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Han R, Mattiat J, Luber S. Automatic purpose-driven basis set truncation for time-dependent Hartree-Fock and density-functional theory. Nat Commun 2023; 14:106. [PMID: 36609507 PMCID: PMC9822955 DOI: 10.1038/s41467-022-35694-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/14/2022] [Indexed: 01/09/2023] Open
Abstract
Real-time time-dependent density-functional theory (RT-TDDFT) and linear response time-dependent density-functional theory (LR-TDDFT) are two important approaches to simulate electronic spectra. However, the basis sets used in such calculations are usually the ones designed mainly for electronic ground state calculations. In this work, we propose a systematic and robust scheme to truncate the atomic orbital (AO) basis set employed in TDDFT and TD Hartree-Fock (TDHF) calculations. The truncated bases are tested for both LR- and RT-TDDFT as well as RT-TDHF approaches, and provide an acceleration up to an order of magnitude while the shifts of excitation energies of interest are generally within 0.2 eV. The procedure only requires one extra RT calculation with 1% of the total propagation time and a simple modification on basis set file, which allows an instant application in any quantum chemistry package supporting RT-/LR-TDDFT calculations. Aside from the reduced computational effort, this approach also offers valuable insight into the effect of different basis functions on computed electronic excitations and further ideas on the design of basis sets for special purposes.
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Affiliation(s)
- Ruocheng Han
- grid.7400.30000 0004 1937 0650Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Johann Mattiat
- grid.7400.30000 0004 1937 0650Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Sandra Luber
- grid.7400.30000 0004 1937 0650Department of Chemistry, University of Zurich, Zurich, Switzerland
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Yuan ZH, Zhang XP, Guan J, Chen LL, Li SK, Liu M, Qin YJ, Yang YS, Zhu HL. Introducing ortho-methoxyl group as a fluorescence-enhancing and bathochromic-shift bi-functional strategy for typical cysteine sensors. Talanta 2020; 219:121217. [PMID: 32887118 DOI: 10.1016/j.talanta.2020.121217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 11/29/2022]
Abstract
A practical strategy of introducing ortho-methoxyl group was explored to achieve the fluorescence-enhancing and bathochromic-shift bi-functional optimization. It was tested in the Cys sensing ISOPH-X series, thus the successful case, ISOPH-2, was obtained. It realized the optimization in a simple and compatible way. The corresponding strategy was basically established during the confirmation of checkpoints including applicable steadiness (over 24 h), wide pH range (7.0-9.0), rapid response (20 min), good biocompatibility, high sensitivity (LOD = 0.072 nm), high selectivity and biological monitoring of Cys in living cells as well as C. elegans. In this work, the o-methoxyl introduction strategy led to a 15 nm red shift and a near 4-fold fluorescence enhancement. This strategy could be combined with the double bond-introducing approach. Compared with reported strategies, by breaking the dilemma between red shift and strong fluorescent intensity, this strategy might offer beneficial information for exploiting better sensors with more fluorophores and mechanisms for their targets.
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Affiliation(s)
- Zeng-Hui Yuan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xu-Ping Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Guan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Li-Li Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shu-Kai Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ming Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ya-Juan Qin
- Department of Medicinal Chemistry, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Yu-Shun Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Cabir B, Yildiko U, Ağırtaş MS, Horoz S. Computational DFT calculations, photovoltaic properties and synthesis of (2R, 3S)-2, 3, 4-trihydroxybutoxy substituted phthalocyanines. INORG NANO-MET CHEM 2020. [DOI: 10.1080/24701556.2020.1725051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Beyza Cabir
- Department of Chemistry, Faculty of Science, Van Yuzuncu Yıl University, Van, Turkey
| | - Umit Yildiko
- Architecture and Engineering Faculty, Department of Bioengineering, Kafkas University, Kars, Turkey
| | - Mehmet Salih Ağırtaş
- Department of Chemistry, Faculty of Science, Van Yuzuncu Yıl University, Van, Turkey
| | - Sabit Horoz
- Faculty of Engineering and Architecture Department of Electrical and Electronic Engineering, Siirt University, Siirt, Turkey
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Belosludov RV, Nevonen D, Rhoda HM, Sabin JR, Nemykin VN. Simultaneous Prediction of the Energies of Qx and Qy Bands and Intramolecular Charge-Transfer Transitions in Benzoannulated and Non-Peripherally Substituted Metal-Free Phthalocyanines and Their Analogues: No Standard TDDFT Silver Bullet Yet. J Phys Chem A 2018; 123:132-152. [DOI: 10.1021/acs.jpca.8b07647] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Rodion V. Belosludov
- Institute for Materials Research, Tohoku University, Katahira 2-1-1,
Aoba-ku Sendai 980-8577, Japan
| | - Dustin Nevonen
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Hannah M. Rhoda
- Department of Chemistry & Biochemistry, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Jared R. Sabin
- Department of Chemistry & Biochemistry, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Victor N. Nemykin
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Chemistry & Biochemistry, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
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Cao HY, Si DH, Tang Q, Zheng XF, Hao C. Electronic structures and solvent effects of unsymmetrical neo-confused porphyrin: DFT and TDDFT–IEFPCM investigations. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.01.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Hao L, Wang J, Bai FQ, Xie M, Zhang HX. Theoretical studies of fluorine substituent effect on organic photo-sensitizers in dye sensitized solar cells. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Safonova EA, Martynov AG, Zolotarevskii VI, Nefedov SE, Gorbunova YG, Tsivadze AY. Design of UV-Vis-NIR panchromatic crown-phthalocyanines with controllable aggregation. Dalton Trans 2015; 44:1366-78. [PMID: 25423480 DOI: 10.1039/c4dt02759k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel magnesium and zinc phthalocyaninates, bearing four lateral electron-rich 15-crown-5-oxanthrene fragments, were synthesized starting from benzo-15-crown-5. Being almost insoluble in common organic solvents, these complexes could be solubilised by interaction with potassium acetate due to the formation of well-defined cofacial supramolecular dimers. A characteristic feature of these dimers is the presence of additional bands in their UV-Vis spectra, which affords the expansion of light absorption region up to ∼750 nm. This new band corresponds to the charge transfer from the peripheral groups to the Pc core, as evidenced by TDDFT calculations. Potassium cations can be reversibly removed from these dimers by [2.2.2]cryptand, resulting in the formation of monodisperse nanoparticles exhibiting absorbances up to 900 nm. This approach can be further used for the fabrication of nanostructured optoelectronic materials based on the synthesized donor-acceptor panchromatic crown-phthalocyanines.
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Affiliation(s)
- Evgeniya A Safonova
- A.N. Frumkin, Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071, Leninskiy pr., 31, bldg. 4, Moscow, Russia.
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Fu H, Cao M, She Y, Sun Z, Yu Y. Electronic effects of the substituent on the dioxygen-activating abilities of substituted iron tetraphenylporphyrins: a theoretical study. J Mol Model 2015; 21:92. [DOI: 10.1007/s00894-015-2619-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 02/15/2015] [Indexed: 10/23/2022]
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Gao Y, Nemykin VN. Modeling of the energies and splitting of the Qx and Qy bands in positional isomers of zinc pyridinoporphyrazines by TDDFT approach: can TDDFT help distinguishing the structural isomers? J Mol Graph Model 2013; 42:73-80. [PMID: 23567934 DOI: 10.1016/j.jmgm.2013.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/07/2013] [Accepted: 03/08/2013] [Indexed: 10/27/2022]
Abstract
Electronic structures, energies and splitting of the Qx and Qy bands for positional isomers of zinc mono-, di-, tri-, and tetra pyridinoporphyrazines as well as parent zinc phthalocyanine were investigated using density functional theory (DFT) and time-dependent (TD) DFT approaches. The influence of the Hartree-Fock exchange on excited state energies and Qx and Qy bands splitting were studied using GGA BP86 and hybrid B3LYP and PBE1PBE exchange-correlation functionals. Solvent effects were estimated using the polarized continuum model (PCM) approach and cyclohexane, toluene, or DMSO as solvents. It was found that general trends in the Qx and Qy band energies and splitting correlate very well with the available experimental data on pyridinoporphyrazines and follow the trends in HOMO-LUMO and HOMO-LUMO+1 energy gaps as well as LUMO-LUMO+1 splitting. TDDFT trends allow estimation of the Qx and Qy band energies and splitting in unknown tripyridinoporphyrazines and in individual positional isomers of tetrapyridinoporphyrazines.
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Affiliation(s)
- Yunling Gao
- Department of Chemistry and Biochemistry, University of Minnesota-Duluth, Duluth, MN 55812, USA
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