yu Kosyanov
- Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russian Federation.,Institute of Automation and Control Processes, Far Eastern Branch, Russian Academy of Sciences, 5 Radio Street, 690041 Vladivostok, Russian Federation
| | - Ilya S Samoilov
- Kamchatka Branch of the Geophysical Survey of the Russian Academy of Sciences, Piip blvd. 9, 683023 Petropavlovsk-Kamchatsky, Russian Federation. .,Department of Photonics, Saint Petersburg State University, 7-9 Universitetskaya Embankment, 199034 St. Petersburg, Russian Federation
| | - Anna D Skitnevskaya
- Laboratory of Quantum Chemical Modeling of Molecular Systems, Irkutsk State University, Karl Marx Str. 1, 664003 Irkutsk, Russian Federation
| | - Alexander B Trofimov
- Laboratory of Quantum Chemical Modeling of Molecular Systems, Irkutsk State University, Karl Marx Str. 1, 664003 Irkutsk, Russian Federation.,Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky St., 664033 Irkutsk, Russian Federation
| | - Elena V Antina
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Str. 1, 153045 Ivanovo, Russian Federation
| | - Mikhail B Berezin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Str. 1, 153045 Ivanovo, Russian Federation
| | - Vitaliy I Vovna
- Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russian Federation
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13
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Cárdenas G, Lucia‐Tamudo J, Mateo‐delaFuente H, Palmisano VF, Anguita‐Ortiz N, Ruano L, Pérez‐Barcia Á, Díaz‐Tendero S, Mandado M, Nogueira JJ. MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations. J Comput Chem 2023; 44:516-533. [PMID: 36507763 PMCID: PMC10107847 DOI: 10.1002/jcc.27018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022]
Abstract
We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch case.
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Affiliation(s)
- Gustavo Cárdenas
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
| | | | | | | | | | - Lorena Ruano
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
| | | | - Sergio Díaz‐Tendero
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Universidad Autónoma de MadridMadridSpain
- Condensed Matter Physics Center (IFIMAC)Universidad Autónoma de MadridMadridSpain
| | - Marcos Mandado
- Department of Physical ChemistryUniversity of VigoVigoSpain
| | - Juan J. Nogueira
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Universidad Autónoma de MadridMadridSpain
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14
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Kotaru S, Kähler S, Alessio M, Krylov AI. Magnetic exchange interactions in binuclear and tetranuclear iron(III) complexes described by spin-flip DFT and Heisenberg effective Hamiltonians. J Comput Chem 2023; 44:367-380. [PMID: 35699152 PMCID: PMC10084445 DOI: 10.1002/jcc.26941] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/07/2022] [Accepted: 04/22/2022] [Indexed: 12/31/2022]
Abstract
Low-energy spectra of single-molecule magnets (SMMs) are often described by Heisenberg Hamiltonians. Within this formalism, exchange interactions between magnetic centers determine the ground-state multiplicity and energy separation between the ground and excited states. In this contribution, we extract exchange coupling constants (J) for a set of iron (III) binuclear and tetranuclear complexes from all-electron calculations using non-collinear spin-flip time-dependent density functional theory (NC-SF-TDDFT). For 12 binuclear complexes with J-values ranging from -6 to -132 cm-1 , our benchmark calculations using the short-range hybrid ωPBEh functional and 6-31G(d,p) basis set agree well with the experimentally derived values (mean absolute error of 4.7 cm-1 ). For the tetranuclear SMMs, the computed J constants are within 6 cm-1 from the experimentally derived values. We explore the range of applicability of the Heisenberg model by analyzing bonding patterns in these Fe(III) complexes using natural orbitals (NO), their occupations, and the number of effectively unpaired electrons. The results illustrate the efficiency of the spin-flip protocol for computing the exchange couplings and the utility of the NO analysis in assessing the validity of effective spin Hamiltonians.
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Affiliation(s)
- Saikiran Kotaru
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Sven Kähler
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Maristella Alessio
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Anna I. Krylov
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCalifornia
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15
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Gamboa-Arancibia ME, Caro N, Gamboa A, Morales JO, González Casanova JE, Rojas Gómez DM, Miranda-Rojas S. Improving Lurasidone Hydrochloride's Solubility and Stability by Higher-Order Complex Formation with Hydroxypropyl-β-cyclodextrin. Pharmaceutics 2023; 15:pharmaceutics15010232. [PMID: 36678861 PMCID: PMC9861442 DOI: 10.3390/pharmaceutics15010232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
The biopharmaceutical classification system groups low-solubility drugs into two groups: II and IV, with high and low permeability, respectively. Most of the new drugs developed for common pathologies present solubility issues. This is the case of lurasidone hydrochloride-a drug used for the treatment of schizophrenia and bipolar depression. Likewise, the stability problems of some drugs limit the possibility of preparing them in liquid pharmaceutical forms where hydrolysis and oxidation reactions can be favored. Lurasidone hydrochloride presents the isoindole-1,3-dione ring, which is highly susceptible to alkaline hydrolysis, and the benzisothiazole ring, which is susceptible to a lesser extent to oxidation. Herein, we propose to study the increase in the solubility and stability of lurasidone hydrochloride by the formation of higher-order inclusion complexes with hydroxypropyl-β-cyclodextrin. Several stoichiometric relationships were studied at between 0.5 and 3 hydroxypropyl-β-cyclodextrin molecules per drug molecule. The obtained products were characterized, and their solubility and stability were assessed. According to the obtained results, the formation of inclusion complexes dramatically increased the solubility of the drug, and this increased with the increase in the inclusion ratio. This was associated with the loss of crystalline state of the drug, which was in an amorphous state according to infrared spectroscopy, calorimetry, and X-ray analysis. This was also correlated with the stabilization of lurasidone by the cyclodextrin inhibiting its recrystallization. Phase solubility,1H-NMR, and docking computational characterization suggested that the main stoichiometric ratio was 1:1; however, we cannot rule out a 1:2 ratio, where a second cyclodextrin molecule could bind through the isoindole-1,3-dione ring, improving its stability as well. Finally, we can conclude that the formation of higher-order inclusion complexes of lurasidone with hydroxypropyl-β-cyclodextrin is a successful strategy to increase the solubility and stability of the drug.
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Affiliation(s)
- María Elena Gamboa-Arancibia
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Estación Central, Santiago 9170022, Chile
- Correspondence: (M.E.G.-A.); (S.M.-R.); Tel.: +56-2-2-7181166 (M.E.G.-A.); +56-2-2-6618341 (S.-M.R.)
| | - Nelson Caro
- Centro de Investigación Austral Biotech, Facultad de Ciencias, Universidad Santo Tomas, Avenida Ejército 146, Santiago 8370003, Chile
| | - Alexander Gamboa
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Estación Central, Santiago 9170022, Chile
- Centro de Investigación Austral Biotech, Facultad de Ciencias, Universidad Santo Tomas, Avenida Ejército 146, Santiago 8370003, Chile
| | - Javier Octavio Morales
- Department of Pharmaceutical Science and Technology, School of Chemical and Pharmaceutical Sciences, University of Chile, Santiago 8380494, Chile
- Advanced Center for Chronic Diseases, Santiago 8380494, Chile
- Center of New Drugs for Hypertension, Santiago 8380494, Chile
| | | | - Diana Marcela Rojas Gómez
- Escuela de Nutrición y Dietética, Facultad de Medicina, Universidad Andrés Bello, Santiago 8370321, Chile
| | - Sebastián Miranda-Rojas
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
- Correspondence: (M.E.G.-A.); (S.M.-R.); Tel.: +56-2-2-7181166 (M.E.G.-A.); +56-2-2-6618341 (S.-M.R.)
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16
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Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020505. [PMID: 36677562 PMCID: PMC9863226 DOI: 10.3390/molecules28020505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
We report the results of a computational study of the mechanism of the light-induced chemical reaction of chromophore hydration in the fluorescent protein Dreiklang, responsible for its switching from the fluorescent ON-state to the dark OFF-state. We explore the relief of the charge-transfer excited-state potential energy surface in the ON-state to locate minimum energy conical intersection points with the ground-state energy surface. Simulations of the further evolution of model systems allow us to characterize the ground-state reaction intermediate tentatively suggested in the femtosecond studies of the light-induced dynamics in Dreiklang and finally to arrive at the reaction product. The obtained results clarify the details of the photoswitching mechanism in Dreiklang, which is governed by the chemical modification of its chromophore.
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17
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Sarangi R, Nanda KD, Krylov AI. Charge-transfer-to-solvent states provide a sensitive spectroscopic probe of the local solvent structure around anions. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2148582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ronit Sarangi
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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18
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Kramarova EP, Negrebetskii VV, Volodin AD, Buikin PA, Lalov AV, Novikov RA, Aliev TM, Korlyukov AA, Vologzhanina AV. Synthesis, Crystal Structure, and Properties of Phenylsilicon(IV) Bis-catecholate Complexes. RUSS J COORD CHEM+ 2022. [DOI: 10.1134/s1070328422090019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Gatti C, Danten Y, Frayret C. Atomic Group Decomposition of Charge Transfer Excitation Global Indexes. J Phys Chem A 2022; 126:6314-6328. [PMID: 36053727 PMCID: PMC9483980 DOI: 10.1021/acs.jpca.2c04607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A model for decomposing the Le Bahers, Adamo, and Ciofini Charge Transfer (CT) Excitations global indexes ( J. Chem. Theory Comput. 2011, 7, 2498-2506) into molecular subdomains contributions is presented and a software, DOCTRINE (atomic group Decomposition Of the Charge TRansfer INdExes) for the implementation of this novel model has been coded. Although our method applies to any fuzzy or to any disjoint exhaustive partitioning of the real space, it is here applied using a definition of chemically relevant molecular subdomains based on the Atoms in Molecules Bader basins. This choice has the relevant advantage of associating intra or inter subdomain contributions to rigorously defined quantum objects, yet bearing a clear chemical meaning. Our method allows for a quantitative evaluation of the subdomain contributions to the charge transfer, the charge transfer excitation length and the dipole moment change upon excitation. All these global indexes may be obtained either from the electron density increment or the electron density depletion upon excitation. However, the subdomain contributions obtained from the two distributions generally differ, therefore allowing to distinguish whether the contribution to a given property of a given subdomain is dominated by one of the two distributions or if both are playing a significant role. As a toy system for the first application of our model, a typical [D-π-A, π = conjugated bridge] compound belonging to the merocyanine dyes family is selected, and the first four excited states of this compound in a strongly polar protic solvent and in a weakly polar solvent are thoroughly investigated.
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Affiliation(s)
- Carlo Gatti
- CNR Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", CNR SCITEC, Sede Via C. Golgi, 19, 20133 Milano, Italy.,Istituto Lombardo, Accademia di Scienze e Lettere, via Brera 76, 20121 Milano, Italy
| | - Yann Danten
- Institut des Sciences Moléculaires, UMR CNRS 5255, Université de Bordeaux, 351 Cours de la Libération, 33405 Talence, France
| | - Christine Frayret
- Laboratoire de Réactivité et Chimie des Solides (LRCS), UMR CNRS 7314, Université de Picardie Jules Verne, Hub de l'Energie, 15 Rue Baudelocque, 80000 Amiens Cedex, France.,Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens Cedex, France
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20
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Wójcik P, Hudson ER, Krylov AI. On the prospects of optical cycling in diatomic cations: effects of transition metals, spin–orbit couplings, and multiple bonds. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2107582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Paweł Wójcik
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Eric R. Hudson
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA, USA
- UCLA Center for Quantum Science and Engineering, Los Angeles, CA, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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21
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Giudetti G, Polyakov I, Grigorenko BL, Faraji S, Nemukhin AV, Krylov AI. How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur. J Chem Theory Comput 2022; 18:5056-5067. [PMID: 35797455 DOI: 10.1021/acs.jctc.2c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work explores the level of transparency in reporting the details of computational protocols that is required for practical reproducibility of quantum mechanics/molecular mechanics (QM/MM) simulations. Using the reaction of an essential SARS-CoV-2 enzyme (the main protease) with a covalent inhibitor (carmofur) as a test case of chemical reactions in biomolecules, we carried out QM/MM calculations to determine the structures and energies of the reactants, the product, and the transition state/intermediate using analogous QM/MM models implemented in two software packages, NWChem and Q-Chem. Our main benchmarking goal was to reproduce the key energetics computed with the two packages. Our results indicate that quantitative agreement (within the numerical thresholds used in calculations) is difficult to achieve. We show that rather minor details of QM/MM simulations must be reported in order to ensure the reproducibility of the results and offer suggestions toward developing practical guidelines for reporting the results of biosimulations.
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Affiliation(s)
- Goran Giudetti
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Igor Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, 9747 AG The Netherlands
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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22
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Buikin PA, Vologzhanina AV, Arkhipov DE, Korlyukov AA. Electronic structure of substituted catecholate complexes of hexacoordinated silicon: a quantum chemical study. Russ Chem Bull 2022. [DOI: 10.1007/s11172-022-3511-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Pletzer M, Plasser F, Rimmele M, Heeney M, Glöcklhofer F. [2.2.2.2]Paracyclophanetetraenes (PCTs): cyclic structural analogues of poly( p‑phenylene vinylene)s (PPVs). OPEN RESEARCH EUROPE 2022; 1:111. [PMID: 37645175 PMCID: PMC10445936 DOI: 10.12688/openreseurope.13723.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/03/2022] [Indexed: 08/31/2023]
Abstract
Background: Poly( p-phenylene vinylene)s ( PPVs) and [2.2.2.2]paracyclophanetetraene ( PCT) are both composed of alternating π-conjugated para-phenylene and vinylene units. However, while the former constitute a class of π-conjugated polymers that has been used in organic electronics for decades, the latter is a macrocycle that only recently revealed its potential for applications such as organic battery electrodes. The cyclic structure endows PCT with unusual properties, and further tuning of these may be required for specific applications. Methods: In this article, we adopt an approach often used for tuning the properties of PPVs, the introduction of alkoxy (or alkylthio) substituents at the phenylene units, for tuning the optoelectronic properties of PCT. The resulting methoxy- and methylthio-substituted PCTs, obtained by Wittig cyclisation reactions, are studied by UV-vis absorption, photoluminescence, and cyclic voltammetry measurements, and investigated computationally using the visualisation of chemical shielding tensors (VIST) method. Results: The measurements show that substitution leads to slight changes in terms of absorption/emission energies and redox potentials while having a pronounced effect on the photoluminescence intensity. The computations show the effect of the substituents on the ring currents and chemical shielding and on the associated local and global (anti)aromaticity of the macrocycles, highlighting the interplay of local and global aromaticity in various electronic states. Conclusions: The study offers interesting insights into the tuneability of the properties of this versatile class of π-conjugated macrocycles.
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Affiliation(s)
- Matthias Pletzer
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Centre for Processable Electronics, Imperial College London, London, W12 0BZ, UK
| | - Felix Plasser
- Department of Chemistry, Loughborough University, Loughborough, LE11 3TU, UK
| | - Martina Rimmele
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Centre for Processable Electronics, Imperial College London, London, W12 0BZ, UK
| | - Martin Heeney
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Centre for Processable Electronics, Imperial College London, London, W12 0BZ, UK
| | - Florian Glöcklhofer
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Centre for Processable Electronics, Imperial College London, London, W12 0BZ, UK
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24
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Affiliation(s)
- Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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25
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 412] [Impact Index Per Article: 137.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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26
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Rimmele M, Nogala W, Seif-Eddine M, Roessler MM, Heeney M, Plasser F, Glöcklhofer F. Functional group introduction and aromatic unit variation in a set of π-conjugated macrocycles: revealing the central role of local and global aromaticity. Org Chem Front 2021; 8:4730-4745. [PMID: 34484800 PMCID: PMC8382046 DOI: 10.1039/d1qo00901j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/17/2021] [Indexed: 12/18/2022]
Abstract
π-Conjugated macrocycles are molecules with unique properties that are increasingly exploited for applications and the question of whether they can sustain global aromatic or antiaromatic ring currents is particularly intriguing. However, there are only a small number of experimental studies that investigate how the properties of π-conjugated macrocycles evolve with systematic structural changes. Here, we present such a systematic experimental study of a set of [2.2.2.2]cyclophanetetraenes, all with formally Hückel antiaromatic ground states, and combine it with an in-depth computational analysis. The study reveals the central role of local and global aromaticity for rationalizing the observed optoelectronic properties, ranging from extremely large Stokes shifts of up to 1.6 eV to reversible fourfold reduction, a highly useful feature for charge storage/accumulation applications. A recently developed method for the visualization of chemical shielding tensors (VIST) is applied to provide unique insight into local and global ring currents occurring in different planes along the macrocycle. Conformational changes as a result of the structural variations can further explain some of the observations. The study contributes to the development of structure-property relationships and molecular design guidelines and will help to understand, rationalize, and predict the properties of other π-conjugated macrocycles. It will also assist in the design of macrocycle-based supramolecular elements with defined properties.
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Affiliation(s)
- Martina Rimmele
- Department of Chemistry, Imperial College London London W12 0BZ UK .,Centre for Processable Electronics, Imperial College London London W12 0BZ UK
| | - Wojciech Nogala
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | | | - Maxie M Roessler
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - Martin Heeney
- Department of Chemistry, Imperial College London London W12 0BZ UK .,Centre for Processable Electronics, Imperial College London London W12 0BZ UK
| | - Felix Plasser
- Department of Chemistry, Loughborough University Loughborough LE11 3TU UK
| | - Florian Glöcklhofer
- Department of Chemistry, Imperial College London London W12 0BZ UK .,Centre for Processable Electronics, Imperial College London London W12 0BZ UK
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27
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Alessio M, Krylov AI. Equation-of-Motion Coupled-Cluster Protocol for Calculating Magnetic Properties: Theory and Applications to Single-Molecule Magnets. J Chem Theory Comput 2021; 17:4225-4241. [PMID: 34191507 DOI: 10.1021/acs.jctc.1c00430] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We present a new computational protocol for computing macroscopic magnetic properties of transition-metal complexes using the equation-of-motion coupled-cluster (EOM-CC) framework. The approach follows a two-step state-interaction scheme: we first compute zero-order states using nonrelativistic EOM-CC and then use these states to evaluate matrix elements of the spin-orbit and Zeeman operators. Diagonalization of the resulting Hamiltonian yields spin-orbit- and field-perturbed eigenstates. Temperature- and field-dependent magnetization and susceptibility are computed by numerical differentiation of the partition function. To compare with powder-sample experiments, these quantities are numerically averaged over field orientations. We applied this protocol to several single-molecule magnets (SMMs) with Fe(II) and Fe(III) in trigonal pyramidal, linear, and trigonal bipyramidal coordination environments. We described the underlying electronic structure by the electron-attachment (EOM-EA) and spin-flip (EOM-SF) variants of EOM-CC. The computed energy barriers for spin inversion, and macroscopic magnetization and susceptibility agree well with experimental data. Trends in magnetic anisotropy and spin-reversal energy barriers are explained in terms of a molecular orbital picture rigorously distilled from spinless transition density matrices between many-body states. The results illustrate excellent performances of EOM-CC in describing magnetic behavior of mononuclear transition-metal SMMs.
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Affiliation(s)
- Maristella Alessio
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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28
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Chen Z, Pascal S, Daurat M, Lichon L, Nguyen C, Godefroy A, Durand D, Ali LMA, Bettache N, Gary-Bobo M, Arnoux P, Longevial JF, D'Aléo A, Marchand G, Jacquemin D, Siri O. Modified Indulines: From Dyestuffs to In Vivo Theranostic Agents. ACS APPLIED MATERIALS & INTERFACES 2021; 13:30337-30349. [PMID: 34159778 DOI: 10.1021/acsami.1c05933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The efficient, versatile, and straightforward synthesis of the first N-alkyl analogues of induline 3B (8a and 8b) is reported. Thanks to the introduction of lipophilic substituents and their attractive photophysical properties (far-red emission and production of singlet oxygen), phenazinium 8b can be used as a theranostic agent and shows, at very low concentrations (100 nM), a remarkable ability to (i) image cells and zebrafish embryos with high quality under both mono- (514 nm) and biphotonic (790 and 810 nm) excitations, (ii) efficiently and quickly penetrate cancer cells rather than healthy fibroblasts, and (iii) induce a total or almost total cancer cell death in vitro and in vivo after illumination (λexc = 540-560 nm). The molecular structure of 8b is based on a triamino-phenazinium core only, with no need for additional components, highlighting the emergence of a minimalistic and versatile class of fluorescent probes for targeted photodynamic cancer therapy.
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Affiliation(s)
- Zhongrui Chen
- Aix Marseille Université, CNRS, CINaM, UMR 7325, Campus de Luminy, 13288 Marseille Cedex 09, France
| | - Simon Pascal
- Aix Marseille Université, CNRS, CINaM, UMR 7325, Campus de Luminy, 13288 Marseille Cedex 09, France
| | - Morgane Daurat
- Faculté de Pharmacie, NanoMedSyn, 15 Avenue Charles Flahault, 34093 Montpellier, Cedex 5 France
| | - Laure Lichon
- Université Montpellier, CNRS, IBMM, UMR 5247, ENSCM, 34093 Montpellier, France
| | - Christophe Nguyen
- Université Montpellier, CNRS, IBMM, UMR 5247, ENSCM, 34093 Montpellier, France
| | - Anastasia Godefroy
- Faculté de Pharmacie, NanoMedSyn, 15 Avenue Charles Flahault, 34093 Montpellier, Cedex 5 France
| | - Denis Durand
- Université Montpellier, CNRS, IBMM, UMR 5247, ENSCM, 34093 Montpellier, France
| | - Lamiaa M A Ali
- Université Montpellier, CNRS, IBMM, UMR 5247, ENSCM, 34093 Montpellier, France
- Department of Biochemistry Medical Research Institute, University of Alexandria, 21561 Alexandria, Egypt
| | - Nadir Bettache
- Université Montpellier, CNRS, IBMM, UMR 5247, ENSCM, 34093 Montpellier, France
| | - Magali Gary-Bobo
- Université Montpellier, CNRS, IBMM, UMR 5247, ENSCM, 34093 Montpellier, France
| | - Philippe Arnoux
- Université de Lorraine, CNRS, LRGP, UMR 7274, 54000 Nancy, France
| | - Jean-François Longevial
- Aix Marseille Université, CNRS, CINaM, UMR 7325, Campus de Luminy, 13288 Marseille Cedex 09, France
| | - Anthony D'Aléo
- Aix Marseille Université, CNRS, CINaM, UMR 7325, Campus de Luminy, 13288 Marseille Cedex 09, France
| | - Gabriel Marchand
- Université de Nantes, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France
| | | | - Olivier Siri
- Aix Marseille Université, CNRS, CINaM, UMR 7325, Campus de Luminy, 13288 Marseille Cedex 09, France
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29
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Polik WF, Schmidt JR. WebMO
: Web‐based computational chemistry calculations in education and research. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1554] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - J. R. Schmidt
- Theoretical Chemistry Institute and Department of Chemistry University of Wisconsin—Madison Madison Wisconsin USA
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30
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Nanda KD, Krylov AI. The orbital picture of the first dipole hyperpolarizability from many-body response theory. J Chem Phys 2021; 154:184109. [PMID: 34241029 DOI: 10.1063/5.0049184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We present an approach for obtaining a molecular orbital picture of the first dipole hyperpolarizability (β) from correlated many-body electronic structure methods. Ab initio calculations of β rely on quadratic response theory, which recasts the sum-over-all-states expression of β into a closed-form expression by calculating a handful of first- and second-order response states; for resonantly enhanced β, damped response theory is used. These response states are then used to construct second-order response reduced one-particle density matrices (1PDMs), which, upon visualization in terms of natural orbitals (NOs), facilitate a rigorous and black-box mapping of the underlying electronic structure with β. We explain the interpretation of different components of the response 1PDMs and the corresponding NOs within both the undamped and damped response theory framework. We illustrate the utility of this new tool by deconstructing β for cis-difluoroethene, para-nitroaniline, and hemibonded OH· + H2O complex, computed within the framework of coupled-cluster singles and doubles response theory, in terms of the underlying response 1PDMs and NOs for a range of frequencies.
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Affiliation(s)
- Kaushik D Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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31
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Loos PF, Comin M, Blase X, Jacquemin D. Reference Energies for Intramolecular Charge-Transfer Excitations. J Chem Theory Comput 2021; 17:3666-3686. [DOI: 10.1021/acs.jctc.1c00226] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, F-31400 Toulouse, France
| | | | - Xavier Blase
- Univ. Grenoble Alpes, CNRS, Inst NEEL, F-38042 Grenoble, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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32
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Exploitation of Baird Aromaticity and Clar’s Rule for Tuning the Triplet Energies of Polycyclic Aromatic Hydrocarbons. CHEMISTRY 2021. [DOI: 10.3390/chemistry3020038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH) are a prominent substance class with a variety of applications in molecular materials science. Their electronic properties crucially depend on the bond topology in ways that are often highly non-intuitive. Here, we study, using density functional theory, the triplet states of four biphenylene-derived PAHs finding dramatically different triplet excitation energies for closely related isomeric structures. These differences are rationalised using a qualitative description of Clar sextets and Baird quartets, quantified in terms of nucleus independent chemical shifts, and represented graphically through a recently developed method for visualising chemical shielding tensors (VIST). The results are further interpreted in terms of a 2D rigid rotor model of aromaticity and through an analysis of the natural transition orbitals involved in the triplet excited states showing good consistency between the different viewpoints. We believe that this work constitutes an important step in consolidating these varying viewpoints of electronically excited states.
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33
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Herbert JM. Dielectric continuum methods for quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry The Ohio State University Columbus Ohio USA
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34
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Gulania S, Kjønstad EF, Stanton JF, Koch H, Krylov AI. Equation-of-motion coupled-cluster method with double electron-attaching operators: Theory, implementation, and benchmarks. J Chem Phys 2021; 154:114115. [PMID: 33752380 DOI: 10.1063/5.0041822] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report a production-level implementation of the equation-of-motion (EOM) coupled-cluster (CC) method with double electron-attaching (DEA) EOM operators of 2p and 3p1h types, EOM-DEA-CCSD. This ansatz, suitable for treating electronic structure patterns that can be described as two-electrons-in-many orbitals, represents a useful addition to the EOM-CC family of methods. We analyze the performance of EOM-DEA-CCSD for energy differences and molecular properties. By considering reduced quantities, such as state and transition one-particle density matrices, we compare EOM-DEA-CCSD wave functions with wave functions computed by other EOM-CCSD methods. The benchmarks illustrate that EOM-DEA-CCSD is capable of treating diradicals, bond-breaking, and some types of conical intersections.
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Affiliation(s)
- Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Eirik F Kjønstad
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - John F Stanton
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, USA
| | - Henrik Koch
- Scuola Normale Superiore, Piazza dei Cavaleri 7, 56126 Pisa, Italy
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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35
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Skomorowski W, Krylov AI. Feshbach–Fano approach for calculation of Auger decay rates using equation-of-motion coupled-cluster wave functions. II. Numerical examples and benchmarks. J Chem Phys 2021; 154:084125. [DOI: 10.1063/5.0036977] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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36
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Skomorowski W, Krylov AI. Feshbach-Fano approach for calculation of Auger decay rates using equation-of-motion coupled-cluster wave functions. I. Theory and implementation. J Chem Phys 2021; 154:084124. [PMID: 33639760 DOI: 10.1063/5.0036976] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
X-ray absorption creates electron vacancies in the core shell. These highly excited states often relax by Auger decay-an autoionization process in which one valence electron fills the core hole and another valence electron is ejected into the ionization continuum. Despite the important role of Auger processes in many experimental settings, their first-principles modeling is challenging, even for small systems. The difficulty stems from the need to describe many-electron continuum (unbound) states, which cannot be tackled with standard quantum-chemistry methods. We present a novel approach to calculate Auger decay rates by combining Feshbach-Fano resonance theory with the equation-of-motion coupled-cluster single double (EOM-CCSD) framework. We use the core-valence separation scheme to define projectors into the bound (square-integrable) and unbound (continuum) subspaces of the full function space. The continuum many-body decay states are represented by products of an appropriate EOM-CCSD state and a free-electron state, described by a continuum orbital. The Auger rates are expressed in terms of reduced quantities, two-body Dyson amplitudes (objects analogous to the two-particle transition density matrix), contracted with two-electron bound-continuum integrals. Here, we consider two approximate treatments of the free electron: a plane wave and a Coulomb wave with an effective charge, which allow us to evaluate all requisite integrals analytically; however, the theory can be extended to incorporate a more sophisticated description of the continuum orbital.
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Affiliation(s)
- Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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37
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Véril M, Scemama A, Caffarel M, Lipparini F, Boggio‐Pasqua M, Jacquemin D, Loos P. QUESTDB
: A database of highly accurate excitation energies for the electronic structure community. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1517] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mickaël Véril
- Laboratoire de Chimie et Physique Quantiques Université de Toulouse, CNRS, UPS Toulouse France
| | - Anthony Scemama
- Laboratoire de Chimie et Physique Quantiques Université de Toulouse, CNRS, UPS Toulouse France
| | - Michel Caffarel
- Laboratoire de Chimie et Physique Quantiques Université de Toulouse, CNRS, UPS Toulouse France
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale University of Pisa Pisa Italy
| | - Martial Boggio‐Pasqua
- Laboratoire de Chimie et Physique Quantiques Université de Toulouse, CNRS, UPS Toulouse France
| | | | - Pierre‐François Loos
- Laboratoire de Chimie et Physique Quantiques Université de Toulouse, CNRS, UPS Toulouse France
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38
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Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, Kar RK, Kemmler L, Kim SS, Kongsted J, Krylov AI, Lahav Y, Lazaratos M, NasserEddin Q, Navizet I, Nemukhin A, Olivucci M, Olsen JMH, Pérez de Alba Ortíz A, Pieri E, Rao AG, Rhee YM, Ricardi N, Sen S, Solov'yov IA, De Vico L, Wesolowski TA, Wiebeler C, Yang X, Schapiro I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol 2021; 97:243-269. [PMID: 33369749 DOI: 10.1111/php.13372] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
Abstract
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
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Affiliation(s)
| | - Suliman Adam
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil S Amoyal
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Barnoy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Veniamin A Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Department Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | | | - Ofer Filiba
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | - Ronald González
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lukas Kemmler
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Yigal Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,MIGAL - Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Qays NasserEddin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Navizet
- MSME, Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris Est Creteil, Marne-la-Vallée, France
| | - Alexander Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy.,Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alberto Pérez de Alba Ortíz
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Elisa Pieri
- Aix-Marseille Univ, CNRS, ICR, Marseille, France
| | - Aditya G Rao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Niccolò Ricardi
- Département de Chimie Physique, Université de Genève, Genève, Switzerland
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | | | - Christian Wiebeler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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39
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Quintas-Sánchez E, Dawes R. Spectroscopy and Scattering Studies Using Interpolated Ab Initio Potentials. Annu Rev Phys Chem 2021; 72:399-421. [PMID: 33503385 DOI: 10.1146/annurev-physchem-090519-051837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Born-Oppenheimer potential energy surface (PES) has come a long way since its introduction in the 1920s, both conceptually and in predictive power for practical applications. Nevertheless, nearly 100 years later-despite astonishing advances in computational power-the state-of-the-art first-principles prediction of observables related to spectroscopy and scattering dynamics is surprisingly limited. For example, the water dimer, (H2O)2, with only six nuclei and 20 electrons, still presents a formidable challenge for full-dimensional variational calculations of bound states and is considered out of reach for rigorous scattering calculations. The extremely poor scaling of the most rigorous quantum methods is fundamental; however, recent progress in development of approximate methodologies has opened the door to fairly routine high-quality predictions, unthinkable 20 years ago. In this review, in relation to the workflow of spectroscopy and/or scattering studies, we summarize progress and challenges in the component areas of electronic structure calculations, PES fitting, and quantum dynamical calculations.
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Affiliation(s)
- Ernesto Quintas-Sánchez
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, USA;
| | - Richard Dawes
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, USA;
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40
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Sarkar R, Boggio-Pasqua M, Loos PF, Jacquemin D. Benchmarking TD-DFT and Wave Function Methods for Oscillator Strengths and Excited-State Dipole Moments. J Chem Theory Comput 2021; 17:1117-1132. [DOI: 10.1021/acs.jctc.0c01228] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, 31400 Toulouse, France
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, 31400 Toulouse, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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41
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Sen T, Ma Y, Polyakov IV, Grigorenko BL, Nemukhin AV, Krylov AI. Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang. J Phys Chem B 2021; 125:757-770. [PMID: 33411528 DOI: 10.1021/acs.jpcb.0c09221] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the results of high-level electronic structure and dynamics simulations of the photoactive protein Dreiklang. With the goal of understanding the details of the Dreiklang photocycle, we carefully characterize the excited states of the ON- and OFF-forms of Dreiklang. The key finding of our study is the existence of a low-lying excited state of a charge-transfer character in the neutral ON form and that population of this state, which is nearly isoenergetic with the locally excited bright state, initiates a series of steps that ultimately lead to the formation of the hydrated dark chromophore (OFF state). These results allow us to refine the mechanistic picture of Dreiklang's photocycle and photoactivation.
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Affiliation(s)
- Tirthendu Sen
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Yingying Ma
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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42
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Zhang J, Xiang Y, Zheng S. From Y6 to BTPT-4F: a theoretical insight into the influence of the individual change of fused-ring skeleton length or side alkyl chains on molecular arrangements and electron mobility. NEW J CHEM 2021. [DOI: 10.1039/d1nj01515j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Organic solar cells (OSCs) based on non-fullerene acceptor (NFA) Y6 have drawn tremendous attention due to the great progress in their power conversion efficiencies (PCEs).
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Affiliation(s)
- Jie Zhang
- School of Materials and Energy
- Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies
- Southwest University
- Chongqing
- China
| | - Yunjie Xiang
- School of Materials and Energy
- Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies
- Southwest University
- Chongqing
- China
| | - Shaohui Zheng
- School of Materials and Energy
- Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies
- Southwest University
- Chongqing
- China
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43
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Exploring the effects of axial halogen substitutions of subphthalocyanine on the charge transfer nature in subPC/C60 solar cells. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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44
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Chrayteh A, Blondel A, Loos PF, Jacquemin D. Mountaineering Strategy to Excited States: Highly Accurate Oscillator Strengths and Dipole Moments of Small Molecules. J Chem Theory Comput 2020; 17:416-438. [DOI: 10.1021/acs.jctc.0c01111] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Amara Chrayteh
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Aymeric Blondel
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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45
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Wrighton-Araneda K, Valdebenito C, Abarca G, Cortés-Arriagada D. Data of interaction of supported ionic liquids phases onto copper nanoparticles: A density functional theory study. Data Brief 2020; 33:106562. [PMID: 33304960 PMCID: PMC7708792 DOI: 10.1016/j.dib.2020.106562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 11/28/2022] Open
Abstract
This work contains data on the computational, structural, and electronic characterization of supported ionic liquids phases anchored to copper nanoparticles using Density Functional theory calculations. The data supplement the paper "Interaction of supported ionic liquids phases onto copper nanoparticles: A Density Functional Theory study" [1], based on the adsorption of ionic liquid onto a Cu nanoparticle is analyzed from a chemical and physical point of view. The chemical analysis is based on Atoms in Molecule theory (AIM) and allows us to differentiate the chemical binding nature between ionic liquid and copper nanoparticle. On the other hand, the energy decomposition analysis based on absolutely localized molecular orbital (ALMO-EDA) describes the physical contributions that govern the interaction between ionic liquid and the copper nanoparticles. Herein, detailed and extended information in the synthesis and computational characterization are presented.
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Affiliation(s)
- Kerry Wrighton-Araneda
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación. Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O. Box, San Joaquín, Santiago 8940577, Chile
| | - Cristián Valdebenito
- Universidad Bernardo O'Higgins, Escuela de Obstetricia y Puericultura, Centro Integrativo de Biología y Química Aplicada (CIBQA), Santiago 8370993, Chile
| | - Gabriel Abarca
- Universidad Bernardo O'Higgins, Escuela de Obstetricia y Puericultura, Centro Integrativo de Biología y Química Aplicada (CIBQA), Santiago 8370993, Chile
| | - Diego Cortés-Arriagada
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación. Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O. Box, San Joaquín, Santiago 8940577, Chile
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46
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Parenti KR, He G, Sanders SN, Pun AB, Kumarasamy E, Sfeir MY, Campos LM. Bridge Resonance Effects in Singlet Fission. J Phys Chem A 2020; 124:9392-9399. [PMID: 33138366 DOI: 10.1021/acs.jpca.0c08427] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A major benefit of intramolecular singlet fission (iSF) materials, in which through-bond interactions mediate triplet pair formation, is the ability to control the triplet formation dynamics through molecular engineering. One common design strategy is the use of molecular bridges to mediate interchromophore interactions, decreasing electronic coupling by increasing chromophore-chromophore separation. Here, we report how the judicious choice of aromatic bridges can enhance chromophore-chromophore electronic coupling. This molecular engineering strategy takes advantage of "bridge resonance", in which the frontier orbital energies are nearly degenerate with those of the covalently linked singlet fission chromophores, resulting in fast iSF even at large interchromophore separations. Using transient absorption spectroscopy, we investigate this bridge resonance effect in a series of pentacene and tetracene-bridged dimers, and we find that the rate of triplet formation is enhanced as the bridge orbitals approach resonance. This work highlights the important role of molecular connectivity in controlling the rate of iSF through chemical bonds and establishes critical design principles for future use of iSF materials in optoelectronic devices.
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Affiliation(s)
- Kaia R Parenti
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Guiying He
- Department of Physics, Graduate Center, City University of New York, New York, New York 10016, United States.,Photonics Initiative, Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Samuel N Sanders
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Andrew B Pun
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Elango Kumarasamy
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Matthew Y Sfeir
- Department of Physics, Graduate Center, City University of New York, New York, New York 10016, United States.,Photonics Initiative, Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Luis M Campos
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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47
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Vidal ML, Epshtein M, Scutelnic V, Yang Z, Xue T, Leone SR, Krylov AI, Coriani S. Interplay of Open-Shell Spin-Coupling and Jahn-Teller Distortion in Benzene Radical Cation Probed by X-ray Spectroscopy. J Phys Chem A 2020; 124:9532-9541. [PMID: 33103904 DOI: 10.1021/acs.jpca.0c08732] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We report a theoretical investigation and elucidation of the X-ray absorption spectra of neutral benzene and of the benzene cation. The generation of the cation by multiphoton ultraviolet (UV) ionization and the measurement of the carbon K-edge spectra of both species using a table-top high-harmonic generation source are described in the companion experimental paper [Epshtein, M.; et al. J. Phys. Chem. A http://dx.doi.org/10.1021/acs.jpca.0c08736]. We show that the 1sC → π transition serves as a sensitive signature of the transient cation formation, as it occurs outside of the spectral window of the parent neutral species. Moreover, the presence of the unpaired (spectator) electron in the π-subshell of the cation and the high symmetry of the system result in significant differences relative to neutral benzene in the spectral features associated with the 1sC → π* transitions. High-level calculations using equation-of-motion coupled-cluster theory provide the interpretation of the experimental spectra and insight into the electronic structure of benzene and its cation. The prominent split structure of the 1sC → π* band of the cation is attributed to the interplay between the coupling of the core → π* excitation with the unpaired electron in the π-subshell and the Jahn-Teller distortion. The calculations attribute most of the splitting (∼1-1.2 eV) to the spin coupling, which is visible already at the Franck-Condon structure, and we estimate the additional splitting due to structural relaxation to be around ∼0.1-0.2 eV. These results suggest that X-ray absorption with increased resolution might be able to disentangle electronic and structural aspects of the Jahn-Teller effect in the benzene cation.
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Affiliation(s)
- Marta L Vidal
- DTU Chemistry - Department of Chemistry, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Michael Epshtein
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Valeriu Scutelnic
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Zheyue Yang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Tian Xue
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Stephen R Leone
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Department of Physics, University of California, Berkeley, California 94720, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Sonia Coriani
- DTU Chemistry - Department of Chemistry, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
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48
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Nanda KD, Krylov AI. Cherry-picking resolvents: A general strategy for convergent coupled-cluster damped response calculations of core-level spectra. J Chem Phys 2020; 153:141104. [DOI: 10.1063/5.0020843] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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49
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Vidal ML, Pokhilko P, Krylov AI, Coriani S. Equation-of-Motion Coupled-Cluster Theory to Model L-Edge X-ray Absorption and Photoelectron Spectra. J Phys Chem Lett 2020; 11:8314-8321. [PMID: 32897075 DOI: 10.1021/acs.jpclett.0c02027] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We present an extension of the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) theory for computing X-ray L-edge spectra, both in the absorption (XAS) and in the photoelectron (XPS) regimes. The approach is based on the perturbative evaluation of spin-orbit couplings using the Breit-Pauli Hamiltonian and nonrelativistic wave functions described by the fc-CVS-EOM-CCSD ansatz (EOM-CCSD within the frozen-core core-valence separated (fc-CVS) scheme). The formalism is based on spinless one-particle density matrices. The approach is illustrated by modeling XAS and XPS of several model systems ranging from Ar to small molecules containing sulfur and silicon.
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Affiliation(s)
- Marta L Vidal
- DTU Chemistry - Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark
| | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Sonia Coriani
- DTU Chemistry - Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark
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50
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Senthooran R, Curnow OJ, Brenner T, Weiss R, Ferreras M, Crittenden DL. A Series of Discrete Dichloride Dihydrates: Characterisation and Symmetry Effects. Chempluschem 2020; 85:2272-2280. [PMID: 32897648 DOI: 10.1002/cplu.202000563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/16/2020] [Indexed: 11/07/2022]
Abstract
A series of three discrete dichloride dihydrates [Cl2 (H2 O)2 ]2- have been isolated with different triaminocyclopropenium (TAC) cations and with different crystallographic symmetries. The cluster exhibits D2h symmetry with the tris(dimethylamino)cyclopropenium cation [C3 (NMe2 )3 ]+ , C2h symmetry with the fluorinated cation [C3 (N(CH2 CF3 )2 )(NBu2 )2 ]+ (containing two 2,2,2-trifluoroethyl substituents) and C2v symmetry with the more fluorinated [C3 (N(CH2 CF3 )2 )2 (NBu2 )]+ cation. The effect of symmetry on the infrared spectra of the dichloride ion-pair clusters, as well as deuterated analogues, has been investigated. The D2h - and C2h -symmetric clusters each exhibit two stretching bands in the infrared at 3427 and 3368 cm-1 for D2h symmetry and 3444 and 3392 cm-1 for C2h symmetry, whereas the C2v -symmetric cluster exhibits three bands at 3475, 3426 and 3373 cm-1 . Computational studies were carried out on a [Cl2 (H2 O)2 ]2- cluster with C2v symmetry to aid the infrared band assignments.
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Affiliation(s)
- Rathiga Senthooran
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Owen J Curnow
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Thomas Brenner
- Institut für Organische Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054, Erlangen, Germany
| | - Robert Weiss
- Institut für Organische Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054, Erlangen, Germany
| | - Manuel Ferreras
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Deborah L Crittenden
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
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