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Müller K, Schellhammer KS, Gräßler N, Debnath B, Liu F, Krupskaya Y, Leo K, Knupfer M, Ortmann F. Directed exciton transport highways in organic semiconductors. Nat Commun 2023; 14:5599. [PMID: 37699907 PMCID: PMC10497625 DOI: 10.1038/s41467-023-41044-9] [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: 06/02/2022] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
Exciton bandwidths and exciton transport are difficult to control by material design. We showcase the intriguing excitonic properties in an organic semiconductor material with specifically tailored functional groups, in which extremely broad exciton bands in the near-infrared-visible part of the electromagnetic spectrum are observed by electron energy loss spectroscopy and theoretically explained by a close contact between tightly packing molecules and by their strong interactions. This is induced by the donor-acceptor type molecular structure and its resulting crystal packing, which induces a remarkable anisotropy that should lead to a strongly directed transport of excitons. The observations and detailed understanding of the results yield blueprints for the design of molecular structures in which similar molecular features might be used to further explore the tunability of excitonic bands and pave a way for organic materials with strongly enhanced transport and built-in control of the propagation direction.
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Affiliation(s)
- Kai Müller
- Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Karl S Schellhammer
- Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
- Dresden Integrated Center for Applied Physics and Photonic Materials (IAPP) and Institute for Applied Physics, Technische Universität Dresden, 01062, Dresden, Germany
| | - Nico Gräßler
- Dresden Integrated Center for Applied Physics and Photonic Materials (IAPP) and Institute for Applied Physics, Technische Universität Dresden, 01062, Dresden, Germany
- Leibniz Institute for Solid State and Materials Research Dresden, Helmholtzstr. 20, 01069, Dresden, Germany
| | - Bipasha Debnath
- Leibniz Institute for Solid State and Materials Research Dresden, Helmholtzstr. 20, 01069, Dresden, Germany
| | - Fupin Liu
- Leibniz Institute for Solid State and Materials Research Dresden, Helmholtzstr. 20, 01069, Dresden, Germany
| | - Yulia Krupskaya
- Leibniz Institute for Solid State and Materials Research Dresden, Helmholtzstr. 20, 01069, Dresden, Germany
| | - Karl Leo
- Dresden Integrated Center for Applied Physics and Photonic Materials (IAPP) and Institute for Applied Physics, Technische Universität Dresden, 01062, Dresden, Germany
| | - Martin Knupfer
- Leibniz Institute for Solid State and Materials Research Dresden, Helmholtzstr. 20, 01069, Dresden, Germany
| | - Frank Ortmann
- Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany.
- Department of Chemistry, TUM School of Natural Sciences, Technische Universität München, Lichtenbergstr. 4, 85748, Garching b. München, Germany.
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Nisha S, Joe IH. Quantum chemical computation and spectroscopic investigation on antiviral drug Acyclovir:-In-silico and in-vitro analysis. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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3
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Interaction energy profile for diphenyl diselenide in complex with δ-aminolevulinic acid dehydratase enzyme using quantum calculations and a molecular fragmentation method. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.comtox.2018.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Chandraboss VL, Karthikeyan B, Senthilvelan S. Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO2 clusters of sol–gel silicate material for understanding DNA photodamage. Phys Chem Chem Phys 2015; 17:12100-14. [DOI: 10.1039/c5cp00451a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A sol–gel silicate matrix containing entrapped guanine was prepared. The SiO2 matrix provides UVA protection by reducing the light penetration to the entrapped guanine molecules.
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5
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Lima Neto JX, Fulco UL, Albuquerque EL, Corso G, Bezerra EM, Caetano EWS, da Costa RF, Freire VN. A quantum biochemistry investigation of willardiine partial agonism in AMPA receptors. Phys Chem Chem Phys 2015; 17:13092-103. [DOI: 10.1039/c4cp05630b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ quantum biochemistry methods based on the Density Functional Theory (DFT) approach to unveil detailed binding energy features of willardiines co-crystallized with the AMPA receptor.
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Affiliation(s)
- José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Gilberto Corso
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Eveline M. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Roner F. da Costa
- Departamento de Física
- Universidade Federal Rural do Semi-Árido
- 59780-000 Caraúbas-RN
- Brazil
| | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
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Zanatta G, Gottfried C, Silva AM, Caetano EWS, Sales FAM, Freire VN. L-Asparagine crystals with wide gap semiconductor features: optical absorption measurements and density functional theory computations. J Chem Phys 2014; 140:124511. [PMID: 24697463 DOI: 10.1063/1.4869179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Results of optical absorption measurements are presented together with calculated structural, electronic, and optical properties for the anhydrous monoclinic L-asparagine crystal. Density functional theory (DFT) within the generalized gradient approximation (GGA) including dispersion effects (TS, Grimme) was employed to perform the calculations. The optical absorption measurements revealed that the anhydrous monoclinic L-asparagine crystal is a wide band gap material with 4.95 eV main gap energy. DFT-GGA+TS simulations, on the other hand, produced structural parameters in very good agreement with X-ray data. The lattice parameter differences Δa, Δb, Δc between theory and experiment were as small as 0.020, 0.051, and 0.022 Å, respectively. The calculated band gap energy is smaller than the experimental data by about 15%, with a 4.23 eV indirect band gap corresponding to Z → Γ and Z → β transitions. Three other indirect band gaps of 4.30 eV, 4.32 eV, and 4.36 eV are assigned to α3 → Γ, α1 → Γ, and α2 → Γ transitions, respectively. Δ-sol computations, on the other hand, predict a main band gap of 5.00 eV, just 50 meV above the experimental value. Electronic wavefunctions mainly originating from O 2p-carboxyl, C 2p-side chain, and C 2p-carboxyl orbitals contribute most significantly to the highest valence and lowest conduction energy bands, respectively. By varying the lattice parameters from their converged equilibrium values, we show that the unit cell is less stiff along the b direction than for the a and c directions. Effective mass calculations suggest that hole transport behavior is more anisotropic than electron transport, but the mass values allow for some charge mobility except along a direction perpendicular to the molecular layers of L-asparagine which form the crystal, so anhydrous monoclinic L-asparagine crystals could behave as wide gap semiconductors. Finally, the calculations point to a high degree of optical anisotropy for the absorption and complex dielectric function, with more structured curves for incident light polarized along the 100 and 101 directions.
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Affiliation(s)
- G Zanatta
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, 90035-003 Porto Alegre-RS, Brazil
| | - C Gottfried
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, 90035-003 Porto Alegre-RS, Brazil
| | - A M Silva
- Universidade Estadual do Piauí, 64260-000 Piripiri-Pi, Brazil
| | - E W S Caetano
- Instituto de Educação, Ciência e Tecnologia do Ceará, 60040-531 Fortaleza-CE, Brazil
| | - F A M Sales
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60455-760 Fortaleza-CE, Brazil
| | - V N Freire
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60455-760 Fortaleza-CE, Brazil
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da Silva Ribeiro TC, da Costa RF, Bezerra EM, Freire VN, Lyra ML, Manzoni V. The quantum biophysics of the isoniazid adduct NADH binding to its InhA reductase target. NEW J CHEM 2014. [DOI: 10.1039/c3nj01453c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Iwasaka M, Mizukawa Y. Light reflection control in biogenic micro-mirror by diamagnetic orientation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:4328-4334. [PMID: 23470105 DOI: 10.1021/la400046a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
As has become known, most materials, such as proteins and DNA, show orientation under strong magnetic fields. However, the critical threshold for the magnetic field of the magnetomechanical phenomena is still unknown. We demonstrate that a thin micro-mirror from a fish scale with high reflectivity exhibits a distinct magnetic response at 100 mT. A dramatic event under a magnetic field is the decrease of light scattering from guanine crystals as well as rapid rotation against the applied magnetic field. Enhancement of light scattering intensity is also observed when the three vectors of light incidence, magnetic field, and observation are orthogonally directed. The results indicate that biogenic guanine crystals have a large diamagnetic anisotropy along the surface parallel and normal directions. The micrometer to submicrometer scale of thin biogenic plates can act as a noninvasively, magnetically controlled micro-mirror for light irradiation control in the micrometer-scale region.
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KOLB BRIAN, THONHAUSER T. MOLECULAR BIOLOGY AT THE QUANTUM LEVEL: CAN MODERN DENSITY FUNCTIONAL THEORY FORGE THE PATH? ACTA ACUST UNITED AC 2012. [DOI: 10.1142/s1793984412300063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory — a framework that can treat thousands of atoms on firm theoretical ground — can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within the density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent work utilizing these methods to study biologically relevant systems will be highlighted, and a vision for the future of density functional theory within molecular biology will be discussed.
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Affiliation(s)
- BRIAN KOLB
- Department of Physics, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA
| | - T. THONHAUSER
- Department of Physics, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA
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10
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Nikan M, Patrick BO, Sherman JC. Crystal Structure of a Template-Assembled Synthetic G-Quadruplex. Chembiochem 2012; 13:1413-5. [DOI: 10.1002/cbic.201200262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Indexed: 01/24/2023]
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11
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Barroso-Neto IL, Marques JPC, da Costa RF, Caetano EWS, Cavada BS, Gottfried C, Freire VN. Inactivation of Ovine Cyclooxygenase-1 by Bromoaspirin and Aspirin: A Quantum Chemistry Description. J Phys Chem B 2012; 116:3270-9. [DOI: 10.1021/jp206397z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ito L. Barroso-Neto
- Department of Biochemistry, Universidade Federal do Ceará, Fortaleza 60455-760, Ceará, Brazil
| | - João Paulo C. Marques
- Department of Physics, Universidade Federal do Ceará, Fortaleza 60455-760,
Ceará, Brazil
| | - Roner F. da Costa
- Department of Physics, Universidade Federal do Ceará, Fortaleza 60455-760,
Ceará, Brazil
| | - Ewerton W. S. Caetano
- Instituto
Federal de Educação, Ciência e Tecnologia do Ceará, Fortaleza 60040-531, Ceará,
Brazil
| | - Benildo S. Cavada
- Department of Biochemistry, Universidade Federal do Ceará, Fortaleza 60455-760, Ceará, Brazil
| | - Carmem Gottfried
- Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre
90035-003, Rio Grande do Sul, Brazil
| | - Valder N. Freire
- Department of Physics, Universidade Federal do Ceará, Fortaleza 60455-760,
Ceará, Brazil
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12
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Frazão NF, Albuquerque EL, Fulco UL, Azevedo DL, Mendonça GLF, Lima-Neto P, Caetano EWS, Santana JV, Freire VN. Four-level levodopa adsorption on C60 fullerene for transdermal and oral administration: a computational study. RSC Adv 2012. [DOI: 10.1039/c2ra20606d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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da Costa RF, Freire VN, Bezerra EM, Cavada BS, Caetano EWS, de Lima Filho JL, Albuquerque EL. Explaining statin inhibition effectiveness of HMG-CoA reductase by quantum biochemistry computations. Phys Chem Chem Phys 2011; 14:1389-98. [PMID: 22159045 DOI: 10.1039/c1cp22824b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
By taking advantage of the crystallographic data of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) complexed with statins, a quantum biochemistry study based on the density functional theory is performed to estimate the interaction energy for each statin when one considers binding pockets of different sizes. Assuming a correlation between statin potency and the strength of the total HMGR-statin binding energy, clinical data as well as IC(50) values of these cholesterol-lowering drugs are successfully explained only after stabilization of the calculated total binding energy for a larger size of the ligand-interacting HGMR region, one with a radius of at least 12.0 Å. Actually, the binding pocket radius suggested by classic works, which was based solely on the interpretation of crystallographic data of the HMGR-statin complex, is smaller than that necessary to achieve total binding energy convergence in our simulations. Atorvastatin and rosuvastatin are shown to be the most strongly bound HMGR inhibitors, while simvastatin and fluvastatin are the weakest ones. A binding site, interaction energy between residues and statin atoms, and residues domain (BIRD) panel is constructed, indicating clear quantum biochemistry-based routes for the development of new statin derivatives.
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Affiliation(s)
- Roner F da Costa
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici, Fortaleza, Brazil
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14
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Maia FF, Freire VN, Caetano EWS, Azevedo DL, Sales FAM, Albuquerque EL. Anhydrous crystals of DNA bases are wide gap semiconductors. J Chem Phys 2011; 134:175101. [DOI: 10.1063/1.3584680] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Ortmann F, Bechstedt F, Hannewald K. Characteristics of small- and large-polaron motion in organic crystals. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:465802. [PMID: 21403376 DOI: 10.1088/0953-8984/22/46/465802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Based on a generalized theory of charge transport in organic crystals we investigate the motion of polarons of arbitrary size. Within this theory, we analyze the influence of characteristic electronic, vibronic, and thermal energies and their role for the transport regimes. The polaron bandwidth is identified as the central temperature-dependent quantity. The size of the dressed charge carriers is used to analyze the correlation between the polaron size and transport mechanism. In addition, we propose that the band and hopping transport can be distinguished by investigating the mobility anisotropy. To do this only electronic structure parameters are necessary for comparison.
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Friedlein R, Wang Y, Fleurence A, Bussolotti F, Ogata Y, Yamada-Takamura Y. Stacks of Nucleic Acids as Molecular Wires: Direct Measurement of the Intermolecular Band Dispersion in Multilayer Guanine Assemblies. J Am Chem Soc 2010; 132:12808-10. [DOI: 10.1021/ja104839d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rainer Friedlein
- School of Materials Science & Research Center for Integrated Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan.
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Lopes LMF, Garcia AR, Fidalgo A, Ilharco LM. Encapsulation of ruthenium nitrosylnitrate and DNA purines in nanostructured sol-gel silica matrices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:10243-10250. [PMID: 19499946 DOI: 10.1021/la901046f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The interactions between DNA purines (guanine and adenine) and the ruthenium complex Ru(NO)(NO(3))(3) were studied within nanostructured silica matrices prepared by a two-step sol-gel process. By infrared analysis in diffuse reflectance mode, it was proved that encapsulation induces a profound modification on the complex, whereas guanine and adenine preserve their structural integrity. The complex undergoes nitrate ligand exchange and co-condenses with the silica oligomers, but the nitrosyl groups remain stable, which is an unusual behavior in Ru nitrosyl complexes. In turn, the doping molecules affect the sol-gel reactions and eventually the silica structure as it forms: the complex yields a microporous structure, and the purine bases are responsible for the creation of macropores due to hydrogen bonding with the silanol groups of the matrix. In a confined environment, the interactions are much stronger for the coencapsulated pair guanine complex. While adenine only establishes hydrogen bonds or van der Waals interactions with the complex, guanine bonds covalently to Ru by one N atom of the imidazole ring, which becomes strongly perturbed, resulting in a deformation of the complex geometry.
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Affiliation(s)
- Luís M F Lopes
- Centro de Quimica-Fisica Molecular (CQFM) and Institute of Nanoscience and Nanotechnology (IN), Instituto Superior Tecnico, Universidade Tecnica de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisboa, Portugal
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Ortmann F, Hannewald K, Bechstedt F. Charge Transport in Guanine-Based Materials. J Phys Chem B 2009; 113:7367-71. [DOI: 10.1021/jp901029t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frank Ortmann
- Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität Jena and European Theoretical Spectroscopy Facility (ETSF), Max-Wien-Platz 1, 07743 Jena, Germany
| | - Karsten Hannewald
- Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität Jena and European Theoretical Spectroscopy Facility (ETSF), Max-Wien-Platz 1, 07743 Jena, Germany
| | - Friedhelm Bechstedt
- Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität Jena and European Theoretical Spectroscopy Facility (ETSF), Max-Wien-Platz 1, 07743 Jena, Germany
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