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Navarro A, Ruiz-Arias A, Fueyo-González F, Izquierdo-García C, Peña-Ruiz T, Gutiérrez-Rodríguez M, Herranz R, Cuerva JM, González-Vera JA, Orte A. Multiple pathways for lanthanide sensitization in self-assembled aqueous complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 323:124926. [PMID: 39116593 DOI: 10.1016/j.saa.2024.124926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024]
Abstract
Lanthanide photoluminescence (PL) emission has attracted much attention for technological and bioimaging applications because of its particularly interesting features, such as narrow emission bands and very long PL lifetimes. However, this emission process necessitates a preceding step of energy transfer from suitable antennas. While biocompatible applications require luminophores that are stable in aqueous media, most lanthanide-based emitters are quenched by water molecules. Previously, we described a small luminophore, 8-methoxy-2-oxo-1,2,4,5-tetrahydrocyclopenta[de]quinoline-3-phosphonic acid (PAnt), which is capable of dynamically coordinating with Tb(III) and Eu(III), and its exchangeable behavior improved their performance in PL lifetime imaging microscopy (PLIM) compared with conventional lanthanide cryptate imaging agents. Herein, we report an in-depth photophysical and time-dependent density functional theory (TD-DFT) computational study that reveals different sensitization mechanisms for Eu(III) and Tb(III) in stable complexes formed in water. Understanding this unique behavior in aqueous media enables the exploration of different applications in bioimaging or novel emitting materials.
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Affiliation(s)
- Amparo Navarro
- Departamento de Química Física y Analítica, Universidad de Jaén, Facultad de Ciencias Experimentales, 23071 Jaén, Spain
| | - Alvaro Ruiz-Arias
- Nanoscopy-UGR Laboratory, Departamento de Fisicoquímica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, University of Granada, Campus Cartuja, 18071, Granada, Spain
| | | | | | - Tomás Peña-Ruiz
- Departamento de Química Física y Analítica, Universidad de Jaén, Facultad de Ciencias Experimentales, 23071 Jaén, Spain
| | - Marta Gutiérrez-Rodríguez
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; PTI-Global Health CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Rosario Herranz
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Juan M Cuerva
- Departamento de Química Orgánica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, University of Granada, Campus Fuentenueva, 18071 Granada, Spain
| | - Juan A González-Vera
- Nanoscopy-UGR Laboratory, Departamento de Fisicoquímica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, University of Granada, Campus Cartuja, 18071, Granada, Spain; Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Angel Orte
- Nanoscopy-UGR Laboratory, Departamento de Fisicoquímica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, University of Granada, Campus Cartuja, 18071, Granada, Spain.
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2
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Wang Y, Li W, Zhou P. Sensing mechanism of the benzo-bodipy based fluorescent probe for Hypochlorous acid detection: Invalidity of photoinduced electron transfer. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 323:124923. [PMID: 39096669 DOI: 10.1016/j.saa.2024.124923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 07/24/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
In vivo real-time detection of hypochlorous acid (HClO) in biological systems plays a crucial role in diagnosing immune-related diseases. Experimentally, a benzo-bodipy probe based on the photo-induced electron transfer (PeT) sensing mechanism has been developed for live fluorescence imaging. However, there have been no theoretical studies conducted to substantiate the precision of the sensing mechanism. This paper employs density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods to investigate the fluorescence detection mechanism of benzo-bodipy derivatives (BBy-T and BBy-TO), proposing a detection approach based on dark nπ* state quenching. The study reveals that the fluorescence quenching mechanism of BBy-T is primarily regulated by a thiomorpholine moiety, involving a dark nπ* state transition non-radiatively. Furthermore, this paper explains the fluorescence enhancement observed in BBy-TO. Theoretical investigations demonstrate, based on frontier molecular orbitals (FMOs) and hole-electron analysis, that the fluorescence enhancement for BBy-TO is not governed by the previously proposed intramolecular charge transfer (ICT) mechanism in experiments but rather follows a locally excited (LE) ππ* pattern. This work offers new insights for the design of novel fluorescence probes based on bodipy and benzo derivatives, expanding the understanding of their fluorescence properties.
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Affiliation(s)
- Yuxi Wang
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, China
| | - Wenzhi Li
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, China
| | - Panwang Zhou
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, China; State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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3
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Böhmer T, Kleinschmidt M, Marian CM. Toward the improvement of vibronic spectra and non-radiative rate constants using the vertical Hessian method. J Chem Phys 2024; 161:094114. [PMID: 39234963 DOI: 10.1063/5.0220361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/15/2024] [Indexed: 09/06/2024] Open
Abstract
For the computation of vibrationally resolved electronic spectra, various approaches can be employed. Adiabatic approaches simulate vibronic transitions using harmonic potentials of the initial and final states, while vertical approaches extrapolate the final state potential from the gradients and Hessian at the Franck-Condon point, avoiding a full exploration of the potential energy surface of the final state. Our implementation of the vertical Hessian (VH) method has been validated with a benchmark set of four small molecules, each presenting unique challenges, such as complex topologies, problematic low-frequency vibrations, or significant geometrical changes upon electronic excitation. We assess the quality of both adiabatic and vertical approaches for simulating vibronic transitions. For two types of donor-acceptor compounds with promising thermally activated delayed fluorescence properties, our computations confirm that the vertical approaches outperform the adiabatic ones. The VH method significantly reduces computational costs and yields meaningful emission spectra, where adiabatic models fail. More importantly, we pioneer the use of the VH method for the computation of rate constants for non-radiative processes, such as intersystem crossing and reverse intersystem crossing along a relaxed interpolated pathway of a donor-acceptor compound. This study highlights the potential of the VH method to advance computational vibronic spectroscopy by providing meaningful simulations of intricate decay pathway mechanisms in complex molecular systems.
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Affiliation(s)
- Tobias Böhmer
- Institute for Theoretical and Computational Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Martin Kleinschmidt
- Institute for Theoretical and Computational Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Christel M Marian
- Institute for Theoretical and Computational Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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4
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Raïch Panisello O, Jover J, Puigjaner C, Ferrer M, Martínez M. No Switching Cooperativity between Coordinated Azo Ligands on Complexes Having {M II(phosphane-κ 2P)} 2+ (M = Pd, Pt) Scaffolds. Inorg Chem 2024; 63:16251-16263. [PMID: 39167678 PMCID: PMC11372757 DOI: 10.1021/acs.inorgchem.4c02169] [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
A series of square-planar palladium and platinum compounds with cis-blocking phosphanes and terminal azobenzene ligands [M(dppp)(azo)2](OTf)2 (azo = CN(C6H4)-N═N-(C6H4)CN (iso-cyano), CN(C6H4)-N═N-(C6H5) (iso-Ph)) and [{M2(tpbz)}(azo)4](OTf)4 (azo = CN(C6H4)-N═N-(C6H5) (iso-Ph)) have been synthesized and fully characterized. Similarly to the uncoordinated ligands, the new coordination compounds have shown to be photochemically active with respect to their trans-to-cis isomerization process. Their cis-to-trans back spontaneous reaction have been studied as a function of solvent, temperature and pressure and the corresponding activation parameters determined in order to investigate the mechanism of these transformations. The results obtained are indicative of the operation of a rotational mechanism with no cooperativity between the azo ligands attached to the same metal. Density functional theory calculations have been carried out in order to estimate the relative energies of the different photoisomers for the theoretical interpretation of the experimental data.
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Affiliation(s)
- Ot Raïch Panisello
- Secció de Química Inorgànica, Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Jesús Jover
- Secció de Química Inorgànica, Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Cristina Puigjaner
- Unitat de Difracció de RX, Centres Científics i Tecnològics de la Universitat de Barcelona (CCiTUB), Universitat de Barcelona, Solé i Sabarís 1-3, 08028 Barcelona, Spain
| | - Montserrat Ferrer
- Secció de Química Inorgànica, Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Manuel Martínez
- Secció de Química Inorgànica, Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
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5
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Kaczmarek K, Artym J, Bojarska J, Pacholczyk-Sienicka B, Waśko J, Jelemenska I, Wolf WM, Breza M, Zimecki M. The Immunosuppressive Properties of Cyclo-[ D-Pro-Pro- β3-HoPhe-Phe-] Tetrapeptide Selected from Stereochemical Variants of Cyclo-[Pro-Pro- β3-HoPhe-Phe-] Peptide. Pharmaceutics 2024; 16:1106. [PMID: 39204451 PMCID: PMC11359963 DOI: 10.3390/pharmaceutics16081106] [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: 07/18/2024] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The anti-inflammatory, antiviral, and anti-cancer properties, as well as the mechanism of action of cyclo-[Pro-Pro-β3-HoPhe-Phe-] tetrapeptide (denoted as 4B8M), were recently described. The aim of this work was to synthesize and evaluate the immunosuppressive actions of the stereochemical variants of 4B8M by sequential substitution of L-amino acids by D-amino acids (a series of peptides denoted as P01-P07) using parent 4B8M as a reference compound. In addition, diverse available bioinformatics tools using machine learning and artificial intelligence were tested to find the bio-pharmacokinetic and polypharmacological attributes of analyzed stereomers. All peptides were non-toxic to human peripheral blood mononuclear cells (PBMCs) and only cyclo-[D-Pro-Pro-β3-HoPhe-Phe-] peptide (P03) was capable of inhibiting mitogen-induced PBMC proliferation. The peptides inhibited the lipopolysaccharide (LPS)-induced production of tumor necrosis factor-alpha (TNF-α) to various degrees, with P04 (cyclo-[Pro-Pro-D-β3-HoPhe-Phe-]) and P03 being the most potent. For further in vivo studies, P03 was selected because it had the combined properties of inhibiting cell proliferation and TNF-α production. P03 demonstrated a comparable ability to 4B8M in the inhibition of auricle edema and lymph node cell number and in the normalization of a distorted blood cell composition in contact sensitivity to the oxazolone mouse model. In the mouse model of carrageenan-induced inflammation of the air pouch, P03 exhibited a similar inhibition of the cell number in the air pouches as 4B8M, but its inhibitory effects on the percentage of neutrophils and eosinophils in the air pouches and blood, as well as on mastocyte degranulation in the air pouches, were stronger in comparison to 4B8M. Lastly, in a mouse model of dextran sulfate-induced colitis, similar effects to 4B8M regarding thymocyte number restoration and normalization of the blood cell pictures by P03 were observed. In summary, depending on either experimental findings or in silico predictions, P03 demonstrated comparable, or even better, anti-inflammatory and bio-pharmacokinetic properties to 4B8M and may be considered as a potential therapeutic. The possibility of P00 and P03 identification by circular dichroism measurements was tested by quantum-chemical calculations.
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Affiliation(s)
- Krzysztof Kaczmarek
- Institute of Organic Chemistry, Łódź University of Technology, S. Żeromskiego Str. 116, 90-924 Łódź, Poland; (B.P.-S.); (J.W.)
| | - Jolanta Artym
- Department of Experimental Therapy, Hirszfeld Institute of Immunology and Experimental Therapy, R. Weigla Str. 12, 53-114 Wrocław, Poland; (J.A.); (M.Z.)
| | - Joanna Bojarska
- Institute of Inorganic and Ecological Chemistry, Chemistry Department, Łódź University of Technology, S. Żeromskiego Str. 116, 90-924 Łódź, Poland;
| | - Barbara Pacholczyk-Sienicka
- Institute of Organic Chemistry, Łódź University of Technology, S. Żeromskiego Str. 116, 90-924 Łódź, Poland; (B.P.-S.); (J.W.)
| | - Joanna Waśko
- Institute of Organic Chemistry, Łódź University of Technology, S. Żeromskiego Str. 116, 90-924 Łódź, Poland; (B.P.-S.); (J.W.)
| | - Ingrid Jelemenska
- Department of Physical Chemistry, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovakia; (I.J.); (M.B.)
| | - Wojciech M. Wolf
- Institute of Inorganic and Ecological Chemistry, Chemistry Department, Łódź University of Technology, S. Żeromskiego Str. 116, 90-924 Łódź, Poland;
| | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovakia; (I.J.); (M.B.)
| | - Michał Zimecki
- Department of Experimental Therapy, Hirszfeld Institute of Immunology and Experimental Therapy, R. Weigla Str. 12, 53-114 Wrocław, Poland; (J.A.); (M.Z.)
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6
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Ihara M, Tsuchida N, Sumida M, Himiyama T, Kitayama T, Shirasaka N, Fukuta Y. Crystal Structure of the Native Chromoprotein from Pleurotus salmoneostramineus Provides Insights into the Pigmentation Mechanism. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17626-17632. [PMID: 39073883 PMCID: PMC11311226 DOI: 10.1021/acs.jafc.4c02951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024]
Abstract
The pink-colored protein from the fungus Pleurotus salmoneostramineus (PsPCP) possesses unusual primary sequences with little resemblance to those of known proteins and exhibits a red color in aqueous solution. To understand the pigmentation mechanism of PsPCP, we elucidated the X-ray crystal structure of the native PsPCP. We identified a highly conjugated polyene ligand 2-dehydro-3-deoxylaetiporic acid A as a chromophore ligand, whose solution exhibits yellow. The crystal structure of PsPCP indicated that the ligand is secured in the central cavity and anchored at both termini by hydrophilic interactions and that surrounding residues show CH-pi and C-H···O hydrogen bondings. Geometrical analyses of the bound ligand demonstrated that the conjugated C-C and C═C bonds exhibit similar bond distances. The result indicated enhanced electron delocalization within the conjugated CC bond system, resulting in a redshift of the chromophore ligand. The computational estimates of the UV-vis spectra support the view that the electron delocalization within the conjugated CC bonds system of the bound ligand, induced by the specific ligand geometry within a limited space of PsPCP cavity, is responsible for the red pigmentation of PsPCP. Thus, we propose that the coloring mechanism of PsPCP, which constrains the geometry of a highly conjugated polyene ligand, is a novel type of pigment chemistry.
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Affiliation(s)
- Makoto Ihara
- Faculty
of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Nara 631-8505, Japan
| | - Noriko Tsuchida
- Faculty
of Medicine, Saitama Medical University, 38 Moroyama, Saitama 350-8550, Japan
| | - Marina Sumida
- Faculty
of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Nara 631-8505, Japan
| | - Tomoki Himiyama
- National
Institute of Advanced Industrial Science and Technology, 1-8-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Takashi Kitayama
- Faculty
of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Nara 631-8505, Japan
| | - Norifumi Shirasaka
- Faculty
of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Nara 631-8505, Japan
| | - Yasuhisa Fukuta
- Faculty
of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Nara 631-8505, Japan
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7
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Zavalishin MN, Kiselev AN, Gamov GA. Schiff Bases Derived from Pyridoxal 5'-Phosphate and 2-X-Phenylamine (X = H, OH, SH): Substituent Effects on UV-Vis Spectra and Hydrolysis Kinetics. Molecules 2024; 29:3504. [PMID: 39124909 PMCID: PMC11314395 DOI: 10.3390/molecules29153504] [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: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Schiff bases are compounds that are widely distributed in nature and have practical value for industry and biomedicine. Another important use of Schiff bases is identifying metal ions and different molecules, including proteins. Their proneness to hydrolysis limits the utilization of Schiff bases to mainly non-aqueous solutions. However, by introducing -OH and -SH substituents to aromatic amine-bearing rings, it is possible to increase the resilience of the Schiff base to destruction in water. The present paper discusses how the hydroxyl or thiol group influences the spectral properties and kinetics of the hydrolysis and formation of Schiff bases derived from pyridoxal 5'-phosphate and aniline, 2-hydroxyaniline, and 2-mercaptoaniline using quantum chemical data. The spectral variation between different imines can be explained by taking into account the geometry and frontier molecular orbital alteration induced by the substituents. The changes in the hydrolysis rate are analyzed using the computed values of local reactivity indices.
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Affiliation(s)
- Maksim N. Zavalishin
- Department of General Chemical Technology, Ivanovo State University of Chemistry and Technology, Sheremetevskii Pr. 7, Ivanovo 153000, Russia;
| | - Aleksei N. Kiselev
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Science, Akademicheskaya Str. 1, Ivanovo 153045, Russia;
| | - George A. Gamov
- Department of General Chemical Technology, Ivanovo State University of Chemistry and Technology, Sheremetevskii Pr. 7, Ivanovo 153000, Russia;
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8
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Kumar R, Singh B, Gahlyan P, Verma A, Bhandari M, Kakkar R, Pani B. An innovative Schiff-base colorimetric chemosensor for the selective detection of Cu 2+ ions and its applications. RSC Adv 2024; 14:23083-23094. [PMID: 39040695 PMCID: PMC11261578 DOI: 10.1039/d4ra03097d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024] Open
Abstract
A novel Schiff base moiety, (E)-4-(1-hydrazonoethyl)benzene-1,3-diol (2), and 2,4-dihydroxybenzaldehyde were condensed in a 1 : 1 molar ratio to generate 4-((E)-1-(((Z)-2,4dihydroxybenzylidene)hydrazono)ethyl)benzene-1,3-diol (L), which was then characterized using high-resolution mass spectrometry (HRMS), 1H-NMR, 13C NMR, and single-crystal XRD techniques. UV-vis absorbance measurements were used to determine whether the Schiff base could detect the cupric ions more effectively than the other transition metal ions. When Cu2+ ions were involved, a new band was observed at 462 nm. From the Job plot, the binding stoichiometry for the anticipated L : Cu2+ partnership is determined to be 1 : 1. For the purpose of validating structural correlations and absorption data, DFT simulations were performed. Further, docking studies for L indicated high binding affinity for human hemoglobin, providing vital information about the ligand's favorable binding locations inside hemoglobin binding sites and the consequent interactions with HHb. The binding coefficient and limit of detection were found to be 3.02 × 104 M-1 and 42.09 nM, respectively. Reversibility of the complex was seen upon the addition of EDTA to the L-Cu2+ solution, and a colorimetric variation simulating the "INHIBIT" molecular logic gate was seen upon the addition of Cu2+ and EDTA to L. Furthermore, the chemosensor's potential application in the detection of Cu2+ in the solid state by chemosensor L also confirms its usefulness in real-world applications emphasizing its versatility and practical utility.
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Affiliation(s)
- Ram Kumar
- Department of Chemistry, University of Delhi Delhi 110007 India
- Department of Chemistry, Bhaskaracharya College of Applied Sciences, University of Delhi New Delhi 110075 India
| | - Bholey Singh
- Department of Chemistry, Swami Shraddhanand College, University of Delhi Delhi 110036 India
| | - Parveen Gahlyan
- Department of Chemistry, University of Delhi Delhi 110007 India
| | - Abhishek Verma
- Department of Chemistry, Kirori Mal College, University of Delhi Delhi 110007 India
| | - Mamta Bhandari
- Computational Chemistry Group, Department of Chemistry, University of Delhi Delhi 110007 India
| | - Rita Kakkar
- Computational Chemistry Group, Department of Chemistry, University of Delhi Delhi 110007 India
| | - Balaram Pani
- Department of Chemistry, Bhaskaracharya College of Applied Sciences, University of Delhi New Delhi 110075 India
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9
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Shen T, Liu X. Photoinduced Charge Centralization Quenches the Fluorescence of Conjugation-Fused Tetrazine Labels with Red-to-Near-Infrared Emissions. Bioconjug Chem 2024; 35:1024-1032. [PMID: 38963403 DOI: 10.1021/acs.bioconjchem.4c00227] [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: 07/05/2024]
Abstract
Tetrazine-derived fluorogenic labels are extensively studied for their potential in biological and medical imaging. Nonetheless, the fluorescence quenching mechanism in numerous precursors continues to be debated, particularly as the wavelengths extend into the red and near-infrared (NIR) regions. This challenge poses obstacles to systematically optimizing their fluorogenicity, i.e., achieving red-shifted wavelengths and improved fluorescence turn-on signals through click reactions. This paper highlights the significance of photoinduced charge centralization (PCC), a quenching mechanism observed in tetrazine-fused fluorogenic labels with integrated π-conjugations. PCC is primarily responsible for the quenching effects observed in such labels emitting in the red-to-NIR spectrum. Drawing from structure-property relationships, this study proposes two molecular design strategies that incorporate the PCC mechanism and constitutional isomerization to develop high-performance tetrazine-based labels. These strategies facilitate multiplex fluorescence imaging following click reactions, promising significant advancements in bio-orthogonal imaging techniques.
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Affiliation(s)
- Tianruo Shen
- Science, Mathematics and Technology Cluster, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore
| | - Xiaogang Liu
- Science, Mathematics and Technology Cluster, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore
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10
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Karthika AM, Thomas T, Augustine C. Computational studies on a selection of phosphite esters as antioxidants for polymeric materials. J Mol Model 2024; 30:244. [PMID: 38958769 DOI: 10.1007/s00894-024-06045-5] [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: 05/17/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
CONTEXT Phosphite esters, a class of organo-phosphorus compounds, are widely used as non-discolouring antioxidants in many polymeric products. Apart from normal radical scavenging, they prevent the splitting of hydroperoxides (ROOH), one of the initial products of autoxidation, from forming extremely reactive free radicals such as alkoxy (RO.) and hydroxy (.OH) radicals. The inherent molecular properties of antioxidants and the chemistry of their action are essential for researchers working in this field of science. Four organo-phosphorous compounds well-known for their antioxidant activity are selected here for theoretical analysis: Tri(m-methylphenyl) phosphite (m-TMPP), Tri(4-methyl-2,6-di-tert-butylphenyl) phosphite (TMdtBPP), Tri(allylphenyl) phosphite (TAPP) and Tri(mercaptobenzothiazoyl) thiophosphate (TMBTTP). The antioxidant activity exhibited by these compounds is theoretically verified, and the results are consistent with the available experimental data. Such theoretical predictions offer advantages in scientific research, particularly when researchers need to select certain molecules as antioxidants for experiments from a pool of molecular systems. METHODS The chemical computations presented in this report are done in Gaussian 16 program package. The procedure of density functional theory (DFT) with the model chemistry B3LYP/6-31G(d,p) is used to generate computational data. Global reactivity indices, thermochemical data, Fukui functions, molecular electrostatic potential and NMR spectra are computed for the chosen molecular systems from their optimized geometries.
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Affiliation(s)
- A M Karthika
- Department of Chemistry, St. Berchmans College (Autonomous), Mahatma Gandhi University, Kottayam, India
| | - Tiju Thomas
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Cyril Augustine
- Department of Chemistry, St. Berchmans College (Autonomous), Mahatma Gandhi University, Kottayam, India.
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Madras, Chennai, India.
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11
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Menon LV, Manoj E. Copper perchlorate catalyzed oxidative cyclisation of a novel bishydrazone ligand, formation of an unusual copper complex and in vitro biological implications. J Inorg Biochem 2024; 255:112538. [PMID: 38547785 DOI: 10.1016/j.jinorgbio.2024.112538] [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: 01/11/2024] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 04/16/2024]
Abstract
A novel hexadentate bishydrazone ligand, 1,10-bis(di(2-pyridyl)ketone) adipic acid dihydrazone (H2L1) is synthesized and characterized. With copper perchlorate as a catalytic oxidant, the ligand undergoes oxidative cyclisation and resulted in the formation of an unusual copper complex [Cu(L1a)2Cl]ClO4 (1), where L1a is 3-(2-pyridyl)triazolo[1,5-a]-pyridine. The Cu(II) complex was characterized physicochemically, while the molecular structure was confirmed by single crystal X- ray diffraction. In the complex cation, copper(II) is in a distorted trigonal bipyramidal coordination environment, surrounded by two triazolo nitrogen atoms and two pyridyl nitrogen atoms of L1a and a chloride atom. The relevant non covalent intermolecular interactions of the complex quantified using Hirshfeld surface analysis reveals that the O···H/ H···O (27.2%) contacts has the highest contribution. The solution phase bandgaps of the compounds were calculated using Tauc plot, whereas the solid-state band gaps were calculated by Kubelka-Munk model. DFT studies of the compounds indicate that the theoretical calculations corroborate with the experimental data. DPPH antioxidant activity assay of the synthesized compounds showed that the proligand H2L1 has a lower IC50 value (24.1 μM) than that of complex 1 (29.7 μM). The in vitro antibacterial activity was evaluated against Escherichia coli and Staphylococcus aureus, which revealed that complex 1 have excellent activity against E. coli, much as the standard ciprofloxacin. The cytotoxic efficacy investigation of the compounds against A549 (lung) adenocarcinoma cells suggested that H2L1 has more anticancer activity (IC50 value of 149.08 μM) than that of complex 1(IC50 value of 176.70 μM).
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Affiliation(s)
- Lakshmi V Menon
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, Kerala 682 022, India
| | - E Manoj
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, Kerala 682 022, India.
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12
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Tauchi D, Kanno K, Hasegawa M, Mazaki Y, Tsubaki K, Sugiura KI, Shiga T, Mori S, Nishikawa H. Aggregation-induced enhanced fluorescence emission of chiral Zn(II) complexes coordinated by Schiff-base type binaphthyl ligands. Dalton Trans 2024; 53:8926-8933. [PMID: 38687172 DOI: 10.1039/d4dt00903g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
A pair of novel chiral Zn(II) complexes coordinated by Schiff-base type ligands derived from BINOL (1,1'-bi-2-naphthol), R-/S-Zn, were synthesized. X-ray crystallography revealed the presence of two crystallographically independent complexes; one has a distorted trigonal-bipyramidal structure coordinated by two binaphthyl ligands and one disordered methanol molecule (molecule A), while the other has a distorted tetrahedral structure coordinated by two binaphthyl ligands (molecule B). Numerous CH⋯π and CH⋯O interactions were identified, contributing to the formation of a 3-dimensional rigid network structure. Both R-/S-Zn exhibited fluorescence in both CH2Cl2 solutions and powder samples, with the photoluminescence quantum yields (PLQYs) of powder samples being twice as large as those in solutions, indicating aggregation-induced enhanced emission (AIEE). The AIEE properties were attributed to the restraint of the molecular motion arising from the 3-dimensional intermolecular interactions. CD and CPL spectra were observed for R-/S-Zn in both solutions and powders. The dissymmetry factors, gabs and gCPL values, were within the order of 10-3 to 10-4 magnitudes, comparable to those reported for chiral Zn(II) complexes in previous studies.
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Affiliation(s)
- Daiki Tauchi
- Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan.
| | - Katsuya Kanno
- Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan.
| | - Masashi Hasegawa
- Graduate School of Science, Kitasato University, Kanagawa 252-0373, Japan
| | - Yasuhiro Mazaki
- Graduate School of Science, Kitasato University, Kanagawa 252-0373, Japan
| | - Kazunori Tsubaki
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Ken-Ichi Sugiura
- Graduate School of Science, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Takuya Shiga
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Seiji Mori
- Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan.
| | - Hiroyuki Nishikawa
- Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan.
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13
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García-García A, Medina-O'donnell M, Rojas S, Cano-Morenilla M, Morales J, Quesada-Moreno MM, Sainz J, Vitorica-Yrezabal IJ, Rodríguez-Diéguez A, Navarro A, Reyes-Zurita FJ. Modulating anti-inflammatory and anticancer properties by designing a family of metal-complexes based on 5-nitropicolinic acid. Dalton Trans 2024; 53:8988-9000. [PMID: 38721696 DOI: 10.1039/d4dt00265b] [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: 05/29/2024]
Abstract
A new family of six complexes based on 5-nitropicolinic acid (5-npic) and transition metals has been obtained: [M(5-npic)2]n (MII = Mn (1) and Cd (2)), [Cu(5-npic)2]n (3), and [M(5-npic)2(H2O)2] (MII = Co (4), Ni (5), and Zn (6)), which display 1D, 2D, and mononuclear structures, respectively, thanks to different coordination modes of 5-npic. After their physicochemical characterization by single-crystal X-ray diffraction (SCXRD), elemental analyses (EA), and spectroscopic techniques, quantum chemical calculations using Time-Dependent Density Functional Theory (TD-DFT) were performed to further study the luminescence properties of compounds 2 and 6. The potential anticancer activity of all complexes was tested against three tumor cell lines, B16-F10, HT29, and HepG2, which are models widely used for studying melanoma, colon cancer, and liver cancer, respectively. The best results were found for compounds 2 and 4 against B16-F10 (IC50 = 26.94 and 45.10 μg mL-1, respectively). In addition, anti-inflammatory studies using RAW 264.7 cells exhibited promising activity for 2, 3, and 6 (IC50 NO = 5.38, 24.10, and 17.63 μg mL-1, respectively). This multidisciplinary study points to complex 2, based on CdII, as a promising anticancer and anti-inflammatory material.
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Affiliation(s)
- Amalia García-García
- Department of Inorganic Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
| | - Marta Medina-O'donnell
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
| | - Sara Rojas
- Department of Inorganic Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
| | - Mariola Cano-Morenilla
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
| | - Juan Morales
- Department of Physical and Analytical Chemistry, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain.
| | - María Mar Quesada-Moreno
- Department of Physical and Analytical Chemistry, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain.
| | - Juan Sainz
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Av. de la Ilustración 114, 18016, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs. Granada, Av. de Madrid 15, 18012, Granada, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Iñigo J Vitorica-Yrezabal
- Department of Inorganic Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
| | - Antonio Rodríguez-Diéguez
- Department of Inorganic Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
| | - Amparo Navarro
- Department of Physical and Analytical Chemistry, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain.
| | - Fernando J Reyes-Zurita
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
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14
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Kuranova NN, Pimenov OA, Zavalishin MN, Gamov GA. Complexes of Gold(III) with Hydrazones Derived from Pyridoxal: Stability, Structure, and Nature of UV-Vis Spectra. Int J Mol Sci 2024; 25:5046. [PMID: 38732264 PMCID: PMC11084471 DOI: 10.3390/ijms25095046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
Pyridoxal and pyridoxal 5'-phosphate are aldehyde forms of B6 vitamin that can easily be transformed into each other in the living organism. The presence of a phosphate group, however, provides the related compounds (e.g., hydrazones) with better solubility in water. In addition, the phosphate group may sometimes act as a binding center for metal ions. In particular, a phosphate group can be a strong ligand for a gold(III) ion, which is of interest for researchers for the anti-tumor and antimicrobial potential of gold(III). This paper aims to answer whether the phosphate group is involved in the complex formation between gold(III) and hydrazones derived from pyridoxal 5'-phosphate. The answer is negative, since the comparison of the stability constants determined for the gold(III) complexes with pyridoxal- and pyridoxal 5'-phosphate-derived hydrazones showed a negligible difference. In addition, quantum chemical calculations confirmed that the preferential coordination of two series of phosphorylated and non-phosphorylated hydrazones to gold(III) ion is similar. The preferential protonation modes for the gold(III) complexes were also determined using experimental and calculated data.
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Affiliation(s)
| | | | | | - George A. Gamov
- Department of General Chemical Technology, Ivanovo State University of Chemistry and Technology, Sheremetevskii pr. 7, Ivanovo 153000, Russia; (N.N.K.); (O.A.P.); (M.N.Z.)
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15
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Das P, Grinalds NJ, Ghiviriga I, Abboud KA, Dobrzycki Ł, Xue J, Castellano RK. Dicyanorhodanine-Pyrrole Conjugates for Visible Light-Driven Quantitative Photoswitching in Solution and the Solid State. J Am Chem Soc 2024; 146:11932-11943. [PMID: 38629510 DOI: 10.1021/jacs.4c00983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Small molecule photoswitches capable of toggling between two distinct molecular states in response to light are versatile tools to monitor biological processes, control photochemistry, and design smart materials. In this work, six novel dicyanorhodanine-based pyrrole-containing photoswitches are reported. The molecular design avails both the Z and E isomers from synthesis, where each can be isolated using chromatographic techniques. Inter- and intramolecular hydrogen bonding (H-bonding) interactions available to the E and Z isomers, respectively, uniquely impart thermal stability to each isomer over long time periods. Photoisomerization could be assessed by solution NMR and UV-vis spectroscopic techniques along with complementary ground- and excited-state computational studies, which show good agreement. Quantitative E → Z isomerization occurs upon 523 nm irradiation of the parent compound (where R = H) in solution, whereas Z → E isomerization using 404 nm irradiation offers a photostationary state (PSS) ratio of 84/16 (E/Z). Extending the π-conjugation of the pyrrole unit (where R = p-C6H4-OMe) pushes the maximum absorption to the yellow-orange region of the visible spectrum and allows bidirectional quantitative isomerization with 404 and 595 nm excitation. Comparator molecules have been prepared to report how the presence or absence of H-bonding affects the photoswitching behavior. Finally, studies of the photoswitches in neat films and photoinactive polymer matrices reveal distinctive structural and optical properties of the Z and E isomers and ultimately afford reversible photoswitching to spectrally unique PSSs using visible light sources including the Sun.
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Affiliation(s)
- Parag Das
- Department of Chemistry, University of Florida, P. O. Box 117200, Gainesville, Florida 32611, United States
| | - Nathan J Grinalds
- Department of Materials Science and Engineering, University of Florida, P. O. Box 116400, Gainesville, Florida 32611, United States
| | - Ion Ghiviriga
- Department of Chemistry, University of Florida, P. O. Box 117200, Gainesville, Florida 32611, United States
| | - Khalil A Abboud
- Department of Chemistry, University of Florida, P. O. Box 117200, Gainesville, Florida 32611, United States
| | - Łukasz Dobrzycki
- Department of Chemistry, University of Florida, P. O. Box 117200, Gainesville, Florida 32611, United States
| | - Jiangeng Xue
- Department of Materials Science and Engineering, University of Florida, P. O. Box 116400, Gainesville, Florida 32611, United States
| | - Ronald K Castellano
- Department of Chemistry, University of Florida, P. O. Box 117200, Gainesville, Florida 32611, United States
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16
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Li G, Liu Y, Lei D, Li J, Dou X. Amination and Protonation Facilitated Novel Isoxazole Derivative for Highly Efficient Electron and Hole Separation. J Phys Chem A 2024. [PMID: 38656182 DOI: 10.1021/acs.jpca.4c01324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
It is of great importance to understand the intrinsic relationship between phototautomerization and photoelectric properties for the exploration of novel organic materials. Here, in order to chemically control the protonation process, the aminated isoxazole derivative (2,2'-(isoxazolo[5,4-d]isoxazole-3,6-diyl)dibenzenaminium, DP-DA-DPIxz) with -N═ as the proton acceptor was designed to achieve the twisted intramolecular charge transfer (TICT) state which was triggered by an excited-state intramolecular proton transfer (ESIPT) process. This kind of protonation enhanced the intramolecular hydrogen bonding, conjugative effect, and steric hindrance effects, ensuring a barrierless spontaneous TICT process. Through the intramolecular proton transfer, the configuration torsion and conjugation dissociation of the DP-DA-DPIxz molecule was favored, which led to efficient charge separation and remarkable variations in light-emitting properties. We hope the present investigation will provide a new approach to design novel optoelectronic organic materials and shine light on the understanding of the charge transfer and separation process in molecular science.
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Affiliation(s)
- Gaosheng Li
- School of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Yali Liu
- Xinjiang Key Laboratory of Trace Chemical Substances Sensing, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Da Lei
- Xinjiang Key Laboratory of Trace Chemical Substances Sensing, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Jiguang Li
- Xinjiang Key Laboratory of Trace Chemical Substances Sensing, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xincun Dou
- School of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang 830046, China
- Xinjiang Key Laboratory of Trace Chemical Substances Sensing, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Gish MK, Karunasena CD, Carr JM, Kopcha WP, Greenaway AL, Mohapatra AA, Zhang J, Basu A, Brosius V, Pratik SM, Bredas JL, Coropceanu V, Barlow S, Marder SR, Ferguson AJ, Reid OG. The Excited-State Lifetime of Poly(NDI2OD-T2) Is Intrinsically Short. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2024; 128:6392-6400. [PMID: 38655059 PMCID: PMC11033933 DOI: 10.1021/acs.jpcc.4c00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Conjugated polymers composed of alternating electron donor and acceptor segments have come to dominate the materials being considered for organic photoelectrodes and solar cells, in large part because of their favorable near-infrared absorption. The prototypical electron-transporting push-pull polymer poly(NDI2OD-T2) (N2200) is one such material. While reasonably efficient organic solar cells can be fabricated with N2200 as the acceptor, it generally fails to contribute as much photocurrent from its absorption bands as the donor with which it is paired. Moreover, transient absorption studies have shown N2200 to have a consistently short excited-state lifetime (∼100 ps) that is dominated by a ground-state recovery. In this paper, we investigate whether these characteristics are intrinsic to the backbone structure of this polymer or if these are extrinsic effects from ubiquitous solution-phase and thin-film aggregates. We compare the solution-phase photophysics of N2200 with those of a pair of model compounds composed of alternating bithiophene (T2) donor and naphthalene diimide (NDI) acceptor units, NDI-T2-NDI and T2-NDI-T2, in a dilute solution. We find that the model compounds have even faster ground-state recovery dynamics (τ = 45, 27 ps) than the polymer (τ = 133 ps), despite remaining molecularly isolated in solution. In these molecules, as in the case of the N2200 polymer, the lowest excited state has a T2 to NDI charge-transfer (CT) character. Electronic-structure calculations indicate that the short lifetime of this state is due to fast nonradiative decay to the ground state (GS) promoted by strong CT-GS electronic coupling and strong electron-vibrational coupling with high-frequency (quantum) normal modes.
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Affiliation(s)
- Melissa K. Gish
- Materials,
Chemical, and Computational Science Directorate, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Chamikara D. Karunasena
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721-0041, United States
| | - Joshua M. Carr
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80309, United States
| | - William P. Kopcha
- Materials,
Chemical, and Computational Science Directorate, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Ann L. Greenaway
- Materials,
Chemical, and Computational Science Directorate, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Aiswarya Abhisek Mohapatra
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Junxiang Zhang
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Aniruddha Basu
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Victor Brosius
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Saied Md Pratik
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721-0041, United States
| | - Jean-Luc Bredas
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721-0041, United States
| | - Veaceslav Coropceanu
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721-0041, United States
| | - Stephen Barlow
- Materials,
Chemical, and Computational Science Directorate, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Seth R. Marder
- Materials,
Chemical, and Computational Science Directorate, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80309, United States
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Department
of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Andrew J. Ferguson
- Materials,
Chemical, and Computational Science Directorate, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Obadiah G. Reid
- Materials,
Chemical, and Computational Science Directorate, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80309, United States
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18
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Bondanza M, Nottoli T, Nottoli M, Cupellini L, Lipparini F, Mennucci B. The OpenMMPol library for polarizable QM/MM calculations of properties and dynamics. J Chem Phys 2024; 160:134106. [PMID: 38557842 DOI: 10.1063/5.0198251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
We present a new library designed to provide a simple and straightforward way to implement QM/AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) and other polarizable QM/MM (Molecular Mechanics) methods based on induced point dipoles. The library, herein referred to as OpenMMPol, is free and open-sourced and is engineered to address the increasing demand for accurate and efficient QM/MM simulations. OpenMMPol is specifically designed to allow polarizable QM/MM calculations of ground state energies and gradients and excitation properties. Key features of OpenMMPol include a modular architecture facilitating extensibility, parallel computing capabilities for enhanced performance on modern cluster architectures, a user-friendly interface for intuitive implementation, and a simple and flexible structure for providing input data. To show the capabilities offered by the library, we present an interface with PySCF to perform QM/AMOEBA molecular dynamics, geometry optimization, and excited-state calculation based on (time-dependent) density functional theory.
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Affiliation(s)
- Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Tommaso Nottoli
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Michele Nottoli
- Institute of Applied Analysis and Numerical Simulation, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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19
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Feng Y, Lei D, Zu B, Li J, Li Y, Dou X. A Self-Accelerating Naphthalimide-Based Probe Coupled with Upconversion Nanoparticles for Ultra-Accurate Tri-Mode Visualization of Hydrogen Peroxide. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309182. [PMID: 38240462 PMCID: PMC10987149 DOI: 10.1002/advs.202309182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/29/2023] [Indexed: 04/04/2024]
Abstract
The design and development of ultra-accurate probe is of great significance to chemical sensing in complex practical scenarios. Here, a self-accelerating naphthalimide-based probe with fast response and high sensitivity toward hydrogen peroxide (H2O2) is designed. By coupling with the specially selected upconversion nanoparticles (UCNPs), an ultra-accurate colorimetric-fluorescent-upconversion luminescence (UCL) tri-mode platform is constructed. Owing to the promoted reaction process, this platform demonstrates rapid response (< 1 s), an ultra-low detection limit (4.34 nM), and superb anti-interferent ability even in presence of > 21 types of oxidants, explosives, metallic salts, daily compounds, colorful or fluorescent substances. In addition, the effectiveness of this design is further verified by a sponge-based sensing chip loaded with the UCNPs/probe in recognizing trace H2O2 vapor from interferents with the three characteristic colors existing simultaneously. The proposed design of probe and tri-mode visualization detection platform is expected to open up a brand-new methodology for ultra-accurate sensing.
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Affiliation(s)
- Yanan Feng
- Hebei Provincial Key Laboratory of Photoelectric Control on Surface and InterfaceCollege of ScienceHebei University of Science and TechnologyShijiazhuang050018China
- Xinjiang Key Laboratory of Trace Chemical Substances SensingXinjiang Technical Institute of Physics and ChemistryChinese Academy of SciencesUrumqi830011China
| | - Da Lei
- Xinjiang Key Laboratory of Trace Chemical Substances SensingXinjiang Technical Institute of Physics and ChemistryChinese Academy of SciencesUrumqi830011China
| | - Baiyi Zu
- Xinjiang Key Laboratory of Trace Chemical Substances SensingXinjiang Technical Institute of Physics and ChemistryChinese Academy of SciencesUrumqi830011China
- Key Laboratory of Improvised Explosive Chemicals for State Market RegulationUrumqi830011China
| | - Jiguang Li
- Xinjiang Key Laboratory of Trace Chemical Substances SensingXinjiang Technical Institute of Physics and ChemistryChinese Academy of SciencesUrumqi830011China
| | - Yajuan Li
- Hebei Provincial Key Laboratory of Photoelectric Control on Surface and InterfaceCollege of ScienceHebei University of Science and TechnologyShijiazhuang050018China
| | - Xincun Dou
- Xinjiang Key Laboratory of Trace Chemical Substances SensingXinjiang Technical Institute of Physics and ChemistryChinese Academy of SciencesUrumqi830011China
- Key Laboratory of Improvised Explosive Chemicals for State Market RegulationUrumqi830011China
- Center of Materials Science and Optoelectronics EngineeringUniversity of Chinese Academy of SciencesBeijing100049China
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20
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Deng Y, Shen T, Yu X, Li J, Zou P, Gong Q, Zheng Y, Sun H, Liu X, Wu H. Tetrazine-Isonitrile Bioorthogonal Fluorogenic Reactions Enable Multiplex Labeling and Wash-Free Bioimaging of Live Cells. Angew Chem Int Ed Engl 2024; 63:e202319853. [PMID: 38242857 DOI: 10.1002/anie.202319853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/21/2024]
Abstract
Developing fluorogenic probes for simultaneous live cell labeling of multiple targets is crucial for understanding complex cellular events. The emerging [4+1] cycloaddition between tetrazine and isonitriles holds promise as a bioorthogonal tool, yet existing tetrazine probes lack reactivity and fluorogenicity. Here, we present the development of a series of tetrazine-functionalized bioorthogonal probes. By incorporating pyrazole adducts into the fluorophore scaffolds, the post-reacted probes displayed remarkable fluorescence turn-on ratios, up to 3184-fold. Moreover, these modifications are generalizable to various fluorophores, enabling a broad emission range from 473 to 659 nm. Quantum chemical calculations further elucidate the turn-on mechanisms. These probes enable the simultaneous labeling of multiple targets in live cells, without the need for a washing step. Consequently, our findings pave the way for advanced multiplex imaging and detection techniques for cellular studies.
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Affiliation(s)
- Yingqiao Deng
- Department of Radiology and Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province and Frontiers Science Center for Disease Related Molecular Network, West China Hospital, Sichuan University, Huaxi Research Building, 001 4th Keyuan Road, 610041, Chengdu, China
| | - Tianruo Shen
- Science, Mathematics and Technology Cluster, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore, Singapore
| | - Xinyu Yu
- Department of Radiology and Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province and Frontiers Science Center for Disease Related Molecular Network, West China Hospital, Sichuan University, Huaxi Research Building, 001 4th Keyuan Road, 610041, Chengdu, China
| | - Jie Li
- Department of Radiology and Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province and Frontiers Science Center for Disease Related Molecular Network, West China Hospital, Sichuan University, Huaxi Research Building, 001 4th Keyuan Road, 610041, Chengdu, China
| | - Peixuan Zou
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, No.17 People's South Road, 610041, Chengdu, China
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, No.17 People's South Road, 610041, Chengdu, China
| | - Qiyong Gong
- Department of Radiology and Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province and Frontiers Science Center for Disease Related Molecular Network, West China Hospital, Sichuan University, Huaxi Research Building, 001 4th Keyuan Road, 610041, Chengdu, China
| | - Yongxiang Zheng
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, No.17 People's South Road, 610041, Chengdu, China
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, No.17 People's South Road, 610041, Chengdu, China
| | - Hongbao Sun
- Department of Radiology and Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province and Frontiers Science Center for Disease Related Molecular Network, West China Hospital, Sichuan University, Huaxi Research Building, 001 4th Keyuan Road, 610041, Chengdu, China
| | - Xiaogang Liu
- Science, Mathematics and Technology Cluster, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore, Singapore
| | - Haoxing Wu
- Department of Radiology and Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province and Frontiers Science Center for Disease Related Molecular Network, West China Hospital, Sichuan University, Huaxi Research Building, 001 4th Keyuan Road, 610041, Chengdu, China
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, No.17 People's South Road, 610041, Chengdu, China
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21
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Crisci L, Coppola F, Petrone A, Rega N. Tuning ultrafast time-evolution of photo-induced charge-transfer states: A real-time electronic dynamics study in substituted indenotetracene derivatives. J Comput Chem 2024; 45:210-221. [PMID: 37706600 DOI: 10.1002/jcc.27231] [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: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
Photo-induced charge transfer (CT) states are pivotal in many technological and biological processes. A deeper knowledge of such states is mandatory for modeling the charge migration dynamics. Real-time time-dependent density functional theory (RT-TD-DFT) electronic dynamics simulations are employed to explicitly observe the electronic density time-evolution upon photo-excitation. Asymmetrically substituted indenotetracene molecules, given their potential application as n-type semiconductors in organic photovoltaic materials, are here investigated. Effects of substituents with different electron-donating characters are analyzed in terms of the overall electronic energy spacing and resulting ultrafast CT dynamics through linear response (LR-)TD-DFT and RT-TD-DFT based approaches. The combination of the computational techniques here employed provided direct access to the electronic density reorganization in time and to its spatial and rational representation in terms of molecular orbital occupation time evolution. Such results can be exploited to design peculiar directional charge dynamics, crucial when photoactive materials are used for light-harvesting applications.
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Affiliation(s)
- Luigi Crisci
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
- Scuola Normale Superiore di Pisa, Pisa, Italy
| | | | - Alessio Petrone
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
- Scuola Superiore Meridionale, Naples, Italy
- Istituto Nazionale Di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di M.S. Angelo ed. 6, Naples, Italy
| | - Nadia Rega
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
- Scuola Superiore Meridionale, Naples, Italy
- Istituto Nazionale Di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di M.S. Angelo ed. 6, Naples, Italy
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22
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Deng YH, Li Q, Li M, Wang L, Sun TY. Rational design of super reductive EDA photocatalyst for challenging reactions: a theoretical and experimental study. RSC Adv 2024; 14:1902-1908. [PMID: 38192317 PMCID: PMC10772736 DOI: 10.1039/d3ra07558c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024] Open
Abstract
We reported a novel electron-donor-acceptor (EDA) photocatalyst formed in situ from isoquinoline, a diboron reagent, and a weak base. To further optimize the efficiency of this photocatalyst, Density Functional Theory (DFT) calculations were conducted to investigate the substituent effects on the properties of vertical excitation energy and redox potential. Subsequently, we experimentally validated these effects using a broader range of substituents and varying substitution positions. Notably, the 4-NH2 EDA complex derived from 4-NH2-isoquinoline exhibits the highest photocatalytic efficiency, enabling feasible metal free borylation of aromatic C-H bond and detosylaion of Ts-anilines under green and super mild conditions. These experimental results demonstrate the effectiveness of our strategy for photocatalyst optimization.
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Affiliation(s)
- Yi-Hui Deng
- Shenzhen Bay Laboratory Shenzhen 518132 P. R. China
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School Shenzhen 518055 P. R. China
| | - Qini Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University No.66, Gongchang Road Shenzhen 518107 P. R. China
| | - Manhong Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University No.66, Gongchang Road Shenzhen 518107 P. R. China
| | - Leifeng Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University No.66, Gongchang Road Shenzhen 518107 P. R. China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory Shenzhen 518132 P. R. China
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23
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Suda K, Yokogawa D. Theoretical Study of Raman Intensities of p-Nitroaniline in Different Solvent Conditions by Using a Reference Interaction Site Model Self-Consistent Field Explicitly Including Constrained Spatial Electron Density Distribution. J Phys Chem B 2023; 127:11023-11030. [PMID: 38100491 DOI: 10.1021/acs.jpcb.3c04983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Raman spectroscopy is one of the most powerful tools to understand and characterize the states and structures of systems in several environments. To obtain highly accurate changes in Raman intensities of systems in solution, theoretical treatment, which can deal with not only the states and structures of systems but also the environment around molecules, proves to be significant. Hence, in this study, we developed the calculation of changes in Raman intensities of systems in different solvent conditions by using the reference interaction site model self-consistent field study explicitly including constrained spatial electron density distribution; this model is designed based on elements from both quantum mechanics and statistical mechanics. We showed that our calculation method could reproduce the changes in Raman intensities of p-nitroaniline (pNA) under different solvent conditions, including supercritical water, which has been observed in previous experimental studies. Based on the analysis of the calculation results, we observed that the ratio of the Raman intensity change of pNA in different solvent conditions is strongly correlated with the charge-transfer character of pNA.
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Affiliation(s)
- Kayo Suda
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Daisuke Yokogawa
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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24
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Zaier R, Martel A, Antosiewicz TJ. Effect of Benzothiadiazole-Based π-Spacers on Fine-Tuning of Optoelectronic Properties of Oligothiophene-Core Donor Materials for Efficient Organic Solar Cells: A DFT Study. J Phys Chem A 2023; 127:10555-10569. [PMID: 38086177 PMCID: PMC10749456 DOI: 10.1021/acs.jpca.3c04866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/22/2023]
Abstract
In this work, five novel A-π-D-π-A type molecules D1-D5 were designed by adding unusual benzothiadiazole derivatives as π-spacer blocks to the efficient reference molecule DRCN5T for application as donor materials in organic solar cells (OSCs). Based on a density functional theory approach, a comprehensive theoretical study was performed with different functionals (B3LYP, B3LYP-GD3, B3LYP-GD3BJ, CAM-B3LYP, M06, M062X, and wB97XD) and with different solvent types (PCM and SMD) at the extended basis set 6-311+g(d,p) to evaluate the structural, optoelectronic, and intramolecular charge transfer properties of these molecules. The B3LYP-GD3BJ hybrid functional was used to optimize the studied molecules in CHCl3 solution with the SMD model solvent as it provided the best results compared to experimental data. Transition density matrix maps were simulated to examine the hole-electron localization and the electronic excitation processes in the excited state, and photovoltaic parameters including open-circuit photovoltage and fill factor were investigated to predict the efficiency of these materials. All the designed materials showed promising optoelectronic and photovoltaic characteristics, and for most of them, a red shift. Out of the proposed molecules, [1,2,5]thiadiazolo[3,4-d]pyridazine was selected as a promising π-spacer block to evaluate its interaction with PC61BM in a composite to understand the charge transfer between the donor and acceptor subparts. Overall, this study showed that adding π-spacer building blocks to the molecular structure is undoubtedly a potential strategy to further enhance the performance of donor materials for OSC applications.
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Affiliation(s)
- Rania Zaier
- Faculty
of Physics, University of Warsaw, Pasteura 5, PL-02-093 Warsaw, Poland
| | - Arnaud Martel
- Institut
des Molécules et Matériaux du Mans, UMR 6283 CNRS-Université du Maine, Avenue Olivier Messiaen, 72085 Cedex Le Mans, France
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25
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Bekri L, Elhorri AM, Hedidi M, Zouaoui-Rabah M. Theoretical study of the Tetraaminelithium and Tetraaminesodium molecules complexed with H -, Li - and Na - anions: static and dynamic NLO parameters. J Mol Model 2023; 30:8. [PMID: 38091098 DOI: 10.1007/s00894-023-05801-3] [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: 10/28/2023] [Accepted: 12/01/2023] [Indexed: 01/11/2024]
Abstract
CONTEXT This work focuses on the study of six molecules composed of the TetraAmineLithium (TALi+) and TetraAmineSodium (TANa+) structures linked with the anions H-, Li- and Na-. The NLO results obtained by these calculations showed significant values of static first hyperpolarizabilities (βtot) ranging from 8.74 * 10-30 to 691.99 * 10-30 esu. The two molecules TALi-Li and TALi-Na gave the highest values of static βtot equal to 563.20 and 691.99 * 10-30 esu respectively and static second hyperpolarizabilities (γav) of 680.02 and 779.05 * 10-35 esu. The highest dynamic first hyperpolarizabilities (β||) values are around 1474080.00 * 10-30 esu and 6,145,080.00 * 10-30 esu at 720 nm lasers and which are attributed to the two molecules TANa-Li and TANa-Na respectively. Four molecules have push-pull behavior where the anions are donor groups, the Li+-NH3 and Na+-NH3 groups are acceptor groups and a bridge composed by the three remaining NH3 ligands. The maximum wavelengths (λmax) in vacuum and in the presence of solvents for all molecules are in the range 240 to 870 nm. METHOD The software used in this study is Gaussian 16. The optimizations of the molecules were calculated by B3LYP-D3/6-31 + + G(d,p). The static first hyperpolarizability (βtot) was calculated by different functionals: CAM-B3LYP, LC-wPBE, LC-BLYP, M11, wB97X, HSEh1PBE and M06-2X and the MP2 method, the basis-set used is 6-31 + + G(d,p). Other calculations of static βtot were carried out by the CAM-B3LYP functional combined with several basis-sets: 6-31G(d,p), 6-31 + + G(d,p), cc-pVDZ, AUG-cc- pVDZ, 6-311G(d,p), 6-311 + + G(d,p), cc-pVTZ and AUG-cc-pVTZ. The calculations of the first (β||) and second (γ||) hyperpolarizabilities in second harmonic generation (SHG) were calculated by CAM-B3LYP/6-31 + + G(d,p). The delocalization energies (E(2)) were determined by the NBO approach and calculated by the same functional and basis-set cited before. The solvation Gibbs energies (ΔGsolv) were calculated using the implicit SMD model. Maximum wavelengths (λmax) and oscillator strengths ([Formula: see text]) were calculated by TD-CAM-B3LYP/6-31 + + G(d,p) in the presence of the implicit CPCM model.
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Affiliation(s)
- Lahcène Bekri
- Department of Chemistry, Faculty of Exact Sciences, Mustapha Stambouli, University of Mascara, Av. Cheikh El Khaldi, 29000, Mascara, Algeria
| | - Abdelkader M Elhorri
- Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba BenBouali University, Chlef, Ouled Fares, P.O. Box 78C, 02180, Chlef, Algeria.
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba BenBouali University, Chlef, Ouled Fares, P.O. Box 78C, 02180, Chlef, Algeria.
| | - Madani Hedidi
- Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba BenBouali University, Chlef, Ouled Fares, P.O. Box 78C, 02180, Chlef, Algeria
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba BenBouali University, Chlef, Ouled Fares, P.O. Box 78C, 02180, Chlef, Algeria
| | - Mourad Zouaoui-Rabah
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba BenBouali University, Chlef, Ouled Fares, P.O. Box 78C, 02180, Chlef, Algeria
- Department of Preparatory Education in Science and Technology, National Polytechnic School of Oran Maurice Audin, Oran El M'naouer, Box B.P. 1523, Oran, Algeria
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26
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Buttarazzi E, Perrella F, Rega N, Petrone A. Watching the Interplay between Photoinduced Ultrafast Charge Dynamics and Nuclear Vibrations. J Chem Theory Comput 2023; 19:8751-8766. [PMID: 37991892 PMCID: PMC10720350 DOI: 10.1021/acs.jctc.3c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023]
Abstract
Here is presented the ultrafast hole-electron dynamics of photoinduced metal to ligand charge-transfer (MLCT) states in a Ru(II) complex, [Ru(dcbpy)2(NCS)2]4- (dcbpy = 4,4'-dicarboxy-2,2'-bipyridine), a photoactive molecule employed in dye sensitized solar cells. Via cutting-edge computational techniques, a tailored computational protocol is here presented and developed to provide a detailed analysis of the electronic manifold coupled with nuclear vibrations to better understand the nonradiative pathways and the resulting overall dye performances in light-harvesting processes (electron injection). Thus, the effects of different vibrational modes were investigated on both the electronic levels and charge transfer dynamics through a theoretical-computational approach. First, the linear response time-dependent density functional (LR-TDDFT) formalism was employed to characterize excitation energies and spacing among electronic levels (the electronic layouts). Then, to understand the ultrafast (femtosecond) charge dynamics on the molecular scale, we relied on the nonperturbative mean-field quantum electronic dynamics via real-time (RT-) TDDFT. Three vibrational modes were selected, representative for collective nuclear movements that can have a significant influence on the electronic structure: two involving NCS- ligands and one involving dcbpy ligands. As main results, we observed that such MLCT states, under vibrational distortions, are strongly affected and a faster interligand electron transfer mechanism is observed along with an increasing MLCT character of the adiabatic electronic states approaching closer in energy due to the vibrations. Such findings can help both in providing a molecular picture of multidimensional vibro-electronic spectroscopic techniques, used to characterize ultrafast coherent and noncoherent dynamics of complex systems, and to improve dye performances with particular attention to the study of energy or charge transport processes and vibronic couplings.
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Affiliation(s)
- Edoardo Buttarazzi
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di Monte S. Angelo, Via Cintia 21, I-80126 Napoli, Italy
| | - Fulvio Perrella
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Nadia Rega
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di Monte S. Angelo, Via Cintia 21, I-80126 Napoli, Italy
- Istituto
Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario
di Monte S. Angelo ed. 6, Via Cintia, I-80126 Napoli, Italy
| | - Alessio Petrone
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di Monte S. Angelo, Via Cintia 21, I-80126 Napoli, Italy
- Istituto
Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario
di Monte S. Angelo ed. 6, Via Cintia, I-80126 Napoli, Italy
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Zouaoui-Rabah M, Bekri L, Hedidi M, Elhorri AM, Madaoui Y. Characteristics of new pyrrolic derivatives and their oligomers using DFT and TD-DFT calculations. J Mol Model 2023; 29:364. [PMID: 37945908 DOI: 10.1007/s00894-023-05763-6] [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: 08/31/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023]
Abstract
CONTEXT This article is based on the study of pyrrolic derivatives and their oligomers. Knowing that, pyrrolic derivatives are widely studied on an industrial scale. The aim of this work is to find pyrrolic derivatives having the same physicochemical characteristics such as the pyrrolic edifice. Six derivatives were studied by substituting the hydrogens in the β position of the pyrroles with the following radicals: -CHO, -Cl, -CN, -NO, and -OH. The study was carried out theoretically using ab initio and density functional of theory (DFT) methods. In the first step, molecules of four units were taken into consideration in order to make the comparison between them. This comparison showed that the majority of molecules exhibited high intramolecular charge transfer (ICT) compared to the molecule composed of four pyrrolic units (OP4), and also exhibited strong nucleophilic and electrophilic characteristics. Natural bond orbital (NBO) analysis has shown continuous ICT mechanisms for certain molecules. The studied derivatives showed good solvation in several solvents compared to OP4. The molecules substituted by the radicals -CHO, -CN, -OH, and -NO generated several peaks in the excited states, which is the opposite case for the other molecules with a single peak. The effects of chain elongation revealed exponential equations generated by the two parameters energy gaps (ΔEH-L) and maximum wavelengths (λmax) as a function of the number of units (n). These equations were used to predict the maximum and minimum values of the above parameters for more elongated oligomers. METHOD The software used to make the calculations is Gaussian 16. All geometries were calculated by B3LYP functional and 6-31++G(d,p) basis set. The electronic parameters ΔEH-L were calculated by the following functionals: B3LYP, CAM-B3LYP, LC-wPBE, LC-BLYP, wB97X, M062X, M06HF, and M11 in addition to the second-order Møller-Plesset method (MP2) while always keeping the basis set mentioned before. An effect of basis set variation was studied by the optimal functional in combination with the following basis sets: 6-31G(d,p), 6-31++G(d,p), cc-pVDZ, AUG-cc-pVDZ, 6-311G(d,p), 6-311++G(d,p), cc-pVTZ, and AUG-cc-pVTZ. The NBO study was carried out with the M06HF/6-31++G(d,p) functional using the NBO method. The solvation parameters were calculated by M06HF/6-31++G(d,p) in the presence of the implicit solvation model Solvation Model based on Density (SMD). The excited states were calculated by M06HF/6-31++G(d,p) by the implicit solvation model Conductor Polarizable Continuum Model (CPCM).
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Affiliation(s)
- Mourad Zouaoui-Rabah
- Department of Preparatory Education in Science and Technology, National Polytechnic School of Oran Maurice Audin, P.O. Box 1523, Oran, El M'naouer, Algeria
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
| | - Lahcène Bekri
- Departement of Chemistry, Faculty of Exact Sciences, Mustapha Stambouli, University of Mascara, Av. Cheikh El Khaldi, 29000, Mascara, Algeria
| | - Madani Hedidi
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
- Departement of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
| | - Abdelkader M Elhorri
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria.
- Departement of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria.
| | - Yemouna Madaoui
- Departement of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
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28
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Ovchinnikov MY, Kuzmina EV, Karaseva EV, Khursan SL, Kolosnitsyn VS. DFT Model of Elemental Sulfur in Sulfolane Solutions. J Phys Chem A 2023; 127:8971-8984. [PMID: 37862674 DOI: 10.1021/acs.jpca.3c04104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The structure and the thermodynamic and optical (UV) properties of elemental sulfur solution in sulfolane (Sl) have been studied using density functional theory methods. The cyclic molecular form of sulfur (S8 "crown") was found using PBE1PBE/6-311+G(d,p) approximation in combination with a polarizable continuum model (the integral equation formalism variant) to exist in sulfolane medium as a Sl-S8-Sl solvate. It has been theoretically established that sulfur can form stable (S8)n clusters in concentrated solutions. An increase in the extent of association (n) of the sulfur cluster leads to a decrease in the extinction coefficient [TD-DFT(TPSSTPSS/6-311+G(d,p))] of the most intense absorption maximum lying at about 50,000 cm-1 while maintaining the shape of the remaining part of the spectrum. The observed pattern qualitatively expresses the spectral regularities of solutions with different concentrations of sulfur in sulfolane. It has been proposed that a model of the absorption spectrum of elemental sulfur suggests a minor contribution of the S12 molecular form (G298°((S12)2) - G298°((S8)3) ≈ -15.5 kJ mol-1). The findings of the study will provide deeper insights into the transformation of molecular forms of sulfur and more precisely analyze processes involving sulfur as an acting species using electronic spectroscopy.
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29
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Fontes LFB, Rocha J, Silva AMS, Guieu S. Excited-State Proton Transfer in Luminescent Dyes: From Theoretical Insight to Experimental Evidence. Chemistry 2023; 29:e202301540. [PMID: 37450664 DOI: 10.1002/chem.202301540] [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: 05/16/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
The effective utilization of luminescent dyes often relies on a comprehensive understanding of their excitation and relaxation pathways. One such pathway, Excited-State Proton Transfer (ESPT), involves the tautomerization of the dye in its excited state, resulting in a new structure that exhibits distinct emission properties, such as a very large Stokes' shift or dual-emission. Although the ESPT phenomenon is well-explained theoretically, its experimental demonstration can be challenging due to the presence of numerous other phenomena that can yield similar experimental observations. In this review, we propose that an all-encompassing methodology, integrating experimental findings, computational analyses, and a thorough evaluation of diverse mechanisms, is essential for verifying the occurrence of ESPT in luminescent dyes. Investigations have offered significant understanding of the elements impacting the ESPT process and the array of approaches that can be used to validate the existence of ESPT. These discoveries hold crucial ramifications for the advancement of molecular probes, sensors, and other applications that depend on ESPT as a detection mechanism.
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Affiliation(s)
- Luís F B Fontes
- LAQV-REQUIMTE & Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
- CICECO-Aveiro Institute of Materials & Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
| | - João Rocha
- CICECO-Aveiro Institute of Materials & Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Artur M S Silva
- LAQV-REQUIMTE & Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Samuel Guieu
- LAQV-REQUIMTE & Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
- CICECO-Aveiro Institute of Materials & Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
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Breza M. On the Jahn-Teller Effect in Silver Complexes of Dimethyl Amino Phenyl Substituted Phthalocyanine. Molecules 2023; 28:7019. [PMID: 37894497 PMCID: PMC10609293 DOI: 10.3390/molecules28207019] [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: 09/09/2023] [Revised: 10/03/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The structures of Ag complexes with dimethyl amino phenyl substituted phthalocyanine m[dmaphPcAg]q of various charges q and in the two lowest spin states m were optimized using the B3LYP method within the D4h symmetry group and its subgroups. The most stable reaction intermediate in the supposed photoinitiation reaction is 3[dmaphPcAg]-. Group-theoretical analysis of the optimized structures and of their electron states reveals two symmetry-descent mechanisms. The stable structures of maximal symmetry of complexes 1[dmaphPcAg]+, 3[dmaphPcAg]+, 2[dmaphPcAg]0, and 4[dmaphPcAg]2- correspond to the D4 group as a consequence of the pseudo-Jahn-Teller effect within unstable D4h structure. Complexes 4[dmaphPcAg]0, 1[dmaphPcAg]-, 3[dmaphPcAg]-, and 2[dmaphPcAg]2- with double degenerate electron ground states in D4h symmetry structures undergo a symmetry descent to stable structures corresponding to maximal D2 symmetry, not because of a simple Jahn-Teller effect but due to a hidden pseudo-Jahn-Teller effect (strong vibronic interaction between excited electron states). The reduction of the neutral photoinitiator causes symmetry descent to its anionic intermediate because of vibronic interactions that must significantly affect the polymerization reactions.
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Affiliation(s)
- Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovakia
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31
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Gong Q, Li Y, Nie X, Liu F. Theoretical Insights into Aggregation-Induced Emission with the Ionic π Fluorophore: The Importance of Choosing the Dimer QM Model in the ONIOM Study. J Phys Chem A 2023; 127:7148-7155. [PMID: 37595363 DOI: 10.1021/acs.jpca.3c02952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
In understanding the mechanism of aggregation-induced emission (AIE), the multilevel ONIOM framework has been demonstrated as one of the efficient tools that can capture the essential mechanistic information by choosing a single fluorophore as the quantum mechanics (QM) model and putting all surrounding molecules in the low-level region. Recently, the ionic styryl-pyridine salt (namely, SPH) has been reported as a new class of AIEgen with a high fluorescence yield. In the SPH crystal, a pair of ionic SPH molecules are closely stacked with each other in an antiparallel, head-to-tail pattern, thus the choice of QM models (an individual or dimeric structure) becomes critical in the ONIOM study. Herein we report the AIE mechanism of the ionic SPH at the QM ((TD)-CAM-B3LYP) and ONIOM(QM:MM) levels. As usual, the fluorescence quenching of SPH in tetrahydrofuran (THF) solution is attributed to a nonradiative relaxation via the central C═C bond rotation, with a rather low barrier of 2.7 kcal/mol. In crystals, either with a monomer or dimer model, the fluorescence quenching channel is found to be restricted due to the obvious C═C rotation barriers. Compared with the monomer model, the dimer model, by treating the orbital interaction of the two SPH molecules at the QM level, provides significantly increased barriers and a red-shifted emission wavelength that better matches the experimental value. In addition, the calculated exciton coupling in the fluorescence emission state can be discovered only by a dimer model. The findings here emphasize not only the importance of choosing a proper model in the ONIOM study of AIE but also expanding our understanding of novel AIE systems.
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Affiliation(s)
- Qianqian Gong
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710062, P. R. China
| | - Yazhen Li
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710062, P. R. China
| | - Xiaoke Nie
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710062, P. R. China
| | - Fengyi Liu
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710062, P. R. China
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32
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McGarry RJ, Varvarezos L, Pryce MT, Long C. Excited-State Dynamics Leading Either to Triplet Formation or Coordinative Expansion following Photolysis of Cu(II)-Porphyrins: A DFT, TD-DFT, Luminescence and Femtosecond Time-Resolved Absorbance Study. Molecules 2023; 28:6310. [PMID: 37687139 PMCID: PMC10488807 DOI: 10.3390/molecules28176310] [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: 07/18/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The photophysical properties of Cu(II) complexes with 5,10,15,20-meso-tetrakis(phenyl)porphyrin and 5,10,15,20-meso-tetrakis(N-methylpyridium-4-yl)porphyrin are examined via the luminescence and femtosecond time-resolved absorbance methods, respectively. These studies are supported by DFT and TD-DFT calculations, which highlight the important role played by ligand-to-metal charge-transfer states in directing the system toward either intersystem crossing to the triplet hypersurface or coordinative expansion to a five-coordinate quasi-stable intermediate. The latter processes occur when the porphyrin is photolyzed in the presence of suitably located Lewis bases. Femtosecond time-resolved absorbance measurements of Cu(II)-5,10,15,20-meso-tetrakis(N-methylpyridium-4-yl)porphyrin confirm that the coordinative expansion in water occurs in approximately 700 fs, while crossing to the triplet hypersurface takes approximately 140 fs in the same solvent. These processes are mutually exclusive, although both can occur simultaneously depending on the environment of the porphyrin. The ratio of the two processes depends on the relative orientation of the Lewis base with respect to the copper atom at the time of excitation. As a consequence, copper porphyrins such as these are excellent probes in the environment of the porphyrin and can be used to identify the location of the porphyrin when interacting with DNA fragments.
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Affiliation(s)
- Ross J. McGarry
- School of Chemical Sciences, Dublin City University, D09 V209 Dublin, Ireland; (R.J.M.); (M.T.P.)
| | - Lazaros Varvarezos
- School of Physical Sciences, Dublin City University, D09 V209 Dublin, Ireland;
| | - Mary T. Pryce
- School of Chemical Sciences, Dublin City University, D09 V209 Dublin, Ireland; (R.J.M.); (M.T.P.)
| | - Conor Long
- School of Chemical Sciences, Dublin City University, D09 V209 Dublin, Ireland; (R.J.M.); (M.T.P.)
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Štellerová D, Lukeš V, Breza M. On the Potential Role of the (Pseudo-) Jahn-Teller Effect in the Membrane Transport Processes: Enniatin B and Beauvericin. Molecules 2023; 28:6264. [PMID: 37687093 PMCID: PMC10488337 DOI: 10.3390/molecules28176264] [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: 08/09/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
The molecular structure of mycotoxins enniatin B and beauvericin, which are used as ionophores, was studied using density functional theory in various symmetry groups and singly charged states. We have shown that the charge addition or removal causes significant structural changes. Unlike the neutral C3 molecules, the stability of the charged C1 structures was explained by the Jahn-Teller or Pseudo-Jahn-Teller effect. This finding agrees with the available experimental X-ray structures of their metal complexes where electron density transfer from the metal can be expected. Hence, the membrane permeability of metal sandwich-structure complexes possessing antimicrobial activities is modulated by the conformational changes.
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Affiliation(s)
| | | | - Martin Breza
- Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology in Bratislava (STU), Radlinskeho 9, SK-81237 Bratislava, Slovakia; (D.Š.); (V.L.)
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34
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Bousquet MHE, Papineau TV, Veys K, Escudero D, Jacquemin D. Extensive Analysis of the Parameters Influencing Radiative Rates Obtained through Vibronic Calculations. J Chem Theory Comput 2023; 19:5525-5547. [PMID: 37494031 DOI: 10.1021/acs.jctc.3c00191] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Defining a theoretical model systematically delivering accurate ab initio predictions of the fluorescence quantum yields of organic dyes is highly desirable for designing improved fluorophores in a systematic rather than trial-and-error way. To this end, the first required step is to obtain reliable radiative rates (kr), as low kr typically precludes effective emission. In the present contribution, using a series of 10 substituted phenyls with known experimental kr, we analyze the impact of the computational protocol on the kr determined through the thermal vibration correlation function (TVCF) approach on the basis of time-dependent density functional theory (TD-DFT) calculations of the energies, structures, and vibrational parameters. Both the electronic structure (selected exchange-correlation functional, application or not of the Tamm-Dancoff approximation) and the vibronic parameters (line-shape formalism, coordinate system, potential energy surface model, and dipole expansion) are tackled. Considering all possible combinations yields more than 3500 cases, allowing to extract statistically-relevant information regarding the impact of each computational parameter on the magnitude of the estimated kr. It turns out that the selected vibronic model can have a significant impact on the computed kr, especially the potential energy surface model. This effect is of the same order of magnitude as the difference noted between B3LYP and CAM-B3LYP estimates. For the treated compounds, all evaluated functionals do deliver reasonable trends, fitting the experimental values.
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Affiliation(s)
| | | | - Koen Veys
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
| | | | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
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Rajh T, Masson E, Latt KZ, Smith A, Brugh AM, Dandu N, Trainer D, Curtiss LA, Ngo AT, Hla SW. Light- and Chemical-Doping-Induced Magnetic Behavior of Eu Molecular Systems. Inorg Chem 2023; 62:12721-12729. [PMID: 37506323 DOI: 10.1021/acs.inorgchem.3c01154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Variable temperature electron paramagnetic resonance (VT-EPR) was used to investigate the role of the environment and oxidation states of several coordinated Eu compounds. We find that while Eu(III) chelating complexes are diamagnetic, simple chemical reduction results in the formation of paramagnetic species. In agreement with the distorted D3h symmetry of Eu molecular complexes investigated in this study, the EPR spectrum of reduced complexes showed axially symmetric signals (g⊥ = 2.001 and g∥ = 1.994) that were successfully simulated with two Eu isotopes with nuclear spin 5/2 (151Eu and 153Eu with 48% and 52% natural abundance, respectively) and nuclear g-factors 151Eu/153Eu = 2.27. Illumination of water-soluble complex Eu(dipic)3 at 4 K led to the ligand-to-metal charge transfer (LMCT) that resulted in the formation of Eu(II) in a rhombic environment (gx = 2.006, gy = 1.995, gz = 1.988). The existence of LMCT affects the luminescence of Eu(dipic)3, and pre-reduction of the complex to Eu(II)(dipic)3 reversibly reduces red luminescence with the appearance of a weak CT blue luminescence. Furthermore, encapsulation of a large portion of the dipic ligand with Cucurbit[7]uril, a pumpkin-shaped macrocycle, inhibited ligand-to-metal charge transfer, preventing the formation of Eu(II) upon illumination.
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Affiliation(s)
- Tijana Rajh
- Nanoscience and Technology Division, Argonne National Laboratory, 9700 S Cass Ave, Argonne, Illinois 60540, United States
- School of Molecular Sciences, Arizona State University, 551 E University Dr, Tempe, Arizona 85281, United States
| | - Eric Masson
- Department of Chemistry, Ohio University, Athens, Ohio 45701, United States
| | - Kyaw Zin Latt
- Nanoscience and Technology Division, Argonne National Laboratory, 9700 S Cass Ave, Argonne, Illinois 60540, United States
| | - Ashton Smith
- Department of Chemistry, Ohio University, Athens, Ohio 45701, United States
| | - Alexander M Brugh
- School of Molecular Sciences, Arizona State University, 551 E University Dr, Tempe, Arizona 85281, United States
| | - Naveen Dandu
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60608, United States
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Daniel Trainer
- Nanoscience and Technology Division, Argonne National Laboratory, 9700 S Cass Ave, Argonne, Illinois 60540, United States
| | - Larry A Curtiss
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Anh T Ngo
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60608, United States
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Saw-Wai Hla
- Nanoscience and Technology Division, Argonne National Laboratory, 9700 S Cass Ave, Argonne, Illinois 60540, United States
- Nanoscale & Quantum Phenomena Institute, and Department of Physics & Astronomy, Ohio University, Athens, Ohio 45701, United States
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36
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O'Connor MS, Bragg ZT, Dearworth JR, Hendrickson HP. Quantum Mechanics/Molecular mechanics calculations predict A1, not A2, is present in melanopsin (Opn4m) of red-eared slider turtles (Trachemys scripta elegans). Vision Res 2023; 209:108245. [PMID: 37290221 DOI: 10.1016/j.visres.2023.108245] [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: 01/12/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 06/10/2023]
Abstract
Melanopsin is a photopigment that plays a role in non-visual, light-driven, cellular processes such as modulation of circadian rhythms, retinal vascular development, and the pupillary light reflex (PLR). In this study, computational methods were used to understand which chromophore is harbored by melanopsin in red-eared slider turtles (Trachemys scripta elegans). In mammals, the vitamin A derivative 11-cis-retinal (A1) is the chromophore, which provides functionality for melanopsin. However, in red-eared slider turtles, a member of the reptilian class, the identity of the chromophore remains unclear. Red-eared slider turtles, similar to other freshwater vertebrates, possess visual pigments that harbor a different vitamin A derivative, 11-cis-3,4-didehydroretinal (A2), making their pigments more sensitive to red-light than blue-light, therefore, suggesting the chromophore to be the A2 derivative instead of the A1. To help resolve the chromophore identity, in this work, computational homology models of melanopsin in red-eared slider turtles were first constructed. Next, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to compare how A1 and A2 derivatives bind to melanopsin. Time dependent density functional theory (TDDFT) calculations were then used to determine the excitation energy of the pigments. Lastly, calculated excitation energies were compared to experimental spectral sensitivity data from responses by the irises of red-eared sliders. Contrary to what was expected, our results suggest that melanopsin in red-eared slider turtles is more likely to harbor the A1 chromophore than the A2. Furthermore, a glutamine (Q622.56) and tyrosine (Y853.28) residue in the chromophore binding pocket are shown to play a role in the spectral tuning of the chromophore.
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Affiliation(s)
- Michael S O'Connor
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States
| | - Zoey T Bragg
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States
| | - James R Dearworth
- Department of Biology, Lafayette College, Easton, PA 18042, United States
| | - Heidi P Hendrickson
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States.
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37
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Maranzana A, Tonachini G. Mechanism of the Photochemical Isomerization and Oxidation of 2-Butenedial: A Theoretical Study. Molecules 2023; 28:4994. [PMID: 37446656 DOI: 10.3390/molecules28134994] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Under tropospheric conditions, 2-butenedial is photochemically removed to produce secondary organic aerosol. Upon solar irradiation in the lower troposphere, the main photochemical products are ketene-enol (a key intermediate product), furanones, and maleic anhydride. The oxidative reaction mechanism was studied using the multireference method CASSCF to explore the hypersurface of the two most accessible singlet excited states, and by DFT for the ground state. Photoisomerization of 2-butenedial in the first excited state directly produces ground state ketene-enol upon nonradiative relaxation. From this intermediate, furan-2-ol and successively 3H-furan-2-one and 5H-furan-2-one are formed. The cooperative effect of two water molecules is essential to catalyze the cyclization of ketene-enol to furan-2-ol, followed by hydrogen transfers to furanones. Two water molecules are also necessary to form maleic anhydride from furan-2-ol. For this last reaction, in which one extra oxygen must be acquired, we hypothesize a mechanism with singlet oxygen as the oxidant.
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Affiliation(s)
- Andrea Maranzana
- Dipartimento di Chimica, Università di Torino, Corso Massimo D'Azeglio 48, I-10125 Torino, Italy
| | - Glauco Tonachini
- Dipartimento di Chimica, Università di Torino, Corso Massimo D'Azeglio 48, I-10125 Torino, Italy
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38
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Rajapaksha IN, Wang J, Leszczynski J, Scott CN. Investigating the Effects of Donors and Alkyne Spacer on the Properties of Donor-Acceptor-Donor Xanthene-Based Dyes. Molecules 2023; 28:4929. [PMID: 37446594 DOI: 10.3390/molecules28134929] [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: 05/04/2023] [Revised: 06/08/2023] [Accepted: 06/18/2023] [Indexed: 07/15/2023] Open
Abstract
NIR dyes have become popular for many applications, including biosensing and imaging. For this reason, the molecular switch mechanism of the xanthene dyes makes them useful for in vivo detection and imaging of bioanalytes. Our group has been designing NIR xanthene-based dyes by the donor-acceptor-donor approach; however, the equilibrium between their opened and closed forms varies depending on the donors and spacer. We synthesized donor-acceptor-donor NIR xanthene-based dyes with an alkyne spacer via the Sonogashira coupling reaction to investigate the effects of the alkyne spacer and the donors on the maximum absorption wavelength and the molecular switching (ring opening) process of the dyes. We evaluated the strength and nature of the donors and the presence and absence of the alkyne spacer on the properties of the dyes. It was shown that the alkyne spacer extended the conjugation of the dyes, leading to absorption wavelengths of longer values compared with the dyes without the alkyne group. In addition, strong charge transfer donors shifted the absorption wavelength towards the NIR region, while donors with strong π-donation resulted in xanthene dyes with a smaller equilibrium constant. DFT/TDDFT calculations corroborated the experimental data in most of the cases. Dye 2 containing the N,N-dimethylaniline group gave contrary results and is being further investigated.
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Affiliation(s)
- Ishanka N Rajapaksha
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jing Wang
- Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA
| | - Jerzy Leszczynski
- Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA
| | - Colleen N Scott
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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Shtepliuk I. A DFT Study of Phosphate Ion Adsorption on Graphene Nanodots: Implications for Sensing. SENSORS (BASEL, SWITZERLAND) 2023; 23:5631. [PMID: 37420797 DOI: 10.3390/s23125631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/09/2023]
Abstract
The optical properties of graphene nanodots (GND) and their interaction with phosphate ions have been investigated to explore their potential for optical sensing applications. The absorption spectra of pristine GND and modified GND systems were analyzed using time-dependent density functional theory (TD-DFT) calculation investigations. The results revealed that the size of adsorbed phosphate ions on GND surfaces correlated with the energy gap of the GND systems, leading to significant modifications in their absorption spectra. The introduction of vacancies and metal dopants in GND systems resulted in variations in the absorption bands and shifts in their wavelengths. Moreover, the absorption spectra of GND systems were further altered upon the adsorption of phosphate ions. These findings provide valuable insights into the optical behavior of GND and highlight their potential for the development of sensitive and selective optical sensors for phosphate detection.
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Affiliation(s)
- Ivan Shtepliuk
- Semiconductor Materials Division, Department of Physics, Chemistry and Biology-IFM, Linköping University, S-58183 Linköping, Sweden
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40
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Dalmau D, Crespo O, Matxain JM, Urriolabeitia EP. Fluorescence Amplification of Unsaturated Oxazolones Using Palladium: Photophysical and Computational Studies. Inorg Chem 2023. [PMID: 37315074 DOI: 10.1021/acs.inorgchem.3c00601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Weakly fluorescent (Z)-4-arylidene-5-(4H)-oxazolones (1), ΦPL < 0.1%, containing a variety of conjugated aromatic fragments and/or charged arylidene moieties, have been orthopalladated by reaction with Pd(OAc)2. The resulting dinuclear complexes (2) have the oxazolone ligands bonded as a C^N-chelate, restricting intramolecular motions involving the oxazolone. From 2, a variety of mononuclear derivatives, such as [Pd(C^N-oxazolone)(O2CCF3)(py)] (3), [Pd(C^N-oxazolone)(py)2](ClO4) (4), [Pd(C^N-oxazolone)(Cl)(py)] (5), and [Pd(C^N-oxazolone)(X)(NHC)] (6, 7), have been prepared and fully characterized. Most of complexes 3-6 are strongly fluorescent in solution in the range of wavelengths from green to yellow, with values of ΦPL up to 28% (4h), which are among the highest values of quantum yield ever reported for organometallic Pd complexes with bidentate ligands. This means that the introduction of the Pd in the oxazolone scaffold produces in some cases an amplification of the fluorescence of several orders of magnitude from the free ligand 1 to complexes 3-6. Systematic variations of the substituents of the oxazolones and the ancillary ligands show that the wavelength of emission is tuned by the nature of the oxazolone, while the quantum yield is deeply influenced by the change of ligands. TD-DFT studies of complexes 3-6 show a direct correlation between the participation of the Pd orbitals in the HOMO and the loss of emission through non-radiative pathways. This model allows the understanding of the amplification of the fluorescence and the future rational design of new organopalladium systems with improved properties.
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Affiliation(s)
- David Dalmau
- Instituto de Síntesis Química y Catálisis Homogénea, ISQCH (CSIC-Universidad de Zaragoza), Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Olga Crespo
- Instituto de Síntesis Química y Catálisis Homogénea, ISQCH (CSIC-Universidad de Zaragoza), Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Jon M Matxain
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU and Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Euskadi, Spain
| | - Esteban P Urriolabeitia
- Instituto de Síntesis Química y Catálisis Homogénea, ISQCH (CSIC-Universidad de Zaragoza), Pedro Cerbuna 12, 50009 Zaragoza, Spain
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41
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Zhao XR, Sun XR, Zhang XJ, Wu XW, Cheng B, Ni DX, Huang JB, Zhang RH, Li XL, Xiao WL. Nudifloids A-N, structurally diverse 3,4-seco-labdane diterpenoids from Callicarpa nudiflora with inflammatory inhibitory activity. PHYTOCHEMISTRY 2023; 210:113665. [PMID: 37044361 DOI: 10.1016/j.phytochem.2023.113665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Fourteen undescribed seco-type diterpenoids, named nudifloids A-N, together with ten known analogs, were isolated from the leaves of Callicarpa nudiflora. Nudifloids A-N had a characteristic 3,4-seco-labdane-type diterpenoid skeleton, whereas nudifloids A-C and K-N were 3,4-seco-norditerpenoids. Nudifloid A was the first example of a 3,4-seco-12,13,14,15,16-quartnor-labdane diterpenoid, with a seven-membered lactone ring formed through esterification between C-3 and C-11. Nudifloids B and C were a pair of highly modified 3,4-seco-labdane nor-diterpenoid epimers, of which C-2 and C-18 were cyclized together to form a cyclohexene fragment. The structures of these undescribed diterpenoids were established by spectroscopic analysis and reference data. The anti-inflammatory activity of diterpenoids in rich yield was evaluated by analyzing the inhibition of lipopolysaccharide plus nigericin-induced pyroptosis in J774A.1 cells. Nudifloids D and E exhibited prominent anti-NLRP3 inflammasome activity, with IC50 values of 1.80 and 1.59 μM, respectively. Cell permeability assays revealed that nudifloid D inhibited pyroptosis, which could ameliorate inflammation by blocking the activation of the NLRP3 inflammasome.
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Affiliation(s)
- Xue-Rong Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Xiao-Rong Sun
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Xing-Jie Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Xue-Wen Wu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Bin Cheng
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Dong-Xuan Ni
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Jia-Bi Huang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Rui-Han Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Xiao-Li Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China.
| | - Wei-Lie Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China.
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42
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Pieńkos M, Zadykowicz B. What Other Than Acridinium Esters? Computational Search for New Acridinium-Based Chemiluminogens. Int J Mol Sci 2023; 24:ijms24119468. [PMID: 37298422 DOI: 10.3390/ijms24119468] [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: 05/09/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
The rapid increase in disease prevalence in the world makes it extremely important to search for new or develop existing diagnostic methods, for example, chemiluminescent labeling used in immunodiagnostics. At present, acridinium esters are willingly used as chemiluminogenic fragments of labels. However, the search for new chemiluminogens that are particularly efficient is the main task of our studies. The density functional theory (DFT) and time-dependent (TD) DFT methods were used to obtain thermodynamic and kinetic results concerning the chemiluminescence and competitive dark reactions, which indicated whether some of the scrutinized derivatives have better characteristics than the chemiluminogens used so far. Synthesis of these candidates for efficient chemiluminogens, followed by studies of their chemiluminescent properties, and ultimately in chemiluminescent labeling, are further steps to confirm their potential applicability in immunodiagnostics.
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Affiliation(s)
- Milena Pieńkos
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Beata Zadykowicz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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43
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Pimenov OA, Grazhdan KV, Zavalishin MN, Gamov GA. Geometry and UV-Vis Spectra of Au 3+ Complexes with Hydrazones Derived from Pyridoxal 5'-Phosphate: A DFT Study. Int J Mol Sci 2023; 24:ijms24098412. [PMID: 37176119 PMCID: PMC10179053 DOI: 10.3390/ijms24098412] [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: 04/20/2023] [Revised: 05/05/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023] Open
Abstract
Gold(III) complexes with different ligands can provide researchers with a measure against pathogenic microorganisms with antibiotic resistance. We reported in our previous paper that the UV-Vis spectra of different protonated species of complexes formed by gold(III) and five hydrazones derived from pyridoxal 5'-phosphate are similar to each other and to the spectra of free protonated hydrazones. The present paper focuses on the reasons of the noted similarity in electron absorption spectra. The geometry of different protonated species of complexes of gold(III) and hydrazones (15 structures in total) was optimized using the density functional theory (DFT). The coordination polyhedron of gold(III) bond critical points were further studied to identify the symmetry of the gold coordination sphere and the type of interactions that hold the complex together. The UV-Vis spectra were calculated using TD DFT methods. The molecular orbitals were analyzed to interpret the calculated spectra.
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Affiliation(s)
- Oleg A Pimenov
- General Chemical Technology Department, Ivanovo State University of Chemistry and Technology, Sheremetevskii pr. 7, 153000 Ivanovo, Russia
| | - Konstantin V Grazhdan
- General Chemical Technology Department, Ivanovo State University of Chemistry and Technology, Sheremetevskii pr. 7, 153000 Ivanovo, Russia
| | - Maksim N Zavalishin
- General Chemical Technology Department, Ivanovo State University of Chemistry and Technology, Sheremetevskii pr. 7, 153000 Ivanovo, Russia
| | - George A Gamov
- General Chemical Technology Department, Ivanovo State University of Chemistry and Technology, Sheremetevskii pr. 7, 153000 Ivanovo, Russia
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44
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Bhat V, Callaway CP, Risko C. Computational Approaches for Organic Semiconductors: From Chemical and Physical Understanding to Predicting New Materials. Chem Rev 2023. [PMID: 37141497 DOI: 10.1021/acs.chemrev.2c00704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
While a complete understanding of organic semiconductor (OSC) design principles remains elusive, computational methods─ranging from techniques based in classical and quantum mechanics to more recent data-enabled models─can complement experimental observations and provide deep physicochemical insights into OSC structure-processing-property relationships, offering new capabilities for in silico OSC discovery and design. In this Review, we trace the evolution of these computational methods and their application to OSCs, beginning with early quantum-chemical methods to investigate resonance in benzene and building to recent machine-learning (ML) techniques and their application to ever more sophisticated OSC scientific and engineering challenges. Along the way, we highlight the limitations of the methods and how sophisticated physical and mathematical frameworks have been created to overcome those limitations. We illustrate applications of these methods to a range of specific challenges in OSCs derived from π-conjugated polymers and molecules, including predicting charge-carrier transport, modeling chain conformations and bulk morphology, estimating thermomechanical properties, and describing phonons and thermal transport, to name a few. Through these examples, we demonstrate how advances in computational methods accelerate the deployment of OSCsin wide-ranging technologies, such as organic photovoltaics (OPVs), organic light-emitting diodes (OLEDs), organic thermoelectrics, organic batteries, and organic (bio)sensors. We conclude by providing an outlook for the future development of computational techniques to discover and assess the properties of high-performing OSCs with greater accuracy.
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Affiliation(s)
- Vinayak Bhat
- Department of Chemistry & Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Connor P Callaway
- Department of Chemistry & Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Chad Risko
- Department of Chemistry & Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506-0055, United States
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45
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Antony A, Thomas T, Augustine C. On the coordination chemistry of a bacterial siderophore cepabactin from a theoretical perspective. J Mol Model 2023; 29:167. [PMID: 37126124 DOI: 10.1007/s00894-023-05565-w] [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: 07/19/2022] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Iron is one of the essential metals required by almost all living organisms. However, nature has certain constraints in distributing this element among tissues. Since polymeric oxide-bridged Fe (III) is the prominent source of Fe (III) ions, the insolubility of Fe (III) ions in aqueous systems reduces the direct uptake by cells. Secondly, the free-Fe entities which generate .OH radicals pave the way to the destruction of the cells. Hence, a protective coordination environment via sophisticated chemical systems is required for the acquisition of Fe, its successive transport, storage, and effective utilization in various tissues. Siderophores are polydentate ligands used by bacterial cells for Fe acquisition, with a relatively high affinity for Fe (III) ions. Secreted from the bacterial cells into the external aqueous medium, they sequester Fe to give a soluble complex which re-enters the organism at a specific receptor. Once it gets inside the cell, the Fe is released from the complex and utilized for essential biochemical reactions. The medicinal applications of these natural ligands, developing progressively in various research groups, necessitate the theoretical aspects of their coordination chemistry. This research paper deals with the coordination chemistry of one of the siderophores, cepabactin (Cep). The chemical computations confirm that the FeIII(Cep)3 complex is octahedral and high spin. The oxygen atoms of Cep, which are hard and negatively charged, thus act as electron donors in the FeIII(Cep)3 complex formation. This in turn makes the siderophores relatively less attractive towards Fe (II) ions.
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Affiliation(s)
- Arsha Antony
- Department of Chemistry, St. Berchmans College, Mahatma Gandhi University, Kottayam, India
| | - Tiju Thomas
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Cyril Augustine
- Department of Chemistry, St. Berchmans College, Mahatma Gandhi University, Kottayam, India.
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46
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Odachowski M, Neven R, Perversi G, Romano D, Slabber CA, Hadiji M, Honing M, Zhao Y, Munro OQ, Blom B. Ionic mononuclear [Fe] and heterodinuclear [Fe,Ru] bis(diphenylphosphino)alkane complexes: Synthesis, spectroscopy, DFT structures, cytotoxicity, and biomolecular interactions. J Inorg Biochem 2023; 242:112156. [PMID: 36801621 DOI: 10.1016/j.jinorgbio.2023.112156] [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: 11/11/2022] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/06/2023]
Abstract
Iron(II) and Ru(II) half-sandwich compounds encompass some promising pre-clinical anticancer agents whose efficacy may be tuned by structural modification of the coordinated ligands. Here, we combine two such bioactive metal centres in cationic bis(diphenylphosphino)alkane-bridged heterodinuclear [Fe2+, Ru2+] complexes to delineate how ligand structural variations modulate compound cytotoxicity. Specifically, Fe(II) complexes of the type [(η5-C5H5)Fe(CO)2(κ1-PPh2(CH2)nPPh2)]{PF6} (n = 1-5), compounds 1-5, and heterodinuclear [Fe2+, Ru2+] complexes, [(η5-C5H5)Fe(CO)2(μ-PPh2(CH2)nPPh2))(η6-p-cymene)RuCl2]{PF6} (n = 2-5) (compounds 7-10), were synthesized and characterised. The mononuclear complexes were moderately cytotoxic against two ovarian cancer cell lines (A2780 and cisplatin resistant A2780cis) with IC50 values ranging from 2.3 ± 0.5 μM to 9.0 ± 1.4 μM. For 7-10, the cytotoxicity increased with increasing Fe⋅⋅⋅Ru distance, consistent with their DNA affinity. UV-visible spectroscopy suggested the chloride ligands in heterodinuclear 8-10 undergo stepwise substitution by water on the timescale of the DNA interaction experiments, probably affording the species [RuCl(OH2)(η6-p-cymene)(PRPh2)]2+ and [Ru(OH)(OH2)(η6-p-cymene)(PRPh2)]2+ (where PRPh2 has R = [-(CH2)5PPh2-Fe(C5H5)(CO)2]+). One interpretation of the combined DNA-interaction and kinetic data is that the mono(aqua) complex may interact with dsDNA through nucleobase coordination. Heterodinuclear 10 reacts with glutathione (GSH) to form stable mono- and bis(thiolate) adducts, 10-SG and 10-SG2, with no evidence of metal ion reduction (k1 = 1.07 ± 0.17 × 10-1 min-1 and k2 = 6.04 ± 0.59 × 10-3 min-1 at 37 °C). This work highlights the synergistic effect of the Fe2+/Ru2+ centres on both the cytotoxicity and biomolecular interactions of the present heterodinuclear complexes.
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Affiliation(s)
- Matylda Odachowski
- Maastricht Science Programme, Faculty of Science and Engineering, Maastricht University, Paul Henri Spaaklaan 1, 6229 EN Maastricht, The Netherlands
| | - Robin Neven
- Maastricht Science Programme, Faculty of Science and Engineering, Maastricht University, Paul Henri Spaaklaan 1, 6229 EN Maastricht, The Netherlands
| | - Giuditta Perversi
- Maastricht Science Programme, Faculty of Science and Engineering, Maastricht University, Paul Henri Spaaklaan 1, 6229 EN Maastricht, The Netherlands
| | - Dario Romano
- King Abdullah University of Science and Technology, Department of Chemical Sciences, Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Cathryn A Slabber
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO WITS 2050 Johannesburg, South Africa
| | - Mouna Hadiji
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH1015 Lausanne, Switzerland
| | - Maarten Honing
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry Maastricht University, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
| | - Yuandi Zhao
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry Maastricht University, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
| | - Orde Q Munro
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO WITS 2050 Johannesburg, South Africa.
| | - Burgert Blom
- Maastricht Science Programme, Faculty of Science and Engineering, Maastricht University, Paul Henri Spaaklaan 1, 6229 EN Maastricht, The Netherlands.
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Weight BM, Sifain AE, Gifford BJ, Htoon H, Tretiak S. On-the-Fly Nonadiabatic Dynamics Simulations of Single-Walled Carbon Nanotubes with Covalent Defects. ACS NANO 2023; 17:6208-6219. [PMID: 36972076 DOI: 10.1021/acsnano.2c08579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) with covalent surface defects have been explored recently due to their promise for use in single-photon telecommunication emission and in spintronic applications. The all-atom dynamic evolution of electrostatically bound excitons (the primary electronic excitations) in these systems has only been loosely explored from a theoretical perspective due to the size limitations of these large systems (>500 atoms). In this work, we present computational modeling of nonradiative relaxation in a variety of SWCNT chiralities with single-defect functionalizations. Our excited-state dynamics modeling uses a trajectory surface hopping algorithm accounting for excitonic effects with a configuration interaction approach. We find a strong chirality and defect-composition dependence on the population relaxation (varying over 50-500 fs) between the primary nanotube band gap excitation E11 and the defect-associated, single-photon-emitting E11* state. These simulations give direct insight into the relaxation between the band-edge states and the localized excitonic state, in competition with dynamic trapping/detrapping processes observed in experiment. Engineering fast population decay into the quasi-two-level subsystem with weak coupling to higher-energy states increases the effectiveness and controllability of these quantum light emitters.
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Affiliation(s)
- Braden M Weight
- Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, United States
- Center for Integrated Nanotechnologies, Center for Nonlinear Studies, and Theoretical Division Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Andrew E Sifain
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540 United States
| | - Brendan J Gifford
- Center for Integrated Nanotechnologies, Center for Nonlinear Studies, and Theoretical Division Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Han Htoon
- Center for Integrated Nanotechnologies, Center for Nonlinear Studies, and Theoretical Division Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sergei Tretiak
- Center for Integrated Nanotechnologies, Center for Nonlinear Studies, and Theoretical Division Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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48
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Petrusevich EF, Bousquet MHE, Ośmiałowski B, Jacquemin D, Luis JM, Zaleśny R. Cost-Effective Simulations of Vibrationally-Resolved Absorption Spectra of Fluorophores with Machine-Learning-Based Inhomogeneous Broadening. J Chem Theory Comput 2023; 19:2304-2315. [PMID: 37096370 PMCID: PMC10134414 DOI: 10.1021/acs.jctc.2c01285] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
The results of electronic and vibrational structure simulations are an invaluable support for interpreting experimental absorption/emission spectra, which stimulates the development of reliable and cost-effective computational protocols. In this work, we contribute to these efforts and propose an efficient first-principle protocol for simulating vibrationally-resolved absorption spectra, including nonempirical estimations of the inhomogeneous broadening. To this end, we analyze three key aspects: (i) a metric-based selection of density functional approximation (DFA) so to benefit from the computational efficiency of time-dependent density function theory (TD-DFT) while safeguarding the accuracy of the vibrationally-resolved spectra, (ii) an assessment of two vibrational structure schemes (vertical gradient and adiabatic Hessian) to compute the Franck-Condon factors, and (iii) the use of machine learning to speed up nonempirical estimations of the inhomogeneous broadening. In more detail, we predict the absorption band shapes for a set of 20 medium-sized fluorescent dyes, focusing on the bright ππ★ S0 → S1 transition and using experimental results as references. We demonstrate that, for the studied 20-dye set which includes structures with large structural variability, the preselection of DFAs based on an easily accessible metric ensures accurate band shapes with respect to the reference approach and that range-separated functionals show the best performance when combined with the vertical gradient model. As far as band widths are concerned, we propose a new machine-learning-based approach for determining the inhomogeneous broadening induced by the solvent microenvironment. This approach is shown to be very robust offering inhomogeneous broadenings with errors as small as 2 cm-1 with respect to genuine electronic-structure calculations, with a total CPU time reduced by 98%.
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Affiliation(s)
- Elizaveta F. Petrusevich
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | | | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University, Gagarina Street 7, PL-87-100 Toruń, Poland
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Josep M. Luis
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | - Robert Zaleśny
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
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49
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Antón-Cánovas T, Achelle S, Paz Fernández-Liencres M, Navarro A, Alonso F, Rodríguez-López J. Acidochromism of amino-substituted indolizine chromophores: towards white light emission. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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50
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Dewangan S, Mishra A, Halder B, Mishra A, Dhiman R, Chatterjee S. Unsymmetrically bi-functionalized 1,1’-ferrocenyl bi-hydrazone and hydrazone-cyanovinyl molecules as fluorescent “on-off” sensor: Synthesis, cytotoxicity and cancer cell imaging behavior. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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