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Makarov D, Volkov OM, Kákay A, Pylypovskyi OV, Budinská B, Dobrovolskiy OV. New Dimension in Magnetism and Superconductivity: 3D and Curvilinear Nanoarchitectures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2101758. [PMID: 34705309 DOI: 10.1002/adma.202101758] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/16/2021] [Indexed: 06/13/2023]
Abstract
Traditionally, the primary field, where curvature has been at the heart of research, is the theory of general relativity. In recent studies, however, the impact of curvilinear geometry enters various disciplines, ranging from solid-state physics over soft-matter physics, chemistry, and biology to mathematics, giving rise to a plethora of emerging domains such as curvilinear nematics, curvilinear studies of cell biology, curvilinear semiconductors, superfluidity, optics, 2D van der Waals materials, plasmonics, magnetism, and superconductivity. Here, the state of the art is summarized and prospects for future research in curvilinear solid-state systems exhibiting such fundamental cooperative phenomena as ferromagnetism, antiferromagnetism, and superconductivity are outlined. Highlighting the recent developments and current challenges in theory, fabrication, and characterization of curvilinear micro- and nanostructures, special attention is paid to perspective research directions entailing new physics and to their strong application potential. Overall, the perspective is aimed at crossing the boundaries between the magnetism and superconductivity communities and drawing attention to the conceptual aspects of how extension of structures into the third dimension and curvilinear geometry can modify existing and aid launching novel functionalities. In addition, the perspective should stimulate the development and dissemination of research and development oriented techniques to facilitate rapid transitions from laboratory demonstrations to industry-ready prototypes and eventual products.
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Affiliation(s)
- Denys Makarov
- Helmholtz-Zentrum Dresden - Rossendorf e.V., Institute of Ion Beam Physics and Materials Research, 01328, Dresden, Germany
| | - Oleksii M Volkov
- Helmholtz-Zentrum Dresden - Rossendorf e.V., Institute of Ion Beam Physics and Materials Research, 01328, Dresden, Germany
| | - Attila Kákay
- Helmholtz-Zentrum Dresden - Rossendorf e.V., Institute of Ion Beam Physics and Materials Research, 01328, Dresden, Germany
| | - Oleksandr V Pylypovskyi
- Helmholtz-Zentrum Dresden - Rossendorf e.V., Institute of Ion Beam Physics and Materials Research, 01328, Dresden, Germany
- Kyiv Academic University, Kyiv, 03142, Ukraine
| | - Barbora Budinská
- Superconductivity and Spintronics Laboratory, Nanomagnetism and Magnonics, Faculty of Physics, University of Vienna, Vienna, 1090, Austria
| | - Oleksandr V Dobrovolskiy
- Superconductivity and Spintronics Laboratory, Nanomagnetism and Magnonics, Faculty of Physics, University of Vienna, Vienna, 1090, Austria
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Pylypovskyi OV, Kononenko DY, Yershov KV, Rößler UK, Tomilo AV, Fassbender J, van den Brink J, Makarov D, Sheka DD. Curvilinear One-Dimensional Antiferromagnets. NANO LETTERS 2020; 20:8157-8162. [PMID: 32986440 DOI: 10.1021/acs.nanolett.0c03246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antiferromagnets host exotic quasiparticles, support high frequency excitations and are key enablers of the prospective spintronic and spin-orbitronic technologies. Here, we propose a concept of a curvilinear antiferromagnetism where material responses can be tailored by a geometrical curvature without the need to adjust material parameters. We show that an intrinsically achiral one-dimensional (1D) curvilinear antiferromagnet behaves as a chiral helimagnet with geometrically tunable Dzyaloshinskii-Moriya interaction (DMI) and orientation of the Néel vector. The curvature-induced DMI results in the hybridization of spin wave modes and enables a geometrically driven local minimum of the low-frequency branch. This positions curvilinear 1D antiferromagnets as a novel platform for the realization of geometrically tunable chiral antiferromagnets for antiferromagnetic spin-orbitronics and fundamental discoveries in the formation of coherent magnon condensates in the momentum space.
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Affiliation(s)
- Oleksandr V Pylypovskyi
- Helmholtz-Zentrum Dresden-Rossendorf e.V., Institute of Ion Beam Physics and Materials Research, Dresden 01328, Germany
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | - Denys Y Kononenko
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
- Institute for Theoretical Solid State Physics, IFW Dresden, Dresden 01069, Germany
| | - Kostiantyn V Yershov
- Institute for Theoretical Solid State Physics, IFW Dresden, Dresden 01069, Germany
- Bogolyubov Institute for Theoretical Physics of National Academy of Sciences of Ukraine, Kyiv 03143, Ukraine
| | - Ulrich K Rößler
- Institute for Theoretical Solid State Physics, IFW Dresden, Dresden 01069, Germany
| | - Artem V Tomilo
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | - Jürgen Fassbender
- Helmholtz-Zentrum Dresden-Rossendorf e.V., Institute of Ion Beam Physics and Materials Research, Dresden 01328, Germany
| | - Jeroen van den Brink
- Institute for Theoretical Solid State Physics, IFW Dresden, Dresden 01069, Germany
- Institute for Theoretical Physics, TU Dresden, Dresden 01069, Germany
| | - Denys Makarov
- Helmholtz-Zentrum Dresden-Rossendorf e.V., Institute of Ion Beam Physics and Materials Research, Dresden 01328, Germany
| | - Denis D Sheka
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
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Orimoto Y, Aoki Y. Computational Study of Cu-Containing Artificial DNA: Twist Angle Dependence of Magnetism. ChemistrySelect 2016. [DOI: 10.1002/slct.201600940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences; Kyushu University; 6-1 Kasuga-Park Fukuoka 816-8580 Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences; Kyushu University; 6-1 Kasuga-Park Fukuoka 816-8580 Japan
- Japan Science and Technology Agency; CREST; 4-1-8 Hon-chou, Kawaguchi Saitama 332-0012 Japan
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Tanaka Y, Kondo J, Sychrovský V, Šebera J, Dairaku T, Saneyoshi H, Urata H, Torigoe H, Ono A. Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs. Chem Commun (Camb) 2015; 51:17343-60. [DOI: 10.1039/c5cc02693h] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this feature article, recent progress and future perspectives of metal-mediated base-pairs such as T–Hg(ii)–T and C–Ag(i)–C are presented.
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Affiliation(s)
- Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences
- Tokushima Bunri University
- Tokushima
- Japan
- Graduate School of Pharmaceutical Sciences
| | - Jiro Kondo
- Department of Materials and Life Sciences
- Faculty of Science and Technology
- Sophia University
- Chiyoda-ku
- Japan
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
- Institute of Physics
| | - Takenori Dairaku
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai
- Japan
| | - Hisao Saneyoshi
- Department of Material & Life Chemistry
- Kanagawa University
- Yokohama
- Japan
| | - Hidehito Urata
- Osaka University of Pharmaceutical Sciences
- Takatsuki
- Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry
- Faculty of Science
- Tokyo University of Science
- Shinjuku-ku
- Japan
| | - Akira Ono
- Department of Material & Life Chemistry
- Kanagawa University
- Yokohama
- Japan
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Samanta PK, Pati SK. Structural and magnetic properties of a variety of transition metal incorporated DNA double helices. Chemistry 2013; 20:1760-4. [PMID: 24382746 DOI: 10.1002/chem.201302628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 10/30/2013] [Indexed: 12/22/2022]
Abstract
By using density functional theory calculations, the structural, energetic, magnetic, and optical properties for a variety of transition metal (M = Mn, Fe, Co, Ni and Cu) ions incorporated modified-DNA (M-DNA) double helices has been investigated. The DNA is modified with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S-en) metalated bases. We find the formation of extended M-O network leading to the ferromagnetic interactions for the case of H-DNA for all the metal ions. More ordered stacking arrangement was found for S-en-DNA. We calculate the exchange coupling constant (J) considering Heisenberg Hamiltonian for quantitative description of magnetic interactions. The ferromagnetic and antiferromagnetic interactions are obtained by varying different transition metal ions. The extent of the magnetic interaction depends on the number of transition metal ions. Optical profiles show peaks below 2 eV, a clear signature of spin-spin coupling.
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Affiliation(s)
- Pralok K Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80-2208-2766/2767, Hompage: http://www.jncasr.ac.in/pati
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Samanta PK, Pati SK. Structural, electronic and photophysical properties of analogous RNA nucleosides: a theoretical study. NEW J CHEM 2013. [DOI: 10.1039/c3nj00633f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Samanta PK, Manna AK, Pati SK. Thieno analogues of RNA nucleosides: a detailed theoretical study. J Phys Chem B 2012; 116:7618-26. [PMID: 22671305 DOI: 10.1021/jp301752k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We use first-principles density functional theory calculations to investigate the structural, energetic, bonding aspects, and optical properties of recently synthesized thieno-analogues of RNA nucleosides. The results are compared against the findings obtained for both the natural nucleosides as well as available experimental data. We find that the modified nucleosides form the hydrogen bonded Watson-Crick (WC) base pairing with similar H-bonding energy as obtained for the natural nucleosides. We have calculated and compared the charge transfer integrals for the H-bonded natural and thieno-modified nucleosides. We find that the thieno modification of these nucleosides strongly affects the charge transfer integrals due to the difference in extent of orbital delocalization in these two types of nucleosides. We also find that the degree of reduction of charge transfer integrals is larger for the H-bonded A-U pair than in the G-C pair. We also focus on the optical absorption properties of these thieno-modified nucleosides and their WC H-bonded base pairs in gas phase as well as with implicit water. Our calculated results show that the low energy peaks in the absorption spectra mainly arise because of the π-π* electronic transition for both the nucleosides, and the observed red shift for thieno-nucleosides compared to natural nucleosides are consistent with the calculated decrease in electronic gaps. Our results demonstrate that the thieno modification of natural nucleosides significantly modifies their electronic and optical properties, although the basic structural and bonding aspects remained the same. It also gives a microscopic understanding of the experimentally observed optical behaviors.
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Affiliation(s)
- Pralok K Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India
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Matsui T, Miyachi H, Baba T, Shigeta Y. Theoretical Study on Reaction Scheme of Silver(I) Containing 5-Substituted Uracils Bridge Formation. J Phys Chem A 2011; 115:8504-10. [DOI: 10.1021/jp200871f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Brancolini G, Felice RD. Combined effects of metal complexation and size expansion in the electronic structure of DNA base pairs. J Chem Phys 2011; 134:205102. [DOI: 10.1063/1.3593272] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Nakanishi Y, Matsui T, Kitagawa Y, Shigeta Y, Saito T, Kataoka Y, Kawakami T, Okumura M, Yamaguchi K. Electron Conductivity in Modified Models of Artificial Metal–DNA Using Green’s Function-Based Elastic Scattering Theory. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20100207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Matsui T, Miyachi H, Nakanishi Y, Shigeta Y, Sato T, Kitagawa Y, Okumura M, Hirao K. Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNA. J Phys Chem B 2009; 113:12790-5. [PMID: 19708672 DOI: 10.1021/jp9045319] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We evaluated the stability, UV-vis spectra, and possibility of stacking of [S-M(II)-S] (M=Ni, Pd, Pt, S: hydroxypyridinethione) using density functional theory (DFT). We calculated the formation energies of modified bases with possible combinations of chalcogen atoms and metal cations. The results confirmed that [H-Ni(II)-H] (H: hydroxypyridone), [H-Cu(II)-H], and [S-Cu(II)-S] would form stable metal-base pairing; on the other hand, [H-Zn(II)-H], [S-Zn(II)-S], and [H-Pt(II)-H] would not. We predicted UV-vis excitations at 400-410 nm, mainly dominated by a d-pi* transition accompanied by a pi-pi* transition in [S-M(II)-S], where a metal-to-ligand charge transfer shifts the peak of S (without metal cations) by performing time-dependent density functional theory (TDDFT) calculations. By adding the Andersson-Langreth-Lundqvist van der Waals correction to the hybrid DFT results, we estimated the interaction energy between base pairs of [S-M(II)-S]. According to the results, the interaction between [S-M(II)-S] monomers for all cases is attractive, so that the selectivity of formation of the metal-containing DNA is governed mainly by the formation of the base pair in the aqueous phase and only slightly by the pi-pi stacking interaction between the modified bases.
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Affiliation(s)
- Toru Matsui
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8656, Japan.
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Mallajosyula SS, Pati SK. Conformational tuning of magnetic interactions in metal-DNA complexes. Angew Chem Int Ed Engl 2009; 48:4977-81. [PMID: 19472237 DOI: 10.1002/anie.200806056] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The alignment of Cu(2+) ions along a modified DNA helix is studied with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S-en) metalated base pairs (MBPs). The conformational motion of H-MBP leads to the interlinking of the H-MBPs by an extended Cu-O network that is ferromagnetic, whereas the conformational freezing of the S-en-MBP leads to an ordered pairwise-stacked arrangement that is weakly antoferrimagnetic.
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Affiliation(s)
- Sairam S Mallajosyula
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
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Woiczikowski PB, Kubar T, Gutiérrez R, Caetano RA, Cuniberti G, Elstner M. Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories. J Chem Phys 2009; 130:215104. [PMID: 19508103 DOI: 10.1063/1.3146905] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. [J. Am. Chem. Soc. 126, 11471 (2004)]. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.
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Affiliation(s)
- P Benjamin Woiczikowski
- Department of Physical and Theoretical Chemistry, Technische Universitat Braunschweig, D-38106 Braunschweig, Germany
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Nakanishi Y, Kitagawa Y, Shigeta Y, Saito T, Matsui T, Miyachi H, Kawakami T, Okumura M, Yamaguchi K. Theoretical studies on magnetic interactions between Cu(II) ions in salen nucleobases. Polyhedron 2009. [DOI: 10.1016/j.poly.2008.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Theoretical studies on magnetic interactions between Cu(II) ions in hydroxypyridone nucleobases. Polyhedron 2009. [DOI: 10.1016/j.poly.2008.10.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mallajosyula S, Pati S. Conformational Tuning of Magnetic Interactions in Metal-DNA Complexes. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806056] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Matsui T, Miyachi H, Sato T, Shigeta Y, Hirao K. Structural Origin of Copper Ion Containing Artificial DNA: A Density Functional Study. J Phys Chem B 2008; 112:16960-5. [DOI: 10.1021/jp8080707] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Toru Matsui
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hideaki Miyachi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Takeshi Sato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yasuteru Shigeta
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Kimihiko Hirao
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
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Brancolini G, Di Felice R. Electronic Properties of Metal-Modified DNA Base Pairs. J Phys Chem B 2008; 112:14281-90. [DOI: 10.1021/jp806419t] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Giorgia Brancolini
- National Research Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41100 Modena, Italy
| | - Rosa Di Felice
- National Research Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41100 Modena, Italy
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Affiliation(s)
- Jens Müller
- Faculty of Chemistry, Dortmund University of Technology, Otto‐Hahn‐Str. 6, 44227 Dortmund, Germany, Fax: +49 231 755 3797
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He W, Franzini RM, Achim C. Metal-Containing Nucleic Acid Structures Based on Synergetic Hydrogen and Coordination Bonding. PROGRESS IN INORGANIC CHEMISTRY 2008. [DOI: 10.1002/9780470144428.ch8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Sponer J, Riley KE, Hobza P. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys Chem Chem Phys 2008; 10:2595-610. [PMID: 18464974 DOI: 10.1039/b719370j] [Citation(s) in RCA: 270] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.
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Affiliation(s)
- Jirí Sponer
- Institute of Organic Chemistry and Biochemistry, vvi, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague 6, Czech Republic
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Ullien D, Cohen H, Porath D. The effect of the number of parallel DNA molecules on electric charge transport through 'standing DNA'. NANOTECHNOLOGY 2007; 18:424015. [PMID: 21730448 DOI: 10.1088/0957-4484/18/42/424015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present morphological and electrical characterization of double-stranded DNA (dsDNA) molecules covalently bound to two metal electrodes: an underlying gold surface and a gold nanoparticle (GNP). Conductive atomic force microscope (cAFM) with a metallized tip is used to perform current-voltage (I-V) measurements through dsDNA molecules, connected to GNPs of different diameters 5, 10 and 20 nm. The number of DNA molecules coating the GNP is expected to vary with the surface area of the GNP. This number and the portion of the GNP surface area enabling hybridization of the DNA determine the number of DNA molecules connecting the GNP to the gold surface. The larger the diameter of the GNP the higher the expected number of dsDNA molecules connecting it to the gold surface and thus the expected current. Our results show similar currents for all three GNP sizes, indicating that current flows through the same number of molecules regardless of the diameter of the measured GNP. The measured currents, 220 nA at 2 V, are in accordance with our previous reports (Cohen et al 2005 Proc. Natl Acad. Sci. USA 102 11589-93; Cohen et al 2006 Faraday Discuss. 131 367-76) in which we demonstrated the validity of the experimental system. In particular, for the 5 nm GNP, we conclude that the current possibly flows through two to three molecules, likely only one, and that a single short dsDNA molecule can support at least ∼70 nA, and probably 220 nA.
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Affiliation(s)
- Daniela Ullien
- Physical Chemistry Department and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904, Israel
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Kirin SI, Yennawar HP, Williams ME. Synthesis and Characterization of CuII Complexes with Amino Acid Substituted Di(2-pyridyl)amine Ligands. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700273] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Recent developments show encouraging results for the use of DNA as a construction material for nanometer-sized objects. Today, however, DNA-based molecular nanoarchitectures are constructed with mainly unmodified or at best end-modified oligonucleotides, thus shifting the development of functionalized DNA structures into the limelight. One of most recent developments in this direction is the substitution of the canonical Watson-Crick base pairs by metal complexes. In this way "metal-base pairs" are created, which could potentially impart magnetic or conductive properties to DNA-based nanostructures. This review summarizes research which started almost 45 years ago with the investigation of how metal ions interact with unmodified DNA and which recently culminated in the development of artificial ligand-like nucleobases so far able to coordinate up to ten metal ions inside a single DNA duplex in a programmable fashion.
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Affiliation(s)
- Guido H Clever
- Department of Chemistry and Biochemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, Haus F, 81377 Munich, Germany
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Abstract
We report the results of density functional theory (DFT) studies on the formation of the complex H1--Cu2+-H1- consisting of two deprotonated hydroxypyridone ligands (H1-) and a Cu2+ ion. We compare the total energies of three possible structures with different symmetries and show that the structure with plane reflection symmetry has the lowest energy. The electronic structure of the periodic extended DNA-like double helix consisting of stacked H1--Cu2+-H1- units is then calculated within the density functional method, and the double helix is found to be an insulating ferromagnet.
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Affiliation(s)
- Radi A Jishi
- Department of Physics, California State University, Los Angeles, California 90032, USA
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27
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Mallajosyula SS, Pati SK. Structure and transport characteristics of modified DNA with magnetic ions. PHYSICAL REVIEW LETTERS 2007; 98:136601. [PMID: 17501225 DOI: 10.1103/physrevlett.98.136601] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Indexed: 05/15/2023]
Abstract
Motivated by recent experiments we study the alignment of magnetic ions Cu2+ and Mn2+ along the modified DNA helix. We find that doping with magnetic ions induces conducting states in the gap region of natural DNA. These magnetic ions are found to interact ferromagnetically along the DNA helix. Calculations of optical conductivity about the helical axis suggest that the origin of magnetic characteristics depend on the metal ions; while Cu-DNA favors in-plane sigma-like delocalization over the base pairs, the Mn-DNA favors out-of-plane (pi) delocalizations. Such an alignment of magnetic ions offers promising perspectives for creating low-dimensional polarized spin channel within the DNA helix.
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Affiliation(s)
- Sairam S Mallajosyula
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India
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Cavallari M, Calzolari A, Garbesi A, Di Felice R. Stability and migration of metal ions in G4-wires by molecular dynamics simulations. J Phys Chem B 2007; 110:26337-48. [PMID: 17181293 DOI: 10.1021/jp064522y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a molecular dynamics investigation of guanine quadruple helices based on classical force fields. We analyze the dependence of the helical conformation on various compositional factors, such as the length of the G4-wire, as well as the incorporation into the helix channel of alkali ions of different species and in different amounts. In compliance with previous indications, our results suggest that monovalent alkali cations assist the stability of the quadruplex arrangement against disruption on the few nanoseconds time scale in the order of increasing van der Waals radius. Whereas very short G4-wire fragments immediately unfold in the absence of coordinating metal ions or in the presence of tiny ions (e.g., Li+) in agreement with the experimental evidence that empty short guanine quadruplexes are not formed in any synthetic conditions, our simulations show that longer empty helices do not discompose. This finding supports the possibility of producing long G4-wires with different guanine-cation stoichiometries than those routinely known. The classical trajectories allow us to identify different stationary axial sites for the different metal species, which are confirmed by complementary quantum calculations.
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Affiliation(s)
- Manuela Cavallari
- National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi 213/A, 41100 Modena, Italy. cavallari.
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