1
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Gunes BA, Kirlangic OF, Kilic M, Sunguroglu A, Ozgurtas T, Sezginer EK, Boyacioglu B, Unver H, Yildiz M. Palladium Metal Nanocomposites Based on PEI-Functionalized Nitrogen-Doped Graphene Quantum Dots: Synthesis, Characterization, Density Functional Theory Modeling, and Cell Cycle Arrest Effects on Human Ovarian Cancer Cells. ACS OMEGA 2024; 9:13342-13358. [PMID: 38524449 PMCID: PMC10956410 DOI: 10.1021/acsomega.3c10324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/14/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024]
Abstract
In this study, the synthesis, characterization, density functional theory calculations (DFT), and effect of polyethylenimine (PEI)-functionalized nitrogen-doped graphene quantum dots (PEI N-GQDs) and their palladium metal nanoparticles nanocomposites (PdNPs/PEI N-GQDs) on cancer cells were extensively investigated. The focus also includes investigating their cytotoxic and apoptotic effects on ovarian cancer cells, which pose a serious risk to women's health and have high death rates from delayed diagnosis, inadequate response to treatment, and decreased survival. Graphene quantum dots and their palladium nanocomposites were differentially effective against ovarian cancer cell lines. In particular, the smaller particle size and morphology of PdNPs/PEI N-GQDs nanocomposites compared with PEI N-GQDs probably enhance their activity through highly improved uptake by cells. These findings emphasize the importance of particle size in composite drugs for efficient cancer treatment. DFT results revealed that the Pd-containing nanocomposite, with a smaller highest occupied molecular orbital-lowest unoccupied molecular orbital gap, exhibited higher reactivity and anticancer effects in human ovarian cancer cell line, OVCAR-3. Significantly, the application of nanocomposites to ovarian cancer cells initiated apoptosis, offering valuable insights into the intricate interplay between nanomaterials and cancer biology.
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Affiliation(s)
- Buket Altinok Gunes
- Vocational
School of Health Services, Ankara University, Ankara 06290, Turkiye
| | | | - Murat Kilic
- Vocational
School of Health Services, Ankara University, Ankara 06290, Turkiye
| | - Asuman Sunguroglu
- Department
of Medical Biology, School of Medicine, Ankara University, Ankara 06620, Turkiye
| | - Taner Ozgurtas
- Department
of Medical Biochemistry, Gulhane School of Medicine, University of Health Sciencies, Ankara 06018, Turkiye
| | - Ecem Kaya Sezginer
- Department
of Biochemistry, Faculty of Pharmacy, Ankara
University, Ankara 06100, Turkiye
| | - Bahadir Boyacioglu
- Vocational
School of Health Services, Ankara University, Ankara 06290, Turkiye
| | - Huseyin Unver
- Department
of Physics, Faculty of Science, Ankara University, Ankara 06100, Turkiye
| | - Mustafa Yildiz
- Department
of Chemistry, Faculty of Sciences, Canakkale
Onsekiz Mart University, Canakkale 17100, Turkiye
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2
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Adjir K, Berrekhchi-Berrahma AC, Sekkal-Rahal M. Theoretical characterization and biological activity investigation of indirubins, cyclin dependent kinases inhibitors. J Biomol Struct Dyn 2023:1-10. [PMID: 38100566 DOI: 10.1080/07391102.2023.2294182] [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: 04/14/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
Up to now, significant research efforts have been directed towards investigating indirubin and its derivatives as potential candidates for developing new compounds with multiple biological activities. In the present work, natural indirubin and numerous of its chemical derivatives referred to as indirubins have been investigated computationally using DFT method with the B3LYP/6-311 + G(d,p) level of theory, in order to reveal structure- biological activity relationship. We started with a structural properties description. Results analysis indicated that extra interaction sites were provided through the set of substitutions in compounds (1): Indirubin-3'-monoxime, (2): Indirubin-5-sulfonic acid, (3): 5-Nitro-indirubinoxime, (4): 5'-OH-5-nitro-indirubinoxime (AGM130), (5): 7-Bromo-5'-carboxyindirubin-3'-oxime, and (6): 7 BIO and consequently, extra hydrogen bonds may be formed with the active sites of molecular targets, such as GSK-3, CDKs, and Aurora kinases, as well as the aryl hydrocarbon receptor. Subsequently, to get more information on the electronic properties of indirubin and its analogues, HOMO, LUMO, Egap, and further electronic parameters were carried out. The indirubin derivatives showed an easier interaction with its environment than indirubin, the parent compound. The UV-Visible spectra of indirubin and compounds 1-6 were also produced using TD-DFT with B3LYP functional and 6-311 + G(2d,p) basis set. The relationship between absorption and chemical structure is discussed. Two phototoxic brominated compounds showed important absorption spectra modifications. It was also found that the main absorption bands of all compounds derived from π→π*(HOMO→LUMO) transitions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khadidja Adjir
- Laboratory of Thermodynamics and Molecular Modeling, Faculty of Chemistry, Bab Ezzouar, Algiers, Algeria
| | - Amina C Berrekhchi-Berrahma
- Laboratoire de Chimie Théorique de Bio- et Nanosystèmes (LCTBN), Faculty of Exact Sciences, University Djillali Liabes of Sidi Bel Abbès, Sidi Bel Abbès, Algeria
| | - Majda Sekkal-Rahal
- Laboratoire de Chimie Théorique de Bio- et Nanosystèmes (LCTBN), Faculty of Exact Sciences, University Djillali Liabes of Sidi Bel Abbès, Sidi Bel Abbès, Algeria
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3
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Lupo Pasini M, Mehta K, Yoo P, Irle S. Two excited-state datasets for quantum chemical UV-vis spectra of organic molecules. Sci Data 2023; 10:546. [PMID: 37604820 PMCID: PMC10442335 DOI: 10.1038/s41597-023-02408-4] [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: 03/07/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
We present two open-source datasets that provide time-dependent density-functional tight-binding (TD-DFTB) electronic excitation spectra of organic molecules. These datasets represent predictions of UV-vis absorption spectra performed on optimized geometries of the molecules in their electronic ground state. The GDB-9-Ex dataset contains a subset of 96,766 organic molecules from the original open-source GDB-9 dataset. The ORNL_AISD-Ex dataset consists of 10,502,904 organic molecules that contain between 5 and 71 non-hydrogen atoms. The data reveals the close correlation between the magnitude of the gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the excitation energy of the lowest singlet excited state energies quantitatively. The chemical variability of the large number of molecules was examined with a topological fingerprint estimation based on extended-connectivity fingerprints (ECFPs) followed by uniform manifold approximation and projection (UMAP) for dimension reduction. Both datasets were generated using the DFTB+ software on the "Andes" cluster of the Oak Ridge Leadership Computing Facility (OLCF).
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Affiliation(s)
- Massimiliano Lupo Pasini
- Oak Ridge National Laboratory, Computational Sciences and Engineering Division, Oak Ridge, 37831, USA.
| | - Kshitij Mehta
- Oak Ridge National Laboratory, Computer Science and Mathematics Division, Oak Ridge, 37831, USA
| | - Pilsun Yoo
- Oak Ridge National Laboratory, Computational Sciences and Engineering Division, Oak Ridge, 37831, USA
| | - Stephan Irle
- Oak Ridge National Laboratory, Computational Sciences and Engineering Division, Oak Ridge, 37831, USA.
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4
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Ashtari-Jafari S, Jamshidi Z, Visscher L. Efficient simulation of resonance Raman spectra with tight-binding approximations to Density Functional Theory. J Chem Phys 2022; 157:084104. [DOI: 10.1063/5.0107220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Resonance Raman spectroscopy has long been established as one of the most sensitive techniques for detection, structure characterization and probing the excited-state dynamics of biochemical systems. However, the analysis of resonance Raman spectra is much facilitated when measurements are accompanied by Density Functional Theory (DFT) calculations which are expensive for large biomolecules. In this work, resonance Raman spectra are therefore computed with the Density Functional Tight-Binding (DFTB) method in the time-dependent excited-state gradient approximation. To test the accuracy of the tight-binding approximations, this method is first applied to typical resonance Raman benchmark molecules like β-carotene and compared to results obtained with pure and range-separated exchange-correlation (xc) functionals. We then demonstrate the efficiency of the approach by considering a computationally challenging heme variation. Overall, we find that the vibrational frequencies and excited-state properties (energies and gradients) which are needed to simulate the spectra are reasonably accurate and suitable for interpretation of experiments. We can therefore recommend DFTB as a fast computational method to interpret resonance Raman spectra.
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Affiliation(s)
- Sahar Ashtari-Jafari
- Chemistry & Chemical Engineering Research Center of Iran (CCERCI), Iran, Islamic Republic of
| | - Zahra Jamshidi
- Chemistry, Sharif University of Technology, Iran, Islamic Republic of
| | - Lucas Visscher
- Division of Theoretical Chemistry, Vrije Universiteit Amsterdam, Netherlands
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5
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Amino-functionalized nitrogen-doped graphene quantum dots and silver-graphene based nanocomposites: Ultrafast charge transfer and a proof-of-concept study for bioimaging applications. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2021.113741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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6
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Lafiosca P, Gómez S, Giovannini T, Cappelli C. Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach. J Chem Theory Comput 2022; 18:1765-1779. [PMID: 35184553 PMCID: PMC8908768 DOI: 10.1021/acs.jctc.1c01066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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We report on the
first formulation of a novel polarizable QM/MM
approach, where the density functional tight binding (DFTB) is coupled
to the fluctuating charge (FQ) force field. The resulting method (DFTB/FQ)
is then extended to the linear response within the TD-DFTB framework
and challenged to study absorption spectra of large condensed-phase
systems.
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Affiliation(s)
- Piero Lafiosca
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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7
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Karatay A, Yılmaz H, Yildiz EA, Sevinç G, Hayvali M, Boyacioglu B, Unver H, Elmali A. Two-photon absorption and triplet excited state quenching of near-IR region aza-BODIPY photosensitizers via a triphenylamine moiety despite heavy bromine atoms. Phys Chem Chem Phys 2022; 24:25495-25505. [DOI: 10.1039/d2cp02960j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Aza-BODIPY compounds with methoxy groups at -3 and -5 positons and triphenylamine moieties at -1, -7 positions with and without heavy bromine atoms at -2, -6 positions have been designed and synthesized.
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Affiliation(s)
- Ahmet Karatay
- Department of Engineering Physics, Faculty of Engineering, Ankara University, 06100 Beşevler, Ankara, Turkey
| | - Halil Yılmaz
- Department of Chemistry, Faculty of Science, Ankara University, Beşevler, 06100 Ankara, Turkey
| | - Elif Akhuseyin Yildiz
- Department of Engineering Physics, Faculty of Engineering, Ankara University, 06100 Beşevler, Ankara, Turkey
| | - Gökhan Sevinç
- Department of Chemistry, Faculty of Science and Literature, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
| | - Mustafa Hayvali
- Department of Chemistry, Faculty of Science, Ankara University, Beşevler, 06100 Ankara, Turkey
| | - Bahadir Boyacioglu
- Vocational School of Health Services, Ankara University, 06290 Kecioren-Ankara, Turkey
| | - Huseyin Unver
- Department of Physics, Faculty of Science, Ankara University, 06100 Besevler-Ankara, Turkey
| | - Ayhan Elmali
- Department of Engineering Physics, Faculty of Engineering, Ankara University, 06100 Beşevler, Ankara, Turkey
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8
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Din NU, Turkowski V, Rahman TS. Excited states in hydrogenated single-layer MoS 2. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:075201. [PMID: 33176289 DOI: 10.1088/1361-648x/abc971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Our calculations of the excitation spectrum of single-layer MoS2 at several hydrogen coverages, using a density-matrix based time-dependent density-functional theory (TDDFT) show that the fully hydrogenated system is metallic, while at lower coverages the spectrum consists of spin-polarized partially filled localized mid-gap states. The calculated absorption spectrum of the system reveals standard excitonic peaks corresponding to the bound valence-band hole and conduction-band electron, as well as excitonic peaks that involve the mid-gap states. Binding energies of the excitons of the hydrogenated system are found to be relatively large (few tens of meV), making their experimental detection facile and suggesting hydrogenation as a knob for tuning the optical properties of single-layer MoS2. Importantly, we find hydrogenation to suppress visible light photoluminescence, in agreement with experimental observations. In contrast, both Li and Na atoms transform the system into an n-doped non-magnetic semiconductor that does not allow excitonic states.
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Affiliation(s)
- Naseem Ud Din
- Department of Physics, University of Central Florida, Orlando, FL 32816-2385, United States of America
| | - Volodymyr Turkowski
- Department of Physics, University of Central Florida, Orlando, FL 32816-2385, United States of America
| | - Talat S Rahman
- Department of Physics, University of Central Florida, Orlando, FL 32816-2385, United States of America
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9
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Liu Z, Alkan F, Aikens CM. TD-DFTB study of optical properties of silver nanoparticle homodimers and heterodimers. J Chem Phys 2020; 153:144711. [PMID: 33086806 DOI: 10.1063/5.0025672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The absorption spectra for face-centered cubic nanoparticle dimers at various interparticle distances are investigated using time-dependent density functional tight binding. Both homodimers and heterodimers are investigated in this work. By studying nanoparticles at various interparticle distances and analyzing their vertical excitations, we found that as the interparticle distance decreases, a red shift arises from contributions of the transition dipole moment that are aligned along the z-axis with nondegenerate features; blue shifts occur for peaks that originate from transition dipole moment components in the x and y directions with double degeneracy. When the nanoparticles are similar in size, the features in the absorption spectra become more sensitive to the interparticle distances. The best-fit curves from vertical excitation energy in the form of AR-b for ΔEredshift/ΔEblueshift vs R are determined. In this way, we determined trends for absorption peak shifts and how these depend on the interparticle distance.
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Affiliation(s)
- Zhen Liu
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Fahri Alkan
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Christine M Aikens
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
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10
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Belić J, van Beek B, Menzel JP, Buda F, Visscher L. Systematic Computational Design and Optimization of Light Absorbing Dyes. J Phys Chem A 2020; 124:6380-6388. [PMID: 32649188 PMCID: PMC7416309 DOI: 10.1021/acs.jpca.0c04506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We present a workflow
to aid the discovery of new dyes for the
role of a photosensitive unit in the dye-sensitized photo-electrochemical
cells (DS-PECs). New structures are generated in a fully automated
way using the Compound Attachment Tool (CAT) introduced in this work.
These structures are characterized with efficient approximate density
functional theory (DFT) methods, and molecules with favorable optical
properties are suggested for possible further use in DS-PECs. As around
2500 structures are generated in this work, and as we aim for still
larger volumes of compounds to screen in subsequent applications,
we have assessed the reliability of low-cost screening methods and
show that simplified time-dependent density functional theory (sTDDFT)
provides a satisfying accuracy/cost ratio. From the dyes considered,
we propose a set that can be suitable for panchromatic sensitization
of the photoelectrode in DS-PECs to further increase DS-PEC efficiency.
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Affiliation(s)
- Jelena Belić
- Vrije Uversiteit Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands
| | - Bas van Beek
- Vrije Uversiteit Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands
| | - Jan Paul Menzel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, P.O. Box 9502, Leiden 2300 RA, The Netherlands
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, P.O. Box 9502, Leiden 2300 RA, The Netherlands
| | - Lucas Visscher
- Vrije Uversiteit Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands
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11
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Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M. Density-functional tight-binding: basic concepts and applications to molecules and clusters. ADVANCES IN PHYSICS: X 2020; 5:1710252. [PMID: 33154977 PMCID: PMC7116320 DOI: 10.1080/23746149.2019.1710252] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023] Open
Abstract
The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
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Affiliation(s)
- Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Nathalie Tarrat
- CEMES, Université de Toulouse (UPS), CNRS, UPR8011, Toulouse, Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Leo Dontot
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Evgeny Posenitskiy
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, UMR5589, Université de Toulouse (UPS) and CNRS, Toulouse, France
| | - Carles Martí
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
- Laboratoire de Chimie, UMR5182, Ecole Normale Supérieure de Lyon, Université de Lyon and CNRS, Lyon, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
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12
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Nishimoto Y. Time-Dependent Long-Range-Corrected Density-Functional Tight-Binding Method Combined with the Polarizable Continuum Model. J Phys Chem A 2019; 123:5649-5659. [PMID: 31150233 DOI: 10.1021/acs.jpca.9b03713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, excited-state free energies and geometries were efficiently evaluated using a linear-response time-dependent long-range-corrected density-functional tight-binding method integrated with the polarizable continuum model (TD-LC-DFTB2/PCM). Although the LC-DFTB method required the evaluation of the exchange-type term, which was moderately computationally expensive, a single evaluation of the excited-state gradient for a system consisting of more than 1000 atoms in a vacuum was completed within 30 min using one CPU core. Benchmark calculations were conducted for 3-hydroxyflavone, which exhibits dual emission: the absorption and enol-form emission wavelengths calculated by TD-LC-DFTB2/PCM agreed well with those predicted based on the density functional theory using a long-range corrected functional; however, there was a large error in the predicted keto-form emission wavelength. Further benchmark calculations for more than 20 molecules indicated that the conventional TD-DFTB method underestimated the absorption and 0-0 transition energies compared with those which were measured experimentally, whereas the TD-LC-DFTB2 method systematically overestimated these metrics. Nevertheless, the agreement of the results of the TD-LC-DFTB2 method with those obtained by the CAM-B3LYP method demonstrates the potential of the TD-LC-DFTB2/PCM method. Moreover, changing the range separation parameter to 0.15 minimized this deviation.
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Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry , Kyoto University , 34-4 Takano Nishihiraki-cho , Sakyo-ku, Kyoto 606-8103 , Japan
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13
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Teodoro TQ, Koenis MAJ, Galembeck SE, Nicu VP, Buma WJ, Visscher L. Frequency Range Selection Method for Vibrational Spectra. J Phys Chem Lett 2018; 9:6878-6882. [PMID: 30449106 PMCID: PMC6287222 DOI: 10.1021/acs.jpclett.8b02963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/18/2018] [Indexed: 06/09/2023]
Abstract
Theoretical calculations of vibrational properties are widely used to explain and predict experimental spectra. However, with standard quantum chemical methods all molecular motions are considered, which is rather time-consuming for large molecules. Because typically only a specific spectral region is of experimental interest, we propose here an efficient method that allows calculation of only a selected frequency interval. After a computationally cheap low-level estimate of the molecular motions, the computational time is proportional to the number of normal modes needed to describe this frequency range. Results for a medium-sized molecule show a reduction in computational time of up to 1 order of magnitude with negligible loss in accuracy. We also show that still larger computational savings are possible by using an additional intensity-selection procedure.
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Affiliation(s)
- T. Q. Teodoro
- Amsterdam
Center for Multiscale Modeling, Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Departamento
de Química, FFCLRP, Universidade
de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, 14040-901 São Paulo, Brazil
| | - M. A. J. Koenis
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - S. E. Galembeck
- Departamento
de Química, FFCLRP, Universidade
de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, 14040-901 São Paulo, Brazil
| | - V. P. Nicu
- Department
of Environmental Science, Physics, Physical Education and Sport, Lucian Blaga University of Sibiu, loan Ratiu Street, Nr. 7-9, 550012 Sibiu, Romania
| | - W. J. Buma
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - L. Visscher
- Amsterdam
Center for Multiscale Modeling, Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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14
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Alkan F, Aikens CM. TD-DFT and TD-DFTB Investigation of the Optical Properties and Electronic Structure of Silver Nanorods and Nanorod Dimers. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2018; 122:23639-23650. [PMID: 30364415 PMCID: PMC6196343 DOI: 10.1021/acs.jpcc.8b05196] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Indexed: 05/13/2023]
Abstract
Here, we perform theoretical investigation using time-dependent density functional theory (TD-DFT) and time-dependent density functional tight binding (TD-DFTB) for the electronic structure and optical properties of silver nanorods. TD-DFTB generally performs well for the accurate description of optical properties with respect to the size and type of dimer assembly of silver nanorods compared to TD-DFT. However, the energies and intensities of the longitudinal and transverse peaks of the nanorods are somewhat underestimated with TD-DFTB compared to the values calculated at the TD-DFT level. By exploiting the computational efficiency of TD-DFTB, we also extend our investigation to longer nanorods and their dimers containing up to ∼2000 atoms. Our results show that the coupling between nanorods and the resulting optical properties of the dimer assemblies are quite dependent on the length of the monomers. In all cases, the energy shifts in dimers as a function of the gap distance deviate significantly from the dipole-dipole interaction model. Moreover, a comparison of the best-fit curves for the dependence of the fractional shifts (Δλ/λ0) on nanorod length indicates that the parameters of the plasmon ruler equation depend on the length of the nanorods and the type of the assembly rather than approaching a universal value. These insights are enabled by the computational efficiency of TD-DFTB and its ability to treat quantum mechanical effects in large nanorod dimer systems.
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15
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Darghouth AAMHM, Correa GC, Juillard S, Casida ME, Humeniuk A, Mitrić R. Davydov-type excitonic effects on the absorption spectra of parallel-stacked and herringbone aggregates of pentacene: Time-dependent density-functional theory and time-dependent density-functional tight binding. J Chem Phys 2018; 149:134111. [PMID: 30292200 DOI: 10.1063/1.5025624] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Exciton formation leads to J-bands in solid pentacene. Describing these exciton bands represents a challenge for both time-dependent (TD) density-functional theory (DFT) and for its semi-empirical analog, namely, for TD density-functional tight binding (DFTB) for three reasons: (i) solid pentacene and pentacene aggregates are bound only by van der Waals forces which are notoriously difficult to describe with DFT and DFTB, (ii) the proper description of the long-range coupling between molecules, needed to describe Davydov splitting, is not easy to include in TD-DFT with traditional functionals and in TD-DFTB, and (iii) mixing may occur between local and charge transfer excitons, which may, in turn, require special functionals. We assess how far TD-DFTB has progressed toward a correct description of this type of exciton by including both a dispersion correction for the ground state and a range-separated hybrid functional for the excited state and comparing the results against corresponding TD-CAM-B3LYP/CAM-B3LYP+D3 results. Analytic results for parallel-stacked ethylene are derived which go beyond Kasha's exciton model [M. Kasha, H. R. Rawls, and A. El-Bayoumi, Pure Appl. Chem. 11, 371 (1965)] in that we are able to make a clear distinction between charge transfer and energy transfer excitons. This is further confirmed when it is shown that range-separated hybrids have a markedly greater effect on charge-transfer excitons than on energy-transfer excitons in the case of parallel-stacked pentacenes. TD-DFT calculations with the CAM-B3LYP functional and TD-lc-DFT calculations lead to negligible excitonic corrections for the herringbone crystal structure, possibly because of an overcorrection of charge-transfer effects (CAM refers to Coulomb attenuated method). In this case, TD-DFT calculations with the B3LYP functional or TD-DFTB calculations parameterized to B3LYP give the best results for excitonic corrections for the herringbone crystal structure as judged from comparison with experimental spectra and with Bethe-Salpeter equation calculations from the literature.
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Affiliation(s)
- Ala Aldin M H M Darghouth
- Laboratoire de Chimie Théorique, Département de Chimie Moléculaire (DCM), Institut de Chimie Moléculaire de Grenoble (ICMG), Université Grenoble-Alpes, 301 Rue de la Chimie, CS 40700, 38058 Grenoble Cedex 9, France
| | - Gabriela Calinao Correa
- Laboratoire de Chimie Théorique, Département de Chimie Moléculaire (DCM), Institut de Chimie Moléculaire de Grenoble (ICMG), Université Grenoble-Alpes, 301 Rue de la Chimie, CS 40700, 38058 Grenoble Cedex 9, France
| | - Sacha Juillard
- Laboratoire de Chimie Théorique, Département de Chimie Moléculaire (DCM), Institut de Chimie Moléculaire de Grenoble (ICMG), Université Grenoble-Alpes, 301 Rue de la Chimie, CS 40700, 38058 Grenoble Cedex 9, France
| | - Mark E Casida
- Laboratoire de Chimie Théorique, Département de Chimie Moléculaire (DCM), Institut de Chimie Moléculaire de Grenoble (ICMG), Université Grenoble-Alpes, 301 Rue de la Chimie, CS 40700, 38058 Grenoble Cedex 9, France
| | - Alexander Humeniuk
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Straße 42, D-97074 Würzburg, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Straße 42, D-97074 Würzburg, Germany
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16
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Ghosh S, Andersen A, Gagliardi L, Cramer CJ, Govind N. Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians. J Chem Theory Comput 2017; 13:4410-4420. [DOI: 10.1021/acs.jctc.7b00618] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soumen Ghosh
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Amity Andersen
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99338, United States
| | - Laura Gagliardi
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Christopher J. Cramer
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Niranjan Govind
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99338, United States
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17
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Rüger R, van Lenthe E, Lu Y, Frenzel J, Heine T, Visscher L. Correction to Efficient Calculation of Electronic Absorption Spectra by Means of Intensity-Selected Time-Dependent Density Functional Tight Binding. J Chem Theory Comput 2017; 13:3424-3425. [PMID: 28594554 DOI: 10.1021/acs.jctc.7b00564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Rüger R, van Lenthe E, Heine T, Visscher L. Tight-binding approximations to time-dependent density functional theory - A fast approach for the calculation of electronically excited states. J Chem Phys 2017; 144:184103. [PMID: 27179467 DOI: 10.1063/1.4948647] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of two compared to TD-DFTB.
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Affiliation(s)
- Robert Rüger
- Scientific Computing & Modelling NV, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Erik van Lenthe
- Scientific Computing & Modelling NV, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Thomas Heine
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig, Germany
| | - Lucas Visscher
- Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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19
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Kłos J, Kim M, Alexander MH, Wang Y. Chemical Control and Spectral Fingerprints of Electronic Coupling in Carbon Nanostructures. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:29476-29483. [PMID: 28819465 PMCID: PMC5555747 DOI: 10.1021/acs.jpcc.6b09612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The optical and electronic properties of atomically thin materials such as single-walled carbon nanotubes and graphene are sensitively influenced by substrates, the degree of aggregation, and the chemical environment. However, it has been experimentally challenging to determine the origin and quantify these effects. Here we use time-dependent density-functional-theory calculations to simulate these properties for well-defined molecular systems. We investigate a series of core-shell structures containing C60 enclosed in progressively larger carbon shells and their perhydrogenated or perfluorinated derivatives. Our calculations reveal strong electronic coupling effects that depend sensitively on the interparticle distance and on the surface chemistry. In many of these systems we predict considerable orbital mixing and charge transfer between the C60 core and the enclosing shell. We predict that chemical functionalization of the shell can modulate the electronic coupling to the point where the core and shell are completely decoupled into two electronically independent chemical systems. Additionally, we predict that the C60 core will oscillate within the confining shell, at a frequency directly related to the strength of the electronic coupling. This low-frequency motion should be experimentally detectable in the IR region.
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Affiliation(s)
- Jacek Kłos
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Mijin Kim
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Millard H. Alexander
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland 20742, United States
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20
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Mikulecký P, Zahradník J, Kolenko P, Černý J, Charnavets T, Kolářová L, Nečasová I, Pham PN, Schneider B. Crystal structure of human interferon-γ receptor 2 reveals the structural basis for receptor specificity. Acta Crystallogr D Struct Biol 2016; 72:1017-25. [PMID: 27599734 PMCID: PMC5013595 DOI: 10.1107/s2059798316012237] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/27/2016] [Indexed: 11/10/2022] Open
Abstract
Interferon-γ receptor 2 is a cell-surface receptor that is required for interferon-γ signalling and therefore plays a critical immunoregulatory role in innate and adaptive immunity against viral and also bacterial and protozoal infections. A crystal structure of the extracellular part of human interferon-γ receptor 2 (IFNγR2) was solved by molecular replacement at 1.8 Å resolution. Similar to other class 2 receptors, IFNγR2 has two fibronectin type III domains. The characteristic structural features of IFNγR2 are concentrated in its N-terminal domain: an extensive π-cation motif of stacked residues KWRWRH, a NAG-W-NAG sandwich (where NAG stands for N-acetyl-D-glucosamine) and finally a helix formed by residues 78-85, which is unique among class 2 receptors. Mass spectrometry and mutational analyses showed the importance of N-linked glycosylation to the stability of the protein and confirmed the presence of two disulfide bonds. Structure-based bioinformatic analysis revealed independent evolutionary behaviour of both receptor domains and, together with multiple sequence alignment, identified putative binding sites for interferon-γ and receptor 1, the ligands of IFNγR2.
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Affiliation(s)
- Pavel Mikulecký
- Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jirí Zahradník
- Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Petr Kolenko
- Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Tatsiana Charnavets
- Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Lucie Kolářová
- Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Iva Nečasová
- Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Phuong Ngoc Pham
- Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
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21
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Grimme S, Bannwarth C. Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB). J Chem Phys 2016; 145:054103. [DOI: 10.1063/1.4959605] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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22
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Lutsker V, Aradi B, Niehaus TA. Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method. J Chem Phys 2016; 143:184107. [PMID: 26567646 DOI: 10.1063/1.4935095] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.
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Affiliation(s)
- V Lutsker
- Department of Theoretical Physics, University of Regensburg, 93040 Regensburg, Germany
| | - B Aradi
- BCCMS, University of Bremen, 28359 Bremen, Germany
| | - T A Niehaus
- Department of Theoretical Physics, University of Regensburg, 93040 Regensburg, Germany
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23
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Bannwarth C, Grimme S. Electronic Circular Dichroism of Highly Conjugated π-Systems: Breakdown of the Tamm–Dancoff/Configuration Interaction Singles Approximation. J Phys Chem A 2015; 119:3653-62. [DOI: 10.1021/acs.jpca.5b01680] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Bannwarth
- Mulliken
Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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