1
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Schreder L, Luber S. Implementation of frozen density embedding in CP2K and OpenMolcas: CASSCF wavefunctions embedded in a Gaussian and plane wave DFT environment. J Chem Phys 2024; 161:144110. [PMID: 39387407 DOI: 10.1063/5.0222409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 09/18/2024] [Indexed: 10/15/2024] Open
Abstract
Most chemical processes happen at a local scale where only a subset of molecular orbitals is directly involved and only a subset of covalent bonds may be rearranged. To model such reactions, Density Functional Theory (DFT) is often inadequate, and the use of computationally more expensive correlated wavefunction (WF) methods is required for accurate results. Mixed-resolution approaches backed by quantum embedding theory have been used extensively to approach this imbalance. Based on the frozen density embedding freeze-and-thaw algorithm, we describe an approach to embed complete active space self-consistent field simulations run in the OpenMolcas code in a DFT environment calculated in CP2K without requiring any external tools. This makes it possible to study a local, active part of a chemical system in a larger and relatively static environment with a computational cost balanced between the accuracy of a WF method and the efficiency of DFT, which we test on environment-subsystem pairs. Finally, we apply the implementation to an oxygen molecule leaving an aluminum (111) surface and a ruthenium(IV) oxide (110) surface.
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Affiliation(s)
- Lukas Schreder
- University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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2
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Wang H, Sun L, Zhao Y, Qiu Y. DFT Study on the Second-Order NLO Responses of 2-Phenyl Benzoquinoline Ir(III) Complexes by Substituents and Redox Effects. J Phys Chem A 2024; 128:8709-8716. [PMID: 39344984 DOI: 10.1021/acs.jpca.4c05008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Metal complexes have received extensive attention in nonlinear optical (NLO) materials because of their advantages, such as shorter response times and more flexible structural properties. Density functional theory is used in investigating the geometric structures, electronic structures, charge centroid, and first hyperpolarizability (βtot) of a series of selected 15 coordinated Ir(III) complexes. The substitute effect and one-electron redox process effects on the structures and properties of 15 coordinated Ir(III) complexes are considered. When the electron-withdrawing group is introduced into the ligand, the HOMO-LUMO energy gap decreases and the βtot value increases, positively correlating with the electron-withdrawing ability. The single electron redox process can also improve the NLO responses of complexes, especially the reduction process. The βtot value of complex 4- is the largest, 2078 times higher than that of complex 4. The analysis shows that the variation of NLO responses of complexes is ascribed to the change of electronic structures and the charge transfer modes induced by the ligand modification and redox process, which are considered to be two effective methods in enhancing the NLO responses of 2-phenyl benzoquinoline Ir(III) complexes. This study aims to offer design insights into high-performance nonlinear optical materials.
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Affiliation(s)
- Hequn Wang
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Liting Sun
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Yuanyuan Zhao
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Yongqing Qiu
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
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3
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Tatarin SV, Bezzubov SI. Synthesis, Structure, and Properties of Nontrivial Iridium(III) Complexes Based on Anthracene-Decorated Benzimidazole Ligand. Inorg Chem 2024; 63:18642-18654. [PMID: 39321335 DOI: 10.1021/acs.inorgchem.4c02414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Reactions of iridium trichloride hydrate with bulky 2-(9-anthracenyl)-1-phenyl-benzimidazole (anbi) in the presence of N-donor ligands afforded a number of unique noncyclometalated complexes, while attempts to prepare a common μ-chloro-bridged bis-cyclometalated dimer systematically gave a monocyclometalated complex cis-[Ir(C,N-anbi)(N-anbi)Cl2] instead. The obtained complexes were characterized by 1H NMR, high-resolution mass spectrometry, single-crystal and powder X-ray diffraction, UV-vis spectroscopy, and cyclic voltammetry. The noncyclometalated complexes fac-[Ir(N-anbi)(N^N)Cl3)], where N^N are 4,4'-disubstituted 2,2'-bipyridines, are octahedral and contain the anthracene and 2,2'-bipyridine units in a close cofacial arrangement. These complexes were found to be exceptionally inert to the chloride ligand exchange even in the presence of silver triflate, forming a rare trinuclear Ir-μ-Cl3-Ag-μ-Cl3-Ir structure instead. In the monocyclometalated complex, the Ir(III) ion is pentacoordinated in a rare square-pyramidal geometry, where the bulky anthracene fragment is involved in the steric shielding of the metal center. This is in line with the results of gas-phase density functional theory calculations, demonstrating that the experimentally observed structure is energetically most preferable. The monocyclometalated complex is deeply colored due to intense charge-transfer absorption bands in the range 450-650 nm with ε = 2000-5000 M-1 cm-1, superior to the noncyclometalated complexes. The synthesis, structures, and properties of the new complexes are discussed in the context of the related mono-, bis-, and noncyclometalated iridium(III) compounds.
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Affiliation(s)
- Sergei V Tatarin
- N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| | - Stanislav I Bezzubov
- N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
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4
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Nguyen Thi Minh N, König C. The role of microenvironments on computed vibrationally-resolved emission spectra: The case of oxazines. J Comput Chem 2024; 45:2232-2241. [PMID: 38831461 DOI: 10.1002/jcc.27385] [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: 09/27/2023] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 06/05/2024]
Abstract
Oxazine dyes act as reporters of their near environment by the response of their fluorescence spectra. At the same time, their fluorescence spectra exhibit a pronounced vibrational progression. In this work, we computationally investigate the impact of near-environment models consisting of aggregated water as well as betaine molecules on the vibrational profile of fluorescence spectra of different oxazine derivatives. For aggregated betaine and a water molecule located above the plane of the dyes, we observe a distinct modification of the vibrational profile, which is more pronounced than the effect of a continuum description of a solvent environment. Our analysis shows that this effect cannot be explained by a pure change in the electronic structure, but that also vibrational degrees of freedom of the environment can be decisive for the vibrational profile and should, hence, not generally be neglected.
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Affiliation(s)
- Nghia Nguyen Thi Minh
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Hannover, Germany
| | - Carolin König
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Hannover, Germany
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Samanta S, Mondal P. A Comprehensive Computational Study on the Thermodynamics and Kinetics of Tetrahydrobiopterin Regeneration Process. Chemphyschem 2024; 25:e202400401. [PMID: 38861155 DOI: 10.1002/cphc.202400401] [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: 04/09/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/12/2024]
Abstract
One of the most crucial enzymatic cofactors in the human body is tetrahydrobiopterin, which is acquired through biological synthesis and self-regeneration. During this regenerative process, it undergoes oxidation, deprotonation, further oxidation, and subsequent deprotonation, resulting in the formation of quinonoid-dihydrobiopterin, which then undergoes tautomerization to yield dihydrobiopterin. This study presents the thermodynamic and kinetic properties associated with each stage of the regeneration process using theoretical calculations. The redox potentials for oxidation steps and the pKa values for deprotonation steps are determined employing the Born-Haber cycle and the direct change of free energy in implicit solvent models. The redox metabolites are characterized and confirmed from their calculated absorption spectra using the time-dependent density functional theory method. For the tautomerization steps, an IRC calculation is executed, and rate constants are computed using Eyring's Transition State Theory (TST). The tunnelling probability of the H atom during the tautomerization process is incorporated using Wigner's tunnelling correction in the calculation of the rate constant. Notably, we identify the N3 atom as the most probable deprotonation site for H3B+ and predict its geometry based on our calculations. Furthermore, we elucidate the spectral properties of intermediates involved in the regeneration process, highlighting key electronic transitions responsible for their excitations. Our results indicate that each step of tautomerization occurs along vibrational bending modes. We have observed that these tautomerization processes have high activation energies by optimising transition states. Additionally, considering tunnelling correction can significantly affect the reaction rates associated with these processes. These results provide a comprehensive understanding of the thermodynamics and kinetics of the regeneration process of tetrahydrobiopterin, which will help in the modulation of its biological activity.
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Affiliation(s)
- Suvadip Samanta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati, India
| | - Padmabati Mondal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati, India
- Center for Atomic, Molecular and Optical Sciences and Technologies, Indian Institute of Science Education and Research (IISER), Tirupati, India
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Parveen M, Uzma, Khan AA, Nami SAA, Kataria R, Malik A, Amali NAM, Abd Kadir NH, Alam M. Isolation, Characterization, and Single-Crystal X-ray Analysis of Lantabetulic Acid from Rhus alata: Insights into HSA and BSA Binding Interactions, with In-Silico Study. ACS OMEGA 2024; 9:39484-39502. [PMID: 39346876 PMCID: PMC11425619 DOI: 10.1021/acsomega.4c03406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 09/01/2024] [Accepted: 09/04/2024] [Indexed: 10/01/2024]
Abstract
This study investigated the bioactive potential of Rhus alata, a plant known for its rich phytochemicals. A previously unreported compound was isolated from R. alata and characterized using various spectroscopic techniques (IR, UV, NMR, MS) and confirmed for the first time by X-ray crystallography. In isolated compound 1, noncovalent interactions between H···H/H···H, C···C/C···C and O···H/H···O play a major role in its packing arrangement. This observation is consistent with the results of Hirshfeld surface analysis, which quantified these interactions as 14.2%, 84.6%, and 1.2%, respectively. The isolated compound was identified as lantabetulic acid (1) (3β,25-expoxy-3α-hydroxylup-20(29)-en-28-oic acid). To understand its potential biological interactions, the binding affinity of lantabetulic acid to biomolecules such as bovine serum albumin (BSA), and human serum albumin (HSA), was assessed. The results showed significant binding efficacy, indicating potential interactions with these molecules. Furthermore, the DPPH assay demonstrated the potent antioxidant activity of this compound. We used in silico molecular docking to clarify the binding affinity between lantabetulic acid and a particular receptor. Furthermore, molecular dynamic simulation studies also explored the binding interaction. As well, MM/GBSA calculations corroborate the simulation results and the stability of the complex. Docking and dynamics studies revealed promising binding scores, suggesting further investigation into their potential therapeutic applications. Geometric parameters and the absorption spectrum of compound 1 were also determined using the DFT approach and compared with experimental findings.
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Affiliation(s)
- Mehtab Parveen
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Uzma
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Shahab A A Nami
- Department of Industrial Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Ramesh Kataria
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Abdul Malik
- Department of Pharmaceutics. College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nurul Afiqah Muhammad Amali
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Nurul Huda Abd Kadir
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Mahboob Alam
- Department of Safety Engineering, Dongguk University, 123 Dongdae-ro, Gyeongju, Gyeongbuk 780714, Republic of Korea
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Howe J, Abou-Hatab S, Matsika S. Modeling the effect of substituents on the electronically excited states of indole derivatives. J Comput Chem 2024. [PMID: 39302059 DOI: 10.1002/jcc.27502] [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: 06/24/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/22/2024]
Abstract
A proper understanding of excited state properties of indole derivatives can lead to rational design of efficient fluorescent probes. The optically activeL a $$ {L}_a $$ andL b $$ {L}_b $$ excited states of a series of substituted indoles, where a substituent was placed on position four, were calculated using equation of motion coupled cluster and time dependent density functional theory. The results indicate that most substituted indoles have a brighter second excited state corresponding to experimental absorption maxima, but a few with electron withdrawing substituents absorb more on the first excited state. Absorption on the first excited state may increase their fluorescence quantum yield, making them better probes. Electronic structure methods were found to predict the energies of the systems with electron withdrawing substituents more accurately than those with electron donating substituents. The excited states of both states correlated well with electrophilicity, similar to the experimental trends for the absorption maxima. Overall, these computational studies indicate that theory can be used to predict excited state properties of substituted indoles, when the substituent is an electron withdrawing group.
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Affiliation(s)
- Jordan Howe
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, USA
| | | | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, USA
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8
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Batista ANL, Valverde AL, Nafie LA, Batista JM. Stereochemistry of natural products from vibrational circular dichroism. Chem Commun (Camb) 2024; 60:10439-10450. [PMID: 39234927 DOI: 10.1039/d4cc02481h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Secondary metabolites from land and marine (micro)organisms have been at the focus of the drug discovery process for many years. One of the reasons for this success is nature's incredible ability to create intricate molecular scaffolds. Such structural richness, however, makes the structural elucidation, and the absolute configuration assignment in particular, a challenging process. Vibrational circular dichroism (VCD) has emerged as one of the most reliable and versatile methods to unambiguously assign both the absolute configuration and conformations of chiral molecules in solution. Although VCD is no longer a curiosity in the field of molecular spectroscopy after 50 years since its first report, it is still underutilized by natural product chemists worldwide for varying reasons. Herein, we highlight the evolution of the application of VCD to natural product chemistry, focusing on its strengths as well as points that still need improvement. General guidelines for the correct application of VCD to stereochemical studies are also provided.
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Affiliation(s)
- Andrea N L Batista
- Institute of Chemistry, Fluminense Federal University, Outeiro de São João Batista s/n, 24020-141, Niterói-RJ, Brazil
| | - Alessandra L Valverde
- Institute of Chemistry, Fluminense Federal University, Outeiro de São João Batista s/n, 24020-141, Niterói-RJ, Brazil
| | - Laurence A Nafie
- Department of Chemistry, 1-014CST, Syracuse University, 13244-4100, Syracuse-NY, USA
| | - João M Batista
- Federal University of São Paulo, Institute of Science and Technology, R. Talim 330, 12231-280, São José dos Campos-SP, Brazil.
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Wang DD, Zhang R, Tang LY, Long GQ, Yan H, Yang YC, Guo ZF, Zheng YY, Wang Y, Jia JM, Wang AH. (±)-Salvicatone A: A Pair of C 27-Meroterpenoid Enantiomers with Skeletons from the Roots and Rhizomes of Salvia castanea Diels f. tomentosa Stib. J Org Chem 2024; 89:12894-12901. [PMID: 37976373 DOI: 10.1021/acs.joc.3c01664] [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: 11/19/2023]
Abstract
(±)-Salvicatone A (1), a C27-meroterpenoid featuring a unique 6/6/6/6/6-pentacyclic carbon skeleton with a 7,8,8a,9,10,10a-hexahydropyren-1 (6H)-one motif, was isolated from the roots and rhizomes of Salvia castanea Diels f. tomentosa Stib. Its structure was characterized by comprehensive spectroscopic analyses along with computer-assisted structure elucidation, including ACD/structure elucidator and quantum chemical calculations with 1H/13C NMR and electronic circular dichroism. Biogenetically, compound 1 was constructed from decarboxylation following [4 + 2] Diels-Alder cycloaddition reaction between caffeic acid and miltirone analogue. Bioassays showed that (-)-1 and (+)-1 inhibited nitric oxide production in lipopolysaccharide-induced RAW264.7 macrophage cells with an IC50 value of 6.48 ± 1.25 and 15.76 ± 5.55 μM, respectively. The structure-based virtual screening based on the pharmacophores in ePharmaLib, as well as the molecular docking and molecular dynamics simulations study, implied that (-)-1 and (+)-1 may potentially bind to retinoic acid receptor-related orphan receptor C to exert anti-inflammatory activities.
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Affiliation(s)
- Dong-Dong Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Rui Zhang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Lian-Yu Tang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Guo-Qing Long
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Hui Yan
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yong-Cheng Yang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zi-Feng Guo
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Ying-Ying Zheng
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yong Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Jing-Ming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - An-Hua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
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10
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Rodríguez-Kessler PL, Muñoz-Castro A. Intermediate Intercluster Bond Orders. Electronic Communication in Au 38(SR) 24 Superatomic Molecules. Chemphyschem 2024; 25:e202400183. [PMID: 38831496 DOI: 10.1002/cphc.202400183] [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: 02/20/2024] [Revised: 04/23/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
Ligand-protected gold clusters remain potential building blocks for envisaged molecular materials. The archetypal Au38(SR)24 cluster can be viewed as a robust template for the fusion of two Au25(SR)18 - cluster units, retaining a bi-icosahedral Au23 core. Via electrochemical properties, the overall charge state can be selectively tuned, enabling the access of 14 valence electron (ve) species featuring a single intercluster bond and nearby charge from -1 to +3, achieving related species bearing 15- to 11-ve with variable intercluster bond orders. Here, we explore the characteristics of intermediate intercluster bond orders in order to provide insights into the plausible electron communication between the constituent building blocks, with Au38(SR)24, as a representative template. Our results denote a small structural variation along -1 to +3 charge states, provided by the core-protecting ligand interaction, which is enhanced towards more oxidized species. The remaining unpaired electron from intermediate intercluster bond orders of 1.5 for Au38(SR)24 1-, 1.5 for Au38(SR)24 1+, and 2.5 for Au38(SR)24 3+, holds delocalized characteristics between the building block units, favoring electron communication for conductive and cooperative cluster aggregates. Such features are relevant for the formation of molecular electronic device applications, favoring the rationalization prior to engaging in explorative synthesis of larger ligand-protected cluster aggregates.
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Affiliation(s)
- Peter L Rodríguez-Kessler
- Centro de Investigaciones en Óptica A.C., Loma del Bosque 115, Col. Lomas del Campestre, León, Guanajuato, 37150, Mexico
| | - Alvaro Muñoz-Castro
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista 7, Santiago, 8420524, Chile
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11
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Giovannini T. Kohn-Sham fragment energy decomposition analysis. J Chem Phys 2024; 161:104110. [PMID: 39268825 DOI: 10.1063/5.0216596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/15/2024] [Indexed: 09/15/2024] Open
Abstract
We introduce the concept of Kohn-Sham fragment localized molecular orbitals (KS-FLMOs), which are Kohn-Sham molecular orbitals (MOs) localized in specific fragments constituting a generic molecular system. In detail, we minimize the local electronic energies of various fragments, while maximizing the repulsion between them, resulting in the effective localization of the MOs. We use the developed KS-FLMOs to propose a novel energy decomposition analysis, which we name Kohn-Sham fragment energy decomposition analysis, which allows for rationalizing the main non-covalent interactions occurring in interacting systems both in vacuo and in solution, providing physical insights into non-covalent interactions. The method is validated against state-of-the-art energy decomposition analysis techniques and with high-level calculations.
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Affiliation(s)
- Tommaso Giovannini
- Department of Physics, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy and Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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12
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Wu H, Hemmingsen L, Sauer SPA. On the geometry dependence of the nuclear magnetic resonance chemical shift of mercury in thiolate complexes: A relativistic density functional theory study. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:648-669. [PMID: 38773942 DOI: 10.1002/mrc.5452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024]
Abstract
Thiolate containing mercury(II) complexes of the general formula [Hg(SR)n ]2 - n have been of great interest since the toxicity of mercury was recognized. 199Hg nuclear magnetic resonance spectroscopy (NMR) is a powerful tool for characterization of mercury complexes. In this work, the Hg shielding constants in a series of [Hg(SR)n ]2 - n complexes are therefore investigated computationally with particular emphasis on their geometry dependence. Geometry optimizations and NMR chemical shift calculations are performed at the density functional theory (DFT) level with both the zeroth-order regular approximation (ZORA) and four-component relativistic methods. The four exchange-correlation (XC) functionals PBE0, PBE, B3LYP, and BLYP are used in combination with either Dyall's Gaussian-type (GTO) or Slater-type orbitals (STOs) basis sets. Comparing ZORA and four-component calculations, one observes that the calculated shielding constants for a given molecular geometry have a constant difference of ∼ 1070 ppm. This confirms that ZORA is an acceptable relativistic method to compute NMR chemical shifts. The combinations of four-component/PBE0/v3z and ZORA/PBE0/QZ4P are applied to explore the geometry dependence of the isotropic shielding. For a given coordination number, the distance between mercury and sulfur is the key factor affecting the shielding constant, while changes in bond and dihedral angles and even different side groups have relatively little impact.
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Affiliation(s)
- Haide Wu
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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13
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Saetta C, Barlocco I, Liberto GD, Pacchioni G. Key Ingredients for the Screening of Single Atom Catalysts for the Hydrogen Evolution Reaction: The Case of Titanium Nitride. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2401058. [PMID: 38671564 DOI: 10.1002/smll.202401058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/10/2024] [Indexed: 04/28/2024]
Abstract
A computational screening of Single Atom Catalysts (SACs) bound to titanium nitride (TiN) is presented, for the Hydrogen Evolution Reaction (HER), based on density functional theory. The role of fundamental ingredients is explored to account for a reliable screening of SACs. Namely, the formation of H2-complexes besides the classical H* one impacts the predicted HER activity, in line with previous studies on other SACs. Also, the results indicate that one needs to adopt self-interaction-corrected functionals. Finally, predicting an active catalyst is of little help without an assessment of its stability. Thus, it is included in the theoretical framework the analysis of the stability of the SACs in working conditions of pH and voltage. Once unconventional intermediates and stability are considered in a self-interaction corrected scheme, the number of potential good catalysts for HER is strongly reduced since i) some potentially good catalysts are not stable against dissolution and ii) the formation of unconventional intermediates leads to thermodynamic barriers. This study highlights the importance of including ingredients for the prediction of new systems, such as the formation of unconventional intermediates, estimating the stability of SACs, and the adoption of self-interaction corrected functionals. Also, this study highlights some interesting candidates deserving of dedicated work.
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Affiliation(s)
- Clara Saetta
- Dipartimento di Scienza dei Materiali, Università degli studi di Milano Bicocca, Via R. Cozzi 55, Milano, 20125, Italy
| | - Ilaria Barlocco
- Dipartimento di Scienza dei Materiali, Università degli studi di Milano Bicocca, Via R. Cozzi 55, Milano, 20125, Italy
| | - Giovanni Di Liberto
- Dipartimento di Scienza dei Materiali, Università degli studi di Milano Bicocca, Via R. Cozzi 55, Milano, 20125, Italy
| | - Gianfranco Pacchioni
- Dipartimento di Scienza dei Materiali, Università degli studi di Milano Bicocca, Via R. Cozzi 55, Milano, 20125, Italy
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14
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Ulukan P, Lognon E, Catak S, Monari A. Intersystem crossing in a dibenzofuran-based room temperature phosphorescent luminophore investigated by non-adiabatic dynamics. Phys Chem Chem Phys 2024; 26:22261-22268. [PMID: 39136100 DOI: 10.1039/d4cp02474e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The use of phosphorescent luminophores is highly beneficial in diverse high-technological and biological applications. Yet, because of the formally forbidden character of intersystem crossing, the use of heavy metals or atoms is usually necessary to achieve high quantum yields. This choice imposes serious constraints in terms of high device cost and inherent toxicity. In this contribution we resort to density functional based surface hopping non-adiabatic dynamics of a potential organic luminophore intended for room-temperature applications. We confirm that intersystem crossing is operative in a ps time-scale without requiring the activation of large-scale movements, thus confirming the suitability of the El Sayed-based strategy for the rational design of fully organic phosphorescent emitters.
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Affiliation(s)
- Pelin Ulukan
- Bogazici University, 34342 Bebek/Istanbul, Turkey
| | - Elise Lognon
- Université Paris Cité and CNRS, ITODYS, F-75006 Paris, France.
| | - Saron Catak
- Bogazici University, 34342 Bebek/Istanbul, Turkey
| | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS, F-75006 Paris, France.
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15
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Garcia-Alvarez JC, Gozem S. Absorption Intensities of Organic Molecules from Electronic Structure Calculations versus Experiments: the Effect of Solvation, Method, Basis Set, and Transition Moment Gauge. J Chem Theory Comput 2024; 20. [PMID: 39141425 PMCID: PMC11360136 DOI: 10.1021/acs.jctc.4c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024]
Abstract
Recently, we derived experimental oscillator strengths (OSs) from well-defined UV-visible absorption spectral peaks of 100 molecules in solution. Here, we focus on a subset of transitions with the highest reliability to further benchmark the OSs from several wave function methods and density functionals. We consider multiple basis sets, transition moment gauges (length, velocity, and mixed), and solvent corrections. Most transitions in the comparison set come from conjugated molecules and have π → π* character. We use an automated algorithm to assign computed transitions to experimental bands. OSs computed using the Tamm-Dancoff approximation (TDA), CIS, or EOM-CCSD exhibited a strong gauge dependence, which is diminished in linear response theories (TD-DFT, TD-HF, and to a smaller degree LR-CCSD). OSs calculated from TD-DFT with PCM solvent models are systematically larger than apparent OSs derived from experimental spectra. For example, fcomp from hybrid functionals and PCM have mean absolute errors that are ∼10% of n·fexp, where n is a solvent refractive index factor that arises from the energy flux of the radiation field in a dielectric (solvent). Theoretical cavity field corrections considering spherical cavities do not improve the agreement between computed and experimental data. Corrections that account for the molecular shape and the direction of transition dipole moments, or that explicitly account for the effect of solvent molecules on the local field, should be more appropriate.
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Affiliation(s)
| | - Samer Gozem
- Department of Chemistry, Georgia
State University, Atlanta, Georgia 30302, United States
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16
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Mydlova L, Sahraoui B, El-Ghayoury A, Berdowski J, Migalska-Zalas A, Makowska-Janusik M. Hierarchical Modeling of the Nonlinear Optical Response of Composite Materials Based on Tetrathiafulvalene Derivatives. Molecules 2024; 29:3720. [PMID: 39202800 PMCID: PMC11356877 DOI: 10.3390/molecules29163720] [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: 07/04/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 09/03/2024] Open
Abstract
The presented work concerns computational investigations of the physical properties of composite materials based on polymer matrix and nonlinear optical (NLO) active chromophores. The structural, electronic, and optical properties of selected tetrathiafulvalene (TTF)-based chromophores have been calculated using quantum chemical methods. The polymer matrix changes the physical properties of the inserted chromophores influencing their optical parameters. To explain the mechanism of the NLO signal occurrence from the composites based on poly(methyl methacrylate) (PMMA) matrix and TTF chromophores, their structures are modeled using the classical molecular dynamics. In consequence, the structural properties of the composites are discussed according to the NLO requirements. By developing the theoretical model based on a discrete multipole local field approach, the impact of polymer matrix on the optical properties of chromophores is explained.
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Affiliation(s)
- Lucia Mydlova
- Faculty of Science and Technology, Jan Dlugosz University, Al. Armii Krajowej 13/15, 42-200 Czestochowa, Poland; (L.M.); (J.B.); (A.M.-Z.)
| | - Bouchta Sahraoui
- LPHIA, University of Angers, Bd Lavoisier 2, 49045 Angers, France;
| | | | - Janusz Berdowski
- Faculty of Science and Technology, Jan Dlugosz University, Al. Armii Krajowej 13/15, 42-200 Czestochowa, Poland; (L.M.); (J.B.); (A.M.-Z.)
| | - Anna Migalska-Zalas
- Faculty of Science and Technology, Jan Dlugosz University, Al. Armii Krajowej 13/15, 42-200 Czestochowa, Poland; (L.M.); (J.B.); (A.M.-Z.)
| | - Malgorzata Makowska-Janusik
- Faculty of Science and Technology, Jan Dlugosz University, Al. Armii Krajowej 13/15, 42-200 Czestochowa, Poland; (L.M.); (J.B.); (A.M.-Z.)
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17
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Nagy D, Reinholdt P, Jensen PWK, Kjellgren ER, Ziems KM, Fitzpatrick A, Knecht S, Kongsted J, Coriani S, Sauer SPA. Electric Field Gradient Calculations for Ice VIII and IX Using Polarizable Embedding: A Comparative Study on Classical Computers and Quantum Simulators. J Phys Chem A 2024; 128:6305-6315. [PMID: 39020525 DOI: 10.1021/acs.jpca.4c02697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
We test the performance of the polarizable embedding variational quantum eigensolver self-consistent field (PE-VQE-SCF) model for computing electric field gradients with comparisons to conventional complete active space self-consistent-field (CASSCF) calculations and experimental results. We compute quadrupole coupling constants for ice VIII and ice IX. We find close agreement of the quantum-computing PE-VQE-SCF results with the results from the classical PE-CASSCF calculations and with experiment. Furthermore, we observe that the inclusion of the environment is crucial for obtaining results that match the experimental data. The calculations for ice VIII are within the experimental uncertainty for both CASSCF and VQE-SCF for oxygen and lie close to the experimental value for ice IX as well. With the VQE-SCF, which is based on an adaptive derivative-assembled problem-tailored (ADAPT) ansatz, we find that the inclusion of the environment and the size of the different basis sets do not directly affect the gate counts. However, by including an explicit environment, the wavefunction and therefore the optimization problem become more complicated, which usually results in the need to include more operators from the operator pool, thereby increasing the depth of the circuit.
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Affiliation(s)
- Dániel Nagy
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Phillip W K Jensen
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Erik Rosendahl Kjellgren
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Karl Michael Ziems
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | | | - Stefan Knecht
- Algorithmiq Ltd, Kanavakatu 3C, FI-00160 Helsinki, Finland
- Department of Chemistry and Applied Life Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, CH-8093 Zürich, Switzerland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
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18
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Khanna A, Shedge SV, Zuehlsdorff TJ, Isborn CM. Calculating absorption and fluorescence spectra for chromophores in solution with ensemble Franck-Condon methods. J Chem Phys 2024; 161:044121. [PMID: 39077907 DOI: 10.1063/5.0217080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Accurately modeling absorption and fluorescence spectra for molecules in solution poses a challenge due to the need to incorporate both vibronic and environmental effects, as well as the necessity of accurate excited state electronic structure calculations. Nuclear ensemble approaches capture explicit environmental effects, Franck-Condon methods capture vibronic effects, and recently introduced ensemble-Franck-Condon approaches combine the advantages of both methods. In this study, we present and analyze simulated absorption and fluorescence spectra generated with combined ensemble-Franck-Condon approaches for three chromophore-solvent systems and compare them to standard ensemble and Franck-Condon spectra, as well as to the experiment. Employing configurations obtained from ground and excited state ab initio molecular dynamics, three combined ensemble-Franck-Condon approaches are directly compared to each other to assess the accuracy and relative computational time. We find that the approach employing an average finite-temperature Franck-Condon line shape generates spectra nearly identical to the direct summation of an ensemble of Franck-Condon spectra at one-fourth of the computational cost. We analyze how the spectral simulation method, as well as the level of electronic structure theory, affects spectral line shapes and associated Stokes shifts for 7-nitrobenz-2-oxa-1,3-diazol-4-yl and Nile red in dimethyl sulfoxide and 7-methoxy coumarin-4-acetic acid in methanol. For the first time, our studies show the capability of combined ensemble-Franck-Condon methods for both absorption and fluorescence spectroscopy and provide a powerful tool for simulating linear optical spectra.
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Affiliation(s)
- Ajay Khanna
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
| | - Sapana V Shedge
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
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19
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Kiataki MB, Coutinho K, Varella MTDN. Toward a numerically efficient description of bulk-solvated anionic states. J Chem Phys 2024; 161:034301. [PMID: 39007383 DOI: 10.1063/5.0203247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute-solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute-solvent and solvent-solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models.
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Affiliation(s)
- Matheus B Kiataki
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
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20
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Bashirova D, Zuehlsdorff TJ. First-Principles Modeling of the Absorption Spectrum of Crystal Violet in Solution: The Importance of Environmentally Driven Symmetry Breaking. J Phys Chem A 2024; 128:5229-5242. [PMID: 38938007 DOI: 10.1021/acs.jpca.4c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Theoretical spectroscopy plays a crucial role in understanding the properties of the materials and molecules. One of the most promising methods for computing optical spectra of chromophores embedded in complex environments from the first principles is the cumulant approach, where both (generally anharmonic) vibrational degrees of freedom and environmental interactions are explicitly accounted for. In this work, we verify the capabilities of the cumulant approach in describing the effect of complex environmental interactions on linear absorption spectra by studying Crystal Violet (CV) in different solvents. The experimental absorption spectrum of CV strongly depends on the nature of the solvent, indicating strong coupling to the condensed-phase environment. We demonstrate that these changes in absorption line shape are driven by an increased splitting between absorption bands of two low-lying excited states that is caused by a breaking of the D3 symmetry of the molecule and that in polar solvents, this symmetry breaking is mainly driven by electrostatic interactions with the condensed-phase environment rather than distortion of the structure of the molecule, in contrast with conclusions reached in a number of previous studies. Our results reveal the importance of explicitly including a counterion in the calculations in nonpolar solvents due to electrostatic interactions between CV and the ion. In polar solvents, these interactions are strongly reduced due to solvent screening effects, thus minimizing the symmetry breaking. Computed spectra in methanol are found to be in reasonable agreement with the experiment, demonstrating the strengths of the outlined approach in modeling strong environmental interactions.
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Affiliation(s)
- Dayana Bashirova
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
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21
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Soler-Orenes JA, Monari A, Miranda MA, Hernández-Gil J, Lhiaubet-Vallet V. Environmentally sensitive fluorescence of the topical retinoid adapalene. Front Chem 2024; 12:1438751. [PMID: 39040091 PMCID: PMC11260622 DOI: 10.3389/fchem.2024.1438751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 06/14/2024] [Indexed: 07/24/2024] Open
Abstract
Intrinsic fluorescence of drugs brings valuable information on their localization in the organism and their interaction with key biomolecules. In this work, we investigate the absorption and emission properties of the topical retinoid adapalene in different solvents and biological media. While the UVA/UVB absorption band does not exhibit any significant solvent-dependent behavior, a strong positive solvatochromism is observed for the emission. These results are in line with molecular modeling and simulations that show the presence of two quasi-degenerate states, i.e., a local π-π* and an intermolecular charge-transfer (ICT) state. However, molecular modeling also revealed that, whatever the solvent, at the corresponding equilibrium geometry the lowest and emissive excited state is the local π-π*. Finally, the potential of adapalene to act as a biological probe is demonstrated using albumin, DNA and micelles.
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Affiliation(s)
- Juan A. Soler-Orenes
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - Miguel A. Miranda
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Javier Hernández-Gil
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Valencia, Spain
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22
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Karibayev M, Myrzakhmetov B, Bekeshov D, Wang Y, Mentbayeva A. Atomistic Modeling of Quaternized Chitosan Head Groups: Insights into Chemical Stability and Ion Transport for Anion Exchange Membrane Applications. Molecules 2024; 29:3175. [PMID: 38999128 PMCID: PMC11243541 DOI: 10.3390/molecules29133175] [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: 05/12/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
The chemical stability and ion transport properties of quaternized chitosan (QCS)-based anion exchange membranes (AEMs) were explored using Density Functional Theory (DFT) calculations and all-atom molecular dynamics (MD) simulations. DFT calculations of LUMO energies, reaction energies, and activation energies revealed an increasing stability trend among the head groups: propyl trimethyl ammonium chitosan (C) < oxy propyl trimethyl ammonium chitosan (B) < 2-hydroxy propyl trimethyl ammonium chitosan (A) at hydration levels (HLs) of 0 and 3. Subsequently, all-atom MD simulations evaluated the diffusion of hydroxide ions (OH-) through mean square displacement (MSD) versus time curves. The diffusion coefficients of OH- ions for the three types of QCS (A, B, and C) were observed to increase monotonically with HLs ranging from 3 to 15 and temperatures from 298 K to 350 K. Across different HLs and temperatures, the three QCS variants exhibited comparable diffusion coefficients, underlining their effectiveness in vehicular transport of OH- ions.
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Affiliation(s)
- Mirat Karibayev
- Department of Chemical & Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Astana 010000, Kazakhstan
| | - Bauyrzhan Myrzakhmetov
- Center for Energy and Advanced Materials Science, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Dias Bekeshov
- Department of Chemical & Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Astana 010000, Kazakhstan
| | - Yanwei Wang
- Department of Chemical & Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Astana 010000, Kazakhstan
- Center for Energy and Advanced Materials Science, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Almagul Mentbayeva
- Department of Chemical & Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Astana 010000, Kazakhstan
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23
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Josephy T, Kumar R, Bleher K, Röhs F, Glaser T, Rajaraman G, Comba P. Synthesis, Characterization, and Reactivity of Bispidine-Iron(IV)-Tosylimido Species. Inorg Chem 2024; 63:12109-12119. [PMID: 38875304 DOI: 10.1021/acs.inorgchem.4c01237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Reported are the synthesis and detailed studies of the iron(IV)-tosylimido complexes of two isomeric pentadentate bispidine ligands (bispidines are 3,7-diazabicyclo[3.3.1]nonane derivatives). This completes a series of five tosylimido complexes with comparable pentadentate amine/pyridine ligands, where the corresponding [(L)FeIV═O]2+ oxidants have been studied in detail. The characterization of the two new complexes in solution (UV-vis-NIR, Mössbauer, HR-ESI-MS) shows that these oxidants have an intermediate spin (S = 1) electronic ground state. The reactivities have been studied as oxidants in C-H activation at 1,3-cyclohexadiene and nitrogen atom transfer to thioanisole. For the latter substrate, the entire set of data for the five ligands and for both nitrogen and oxygen atom transfer is now available and the interesting observation is that oxygen atom transfer is, as expected, generally faster than nitrogen atom transfer, with the exception of the two ligands that have four and three pyridine groups oriented parallel to the Fe-O and Fe-N axes. A thorough DFT analysis indicates that this is due to steric effects in the case of the [(L)FeIV═O]2+ species, which are less important in the [(L)FeIV═NTs]2+ compounds due to partial electron transfer from the thioanisole substrate to the iron(IV)-tosylimido oxidant.
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Affiliation(s)
- Thomas Josephy
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270,Heidelberg D-69120, Germany
| | - Ravi Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Katharina Bleher
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270,Heidelberg D-69120, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
| | - Fridolin Röhs
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Thorsten Glaser
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Peter Comba
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270,Heidelberg D-69120, Germany
- Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), Universität Heidelberg, Heidelberg 69120, Germany
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24
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Hao Y, Xia Y, Liu W, Sun G, Feng L, Zhou X, Iqbal S, Tian Z, Zhang Z, Li Y, Zhang X, Jiang Y. Tuning the Solvation Structure in Water-Based Solution Enables Surface Reconstruction of Layered Oxide Cathodes toward Long Lifespan Sodium-Ion Batteries. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401514. [PMID: 38696613 PMCID: PMC11234404 DOI: 10.1002/advs.202401514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/02/2024] [Indexed: 05/04/2024]
Abstract
Layered oxides of sodium-ion batteries suffer from severe side reactions on the electrode/electrolyte interface, leading to fast capacity degradation. Although surface reconstruction strategies are widely used to solve the above issues, the utilization of the low-cost wet chemical method is extremely challenging for moisture-sensitive Na-based oxide materials. Here, the solvation tuning strategy is proposed to overcome the deterioration of NaNi1/3Mn1/3Fe1/3O2 in water-based solution and conduct the surface reconstruction. When capturing the water molecules by the solvation structure of cations, here is Li+, the structural collapse and degradation of layered oxides in water-based solvents are greatly mitigated. Furthermore, Li(H2O)3EA+ promotes the profitable Li+/Na+ exchange to build a robust surface, which hampers the decomposition of electrolytes and the structural evolution upon cycling. Accordingly, the lifespan of Li-reinforced materials is prolonged to three times that of the pristine one. This work represents a step forward in understanding the surface reconstruction operated in a water-based solution for high-performance sodium layered oxide cathodes.
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Affiliation(s)
- Youchen Hao
- School of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- Future Science Research InstituteZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou311215China
| | - Yufan Xia
- School of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
| | - Wen Liu
- Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhen518055China
| | - Guojie Sun
- School of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- Future Science Research InstituteZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou311215China
| | - Lihua Feng
- School of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- Future Science Research InstituteZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou311215China
| | - Xiaochong Zhou
- School of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
| | - Sikandar Iqbal
- School of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- Future Science Research InstituteZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou311215China
| | - Ziqi Tian
- Huzhou Horizontal Na Energy Technology Co., Ltd.Huzhou313000China
| | - Zhongcai Zhang
- Huzhou Horizontal Na Energy Technology Co., Ltd.Huzhou313000China
| | - Yong Li
- School of Physics and Materials ScienceNanchang UniversityNanchangJiangxi330031China
| | - Xuan Zhang
- School of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- Future Science Research InstituteZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou311215China
| | - Yinzhu Jiang
- School of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- Future Science Research InstituteZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou311215China
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25
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Gómez S, Cappelli C. The Role of Hydrogen Bonding in the Raman Spectral Signals of Caffeine in Aqueous Solution. Molecules 2024; 29:3035. [PMID: 38998986 PMCID: PMC11243038 DOI: 10.3390/molecules29133035] [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: 06/06/2024] [Revised: 06/22/2024] [Accepted: 06/23/2024] [Indexed: 07/14/2024] Open
Abstract
The identification and quantification of caffeine is a common need in the food and pharmaceutical industries and lately also in the field of environmental science. For that purpose, Raman spectroscopy has been used as an analytical technique, but the interpretation of the spectra requires reliable and accurate computational protocols, especially as regards the Resonance Raman (RR) variant. Herein, caffeine solutions are sampled using Molecular Dynamics simulations. Upon quantification of the strength of the non-covalent intermolecular interactions such as hydrogen bonding between caffeine and water, UV-Vis, Raman, and RR spectra are computed. The results provide general insights into the hydrogen bonding role in mediating the Raman spectral signals of caffeine in aqueous solution. Also, by analyzing the dependence of RR enhancement on the absorption spectrum of caffeine, it is proposed that the sensitivity of the RR technique could be exploited at excitation wavelengths moderately far from 266 nm, yet achieving very low detection limits in the quantification caffeine content.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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26
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Obeng A, Autschbach J. How Much Electron Donation Is There In Transition Metal Complexes? A Computational Study. J Chem Theory Comput 2024; 20:4965-4976. [PMID: 38857528 DOI: 10.1021/acs.jctc.4c00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
The "dative" covalent interactions between metals and ligands in coordination compounds, i.e., metal-to-ligand and ligand-to-metal donation, are manifestations of electron delocalization and subject to errors in approximate calculations. This work addresses the extent of dative bonding/donation in a series of closed-shell transition metal complexes. Several Kohn-Sham density functionals, representing different "rungs" of approximations, along with post-Hartree-Fock methods are assessed in comparison to CCSD(T). Two widely used nonhybrid and global hybrid density functionals (B3LYP, PBE0) tend to produce notably too strong donation. Global hybrids with elevated fractions of exact exchange (40 to 50%) and the range-separated exchange functional CAM-B3LYP tend to perform better for the description of the donation. The performance of a double-hybrid functional is found to be quite satisfactory, correcting errors seen in MP2 calculations. A fast approximate coupled-cluster model (DLPNO-CCSD) also gives a reasonable description of the donation, with a tendency to underestimate its extent.
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Affiliation(s)
- Augustine Obeng
- Department of Chemistry, University at Buffalo State University of New York Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York Buffalo, New York 14260-3000, United States
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27
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Hu T, Han G, Guo Y, Yu K, Yi Y. Efficient and Accurate Estimation of Electronic Polarization Energies for Organic Semiconductors: An Embedding Charge Quantum Mechanics/Continuum Dielectric Model. J Chem Theory Comput 2024; 20:5115-5121. [PMID: 38870475 DOI: 10.1021/acs.jctc.4c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Electronic polarization plays a pivotal role in determining the molecular energy levels of organic semiconductors (OSCs) in the condensed phase. However, accurate estimation of the electronic polarization energy is a challenging task due to the intricate imbalance between the precision and efficiency. In this work, we have developed an embedding charge quantum mechanics/continuum dielectric (EC-QM/CD) model, which enables quantitative evaluation of the ionization potential (IP), electron affinity (EA), and polarization energy in both crystalline and amorphous solids for OSCs. The benchmark calculations on both p-type OSCs of oligoacenes and n-type OSCs of A-D-A small-molecule acceptors show that the values of IP, EA, and polarization energy obtained by EC-QM/CD are in good accordance with the experimental measurements or the results by high-precision methods, while the computational costs are substantially reduced. Given its balance between the accuracy and efficiency, the EC-QM/CD model exhibits considerable potential to broaden the applications in the field of OSCs, for instance, high-throughput screening by using solid-state energy levels or polarization energies as critical descriptors.
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Affiliation(s)
- Taiping Hu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangchao Han
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuan Guo
- Faculty of Light Industry, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Kuang Yu
- Tsinghua-Berkeley Shenzhen Institute and Institute of Materials Research (iMR), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Yuanping Yi
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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28
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Huang H, Peng J, Zhang Y, Gu FL, Lan Z, Xu C. The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications. J Chem Phys 2024; 160:234101. [PMID: 38884395 DOI: 10.1063/5.0215036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024] Open
Abstract
Understanding the nonadiabatic dynamics of complex systems is a challenging task in computational photochemistry. Herein, we present an efficient and user-friendly quantum mechanics/molecular mechanics (QM/MM) interface to run on-the-fly nonadiabatic dynamics. Currently, this interface consists of an independent set of codes designed for general-purpose use. Herein, we demonstrate the ability and feasibility of the QM/MM interface by integrating it with our long-term developed JADE package. Tailored to handle nonadiabatic processes in various complex systems, especially condensed phases and protein environments, we delve into the theories, implementations, and applications of on-the-fly QM/MM nonadiabatic dynamics. The QM/MM approach is established within the framework of the additive QM/MM scheme, employing electrostatic embedding, link-atom inclusion, and charge-redistribution schemes to treat the QM/MM boundary. Trajectory surface-hopping dynamics are facilitated using the fewest switches algorithm, encompassing classical and quantum treatments for nuclear and electronic motions, respectively. Finally, we report simulations of nonadiabatic dynamics for two typical systems: azomethane in water and the retinal chromophore PSB3 in a protein environment. Our results not only illustrate the power of the QM/MM program but also reveal the important roles of environmental factors in nonadiabatic processes.
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Affiliation(s)
- Haiyi Huang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- MOE Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiawei Peng
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yulin Zhang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
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29
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Soto M, Fink K, Zweifel C, Weddle PJ, Spotte-Smith EWC, Veith GM, Persson KA, Colclasure AM, Tremolet de Villers BJ. Solubilities of Ethylene and Carbon Dioxide Gases in Lithium-Ion Battery Electrolyte. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2024; 69:2236-2243. [PMID: 38895647 PMCID: PMC11181333 DOI: 10.1021/acs.jced.3c00692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/21/2024]
Abstract
During Li-ion battery operation, (electro)chemical side reactions occur within the cell that can promote or degrade performance. These complex reactions produce byproducts in the solid, liquid, and gas phases. Studying byproducts in these three phases can help optimize battery lifetimes. To relate the measured gas-phase byproducts to species dissolved in the liquid-phase, equilibrium proprieties such as the Henry's law constants are required. The present work implements a pressure decay experiment to determine the thermodynamic equilibrium concentrations between the gas and liquid phases for ethylene (C2H4) and carbon dioxide (CO2), which are two gases commonly produced in Li-ion batteries, with an electrolyte of 1.2 M LiPF6 in 3:7 wt/wt ethylene carbonate/ethyl methyl carbonate and 3 wt % fluoroethylene carbonate (15:25:57:3 wt % total composition). The experimentally measured pressure decay curve is fit to an analytical dissolution model and extrapolated to predict the final pressure at equilibrium. The relationship between the partial pressures and concentration of dissolved gas in electrolyte at equilibrium is then used to determine Henry's law constants of 2.0 × 104 kPa for C2H4 and k CO2 = 1.1 × 104 kPa for CO2. These values are compared to Henry's law constants predicted from density functional theory and show good agreement within a factor of 3.
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Affiliation(s)
- Mel Soto
- National
Renewable Energy Laboratory (NREL), 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Kae Fink
- National
Renewable Energy Laboratory (NREL), 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Christof Zweifel
- National
Renewable Energy Laboratory (NREL), 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Peter J. Weddle
- National
Renewable Energy Laboratory (NREL), 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Evan Walter Clark Spotte-Smith
- Department
of Materials Science and Engineering, University
of California, Berkeley, California 94720, United States
- Materials
Science Division, Lawerence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Gabriel M. Veith
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Kristin A. Persson
- Department
of Materials Science and Engineering, University
of California, Berkeley, California 94720, United States
- Materials
Science Division, Lawerence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Molecular
Foundry, Lawerence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew M. Colclasure
- National
Renewable Energy Laboratory (NREL), 15013 Denver West Parkway, Golden, Colorado 80401, United States
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30
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Mondal H, Chattaraj PK. Frustrated Lewis pair-mediated hydro-dehalogenation: crucial role of non-covalent interactions. J Mol Model 2024; 30:198. [PMID: 38842625 DOI: 10.1007/s00894-024-05997-y] [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: 01/16/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024]
Abstract
CONTEXT Organic halides stand as invaluable reagents with diverse applications in synthetic chemistry and various industrial processes. Despite their utility, concerns arise due to their inherent toxicity. Addressing these apprehensions, hydro-dehalogenation has emerged as a promising strategy involving the replacement of halogen atoms with hydrogen atoms to transform toxic organic halides into hydrocarbons. This study delves into the computational exploration of hydro-dehalogenation reactions of benzyl halide, mediated by frustrated Lewis pairs (FLPs), using density functional theory (DFT). The reactions entail the formation of FLP1 or FLP2 in the presence of TMP or lutidine with B(C6F5)3, respectively. This is followed by heterolytic cleavage of dihydrogen and subsequent reaction with benzyl halides. Non-covalent interaction analysis underscores the significance of π-π stacking and CH-π interactions in stabilizing transition states. Additionally, the activation strain model (ASM) dissects activation energies, revealing the substantial impact of strain energy on reaction barriers. Energy decomposition analysis (EDA) offers insights into the contributions of electrostatic, orbital, and dispersion energies to the overall attractive interaction energy. The investigation extends to hydro-dehalogenation reactions of ethyl halides, uncovering distinct mechanisms and activation barriers. This comprehensive analysis illuminates the intricacies of hydro-dehalogenation reactions, providing valuable insights into their mechanisms and paving the way for future studies in this field. METHODS Geometry optimizations were carried out at the M06-2X/def2-SVP level of theory, which was performed using the Gaussian 16 program. Solvent-corrected single-point energies were also calculated using the polarizable continuum model (PCM) at the PCM(chloroform)-M06-2X/def2-TZVP//M06-2X/def2-SVP level of theory. The Gibbs free energy correction was determined from computations performed at the M06-2X/def2-SVP level of theory. Principal interacting orbital (PIO) analysis was conducted using the NBO 6.0 software. The nature of bonding in the respective transition state (TS) structures was analyzed using atoms-in-molecules (AIM) analyses. Additionally, the presence of non-covalent interactions (NCI) was exemplified using Multiwfn software.
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Affiliation(s)
- Himangshu Mondal
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India.
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31
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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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32
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Nikulshin PV, Makarov AY, Koskin IP, Becker CS, Kazantsev MS, Beckmann J, Balmohammadi Y, Grabowsky S, Mebs S, Naumova OV, Protasov DY, Svit KA, Irtegova IG, Radiush EA, Bagryanskaya IY, Shundrin LA, Zibarev AV. 1,2,3,4-Tetrafluorobiphenylene: A Prototype Janus-Headed Scaffold for Ambipolar Materials. Chempluschem 2024; 89:e202300692. [PMID: 38052725 DOI: 10.1002/cplu.202300692] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
The title compound was synthesized by Ullmann cross-coupling in low yield as the first representative of [n]phenylene containing hydrocarbon and fluorocarbon rings. Stille/Suzuki-Miyaura cross-coupling reactions, as well as substitution of fluorine in suitable starting compounds, failed to give the same product. The geometric and electronic structures of the title compound were studied by X-ray diffraction, cyclic voltammetry and density functional theory calculations, together with Hirshfeld surface and reduced density gradient analyses. The crystal structure features head-to-tail π-stacking and other fluorine-related secondary bonding interactions. From the nucleus-independent chemical shifts descriptor, the four-membered ring of the title compound is antiaromatic, and the six-membered rings are aromatic. The Janus molecule is highly polarized; and the six-membered fluoro- and hydrocarbon rings are Lewis π-acidic and π-basic, respectively. The electrochemically-generated radical cation of the title compound is long-lived as characterized by electron paramagnetic resonance, whereas the radical anion is unstable in solution. The title compound reveals electrical properties of an insulator. On expanding its molecular scaffold towards partially fluorinated [n]phenylenes (n≥2), the properties presumably can be transformed into those of semiconductors. In this context, the title compound is suggested as a prototype scaffold for ambipolar materials for organic electronics and spintronics.
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Affiliation(s)
- Pavel V Nikulshin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Current address: Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Alexander Yu Makarov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Igor P Koskin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Christina S Becker
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Maxim S Kazantsev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Jens Beckmann
- Institute for Inorganic Chemistry and Crystallography, University of Bremen, 28359, Bremen, Germany
| | - Yaser Balmohammadi
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Stefan Mebs
- Institute for Experimental Physics, Free University of Berlin, 14195, Berlin, Germany
| | - Olga V Naumova
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Dmitry Yu Protasov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Kirill A Svit
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina G Irtegova
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Ekaterina A Radiush
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina Yu Bagryanskaya
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Leonid A Shundrin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Andrey V Zibarev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
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33
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Insuasty D, Mutis M, Trilleras J, Illicachi LA, Rodríguez JD, Ramos-Hernández A, San-Juan-Vergara HG, Cadena-Cruz C, Mora JR, Paz JL, Méndez-López M, Pérez EG, Aliaga ME, Valencia J, Márquez E. Synthesis, Photophysical Properties, Theoretical Studies, and Living Cancer Cell Imaging Applications of New 7-(Diethylamino)quinolone Chalcones. ACS OMEGA 2024; 9:18786-18800. [PMID: 38708212 PMCID: PMC11064003 DOI: 10.1021/acsomega.3c07242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/11/2023] [Accepted: 01/10/2024] [Indexed: 05/07/2024]
Abstract
In this article, three unsymmetrical 7-(diethylamino)quinolone chalcones with D-π-A-D and D-π-A-π-D type push-pull molecular arrangements were synthesized via a Claisen-Schmidt reaction. Using 7-(diethylamino)quinolone and vanillin as electron donor (D) moieties, these were linked together through the α,β-unsaturated carbonyl system acting as a linker and an electron acceptor (A). The photophysical properties were studied, revealing significant Stokes shifts and strong solvatofluorochromism caused by the ICT and TICT behavior produced by the push-pull effect. Moreover, quenching caused by the population of the TICT state in THF-H2O mixtures was observed, and the emission in the solid state evidenced a red shift compared to the emission in solution. These findings were corroborated by density functional theory (DFT) calculations employing the wb97xd/6-311G(d,p) method. The cytotoxic activity of the synthesized compounds was assessed on BHK-21, PC3, and LNCaP cell lines, revealing moderate activity across all compounds. Notably, compound 5b exhibited the highest activity against LNCaP cells, with an LC50 value of 10.89 μM. Furthermore, the compounds were evaluated for their potential as imaging agents in living prostate cells. The results demonstrated their favorable cell permeability and strong emission at 488 nm, positioning them as promising candidates for cancer cell imaging applications.
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Affiliation(s)
- Daniel Insuasty
- Departamento
de Química y Biología, División de Ciencias Básicas, Universidad del Norte, Km 5 vía Puerto Colombia, Puerto Colombia 081007, Colombia
| | - Mario Mutis
- Grupo
de Investigación en Compuestos Heterocíclicos, Facultad
de Ciencias Básicas, Universidad
del Atlántico, Puerto Colombia 081007, Colombia
| | - Jorge Trilleras
- Grupo
de Investigación en Compuestos Heterocíclicos, Facultad
de Ciencias Básicas, Universidad
del Atlántico, Puerto Colombia 081007, Colombia
| | - Luis A. Illicachi
- Grupo
de Investigación en Química y Biotecnología,
Facultad de Ciencias Básicas, Universidad
Santiago de Cali, Calle 5. No. 62-00, Cali 760032, Colombia
| | - Juan D. Rodríguez
- Programa
de medicina, Facultad de Ciencias de la Salud, Universidad Libre, Km 7 vía Puerto Colombia, Puerto Colombia 081007, Colombia
| | - Andrea Ramos-Hernández
- Grupo
Química Supramolecular Aplicada, Semillero Electroquímica
Aplicada, Facultad de Ciencias Básicas, Universidad del Atlántico, Puerto Colombia 081007, Colombia
| | - Homero G. San-Juan-Vergara
- Departamento
de Medicina, División Ciencias de la Salud, Universidad del Norte, Km 5 vía Puerto Colombia, Puerto Colombia 081007, Colombia
| | - Christian Cadena-Cruz
- Departamento
de Medicina, División Ciencias de la Salud, Universidad del Norte, Km 5 vía Puerto Colombia, Puerto Colombia 081007, Colombia
| | - José R. Mora
- Instituto
de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería
Química, Universidad San Francisco
de Quito, Diego de Robles y Vía Interoceánica, Quito 170901, Ecuador
| | - José L. Paz
- Departamento
Académico de Química Inorgánica, Facultad de
Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Apartado, 15081 Lima, Perú
| | - Maximiliano Méndez-López
- Departamento
de Química y Biología, División de Ciencias Básicas, Universidad del Norte, Km 5 vía Puerto Colombia, Puerto Colombia 081007, Colombia
| | - Edwin G. Pérez
- Organic
Chemistry Department, Faculty of Chemistry and Pharmacy, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Margarita E. Aliaga
- Physical
Chemistry Department, Faculty of Chemistry and Pharmacy, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Jhesua Valencia
- Departamento
de Química y Biología, División de Ciencias Básicas, Universidad del Norte, Km 5 vía Puerto Colombia, Puerto Colombia 081007, Colombia
| | - Edgar Márquez
- Departamento
de Química y Biología, División de Ciencias Básicas, Universidad del Norte, Km 5 vía Puerto Colombia, Puerto Colombia 081007, Colombia
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34
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Pal AK, Datta A. First-principles design of heavy-atom-free singlet oxygen photosensitizers for photodynamic therapy. J Chem Phys 2024; 160:164720. [PMID: 38682739 DOI: 10.1063/5.0196557] [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: 01/08/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
In photodynamic therapy (PDT) treatment, heavy-atom-free photosensitizers (PSs) are a great source of singlet oxygen photosensitizer. Reactive oxygen species (ROS) are produced by an energy transfer from the lowest energy triplet excited state to the molecular oxygen of cancer cells. To clarify the photophysical characteristics in the excited states of a few experimentally identified thionated (>C=S) molecules and their oxygenated congeners (>C=O), a quantum chemical study is conducted. This study illustrates the properties of the excited states in oxygen congeners that render them unsuitable for PDT treatment. Concurrently, a hierarchy is presented based on the utility of the lowest-energy triplet excitons of thionated compounds. Their non-radiative decay rates are calculated for reverse-ISC and inter-system crossover (ISC) processes. In addition, the vibronic importance of C=O and C=S bonds is clarified by the computation of the Huang-Rhys factor, effective vibrational mode, and reorganization energy inside the Marcus-Levich-Jörtner system. ROS generation in thionated PSs exceeds their oxygen congeners as kf ≪ kISC, where radiative decay rate is designated as kf. As a result, the current work offers a calculated strategy for analyzing the effectiveness of thionated photosensitizers in PDT.
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Affiliation(s)
- Arun K Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, West Bengal, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, West Bengal, India
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35
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Patel K, Khatua R, Patrikar K, Mondal A. Exploring structure-property landscape of non-fullerene acceptors for organic solar cells. J Chem Phys 2024; 160:144709. [PMID: 38606738 DOI: 10.1063/5.0191650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/10/2024] [Indexed: 04/13/2024] Open
Abstract
We present a comprehensive analysis of the structure-property relationship in small molecule non-fullerene acceptors (NFAs) featuring an acceptor-donor-acceptor configuration employing state-of-the-art quantum chemical computational methods. Our focus lies in the strategic functionalization of halogen groups at the terminal positions of NFAs as an effective means to mitigate non-radiative voltage losses and augment photovoltaic and photophysical properties relevant to organic solar cells. Through photophysical studies, we observe a bathochromic shift in the visible region for all halogen-functionalized NFAs, except type-2, compared to the unmodified compound. Most of these functionalized compounds exhibit exciton binding energies below 0.3 eV and ΔLUMO less than 0.3 eV, indicating their potential as promising candidates for organic solar cells. Selected candidate structures undergo an analysis of charge transport properties using the semi-classical Marcus theory based on hopping transport formalism. Molecular dynamics simulations followed by charge transport simulations reveal an ambipolar nature of charge transport in the investigated NFAs, with equivalent hole and electron mobilities compared to the parent compound. Our findings underscore the crucial role of end-group functionalization in enhancing the photovoltaic and photophysical characteristics of NFAs, ultimately improving the overall performance of organic solar cells. This study advances our understanding of the structure-property relationships in NFAs and provides valuable insights into the design and optimization of organic solar cell materials.
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Affiliation(s)
- Khantil Patel
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Rudranarayan Khatua
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Kalyani Patrikar
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Anirban Mondal
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
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36
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Losantos R, Prampolini G, Monari A. A Portrait of the Chromophore as a Young System-Quantum-Derived Force Field Unraveling Solvent Reorganization upon Optical Excitation of Cyclocurcumin Derivatives. Molecules 2024; 29:1752. [PMID: 38675572 PMCID: PMC11052401 DOI: 10.3390/molecules29081752] [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: 02/01/2024] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
The study of fast non-equilibrium solvent relaxation in organic chromophores is still challenging for molecular modeling and simulation approaches, and is often overlooked, even in the case of non-adiabatic dynamics simulations. Yet, especially in the case of photoswitches, the interaction with the environment can strongly modulate the photophysical outcomes. To unravel such a delicate interplay, in the present contribution we resorted to a mixed quantum-classical approach, based on quantum mechanically derived force fields. The main task is to rationalize the solvent reorganization pathways in chromophores derived from cyclocurcumin, which are suitable for light-activated chemotherapy to destabilize cellular lipid membranes. The accurate and reliable decryption delivered by the quantum-derived force fields points to important differences in the solvent's reorganization, in terms of both structure and time scale evolution.
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Affiliation(s)
- Raúl Losantos
- Departamento de Química, Instituto de Investigación en Química (IQUR), Universidad de La Rioja, Madre de Dios 53, 26006 Logroño, Spain
- ITODYS, Université Paris Cité and CNRS, F-75006 Paris, France
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy;
| | - Antonio Monari
- ITODYS, Université Paris Cité and CNRS, F-75006 Paris, France
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37
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Rode JE, Wasilczenko J, Górecki M. Differentiation of solvatomorphs of active pharmaceutical ingredients (API) by solid-state vibrational circular dichroism (VCD). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123851. [PMID: 38295593 DOI: 10.1016/j.saa.2024.123851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
Here, we present the new application of solid-state Vibrational Circular Dichroism (VCD) spectroscopy to differentiate several dutasteride (DS) solvatomorphs - the model active pharmaceutical ingredient (API). Several crystalline DS hydrochloride hydrates solvated with methanol, ethanol, acetonitrile, acetone, and acetic acid were prepared. In contrast to almost identical IR spectra, the VCD ones were very sensitive to changes in the sample composition. We marked significant differences in the shape of VCD spectra of studied DS solvatomorphs, DS hydrates, and DS polymorphic forms. Our findings, supported by DFT calculations, show that VCD spectroscopy has the pronounced ability to distinguish their crystal arrangements. We believe that this contribution will extend the use of VCD in the pharmaceutical industry for developing and designing new chiral drug products for the identification, description, and in-depth probing of several pharmaceutical solvatomorphs in the future.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, Dorodna 16 St., 03-195 Warsaw, Poland
| | - Justyna Wasilczenko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224 Warsaw, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224 Warsaw, Poland.
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38
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Mondal H, Chattaraj PK. Unraveling Reactivity Pathways: Dihydrogen Activation and Hydrogenation of Multiple Bonds by Pyramidalized Boron-Based Frustrated Lewis Pairs. ChemistryOpen 2024; 13:e202300179. [PMID: 38117941 PMCID: PMC11004477 DOI: 10.1002/open.202300179] [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: 08/29/2023] [Revised: 11/24/2023] [Indexed: 12/22/2023] Open
Abstract
The activation of H2 by pyramidalized boron-based frustrated Lewis Pairs (FLPs) (B/E-FLP systems where "E" refers to N, P, As, Sb, and Bi) have been explored using density functional theory (DFT) based computational study. The activation pathway for the entire process is accurately characterized through the utilization of the activation strain model (ASM) of reactivity, shedding light on the underlying physical factors governing the process. The study also explores the hydrogenation process of multiple bonds with the help of B/N-FLP. The research findings demonstrate that the liberation of activated dihydrogen occurs in a synchronized, albeit noticeably asynchronous, fashion. The transformation is extensively elucidated using the activation strain model and the energy decomposition analysis. This approach suggests a co-operative double hydrogen-transfer mechanism, where the B-H hydride triggers a nucleophilic attack on the carbon atom of the multiple bonds, succeeded by the migration of the protic N-H.
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Affiliation(s)
- Himangshu Mondal
- Department of ChemistryIndian Institute of TechnologyKharagpur721302India
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39
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Kjellgren ER, Reinholdt P, Fitzpatrick A, Talarico WN, Jensen PWK, Sauer SPA, Coriani S, Knecht S, Kongsted J. The variational quantum eigensolver self-consistent field method within a polarizable embedded framework. J Chem Phys 2024; 160:124114. [PMID: 38533884 DOI: 10.1063/5.0190594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/10/2024] [Indexed: 03/28/2024] Open
Abstract
We formulate and implement the Variational Quantum Eigensolver Self Consistent Field (VQE-SCF) algorithm in combination with polarizable embedding (PE), thereby extending PE to the regime of quantum computing. We test the resulting algorithm, PE-VQE-SCF, on quantum simulators and demonstrate that the computational stress on the quantum device is only slightly increased in terms of gate counts compared to regular VQE-SCF. On the other hand, no increase in shot noise was observed. We illustrate how PE-VQE-SCF may lead to the modeling of real chemical systems using a simulation of the reaction barrier of the Diels-Alder reaction between furan and ethene as an example.
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Affiliation(s)
- Erik Rosendahl Kjellgren
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | | - Walter N Talarico
- Algorithmiq Ltd., Kanavakatu 3C, FI-00160 Helsinki, Finland
- Department of Applied Physics, QTF Centre of Excellence, Center for Quantum Engineering, Aalto University School of Science, FIN-00076 AALTO Espoo, Finland
| | - Phillip W K Jensen
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Sonia Coriani
- DTU Chemistry - Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Stefan Knecht
- Algorithmiq Ltd., Kanavakatu 3C, FI-00160 Helsinki, Finland
- ETH Zürich, Department of Chemistry and Applied Life Sciences, Vladimir-Prelog-Weg 1-5/10, CH-8093 Zürich, Switzerland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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40
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Moscato D, Mandelli G, Bondanza M, Lipparini F, Conte R, Mennucci B, Ceotto M. Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine. J Am Chem Soc 2024; 146:8179-8188. [PMID: 38470354 DOI: 10.1021/jacs.3c12700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
We introduce a quantum mechanics/molecular mechanics semiclassical method for studying the solvation process of molecules in water at the nuclear quantum mechanical level with atomistic detail. We employ it in vibrational spectroscopy calculations because this is a tool that is very sensitive to the molecular environment. Specifically, we look at the vibrational spectroscopy of thymidine in liquid water. We find that the C═O frequency red shift and the C═C frequency blue shift, experienced by thymidyne upon solvation, are mainly due to reciprocal polarization effects, that the molecule and the water solvent exert on each other, and nuclear zero-point energy effects. In general, this work provides an accurate and practical tool to study quantum vibrational spectroscopy in solution and condensed phase, incorporating high-level and computationally affordable descriptions of both electronic and nuclear problems.
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Affiliation(s)
- Davide Moscato
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Giacomo Mandelli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
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41
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Yan P, Stegbauer S, Wu Q, Kolodzeiski E, Stein CJ, Lu P, Bach T. Enantioselective Intramolecular ortho Photocycloaddition Reactions of 2-Acetonaphthones. Angew Chem Int Ed Engl 2024; 63:e202318126. [PMID: 38275271 DOI: 10.1002/anie.202318126] [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: 11/27/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 01/27/2024]
Abstract
2-Acetonaphthones, which bear an alkenyl group tethered to its C1 carbon atom via an oxygen atom, were found to undergo an enantioselective intramolecular ortho photocycloaddition reaction. A chiral oxazaborolidine Lewis acid leads to a bathochromic absorption shift of the substrate and enables an efficient enantioface differentiation. Visible light irradiation (λ=450 nm) triggers the reaction which is tolerant of various groups at almost any position except carbon atom C8 (16 examples, 53-99 % yield, 80-97 % ee). Consecutive reactions were explored including a sensitized rearrangement to tetrahydrobiphenylenes, which occurred with full retention of configuration. Evidence was collected that the catalytic photocycloaddition occurs via triplet intermediates, and the binding mode of the acetonaphthone to the chiral Lewis acid was elucidated by DFT calculations.
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Affiliation(s)
- Peng Yan
- Research Center for Molecular Recognition and Synthesis, Department of Chemistry, Fudan University, 220 Handan Lu, Shanghai, 200433, China
| | - Simone Stegbauer
- Department Chemie and Catalysis Research Center (CRC) School of Natural Sciences, Technische Universität München, Lichtenbergstraße 4, D-85747, Garching, Germany
| | - Qinqin Wu
- Research Center for Molecular Recognition and Synthesis, Department of Chemistry, Fudan University, 220 Handan Lu, Shanghai, 200433, China
| | - Elena Kolodzeiski
- Department Chemie and Catalysis Research Center (CRC) School of Natural Sciences, Technische Universität München, Lichtenbergstraße 4, D-85747, Garching, Germany
| | - Christopher J Stein
- Department Chemie and Catalysis Research Center (CRC) School of Natural Sciences, Technische Universität München, Lichtenbergstraße 4, D-85747, Garching, Germany
| | - Ping Lu
- Research Center for Molecular Recognition and Synthesis, Department of Chemistry, Fudan University, 220 Handan Lu, Shanghai, 200433, China
| | - Thorsten Bach
- Department Chemie and Catalysis Research Center (CRC) School of Natural Sciences, Technische Universität München, Lichtenbergstraße 4, D-85747, Garching, Germany
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42
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Sparks NE, Smith C, Stahl T, Amarasekara DL, Hamadani C, Lambert E, Tang SW, Kulkarni A, Derbigny BM, Dasanayake GS, Taylor G, Ghazala M, Hammer NI, Sokolov AY, Fitzkee NC, Tanner EEL, Watkins DL. NIR-II emissive donor-acceptor-donor fluorophores for dual fluorescence bioimaging and photothermal therapy applications. JOURNAL OF MATERIALS CHEMISTRY. C 2024; 12:4369-4383. [PMID: 38525159 PMCID: PMC10955863 DOI: 10.1039/d3tc04747d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/26/2024]
Abstract
Fluorescence bioimaging with near-infrared II (NIR-II) emissive organic fluorophores has proven to be a viable noninvasive diagnostic technique. However, there is still the need for the development of fluorophores that possess increased stability as well as functionalities that impart stimuli responsiveness. Through strategic design, we can synthesize fluorophores that possess not only NIR-II optical profiles but also pH-sensitivity and the ability to generate heat upon irradiation. In this work, we employ a donor-acceptor-donor (D-A-D) design to synthesize a series of NIR-II fluorophores. Here we use thienothiadiazole (TTD) as the acceptor, 3-hexylthiophene (HexT) as the π-spacer and vary the alkyl amine donor units: N,N-dimethylaniline (DMA), phenylpiperidine (Pip), and phenylmorpholine (Morp). Spectroscopic analysis shows that all three derivatives exhibit emission in the NIR-II region with λemimax ranging from 1030 to 1075 nm. Upon irradiation, the fluorophores exhibited noticeable heat generation through non-radiative processes. The ability to generate heat indicates that these fluorophores will act as theranostic (combination therapeutic and diagnostic) agents in which simultaneous visualization and treatment can be performed. Additionally, biosensing capabilities were supported by changes in the absorbance properties while under acidic conditions as a result of protonation of the alkyl amine donor units. The fluorophores also show minimal toxicity in a human mammary cell line and with murine red blood cells. Overall, initial results indicate viable NIR-II materials for multiple biomedical applications.
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Affiliation(s)
- Nicholas E Sparks
- Department of Chemistry and Biochemistry, The Ohio State University Columbus Ohio 43210 USA
| | - Cameron Smith
- Department of Chemistry and Biochemistry, University of Mississippi University Oxford MS USA
| | - Terrence Stahl
- Department of Chemistry and Biochemistry, The Ohio State University Columbus Ohio 43210 USA
| | - Dhanush L Amarasekara
- Department of Chemistry, Mississippi State University Mississippi State MS 39762 USA
| | - Christine Hamadani
- Department of Chemistry and Biochemistry, University of Mississippi University Oxford MS USA
| | - Ethan Lambert
- Department of Chemistry and Biochemistry, University of Mississippi University Oxford MS USA
| | - Sheng Wei Tang
- Department of Chemistry and Biochemistry, The Ohio State University Columbus Ohio 43210 USA
| | - Anuja Kulkarni
- Department of Chemistry and Biochemistry, The Ohio State University Columbus Ohio 43210 USA
| | - Blaine M Derbigny
- Department of Chemistry and Biochemistry, The Ohio State University Columbus Ohio 43210 USA
| | - Gaya S Dasanayake
- Department of Chemistry and Biochemistry, University of Mississippi University Oxford MS USA
| | - George Taylor
- Department of Chemistry and Biochemistry, University of Mississippi University Oxford MS USA
| | - Maryam Ghazala
- Department of Chemistry and Biochemistry, The Ohio State University Columbus Ohio 43210 USA
| | - Nathan I Hammer
- Department of Chemistry and Biochemistry, University of Mississippi University Oxford MS USA
| | - Alexander Y Sokolov
- Department of Chemistry and Biochemistry, The Ohio State University Columbus Ohio 43210 USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University Mississippi State MS 39762 USA
| | - Eden E L Tanner
- Department of Chemistry and Biochemistry, University of Mississippi University Oxford MS USA
| | - Davita L Watkins
- Department of Chemistry and Biochemistry, The Ohio State University Columbus Ohio 43210 USA
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University 151 W Woodruff Ave. Columbus OH 43210 USA
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43
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Miao L, Jia W, Cao X, Jiao L. Computational chemistry for water-splitting electrocatalysis. Chem Soc Rev 2024; 53:2771-2807. [PMID: 38344774 DOI: 10.1039/d2cs01068b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Electrocatalytic water splitting driven by renewable electricity has attracted great interest in recent years for producing hydrogen with high-purity. However, the practical applications of this technology are limited by the development of electrocatalysts with high activity, low cost, and long durability. In the search for new electrocatalysts, computational chemistry has made outstanding contributions by providing fundamental laws that govern the electron behavior and enabling predictions of electrocatalyst performance. This review delves into theoretical studies on electrochemical water-splitting processes. Firstly, we introduce the fundamentals of electrochemical water electrolysis and subsequently discuss the current advancements in computational methods and models for electrocatalytic water splitting. Additionally, a comprehensive overview of benchmark descriptors is provided to aid in understanding intrinsic catalytic performance for water-splitting electrocatalysts. Finally, we critically evaluate the remaining challenges within this field.
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Affiliation(s)
- Licheng Miao
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Wenqi Jia
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Xuejie Cao
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Lifang Jiao
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China.
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44
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Plett C, Stahn M, Bursch M, Mewes JM, Grimme S. Improving Quantum Chemical Solvation Models by Dynamic Radii Adjustment for Continuum Solvation (DRACO). J Phys Chem Lett 2024; 15:2462-2469. [PMID: 38407047 DOI: 10.1021/acs.jpclett.3c03551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
We present the Dynamic Radii Adjustment for COntinuum solvation (DRACO) approach, which employs precomputed atomic partial charges and coordination numbers of the solute atoms to improve the solute cavity. As such, DRACO is compatible with major solvation models, improving their performance significantly and robustly at virtually no extra cost, especially for charged solutes. Combined with the purely electrostatic CPCM and COSMO models, DRACO reduces the mean absolute deviation (MAD) of the solvation free energy by up to 4.5 kcal mol-1 (67%) for a large data set of polar and ionic solutes. Even in combination with the highly empirical universal solvation model (SMD), DRACO substantially reduces the MAD for charged solutes by up to 1.5 kcal mol-1 (39%), while neutral solutes are slightly improved (0.2 kcal mol-1 or 16%). We present an interface of DRACO with two computationally efficient atomic charge models that enables fully automated, out-of-the-box calculations with the widely used program packages Orca and TurboMole.
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Affiliation(s)
- Christoph Plett
- Mulliken Center for Theoretical Chemistry, 53115 Bonn, Germany
| | - Marcel Stahn
- Mulliken Center for Theoretical Chemistry, 53115 Bonn, Germany
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, 53115 Bonn, Germany
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Jan-Michael Mewes
- Mulliken Center for Theoretical Chemistry, 53115 Bonn, Germany
- beeOLED GmbH, 01257 Dresden, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, 53115 Bonn, Germany
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45
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Małecka M, Sobiesiak M, Chęcińska L, Kozakiewicz-Piekarz A, Napiórkowska-Mastalerz M, Ziomkowska B, Stepniak A, Kupcewicz B. Fluorescent properties in solid-state and solution of novel tricyclic derivatives of chloro/bromophenylchromanones and 2-methylpyrazoline. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123715. [PMID: 38103355 DOI: 10.1016/j.saa.2023.123715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/19/2023]
Abstract
In this work, we reported the synthesis and spectroscopic characterization of seven novel tricyclic compounds resulting from the reaction of 3-benzylidenechromanone with Cl or Br substituent in different positions and without halogen with methylhydrazine. The structural characterization of compounds was done through different techniques i.e., FTIR,1HNMR,a single and powder X-Ray diffraction. Moreover, fluorescence quantum yield and lifetime assessed their fluorescent properties in the solid state and various solvents. Derivatives with Cl or Br substituent in positions 2 and 4 are isostructural. 4-Cl, 4-Br and 3-Cl compounds exhibit fluorescence with moderate efficiency (quantum yield 0.11-0.26) in solid state due to specific arrangements, so-called π-stack brick stone with head-to-tail self-assembly. Other crystalline compounds (2-Cl, 2-Br and 3-Br) that exhibit negligible fluorescence quantum yield have crossed V-type arrangement. In the solution, the nonhalogenated compound shows the best fluorescence efficiency. In turn, the presence of halogen atoms results in fluorescence decreasing. TD-DFT study revealed that unsubstituted compound higher emissive in solution has a different electron density distribution at HOMO and LUMO levels than less emissive substituted compounds (A3 and A3).
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Affiliation(s)
- Magdalena Małecka
- University of Lodz, Faculty of Chemistry, Department of Physical Chemistry, Pomorska 163/165, 90-236 Lodz, Poland.
| | - Marta Sobiesiak
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland.
| | - Lilianna Chęcińska
- University of Lodz, Faculty of Chemistry, Department of Physical Chemistry, Pomorska 163/165, 90-236 Lodz, Poland
| | - Anna Kozakiewicz-Piekarz
- Department of Biomedical and Polymer Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100 Torun, Poland
| | - Marta Napiórkowska-Mastalerz
- Department of Biophysics, Faculty of Pharmacy, Nicolaus Copernicus University, Jagiellonska 15, 85-089 Bydgoszcz, Poland
| | - Blanka Ziomkowska
- Department of Biophysics, Faculty of Pharmacy, Nicolaus Copernicus University, Jagiellonska 15, 85-089 Bydgoszcz, Poland
| | - Artur Stepniak
- University of Lodz, Faculty of Chemistry, Department of Physical Chemistry, Pomorska 163/165, 90-236 Lodz, Poland
| | - Bogumiła Kupcewicz
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland
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46
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Wang S, Yam C, Chen S, Hu L, Li L, Hung FF, Fan J, Che CM, Chen G. Predictions of photophysical properties of phosphorescent platinum(II) complexes based on ensemble machine learning approach. J Comput Chem 2024; 45:321-330. [PMID: 37861354 DOI: 10.1002/jcc.27238] [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: 07/26/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/21/2023]
Abstract
Cyclometalated Pt(II) complexes are popular phosphorescent emitters with color-tunable emissions. To render their practical applications as organic light-emitting diodes emitters, it is required to develop Pt(II) complexes with high radiative decay rate constant and photoluminescence (PL) quantum yield. Here, a general protocol is developed for accurate predictions of emission wavelength, radiative decay rate constant, and PL quantum yield based on the combination of first-principles quantum mechanical method, machine learning, and experimental calibration. A new dataset concerning phosphorescent Pt(II) emitters is constructed, with more than 200 samples collected from the literature. Features containing pertinent electronic properties of the complexes are chosen and ensemble learning models combined with stacking-based approaches exhibit the best performance, where the values of squared correlation coefficients are 0.96, 0.81, and 0.67 for the predictions of emission wavelength, PL quantum yield and radiative decay rate constant, respectively. The accuracy of the protocol is further confirmed using 24 recently reported Pt(II) complexes, which demonstrates its reliability for a broad palette of Pt(II) emitters.
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Affiliation(s)
- Shuai Wang
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - ChiYung Yam
- Hong Kong Quantum AI Lab Limited, Hong Kong, China
- Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China, Shenzhen, China
| | - Shuguang Chen
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
- Hong Kong Quantum AI Lab Limited, Hong Kong, China
| | - LiHong Hu
- School of Information Science and Technology, Northeast Normal University, Changchun, China
| | - Liping Li
- Hong Kong Quantum AI Lab Limited, Hong Kong, China
| | - Faan-Fung Hung
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
- Hong Kong Quantum AI Lab Limited, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry, HKU-CAS Joint Laboratory on New Materials, The University of Hong Kong, Hong Kong, China
| | - Jiaqi Fan
- Hong Kong Quantum AI Lab Limited, Hong Kong, China
| | - Chi-Ming Che
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
- Hong Kong Quantum AI Lab Limited, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry, HKU-CAS Joint Laboratory on New Materials, The University of Hong Kong, Hong Kong, China
| | - GuanHua Chen
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
- Hong Kong Quantum AI Lab Limited, Hong Kong, China
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47
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Różanowska M, Szczupaj G, Nowakowski M, Rajagopal P, Lipiński PFJ, Matalińska J, Misicka A, Lisowski M, Jaremko Ł, Jaremko M. Applications of biaryl cyclization in the synthesis of cyclic enkephalin analogs with a highly restricted flexibility. Amino Acids 2024; 56:18. [PMID: 38427104 PMCID: PMC10907494 DOI: 10.1007/s00726-023-03371-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 03/02/2024]
Abstract
A series of 10 cyclic, biaryl analogs of enkephalin, with Tyr or Phe residues at positions 1 and 4, were synthesized according to the Miyaura borylation and Suzuki coupling methodology. Biaryl bridges formed by side chains of the two aromatic amino acid residues are of the meta-meta, meta-para, para-meta, and para-para configuration. Conformational properties of the peptides were studied by CD and NMR. CD studies allowed only to compare conformations of individual peptides while NMR investigations followed by XPLOR calculations provided detailed information on their conformation. Reliability of the XPLOR calculations was confirmed by quantum chemical ones performed for one of the analogs. No intramolecular hydrogen bonds were found in all the peptides. They are folded and adopt the type IV β-turn conformation. Due to a large steric strain, the aromatic carbon atoms forming the biaryl bond are distinctly pyramidalized. Seven of the peptides were tested in vitro for their affinity for the µ-opioid receptor.
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Affiliation(s)
| | - Gabriela Szczupaj
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Michał Nowakowski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Priyadharshni Rajagopal
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Marek Lisowski
- Faculty of Chemistry, University of Wrocław, Wrocław, Poland
| | - Łukasz Jaremko
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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48
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Allan L, Zuehlsdorff TJ. Taming the third order cumulant approximation to linear optical spectroscopy. J Chem Phys 2024; 160:074108. [PMID: 38380749 DOI: 10.1063/5.0182745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
The second order cumulant method offers a promising pathway to predicting optical properties in condensed phase systems. It allows for the computation of linear absorption spectra from excitation energy fluctuations sampled along molecular dynamics (MD) trajectories, fully accounting for vibronic effects, direct solute-solvent interactions, and environmental polarization effects. However, the second order cumulant approximation only guarantees accurate line shapes for energy gap fluctuations obeying Gaussian statistics. A third order correction has recently been derived but often yields unphysical spectra or divergent line shapes for moderately non-Gaussian fluctuations due to the neglect of higher order terms in the cumulant expansion. In this work, we develop a corrected cumulant approach, where the collective effect of neglected higher order contributions is approximately accounted for through a dampening factor applied to the third order cumulant term. We show that this dampening factor can be expressed as a function of the skewness and kurtosis of energy gap fluctuations and can be parameterized from a large set of randomly sampled model Hamiltonians for which exact spectral line shapes are known. This approach is shown to systematically remove unphysical contributions in the form of negative absorbances from cumulant spectra in both model Hamiltonians and condensed phase systems sampled from MD and dramatically improves over the second order cumulant method in describing systems exhibiting Duschinsky mode mixing effects. We successfully apply the approach to the coumarin-153 dye in toluene, obtaining excellent agreement with experiment.
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Affiliation(s)
- Lucas Allan
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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49
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Ozaki Y, Morisawa Y, Tanabe I. ATR-far-ultraviolet spectroscopy: a challenge to new σ chemistry. Chem Soc Rev 2024; 53:1730-1768. [PMID: 38287893 DOI: 10.1039/d3cs00437f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
This review reports the recent progress on ATR-far ultraviolet (FUV) spectroscopy in the condensed phase. ATR-FUV spectroscopy for liquids and solids enables one to explore various topics in physical chemistry, analytical chemistry, nanoscience and technology, materials science, electrochemistry, and organic chemistry. In this review, we put particular emphasis on the three major topics: (1) studies on electronic transitions and structures of various molecules, which one cannot investigate via ordinary UV spectroscopy. The combined use of ATR-FUV spectroscopy and quantum chemical calculations allows for the investigation of various electronic transitions, including σ, n-Rydberg transitions. ATR-FUV spectroscopy may open a new avenue for σ-chemistry. (2) ATR-FUV spectroscopy enables one to measure the first electronic transition of water at approximately 160 nm without peak saturation. Using this band, one can study the electronic structure of water, aqueous solutions, and adsorbed water. (3) ATR-FUV spectroscopy has its own advantages of the ATR method as a surface analysis method. ATR-FUV spectroscopy is a powerful technique for exploring a variety of top surface phenomena (∼50 nm) in adsorbed water, polymers, graphene, organic materials, ionic liquids, and so on. This review briefly describes the principles, characteristics, and instrumentation of ATR-FUV spectroscopy. Next, a detailed description about quantum chemical calculation methods for FUV and UV regions is given. The recent application of ATR-FUV-UV spectroscopy studies on electronic transitions from σ orbitals in various saturated molecules is introduced first, followed by a discussion on the applications of ATR-FUV spectroscopy to studies on water, aqueous solutions, and adsorbed water. Applications of ATR-FUV spectroscopy in the analysis of other materials such as polymers, ionic liquids, inorganic semiconductors, graphene, and carbon nanocomposites are elucidated. In addition, ATR-FUV-UV-vis spectroscopy focusing on electrochemical interfaces is outlined. Finally, FUV-UV-surface plasmon resonance studies are discussed.
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Affiliation(s)
- Yukihiro Ozaki
- School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo 669-1330, Japan.
- Toyota Physical and Chemical Research Institute, Nagakute, Aichi 480-1192, Japan
| | - Yusuke Morisawa
- School of Science and Engineering, Kindai University, Higashi-Osaka, Osaka 577-8502, Japan.
| | - Ichiro Tanabe
- Department of Chemistry, School of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan.
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Imamura K, Yokogawa D, Sato H. Recent developments and applications of reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED): A hybrid model of quantum chemistry and integral equation theory of molecular liquids. J Chem Phys 2024; 160:050901. [PMID: 38341702 DOI: 10.1063/5.0190116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/13/2024] Open
Abstract
The significance of solvent effects in electronic structure calculations has long been noted, and various methods have been developed to consider this effect. The reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED) is a hybrid model that combines the integral equation theory of molecular liquids with quantum chemistry. This method can consider the statistically convergent solvent distribution at a significantly lower cost than molecular dynamics simulations. Because the RISM theory explicitly considers the solvent structure, it performs well for systems where hydrogen bonds are formed between the solute and solvent molecules, which is a challenge for continuum solvent models. Taking advantage of being founded on the variational principle, theoretical developments have been made in calculating various properties and incorporating electron correlation effects. In this review, we organize the theoretical aspects of RISM-SCF-cSED and its distinctions from other hybrid methods involving integral equation theories. Furthermore, we carefully present its progress in terms of theoretical developments and recent applications.
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Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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